# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosopelagicus_brevis-ASM81218v1/GCA_000812185.1_ASM81218v1_protein.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosopelagicus_brevis-ASM81218v1/GCA_000812185.1_ASM81218v1_protein.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Nitrosopelagicus_brevis-ASM81218v1/GCA_000812185.1_ASM81218v1_protein.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       AJA91819.1  [L=62]
Description: hypothetical protein T478_0858 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-06   25.6   4.0    1.4e-05   24.6   4.0    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
       0.07   13.0   0.4       0.07   13.0   0.4    1.6  2  TFIIS_C         Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   4.0   1.6e-09   1.4e-05       1      32 []      19      52 ..      19      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-09
                    -B-SSS--B----SSS...----SSS-----B--- CS
  DNA_RNApol_7kD  1 YiCgeCgaevslkkgd...piRCkeCGhRilYKkR 32
                    Y+C++Cg+e+ l++ +    i+C  CG+R++ KkR
      AJA91819.1 19 YKCMRCGHETALEELArlpEIKCI-CGFRVFTKKR 52
                    9********99776653337***9.*********9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   7.8e-06      0.07      27      37 ..      17      27 ..      11      28 .. 0.87
   2 ?   -2.5   0.2      0.56     5e+03      31      35 ..      41      44 ..      39      46 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.8e-06
     TFIIS_C 27 vfykCtkCghr 37
                vfykC+ Cgh+
  AJA91819.1 17 VFYKCMRCGHE 27
                8********96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.56
     TFIIS_C 31 CtkCg 35
                C  Cg
  AJA91819.1 41 C-ICG 44
                4.355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 416.90
//
Query:       AJA91820.1  [L=98]
Description: hypothetical protein T478_0562 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
          1   10.0   9.6        3.9    8.1   9.5    1.9  1  Lactococcin_972  Bacteriocin (Lactococcin_972)
        6.7    6.3  23.9        8.1    6.0  23.9    1.1  1  DDRGK            DDRGK domain


Domain annotation for each model (and alignments):
>> Lactococcin_972  Bacteriocin (Lactococcin_972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.5   0.00044       3.9      14      59 ..      11      55 ..       4      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00044
  Lactococcin_972 14 glvysnYyHgtkcHgstvvlGkrtrkseaaaGkwskAsasraltnn 59
                     ++ +s+Y   +k+H s ++  ++t++ +++ ++++kA+a+++ + +
       AJA91820.1 11 NQSRSEYKAKKKKHPSRAN-KTKTNQIRERYEAKAKAKAEQKTRAQ 55
                     6789***************.77777777767777777765555444 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  23.9   0.00091       8.1      16      99 ..       5      88 ..       2      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00091
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       DDRGK 16 kkrqqreaeeeereerkkleekreeerkekeekeeekekkkeeeerkkeeekerkeqeeyeklksefvveeegtekesaeeeek 99
                k +++r++ + e++ +kk++  r ++ k ++ +e+ ++k+k+++e+k ++++ r      + +k e  v ++  ++++a   +k
  AJA91820.1  5 KAKKKRNQSRSEYKAKKKKHPSRANKTKTNQIRERYEAKAKAKAEQKTRAQQSRASRRSGKSMKTEGKVTKSTSKAKEARSSKK 88
                346677888899999999999999999999999999999999999999999999999999******999999999888877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3382  (0.188633); expected 358.6 (0.02)
Passed bias filter:                      713  (0.039768); expected 358.6 (0.02)
Passed Vit filter:                       159  (0.00886831); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 705.09
//
Query:       AJA91821.1  [L=449]
Description: beta-lactamase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-12   46.6   0.0      6e-12   45.7   0.0    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00065   19.3   0.0     0.0011   18.6   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.031   14.3   0.1    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
       0.13   12.2   0.0       0.32   11.0   0.0    1.6  1  Sdh5           Flavinator of succinate dehydrogenase


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   1.3e-15     6e-12       1      67 [.       2      81 ..       2     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.3e-15
  Lactamase_B_3  1 eltwlghnsflletagarilvDPfkanlgyeppa.............eeaDlvlisqaledHahletlkqlaenvkvlee 67
                   ++t+l ++s+l+e+++++il+DP+  + +y  ++             +++D + is+ ++dH+   tl +l+++++++ +
     AJA91821.1  2 KITYLNSASVLIEDKNVKILCDPWLDGEEYFGSWgiyppydfrpeifDDVDFIHISHIHPDHCSSSTLSKLNKKIPIIIH 81
                   69**********************88666666667888899999***************************999888866 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.4e-07    0.0011       3     110 ..      20     121 ..      18     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                    EEES--TT...HHHHHTCGG.S--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TT CS
  Lactamase_B_2   3 iLiDagpd...lrqqalral.qPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwg 93 
                    iL+D+++d    ++        P   + + ++++d++ ++h H DH+    tl +l  kk+p++ +k   + l++ +      +  + +v el+ +
     AJA91821.1  20 ILCDPWLDgeeYFGS--WGIyPPYDfRPEIFDDVDFIHISHIHPDHC-SSSTLSKLN-KKIPIIIHKFPEKFLKSFLE-----NL-GFDVIELEHN 105
                    999999997773344..2222455555666999**************.579999975.469*9999877777777743.....33.5556677777 PP

                    SEEEECSTTEEEEEEEE CS
  Lactamase_B_2  94 esfelgdggleitatpa 110
                    ++++l+ ++++i + +a
     AJA91821.1 106 KRTKLK-ENVHINVLAA 121
                    777776.4666766665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     7e-06     0.031       6      84 ..       8      90 ..       4     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7e-06
                 SEEEEEEETTCEEEES--SCHHHHHHHH....HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
  Lactamase_B  6 vnsyliegdggviLiDtGtsteaaraal....elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84
                 + s+lie+++  iL D+ +++e+    +     +  +    +dvd + ++H H+DH++     +   ++p+++++  ++ l+ 
   AJA91821.1  8 SASVLIEDKNVKILCDPWLDGEEYFGSWgiypPYDFRPEIFDDVDFIHISHIHPDHCSSSTLSKLNKKIPIIIHKFPEKFLKS 90
                 5667777777777777777777777777665444444444579***************9999999999999998766666555 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.2e-05      0.32      31      67 ..     381     417 ..     376     422 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-05
                 --HHHHHHHHHHHTS-.-HHHHHHHHT-.---S-HHHH CS
        Sdh5  31 lseeeldaferLLdle.DpdLldwltgrkeepedaela 67 
                  +++e+++f+++L +  D+ Ll+w+++  +  ++++ a
  AJA91821.1 381 CTAKEIQKFNQFLMMTlDNRLLRWILQG-PRKAHWSIA 417
                 6899********99999**********9.888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3294.34
//
Query:       AJA91822.1  [L=88]
Description: putative aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00051   20.3   0.1    0.00081   19.6   0.1    1.5  1  Glu-tRNAGln    Glu-tRNAGln amidotransferase C subunit
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.17   12.0   0.0    1.2  1  Peptidase_C23  Carlavirus endopeptidase


Domain annotation for each model (and alignments):
>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     9e-08   0.00081      11      59 ..      26      81 ..       2      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9e-08
                 HHHHHHHHHHTTCGCS--TT----S......-EB-S-.-..HHHHHTT-SSEETTE CS
  Glu-tRNAGln 11 kelnsildyveqLqevdttgveplthp....vlReDe.v..reelLknApetedgy 59
                 +  +++l+y++ L+++d++  e +++      lR+D+ +  +++l +  ++ ++ y
   AJA91822.1 26 SRVKKMLEYFDILDQIDLSSEEIMSQQkslnELRKDQfIpyDKKLIESLKNFREHY 81
                 66789*************9************9****75367666655555555555 PP

>> Peptidase_C23  Carlavirus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.9e-05      0.17      38      70 ..      19      51 ..       5      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
  Peptidase_C23 38 eGrGlsiedvesvleildivgdvnvggklivln 70
                   e +G  +  v+++le +di  ++++  ++i+  
     AJA91822.1 19 EDHGEHVSRVKKMLEYFDILDQIDLSSEEIMSQ 51
                   66899999**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 675.72
//
Query:       AJA91823.1  [L=54]
Description: hypothetical protein T478_0109 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 423.50
//
Query:       AJA91824.1  [L=52]
Description: hypothetical protein T478_0033 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.8   1.5      0.064   13.7   1.5    1.0  1  MerC      MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.5   3.6e-06     0.064      41      84 ..       2      45 ..       1      51 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-06
        MerC 41 vllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg 84
                v++  ++a++++ l+vg+ ++ ++   ++g+lG+++++ ++f++
  AJA91824.1  2 VIFGAFIALAIAPLAVGVESTIEFVGSLIGILGVVFMISGMFYK 45
                677889************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 389.17
//
Query:       AJA91825.1  [L=149]
Description: SUF system FeS assembly protein, NifU family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-26   92.1   0.0    3.5e-26   91.9   0.0    1.1  1  NifU_N    NifU-like N terminal domain
     0.0022   17.8   0.0     0.0029   17.4   0.0    1.2  1  SufE      Fe-S metabolism associated domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   3.9e-30   3.5e-26       2     125 ..       7     130 ..       6     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 3.9e-30
                 SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHCCCCHHHHHHHHTC. CS
      NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgktleealkitnkeiaeelgg. 99 
                 y++ ++++ +nP n G++ +++   +  +  +p cGD++ L++++d+  ++i ++kF++ GC++ +A+ss+lte++kgk+le+++k  ++e  +elg  
  AJA91825.1   7 YTEMIIEYSRNPSNFGKIVDAH---IHQHDANPLCGDTIDLYLNIDD--NKISEVKFDGHGCAICMACSSVLTEMIKGKSLEDVKKFDKDELLSELGLe 100
                 99******************99...5778899***************..5******************************************9998866 PP

                 ....SCSSSCHCSCHHHHHHHHHHHHHHHH CS
      NifU_N 100 ....lpkeklhcsvlaedalkaavkkYkak 125
                       +++++c+ l+ + lk ++++Y a 
  AJA91825.1 101 hlvkTSPVRIKCALLSLKSLKYGIYSYFAD 130
                 7777899********************875 PP

>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.3e-07    0.0029      16     104 ..      10     103 ..       6     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.3e-07
                 HHHHHHHTS----C.....CCCCCCEEECTSSSEEEEEEEEETTS...EEEEEEESSHHHHHHHHHHHHHCTTEECCCCTCC-TCHHHHHTTSHHHH CS
        SufE  16 ylielgkklpplpe.....elkteenkvkGCqsqvwlaaeledgk...lkfeadsdarivkGllalllevlsgktpeeilavdledfleelglsehl 104
                 ++ie++++  ++ +      +++++n    C  ++ l  +++d+k   +kf+++   +i  +  ++l e+++gk+ e++ ++d +++l+elgl++ +
  AJA91825.1  10 MIIEYSRNPSNFGKivdahIHQHDANPL--CGDTIDLYLNIDDNKiseVKFDGHG-CAICMACSSVLTEMIKGKSLEDVKKFDKDELLSELGLEHLV 103
                 5666666666555555433334444444..4444445555555555457777765.56888999*****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 898.30
//
Query:       AJA91826.1  [L=355]
Description: glucose-1-phosphate thymidylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-56  190.9   0.0    3.7e-56  190.5   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    1.2e-09   37.5  21.0    4.9e-06   26.1   6.7    3.9  3  Hexapep          Bacterial transferase hexapeptide (six repea
    2.7e-09   37.6   0.0    3.5e-09   37.2   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0056   16.4  13.1     0.0064   16.2   5.8    3.1  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.25   10.2   1.4       0.43    9.5   1.4    1.3  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.0     1e-59   3.7e-56       1     245 [.       2     234 ..       2     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 1e-59
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      k++IL+GG GtRL+PLt+t +k+l+p+++k ++ +++l+ + + gi++i +++    s  v+e++++g++fgv+++++ ++e++g+A+A+ l +
       AJA91826.1   2 KGIILHGGHGTRLRPLTHTGPKQLLPIANK-PMSEYCLNSIKETGITDIAIIIGGLGSKKVKEYYGNGENFGVKITYVEQDEPRGIAHAINLCK 94 
                      79****************************.*************************************************************** PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      +++++ek    +lv+ gD +i+  ++++vk++ +++   ++t+++ +v++++++G++e+++ ++++++vEKPk++  s+la++GiY+ ++++++
       AJA91826.1  95 DFINNEK----FLVFLGDNIIQRSISDFVKNFDKSNF--DATLLLCEVDNPSRFGIAEIKN-KKIIKIVEKPKNPL-SNLAVTGIYLLTPKIFE 180
                      ******9....799999999999**************..9*******************98.69**********99.***************** PP

                      HHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHH CS
  NTP_transferase 189 flakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekl 245
                      ++ ++l++++r e eitd+l  +l++ ++    + +d  yW+D+Gt+++++ an ++
       AJA91826.1 181 II-ENLKPSWRNELEITDALDILLNKNNNLSFEIITD--YWKDTGTPQDIIHANGEV 234
                      **.89********************987776666666..9************99766 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   6.3   2.9e-09   1.1e-05       3      35 ..     257     289 ..     255     290 .. 0.95
   2 !   26.1   6.7   1.4e-09   4.9e-06       2      30 ..     274     302 ..     273     305 .. 0.92
   3 !    5.4   4.6    0.0043        16       1      24 [.     291     318 ..     291     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.9e-09
                 EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                  +G+n++I ++++i g+V+IG+n+ I +gv ig
  AJA91826.1 257 LTGKNSIIEKNVIITGPVIIGENCQINSGVIIG 289
                 69*****************************98 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.4e-09
                 EEEETTEEE-TTEEEETTEEE-TTEEEET CS
     Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIga 30 
                 ++IG+n++I ++++ig+n+ IG+n++I  
  AJA91826.1 274 VIIGENCQINSGVIIGPNTSIGNNSIINQ 302
                 79************************976 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0043
                 TEEEETTEEE-T....TEEEETTEEE-T CS
     Hexapep   1 stvIGsnvlIgp....faviggnVkIGd 24 
                 +t IG+n++I      +++i++n++I +
  AJA91826.1 291 NTSIGNNSIINQgnieNSIIMENCEINS 318
                 689*********99999****9999965 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   9.7e-13   3.5e-09       1     118 [.       3     129 ..       3     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 9.7e-13
                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHH...TTCTS-EEE-TTSS.-SHHHHHHHHHHHH.S CS
  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd...eevlaal...arlgvrvvededpg.kgplaslaaalraaad 85 
                   ++iL GG+++R+      g+K+llp+++kp+ e++l+++++ g+ ++ ++ g    ++v++++   + +gv++++ e+ + +g+++++    + + +
    AJA91826.1   3 GIILHGGHGTRLRplthtGPKQLLPIANKPMSEYCLNSIKETGITDIAIIIGGlgsKKVKEYYgngENFGVKITYVEQDEpRGIAHAINLCKDFI-N 98 
                   79**********6554447*************************99999977656556665543337778887655544339******9999999.8 PP

                   SSCEEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
  NTP_transf_3  86 adavlvlacDmPlltpelverllaaaaasgadv 118
                   ++ +lv+++D +   +  +  +++++++s+ d+
    AJA91826.1  99 NEKFLVFLGDNII--QRSISDFVKNFDKSNFDA 129
                   **********966..677888888887777655 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   5.8   1.8e-06    0.0064       5      33 ..     259     289 ..     255     290 .. 0.92
   2 !   12.7   7.9   2.2e-05     0.079       1      27 [.     273     301 ..     273     305 .. 0.91
   3 !    4.4   3.8    0.0086        31       2      17 ..     286     303 ..     285     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                 -TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
   Hexapep_2   5 GdnCliGanagi..GvslGdncvvgaGvvit 33 
                 G+n++i +n +i  +v++G+nc + +Gv+i 
  AJA91826.1 259 GKNSIIEKNVIItgPVIIGENCQINSGVIIG 289
                 9**********9955**************96 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.2e-05
                 .EEE-TT-EE-TT-EES..EEE-TT-EE- CS
   Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvvg 27 
                 pviIG+nC i +  +iG  +s+G+n+++ 
  AJA91826.1 273 PVIIGENCQINSGVIIGpnTSIGNNSIIN 301
                 8*********999999999*******995 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0086
                 EEE-TT-EE-TT-EE..S CS
   Hexapep_2   2 viIGdnCliGanagi..G 17 
                 viIG n+ iG n++i  G
  AJA91826.1 286 VIIGPNTSIGNNSIInqG 303
                 899999999999998555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   0.00012      0.43     278     339 ..     261     320 ..     224     338 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
  Fucokinase 278 nSvlessvsvgegsvi.ehsslkgnvsigsnsivsglelesseeslelpddtilqtlslklsk 339
                 nS++e++v +    +i e+++++++v ig n+ + + ++ ++ +   + + +i+ + ++++s+
  AJA91826.1 261 NSIIEKNVIITGPVIIgENCQINSGVIIGPNTSIGNNSIINQGN---IENSIIMENCEINSSG 320
                 56666666555444443577777666666666666666665444...7777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2075.75
//
Query:       AJA91827.1  [L=543]
Description: thermosome subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.8e-178  594.2  22.1   2.1e-178  594.0  22.1    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
    4.5e-05   23.4   1.3       0.33   10.8   0.0    2.9  3  Dak2        DAK2 domain


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.0  22.1  2.3e-182  2.1e-178       1     488 [.      38     526 ..      38     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 594.0 bits;  conditional E-value: 2.3e-182
                 HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                 +adivk++lGP+G+dKmlv++ g+v++TnDGatilke++ +hPaak+++e++++ d+evGDGTt+ vi+ag+Ll +ae+l++++vh ++iieg++ a e
  AJA91827.1  38 VADIVKSSLGPRGLDKMLVDSLGDVTITNDGATILKEIDAQHPAAKMMIEISKTIDTEVGDGTTSSVIFAGTLLAKAEELLKKDVHSSVIIEGFQAASE 136
                 69************************************************************************************************* PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTS CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene..keldlgrikvvkieggsledselveGlvldkgvlspdm 195
                 kale L ei++++    +dre+Llk+a+ts+ skl+s+++e lsk+vvd++ +++e+++   ++dl++ kv+k+ ggs++d+ l++G+vldk+v+++ m
  AJA91827.1 137 KALEVLAEISKKVTA--DDRETLLKIASTSMESKLISEDSEPLSKIVVDSImSITETRDnkASIDLDNLKVEKKAGGSIQDTALIKGIVLDKEVVHSGM 233
                 *********666665..59********************************66666555999************************************* PP

                 SCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT CS
  Cpn60_TCP1 196 pkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatG 294
                 p+k+++ak++ll++ +e ekte++++++++d+++++ ++++e+++++ +++ki++ g+nvv+cqkgidd+a+hfl k+gila+rrvk++d+ +lakatG
  AJA91827.1 234 PTKIQQAKIALLNTAMEVEKTEMSAEIRINDPTQMQMFLEEENRMIKTMVDKIHSIGANVVICQKGIDDMAQHFLSKHGILAVRRVKESDMTKLAKATG 332
                 *************************************************************************************************** PP

                 --EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
  Cpn60_TCP1 295 atavssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                 +++ s++ed+++++lG a+ v+++k++s+k+++ie++k+++++t+l+rg ++ v+de+ r+i+d+l vvk +ie++++v+GGGa e  la+ lk+++++
  AJA91827.1 333 GRITSNIEDISEKDLGGANLVQQKKVESDKWVFIEGCKNPQSVTLLIRGGSQRVVDEVDRSIHDSLMVVKDVIEKPEIVAGGGAPEALLASFLKDWSER 431
                 *************************************************************************************************** PP

                 SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEX CS
  Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiik 488
                  +g++qlai++fa+ALe+ip t+aeNaG+dpi+++ klra++++g+k+ gi++++g++ d++++++v+p+ vk+q++ksAteaas+iLrid++i 
  AJA91827.1 432 FEGRQQLAINKFAEALEIIPLTIAENAGMDPIDTMVKLRARQSEGKKWSGINAKEGRVADMLTQNIVEPVVVKEQIIKSATEAASMILRIDDVIA 526
                 *********************************************************************************************95 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.5   7.3e-05      0.66      17      92 ..      70     148 ..      62     197 .. 0.74
   2 ?   -2.0   0.0      0.32   2.9e+03      97     120 ..     280     304 ..     276     350 .. 0.64
   3 !   10.8   0.0   3.7e-05      0.33      14      98 ..     382     465 ..     379     475 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7.3e-05
                 HHHHHHHC---SSHHHHHHHHHHHHHHH--..STHHHHHHHHHHHHHHHC........TT---HHHHHHHHHHHHHHHH-- CS
        Dak2  17 avlkaleeleeaslaevlkalakallsgag..GtsGvlysqflralakalkekee...ldaedlaaalkaaleaiqavgka 92 
                  +lk++++  ++ +a+++ +++k++ +++g   ts v+++  l+a a++l +k+    + +e ++aa ++ale + +++k 
  AJA91827.1  70 TILKEIDA--QHPAAKMMIEISKTIDTEVGdgTTSSVIFAGTLLAKAEELLKKDVhssVIIEGFQAASEKALEVLAEISKK 148
                 55666665..588889999999999888854379*******9999999997766633356666666666666666666544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.32
                 SSTHHHHHHHHHHHHT......... CS
        Dak2  97 kTmlDvlrpavealekakd.gedlk 120
                 kTm+D ++ +  ++  +++  +d++
  AJA91827.1 280 KTMVDKIHSIGANVVICQKgIDDMA 304
                 7888877777776666554433333 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 3.7e-05
                 HHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH---TTSSS CS
        Dak2  14 gaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavgkarpgdkT 98 
                 g++ v++++++   +sl  v + + k  + + gG+  +l+++fl+  ++ ++++++l ++++a+al+    +i + ++++p d T
  AJA91827.1 382 GSQRVVDEVDRSIHDSLMVVKDVIEKPEIVAGGGAPEALLASFLKDWSERFEGRQQLAINKFAEALEIIPLTIAENAGMDPID-T 465
                 67777777777777777777777777777788999*******************************99999998888888877.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 3182.96
//
Query:       AJA91828.1  [L=241]
Description: uracil-DNA glycosylase, family 4 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-43  149.0   0.0    1.3e-43  148.7   0.0    1.2  1  UDG          Uracil DNA glycosylase superfamily
     0.0005   19.0   0.0    0.00072   18.5   0.0    1.1  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.058   14.0   0.6       0.35   11.5   0.0    2.1  2  DUF1053      Domain of Unknown Function (DUF1053)
       0.12   10.8   0.0       0.15   10.4   0.0    1.1  1  IDH          Monomeric isocitrate dehydrogenase
       0.81    9.9   6.2        4.5    7.5   1.8    2.6  2  Fer4_9       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.0   3.6e-47   1.3e-43       1     150 [.      28     171 ..      28     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 3.6e-47
                 HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEE CS
         UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikacaplleeeiellkprlivll 99 
                 pg g+ da+v++vGeaPg++ed +g+pF+g+ag++l+ +l+++g++r     ++vyitn+vkcrpp+nr  p+++e + c +++++eie+++p++i+++
  AJA91828.1  28 PGKGNFDADVIFVGEAPGRNEDIHGEPFVGAAGKRLDMILEDTGIDR-----KDVYITNIVKCRPPKNR-VPSKKEEESCNDFIKQEIEIINPKIICVM 120
                 688999*****************************************.....*****************.9999999********************** PP

                 SHHHHHH...HHHHSCESCCCSCT..SEEEEES-SSTTTTTTTTSHHHHHHHH CS
         UDG 100 Gktaakall.geklgklrgklleak.irvlplphPsplnrnffksnpelkaea 150
                 G+ta+ +ll g++++k +gk++e++  ++++++hP++  +n  ++  e+++e 
  AJA91828.1 121 GNTAYGTLLdGKEITKNHGKIVEKDgRKFFVTFHPAATIYN--QKLVEELKED 171
                 ********9999************99***************..2323333333 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     2e-07   0.00072     140     213 ..     110     178 ..      97     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                  TT--GGGEEE---HHHHHHHHHHHHHH...T-HHHHHH--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHH CS
  Epimerase_2 140 egeeeerifvvGntviDalllskeeieeklkaseilkelkekkyvlvtlHrrenedeperlkeilealkalake 213
                  e ++++ i v Gnt++ +ll  ke  +++    +i +  k+ + + vt+H++++  +++ ++e+ e +++lak 
   AJA91828.1 110 EIINPKIICVMGNTAYGTLLDGKEITKNHG---KIVE--KDGRKFFVTFHPAATIYNQKLVEELKEDFRKLAKF 178
                  4468999**************999988544...8855..5888899**********999999999999999986 PP

>> DUF1053  Domain of Unknown Function (DUF1053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.7e-05      0.35      43      73 ..      88     118 ..      67     130 .. 0.86
   2 ?    0.2   0.2       0.3   1.1e+03      69     100 ..     161     193 ..     154     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.7e-05
     DUF1053  43 ersasekarleeelderleqaIdglsskklw 73 
                  +++ ++++ ee ++++++q I++++ k ++
  AJA91828.1  88 PKNRVPSKKEEESCNDFIKQEIEIINPKIIC 118
                 5789999******************988766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.3
     DUF1053  69 skklw.krsedlkkftliFkekslEkkYrqlre 100
                 ++kl  + +ed++k+  + + k+  k+Y + r 
  AJA91828.1 161 NQKLVeELKEDFRKLAKFLETKDEPKQYEERRC 193
                 566665678999999998888998899987765 PP

>> IDH  Monomeric isocitrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.3e-05      0.15     622     692 ..     114     184 ..      99     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.3e-05
                 HHHHHHHHHHHHHHHHHTT-S--SSTTS--HHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHHHHHHHTHH CS
         IDH 622 akvladtldkateklLendksPsrkvgelDnrgshfylalywaealaaqtedaelkakfakvakeleenee 692
                  k+++   ++a ++lL+ +   +++ + +++ g +f+++ + a ++ +q+  +elk+ f+k+ak le+++e
  AJA91828.1 114 PKIICVMGNTAYGTLLDGKEITKNHGKIVEKDGRKFFVTFHPAATIYNQKLVEELKEDFRKLAKFLETKDE 184
                 5677777789999999999888888788888899********************************98765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.019        67      35      43 ..      13      21 ..       3      35 .. 0.71
   2 ?    7.5   1.8    0.0013       4.5       4      40 ..     192     225 ..     191     226 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.019
      Fer4_9 35 aCigCgaCv 43
                +C +C+ C+
  AJA91828.1 13 ECQKCELCE 21
                355555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0013
      Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraase.eaCigCg 40 
                 +C++C+++ +++vvv+ ++ +     ++++  +C++C+
  AJA91828.1 192 RCDYCMAKTKHEVVVMPKVVTR----KRRWlFKCTECN 225
                 4666666666666655444444....4444468****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1483.15
//
Query:       AJA91829.1  [L=819]
Description: ABC transporter, substrate-binding protein, family 5 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      6e-26   91.3  11.7    9.9e-22   77.4   0.0    2.8  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0   5.5e-26   9.9e-22     150     362 ..      25     252 ..      19     264 .. 0.84
   2 !   12.8   9.3   2.3e-06     0.042      21     160 ..     455     679 ..     438     715 .. 0.70

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 5.5e-26
                 SSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT....STGGGSHHHHHHHHHHS-HHHHHHHCTTTS CS
   SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtk....kppfddkrvRqAlsyAiDreeivkavlegy 244
                  ++d+i+f  + d++++++++++G++d + ++  sd  +  e+ ++ + +++ +gg++ + +N +     +pf+ ++vR A++  +Dr+ iv+++l+gy
  AJA91829.1  25 TYVDEIKFIQYLDENTALEEVKNGNLDMYYYRISSDRLEDSESRDTLK-VYESTGGYYSILLNPTdegpFNPFSIQEVRYAVNFLVDRNLIVNELLGGY 122
                 69************************8886555555555555555555.68888888888899998888779*************************** PP

                 SEEESSSSTTTSTTCCSCHCCCSHH...SHHHHHHHHHHHTT-BCSSTSCEETC.......EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE CS
   SBP_bac_5 245 atpansllppsspgadeeykpayka...ydpekAkklLkeaGykdgdggglrek.......klkltlllasgspaekaiaeliqqqlkkiGikvevktv 333
                 +tp+ s  ++ s+ +    +  ++    y+p  A++++ +     g ++ ++         + ++t+++ s++p++kai e++ ++l++iG+kv+ +  
  AJA91829.1 123 GTPMFSNYGSFSAEYLRVLDVIETFqfrYNPSFAENIISDELSARGAEK-ID-GiwnyesePIEITFFIRSDDPVRKAIGEILSSELEEIGFKVNKEFG 219
                 *******999999999888887666999*******99776655555432.21.13455669************************************** PP

                 CHH....HHHHHHHHCTTESEEEEEEECTTSTT CS
   SBP_bac_5 334 dwa....atylervkdgdfdmillgwgadypdp 362
                 d +     +y +   +++++++  gwg++ ++ 
  AJA91829.1 220 DLNkayvVVYGSNPAEQKWSLYTEGWGSSGFTR 252
                 8888***999999**************997665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.3e-06
                 EEEE-TT-B-TTSSB-SHHHHHHH........HHHHHTGGGHCTTHHHHHC..........TCTEEEEEEEETTEEEEEESSETT.......TTTTHCH CS
   SBP_bac_5  21 tfkLRkgvkFsDGtpltAeDvvfs........ferlldpdtasgyasllee..........dqdikkveavddytvrftlkkpna.......lfltlla 94 
                 t+ L+   +++ G +++  D+++s                t   +++   +           ++ k++ ++d++t+++++   ++         +   +
  AJA91829.1 455 TYDLKF-NQWHHGPEMNMNDIIYSvyflsewgS-----ERTEDDRTY---DadfspqasqiLNTLKGIRVIDENTIEVYTDFWHFdsgeiasWGSVWSS 544
                 555555.37**************9665333331.....333333333...2224667778878****************88886678777763333333 PP

                 HHHHHHGC................................................................CHTCTCTTT.TTGTTTSE-BSSSEEEE CS
   SBP_bac_5  95 avpasiak................................................................kaaekeddk.dkdtnekpvgtGPYklk 128
                 +++  +a+                                                                  + ++++k  +++n +++++GP+ l+
  AJA91829.1 545 MPWEIMASmekivmdgkssfsrtesitkninwlsliipndanqvkmqldtfeknehtpdaliqfnpqndfqnI-RYDSSKKwIDENNHAVISNGPFYLD 642
                 333333336667777999*****************************************************63.444444405666666677******* PP

                 EEETTT.EEEEEE-TT..ST..TTSCSSSSEEEEEE- CS
   SBP_bac_5 129 efkpgq.kivlernpd..Yw..gggkpkldriefkvi 160
                 +++p++ +iv++ +++  Y   +g+   ++ ++f  i
  AJA91829.1 643 RYSPDSrTIVIKSFDYgnYVfeQGKWKDFENVKFPSI 679
                 ****994455555555555366333334444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (819 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4973.01
//
Query:       AJA91830.1  [L=117]
Description: hypothetical protein T478_1385 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 879.90
//
Query:       AJA91831.1  [L=222]
Description: ScpA/B-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.5   2.6    0.00094   19.2   0.1    2.2  2  SMC_ScpA  Segregation and condensation protein ScpA
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.022   14.9   0.0    1.4  1  DUF2582   Winged helix-turn-helix domain (DUF2582)
      0.014   15.2   0.1      0.024   14.5   0.1    1.3  1  CNDH2_C   Condensin II complex subunit CAP-H2 or CNDH2, C-ter


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.6     2e-05      0.12       6      67 ..      26      86 ..      24     100 .. 0.90
   2 !   19.2   0.1   1.6e-07   0.00094     182     241 .]     163     221 ..     141     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                HHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXXXXXXX CS
    SMC_ScpA  6 eldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqveeeede 67
                + dv+d++++++    l+ ++    k +l  ++ + + +s + +lK +s++ l++ + e+ +
  AJA91831.1 26 KRDVWDIDLIQILSMLLKILEKT-DKKDLRVAGMAALSSSLIYKLKVESIFALQKAAMEKKP 86
                559*******************9.***************************99999887665 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.6e-07
                 ....HHH..TS-EEGGGSSTT...--HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEEEE- CS
    SMC_ScpA 182 kevLldl..rswvdlseLladnkledkkelvgvFlAlLeLiknqavaleQeeflddLqvsll 241
                 + vL +l   +   l+++++     d  + + +F+A+L L +++++++ Qee  +++ v+l+
  AJA91831.1 163 DLVLRKLqaNGSLLLEKIVEE---LDTTDSIRCFFAILFLARDEKIDILQEEGEEEIRVTLI 221
                 446777743345556666666...88999*****************************9975 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.7e-06     0.022       4      63 ..     156     216 ..     153     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                 HHHHHHHHHHHHHHCCSSSEEHHHHHHHCT-.SCHHHHHHHHHHHCTTSEEEEEETTEEEE CS
     DUF2582   4 eiiGenAGkvwhlLnengeislkelkrktgl.sdkelalAiGWLaREdKivierkekelfv 63 
                 +iiGe    v + L+ ng + l+++ ++ +  ++   + Ai  LaR +Ki+i ++e+e  +
  AJA91831.1 156 NIIGEYQDLVLRKLQANGSLLLEKIVEELDTtDSIRCFFAILFLARDEKIDILQEEGEEEI 216
                 689999999*****************999993455799*****************998766 PP

>> CNDH2_C  Condensin II complex subunit CAP-H2 or CNDH2, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     4e-06     0.024     214     276 ..     158     216 ..     148     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
     CNDH2_C 214 IHeYGdriiesleekarvgetvsFaevVkgkekyevcRlflAsLqLANdgnVeidskdalees 276
                 I eY d ++++l+    ++     +++V++ ++++  R+f A L LA d  + i +++++ee 
  AJA91831.1 158 IGEYQDLVLRKLQ----ANGSLLLEKIVEELDTTDSIRCFFAILFLARDEKIDILQEEGEEEI 216
                 6688899999999....47899*******************************8887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 1210.76
//
Query:       AJA91832.1  [L=181]
Description: hypothetical protein T478_1318 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00089   19.6   0.1      0.036   14.5   0.1    2.3  1  RuvX      Holliday junction resolvase
     0.0037   17.0   0.1     0.0078   15.9   0.1    1.5  1  DUF460    Protein of unknown function (DUF460)
  ------ inclusion threshold ------
      0.085   12.9   0.1       0.17   11.9   0.0    1.6  2  T2SSS_2   Type II secretion system (T2SS) pilotin, S protein


Domain annotation for each model (and alignments):
>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     6e-06     0.036       3     128 ..      59     164 ..      57     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6e-06
                 EEEEEESSSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHHHHT...T-EEEEE--S---- CS
        RuvX   3 ilglDvGtkriGvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeLakrl.kklpvelvDErlttv 100
                 +lg+D G+ riGv v+  ++ +a+++ +   k     +  l ++++e  +++ +v +    +g     +k ++k+ + L+ ++ +k+++e+vDE+ tt 
  AJA91832.1  59 VLGIDPGQ-RIGVSVTYLENEIARAFFVSLDK----LIPYLISILAELPAARKIVKI---GNG----DMKTANKILQMLNLQFcSKFEIEFVDESSTTL 145
                 78899985.78999999888888888776666....555555555555555555422...233....34444455555554443577***********9 PP

                 XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        RuvX 101 eaerilresglsrkkrkkvvDklaAvii 128
                 + +++          ++++ D l+A++i
  AJA91832.1 146 KIKNHN---------QRGKRDMLSAQFI 164
                 988655.........4555566666655 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-06    0.0078      24      53 ..      50      79 ..      33      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
      DUF460 24 lkkkrkkklivGiDPGittgiavldldgev 53
                +++++++kl++GiDPG  +g++v  l+ e+
  AJA91832.1 50 NSTTNSSKLVLGIDPGQRIGVSVTYLENEI 79
                34677899***************9999876 PP

>> T2SSS_2  Type II secretion system (T2SS) pilotin, S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.89   5.3e+03      38      48 ..      23      33 ..      10      63 .. 0.57
   2 ?   11.9   0.0   2.9e-05      0.17      47     101 ..     113     166 ..      87     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                EEEEEEE--TT CS
     T2SSS_2 38 tveimllYnqd 48
                 + + +l+++ 
  AJA91832.1 23 QISMPMLFDEI 33
                55666665543 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.9e-05
                 TTSTT---HHHHHHHHHHHHHHSHHHHHHHHHT-EEEEEEE-TT--..EEEEEEE-G CS
     T2SSS_2  47 qdakgakpleqvlkssiasyCenkevkanldaGvsYrikirnsrGq..llvdqlvsk 101
                 +d    k+++++l+    ++C++ e++   ++  + +ik +n+rG+  +l  q++s+
  AJA91832.1 113 GD---MKTANKILQMLNLQFCSKFEIEFVDESSTTLKIKNHNQRGKrdMLSAQFISQ 166
                 33...35789***********************************832355666766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 1067.02
//
Query:       AJA91833.1  [L=950]
Description: PF03699 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-38  131.2  12.3    2.2e-37  128.7  12.3    1.9  1  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7  12.3   1.2e-41   2.2e-37       6     757 ..      23     766 ..      19     767 .. 0.71

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 1.2e-41
     UPF0182   6 avlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvf.............lllalllllnlllaerl..................ell. 72 
                  ++a++ +++ +la   + +l ++ +++ +vf++ l+ +l+  +  +                                                + + 
  AJA91833.1  23 GIIAIIGIIIFALAGNQAVVLSMNVTEFADVFTKPLMFSLIGGISLAsiallrvnavkrsS---------------IfwffintainmmnrgpqdQ-Vq 105
                 5566666667788888888888888889999998888776655544422223333332222...............13333333333344445540.04 PP

     UPF0182  73 .............eklerlrealekklkllllaialvlsllvglvassq...wekvllflnstsf..gvkDpifgkDisFYvFklPflelllslllalv 153
                               +++  + +    l  ++  ++l++++ + ++++++   +e++   l s +f    +Dp f +D    +  +P+l ++   +++++
  AJA91833.1 106 qtvpnfseyklsgGHFALWQVTKILLLGAFF--ANLMFGFGLLYMIEGNdlgVENIT-TLFSLPFvtPPNDPTFAMDNV--TPMIPALLIVIPPIIGAI 199
                 4456666543322222222222222222223..333333333334444433444444.444445511568*****9985..566899999999999999 PP

     UPF0182 154 llaliavllvyllsgeslgirlkfaelskaarrhlsvllallllllalsywLdryellyskrgvvtGagYtdvnavlpaktilavialvvavlllvaiv 252
                  l li+ + ++++ + ++   l  +++++   r l   +a++ ++++++++ + +++ ++++        +d n++  +   ++v  +++a+ ++ ++ 
  AJA91833.1 200 GLRLILFVGIHYIIKVVT---LYLHDTKEGKPRYL-NYMATIEAVIGIGIIWAAFNMFFTDT--------IDYNTRYAIGGTFVVGFALIAFSVFDRMR 286
                 999999999999999443...43334444444444.44555666778888888888888852........44455444444444444444444444443 PP

     UPF0182 253 lkklklpl...ialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIeaTreAygLdkveveefeaeael.....taedleenaetienirLl 343
                  + l+ ++   + + + +++ai+l v +++ v++ + + +++e   pY +++I + r   +Ld +++++ e++ +       ++ +++n++++++ir++
  AJA91833.1 287 ARVLTHMFkrdVYIRVAAIIAIALIVGIAMGVNNSVADAKKIEYLGPYTAQQIGVNRYLAELDMINENTHEVQITSvnpnvIESYIDQNEDVLSKIRVW 385
                 33222222111233333333344445567789999*******************************9999866655544335888999*********** PP

     UPF0182 344 DprplletfrqlqqirnYYkFedldvdrYtidgeerqvviaaREldysalpeeaktwvnkhlvYTHG.yGvvaspvnkvteeGlpeflvkdipseeees 441
                 D+++  +  +    + +Y +Fed d+ r++ +        + + +  s+++  +++w n+hlvYTH   G+ + ++++ t          d       s
  AJA91833.1 386 DWNAAFAKLKPEIGLIPYVDFEDNDILRFDDKL---YWTASMKPILPSSVSL-ENQWYNEHLVYTHVpDGFLTLEATEGTI--------VDS------S 466
                 ****************************97654...4677899999999965.599**********526887777666542........222......2 PP

     UPF0182 442 lkieepriYfGel.tndyvivgtkvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnikeRvekvaPfLtlD 539
                    e+  iY+Ge    d    g  v+ +d  +    +  +YdG gGv++  +l+ ++f     +++++ls    ++  i+ +++++eR++++ P++ ++
  AJA91833.1 467 ELFEQRAIYYGEGgLLDDTWSGYPVNRVDSAEL---NGAKYDGAGGVDVPPPLS-WIF-----EPNFILSYP-GESLHIMRYKDVNERMQTLYPYFLYN 555
                 2467899*****953344455556667887744...4689*********77665.444.....899999865.66779*****************9996 PP

     UPF0182 540 s.....dpYlvvadgrlyWivD...aYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvklYvvdeeDPiikawskiFpglfkplsempeeL 630
                       d Y+v+  ++ yW+v    ++ t ++ PyS             Y+R +  ++vD ydG+++l   + +D   +  +  + + +    e p+ L
  AJA91833.1 556 MfgkelDSYPVTDGKNTYWLVPlivGFDT-RDVPYSAG---------NPYLRLAGFALVDTYDGDISLI-KNGDDFFSNMLMAQYDDQII---EAPAWL 640
                 4444449************8763337765.568***77.........27******************95.56689999999999998776...68**** PP

     UPF0182 631 rshlrYPedlFkvqsellakYHvtdpevFYnredlWevpkeeeeqpvePyYlilklpgeekeefillspftp..ssrenliawlaarsdgenygkllly 727
                 ++++rYP++lF+ ++e+++ YHvtd+e+F + +++ e+p+       + yY+ +k pg e++efi l+ +    s+  nl++++++++d ++ gk++ y
  AJA91833.1 641 EEQIRYPQELFNWKTEMYNIYHVTDVETFIQANEFYEIPRG-----LDTYYIQAKPPGFEQTEFIGLLSLELrgSQGRNLAGYMIVENDMDKLGKMTFY 734
                 ****************************************9.....******************96655544228889********************* PP

     UPF0182 728 elpkq..elvyGpeqiearinqdpeisqqlsL 757
                 e+p +  +++ Gp+ + + ++ dp+ +q  +L
  AJA91833.1 735 EVPLDseTKLLGPTSVREALDRDPDFAQLKTL 766
                 *9965227789*************99987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (950 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.35s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 5171.31
//
Query:       AJA91834.1  [L=819]
Description: hypothetical protein T478_0680 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (819 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 5479.99
//
Query:       AJA91835.1  [L=260]
Description: hypothetical protein T478_0487 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.075   13.2   0.3       0.14   12.3   0.3    1.3  1  RGS_DHEX       Regulator of G-protein signalling DHEX domain
        1.2    8.1   2.8        1.8    7.5   2.8    1.3  1  TMEM171        Transmembrane protein family 171
        1.4    9.0   6.6       0.98    9.6   0.3    2.4  2  DUF3408        Protein of unknown function (DUF3408)


Domain annotation for each model (and alignments):
>> RGS_DHEX  Regulator of G-protein signalling DHEX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   2.3e-05      0.14      27      72 ..     197     242 ..     192     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
    RGS_DHEX  27 nkqrleeyekealnklqkllakkwefiimqaeeqlkvdkerkkadk 72 
                 ++++le+yeke l++l+++  +  + + + a++ + ++  + ++++
  AJA91835.1 197 KQAQLEDYEKEYLARLEQKKVDDAKAVAEAAKAEAAAAAAKVQSNR 242
                 4567************************999999888877777766 PP

>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.8    0.0003       1.8     220     248 ..     174     202 ..     168     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0003
     TMEM171 220 PPPPPpyfaessasavtkspgassllase 248
                 PPPPPp  +e++asa + s g s+  + e
  AJA91835.1 174 PPPPPPPQPEPQASAGSASDGKSKQAQLE 202
                 89999999*******99998876654433 PP

>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.1     0.032   1.9e+02       4      49 ..       9      57 ..       4      82 .. 0.54
   2 ?    9.6   0.3   0.00016      0.98      46      79 ..     181     213 ..     150     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.032
     DUF3408  4 Eellkelivkkiplksk...peeeetpakeekeeakeeeeeeaeeeeek 49
                E+ l++l +++ p  ++   p  +e p++ +k +++++ e    +  ++
  AJA91835.1  9 EKRLSNLAEAPKPAPKEapkPAPKEAPKPAPKPAEAKKPEGGGGPHAHD 57
                5566666644444433344444444444444444444444444444444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00016
     DUF3408  46 eeekekkekkkrisekkrktsledYeetFLkrkk 79 
                 ++e+++++  +   +k+++++ledYe+++L+r +
  AJA91835.1 181 QPEPQASAG-SASDGKSKQAQLEDYEKEYLARLE 213
                 223333322.35578999************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1313  (0.0732333); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 1725.01
//
Query:       AJA91836.1  [L=306]
Description: 2-phospho-L-lactate transferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-55  186.1   0.0      1e-54  185.8   0.0    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.8   0.0   5.6e-59     1e-54       1     277 [.       2     282 ..       2     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 5.6e-59
                 EEEEE-CHHHHHHHHHHCCSSCEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH...--S-C..........HHHHHCH-B-SS........SS CS
     UPF0052   1 vvvlgGGtGlskllrglkevtaeltavvtvaDdggssGelrrelgllaigDirnvlval...idder..........lleeLfqyRfkg........dg 78 
                 +++l+GGtG  k++rg+ ++ +e+t++ +v+D+ ++ G       +++++Di+++++ l   +d+e+          +l+++  +   g        d+
  AJA91836.1   2 ITILAGGTGSIKMVRGFAAHDQEVTVISNVGDNYWLYG-------MYVCPDIDTIIYGLsgiLDEEKgwgvkkdtnnFLRQMEVF---GeetwfrvgDR 90 
                 899***********************************.......**************99777777999666655533333333...256688888** PP

                 SSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS-EEE.STTTGGGG-S...-EEE.EEEESTT----HHHHHHHH CS
     UPF0052  79 dlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledGeeit.geskisearklkapikr.vflepegaeaapevleaik 174
                 d a+h+ ++ +L++     g +l+++++ +++ ++++ +++P+td++ve++++  +Ge ++ +e +++++   + +i+   ++++++a+++p++++ai+
  AJA91836.1  91 DAATHLTRTNMLKN-----GkNLSDITQWMCEKFAIESKIIPITDNTVETRITA-NGEDLHlQEFWVKHR--GRGTIEGiQYVGADKARPNPDAIAAIQ 181
                 **************.....99******************************998.************444..457****99****************** PP

                 H-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSEEEEE--SB--TTTSTT-BHHHHHHHHHHCH-........SS....S...-SEEEEE-S---HHH CS
     UPF0052 175 eAdlivlgpGslytSiiPiLlvpgiaealreskakkvlvsnimtqkGetdgfsvsdhvkaieravg........kgvakay...vdavlvntsevpeel 262
                 +A+l+v++pG+++tSi+P++ ++g++++l ++k+k+v+vs++++      ++s+s++++++++a+g        ++    y   ++ ++++t+    + 
  AJA91836.1 182 DAELVVIAPGNPLTSIGPMMGIKGVRKELTKNKKKVVAVSPLIG------NKSFSGPADKYMEAAGievsvfglAQF---YadvCSKMIIDTK----DK 267
                 *******************************************9......****************87777554333...3444888899888....33 PP

                 HHHHHTTT--B-B-- CS
     UPF0052 263 lekyaaegkepvelD 277
                  +k + eg +   lD
  AJA91836.1 268 AQKSKIEGLDIRVLD 282
                 444444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2351.20
//
Query:       AJA91837.1  [L=184]
Description: flavodoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-22   78.1   0.0    8.9e-22   77.8   0.0    1.1  1  Flavodoxin_1  Flavodoxin
  ------ inclusion threshold ------
      0.074   13.1   0.1       0.12   12.4   0.1    1.3  1  ANAPC5        Anaphase-promoting complex subunit 5
       0.16   12.3   0.0          2    8.8   0.0    2.1  2  RuvX          Holliday junction resolvase


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   1.5e-25   8.9e-22       2     143 .]       6     174 ..       5     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.5e-25
                   EEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSCGGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCHHGCCSTTTTEEEEEEEEECT CS
  Flavodoxin_1   2 lYgSetGnteklAkqlaeelgehgfnadvvslsdydeslseieeealllvvtsTfgnGdppengesffqdllelkgdeledgdlsgvrfavfglGds 98 
                    +g++tG+te++   ++e+lg++  n  + ++ + d  l ++   + l+ +++T++ G  +     +++d+l +k     + dl+g+ +avfglGds
    AJA91837.1   6 YFGTQTGKTETVCGIIKEQLGDAVAN--AKDVTESD--LADFAGLDGLICGIPTWNTGAEELRSG-TAWDDLLEK---IGALDLKGKPVAVFGLGDS 94 
                   79*******************75544..44444444..669*****************8887777.899998888...58999************** PP

                   TSSS..TTHHHHHHHHHHHHTTCEEES................................SSEEEETTST.HGHHHHHHHH CS
  Flavodoxin_1  99 ayen..FcaagkkldekleelGaerll................................kllegdednq.egqeeafrkW 143
                    +++  + +a+ +l+  +e++Ga++++                                 +l +ded + + ++e+++ W
    AJA91837.1  95 VGYGqdYVDAMEELHRYFEKAGAKMVGyvsldgyenftssrcliphlneitppedgekfCGLPVDEDSEnDRTQERVENW 174
                   ***********************************************************99******************9 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.1e-05      0.12      12      31 ..      99     118 ..      94     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
      ANAPC5  12 kdYqqaldsLhryFDyvlsq 31 
                 +dY +a+++LhryF  +  +
  AJA91837.1  99 QDYVDAMEELHRYFEKAGAK 118
                 8*************887665 PP

>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.057   3.4e+02      13      70 ..       3      64 ..       1      80 [. 0.66
   2 ?    8.8   0.0   0.00034         2      57      85 ..     154     182 ..     130     184 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.057
                EEEEEE-S--SS---EEEEE---H..HHHHHHHHH..HHHHTT--EEEEE------SSS--- CS
        RuvX 13 iGvAvsdplgilaspletierksk..ekdleelke..lvkeeeveeiVvGlPlnldgseges 70
                iG+  + ++g++ +   +i+++ +   ++++++ e  l++   ++ ++ G+P+   g e+ +
  AJA91837.1  3 IGLYFGTQTGKTETVCGIIKEQLGdaVANAKDVTEsdLADFAGLDGLICGIPTWNTGAEELR 64
                77777777777777777777664422344444433114555589999999998888877654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00034
                 EE------SSS---SSTTHHHHHHHHHT. CS
        RuvX  57 vGlPlnldgsegesakkvrkfaeeLakrl 85 
                  GlP++ d ++ +++++v++++ +L+k++
  AJA91837.1 154 CGLPVDEDSENDRTQERVENWCAQLKKEM 182
                 7*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1289.07
//
Query:       AJA91838.1  [L=401]
Description: ATPase, AAA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-38  132.5   0.0    3.3e-38  131.1   0.0    1.7  1  AAA              ATPase family associated with various cellul
    5.9e-07   29.7   0.0    1.1e-06   28.8   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
      7e-07   29.2   0.0    2.5e-06   27.4   0.0    2.0  1  Vps4_C           Vps4 C terminal oligomerisation domain
      7e-06   26.4   0.1     0.0014   18.9   0.0    3.3  3  AAA_22           AAA domain
    8.4e-06   26.3   0.0     0.0036   17.7   0.0    2.7  2  AAA_16           AAA ATPase domain
    2.8e-05   23.8   0.0    8.7e-05   22.3   0.0    1.9  1  AAA_lid_3        AAA+ lid domain
      3e-05   24.0   4.6    5.8e-05   23.1   4.6    1.5  1  MIT              MIT (microtubule interacting and transport) 
    6.6e-05   22.9   0.1     0.0024   17.8   0.1    2.8  1  AAA_5            AAA domain (dynein-related subfamily)
    6.8e-05   22.7   0.0    0.00033   20.4   0.0    2.1  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00013   22.1   0.2      0.004   17.3   0.0    2.7  2  AAA_33           AAA domain
     0.0019   17.8   0.0     0.0037   16.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0022   18.0   0.0     0.0048   16.9   0.0    1.6  1  AAA_14           AAA domain
      0.004   16.9   0.0     0.0071   16.1   0.0    1.4  1  AAA_24           AAA domain
     0.0043   17.0   0.0        3.3    7.6   0.0    2.6  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0046   16.4   0.1     0.0098   15.3   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0086   15.8   0.2       0.71    9.6   0.1    3.2  3  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.062   12.9   0.0    2.1  2  AAA_25           AAA domain
      0.012   14.8   0.0      0.025   13.8   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.016   15.0   0.0      0.031   14.0   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.03   14.3   0.0       0.37   10.7   0.0    2.3  2  NACHT            NACHT domain
       0.04   13.1   0.0       0.17   11.1   0.0    1.9  2  KAP_NTPase       KAP family P-loop domain
      0.052   13.3   0.2       0.21   11.3   0.0    1.9  2  AAA_11           AAA domain
      0.061   13.6   0.1       0.33   11.2   0.0    2.1  2  HTH_Tnp_Tc3_2    Transposase
      0.062   13.7   0.1       0.37   11.2   0.0    2.3  2  RNA_helicase     RNA helicase
      0.076   12.2   0.0        2.1    7.5   0.0    2.2  2  NB-ARC           NB-ARC domain
       0.11   12.2   0.0       0.37   10.5   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
       0.11   11.7   0.0       0.61    9.3   0.0    2.0  2  Zeta_toxin       Zeta toxin
       0.12   11.7   0.1        1.5    8.1   0.1    2.3  2  ATPase           KaiC
       0.15   12.7   0.1        3.7    8.3   0.0    2.8  3  Tn7_Tnp_TnsA_C   TnsA endonuclease C terminal


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   5.3e-41   3.3e-38       1     131 [.     156     290 ..     156     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 5.3e-41
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqLlteldg 95 
                 +llyGppGtGKT+la a a+el+ +f+++++++++sk++ge+ek++++lf+ a++ +    kp+ilfiDE+d+l ++r +se + e r+ nq+l+eldg
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELDGYFINVDAASMMSKWLGEAEKNVSKLFTMARKYNeregKPVILFIDEVDSLLGDR-NSEVGGEIRAKNQFLSELDG 253
                 89***************************************************9999999999***************.89999*************** PP

                 TTTS..SSTEEEEEEESSGGGSTHHHHSTTSSEEEETT CS
         AAA  96 vkkk..eskvivigatnrpdkldpallrgRfdrkieie 131
                 v+ k  e  + vigatn+p++ld+++l +Rf+++i+++
  AJA91838.1 254 VNGKgkETMMYVIGATNKPWSLDEPFL-RRFQKRIYVS 290
                 *9997777799****************.7******997 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.8e-09   1.1e-06       6      80 ..     156     229 ..     154     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.8e-09
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTS.EEEEETGGG- CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegG.ivllDEidKi 80 
                 +ll gp g+Gkt+la a+a+ l+      +i +da +++     e+e+ vs+l   +  y+++e +  i+++DE+d  
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELDG----YFINVDAASMMSkwLGEAEKNVSKLFTMARKYNEREGKPvILFIDEVDSL 229
                 5789******************95....9******99999776899**************999988867899***965 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.1e-09   2.5e-06      26      61 .]     363     399 ..     350     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.1e-09
      Vps4_C  26 eP.pvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                  P ++t+ Df+++ ++ +p+Vs e ++ + ++ ++fG
  AJA91838.1 363 DPrELTMADFKDIKARRKPSVSTENIRAYHKWSESFG 399
                 5659********************************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.5   3.4e+03      43      71 ..      40      74 ..       9     101 .. 0.66
   2 !   18.9   0.0   2.3e-06    0.0014       8     104 ..     156     230 ..     153     271 .. 0.70
   3 ?   -0.5   0.0       2.2   1.4e+03      54      84 ..     294     321 ..     250     346 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.5
      AAA_22 43 v..fvtlpsstsskdllrellralglelka....e 71
                +  ++ l   +s+ +++++  ++++++ ka    +
  AJA91838.1 40 LlkLMRLYPTSSLNKIYQQSYQKYQERIKAlretR 74
                33556666666777888888888887777644440 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2.3e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlr 104
                 ++++G++GtGKT+l++  +++l         +  ++ v+++s +      ++ l + +    +   + + l+++ +++ ++ +++++l iDE++ l 
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANEL---------DGYFINVDAASMM------SKWLGEAE----K---NVSKLFTMARKYNEREGKPVILFIDEVDSLL 230
                 689******************9.........5666677777766......22222222....2...6667777777777777777777788888754 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.2
      AAA_22  54 kdllrellralglelkaerlsseellealeq 84 
                 +d +++l+++++++lk+   s++  ++ l++
  AJA91838.1 294 QDARHKLFEQYTNPLKK---STRFNIASLAK 321
                 45567777777777777...33333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.9e-06    0.0036      24      57 ..     153     183 ..     147     199 .. 0.83
   2 ?    5.5   0.0     0.033        20     123     146 ..     205     228 ..     192     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.9e-06
      AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflr 57 
                 p+ +ll+G++G+GK+ l+ + +++l    g+f++
  AJA91838.1 153 PRGMLLYGPPGTGKTMLAAATANELD---GYFIN 183
                 6899**************99998776...56665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
      AAA_16 123 lkrllallsrderplvlvlDdlqw 146
                 ++ + ++ +r+++p++l++D+++ 
  AJA91838.1 205 FTMARKYNEREGKPVILFIDEVDS 228
                 44455889999***********94 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.4e-07   8.7e-05       2      36 ..     314     348 ..     313     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.4e-07
   AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                 ++++ LA++ +GyS  D++ +c+ A ll + + + 
  AJA91838.1 314 FNIASLAKQFDGYSASDIKDVCQGAQLLVVNELFR 348
                 699************************99998433 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   4.6   9.4e-08   5.8e-05       3      65 .]       9      72 ..       7      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 9.4e-08
         MIT  3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalk.ekneerrellrekieeYleRaeeLke 65
                +A +++ +A+ +D++g    A+  Y++a e Ll++++   +++  + +++  ++Y+eR++ L+e
  AJA91838.1  9 SASKYAAAAIRADSQGAAGMAITDYQNASETLLKLMRlYPTSSLNKIYQQSYQKYQERIKALRE 72
                7999*********************************55888******************9975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1     4e-06    0.0024       2     138 .]     156     283 ..     155     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.......G-SEEEEESGGG--HHHHHHHHHHHHSSE CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.......egeilvlDEveraesevlnsLlslleerr 93 
                 +lL GppGtgK++la   a  l   +  v   + ++      ++    g+++   s+l + ar       ++ il++DEv+ +  +  +++   +  + 
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELDGYFINVDAASMMS------KWL---GEAEKNVSKLFTMARkyneregKPVILFIDEVDSLLGDRNSEVGGEIRAKN 245
                 79*************999998876665554444333......333...333344466666666677777788899999999666555555555555555 PP

                 EE..-SSSEEE---.......-EEEEEESS--.-TT-TTHHHHTT- CS
       AAA_5  94 llleeggelvkaknddller.frviatanpldrslnelspalrsRf 138
                   l e++++ ++ ++    + ++vi+++n++     +l++++++Rf
  AJA91838.1 246 QFLSELDGVNGKGKE----TmMYVIGATNKPW----SLDEPFLRRF 283
                 555555555544443....1488888888888....7888888887 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.3e-07   0.00033      36      96 ..     156     229 ..     120     288 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.3e-07
      RuvB_N  36 vllyGpPGlGkttlakiiakelgvk.lkitsgPvlek.....agdlaallt...nleekd....vlfideihrl 96 
                 +llyGpPG Gkt la+  a+el+   +++ ++ +++k     +++++ l+t   + +e++    +lfide+  l
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELDGYfINVDAASMMSKwlgeaEKNVSKLFTmarKYNEREgkpvILFIDEVDSL 229
                 79********************8651445555555432222133444444311144444355557888888766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.42   2.6e+02      63     119 ..      44      99 ..      12     116 .. 0.55
   2 !   17.3   0.0   6.5e-06     0.004       3      35 ..     157     189 ..     156     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.42
      AAA_33  63 arkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRa 119
                  r + ++  n i  + + + +er + l+  r ++v+  +v+ ++++e+ k+ la+ +
  AJA91838.1  44 MRLYPTSSLNKIYQQSYQKYQERIKALRETRGANVE-PVVDPNASPEEQKKALARAQ 99 
                 444444444444444444444444444444444433.44555555555444444333 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6.5e-06
      AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrr 35 
                 ll G+pG+GK+ la   +++l++++++ d+++ 
  AJA91838.1 157 LLYGPPGTGKTMLAAATANELDGYFINVDAASM 189
                 688**************************9554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.9e-06    0.0037      36     110 ..     156     227 ..     153     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.9e-06
       AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklek..rrkgvygPpggkklvvFvDDln 110
                 +ll+Gp GtGKt+++  + ++ld       +in+ a    ++     e+++ k     + y    gk +++F+D+++
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELD-----GYFINVDAASMMSKWLGEAEKNVSKlfTMARKYNEREGKPVILFIDEVD 227
                 89********************9.....77888888888888888888888883335689**************986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.8e-06    0.0048       5     102 ..     156     270 ..     153     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-06
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd......kkladpekllelileklke..ekktylflDEiqev...............pewe 80 
                 +++ G+  +GKT+l+   ++el        +in+d  +       +++++ +kl ++ ++   e   k  +lf+DE+  +               +++ 
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELD-----GYFINVDAASMmskwlgEAEKNVSKLFTMARKYN-EreGKPVILFIDEVDSLlgdrnsevggeirakNQFL 248
                 6799**************98877.....3444444444422332211112223333333331.13246778******9988888888888887777777 PP

      AAA_14  81 kalkslvdegknldvivtGSns 102
                 + l ++  +gk+  ++v G  +
  AJA91838.1 249 SELDGVNGKGKETMMYVIGATN 270
                 7777777777777777777665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.2e-05    0.0071       5      77 ..     156     229 ..     153     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
      AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                 +l+yGp+g+GKT+la+    + +  fi++++ +  +  + ++  +++ ++   + + ++ + +  +l+iD +d l
  AJA91838.1 156 MLLYGPPGTGKTMLAAATanELDGYFINVDAAS-MMSKWLGEAEKNVSKLFTMARKYNEREGKPVILFIDEVDSL 229
                 79*************998676677788888833.55666555445555555555555555555556777777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0      0.01       6.5      24      45 ..     157     178 ..     153     187 .. 0.86
   2 !    7.6   0.0    0.0054       3.3      93     131 ..     192     230 ..     181     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
    ATPase_2  24 fiYGpegsGKtaLlkeiienle 45 
                 ++YGp g GKt L    +++l+
  AJA91838.1 157 LLYGPPGTGKTMLAAATANELD 178
                 79***********999999885 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0054
    ATPase_2  93 eilkeksklvfkaielllekikkkgkkiiiiiDelqkli 131
                 + l e  k+v k ++ + +  +++gk +i++iDe+  l 
  AJA91838.1 192 KWLGEAEKNVSKLFTMARKYNEREGKPVILFIDEVDSLL 230
                 444588899999999999999999999********8876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.6e-05    0.0098      25      42 ..     156     173 ..     153     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                   +ll+GppG+GKtmla++ 
    AJA91838.1 156 MLLYGPPGTGKTMLAAAT 173
                   89************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.84   5.2e+02     144     175 ..      45      76 ..      25      84 .. 0.80
   2 !    9.6   0.1    0.0011      0.71      21      81 ..     156     209 ..     153     235 .. 0.60
   3 ?    1.5   0.0      0.34   2.1e+02      13      40 ..     241     268 ..     230     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.84
      AAA_30 144 agigtaeLtevvRqkeseeraaalalregdae 175
                 +  +t +L++++ q+ +++++  +alre + +
  AJA91838.1  45 RLYPTSSLNKIYQQSYQKYQERIKALRETRGA 76 
                 4678999*******999999999999987665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
      AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk 81 
                 ++l Gp+GtGKt++ +a ++ ++  g     +  +  aA  +++ lg + +++ kl +  +
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELD--G-----YFINVDAASMMSKWLGEAEKNVSKLFTMAR 209
                 5789********98877765444..3.....233334445555555555555555555555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.34
      AAA_30  13 lltsgdrvavltGpAGtGKttalkalre 40 
                 + ++++ ++ l G+ G GK t++ ++ +
  AJA91838.1 241 IRAKNQFLSELDGVNGKGKETMMYVIGA 268
                 66777788889999*****999988744 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.062      24      54 ..     146     174 ..     131     177 .. 0.74
   2 ?   -0.8   0.0       1.5   9.5e+02     133     161 ..     207     237 ..     182     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
      AAA_25  24 wlvk.gllpagelallaGapgtGKttlaldla 54 
                 +l++ g+ p+g   ll+G+pgtGKt+la   a
  AJA91838.1 146 DLFPlGW-PRG--MLLYGPPGTGKTMLAAATA 174
                 5555444.544..58************98765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
      AAA_25 133 leaaieeveg.vrlvviDplsralgg.dens 161
                 ++++ +e+eg ++ + iD ++++lg  +++ 
  AJA91838.1 207 MARKYNEREGkPVILFIDEVDSLLGDrNSEV 237
                 5667777777899999999999998754444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     4e-05     0.025      51      91 ..     154     192 ..     151     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                 r++Ll Gp+gtGkt la a ++el     f+ + ++ + s 
  AJA91838.1 154 RGMLLYGPPGTGKTMLAAATANELD--GYFINVDAASMMSK 192
                 899********************97..56777777776665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-05     0.031      49      71 ..     155     177 ..     151     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-05
   IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                 +++l Gp+G+GK+ la+a + e 
  AJA91838.1 155 GMLLYGPPGTGKTMLAAATANEL 177
                 5799**************98764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00059      0.37       3      23 ..     156     176 ..     154     182 .. 0.86
   2 ?    0.7   0.0      0.73   4.5e+02       5      31 ..     251     277 ..     248     324 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l G++G GKT+L++  a +
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANE 176
                 799************987766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.73
                 EEC-TTTCHHHHHHHHHHHHCTS-SCC CS
       NACHT   5 lqGeaGsGKTtLlqklalawaegklpq 31 
                 l G +G+GK t++  +  + + + l++
  AJA91838.1 251 LDGVNGKGKETMMYVIGATNKPWSLDE 277
                 67999***9999887766666665555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.91   5.6e+02      24      45 ..     157     178 ..     152     192 .. 0.82
   2 ?   11.1   0.0   0.00028      0.17     152     194 ..     196     238 ..     163     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.91
  KAP_NTPase  24 gLygkWGsGKssllnkledelk 45 
                  Lyg+ G+GK+ l +   +el+
  AJA91838.1 157 LLYGPPGTGKTMLAAATANELD 178
                 699*********9988888775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00028
  KAP_NTPase 152 klqteveelladmektLdalqkrlVvviDdLDrceteevlqll 194
                 +  + v++l++++ k+ +++ k+++++iD+ D++  ++  ++ 
  AJA91838.1 196 EAEKNVSKLFTMARKYNEREGKPVILFIDEVDSLLGDRNSEVG 238
                 56678888**************************999988775 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       2.4   1.5e+03     129     145 ..      56      72 ..       8     122 .. 0.49
   2 ?   11.3   0.0   0.00034      0.21      20      43 ..     156     191 ..     143     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
      AAA_11 129 iskeleklakelrafee 145
                  +++ +k+++ ++a  e
  AJA91838.1  56 YQQSYQKYQERIKALRE 72 
                 22222222222222211 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
      AAA_11  20 tliqGPPGtgKTktivellsqll............s 43 
                  l+ GPPGtgKT   ++  ++l             s
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANELDgyfinvdaasmmS 191
                 5899********999999999965555555544430 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.1   1.9e+03       4      26 ..      40      62 ..      38      69 .. 0.80
   2 ?   11.2   0.0   0.00054      0.33      37      67 ..     365     395 ..     364     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.1
  HTH_Tnp_Tc3_2  4 IvrlvrkdPritlreLanelkee 26
                   +++l+r  P+ +l ++ +++ ++
     AJA91838.1 40 LLKLMRLYPTSSLNKIYQQSYQK 62
                   78899999********9988766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00054
  HTH_Tnp_Tc3_2  37 rrLrkaglkkrkprkkplLskknrkaRLeFA 67 
                    r L +a++k  k+r+kp +s++n++a  +++
     AJA91838.1 365 RELTMADFKDIKARRKPSVSTENIRAYHKWS 395
                    7899********************9866665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0006      0.37       2      25 ..     157     180 ..     156     226 .. 0.84
   2 ?   -0.7   0.0       3.1   1.9e+03       5      20 ..     253     268 ..     249     336 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0006
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                   +lyGp+g+GK++la   a++l + 
    AJA91838.1 157 LLYGPPGTGKTMLAAATANELDGY 180
                   79************9988887655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.1
  RNA_helicase   5 GpsgeGKStlakeLak 20 
                   G +g GK t+++ + +
    AJA91838.1 253 GVNGKGKETMMYVIGA 268
                   6678888888877443 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0034       2.1      23      44 ..     156     177 ..     153     207 .. 0.87
   2 ?    2.3   0.0      0.12        77      24      79 ..     250     311 ..     241     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0034
                 EEEEESTTSSHHHHHHHHCCSH CS
      NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                 + l+G +G GKt la+   n++
  AJA91838.1 156 MLLYGPPGTGKTMLAAATANEL 177
                 789************9988875 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                 EEEESTTSSHHHHHHHH..CCSHCCCC....CCBTEEEEEEEESXXHHHHHHHXXHHHHHCC CS
      NB-ARC  24 alvGmgGvGKttlakqi..lnksdeve....grFdsvawvvvsktdkseeiletilkeLsls 79 
                  l G  G GK t++  i   nk  +++    +rF   ++v++  +d  ++++e+  + L++s
  AJA91838.1 250 ELDGVNGKGKETMMYVIgaTNKPWSLDepflRRFQKRIYVSLPAQDARHKLFEQYTNPLKKS 311
                 577888999999987762233333333222279999999**99******9999999999776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0006      0.37      25      66 ..     156     194 ..     151     236 .. 0.71
   2 ?   -2.4   0.0       5.5   3.4e+03      28      42 ..     252     266 ..     241     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0006
                      EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH CS
  Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeell 66 
                      +l+ G  GtGK++la a  ++    ++ f++v+ a++ ++ l
       AJA91838.1 156 MLLYGPPGTGKTMLAAATANE---LDGYFINVDAASMMSKWL 194
                      79*************997654...568999999998865544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.5
                      ECSTTSSHHHHHHHH CS
  Sigma54_activat  28 tGesGtGKellarai 42 
                       G +G GKe++   i
       AJA91838.1 252 DGVNGKGKETMMYVI 266
                      577788887766555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00098      0.61      16      51 ..     153     186 ..     147     191 .. 0.87
   2 ?   -1.0   0.0       1.4   8.9e+02     132     173 ..     198     254 ..     196     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00098
  Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                 P  +ll G pG GK+ la+++++el  +g ++ +d+
  AJA91838.1 153 PRGMLLYGPPGTGKTMLAAATANEL--DGYFINVDA 186
                 5667999******************..899998887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
  Zeta_toxin 132 kkelSrlgvldRyeeevae..............g.Rlvpkeehdeafeglresveal 173
                 +k++S l++++R  +e ++              g R+ ++   ++a +++ ++++ +
  AJA91838.1 198 EKNVSKLFTMARKYNEREGkpvilfidevdsllGdRNSEVGGEIRAKNQFLSELDGV 254
                 788999999999888833345677777777777567777777777777777776665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0025       1.5      21      37 ..     155     171 ..     146     176 .. 0.86
   2 ?    0.8   0.0      0.41   2.6e+02      81     153 ..     179     250 ..     172     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
      ATPase  21 vvlitGepGtGKtifal 37 
                  +l++G pGtGKt++a+
  AJA91838.1 155 GMLLYGPPGTGKTMLAA 171
                 489***********986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.41
      ATPase  81 gklaiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkk 153
                 g ++ +da++++++    + ++++++l +  +++ ++ +    + iD +++l   ++++++  ++r   ++l++
  AJA91838.1 179 GYFINVDAASMMSKWLG-EAEKNVSKLFTMARKYNEREGKpVILFIDEVDSL-LGDRNSEVGGEIRAKNQFLSE 250
                 66777888888776443.788889998888777765444427788******9.777777777777766666655 PP

>> Tn7_Tnp_TnsA_C  TnsA endonuclease C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.6     1e+03      29      55 ..      33      59 ..      19      76 .. 0.57
   2 ?   -1.2   0.0       5.3   3.3e+03      33      66 ..     187     218 ..     173     222 .. 0.75
   3 ?    8.3   0.0    0.0059       3.7      12      65 ..     279     333 ..     278     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.6
  Tn7_Tnp_TnsA_C 29 leelaelllerlrenpdttlrellkel 55
                    +++  e ll+ +r  p+++l+++ ++ 
      AJA91838.1 33 YQNASETLLKLMRLYPTSSLNKIYQQS 59
                    555555566655555666666555554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.3
  Tn7_Tnp_TnsA_C  33 aelllerlrenpdttlrellkelDkeyslergts 66 
                     a+ +++ l e+ ++++++l++   ++y+ ++g+ 
      AJA91838.1 187 ASMMSKWLGEA-EKNVSKLFTMA-RKYNEREGKP 218
                     45555666677.99999999999.9999999875 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0059
  Tn7_Tnp_TnsA_C  12 wlhpyrriedddlseeel.eelaelllerlrenpdttlrellkelDkeyslergt 65 
                     +l++++++   +l++++  + l+e++ + l+++   ++ +l+k++D     +  +
      AJA91838.1 279 FLRRFQKRIYVSLPAQDArHKLFEQYTNPLKKSTRFNIASLAKQFDGYSASDIKD 333
                     677777777777777777799************************9877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 2698.76
//
Query:       AJA91839.1  [L=123]
Description: hypothetical protein T478_0945 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.067   13.2   0.2       0.12   12.4   0.2    1.4  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.12   12.2   0.0       0.13   12.2   0.0    1.1  1  DUF4572        Domain of unknown function (DUF4572)


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.3e-05      0.12      19      33 ..      99     113 ..      93     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
  Zn_Tnp_IS1595  19 fvCPhCgsrkayrik 33 
                    f CPhCg+ ++y++ 
     AJA91839.1  99 FSCPHCGHITPYETV 113
                    78*****99999875 PP

>> DUF4572  Domain of unknown function (DUF4572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05      0.13      56     121 ..      44     108 ..      24     123 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
     DUF4572  56 gekdegtlisetheqlsqvllkkefkeiktrksllneeslasailerdeglpktgfgavlprhppd 121
                 g+ d+++++++ +e l+ +  +++f+ i+ r  ++  es+a   +erd ++ ++g+ +     +  
  AJA91839.1  44 GTIDTNEVVTSIKEFLESIGEQRNFAVIS-RGEIISIESIAGKTIERDSKQSAEGLFSCPHCGHIT 108
                 78899999*********************.*******************99999965544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 853.09
//
Query:       AJA91840.1  [L=166]
Description: DNA-binding helix-turn-helix protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-10   38.7   0.6    2.1e-09   37.3   0.3    1.8  2  HTH_20           Helix-turn-helix domain
    2.2e-06   27.4   1.0    2.2e-05   24.3   0.5    2.5  2  HTH_5            Bacterial regulatory protein, arsR family
    0.00029   21.0   2.1     0.0006   20.0   1.9    1.7  1  FUR              Ferric uptake regulator family
  ------ inclusion threshold ------
      0.014   15.3   1.3      0.016   15.1   1.3    1.3  1  AbiH             Bacteriophage abortive infection AbiH
      0.022   15.2   6.6      0.023   15.1   1.1    2.1  2  eIF3_N           eIF3 subunit 6 N terminal domain
      0.037   13.6   0.2      0.056   13.1   0.2    1.3  1  DUF2240          Uncharacterized protein conserved in archaea
      0.048   13.7   0.1       0.12   12.4   0.1    1.7  1  DUF4485          Domain of unknown function (DUF4485)
      0.061   13.4   0.5       0.13   12.3   0.5    1.7  1  SEA              SEA domain
      0.067   13.2   0.4        0.2   11.7   0.4    1.8  1  HTH_12           Ribonuclease R winged-helix domain
       0.16   11.0   1.1       0.18   10.9   1.1    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.3   1.2e-12   2.1e-09       4      59 ..      22      81 ..      19      83 .. 0.90
   2 ?   -1.4   0.0       1.4   2.6e+03      27      36 ..     119     129 ..     115     136 .. 0.58

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.2e-12
                HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20  4 aeALahPvRrrilraLaraegltaselaerl.....dlskntlsyHLrvLeeagLvevvre 59
                a+A+ +P R+++l++L  ++ l a+++ ++l       + +t ++HL++L ea+L+evv+ 
  AJA91840.1 22 AKAIEDPARAKVLQLL-YRKHLNAEQITAQLkksgfKKALTTTRHHLEILKEAELIEVVKI 81
                89**************.9*************665444*********************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                 HHHHHHHHT.S CS
      HTH_20  27 aselaerld.l 36 
                  +++ ++ld l
  AJA91840.1 119 SKQIEQLLDaL 129
                 45555555434 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   1.2e-08   2.2e-05       1      46 [.      27      77 ..      27      78 .. 0.90
   2 ?   -1.9   0.0       1.8   3.3e+03       6      19 ..     124     139 ..     123     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                SHHHHHHHHHHTTSSEEHHHHHHHHTS-H.....HHHHHHHHHHHHTTSEE CS
       HTH_5  1 dptRlkILklLaegelcvcelaeelglsq.....stvShHLkkLreaGLVe 46
                dp+R k+L+lL ++ l + +++++l++s       t++hHL +L+ea L+e
  AJA91840.1 27 DPARAKVLQLLYRKHLNAEQITAQLKKSGfkkalTTTRHHLEILKEAELIE 77
                8************************9984444449**************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.8
                 HHHHHHTT..SSEEHH CS
       HTH_5   6 kILklLae..gelcvc 19 
                 ++L +L++  g+++ +
  AJA91840.1 124 QLLDALSKktGKAKTS 139
                 5788888866666555 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.9   3.3e-07    0.0006       9      67 ..      29      85 ..      26     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.3e-07
                HHHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSE CS
         FUR  9 qRekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedge 67
                 R k+l++l+  ++hl+ae+++ +lk+ + +  l+T    L++l+ea+l++ +++e+++
  AJA91840.1 29 ARAKVLQLLY--RKHLNAEQITAQLKKSGFKKALTTTRHHLEILKEAELIEVVKIEEKR 85
                6899999997..57***************************************999654 PP

>> AbiH  Bacteriophage abortive infection AbiH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.3   8.8e-06     0.016      35     106 ..      85     155 ..      26     166 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.8e-06
        AbiH  35 nelleellkkenkasekekWsdlEkelgellkklekkdveeliddikdalteylkdsedesdkdvysekake 106
                   ++ +++ ++ k  + e+  d+Ek++++++k+ +k ++e+l+d ++++  + +++++++++++++ +++ +
  AJA91840.1  85 RGAMIKYYGTSTKLLDYETPKDFEKKYSTVIKSTSK-QIEQLLDALSKKTGKAKTSQNKQEYSQYLMMEIVN 155
                 23333455689999999999**********987666.56999999999999999999999999988766655 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5     0.061   1.1e+02      68     119 ..      27      77 ..       5      83 .. 0.69
   2 ?   15.1   1.1   1.3e-05     0.023      45     115 ..      87     152 ..      83     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.061
      eIF3_N  68 ekkreevleeleeleeeaekvlelledeevvsnlrsdkkqnlefLkeehgit 119
                 +  r++vl+ l +   +ae+++  l+++ ++++l+ + ++ le+Lke   i+
  AJA91840.1  27 DPARAKVLQLLYRKHLNAEQITAQLKKSGFKKALT-TTRHHLEILKEAELIE 77 
                 34678888888888888899999998888888885.5566778888766555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.3e-05
      eIF3_N  45 nmvdyaadlykelegeeevpeelekkreevleeleeleeeaekvlelledeevvsnlrsdkkqnlefLkee 115
                  m+ y  +  k l  + e+p+++ekk ++v++     ++++e++l+ l++++ +++ +++k++ +++L  e
  AJA91840.1  87 AMIKYYGTSTKLL--DYETPKDFEKKYSTVIKS---TSKQIEQLLDALSKKTGKAKTSQNKQEYSQYLMME 152
                 6888888888888..4689***********985...5567***************************9755 PP

>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   3.1e-05     0.056      15     104 ..      48     139 ..      40     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
     DUF2240  15 kdklsesdfvfalsldrkwls...pdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpdeell..kekstferildaiaastgiekke 104
                 +++l++s f  al+  r+ l+     +  +++++ e++g + k  g  +   d+   e P++F+ + ++    + + +e++lda++++tg+ k++
  AJA91840.1  48 TAQLKKSGFKKALTTTRHHLEilkEAELIEVVKIEEKRGAMIKYYGTSTKLLDY---ETPKDFEKKYSTVikSTSKQIEQLLDALSKKTGKAKTS 139
                 678888888888888877655100444456667777888888866666666665...56****9998888888999*************998864 PP

>> DUF4485  Domain of unknown function (DUF4485)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.7e-05      0.12      25      71 ..     119     164 ..     104     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.7e-05
     DUF4485  25 kervaeWlkkLcepekenleekknRNdYlqlLlkmlqngrlegPFnk 71 
                  + +++ l+ L++++  +++  +n+ +Y q+L++ + n+ ++++F+k
  AJA91840.1 119 SKQIEQLLDALSKKTG-KAKTSQNKQEYSQYLMMEIVNRAVTTVFEK 164
                 5566777899999999.9***************************98 PP

>> SEA  SEA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   7.4e-05      0.13       2      44 ..      91     133 ..      90     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.4e-05
         SEA   2 yftgsftitnveyspdladpsSaefkslardieelldevfqks 44 
                 y+  s ++ + e  +d++++ S+  ks++++ie+lld + +k+
  AJA91840.1  91 YYGTSTKLLDYETPKDFEKKYSTVIKSTSKQIEQLLDALSKKT 133
                 666677777778889**********************998883 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00011       0.2      13      50 ..      41      78 ..      32      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
      HTH_12 13 pigakeiaeeLkkrgydigeravRyrLrkleergltrr 50
                 + a++i  +Lkk g +    + R +L +l e +l++ 
  AJA91840.1 41 HLNAEQITAQLKKSGFKKALTTTRHHLEILKEAELIEV 78
                47899*************9***************9985 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.1    0.0001      0.18      44     145 ..      43     149 ..      16     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
  ABC2_membrane_3  44 lsqqlvealeaspsve......lvyevdseeeakkalkngdidgilvipkgfskdllkgesa.tvtvlinssnlnsskailnalnsllqqlnas 130
                      +++q++++l++s+  +       + e+  e+e+ + +k ++  g+++ + g s +ll++e++ +++  +++   ++sk+i++ l++l+++ +++
       AJA91840.1  43 NAEQITAQLKKSGFKKaltttrHHLEILKEAELIEVVKIEEKRGAMIKYYGTSTKLLDYETPkDFEKKYSTVIKSTSKQIEQLLDALSKKTGKA 136
                      6777888888776544666755566677788888**************999999999555554999999*****************99999987 PP

  ABC2_membrane_3 131 alvlqseatstsani 145
                      +++  +++++ s+ +
       AJA91840.1 137 KTS--QNKQEYSQYL 149
                      765..4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2397  (0.133694); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1251.87
//
Query:       AJA91841.1  [L=298]
Description: ribonuclease Z [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-17   62.9   0.0    3.5e-08   33.2   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.9e-08   34.6   0.0    1.1e-07   32.0   0.0    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    6.9e-05   22.5   0.0    0.00012   21.7   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.18   11.9   0.0    1.3  1  DUF4130        Domain of unknown function (DUF4130


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   7.7e-12   3.5e-08       5     138 ..      33     154 ..      30     176 .. 0.78
   2 !   27.7   0.0   3.7e-10   1.7e-06     132     201 .]     197     266 ..     189     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7.7e-12
                    ES--TTHHHH.HTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TT CS
  Lactamase_B_2   5 iDagpdlrqq.alralqPve.lrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyapkgvlavleanfvylaleeepavnvheldwg 93 
                    +Dag +  +q a  +l ++  ++++  + + +++th H DH+ g+l l +   l+++   +++y+p+g+ + ++an++ l+++ +++v ++ +d g
     AJA91841.1  33 FDAGEG--AQvA--YL-KAGlPWNK--KMK-IFVTHLHGDHCLGILGLLQtmsLQKRTeaVEIYGPAGIEEFITANIKVLNFGLPFPVFITIVDEG 120
                    666666..2311..11.12223444..666.9******************9873333358************************988888888888 PP

                    SEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEE CS
  Lactamase_B_2  94 esfelgdggleitatparhksgrrldrnagdtlGlriegggkrvy 138
                    + ++ +  + +i + +a+h+ +          +++++e+++++ +
     AJA91841.1 121 NVVKEK--NYQINCCEAQHGIPA---------FSYCFEENERAGV 154
                    877776..789*********998.........9999996666533 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 3.7e-10
                    CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
  Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                    ++gk++  +gDt  ++ +++e +++ d l +d+t+  + + ++ +  H+t +ea+e+a+++++k l+l+H+
     AJA91841.1 197 RPGKKIGISGDTRPTQ-KLKEFFENSDYLSFDCTFSYELKDRAiETNHSTAKEAAELAKEANVKNLILTHF 266
                    6899*********888.7799*************9988775559**************************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.6e-11   1.1e-07       8      87 ..      21      95 ..      15     127 .. 0.84
   2 ?   -0.3   0.0       0.2     9e+02      34      53 ..     247     266 ..     226     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.6e-11
                 EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHH CS
  Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeea 87
                 ++ ++ +++v+++D+G +++ a ++     +gl++++   +++THlH DH+ g  gl ++    ++ +a e + + + e+
   AJA91841.1 21 CICLVRENEVLMFDAGEGAQVAYLK-----AGLPWNKKMKIFVTHLHGDHCLGILGLLQTMSLQKRTEAVEIYGPAGIEE 95
                 5566799*****************8.....8**************************99988888888877776666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                  HHHHHTSGGGGEEEEE-SBS CS
  Lactamase_B  34 elaalglkpkdvdavilTHl 53 
                  + aa+  k  +v+ +ilTH+
   AJA91841.1 247 KEAAELAKEANVKNLILTHF 266
                  45678889999********6 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.6e-08   0.00012       4      60 ..      11      65 ..       8      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.6e-08
  Lactamase_B_4  4 ttptsDtsgPlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswss 60
                   ++pt++ s ++++L  +++  +f + gEg Q a  + ++  +k  +iF+t+ +  ++
     AJA91841.1 11 AAPTVERSLTCICLVRENEVLMF-DAGEGAQVAYLKAGLPWNKKMKIFVTHLH-GDH 65
                   799********************.***************************98.554 PP

>> DUF4130  Domain of unknown function (DUF4130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     4e-05      0.18      63      97 ..     250     284 ..     240     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
     DUF4130  63 akiePkhnvlellaehFadRfadekwlIldekrkl 97 
                 a+++ + nv +l+++hF+ R++de+ lI + k+  
  AJA91841.1 250 AELAKEANVKNLILTHFSARYNDESVLIDEAKQTH 284
                 6778899*******************998766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1923.62
//
Query:       AJA91842.1  [L=104]
Description: hypothetical protein T478_1491 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0071   16.2   5.6      0.012   15.5   5.5    1.5  1  DUF4013    Protein of unknown function (DUF4013)
  ------ inclusion threshold ------
      0.011   15.4   0.2      0.014   15.1   0.2    1.1  1  CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
      0.048   13.9   2.8      0.062   13.5   2.8    1.1  1  DUF3397    Protein of unknown function (DUF3397)
        1.2    9.3   3.8        7.7    6.7   2.0    2.0  2  YrhC       YrhC-like protein
        1.2    9.8   5.5        0.6   10.9   1.4    1.9  2  PrgI       PrgI family protein


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   5.5   3.3e-06     0.012      34      97 ..      35      85 ..      12      93 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.3e-06
     DUF4013 34 lPefddwgkllvdGlkafvvslvYlliplii..........alltllvalaslaagdsaagallvlallgllla 97
                lP    w+kl  +G+ ++v+s++Y + p+ii                               l + ++++l+la
  AJA91842.1 35 LPS---WKKLSTQGVAMIVLSVIYVIAPAIIvtregqthveP--------------------LWMSIVVMLALA 85
                455...589**********************44444433331....................222222222222 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   3.8e-06     0.014      84     139 ..      29      96 ..      18     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
   CPP1-like  84 lqesldtPssedlliraavflvlavltlvapaes............vpalllalglgasiyflnrKek 139
                 +++ ++ Ps ++l +++++++vl+v+ ++apa               ++++++l+l+++++f+ r++k
  AJA91842.1  29 ISRGIKLPSWKKLSTQGVAMIVLSVIYVIAPAIIvtregqthveplWMSIVVMLALAVTLFFQARRSK 96 
                 677899*************************98889999***999989999999**********9986 PP

>> DUF3397  Protein of unknown function (DUF3397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.8   1.7e-05     0.062       2      80 ..      13      95 ..      12     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
     DUF3397  2 ltiillpllvlllvyiivkkfslkk.kk..aklkalDvttpflilavhllseelfgksfl.pllllvllllaillliiqarkk 80
                l+++++p+++l ++ +i++ ++l + kk   +  a+ v+ +++++a +++++   ++++   ++ +v++l++ + l++qar++
  AJA91842.1 13 LAFTIYPFIALGIIELISRGIKLPSwKKlsTQGVAMIVLSVIYVIAPAIIVTREGQTHVEpLWMSIVVMLALAVTLFFQARRS 95
                6899**************99988884431135567777888888888888888888888755667777777777778888765 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3    0.0086        31      10      57 ..      15      62 ..       9      70 .. 0.82
   2 ?    6.7   2.0    0.0021       7.7      15      61 ..      48      94 ..      47      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0086
        YrhC 10 YkrFafvLLalsaFLyiGlviPseaketlkksillgaivvfLllaflf 57
                ++ + f+ L ++  +  G+ +Ps +k  ++   +++ +v+ +++  ++
  AJA91842.1 15 FTIYPFIALGIIELISRGIKLPSWKKLSTQGVAMIVLSVIYVIAPAII 62
                56688899999999999999***9999999999999999988875544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0021
        YrhC 15 fvLLalsaFLyiGlviPseaketlkksillgaivvfLllaflflrrs 61
                ++ L+++  +   +++  e++++++  ++  +++++L++ ++f  r 
  AJA91842.1 48 MIVLSVIYVIAPAIIVTREGQTHVEPLWMSIVVMLALAVTLFFQARR 94
                56666666666666777777777777777777777777776665544 PP

>> PrgI  PrgI family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.13   4.7e+02      52      65 ..      14      27 ..       7      40 .. 0.73
   2 ?   10.9   1.4   0.00017       0.6      14      67 ..      38      93 ..      31     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
        PrgI 52 illavPvaalgfyk 65
                 +++ P++alg+++
  AJA91842.1 14 AFTIYPFIALGIIE 27
                56789999999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00017
        PrgI 14 ffgLtlRQliflvlall.vaiglylllrafl.eelasvlvillavPvaalgfykkd 67
                + +L+   ++++vl ++ v +++++++r+      ++++ i++++ +a+  f++ +
  AJA91842.1 38 WKKLSTQGVAMIVLSVIyVIAPAIIVTREGQtHVEPLWMSIVVMLALAVTLFFQAR 93
                6777777788888877733444444444444788999************9999643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 711.97
//
Query:       AJA91843.1  [L=89]
Description: hypothetical protein T478_1204 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-08   33.1   2.5    6.4e-08   33.1   2.5    1.8  2  Trm112p          Trm112p-like protein
      0.006   16.6   0.1      0.006   16.6   0.1    1.4  2  Elf1             Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
      0.025   14.7   1.9       0.12   12.5   1.9    2.0  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
      0.086   13.2   0.1       0.11   12.9   0.1    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
        1.2    9.6   5.4        1.3    9.4   0.7    2.3  2  zf-C2H2_jaz      Zinc-finger double-stranded RNA-binding


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   2.5   1.8e-11   6.4e-08       1      67 [.       2      49 ..       2      50 .. 0.79
   2 ?   -2.3   0.0       1.9   6.9e+03      32      37 ..      67      73 ..      55      83 .. 0.53

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.8e-11
                BTGGCCC-B-TTTHH.C--HHHHHHHHHTT---S-SS----S..CHHTTEECCCCEEEETTTTEEEEEET CS
     Trm112p  1 kllllniLaCpackg.pLdwealvevaalglnelpkekpedy..ellleldieegeLvCpncgraYpIkd 67
                k++ll+iLaCp+ck+ pL  e + e                   +     +i+eg+++C  c r + I +
  AJA91843.1  2 KRKLLDILACPMCKKhPL--ELI-EI---------------KtkN----DEIVEGAIYCDTCERYFLIIE 49
                789*************99..122.11...............1212....69*****************87 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                -.S-SS- CS
     Trm112p 32 e.lpkek 37
                e l+k+k
  AJA91843.1 67 EfLQKNK 73
                2333333 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.7e-06     0.006      16      55 ..       3      45 ..       1      53 [. 0.83
   2 ?   -3.0   0.2       2.2     8e+03       5      17 ..      63      75 ..      60      79 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
        Elf1 16 kklptkFdCpfCnheksvevkldkkek...iaevsCkvCgesf 55
                +kl     Cp+C+++    +++++k++    + + C +C+ +f
  AJA91843.1  3 RKLLDILACPMCKKHPLELIEIKTKNDeivEGAIYCDTCERYF 45
                56888999*****997767778777777799********9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
        Elf1  5 kkakkrkkkkkkk 17
                k++++  +k+k++
  AJA91843.1 63 KQENEFLQKNKDS 75
                3333444555554 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.9   3.3e-05      0.12      10      31 ..      27      48 ..       8      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
  zf-RRPl_C4 10 kklknlnetvyCeaCeiyfkvk 31
                k+ + ++  +yC++Ce yf + 
  AJA91843.1 27 KNDEIVEGAIYCDTCERYFLII 48
                3344566789********9854 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     3e-05      0.11       3      36 ..       8      43 ..       6      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
  Lar_restr_allev  3 LkpCPfCggra.vlersqrvvaeigq.cvyCadCga 36
                     ++ CP C++ + +l++ + +  ei +  +yC+ C+ 
       AJA91843.1  8 ILACPMCKKHPlELIEIKTKNDEIVEgAIYCDTCER 43
                     789****99883566666666666668*******86 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3     0.057     2e+02       4      10 ..      11      17 ..       8      17 .. 0.87
   2 ?    9.4   0.7   0.00036       1.3       2      11 ..      36      45 ..      35      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                 BTTTTBB CS
  zf-C2H2_jaz  4 CvlCdKy 10
                 C+ C+K+
   AJA91843.1 11 CPMCKKH 17
                 *****97 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00036
                 CBBTTTTBBB CS
  zf-C2H2_jaz  2 fYCvlCdKyF 11
                  YC +C++yF
   AJA91843.1 36 IYCDTCERYF 45
                 5********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 650.28
//
Query:       AJA91844.1  [L=181]
Description: hypothetical protein T478_0144 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1265.18
//
Query:       AJA91845.1  [L=138]
Description: DNA-binding helix-turn-helix protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-05   23.9   0.2    0.00029   20.9   0.1    2.2  2  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
      0.042   13.9   0.0       0.23   11.5   0.0    2.0  2  Cro             Cro
      0.051   13.6   0.1        0.2   11.7   0.1    2.0  2  HTH_19          Helix-turn-helix domain
      0.059   13.2   0.0       0.35   10.8   0.0    2.3  3  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.077   12.8   0.1       0.12   12.2   0.1    1.5  1  DUF2570         Protein of unknown function (DUF2570)
      0.082   13.1   0.3        3.8    7.8   0.0    2.8  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
        0.1   12.6   0.5        1.2    9.2   0.0    2.2  2  UPF0154         Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.1e-07   0.00029      11      45 ..      31      64 ..      22      71 .. 0.84
   2 ?    1.0   0.1      0.18   4.5e+02      10      28 ..      76      93 ..      61      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                HHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHH CS
       HTH_3 11 sqeeLAeklGvsrstisriEnGernPsletlkkla 45
                  e+++++lGv++++is++++G ++ ++e +kkl+
  AJA91845.1 31 REEMISKMLGVTQAAISNYIRG-TRGDPELIKKLS 64
                56899*****************.558888888887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                HHHHHHHHHHTSSHHHHHH CS
       HTH_3 10 lsqeeLAeklGvsrstisr 28
                +sq  +++++  ++st+s+
  AJA91845.1 76 ISQNLASDMA-YTPSTLSK 93
                5555555555.57888887 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     9e-05      0.23      19      37 ..      36      54 ..      29      62 .. 0.89
   2 ?   -0.3   0.0      0.44   1.1e+03      11      33 ..      74      95 ..      66     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9e-05
                HHHHTS-HHHHHHHHHCT- CS
         Cro 19 AkdlgvkqsaIsKAlkakR 37
                 k+lgv+q+aIs  ++  R
  AJA91845.1 36 SKMLGVTQAAISNYIRGTR 54
                69**********9998777 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.44
                HHHHHHHHHHHHTS-HHHHHHHH CS
         Cro 11 tkvGQaktAkdlgvkqsaIsKAl 33
                +++ Q   A+d+  ++s +sK +
  AJA91845.1 74 QEISQN-LASDMAYTPSTLSKFI 95
                555553.6899999999999965 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.8e-05       0.2      16      48 ..      33      63 ..      22      81 .. 0.79
   2 ?   -0.2   0.0       0.4     1e+03      18      34 ..      80      96 ..      67     125 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
      HTH_19 16 eelaerlgisrskisaiEngkkdvpsaelllki 48
                e+++++lg++++ is+++ g + +p+  l++k+
  AJA91845.1 33 EMISKMLGVTQAAISNYIRGTRGDPE--LIKKL 63
                899*****************998986..44333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.4
      HTH_19 18 laerlgisrskisaiEn 34
                la++   ++s +s++++
  AJA91845.1 80 LASDMAYTPSTLSKFIG 96
                34444445888888774 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.35      16      42 ..      37      62 ..      32      72 .. 0.82
   2 ?   -1.4   0.0      0.87   2.2e+03      13      29 ..      79      95 ..      71     102 .. 0.81
   3 ?   -2.6   0.0       2.1   5.3e+03      54      62 ..     112     120 ..     111     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
  YdaS_antitoxin 16 ealgvsqqaVsqWlkgkkqvpaervpe 42
                    + lgv+q+a+s+ ++g+++ ++e + +
      AJA91845.1 37 KMLGVTQAAISNYIRGTRG-DPELIKK 62
                    569************9776.7777765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
  YdaS_antitoxin 13 aLAealgvsqqaVsqWl 29
                     LA     ++++ s+++
      AJA91845.1 79 NLASDMAYTPSTLSKFI 95
                    68888888999998876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.1
  YdaS_antitoxin  54 eeLRpDvdw 62 
                     +eL  D+d 
      AJA91845.1 112 HELESDIDE 120
                     899999997 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.5e-05      0.12      43      81 ..      53      91 ..      12     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
     DUF2570 43 qkanqrLteqLeqerqavekqqkianelkakveeekeev 81
                 + + +L+++L  e+q  e +q+i+++l   +  +  ++
  AJA91845.1 53 TRGDPELIKKLSAEKQVSEMIQEISQNLASDMAYTPSTL 91
                556779**********************99998766655 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0015       3.8      10      41 ..      16      48 ..      15      52 .. 0.81
   2 ?    0.5   0.0      0.27     7e+02      39      48 ..      69      78 ..      61      79 .. 0.85
   3 ?    1.3   0.0      0.16   4.1e+02      27      43 ..      79      95 ..      76      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                    HHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHH CS
  Fe_dep_repress 10 LetIYtlse.ekkvvktkdlaerLnvspssVse 41
                    L++I+  +  e+  v+  ++++ L+v  + +s 
      AJA91845.1 16 LRAILAKDLsENHNVREEMISKMLGVTQAAISN 48
                    67777666668888999*********9999886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                    HHHHHHHHHH CS
  Fe_dep_repress 39 VsemlkkLek 48
                    Vsem+++ ++
      AJA91845.1 69 VSEMIQEISQ 78
                    8999999876 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.16
                    HHHHHHTS-HHHHHHHH CS
  Fe_dep_repress 27 dlaerLnvspssVseml 43
                    +la+ ++  ps+ s+ +
      AJA91845.1 79 NLASDMAYTPSTLSKFI 95
                    7999********99865 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00047       1.2      17      39 ..      17      39 ..      14      41 .. 0.91
   2 ?    1.2   0.1      0.15   3.7e+02      48      59 ..      66      77 ..      61      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00047
     UPF0154 17 rkymkkqlkenPpinekmiramm 39
                r ++ k+l+en  + e+mi +m+
  AJA91845.1 17 RAILAKDLSENHNVREEMISKML 39
                78999***************996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
     UPF0154 48 ekqikqvmrsmk 59
                ekq+ ++++++ 
  AJA91845.1 66 EKQVSEMIQEIS 77
                788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 992.67
//
Query:       AJA91846.1  [L=245]
Description: coenzyme F420-0:L-glutamate ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-55  187.6   1.9    2.9e-55  187.3   1.9    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   1.9   1.6e-59   2.9e-55       6     244 .]      13     222 ..      11     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 1.6e-59
                  ---TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..................HHHHHHHHTEEEE CS
  F420_ligase   6 likegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLkalakatrkvevvlsepsde 103
                   +++ ddl +++++s k++   le+gD++v+++k+++k eg++v+l++i pse  + ia+++  +dp                  + v+++lse++++
   AJA91846.1  13 DVQPTDDLIDLLLSSSKTS---LENGDVLVISQKIISKHEGRVVNLDSIIPSELSIGIASAY-DKDP------------------KLVQAILSESQRI 88 
                  699**************66...****************************************.****..................************* PP

                  EE-...S-EEEE.......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEE CS
  F420_ligase 104 vgn...qlidekytdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkertgkdveVliygkDpegriweladpvvaigtsglealr 198
                  v+    ++i+++       ++G++++nagidesnve+g+++llP+d+dksa++i+ k+ ++tgk+v+V+i  +D++gr++++++++ aig+sg+  + 
   AJA91846.1  89 VRMehgVIIVQT-------NHGFICANAGIDESNVENGYATLLPKDSDKSADNIRLKILQQTGKKVAVII--SDTFGRPFRMGQTDHAIGVSGIDTIL 177
                  **9998888888.......***************************************************..************************** PP

                  E-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
  F420_ligase 199 dlrgkkdldgkelgttpravtdelgsladLvsGsadegtPvvlvrg 244
                  +++g+ d +gk l++t  a++del+s+a+Lv+G++ +++P++++++
   AJA91846.1 178 HYEGTPDTFGKILRVTATAIVDELCSAAELVMGKT-KKCPAAIIKN 222
                  **********************************9.899**99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1632.92
//
Query:       AJA91847.1  [L=284]
Description: HpcH/HpaI aldolase/citrate lyase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-46  155.9   0.0    9.5e-46  155.7   0.0    1.1  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
      1e-12   47.9   0.5    3.4e-06   26.4   0.1    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
     0.0048   15.8   0.7      0.008   15.1   0.7    1.3  1  PK              Pyruvate kinase, barrel domain
     0.0083   16.2   1.4       0.24   11.5   0.7    2.8  2  Exog_C          Endo/exonuclease (EXOG) C-terminal domain


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0   2.1e-49   9.5e-46       1     221 []       6     224 ..       6     224 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 2.1e-49
                 EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG.HHHTTSSEEEESS--SHHH CS
   HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle.vldlgaqvvlvPkvetaee 98 
                 r+++f+pg+n++ +eka     D v +DlEd+v  +eK++AR+l+++ lk+ +     +++v+ R ns +s+ +  dle ++++g++++++Pkv++a+e
  AJA91847.1   6 RSLVFVPGNNPRFLEKAKSLSGDIVCFDLEDSVPDKEKQNARTLIAKKLKERKD---FKASVFARTNSPQSGKVPSDLEkIVQKGLDGIVIPKVDSAKE 101
                 789******************************************998888766...4457************************************** PP

                 HHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HHHHHHHTT-TTSTTSHHHH.HHHHHHHHTTHCEEEEEEE.E-SSH CS
   HpcH_HpaI  99 alevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGaeDlsadlgtkrspegtevl.dareriltaaraagiaaldtvasdi 195
                 ++++++++ + e   +++ k++r++  iEsa+gv n  eIa a++++d++++G  Dl  d+  + +++ +    ++r r+  aa aagi a+d+++ +i
  AJA91847.1 102 LKKIEKIISSLE--KKRKLKTIRIIPSIESALGVINCYEIAsASKRIDAIVFGIFDLLNDMQIEYTKGNPVGGkYSRYRVPVAAAAAGIPAIDGIWQEI 198
                 ***********9..55567*******************************************998777765558************************* PP

                 HHHHHHHHTTHCEEEEEEHHHHHHHH CS
   HpcH_HpaI 196 ddaegflaegalfvalGfdgkllinp 221
                 +d++g+ ++ +l+++lG++gk++i+p
  AJA91847.1 199 KDKKGLEQDCKLGKELGYSGKSIIHP 224
                 *************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   7.7e-10   3.4e-06      34     141 ..      29     130 ..       7     152 .. 0.73
   2 !   20.2   0.0   5.9e-08   0.00027     248     314 ..     199     269 ..     136     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.7e-10
  C-C_Bond_Lyase  34 slvlclEDavseeeveaAeenlkellkelaeaekekekeelpllFvRvRspeqlkellerlgealelltGfvlPkftse.sleeylealkkanek 127
                      ++++lED+v ++e ++A + +++ lke ++            +F R  sp+  k   +  +   + l+G+v+Pk++s+ +l+++ ++++++++k
      AJA91847.1  29 IVCFDLEDSVPDKEKQNARTLIAKKLKERKD--------FKASVFARTNSPQSGKVPSDLEKIVQKGLDGIVIPKVDSAkELKKIEKIISSLEKK 115
                     467889*************999998887666........45679****9999877666655557889*********8761567777777776655 PP

  C-C_Bond_Lyase 128 lg.kklllmPilEte 141
                      + k++ ++P +E++
      AJA91847.1 116 RKlKTIRIIPSIESA 130
                     441568899999996 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.9e-08
  C-C_Bond_Lyase 248 kdldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldiles.akg...gvfkseyankmn 314
                     kd  gl +  +l k+ G  GK++IhP qi+  ++++  + +e +  + ++++ +k+   g  +  + +km+
      AJA91847.1 199 KDKKGLEQDCKLGKELGYSGKSIIHPDQIETTHKIFHPNSSEITWSKLVVKEyEKStkkGRGAIVVDGKMI 269
                     45679*******************************99999999999999875442233444444555665 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.7   1.8e-06     0.008     145     241 ..      43     144 ..      26     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-06
                 EEEEEESS-EEE-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHT...CCC..TTSEEEEEE-SCHHHHTHHHHHH CS
          PK 145 eleveventgvlgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevle...eeg..keikiiakienqegvenldeile 238
                 + + ++  + +l+++k   +   +      s k  +dl+  v++g+d i++  v +a+++k++ +++    ++   k+i+ii  ie++ gv n  ei  
  AJA91847.1  43 KQNARTLIAKKLKERKDFKASVFARTNSPQSGKVPSDLEKIVQKGLDGIVIPKVDSAKELKKIEKIISsleKKRklKTIRIIPSIESALGVINCYEIAS 141
                 455666666667777777666555555556778889****************************99752213334678*******************98 PP

                 HSS CS
          PK 239 asD 241
                 as 
  AJA91847.1 142 ASK 144
                 875 PP

>> Exog_C  Endo/exonuclease (EXOG) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.7   5.4e-05      0.24      14      34 ..      95     115 ..      91     122 .. 0.92
   2 ?    2.2   0.0     0.041   1.8e+02      24      42 ..     191     210 ..     183     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
      Exog_C  14 KvesArtlkRLekvmkeLkea 34 
                 Kv+sA+ lk++ek+++ L+++
  AJA91847.1  95 KVDSAKELKKIEKIISSLEKK 115
                 9*****************975 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.041
      Exog_C  24 LekvmkeLke.agiepDeyL 42 
                 ++ +++e+k+ +g+e D +L
  AJA91847.1 191 IDGIWQEIKDkKGLEQDCKL 210
                 6789****962699999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1909.15
//
Query:       AJA91848.1  [L=210]
Description: proteasome endopeptidase complex, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-53  181.2   0.1    1.6e-53  181.0   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.1   9.1e-58   1.6e-53       3     189 ..      11     190 ..       9     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 9.1e-58
                 HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTT CS
  Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgr 101
                 +Gtt+vGik++dgvvl+ad+ra+ag  +++++   Ki ki +h+g+++aG +aDa+++v+ +r++a+l+r+++++pipv     ++a++++ +  +++ 
  AJA91848.1  11 HGTTTVGIKATDGVVLCADMRASAGYFIANNN-TMKIQKIEQHVGLTLAGGVADAQNIVDVLRYHANLHRIQNQEPIPVN----SLARLTSLMFHQNRG 104
                 9***************************7777.5**********************************************....999999999999999 PP

                 TTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
  Proteasome 102 rpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievav 189
                  pf++ +l++gvd +g p+L++id+ Gs+    ++v++Gsgs +a+++le+ey++dltle+a+ +a++a+k+a+ r   +g++i+va 
  AJA91848.1 105 YPFIADILVGGVDAKG-PSLFNIDMFGSVENK-NYVTTGSGSPVAYGLLEEEYNKDLTLEDAKVVALRAVKAAITRNIGTGDGINVAL 190
                 *************888.*************99.7****************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1545.12
//
Query:       AJA91849.1  [L=360]
Description: putative modification methylase BspRI [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-59  199.8   0.1    1.2e-58  199.1   0.1    1.2  1  DNA_methylase  C-5 cytosine-specific DNA methylase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.1   0.1   6.8e-63   1.2e-58       4     333 ..       7     349 ..       5     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 199.1 bits;  conditional E-value: 6.8e-63
                    EEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.....-SEEEES-TTTS-GS--.-SEEEE---GGGTECTSEE--TTSGGGHHHHHHH CS
  DNA_methylase   4 idLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk....kvsigDitkidkkklpediDlLvgGfPCqpfSvaGkqkgfedtrgtLffeii 95 
                      LfaG GG +lg+ +agf+ v+a++++++a++t++ +f+    k++ ++ +  ++k++  +  +++gGfPCq+fS aG  +  +d+r++L+ e  
     AJA91849.1   7 ATLFAGGGGDSLGFTSAGFDLVFANDNNPDACETLRSRFEngsgKKIVHKGNVEKIKNFG-NANVITGGFPCQGFSLAG-PREVKDKRNSLYQELK 100
                    67*************************************976665555555666666777.5*****************.899************* PP

                    HHHHHH--SEEEEEEEGGGGGGCCS...............HHHHHHHHHHHHHT..EEEEEEEEEGGGTT-SB--EEEEEEEEEGGG--------- CS
  DNA_methylase  96 riikekkPkvfllENVkgLlkhdkg...............ktlkvilekleelG..YevsykllnasdyGvpQnReRvfivgirkdlelnvlvkvk 174
                    r i   +P++f+ ENVkgL++  ++               k+ + i+++l+e+G  Y+vsy+l  a+d+G+pQ+ReR++ivg+rkd +        
     AJA91849.1 101 RAISLVNPEFFIGENVKGLVTIGEKskakyfhngkivklgKVAEAIIKELSEVGkgYNVSYQLHSAKDFGIPQDRERIIIVGVRKDIN-------F 189
                    ********************9877777899***********************999*****************************964.......7 PP

                    -SS---GGG.....TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---H.HHTS--B--TTS...-B----S-STT-......-B-TT CS
  DNA_methylase 175 efrfpkkkdleasktlrdlleekseldeektalsdklvekeekikkttkaseegypk.elsrnridkveelkglsatrrksgrge......kleke 263
                    ef+fpk+ +    k l+ +       + e+  ++d  ++++e +++++++ ++ +++ ++srnri+k++e   +s+t+ +  ++       k +++
     AJA91849.1 190 EFKFPKPTH---GKGLKPYV------TMEEFGIKDIPLKDDEVFREAKGKRKDFFSSrYMSRNRIRKWNE---TSFTIPAEASQVpahpssKKMWN 273
                    888888853...44444444......45788888888889999988888888888888999999999999...55555555554422344433444 PP

                    S---EEEETTEEE--T...........TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHH CS
  DNA_methylase 264 laeagklqknkerfkp..........viekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakei 333
                    +  +g+++ +++   +           i+ k   rL+ r +a +qGfP+d  f+++  + ykqiGn+Vp+ +++++a+ i
     AJA91849.1 274 VDVTGENRPKDS---EwaefrkkhekDIS-KSLVRLSWRQCAAIQGFPKDHPFSGDVVSIYKQIGNAVPPLLMQKVAECI 349
                    444444444433...15557777774444.45557*****************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2612.83
//
Query:       AJA91850.1  [L=108]
Description: hypothetical protein T478_0297 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 835.20
//
Query:       AJA91851.1  [L=103]
Description: PF13031 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-07   29.4   0.3    1.1e-06   29.1   0.3    1.2  1  DUF3892   Protein of unknown function (DUF3892)
  ------ inclusion threshold ------
      0.044   14.4   1.2        2.2    8.9   0.5    2.2  2  ASCH      ASCH domain


Domain annotation for each model (and alignments):
>> DUF3892  Protein of unknown function (DUF3892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.3   1.2e-10   1.1e-06      14      76 .]      19      99 ..       8      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.2e-10
     DUF3892 14 erItevk....gsntlstgekyskeeaislikngkkagVevvrsk...............dGekYlrtkadgtetdNLlsLp 76
                 +It+v+     +++ +++e+++k+++ s ik+gkk ++++ +++               +Ge ++rt+ +++  d L+ Lp
  AJA91851.1 19 ANITHVQvhedFEGQFGKPEIIDKKTLASHIKKGKK-YITIYKKNetdwepgeiinayvlNGETHIRTDSNKVDGDRLGTLP 99
                6899999999666799********************.66666666999999999999999*********************9 PP

>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0059        53       6      17 ..       3      14 ..       1      31 [. 0.81
   2 ?    8.9   0.5   0.00025       2.2       6      27 ..      42      66 ..      25      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0059
                THHHHHHTTS-- CS
        ASCH  6 elaslivsGkKt 17
                ++a+ +vsG+K+
  AJA91851.1  3 KWADFVVSGIKK 14
                7**********8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00025
                T..HHHHHHTTS--EE.EESSTTTG CS
        ASCH  6 e..laslivsGkKtae.irvwdeel 27
                +  las i++GkK ++ +++++++ 
  AJA91851.1 42 KktLASHIKKGKKYITiYKKNETDW 66
                0459************655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 724.38
//
Query:       AJA91852.1  [L=248]
Description: 2OG-Fe(II) oxygenase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.9   0.0    1.8e-09   38.3   0.0    1.2  1  2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
    6.6e-06   26.5   0.0    1.6e-05   25.2   0.0    1.5  1  2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
  ------ inclusion threshold ------
      0.093   13.4   0.0       0.23   12.1   0.0    1.7  1  2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> 2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   3.1e-13   1.8e-09       5      95 ..     123     236 ..     119     237 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3.1e-13
                     EE-TT-EEEEE-SS--......--TT.-.EEEEEEEEE....ET-B--EEE................................---TT-EEEEE- CS
  2OG-FeII_Oxy_3   5 rygegqeykpHvDnfe......keegsgqrrltvllyLnekeseeGGelelyekdk......................eavkikpkkgrlvlFes 71 
                     ++g+ +  + H Dn++      +  ++ + +l+++lyL+  ++e+GGel++y+k                        +++ki+p +g++vl + 
      AJA91852.1 123 IHGNDDSVHLHRDNSNfemsdyN-VSNLKNQLSAILYLQ--SPEQGGELTIYHKLWnkedermrepdfgyssaliedvHKTKISPIEGNMVLLNP 214
                     456778899****9999999953.44488*********4..569*******999889999*****************99999************* PP

                     ..B-TEEE--B.-SS-EEEEEEEE CS
  2OG-FeII_Oxy_3  72 dellpHevlpvtkggeRlsltgwi 95 
                     +    H+++ v+ +++R+s+ +++
      AJA91852.1 215 KFY--HQIESVSGSRSRISIGFFF 236
                     766..******8766****99987 PP

>> 2OG-FeII_Oxy_5  Putative 2OG-Fe(II) oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.7e-09   1.6e-05      22     100 ..     152     234 ..     148     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.7e-09
  2OG-FeII_Oxy_5  22 vlSgvyYlsvpkeagalkledpr...lavelgaparkeeak.eenqslvdvkpkeGdlvlFPswlrHevlpnegeeeRisisf 100
                      lS++ Yl+ p++ g+l ++++    +   + +p+  ++ +  e+ + + ++p eG++vl   +++H++   +g+++Risi f
      AJA91852.1 152 QLSAILYLQSPEQGGELTIYHKLwnkEDERMREPDFGYSSAlIEDVHKTKISPIEGNMVLLNPKFYHQIESVSGSRSRISIGF 234
                     79**************9999876443444466777777766356688999*******************************88 PP

>> 2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05      0.23      22      90 ..     150     234 ..     129     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
  2OG-FeII_Oxy_4  22 eRrvayilyleeeWkeddGGaLlls.......ddeg...............dv.tksivPkwnqlvlFevkeshsvaevasvaekeRlsisg 90 
                     + +++ ilyl+   ++++GG+L ++       d  +               dv  ++i+P  +++vl + k  h++++v    +++R+si  
      AJA91852.1 150 KNQLSAILYLQ---SPEQGGELTIYhklwnkeD--ErmrepdfgyssalieDVhKTKISPIEGNMVLLNPKFYHQIESVSG--SRSRISIGF 234
                     45678899998...4799999977745554320..1222232333333332334569*************999*****996..789999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1757.61
//
Query:       AJA91853.1  [L=291]
Description: NADP oxidoreductase coenzyme F420-dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-40  138.9   1.5    2.6e-40  138.2   1.5    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.6e-20   73.5   0.1      3e-20   72.7   0.1    1.5  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
    4.3e-08   33.6   0.2    1.2e-07   32.1   0.2    1.8  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.7e-06   27.5   0.2    2.7e-06   26.9   0.2    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    5.9e-06   26.4   0.2      1e-05   25.6   0.2    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    1.1e-05   25.1   0.2    2.1e-05   24.2   0.2    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0002   21.0   0.1    0.00034   20.3   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0004   20.3   0.1     0.0012   18.7   0.1    1.8  2  Rossmann-like   Rossmann-like domain
    0.00073   19.6   0.2      0.017   15.1   0.2    2.4  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0041   16.7   1.2      0.058   13.0   0.4    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0045   16.9   2.2     0.0085   16.0   0.4    2.4  4  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.027   14.0   0.1      0.044   13.3   0.1    1.3  1  NmrA            NmrA-like family
      0.042   13.7   0.0      0.066   13.1   0.0    1.4  1  NAD_binding_10  NAD(P)H-binding
      0.058   13.6   0.2       0.17   12.2   0.2    1.9  1  TrkA_N          TrkA-N domain
      0.083   13.3   0.3       0.16   12.4   0.3    1.7  1  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   1.5   2.2e-43   2.6e-40       1     156 [.       3     160 ..       3     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 2.2e-43
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS...HCCC--TT-EEEE-S--- CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg...llealkkgdilidgstss 93 
                    kig++G+G++G+   l+ll+ gyk++v+nr+kek+e+l ++ga +++s+++++++ ++vi++vk+ +av++v++g   +l+  ++g ++ d+st++
     AJA91853.1   3 KIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENKGALVVDSPKNVAENSELVIMVVKDANAVKDVVFGdcgILAGRHEGMCIADMSTIN 98 
                    79********************************************************************************************** PP

                    HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEEEE CS
  NAD_binding_2  94 pedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvthv 156
                    p++tre++k+++e g++++++PV GG + A +G+L im++G++e+fe+ k ++e+i+ + + +
     AJA91853.1  99 PNSTREISKKVTEDGIDYMEIPVMGGPNVAINGKLVIMASGKKEVFEKFKTIFESIADQSI-Y 160
                    *********************************************************9776.4 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.1   2.5e-23     3e-20       1     121 [.     165     284 ..     165     285 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 2.5e-23
  NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKDlglalelareagaplpll 95 
                     G+++ +Kl+ nl +a+  + +sE+++l +kaG dpe +l+v+n+   +  ++e k   ++++++ +p+F+l+ + KDl+ ++++a++++a+lp++
      AJA91853.1 165 GTAHSIKLAMNLQIAMLALSLSEGITLTKKAGFDPEIFLKVLNSTYFKTGMSEGKAH-KMINDSVKPTFTLANLKKDLDTINDAAESFDAELPMA 258
                     899**************************************************9998.69*********************************** PP

  NAD_binding_11  96 alaeqlyaaaaaegggdaDhsaivrl 121
                     + a+++ya a  +g gd D++ i+ +
      AJA91853.1 259 KIARKIYADATDAGFGDIDYTGIISY 284
                     **********************9976 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.2     1e-10   1.2e-07       1      73 [.       3      69 ..       3      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-10
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkped 73
                   kigi+G+G +gea+ + ll  g   ++i+v  +r++ek e+l+++ g+ v   + + +ae+++ v+  vk ++
     AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVG---YKITVF-NRSKEKTEKLENK-GALVVD-SPKNVAENSELVIMVVKDAN 69
                   7*********************...****77.**********887.567777.9*************999654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.2   2.3e-09   2.7e-06      37     101 ..       2      67 ..       1      75 [. 0.90

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.3e-09
                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S-- CS
  2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlpl 101
                   +++Gi+G+G +G+av   l  +g k+++++rsk+k+e+ e++g+  ++s +++ ++s+ v++++  
    AJA91853.1   2 MKIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENKGAlVVDSPKNVAENSELVIMVVKD 67 
                   589**********************************99999996667************998865 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   8.6e-09     1e-05      14      81 ..       3      63 ..       1     111 [. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 8.6e-09
                  EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
  Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                  k+ ++G+G+++e v  hLl+ g+k ++v+NR+ e+ ++l ++       al +++ k++ +++++vi+
    AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVGYK-ITVFNRSKEKTEKLENKG------ALVVDSPKNVAENSELVIM 63
                  899********************9.**************8775......3445555566666666665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   1.7e-08   2.1e-05       6      72 ..       3      69 ..       1      77 [. 0.91

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.7e-08
                -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH CS
        IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel 72
                ki ++G G  G+a +l l d g +++v +r+++k+ k  ++ ++ v + +++++++++v++++ D  
  AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENKGALVVDSPKNVAENSELVIMVVKDAN 69
                89*******************************988888888899999**************99964 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.9e-07   0.00034       1      47 [.       4      51 ..       4      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
        ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                i i+G+G +G  ++ +L   g+++t+ +rs+ + e+l+++G  + ++ 
  AJA91853.1  4 IGIVGTGMLGEAVGLHLLDVGYKITVFNRSKeKTEKLENKGALVVDSP 51
                79**********************************999998888776 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   9.8e-07    0.0012      11      87 ..       2      77 ..       1     114 [. 0.71
   2 ?   -1.3   0.0       1.5   1.8e+03      56      81 ..     118     143 ..      88     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.8e-07
  Rossmann-like 11 lsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdae.lpglvkg 87
                   +++Gi+++G +G a+g  l  +g++++  +  s+   e+ e++     v + ++va+++el+++ v da+ + ++v g
     AJA91853.1  2 MKIGIVGTGMLGEAVGLHLLDVGYKITVFNR-SKEKTEKLENK-GALVVDSPKNVAENSELVIMVVKDANaVKDVVFG 77
                   689**********************986543.33333333333.2333445679**************9724556654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
  Rossmann-like  56 dvpvlevedvaaraellllavPdael 81 
                    ++pv+  ++va + +l+++a    e+
     AJA91853.1 118 EIPVMGGPNVAINGKLVIMASGKKEV 143
                    56777777888888888888766655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.4e-05     0.017       1      42 [.       3      44 ..       3     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
  NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42
                    ki+++G+G+ G a+  +l + g +++++ r++e +e+++++ 
      AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENKG 44
                    79**********************************998764 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   4.8e-05     0.058       1      47 [.       2      48 ..       2      74 .. 0.90
   2 ?    1.4   0.0      0.17     2e+02     115     155 ..      89     127 ..      81     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                    SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS- CS
  UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy 47
                    mki ++G+G +G   ++ l  +g ++++   ++ek +kl+++   ++
      AJA91853.1  2 MKIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENKGALVV 48
                    89*************************************87665554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                     EEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEEEE---- CS
  UDPG_MGDP_dh_N 115 kvvvvkSTvpvgtaeelvkkileeaskkkgvdfdvvsnPEf 155
                       +   ST+ + +++e+ kk+ e+  +   +++ v+  P  
      AJA91853.1  89 MCIADMSTINPNSTREISKKVTEDGID--YMEIPVMGGPNV 127
                     567788*********999999998766..356666666655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   7.1e-06    0.0085       1      41 [.       3      43 ..       3      81 .. 0.87
   2 ?   -0.6   0.0       0.9   1.1e+03      74     104 ..      52      83 ..      38     111 .. 0.74
   3 ?   -3.1   0.0       5.2   6.2e+03      93     171 ..     140     155 ..     133     164 .. 0.54
   4 ?   -1.7   0.0       1.9   2.3e+03      52      80 ..     220     248 ..     174     270 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.1e-06
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalek 41
                k++++G+G++G+ +   ++  g++++++++s+e+ ek ++k
  AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKEKTEKLENK 43
                69******************************999998776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.9
                 HHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS CS
     3HCDH_N  74 eeav.dadlviEavvEnlelKrkvfaelekia 104
                 ++++ + +lvi  v +  ++K  vf ++  +a
  AJA91853.1  52 KNVAeNSELVIMVVKDANAVKDVVFGDCGILA 83 
                 45556899999999999999999998877666 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.2
                 HHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHTT CS
     3HCDH_N  93 KrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvatvvelakkig 171
                 K                                                               +e+++++++++++i 
  AJA91853.1 140 K---------------------------------------------------------------KEVFEKFKTIFESIA 155
                 4...............................................................444555555555544 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.9
                 TTSS-HHHHCCCHHCEEEES-HHHHHC-S CS
     3HCDH_N  52 kgklkeeeveaalarisfttdleeavdad 80 
                 ++k+ +++v+ +++  + ++dl+++ da 
  AJA91853.1 220 AHKMINDSVKPTFTLANLKKDLDTINDAA 248
                 33333466666666666666666666554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.7e-05     0.044       6      68 ..       8      71 ..       4      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                TTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE...ES-TT-HHHHHHHHTT-SEE CS
        NmrA  6 aTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv...kgdlddkeslvealkgvdvv 68
                +TG +G++v  +ll++g+k+ +  R  ++e+ ++l+++G+ +v   k+ +++ e++  ++k++++v
  AJA91853.1  8 GTGMLGEAVGLHLLDVGYKITVFNR--SKEKTEKLENKGALVVdspKNVAENSELVIMVVKDANAV 71
                7******************988766..678899**********53223355777777778877765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05     0.066       2      64 ..       8      71 ..       8     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                    TTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE-..-T.T-CCHHHHHHTT-SEE CS
  NAD_binding_10  2 AtGkvGrllvkellargghevtalvRnpeklaeleaeeglevveg..dv.tdvedlaealkgadaV 64
                    +tG  G ++  +ll+  g+++t++ R++ek+++le ++g+ vv+   +v +++e +  ++k+a+aV
      AJA91853.1  8 GTGMLGEAVGLHLLDV-GYKITVFNRSKEKTEKLE-NKGALVVDSpkNVaENSELVIMVVKDANAV 71
                    69**************.5****************8.688888875223314556677777788777 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00014      0.17       3      45 ..       6      48 ..       4      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                EES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
      TrkA_N  3 iiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45
                i+G G +G+++   L + g+ +++v  +++e+ e+l+++g+ vv
  AJA91853.1  6 IVGTGMLGEAVGLHLLDvGY-KITVFNRSKEKTEKLENKGALVV 48
                9****************999.5******************8877 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00014      0.16       9      77 ..       3      73 ..       1     153 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev..keeleelvklaeeelekdlegadlviaatddrelner 77
                   k+ +vG G +++    +ll+ g k+tv       +e+le++  l  +  ++  e+ +lvi++++d++  + 
     AJA91853.1  3 KIGIVGTGMLGEAVGLHLLDVGYKITVFNRSKekTEKLENKGALVVDSPKNVAENSELVIMVVKDANAVKD 73
                   5779***********************98882112333333334444446778889999999988765444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2047.29
//
Query:       AJA91854.1  [L=274]
Description: hypothetical protein T478_1360 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1967.23
//
Query:       AJA91855.1  [L=160]
Description: hypothetical protein T478_0676 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.06   12.9   0.1      0.087   12.4   0.1    1.2  1  GNAT_acetyltran  GNAT acetyltransferase
      0.091   12.7   0.0       0.12   12.3   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
       0.15   11.3   0.0       0.25   10.6   0.0    1.3  1  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr


Domain annotation for each model (and alignments):
>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.5e-05     0.087      28     135 ..      39     142 ..      29     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
  GNAT_acetyltran  28 lekpksalivlgdfvflaGe.pneefaeelvleekekkeekrfilvpqseeweelieeilgeklkkitryaikkeeeafdkekLeklaeslpee 120
                      +++p+  +i+ g f++ aG  ++ e+++ + +++++ ++++   ++      ++l ++  g++++k +r  + +++e++  +   kla++l+ee
       AJA91855.1  39 SKEPEEDAIFFGVFLYKAGTpHDYESKQGITYYYNNIERNDLPPIT------KSLKKKFGGNEYEKGERIFLVDSKEIYAAKDIAKLAKELQEE 126
                      56899999************55545556666666665555543333......23445666899999*****99999****************** PP

  GNAT_acetyltran 121 yelkkide.elyeear 135
                      +++++i + el ++++
       AJA91855.1 127 FTINPIITiELHDTTQ 142
                      *****98744444433 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.9e-05      0.12      50      91 ..      51      90 ..      50     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                  EEEE-TTS-EEEEE-TTSEEEEEEEEE---GGGGGGG---EE CS
  AraC_binding 50 lfLlppgepHdyesdsedgweyrwlyfegelleriledssil 91
                  +fL + g+pHdyes    g++y++ ++e   l  i+++    
    AJA91855.1 51 VFLYKAGTPHDYESKQ--GITYYYNNIERNDLPPITKSLKKK 90
                  79**************..*****9999998888888766644 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.1e-05      0.25      32      95 ..      86     154 ..      81     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXX CS
    HlyD_D23  32 klyvnatgdkVkkGqpLaelyspelvaaqeeyllalkakkklkkke.....lleaarerLrllgvseeq 95 
                 +l+ ++ g++ +kG++++ ++s+e++aa++   la++ +++ + +      l ++ +e+L+ +g +e++
  AJA91855.1  86 SLKKKFGGNEYEKGERIFLVDSKEIYAAKDIAKLAKELQEEFTINPiitieLHDTTQEKLKEWGYPEAK 154
                 57778889999*****************99888888888888767799999999**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1041.85
//
Query:       AJA91856.1  [L=225]
Description: ribose 5-phosphate isomerase A [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-52  175.3   0.1      1e-51  175.0   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    1.3e-05   25.2   0.2      0.017   15.1   0.1    2.8  3  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.035   13.6   0.2      0.048   13.2   0.2    1.1  1  DUF4147         Domain of unknown function (DUF4147)


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.1   1.7e-55     1e-51       2     173 .]      52     219 ..      51     219 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 1.7e-55
                     EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTSS-EEEEE-GGGHHHH CS
  Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgkfpvPveVlpfaleav 96 
                     +vptS q +  ae+ g++l++ d++++idl++DGaD++d+++ liKGgGgall+E i+ +aakk+i++ad+sK+v++++   +P+eV p a++ v
      AJA91856.1  52 CVPTSMQIKLIAEKGGLELIDADQIDKIDLVFDGADQIDKNKFLIKGGGGALLKENILISAAKKVIIMADSSKFVKDFN-RTIPIEVQPSARQIV 145
                     9****************************************************************************96.89************* PP

                     HHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S--SEEEEEETTC CS
  Rib_5-P_isom_A  97 arelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlgladkvlvgkedg 173
                      +++e+l  gkpelR+  +++ p++T+n n+ilD+ f + i++p+ l+++l +ipGV+e+G+F++  d ++ +k++g
      AJA91856.1 146 WKKIERL-SGKPELRT-LDRGYPFFTENSNIILDCGF-GVIKNPKILQQKLLNIPGVIEVGIFTRKPDIIYKAKANG 219
                     *****75.99*****9.7789****************.6899*****************************999876 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0013       7.6      13      41 ..      14      42 ..       8      71 .. 0.85
   2 !   15.1   0.1   2.8e-06     0.017      93     141 ..      79     127 ..      73     137 .. 0.81
   3 ?   -0.1   0.0      0.14   8.1e+02      18      65 ..     169     223 ..     165     225 .] 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0013
       DeoRC 13 AaeliedgdtifldaGtTtlelaraLaek 41
                A++ ++dg++i l++G  +++l++ L++ 
  AJA91856.1 14 ALKNVKDGHVIGLGSGRAATALVKSLSKY 42
                8999********************99875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.8e-06
       DeoRC  93 vdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgk 141
                 +d++f ga+ id+++ l++        ++ li+aa++vi++aDssKf k
  AJA91856.1  79 IDLVFDGADQIDKNKFLIKGGGGALLKENILISAAKKVIIMADSSKFVK 127
                 78889999999988777777777777778899***************76 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.14
       DeoRC  18 edgdtifldaGtTtlelaraLaekk.......nltvvTnslnvaeeLsekedikv 65 
                  +++ i+ld+G  +    + L++k        ++ ++T + +++ + +++ ++++
  AJA91856.1 169 TENSNIILDCGFGVIKNPKILQQKLlnipgviEVGIFTRKPDIIYKAKANGKFEI 223
                 6788899999988877766666665666677777888888888888777777765 PP

>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   8.1e-06     0.048      33     125 ..      18     106 ..       3     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-06
                 ...-SEEEEEESTTHHHHHHHHH.HHHGEEEEEEETT-----TT-EE..EEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS-- CS
     DUF4147  33 skkkrvvvvgaGKAaaamaaaleeealksgvvvvkkghaeekeriev..leaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaa 125
                  k ++v+ +g G+Aa a+++ l+ +++k++ + vk   +  + +i++   +++  l d++ ++  + + + a+++++++   +li GGg All  
  AJA91856.1  18 VKDGHVIGLGSGRAATALVKSLS-KYIKTKKIAVKCVPT--SMQIKLiaEKGGLELIDADQIDKIDLVFDGADQIDKNK---FLIKGGGGALLKE 106
                 35678888999************.788877777765433..334555215668889*****999999999999998887...6789******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1641.42
//
Query:       AJA91857.1  [L=37]
Description: hypothetical protein T478_1383 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 278.80
//
Query:       AJA91858.1  [L=314]
Description: tubulin/FtsZ family, GTPase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-16   60.5   3.9    6.6e-15   55.8   0.5    2.7  3  Tubulin   Tubulin/FtsZ family, GTPase domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1   0.00051       9.1       2      25 ..       9      32 ..       8      56 .. 0.75
   2 !   55.8   0.5   3.7e-19   6.6e-15      58     195 ..      33     157 ..      28     159 .. 0.83
   3 ?   -1.3   0.0      0.12   2.1e+03      71     106 ..     187     222 ..     168     267 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00051
                EEEEEEHHHHHHHHHHHHH...HH CS
     Tubulin  2 iivigvGqcGnqignelwellake 25
                ++v+g+G++G+++++e+ ++l  +
  AJA91858.1  9 VLVVGLGGAGIKLASEMRDVLDAD 32
                789**************9966544 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 3.7e-19
                 HHHHHTS-GS......EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEEEE CS
     Tubulin  58 pqvlneikagselfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvvvl 156
                   ++++ k++  + ++n++++++++     ++   ++ + +a e +e+i+++++  ++   ++i+a l+G +G +l+pv+ +++ke+  ++ v+++ ++
  AJA91858.1  33 LLKISQDKKD--VSEHNSIHISTKS----IINPSVQLIRGCAMEQSEKIEEHMSTYET---VIIMANLAGKSGAALAPVVSSICKEQ--NKNVLSFAIM 120
                 4444444444..8888888885554....4445555556678888999**99999999...**************************..999******* PP

                 --GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCC CS
     Tubulin 157 PsefsevvvepynailalkelieesdavividNdaLlki 195
                 P++f  ++ ++ ++  +lk+l+ +sd++i+idNda+l+ 
  AJA91858.1 121 PFKF--EKNRIFQSGISLKRLRMNSDSTIIIDNDAILDS 157
                 ****..789**************************9985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.12
                 ...EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHH CS
     Tubulin  71 fnpnklllgkegagnngaggypevgkeaaeeileei 106
                  + +++++ + +++n   + + ++   ++++  + i
  AJA91858.1 187 TDDTNIMSTSRSTENIEESVKDSIKMLYEDAPPNSI 222
                 444444444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2234.47
//
Query:       AJA91859.1  [L=477]
Description: hypothetical protein T478_0501 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-08   33.4   0.1      0.016   15.7   0.0    4.0  4  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
      2e-06   27.8   0.0     0.0052   16.9   0.0    3.5  3  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.16   12.2   0.1       0.16   12.2   0.1    3.4  4  Gmad2         Immunoglobulin-like domain of bacterial spore g
       0.19   11.6   4.9        0.2   11.5   0.8    2.8  3  FlgD_ig       FlgD Ig-like domain
       0.21   11.9   1.7       0.91    9.9   0.1    2.7  3  CBM_2         Cellulose binding domain
       0.34   10.7   7.6       0.68    9.7   7.6    1.5  1  PmbA_TldD     Putative modulator of DNA gyrase
        7.9    7.7   7.2       0.89   10.7   0.1    3.0  3  PPC           Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   9.5e-05      0.24      14      98 ..      21      96 ..      19      97 .. 0.78
   2 ?   -3.2   0.0       4.8   1.2e+04      37      68 ..     100     134 ..      99     139 .. 0.67
   3 !   15.7   0.0   6.1e-06     0.016      14      98 ..     227     305 ..     224     306 .. 0.76
   4 ?   -0.2   0.0      0.54   1.4e+03      50      81 ..     415     450 ..     404     452 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.5e-05
                 EESSEEEEETTEEEEEEEESSSSBEEEEET..TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind 14 FetkeitvkkgekvtfvnlavmgHNvvldk..dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98
                 F ++++t+  g  vtf n+++ +H     +  dg p+g+ ++ + +         G ++++   +ag+Y +fC  H    M+g v+v
   AJA91859.1 21 FLPSTVTIGVGGMVTFANNDSAAHTSTSGTpaDG-PNGIWDSSLVM--------MGAAYTTPALDAGEYPYFCMVHP--WMEGLVIV 96
                 7899999999999999999999997665544344.44444444444........59999999999************..68**9998 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.8
                  BEEEEET...TSSTTTGGGTTSCTTCEEEEBSTTE CS
  Copper-bind  37 HNvvldk...dgvpagvdkdkvkaedetkliggGe 68 
                  HN v+++   + ++  +dk+  + +d   ++g+G 
   AJA91859.1 100 HNAVTSTpsiGPLSFYIDKTTYTTGDTIIVTGSGA 134
                  77777776666666677777777777666777775 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 6.1e-06
                  EESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEE.EEEEETTTTTTTSEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagt.YkffCsPHaaagMkgkvtv 98 
                  F ++ + v++g+ vtfvn+++ gH      +  ++g d +        +l+++G  + v f+  +ag+ + +fC  H    M+g+++v
   AJA91859.1 227 FIPSFLIVDPGDIVTFVNNDSAGHTSTS--GTPADGPDGNWD-----SSLMSPGYGMDVIFEisDAGQeFPYFCMVHP--WMEGTIIV 305
                  7788999*****************6544..333334443333.....3478888888888887666668*********..69****98 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.54
                  GGGTTSCTTCEEEEBSTTEEEEEEEE....SSEEEE CS
  Copper-bind  50 vdkdkvkaedetkliggGekdsvtfd....eagtYk 81 
                   +++ ++ ++ t + g+G++  + ++    eagtY+
   AJA91859.1 415 SNNTTISLSHVTGMLGAGQTLDQVLSympsEAGTYT 450
                  56778888889999******9999988887778787 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06    0.0052      32     104 .]      21      96 ..       3      96 .. 0.90
   2 !    5.5   0.0    0.0068        17      82     104 .]     283     305 ..     225     305 .. 0.73
   3 ?    0.6   0.2      0.24   6.2e+02      18      59 ..     366     406 ..     350     425 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
  Cupredoxin_1  32 fePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   f Ps++++  g    +++ n+d+ +++ +s         ++ +  +++g+++t   ++l++GeY+++c  h+ ++G +iV
    AJA91859.1  21 FLPSTVTIGVGG--MVTFANNDSAAHTSTSGTpadgpngIWDSSLVMMGAAYTT--PALDAGEYPYFCMVHPWMEGLVIV 96 
                   789999998887..78999******9999999999***99999999***99994..78**************99***998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0068
  Cupredoxin_1  82 plkpGeYeftcdmhmdakGkliV 104
                    +   e++++c  h+ ++G++iV
    AJA91859.1 283 SDAGQEFPYFCMVHPWMEGTIIV 305
                   344459*********99*****9 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.24
  Cupredoxin_1  18 aaektveitvkdggfePskievkagekvklkiknkdktpeef 59 
                   a+++  + +++  +   +++ v++  ++++ ++n+++  ++f
    AJA91859.1 366 AEAAAAAAEAA-SQQAIAELSVNEKIEITMDFTNDSDVQQSF 406
                   33333333333.334667888888888888888888776665 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.3e-05      0.16      14      85 ..     124     191 ..     118     192 .. 0.84
   2 ?   -2.5   0.4       2.4   6.2e+03      36      55 ..     324     343 ..     309     361 .. 0.71
   3 ?   -2.9   2.3       3.2   8.3e+03      23      53 ..     345     375 ..     334     393 .. 0.70
   4 ?    3.7   0.0     0.028        71      30      76 ..     408     452 ..     403     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
       Gmad2  14 tspvkvsGkarvFEatvnvrlrddagevlaegfvtAdegapkfgdFeatvefkapepgkgtlevyelsakdG 85 
                 ++++ v+G+  + E +v + + d +g ++     ++++g+ + g Fe+t++ ++  +  g+  +y+l+ +dG
  AJA91859.1 124 GDTIIVTGSGASPESSVVILVNDPDGDMVL----VTQTGVNSDGSFETTIPTDPTGTLWGQEGFYSLDVSDG 191
                 47899***********************85....6688999***********97556666666888888887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
       Gmad2  36 ddagevlaegfvtAdegapk 55 
                 d+a++++a +++ A+++a++
  AJA91859.1 324 DAAERIAAAEAAAAAAEAEA 343
                 34445555666666666655 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.2
       Gmad2  23 arvFEatvnvrlrddagevlaegfvtAdega 53 
                 ar  Ea+   r+  ++   +a +++ A+++a
  AJA91859.1 345 ARIAEAEAAARIAAAEAAAAAAEAAAAAAEA 375
                 5667777778888777777775555555443 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.028
       Gmad2  30 vnvrlrddagevlaegfvtAdegapkfgdFeatvefkapepgkgtle 76 
                 + v+++d++++ ++ ++vt+  g  +  + +  +++ ++e+g++t+e
  AJA91859.1 408 LIVQIKDSNNTTISLSHVTGMLG--AGQTLDQVLSYMPSEAGTYTVE 452
                 6799***************6665..7788889999999999999997 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   7.8e-05       0.2      10      74 ..     125     189 ..     117     191 .. 0.81
   2 ?    0.2   0.0      0.27     7e+02      25      38 ..     408     421 ..     383     434 .. 0.78
   3 ?   -3.7   0.0       4.3   1.1e+04      65      72 ..     445     452 ..     443     452 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                 --EEEEEE.ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B-.-SEEEEEEEE CS
     FlgD_ig  10 geaplgvelpeaadevtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkl.adGaYtvkvt 74 
                  +  ++ + +++ ++v++ ++D  G+ V   + g  s G+++ t + td  G+   ++G Y++ v+
  AJA91859.1 125 DTIIVTGSGASPESSVVILVNDPDGDMVLVTQTGVNSDGSFETTIP-TDPTGTLWgQEGFYSLDVS 189
                 33445555899***********************************.9999997635788888775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                 EEEEEE-SS--EEE CS
     FlgD_ig  25 vtvtikDasGevVr 38 
                 + v+ikD++++++ 
  AJA91859.1 408 LIVQIKDSNNTTIS 421
                 5699*****99984 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.3
                 -SEEEEEE CS
     FlgD_ig  65 adGaYtvk 72 
                 ++G+Ytv+
  AJA91859.1 445 EAGTYTVE 452
                 58999986 PP

>> CBM_2  Cellulose binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.8   7.1e+03      47      54 ..      58      65 ..      26      75 .. 0.54
   2 ?   -0.6   0.0      0.66   1.7e+03      50      88 ..     249     288 ..     239     296 .. 0.77
   3 ?    9.9   0.1   0.00036      0.91       3      72 ..     394     462 ..     392     469 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                EESEEEEE CS
       CBM_2 47 lWnatvsq 54
                 W+++++ 
  AJA91859.1 58 IWDSSLVM 65
                34444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.66
                 EEEEEETTEEEEEE-STT-EE.-TTEEEEEEEEEEE-SS- CS
       CBM_2  50 atvsqsGnsvtatnvswNgti.apGgsasfGfqgsktgsn 88 
                 +++s+sG++    + +w +++  pG  +++ f++s +g++
  AJA91859.1 249 GHTSTSGTPADGPDGNWDSSLmSPGYGMDVIFEISDAGQE 288
                 5678899999999999998862579999999999999875 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00036
                 EEEEEEEE-SSEEEEEEEEEE-SSS-EES-EEEEE--TTEEEEEEESEEEEEETTEEEEEE-STT-EE-T CS
       CBM_2   3 atyavtseWetGftasvtvkNsgssaingWtvewtlpagqrvtqlWnatvsqsGnsvtatnvswNgtiap 72 
                 ++++ +s+ ++ f   v++k s +++i+  +v+  l agq++ q+ +   s++G ++t+++  wN+   p
  AJA91859.1 394 MDFTNDSDVQQSFALIVQIKDSNNTTISLSHVTGMLGAGQTLDQVLSYMPSEAG-TYTVEKFLWNNFADP 462
                 57888999999************************************9999995.79********97655 PP

>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.6   0.00026      0.68      37     100 ..     305     389 ..     300     453 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                 EETTEEEEEE...ESS...........HHHHHHHHHHHHHHCCS---TT-GGS-HHHHHHHHHHHHHH.CHCST..........T CS
   PmbA_TldD  37 ikggrlgfastldtsd...........ealeeaveraveiaklapedpeaeevsaeekielleelekalrsadp..........k 100
                 ++gg   ++s  ++s+           ++ ++a+ +a+++a+ a+ +  a+   ae + + +e++++a+++a++          k
  AJA91859.1 305 VSGGGATSSSQAESSQaqddaaeriaaAEAAAAAAEAEAAARIAEAEAAARIAAAEAAAAAAEAAAAAAEAASQqaiaelsvneK 389
                 3344333444444554564333333331222222224444433333332211111111111222222222222233222222220 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       6.9   1.8e+04      53      64 ..      70      80 ..      35      83 .. 0.49
   2 ?   -0.9   0.4       1.5   3.7e+03      10      47 ..     122     166 ..     117     194 .. 0.54
   3 ?   10.7   0.1   0.00035      0.89       9      67 ..     384     452 ..     382     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.9
                TS-EE-SSSEEE CS
         PPC 53 yieftapqaGtY 64
                y + +a++aG Y
  AJA91859.1 70 YTT-PALDAGEY 80
                333.55677776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                 -TT-EEEEEES-TT.....SEEEEE-TT.......-SS-EE-STT- CS
         PPC  10 pagdsltididggti...dldLylldsng.....tsvaaydansap 47 
                 ++gd+++++  +g+    ++ + + d++g     t++  ++++s++
  AJA91859.1 122 TTGDTIIVT-GSGASpesSVVILVNDPDGdmvlvTQTGVNSDGSFE 166
                 566667666.333334643334455555433322333333344433 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00035
                 E-TT-EEEEEES-TT..SE........EEEE-TT..-SS-EE-ST...T-TTS-TTS-EE-SSSEEEEEE CS
         PPC   9 vpagdsltididggtidld........Lylldsngtsvaaydans...apsgsdeyieftapqaGtYyva 67 
                 ++++ +++i++d ++ d+d        +++ dsn+t+++ ++ ++   a ++ d  +++ + +aGtY v+
  AJA91859.1 384 LSVNEKIEITMDFTN-DSDvqqsfaliVQIKDSNNTTISLSHVTGmlgAGQTLDQVLSYMPSEAGTYTVE 452
                 667777777776666.4444466668889*****999999999999999999******999******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1667  (0.0929779); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3104.29
//
Query:       AJA91860.1  [L=233]
Description: PAC2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-25   89.0   0.0    5.2e-25   88.7   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.0   2.9e-29   5.2e-25       2     208 ..      17     223 ..      16     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 2.9e-29
                 EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.......SEEEEEEE..E-HSCHHH...HHHHHHH CS
        PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsg......srdllvlqg..repilqye...efakall 89 
                 i+++ ++GnVg+++v+++  sl+   + +  s+   p     p+ ++++g+ +e p+      +      ++d++v+ g    ++  +e   e+++ ++
  AJA91860.1  17 IAAMQDMGNVGSIVVNHINKSLGTASFRHATSSR--P-----PY-VYDKGGYIEIPE------EkweyrfGKDIIVFGGgrG-QPQENEelnELCQDVI 100
                 78999*****************999999999988..4.....44.444453333333......234444469*******953.4444445889****** PP

                 HHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT.......-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC.--HHHHH CS
        PAC2  90 dwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.ees.......eyggivgitglLlsaakergipavgllaevphyl.pdPkaaa 179
                 ++a++++ k ++++gg+++ ++   + + p  +t++ t+ + + +l   +       ++++i+g++gl+l+ ak +gi+++gl++e  +   p  +aa+
  AJA91860.1 101 NVAKRYDAKFIYTVGGYHTSRS---FGKSP--TTYVTTTSQDILKLvR-KlgiettpTESVITGFNGLILGYAKLNGINGIGLYGELLEPRiPQYRAAR 193
                 ******************7654...45555..6777777777766733.22445578*****************************999655******* PP

                 HHHHHHHHHHT--.-HCHHHHHHHHHHHHH CS
        PAC2 180 alleflskllgle.vdtedLeedaeeleeq 208
                 +++e l+kl+  +  dt++L+ +ae++e++
  AJA91860.1 194 TIIETLEKLTYQKlGDTKELSVKAEAVESR 223
                 **********66637799********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1705.01
//
Query:       AJA91861.1  [L=375]
Description: transporter, major facilitator family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-25   88.1  42.0      1e-20   74.0  31.8    2.1  2  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.022   13.6  34.1       0.72    8.6  33.4    2.3  1  MFS_1_like  MFS_1 like family
       0.96    9.4   7.3        4.1    7.4   0.2    3.9  3  Tail_VII    Inovirus G7P protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0  31.8   1.7e-24     1e-20       4     330 ..      14     312 ..      13     317 .. 0.83
   2 !   21.4   1.8   1.7e-08    0.0001     119     178 ..     313     370 ..     310     375 .] 0.87

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.7e-24
       MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fasslwlllvlrvlqGlgag 100
                 ++f+ + +++i+++++p ++a+    s+ eig++++ +a++++++   +Gr+sdr   r  ++ +g++l a++ + l  fa + ++l+++r+ +G+++g
  AJA91861.1  14 TTFFQHSGIAITFVFMP-IIASVVAKSVFEIGIIVASFAFAQILTETYFGRMSDRKAKRLlFIRVGFILCAIT-FGLHyFADNTTYLIIARLGAGIASG 110
                 57999999*********.9999999******************************989999************.44445877766************** PP

       MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpa 199
                 +++p ++a++ +  ++    + ++ + ++ +lG + g +++g+        ++f++   +++++f+   + l  ++ + ++   +e+       ++++ 
  AJA91861.1 111 IMIPPMLAYAYEAGKG---KSKVASVISFHALGWLAGIVAAGIAN---DEKLIFVVSSCFFIIGFL---ISLKLPKIQTEKI--VEK-------GIIK- 190
                 ************9998...33344455678888888889999999...6689************77...5555555555555..333.......4444. PP

       MFS_1 200 wkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavts 298
                  k+++k++ +  l+ +ll+ ++g +++ t lp++l+e +g   l+++++++ +  l +   +l+   +s+r++ ++++ + +++++++ +++ l+  t 
  AJA91861.1 191 -KIIVKNK-F--LFSSLLVRHVGAAAAWTVLPIMLMEYFGAE-LYQVSMVYVANTLTA---FLVMNLMSKRIQIQNITKFKIGIGMTVIVFVGLALIT- 280
                 .5555666.5..899999999999******************.999998888888887...77999999**888888888888888888888888888. PP

       MFS_1 299 savllllvlvliGfglgfvfpsllalasdlap 330
                 + ++++ +++++G+ ++f f+  +  ++++ p
  AJA91861.1 281 EWWMAWPFMAIVGCSWAFLFIGGNFHLMENNP 312
                 6677777************9998888877765 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.7e-08
       MFS_1 119 rgraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                 r+  ++++s++ ++++++gp+++g +a +  ++av++++ ivs+ af++     + ++++
  AJA91861.1 313 RSTSTAIFSSTLAISTVIGPVIAGSIAYYTDYTAVMVFAIIVSFSAFII--STRMKSEKP 370
                 77889*****************************************997..665555555 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  33.4   0.00012      0.72       7     383 ..      14     350 ..      10     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00012
  MFS_1_like   7 lyFfffaalgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdv 105
                 + Ff+ + ++  + ++ i  +    ++ eigii++   + +il +  +g ++Dr +kr   ++++ +l a++f   +                      
  AJA91861.1  14 TTFFQHSGIAITFVFMPIIASVVAKSVFEIGIIVASFAFAQILTETYFGRMSDRKAKRLLFIRVGFILCAITFGLHY---------------------- 90 
                 5688888888888888888888888899*********************************************9333...................... PP

  MFS_1_like 106 daektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnete 204
                  +  +  +l++ ++ a + +  +++ + a ++++ g+ + + + ++ f ++G+    ++ Gi+ d           +++v   +++i +l++l+l++ +
  AJA91861.1  91 -FADNTTYLIIARLGAGIASGIMIPPMLAYAYEA-GKGKSKVASVISFHALGWLAGIVAAGIANDEKL--------IFVVSSCFFIIGFLISLKLPKIQ 179
                 .445556666677777777777777777777665.8888889*******************9977644........58999**********99998887 PP

  MFS_1_like 205 kesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvkll..iiallay 300
                  e+ ++       +++i+ + +  +++  +l+ ++  +++++ l + L +  ga  + ++++    v+ +++ f++++ + +++ ++++    i++ ++
  AJA91861.1 180 TEKIVEKGI----IKKIIVKNK--FLFSSLLVRHVGAAAAWTVLPIMLmEYFGAELYQVSMVY---VANTLTAFLVMNLMSKRIQIQNITkfKIGIGMT 269
                 776655553....334444444..455566666666777777788888666688777777655...566677777777777777777775226899*** PP

  MFS_1_like 301 ilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGll..wdlksaiflF 383
                 ++ f+++a+i+++w++ p+ ++ g+s + l+  + ++  +  p+s+ +   +++s++   + + +G +i+G +  +  ++a+++F
  AJA91861.1 270 VIVFVGLALITEWWMAWPFMAIVGCSWAFLFIGGNFHLMENNPRSTST---AIFSST-LAISTVIGPVIAGSIayYTDYTAVMVF 350
                 ************************************999999987666...777776.677888888887754214667777766 PP

>> Tail_VII  Inovirus G7P protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4     0.088   5.2e+02       1      23 [.      29      51 ..      29      55 .. 0.83
   2 ?    7.4   0.2   0.00069       4.1      18      37 ..     133     153 ..     128     154 .. 0.81
   3 ?    2.5   0.1     0.022   1.3e+02       7      32 ..     318     339 ..     312     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.088
    Tail_VII  1 MesveDavawsticiglVlvWFv 23
                M+  +  va s+  ig+++  F+
  AJA91861.1 29 MPIIASVVAKSVFEIGIIVASFA 51
                77888889999999999998887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00069
    Tail_VII  18 VlvWFvLGrlAGsvA.GmFnd 37 
                 V+ + +LG lAG vA G+ nd
  AJA91861.1 133 VISFHALGWLAGIVAaGIAND 153
                 89989*******996377776 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.022
    Tail_VII   7 avawsticiglVlvWFvLGrlAGsvA 32 
                 a+  st  i+ V+       +AGs+A
  AJA91861.1 318 AIFSSTLAISTVIG----PVIAGSIA 339
                 89999999999998....67888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2718.57
//
Query:       AJA91862.1  [L=250]
Description: putative phosphoesterase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   42.2   1.9      6e-10   40.0   1.9    2.1  1  Metallophos      Calcineurin-like phosphoesterase
    4.2e-08   33.5   0.0    6.4e-08   33.0   0.0    1.2  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    0.00083   18.3   0.1     0.0017   17.3   0.0    1.5  2  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.077   12.9   1.6       0.16   11.8   1.6    1.6  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   1.9   1.3e-13     6e-10       4     152 ..      23     177 ..      21     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.3e-13
                  EEEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHHTSEEEEEC-TTS........ CS
  Metallophos   4 lvigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrg......dlekellellaalvkypipvylllGNHe........ 75 
                  lvi+DlH+             + + ++ d++  +++++++e+pd ++l+GD+          +++  + +++++  +    ++l++GNH+        
   AJA91862.1  23 LVISDLHIgfehkfssnkntIENNSSIKDIISNIKKIIKKENPDTLILLGDVKSSIqnitktEWND-VPYFFEEIKN-SLDIILIPGNHDsnidrlip 118
                  89***************777777777777777778889999**********777764444446666.5555444444.5888********32222222 PP

                  ......CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEESECEEE.......THHHHHHHHHHHSCHHHHCC.HHHHH CS
  Metallophos  76 ......gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs...lkvlllhGgspel.......lvsldklgslnleleapepg.dewlk 152
                        g                              +          +++ll hG++ +        +     ++ + +++++  +g  +w++
   AJA91862.1 119 ndvtliG------------------------------SK-----GmiiDDILLTHGHTMPSknysnvnNIIMGHIHPVYFDQNSLLNGeRIWIS 177
                  2222220..............................22.....12233677777773222222233333333333333333333333444444 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   1.4e-11   6.4e-08       4     132 ..      23     163 ..      21     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.4e-11
  Metallophos_2   4 aiiSDlH..................snldaleavlealkevgvdaiihaGDl.eeeep......evleellela....pvlaVrGNnDeevveedv 70 
                    ++iSDlH                  s  d++ ++ +++k++++d++i++GD+   ++       + +  ++e      +++ ++GN+D        
     AJA91862.1  23 LVISDLHigfehkfssnkntiennsSIKDIISNIKKIIKKENPDTLILLGDVkSSIQNitktewNDVPYFFEEIknslDIILIPGNHD-------- 110
                    89*************999999988766777888899***************652222244455545555554445667**********........ PP

  Metallophos_2  71 lreaaelgtdlpeeaelelagek......vlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpev 132
                          +++ +p++ +l   g k      +ll+Hg+          + ++++++++ +++GH+H  + 
     AJA91862.1 111 ----SNIDRLIPNDVTLI--GSKgmiiddILLTHGH---------TMPSKNYSNVNNIIMGHIHPVYF 163
                    ....56667777666666..222344666******9.........4555556677789******7655 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.9e-07    0.0017      25      80 ..      21      77 ..       2      83 .. 0.79
   2 ?   -2.8   0.0       0.5   2.3e+03     147     195 ..     121     165 ..     117     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-07
                 THHHHHHTT----SEEE-..--S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHH CS
  Epimerase_2 25 gdtvfeeleiekpdydln..sdsqslakstgrvligleevleeekpDlvlvlGDtnet 80
                 ++ v ++l+i   +++++  +++ + + s+  +++++++++++e+pD +++lGD  + 
   AJA91862.1 21 KNLVISDLHI-GFEHKFSsnKNTIENNSSIKDIISNIKKIIKKENPDTLILLGDVKSS 77
                 4556668888.5555555215557778999************************9886 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.5
                  EEE---..HHHHHHHHHHHHHH...T-HHHHHH--SS-EEEEE---HHHHT CS
  Epimerase_2 147 ifvvGn..tviDalllskeeieeklkaseilkelkekkyvlvtlHrrened 195
                  ++ +G+  ++iD +ll++ +   +    +     + +++++  +H++   +
   AJA91862.1 121 VTLIGSkgMIIDDILLTHGHTMPSK---NY---SNVNNIIMGHIHPVYFDQ 165
                  5666652234577766655554333...44...244677777888876655 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6   3.7e-05      0.16      10      99 ..      45     140 ..      37     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
  Exo_endo_phos_2  10 psdelenlestlekllselkspkiiilGDf.....NakhplWgsedtds......sargeeLiefleehslsllnllksgptfkssngsstiDl 92 
                      ++++++++ s+++k++++ +  ++i+lGD+     N ++++W++    +       ++  ++i +  +h+ ++  l ++  t + s+g  +iD 
       AJA91862.1  45 NNSSIKDIISNIKKIIKKENPDTLILLGDVkssiqNITKTEWND----VpyffeeIKNSLDIILIPGNHDSNIDRLIPNDVTLIGSKG-MIIDD 133
                      445899*************988*******866666888888877....1335656677778888889999998899999999999998.77765 PP

  Exo_endo_phos_2  93 tltsdnl 99 
                      +l ++  
       AJA91862.1 134 ILLTHGH 140
                      5554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1793.48
//
Query:       AJA91863.1  [L=292]
Description: 3-beta hydroxysteroid dehydrogenase/isomerase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-19   70.8   0.0    1.4e-19   70.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    4.1e-15   56.0   0.1    1.8e-14   53.9   0.1    2.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-10   40.7   0.3    6.7e-10   38.4   0.3    2.0  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.1e-09   35.7   0.0    7.4e-09   35.1   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
    4.9e-08   32.5   0.0    0.00051   19.3   0.0    2.2  2  NAD_binding_4    Male sterility protein
     0.0031   16.7   0.5       0.44    9.6   0.2    2.7  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.051   13.7   0.0    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.034   13.6   0.0      0.059   12.8   0.0    1.4  1  adh_short        short chain dehydrogenase
      0.053   13.4   0.0       0.07   13.0   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0     7e-23   1.4e-19       1     228 [.       3     207 ..       3     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 7e-23
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHHHHSHHHHHHHHTHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa.vggvaassedpadfieknlqgtlnl 98 
                 +lVtGa GfiGs l+k+l  +g+ev g  ++s ++     e  +++++dlt+++   ++ + +++d+v+hlAa    v+++ ++     ++n  gt+nl
  AJA91863.1   3 VLVTGAGGFIGSRLAKKLILEGHEVYGTIHDSPSQV----EGMQIINADLTNDE--FEIPD-VRFDVVFHLAAaTPLVKDKKKQ----KRINYDGTVNL 90 
                 79*****************************44443....4459*******988..55555.8********9867777665555....578******** PP

                 HHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTS CS
   Epimerase  99 leaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegk 197
                 ++ ++++    ++++s   v+G+++ +  +e++   p+kp + +    l + k +e+  +++++ + +     +yG +      s +   +++k+++g 
  AJA91863.1  91 FNKIKDKTE-FIIYASGLGVFGNPNGT-VDEQS---PIKPDTDFVKIRLDAQKFLENSCKENNIGFSVCYFGDVYGDG------SWFTEMVVKKLKSGM 178
                 ****97744.89**********88885.66666...******************************************......888888999999997 PP

                 SSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
   Epimerase 198 qevtllgdgtalRdflyveDvaeaillvleh 228
                    +  g+g+    f++v+D++ +++ ++++
  AJA91863.1 179 --MKTPGKGDYDKCFIHVDDAVGILISIAKN 207
                 ..9999****************999999888 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   8.8e-18   1.8e-14       1     269 [.       4     238 ..       4     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.8e-18
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---.HHHHTTSH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqsh.VdvsfekP 95 
                    L+TG  GfiGs la++L+ +g+ev+g++++s s    ++e             ++++++Dlt+ +     + +v++d v++LAA    V+ +    
     AJA91863.1   4 LVTGAGGFIGSRLAKKLILEGHEVYGTIHDSPS----QVE------------GMQIINADLTNDEF---EIPDVRFDVVFHLAAATPlVKDKK--- 77 
                    9*************************9988776....233............356899****9874...5889**********9976244443... PP

                    HHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TT CS
  GDP_Man_Dehyd  96 eytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrget 191
                     +  ++n  Gt++L++ i++        ++ aS   v+G+++   ++E+ p++P   +   +l a+ + +n  ++ ++  ++  +   ++      
     AJA91863.1  78 -KQKRINYDGTVNLFNKIKDKT----EFIIYASGLGVFGNPN-GTVDEQSPIKPDTDFVKIRLDAQKFLENSCKENNIGFSVCYFGDVYGDGS--- 164
                    .4588999**********9843....34678999******96.789********************************999888888999883... PP

                    SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS.---EEE-TT-EEECHHCHHCCHHCCCHH CS
  GDP_Man_Dehyd 192 fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdk.pedyviatgethsvrefvelaflelgkt 269
                      t+ +   v + + g  +++  G++d  + + hv+D v ++  + +++   + yv+a+ ++++ +efv+ ++ ++g +
     AJA91863.1 165 WFTEMV---VKKLKSGMMKTP--GKGDYDKCFIHVDDAVGILISIAKNNLrDQAYVCADSTSVTFKEFVDYTADKIGAK 238
                    344443...456678887777..999999***************9988651567******************9999865 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.3   3.4e-13   6.7e-10       1     269 [.       4     236 ..       4     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 3.4e-13
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 +vtG++GF+G++l k+L+ +++  e  v+   ++++      +v+  ++i++D+t+ +  e      dvv+hla+++++ +  +++   ++n+ GT n+
  AJA91863.1   4 LVTGAGGFIGSRLAKKLILEGH--E--VYGTIHDSPS-----QVEGMQIINADLTNDEF-EIPDVRFDVVFHLAAATPLVKDKKKQ--KRINYDGTVNL 90 
                 69*******************6..4..4544444433.....45555567999987553.33444689*************77766..8********** PP

   3Beta_HSD 100 leacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak 198
                  +  +    ++++Y S ++v g+        ng  +++ + ++   + + +  a k++ ++     +n   +  c      +yG+g+ +++ ++k  +k
  AJA91863.1  91 FNKIK-DKTEFIIYASGLGVFGN-------PNGTVDEQSPIKPDTDFVKIRLDAQKFLENSCK---ENNIGFSVCYF--GDVYGDGSWFTEMVVK-KLK 175
                 *9865.567***********999.......344444444555566666666666666655555...33335777766..4689999877665554.456 PP

   3Beta_HSD 199 lglalfkigdeevlsdrvYvgNvawahi.lAaralqdpkkkssvagqayfisddsPvesyddfnltllkelg 269
                 +g  +   g+ +  + ++ v+  + + i +A  +l+d         qay + d + v+ +++f+     ++g
  AJA91863.1 176 SG-MMKTPGKGDYDKCFIHVDDAVGILIsIAKNNLRD---------QAYVCADSTSVT-FKEFVDYTADKIG 236
                 66.4555566666666777766555444133334444.........577777777777.7777766666665 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.7e-12   7.4e-09       1     167 [.       1     174 [.       1     292 [] 0.74

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.7e-12
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......T--TTSHHHHHHHH..HHH--SEEEE------HHHHHHSHHHHHHHHTHHHHHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre......eldltdaeavaell..keakpdvvvnaAAytavDkaEseeeaayavnaeavealAea 88 
                    mk+lvtGa+G +Gs Lak+l  eg+ev+++  +       +++ +a+  ++ +   +++ dvv ++AA t   k   +++++ ++n +++ +l + 
     AJA91863.1   1 MKVLVTGAGGFIGSRLAKKLILEGHEVYGTIHDspsqveGMQIINADLTNDEFeiPDVRFDVVFHLAAATPLVK---DKKKQKRINYDGTVNLFNK 93 
                    89***************************95555788884555555555444322799************9875...889999************* PP

                    HHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEE....EEE-SEESSSSS-HHHHHHHHH CS
  RmlD_sub_bind  89 aaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkali....vRtswvygekgknfvktmlrla 167
                     +    ++i+ S   VF G+ +    e+++ +P + + + +l+  +  ++++k+  i      ++ vyg+ g  f + +++++
     AJA91863.1  94 IKDKTEFIIYASGLGVF-GNPNGTVDEQSPIKPDTDFVKIRLDAQKFLENSCKENNIgfsvCYFGDVYGD-GSWFTEMVVKKL 174
                    *****************.6778889***********9999999988888877765541110455555554.555555555554 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   3.8e-05     0.076       1      49 [.       5      52 ..       5      58 .. 0.82
   2 !   19.3   0.0   2.6e-07   0.00051      85     157 ..      57     141 ..      39     180 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-.SSSHHHHHHHHHHHT-SS- CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvR.aksgesaeeRleeelekke 49
                   +TGa GF+G++L +kL+ +    ++y  ++ + s+ ++++ +++ l+++e
     AJA91863.1  5 VTGAGGFIGSRLAKKLILEGH--EVYGTIHdSPSQVEGMQIINADLTNDE 52
                   7***************98887..799999955566688888888777765 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.6e-07
                    HHH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.................. CS
  NAD_binding_4  85 aeevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeege..............k 157
                      + dv++h aA + ++++ k+ +r+N +Gt+++++  k   k++ +++ S   v g+ +g+v+e+   +++              +
     AJA91863.1  57 DVRFDVVFHLAAATPLVKDKKKQKRINYDGTVNLFNKIK--DKTEFIIYASGLGVFGNPNGTVDEQSPIKPDtdfvkirldaqkflE 141
                    45689****************************999777..4445789999955555555577776544444566666665544433 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2   0.00022      0.44       1      20 [.       3      22 ..       3      43 .. 0.89
   2 ?   -0.2   0.0      0.22   4.4e+02      75      94 ..      57      74 ..      42     102 .. 0.72
   3 ?    3.2   0.0      0.02        39     154     239 ..     142     227 ..     133     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00022
                     EEEETTTSHHHHHHHHHHHH CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilk 20
                     vlvtGagG iGs+l ++++ 
       AJA91863.1  3 VLVTGAGGFIGSRLAKKLIL 22
                     8**************99875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                     ..T-SEEEE------HHHHH CS
  Polysacc_synt_2 75 elkvdvvfhaAAlKhVPlve 94
                     +++ dvvfh AA    Plv 
       AJA91863.1 57 DVRFDVVFHLAAA--TPLVK 74
                     56789****9996..45555 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.02
                      G--SSS--EEEEEEE-EETTGTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHH CS
  Polysacc_synt_2 154 keseekktkfvvvRfGNVlgSrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdl 239
                      ++ +e++  f+v  fG V g       +  k++k+g   t    +  + f+ +++av ++++ +++  + + +v     +v+ ++ 
       AJA91863.1 142 NSCKENNIGFSVCYFGDVYGDGSWFTEMVVKKLKSGMMKTPGKGDYDKCFIHVDDAVGILISIAKNNLRDQAYVCADSTSVTFKEF 227
                      44456678999999***9996555667889999999999999999**************999999999999999877777777665 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.051       1      46 [.       1      45 [.       1      70 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHH CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdage 46
                +kv+v+Ga G +G++++k +   e++e+ + ++ ++s++eg+++ +
  AJA91863.1  1 MKVLVTGAGGFIGSRLAKKLIL-EGHEVYGTIHDSPSQVEGMQIIN 45
                89*****************999.9************9999988854 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     3e-05     0.059       3      37 ..       3      38 ..       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHH CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvv.vdrseekl 37
                vlvtGa++ IG  +ak+l+ eG +v+  +  s++++
  AJA91863.1  3 VLVTGAGGFIGSRLAKKLILEGHEVYGtIHDSPSQV 38
                9************************87555555444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.5e-05      0.07       1      52 [.       7      52 ..       7     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
                    TTTSHHHHHHHHHHHHC-T-EEEEEETT.HHHCHHHHCTTTCEEEE--TT-CC CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRn.peklaeleaeeglevvegdvtdve 52
                    GA G +G++l+k+l+ +g hev   + + p++++      g++++ +d+t+ e
      AJA91863.1  7 GAGGFIGSRLAKKLILEG-HEVYGTIHDsPSQVE------GMQIINADLTNDE 52
                    9****************5.***887766377776......7899999999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2053.73
//
Query:       AJA91864.1  [L=364]
Description: inositol-3-phosphate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-27   96.3   0.0    2.1e-27   95.5   0.0    1.4  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   1.2e-31   2.1e-27       1     108 [.     199     306 ..     199     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 1.2e-31
                     SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GGGTTEEEEEEEEEEEE CS
  Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpylgDsKvaldeiesei 92 
                     G+T+++++La+l+ erg k+++++++N++Gn+D++n++e+er+ sKkisK++ v++++ + +l  +d ++++   +++p+lg++K ++++ie++ 
      AJA91864.1 199 GATIVHRTLARLCDERGTKIEKTYQINVGGNTDFLNMKEQERLISKKISKTESVQSQLTD-RL--DDDNIYVgpsDFIPFLGNTKLMFMRIEGRQ 290
                     9********************************************************998.44..35679999********************** PP

                     GGGEEEEEEEEEEEEH CS
  Inos-1-P_synth  93 flggkntielkleceD 108
                     + +++ ++e++le++D
      AJA91864.1 291 WANIPYNMEVRLEVDD 306
                     **************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2719.53
//
Query:       AJA91865.1  [L=187]
Description: TATA-box-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-53  176.7   0.0    3.1e-26   91.1   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.6e-06   27.0   0.0       0.11   12.6   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   3.5e-30   3.1e-26       3      84 ..       9      88 ..       7      89 .. 0.96
   2 !   83.8   0.0   6.7e-28     6e-24       2      83 ..      99     178 ..      98     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 3.5e-30
                EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                 ++Nvvasa++++++dL+ + +k    ++eY p++fpglv+rl++p+++ liF++Gk+v+tGaksee + +a++++++ l+k
  AJA91865.1  9 SVENVVASASVDQKVDLNDITKKF--PDTEYHPDQFPGLVFRLESPRTATLIFRTGKMVCTGAKSEEMAVKAVQTVVKQLRK 88
                79******************7665..*****************************************************997 PP

  == domain 2  score: 83.8 bits;  conditional E-value: 6.7e-28
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 +++qN+va +nlg +++Le+ a+k+    + Yepe+fpgl+ r+ +pk+++l+F+sGk+v+tGak+e ++++ ++++   l+
  AJA91865.1  99 ITVQNIVAAINLGGKIHLEQAARKL--PRSMYEPEQFPGLIHRMLDPKTVILLFASGKLVCTGAKKEADVYRSVHNLHSTLE 178
                 68*******************9998..*********************************************9999887775 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   1.7e-05      0.15      12      62 ..      26      77 ..      17      88 .. 0.83
   2 !   12.6   0.0   1.2e-05      0.11      24      63 ..     130     167 ..     119     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
     DUF3378 12 kkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAsk 62
                + +++++ +      + p+ vf+ +++ t   +++ gK +  G++ e+ A k
  AJA91865.1 26 NDITKKFPDTeYHPDQFPGLVFRLESPRTATLIFRTGKMVCTGAKSEEMAVK 77
                55555555443667899*******************************9987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.2e-05
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeAskw 63 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e  A  +
  AJA91865.1 130 PEQFPGLIHRMLDPKTVILLFASGKLVCTGAKKE--ADVY 167
                 678899999999***************8776555..5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1328.00
//
Query:       AJA91866.1  [L=518]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-66  222.9  19.9    4.9e-66  222.9  19.9    2.4  3  Proton_antipo_M  Proton-conducting membrane transporter
    0.00021   21.3   0.1     0.0013   18.7   0.1    2.5  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.4      0.94   8.4e+03       7      23 ..      32      48 ..      30      50 .. 0.76
   2 !  222.9  19.9   5.5e-70   4.9e-66       1     278 [.     157     430 ..     157     435 .. 0.96
   3 ?    0.0   1.1     0.044   3.9e+02      40      97 ..     441     498 ..     433     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 0.94
  Proton_antipo_M  7 lylglElvllplylLig 23
                      ++ ++l l ++++Li+
       AJA91866.1 32 TWFTFGLLLYCTVILIN 48
                     57888888888888886 PP

  == domain 2  score: 222.9 bits;  conditional E-value: 5.5e-70
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94 
                      +++L+ +y+++E++l+p+++L++++++  ++ + +l +++ t +g ++LLlg+l++    g+ +f ++++a    ++   l++ ++++++gl v
       AJA91866.1 157 STNLIEFYIFFEVMLIPSFFLVAFYGDG-NRRRIALQFLFWTHVGAVVLLLGFLAIGLSVGSFDFVDIVEA---EIDPDILVVSAVAIILGLGV 246
                      78***********************988.77788899999*******************************...8888889999********** PP

  Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGyml 187
                      K+a++ +h+Wlp a+ +aPtp+sall+  +  +g+++l+rl++ +  + +++is++l i ++++m++g+ +al q d Kr+lAySsis++Gy+l
       AJA91866.1 247 KLAAFVFHVWLPYAHGAAPTPISALLSPAMIGIGAYGLFRLIVEFLpQTYGDISIMLNIWGVVTMFYGGAMALMQDDFKRMLAYSSISQMGYLL 340
                      **************************888**************99999********************************************** PP

  Proton_antipo_M 188 ialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                       a++  + yg+++a +  ++h+l k llF+ a +vi  ++ tr+++++ggLa kmPi+a++ +++ l+++G+Ppt+gF+++++++++a++ 
       AJA91866.1 341 FAIGSFSTYGLAGAEMMYISHGLGKGLLFMTA-GVIIVQVGTRSFKKLGGLASKMPITAVCAVIGGLTIMGIPPTSGFMGEWMVFYGALET 430
                      ********************************.5556777**********************************************99875 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.044
  Proton_antipo_M  40 lltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllvKsa 97 
                      l+++lg ++  l +++++++   + f +l ++l+++++ +  +l+ +++l+g+ + ++
       AJA91866.1 441 LMFALGLIATALTMSYILWMLKRVFFGKLPENLQNVKEGSWYMLAPMMVLAGFTIVVG 498
                      677888888889999999*999999999999999999999999999999999987665 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.5e-07    0.0013       5      46 ..      62     100 ..      58     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-07
  Proton_antipo_N   5 lsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMad 46 
                      ++   +  e+gfllD+l   +++++ ++ ++  lYS  YM +
       AJA91866.1  62 TT---MFGEFGFLLDGLATPFAIIIYVLCTVLALYSKPYMVH 100
                      44...3348*******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 3282.14
//
Query:       AJA91867.1  [L=923]
Description: copper resistance protein D [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-13   50.8   4.3    1.4e-12   47.9   0.5    2.7  2  CopD      Copper resistance protein D
    7.8e-10   39.7   0.0      2e-09   38.4   0.0    1.8  1  CopC      CopC domain
    1.5e-09   37.8   0.1      0.018   14.6   0.0    4.2  4  SGL       SMP-30/Gluconolactonase/LRE-like region
    0.00071   20.1   0.1      0.025   15.2   0.0    2.6  2  YtkA      YtkA-like
     0.0052   16.8   0.1      0.087   12.9   0.0    3.0  2  DUF5074   Domain of unknown function (DUF5074)
  ------ inclusion threshold ------
      0.011   16.1   1.7      0.011   16.1   1.7    2.9  3  DUF4149   Domain of unknown function (DUF4149)
      0.018   16.1   1.6      0.075   14.1   1.6    2.0  1  PPC       Bacterial pre-peptidase C-terminal domain
      0.025   14.7  10.8    2.6e+02    2.4   0.0    7.5  8  Reg_prop  Two component regulator propeller
       0.25   10.5   0.1        0.4    9.8   0.1    1.2  1  TMEM173   Transmembrane protein 173


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.052     1e+02       6      58 ..     186     243 ..     181     250 .. 0.76
   2 !   47.9   0.5   6.9e-16   1.4e-12       4     105 .]     330     429 ..     327     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.052
        CopD   6 rFsrlalaavavvlvtGvvnallrvg.....lagllttayGrlllaKlalllvllala 58 
                 +Fs+++ + v++++++ +++  +++      + + ++t+ G ++l+ ++  +++++l 
  AJA91867.1 186 KFSKIIGIGVIATFASNFIMLGVQTWrletsPLDVIGTTFGTTWLIRMIITIIIIGLW 243
                 69************99999985553333244677778999998888888887777764 PP

  == domain 2  score: 47.9 bits;  conditional E-value: 6.9e-16
        CopD   4 lrrFsrlalaavavvlvtGvvnallrvg..lagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlrrsaalelvlalvvll 100
                 ++rFs l ++a++++++tG ++ + +    +a+l++++yG+l+l+K+a  +++++++++ +   ++ +    + ++    +++ + +  e++l+++ l+
  AJA91867.1 330 IPRFSGLFIIAIGILIITGPTLLWFL-DdnVASLTDSTYGKLILIKIAIAAAMIGFGGMYQIKFLKNM---SDLEKLNISRKISKPLKFEAGLGIALLA 424
                 78********************7777.5588***********************************99...4455666667****************** PP

        CopD 101 laaal 105
                 ++a+l
  AJA91867.1 425 VVALL 429
                 **987 PP

>> CopC  CopC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0     1e-12     2e-09       1      92 []      22     117 ..      22     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1e-12
        CopC   1 HaalvsstPaagatvaaapeevtLtFsepvel..skvkvtdpdgke.evetvdaktveaelkvplpelaaGtYtVewrvvsa.DGHpvsGsfsFtv 92 
                 H+ l +s+P +g+   a  +++  ++se+ve   s+++v+d++g++ + +++  +  e++l v+ p+l++G Yt++ +v+s+ DGH v+ +++F v
  AJA91867.1  22 HPFLLDSEPGQGQNAPAGTTQIITNYSEAVEIgfSELRVYDANGNQiDNKDTAYNGGETSLIVTTPPLEDGVYTITSKVLSKiDGHLVQAAIVFGV 117
                 8999****************************************8884444455557788999999999************88***********87 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00064       1.3     186     223 ..     615     657 ..     585     664 .. 0.71
   2 !   14.6   0.0     9e-06     0.018     147     220 ..     630     702 ..     623     716 .. 0.81
   3 !    6.7   0.0    0.0024       4.9     144     213 ..     718     782 ..     710     798 .. 0.71
   4 !   11.2   0.0   9.8e-05       0.2     184     232 ..     796     845 ..     784     856 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00064
         SGL 186 pDGla...vDa..eGnvwvAvwgggkvvrfdpdGklieeiklp 223
                 +DGl+   +D   +G++w +   ++k+  fdp+ +  e+i+lp
  AJA91867.1 615 FDGLTtifMDIgkDGKIWFTDTPNSKIGSFDPKTEKFETIQLP 657
                 6665322256555999999999999999999999999999999 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9e-06
         SGL 147 tlYlaDsltrkiwaydvdaeggklsnrrvf.adlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGklieei 220
                 ++ ++D+++ ki ++d ++e+ +  +   f + +kk    p ++ vD+e+ vwvAv++++ + ++++  k  + +
  AJA91867.1 630 KIWFTDTPNSKIGSFDPKTEKFETIQLPQFnLAIKKSL--PTSVGVDNENDVWVAVIDQSLLLEYNQSTKKFKIV 702
                 4568*************999988888888856666665..********************999999987766655 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0024
         SGL 144 dgktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpd 213
                 d + + +a+sl +k+ ++d +  +++l++ +   +++++  ep  l++D+e nvw+A   g  +++f+p 
  AJA91867.1 718 DANNVWFAESLVGKLGKIDGE--TKELTEFT--PQGEPM-AEPFALMIDKEENVWIAEHIGPAITKFNPI 782
                 555666777777777777763..33333333..334444.46999**********************996 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 9.8e-05
         SGL 184 gepDGlavDaeGnvwvAvwgggkvvrfdpd.Gklieeiklpak.rvtscaF 232
                 + p G+a D+ +n+wvA+   + +v++d+  G++ie i++p++   t  + 
  AJA91867.1 796 SLPFGMAFDKYDNMWVAQHVIDSLVVYDQSsGQIIE-IAIPTEgSFTQFVI 845
                 4577**************************777655.****8877777665 PP

>> YtkA  YtkA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.18   3.6e+02      42      72 ..      68      97 ..      48     104 .. 0.72
   2 !   15.2   0.0   1.2e-05     0.025       7      85 ..     460     539 ..     456     540 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.18
        YtkA 42 vefwmpameGmeemttkvelkesedGvYeae 72
                ++  ++a +G+e ++  v++ + edGvY ++
  AJA91867.1 68 IDNKDTAYNGGE-TSLIVTTPPLEDGVYTIT 97
                444455656666.5788888889*****998 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.2e-05
        YtkA   7 levelvspeepkagentivv.tvtqggkpVedad.vkvefwmpameGmeemttkvelke...sedGvYeaevnfsmeGtWqvql 85 
                 +++++ +  ++  g+nti+v + ++++kp+ d +  k++++ p+ ++ ++   ++e++e   +   +Y+a ++f+  G Wq++l
  AJA91867.1 460 AKFDVKVL-PAGIGSNTISViVTSYDDKPLVDISgLKIKVSNPQ-KNISP--IEAEVTEnvqDSVTKYSADATFGFVGNWQIEL 539
                 55666554.56789****883577*********99********8.55666..555555541234567***************98 PP

>> DUF5074  Domain of unknown function (DUF5074)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   4.4e-05     0.087       4      36 ..     626     662 ..     625     670 .. 0.86
   2 ?   -0.5   0.0      0.62   1.2e+03       5      12 ..     762     769 ..     717     798 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
     DUF5074   4 skDGnvWaa..sgtkLvkinpktlevktvelpe..ls 36 
                 +kDG++W +   + k+  ++pkt + +t++lp+  l+
  AJA91867.1 626 GKDGKIWFTdtPNSKIGSFDPKTEKFETIQLPQfnLA 662
                 59******988889******************94444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.62
     DUF5074   5 kDGnvWaa 12 
                 k+ nvW+a
  AJA91867.1 762 KEENVWIA 769
                 34455555 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.4      0.96   1.9e+03       3      21 ..     221     239 ..     220     282 .. 0.73
   2 ?   16.1   1.7   5.3e-06     0.011       2      61 ..     295     359 ..     294     391 .. 0.78
   3 ?   -3.0   0.1       4.7   9.5e+03      45      55 ..     419     429 ..     412     442 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.96
     DUF4149   3 lglllGsqlwvtfvvapvl 21 
                 +g+++G+++ +  + ++++
  AJA91867.1 221 IGTTFGTTWLIRMIITIII 239
                 6788888888888877765 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.3e-06
     DUF4149   2 slglllGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevavg......s 61 
                 + ++++G+++++ fv+ p++ ++ ++   +++   l p++ gl ++  ++l++t +          
  AJA91867.1 295 LSSIWIGGVIFFAFVALPTITKT-ENSIKEKITLSLIPRFSGLFIIAIGILIITGPTLLwflddnV 359
                 6789*******************.7778899***********************998776665553 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.7
     DUF4149  45 glalsvllllt 55 
                 g+al+++++l+
  AJA91867.1 419 GIALLAVVALL 429
                 33333333332 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.6   3.8e-05     0.075       9      66 ..      36      96 ..      35      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                E-TT-E.EEEEES-TT...SE.EEEE-TT..-SS-EE-STT-TTS-TTS-EE-.SSSEEEEE CS
         PPC  9 vpagds.ltididggti.dld.Lylldsngtsvaaydansapsgsdeyiefta.pqaGtYyv 66
                +pag++ ++ + +      ++ L+++d+ng+++++  ++++++g  ++i  t+ +++G+Y +
  AJA91867.1 36 APAGTTqIITNYSEAVEiGFSeLRVYDANGNQIDN-KDTAYNGGETSLIVTTPpLEDGVYTI 96
                6777775555543333236668*******998888.888899999899986668******98 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3         9   1.8e+04      18      22 ..     298     302 ..     297     302 .. 0.84
   2 ?   -0.5   0.0       1.2   2.4e+03      14      21 ..     585     593 ..     581     595 .. 0.80
   3 ?    1.8   0.1       0.2     4e+02      13      20 ..     626     633 ..     617     636 .. 0.75
   4 ?    1.4   0.0      0.28   5.6e+02       9      21 ..     670     682 ..     666     685 .. 0.84
   5 ?    2.2   0.0      0.15   3.1e+02       8      21 ..     712     725 ..     708     725 .. 0.89
   6 ?    2.2   0.0      0.15   3.1e+02       9      21 ..     757     769 ..     753     769 .. 0.89
   7 ?    2.3   0.0      0.14   2.8e+02       9      21 ..     800     812 ..     793     813 .. 0.85
   8 ?    2.4   0.0      0.13   2.6e+02      11      20 ..     845     854 ..     836     855 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9
                 EEEEE CS
    Reg_prop  18 lWvGt 22 
                 +W+G+
  AJA91867.1 298 IWIGG 302
                 8**96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                 TTS.CEEEE CS
    Reg_prop  14 sdG.rlWvG 21 
                  dG ++W++
  AJA91867.1 585 YDGeNIWIS 593
                 48889**97 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.2
                 -TTSCEEE CS
    Reg_prop  13 DsdGrlWv 20 
                  +dG++W+
  AJA91867.1 626 GKDGKIWF 633
                 67*****9 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.28
                 EEEE-TTSCEEEE CS
    Reg_prop   9 aileDsdGrlWvG 21 
                 ++  D+++++Wv+
  AJA91867.1 670 SVGVDNENDVWVA 682
                 5668********8 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.15
                 EEEEE-TTSCEEEE CS
    Reg_prop   8 taileDsdGrlWvG 21 
                 tai  D  +++W++
  AJA91867.1 712 TAIEIDDANNVWFA 725
                 58999*******96 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.15
                 EEEE-TTSCEEEE CS
    Reg_prop   9 aileDsdGrlWvG 21 
                 a++ D++ ++W++
  AJA91867.1 757 ALMIDKEENVWIA 769
                 8999*******96 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.14
                 EEEE-TTSCEEEE CS
    Reg_prop   9 aileDsdGrlWvG 21 
                  ++ D+  ++Wv+
  AJA91867.1 800 GMAFDKYDNMWVA 812
                 5788*******97 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.13
                 EE-TTSCEEE CS
    Reg_prop  11 leDsdGrlWv 20 
                   D +G++W+
  AJA91867.1 845 IADDNGDIWF 854
                 349******8 PP

>> TMEM173  Transmembrane protein 173
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0002       0.4      49     124 ..     230     301 ..     210     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0002
                 XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX-TCHHHHHHHHHHC CS
     TMEM173  49 lnlkslvllllllllylalssdlglslllalallslckllvll.lglqklslvevseirekkklnvAhGlAwsyYiG 124
                 l + +++++++ l +++  +++++ +  + l+++sl+   + + +g   ++++e+ +i     l++ h l +s +iG
  AJA91867.1 230 LIRMIITIIIIGLWFWMEKKNEITIKGQIPLLIASLILIATTTmMGHGASTELEAPWI-----LDYSHNLLSSIWIG 301
                 556678888899999999999999999999999998776666669*************.....*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (923 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.41
# Mc/sec: 6813.79
//
Query:       AJA91868.1  [L=177]
Description: hypothetical protein T478_0322 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1280.14
//
Query:       AJA91869.1  [L=369]
Description: hypothetical protein T478_1271 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.5   0.6      0.011   15.5   0.6    2.6  2  PKD       PKD domain
      0.019   15.1   0.0      0.066   13.4   0.0    1.8  2  ASH       Abnormal spindle-like microcephaly-assoc'd, ASPM-SP
      0.068   11.8   0.1      0.083   11.5   0.1    1.1  1  NPAT_C    NPAT C terminus
      0.074   12.9   0.0       0.12   12.2   0.0    1.2  1  Carot_N   Orange carotenoid protein, N-terminal


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.3   1.4e+03      28      43 ..     131     143 ..     103     147 .. 0.55
   2 ?   15.5   0.6   2.5e-06     0.011      19      67 ..     304     353 ..     281     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                 EEEE--SS--EEEEET CS
         PKD  28 ysWdfgdgsvvqvlse 43 
                  +W++g    vq l++
  AJA91869.1 131 IRWNVGE---VQWLES 143
                 2377777...666655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.5e-06
                 ES.-SS-SEEE..EE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
         PKD  19 avpdganvtys..WdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                 +v+dg+ vt s  W +g+  +++++ +p  + ++++ G+Ye+tv ++ +v 
  AJA91869.1 304 QVQDGNGVTVSlaWITGQ-LAAGQSFSPALSWIPTASGSYEATVFVWESVD 353
                 457877777777799999.*************************9998775 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   6.2e+03      69      93 ..     184     208 ..     181     211 .. 0.80
   2 ?   13.4   0.0   1.5e-05     0.066      18      87 ..     276     347 ..     271     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                 XXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  69 tltvtwtPteegavrevLqflvndv 93 
                 +l++t t+ ++g    ++ f+ +d 
  AJA91869.1 184 SLMITETNEATGIFEGTVSFTADDE 208
                 6778888888999999999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                 ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete..levqpgesvtltvtwtPteegavrevLq 87 
                 +v v +  + + +++N+++ +++ ++   +++ +g++v+ ++   ++++g+s++  ++w Pt++g+  +++ 
  AJA91869.1 276 EVSVDQQVQIEADLVNGQDRDQSFAYLVQVQDGNGVTVSLAWitGQLAAGQSFSPALSWIPTASGSYEATVF 347
                 6888888899999********9999999999********999999********************9998875 PP

>> NPAT_C  NPAT C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.9e-05     0.083       6     130 ..     243     369 .]     241     369 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
      NPAT_C   6 isgenlptiilSspaKspeknaelskclsseetagaevkdsalveQkllvlkpkd.saasslniqneectvfsla.gtsnvskdggf...iqLlpatst 99 
                 i+g  +   i+ + +++p++na+++++   + + +  v +  ++e  l+  + +d s+a  +++q +++++ sla +t +++    f   +  +p++s 
  AJA91869.1 243 ITGTAIVGTIVPPLERAPAANARVVDSFGNSLS-EVSVDQQVQIEADLVNGQDRDqSFAYLVQVQDGNGVTVSLAwITGQLAAGQSFspaLSWIPTASG 340
                 8999999999************99997665544.33488889999999987755428899999999998877776489999987665322556999999 PP

      NPAT_C 100 afgnsnniliatCvtdpaalgttvtqsnvvv 130
                 +++ +  ++    v +p+al+ tv+ s  vv
  AJA91869.1 341 SYEATVFVW--ESVDNPTALSDTVSVSIRVV 369
                 999875555..78***********9997665 PP

>> Carot_N  Orange carotenoid protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.12      45      85 ..     261     301 ..     250     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                 HHHHCCCHHHHHHHHCS-HHHHHHHHHHHHCT--SHHHHHH CS
     Carot_N  45 aaelelaekllnqikqlseeeQlqvmrdlvnkkdteisraY 85 
                 aa+ ++++++ n ++++s ++Q+q+  dlvn +d + s aY
  AJA91869.1 261 AANARVVDSFGNSLSEVSVDQQVQIEADLVNGQDRDQSFAY 301
                 688899999999***********************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2717.38
//
Query:       AJA91870.1  [L=268]
Description: hypothetical protein T478_0831 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-30  105.5  10.9    2.1e-30  105.1  10.9    1.2  1  CdvA         CdvA-like coiled-coil domain
     0.0078   16.2   1.0      0.012   15.6   1.0    1.2  1  PDDEXK_7     PD-(D/E)XK nuclease superfamily
     0.0088   15.5  13.2      0.013   15.0  13.2    1.3  1  DUF4775      Domain of unknown function (DUF4775)
  ------ inclusion threshold ------
       0.13   12.5   3.0       0.26   11.5   2.7    1.7  1  YbaB_DNA_bd  YbaB/EbfC DNA-binding family


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1  10.9   4.7e-34   2.1e-30       1     122 [.      84     205 ..      84     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 4.7e-34
        CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleeke 99 
                 +r++AL+e+vs++d +ks++e i+ek++++l++l++++ e++++l++r+ e+e+q ks++ +l+++k++ +s+Ei+ e++++++++++e+l+++++ek+
  AJA91870.1  84 RRLNALMEIVSDNDSMKSDAEIIHEKYNTKLMTLQRTEFEISSELDNRVVEIEEQEKSVKVLLFDAKVQLKSNEISQETFDHVQSETDEMLQHMKHEKD 182
                 89************************************************************************************************* PP

        CdvA 100 eikklleklskleleeeeveetk 122
                 ei+k++++l++l+le++ +e+++
  AJA91870.1 183 EISKVKSRLANLSLEDMIPEVSP 205
                 **************998887765 PP

>> PDDEXK_7  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.0   2.6e-06     0.012      23     141 ..      70     184 ..      58     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
    PDDEXK_7  23 vkeqnllkvkekglrvqlekgraakllferlsdgeeielaynprfsrkeekq.ssytvtqkPD.ivleitkkekkkvlivfDAKYRidaaeekleeeek 119
                 + +q+llk+ke  +  +l+  ++  ++ ++ s + ++e+++++++++  + q + + ++ + D  v+ei+++ek+  +++fDAK  ++++e +   +e+
  AJA91870.1  70 LDSQRLLKQKEL-VIRRLNALME--IVSDNDSMKSDAEIIHEKYNTKLMTLQrTEFEISSELDnRVVEIEEQEKSVKVLLFDAKVQLKSNEIS---QET 162
                 555666555333.3445555555..677777888899999999998776666655566666662699********************999998...455 PP

    PDDEXK_7 120 eeedegpkedalnkmhrYrdai 141
                  ++ + ++++ l++m   +d i
  AJA91870.1 163 FDHVQSETDEMLQHMKHEKDEI 184
                 6677777788899888888877 PP

>> DUF4775  Domain of unknown function (DUF4775)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  13.2   2.8e-06     0.013     248     324 ..     181     263 ..      96     268 .] 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
     DUF4775 248 adatvedeav.vdkkseekaaavsess....eePk.eesePakeptPePmevDsssksstetaksstPvkevvaaeaasesaa 324
                 +d+ ++ ++   +   e+ + +vs s+      P+ +  eP+    PeP  v+sss+ s+et+ ++ P++e+ +ae++s+  +
  AJA91870.1 181 KDEISKVKSRlANLSLEDMIPEVSPSAmpgtYLPQpSDDEPIETRLPEPPSVESSSQKSSETQVMTIPAQEQIPAEPESDWIK 263
                 222222222222333344444444444332133666789**************************************998555 PP

>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.7   5.9e-05      0.26       8      63 ..     118     177 ..     112     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                  HHHHHHHHHHHTTSEEEEEETTTTEEE.EEETT--EEEEEE-GGGG....GS-HHHHHHH CS
  YbaB_DNA_bd   8 qkkmeeaqeelaekevegssggglVkV.tvngkgevksikIdpslld...pedkemLedl 63 
                  q+   e+  el++  ve + +++ VkV  +++k ++ks +I+++ +d    e  emL+++
   AJA91870.1 118 QRTEFEISSELDNRVVEIEEQEKSVKVlLFDAKVQLKSNEISQETFDhvqSETDEMLQHM 177
                  555558899******************778***************998875557999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1920  (0.107089); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1855.44
//
Query:       AJA91871.1  [L=516]
Description: ABC1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-24   85.4   0.3    9.2e-24   83.9   0.0    1.9  2  ABC1      ABC1 family
     0.0033   16.8   1.1     0.0091   15.4   1.1    1.8  1  Pkinase   Protein kinase domain
     0.0046   16.9   0.0      0.025   14.5   0.0    2.0  2  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.011   15.4   0.4      0.011   15.4   0.4    1.9  2  WaaY      Lipopolysaccharide core biosynthesis protein (WaaY)
       0.11   11.3   0.7       0.18   10.6   0.7    1.3  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   2.6e-27   9.2e-24       6     119 .]     105     218 ..     101     218 .. 0.91
   2 ?   -2.1   0.0       1.2   4.2e+03      49      80 ..     399     433 ..     395     461 .. 0.53

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.6e-27
        ABC1   6 kleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakll.kkflkelrldleelvdefskslleEldferEAknaekf 103
                 k++e F++++ +++  AS++qV+r++ ++g++++vKv+rpg++k +++Dl++l  ++  + k + ++lr ++  ++++f +s+ eEld+++E+ n +++
  AJA91871.1 105 KIDEKFDSLETTALSGASLGQVYRGT-RNGQQIIVKVKRPGIEKVVEKDLKVLMKIIPFAmKFVDPNLRFSIIPIMKQFVESMHEELDYTKESDNLKTI 202
                 799*********************96.79*********************98777776650555678889***************************** PP

        ABC1 104 renfaklkevkvPkvy 119
                 ++n+a +++v +P+v+
  AJA91871.1 203 KKNMAPYNNVVIPEVH 218
                 **************95 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
        ABC1  49 kriksDlellkllakllkk..flkelr.ldleelv 80 
                 ++ k D++ +k+l ++l++  ++k+   +++++  
  AJA91871.1 399 HTHKVDFKFIKVLGQILEEesLIKDAYvEEIKRSF 433
                 56666777776666666541122222223333333 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.1   2.5e-06    0.0091      43     153 ..     184     304 ..     121     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                 HHHHHHHHHHHHHS.CTTB--EEEEEEE..........SSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGE CS
     Pkinase  43 kkvlrEikilkklk.hpnivrlyevfee..........kdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNi 129
                 +++ +E+ + k+++  + i + +  +++          +++ +l +ey++g +++d+ + +++ ++ +++   +++++     l +++i+H D  p Ni
  AJA91871.1 184 ESMHEELDYTKESDnLKTIKKNMAPYNNvvipevhddySTKNILTMEYIPGIKVTDIQSlDEKGIDRQQLVIDVHKVFFT--MLLKHSIFHADPHPGNI 280
                 45555555555555444444444444445555666556777789********9999999766667777777777777654..467889*********** PP

                 EEETTTEEEE-SGTTSEESSSSCS CS
     Pkinase 130 LidekgelKitDFGlakelesssk 153
                  ++++g l + DFG+  +++ +++
  AJA91871.1 281 SVKDDGTLILYDFGMIGRINDETR 304
                 ***************999998765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.27   9.8e+02       7      31 ..     119     144 ..     114     158 .. 0.78
   2 !   14.5   0.0   6.8e-06     0.025     141     196 ..     244     296 ..     204     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                 -.SSCEEEEEEETT.--EEEEEE-TT CS
         APH   7 ggasnrtylvttpa.gryvlrrnppa 31 
                 +gas  +++++t + ++ ++++++p+
  AJA91871.1 119 SGASLGQVYRGTRNgQQIIVKVKRPG 144
                 5688888999999967*********9 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.8e-06
                 TCC..HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
         APH 141 lld..lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                  ++  ++++l   v   +   l+   ++++ H D+hpgN+ v++d++ +  + Df++ 
  AJA91871.1 244 DEKgiDRQQLVIDVHKVFFTMLL---KHSIFHADPHPGNISVKDDGTLI--LYDFGMI 296
                 44444455555556666666666...79***************999998..9999986 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   3.1e-06     0.011     114     176 ..     221     290 ..     179     312 .. 0.79
   2 ?   -2.2   0.1      0.73   2.6e+03      32      70 ..     404     441 ..     394     463 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
        WaaY 114 yvkvyimiieyiegielvdmpeiddevkak..i.....kqsieklhqlgmvsgdphrgnfivkkdevrii 176
                 y    i+ +eyi gi+++d+ ++d++  ++  +     k  ++ l ++++   dph gn+ vk+d+  i+
  AJA91871.1 221 YSTKNILTMEYIPGIKVTDIQSLDEKGIDRqqLvidvhKVFFTMLLKHSIFHADPHPGNISVKDDGTLIL 290
                 7778899***************99874333012111113344568899****************998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.73
        WaaY  32 nfkvikvlrniddtkvvlidtdygkyilkvfspkvkrne 70 
                 +fk ikvl +i +   +li+  y   i + fs  +k  e
  AJA91871.1 404 DFKFIKVLGQILEEE-SLIKDAYVEEIKRSFSRFAKTIE 441
                 567777777776544.56777777777777776665554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   4.9e-05      0.18     344     430 ..     420     513 ..     392     516 .] 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.9e-05
     DUF2207 344 kkskkkakkfkkalkkwksavkk......kergyfdkkg..kkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllf 430
                   ++++ +++k++++++++ +++      + ++++++++  +++  k + + l++ i++ +++l++++ +++ +   ++l++i   ++i++ +lf
  AJA91871.1 420 LIKDAYVEEIKRSFSRFAKTIEDtltiapEIKKFMEDTKlmQQQSGKKNNAMLAGSIFAAAVFLGSAFMFQS-NETVGVLGMIASGVIIGISALF 513
                 344558899********************8889998888665566666666666666777777777777777.5555555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3208.55
//
Query:       AJA91872.1  [L=164]
Description: ribosomal protein L13 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-09   37.1   0.3    2.7e-07   30.9   0.1    2.6  2  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   1.5e-11   2.7e-07       4     114 ..      24     124 ..      21     134 .. 0.87
   2 ?   -1.2   0.0      0.13   2.3e+03      46      70 ..     137     161 ..     129     163 .. 0.53

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.5e-11
                    EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-.. CS
  Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLp.. 97 
                    v+D ++ + grlas++ak+Lr             G+ v ++n++k+ ++gkk +    y++   + ++ + +    + ++p+ i+ ++++gmLp  
     AJA91872.1  24 VVDGTHLIAGRLASNVAKLLR------------KGNRVTIVNCDKIMMSGKKFSIIGEYEEFLKINSIINYKHGPKHPRRPDTIISRMIRGMLPfe 107
                    789999999999999999997............5899****************98888888888888888888889******************54 PP

                    SSHHHHHHGCTEEEESS CS
  Ribosomal_L13  98 knklgrrrlkrLkvyag 114
                     +  g++ + rL+ y g
     AJA91872.1 108 DKPSGKTDFARLRTYIG 124
                    466999999***99977 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.13
                    GGCBB-SSTHHTT-EEEEE-SSTTS CS
  Ribosomal_L13  46 aekvaltgkkleqkvyyrhtgypgg 70 
                     ek ++t +  +  ++ + ++y+gg
     AJA91872.1 137 FEKAKITKDSSRYTTMAEISRYIGG 161
                    3444444455555555555666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1164.76
//
Query:       AJA91873.1  [L=174]
Description: hypothetical protein T478_0213 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 1019.77
//
Query:       AJA91874.1  [L=109]
Description: hypothetical protein T478_0925 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0054   16.5   0.4       0.01   15.6   0.4    1.4  1  TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding d
  ------ inclusion threshold ------
      0.037   12.8   0.1       0.04   12.7   0.1    1.1  1  Glycolytic     Fructose-bisphosphate aldolase class-I


Domain annotation for each model (and alignments):
>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   1.2e-06      0.01       7      25 ..      38      56 ..      35      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-06
  TRAF_BIRC3_bd  7 saLetkvatFEnIVsVLnr 25
                   ++Le+k  +FE IV++L +
     AJA91874.1 38 ETLEEKEDVFEEIVCTLTQ 56
                   58***************76 PP

>> Glycolytic  Fructose-bisphosphate aldolase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.5e-06      0.04      45     100 ..      15      70 ..       5      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-06
                 HHHHHHT-TT.GGGTEEEEEE-HHHHT-B-TTS-BHHHHHHHTT-EEEEE----EE CS
  Glycolytic  45 yrelLfttdkeleeyisGvilfeetlyqkaddgkplvellkekgiipGiKvdkgvv 100
                  +elL+++ + ++++ + ++l+ etl +k+d  +++v +l++ ++i  + v  g+v
  AJA91874.1  15 LQELLVKATNFISQTNTPIVLYRETLEEKEDVFEEIVCTLTQDHVIEQVIVSGGMV 70 
                 679*******************************************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 781.96
//
Query:       AJA91875.1  [L=327]
Description: glycosyltransferases group 1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-05   25.6   0.0    1.9e-05   25.0   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     1e-09   1.9e-05       9      91 ..     233     319 ..     179     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1e-09
  Glyco_trans_1_2   9 espnlrlfEaaacGafaltdda...egleelftpgkevilfedleelaekiryllanpee..rraiaeaarervlaehtydhraeqll 91 
                        p+l++ E aa+G++   + +   +g+   f+++k++i++ ++ + +ek++++l++p+   +++ia+a+r+++  e++ d+++++++
       AJA91875.1 233 FYPTLKYWENAAAGCLTFMEITnknDGYFIGFENEKSAIFI-NERNYQEKFQEFLSDPDNpkWEEIANAGRKFAMDELNNDKAVQKIV 319
                      57999**********99988557678888889***999999.7799**********886444*******************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2506.23
//
Query:       AJA91876.1  [L=156]
Description: hypothetical protein T478_1279 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.095   12.9   1.0       0.16   12.1   0.9    1.5  1  Big_3_5   Bacterial Ig-like domain (group 3)
        2.1    8.4   5.3          6    6.9   0.9    2.3  2  DUF4514   Domain of unknown function (DUF4514)


Domain annotation for each model (and alignments):
>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.9   1.8e-05      0.16      43      76 ..      83     116 ..      36     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                 --TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S CS
     Big_3_5  43 lsanGtAtltvsalaaGthsitAtYsGdanyaas 76 
                  s + +A+l++++ +aG+  it + +Gd+ ++ s
  AJA91876.1  83 ASFKNKANLSWTSITAGQTIITIQNTGDSEFTES 116
                 222579*************************988 PP

>> DUF4514  Domain of unknown function (DUF4514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9   0.00067         6      21      34 ..       4      17 ..       2      20 .. 0.93
   2 ?    3.2   0.2    0.0094        85      20      41 ..     128     152 ..     124     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00067
     DUF4514 21 KYaiiGtalGvais 34
                K++iiG+++G ais
  AJA91876.1  4 KFTIIGIIIGSAIS 17
                99***********9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0094
     DUF4514  20 iKYaiiGtalGvai...sAgFLALK 41 
                 + Y i+ ++ Gv+i   sAgF A K
  AJA91876.1 128 FTYSILVIIAGVVIigfSAGFSARK 152
                 5688877888877656699998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1304.03
//
Query:       AJA91877.1  [L=154]
Description: thioesterase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-16   60.0   0.1    3.2e-16   59.4   0.1    1.3  1  4HBT             Thioesterase superfamily
    2.4e-05   23.9   0.3    3.3e-05   23.4   0.3    1.2  1  MaoC_dehydratas  MaoC like domain
     0.0053   16.9   0.2      0.019   15.1   0.2    1.8  1  DUF4442          Domain of unknown function (DUF4442)


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.1   5.4e-20   3.2e-16       2      76 ..      25      98 ..      24     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 5.4e-20
                SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSC CS
        4HBT  2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgr 76
                G+v+gG++l+ +D +ag+++ +   +  +v+v+ ++i fl+pv +g++l v+arv+++ ++s+++ev v +ed  
  AJA91877.1 25 GNVFGGAILKHIDMVAGIVAQRFSQT-NAVTVSMDKISFLKPVFVGNVLFVKARVNYVQKSSMEIEVNVEAEDIA 98
                9*************************.********************************************9976 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   5.5e-09   3.3e-05      62     118 ..      39      95 ..      28     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.5e-09
                      HHHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEE CS
  MaoC_dehydratas  62 vaklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtke 118
                      va++v++++ + ++  v ++k++F kpV++g+ l v++ v+ +++  ++++v v+ e
       AJA91877.1  39 VAGIVAQRFSQTNAVTVSMDKISFLKPVFVGNVLFVKARVNYVQKSSMEIEVNVEAE 95 
                      7899999999999***************************99999998888887765 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   3.2e-06     0.019      30     125 ..       9     105 ..       3     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-06
                 EEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEEE-S-..--S-EEEEEE-TTS-TT--EEEEEEEEEEE.TTE.EEEE CS
     DUF4442  30 raevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevdYlak..atgdltavaelepedvgekeelvvevevrd.ekgeevvr 125
                 +aev ++  +   N  g v+++Ai    ++++G++a++ + +t  + +   ++++l++      l   a+++  +   + e++v+ve++d +kg+ v +
  AJA91877.1   9 KAEVIIRMFPSDANPAGNVFGGAILKHIDMVAGIVAQR-FSQTNAVTVSMDKISFLKPvfVGNVLFVKARVNYVQKS-SMEIEVNVEAEDiAKGTRVHT 105
                 6788888888899********************99986.6667777778889*****96334455566666665544.677777777777334555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 1031.73
//
Query:       AJA91878.1  [L=254]
Description: PF11906 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-15   56.9   0.1    2.1e-09   37.7   0.1    2.3  2  DUF3426     Protein of unknown function (DUF3426)
     0.0013   18.8   5.6       0.35   10.8   0.9    2.5  2  DUF2393     Protein of unknown function (DUF2393)
  ------ inclusion threshold ------
      0.022   14.4   0.3        1.9    8.1   0.0    2.1  2  DUF3157     Protein of unknown function (DUF3157)
      0.072   13.7   0.2       0.25   12.0   0.1    1.9  2  Cadherin_4  Bacterial cadherin-like domain
      0.078   13.0   0.2        2.5    8.1   0.0    2.3  2  Cadherin_5  Cadherin-like domain
      0.093   12.2   2.5       0.32   10.4   0.1    2.0  2  GbpC        Glucan-binding protein C
        0.2   12.0   3.9       0.98    9.7   0.3    2.4  2  DUF4352     Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF3426  Protein of unknown function (DUF3426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.2e-06    0.0057      67      99 ..      34      67 ..      22      70 .. 0.87
   2 !   37.7   0.1   8.3e-13   2.1e-09      45     143 ..     112     201 ..      90     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
     DUF3426 67 n.lvlegtlrNradkpqalpaleltLtDaqgqvv 99
                + + + g+++N+++ p   +++ +tLtD++g+vv
  AJA91878.1 34 GiMHIVGEIKNESKSPVNKIKIIATLTDENGKVV 67
                258899**************************99 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 8.3e-13
     DUF3426  45 pprdielisiessslrekageanlvlegtlrNradkpqalpaleltLtDaqgqvv.arrvlspaeyllanqaantglapgseipfalvlev..pgkrva 140
                 +p++ + i i ss++++++ +  l+++gt+ N+ + +  ++++ +tL+D++g+v+ +++v++  ++          l++g+e +f++++++  ++ +v+
  AJA91878.1 112 APKN-QVIEIVSSDMKRDQLNN-LIISGTIENNGEITANMINIVATLYDRDGKVLtVSKVQTQPDF----------LRAGEESHFVVPIYEknQSIDVV 198
                 4444.8899******9988888.******************************9845777766666..........99***********9844556677 PP

     DUF3426 141 gyr 143
                 +y+
  AJA91878.1 199 DYS 201
                 775 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.9   0.00014      0.35      62      97 ..      35      69 ..       4     110 .. 0.75
   2 !   10.2   0.3   0.00022      0.57      47      93 ..     118     163 ..     110     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
     DUF2393 62 afvvdgtitNeGkftikeCkleiklvnkshnkkske 97
                 + + g+i+Ne+k ++++ k+ ++l +++ +  +++
  AJA91878.1 35 IMHIVGEIKNESKSPVNKIKIIATLTDENGKV-VDK 69
                566889******************99988777.333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
     DUF2393  47 aeltilsqkrllyteafvvdgtitNeGkftikeCkleiklvnkshnk 93 
                 +e+  ++ kr + ++ ++++gti N+G+ t +   + ++l++ + + 
  AJA91878.1 118 IEIVSSDMKRDQLNN-LIISGTIENNGEITANMINIVATLYDRDGKV 163
                 778888888888875.899*****************99999988765 PP

>> DUF3157  Protein of unknown function (DUF3157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0094        24     111     150 ..      33      72 ..      11      80 .. 0.82
   2 ?    8.1   0.0   0.00075       1.9      99     151 ..     117     170 ..     109     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0094
     DUF3157 111 dgrLgLtfeltsqSsesvivvelevslyddsGellktekv 150
                 dg + ++ e++++S+  v  +++   l d++G+++++ + 
  AJA91878.1  33 DGIMHIVGEIKNESKSPVNKIKIIATLTDENGKVVDKIDG 72 
                 47788899*************************9987655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00075
     DUF3157  99 Gvkvslskakyed.grLgLtfeltsqSsesvivvelevslyddsGellktekvt 151
                  ++++ s+ k ++ ++L ++  ++++ +    ++++   lyd +G++l   kv+
  AJA91878.1 117 VIEIVSSDMKRDQlNNLIISGTIENNGEITANMINIVATLYDRDGKVLTVSKVQ 170
                 588999999999999*********************************999886 PP

>> Cadherin_4  Bacterial cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.9   4.8e+03      38      63 ..      57      67 ..      21      74 .. 0.57
   2 ?   12.0   0.1   9.8e-05      0.25      20      58 ..     136     174 ..     126     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
  Cadherin_4 38 andtDvdgddltvtavtvagtyGtlt 63
                a               t++ ++G ++
  AJA91878.1 57 A---------------TLTDENGKVV 67
                2...............2344455544 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.8e-05
  Cadherin_4  20 satvtedtpltitagnvlandtDvdgddltvtavtvagt 58 
                 s+t++ ++ +t +  n+ a+ +D dg  ltv+ v+++++
  AJA91878.1 136 SGTIENNGEITANMINIVATLYDRDGKVLTVSKVQTQPD 174
                 568888999999999*******************99885 PP

>> Cadherin_5  Cadherin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.056   1.4e+02      47      63 ..      58      74 ..      42      78 .. 0.77
   2 ?    8.1   0.0   0.00097       2.5      14      49 ..     137     172 ..     126     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.056
  Cadherin_5 47 tadaenGtvvdngdGtf 63
                t+++enG+vvd+ dG++
  AJA91878.1 58 TLTDENGKVVDKIDGKI 74
                346779********986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00097
  Cadherin_5  14 aagseDtaltitaaqLLanasDvdgdtLsvssltad 49 
                 ++++++ ++t ++ +++a   D dg+ L+vs+++++
  AJA91878.1 137 GTIENNGEITANMINIVATLYDRDGKVLTVSKVQTQ 172
                 56777889999999*******************644 PP

>> GbpC  Glucan-binding protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.056   1.4e+02     142     181 ..      32      69 ..      24      78 .. 0.69
   2 ?   10.4   0.1   0.00013      0.32     122     183 ..     106     168 ..     100     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.056
                 SSTTT-EEEEE---SSSS--EEEEEEEEEEE-TTS-B--- CS
        GbpC 142 kDPtvtifagaktgnaekktkieikmkvkfYdedGkeidp 181
                 +D ++ i+ + k++   k    +ik+ +++ de+Gk++d 
  AJA91878.1  32 NDGIMHIVGEIKNES--KSPVNKIKIIATLTDENGKVVDK 69 
                 555555555544444..44456889999999******985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                 EEEEEEE-S.SSSSEEEEEE-SSTTT-EEEEE---SSSS--EEEEEEEEEEE-TTS-B---TT CS
        GbpC 122 ykytlkssp.ngegklklvlekDPtvtifagaktgnaekktkieikmkvkfYdedGkeidpdk 183
                 ++y l +   +  + +   +++D    ++++  ++n ++ t   i++ +++Yd dGk+++++k
  AJA91878.1 106 FEYKLAAPKnQVIEIVSSDMKRDQLNNLIISGTIENNGEITANMINIVATLYDRDGKVLTVSK 168
                 5666654333555667778999999999999999999999999****************9998 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.04     1e+02      46      73 ..      42      69 ..      36     111 .. 0.82
   2 ?    9.7   0.3   0.00038      0.98      38      74 ..     131     167 ..     106     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.04
                EEE-SSS-EEEEGGGEEEEETTEEE-BE CS
     DUF4352 46 vkNkgkealtvnssqfkLkdgdgkeyda 73
                +kN++k++++  ++  +L+d++gk +d 
  AJA91878.1 42 IKNESKSPVNKIKIIATLTDENGKVVDK 69
                99**********************9983 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
                 EEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEE CS
     DUF4352  38 eflivdvtvkNkgkealtvnssqfkLkdgdgkeydad 74 
                   li++ t++N+g+ + ++  +  +L+d+dgk  + +
  AJA91878.1 131 NNLIISGTIENNGEITANMINIVATLYDRDGKVLTVS 167
                 4589999************************987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1719.38
//
Query:       AJA91879.1  [L=96]
Description: nucleic acid-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   24.7   0.6    1.9e-05   24.5   0.6    1.1  1  REPA_OB_2        Replication protein A OB domain
    0.00027   20.9   0.2    0.00036   20.5   0.2    1.2  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.038   14.1   0.1      0.047   13.8   0.1    1.1  1  bPH_1            Bacterial PH domain


Domain annotation for each model (and alignments):
>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.6   3.2e-09   1.9e-05       9      84 ..      10      81 ..       3      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.2e-09
   REPA_OB_2  9 kdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFgg 84
                  s + v g v++ ee++++++k+++ +++  + +lvD+ g+++++tlW ++a+++++   + + + ++  ++F+g
  AJA91879.1 10 MRSGINVEGTVERKEEIRTVNTKAGS-TVDVANAMLVDN-GMEIKITLWAEDANNIQN--GDKIKIENGYTNEFKG 81
                45668999****************99.9**********7.799************874..4446667777777776 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   6.1e-08   0.00036       2      68 ..      15      85 ..      14      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.1e-08
                     EEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
  tRNA_anti-codon  2 tvaGrvtsis........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelel 68
                     +v+G v +++        ++s+  v+++ l D+  +i+++l+     + a+n+++Gd ++++ G+ ++++g+ ++l
       AJA91879.1 15 NVEGTVERKEeirtvntkAGSTVDVANAMLVDNGMEIKITLWA----EDANNIQNGDKIKIEnGYTNEFKGE-VQL 85
                     58889999999988888888888899999**************....**********************988.876 PP

>> bPH_1  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.8e-06     0.047      53     108 ..      14      68 ..      13      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.8e-06
                 EE---SSS--EEEEEEETTTEEEEEEEEESTTSSEEEEEEEETTTCCEEEEECGCC CS
       bPH_1  53 vdkqgvtgkKkeyksipyssIsevsiEtagtfDldaeLkiwisgeeepikvefkkk 108
                 ++++g + +K e+++++ ++ s+v + +a  +D  +e+ki++  e++  +++   k
  AJA91879.1  14 INVEGTVERKEEIRTVNTKAGSTVDVANAMLVDNGMEIKITLWAEDA-NNIQNGDK 68 
                 6889999*********************************9955544.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 698.41
//
Query:       AJA91880.1  [L=244]
Description: peptidyl-prolyl cis-trans isomerase, FKBP-type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   44.5   0.7    1.6e-10   41.2   0.2    2.6  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    5.2e-10   39.3   1.0    1.1e-09   38.2   1.0    1.6  1  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.2   1.7e-14   1.6e-10       5      91 ..       3     146 ..       1     149 [. 0.71
   2 ?    2.4   0.1     0.022     2e+02      10      34 ..     128     151 ..     122     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.7e-14
                 B-TTCEEEEEEEEEET.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTTTBCTTT..B.TT... CS
      FKBP_C   5 akegdtVtvhykgkle.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaYgekglaggv..ippn... 84 
                  k+g+ + ++y++k++  g+vf+++           +   ++ p  + vG+  v+kG+++al + k+Gek+t+++  e ++g+++  g+v  ip     
  AJA91880.1   3 FKKGQLILLDYTAKIKdSGEVFETTneddakkhsiHDpniKYMPKLVSVGEAWVLKGLDDALPETKAGEKKTIEVSAEKGFGARDK-GKVrmIPLRklg 100
                 589*************77*******899988877622667*******************************************777.444454333333 PP

                 .......................................SEEEEEE CS
      FKBP_C  85 .......................................atLvFev 91 
                                                        +t+v++v
  AJA91880.1 101 edaekvsvgdtveidnkkgiirfigsgrvqidynhrfagKTIVYDV 146
                 3333344444444444444444444445555555555556666666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.022
                 EEEEEEEEEETTSSEEEEHCCHTSE CS
      FKBP_C  10 tVtvhykgkledgkvfdssrsrakp 34 
                 +V+++y+ ++++++++ +  + +k 
  AJA91880.1 128 RVQIDYNHRFAGKTIVYDV-DIKKS 151
                 7888888888644433333.33333 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.0   1.2e-13   1.1e-09       1      72 []     155     225 ..     155     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.2e-13
                 HHHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEEE CS
    FKBP26_C   1 dkekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdefe 72 
                 d +k++e+ k ++P ++ +k++++ ++++v I++pee + ++++ ++k    +d++k+++   kV+Fv+ +e
  AJA91880.1 155 DDDKVTEILKSRLP-VENDKINFKKTGGVVDITIPEEIYRADGLAIIKHFTQMDLFKFVPALTKVNFVESYE 225
                 579***********.666***************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1898.47
//
Query:       AJA91881.1  [L=127]
Description: ribosomal protein S8.e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-20   72.3   4.8    4.9e-20   72.1   4.8    1.1  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   4.8   2.8e-24   4.9e-20       1     137 []       1     126 [.       1     126 [. 0.87

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 2.8e-24
                    XXXBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEECSSSTCHHHHTTC- CS
  Ribosomal_S8e   1 mgisrdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVkknpsnneyvrlgvl 96 
                    m+ s ++ ++ k+tGg +++l+ ++k+e  r ++++ +g+e+    r   G+ +k++l++ +        +++k+ kI++V +n++nn+y r+g++
     AJA91881.1   1 MKKSVENLKTSKITGGLRHPLKTRQKFETDRYPNEAEMGEEQQTITRKTRGNNRKTGLKIASFVNLVMADSKVKRSKIIKVLENQTNNDYQRRGII 96 
                    556667788999***************************8888888888887777777776655555566667779******************** PP

                    -TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
  Ribosomal_S8e  97 tKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                    tKgai+e++ ++            ++ srPgq+G v ++l+
     AJA91881.1  97 TKGAIVETEDGK-----------CRIVSRPGQSGTVSGILV 126
                    ************...........9**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 949.73
//
Query:       AJA91882.1  [L=141]
Description: hypothetical protein T478_0838 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1672  (0.0932567); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); expected 17.9 (0.001)
Passed Fwd filter:                        68  (0.00379274); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.88u 0.26s 00:00:01.14 Elapsed: 00:00:00.43
# Mc/sec: 978.20
//
Query:       AJA91883.1  [L=262]
Description: hypothetical protein T478_1395 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        1.4    8.4   4.4        5.7    6.5   0.7    2.3  2  zf-ribbon_3  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7   0.00032       5.7      16      25 ..       2      11 ..       2      12 .. 0.86
   2 ?    3.1   0.2    0.0036        64       3      13 ..      17      26 ..      15      31 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00032
  zf-ribbon_3 16 dnvCpyCGtk 25
                 +++C++CG+k
   AJA91883.1  2 AQKCTHCGKK 11
                 579*****86 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0036
  zf-ribbon_3  3 vrCPnCGapls 13
                 ++CP C ++ s
   AJA91883.1 17 KSCPFCSNN-S 26
                 789999666.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1837.62
//
Query:       AJA91884.1  [L=64]
Description: zinc finger, C2H2 type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-06   27.7   6.7    0.00023   21.4   0.5    2.3  2  zf-C2H2          Zinc finger, C2H2 type
    2.4e-06   27.9   7.9     0.0018   19.0   1.1    2.2  2  zf-C2H2_4        C2H2-type zinc finger
    7.7e-05   22.0   0.6       0.31   10.5   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
    0.00012   21.8   4.7       0.26   11.1   3.6    2.9  2  zf-C2H2_11       zinc-finger C2H2-type
    0.00017   21.2   2.0       0.23   11.2   0.2    2.4  2  zinc_ribbon_2    zinc-ribbon domain
    0.00042   20.4   3.7       0.28   11.3   0.1    2.3  2  Zn-ribbon_8      Zinc ribbon domain
     0.0015   18.0   2.0          1    8.9   0.1    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0015   18.3   2.9     0.0015   18.3   2.9    3.1  3  zf-C2HC_2        zinc-finger of a C2HC-type
     0.0019   17.6   1.7       0.23   11.0   0.1    2.2  2  DUF2688          Protein of unknown function (DUF2688)
     0.0054   16.5   5.0        0.3   10.9   1.3    2.2  2  zf-HYPF          HypF finger
     0.0055   16.7   5.2       0.32   11.0   0.7    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0066   16.5   4.0     0.0094   16.0   4.0    1.4  1  DZR              Double zinc ribbon
     0.0074   16.2   0.5     0.0074   16.2   0.5    2.5  3  zinc_ribbon_4    zinc-ribbon domain
     0.0083   16.0   1.9      0.023   14.6   1.9    1.8  1  C1_1             Phorbol esters/diacylglycerol binding domain
  ------ inclusion threshold ------
      0.011   15.4   0.4        1.6    8.5   0.0    2.2  2  Ribosomal_S27e   Ribosomal protein S27
      0.013   15.6   3.7       0.63   10.1   0.6    2.4  2  XPA_N            XPA protein N-terminal
      0.013   15.3   1.6       0.53   10.1   0.1    2.1  2  Ephrin_rec_like  Putative ephrin-receptor like
      0.013   15.4   0.9        1.6    8.7   0.1    2.3  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.018   15.1   2.7       0.41   10.7   2.8    2.0  2  CpXC             CpXC protein
      0.018   14.7   5.0        2.3    8.0   0.1    2.6  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.024   14.2   1.8        1.6    8.4   0.2    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.031   15.0   3.3      0.038   14.7   3.3    1.3  1  zinc_ribbon_15   zinc-ribbon family
      0.035   14.0   5.5          1    9.3   1.2    2.4  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.057   13.3   1.1        6.7    6.7   0.1    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.057   13.8   1.6        6.6    7.2   0.2    2.1  2  DUF983           Protein of unknown function (DUF983)
      0.064   13.5   1.6      0.073   13.4   1.6    1.1  1  zf-C2H2_8        C2H2-type zinc ribbon
      0.072   13.0   3.6        2.5    8.0   0.2    2.4  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.073   13.5   2.7       0.68   10.4   2.6    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.092   12.4   1.4          6    6.6   0.2    2.1  2  zf_C2H2_ZHX      Zinc-fingers and homeoboxes C2H2 finger doma
       0.13   12.6   4.9          2    8.8   0.2    2.0  2  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
       0.18   11.6   3.4        4.9    7.0   0.3    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.22   11.5   7.4       0.35   10.9   0.7    2.5  2  zf-BED           BED zinc finger
       0.25   11.3   8.8       0.29   11.1   6.9    1.9  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.25   11.1   7.8       0.89    9.4   2.9    2.3  2  zinc_ribbon_5    zinc-ribbon domain
       0.41   10.8   0.2       0.41   10.8   0.2    2.7  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.45   10.7   6.4        6.4    7.0   1.4    2.6  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.54   10.1   9.9        1.7    8.5   0.3    2.8  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
        5.5    7.5  10.9         46    4.5   6.3    2.8  2  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.0    0.0028       1.3       2      23 .]      13      35 ..      12      35 .. 0.95
   2 !   21.4   0.5     5e-07   0.00023       2      21 ..      42      61 ..      41      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                kC++Cg    + + LkrH ++ H
  AJA91884.1 13 KCKKCGSELHDAERLKRHEKIaH 35
                8*****************99988 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 5e-07
                EETTTTEEESSHHHHHHHHH CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHir 21
                kC  Cg  F+++++L++H +
  AJA91884.1 42 KCRNCGTEFRDPDDLRKHKK 61
                8*****************87 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.8   0.00028      0.13       2      24 .]      13      35 ..      12      35 .. 0.93
   2 !   19.0   1.1   3.7e-06    0.0018       2      22 ..      42      62 ..      41      64 .] 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00028
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                kC+ Cg   ++ ++L+rH k  H
  AJA91884.1 13 KCKKCGSELHDAERLKRHEKIAH 35
                8*****************99877 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.7e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkt 22
                kC+ Cg+ F+++++L++H k+
  AJA91884.1 42 KCRNCGTEFRDPDDLRKHKKK 62
                8*****************997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00066      0.31      14      26 .]       9      21 ..       6      21 .. 0.85
   2 !    9.7   0.1    0.0011      0.54      16      25 ..      40      49 ..      38      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
  zf-ribbon_3 14 sddnvCpyCGtkl 26
                 ++ ++C++CG++l
   AJA91884.1  9 ESSTKCKKCGSEL 21
                 7889******986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
  zf-ribbon_3 16 dnvCpyCGtk 25
                 d++C +CGt+
   AJA91884.1 40 DVKCRNCGTE 49
                 789*****97 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   3.6   0.00055      0.26       1      28 [.       8      35 ..       8      35 .. 0.95
   2 !    8.4   0.0    0.0037       1.7       5      23 ..      41      59 ..      40      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
  zf-C2H2_11  1 destcqCleCGlcftSqlsLsRHlfIvH 28
                +es+ +C +CG     +  L+RH  I H
  AJA91884.1  8 EESSTKCKKCGSELHDAERLKRHEKIAH 35
                58************************99 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0037
  zf-C2H2_11  5 cqCleCGlcftSqlsLsRH 23
                ++C+ CG  f     L++H
  AJA91884.1 41 VKCRNCGTEFRDPDDLRKH 59
                69*****999777777777 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00048      0.23       1      11 [.      13      23 ..       8      26 .. 0.83
   2 !    9.3   0.1    0.0019      0.91       1       8 [.      42      49 ..      40      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
  zinc_ribbon_2  1 fCpnCGaelqd 11
                   +C++CG el d
     AJA91884.1 13 KCKKCGSELHD 23
                   79999999866 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
  zinc_ribbon_2  1 fCpnCGae 8 
                   +C nCG+e
     AJA91884.1 42 KCRNCGTE 49
                   57777765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00059      0.28      21      36 ..       6      21 ..       2      27 .. 0.78
   2 !   10.0   0.8    0.0016      0.74       6      16 ..      41      51 ..      40      64 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00059
  Zn-ribbon_8 21 isdapltaCPeCgsev 36
                  s+++ t+C++Cgse+
   AJA91884.1  6 KSEESSTKCKKCGSEL 21
                 46778899*****976 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
  Zn-ribbon_8  6 YrCeeCghefe 16
                  +C++Cg+ef 
   AJA91884.1 41 VKCRNCGTEFR 51
                 69********7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0022         1       2      17 ..      13      26 ..      10      29 .. 0.79
   2 !    8.6   0.3    0.0027       1.3       2      16 ..      42      54 ..      41      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                  EETTTTCEECHEETST CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDper 17
                  kC++Cgs+  + D+er
    AJA91884.1 13 KCKKCGSE--LHDAER 26
                  89999998..677665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
                  EETTTTCEECHEETS CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpe 16
                  kC nCg+++  +Dp+
    AJA91884.1 42 KCRNCGTEF--RDPD 54
                  9*****995..7765 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.6      0.34   1.6e+02       4       9 ..      13      18 ..      12      18 .. 0.89
   2 ?    5.4   0.1     0.038        18      15      23 ..      25      33 ..      23      33 .. 0.89
   3 !   18.3   2.9   3.3e-06    0.0015       3      25 .]      41      64 .]      41      64 .] 0.97

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.34
   zf-C2HC_2  4 pCpkCg 9 
                +C+kCg
  AJA91884.1 13 KCKKCG 18
                7****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.038
   zf-C2HC_2 15 drlekHepv 23
                +rl +He++
  AJA91884.1 25 ERLKRHEKI 33
                8******97 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3.3e-06
   zf-C2HC_2  3 vpCpkCgRsF.npdrlekHepvCk 25
                v+C++Cg  F  pd l kH+++Ck
  AJA91884.1 41 VKCRNCGTEFrDPDDLRKHKKKCK 64
                79*********************8 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00048      0.23       7      21 ..      11      25 ..       6      28 .. 0.84
   2 ?    6.1   0.1     0.016       7.4       6      18 ..      39      51 ..      37      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00048
     DUF2688  7 tTqCrRCGkslstls 21
                +T+C++CG  l   +
  AJA91884.1 11 STKCKKCGSELHDAE 25
                8*******9998765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
     DUF2688  6 VtTqCrRCGksls 18
                V  +Cr CG+  +
  AJA91884.1 39 VDVKCRNCGTEFR 51
                5679*****9876 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0085         4       2      13 ..      14      25 ..      12      34 .. 0.71
   2 !   10.9   1.3   0.00064       0.3       2      18 ..      43      59 ..      42      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0085
                -HHHHHHHC-TT CS
     zf-HYPF  2 CedClrEykdpl 13
                C++C  E++d +
  AJA91884.1 14 CKKCGSELHDAE 25
                888888888866 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00064
                -HHHHHHHC-TTSTTTT CS
     zf-HYPF  2 CedClrEykdpldRRfh 18
                C +C  E++dp d R h
  AJA91884.1 43 CRNCGTEFRDPDDLRKH 59
                *************8877 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.4    0.0032       1.5      61      84 ..       2      25 ..       1      33 [. 0.76
   2 !   11.0   0.7   0.00068      0.32      66      92 ..      36      63 ..      23      64 .] 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                EEEEEEE--EEEETTTS-EEECHH CS
        HypA 61 eLeieevpvkvrCreCgkefelee 84
                +L  ++++ +++C++Cg+e + +e
  AJA91884.1  2 KLFTKSEESSTKCKKCGSELHDAE 25
                566788899999999999887554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00068
                EE--EEEETTTS-EEECHHH.HHS-TTT CS
        HypA 66 evpvkvrCreCgkefeleek.alrCpkC 92
                  +v v+Cr+Cg+ef+  ++ + + +kC
  AJA91884.1 36 GRRVDVKCRNCGTEFRDPDDlRKHKKKC 63
                56799**********9554332223333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.0     2e-05    0.0094       8      38 ..       7      50 ..       4      64 .] 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
         DZR  8 lppdarfCseCgtklkavaa.............edrCpsCgekv 38
                 ++++  C++Cg++l  +++               +C +Cg++ 
  AJA91884.1  7 SEESSTKCKKCGSELHDAERlkrhekiahgrrvDVKCRNCGTEF 50
                5678889********98888*********************984 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.036        17      25      32 ..      11      18 ..       5      20 .. 0.78
   2 !   16.2   0.5   1.6e-05    0.0074      17      36 .]      31      51 ..      29      51 .. 0.85
   3 ?   -2.3   0.1       9.5   4.5e+03      21      25 ..      58      62 ..      52      64 .] 0.49

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.036
  zinc_ribbon_4 25 kvrCskCg 32
                   + +C+kCg
     AJA91884.1 11 STKCKKCG 18
                   56899998 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.6e-05
  zinc_ribbon_4 17 eklp.akgvkvrCskCghvFr 36
                   ek++ +++v v+C +Cg+ Fr
     AJA91884.1 31 EKIAhGRRVDVKCRNCGTEFR 51
                   788868888*********996 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.5
  zinc_ribbon_4 21 akgvk 25
                   ++++k
     AJA91884.1 58 KHKKK 62
                   44443 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.9   4.8e-05     0.023       9      37 ..       9      49 ..       3      64 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.8e-05
                SS--B-TTT-SB-............-SSSS-EEEETTT--E CS
        C1_1  9 kqptfCkhCgefl............wgkekqglkCswCkll 37
                +++t+Ck+Cg+ l             +++++ +kC++C+  
  AJA91884.1  9 ESSTKCKKCGSELhdaerlkrhekiAHGRRVDVKCRNCGTE 49
                789*****************999966699999******865 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.031        15      25      36 ..      10      21 ..       3      24 .. 0.71
   2 ?    8.5   0.0    0.0034       1.6       3      16 ..      36      49 ..      34      54 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.031
                    S-EEESSSTCEE CS
  Ribosomal_S27e 25 tvvkCisCgkvL 36
                    +  kC +Cg+ L
      AJA91884.1 10 SSTKCKKCGSEL 21
                    556888888766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
                    --EEEEE-TTTS-E CS
  Ribosomal_S27e  3 skFldvkCpdCene 16
                    ++ +dvkC +C+ e
      AJA91884.1 36 GRRVDVKCRNCGTE 49
                    55678888888764 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6    0.0013      0.63       2      13 ..      12      23 ..      11      25 .. 0.90
   2 ?    6.2   0.1     0.023        11       3      13 ..      42      52 ..      41      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
       XPA_N  2 pkCdeCgkefld 13
                +kC++Cg+e++d
  AJA91884.1 12 TKCKKCGSELHD 23
                69********99 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.023
       XPA_N  3 kCdeCgkefld 13
                kC  Cg ef d
  AJA91884.1 42 KCRNCGTEFRD 52
                7********87 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0011      0.53      20      38 ..       6      24 ..       4      31 .. 0.85
   2 ?    4.9   0.1     0.047        22      26      47 ..      41      62 ..      36      63 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
  Ephrin_rec_like 20 qneegqlsClaCPlgtttk 38
                     ++ee++++C++C+++ ++ 
       AJA91884.1  6 KSEESSTKCKKCGSELHDA 24
                     57999********988765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
  Ephrin_rec_like 26 lsClaCPlgtttkkpgatsesd 47
                     ++C +C++++++  +  + +++
       AJA91884.1 41 VKCRNCGTEFRDPDDLRKHKKK 62
                     79****9998877665555555 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.037        17      23      30 ..      13      20 ..       3      22 .. 0.66
   2 ?    8.7   0.1    0.0034       1.6      21      31 ..      39      50 ..      33      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.037
                    EESSSS-E CS
  RNA_POL_M_15KD 23 eCrqCgYe 30
                     C +Cg+e
      AJA91884.1 13 KCKKCGSE 20
                    49999886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
                    E.EEESSSS-EE CS
  RNA_POL_M_15KD 21 n.feCrqCgYee 31
                    + + Cr+Cg e+
      AJA91884.1 39 VdVKCRNCGTEF 50
                    3689****9886 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4      0.16        76      37      47 ..      11      21 ..       2      26 .. 0.78
   2 ?   10.7   2.8   0.00087      0.41      22      57 ..      25      60 ..      12      64 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.16
        CpXC 37 eatCpkCgata 47
                +++C kCg + 
  AJA91884.1 11 STKCKKCGSEL 21
                68899999765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00087
        CpXC 22 edpelkeklldgslfeatCpkCgatakleapllyhd 57
                e+ + +ek+ +g+  +++C +Cg++++ + +l+ h+
  AJA91884.1 25 ERLKRHEKIAHGRRVDVKCRNCGTEFRDPDDLRKHK 60
                5667789******************99777777666 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0049       2.3      16      25 ..      10      19 ..       4      21 .. 0.80
   2 ?    7.6   1.9    0.0063         3      18      24 ..      41      47 ..      24      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0049
                    S----SSS-- CS
  DNA_RNApol_7kD 16 dpiRCkeCGh 25
                     + +Ck+CG+
      AJA91884.1 10 SSTKCKKCGS 19
                    5679*****7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0063
                    ---SSS- CS
  DNA_RNApol_7kD 18 iRCkeCG 24
                    ++C++CG
      AJA91884.1 41 VKCRNCG 47
                    8****** PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0033       1.6       3      17 ..      12      26 ..      10      31 .. 0.84
   2 ?    5.7   0.1     0.024        11       3      20 ..      41      59 ..      39      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0033
      zf_UBZ  3 ylCerCgkeipesel 17
                  C++Cg+e+ ++e+
  AJA91884.1 12 TKCKKCGSELHDAER 26
                68*******999976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.024
      zf_UBZ  3 ylCerCgkeipes.elqEH 20
                + C  Cg+e+ ++ +l  H
  AJA91884.1 41 VKCRNCGTEFRDPdDLRKH 59
                68********998777666 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.3   8.1e-05     0.038      33      76 ..       7      51 ..       1      64 [] 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.1e-05
  zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkesse.kkeCknCgkeve 76
                    +++   +c+kC+s l++ ++l+++ + ++ ++   +C+nCg+e  
      AJA91884.1  7 SEESSTKCKKCGSELHDAERLKRHEKIAHGRRvDVKCRNCGTEFR 51
                    347889*********999855444333333336889*****9875 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.013       6.1       4      17 ..      11      24 ..       8      27 .. 0.82
   2 ?    9.3   1.2    0.0022         1       4      20 ..      40      56 ..      37      64 .] 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
  Prok-RING_1  4 gkkCpvCgkelkee 17
                  +kC+ Cg el+++
   AJA91884.1 11 STKCKKCGSELHDA 24
                 689999*9999986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
  Prok-RING_1  4 gkkCpvCgkelkeedDi 20
                 + kC  Cg e+++ dD+
   AJA91884.1 40 DVKCRNCGTEFRDPDDL 56
                 689***********996 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.031        14      12      19 ..      12      19 ..      12      27 .. 0.81
   2 ?    6.7   0.1     0.014       6.7      13      21 ..      42      50 ..      41      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
     DUF35_N 12 qrCpdCGt 19
                ++C++CG+
  AJA91884.1 12 TKCKKCGS 19
                68999997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
     DUF35_N 13 rCpdCGtvq 21
                +C++CGt +
  AJA91884.1 42 KCRNCGTEF 50
                7****9966 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.014       6.6       8      22 ..      11      25 ..       4      27 .. 0.82
   2 ?    6.2   0.1     0.029        13       7      20 ..      39      52 ..      37      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
      DUF983  8 adaCeaCgldlshar 22
                  +C++Cg +l+ a+
  AJA91884.1 11 STKCKKCGSELHDAE 25
                679*******99765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
      DUF983  7 vadaCeaCgldlsh 20
                v  +C++Cg++++ 
  AJA91884.1 39 VDVKCRNCGTEFRD 52
                5679******9974 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6   0.00015     0.073      40      89 ..      14      63 ..       2      64 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
   zf-C2H2_8 40 tascaetfpsmqelvahtklhykpnryfkcencllrfrthrslfkhlhvc 89
                ++ c   +   + l  h k+ +      kc nc   fr    l kh + c
  AJA91884.1 14 CKKCGSELHDAERLKRHEKIAHGRRVDVKCRNCGTEFRDPDDLRKHKKKC 63
                3457777888889999****9999999*******************9988 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.027        13       2       8 ..      13      19 ..       8      21 .. 0.74
   2 ?    8.0   0.2    0.0054       2.5      29      39 .]      41      51 ..      36      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
     TFIIS_C  2 kCpkCgs 8 
                kC+kCgs
  AJA91884.1 13 KCKKCGS 19
                6777776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0054
     TFIIS_C 29 ykCtkCghrWr 39
                +kC +Cg ++r
  AJA91884.1 41 VKCRNCGTEFR 51
                89*****9997 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.021        10      28      52 ..      11      32 ..       2      36 .. 0.67
   2 ?   10.4   2.6    0.0014      0.68       5      53 ..      13      62 ..      11      64 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
  Lar_restr_allev 28 cvyCadCgastpwfkiaedeaeaek 52
                        C++Cg    + + ae+ +++ek
       AJA91884.1 11 STKCKKCGS---ELHDAERLKRHEK 32
                     678*****9...5555665555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0014
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigq....cvyCadCgastpwfkiaedeaeaeke 53
                      C  Cg++    ++ +++++i++     v C +Cg    +f+  +d  +++k+
       AJA91884.1 13 KCKKCGSELHDAERLKRHEKIAHgrrvDVKCRNCGT---EFRDPDDLRKHKKK 62
                     5888998877666666666666688889********...88888888888776 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.013         6       6      28 ..      13      35 ..       8      42 .. 0.87
   2 ?    5.6   0.0     0.026        12       7      27 ..      43      63 ..      39      64 .] 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
  zf_C2H2_ZHX  6 vCveCsfsakkfegLalHNarsH 28
                  C +C+    + e L+ H   +H
   AJA91884.1 13 KCKKCGSELHDAERLKRHEKIAH 35
                 69****************98888 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
  zf_C2H2_ZHX  7 CveCsfsakkfegLalHNars 27
                 C +C+   ++ ++L +H  ++
   AJA91884.1 43 CRNCGTEFRDPDDLRKHKKKC 63
                 99***************8776 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9     0.017         8      49      70 ..      10      31 ..       1      40 [. 0.79
   2 ?    8.8   0.2    0.0042         2      50      72 ..      40      62 ..      31      64 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.017
   zf-C2H2_2 49 ekleClyCekefkslealreHm 70
                ++ +C  C++e ++ e l+ H 
  AJA91884.1 10 SSTKCKKCGSELHDAERLKRHE 31
                4689*******99******994 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0042
   zf-C2H2_2 50 kleClyCekefkslealreHmkk 72
                +++C  C++ef++ ++lr+H kk
  AJA91884.1 40 DVKCRNCGTEFRDPDDLRKHKKK 62
                579*****************765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.033        15       3       9 ..      14      20 ..      13      23 .. 0.77
   2 ?    7.0   0.3      0.01       4.9       3      10 ..      43      50 ..      42      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.033
  Rubredoxin_2  3 CsqCGfe 9 
                  C++CG+e
    AJA91884.1 14 CKKCGSE 20
                  9999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
  Rubredoxin_2  3 CsqCGfes 10
                  C++CG e+
    AJA91884.1 43 CRNCGTEF 50
                  99999886 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00074      0.35       7      38 ..       4      30 ..       2      36 .. 0.83
   2 ?    4.3   2.4     0.089        42       4      27 ..      28      51 ..      25      64 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00074
                S----GGSS--EETTTTEE----SSTHHHHHH CS
      zf-BED  7 ftpvslkeqkavCryCgkilsrgggttnLkrH 38
                ft+ +  e +++C+ Cg +l +     +LkrH
  AJA91884.1  4 FTKSE--ESSTKCKKCGSELHDA---ERLKRH 30
                77777..99*********99886...777777 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.089
                TSSS----GGSS--EETTTTEE-- CS
      zf-BED  4 WkyftpvslkeqkavCryCgkils 27
                +++ +++  ++  ++Cr Cg ++ 
  AJA91884.1 28 KRHEKIAHGRRVDVKCRNCGTEFR 51
                5677777788888******98775 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.9   0.00061      0.29      24      56 ..       7      50 ..       2      57 .. 0.82
   2 ?    4.7   0.9     0.062        29      30      40 ..      42      52 ..      40      64 .] 0.54

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00061
  OrfB_Zn_ribbon 24 payTSktCseCgsknke...........alsgrtfkCpnCgfea 56
                     + +S++C +Cgs++ +              +  +kC+nCg+e+
      AJA91884.1  7 SEESSTKCKKCGSELHDaerlkrhekiaHGRRVDVKCRNCGTEF 50
                    4569**********9999999988886555555789*****985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.062
  OrfB_Zn_ribbon 30 tCseCgsknke 40
                    +C +Cg + ++
      AJA91884.1 42 KCRNCGTEFRD 52
                    56666666665 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.048        22       3      33 ..      12      19 ..       5      32 .. 0.74
   2 ?    9.4   2.9    0.0019      0.89       3      26 ..      41      63 ..      39      64 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.048
  zinc_ribbon_5  3 irCpdCdtkFklvdsklKksgkkVrCakCae 33
                   +                       +C kC++
     AJA91884.1 12 T-----------------------KCKKCGS 19
                   3.......................5555553 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
  zinc_ribbon_5  3 irCpdCdtkFklvdsklKksgkkV 26
                   ++C +C+t F+ + + l+k  kk 
     AJA91884.1 41 VKCRNCGTEFR-DPDDLRKHKKKC 63
                   68*********.555667777775 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00087      0.41       2      13 ..      12      23 ..      12      30 .. 0.87
   2 ?    3.5   0.6      0.16        75       2       9 ..      41      48 ..      41      49 .. 0.87
   3 ?   -1.6   0.1       6.4     3e+03      15      21 ..      55      61 ..      54      64 .] 0.54

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00087
      zf-ACC  2 tKCpsCgemlyk 13
                tKC +Cg+ l+ 
  AJA91884.1 12 TKCKKCGSELHD 23
                8******99985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.16
      zf-ACC  2 tKCpsCge 9 
                +KC  Cg+
  AJA91884.1 41 VKCRNCGT 48
                69****96 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 6.4
      zf-ACC 15 eLernly 21
                +L+++++
  AJA91884.1 55 DLRKHKK 61
                5666654 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.4     0.017         8      12      31 ..       7      26 ..       3      36 .. 0.74
   2 ?    7.0   1.4     0.014       6.4      10      24 ..      34      48 ..      27      64 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
    zf-Mss51 12 pkhvdfeCpdCGiptycsee 31
                +++ + +C++CG   +  e 
  AJA91884.1  7 SEESSTKCKKCGSELHDAER 26
                5677899*****99887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
    zf-Mss51 10 tapkhvdfeCpdCGi 24
                ++ ++vd++C +CG 
  AJA91884.1 34 AHGRRVDVKCRNCGT 48
                35899*********6 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3    0.0036       1.7       8      20 ..       6      18 ..       2      25 .. 0.79
   2 ?    5.1   3.4     0.043        21      14      39 ..      41      64 .]      32      64 .] 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
   zf-C2H2_3  8 qksfgasqCkeCg 20
                +++ ++++Ck+Cg
  AJA91884.1  6 KSEESSTKCKKCG 18
                55556688****9 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.043
   zf-C2H2_3 14 sqCkeCgMvYnpgspeDeklHkkfHa 39
                ++C +Cg ++   +p+D + Hkk ++
  AJA91884.1 41 VKCRNCGTEF--RDPDDLRKHKKKCK 64
                56999*9998..59********9886 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.3     0.097        46       2      21 ..      12      31 ..      11      47 .. 0.80
   2 ?   -0.4   0.2       3.3   1.6e+03      36      43 ..      57      64 .]      55      64 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.097
     zf-IS66  2 rtCpcCGgllkpigedrvre 21
                ++C++CG++l+ ++  ++ e
  AJA91884.1 12 TKCKKCGSELHDAERLKRHE 31
                78******999988775445 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.3
     zf-IS66 36 irpkyaCp 43
                + +k++C+
  AJA91884.1 57 RKHKKKCK 64
                67999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 447.58
//
Query:       AJA91885.1  [L=351]
Description: TIGR00303 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.1   0.0    1.5e-13   50.7   0.0    1.2  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   8.2e-18   1.5e-13     100     273 ..      99     269 ..      89     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 8.2e-18
                 EEEEEE-S.--T....EE--SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTCHHHHHHHHHHHHT--HHHH---TTT--HH CS
     DBI_PRT 100 rvvDvgva.dle....vdrkvrrgtaniakepAmtreeaeaaleaGieladeladagadllalGemGigNttaaaallaallglepeevvGrGtgldde 193
                  vv++g +   +     d+ +    +ni++ pAm+ e+++  +e+G +l +  +++++d+l++Ge+  g tt+a  +l a+  le +      + ++++
  AJA91885.1  99 FVVNAGSKvA-PslcyFDADILP-GKNISESPAMSIEQVKSGIEYGKNLGKI-MSQNTDCLVIGECIPGGTTTALTVLRAFG-LECN----VSSSMQNN 189
                 5666664321.124454445544.489*********************9987.5789*****************99998874.3333....3567899* PP

                 HHHHHHHHHHHHHHCH-TT.HHHHHHHHS-HHHHHHHHHHHHHHHTT--EEE-SHHHHHHHHHHHHHSGGGGGGEEE-B- CS
     DBI_PRT 194 glarKiavieqalarhaekdplevLakvGGleiaalaGailgAaarripvvlDGfistaAalvAvrlapevkdyliashr 273
                  l  K +++++al+r +++d+le++a++G   + + aG++ +A ++  +++  G  + a   +A+++  ++++  i ++ 
  AJA91885.1 190 PLDLKNKIVSDALKRKKSDDALEIIANFGDPMMPVCAGMLSSASKNCHVILAGGTQMLAVLQLAKQIGYNAENSAIGCTS 269
                 ****************767**************99999888888877777777788888888999999998888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2210.82
//
Query:       AJA91886.1  [L=222]
Description: EMG1/NEP1 methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-43  148.5   2.5    1.9e-43  148.4   2.5    1.0  1  EMG1            EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
        0.2   11.6   0.0        0.3   11.1   0.0    1.2  1  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   2.5   2.2e-47   1.9e-43       1     194 []       4     217 ..       4     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 2.2e-47
                 EEEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEEEEEETTSEEEEE-TT--- CS
        EMG1   1 ivLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqvyihttknvlIevnpqtRi 83 
                 i+L e+sLel++++                + s++LL+++ h  ++k l++e k++RpDIvH +Ll++  sp   ++++qv++ht ++++I++n++tR+
  AJA91886.1   4 IILVESSLELIPTElsnhqsvlayskkfkkNISNTLLDNSWHFGAMKGLENEIKRGRPDIVHLTLLSICTSPAFYQNKIQVFVHTINDEIISINNNTRL 102
                 89**************************99999****************************************************************** PP

                 -SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTSEE-..............EEEE-SSSS.......---HHEEESS CS
        EMG1  84 PrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesaekk.lvdleefvvkpvvfvigamskgsvki...dykeeeisis 176
                 P++++rF+gLm++L+ +++i+++++   L+++ ++++++++++    +ii+l+++++k+   +l++ ++++ +++ig+++kg+ +    ++ e+++si 
  AJA91886.1 103 PKSYHRFQGLMEKLFLTKKIESESEI--LIQMENSSLSKLISKinPDEIIGLTTQGQKTtFEKLTHQIKENSCILIGGFQKGHFNKeteKIIETSFSIH 199
                 *********************99875..**************98889**********6633355666699************555522355556***** PP

                 SS---HHHHHHHHHHHCH CS
        EMG1 177 nypLsaavvcskiltafE 194
                 + +L+a++v+s+++ ++E
  AJA91886.1 200 DSSLEAHLVASRLVYEYE 217
                 *************99987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.3e-05       0.3      52     108 ..      40      94 ..      15     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.3e-05
  Glyco_transf_4  52 krllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye 108
                      ++ + + +++ l + +kr++pD+vH      +   +++    +   +V+t+ +   
      AJA91886.1  40 LDNSWHFGAMKGLENEIKRGRPDIVHLTLLSICTSPAFYQN--KIQVFVHTINDEII 94 
                     56778899999***************988666666655555..46666777766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1666.03
//
Query:       AJA91887.1  [L=272]
Description: putative RNA methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-46  157.2   0.0    6.8e-46  157.1   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
  ------ inclusion threshold ------
      0.042   14.0   0.0        2.1    8.5   0.0    2.2  2  SpoU_methylase   SpoU rRNA Methylase family
      0.048   13.5   0.0       0.72    9.7   0.0    2.1  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.0   1.1e-49   6.8e-46       2     284 ..       3     263 ..       2     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 1.1e-49
  Methyltrn_RNA_3   2 vsiaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhkelkyaglLppldap 95 
                      +siaiP s +++ +++e kt+++ qIARaa iF+V+ i++++d+ + e+    +s++l+++L++letP++ rk+l+p+   l+++g L p+++p
       AJA91887.1   3 LSIAIPDSSLKDEKKHENKTRKIFQIARAAGIFQVNNIIIYKDGREFEN----DSKLLSTILRFLETPQNFRKRLYPKSGLLQFVGALSPIKMP 92 
                      79*****************************************997764....78*************************************** PP

  Methyltrn_RNA_3  96 hhl.....rsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklsseesveakvVspsepreeaglywGYsVrlaks 184
                              ++ ++g++reGv+ +++   k+   +++iG+++++  +   + +   R  Vk+  ++      V+  e+  +    w Y+V+   +
       AJA91887.1  93 NQTvtsdaKQVKKGDVREGVIFPRDG--KK---FIDIGIDHSIPYHG--KKQIDKRAIVKI--KDILPDFSVHDIEK-DQLPNFWSYNVKHGGN 176
                      **99998766779**********965..55...**********8888..555688999999..66888888998888.59999*********** PP

  Methyltrn_RNA_3 185 lsavftespfeggydlsigtsergekveeklaelekkk.efkhllivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtE 276
                      l +++te         +i+ts++++k++++    +k   +++++l+vfG   +g+ ++l+++       +++++ F + +n++p+qg++t+r+E
       AJA91887.1 177 LFSLLTEW-----KGPKILTSRKSKKIKNEDM--QKILsSKEEILVVFGTtDKGIHEMLDKK------ISNIQN-FKA-WNFFPHQGTETVRLE 255
                      *******8.....4679*****9987776655..4456579*********99*******655......455655.665.6999*********** PP

  Methyltrn_RNA_3 277 EavliaLa 284
                      Ea+l  La
       AJA91887.1 256 EAILGCLA 263
                      ***98887 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.016        93      17      38 ..      27      48 ..      24      64 .. 0.80
   2 ?    8.5   0.0   0.00035       2.1      62     117 ..     175     233 ..     163     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.016
                    HHHHHHHHTT-SEEEEESGSSC CS
  SpoU_methylase 17 aiaRtakafgaselvlvkprsa 38
                     iaR+a +f+++++++ k+ ++
      AJA91887.1 27 QIARAAGIFQVNNIIIYKDGRE 48
                    59**************996554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00035
                     SSHHHHHHHHCCCTEEEEEESTT-SEGC.....CS.HHHTTEEEEEEBTTTBS-HHHHCTSS CS
  SpoU_methylase  62 dsleealkelkeegfalvatslkgksls.....ei.dlkekvalvfGnEdkGlsnellelad 117
                     ++l ++l+e+k      + ts+k+k+++     +i + ke++++vfG+ dkG+++ l ++++
      AJA91887.1 175 GNLFSLLTEWKGP---KILTSRKSKKIKnedmqKIlSSKEEILVVFGTTDKGIHEMLDKKIS 233
                     5555566666655...24445555555522121445666**************998777765 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.036   2.1e+02      28      63 ..      25      63 ..      21     100 .. 0.81
   2 ?    9.7   0.0   0.00012      0.72     112     159 ..     193     236 ..     172     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.036
                     HHHHHHHHHHTT-SEEEEE--...-HHHHHHHHHHHHHH CS
  Methyltrn_RNA_4 28 lhDiaRsartygvkkyyvvtp...leaqrelverilehW 63
                     +  iaR+a  ++v++  + ++   +e+  +l+++il++ 
       AJA91887.1 25 IFQIARAAGIFQVNNIIIYKDgreFENDSKLLSTILRFL 63
                     678************999875222566777777777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                      --SS-B-HHHHHHHHHH--S-EEEEE--T.T---HHHHTT-SEEB--TT CS
  Methyltrn_RNA_4 112 kkentvsyeelrelleeeekpvlllfGtg.wGlaeevlekadyiLepir 159
                      +k+++++ e+++++l ++++++l++fGt+  G++e    + d  ++ i+
       AJA91887.1 193 RKSKKIKNEDMQKIL-SSKEEILVVFGTTdKGIHE----MLDKKISNIQ 236
                      46889999****999.99999******97245544....3333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2109.35
//
Query:       AJA91888.1  [L=186]
Description: putative phosphoheptose isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-26   91.9   0.4    5.1e-26   91.3   0.4    1.2  1  SIS_2         SIS domain
      2e-08   34.2   0.9    1.1e-05   25.2   0.1    2.2  2  SIS           SIS domain
  ------ inclusion threshold ------
       0.04   13.7   0.1      0.074   12.8   0.1    1.6  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
      0.091   13.0   0.2       0.19   12.0   0.2    1.5  1  Fer4_12       4Fe-4S single cluster domain
        0.1   13.0   0.1       0.21   12.0   0.1    1.4  1  OmpA          OmpA family
       0.11   12.4   0.1       0.23   11.4   0.1    1.5  1  TBPIP         TBPIP/Hop2 winged helix domain
       0.16   12.2   0.1         15    5.8   0.0    2.8  3  AAA_lid_6     AAA lid domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.3   0.4     2e-29   5.1e-26      15     138 .]      20     143 ..      10     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.3 bits;  conditional E-value: 2e-29
                 HHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHHTT-TTHHHHHHHH..TT--TT-EEEEE- CS
       SIS_2  15 etqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeatkssalerdegyakqilrl..vrlkpgDvLlviS 111
                 ++ +++ie+ ++ i ++l+n +k+++fG+G+Saa+a+++aa+++g+++ er  lpa+ l+td+  ++ + +++d  ++++++r+  + +++gDv + iS
  AJA91888.1  20 TSLSNEIEESIQKIIECLKNQKKIILFGNGGSAADAQHIAAEFIGRFKKERNSLPAISLTTDT--SIITSISNDYSFDNIFSRQceSLVNSGDVVIAIS 116
                 678999*******************************************************98..666666666666666666633337********** PP

                 SS--SHHHHHHHHHHHHHT-EEEEEE- CS
       SIS_2 112 nsGnnavvveaaeaakergmkviAlts 138
                 +sGn++++   ++a k+ g+ vi+l++
  AJA91888.1 117 TSGNSKNIELGINASKQNGALVIGLLG 143
                 ************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0012       2.9       2      27 ..      37      62 ..      36      68 .. 0.91
   2 !   25.2   0.1   4.4e-09   1.1e-05      48     110 ..     103     165 ..      83     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                HCTSSEEEEEESHHHHHHHHHHHHHH CS
         SIS  2 LakakriyvlGaGtsyaiakelalkl 27
                L ++k+i+++G G s+a a+ +a+ +
  AJA91888.1 37 LKNQKKIILFGNGGSAADAQHIAAEF 62
                7899***************9999877 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 4.4e-09
                 GGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
         SIS  48 lalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyinaepet 110
                  +l++++d+vi+is+sg++k+  + ++  k++ga +i++ +++g  + +  d+ + in+ + +
  AJA91888.1 103 ESLVNSGDVVIAISTSGNSKNIELGINASKQNGALVIGLLGNNGGMVRELVDIPIVINSTDTA 165
                 589*************************************99999998888888888777666 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.9e-05     0.074       1      89 [.      30     120 ..      30     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT.....-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSS CS
  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklg.....iPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfd 89 
                   i+k++e lk+ k+ +il+G+g + ++a++ ++e++ +++     +P ++     ++i + +  y  +++ + s+++  ++++ D+v+a+ +  +
    AJA91888.1  30 IQKIIECLKNQKK-IILFGNGGSAADAQHIAAEFIGRFKkernsLPAISLTTDTSIITSISNDY--SFDNIFSRQCESLVNSGDVVIAISTSGN 120
                   7899999999877.6788999999**********966543333389988888888888766655..5677779999999999999999987654 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.5e-05      0.19      38     134 ..      27     132 ..      14     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
     Fer4_12  38 kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp.ekdiwlyt.gytleelskk.........ekeellkeidvlvdGkfeesled 125
                 +e +++iie lk+++++ l   GG       + + +e++ ++k+e    + i l+t  +++  +s++         + e+l++  dv++    + + ++
  AJA91888.1  27 EESIQKIIECLKNQKKIILFGNGGSAAD--AQHIAAEFIGRFKKERNsLPAISLTTdTSIITSISNDysfdnifsrQCESLVNSGDVVIAISTSGNSKN 123
                 6788999999988888777777787777..999*********99985334444443134555555556666666669999**********999999999 PP

     Fer4_12 126 eslrfrgss 134
                  +l +++s+
  AJA91888.1 124 IELGINASK 132
                 999999987 PP

>> OmpA  OmpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.1e-05      0.21       5      37 ..      18      53 ..      17      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                TS--B-GGGHHHHHHHHHHHHS-S--EEEEE-....- CS
        OmpA  5 gsseLtpkaksaldkiaellkkpeqkitveGh....t 37
                +s++L++++++ ++ki+e lk +++ki++ G     +
  AJA91888.1 18 NSTSLSNEIEESIQKIIECLK-NQKKIILFGNggsaA 53
                89*******************.6777**999844333 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   8.9e-05      0.23      32      49 ..      27      44 ..      10      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.9e-05
       TBPIP 32 KtavqkaLdeLvdegkii 49
                 +++qk++++L++++kii
  AJA91888.1 27 EESIQKIIECLKNQKKII 44
                578**************8 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3   3.4e+03      27      37 ..       2      12 ..       1      19 [. 0.82
   2 ?    5.8   0.0     0.006        15       4      26 ..      27      52 ..      24      63 .. 0.75
   3 ?    3.2   0.0     0.041   1.1e+02      22      31 ..     145     154 ..     140     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
   AAA_lid_6 27 Rnllekairrq 37
                +nl+e++i  +
  AJA91888.1  2 KNLIEESILSR 12
                69999999766 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.006
   AAA_lid_6  4 eevlrelle...rrrrdenfGNARfV 26
                ee +++++e    ++++  fGN++ +
  AJA91888.1 27 EESIQKIIEclkNQKKIILFGNGGSA 52
                455555666554888999*****987 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.041
   AAA_lid_6  22 NARfVRnlle 31 
                 N+++VR l++
  AJA91888.1 145 NGGMVRELVD 154
                 9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1387.73
//
Query:       AJA91889.1  [L=312]
Description: 3-beta hydroxysteroid dehydrogenase/isomerase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-39  136.1   0.0    1.7e-39  135.7   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.2e-29  102.4   0.1    4.3e-29  102.0   0.1    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.3e-28   97.7   0.0    8.2e-28   97.3   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    3.2e-19   69.0   2.0      4e-19   68.7   2.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.7e-17   62.9   0.7    2.1e-16   59.9   0.7    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    2.6e-11   43.2   0.0    4.9e-08   32.4   0.1    2.5  2  NAD_binding_4    Male sterility protein
    3.1e-06   27.2   0.0    4.6e-06   26.6   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
     0.0077   16.0   0.0      0.015   15.1   0.0    1.4  1  O-FucT           GDP-fucose protein O-fucosyltransferase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.0   7.7e-43   1.7e-39       2     241 .]      12     239 ..      11     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 7.7e-43
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STT.TTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssa.sntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 l+tGa+GfiG++++k++ + +y++i+l++++++ +n++ ++++ +   d++d+s +e++++ ++pd+v+hlA  g  ++  ++p++++++n++g +n+l
  AJA91889.1  12 LITGANGFIGTNFIKKFHN-NYDIIALTHNNNSlKNFSGIKNIIIESNDILDNSIIEKIVS-YNPDVVLHLANFGYLRDCENNPEKTYQTNVVGLRNIL 108
                 9****************97.69******99877245555666699999***********99.69*********************************** PP

                 HHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSS CS
   Epimerase 100 eaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkq 198
                 + ++k +  +++f sS evYG+  +   e +++t++l+pn+  + +K+++e+l+ +  +  +++++ilrl+n++Gp+    ++s+v+  +++++l++k 
  AJA91889.1 109 QICQKINS-KIIFTSSREVYGETIR---ETSSETDELNPNNVLGKTKILSENLIISNSDISKFDYTILRLSNVFGPH----SPSSVVGLMLTHALKEK- 198
                 ********.************6665...6777778**********************9999****************....****************9. PP

                 SEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 199 evtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 +++++g g++   ++y++ v+++i  ++  ++   k++i+niG
  AJA91889.1 199 KIIVYG-GKQTLNLVYIDYVIDIIDKIICSPEL-TKNKILNIG 239
                 *****9.***********************998.6789****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.1   1.9e-32   4.3e-29       1     331 [.      12     301 ..      12     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 1.9e-32
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    LiTG +GfiG ++++++ +++  +  + +++s+ n++ i+++             + + D+ D+s +e++++ ++pd v++LA     +   ++Pe
     AJA91889.1  12 LITGANGFIGTNFIKKFHNNYDIIALTHNNNSLKNFSGIKNI------------IIESNDILDNSIIEKIVS-YNPDVVLHLANFGYLRDCENNPE 94 
                    9****************9986666666666677777766665............46789****999999886.67********************* PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf 192
                    +t+++nv+G  ++L+++++++     +++++S+ EvYG++ +   +Et  ++P++  + +K+ ++ ++++  +  ++  ++ +l+n  +p+   + 
     AJA91889.1  95 KTYQTNVVGLRNILQICQKIN----SKIIFTSSREVYGETIRETSSETDELNPNNVLGKTKILSENLIISNSDISKFDYTILRLSNVFGPHSPSS- 185
                    ******************997....4899**************************************************************6444. PP

                    CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTG CS
  GDP_Man_Dehyd 193 vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgk 288
                        + ++++++++ +++++++G ++++    +++ +++++++++ + +     + +++  ++++  ++++++l ++++                +
     AJA91889.1 186 ---VVGLMLTHALK-EKKIIVYG-GKQTLNLVYIDYVIDIIDKIICSPE-----LTKNKILNIGSNENITIIDLARKLTNLF-------------N 258
                    ...45555555555.45778888.5678889999999999999998877.....6788888888888888888888766432.............2 PP

                    GCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHH CS
  GDP_Man_Dehyd 289 vvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvre 331
                    +++ + +   r++e +    + +k++e  +++ k +++e ++e
     AJA91889.1 259 EKIDILKLEPRDSETKYFKPNLQKIHELFNFNSKKTINEELKE 301
                    3455555556777888888888888888888888888887776 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   3.6e-31   8.2e-28       2     235 ..      10     261 ..       9     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 3.6e-31
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHHTHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavnaea 81 
                    k+l+tGanG +G++ +k+++ ++++++alt +                + d+ d++ ++++++  +pdvv ++A +     +E+++e+ y+ n+ +
     AJA91889.1  10 KLLITGANGFIGTNFIKKFH-NNYDIIALTHNnnslknfsgikniiieSNDILDNSIIEKIVSY-NPDVVLHLANFGYLRDCENNPEKTYQTNVVG 103
                    79*****************9.668*****9998999*******999999999999999999987.9****************************** PP

                    HHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEEE-SEESS.SSS-HHHHHHHHHHH-SE CS
  RmlD_sub_bind  82 vealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkkalivRtswvyge.kgknfvktmlrlakeree 172
                     +++ + ++++++++i+ S+  V+  +  +  +e+de +P nv G+tK++ E+ + +    ++ +++i+R s v+g  +  + v  ml  a ++++
     AJA91889.1 104 LRNILQICQKINSKIIFTSSREVYGETIRETSSETDELNPNNVLGKTKILSENLIISnsdiSKFDYTILRLSNVFGPhSPSSVVGLMLTHALKEKK 199
                    ************************9999999************************99555555699*********9835678999**********9 PP

                    EEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG..-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
  RmlD_sub_bind 173 lkvvaDqlgsPTsardlAevllqllekaaeekel..agvyHlanegetswlefArailkeagads 235
                    + v     g+ T      ++++++++k+++++el  ++++ ++++++++  ++Ar+  + ++++ 
     AJA91889.1 200 IIVYG---GKQTLNLVYIDYVIDIIDKIICSPELtkNKILNIGSNENITIIDLARKLTNLFNEKI 261
                    99975...667888888999999999999999988899*****************9999888765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   2.0   1.8e-22     4e-19       1     224 [.      12     220 ..      12     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.8e-22
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleeale.gvdvvihlaslvdvag.kltedeimkvnvkGTr 97 
                 ++tG+ GF+G + +k++ +  +     ++ l ++++ l+++s ++++ +   D++d++ +e+ +  + dvv+hla    ++  + + ++ ++ nv G r
  AJA91889.1  12 LITGANGFIGTNFIKKFHNNYD-----IIALTHNNNSLKNFSGIKNIIIESNDILDNSIIEKIVSyNPDVVLHLANFGYLRDcENNPEKTYQTNVVGLR 105
                 69**************977765.....7888999999999999999978889**********986378*************988999************ PP

   3Beta_HSD  98 nvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkql 196
                 n+l+ c k +  ++++tSs ev g+      i++   +++ e ++++++ ++K l+E+l+++       +++++    LR + ++G+ ++  v  l  +
  AJA91889.1 106 NILQICQKIN-SKIIFTSSREVYGE-----TIRE-TSSETDELNPNNVLGKTKILSENLIISNS-----DISKFDYTILRLSNVFGPHSPSSVVGLMLT 192
                 ******9998.679********999.....5553.33445577899**************9655.....589998889************999988777 PP

   3Beta_HSD 197 aklglalfkigdeevlsdrvYvgNvawa 224
                   l+++++ +   +++ + vY + v ++
  AJA91889.1 193 HALKEKKIIVYGGKQTLNLVYIDYVIDI 220
                 77777777777777779****9988765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.7   9.5e-20   2.1e-16       1     251 [.      11     261 ..      11     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 9.5e-20
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +l+tGa G iG ++++++ +     ii l ++ ++l +++  +     +  +  e      d+ d++ +ek+++ +++dvv+h A +  +  +e
       AJA91889.1  11 LLITGANGFIGTNFIKKFHN--NYDIIALTHNNNSLKNFSGIK-----NIII--E----SNDILDNSIIEKIVS-YNPDVVLHLANFGYLRDCE 90 
                      59***************975..568999999999999988754.....3222..2....469***********9.******************* PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEE..............EGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT. CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliS..............tDKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlg. 173
                      +np ++ +tNv+g +n+++++++ + k + + S              t    nP nv+G tK l+e l+++ ++ s   k  +++ R  NV+g 
       AJA91889.1  91 NNPEKTYQTNVVGLRNILQICQKINSKIIFTSSrevygetiretsseT-DELNPNNVLGKTKILSENLIISNSDIS---KFDYTILRLSNVFGp 180
                      *********************999865444333222222222222222.3579*****************999998...89***********86 PP

                      .GTTSSHHHHHHHHHTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--...-EEEHHHHHHHH........ CS
  Polysacc_synt_2 174 .SrGSviplFkkqikeggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmG..epvkivdlakalielsglee 251
                       S  Sv+ l      +++++ v   + t  ++ i+  ++++ + +   +  +  +l++G  e ++i+dla++l +l++ + 
       AJA91889.1 181 hSPSSVVGLMLTHALKEKKIIVYGGKQTLNLVYIDYVIDIIDKIICSPELTKNKILNIGsnENITIIDLARKLTNLFNEKI 261
                      6889************************9999999999999776655555544445554228999********99997654 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00037      0.83       1      44 [.      13      53 ..      13      84 .. 0.70
   2 !   32.4   0.1   2.2e-11   4.9e-08      99     256 ..      88     220 ..      61     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleee 44
                   +TGa GF+G+ +++k  ++     i++l +++++ +    +++ 
     AJA91889.1 13 ITGANGFIGTNFIKKFHNNY---DIIALTHNNNSLKNFSGIKNI 53
                   8*************987665...599999988776666666554 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 2.2e-11
                    S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH CS
  NAD_binding_4  99 nfdepykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrs 194
                    + +++ ++ +++Nv G r++l++++k++++  +++ S+  v+ge  +                ++ +++++ + +n   ++K l+E+l+ + ++ s
     AJA91889.1  88 DCENNPEKTYQTNVVGLRNILQICQKINSK--IIFTSSREVYGETIR----------------ETSSETDELNPNNVLGKTKILSENLIISNSDIS 165
                    445567789******************999..999999555555442................2345566677788999***************** PP

                    ---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHHHHHHH CS
  NAD_binding_4 195 glpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgdkeavldlvpvDyvana 256
                    ++  +i+R+s++ g  ++ ++ g       l  + +++++   ++  +++l+lv +Dyv+++
     AJA91889.1 166 KFDYTILRLSNVFGPHSPSSVVGLM-----LTHALKEKKII--VYGGKQTLNLVYIDYVIDI 220
                    **************55553333333.....33333333333..3333456777777777765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.1e-09   4.6e-06       1     145 [.      15     176 ..      15     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.1e-09
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-.SEEEES-.........--TCCHHHH........ CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga.daVvsal.........ggggkdeeg........ 77 
                     GA+G +G   +k+  ++  +++ al+ n ++l++++  +++ + + d++d + +++ ++   d+V+  +         +                
      AJA91889.1  15 GANGFIGTNFIKKFHNN--YDIIALTHNNNSLKNFSGIKNIIIESNDILDNSIIEKIVSYNpDVVLHLAnfgylrdceN-------Npektyqtn 100
                     9*************998..8***************9889999999999*9**9***99866155555555555544442.......122334456 PP

                     ...HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHH.CCHHHH.HHHHHHHHHHHH....SSSEEEEEEE-C CS
  NAD_binding_10  78 ...aknivdaakeagvkRfvlvsaigvgdevpgefgewnke.llkayl.aakraaeellra....sgldwTivrpgg 145
                         +ni++ +++ +  ++++ s+  v+ e+ +e+++ ++e + +++l + k  +e+l+ +    s++d+Ti+r + 
      AJA91889.1 101 vvgLRNILQICQKINS-KIIFTSSREVYGETIRETSSETDElNPNNVLgKTKILSENLIISnsdiSKFDYTILRLSN 176
                     788********99876.8999999999987666655444432667777677889999987668999********876 PP

>> O-FucT  GDP-fucose protein O-fucosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.5e-06     0.015     231     325 ..      92     186 ..      79     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.5e-06
      O-FucT 231 tpeecvpsleeialqlkgllkelkltsvfvAtdeiyggeelkelkkefpnlv...kvtkeklaskeelekfkdgsvaaiDqiicsrsdvFigtyeStf 325
                  pe+++++ +  ++++++++++++ + +f ++ e yg+  + e ++e  +l     + k+k+   +e   + +++++  D+ i+  s+vF + + S++
  AJA91889.1  92 NPEKTYQTNVVGLRNILQICQKINSKIIFTSSREVYGET-IRETSSETDELNpnnVLGKTKI--LSENLIISNSDISKFDYTILRLSNVFGPHSPSSV 186
                 589999999999************************987.7777766655444112345554..4444469999999*************98888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2233.44
//
Query:       AJA91890.1  [L=166]
Description: hypothetical protein T478_0302 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-92  308.5  11.7    1.6e-92  308.3  11.7    1.0  1  Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA


Domain annotation for each model (and alignments):
>> Archaeal_AmoA  Archaeal ammonia monooxygenase subunit A (AmoA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.3  11.7     9e-97   1.6e-92      36     183 .]       1     148 [.       1     148 [. 1.00

  Alignments for each domain:
  == domain 1  score: 308.3 bits;  conditional E-value: 9e-97
  Archaeal_AmoA  36 mlvvgaiyyllftgvpgtatyyalimtvyvwvakgawfalgypydfivvpvwlpsamlldlaywatkrnkhaliliggvlvglslplfnmvnlllv 131
                    ml vga yyl+ftgvpgtatyyalimtvy+w+akgawfalgypydfiv+pvwlpsamlldlaywatk+nkh+lil+ggvlvg+slplfnmvnl++v
     AJA91890.1   1 MLTVGACYYLTFTGVPGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLILFGGVLVGMSLPLFNMVNLITV 96 
                    89********************************************************************************************** PP

  Archaeal_AmoA 132 adplevafkyprptlpaymtpiepqvgkfynspvalgagagavlsvtiaalg 183
                    adple+afkyprptlp+ymtpiepqvgkfynspvalgagagavl+ t+aalg
     AJA91890.1  97 ADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGAGAVLACTFAALG 148
                    **************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1161.85
//
Query:       AJA91891.1  [L=133]
Description: hypothetical protein T478_0803 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   12.5   0.1      0.086   12.1   0.1    1.2  1  Pho88     Phosphate transport (Pho88)
      0.074   12.5   0.6       0.17   11.3   0.1    1.6  2  NeuB      NeuB family


Domain annotation for each model (and alignments):
>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.6e-06     0.086      59     102 ..      15      57 ..       3      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.6e-06
       Pho88  59 Dlttlkyvepasplske.eeklvttTvkdYDlaelkkllksilmg 102
                 D   ++yv   +++s++  ek+++ T + +D +++kk++++++m 
  AJA91891.1  15 D--KIRYVGVYNSFSGDvYEKMQNGTARHFDKDQTKKSMTQAIMR 57 
                 4..799***********999*********************9985 PP

>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     2e-05      0.17      14      88 ..      33     111 ..      28     116 .. 0.79
   2 ?    1.4   0.0     0.021   1.8e+02     163     184 ..     107     128 ..      99     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2e-05
                 EEEE--HHHH--GGGGG--......TT-S-HHHH....HHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHH CS
        NeuB  14 KfQtfkaeelvskeakkaeyqkkekekeesqlel....lkklelseeehkelkeyceekgieflstpfdlesvdllesl 88 
                 K+Q+ +a+++ ++++kk+  q+  ++k+++q+       + + + +e+ +++   c + g+ ++st  d++  d+++++
  AJA91891.1  33 KMQNGTARHFDKDQTKKSMTQAIMRWKTRKQFSAeigePEYAMTRYEKVNRITMSCGKDGLLMFSTEVDVHLCDIIDDV 111
                 7888888888888887777777777888777654212146678999************************999999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.021
                 HHHHHHHH-TSEEEEE--SSSS CS
        NeuB 163 aietlkeafgvpvGySDHtlgi 184
                  i+++ +  + +vG SDH+ g 
  AJA91891.1 107 IIDDVTKMVKEHVGESDHEDGS 128
                 578888999999******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 986.67
//
Query:       AJA91892.1  [L=244]
Description: PF02006 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-62  210.7   3.7    1.8e-62  210.0   3.7    1.3  1  PPS_PS        Phosphopantothenate/pantothenate synthetase
  ------ inclusion threshold ------
      0.018   14.8   0.3        1.1    8.9   0.0    2.4  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   3.7     2e-66   1.8e-62       3     172 ..      67     229 ..      65     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 2e-66
      PPS_PS   3 lakkpvisvNGNtaaLvaeeiveLaealgaklevNlfyrteeRvekiaellkeagaeevlgleeda..ripeleseRakvskeGiysaDvvlvplEDGD 99 
                 +a+++visvNGN aaL+++ei++La+++++k+evNlfy +e+R ++i+++lk++ga++vlg+++++  ++++++s+R++v+k+Gi+saDvvlvplEDGD
  AJA91892.1  67 QAQNSVISVNGNFAALCPKEIIQLAKTTNSKIEVNLFYSSEKRKKAISKILKKSGAKQVLGMDKKQsaKLKGIDSARRIVDKNGIFSADVVLVPLEDGD 165
                 79***********************************************************99887789****************************** PP

      PPS_PS 100 RaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkskeeleeivkefdnkkvlkea 172
                 R+ aL+k+ Kkvi+ DLNPlsRta+ta++tivdnv+R+++ l+++ k+  +       ++  +fdnkk+lk++
  AJA91892.1 166 RTIALKKAKKKVITFDLNPLSRTAQTADVTIVDNVTRSMKLLVSESKKSGR-------KV--TFDNKKNLKSS 229
                 ******************************************988776522.......22..35555555544 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00013       1.1       1      40 [.      58      96 ..      58     107 .. 0.92
   2 ?    4.0   0.1    0.0042        38     100     136 ..     170     206 ..     110     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00013
                  HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT- CS
  TPP_enzyme_M  1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgi 40
                  i++aa +l++a++ vi v g  a + + +e+ +la++++ 
    AJA91892.1 58 IKAAAYMLNQAQNSVISVNGNFA-ALCPKEIIQLAKTTNS 96
                  789***************99999.99***********986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0042
                   TTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
  TPP_enzyme_M 100 fapea.kiihididpaeigknyqvdlaivgdvketlea 136
                    ++ + k+i +d +p +   +  +d++iv +v+ +++ 
    AJA91892.1 170 LKKAKkKVITFDLNPLSRTAQT-ADVTIVDNVTRSMKL 206
                   3333449********8888876.89****999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1197  (0.0667633); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1903.83
//
Query:       AJA91893.1  [L=230]
Description: PF01982 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.9e-41  138.6   0.2    1.4e-40  138.2   0.2    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
    0.00043   20.3   0.0    0.00079   19.4   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0011   18.9   0.2     0.0055   16.6   0.0    2.2  2  MarR            MarR family
     0.0011   18.8   0.0     0.0025   17.7   0.0    1.6  1  MarR_2          MarR family
      0.002   18.0   0.1      0.055   13.4   0.0    2.5  2  HTH_36          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.2   1.3      0.021   14.5   0.1    1.9  2  DUF4364         Domain of unknown function (DUF4364)
      0.016   14.8   0.0      0.052   13.1   0.0    1.9  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.023   14.6   0.1      0.092   12.7   0.0    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.031   14.2   0.1       0.06   13.3   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.033   13.6   1.6      0.078   12.4   0.1    2.0  2  RepL            Firmicute plasmid replication protein (RepL)
       0.16   11.8   0.1       0.54   10.1   0.1    1.9  1  LexA_DNA_bind   LexA DNA binding domain


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.2   8.5e-44   1.4e-40       1     121 []     101     223 ..     101     223 .. 0.98

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 8.5e-44
                     EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCC.GHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEEC.CEEEEEEEESS-SS. CS
  CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldee.slelrkaleklkgieiegfedeertfgavkvypakie.kikaavvvperthye 93 
                     ++sG+geG+yy+s++gy++qf++klg+ pypGTLNv+++e+   e+ ++l++++gi+i+ f+d++rtfg+vk+++ ki+ k+++++++ erth++
      AJA91893.1 101 ITSGMGEGAYYMSMKGYTKQFKSKLGYVPYPGTLNVQIKEKkFSEAISQLSNYEGIKINPFSDGKRTFGWVKCFKSKINnKVDCELILLERTHHD 195
                     68***************************************889999*******************************8789************* PP

                     TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
  CTP-dep_RFKase  94 edvlEiiapekLReklelkdgdevevev 121
                     ++++E+i+++++R++l++++ ++v+v++
      AJA91893.1 196 TTIVEFISKHNIRKALKISEKSNVKVKI 223
                     **************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.9e-07   0.00079      25      61 .]      27      63 ..      25      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.9e-07
                B-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
      HTH_20 25 ltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                +t + l ++++ s++++s HL++Le+ g++e+  +gr
  AJA91893.1 27 VTTTSLGKEIGKSQQSASLHLKELESGGFIERIQSGR 63
                57788899999********************998886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.4e-06    0.0055      17      52 ..      26      61 ..      10      64 .. 0.89
   2 ?   -0.3   0.0      0.66   1.1e+03      21      43 ..      67      89 ..      60      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsks 52
                + + + L+k +g s+ +++  l++Le  G+ieR +s
  AJA91893.1 26 NVTTTSLGKEIGKSQQSASLHLKELESGGFIERIQS 61
                56778****************************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.66
                HHHHHHHTS-HHHHHHHHHHHHH CS
        MarR 21 seLakklgvskstvtrvldrLek 43
                +++  k  v+ st+ ++l +L+ 
  AJA91893.1 67 IKITHKGFVELSTLHNLLSKLIS 89
                57888888888888888888876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.5e-06    0.0025       2      56 ..       3      61 ..       2      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                T--HHHHHHHHHHHCTTTS....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
      MarR_2  2 gltpaqarvLaaLgrrpgr....dltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                +l+ +++  La++   +g+    ++t + l ++ g s++++s +lk+L++ G++er  +
  AJA91893.1  3 DLKTQHLLTLAHILSKGGKhnfvNVTTTSLGKEIGKSQQSASLHLKELESGGFIERIQS 61
                677889999********99*99999******************************9865 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.4e-05     0.055       2      55 .]       3      56 ..       2      56 .. 0.95
   2 ?    1.9   0.0      0.14   2.3e+02      19      41 ..     194     217 ..     186     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
      HTH_36  2 rLspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                 L++   l+l +++s  +k + ++ +   l k  g+s +++s ++keLe  G+i
  AJA91893.1  3 DLKTQHLLTLAHILSKGGKHNFVNVTTTSLGKEIGKSQQSASLHLKELESGGFI 56
                59999********************************************98876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
      HTH_36  19 nkngg.cfpsqetlakrlglsknT 41 
                  ++++  f s+  + k+l++s+++
  AJA91893.1 194 HDTTIvEFISKHNIRKALKISEKS 217
                 478899999***********9775 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.3e-05     0.021      39      85 ..      46      92 ..      39      98 .. 0.91
   2 ?   -1.7   0.1       1.3   2.1e+03     114     114 ..     207     207 ..     172     228 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
     DUF4364 39 alseLvesglieeeekenktlykiTekGketlelfenripksireki 85
                 l+eL++ g+ie  ++  k+ +kiT+kG   l++++n ++k i +  
  AJA91893.1 46 HLKELESGGFIERIQSGRKQSIKITHKGFVELSTLHNLLSKLISKSS 92
                699************************************99988766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
     DUF4364 114 y 114
                  
  AJA91893.1 207 I 207
                 2 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.052      19      48 .]      28      57 ..      26      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
      HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                + + L +++g S++  + +lk+Le+ G+I+
  AJA91893.1 28 TTTSLGKEIGKSQQSASLHLKELESGGFIE 57
                778999**********************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05     0.092      23      59 ..      27      63 ..      23      79 .. 0.89
   2 ?   -2.4   0.0       2.9   4.7e+03      24      34 ..     209     219 ..     204     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
        TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                 t++ + +e+g +++++   L++Le+ G++er+++ +
  AJA91893.1 27 VTTTSLGKEIGKSQQSASLHLKELESGGFIERIQSGR 63
                6899999**************************9764 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                 HHCHHCCCTTS CS
        TrmB  24 tadeiaeelgv 34 
                 +a +i+e+++v
  AJA91893.1 209 KALKISEKSNV 219
                 67789999997 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.7e-05      0.06       7      60 ..       9      70 ..       6      73 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                HHHHHCT..TTC..EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE..E.TEE..EEES CS
   HTH_Crp_2  7 Llrlaer..agg..eielpltqeelAsmlGltretvsrilseLkreglis..r.grr..iril 60
                Ll la+   +gg   + +++t + l+  +G ++++ s  l+eL+  g i+  + gr+  i+i+
  AJA91893.1  9 LLTLAHIlsKGGkhNF-VNVTTTSLGKEIGKSQQSASLHLKELESGGFIEriQsGRKqsIKIT 70
                5555442111234456.89*******************************6424443378775 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.8e-05     0.078      62     111 ..      13      62 ..       1      66 [. 0.87
   2 ?    0.1   0.3      0.29   4.8e+02      86     107 ..     201     222 ..     175     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
        RepL  62 yylidnlnsnntliatnRelaeetgislktvsetlkileeanilkkkanG 111
                  +++    ++n + +t+  l +e g s +  s  lk le ++++ ++++G
  AJA91893.1  13 AHILSKGGKHNFVNVTTTSLGKEIGKSQQSASLHLKELESGGFIERIQSG 62 
                 56777777899999********************************9998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
        RepL  86 gislktvsetlkileeanilkk 107
                  is + +++ lki e++n+  k
  AJA91893.1 201 FISKHNIRKALKISEKSNVKVK 222
                 3789999999999999998666 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00033      0.54      38      60 ..      38      60 ..      28      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
                   -.HHHHHHHHHHHHHTTSEE-GG CS
  LexA_DNA_bind 38 kSpsaveehLkaLerKGyierdp 60
                   kS +++  hLk Le  G+ier +
     AJA91893.1 38 KSQQSASLHLKELESGGFIERIQ 60
                   799*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1844.54
//
Query:       AJA91894.1  [L=320]
Description: K+-dependent Na+/Ca+ exchanger family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.9e-40  136.5  44.7    5.1e-21   75.2  19.2    2.1  2  Na_Ca_ex    Sodium/calcium exchanger protein
  ------ inclusion threshold ------
      0.018   14.7   0.5      0.075   12.7   0.5    2.1  1  Spore_YhaL  Sporulation protein YhaL
      0.026   13.5   0.9      0.049   12.6   0.9    1.4  1  Bmp         ABC transporter substrate-binding protein PnrA-li


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6  17.6   1.9e-22   1.2e-18       5     150 ..       8     145 ..       4     146 .. 0.91
   2 !   75.2  19.2   8.5e-25   5.1e-21       2     149 ..     181     318 ..     180     320 .] 0.83

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.9e-22
                 HHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHHHHHHBTTSSCECCHHH CS
    Na_Ca_ex   5 lfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlialigslkvdseslkldl 103
                  ++++l+l+ ++   +vs   ++ak+l+is  ++Glt++A g+s pEl++s+ aa + +++l +gn++Gsni n+++viG++a++++l + + ++ + +
  AJA91894.1   8 SVLAGLILLCIGGYAIVSGGVSLAKKLRISSMIIGLTVVAYGTSTPELAASLLAAFNSHTELILGNIVGSNISNVGMVIGISAIFTPLLISKITVSRWI 106
                 578999999999***************************************************************************999999988888 PP

                 HHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHHH CS
    Na_Ca_ex 104 gllllvallllllvlllllplfvpgrltvleglvllllYalylvlsl 150
                 ++++ v+ll+++  + +       g+++ ++g++l+++ + ++++ +
  AJA91894.1 107 PIMIGVSLLVVA--MSYD------GEISQVDGVILIAALIGFTAYTI 145
                 998888888833..4434......**************999999987 PP

  == domain 2  score: 75.2 bits;  conditional E-value: 8.5e-25
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHHHHHHBTTSSCECC CS
    Na_Ca_ex   2 lfvlfilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlialigslkvdseslk 100
                 +++l++++++++ ++ ++ v+ a +ia++lg+s+ v+G++++A+g+slpEli+siia++++++d+++gn++Gsni n+ll++G++  i +++v +  + 
  AJA91894.1 181 SIGLIVAGVIVLFIGGHLTVDGAVNIAETLGLSQLVIGVVIVAIGTSLPELITSIIAIAKKQTDIGVGNIVGSNIYNILLILGVSSAIVGIPVVPDVFS 279
                 57899*******************************************************************************999977555554432 PP

                 HHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHHHH CS
    Na_Ca_ex 101 ldlgllllvallllllvlllllplfvpgrltvleglvllllYalylvls 149
                 +   +   +++++l+l++ +      ++ + +++g+ l++++++yl+ +
  AJA91894.1 280 NYY-I---MIAFSLVLFIGF------RKYIPRVVGVGLAIAFVVYLASL 318
                 222.2...222222223333......48999999999999999999765 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.3e-05     0.075       5      46 ..     131     174 ..     131     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
  Spore_YhaL   5 vYlviagIlfSgymavktakeEreldqefIEk...EGevylerle 46 
                 v+l+ a I f +y ++kt k+ + + +e IE+   EGe +l r +
  AJA91894.1 131 VILIAALIGFTAY-TIKTVKKQKIQQNETIENealEGEYFLSRYK 174
                 6789999999999.69***************94445999999965 PP

>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   8.3e-06     0.049     183     278 ..     187     280 ..     181     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-06
                 CT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTTCCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-S--TCCHH CS
         Bmp 183 egvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylapenvitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgldeesdvled 278
                  gv v f   ++++ g+++ a+ lgls++vIgv       +    itsii   ++   + + ++++++   ++  ++lg+  ++vg+  ++dv+++
  AJA91894.1 187 AGVIVLFIGGHLTVDGAVNIAETLGLSQLVIGVVIVAIGTSLPELITSIIAIAKKQTDIGVGNIVGSN--IYNILLILGVSSAIVGIPVVPDVFSN 280
                 68888888999*********************************************************..9****************988888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2447.43
//
Query:       AJA91895.1  [L=164]
Description: ribosomal protein L16 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.1e-28   96.9   1.9    1.1e-27   96.7   1.9    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   1.9   5.9e-32   1.1e-27       5     128 ..      13     156 ..       6     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 5.9e-32
                    XXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXEEEEE-.....SS-TTTS CS
  Ribosomal_L16   5 kyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphhpvtkk.....agedRmg 83 
                    +y   r   i+g++  k+ k++ g+        ++L+++ek q+++ ale+ r+a+n+ l+k++g+   + ++rv+ph  ++++     ag+dR++
     AJA91895.1  13 PYANTR--HIKGKPqIKIAKFNSGNkkrqfeycVQLKINEKVQIRHMALESTRLAANKTLEKTTGEtgyNSRLRVYPHVRLRENktiaaAGADRLS 106
                    565556..78**********************99*****************************9999***************************** PP

                    SSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSX CS
  Ribosomal_L16  84 kGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpik 128
                    +G+    Gk +  ++r + gq+i+e+  ++ + e ak alr+a  Klp+ 
     AJA91895.1 107 EGMrrafGKANSLAVRARQGQVIMEMnVDEEHLEAAKSALRKACVKLPGT 156
                    **************************73335999**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1282.13
//
Query:       AJA91896.1  [L=307]
Description: autoinducer 2 aldolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-20   73.2   0.1    3.3e-20   72.7   0.1    1.2  1  DeoC      DeoC/LacD family aldolase
     0.0071   15.7   0.1      0.016   14.6   0.0    1.4  1  ThiG      Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.1   3.6e-24   3.3e-20       2     234 ..      21     228 ..      20     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 3.6e-24
                 EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEE CS
        DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvdevasveeakalGAdavkvv 100
                 ++lavD++  +++ +        edlk++++  l+ ++++ +++ g + + s+  +  ++++++++ gt ++ +   + d   s++ a++l   av + 
  AJA91896.1  21 LMLAVDHGYFLGPTEKL------EDLKKTIAP-LAKHCDSLMITRGAL-RTSVNPDYPVPVVLRVSGGTSIIGEDLSQEDITVSIKDAIRLNVSAVAMS 111
                 58999**9999999999......8******87.5679*******9976.567778888****************99999999***************** PP

                 EEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTE CS
        DeoC 101 vyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpg 198
                 v++   gs++e q + ++++   +++e+g+p+++  ++ ++      k d++    A r +ae Ga i+K+ +            e+f++v+k++pvp 
  AJA91896.1 112 VFV---GSKYEYQTIVNLGKLVNEAEEYGIPVLAVtAVGKEIG---TK-DARYLSLACRTAAEQGAHIVKTYFC-----------ENFEKVVKSCPVP- 191
                 ***...*************************999956666655...34.677*******************999...........9************. PP

                 EEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHHHHT CS
        DeoC 199 vvlsGGv..seedfletvedAvkeagasGvlsGRaifq 234
                 ++++GG    e+d l+   dA+ +aga Gv +GR+i+q
  AJA91896.1 192 IIIAGGKkiPEKDALKLTYDAL-KAGAVGVDMGRNIWQ 228
                 ******9999************.**************9 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.7e-06     0.016     165     239 ..     179     258 ..     175     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                 HHHHHHHHH-SS-BEEES---SHHHHH.....HHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH------ CS
        ThiG 165 ealkiiieeakvPvivDAGigspsdaa.....qamelGadavllntavaeakdpvamArafklaveaGrlaylagriekr 239
                 e+++ +++++ vP+i+  G   p++ a      a++ Ga +v +   + ++++pvam +a++  v+    a +a ++ k+
  AJA91896.1 179 ENFEKVVKSCPVPIIIAGGKKIPEKDAlkltyDALKAGAVGVDMGRNIWQSDNPVAMIKAVHSIVHGSNNAEQAFTLYKQ 258
                 5778899999*********99997644222226999*****************************999999998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1889  (0.10536); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2383.25
//
Query:       AJA91897.1  [L=108]
Description: putative methionine--tRNA ligase, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-23   81.9   0.0    2.9e-23   81.8   0.0    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   1.6e-27   2.9e-23       1      96 []      14     106 ..      14     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.6e-27
                 EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESSCEEEEEESST--TTCE CS
   tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldekevgilelpadveaGek 96 
                 lrv+k+++ e++p++ ++++ ++ +G+ee r+++ g +++y pe+l++k v+vvanl+pkk+ GveS++M+l+a+   +++   l++ +dv+aG+k
  AJA91897.1  14 LRVAKIVSTEKIPEKSRIIKGTISLGDEE-RDVIIGGAQFYDPEDLIGKTVIVVANLEPKKMAGVESNAMLLAAD--IDDKPFWLTVSDDVPAGTK 106
                 79***************************.*********************************************..79999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 768.79
//
Query:       AJA91898.1  [L=107]
Description: hypothetical protein T478_1253 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 813.11
//
Query:       AJA91899.1  [L=99]
Description: hypothetical protein T478_0084 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.3   0.1      0.014   15.1   0.0    1.6  2  DUF3990   Protein of unknown function (DUF3990)


Domain annotation for each model (and alignments):
>> DUF3990  Protein of unknown function (DUF3990)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.06   1.1e+03     104     123 ..       2      21 ..       1      35 [. 0.77
   2 !   15.1   0.0   7.6e-07     0.014      12      61 ..      32      80 ..      27      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.06
     DUF3990 104 vAddkvfstleaylegkisk 123
                 + d ++ + l++y++  i++
  AJA91899.1   2 ITDASTLKSLNDYISRRIQE 21 
                 56888999999999988876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.6e-07
     DUF3990 12 ekpdlsksrkkkDFGkGFYlteskeqAkewakrkskrkgkkevvnvyeld 61
                e+ ++ k+++++DF  G+Y+++++e   ++  +++ r ++  +v ++e++
  AJA91899.1 32 ETKKVWKCENELDFLYGYYVGKIEEATLHYLLKST-RASAGGYVDTFEIR 80
                6778999***********************99887.56666889999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 774.22
//
Query:       AJA91900.1  [L=190]
Description: pyruvate kinase, barrel domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-06   25.5   0.0    8.4e-06   25.1   0.0    1.1  1  HpcH_HpaI     HpcH/HpaI aldolase/citrate lyase family
    1.1e-05   24.6   0.1    1.1e-05   24.5   0.1    1.1  1  PK            Pyruvate kinase, barrel domain
  ------ inclusion threshold ------
      0.021   15.6   0.2      0.021   15.6   0.2    2.4  3  VAPB_antitox  Putative antitoxin
      0.081   11.4   0.7      0.095   11.2   0.7    1.1  1  PEPcase_2     Phosphoenolpyruvate carboxylase


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.9e-09   8.4e-06      89     199 ..      67     182 ..      56     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-09
                 EESS--SHHHHHHHHHHTSHTTTS---....HCCC-EEEEEE-SHHHHHTHHHHH.TST.TEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTH CS
   HpcH_HpaI  89 lvPkvetaeealevvsalrepekgirg....anketrllaqiEsaegvknaeeIa.ave.gldgvflGaeDlsadlgtkrspegtevldareriltaar 181
                 ++P +e++e+++       e  ++ +       +++ ++  iEs +gv+n++eI  a++ + ++v+l  +Dl  ++  k +++ +  +   ++++  + 
  AJA91900.1  67 MIPILENKENVKFFAVSNVESADDLKEflekVPDRISIVPKIESPNGVLNIDEICtALKsKEKVVMLDHDDLFSNILKK-KEDPESFQGYVKKLIEYCE 164
                 67777777777765444444444555566667799********************877646778899999999998544.4666677788999999999 PP

                 CEEEEEEE.E-SSHHHHH CS
   HpcH_HpaI 182 aagiaaldtvasdiddae 199
                 +++++ l tv +   d+e
  AJA91900.1 165 KNNVSLLRTVGVVFSDDE 182
                 999999999877666655 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.4e-09   1.1e-05     187     272 ..      74     165 ..      18     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-09
                 HCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTHHHHHHH....SSEEEEEHHHHHHHSTCCC.....HHHHHHHHHHHHHH CS
          PK 187 kqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenldeilea....sDgimvarGDlGieipaek.....vllvqkklikkcnl 272
                 k++v++ a+s v +a+D+ke    le+   +i i+ kie+ +gv n+dei  a      ++m+   Dl  +i ++k        + kkli+ c++
  AJA91900.1  74 KENVKFFAVSNVESADDLKE---FLEKVPDRISIVPKIESPNGVLNIDEICTAlkskEKVVMLDHDDLFSNILKKKedpesFQGYVKKLIEYCEK 165
                 679**************975...7899999********************765221135678888888776644321111144555666666655 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.7   7.7e+03      22      34 ..      30      42 ..      28      48 .. 0.59
   2 ?   -1.3   0.0      0.85   3.8e+03      49      49 ..      83      83 ..      55     101 .. 0.53
   3 ?   15.6   0.2   4.7e-06     0.021       7      53 ..     136     182 ..     129     190 .] 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
  VAPB_antitox 22 SFsdvIerLlekk 34
                  S s++ e+L++ +
    AJA91900.1 30 SISELEEKLTKNS 42
                  5566666666543 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.85
  VAPB_antitox 49 l 49
                   
    AJA91900.1 83 S 83
                  2 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 4.7e-06
  VAPB_antitox   7 devYekLkklKregeSFsdvIerLlekkkkgkkkellelfgil.seee 53 
                   d+      k K++ eSF   +++L+e+ +k+ +  ll+ +g++ s++e
    AJA91900.1 136 DDLFSNILKKKEDPESFQGYVKKLIEYCEKN-NVSLLRTVGVVfSDDE 182
                   7777888899***************977765.6689999999866665 PP

>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   2.1e-05     0.095      85     196 ..       8     127 ..       1     139 [. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                 ---TTTS-HHHHHHHHHHHHHHHHH.HHHHH..SS-S-SEEEESS--SH.HHHHHHHHHHHHHHH.............HHHHH-SS..---TTSSEEEE CS
   PEPcase_2  85 vPnpkvEkaerkvlaetlesipnsydlaekf.eetkpifevilPmttsa.eelievakyyekvvagkeelelad....lkvkelvg..elkpesievIP 175
                 + n ++  +e +vl + ++      +l+ek+ +++++ f + lP+ + +  +   + + +  + ++ke++++       + ++l++  e  p++i ++P
  AJA91900.1   8 ITNYDISTSEDSVLRINMAWCNSISELEEKLtKNSNSNFFIDLPIGRIKpPNNRYTLDEMIPILENKENVKFFAvsnvESADDLKEflEKVPDRISIVP 106
                 667777778888888888888877778888845888888888888653312333344444445555666555442122222333321134589****** PP

                 EE-SHHHHHTHHHHHHHHHHH CS
   PEPcase_2 176 LiEdkesllnideiveeyvke 196
                  iE  + +lnidei +++ ++
  AJA91900.1 107 KIESPNGVLNIDEICTALKSK 127
                 **************9988744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1424.84
//
Query:       AJA91901.1  [L=507]
Description: hypothetical protein T478_0078 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-79  266.7   2.9    1.9e-79  266.7   2.9    1.9  2  DPRP            Deoxyribodipyrimidine photo-lyase-related pro
     0.0012   18.9   0.1     0.0025   17.8   0.1    1.5  1  NYN_YacP        YacP-like NYN domain
  ------ inclusion threshold ------
       0.03   14.1   2.2      0.064   13.0   0.3    2.4  2  IF4E            Eukaryotic initiation factor 4E
       0.16   12.5   2.2        6.2    7.5   0.5    3.5  3  RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain


Domain annotation for each model (and alignments):
>> DPRP  Deoxyribodipyrimidine photo-lyase-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.7   2.9   4.2e-83   1.9e-79       2     223 .]       7     228 ..       6     228 .. 0.98
   2 ?   -1.7   0.8      0.49   2.2e+03     172     188 ..     459     475 ..     458     501 .. 0.72

  Alignments for each domain:
  == domain 1  score: 266.7 bits;  conditional E-value: 4.2e-83
                 E--TT---TT-HHHCT--TTT-EEEEE--HCCCCSTTS-HHHHHHHHHHHHHHHHHHHHTT-EEEEE-TT-TT--SHHHHHHHHHHHH--SEEEEE--S CS
        DPRP   2 lilgdqLskehsalkeadkkedrvlliEsaqeatyvrhHkqKlvlifaaMrhFaeeLrekgvevtylelddkenesleeelealleelkieelevtepd 100
                 +il dqLsk++s+lk+++k++d++l++E+a+ea+yv+hHk+Klvl+f+aMrhFa+++++kg+++ y ++ ++++ ++++el++++++ k++++++t+p+
  AJA91901.1   7 VILADQLSKDISSLKNFRKDKDKILMMEVANEARYVNHHKKKLVLVFSAMRHFAKDMKSKGYSIIYSKIGESQD-NFTQELAHQCKKIKPKKIVITHPG 104
                 79********************************************************************7654.8*********************** PP

                 SHHHHHHHHCHHHHCTSEEEEE--TTSSS-HHHHHHHHCC-SS--HHHHHHHHHHHHTTTEETTE.EGGGSS--GGGS-------.TTS---------H CS
        DPRP 101 dkrleqrleelaeklelevevledehFltsreefkewakgrkklrmedFYremRkrlgiLmdedgkPvGGkWnfDaeNRkklpkk.levpkplrfepda 198
                 ++r++q+++++ + l+++ve+ ed++F+++ +efk+w +g+k+lrme+FY++mRk+++iL+d+dgkP GGkWn+D +NRk+lpk+ +++pkpl+ +pd+
  AJA91901.1 105 EYRVLQEIKKWEKMLNISVEISEDDRFFCTITEFKKWTEGKKELRMESFYHMMRKKYNILIDKDGKPKGGKWNYDIKNRKSLPKNhPDIPKPLQHKPDD 203
                 ***********999**********************************************************************999************ PP

                 HHHHHHHHHHHH-TTSSS--TT--- CS
        DPRP 199 itkevielvekrfadtfGsleefrw 223
                 it++vi++++krf+++fG+le+f++
  AJA91901.1 204 ITTQVIAEIKKRFSKHFGDLEPFWF 228
                 **********************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.49
                 S--GGGS-------TTS CS
        DPRP 172 WnfDaeNRkklpkklev 188
                 Wnf  +N+kkl+k++++
  AJA91901.1 459 WNFFLKNQKKLEKNPRL 475
                 99999999999999655 PP

>> NYN_YacP  YacP-like NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.6e-07    0.0025      36     101 ..      39     101 ..      11     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.6e-07
                 HHHHHHH--EEEEEE-TTTS---TT----T.T-EEEE--TT--HHHHHHHHHHHC--TT--EEEE- CS
    NYN_YacP  36 anyqsfkgyevivVFDAqkvkgseeeeekaeglevvytkegetADsvIeklvaelrkekeevvVvT 101
                 a+y ++++ ++++VF A+++  ++ +    +g +++y+k ge+ D++ ++l+++ +k k + +V+T
  AJA91901.1  39 ARYVNHHKKKLVLVFSAMRHFAKDMKS---KGYSIIYSKIGESQDNFTQELAHQCKKIKPKKIVIT 101
                 579999***********9988866666...667************************997777777 PP

>> IF4E  Eukaryotic initiation factor 4E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.4e-05     0.064      16      87 ..     110     185 ..      95     198 .. 0.83
   2 ?   -1.3   0.1      0.37   1.7e+03      33      52 ..     471     490 ..     439     499 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                 --SS-SGGG-EEEEEEEEHHHHHHHHHHS--....GGGB-SSEEEEEEETT--SSTTSHHHHS-EEEEEEE----- CS
        IF4E  16 sksenyeeslkkvatfstveeFwslynnlkk....psklkvksdyhlFkkgikPmWEdpankkGGkwvirlkkkek 87 
                 ++ +++e+ l+  +++s+ + F+ + +++kk     ++l+++s yh+++k+ +   + +   kGGkw + +k+++ 
  AJA91901.1 110 QEIKKWEKMLNISVEISEDDRFFCTITEFKKwtegKKELRMESFYHMMRKKYNILIDKDGKPKGGKWNYDIKNRKS 185
                 46788999999999999999998886666662222578999*****************************988554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.37
                 EHHHHHHHHHHS--GGGB-S CS
        IF4E  33 tveeFwslynnlkkpsklkv 52 
                 +   +w++++nlkk+sk ++
  AJA91901.1 471 KNPRLWTVFSNLKKMSKERK 490
                 44567888888888877554 PP

>> RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0014       6.2       8      59 ..      53     113 ..      46     163 .. 0.80
   2 ?   -0.3   0.0      0.36   1.6e+03      23      43 ..     228     248 ..     227     305 .. 0.68
   3 ?    1.9   0.0     0.076   3.4e+02       5      30 ..     473     498 ..     470     503 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0014
                     HHHHCCCCCCCCCCCEE--CCCCT--CHHHHCCSB-SSSSB-GCCT-EEEE.........S CS
  RNA_pol_Rpb5_N   8 frirrTvleMlkdRgYlvaeeelnisleeFkekygdepkevdrekltisas.........k 59 
                     f ++r  ++ +k  gY +  +++ +s ++F+++ +++ k+++ +k++i+           k
      AJA91901.1  53 FSAMRHFAKDMKSKGYSIIYSKIGESQDNFTQELAHQCKKIKPKKIVITHPgeyrvlqeiK 113
                     6677777777999**************************9999999987765555555554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.36
                     EE--CCCCT--CHHHHCCSB- CS
  RNA_pol_Rpb5_N  23 YlvaeeelnisleeFkekygd 43 
                     + v++e+ + sl++F ++  d
      AJA91901.1 228 FAVTHEQAKKSLDDFIKNRLD 248
                     578999999999999887655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.076
                     HHHHHHHCCCCCCCCCCCEE--CCCC CS
  RNA_pol_Rpb5_N   5 krlfrirrTvleMlkdRgYlvaeeel 30 
                      rl+ +   + +M k+R+ +++++  
      AJA91901.1 473 PRLWTVFSNLKKMSKERKKEIENDSK 498
                     59***************988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3553.82
//
Query:       AJA91902.1  [L=191]
Description: hypothetical protein T478_1459 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1502.83
//
Query:       AJA91903.1  [L=285]
Description: putative carboxyvinyl-carboxyphosphonate phosphorylmutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-51  175.2   0.0    1.7e-51  175.0   0.0    1.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    2.8e-13   49.2   0.1    4.1e-13   48.7   0.1    1.2  1  ICL         Isocitrate lyase family
  ------ inclusion threshold ------
      0.038   12.7   0.1      0.055   12.2   0.1    1.3  1  Glycolytic  Fructose-bisphosphate aldolase class-I


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.0   0.0   2.9e-55   1.7e-51       1     227 [.       4     237 ..       4     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 175.0 bits;  conditional E-value: 2.9e-55
  PEP_mutase   1 lra.LhakgeplvlpnawDalsakiveeagfkalatsSlavaasl.GvpDgeelpleellaavraiaevvslPlivDledGygespeevaetvrrliaa 97 
                 lr+ +++k++plv+p ++Da++aki+++ gf+a+  ++++++a+l G+pD   + l+e+ +++r+ia+++s+PlivD+++Gyg+ + +v++  + l  a
  AJA91903.1   4 LRKlINDKSKPLVVPGVYDAIGAKIAQKVGFEAMFQTGYGTSATLlGMPDYGFIGLSETTDNARRIANAISVPLIVDVDTGYGN-ALTVKKLLQDLQVA 101
                 5676788999******************************998888**************************************.88************ PP

  PEP_mutase  98 GvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagagleeaieRaraYaeAGAdgvfvpglqkdaeiaelvaav 191
                 Gv+g+ +ED+    +++  +++++++ ee  ek+aaa++a+++++f+i+ARtda    a +gl+eaieR++ Y++ GAd +fv   ++ +e++++ + +
  AJA91903.1 102 GVSGIFLEDQkwpkRCGHmKGKEVVQKEEYGEKLAAAVDAKQDKDFIIVARTDAR---ATEGLDEAIERGKYYKKIGADLIFVEAPKSIEEMKKIGKSI 197
                 **********887533445888888*****************************3...6899************************************* PP

  PEP_mutase 192 dvplnvvp.lkgt...lsvaelaelGvarislgnhllraa 227
                 ++pl++ + ++g+    s+a+l+++G++++ +  ++l a 
  AJA91903.1 198 NAPLVANMiEGGAtpiSSTATLHKMGFQLVLYPLSILYAN 237
                 *****9996644348899************9987665544 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.1   6.8e-17   4.1e-13     149     254 ..      74     176 ..      59     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 6.8e-17
                 ---EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE--GGGEEEES-TT-GGG CS
         ICL 149 lrpiiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvartdseaatlitstidtrd 247
                   p+i d dtG+G   +v kl + +   G +Gi +edq    k+cGhm Gk +v  +e+ ++l a+  +    + d ++vartd+ a+  +  +i++  
  AJA91903.1  74 SVPLIVDVDTGYGNALTVKKLLQDLQVAGVSGIFLEDQK-WPKRCGHMKGKEVVQKEEYGEKLAAAVDAK--QDKDFIIVARTDARATEGLDEAIERGK 169
                 469******************9999999**********7.579*******************98753322..468*************99999999887 PP

                 GGGEEEE CS
         ICL 248 hafilGa 254
                 ++  +Ga
  AJA91903.1 170 YYKKIGA 176
                 7777776 PP

>> Glycolytic  Fructose-bisphosphate aldolase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   9.2e-06     0.055      86     131 ..     134     178 ..      83     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.2e-06
                 HTT-EEEEE----EEE-TTSSS-EEE---TTHHHHHHHHHHTT--E CS
  Glycolytic  86 ekgiipGiKvdkgvvplagtegetttqGldglaercaqykkdGarF 131
                 +    ++ K dk+++ +a+t +  +t+Gld+  er + ykk Ga+ 
  AJA91903.1 134 KLAAAVDAKQDKDFIIVART-DARATEGLDEAIERGKYYKKIGADL 178
                 4456688999****999999.6899******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2099.83
//
Query:       AJA91904.1  [L=65]
Description: hypothetical protein T478_0905 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 455.58
//
Query:       AJA91905.1  [L=363]
Description: PF06849 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-74  247.5   0.2    1.2e-73  246.6   0.2    1.4  1  DUF1297   Domain of unknown function (DUF1297)
    2.6e-46  156.6   0.0    4.8e-46  155.7   0.0    1.5  1  DUF1246   Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.2   1.4e-77   1.2e-73       1     188 []     177     363 .]     177     363 .] 0.98

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 1.4e-77
                 HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEEEEEEEE-GGGHHHHH CS
     DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvGnipvvlREsllekvf 99 
                 +++ek+ee ++kg+i ++dl+kasiee+ +G+++n+n+f++p++++v+++gi+rR+++n+++++ lpak+qle+++  ++++vG++p+ +REsllekvf
  AJA91905.1 177 DYKEKSEEKIKKGIIARKDLEKASIEELAIGTYLNFNFFHTPISDQVDFIGIERRLQTNIHDYNALPAKQQLEMDIPLQNIEVGHTPASIRESLLEKVF 275
                 89************************************************************************************************* PP

                 HHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
     DUF1297 100 elgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                 ++g+kfv+a+kk+++pGiiGpF+Lqsv+tkdle++v+dvs R++g++  +++ +spy+k+++g+++ +Grria+Eik+a+e+d++++ivt
  AJA91905.1 276 KMGDKFVRAVKKEYAPGIIGPFSLQSVITKDLEMIVYDVSLRVPGNP--IVAtTSPYTKYQYGTTFGIGRRIAMEIKRAVEEDKIKDIVT 363
                 *********************************************54..44449***********************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.7   0.0   5.4e-50   4.8e-46       1     122 []      19     144 ..      19     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 5.4e-50
                 EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTT.TT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHH.C-SS-EES-TTH CS
     DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekf.kvidevivldkfkdilkeevqeklreenailvPhgsfveYvgiekie.elkvpifGnrkl 97 
                 i++l+SHsal+i++gAk+e+f+t++ c+kgre +Y++f +++de+ +++kfkd+++  +q+ +re+n+i+vPh+s+++Y+g++ +e +lkvpifGnrkl
  AJA91905.1  19 IGVLGSHSALEIMDGAKDEDFETVVYCQKGREVPYQRFnRIADEIKIVKKFKDMASPANQKLMRENNTIIVPHRSLTAYLGYDILEnKLKVPIFGNRKL 117
                 89************************************7788********************************************************* PP

                 HHHHCSHHHHHHH..HHHTT-BB--BE CS
     DUF1246  98 lrwEerrekkrky..LekAgiriPkki 122
                 +++Eer++k+++y  L+kAg+++Pk++
  AJA91905.1 118 FQAEERENKRNQYylLKKAGVKYPKIF 144
                 *********999999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2636.63
//
Query:       AJA91906.1  [L=220]
Description: 3-dehydroquinate dehydratase, type I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-53  182.1   0.0    2.2e-53  181.9   0.0    1.0  1  DHquinase_I     Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.081   13.6   0.7       0.33   11.6   0.3    2.0  2  Gly_transf_sug  Glycosyltransferase sugar-binding region cont
      0.087   13.2   1.1        1.3    9.5   0.8    2.5  2  NOP5NT          NOP5NT (NUC127) domain


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.0   3.7e-57   2.2e-53       1     227 [.       6     217 ..       6     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 3.7e-57
                  EEEE--SSHHHHHHHHHHHTTS-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEEEEEGG CS
  DHquinase_I   1 cvpitgktleeilaelesgkekaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyvDvElt 98 
                  cv+i +k+ +++  +l+++ +k+D++E+R D+lk++ +   +   le  ++ +   +++tlr+k+egg f  ++e+e+ ++lr ++e ++ ++DvE+ 
   AJA91906.1   6 CVSIGEKNPKKLKIILKKALSKSDFAEIRFDYLKKS-D---IPIVLESSKK-NLSRCVCTLRPKSEGGLF-IGKEDERKSILRLIAEYNPFLLDVEF- 96 
                  9******************99************765.3...4444444444.4557**************.8*************************. PP

                  -.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHHT-SS-EEEEE-TTTTGHHHCH CS
  DHquinase_I  99 eapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseakeekdeaplIamamGelGkiSRil 196
                  ++++ + k+l++  +++++k+ +S+hdf++tp + +lk++++km+++  +ivKi+++ak+ +D  rllsl+ ++k++    +++a++mG++Gk+SRil
   AJA91906.1  97 NTIQ-KDKNLASYLKKSKCKLLISWHDFKKTPNESQLKSRFKKMEKFS-NIVKIVTVAKNVSDASRLLSLY-SVKSK---NKMVAFCMGDQGKFSRIL 188
                  5565.5559***************************************.*********************9.56664...8***************** PP

                  HHHHTB-EEEEESSS-..SSTT-EEHHHHHH CS
  DHquinase_I 197 gevfGspvtfasleeakasapGqltarelre 227
                  ++ +Gsp+t+ sl++a   apGq++++e+++
   AJA91906.1 189 CLHLGSPFTYVSLGKA--IAPGQFSVDEIKS 217
                  ************9988..**********986 PP

>> Gly_transf_sug  Glycosyltransferase sugar-binding region containing DXD motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.25   1.5e+03      13      49 ..      11      48 ..       3      62 .. 0.72
   2 ?   11.6   0.3   5.5e-05      0.33       8      71 ..     105     166 ..      78     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
  Gly_transf_sug 13 kahpdyqvvvlskelekvrvaildlefllsd.tpwfee 49
                    +++p++  ++l+k l+k   a + +++l+++  p+++e
      AJA91906.1 11 EKNPKKLKIILKKALSKSDFAEIRFDYLKKSdIPIVLE 48
                    67888888888888888888888888888775664444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.5e-05
  Gly_transf_sug   8 ieslakahpdyqvvvlskelekvrvaildlefllsd.tp..wfeeakkllplfialsDllRlaiLyk 71 
                     + s +k+++ + ++++ +  +    ++++ ++l+s  ++  +f+++ k  ++  + sD++Rl+ Ly 
      AJA91906.1 105 LASYLKKSKCKLLISWHDF-K----KTPNESQLKSRfKKmeKFSNIVKIVTVAKNVSDASRLLSLYS 166
                     4555666666667777664.3....355555555554334489999999****************95 PP

>> NOP5NT  NOP5NT (NUC127) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8   0.00021       1.3      12      48 ..     117     153 ..     109     161 .. 0.87
   2 ?    1.2   0.0      0.08   4.8e+02      16      50 ..     168     197 ..     155     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
      NOP5NT  12 LfkvkdkkllkkddlvkdsvsdlekfsklvkLkaFqk 48 
                 L + +d+k++ +++  k  ++++ekfs++vk++  +k
  AJA91906.1 117 LISWHDFKKTPNESQLKSRFKKMEKFSNIVKIVTVAK 153
                 5566888999999999999************998766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.08
      NOP5NT  16 kdkkllkkddlvkdsvsdlekfsklvkLkaFqkFe 50 
                 k k++     +v+  + d  kfs ++ L+  ++F+
  AJA91906.1 168 KSKNK-----MVAFCMGDQGKFSRILCLHLGSPFT 197
                 33333.....46666889999*****999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1655.08
//
Query:       AJA91907.1  [L=248]
Description: ribosomal protein S3 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-20   73.1   0.4    4.4e-20   72.0   0.4    1.6  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    1.4e-13   50.4   0.1      4e-13   49.0   0.1    1.8  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.071   12.9   2.2        2.1    8.2   0.1    3.2  3  KH_1            KH domain
       0.35   11.8   2.9        1.5    9.8   1.3    2.5  3  CSN5_C          Cop9 signalosome subunit 5 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.4   9.8e-24   4.4e-20       2      83 .]     100     182 ..      99     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 9.8e-24
                     HHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEEEEEE CS
  Ribosomal_S3_C   2 aeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGvkVwI 83 
                     a++le++++fRra++ +i+++m+ ga G++i++sG+L+ ++++  ek+++G +p   h ++  + + +a+++t +G iGv+++I
      AJA91907.1 100 ASHLERGTAFRRATMWTIQQIMEGGAMGVEITISGKLR-GDRSAFEKHSQGILPRagHHADVIVSEDIAHVETPMGLIGVRIRI 182
                     899***********************************.9***************99999999*******************98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.1     9e-17     4e-13       4      78 .]      19      90 ..      16      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 9e-17
                HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTGG CS
        KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpel 78
                 +l  +ik+ag s+ e+ +t+ ++++v+++ +pgivIG++G  ik ++++l+ d++ l++ ++   +++++kpel
  AJA91907.1 19 DYLRSKIKDAGFSNAEVSKTPTGTRVVLHVTRPGIVIGRKGTGIKDLTEKLESDFG-LKNPQIA--VEEITKPEL 90
                688999*************************************************8.9999999..899999985 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00047       2.1      12      28 ..      52      68 ..      42      71 .. 0.84
   2 ?    0.2   0.0      0.15   6.9e+02      21      36 ..     116     133 ..     115     146 .. 0.63
   3 ?    1.8   0.1     0.047   2.1e+02      30      61 ..     177     220 ..     175     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00047
                HHHHTGGGHHHHHHHHH CS
        KH_1 12 griIGkgGsnIkeIree 28
                g +IG++G  Ik++ e+
  AJA91907.1 52 GIVIGRKGTGIKDLTEK 68
                89***********9985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                 HHHHHHH.HH.T-EEEEE CS
        KH_1  21 nIkeIre.et.gakIkvp 36 
                 +I++I+e    g+ I++ 
  AJA91907.1 116 TIQQIMEgGAmGVEITIS 133
                 577777733446666654 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.047
                 T-EEEEES.STT...............T.-EEEEEE.SHHHHHHHH CS
        KH_1  30 gakIkvpk.sedeg............sderevtisG.speavekAk 61 
                 g++I++ k ++               ++++e++i+    ea +kA+
  AJA91907.1 177 GVRIRIAKkEK--LipefemkgktqaQKDEEIRIKKeADEALAKAQ 220
                 56666552121..123555666888899999999876666677776 PP

>> CSN5_C  Cop9 signalosome subunit 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         4   1.8e+04      10      18 ..      19      27 ..      16      36 .. 0.74
   2 ?    0.2   0.0      0.33   1.5e+03      16      25 ..      62      71 ..      59      79 .. 0.89
   3 ?    9.8   1.3   0.00034       1.5      41      75 ..     197     231 ..     176     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
      CSN5_C 10 dYatkqisD 18
                dY  ++i+D
  AJA91907.1 19 DYLRSKIKD 27
                666666666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.33
      CSN5_C 16 isDLaeKlek 25
                i+DL+eKle 
  AJA91907.1 62 IKDLTEKLES 71
                99******85 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00034
      CSN5_C  41 seeaseaeekkk....kkkedsqLakvvkdstkiaseaq 75 
                 +++a++     +    kk+ d++Lak+  +s+ i++e++
  AJA91907.1 197 KTQAQKD----EeiriKKEADEALAKAQSESEIIKIEEE 231
                 2222233....23456********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1774.30
//
Query:       AJA91908.1  [L=305]
Description: elongation factor Tu domain 2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-09   36.4   0.1    1.1e-08   35.3   0.1    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   6.3e-13   1.1e-08       1      73 [.     153     219 ..     153     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.3e-13
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  Gtvalg+v sG++   d++     ++   ei   ++s++++  d++e v  a++G+ ++ ++ ++ i +Gd+l
   AJA91908.1 153 GTVALGKVLSGKITQYDKINH--YPS---EIEAMVKSIQMHDDDVKESVSPARVGLSLKNIKHDE-ITRGDVL 219
                  9********************..777...889*********************************.******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2337.02
//
Query:       AJA91909.1  [L=490]
Description: type II/IV secretion system protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-14   51.7   0.0    8.7e-14   51.2   0.0    1.1  1  T2SSE            Type II/IV secretion system protein
    2.2e-06   27.4   0.1    7.5e-06   25.7   0.0    2.0  1  KH_1             KH domain
     0.0003   21.2   0.0    0.00053   20.4   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0023   17.2   0.0     0.0037   16.5   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.004   16.9   0.0     0.0098   15.6   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0051   16.1   0.1       0.02   14.2   0.1    1.8  2  Zeta_toxin       Zeta toxin
     0.0055   15.7   0.0     0.0088   15.0   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0061   17.1   0.0      0.017   15.7   0.0    1.8  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.049   13.5   0.0    2.0  2  NTPase_1         NTPase
      0.014   15.4   0.0      0.031   14.3   0.0    1.6  1  AAA_14           AAA domain
       0.03   14.1   0.0      0.086   12.7   0.0    1.7  1  KH_2             KH domain
      0.031   14.5   0.0      0.054   13.7   0.0    1.5  1  AAA_28           AAA domain
      0.034   13.9   0.0       0.06   13.1   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.035   14.1   0.0      0.062   13.3   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.052   14.1   0.0       0.11   13.0   0.0    1.6  1  ABC_tran         ABC transporter
      0.061   13.7   0.0       0.15   12.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
      0.064   13.0   0.0      0.097   12.4   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.081   12.8   0.0       0.14   12.1   0.0    1.4  1  NACHT            NACHT domain
      0.097   12.4   0.0        0.2   11.4   0.0    1.4  1  AAA_30           AAA domain
      0.099   12.1   0.0       0.19   11.1   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
       0.11   12.4   1.9       0.13   12.2   0.0    2.1  1  KH_4             KH domain
       0.12   12.1   0.0       0.23   11.2   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.14   12.4   0.0       0.32   11.3   0.0    1.6  1  AAA_22           AAA domain
       0.17   12.0   0.0       0.42   10.8   0.0    1.6  1  AAA_33           AAA domain
       0.22   11.4   0.0       0.35   10.7   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
       0.22   11.1   0.0       0.38   10.3   0.0    1.3  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   1.3e-16   8.7e-14      36     243 ..      56     255 ..      24     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.3e-16
       T2SSE  36 lreveelekaalerlisriaalak.ldiseerplqdarlp..ekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrergl 131
                   + ++l+++ le ++++i ++   +++ + ++   ++l    + +r+ +  +P ++  +++i  +  k+++l+d++ +e+l  +    l++       
  AJA91909.1  56 ELDTKTLHRDYLEIITNQILSAIDdETLGNTEISKPGALViqYRDYRIAITRPPFSELLEITIV-HPIKQMSLEDYQLSEKLMSR----LETQ---AEG 146
                 4566788899999999998776651567788888889988778999999999**9999999997.667889*****988766554....4445...588 PP

       T2SSE 132 ilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleg.a.nqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgs 227
                 il+sG+ gsGK+tl+  + +++n s + + t E p+ +q++  + ++++l     +  f++    +L  rPD  +  E+R +e ++i      TG    
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGKIVKTFESPRDLQVDSgVtQYTRL-----DGSFENSADILLLVRPDYTIFDEVRRREDFRIfSDLRLTGVGM- 239
                 9************************88888*********95413133333.....4569999999999*******************77788899777. PP

       T2SSE 228 lsTlHansaagalerL 243
                 ++ +Han++++a++r 
  AJA91909.1 240 VGVVHANTPIDAIQRF 255
                 9*************96 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.1e-08   7.5e-06       2      38 ..     370     407 ..     369     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-08
                 EEEEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEES.S CS
        KH_1   2 lrilvPsslvgriIGkgGsnIkeIreet.gakIkvpk.s 38 
                 +++ v  + ++++IGk G++I+e+++ + g +I+v++ +
  AJA91909.1 370 IKVFVSGDSIPALIGKAGKTIQELEK-SlGLHIDVEEhG 407
                 5789999*******************.77*****98633 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   7.7e-07   0.00053      16      63 ..     137     184 ..     128     262 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7.7e-07
      AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                 ++r+ + + e +l+sG++G+GKs+l+  +++ ++++g i+ + +  ++l
  AJA91909.1 137 MSRLET-QAEGILISGAPGSGKSTLASGIANFFNRSGKIVkTFESPRDL 184
                 344443.4489*******************9999997555455555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.4e-06    0.0037       7      53 ..     131     180 ..     128     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.4e-06
                 HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC...SHCCCCCCBTE CS
      NB-ARC   7 kviekLlekdelqslvvalvGmgGvGKttlakqiln...ksdevegrFds 53 
                 ++ ekL+   e q   + ++G +G+GK+tla+ i n    s ++ ++F+s
  AJA91909.1 131 QLSEKLMSRLETQAEGILISGAPGSGKSTLASGIANffnRSGKIVKTFES 180
                 5789999999999999***************9886500044455556665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-05    0.0098      18      39 ..     141     161 ..     128     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
      AAA_29  18 eidlkgatlltGpsGsGKSTll 39 
                 e + +g +l++G+ GsGKSTl 
  AJA91909.1 141 ETQAEG-ILISGAPGSGKSTLA 161
                 555566.*************95 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.7   1.2e+03      75     123 ..      54     102 ..      46     106 .. 0.66
   2 !   14.2   0.1   2.9e-05      0.02      19      47 ..     147     175 ..     133     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
  Zeta_toxin  75 ltqkdaselvekllqeaiengyniivegtlrspdvvkklaealkkaGYe 123
                 l++ d+++l +  l+ ++++  + i + tl +++  k  a  ++ + Y+
  AJA91909.1  54 LVELDTKTLHRDYLEIITNQILSAIDDETLGNTEISKPGALVIQYRDYR 102
                 5666667777777777777777777777777777766655555555555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
  Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvv 47 
                 il++G+pG+GKs+la+ +++ ++r g++v
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGKIV 175
                 89*****************9999888887 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05    0.0088      17      60 ..     131     175 ..     115     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                 HHHHHHGGG.-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--E CS
        MeaB  17 ellerllak.aGraqvvGltGvPGaGkstlvealglelrrrGkrv 60 
                 +l e+l+++   +a+ + + G PG+Gkstl + ++  + r Gk v
  AJA91909.1 131 QLSEKLMSRlETQAEGILISGAPGSGKSTLASGIANFFNRSGKIV 175
                 444444444134688999***********************9977 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05     0.017       1      21 [.     147     167 ..     147     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
      AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                 Il++G+pG+GK+tla  +++ 
  AJA91909.1 147 ILISGAPGSGKSTLASGIANF 167
                 99*************998654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.2e-05     0.049       2      35 ..     147     180 ..     146     189 .. 0.90
   2 ?   -2.6   0.0       6.6   4.6e+03     137     153 ..     213     229 ..     201     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-05
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35 
                 ++i+G pG+GK+Tl + +++  ++sg  v+ f  
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGKIVKTFES 180
                 79***********************999987765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                 -SHHHHHHHT-TT-EEE CS
    NTPase_1 137 dlalveeirerkdvkvf 153
                 d  + +e+r+r+d+++f
  AJA91909.1 213 DYTIFDEVRRREDFRIF 229
                 45789999999999998 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.5e-05     0.031       5      80 ..     147     227 ..     143     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla....dpekllelileklke....ekktylflDEiqevpewe 80 
                 ++i+Ga  +GK+tl+  ++ + + +++  +  +++++rd + +    ++++l+  + +++ +     +  y ++DE+ + ++++
  AJA91909.1 147 ILISGAPGSGKSTLASGIA-NFF-NRSGKIVKTFESPRDLQVDsgvtQYTRLDGSFENSA-DilllVRPDYTIFDEVRRREDFR 227
                 789***********99998.555.788888999******665522223334555555542.146666889*******9998876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.086      25      60 ..     368     403 ..     348     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                 CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHH CS
        KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdiek 60 
                  r+++++       +IGk G++i++++k l+  i++
  AJA91909.1 368 GRIKVFVSGDSIPALIGKAGKTIQELEKSLGLHIDV 403
                 67888888889999****************998864 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.8e-05     0.054       2      21 ..     147     166 ..     146     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-05
      AAA_28   2 ivitGgestGKTtlleaLaa 21 
                 i i+G++++GK+tl++ +a+
  AJA91909.1 147 ILISGAPGSGKSTLASGIAN 166
                 78*************99985 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.7e-05      0.06      45     116 ..     142     219 ..     123     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-05
   IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvl.fvrvedLvee...lkrarrdgklaralkr..llkvdllilDd 116
                 +++e+i++ G +G GKs la  ++    r+g+ v  f + +dL       +  r dg++++ ++   l+++d  i D+
  AJA91909.1 142 TQAEGILISGAPGSGKSTLASGIANFFNRSGKIVKtFESPRDLQVDsgvTQYTRLDGSFENSADIllLVRPDYTIFDE 219
                 6789*********************99999998852666666654312134556666666655541134556666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.1e-05     0.062       2      31 ..     147     176 ..     146     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-05
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvq 31 
                 +l+ G+pG+gKs+la  +a ++nr+  +v 
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGKIVK 176
                 7899******************99877765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00016      0.11      12      42 ..     145     174 ..     140     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGei 42 
                 e + i G  G+GKStL++ +a+  +  +G+i
  AJA91909.1 145 EGILISGAPGSGKSTLASGIANFFN-RSGKI 174
                 567899***************9997.68888 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.15       1      23 [.     147     169 ..     147     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                 EEEESSTTSSHHHHHHHHHHHHT CS
         AAA   1 vllyGppGtGKTllakavakelg 23 
                 +l++G pG GK++la+ +a+ ++
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFN 169
                 699****************9765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.097       1      21 [.     147     167 ..     147     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
  Viral_helicase1   1 ivvhGvpGcGKStlirkllrt 21 
                      i+++G+pG+GKStl   +++ 
       AJA91909.1 147 ILISGAPGSGKSTLASGIANF 167
                      689**********98888877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.14       3      22 ..     147     166 ..     145     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                 EEEEC-TTTCHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklal 22 
                 +++ G++GsGK+tL+ ++a 
  AJA91909.1 147 ILISGAPGSGKSTLASGIAN 166
                 789**************996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028       0.2      20      49 ..     146     175 ..     133     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
      AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                   ++ G++G+GK+t+ +++++ ++++g+ v
  AJA91909.1 146 GILISGAPGSGKSTLASGIANFFNRSGKIV 175
                 5789******************99998655 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.19       4      33 ..     147     176 ..     146     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                 EEEE--TTSSHHHHHHHHHHHHHHTT--EE CS
       KTI12   4 vvltGlPssGKstrakeLakaleeekrsvv 33 
                 ++++G P sGKst+a+ +a+ ++ +++ v 
  AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGKIVK 176
                 79******************9999887665 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.13      29      52 ..     368     391 ..     347     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
        KH_4  29 veielnvegedlGrvIGkrGrtld 52 
                  +i++ v+g+ +  +IGk G+t++
  AJA91909.1 368 GRIKVFVSGDSIPALIGKAGKTIQ 391
                 689*******************97 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.23      31      60 ..     142     171 ..     124     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
      RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvk 60 
                 ++ + +l++G+PG Gk+tla+ ia+ ++ +
  AJA91909.1 142 TQAEGILISGAPGSGKSTLASGIANFFNRS 171
                 566789*****************9977665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00047      0.32       5      31 ..     144     170 ..     140     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
      AAA_22   5 agilvvtGesGtGKTtllrrlleqlde 31 
                 a  +++ G +G+GK+tl+  +++ +++
  AJA91909.1 144 AEGILISGAPGSGKSTLASGIANFFNR 170
                 55689*************998888754 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00061      0.42       2      20 ..     147     165 ..     147     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00061
      AAA_33   2 vllvGlpGsGKstlaerll 20 
                 +l+ G+pGsGKstla +++
  AJA91909.1 147 ILISGAPGSGKSTLASGIA 165
                 5788***********8765 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00051      0.35       6      32 ..     147     173 ..     142     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
  Ploopntkinase3   6 iylvGqPGaGkstlmaeltkgfdrskv 32 
                     i + G+PG+Gkstl + +++ f+rs  
      AJA91909.1 147 ILISGAPGSGKSTLASGIANFFNRSGK 173
                     7789****************9999854 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00055      0.38      34      54 ..     145     165 ..     133     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
      AAA_25  34 elallaGapgtGKttlaldla 54 
                 e +l+ Gapg+GK+tla+ +a
  AJA91909.1 145 EGILISGAPGSGKSTLASGIA 165
                 55799************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3739.53
//
Query:       AJA91910.1  [L=68]
Description: hypothetical protein T478_1375 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.23   11.8   2.3       0.32   11.3   2.3    1.3  1  Nodulin_late  Late nodulin protein


Domain annotation for each model (and alignments):
>> Nodulin_late  Late nodulin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.3   1.8e-05      0.32      26      51 ..      23      47 ..      11      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
  Nodulin_late 26 akieCktdadCpkkcpkpykvkCing 51
                     +C++++ C+k  +  ++ kC+n+
    AJA91910.1 23 LDNPCVDNDQCEKR-QEAEEQKCFNE 47
                  468***********.7779****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 535.44
//
Query:       AJA91911.1  [L=118]
Description: ribonuclease HI [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.9e-11   41.7   0.0    1.1e-10   41.4   0.0    1.1  1  RVT_3      Reverse transcriptase-like
    2.2e-10   40.9   0.0    2.3e-10   40.8   0.0    1.1  1  RNase_H    RNase H
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.037   13.8   0.0    1.1  1  HAD_SAK_1  HAD domain family 1 in Swiss Army Knife RNA repair


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   1.8e-14   1.1e-10      35     115 ..      32     111 ..      20     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.8e-14
       RVT_3  35 qgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirkllksfesvsvehipReqNr 115
                 +++ ++ +AE+ A++  L++  +  + ++++ +Dsk  v++ln +  +++++l+ l +e ++l+++  + ++ +ipR++N 
  AJA91911.1  32 KSGLTNNQAEYHAIIAVLKKF-QGSLDKITIFSDSKNTVNQLNHEFAINNEQLRILAQESWSLIPKIPELKILWIPRKENL 111
                 57889***********99997.578******************************************************96 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   3.9e-14   2.3e-10       4      83 ..       3      75 ..       1     110 [. 0.74

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.9e-14
                EEEEEEEEEECTTTCEEEEEEECTT..EEEEEEECCCCHHHHHHHHHHHHHHHTT.SC.SEEEEEES-HHHHHHHHCCCHH CS
     RNase_H  4 vvvYtDGsclgnpgeggagavlykegarnisapleeaqtnnraELsAvieaLkalksd.ekvniytDSkYvvkgitqwvhr 83
                v +Y+DG+     +++g+g+++++   + ++++ +   tnn+aE +A+i++Lk+ + +  k++i++DSk++v+ +++   +
  AJA91911.1  3 VSIYVDGAG---GEKSGYGFFVKET-GESFYENKS-GLTNNQAEYHAIIAVLKKFQGSlDKITIFSDSKNTVNQLNH---E 75
                789*****4...4778999988644.467777766.89***************7544469************97665...2 PP

>> HAD_SAK_1  HAD domain family 1 in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.1e-06     0.037     131     180 ..      45      98 ..      30     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-06
   HAD_SAK_1 131 ledlletyk.sleeitiYedrpkhvkkfkefleklnkkkk...pikaeviqvae 180
                 +  +l++++ sl++iti+ d ++ v+++++ ++  n++ +   + ++++i+  +
  AJA91911.1  45 IIAVLKKFQgSLDKITIFSDSKNTVNQLNHEFAINNEQLRilaQESWSLIPKIP 98 
                 5578899988**********************9999998866544677766444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 870.59
//
Query:       AJA91912.1  [L=63]
Description: hypothetical protein T478_0206 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 469.03
//
Query:       AJA91913.1  [L=199]
Description: hypothetical protein T478_0076 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1479.30
//
Query:       AJA91914.1  [L=225]
Description: DNA-directed RNA polymerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-15   55.9   0.0    8.7e-15   54.9   0.0    1.6  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    1.2e-12   48.0   0.0    2.6e-12   46.9   0.0    1.6  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.034   14.2   0.0    1.6  1  S1_2         S1 domain
      0.037   13.9   0.0      0.083   12.8   0.0    1.5  1  BPL_C        Biotin protein ligase C terminal domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0     2e-18   8.7e-15       2      70 .]      37     105 ..      36     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2e-18
                  EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
  SHS2_Rpb7-N   2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70 
                  d+vr++Ps +gstl++a++ +l++kye  ++++lG+i+ v d +    gk ++g+G++++rV+f+al F
   AJA91914.1  37 DIVRIPPSLFGSTLKKAAESILKSKYESMINQELGYIIMVMDAKVEPMGKMIPGDGGTFHRVEFQALTF 105
                  89*****************************************************************98 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   5.9e-16   2.6e-12       2      67 ..     107     181 ..     106     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 5.9e-16
                 STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEETTT CS
          S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvdkdr 67 
                 p+  e+v+Ge++++t++GafV++g + ++++++s++++d              +++++lkvG +++ +++ v   +
  AJA91914.1 107 PKLQEIVQGEIVDITDFGAFVRIG-PTDALLHLSQVMDDylksdvasgmIIANQSGRTLKVGSMLRTRITAVSLGK 181
                 67789*******************.*********************99955689****************997655 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.6e-06     0.034       4      36 ..     112     143 ..     111     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-06
        S1_2   4 intlkvlretdfgyfLqkdesgevlLpkkevpe 36 
                 i++ +++++tdfg+f+  +  ++ lL+ ++v +
  AJA91914.1 112 IVQGEIVDITDFGAFVRIGP-TDALLHLSQVMD 143
                 78899***************.******999864 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.083      12      28 ..     110     126 ..     107     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                 SCEEEEEEEEE-TTSEE CS
       BPL_C  12 dgkveGiavGIdddGaL 28 
                 +++v+G +v+I+d+Ga 
  AJA91914.1 110 QEIVQGEIVDITDFGAF 126
                 6799***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1618.61
//
Query:       AJA91915.1  [L=151]
Description: ribosomal protein L24 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-19   67.4   0.0    1.3e-18   66.6   0.0    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.8e-06   27.7   0.4    3.6e-06   26.7   0.4    1.5  1  KOW       KOW motif


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.5e-22   1.3e-18       2      84 .]       9      87 ..       8      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.5e-22
    Spt5-NGN  2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEvedll 84
                ++a+++t gqE+ v ++l++k    +++ +l+++Sv+ +d+lkGy+++EA++++++  a +g+++v+g  +g+++++E+e++l
  AJA91915.1  9 LFALRTTGGQEKVVLRQLEAK----MRSGELDVQSVLIVDNLKGYVVIEANDPQVMFMATQGLRHVKGQLRGELEFSEIENYL 87
                8********************....78889**************************************************987 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.4   4.1e-10   3.6e-06       2      29 ..      99     128 ..      98     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.1e-10
                 TSEEEESSSTTTTCEEEEEEEETTT..TEE CS
         KOW   2 GdhVkVvsGphkGktGkVvkvdqhk..vrV 29 
                 + +V+V++Gp+kG ++++++vd +k  ++V
  AJA91915.1  99 DGTVEVIGGPFKGMKATITRVDHDKeeATV 128
                 679**********************65555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1095.34
//
Query:       AJA91916.1  [L=378]
Description: calcineurin-like phosphoesterase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-12   46.2   0.0    8.6e-12   45.5   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    3.5e-11   44.0   0.3      8e-11   42.8   0.3    1.6  2  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.53   10.6   5.6        4.6    7.6   2.5    2.6  2  ABC_tran_CTD   ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   1.4e-15   8.6e-12       1     155 [.       1     218 [.       1     230 [. 0.74

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.4e-15
  Metallophos_2   1 MklaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeep......evleellela....pvlaVrGNnD.......... 62 
                    Mk+ +iSD+H             + ++  ++++++  + +vd +i+aGD+  + +p      ++ ++l++l+    +   V G +D          
     AJA91916.1   1 MKFSHISDTHlglvqygleereqDIYNSFNQAIDISINDKVDFVIFAGDVfHTPTPsgtailQMANALKRLKqngiESFFVLGEHDisrvrttpip 96 
                    9******************9999777888888888888889********887777755555523333333336669999****************9 PP

  Metallophos_2  63 .......................eev.veedvlreaaelgtdl.p.eeaelelagekvlliHgdplgvkdalaellkeaeegsd..vvvcGHtHvp 130
                                           +++ +++ + +e ++l++++ + e+   + +g k+l++H+      +++a  +++++ +++  ++++GH H +
     AJA91916.1  97 yvyhnlefskyigreepvyyknvMIIgLDKIRKNEMEGLEEKFsKlESLASKHDGHKILVLHQG-ITEVNKFAGEINSTDLPKNftYYAMGHLHDK 191
                    999888888888887777775443335555555555555555532255555559*********9.555555555555555555559********** PP

  Metallophos_2 131 evekeggv..lvvnPGsvgeprdgdpe 155
                     +++ + +   +v+PGs  + +++ ++
     AJA91916.1 192 FLKQYEHLkgPLVYPGSTDMTSNQGDV 218
                    999998665589*****9998777665 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.3   1.3e-14     8e-11       1     153 [.       1     195 [.       1     217 [. 0.76
   2 ?   -2.9   0.0       1.4   8.2e+03      21      57 ..     261     296 ..     248     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.3e-14
                  EEEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSEEEEEC-TTS.........CH CS
  Metallophos   1 lrilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pipvylllGNHe.........gf 77 
                  +++ +i+D+Hl        +++   ++++++++d  +++ k+d+v++aGD++++  ++   + ++a  +k+    +i  +++lG H+           
   AJA91916.1   1 MKFSHISDTHLglvqygleEREQDIYNSFNQAIDISIND-KVDFVIFAGDVFHTPTPSGTAILQMANALKRlkqnGIESFFVLGEHDisrvrttpiP- 96 
                  7899************99999999999999999777777.**************9888877777777777667779999**********99999953. PP

                  HH.HHHHHHHHHHHHHHHHEHH.................HCEEETSEEEEEETTE..EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.....HHH CS
  Metallophos  78 ee.ellnkygylgifsepwrsd.................aevfnnlplaslgsgs..lkvlllhGgspellvsldklgslnleleapepg.....dew 150
                  +    l++ +y+g+  ++++++                  e+f+ l + +  s++   k+l+lh g  e +++  +++s +l+++ +        d++
   AJA91916.1  97 YVyHNLEFSKYIGREEPVYYKNvmiigldkirknemeglEEKFSKLESLA--SKHdgHKILVLHQGITEVNKFAGEINSTDLPKNFTYYAmghlhDKF 192
                  44466677677777666666667788888888888887777776666666..5556689999999944445555555555555555554455566777 PP

                  HHH CS
  Metallophos 151 lkd 153
                  lk+
   AJA91916.1 193 LKQ 195
                  776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                  HHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHH CS
  Metallophos  21 llkllddllreekpdlvllaGDlvdrgdlekellell 57 
                  l++ +++l ++  +  + + GD+ +r ++e ++ el 
   AJA91916.1 261 LNEKISKLEKK-PIIKIKIKGDNLERDVIERKFTELA 296
                  44444444333.4445555689988888888887774 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.016        98       8      31 ..     130     146 ..     124     165 .. 0.69
   2 ?    7.6   2.5   0.00077       4.6       6      30 ..     247     271 ..     242     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
  ABC_tran_CTD   8 releeleaeIeaLEeeiaeleael 31 
                   +       e+e LEe+ ++le   
    AJA91916.1 130 N-------EMEGLEEKFSKLESLA 146
                   4.......4555555555555554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00077
  ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleae 30 
                   e+ e+e++++ I++L e+i++le++
    AJA91916.1 247 EKIEFEKIDSGIQELNEKISKLEKK 271
                   899*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2552.21
//
Query:       AJA91917.1  [L=471]
Description: amino acid kinase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-29  103.5   0.5    2.7e-29  102.5   0.5    1.5  1  AA_kinase  Amino acid kinase family
     0.0086   15.8   0.7      0.024   14.4   0.7    1.7  1  DUF4116    Domain of unknown function (DUF4116)
  ------ inclusion threshold ------
      0.052   13.1   0.2       0.32   10.5   0.2    2.0  2  DUF5039    Domain of unknown function (DUF5039)
       0.12   11.7   0.0        0.2   10.9   0.0    1.2  1  DUF3810    Protein of unknown function (DUF3810)
       0.43   10.4   4.4       0.21   11.4   0.7    2.4  3  ACT        ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.5   7.5e-33   2.7e-29       1     241 []       3     299 ..       3     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 7.5e-33
                 TEEEEEE-TTCCC.CTCCHHHHHHHHHHHHHHHHTTEEEEEE--.H........HHHHHHHHH....TCCCCCHHHC...................... CS
   AA_kinase   1 krvVvKlGGsslt.dkeeaslrrlaeqiaalkesgnklvvVhGg.g........sftdgllal....ksglssgelaa..................... 64 
                 k+++ K+GGs+++ d+++  + ++++ i+++ +++ klvvV+++          s td +l +    ++                              
  AJA91917.1   3 KLTIAKFGGSAIGiDGKG--IPEIVKRIKEI-QENSKLVVVCSApLtmvegkkrSLTDVILGIgndaAN--------Gnnfdfsivekpymkileyvsd 90 
                 6899**************..***********.************5222333333444444444444422........1334455556677778888777 PP

                 ..............E..HHHHHHHHH..........HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEE.........CCHHHH CS
   AA_kinase  65 ...........glrstleeagevatr..........dalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvd.........aeaiee 133
                            + + +++ea e+at+           ala  ge l++++l+  l++ g+++  + + +  +   +d+n+es +          ++ie+
  AJA91917.1  91 elrnsckevidEFLKNSKEAIELATSkkefldeirsKALAFSGEVLMSHVLNLILRSNGIKSDTISLDDWPI--ITDNNIESTNflfsesisrMDKIEQ 187
                 777777777775555556666666668899999999******************************999999..6777777777778888888****** PP

                 HHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTS..SEEEEEESSSSCESSTTTTCCTT.CECCEEEHHHCHHCSSS.TTTHHHHCHHHH CS
   AA_kinase 134 lleagvvpvltgfigldeege...lgrgssDtiaallAealgA..dkliiltdVdGVydadpkkvpda.rllpeisvdeaeesaselatgGmkvkhpaa 226
                 +le++ v+ ++gfig + +g      rg+sD++aa l+ +++   d++i l   + V +adpk+v++  + ++e+s++ea+      +++Gmk+++p a
  AJA91917.1 188 ILEKNDVISIGGFIGKTKDGIittYERGGSDRTAADLGILFHKkyDTVIDLEKDSSVVSADPKIVKNElEEVNELSYNEARL----AGMFGMKIVDPIA 282
                 *********************88877***************99889************************************....************* PP

                 HH.HHHCTT.-EEEEEE CS
   AA_kinase 227 la.aarrgg.ipvvItn 241
                 ++ ++++g+ ip+ Itn
  AJA91917.1 283 IKeILENGVeIPLTITN 299
                 97255556589999987 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.7   6.7e-06     0.024       8      44 ..      76     114 ..      71     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.7e-06
     DUF4116   8 avkkngs.alkylseeLkn.DkeivlkAvkqngtalsya 44 
                 +v+k  + +l+y+s+eL+n  ke++ + +k+++ a++ a
  AJA91917.1  76 IVEKPYMkILEYVSDELRNsCKEVIDEFLKNSKEAIELA 114
                 567766569**********99***********9998766 PP

>> DUF5039  Domain of unknown function (DUF5039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   9.1e-05      0.32      58     102 ..      82     127 ..      64     134 .. 0.71
   2 ?   -0.4   0.0      0.19     7e+02      31     112 ..     377     462 ..     361     467 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.1e-05
     DUF5039  58 Paslevyrley.kaakdeldkllntykeykelkkklkeavskeekd 102
                  + le + +e  +++k+ +d++l   ke  el +++ke + +   +
  AJA91917.1  82 MKILEYVSDELrNSCKEVIDEFLKNSKEAIELATSKKEFLDEIRSK 127
                 344555555551468999********************88765544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
     DUF5039  31 adyceannkyi....sindvdylkilveeerPaslevyrleykaakdeldkllntykeykelkkklkeavskeekdavsaalsafy 112
                  dy ++n+kyi    +++ v y + +v     +  +v + + ka+ +  d  ln      + ++++   v ++  d+vs a+ + +
  AJA91917.1 377 GDYVKRNEKYIlsfdALATVAYDRGVVTLIGDEMWRVQQIASKASSKIGDAGLNILNMDAQEETSRIIIVIEDTEDSVSKAIESIH 462
                 58999999999433334567787888877777777888888888877777777777776777777777777777788887776655 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.7e-05       0.2     230     296 ..      81     151 ..      79     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
     DUF3810 230 ylsalsyvlnalykadeeayeellktispevledlkeereywek.......yegtveevsdkvndtyLkangqe 296
                 y+++l+yv  +l+++ +e   e+lk+ s+e +e + +++e+ ++       +  + e + + v ++ L++ng++
  AJA91917.1  81 YMKILEYVSDELRNSCKEVIDEFLKN-SKEAIELATSKKEFLDEirskalaF--SGEVLMSHVLNLILRSNGIK 151
                 99**********************99.99999************65554433..34668899999999999987 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.4   5.1e+03      51      65 ..      17      31 ..      14      32 .. 0.84
   2 ?   -2.5   0.1       1.3   4.6e+03      46      65 ..     243     262 ..     237     263 .. 0.82
   3 ?   11.4   0.7   5.8e-05      0.21      14      64 ..     417     463 ..     416     465 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                EHHHHHHHHHHHHTT CS
         ACT 51 deedleevlealkkl 65
                d ++++e+++++k++
  AJA91917.1 17 DGKGIPEIVKRIKEI 31
                788999*****9975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                 EEEEEEHHHHHHHHHHHHTT CS
         ACT  46 vvivvdeedleevlealkkl 65 
                 +v+ +d++ +++ le++++l
  AJA91917.1 243 SVVSADPKIVKNELEEVNEL 262
                 67889999999999999876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 5.8e-05
                 HHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
         ACT  14 LarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                 +++ ++ ++d+g+Ni ++   +      +++++vi+  e+++++++e +++
  AJA91917.1 417 ASKASSKIGDAGLNILNMDAQEET----SRIIIVIEDTEDSVSKAIESIHS 463
                 7899999****************5....69999999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3347.33
//
Query:       AJA91918.1  [L=370]
Description: tryptophan--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      8e-28   97.6   0.0    1.6e-27   96.6   0.0    1.5  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.064   12.2   0.0       0.72    8.7   0.0    2.4  3  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6   0.0   1.7e-31   1.6e-27       3     293 .]      71     349 ..      69     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.7e-31
                   HS--EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTEEEEETHHHHTTHH CS
  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpekaevvlqsewlehle 98 
                    +++ +y+G  P+g+ H+G+lvp     +lq+   ++++f + D + + ++ +  ++++  k + + +      +a g++pek+++++++  +  l 
    AJA91918.1  71 GKKFFLYTGRGPSGNTHIGHLVPWVFAKWLQEkFDVNIYFQLTDDEKFYTKSD-LTLEDTSKFALENALD---FIALGFNPEKTKIIINTRNIRRL- 162
                   578889*************************95578999*********99999.7788888888888888...****************9987654. PP

                   HHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBST CS
  tRNA-synt_1b  99 laellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgl 194
                      + ++++k       ++f   k  +  +++ ++g + Y  Lq+a  +  +   l p G DQ+ +++++rd+a+++nk     kp  + + +++ l
    AJA91918.1 163 -YPIAAQVAK------KINFSNTKAVFGFTNDTNVGMIFYTSLQSAPCFIEDLPvLIPLGVDQDPHFRITRDVAPKINKP----KPALIHNIMIPAL 248
                   .455555555......334444344444444689************998666447***********************98....9988888899999 PP

                   TSSS.BTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC...SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHH CS
  tRNA-synt_1b 195 dGek.KmSKSagnsaIfLddekesvkkkiqkavtdsde...evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaea 287
                   +G   KmS S+++s+I+ +d+++ vkkki+k   + ++   e ++ l +++ ++   +++l  + ++++  ++++++++++++++  g+lk  l e+
    AJA91918.1 249 TGPGgKMSASDEKSTIYTTDSPQVVKKKINKYGFSGGQvdiEKHRELGGNPDIDV-SFQYLRIFFEQDD-DKLKKIYEDYKSGKMLTGELKAILIEK 343
                   87655************************99877777776666778888999999.9999999999998.99************************* PP

                   HHHHHH CS
  tRNA-synt_1b 288 lnelle 293
                   +n++l+
    AJA91918.1 344 INSFLK 349
                   **9985 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0     8e-05      0.72      22      49 ..      71      98 ..      59     113 .. 0.77
   2 ?   -0.3   0.0     0.045     4e+02     290     329 ..     124     163 ..     116     180 .. 0.85
   3 ?   -1.6   0.0      0.11   9.8e+02      65      88 ..     310     334 ..     303     351 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 8e-05
  tRNA-synt_1f 22 kdevvvesGispSGliHiGnlrevltad 49
                   ++  + +G +pSG  HiG l   + a+
    AJA91918.1 71 GKKFFLYTGRGPSGNTHIGHLVPWVFAK 98
                  4578899************987666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.045
  tRNA-synt_1f 290 ltledwlevaepevlrflilrrkPkkakkldldleilrlv 329
                   ltled  ++a ++ l f+ l  +P+k k +    +i rl+
    AJA91918.1 124 LTLEDTSKFALENALDFIALGFNPEKTKIIINTRNIRRLY 163
                   7999********************9998887777888877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.11
  tRNA-synt_1f  65 ilisDdmDglRkvpenlpek.llek 88 
                   i++  d D+l+k++e+  +  +l+ 
    AJA91918.1 310 IFFEQDDDKLKKIYEDYKSGkMLTG 334
                   7788888999999998776656555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2735.59
//
Query:       AJA91919.1  [L=536]
Description: thymidylate synthase ThyX [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-32  112.1   1.7    3.4e-18   66.1   1.6    2.4  2  Thy1      Thymidylate synthase complementing protein
  ------ inclusion threshold ------
        2.6    8.6  14.3        2.7    8.5   0.5    3.6  3  FadA      Adhesion protein FadA


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   2.4e-15   2.1e-11      24     166 ..      46     247 ..      26     266 .. 0.74
   2 !   66.1   1.6   3.8e-22   3.4e-18      36     187 ..     355     504 ..     280     505 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.4e-15
                 SSHHHH......S.GCCHHHHHHHHH.HTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TT.SEEEE--TTTSGCCCTC.....BS--GGGCC.HHHHHH CS
        Thy1  24 eeaeele.....e.eekkeklikkll.khghgsplehasftfeiegvSravlrqlvrHRi.asfsqqSqRYvesskea.....fvippeieqkeeleel 109
                 ++++++      + +++ e++++++l ++g  s+ e   ++++ieg+   +++++   Ri +s+ ++S RYv+ +k+      f   p+i +  ++ ++
  AJA91919.1  46 KSMRKIFldeflKnKNRGEEFYDRVLlEYGDDSVAELGIAQIAIEGLTNIAVKKIEDRRIgFSYLEKSSRYVSWDKKIkgkykFLHEPTIMK-TKFADE 143
                 333444455443223344599999999**********************************************9883369999888888886.566778 PP

                 HHHHHHHHHHHHHHHHHT...............................................TCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHH CS
        Thy1 110 yeeamekaleaykellea...............................................gvarEdaryvLPlatktklvvtmNlrsLlhflel 161
                 y +a++  +e y +++e                                                 +a +++r +LP +t t++ vt+N r++   l+ 
  AJA91919.1 144 YIDACNLDFEVYSKNIEPmlklirerdsinnykfkdkdgkekkfsainddsilkssmriynaatkAKALDALRSLLPASTLTNVGVTGNGRAFEYLLSI 242
                 99999999999966666555556666666666666666666666666666666666666666666779************************9888777 PP

                 HSSTT CS
        Thy1 162 racsr 166
                    s+
  AJA91919.1 243 LFASK 247
                 65554 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 3.8e-22
                 H......HHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTCBS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHTT CS
        Thy1  36 e......klikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRYvesskeafvippeieqkeeleelyeeamekaleaykelleag 128
                 +      + ++k  +h+ ++ +e+a++tf +  +  +++r + rHR   ++ + q  +  +   + +p+e+++   ++++++e m+++   +k++   +
  AJA91919.1 355 KkiilemADLRKNRRHRPSRAFEMAEYTFDLV-TNFGMFRDFHRHRA--LTLERQLLTTHHG--YDMPQEVKD-LGMQKEFKECMNNTDTVFKKIQ--K 445
                 22333333455555777889************.**************..7777888888766..788*99994.446688999****999999994..5 PP

                 CHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSH CS
        Thy1 129 varEdaryvLPlatktklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaP 187
                 + +E a+yv+  +++  ++++mN+r+  h++elr+ ++ ++++r +a++m++ + k++P
  AJA91919.1 446 KYPEEAQYVVNFGYNYPYMMKMNMREAVHMIELRTVPQGHQDYRIVAQKMYQAINKKHP 504
                 68********************************************************9 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   2.0    0.0013        12      32      84 ..     246     297 ..     244     300 .. 0.90
   2 ?    8.5   0.5    0.0003       2.7      61      92 ..     426     457 ..     418     459 .. 0.95
   3 ?   -0.4   0.3      0.18   1.6e+03      53      96 ..     483     527 ..     465     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0013
        FadA  32 aklakkkelkakieeklakleadsevrfykdeYkellkeyksllkelekeike 84 
                  kl+++++l  +i+++l+  + +s vr   d+Y+++l++y + +k+  +++++
  AJA91919.1 246 SKLKEENNLALQIKKELDT-TIKSFVRRSDDKYGKVLQKYLNSVKKSAQNVAK 297
                 68999*************9.889*****************9999998887776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0003
        FadA  61 kdeYkellkeyksllkelekeikekekkianf 92 
                 ++e+ke +++ +++ k+++k+  e+++ + nf
  AJA91919.1 426 QKEFKECMNNTDTVFKKIQKKYPEEAQYVVNF 457
                 69***************************998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.18
        FadA  53 a.dsevrfykdeYkellkeyksllkelekeikekekkianfeklk 96 
                 +  +++r+  +++ + +++   +l+++ k +  ++ ++++fe+ k
  AJA91919.1 483 QgHQDYRIVAQKMYQAINKKHPILSNIMKFVDMNKYELERFESEK 527
                 446777777777777788888888888888888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1343  (0.0749066); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3561.21
//
Query:       AJA91920.1  [L=284]
Description: lysine biosynthesis enzyme LysX [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-30  106.5   0.0    1.5e-30  106.2   0.0    1.1  1  RimK            RimK-like ATP-grasp domain
    1.5e-09   37.6   0.2    1.2e-05   24.7   0.0    2.8  3  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
    2.3e-09   36.9   0.1    2.9e-09   36.6   0.1    1.2  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    4.4e-09   36.6   0.2    1.1e-08   35.3   0.2    1.6  1  ATP-grasp_3     ATP-grasp domain
    5.6e-06   26.0   0.0    2.2e-05   24.1   0.0    1.9  1  ATP-grasp       ATP-grasp domain
    8.9e-05   21.9   0.0       0.33   10.2   0.0    2.2  2  ATPgrasp_YheCD  YheC/D like ATP-grasp
     0.0025   17.4   0.0     0.0046   16.5   0.0    1.4  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
     0.0033   16.9   0.0     0.0057   16.1   0.0    1.4  1  ATP-grasp_5     ATP-grasp domain
  ------ inclusion threshold ------
      0.033   14.0   0.3      0.084   12.7   0.3    1.7  1  HNH_repeat      Homing endonuclease repeat


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   7.7e-34   1.5e-30       3     187 ..      90     278 ..      88     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 7.7e-34
                 -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH......GGG--.EEEEE--SS-SEEEEEEE CS
        RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea......lkeai.lvqeyieeaenediRvlv 94 
                 +K+ +  lL k++i++p+t ++ + e a +  e+i  + P+v+K + gs G  v+  k+++ ++ v+e        + +i  +qe i+    +diRv+ 
  AJA91920.1  90 NKMITSMLLKKNNIPTPKTYFSFSAETALENFENI--GYPLVIKPIIGSWGRSVMPIKDKDTAEAVIENrqvtdgPQDRIyYLQEMIDR-PPRDIRVIT 185
                 7888999***************************9..6**************************9999877655544555678999986.469****** PP

                 ETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEE.ETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
        RimK  95 vddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllr.akrgllvlEvnsspglekiektlgidiakkliea 187
                 v+d+ v+a+ r+   G F++n+ +G+  e  q+++e ++l  k +ka++  ++G+Dl++ +++gl+v Evn  ++ +++ k ++ +i k++i++
  AJA91920.1 186 VGDQAVSAMYRK-SSGGFKTNIALGADPELCQITKEMEDLCEKTSKAVGGGILGIDLMEdKEKGLVVHEVNNTVEFKGLVKVSEKNIPKEMIDY 278
                 ************.6789***************************************88615689999*************************86 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.2e-09   1.2e-05      10      88 ..      79     153 ..      76     166 .. 0.86
   2 ?   -0.7   0.0      0.33   6.7e+02     143     166 ..     180     199 ..     177     210 .. 0.63
   3 !    9.3   0.0    0.0003      0.59     227     267 ..     220     259 ..     215     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.2e-09
  ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqdyl 88 
                  +N+   + +  +K++++ l++++ +++pk++ +++ +  ++++e++       +viKp+ gs+G+ ++ i+++++++ +
   AJA91920.1  79 INKFDVANTCGNKMITSMLLKKNNIPTPKTYFSFSAETALENFENIGYP----LVIKPIIGSWGRSVMPIKDKDTAEAV 153
                  67777888999*********************************98554....59***************887766655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.33
  ATPgrasp_ST 143 tiRvitflkdkkvevmlamlRlgt 166
                  +iRvit+  d+ v    am R + 
   AJA91920.1 180 DIRVITV-GDQAVS---AMYRKSS 199
                  9******.444444...5566555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0003
  ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpg 267
                  e+ +l+ k ++  +g g+lG+D+  d+ekg+++ E+N+++ 
   AJA91920.1 220 EMEDLCEKTSK-AVGGGILGIDLMEDKEKGLVVHEVNNTVE 259
                  66788999998.9999*********************9865 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.5e-12   2.9e-09      12     155 ..     105     245 ..      90     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.5e-12
                 S--EEEES-.HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTT..TS-EEEEE--GGGGG-EEEEEEETTEE-SEEEEEE--SS CS
   GSH-S_ATP  12 ipktlvskd.keeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteeg..kepviaqrylpeikeGDkRillvdGepigyalaRvpaeg 107
                 +pkt  s + ++++++f +    +++KP+ g+ G++v+ +k++d+   +i +  ++ g   +   +q+ ++   + D R++ v  + ++ a+ R + +g
  AJA91920.1 105 TPKTYFSFSaETALENFENIGYPLVIKPIIGSWGRSVMPIKDKDTAEAVIENRQVTDGpqDRIYYLQEMIDRPPR-DIRVITVGDQAVS-AMYRKS-SG 200
                 57888885515679999999999*******************998877776655554411456678999988777.************9.**9975.67 PP

                 -S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTE CS
   GSH-S_ATP 108 evRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdk 155
                  +++n+a g+  e  ++t++ + ++e+ +++    G  + G+D+++dk
  AJA91920.1 201 GFKTNIALGADPELCQITKEMEDLCEKTSKA---VGGGILGIDLMEDK 245
                 8*************************98765...46667799999886 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.2   5.5e-12   1.1e-08       1     155 [.      88     255 ..      88     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5.5e-12
                  HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE.................EEEE---SEEEEEEEEE CS
  ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve..........lvqefieGkplSvslls 81 
                  + +K+ t   Lk++++++P        ++  e++e+  ++lv+Kp+ G+ g sv+ +++k++aea ie+ +           +qe+i+  p  + ++ 
   AJA91920.1  88 CGNKMITSMLLKKNNIPTPktyfsfsAETALENFENIGYPLVIKPIIGSWGRSVMPIKDKDTAEAVIENRQvtdgpqdriyYLQEMIDRPPRDIRVIT 185
                  789****************999988888888999999*******************************999999999998889*****9999999999 PP

                  .SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEE CS
  ATP-grasp_3  82 dgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd.eepyviEvN 155
                   g +++  +  +   ++  k ++  G   p   + ++e+++l+e++ +++    G++G+Dl+  + ++++v EvN
   AJA91920.1 186 VGDQAVSAMYRKSSGGF--KTNIALGAD-PELCQITKEMEDLCEKTSKAV--GGGILGIDLMEDKeKGLVVHEVN 255
                  88777776666666655..334555654.555578899999999999999..579*******7765889999**9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.1e-08   2.2e-05       2     157 ..      99     255 ..      98     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.1e-08
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE----.SEEEEEEEEEETTC-EEE- CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefvpf.ekElsvlvvrsaeGetafy 93 
                 +k+++p+p+ ++  s+e + e +e++g+p+v+K ++ g+ G+  + +++++++e ++e+       +++  ++ e+++   + + v++v ++    a+y
  AJA91920.1  99 KKNNIPTPKTYFSFSAETALENFENIGYPLVIK-PIIGSWGRSVMPIKDKDTAEAVIENRqvtdgpQDRIYYLQEMIDRpPRDIRVITVGDQAV-SAMY 195
                 7899****999999999888999**********.***********************99999999889999999999863699*****988876.4555 PP

                 -EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEE CS
   ATP-grasp  94 pvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnEla 157
                        + +i  l   p     ++ k+ e++++k  +++gg G++++ l + +++ l+v E+ 
  AJA91920.1 196 RKSSGGFKTNI-ALGADPE--LCQITKEMEDLCEKTSKAVGG-GILGIDLMEDKEKGLVVHEVN 255
                 55544444444.3444555..34699999******9999987.9******99988889999985 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00023      0.46      30      82 ..     106     160 ..      80     179 .. 0.62
   2 !   10.2   0.0   0.00017      0.33     186     251 ..     214     277 ..     191     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
  ATPgrasp_YheCD  30 Petellesledleemlekyks.vylKpanGskGkgilriek.eekellllsrekk 82 
                     P+t    s+e+  e +e+ +  +++Kp+ Gs G+ ++ i+  +++e ++ +r+ +
      AJA91920.1 106 PKTYFSFSAETALENFENIGYpLVIKPIIGSWGRSVMPIKDkDTAEAVIENRQVT 160
                     556555455555555555544499***************9933334444444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
  ATPgrasp_YheCD 186 leelalelaealeesfgr..lgElGlDlgidkegkvWllEvNskpgrsifkeagdkeaarksvkrple 251
                     l++++ e+    e++++    g lG+Dl+ dke+ + + EvN     +   ++++k+    + k++++
      AJA91920.1 214 LCQITKEMEDLCEKTSKAvgGGILGIDLMEDKEKGLVVHEVNNTVEFKGLVKVSEKN----IPKEMID 277
                     45555555555555444433589*******************988777777676644....4444444 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.3e-06    0.0046       6     103 ..      95     189 ..      90     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-06
                  HHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SS.SEEEEEEEEEE CS
  CPSase_L_D2   6 kealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkg.pkeiEvevlrD 102
                  + +lkk n+p+ +       ++e+al+  ++igyP +ik+ +g  G+    ++++++ ++++++ + +      ++  ++++++++ p++i v  + D
   AJA91920.1  95 SMLLKKNNIPTPKTYFS--FSAETALENFENIGYPLVIKPIIGSWGRSVMPIKDKDTAEAVIENRQVTD--GPQDRIYYLQEMIDRpPRDIRVITVGD 188
                  56788888999888877..899*************************9999999988877776654443..344555567777776347777766666 PP

                  T CS
  CPSase_L_D2 103 a 103
                  +
   AJA91920.1 189 Q 189
                  6 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-06    0.0057      16      52 ..      95     131 ..      86     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
  ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                    ll+  +ip+++t +  sae a+e +e+igyp v+K
   AJA91920.1  95 SMLLKKNNIPTPKTYFSFSAETALENFENIGYPLVIK 131
                  5689999*****************************9 PP

>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.2e-05     0.084       5      15 ..      16      26 ..      16      27 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
  HNH_repeat  5 ElvQkqAaELG 15
                +l+Qk+A+ELG
  AJA91920.1 16 KLLQKKAEELG 26
                59********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2199.73
//
Query:       AJA91921.1  [L=103]
Description: divalent cation tolerance protein, CutA1 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-35  119.0   0.6    6.9e-35  118.9   0.6    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.6   3.9e-39   6.9e-35       1      98 [.       4     100 ..       4     101 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 3.9e-39
                 EEEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEEEESEEEHHHHHHHHH CS
       CutA1   1 vlvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiialpieagseaYlkWiee 98 
                 v+++ t+p++++ kk+a+alv++klaACvni++ i+SvY Wkgki++d+E+l ++kt++++ + l++++k+lhpy+vpei ++++++++++Yl+W+ +
  AJA91921.1   4 VIIVSTFPNKTVTKKIANALVKKKLAACVNITK-IDSVYSWKGKIQNDSEYLAIFKTTKKNEKTLKNEIKKLHPYDVPEIAEINVNSMNKPYLDWLID 100
                 58999**************************99.*************************************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1419  (0.0791455); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 747.11
//
Query:       AJA91922.1  [L=393]
Description: transaminase, acetylornithine/succinylornithine family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.2e-114  383.2   0.0   1.4e-114  382.9   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    7.7e-05   22.0   0.0    0.00013   21.3   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.036   13.0   0.0      0.051   12.5   0.0    1.2  1  Aminotran_5    Aminotransferase class-V
      0.083   11.9   0.6       0.15   11.0   0.1    1.5  2  Ter            DNA replication terminus site-binding protein 
      0.092   11.8   0.1       0.17   11.0   0.0    1.4  2  IFRD           Interferon-related developmental regulator (IF


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.9   0.0  3.9e-118  1.4e-114       7     404 ..      12     380 ..       7     382 .. 0.98

  Alignments for each domain:
  == domain 1  score: 382.9 bits;  conditional E-value: 3.9e-118
                  --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHH CS
  Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAl 104
                  + +++ ++++ G+ ++d ++k+y+D ++++ v++lGh++++v++a+k+q++k+  v    l n+  +++ e l k+apk+l++v l nsG+eA+e+A+
   AJA91922.1  12 QRFPVTVDRGIGAHVWDTNNKEYIDCMGGYGVALLGHQNERVTNALKSQLEKIITVH-SSLYNKTREEFLENLFKVAPKNLSQVHLNNSGAEAIEAAM 108
                  456799***********************************************7776.99************************************** PP

                  HHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCE CS
  Aminotran_3 105 KlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiq 202
                  K+ark       t kt+++a++g++HG+ +gals+t + +ky++ f+p++ +v++ ++ d                 +e+l+++ +d+++ vi+Epiq
   AJA91922.1 109 KFARK------FTGKTEMVAMNGSYHGKSMGALSITFN-PKYRKSFKPLIEKVSFSPFGD-----------------IEKLRETVNDQTSFVILEPIQ 182
                  *****......***************************.********************9.................9******************** PP

                  TTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHH CS
  Aminotran_3 203 gegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacav 300
                  ge G+ va+++fl+ +r+lc+++++lli DE+q G+GrTGk++A+eh++++pD+++laK+++gG p+ a+l++ e+ + +++g+h+sTfgGnpl ca+
   AJA91922.1 183 GESGIHVAPDGFLQDVRKLCDEKGILLIYDEIQAGLGRTGKMWAHEHWDTPPDILCLAKGIAGGVPMGATLVKPEILDCISKGEHSSTFGGNPLSCAA 280
                  ************************************************************************************************** PP

                  HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHH CS
  Aminotran_3 301 alavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeeidel 398
                   la+++++ ++kl+en +++g+ +++gL +l++k+ vi+evRgkGlmi++elk e++    +il ++ ekG+l+l +G+n++rllppl+it++++ + 
   AJA91922.1 281 GLATMQALTQDKLVENSANMGRLFRQGLDKLKEKHPVIREVRGKGLMIGVELKFEVR----DILMEGIEKGLLLLYSGRNILRLLPPLVITEADVTKS 374
                  ********************************************************9....9************************************ PP

                  HHHHHH CS
  Aminotran_3 399 leilkk 404
                  leil +
   AJA91922.1 375 LEILDE 380
                  *99875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.5e-08   0.00013      17     295 ..      50     311 ..      40     326 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-08
                    SHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEES.HHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
  Aminotran_1_2  17 kptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgs.Gagaliealifllklnpgdeilvpdptyasyknilr 111
                    ++ +++++k + e   +  t+++++ ++   e+ e+l k +        k+ ++v + + Ga a+ +a +f+ k+  ++e ++ + +y   + ++ 
     AJA91922.1  50 NERVTNALKSQLE---KIITVHSSLYNKTREEFLENLFKVAP-------KNLSQVHLNNsGAEAIEAAMKFARKFTGKTEMVAMNGSYHGKSMGAL 135
                    4566666666654...66677777777777888888877777.......44446655540444444444455556666778888888888888888 PP

                    HTTSEEEEEEBEET......TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--.B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHT CS
  Aminotran_1_2 112 lsggevvryplyse......edfhldlealeealkeapegnkktkvilvesphNPtGt.vatleeleklldlakkynlllfvDeaYagfvfgslda 200
                      ++   + +  ++       +   d+e+l e +++      +t ++++e ++  +G  va+   l+++ +l++++++ll+ De+ ag+  + + +
     AJA91922.1 136 SITFNPKYRKSFKPliekvsFSPFGDIEKLRETVND------QTSFVILEPIQGESGIhVAPDGFLQDVRKLCDEKGILLIYDEIQAGLGRTGK-M 224
                    888886666655556765444445688888888888......799************746777899*************************964.5 PP

                    HHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
  Aminotran_1_2 201 vatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael 295
                    +a +   ++ p ++++   + a G++    G++l+++++++++ k   + ++  ++l+ a+  a+  al +q   ++ ++  +++ + +r++L++l
     AJA91922.1 225 WA-HEHWDTPP-DILCLAKGIAGGVPM---GATLVKPEILDCISKGEHSSTFgGNPLSCAAGLATMQAL-TQ---DKLVENSANMGRLFRQGLDKL 311
                    66.55555555.588877777889999...*******************99995555555554444444.33...344444444444444444443 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05     0.051      42     180 ..      69     217 ..      45     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                  HHHHHHHHHHH.HHHHT-.STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE....GGGH CS
  Aminotran_5  42 tkaveearekv.aelina.eseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld....ldel 132
                  ++ ++++re++  +l+++ +++   + + +++  ai+++++ + r++  ++e+v  +  +h++ + +  +    +++  + pl e+ +      +++l
   AJA91922.1  69 SSLYNKTREEFlENLFKVaPKNLSQVHLNNSGAeAIEAAMKFA-RKFTGKTEMVAMNGSYHGKSMGALSITFNPKYRKSFKPLIEKVSFSpfgdIEKL 165
                  5667777766524555541344444555554443999887766.6799999999999999999999988876666666555555555554444478** PP

                  HHH--TTEEEEEEESBETTTTE.B--...HHHHHHHHHHTT-EEEEE-TTTT CS
  Aminotran_5 133 ekllnektklvaithvsnvtGt.iqp...veeigklakkkgalvlvDaaqav 180
                  ++++n++t+ v++  ++ ++G+ + p   ++++ kl+ +kg+l++ D  qa 
   AJA91922.1 166 RETVNDQTSFVILEPIQGESGIhVAPdgfLQDVRKLCDEKGILLIYDEIQAG 217
                  **********************98876779*****************99985 PP

>> Ter  DNA replication terminus site-binding protein (Ter protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   4.2e-05      0.15     109     140 ..      54      85 ..      44      87 .. 0.89
   2 ?   -2.5   0.0      0.55     2e+03      53     109 ..      98     154 ..      89     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.2e-05
         Ter 109 iNklKaeleeiitvesglekeerFefvhrhlp 140
                  N+lK +le+iitv+s+l ++ r ef+ + ++
  AJA91922.1  54 TNALKSQLEKIITVHSSLYNKTREEFLENLFK 85 
                 59************************988665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.55
         Ter  53 ltgeeAlelalshfrrlfikqqseklSskaavRlpGvlcfsvsnaekaelealieei 109
                  +g eA e+a++  r++  k +   +      +  G+l ++ + + +++ + lie++
  AJA91922.1  98 NSGAEAIEAAMKFARKFTGKTEMVAMNGSYHGKSMGALSITFNPKYRKSFKPLIEKV 154
                 578899999988877766666666666666778888998888888888888888876 PP

>> IFRD  Interferon-related developmental regulator (IFRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.7e-05      0.17      29     102 ..      50     123 ..      28     145 .. 0.89
   2 ?   -3.5   0.1       1.2   4.2e+03     161     184 ..     368     391 ..     367     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.7e-05
        IFRD  29 eeeaqedweekLkqaidelteksaktReaaLesllellsshyleefveerlatlldalekslkkgkseEqalAl 102
                 +e ++++ +++L+++i+  +    ktRe+ Le+l+++  +++ +  ++++ a+ ++a +k  +k +++  ++A+
  AJA91922.1  50 NERVTNALKSQLEKIITVHSSLYNKTREEFLENLFKVAPKNLSQVHLNNSGAEAIEAAMKFARKFTGKTEMVAM 123
                 67788899999999999999999*****************************************9999666665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
        IFRD 161 eeeieelmeflleifssdgqsiea 184
                 e+++++++e+l e+f+++ ++++a
  AJA91922.1 368 EADVTKSLEILDELFTNEEKRKNA 391
                 578899999999999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2825.24
//
Query:       AJA91923.1  [L=83]
Description: hypothetical protein T478_0222 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.19   11.8   0.0       0.21   11.6   0.0    1.1  1  Lentiviral_Tat  Lentiviral Tat protein


Domain annotation for each model (and alignments):
>> Lentiviral_Tat  Lentiviral Tat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.2e-05      0.21       3      58 ..       3      58 ..       1      69 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
  Lentiviral_Tat  3 elPrrreagkeeleislfererdtwdyvsirvPgeilqrwlamlrngrlrrkvlre 58
                    el  + +++  + +i+ +e+e +     s   P++ +qr l  l  +++ r++  e
      AJA91923.1  3 ELSMNDKMTLVQYAIEKYENEEELLSKLSSVLPEKDIQRSLDTLIGTQKVRRIGPE 58
                    5556666777788999*************************999988887777555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 626.19
//
Query:       AJA91924.1  [L=248]
Description: proliferating cell nuclear antigen [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-20   71.2   0.1    3.1e-19   68.9   0.0    1.9  2  PCNA_N        Proliferating cell nuclear antigen, N-terminal 
    5.6e-19   68.6   0.2      4e-17   62.6   0.0    2.7  2  PCNA_C        Proliferating cell nuclear antigen, C-terminal 
     0.0027   17.2   0.0     0.0036   16.8   0.0    1.1  1  Rad9          Rad9
  ------ inclusion threshold ------
      0.071   13.1   0.0       0.16   12.0   0.0    1.5  1  Tnp_22_dsRBD  L1 transposable element dsRBD-like domain


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   6.9e-23   3.1e-19       2     111 ..       3     111 ..       2     132 .. 0.86
   2 ?   -0.0   0.0      0.15   6.7e+02      72     112 ..     146     185 ..     125     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 6.9e-23
                 EEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEETTSSEEE CS
      PCNA_N   2 learleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtlkaedeadtla 100
                 + a+ + a   k ++ ai  lv+ea+f++  +Gis + +D shvaL+ ++  +++feky CD ++ +gv +  +sk++k +++++s+ ++  d++  l 
  AJA91924.1   3 FSAKTNGAEEWKAIISAISTLVEEATFEATVEGISFRGMDPSHVALIDINWPNSAFEKYNCDSDIKFGVRIDEFSKLIKRSDKSNSIEINISDDNMLL- 100
                 67888888899******************************************************************************998875544. PP

                 EEEEECTSSEE CS
      PCNA_N 101 lvfesekkdki 111
                 +++ ++kk k+
  AJA91924.1 101 VTIGKNKKYKM 111
                 44555555443 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.15
                 HHHHHHHHTTSTTTSEEEEEEETTSSEEEEEEEECTSSEEE CS
      PCNA_N  72 lnslskilkcannedsvtlkaedeadtlalvfesekkdkia 112
                 ++ +s  l ++ ne+s t++ + ++  + + +e+  +d+i+
  AJA91924.1 146 VQVVSDYLTITSNESSATFSGKGDSGEVDIALETG-QDEIQ 185
                 44455566667777777777777777666666543.44455 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.023     1e+02      73     111 ..      63     101 ..       6     114 .. 0.54
   2 !   62.6   0.0   8.9e-21     4e-17       2     127 ..     123     244 ..     122     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                 ESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEE CS
      PCNA_C  73 lkepvtltfalkYlaeftkatsLservtlslssevPlvv 111
                  +  +++   ++ + +++k +  s+ +++++s++  l+v
  AJA91924.1  63 CDSDIKFGVRIDEFSKLIKRSDKSNSIEINISDDNMLLV 101
                 333444444445556666666666666666666666555 PP

  == domain 2  score: 62.6 bits;  conditional E-value: 8.9e-21
                 ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-.SEE CS
      PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkYlaeftkatsLs.erv 99 
                 +p ++yda ++l++s   +i  d++ +sd ++i+    +  fs +Gd G+ +i l+       ++e  +l++k+  t t++l+Yl+ ++ka   s e v
  AJA91924.1 123 LPKIDYDAKISLTASALDKILGDVQVVSDYLTITSNESSATFSGKGDSGEVDIALET-----GQDEIQELSVKQESTGTYSLEYLNPIIKAVGGSvEAV 216
                 5899***********************************************888875.....5678999**********************9876478* PP

                 EEEEETTSEEEEEEEETTCEEEEEEE-B CS
      PCNA_C 100 tlslssevPlvveykikdvgllayllak 127
                 t + ss  Pl ve+k+ ++g ++++la+
  AJA91924.1 217 TCEYSSAKPLRVEFKVSNLGQIHFYLAP 244
                 **************************98 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     8e-07    0.0036       4     248 ..      16     243 ..      14     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-07
        Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekvkisidekksrlivqllCkh 102
                 ++ ++s + +e  +e++ +g+++r ++ s+ a   ++  +s F+ky  + +++i++ + +  + ++++  s    + + ++i+i++++      ll   
  AJA91924.1  16 IISAISTLVEEATFEATVEGISFRGMDPSHVALIDINWPNSAFEKY--NCDSDIKFGVRIDEFSKLIK-RS---DKSNSIEINISDDNM-----LLVTI 103
                 5778999999************************************..88889999999999999996.34...455678899988764.....55568 PP

        Rad9 103 gvkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitielakervllksyeeeekdnkkalstelsideeeFeqyqlaedveitl 201
                 g  k++k+ l +s    + + k     k++  +  L ++l   +   + +ti  ++ + +++   + +     ++   l  +++e ++++++++   t+
  AJA91924.1 104 GKNKKYKMRLIESSASDTPLPKIDYDAKISLTASALDKILGDVQVVSDYLTITSNESSATFSGKGDSG-----EVDIALETGQDEIQELSVKQESTGTY 197
                 999*************************************************9999888775444433.....45567777899999999999999999 PP

        Rad9 202 slkefkallvfaeslsaslslafdeaGkPllltikklslleakfila 248
                 sl  +  ++  +      ++++++ a kPl +++k ++l +++f la
  AJA91924.1 198 SLEYLNPIIKAVGGSVEAVTCEYSSA-KPLRVEFKVSNLGQIHFYLA 243
                 99999999988888888889999887.88888888777777777776 PP

>> Tnp_22_dsRBD  L1 transposable element dsRBD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.16      24      55 ..     124     155 ..     118     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                   -EEETTTEEEEESSSSEEEESSHHHHHHHHTT CS
  Tnp_22_dsRBD  24 PrllYPakLsiiieGeikvfiDktklrdylst 55 
                   P++ Y ak+s++     k+  D + + dyl++
    AJA91924.1 124 PKIDYDAKISLTASALDKILGDVQVVSDYLTI 155
                   99****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1762.88
//
Query:       AJA91925.1  [L=242]
Description: putative 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-66  224.3   1.1    1.5e-66  224.1   1.1    1.0  1  His_biosynth  Histidine biosynthesis protein
     0.0057   15.5   0.6       0.11   11.3   0.1    2.1  2  Trp_syntA     Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.011   15.2   0.6       0.25   10.8   0.1    2.1  2  PcrB          PcrB family
      0.011   15.1   0.5       0.82    9.1   0.1    2.3  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.021   14.1   0.0      0.044   13.1   0.0    1.5  1  ThiG          Thiazole biosynthesis protein ThiG
      0.023   14.1   0.1        0.1   12.0   0.0    1.8  2  NMO           Nitronate monooxygenase
       0.11   11.6   0.1        8.8    5.3   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   1.1   5.9e-70   1.5e-66       1     227 [.       2     230 ..       2     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 5.9e-70
                   EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
  His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagad 97 
                   +iipa+Dl+dGkvVrl+kGd +++  y+++pve+ak++e+ g d lh+vDlda+  g+++n ++++ei e+++ip+qv GG r+ e++ e+l++ a+
    AJA91925.1   2 KIIPAIDLMDGKVVRLYKGDPKNKIIYSNNPVEIAKKWESLGGDILHIVDLDATL-GSGENSKIIKEISENTSIPLQVAGGLRTEEKISEVLDF-AS 96 
                   59**************************************************996.**************************************.** PP

                   EEEESHHHH.....H-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHH CS
  His_biosynth  98 kviigtaav.....knpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaea 189
                   + +igt a+     ++ +++++ ++ fgs++iv++iD  +g k++++gw+++tg+d+ +  +++ ++g+ e+l t++++dGtl+Gpd+e +k++++ 
    AJA91925.1  97 RAVIGTIAMqlkesEQDNILSDFIQTFGSERIVISIDHVDG-KIVTHGWQNNTGIDLYDATNEFVNYGFTEFLTTNVSKDGTLEGPDIESLKKICQI 192
                   *******98333224566899********************.******************************************************* PP

                   HSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTS CS
  His_biosynth 190 vkipviasGGvgsledlkelksegvdavivgsalyege 227
                    k + iasGG+++++d++++++    +vi+g+alyeg 
    AJA91925.1 193 KKCNAIASGGISKMQDIQDVNEIDPFGVILGKALYEGL 230
                   *********************9999***********96 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   4.4e-05      0.11     187     238 ..      62     113 ..      57     126 .. 0.85
   2 ?    2.5   0.1     0.021        54     190     233 ..     186     230 ..     172     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                 HHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHCTTT CS
   Trp_syntA 187 delverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkieeeae 238
                 +++++++++ t  P+ v  G++t+e++++v   a+ +++G   ++  e+e++
  AJA91925.1  62 SKIIKEISENTSIPLQVAGGLRTEEKISEVLDFASRAVIGTIAMQLKESEQD 113
                 5789************************************877766554444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                 HHHHHHCTSS-EEEESSS-SHHHHHHHHTT-.SEEEE-HHHHHHH CS
   Trp_syntA 190 verlkkltavPvavGFGistkeqvkqvakva.dGvivGSalvkki 233
                 ++++ ++++  +    Gis+ ++++ v+++   Gvi G al + +
  AJA91925.1 186 LKKICQIKKCNAIASGGISKMQDIQDVNEIDpFGVILGKALYEGL 230
                 4555555554455555************77526*****9987655 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   9.9e-05      0.25     157     222 ..      50     115 ..      41     122 .. 0.75
   2 ?    3.0   0.1     0.024        61     169     214 ..     184     229 ..     164     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.9e-05
                 EEEE-.TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-CHHHHHHHCHHHHH CS
        PcrB 157 iYlEa.sGaledveevialkkklekarlivGGGirsaEkAkevveaADvivvGnvveekderkidai 222
                 + l+a  G  e+ + +++++   +++ l v GG+r +Ek  ev+  A   v+G++  + +e+  d+i
  AJA91925.1  50 VDLDAtLGSGENSKIIKEIS-ENTSIPLQVAGGLRTEEKISEVLDFASRAVIGTIAMQLKESEQDNI 115
                 55666445445545555555.45678999*************************9877776665555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.024
                 HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHH CS
        PcrB 169 eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveek 214
                 e ++++  +++k + i  GGi +  + ++v e     ++ G +++e 
  AJA91925.1 184 ESLKKI-CQIKKCNAIASGGISKMQDIQDVNEIdPFGVILGKALYEG 229
                 333333.35678899***********999998877789999999996 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00032      0.82     128     165 ..      62      99 ..      58     104 .. 0.85
   2 ?    4.1   0.0     0.011        28     130     159 ..     185     214 ..     180     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00032
                   HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEE CS
  G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiav 165
                    k+ikei+++++ip+  +G ++t+e++ e+l+    av
    AJA91925.1  62 SKIIKEISENTSIPLQVAGGLRTEEKISEVLDFASRAV 99 
                   589***********977777799******998766666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                   HHCTSTTS...EEEEESS--SHHHHHHHCT CS
  G3P_antiterm 130 vikeikkelkipiiaGGLietkedveealk 159
                    +k+i++  k++ ia+G i++ +d++++ +
    AJA91925.1 185 SLKKICQIKKCNAIASGGISKMQDIQDVNE 214
                   578999999****************98765 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.7e-05     0.044     128     206 ..      27     104 ..      19     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.7e-05
                 EEE-S-HHHHHHHHHTT-SE..BEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH CS
        ThiG 128 pYvsdDlvlarrleevGcaa..vmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnta 206
                  Y ++ + +a++ e +G     ++ l a +Gsg+   n + +k i e++++P+ v  G+++ +++ +++++   av+   a
  AJA91925.1  27 IYSNNPVEIAKKWESLGGDIlhIVDLDATLGSGE---NSKIIKEISENTSIPLQVAGGLRTEEKISEVLDFASRAVIGTIA 104
                 67888888999999999764227899999**995...899********************************999986555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     4e-05       0.1     179     250 ..      59     129 ..      33     140 .. 0.82
   2 ?   -0.8   0.0      0.31   7.9e+02     196     214 ..     197     215 ..     183     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
         NMO 179 kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkklleaklddte 250
                  +  ++++++ +  +iP+  aGG+ +++ +  +L   As + igt  +  kes+  ++    +   + ++++
  AJA91925.1  59 GENSKIIKEISENTSIPLQVAGGLRTEEKISEVLDF-ASRAVIGTIAMQLKESEQDNILSDFIQTFGSERIV 129
                 467789999*************************99.666669***99999999988877766666655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
         NMO 196 viAaGGiidrrgvaaaLal 214
                  iA GGi + ++++ +  +
  AJA91925.1 197 AIASGGISKMQDIQDVNEI 215
                 5899999999999876555 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0034       8.8     173     204 ..      63      94 ..      53     106 .. 0.84
   2 ?    4.3   0.0    0.0069        18     171     217 ..     182     227 ..     169     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0034
                 HHHHHHHHH-SS-EEEESS--SHHHHHHHHHH CS
         Dus 173 eaIkevkqavsipviaNGdIkdaedaqailee 204
                 + Ike+ ++ sip+ + G+ ++ e+++++l+ 
  AJA91925.1  63 KIIKEISENTSIPLQVAGGLRTEEKISEVLDF 94 
                 679*********************99999976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0069
                 -CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
         Dus 171 dweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                 d+e+ k+++q  +   ia G+I +++d+q++ e     gv+ g++ +
  AJA91925.1 182 DIESLKKICQIKKCNAIASGGISKMQDIQDVNEI-DPFGVILGKALY 227
                 5677788888888999*************98776.566777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1755.46
//
Query:       AJA91926.1  [L=92]
Description: bacterial Fe(2+) trafficking domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-06   27.0   2.5    6.2e-06   25.8   2.5    1.8  1  Iron_traffic   Bacterial Fe(2+) trafficking
     0.0086   16.2   1.2      0.012   15.7   1.2    1.2  1  FYVE           FYVE zinc finger
  ------ inclusion threshold ------
      0.022   14.9   1.3      0.031   14.4   1.3    1.3  1  zf-RRPl_C4     Putative ribonucleoprotein zinc-finger pf C4 t
      0.049   13.2   1.1      0.049   13.2   1.1    1.9  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
      0.083   12.7   1.1       0.19   11.6   1.1    1.6  1  ZZ             Zinc finger, ZZ type
       0.19   11.5   2.6       0.68    9.7   0.1    2.2  2  DUF3039        Protein of unknown function (DUF3039)
       0.21   11.4   3.4       0.56   10.0   0.3    2.3  2  zinc_ribbon_2  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Iron_traffic  Bacterial Fe(2+) trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   2.5   2.4e-09   6.2e-06      35      73 ..      28      66 ..       1      78 [. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.4e-09
  Iron_traffic 35 skeawqeWlkkqtmLiNekrLnladpkarkfLeeqmekf 73
                  + + w+eW + + m+iNe +L+l  +++rk+L+++ + f
    AJA91926.1 28 CTKCWNEWKEMKIMVINEMHLDLSLSDHRKVLRKHEKIF 66
                  5689****************************9875544 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   4.7e-06     0.012      34      66 ..       3      35 ..       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
                EE-STTS-EEE.EEGGGTEEEEEEE-HHHHHHH CS
        FYVE 34 vvCekCssklvallekeaeeksvrvCkeClael 66
                ++C+kC ++  ++ + e++ +++ +C++C++e 
  AJA91926.1  3 IICTKCKEEIPENEQLESQAEKYPLCTKCWNEW 35
                89****************************986 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.3   1.2e-05     0.031      53      91 ..       3      36 ..       1      51 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
  zf-RRPl_C4 53 kLCtkCkeknekekeircetfeeylkklklCkeCkerve 91
                ++CtkCke+  ++++++++      +k  lC++C ++ +
  AJA91926.1  3 IICTKCKEEIPENEQLESQ-----AEKYPLCTKCWNEWK 36
                69********997666655.....99********87644 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.1   1.9e-05     0.049       3      19 ..       3      19 ..       2      19 .. 0.90
   2 ?   -1.3   0.1      0.66   1.7e+03       4       8 ..      27      31 ..      26      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
      zf_UBZ  3 ylCerCgkeipeselqE 19
                ++C +C++eipe+e+ E
  AJA91926.1  3 IICTKCKEEIPENEQLE 19
                78***********9877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.66
      zf_UBZ  4 lCerC 8 
                lC +C
  AJA91926.1 27 LCTKC 31
                59999 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   7.3e-05      0.19       5      38 ..       3      36 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                EE-TTT-S..EESSEEEESSSSS-EE-HHHHHH.. CS
          ZZ  5 ytCdgCseapligvRyhclrcsdYDLCqsCfst.h 38
                 +C +C+e ++ ++     +++ Y LC +C ++ +
  AJA91926.1  3 IICTKCKE-EIPENEQLESQAEKYPLCTKCWNEwK 36
                68******.9999999999***********99844 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4     0.081   2.1e+02      45      51 ..       4      10 ..       2      15 .. 0.86
   2 ?    9.7   0.1   0.00027      0.68      39      56 .]      21      38 ..      17      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.081
     DUF3039 45 vCpeCke 51
                +C +Cke
  AJA91926.1  4 ICTKCKE 10
                8*****8 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
     DUF3039 39 dpkkfPvCpeCkeiyesl 56
                +++k+P+C +C + ++++
  AJA91926.1 21 QAEKYPLCTKCWNEWKEM 38
                689********9988877 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00022      0.56       2      14 ..       5      17 ..       4      18 .. 0.91
   2 ?    1.8   0.2      0.08   2.1e+02      15      19 ..      27      31 ..      19      31 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
  zinc_ribbon_2  2 CpnCGaelqdnak 14
                   C++C +e+++n++
     AJA91926.1  5 CTKCKEEIPENEQ 17
                   **********986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.08
  zinc_ribbon_2 15 FCpyC 19
                    C++C
     AJA91926.1 27 LCTKC 31
                   57777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 705.39
//
Query:       AJA91927.1  [L=241]
Description: putative TIGR00161 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-43  147.0   0.0      9e-43  146.8   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   0.0     5e-47     9e-43       2     212 ..      24     225 ..      23     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 5e-47
                 EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE...E-HSCHHHHHHHHHHHHHHHTT CS
        PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg...repilqyeefakalldwaeelg 96 
                 ++Gf+g+G+Vg++avd++i++l++++vg+++s++ lp     p++++ +gr ++p+r+y + d   ++++++ +   +++++ y+ +a a+ldwae+ g
  AJA91927.1  24 FVGFVGAGLVGTIAVDHMINELDMKEVGFLRSKH-LP-----PSTVFMQGRLRHPFRIYSNsD---GSICAIICeivISQDGIYN-IAMAILDWAEKKG 112
                 78********************************.9*.....9****************8855...9******************.************* PP

                 ESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT CS
        PAC2  97 vkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllg 190
                  +e++vL+g++  +      +     + aa + +l + +ee+     ++g+i+gi+g +l+++  r+i ++ lla +++  pdP aaa+++++++++++
  AJA91927.1 113 STEIIVLDGVADKKH-----DGN--AFFAA-EVDLCRVMEENdiqmvPQGFITGISGGILNECLIRKIRGITLLAKADELTPDPVAAATIIDAINRVYD 203
                 **********94433.....222..22222.223332233223456699************************************************** PP

                 ---HCHHHHHHHHHHHHHHHHH CS
        PAC2 191 levdtedLeedaeeleeqleel 212
                 +e++t++L+++ e++   l+el
  AJA91927.1 204 TEINTKNLKKQKEQMSTDLKEL 225
                 ***************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1279  (0.0713369); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1705.56
//
Query:       AJA91928.1  [L=204]
Description: translocator protein, LysE family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-30  103.8  15.6      9e-30  103.6  15.6    1.0  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6  15.6     5e-34     9e-30       2     192 ..      17     203 ..      16     204 .] 0.96

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 5e-34
        LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdakekkveaeksveaslvkpf 100
                 s+++spGp +++ + +g+++g   gi +a+g++i++  lill+ +G+  + +  p + + +++lG++ L+ +++l++r+  ++k++ e ++      pf
  AJA91928.1  17 SGVMSPGPLFAANVMYGLREGKISGIKMAVGHTIVEFPLILLLGIGFFSIEN-VPEIRTAITILGAIGLFGFAFLQIRAVTKQKFSLETKS---GQGPF 111
                 899***********************************************99.****************************9998655555...48*** PP

        LysE 101 lkglllslsNPkailfwlsvisallaka.eqygdagrlilaaglvvasliwfsllaflaarlsrrlsskkvlriinvvvgvlligfavkllle 192
                  +g+lls +NP++i++wl ++ +l+++  +  g  g+++l++ +++ + +w++ +a +++r  ++ls++  ++ i + ++v+l++f++++ll+
  AJA91928.1 112 VAGILLSALNPFFIVWWLTIGLVLISESiQIFGILGIVVLFLFHIWMDYAWLFTIAAFSSRAKNYLSKRN-FKFIIIGLSVVLVYFGIEFLLK 203
                 *******************************************************************997.67*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1364.52
//
Query:       AJA91929.1  [L=585]
Description: glutamine-fructose-6-phosphate transaminase (isomerizing) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-47  158.5   1.4      3e-25   88.6   0.9    2.4  2  SIS             SIS domain
    3.1e-21   76.0   0.0    5.5e-21   75.2   0.0    1.4  1  GATase_6        Glutamine amidotransferase domain
      4e-16   59.0   0.1    1.4e-15   57.3   0.0    1.9  2  GATase_7        Glutamine amidotransferase domain
    2.2e-06   27.7   1.3    0.00013   22.0   0.2    3.2  3  SIS_2           SIS domain
    2.5e-05   23.3   0.0    5.1e-05   22.3   0.0    1.4  1  GATase_4        Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.057   12.4   0.4        2.2    7.3   0.0    2.7  3  Asparaginase_2  Asparaginase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.9     1e-28     3e-25       2     126 ..     281     404 ..     280     409 .. 0.97
   2 !   68.3   0.0   1.9e-22   5.6e-19       2     129 ..     442     566 ..     441     568 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1e-28
                 HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSE CS
         SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadl 100
                 +++ak+iy++G+Gtsy++a+ ++  l +  +i +e   asel+     +i+ed ++i+is+sge++d+++a++ ak+ + kii+I +  +s+l r+ d+
  AJA91929.1 281 IRSAKNIYITGSGTSYNSALIAKQILSKYVKIKSEPIIASELQFA-PETIEEDSVLIAISQSGESADVLEAVRIAKKSNCKIISIVNLLTSSLTRKGDV 378
                 899******************************************.9**************************************************** PP

                 EEEEEEECHCSSSHCHHHHHHHHHHH CS
         SIS 101 alyinaepetlvastksltaqlaald 126
                 +l +n +pe++va+tks+taql++l+
  AJA91929.1 379 VLGMNCGPEIGVAATKSFTAQLIVLY 404
                 ***********************987 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 1.9e-22
                 HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHH.HHHHHHHHHHHTTSEEEEEESSTTSHHHHHSS CS
         SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetk.dlvaaaelakergakiiaITdskgsplaread 99 
                 L +   iy+lG+G +y+ia e+alkl+e+++i++e+ + +elkhg+lal+d d  vi+i +++ t  d++ +a++ k+rgakii++ d +++      d
  AJA91929.1 442 LKDVSDIYILGRGINYPIAIESALKLKELTYIHAEGIPGGELKHGPLALMDTDVFVIVINPNDSTYtDTLTSAREIKARGAKIIGVSDIESDV----YD 536
                 778889******************************************************99999648999999************9655443....47 PP

                 EEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
         SIS 100 lalyinaepetlvastksltaqlaaldala 129
                 +++ i++ +e+l+++   ++ ql+ ++ ++
  AJA91929.1 537 YWIKIPKINEILYPISEIIPIQLLTYYSAL 566
                 889999999998888888888888887665 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.0   1.8e-24   5.5e-21      11     133 ..      64     191 ..      49     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 1.8e-24
    GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall......eelG......eevlerlrGmfa 97 
                  ++++++H+R+a++g  ++  a+P ps++g++++vhNG i+n++el+++l++ +g++f+s++D+e++++ll      +          +++++++G +a
  AJA91929.1  64 PGKIGIGHTRWATHGKVTDLNAHPHPSNSGKIAIVHNGIIENFEELKKQLEN-DGYSFKSETDSEIIANLLqknyesT--KnvkdtiMKTVSAIKGHYA 159
                 4579************977777******************************.****************998666540..155567788889******* PP

    GATase_6  98 faiwdkrentlilardrlgvkplyyavdesglafas 133
                 f+++  ++++  la+ r+  +pl+++v ++++  +s
  AJA91929.1 160 FVAMF-ENGQ--LAAARFH-EPLIIGVGQENIFLSS 191
                 *8765.3444..4444666.7888888777776666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   4.7e-19   1.4e-15      12     117 ..      84     192 ..      71     196 .. 0.88
   2 ?   -2.4   0.0       1.4   4.3e+03      21      50 ..     284     313 ..     279     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 4.7e-19
    GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAfaiwdeeekrlllaRDrlGikP 101
                 +a P   s++g+++iv+nG i N++el+++Le+ g++f++++D+e++++ll++         + + ++++ ++G +Af+ + e+  +l +aR +    P
  AJA91929.1  84 NAHPHP-SNSGKIAIVHNGIIENFEELKKQLENDGYSFKSETDSEIIANLLQKnyestknvkDTIMKTVSAIKGHYAFVAMFENG-QLAAARFH---EP 177
                 455666.5799**************************************************999*****************9998.9999*995...99 PP

    GATase_7 102 LyygedkgdallfaSe 117
                 L++g  + ++++++S 
  AJA91929.1 178 LIIGVGQ-ENIFLSSD 192
                 9999996.57777775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
    GATase_7  21 dgrlvivfnGeiyNykelreeLeakghrfr 50 
                  +++ i+ +G+ yN   + +++ +k ++++
  AJA91929.1 284 AKNIYITGSGTSYNSALIAKQILSKYVKIK 313
                 5678999999****9999999988877666 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12   3.5e+02      30      71 ..     279     322 ..     256     328 .. 0.69
   2 !   22.0   0.2   4.5e-08   0.00013      99     137 ..     327     365 ..     296     366 .. 0.80
   3 ?    2.1   0.0     0.061   1.8e+02     105     136 ..     494     527 ..     487     529 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                 HHHHTT--EEEEESG...GGHHHHHHTSSSTT-BTTEEEE--GGG CS
       SIS_2  30 dslenggkvlvfGsG...hSaalaeelaaragglaeferialpal 71 
                 + +++ + +++ GsG   +Sa++a+++  +++++ + e+i+  +l
  AJA91929.1 279 EYIRSAKNIYITGSGtsyNSALIAKQILSKYVKI-KSEPIIASEL 322
                 567788899*****94455688899988888875.5566666555 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.5e-08
                 TT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
       SIS_2  99 vrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                   +++  vL+ iS+sG++a v+ea++ ak+  +k+i ++
  AJA91929.1 327 ETIEEDSVLIAISQSGESADVLEAVRIAKKSNCKIISIV 365
                 5689999*****************************997 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.061
                 -EEEEE-SS--S..HHHHHHHHHHHHHT-EEEEE CS
       SIS_2 105 DvLlviSnsGnn..avvveaaeaakergmkviAl 136
                 Dv++++ n   +  +  +  a++ k+rg+k+i++
  AJA91929.1 494 DVFVIVINPNDStyTDTLTSAREIKARGAKIIGV 527
                 666666555554335678899***********98 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.7e-08   5.1e-05      71     187 ..      65     175 ..      45     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-08
    GATase_4  71 sknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrfekaepsaeeleralaelake 165
                  k+ + H R at+G+v++ n+hp   + +  ++ + HnG ++++++      ++ ++   +TDsE +   ll   ++++    +s++++++++ + ++ 
  AJA91929.1  65 GKIGIGHTRWATHGKVTDLNAHPHPSNSG--KIAIVHNGIIENFEELKkqleNDGYSFKSETDSEII-ANLL---QKNY----ESTKNVKDTIMKTVSA 153
                 567899*****************976654..56778***9988765443347677888899***965.3444...3444....4667899999999999 PP

    GATase_4 166 iaelGvfnlllsdgralfahas 187
                 i+ +  f  ++ +g+   a+ +
  AJA91929.1 154 IKGHYAFVAMFENGQLAAARFH 175
                 9999999999999997776655 PP

>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.38   1.1e+03      52      78 ..      36      62 ..      21      63 .. 0.82
   2 ?    7.3   0.0   0.00072       2.2     238     295 ..     126     183 ..     116     189 .. 0.81
   3 ?    2.1   0.0     0.027        80     224     282 ..     289     345 ..     277     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.38
                    HHHHCTCCCSSSTTSS-BTTS---EEE CS
  Asparaginase_2 52 rllEddplfnaGkGsvltedgeveldA 78
                    +  E++++ + G+G v + + + +ld 
      AJA91929.1 36 TESENQIELKKGTGKVTEVNSKFQLDT 62
                    45699999************9999996 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00072
                     HHHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETTS-EEEEECSCCCEEEEE CS
  Asparaginase_2 238 adivalmeykglsleeAaekvieeklkrvkgsgGviavdkkGevaaefnsegmlraya 295
                      +i+a + +k+ + ++ ++++i+++++++kg+ +++a+ ++G++aa+   e ++ ++ 
      AJA91929.1 126 SEIIANLLQKNYESTKNVKDTIMKTVSAIKGHYAFVAMFENGQLAAARFHEPLIIGVG 183
                     4566666666999999****************************99887777666665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.027
                     EEE-HHHHCCTTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETTS-EE CS
  Asparaginase_2 224 aTGkGeeiirellaadivalmeykglsleeAaekvieeklkrvkgsgGviavdkkGeva 282
                      TG+G ++   l+a++i++++ +   ++  A+e  +  + + ++++  +ia++++Ge a
      AJA91929.1 289 ITGSGTSYNSALIAKQILSKYVKIKSEPIIASELQF--APETIEEDSVLIAISQSGESA 345
                     69*****************99997777777776655..56667789**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4216.34
//
Query:       AJA91930.1  [L=261]
Description: hypothetical protein T478_0138 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0014   18.7   0.1     0.0029   17.6   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0015   18.1   0.0        0.4   10.2   0.0    2.5  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
       0.19   12.0   0.0       0.66   10.2   0.0    1.8  2  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.9e-07    0.0029      65     107 ..      65     105 ..      27     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-07
  Glyco_trans_4_2  65 klkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvw 107
                      +l++l kk+kPD + +h ++p+g+  +l  r+ + +p+++s++
       AJA91930.1  65 SLIQLNKKFKPDCIVIHSTIPPGTTERLQ-RKIN-SPIIFSAT 105
                      799*********************99885.4444.9****987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0022        13       5      38 ..       6      38 ..       2      49 .. 0.83
   2 !   10.2   0.0   6.7e-05       0.4     114     135 ..      75      96 ..      61     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0022
                    EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
  UDPG_MGDP_dh_N  5 viGlGYvGlvtaavlaeighevigvDideekvdk 38
                    v GlG +Gl+   +l+++  +++g D +e+  +k
      AJA91930.1  6 VAGLGEIGLPILKILSKK-ENIVGYDLNEKLMNK 38
                    78***********99987.6899****9987665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.7e-05
                     EEEEEE-S---TTHHHHCHHHH CS
  UDPG_MGDP_dh_N 114 gkvvvvkSTvpvgtaeelvkki 135
                      + +v+ ST+p+gt+e l +ki
      AJA91930.1  75 PDCIVIHSTIPPGTTERLQRKI 96 
                     67899***********887776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00011      0.66       2      36 ..       5      38 ..       5      48 .. 0.89
   2 ?   -2.0   0.0      0.71   4.3e+03      44      60 ..     148     164 ..     104     165 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
      TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkdeervee 36
                i++GlG++G  +++ Ls+++ ++v+ d +e+ +++
  AJA91930.1  5 IVAGLGEIGLPILKILSKKE-NIVGYDLNEKLMNK 38
                89****************99.5******9998776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.71
                 EEES-TTSHHHHHHTTG CS
      TrkA_N  44 vvvgdatdeevLeeagi 60 
                 +   + t++e+Le a+i
  AJA91930.1 148 IRTKQMTKPETLELAKI 164
                 44456777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2049.78
//
Query:       AJA91931.1  [L=361]
Description: periplasmic solute-binding family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-72  242.7   2.5    4.7e-72  242.5   2.5    1.1  1  ZnuA         Zinc-uptake complex component A periplasmic
  ------ inclusion threshold ------
       0.18    9.9  15.0       0.27    9.3  15.0    1.1  1  DNA_pol_phi  DNA polymerase phi
       0.19   10.0   3.4       0.22    9.8   3.4    1.1  1  CDC45        CDC45-like protein
       0.28   11.2   3.4       0.79    9.7   2.6    2.2  3  DUF3915      Protein of unknown function (DUF3915)
       0.44    9.8  12.1       0.63    9.3  12.1    1.2  1  NOA36        NOA36 protein
        1.5    8.2  10.7        2.1    7.7  10.7    1.1  1  SDA1         SDA1
        3.4    6.7  15.7        4.8    6.2  15.7    1.2  1  DUF2457      Protein of unknown function (DUF2457)
        8.2    4.8   6.7         11    4.4   6.7    1.3  1  RRN3         RNA polymerase I specific transcription initiati


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.5   2.5   2.1e-75   4.7e-72       1     254 [.      53     355 ..      53     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 242.5 bits;  conditional E-value: 2.1e-75
                 EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEEETTTTC............... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
        ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevidlsegv............... 84 
                 ++++++p+++++++vaGd ++v+  +p+g+++H++ep++++++ l++Ad++vyngl++E++++++++s +  ++v ++++segv               
  AJA91931.1  53 ILTSFYPYHEFTKNVAGDFANVKQFMPSGVEAHDWEPRAQEIQSLKDADVFVYNGLGMESYIENIIESGE-FDNVVFLKASEGVellkfeddhddhakh 150
                 78***************************************************************97664.3444555566555444554444444433 PP

                 .CSEBCSS...................................ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                 .xxxxxxx...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ZnuA  85 .eeeeeee...................................DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireela 147
                  +     +                                   DpHiWl+p +++++v+ i+d+L+++dp+n++ ye+na+ y++k+++ld +i ++l+
  AJA91931.1 151 dD-----HddhddhdehakeddhddhdeheegghdghdhdyefDPHIWLDPILVKQQVNVIRDGLIQVDPDNKEHYEENARIYNDKMDALDMKIGSALS 244
                 30.....0344555666777777888889999999**************************************************************** PP

                 TSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-STSSSTSTT.S.TT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xx RF
        ZnuA 148 eipeekrklvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvatlysldslgdeg.s.ae 240
                 ++++++  +v +h+af yl ++y+++++++ g+ ++    aa+ia++++ +k++++k+if+e+l++p+lae +aeea+++v+ + +l++l++++   + 
  AJA91931.1 245 SCQKDT--IVPYHNAFTYLGERYDIHIMALGGMAPDaeasAAEIAEFVDFVKDNDIKVIFSEELVDPRLAEVIAEEANAQVLLFSPLEALSKDEtGtNV 341
                 999888..********************999**999******************************************************888754588 PP

                 SHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxx RF
        ZnuA 241 tYidmmranleslk 254
                 +Yid m+ nl+slk
  AJA91931.1 342 SYIDKMEDNLDSLK 355
                 ************98 PP

>> DNA_pol_phi  DNA polymerase phi
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  15.0   0.00012      0.27     638     730 ..     140     242 ..     129     253 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00012
  DNA_pol_phi 638 fedededeeddeeeeeeddeededseedddeeesdedeededdedvdeid...........elreklaealgesg......ededdddsdsDed.mdD 717
                  fed+++d  + ++ ++ dd+++  +e+d d++++ e+   + ++++ e d           +          ++        d d+++  +++  +  
   AJA91931.1 140 FEDDHDDHAKHDDHDDHDDHDEHAKEDDHDDHDEHEEGGHDGHDHDYEFDphiwldpilvkQ--------QVNVIrdgliqVDPDNKEHYEENArIYN 229
                  45555555555555555555555555555555555544444444444444777666644431........2222244445545666677777777*** PP

  DNA_pol_phi 718 eqMmaLDeqLaei 730
                  ++M aLD ++ ++
   AJA91931.1 230 DKMDALDMKIGSA 242
                  *******998765 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.4   9.8e-05      0.22     124     167 ..     136     177 ..      95     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.8e-05
       CDC45 124 ealeeeeesdeedeeeeeeddddeeeeeeeeedeedeeedeees 167
                 e l++e++ d++  + ++++dd+++++e+ +ed++d+++++ee 
  AJA91931.1 136 ELLKFEDDHDDHA-K-HDDHDDHDDHDEHAKEDDHDDHDEHEEG 177
                 4444444444222.2.2222222222222222222222222221 PP

>> DUF3915  Protein of unknown function (DUF3915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.6   0.00035      0.79      38     104 ..      90     156 ..      55     176 .. 0.81
   2 ?   -0.6   0.5      0.53   1.2e+03      17      37 ..     155     175 ..     150     184 .. 0.56
   3 ?   -2.4   0.0         2   4.5e+03      73      92 ..     313     332 ..     310     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
     DUF3915  38 rekkkerhavcnvlasiavgtelsllsikgnvtfrnvifegfangvalfsalnnkddkdnkddknnq 104
                 r ++ +  +  +v+    +g e  +  i   + f+nv+f   ++gv l+   + +dd+ ++dd+++ 
  AJA91931.1  90 RAQEIQSLKDADVFVYNGLGMESYIENIIESGEFDNVVFLKASEGVELLKFEDDHDDHAKHDDHDDH 156
                 55555666667788888899999999999*******************9998887777666665544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.53
     DUF3915  17 ghccdrdrerereredereke 37 
                  h  + +  +e +++d+ e+e
  AJA91931.1 155 DHDDHDEHAKEDDHDDHDEHE 175
                 333334455566666666655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2
     DUF3915  73 nvifegfangvalfsalnnk 92 
                 +vi e     v lfs l+  
  AJA91931.1 313 EVIAEEANAQVLLFSPLEAL 332
                 68888888899999998532 PP

>> NOA36  NOA36 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  12.1   0.00028      0.63     266     302 ..     133     177 ..      91     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
       NOA36 266 g........ddeddegdedddddddeedddeeeddedeeeeeeee 302
                 +        dd+dd++++dd+dd+d++d++ +edd+d+++e+ee 
  AJA91931.1 133 EgvellkfeDDHDDHAKHDDHDDHDDHDEHAKEDDHDDHDEHEEG 177
                 234555555899999999999999999999999998888888775 PP

>> SDA1  SDA1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  10.7   0.00092       2.1      71     129 ..     133     212 ..     119     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00092
        SDA1  71 eGleLlekwkeeekkekreeeeedsddeddeedwevesdddseedseggwidvesdee........................e 129
                 eG+eLl+ +++ +++ k+  ++ d++d+ de+ +e ++ dd +e +egg    ++d e                        +
  AJA91931.1 133 EGVELLKFEDDHDDHAKH--DDHDDHDDHDEHAKEDDH-DDHDEHEEGGHDGHDHDYEfdphiwldpilvkqqvnvirdgliQ 212
                 899999987666666665..444433333434444444.34456777887777777778888888888777766666655442 PP

>> DUF2457  Protein of unknown function (DUF2457)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  15.7    0.0022       4.8      58     107 ..     141     185 ..      90     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
     DUF2457  58 eddeedeeddddddddedddedddeedededddstvedlseeasdGyetD 107
                 edd +d+ ++dd+dd++d+de  +e+d+d+ +d+++    e   dG++ D
  AJA91931.1 141 EDDHDDHAKHDDHDDHDDHDEHAKEDDHDD-HDEHE----EGGHDGHDHD 185
                 555555555444444444333333333333.22222....2233444433 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   6.7     0.005        11     211     256 ..     135     176 ..      93     256 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.005
        RRN3 211 Veiqveledlddeedeeleeeleededdedddeddeesdlddlssd 256
                 Ve+    +d dd ++++++++   d++de+++edd  +d++d++++
  AJA91931.1 135 VELLKFEDDHDDHAKHDDHDDH--DDHDEHAKEDD--HDDHDEHEE 176
                 4554333333333333332221..11111111111..122222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2541.05
//
Query:       AJA91932.1  [L=145]
Description: hypothetical protein T478_1094 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-08   32.7   0.2    8.6e-08   32.0   0.2    1.3  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.2   4.8e-12   8.6e-08       9      77 ..      28      96 ..      19      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.8e-12
                    S-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS--- CS
  Ribosomal_S24e  9 katpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekk 77
                     ++ +++e  + + k ++ + ++v+  +++++ G+   tG + +Yd++e akk  +  + +R + + kk
      AJA91932.1 28 GGKLKRKEAVDMITKEFNLSDKTVIAINMKNQTGRPNVTGMFYVYDNEELAKKQVNPTIFERLERQAKK 96
                    57899***************************************************9999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1295  (0.0722293); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 994.34
//
Query:       AJA91933.1  [L=173]
Description: THUMP domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-10   40.9   2.1    2.8e-10   40.5   2.1    1.2  1  THUMP     THUMP domain
     0.0028   18.0   0.1     0.0054   17.1   0.1    1.4  1  CDT1_C    DNA replication factor Cdt1 C-terminal domain
  ------ inclusion threshold ------
      0.014   15.8   0.9      0.027   14.9   0.9    1.4  1  KH_10     GLD-3 KH domain 5
      0.047   14.1   0.8      0.074   13.5   0.8    1.2  1  CENP-H    Centromere protein H (CENP-H)


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   2.1   6.3e-14   2.8e-10       2     143 ..      21     156 ..      20     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.3e-14
                 HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEET...HHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS CS
       THUMP   2 eieellkegkvnverveagkgrivvelkgekpeed...eellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf 97 
                 +++e++++++  +e+ ++  g i+v+++  ++++    +e++++    +++ +r+ip+  +ce++le+i + a+e+ + ++ +e  t++++v++r++  
  AJA91933.1  21 NMLERFGDKEALIEKTPFS-GIILVKTSLDNIKVLdnfREIIEDEPWLIKYCSRIIPIQKECETKLEEIRDVAVELSNVMKQNE--TYRITVEKRHS-- 114
                 7788888888888888884.666666665555443111344444444555****************************888776..***********.. PP

                 SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
       THUMP  98 eftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                 +   ++i + +++ + +    kV+len d+ ++v+i+++k+++s+ 
  AJA91933.1 115 SLHTKDIISNIADSLSN----KVSLENSDWEIIVQILRNKTGVSVI 156
                 68899999999888777....9*********************986 PP

>> CDT1_C  DNA replication factor Cdt1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.2e-06    0.0054      25      82 ..      79     147 ..      74     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
      CDT1_C  25 errsallgrlpdvarilrllf.........vaekksalpmeevvkklkdSlrtpvs..keeaekhlrlL 82 
                 ++ +  l+ + dva  l++++         v++++s+l  ++++++++dSl+++vs  ++++e  +++L
  AJA91933.1  79 KECETKLEEIRDVAVELSNVMkqnetyritVEKRHSSLHTKDIISNIADSLSNKVSleNSDWEIIVQIL 147
                 5555666999999999****9********9999******************988774467777777777 PP

>> KH_10  GLD-3 KH domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   5.9e-06     0.027      11      83 ..      69     142 ..      67     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                 HHHHHTSEEEEEEEEEGGGBS---------BEEEE-TTS-EEEEEEEEE--SSSS--..-EEEEEEEEEEEGGGH CS
       KH_10  11 ryiqgLLPvqlifdientDllervkasdrnitlildelrvsvkvtkselEgeellse..dvlrnivslrskEfnl 83 
                 +y   ++P+q  ++ + ++++  v ++  n+++  + +r++v+ ++s+l +++++s+  d l n vsl+ +++ +
  AJA91933.1  69 KYCSRIIPIQKECETKLEEIRD-VAVELSNVMKQNETYRITVEKRHSSLHTKDIISNiaDSLSNKVSLENSDWEI 142
                 788899**************99.99******************************9877999*******999876 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8   1.6e-05     0.074      11      90 ..      70     148 ..      67     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
      CENP-H  11 lssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkksrqrwrvvknvas 90 
                  +s+++ +++e+++++ee+ +v +e  ++ ++n++   +++ ++  + ++k+  ++  ++l +++  + + w+++ ++++
  AJA91933.1  70 YCSRIIPIQKECETKLEEIRDVAVELSNVMKQNETYRITVE-KRHSSLHTKDIISNIADSLSNKVSLENSDWEIIVQILR 148
                 5899999*********************************4.333333444347888999**************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1280.07
//
Query:       AJA91934.1  [L=173]
Description: hypothetical protein T478_0025 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.015   15.5   0.0    1.3  1  CBM_4_9   Carbohydrate binding domain


Domain annotation for each model (and alignments):
>> CBM_4_9  Carbohydrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   8.6e-07     0.015      46      99 ..      47     102 ..      38     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.6e-07
                 STTCEEEEEEECCS-TT-EEEEEEEEEESSTSEEEEEEEEEESSTTS....CTCEEEE CS
     CBM_4_9  46 etwdgqaiditirlekgktYtvsfwvkassgksrtikvkigdtdadg....anydeva 99 
                 e  d+q i+++  + +g tY+++f  +++s+  ++ik++i+++  ++     ++ +++
  AJA91934.1  47 EFNDIQTITSGLGVIEGGTYKIGFVPMGDSP--AKIKLTIKGKWTESyrlePSWRQIF 102
                 5679999999*********************..********99886544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1329.79
//
Query:       AJA91935.1  [L=162]
Description: HEAT repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-20   71.5   0.0    3.1e-13   49.9   0.0    2.1  2  HEAT_2     HEAT repeats
    1.6e-14   52.7   0.4      0.011   15.9   0.0    4.3  4  HEAT       HEAT repeat
    3.9e-09   36.3   0.0       0.14   12.9   0.0    4.3  4  HEAT_PBS   PBS lyase HEAT-like repeat
    8.1e-09   35.8   0.0      0.011   16.2   0.0    4.1  4  HEAT_EZ    HEAT-like repeat
    1.6e-06   28.2   0.1     0.0032   17.5   0.0    3.2  3  Cnd1       non-SMC mitotic condensation complex subunit 1
    0.00015   21.7   0.2       0.41   10.8   0.0    3.7  4  Arm        Armadillo/beta-catenin-like repeat
  ------ inclusion threshold ------
      0.068   11.7   0.0        1.1    7.8   0.0    2.1  2  Adaptin_N  Adaptin N terminal region
        0.2   11.3   0.0         25    4.5   0.0    2.8  4  DUF4042    Domain of unknown function (DUF4042)


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.8e-09   8.5e-06      34      88 .]      25      79 ..      17      79 .. 0.86
   2 !   49.9   0.0   1.4e-16   3.1e-13       5      87 ..      59     141 ..      55     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.8e-09
      HEAT_2 34 paLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaeaLa 88
                +++v+ll+++d  vR  a   L+ +g ++ ++  ++ l+dd++++vR +Aa +L+
  AJA91935.1 25 DYFVKLLDHDDYVVRCRATCILVDLGGEDKVQYIAKVLKDDPNELVRHEAAFSLG 79
                6788999999999999999999999999999999999999999999999988875 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 1.4e-16
      HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvReaAaeaL 87 
                  ++l++dp++ vr++a+ +Lg++   + ++ L ++  +d+++ vR++aa aLg +g+    ++L+++l+d +++ vR +A+ aL
  AJA91935.1  59 AKVLKDDPNELVRHEAAFSLGQMCFSSGIAPLEDATaNDPSMFVRHEAAVALGVVGSTGEPEVLEKALND-PEESVRHSAVVAL 141
                 689999****************************8889****************************9976.5666799999998 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.023        51       4      20 ..      26      42 ..      25      43 .. 0.88
   2 !   15.6   0.0   6.2e-06     0.014       4      28 ..      57      82 ..      55      85 .. 0.86
   3 !   11.6   0.0   0.00012      0.27       9      27 ..      95     113 ..      88     116 .. 0.86
   4 !   15.9   0.0   4.9e-06     0.011       4      27 ..     121     144 ..     120     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.023
                HHHHHHT-SSHHHHHHH CS
        HEAT  4 lllkllsDpspeVReaA 20
                 ++kll +++  VR+ A
  AJA91935.1 26 YFVKLLDHDDYVVRCRA 42
                589***********987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.2e-06
                HHHHHH.T-SSHHHHHHHHHHHHHHH CS
        HEAT  4 lllkll.sDpspeVReaAakaLgala 28
                 + k l  Dp+  VR  Aa +Lg+++
  AJA91935.1 57 YIAKVLkDDPNELVRHEAAFSLGQMC 82
                577788678****************9 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00012
                 HT-SSHHHHHHHHHHHHHH CS
        HEAT   9 lsDpspeVReaAakaLgal 27 
                  +Dps++VR  Aa aLg +
  AJA91935.1  95 ANDPSMFVRHEAAVALGVV 113
                 49**************986 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 4.9e-06
                 HHHHHHT-SSHHHHHHHHHHHHHH CS
        HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                 +l k+l+Dp+ +VR +A+ aL +l
  AJA91935.1 121 VLEKALNDPEESVRHSAVVALSNL 144
                 6899****************9886 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0064        14       1      27 []      38      64 ..      38      64 .. 0.96
   2 !   12.9   0.0   6.4e-05      0.14       1      24 [.      70      93 ..      70      96 .. 0.89
   3 !    7.8   0.0    0.0028       6.2       1      18 [.     102     122 ..     102     128 .. 0.80
   4 ?    3.9   0.0     0.051   1.2e+02       1      12 [.     133     144 ..     133     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0064
                HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
    HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLqd 27
                vR++A+  L  lg e+ ++ + ++L+d
  AJA91935.1 38 VRCRATCILVDLGGEDKVQYIAKVLKD 64
                9********************999998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.4e-05
                HHHHHHHHHHHCTSGGGHHHHHHH CS
    HEAT_PBS  1 vRraAakaLgqlgdeeaipaLlea 24
                vR++Aa++Lgq+     i++L  a
  AJA91935.1 70 VRHEAAFSLGQMCFSSGIAPLEDA 93
                9***********999999999876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0028
                 HHHHHHHHHHHCTS...GGGH CS
    HEAT_PBS   1 vRraAakaLgqlgd...eeai 18 
                 vR++Aa aLg +g+   +e++
  AJA91935.1 102 VRHEAAVALGVVGStgePEVL 122
                 9*********99986665554 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.051
                 HHHHHHHHHHHC CS
    HEAT_PBS   1 vRraAakaLgql 12 
                 vR++A+ aL +l
  AJA91935.1 133 VRHSAVVALSNL 144
                 9********987 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       0.1   2.2e+02      27      49 ..      21      43 ..      13      46 .. 0.67
   2 !    8.7   0.0    0.0011       2.4      33      55 .]      58      81 ..      55      81 .. 0.84
   3 ?    3.3   0.0     0.055   1.2e+02      33      54 ..      90     112 ..      83     113 .. 0.76
   4 !   16.2   0.0     5e-06     0.011      32      55 .]     121     144 ..     118     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.1
     HEAT_EZ 27 peilpaLlalLnddsd.eV.RaaAa 49
                +e  +++++lL +  d  V R+ A 
  AJA91935.1 21 KEDTDYFVKLLDH--DdYVvRCRAT 43
                56667999***55..5444477765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0011
     HEAT_EZ 33 LlalLnddsd.eVRaaAagaLgnl 55
                 ++ L+dd+  +VR  Aa  Lg++
  AJA91935.1 58 IAKVLKDDPNeLVRHEAAFSLGQM 81
                5678989888788*********97 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.055
     HEAT_EZ  33 Ll.alLnddsdeVRaaAagaLgn 54 
                 L  a+ nd+s  VR  Aa aLg 
  AJA91935.1  90 LEdATANDPSMFVRHEAAVALGV 112
                 4436778888899*******995 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 5e-06
     HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgnl 55 
                  L ++Lnd++ +VR  A+ aL+nl
  AJA91935.1 121 VLEKALNDPEESVRHSAVVALSNL 144
                 689*******************97 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0081        18      20      48 ..      52      81 ..      36      93 .. 0.73
   2 ?    3.7   0.0     0.025        56       1      45 [.      69     110 ..      69     116 .. 0.82
   3 !   17.5   0.0   1.4e-06    0.0032      26      59 ..     122     156 ..     119     159 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0081
        Cnd1 20 eylvepLrkrLk.DedpyVRktaaivvakL 48
                e  v+ + k Lk D+++ VR  aa+ + ++
  AJA91935.1 52 EDKVQYIAKVLKdDPNELVRHEAAFSLGQM 81
                555677777777257999999999988877 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.025
        Cnd1   1 liRalairtlgcirvpnlveylvepLrkrLkDedpyVRktaaivv 45 
                 l+R  a  +lg +++++ + +l +   ++ +D+++ VR  aa+++
  AJA91935.1  69 LVRHEAAFSLGQMCFSSGIAPLED---ATANDPSMFVRHEAAVAL 110
                 578888888888888888888887...5779**********9987 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.4e-06
        Cnd1  26 LrkrLkDedpyVRktaaivvakL.ilndmvkekgf 59 
                 L+k+L+D+++ VR  a++++++L + ++++k+++f
  AJA91935.1 122 LEKALNDPEESVRHSAVVALSNLeFMKTLCKSEKF 156
                 899****************************9986 PP

>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0091        20      17      36 ..      27      46 ..      25      49 .. 0.89
   2 ?    0.1   0.0      0.43   9.6e+02      20      36 ..      61      78 ..      55      83 .. 0.76
   3 ?   -0.2   0.0      0.52   1.2e+03      28      37 ..     102     111 ..      96     115 .. 0.90
   4 !   10.8   0.0   0.00018      0.41      16      39 ..     121     144 ..     112     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0091
                HHHHTTTSSHHHHHHHHHHH CS
         Arm 17 LvrLLssedeevqeeAawAL 36
                +v+LL+++d  v++ A++ L
  AJA91935.1 27 FVKLLDHDDYVVRCRATCIL 46
                79*************99866 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                HTT.TSSHHHHHHHHHHH CS
         Arm 20 LLs.sedeevqeeAawAL 36
                 L+ +++e v++eAa  L
  AJA91935.1 61 VLKdDPNELVRHEAAFSL 78
                577799999****99555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.52
                 HHHHHHHHHH CS
         Arm  28 vqeeAawALs 37 
                 v++eAa AL+
  AJA91935.1 102 VRHEAAVALG 111
                 7899****97 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00018
                 HHHHHTTTSSHHHHHHHHHHHHHH CS
         Arm  16 pLvrLLssedeevqeeAawALsNL 39 
                 +L + L+++ e+v++ A+ ALsNL
  AJA91935.1 121 VLEKALNDPEESVRHSAVVALSNL 144
                 5667899****************9 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0092        21      81     138 ..      24      78 ..       8      86 .. 0.73
   2 ?    7.8   0.0   0.00047       1.1      90     179 ..      65     144 ..      55     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0092
                 CHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
   Adaptin_N  81 tnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                 t+ + k l + + ++r+ A + L +++ ++ ++++a+ +k+   d++  vr +Aa ++
  AJA91935.1  24 TDYFVKLLDHDDYVVRCRATCILVDLGGEDKVQYIAKVLKD---DPNELVRHEAAFSL 78 
                 66777778888888888888888888877777766665553...77788888888776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00047
                 SSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHH CS
   Adaptin_N  90 dpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleei 179
                 dpn+l+r  A  +L++++ ++    l++   ++++d+s +vr +Aa+a+  + +  +          ++++l+d + +v  +Av +l  +
  AJA91935.1  65 DPNELVRHEAAFSLGQMCFSSGIAPLED---ATANDPSMFVRHEAAVALGVVGSTGEPE-------VLEKALNDPEESVRHSAVVALSNL 144
                 6777777777777777775554444554...4667888888888888877666664433.......466778888888888888887776 PP

>> DUF4042  Domain of unknown function (DUF4042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3     3e+03      49      61 ..      33      45 ..      12      50 .. 0.65
   2 ?    4.5   0.0     0.011        25      37      67 ..      51      81 ..      42      88 .. 0.86
   3 ?   -1.2   0.0      0.63   1.4e+03      48      65 ..      94     111 ..      84     118 .. 0.83
   4 ?    3.1   0.0      0.03        67      41      67 ..     118     144 ..     111     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
     DUF4042 49 lkDpspkvRaaal 61
                + D  +++Ra  +
  AJA91935.1 33 HDDYVVRCRATCI 45
                3456678888765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
     DUF4042 37 erkseatLltillkDpspkvRaaalqvlaal 67
                ++++ + + ++l+ Dp+  vR  a+  l ++
  AJA91935.1 51 GEDKVQYIAKVLKDDPNELVRHEAAFSLGQM 81
                5667788999****************99999 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.63
     DUF4042  48 llkDpspkvRaaalqvla 65 
                  ++Dps+ vR  a+ +l 
  AJA91935.1  94 TANDPSMFVRHEAAVALG 111
                 578999999999998875 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.03
     DUF4042  41 eatLltillkDpspkvRaaalqvlaal 67 
                 e ++l  +l+Dp+  vR  a+ +l++l
  AJA91935.1 118 EPEVLEKALNDPEESVRHSAVVALSNL 144
                 567788899************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1260.03
//
Query:       AJA91936.1  [L=133]
Description: scavenger mRNA decapping enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.4   0.1    1.9e-23   83.0   0.1    1.2  1  HIT       HIT domain
    1.5e-11   44.8   0.1    1.7e-11   44.6   0.1    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.1   2.2e-27   1.9e-23       4      97 ..      12     105 ..       9     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.2e-27
                 C-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-T CS
         HIT   4 ipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprre 97 
                  p  +++edd+ +a+ld+ p   gh Lvipkk +++++d++++e+a+l+s+v ++a+a+ k   + ++ ++ nng++a q v+h+HiH+ipr+ 
  AJA91936.1  12 LPGFIIFEDDHHVAILDKYPIDTGHSLVIPKKPYEKITDMPKNEVADLFSLVPQIANAILKATGAVAFSIAQNNGKEAKQIVPHVHIHIIPRYA 105
                 67889**************************************************************************************985 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1   1.9e-15   1.7e-11       3     106 ..       3     107 ..       1     115 [. 0.86

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-15
                 HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EEEEE--SCCCT--S-S--EEEE CS
      DcpS_C   3 vfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vdaeelrvgvhyqPsvyhlHlHvi 100
                 +f ++++gk p  +++ed++ v++ D++p ++ h lvipk+  ++++d+ k+++  l +++ ++ ++i +   +   +   + g ++++ v h+H+H+i
  AJA91936.1   3 IFTEIIEGKLPGFIIFEDDHHVAILDKYPIDTGHSLVIPKKPYEKITDMPKNEVADLFSLVPQIANAILKATGAvAFSIAQNNGKEAKQIVPHVHIHII 101
                 7999*********************************************9999998988888888888777766455667789***************9 PP

                 E..... CS
      DcpS_C 101 sldfes 106
                    +++
  AJA91936.1 102 PRYANK 107
                 765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1143.84
//
Query:       AJA91937.1  [L=231]
Description: dethiobiotin synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-40  137.2   0.0    7.5e-40  136.9   0.0    1.0  1  AAA_26    AAA domain
    2.3e-07   30.9   0.0    3.7e-07   30.2   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
      0.001   18.4   0.4      0.025   13.8   0.0    2.4  2  DUF1611   Domain of unknown function (DUF1611_C) P-loop domai
  ------ inclusion threshold ------
       0.12   12.3   0.3       0.27   11.2   0.0    1.7  2  PuR_N     Bacterial purine repressor, N-terminal


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.0   1.7e-43   7.5e-40       2     192 ..       3     206 ..       2     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 1.7e-43
      AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.....ededselikellgldqtyelpeplalsaplspelaarqegedidlekiv... 92 
                 +ifvtgtdt+vGKT vs++ ++++++k++ vg++KP+++g +       ed+e + ++ ++ ++++l +p+ ++ p sp  a +q + +id++k++   
  AJA91937.1   3 SIFVTGTDTDVGKTCVSAAMANYFREKNIDVGVMKPFASGYKatadsVSEDVEILMKYSQTHDSIDLVNPYYFEIPTSPYDACKQLNLEIDISKVIdsy 101
                 7*****************************************6665446699999999999999********************************998 PP

      AAA_26  93 kelekdadivvVEGagglgvpiteellnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp.....envetlekksgipvlG 186
                  +l+  +d+v+VEG+gg+++pi+++ ++ d++  l+++ i+V+ ++ g++n+ +lt+e++rqkn++ +G i+N+  ++     +  ++++  +g +v+G
  AJA91937.1 102 TQLASIHDMVIVEGIGGIMTPISKNYFVSDLISDLNLESIIVTGTKIGSVNHSMLTYEHARQKNLKFKGFIINQNVADgydlsNMKHQIFGLTGHKVFG 200
                 88999*********************************************************************555566555477899999999**** PP

      AAA_26 187 vvPylp 192
                 ++Py +
  AJA91937.1 201 AIPYVE 206
                 ***975 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   8.3e-11   3.7e-07       1     118 [.       4     208 ..       4     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 8.3e-11
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE.EEESSCCCCHHTTEB-HHHH............................................ CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx............................................ RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvD.aDpqannlaileglendiep............................................ 54 
                 i++++t  +vGKT ++a++a ++ +++ +V + + +    +++a  + +++d+e                                             
  AJA91937.1   4 IFVTGTDTDVGKTCVSAAMANYFREKNIDVGVMKpFASGYKATA--DSVSEDVEIlmkysqthdsidlvnpyyfeiptspydackqlnleidiskvids 100
                 789**********************9999999997777777766..5566666669999999************************************* PP

                 ...........................................CCHCCCHHHHHHCHCHHHH......EEEEEEEEESS...-TTCHHHHHHHHHHC.T CS
                 ...........................................xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
        CbiA  55 ...........................................dlkrllellealgkkkall....lkiagvvlnrvdgeneetllkealeelkqry.g 105
                                                            +  +++ + +++ +  +++    lk++g+++n    + ++ + ++    +++ + g
  AJA91937.1 101 ytqlasihdmvivegiggimtpisknyfvsdlisdlnlesiivTGTKIGSVNHSMLTY-EHArqknLKFKGFIINQNVADGYDLSNMK---HQIFGLtG 195
                 ************************************9999999445555555544433.3334678**********888854444433...3333334* PP

                 S-EEEEEE--CCH CS
                 xxxxxxxxxxxxx RF
        CbiA 106 vpvlgviprdeav 118
                  +v+g ip++e +
  AJA91937.1 196 HKVFGAIPYVEPF 208
                 *********9866 PP

>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.6e-06     0.025      14      47 ..       3      36 ..       1      61 [. 0.88
   2 ?    2.8   0.1     0.014        63      81     104 ..     103     124 ..      92     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-06
     DUF1611 14 rvlvvGTdcavGKrttaleleealeerGlkaafv 47
                 ++v GTd +vGK   + ++++ ++e+ ++++++
  AJA91937.1  3 SIFVTGTDTDVGKTCVSAAMANYFREKNIDVGVM 36
                69*************************9999876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
     DUF1611  81 kaaeeeepdlilveGQgsLthpay 104
                 ++a+  + d+++veG g+++ p+ 
  AJA91937.1 103 QLAS-IH-DMVIVEGIGGIMTPIS 124
                 4443.45.99*******9998875 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     6e-05      0.27       8      47 ..      21      60 ..      19      69 .. 0.88
   2 ?   -3.5   0.0       2.3     1e+04      42      57 ..     105     120 ..     103     121 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6e-05
       PuR_N  8 aitkiLlenPnklisltyfaerfeaAKSsiSeDlaiikea 47
                a+ +++ e+  ++  ++ fa  ++a+  s+SeD++i+ + 
  AJA91937.1 21 AMANYFREKNIDVGVMKPFASGYKATADSVSEDVEILMKY 60
                7899999999999999*******************98765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
       PuR_N  42 aiikealekeglGkle 57 
                 a i++++  eg+G + 
  AJA91937.1 105 ASIHDMVIVEGIGGIM 120
                 5566777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1775.43
//
Query:       AJA91938.1  [L=47]
Description: hypothetical protein T478_0601 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.071   12.9   0.2      0.083   12.6   0.2    1.2  1  PI3K_p85B  PI3-kinase family, p85-binding domain


Domain annotation for each model (and alignments):
>> PI3K_p85B  PI3-kinase family, p85-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.6e-06     0.083      13      49 ..       7      46 ..       3      47 .] 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-06
   PI3K_p85B 13 eiKeeLweeakkyplfg...llkdpsdYvFvginqtaeke 49
                ++K++ we+a+ky++ +      ++ ++++v + ++ ++e
  AJA91938.1  7 NLKQDFWENANKYSWSNgeyEFLKEMSFIMVNLHHQNKTE 46
                79************96421134444556666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 385.79
//
Query:       AJA91939.1  [L=357]
Description: alcohol dehydrogenase, catalytic domain, GroES-like family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-26   91.2   0.0    9.4e-26   90.3   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.6e-22   79.5   0.1    2.5e-22   78.8   0.1    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    5.9e-17   63.0   0.0    9.4e-17   62.3   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   1.6e-29   9.4e-26       1     123 [.     184     312 ..     184     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 1.6e-29
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET......TTC.HHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCT CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny......kea.dlverikeltg.gegvdvvfecvGsgatleaalkllkpgGrlvvvGgg 91 
                 gvG++++q+Ak +G++via++s e kl+++k+lGad+++++      ke  ++++++++  g   g+dv+fe++G g+ ++  l+llk+g ++v+ G+ 
  AJA91939.1 184 GVGIFGIQIAKLYGCTVIATASPE-KLDQLKELGADYAVDHrkedwhKEVfKISKELAKEKGeAPGIDVIFEHIG-GSHFNKELTLLKYGATMVTTGAT 280
                 9******************99766.8***************877777666777777777777688**********.**********************6 PP

                 SSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHH CS
  ADH_zinc_N  92 kgeee.fdlrnlllkeksilGsllgslreefke 123
                 +g ++  dlr++++k ++ilGs+ g+ r e++e
  AJA91939.1 281 TGYDVpADLRQIFFKGINILGSTQGT-RAELEE 312
                 655556*******************9.888877 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.1   4.3e-26   2.5e-22       2     109 .]      32     141 ..      31     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 4.3e-26
                 TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTBEETTTS...S-SSSBS CS
       ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeeakllgvs...ldGgfae 97 
                 +evl +vkaa+++  D++ ++g k l v+lp i G +++Gev +vg++vk++kvGdrVv + ++sc  C++C++g+e  C+++ ++g++   l+Gg++e
  AJA91939.1  32 NEVLFRVKAAALNYDDIWGMRG-KPLAVPLPHISGTDAAGEVIAVGEDVKSIKVGDRVVSHGNMSCRVCSRCTSGREFDCKKRIIWGFQtgpLWGGYCE 129
                 79********************.9*************************************************************************** PP

                 EEEECGGGEEEE CS
       ADH_N  98 yvvvpekklvkl 109
                    +pe +++k+
  AJA91939.1 130 IAHLPEINVLKI 141
                 *****9999875 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.0   1.6e-20   9.4e-17       1     133 []     215     354 ..     215     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.6e-20
                   TT-SEEEETTSTTHH............HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-. CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe............aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasa 85 
                   lGAd ++d+r+ed++            ++ +  g+Dv+++ +gg ++  + l++l+ g+++v+ g++    +  +++++ ++  +k   ++  +++ 
    AJA91939.1 215 LGADYAVDHRKEDWHkevfkiskelakEKGEAPGIDVIFEHIGGSHF-NKELTLLKYGATMVTTGAT----TGYDVPADLRQIFFKGINILGSTQGT 306
                   8**********************99874444578*************.8888999887899*99962....33444443555555555555445554 PP

                   -HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--.SSEEEE CS
  ADH_zinc_N_2  86 qadileelaalieeGklrpvvdrvfpleeaaeAhrylesgra.rGKiVl 133
                   +a+ lee + ++ +Gk+++ +d+ f++e+a++Ah ++ +g+  +GKi+l
    AJA91939.1 307 RAE-LEEGFYWMGQGKIKVIIDSIFTFENAVDAHNKMLNGKGlVGKIIL 354
                   677.********************************97776516***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2368.60
//
Query:       AJA91940.1  [L=127]
Description: hypothetical protein T478_0752 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   12.6   0.1      0.092   12.2   0.1    1.2  1  DUF1454   Protein of unknown function (DUF1454)


Domain annotation for each model (and alignments):
>> DUF1454  Protein of unknown function (DUF1454)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.1e-06     0.092      22      58 ..      19      56 ..       6      75 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-06
     DUF1454 22 teetkeealyLlagaPtFdlt.isqfRekynkanptlp 58
                ++  ++++ y  + +P   +t i ++Rek+nk+n++l 
  AJA91940.1 19 NQGPEDTIRYPPTSTPPTGMTgIKEIREKFNKRNASLM 56
                3346677778776666555544**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 964.80
//
Query:       AJA91941.1  [L=264]
Description: hypothetical protein T478_0554 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1964.67
//
Query:       AJA91942.1  [L=316]
Description: von Willebrand factor type A domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-25   90.6   0.1    2.6e-25   89.6   0.1    1.5  2  VWA       von Willebrand factor type A domain
    2.1e-20   73.4   0.0      4e-20   72.4   0.0    1.4  1  VWA_2     von Willebrand factor type A domain
      3e-10   40.3   1.2    3.2e-10   40.2   0.1    1.6  2  BatA      Aerotolerance regulator N-terminal
     0.0021   17.3   0.2       0.01   15.1   0.1    1.9  2  DUF1194   Protein of unknown function (DUF1194)
     0.0035   16.8   0.0      0.009   15.4   0.0    1.6  1  VWA_CoxE  VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.035   13.9   0.0    1.8  2  Ssl1      Ssl1-like


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   5.7e+03      19     109 ..      43      64 ..      28      81 .. 0.59
   2 !   89.6   0.1   8.9e-29   2.6e-25       1     174 [.      89     274 ..      89     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                 HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEE CS
         VWA  19 kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntgkalkyaleklfkssagaRenakkviil 109
                  v                                                                     +k  +s++  R++ + ++il
  AJA91942.1  43 LV---------------------------------------------------------------------KKSASSQSQFRKHLPFILIL 64 
                 22.....................................................................22333333345555555555 PP

  == domain 2  score: 89.6 bits;  conditional E-value: 8.9e-29
                 EEEEEEE-STTS.....CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHH CS
         VWA   1 DivfvlDgSgsm.....geenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysgggttntgkalkyaleklfk 94 
                 ++v+vlDgSgsm      + ++e++k++++ l+e+le   ++++ g++ f s ++t+  l+ ++  ++ + +ln++k+++g t+ +g++l  +++ + +
  AJA91942.1  89 NVVLVLDGSGSMaatdyPPTRLESAKDAAEILIENLE---PNDHTGIILFESGATTVSYLTPFK--DKTIGDLNAIKQRDGATA-IGDGLVLGVDMANS 181
                 79**********88777777888**************...**********************99..89****************.**********8888 PP

                 HHGTSSTTSEEEEEEEESS--CSS..HTHHHHHHHHGCTEEEEEEEE..................SSSHHHHHHHHHSSSSCHHCEEEESSHHHHHHHH CS
         VWA  95 ssagaRenakkviilltdGksndg..dpkeaaneakeqgikvfavGv..................gnadekelLnkiasepgeghvftvtdfeeleelf 173
                   ++     kkv+ill+dG++n g   p+ea++ a +++i+++++G+                   + +eke L  ia+  + g++++  d ++l+e+f
  AJA91942.1 182 IPNK-----KKVVILLSDGDHNAGvvTPNEAVQYAIQKKIQIHTIGMgseepvllgtniygnplyAELNEKE-LIAIATAAN-GKYYKSVDNNSLNEIF 273
                 8888.....**************99***************************************99999999.********9.***************9 PP

                 H CS
         VWA 174 e 174
                 e
  AJA91942.1 274 E 274
                 8 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   1.3e-23     4e-20       1     106 [.      90     195 ..      90     196 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.3e-23
       VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrrkgekr 98 
                 +v+vlD+SgSm+++dy ptrle akda+e l+++l p+d+ g++ f++g+++++ lt  k+k    l+++++++g+t ++++L l  ++ ++ + ++k+
  AJA91942.1  90 VVLVLDGSGSMAATDYPPTRLESAKDAAEILIENLePNDHTGIILFESGATTVSYLTPFKDKTIGDLNAIKQRDGATAIGDGLVLGVDMANSIP-NKKK 187
                 79*********************************66********************999999999***************************8.**** PP

       VWA_2  99 vivlitDg 106
                 v++l++Dg
  AJA91942.1 188 VVILLSDG 195
                 *******9 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   1.1e-13   3.2e-10       3      77 .]       4      77 ..       1      77 [. 0.93
   2 ?   -2.8   0.1         3   8.9e+03      62      67 ..     296     301 ..     284     309 .. 0.51

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.1e-13
        BatA  3 pFlnPllLlallllplpiillyllkrrpqev..vfsslrlleevekdeealqrlkknllllLrllalallvlalArP 77
                +F + ++Llal++lp  ++l+++  + ++    +fs+l+l++++  ++++    +k+l+++L l+a+ l++++lA P
  AJA91942.1  4 EFGYWYVLLALFILPGFYFLYRFYTKTKKSNslKFSNLELVKKSASSQSQ---FRKHLPFILILIAVGLIIIGLADP 77
                5777889*********99999999988888899*****************...**********************99 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
        BatA  62 Lrllal 67 
                   +++l
  AJA91942.1 296 AAVVVL 301
                 111111 PP

>> DUF1194  Protein of unknown function (DUF1194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.21   6.3e+02       5      21 ..      89     105 ..      87     112 .. 0.87
   2 !   15.1   0.1   3.4e-06      0.01      90     158 ..     161     227 ..     151     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.21
     DUF1194   5 eLvLavDvSgSvdeeEl 21 
                 + vL +D SgS+ ++++
  AJA91942.1  89 NVVLVLDGSGSMAATDY 105
                 6799********98876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.4e-06
     DUF1194  90 aaarrtaigeAlefaaallaenpveglrrviDvSGDGpnneglepvtaardaaeakgvtingLaietke 158
                 ++ + taig +l  ++++ ++ p   +++v+ +  DG +n+g+ + ++a + a +k++ i  + ++++e
  AJA91942.1 161 QRDGATAIGDGLVLGVDMANSIPN--KKKVVILLSDGDHNAGVVTPNEAVQYAIQKKIQIHTIGMGSEE 227
                 45566*************999999..899999999*******99999************9988777665 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     3e-06     0.009      59     163 ..      89     197 ..      81     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-06
    VWA_CoxE  59 elvllvDvSgSmaaysaiflallhAllqqlp..........rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpa 147
                 ++vl++D SgSmaa +      l+++ + ++          +t +++F++  + ++     +D  + + +++ a+++++G T ig++l    ++ +   
  AJA91942.1  89 NVVLVLDGSGSMAA-TDYPPTRLESAKDAAEilienlepndHTGIILFESGATTVSYLTPFKD--KTIGDLN-AIKQRDGATAIGDGLVLGVDMANSIP 183
                 79**********98.554444444444443333344558889**************9999555..4556665.5569***********98888877444 PP

    VWA_CoxE 148 LsrravvvlvsDgler 163
                  +++ vv+l+sDg ++
  AJA91942.1 184 -NKKKVVILLSDG-DH 197
                 .6899*******9.44 PP

>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.035       1     141 [.      93     226 ..      93     232 .. 0.81
   2 ?   -1.4   0.0      0.56   1.7e+03     148     173 ..     252     277 ..     240     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                 EEE-SGGGGSSSSSS-HHHHHHHHHHHHHHHHHHHSTT-EEEEEEEETTEEEEEEEEES-HHHHHHHHHHHTTS---S---HHHHHHHHHHHHSSS-TT CS
        Ssl1   1 vlDlsrameekdlkpsrlavviklleefveeffdqnPisqlgliavkdkkaekltelsGnprkhikaLkslreveakgepsLqnaLelalasLkkvpsh 99 
                 vlD s +m+ +d +p+rl+    ++e  +e+     P    g+i  +++ a +++ l+    k i  L++++  +  g +++ ++L l ++  +++p  
  AJA91942.1  93 VLDGSGSMAATDYPPTRLESAKDAAEILIEN-L--EPNDHTGIILFESG-ATTVSYLTPFKDKTIGDLNAIK--QRDGATAIGDGLVLGVDMANSIPNK 185
                 89*****************987777777765.4..56678999988776.899******************9..88999******************75 PP

                 SEEEEEEEE-SS.----SS-HHHHHHHHHHTT-EEEEEEESS- CS
        Ssl1 100 asrevliifssl.stcDPgdiyetidelkkekirvsvigLsae 141
                   + v+i++s     +  +  +e ++   ++ki+++ ig+ +e
  AJA91942.1 186 --KKVVILLSDGdHNAGVVTPNEAVQYAIQKKIQIHTIGMGSE 226
                 ..56777776531444455567788888888888888887665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.56
                 HHHHTTTTEEEE-SHHHHHHHHHHHH CS
        Ssl1 148 laketkgtysvvldethlkelllehv 173
                 +a + +g+y   +d++ l e++ e +
  AJA91942.1 252 IATAANGKYYKSVDNNSLNEIFEEIT 277
                 56777899999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2294.45
//
Query:       AJA91943.1  [L=58]
Description: ribosomal protein L37e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-21   76.6  10.9    1.2e-21   76.5  10.9    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0082   16.1   1.6      0.011   15.7   1.6    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.8   0.5      0.011   15.7   0.5    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.04   13.6   5.4      0.074   12.7   0.9    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.091   12.5   5.5       0.95    9.2   0.6    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        0.2   11.3   0.7       0.36   10.4   0.7    1.5  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.31   11.2   5.1        1.9    8.6   0.4    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.36   10.3   5.0        5.5    6.5   5.2    2.1  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5  10.9   5.6e-25   1.2e-21       1      52 [.       2      53 ..       2      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 5.6e-25
  Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrkynWsaK 52
                    t+Gt+s+Gk++k +tHi+Cr+Cgk+s h + ++CascG+p+ak+rkynW ++
      AJA91943.1  2 TRGTPSMGKHNKAHTHIRCRKCGKNSLHRRLHRCASCGWPDAKWRKYNWIKR 53
                    79***********************************************987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.6   4.7e-06     0.011      21      54 ..      10      40 ..       5      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
  OrfB_Zn_ribbon 21 evnpayTSktCseCgsknkealsgrtfkCpnCgf 54
                    + n+a+T  +C +Cg+++ +   +r+++C +Cg 
      AJA91943.1 10 KHNKAHTHIRCRKCGKNSLH---RRLHRCASCGW 40
                    568999*********87655...*********96 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.5   5.1e-06     0.011      66      98 ..      13      44 ..       4      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                EE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA 66 evpvkvrCreCgkefeleekalrCpkCgsadve 98
                + + ++rCr+Cgk+  +++   rC +Cg  d +
  AJA91943.1 13 KAHTHIRCRKCGKNSLHRR-LHRCASCGWPDAK 44
                667899******8887664.469****987765 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   3.3e-05     0.074      16      28 ..      16      28 ..      10      31 .. 0.79
   2 ?    3.2   0.3     0.032        71      19      24 ..      34      39 ..      33      41 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                    S----SSS----- CS
  DNA_RNApol_7kD 16 dpiRCkeCGhRil 28
                      iRC++CG  +l
      AJA91943.1 16 THIRCRKCGKNSL 28
                    57*******7666 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.032
                    --SSS- CS
  DNA_RNApol_7kD 19 RCkeCG 24
                    RC  CG
      AJA91943.1 34 RCASCG 39
                    777777 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4    0.0049        11       2      10 ..      19      27 ..      19      30 .. 0.81
   2 ?    9.2   0.6   0.00042      0.95       1      13 [.      33      45 ..      33      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0049
  Rubredoxin_2  2 vCsqCGfes 10
                  +C++CG  s
    AJA91943.1 19 RCRKCGKNS 27
                  799999776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00042
  Rubredoxin_2  1 YvCsqCGfesakw 13
                  ++C +CG+  akw
    AJA91943.1 33 HRCASCGWPDAKW 45
                  69******99999 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00016      0.36       2       8 ..       3       9 ..       3       9 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
   MraY_sig1 2 kGTPTMG 8
               +GTP+MG
  AJA91943.1 3 RGTPSMG 9
               6*****9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4   0.00087       1.9       9      24 ..      10      25 ..       4      33 .. 0.76
   2 ?    5.7   0.5    0.0071        16      17      25 ..      33      41 ..      27      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00087
    zf-Mss51  9 qtapkhvdfeCpdCGi 24
                +++++h ++ C +CG 
  AJA91943.1 10 KHNKAHTHIRCRKCGK 25
                4479***********6 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0071
    zf-Mss51 17 feCpdCGip 25
                + C  CG+p
  AJA91943.1 33 HRCASCGWP 41
                57******9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.2    0.0025       5.5       2      23 ..      17      39 ..      16      41 .. 0.90
   2 ?    6.5   0.5    0.0025       5.7       4      14 ..      34      43 ..      31      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0025
  zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCG 23
                 ++rC +CG+  l  +   C++CG
   AJA91943.1 17 HIRCRKCGKnSLHRRLHRCASCG 39
                 689******77***********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
  zf-ribbon_3  4 rCPnCGaplss 14
                 rC +CG+p ++
   AJA91943.1 34 RCASCGWP-DA 43
                 79999999.66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 418.46
//
Query:       AJA91944.1  [L=333]
Description: biotin-(acetyl-CoA-carboxylase) ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-19   69.3   0.0    6.8e-19   68.1   0.0    1.7  1  BPL_LplA_LipB    Biotin/lipoate A/B protein ligase family
      1e-14   54.2   0.1    3.6e-14   52.4   0.1    2.0  1  HTH_11           HTH domain
    1.5e-10   40.8   0.7    2.9e-10   39.9   0.7    1.5  1  BPL_C            Biotin protein ligase C terminal domain
  ------ inclusion threshold ------
       0.03   14.6   0.9      0.062   13.6   0.1    1.9  2  UPF0122          Putative helix-turn-helix protein, YlxM / p1
      0.033   13.7   0.0      0.063   12.8   0.0    1.5  1  BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
       0.04   14.3   0.1        6.3    7.3   0.0    2.6  2  Phage_X          Phage X family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   2.3e-22   6.8e-19       2     131 .]      94     218 ..      93     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.3e-22
                    EEEES-HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTE CS
  BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipv 93 
                    +e i+st+ +++  +  +++e+g++ +++ qt+Gr    + w spkg++++sl++    ++f+ +   l+  l+++a  +++      +   +i +
     AJA91944.1  94 FEEIDSTQNFAQ-NIAADKKENGTIIIAEKQTSGRgrldRKWTSPKGGIWFSLIIH---PKFDVSSSTLIPILSAVALSKSI------KSVLDIET 179
                    677899988666.799999*************************************...55676666666666777777777......7889**** PP

                    EEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
  BPL_LplA_LipB  94 fikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                    ++kwpnD+ +ng+K+aG++v     ++ + ++++g+g+n
     AJA91944.1 180 EVKWPNDITMNGKKVAGVLVDASFqTNSIDYLILGIGIN 218
                    *********************999888899999999998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   1.2e-17   3.6e-14       4      55 .]      13      65 ..      11      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.2e-17
      HTH_11  4 qilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                ++l ++  +++  +sg++L++ L++Sr +v+++Ik++++lg++Ies+++ GYr
  AJA91944.1 13 KVLSFFQTHDSEyLSGQDLSDVLKISRVAVWKHIKKIQTLGYKIESKQKLGYR 65
                5678888899999***************************************8 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.7   9.8e-14   2.9e-10       2      48 .]     288     333 .]     287     333 .] 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 9.8e-14
                 TTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEEE CS
       BPL_C   2 sGqeVtlededgkveGiavGIdddGaLllktddglqpdinsGdislr 48 
                 +G+ +t+ + +gk+ Gi +GId dGaL +kt ++ +++i+ Gd++l+
  AJA91944.1 288 IGKKITINTSNGKISGISQGIDNDGALKIKTKNE-TKKIYVGDVVLS 333
                 8*********************************.*********985 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.1e-05     0.062      24      71 ..      16      63 ..       9      98 .. 0.83
   2 ?   -2.1   0.1       1.5   4.6e+03      59      79 ..     257     276 ..     254     293 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
     UPF0122 24 nylelyyadDlSlsEiAeefnvsrqavydnikrtekllekyEekLkll 71
                ++++ +  + lS +++ +  ++sr av+ +ik++++l  k E+k kl 
  AJA91944.1 16 SFFQTHDSEYLSGQDLSDVLKISRVAVWKHIKKIQTLGYKIESKQKLG 63
                67888888899*****************************99998874 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
     UPF0122  59 kllekyEekLkllekykkree 79 
                 ++l+++E+ L  l+k +k   
  AJA91944.1 257 EFLLQFEKNLFQLDKGEKS-T 276
                 6788999998777766543.3 PP

>> BPL_LplA_LipB_2  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.063      39     130 ..     138     225 ..      95     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
  BPL_LplA_LipB_2  39 adlleaAlvlaPevplakAaamlpvlmvalqdAlgalaPPevavhlewpgtilvngarvGgvrlaaseadeeevPdwlvvglelalekesee 130
                      +  + ++l+++P+ ++++++ +  + +val+ +++ +    +  +++wp++i++ng +v gv + as   +++  d+l++g+ +++  ++++
       AJA91944.1 138 KGGIWFSLIIHPKFDVSSSTLIPILSAVALSKSIKSVLD--IETEVKWPNDITMNGKKVAGVLVDASF--QTNSIDYLILGIGINFDIDAKK 225
                      5567799**************99*************987..667779**************9999987..4556799999998887766654 PP

>> Phage_X  Phage X family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0021       6.3       6      57 ..       8      61 ..       3      65 .. 0.80
   2 ?    4.3   0.0     0.018        53      24      63 ..     189     228 ..     186     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
     Phage_X  6 ivdlaraanltafYallwkeGydlvel..lskatfyrhraeLlkiGidiaqlcn 57
                +v l +    ++   +   +G+dl+ +  +s+  +++h ++  ++G  i  ++ 
  AJA91944.1  8 NVGLVKVLSFFQTHDSEYLSGQDLSDVlkISRVAVWKHIKKIQTLGYKIESKQK 61
                56666666667777777889****9997889999*************9998875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
     Phage_X  24 keGydlvellskatfyrhraeLlkiGidiaqlcnlsefen 63 
                 ++G+++  +l  a+f+++  + l +Gi i+  ++ ++ e+
  AJA91944.1 189 MNGKKVAGVLVDASFQTNSIDYLILGIGINFDIDAKKLEK 228
                 789999999999*******************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2345.91
//
Query:       AJA91945.1  [L=121]
Description: hypothetical protein T478_0620 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.01   15.0   1.0      0.012   14.8   1.0    1.0  1  Vert_IL3-reg_TF  Vertebrate interleukin-3 regulated transcrip
      0.043   14.1   2.1       0.11   12.8   0.3    2.0  2  KxDL             Uncharacterized conserved protein
      0.087   12.9   2.5       0.95    9.6   0.2    2.3  2  COMM_domain      COMM domain


Domain annotation for each model (and alignments):
>> Vert_IL3-reg_TF  Vertebrate interleukin-3 regulated transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.0     2e-06     0.012     202     292 ..      22     111 ..      12     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
  Vert_IL3-reg_TF 202 akamqikvealdsdfdatqklsspvdmsakrhfelekhaapelvhssltPlsvqvtniqdWslk.sehWhqkelegktqnsfktevveikdn 292
                       + mqikve+ d d+d+++     +d  ++ ++ +e +a   ++ + + P+   + n  + +    e+W+++  ++++ + +k +  ei+++
       AJA91945.1  22 KRQMQIKVES-DLDYDSVKIFGEKMDSVTRAKLGVEDAAELAYTTAEHHPYWAVLYNCTEITKTiLEKWKDEV-TSEQLEEMKWNLKEIQNS 111
                      588******7.99*************************************99999888887665257887655.555567777777777765 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.098   5.8e+02      42      68 ..      12      37 ..       4      52 .. 0.66
   2 ?   12.8   0.3   1.8e-05      0.11      32      80 ..      75     121 .]      72     121 .] 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.098
        KxDL 42 rlaklrarfkqgtkllkevkkdLesif 68
                +l+ l ++f++  ++  +v +dL++  
  AJA91945.1 12 ELKILVEKFEKR-QMQIKVESDLDYDS 37
                455566666554.44456777877755 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.8e-05
        KxDL  32 LlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                 L ++ +++++ l+k ++++ +  + l e+k +L+ i+  i++++ k++k
  AJA91945.1  75 LYNCTEITKTILEKWKDEVTS--EQLEEMKWNLKEIQNSISNIENKIKK 121
                 778888888888888888765..679********************986 PP

>> COMM_domain  COMM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.015        87      51      63 ..       4      16 ..       1      32 [. 0.57
   2 ?    9.6   0.2   0.00016      0.95      47      71 ..      92     116 ..      90     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.015
  COMM_domain 51 eqLqeLlneLeei 63
                 +++q +++eL+  
   AJA91945.1  4 NTFQAFYEELKIL 16
                 5556666665533 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00016
  COMM_domain  47 elskeqLqeLlneLeeiqkqlesla 71 
                  e++ eqL+e+  +L+eiq+++++++
   AJA91945.1  92 EVTSEQLEEMKWNLKEIQNSISNIE 116
                  7999****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1702  (0.09493); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 918.24
//
Query:       AJA91946.1  [L=80]
Description: winged helix-turn-helix [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-10   40.7   0.5    2.1e-10   40.4   0.5    1.1  1  HTH_45       Winged helix-turn-helix
     0.0098   15.9   0.0      0.011   15.8   0.0    1.1  1  Baculo_LEF5  Baculoviridae late expression factor 5
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.019   14.4   0.0    1.3  1  HSP33        Hsp33 protein
       0.02   14.7   0.1       0.03   14.1   0.1    1.3  1  FtsK_gamma   Ftsk gamma domain
       0.11   12.3   0.1       0.12   12.2   0.1    1.0  1  AUX_IAA      AUX/IAA family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.5   5.9e-14   2.1e-10       6      76 ..       4      70 ..       1      71 [. 0.85

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.9e-14
      HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleela 76
                +Ii++I    +e++ ++T+i  k n sy+ l kYL+ ++++++i   +++  +T+kG+++  ++ ++++l+
  AJA91946.1  4 DIISAII---QEEDISPTRIQFKCNTSYDKLMKYLEEMQKREIIAR-NGSIGVTDKGKKFHTDYSKINDLI 70
                4444444...48899*****************************76.56789***************9985 PP

>> Baculo_LEF5  Baculoviridae late expression factor 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     3e-06     0.011       8      50 ..      20      64 ..      13      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
  Baculo_LEF5  8 kkfrrnndysklidylkenfPknv..knktfnlsntGhlfhalya 50
                  +f+ n +y+kl++yl e + + +  +n +  +++ G  fh+ y+
   AJA91946.1 20 IQFKCNTSYDKLMKYLEEMQKREIiaRNGSIGVTDKGKKFHTDYS 64
                 69****************99998733677899999******9876 PP

>> HSP33  Hsp33 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.4e-06     0.019     202     243 ..       5      43 ..       2      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                 HHHHHHSTS--EEEEEEE-EE-----HHHHHHHHHTT-CHHH CS
       HSP33 202 llerlfheedvevleekpvefkCrCsrervekaLkslgkeel 243
                 +++ +++eed+   ++++++fkC+ s ++++k+L+ ++k e+
  AJA91946.1   5 IISAIIQEEDI---SPTRIQFKCNTSYDKLMKYLEEMQKREI 43 
                 56666666655...6789*******************99986 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.3e-06      0.03       6      51 ..       1      46 [.       1      52 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
  FtsK_gamma  6 lfeeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgp 51
                ++ +++  +++e+ +S   +Q + +  Y +  + +++++++ i+  
  AJA91946.1  1 MYFDIISAIIQEEDISPTRIQFKCNTSYDKLMKYLEEMQKREIIAR 46
                5788999************************************975 PP

>> AUX_IAA  AUX/IAA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.3e-05      0.12     142     190 ..      20      71 ..      17      80 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX.XXXXX CS
     AUX_IAA 142 vdLkayksYeeLssalekmFssftigqcgsagts..ekdklseskl.ldlld 190
                 + +k ++sY++L + le+m ++ +i++ gs g++  +k++ ++ ++  dl++
  AJA91946.1  20 IQFKCNTSYDKLMKYLEEMQKREIIARNGSIGVTdkGKKFHTDYSKiNDLIS 71 
                 78899*****************999998875543003344444333366665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 597.54
//
Query:       AJA91947.1  [L=303]
Description: putative transcription initiation factor IIB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-30  105.1   6.7    7.8e-15   54.7   0.4    2.5  2  TFIIB            Transcription factor TFIIB repeat
    2.9e-09   36.3   1.0    4.9e-09   35.5   1.0    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0048   16.8   0.2       0.19   11.7   0.0    2.6  2  HTH_11           HTH domain
     0.0085   15.8   0.3      0.017   14.9   0.1    1.6  2  Cyclin_N         Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.039   13.5   0.0    1.8  1  Sigma70_r4       Sigma-70, region 4
      0.021   14.5   0.3       0.29   10.8   0.0    2.5  2  Sigma70_r4_2     Sigma-70, region 4
      0.032   14.1   0.0       0.25   11.2   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.037   13.7   2.0      0.067   12.9   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.05   13.4   0.5       0.54   10.1   0.0    2.7  3  HTH_23           Homeodomain-like domain
      0.067   12.9   0.0        0.1   12.2   0.0    1.3  1  RPW8             Arabidopsis broad-spectrum mildew resistance
      0.078   13.0   0.1       0.14   12.2   0.1    1.5  1  RB_B             Retinoblastoma-associated protein B domain
        0.1   12.3   4.7       0.27   11.0   1.1    2.6  3  Rep_fac-A_C      Replication factor-A C terminal domain
       0.11   13.1   0.0       0.29   11.7   0.0    1.8  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.13   12.5   0.6       0.28   11.3   0.6    1.6  1  zf-piccolo       Piccolo Zn-finger
       0.13   12.3   1.3        1.4    9.0   0.0    3.0  4  Phage_terminase  Phage terminase small subunit
          7    6.6   6.3          2    8.4   1.2    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.4     7e-18   7.8e-15       2      71 .]     127     196 ..     126     196 .. 0.95
   2 !   53.4   1.1   1.8e-17     2e-14       2      71 .]     221     290 ..     220     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 7e-18
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +r+ d+l ++e V ++A +++++al+++++ Grs  +++A++ly Acr  e+ r +k++   ++++ k i
  AJA91947.1 127 NRLKDKLAISESVVEKAAYIYRKALDKGLVRGRSISALMASALYAACRDTETPRNLKDVEIAANIKRKDI 196
                 68889******************************************************99999998865 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 1.8e-17
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                  r+a+++++ ek ++ A +++k a +++  +G+ p g+aAA+ly+ c k+++ +tq++i++ ++V+e+ti
  AJA91947.1 221 ARIASKIGIAEKTKRYAIKVLKIAQDNEASAGKDPMGLAAAALYLSCVKNGEDKTQRDIAEAANVTEVTI 290
                 799*****************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   1.0   4.4e-12   4.9e-09       3      43 .]      11      51 ..      10      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.4e-12
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  CP C   ++v+D+e+ge++C++CG V+ +   ++gpewr f
    AJA91947.1 11 CPRCVKGKMVTDNESGEMFCSKCGFVMSEKLQESGPEWRSF 51
                  ****99889******************************87 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.15   1.7e+02      19      34 ..     127     142 ..     125     144 .. 0.87
   2 !   11.7   0.0   0.00017      0.19      14      42 ..     272     300 ..     264     303 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
      HTH_11  19 eeLAeeLnvSrrtvrr 34 
                 ++L+++L +S+++v +
  AJA91947.1 127 NRLKDKLAISESVVEK 142
                 689*********9976 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00017
      HTH_11  14 gpisgeeLAeeLnvSrrtvrrdIkaLeel 42 
                 ++ +  ++Ae  nv++ t+r++ k L+e+
  AJA91947.1 272 EDKTQRDIAEAANVTEVTIRNRYKGLKES 300
                 5568899***************9999986 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.5e-05     0.017      30     126 ..     119     211 ..      92     212 .. 0.85
   2 ?   -2.4   0.0       3.2   3.6e+03      76      85 ..     258     267 ..     222     290 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                 HHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
    Cyclin_N  30 mRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdl 126
                 +R+ + + l ++  k+ ++++++  a+ ++ + l k  v+ + +  ++a++L+ A++  e+ p +l+d+ ++++  +++++i +  rl++++L+ ++
  AJA91947.1 119 FRQ-AFSELNRLKDKLAISESVVEKAAYIYRKALDKGLVRGRSISALMASALYAACRDTET-PRNLKDVEIAAN--IKRKDIARCYRLLVKELDLKM 211
                 444.444488999999******************************************999.99****999965..9**************998765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                 HHHHHHHHHH CS
    Cyclin_N  76 vgatcLllAa 85 
                 ++a++L+l++
  AJA91947.1 258 LAAAALYLSC 267
                 6677777776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.5e-05     0.039      17      42 ..     267     295 ..     260     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-05
                 H...TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  17 f...geglTleEIgerlgiSrerVrqiek 42 
                     ge+ T+ +I+e  ++++ ++r + k
  AJA91947.1 267 CvknGEDKTQRDIAEAANVTEVTIRNRYK 295
                 34479********************9976 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.34   3.8e+02      30      45 ..     221     236 ..     220     239 .. 0.81
   2 ?   10.8   0.0   0.00026      0.29      25      47 ..     272     294 ..     269     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.34
                   HHHHHHHT--HHHHHH CS
  Sigma70_r4_2  30 kEIAellgisegtVks 45 
                   + IA+++gi e+t ++
    AJA91947.1 221 ARIASKIGIAEKTKRY 236
                   67*********99665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00026
                   S---HHHHHHHHT--HHHHHHHH CS
  Sigma70_r4_2  25 eglsykEIAellgisegtVksrl 47 
                   e++++++IAe  +++e+t+++r+
    AJA91947.1 272 EDKTQRDIAEAANVTEVTIRNRY 294
                   789******************98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.93     1e+03      21      33 ..     221     233 ..     219     241 .. 0.86
   2 ?   11.2   0.0   0.00023      0.25      19      41 ..     275     297 ..     266     298 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.93
  HTH_AsnC-type  21 aeLAervGlSest 33 
                    a++A ++G++e t
     AJA91947.1 221 ARIASKIGIAEKT 233
                    79******99976 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
  HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrL 41 
                    + +++Ae+ +++e t+++R++ L
     AJA91947.1 275 TQRDIAEAANVTEVTIRNRYKGL 297
                    689****************9976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2         1   1.2e+03      16      19 ..      11      14 ..       9      17 .. 0.71
   2 ?   12.9   0.1     6e-05     0.067       8      21 ..      22      35 ..      21      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1
  zinc_ribbon_2 16 CpyC 19
                   Cp+C
     AJA91947.1 11 CPRC 14
                   5555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6e-05
  zinc_ribbon_2  8 elqdnakFCpyCGt 21
                    ++ ++ FC++CG+
     AJA91947.1 22 DNESGEMFCSKCGF 35
                   5899*********7 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         9     1e+04      18      26 ..     191     199 ..     186     201 .. 0.72
   2 ?    0.1   0.0      0.68   7.6e+02      17      33 ..     217     233 ..     204     237 .. 0.86
   3 ?   10.1   0.0   0.00048      0.54      13      39 ..     265     295 ..     258     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 9
      HTH_23  18 lsvreIAre 26 
                 + +++IAr 
  AJA91947.1 191 IKRKDIARC 199
                 568889986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.68
      HTH_23  17 GlsvreIAreLgvsrrT 33 
                  ++v++IA + g+ + T
  AJA91947.1 217 VQCVARIASKIGIAEKT 233
                 67899*******98877 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00048
      HTH_23  13 llae....GlsvreIAreLgvsrrTvyrwlk 39 
                 l  +     +++r+IA++ +v++ T+++  k
  AJA91947.1 265 LSCVkngeDKTQRDIAEAANVTEVTIRNRYK 295
                 4443456689****************95443 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.4e-05       0.1      15     106 ..      73     167 ..      61     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.4e-05
        RPW8  15 ellkaileakkksldfksilkrLestleritP..vvkeiek.lnkeldrpreeieeLkklLekaekLVekcsklkrynvlkkyrYkkklkeLeks 106
                 + l  +++  +k ++ k+   ++++t+er+++  ++ ++ + +  ++ +  +e+++Lk++L   e+ Vek + + r ++ k     + + +L +s
  AJA91947.1  73 MGLATVINPVNKDASGKPLTASMKNTIERLRTwdSRSQVHEpVDRNFRQAFSELNRLKDKLAISESVVEKAAYIYRKALDKGLVRGRSISALMAS 167
                 5688999999********************9844567776515555588888********************99998888887777777777655 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.14      11      83 ..     120     201 ..     115     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
        RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvt...........keelsFkeiikaYr 83 
                 + a + l++L ++L +s+++ ek+  + +++l  ++ l++ R +  ++ +a+Y+ ++ t            ++++ k+i ++Yr
  AJA91947.1 120 RQAFSELNRLKDKLAISESVVEKAAYIYRKAL--DKGLVRGRSISALMASALYAACRDTetprnlkdveiAANIKRKDIARCYR 201
                 6788999***********99999998988888..568********************995554444444444445555555555 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   0.00024      0.27      19      44 ..       9      34 ..       2      43 .. 0.76
   2 ?   -3.6   0.0       7.5   8.4e+03      15      24 ..     167     176 ..     165     185 .. 0.78
   3 ?    2.0   0.0      0.14   1.6e+02      76     117 ..     252     295 ..     220     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                 EB--STT---.B-EEE.TTTEEEETTTT CS
  Rep_fac-A_C 19 kACpsedCnk.Kvvee.edgewrCekCd 44
                 +ACp   C k K+v++ e+ge+ C kC 
   AJA91947.1  9 DACP--RCVKgKMVTDnESGEMFCSKCG 34
                 7***..8876555555388********6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 7.5
                  TTEEEB--ST CS
  Rep_fac-A_C  15 nlvYkACpse 24 
                  +++Y AC+ +
   AJA91947.1 167 SALYAACRDT 176
                  57899*9854 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.14
                  HHHHHSS-HHH..HHHHCCC-HHHHHHHHHHTTT-EEEEEEEEE CS
  Rep_fac-A_C  76 aekllglsaee..lkklkeedeeefekiiekvklkeflfrlrvk 117
                  ++  +gl a    l  +k+ ++++ ++i+e ++++e+++r r k
   AJA91947.1 252 GKDPMGLAAAAlyLSCVKNGEDKTQRDIAEAANVTEVTIRNRYK 295
                  556677666651156678899999999**********9998876 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026      0.29       2      28 ..      11      40 ..      10      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
  RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrlets 28
                    CP C k+k+  ++    +fC+ Cg+ ++ +
      AJA91947.1 11 CPRCVKGKMVTDNesGEMFCSkCGFVMSEK 40
                    ******99988663466***99***99885 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00025      0.28      28      50 ..      27      50 ..       9      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
  zf-piccolo 28 kqvCnlCGFnptphlte.kkeWlc 50
                ++ C++CGF ++ +l+e + eW +
  AJA91947.1 27 EMFCSKCGFVMSEKLQEsGPEWRS 50
                578**************899**76 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.9   5.5e+03      30      41 ..     131     142 ..     126     144 .. 0.80
   2 ?   -0.1   0.0      0.87   9.7e+02      18      30 ..     186     198 ..     185     206 .. 0.83
   3 ?   -2.0   0.0       3.2   3.6e+03      27      39 ..     222     234 ..     216     241 .. 0.83
   4 ?    9.0   0.0    0.0012       1.4      19      41 ..     270     292 ..     253     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.9
  Phage_terminase  30 kvLdvsestvrk 41 
                      + L +ses v k
       AJA91947.1 131 DKLAISESVVEK 142
                      679999999875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.87
  Phage_terminase  18 EsggtlklkdIAk 30 
                      E + ++k kdIA 
       AJA91947.1 186 EIAANIKRKDIAR 198
                      56789******97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.2
  Phage_terminase  27 dIAkvLdvsestv 39 
                       IA  ++++e+t 
       AJA91947.1 222 RIASKIGIAEKTK 234
                      6999999999985 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0012
  Phage_terminase  19 sggtlklkdIAkvLdvsestvrk 41 
                      +g  +  +dIA+  +v e t+r+
       AJA91947.1 270 NGEDKTQRDIAEAANVTEVTIRN 292
                      5778999**************98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.2    0.0018         2      31      56 ..      11      37 ..       8      39 .. 0.83
   2 ?   -0.8   0.0       1.3   1.5e+03       8      23 ..     229     244 ..     227     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
  OrfB_Zn_ribbon 31 CseCgsknke.alsgrtfkCpnCgfea 56
                    C++C + +   ++++ ++ C++Cgf++
      AJA91947.1 11 CPRCVKGKMVtDNESGEMFCSKCGFVM 37
                    9999765555579***********986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
  OrfB_Zn_ribbon   8 leykakeyGikveevn 23 
                     +++k k+y ikv ++ 
      AJA91947.1 229 IAEKTKRYAIKVLKIA 244
                     789*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1833.78
//
Query:       AJA91948.1  [L=86]
Description: hypothetical protein T478_0112 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 656.15
//
Query:       AJA91949.1  [L=209]
Description: restriction endonuclease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-05   23.2   0.0    9.1e-05   22.5   0.0    1.3  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.1e-09   9.1e-05       4      77 ..      83     161 ..      81     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.1e-09
                 T-TTCHHHHHHHHHHHHSSS.EEE---B-TTSSB--EEEETTEEEEEEEEEEE--T.......S-B-HHHHHHHHHHCTTS. CS
     Mrr_cat   4 mspkeFeklvaellealGyk.eveltgrsgDggiDliakkdplgserilvqaKryk.......nkvgvkeVqeligalkkrg 77 
                 +++++Fe++ + +le++G+    +l+ ++    iD+i kk +     +l+ +K++k       +++ +k+++++   ++++ 
  AJA91949.1  83 LTWRDFEAITGIILEENGFDvTKNLVLTKPRMEIDVIGKKMN---LALLIDCKHWKtmsksalDEIVKKQIERVKRYVADED 161
                 689*****************6334666678999******976...56********767644445566666666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1504.88
//
Query:       AJA91950.1  [L=304]
Description: TIGR00269 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      8e-22   77.9   0.0    1.4e-21   77.1   0.0    1.4  1  ATP_bind_3     PP-loop family
      7e-06   25.1   0.0      1e-05   24.5   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
    2.5e-05   23.6   0.0    3.8e-05   22.9   0.0    1.3  1  NAD_synthase   NAD synthase
    9.4e-05   22.5   0.0    0.00019   21.5   0.0    1.5  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.042   13.3   0.1    2.0  1  QueC           Queuosine biosynthesis protein QueC
      0.025   14.1   0.0      0.049   13.2   0.0    1.5  1  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   4.6e-25   1.4e-21       2     180 ..      50     239 ..      49     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4.6e-25
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H............HHCTTSTCCCHHHHHHHHHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv............akkkgknleeaARelRYevl 88 
                 v+v+vSgG DS++Ll +l+k++++ +++++a+++d g+    +e  e+vk++c+kl++++++ + +               +++++       +R ++l
  AJA91950.1  50 VVVGVSGGKDSLVLLSILKKMSETHNFRIIAVTIDEGIPGYRDEALEIVKSFCSKLDVEFRTYSYKElydvtlseslelRDEEKTTSCSICGIFRRRAL 148
                 79***********************************************************99999999999999998845556777779999****** PP

                 HHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT---B--CGGGCTTSHHHHHH CS
  ATP_bind_3  89 kealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvskeeleeylkekkikwveDesNadekyeRnriR 180
                 ++a+++ g++v++++h+ dD + tfl++   g +  ++  +++ s  ++ir + Pl +++ +e+  y+ ++++++ + +  + ++  R  iR
  AJA91950.1 149 DHAAEELGANVIATGHNLDDSLQTFLINTLSGDSN-KIGWMSPGSDSKQIRKIKPLAEIYESEIVFYAFTNNLPFQTEPCPHMNEGIRTEIR 239
                 ******************************99885.77889****9*****************************99998888888888877 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.4e-09     1e-05       3     125 ..      50     165 ..      48     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.4e-09
  tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefleeyeeGrTPnPdvlC 98 
                    vvv++SgG DS v + +lk+        +++++ +e+        +e l+ +++ ++kl++++++ ++++ y  ++ +e le   e +T   +  C
     AJA91950.1  50 VVVGVSGGKDSLVLLSILKKMSETHNFRIIAVTIDEGIP---GYRDEALEIVKSFCSKLDVEFRTYSYKELYDVTL-SESLELRDEEKT-TSCSIC 140
                    9************99999987644443334444443444...478999**********************998765.566666666666.469999 PP

  tRNA_Me_trans  99 NkeiKfgallekakeelgadalatGHY 125
                       i  +  l++a eelga+ +atGH 
     AJA91950.1 141 G--IFRRRALDHAAEELGANVIATGHN 165
                    7..4455667888888**********6 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.3e-08   3.8e-05       4     132 ..      33     167 ..      30     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                   HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEE..EEEE--..SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHH...HHH CS
  NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenv..lalllP..ssvsseedvedalalaenlgievktidikpivrafeq...elk 93 
                   +  + + +y   ++ + vv+G+SGG DS +   + +k+ + +n+  +a+ +        +e +e  + ++ +l++e+ t++ k+ + +  +   el+
    AJA91950.1  33 KAAKTISKYKMIKNDELVVVGVSGGKDSLVLLSILKKMSETHNFriIAVTIDegIPGYRDEALEIVKSFCSKLDVEFRTYSYKELYDVTLSeslELR 129
                   55667777777778899**************999999998877533788887422345677789999******************998877444555 PP

                   HHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHH CS
  NAD_synthase  94 eakedlakgNlkaRiRmailyaianklnllvlgTgnksE 132
                   ++ e++++  ++   R  +l + a++l+  v++Tg++ +
    AJA91950.1 130 DE-EKTTSCSICGIFRRRALDHAAEELGANVIATGHNLD 167
                   55.599999**************************9865 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.5e-08   0.00019       2     155 ..      50     222 ..      49     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.5e-08
                  EEEE--SSCTCHHHHHHHHHHCTTH....EEEEEE-ST..B-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC.....HHHHHHTH CS
  PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv....pvvfvdtgh..efpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee.....aaeriaKv 88 
                  +vv vsgGkdslVll ++ k+ +        v +d g     +e +e v+ + +++++++ +y+ +e  +  + +     +   e      ++ i + 
   AJA91950.1  50 VVVGVSGGKDSLVLLSILKKMSETHnfriIAVTIDEGIpgYRDEALEIVKSFCSKLDVEFRTYSYKELYDVTLSESLELRDE--EkttscSICGIFRR 145
                  5889**************9999884444467788887632468999999999999988877777766544444433322222..13456899****** PP

                  HHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S..........CEEE-CCCT--HHHHHHHHHHCT--B CS
  PAPS_reduct  89 eplkkaLekldedalltGaRrdesksraklpiveidedfek..........slrvfPllnWteedvwqyilrenipy 155
                  ++l  a e+l+++++ tG   d+s +   ++ ++ d+++              ++ Pl++  e ++  y+ ++n+p 
   AJA91950.1 146 RALDHAAEELGANVIATGHNLDDSLQTFLINTLSGDSNKIGwmspgsdskqIRKIKPLAEIYESEIVFYAFTNNLPF 222
                  ************************************99776999******555677******************986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.4e-05     0.042       2      68 ..      50     121 ..      49     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                 EEEE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS CS
        QueC   2 avvllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelg 68 
                 +vv +SGG DS ++l + kk       +++a+t+d g    +++ le++k+++++l+v e ++ + + l +++
  AJA91950.1  50 VVVGVSGGKDSLVLLSILKKMSethnFRIIAVTIDEGIPgyRDEALEIVKSFCSKLDV-EFRTYSYKELYDVT 121
                 5899***********99988653333689******99877577789************.77766666555444 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.049       6     119 ..      50     167 ..      31     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
        ThiI   6 vlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv......kekltivllkrkmlr 98 
                 v++ +SgG DS V  + +lk+  + +   ++ + +  e   + + ++ e++ ++ ++l+v+++++++ke+ +  l+++      ++ + + ++     r
  AJA91950.1  50 VVVGVSGGKDSLVLLS-ILKKMSETHNFRII-AVTIDEGIPGYRDEALEIVKSFCSKLDVEFRTYSYKELYDVTLSESlelrdeEKTTSCSICGIFRRR 146
                 6777899999988655.45666666666664.555667777888899999999999999********99876544444466653444557788888888 PP

        ThiI  99 iAekvaeeegakalvtGesLg 119
                 + ++ aee ga+ + tG +L 
  AJA91950.1 147 ALDHAAEELGANVIATGHNLD 167
                 99999*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2238.19
//
Query:       AJA91951.1  [L=294]
Description: glycosyltransferase, group 2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-24   84.8   0.2    7.9e-24   84.4   0.2    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00022   21.2   0.0     0.0003   20.7   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
       0.16   12.5   0.0       0.29   11.7   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
        1.4    8.8   6.4        2.3    8.2   6.4    1.3  1  Promethin        Promethin
        4.5    7.8   6.1         11    6.6   6.1    1.6  1  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.2   2.2e-27   7.9e-24       2     168 ..       5     162 ..       4     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.2e-27
                      EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS...EEEEEESSEEE CS
  Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd...yilflDaDdep 92 
                      + ip+yNeek+++  ++ l+++     ++iiv DDgS+D t +i e+l     + +vi++e+n G+++a++  + +a+      ++++DaD ++
       AJA91951.1   5 IGIPAYNEEKNIAVIITQLKEI----TDKIIVCDDGSRDLTSKISEDL-----GAIVIKHEKNLGYGAAIRSIFLKAKDLdcdALVTFDADGQH 89 
                      679*******************....**********************.....9***********************997788*********** PP

                      -TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
  Glycos_transf_2  93 dpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealee 168
                        ++++k+++++ +   d+v+g+r+  +ge+   + +k      ++ +k+++ s+k +l++  ++++++++ +l e
       AJA91951.1  90 RIQDISKVIQPIIEKKSDIVIGSRFLDDGEKEVPNYRK---VGIKVITKITNMSIKKELTDSQSGFRAYSKQVLSE 162
                      *****************************999999987...59*****************************9987 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   8.4e-08    0.0003       4     129 ..       3     118 ..       2     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 8.4e-08
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97 
                      la+ +p++nee+ +  ++++l     ++++++v++d+s++ t +  e    +l+++   v+  ++nlg ++++r+++   +  ++d ++ +D+D
       AJA91951.1   3 LAIGIPAYNEEKNIAVIITQLKE---ITDKIIVCDDGSRDLTSKISE----DLGAI---VIKHEKNLGYGAAIRSIFLKAKDLDCDALVTFDAD 86 
                      799*******9999999999887...79**************99555....57776...7888999**************************** PP

  Glyco_tranf_2_3  98 tvvePdtlkrllqffltpkvgavgtpvfllnr 129
                             + ++ q +  +k ++v +++fl+ +
       AJA91951.1  87 GQHRIQDISKVIQPIIEKKSDIVIGSRFLDDG 118
                      87755555555565557788888888777654 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     8e-05      0.29       1      49 [.      10      57 ..      10      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
  Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdrilvydndstDgtrailkelpevkllhvd 49
                     +ne++ +   ++ ++++  d+i+v+d++s+D t++i + l ++ + h +
       AJA91951.1 10 YNEEKNIAVIITQLKEI-TDKIIVCDDGSRDLTSKISEDLGAIVIKHEK 57
                     58999999999999999.9*****************9998776665554 PP

>> Promethin  Promethin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.4   0.00064       2.3      38      89 ..     227     288 ..     204     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00064
   Promethin  38 llsllPlllFltfalstllfalvg..........allfelfvvgvallvLvpvLfitsflal 89 
                  + ++P ++Fl++ ls  + ++            +++++  +v v++++L++++++ s++++
  AJA91951.1 227 KFYGIPSVFFLIIGLSFTIWTIQEyaisgeiitnIAIIAIGCVIVGVVLLLCAILLYSLVSV 288
                 5889************9999988877788888775555666666666666666666666554 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.1    0.0029        11      18      62 ..     236     283 ..     233     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0029
      DUF202  18 lalialglallrffl...tgepsalg.kilglilivlgiltllvglvry 62 
                  ++i+l+++++ ++    +ge   ++ +i++++++++g+++ll+++  y
  AJA91951.1 236 FLIIGLSFTIWTIQEyaiSGE-IITNiAIIAIGCVIVGVVLLLCAILLY 283
                 6799999****9866553222.222458889*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2022.48
//
Query:       AJA91952.1  [L=225]
Description: HEAT repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-12   48.1   0.1    1.4e-05   25.4   0.0    2.5  3  HEAT_2         HEAT repeats
    0.00018   21.5   0.0        1.5    9.3   0.0    4.4  5  HEAT           HEAT repeat
    0.00062   20.2   0.0        3.3    8.3   0.0    3.6  4  HEAT_EZ        HEAT-like repeat
     0.0073   15.9   0.1      0.015   14.9   0.1    1.5  1  ERAP1_C        ERAP1-like C-terminal domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.3  1  DUF1175        Protein of unknown function (DUF1175)
      0.018   14.9   0.2        4.9    7.0   0.0    2.3  2  DUF1495        Winged helix DNA-binding domain (DUF1495)
      0.063   13.2   1.2        0.7    9.8   0.1    2.5  3  LpxI_N         LpxI N-terminal domain
      0.068   13.4   0.2       0.15   12.2   0.0    1.6  2  Sigma_reg_C    Sigma factor regulator C-terminal
      0.079   13.6   0.1        2.3    8.8   0.0    3.0  3  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.9e-07     0.002       6      55 ..      53     102 ..      50     109 .. 0.92
   2 !   25.4   0.0   6.8e-09   1.4e-05       5      83 ..     114     191 ..     110     196 .. 0.90
   3 !   14.1   0.0   2.3e-05     0.046       8      71 ..     147     210 ..     147     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.9e-07
      HEAT_2   6 qalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaL 55 
                 ++le+ +++++r+ ++++L + ++pe++  +++l +ded ++R +a  +L
  AJA91952.1  53 EILESLKNEKLRKSILQTLTQNNDPEIIHEIIQLFDDEDIEIRGEAFSSL 102
                 57778899************************************998877 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 6.8e-09
      HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvReaA 83 
                 +  l ++ +++vr+ +  +L++ +++ a++ +++l +d++  vR  a  aLg +  +++++ L + + d + + v+ aA
  AJA91952.1 114 VLGL-RHDSKNVRAYTTLVLANRNEKNAIEEIIKLTNDSSGLVRTCAYGALGHLEAKQSAKELHKGVFDSNLEAVKSAA 191
                 5557.899*******************************************************9999777779999875 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.3e-05
      HEAT_2   8 lendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigdpealpaLkell 71 
                 l+nd++  vr  a  aLg +  +++ + L++ + d++ +  + aa +L +i+++ + + L+el 
  AJA91952.1 147 LTNDSSGLVRTCAYGALGHLEAKQSAKELHKGVFDSNLEAVKSAAYSLTRIKEKISDKELEELH 210
                 679*************************************************877777777654 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.8   3.5e+03      13      26 ..      60      73 ..      54      77 .. 0.78
   2 ?    4.4   0.0     0.027        54       2      24 ..      80     102 ..      79     102 .. 0.83
   3 ?    0.4   0.0      0.54   1.1e+03       6      24 ..     115     132 ..     109     134 .. 0.74
   4 !    9.3   0.0   0.00075       1.5       4      27 ..     143     166 ..     140     167 .. 0.91
   5 ?    0.2   0.0      0.61   1.2e+03      11      28 ..     181     198 ..     177     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.8
                SHHHHHHHHHHHHH CS
        HEAT 13 speVReaAakaLga 26
                + + R++ +++L++
  AJA91952.1 60 NEKLRKSILQTLTQ 73
                67788888888865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                 HHHHHHHHT-SSHHHHHHHHHHH CS
        HEAT   2 lPlllkllsDpspeVReaAakaL 24 
                 +  +++l  D++ e+R  A+ +L
  AJA91952.1  80 IHEIIQLFDDEDIEIRGEAFSSL 102
                 56699999********9888765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.54
                 HHHHT-SSHHHHHHHHHHH CS
        HEAT   6 lkllsDpspeVReaAakaL 24 
                 l  l+++s +VR+ + + L
  AJA91952.1 115 L-GLRHDSKNVRAYTTLVL 132
                 4.48999*****9887766 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00075
                 HHHHHHT-SSHHHHHHHHHHHHHH CS
        HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                  ++kl +D+s  VR  A  aLg+l
  AJA91952.1 143 EIIKLTNDSSGLVRTCAYGALGHL 166
                 589999****************87 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 0.61
                 -SSHHHHHHHHHHHHHHH CS
        HEAT  11 DpspeVReaAakaLgala 28 
                 D++ e  ++Aa++L+++ 
  AJA91952.1 181 DSNLEAVKSAAYSLTRIK 198
                 777777899****99985 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.07   1.4e+02      27      48 ..      77      98 ..      54     102 .. 0.82
   2 ?    4.8   0.0     0.021        41      31      53 ..     111     133 ..     108     134 .. 0.79
   3 !    8.3   0.0    0.0016       3.3      27      55 .]     138     166 ..     131     166 .. 0.85
   4 ?   -3.5   0.0       8.2   1.6e+04      40      55 .]     182     197 ..     179     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.07
     HEAT_EZ 27 peilpaLlalLnddsdeVRaaA 48
                pei+ + ++l  d++ e+R+ A
  AJA91952.1 77 PEIIHEIIQLFDDEDIEIRGEA 98
                7888888877777777***977 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.021
     HEAT_EZ  31 paLlalLnddsdeVRaaAagaLg 53 
                 + L+ +L++ds++VRa++   L+
  AJA91952.1 111 KDLVLGLRHDSKNVRAYTTLVLA 133
                 558889**********9976665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0016
     HEAT_EZ  27 peilpaLlalLnddsdeVRaaAagaLgnl 55 
                 + ++ + ++l nd+s +VR+ A gaLg l
  AJA91952.1 138 KNAIEEIIKLTNDSSGLVRTCAYGALGHL 166
                 6678889999999999**********976 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.2
     HEAT_EZ  40 dsdeVRaaAagaLgnl 55 
                 ++ e  + Aa+ L+++
  AJA91952.1 182 SNLEAVKSAAYSLTRI 197
                 5555556677777765 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   7.4e-06     0.015     120     222 ..      56     180 ..      36     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.4e-06
                 TS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH...HCSTT.........-S-HHHHHH.........HHHHHH.HHS.-HHHHHHHHHHHHC-SSH CS
     ERAP1_C 120 eshldaqlrslllsaacaagdpevveearklfkaw...legdd.........lippdlrwa.........vycala.ang.geaewdallerykdtsap 195
                 es  + +lr+++l+++ +++dpe + e  +lf++    + g++         +i +dl            +y++l+ an   ++ +++++++ +d+s  
  AJA91952.1  56 ESLKNEKLRKSILQTLTQNNDPEIIHEIIQLFDDEdieIRGEAfsslflnrgNILKDLVLGlrhdsknvrAYTTLVlANRnEKNAIEEIIKLTNDSSG- 153
                 5667899**************************99532112223333333332222222223333333344444442443133356666666322222. PP

                 HHHHHHHHHHCC-S-HHHHHHHHHHCT CS
     ERAP1_C 196 sekeaalralaatpdpellerllnfvl 222
                   ++ a +al++ + ++  ++l + v+
  AJA91952.1 154 LVRTCAYGALGHLEAKQSAKELHKGVF 180
                 447777777777766666666555444 PP

>> DUF1175  Protein of unknown function (DUF1175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.029      25      83 ..     119     178 ..     110     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
     DUF1175  25 edseafrawfvr.iaeeqlrketarweeeerDCaglvryavrEalkkhdarwleksglsg 83 
                 +ds+++ra+ +  +a+++ ++  ++  + ++D +glvr ++  al + +a+++ k+  +g
  AJA91952.1 119 HDSKNVRAYTTLvLANRNEKNAIEEIIKLTNDSSGLVRTCAYGALGHLEAKQSAKELHKG 178
                 7999****98861566666666888889*****************999998887765553 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0025       4.9       1      37 [.      54      89 ..      54      98 .. 0.77
   2 ?    5.7   0.1    0.0064        13      10      84 ..     124     199 ..     117     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0025
     DUF1495  1 ilrslnkSkvRkkvllyLysiypeksnlqeisrrvrs 37
                il+sl++ k+Rk++l  L+++ +  + ++ei++    
  AJA91952.1 54 ILESLKNEKLRKSILQTLTQNND-PEIIHEIIQLFDD 89
                899****************7765.6777777766555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0064
     DUF1495  10 vRkkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessL..ielGLveeeeeseglklYklteeGi 84 
                 vR    l L+ + +ek+ ++ei++ ++ ++  v+ +  G   + ++++s   +++G+  +  e    + Y+lt   +
  AJA91952.1 124 VRAYTTLVLA-NRNEKNAIEEIIKLTNDSSGLVRTCAYGALGHLEAKQSAkeLHKGVFDSNLEAVKSAAYSLTRIKE 199
                 5555556666.7788999**********************9999999986458889999888888888999987555 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00035       0.7      75     121 ..      49      96 ..      48      99 .. 0.82
   2 ?    1.3   0.0      0.15   2.9e+02      73     111 ..     107     147 ..     104     154 .. 0.87
   3 ?   -2.4   0.0         2     4e+03      29      61 ..     192     224 ..     185     225 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00035
      LpxI_N  75 vekpklldlrp.DlralkllaklkdrgddalLravveelekeGikvlg 121
                 ++++++l+ ++ +   +++l+ l++++d ++++++++ + +e+i++ g
  AJA91952.1  49 MNREEILESLKnEKLRKSILQTLTQNNDPEIIHEIIQLFDDEDIEIRG 96 
                 6788888555526777778888**********************9976 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
      LpxI_N  73 GkvekpklldlrpDlralkllak..lkdrgddalLravvee 111
                 G++ k+++l lr+D + ++ +    l++r+ ++ ++++++ 
  AJA91952.1 107 GNILKDLVLGLRHDSKNVRAYTTlvLANRNEKNAIEEIIKL 147
                 8899999999******9999999888899999999999986 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2
      LpxI_N  29 valegeadeelekivdevaevsvgqlgklikaL 61 
                 ++l+   ++   k+ +e +++   ++++++k++
  AJA91952.1 192 YSLTRIKEKISDKELEELHKLDKPEFDRILKFF 224
                 555555555566666778888888888888887 PP

>> Sigma_reg_C  Sigma factor regulator C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.6e-05      0.15      58     131 ..      17      96 ..       5     100 .. 0.82
   2 ?   -2.1   0.0         2     4e+03      89     110 ..     180     201 ..     135     212 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
  Sigma_reg_C  58 teaiGfkvnps.ssekddkkkypkele.....kaeehfislLkylsdqeeivktleeslekeklkerydyvkkngvkiyG 131
                  ++ iGf + ++ s+ + d++ +++e++      ++e+ +++Lk+ + +++i++tl+++++ e + e+++  ++++++i G
   AJA91952.1  17 YAIIGFLPMNTvSRCSVDMRVKYYEDNlnqdrMNREEILESLKNEKLRKSILQTLTQNNDPEIIHEIIQLFDDEDIEIRG 96 
                  66789877666677777777666666678998999*******************977777655************99988 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
  Sigma_reg_C  89 fislLkylsdqeeivktleesl 110
                  f s+L+ ++    ++++++e+ 
   AJA91952.1 180 FDSNLEAVKSAAYSLTRIKEKI 201
                  3444444444444444444444 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   2.7e+03      40      66 ..      34      58 ..      25      76 .. 0.70
   2 ?    8.8   0.0    0.0012       2.3      22      53 ..      73     104 ..      62     117 .. 0.79
   3 ?    0.9   0.0      0.36   7.1e+02      27      51 ..     139     163 ..     114     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
  Vac14_Fab1_bd 40 dsrvRyyacEslyniakvakgevlkll 66
                   d rv+yy  E   n  ++ ++e+l+ l
     AJA91952.1 34 DMRVKYY--EDNLNQDRMNREEILESL 58
                   6678887..445566666666666655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
  Vac14_Fab1_bd  22 keyleeivkpvlkcfsDkdsrvRyyacEslyn 53 
                    ++   ei++ +++ f+D+d ++R  a  sl+ 
     AJA91952.1  73 QNNDPEIIHEIIQLFDDEDIEIRGEAFSSLFL 104
                    555679******************99999983 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.36
  Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEsl 51 
                    + ++ ++k  +D++  vR  a  +l
     AJA91952.1 139 NAIEEIIKLTNDSSGLVRTCAYGAL 163
                    5566666666777666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1605.00
//
Query:       AJA91953.1  [L=58]
Description: PF06348 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-19   69.2   1.0    2.9e-19   69.0   1.0    1.0  1  DUF1059   Protein of unknown function (DUF1059)
  ------ inclusion threshold ------
      0.089   12.7   0.1      0.093   12.7   0.1    1.1  1  Sina      Seven in absentia protein family


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   1.0   3.2e-23   2.9e-19       2      56 .]       3      57 ..       2      57 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 3.2e-23
     DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                k+++C D+g dCg++++a+te+E++ k++eH+ka+H++ e++pe v++ik+ Ik+
  AJA91953.1  3 KSISCHDAGKDCGWSASAPTEDELMVKIEEHVKAEHKEIELTPENVANIKTLIKE 57
                89***************************************************96 PP

>> Sina  Seven in absentia protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     1e-05     0.093      43      83 ..       3      50 ..       1      58 [] 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
        Sina 43 rpysCpcpgakCkwqGdld.......ellkHlrneHkkvetlegesfs 83
                + +sC  +g++C w  +         ++++H++ eHk++e   ++ ++
  AJA91953.1  3 KSISCHDAGKDCGWSASAPtedelmvKIEEHVKAEHKEIELTPENVAN 50
                789***********9975322222225779*********988776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 452.70
//
Query:       AJA91954.1  [L=39]
Description: hypothetical protein T478_0941 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 317.51
//
Query:       AJA91955.1  [L=83]
Description: RNA polymerase Rpb5, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-25   87.0   0.0    6.5e-25   86.8   0.0    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.0   3.6e-29   6.5e-25       3      73 .]      10      80 ..       8      80 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 3.6e-29
                    -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
  RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                    + +H++vPkhe++++++++++l+++++k+++LP i  +Dp++  lg+k+Gd+++Itrks tage+++YR+V
      AJA91955.1 10 VPDHVYVPKHEIMTKKDAQKVLDEFNCKPTELPLIFVTDPAILGLGVKPGDMIRITRKSGTAGESTYYRYV 80
                    679******************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 583.37
//
Query:       AJA91956.1  [L=53]
Description: hypothetical protein T478_1478 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00064   19.7   0.2    0.00085   19.3   0.2    1.3  1  zf-BED       BED zinc finger
     0.0007   19.9   0.4     0.0007   19.9   0.4    1.8  2  zf-C2H2      Zinc finger, C2H2 type
     0.0019   17.9   0.3     0.0031   17.2   0.3    1.3  1  zf-C2H2_11   zinc-finger C2H2-type
     0.0019   18.9   0.2     0.0019   18.9   0.2    1.8  2  zf-C2H2_4    C2H2-type zinc finger
  ------ inclusion threshold ------
      0.011   15.6   2.9      0.015   15.2   0.0    2.0  2  zf-C2HC_2    zinc-finger of a C2HC-type
      0.014   15.2   0.0      0.014   15.2   0.0    1.7  2  zf-C2H2_9    C2H2 type zinc-finger (1 copy)
      0.021   15.2   0.0      0.023   15.0   0.0    1.1  1  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
      0.026   14.3   0.9       0.28   11.1   0.0    2.1  2  zf-C2H2_3    zinc-finger of acetyl-transferase ESCO
      0.029   13.9   0.1      0.031   13.8   0.1    1.1  1  RAG1_imp_bd  RAG1 importin binding
        0.2   10.2   0.0        0.2   10.1   0.0    1.0  1  DUF629       Protein of unknown function (DUF629)


Domain annotation for each model (and alignments):
>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   4.8e-07   0.00085      17      43 ..      16      39 ..       9      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.8e-07
                -EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED 17 avCryCgkilsrgggttnLkrHLrrkH 43
                + Cr+Cg +++    t +L+rH++++H
  AJA91956.1 16 TLCRICGMNFTA---TDRLMRHMVKAH 39
                56*********9...8**********9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   3.9e-07    0.0007       3      23 .]      18      39 ..      17      39 .. 0.97
   2 ?   -1.1   0.8       1.8   3.2e+03       3       6 ..      50      53 .]      49      53 .] 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                ETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  3 CpdCgksFkrksnLkrHirt.H 23
                C +Cg+ F+  + L+rH+ + H
  AJA91956.1 18 CRICGMNFTATDRLMRHMVKaH 39
                9*****************9988 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                ETTT CS
     zf-C2H2  3 CpdC 6 
                Cp C
  AJA91956.1 50 CPNC 53
                **99 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   1.8e-06    0.0031       7      28 ..      18      39 ..      15      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
  zf-C2H2_11  7 CleCGlcftSqlsLsRHlfIvH 28
                C+ CG++ft    L RH+   H
  AJA91956.1 18 CRICGMNFTATDRLMRHMVKAH 39
                ******************7665 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   1.1e-06    0.0019       3      24 .]      18      39 ..      16      39 .. 0.91
   2 ?   -1.2   0.8       3.1   5.6e+03       2       6 ..      49      53 .]      48      53 .] 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
   zf-C2H2_4  3 CpiCgksFsskkaLlrHlkthH 24
                C+iCg +F+  ++L rH+ + H
  AJA91956.1 18 CRICGMNFTATDRLMRHMVKAH 39
                ********99999*****9988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
   zf-C2H2_4  2 kCpiC 6 
                 Cp C
  AJA91956.1 49 SCPNC 53
                59999 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.4e-06     0.015       5      21 ..      18      35 ..      16      43 .. 0.91
   2 ?    0.1   1.5      0.46   8.2e+02       5       8 ..      50      53 .]      49      53 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.4e-06
   zf-C2HC_2  5 CpkCgRsF.npdrlekHe 21
                C++Cg  F ++drl +H+
  AJA91956.1 18 CRICGMNFtATDRLMRHM 35
                *****************5 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.46
   zf-C2HC_2  5 CpkC 8 
                Cp+C
  AJA91956.1 50 CPNC 53
                **** PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     8e-06     0.014       2      30 ..      16      44 ..      15      46 .. 0.87
   2 ?   -1.9   1.5       1.7   3.1e+03       2       7 ..      48      53 .]      47      53 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                -B-TTT--B-SSHHHHHHHHHHHTSSS-- CS
   zf-C2H2_9  2 plCPvCevkfnswkdlseHilsaasksda 30
                +lC +C ++f + ++l  H+++a  k  +
  AJA91956.1 16 TLCRICGMNFTATDRLMRHMVKAHGKAKK 44
                69******************998877655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                -B-TTT CS
   zf-C2H2_9  2 plCPvC 7 
                p CP C
  AJA91956.1 48 PSCPNC 53
                679999 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.3e-05     0.023       2      24 ..      18      40 ..       8      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
   zf-C2H2_2  2 Clfcekkskeveellehmskkhg 24
                C +c ++++  ++l++hm k+hg
  AJA91956.1 18 CRICGMNFTATDRLMRHMVKAHG 40
                89999999999999999999987 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.28      10      27 ..      11      29 ..       4      30 .. 0.68
   2 ?    2.2   0.2      0.09   1.6e+02       9      19 ..      44      53 .]      37      53 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
   zf-C2H2_3 10 sfga.sqCkeCgMvYnpgs 27
                   + + C  CgM +++++
  AJA91956.1 11 VVITgTLCRICGMNFTATD 29
                4334244*******99875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.09
   zf-C2H2_3  9 ksfgasqCkeC 19
                k++g   C++C
  AJA91956.1 44 KDYGP-SCPNC 53
                55555.6**** PP

>> RAG1_imp_bd  RAG1 importin binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.7e-05     0.031     102     125 ..      16      39 ..      11      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                  XXXXXXXXXXXXXXXXXXXXXXXX CS
  RAG1_imp_bd 102 qlCRlCGaslkkdvknrsyevhgp 125
                  +lCR+CG+ + +  + +++ v+++
   AJA91956.1  16 TLCRICGMNFTATDRLMRHMVKAH 39 
                  69**********99999**99764 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00011       0.2      58      83 ..      17      42 ..      14      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
      DUF629 58 vCrtCsekfsdaeeckqHlvqeHvak 83
                 Cr+C  +f+  +  + H+v+ H + 
  AJA91956.1 17 LCRICGMNFTATDRLMRHMVKAHGKA 42
                6**********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 381.35
//
Query:       AJA91957.1  [L=287]
Description: tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-58  196.2   1.7    3.3e-58  195.5   1.7    1.3  1  THF_DHG_CYH_C   Tetrahydrofolate dehydrogenase/cyclohydrolase
    1.6e-38  131.5   0.5    2.7e-38  130.8   0.5    1.4  1  THF_DHG_CYH     Tetrahydrofolate dehydrogenase/cyclohydrolase
     0.0017   18.1   0.3      0.048   13.5   0.1    2.7  3  IF2_N           Translation initiation factor IF-2, N-termina
      0.006   17.0   0.0      0.012   16.1   0.0    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.019   15.3   0.1      0.032   14.5   0.1    1.3  1  Hydrolase       haloacid dehalogenase-like hydrolase
      0.028   13.7   0.0      0.052   12.8   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.5   1.7   1.1e-61   3.3e-58       2     157 ..     124     280 ..     123     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 1.1e-61
                    HHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-..B-G CS
  THF_DHG_CYH_C   2 plnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpel..ika 95 
                    p n+g l  g+ +l++ctp g++e++k ++ielegk+vv+++rsn+vgkpl  lLl++natVt+chsktkdl++i+  +di++++vG+ e+  ++ 
     AJA91957.1 124 PPNVGLLSIGKAMLVACTPSGIIEMCKYYNIELEGKNVVIINRSNLVGKPLYHLLLQNNATVTTCHSKTKDLKKICLDSDIIITGVGNREIfkLTP 219
                    67***************************************************************************************9844679 PP

                    GGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHH CS
  THF_DHG_CYH_C  96 emvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaak 157
                    +m+kegavviDv ++r  +gkl+GD d++e+ e+ s+ +PvpgGVGpmTvamllknt++aa 
     AJA91957.1 220 DMIKEGAVVIDVATTRH-EGKLAGDADYAEIIEKTSYASPVPGGVGPMTVAMLLKNTVTAAA 280
                    *****************.****************************************9986 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.5   8.9e-42   2.7e-38       2     116 .]       6     120 ..       5     120 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 8.9e-42
                  --HHHHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHHHH-TT--EEEE-SS-STT CS
  THF_DHG_CYH   2 ldGkalakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieelneddsvdGilvqlPlpkh 99 
                  +dG ++ak+i+ +++e v++lk+kg++p+La++lvgd+pas++Yvrnk+kaceevGi ++ ++ p+d++++el klie+ln+d++v+GilvqlPlp+h
   AJA91957.1   6 IDGIEVAKSIKVKVAEIVNDLKSKGISPCLATVLVGDNPASATYVRNKHKACEEVGILTKDHTPPTDITQDELNKLIEKLNADETVHGILVQLPLPSH 103
                  89************************************************************************************************ PP

                  S-HHHHHCCS-GGGBTT CS
  THF_DHG_CYH 100 idekaileaispeKDVD 116
                  ++e + + +i peKDVD
   AJA91957.1 104 LNEFNTTTQILPEKDVD 120
                  ****************9 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.6e-05     0.048       8      31 ..      10      32 ..       9      33 .. 0.94
   2 ?    1.6   0.0      0.08   2.4e+02      38      53 ..      72      87 ..      56      88 .. 0.84
   3 ?   -3.4   0.0         3     9e+03      18      31 ..     143     155 ..     138     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
       IF2_N  8 eLAkeLgvkskevikkLfkelGie 31
                e+Ak ++vk++e++  L k++Gi+
  AJA91957.1 10 EVAKSIKVKVAEIVNDL-KSKGIS 32
                89***************.88**96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.08
       IF2_N 38 sLDeetaeliaeefgi 53
                 +++++++++ e++++
  AJA91957.1 72 DITQDELNKLIEKLNA 87
                6999999999999985 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3
       IF2_N  18 kevikkLfkelGie 31 
                   +i+ + k++ ie
  AJA91957.1 143 SGIIEMC-KYYNIE 155
                 5589999.888876 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.9e-06     0.012      28      98 ..     161     233 ..     148     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-06
                     EEEEESTTTTTSBHHHHSG.GGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHHHHHHHTTSEEEESSS CS
  Semialdhyde_dh  28 vvllsssrsaGkklaeavk.aleegkdlkvedvdeeel.kevdivflalpagvskelapklaeagvkviDlss 98 
                     vv++ +s+  Gk+l  +   + +++++   ++ d +++  + di+++ +++    +l+p+++++g++viD + 
      AJA91957.1 161 VVIINRSNLVGKPLYHLLLqNNATVTTCHSKTKDLKKIcLDSDIIITGVGNREIFKLTPDMIKEGAVVIDVAT 233
                     56667777788888887663333344444444666666799*****************************985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.1e-05     0.032     112     189 ..      10      88 ..       5      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                 HHHHTHHBHTTHHHHHHHHHHTTEEEEEEE...SSEHHHHHHHHHHTTGGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTST CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 112 tiadplkvkpeaaeavasLkaagievvllt...gdnpetaeraanqlGddyf.daviasdietvakpspegkvaaireLqgk 189
                 ++a +  +k ++ae v+ Lk++gi  +l+t   gdnp+ a  + n+    +   +++++d +      ++ ++++i++L+++
  AJA91957.1  10 EVAKS--IKVKVAEIVNDLKSKGISPCLATvlvGDNPASATYVRNKHK-ACEeVGILTKDHTPPTDITQDELNKLIEKLNAD 88 
                 56667..9999**************99999999****88888888765.333133444444448888888888888888755 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.052      72     130 ..     182     234 ..     148     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                  TCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETTGG CS
  AlaDh_PNT_C  72 akfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvAid 130
                  + +v++ +s+ + l++ + ++d++i+ v   G++    +t +m+   k+g+V++DvA+ 
   AJA91957.1 182 NATVTTCHSKTKDLKKICLDSDIIITGV---GNREIFKLTPDMI---KEGAVVIDVATT 234
                  4459999*******************95...5555555577776...78********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2102.41
//
Query:       AJA91958.1  [L=420]
Description: translation initiation factor 2, gamma subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-28   99.5   0.2      8e-28   97.3   0.2    1.8  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    3.4e-24   84.9   1.4    9.2e-24   83.5   0.1    2.4  3  eIF2_C        Initiation factor eIF2 gamma, C terminal
      2e-05   24.7   0.0    3.9e-05   23.7   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    0.00017   21.9   0.8    0.00038   20.8   0.4    1.8  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    0.00059   19.8   1.6      0.009   15.9   0.2    2.3  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.035   14.1   0.1    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.052   13.1   0.8        4.7    6.7   0.0    2.4  2  FeoB_N        Ferrous iron transport protein B
      0.095   12.7   0.0       0.19   11.8   0.0    1.4  1  HypA          Hydrogenase/urease nickel incorporation, metall
      0.097   13.2   0.0       0.78   10.3   0.0    2.4  2  ILEI          Interleukin-like EMT inducer


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.2     4e-31     8e-28       3     192 ..      20     211 ..      18     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 4e-31
                 EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE........................TTCSSEEEEEEEE CS
    GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle........................ketkkylinliDt 77 
                  +nig++ghvDhGKt+L+ +L+ k                   +++E +rgiTi +                              + + ++ ++++D+
  AJA91958.1  20 CVNIGTAGHVDHGKTSLIQALTGKWT---------------SVHSQELKRGITIRVGYSDAAfykcpdcepptnystspkcpnckqEGELSRVVSFVDS 103
                 68*******************94443...............4556899999999998887777799999999999999999999754778999****** PP

                 SSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEE CS
    GTP_EFTU  78 PGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfg 173
                 PGH++ + ++  g + +Dga+l+v+a+e  +++q++e+l  ++++g++ i+v+ NK+D +  +e     ++++ k+      ++  g+++  + pv+++
  AJA91958.1 104 PGHESLMANMLSGSALMDGAILLVAANEKvPQMQSKEHLLALQTLGIKqIVVVQNKVDLItYKEAMSNYSDIS-KF------IK--GTNA-AKSPVIPV 192
                 ***************************99579****************999999******8899999999999.66......54..4444.367***** PP

                 BTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 174 Salkgegvktllealvell 192
                 Sa  + ++++l+  + + +
  AJA91958.1 193 SAQANLNLDALIYSIETEI 211
                 *********9998887655 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   5.4e+03      17      32 ..     128     143 ..     107     163 .. 0.68
   2 ?   -2.1   0.0       2.4   4.7e+03      24      48 ..     272     297 ..     261     304 .. 0.75
   3 !   83.5   0.1   4.6e-27   9.2e-24       4      86 .]     337     419 ..     335     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                 SSCCC-----TTEEEE CS
      eIF2_C  17 keekkveklkkkEvLm 32 
                   ++kv ++++kE+L+
  AJA91958.1 128 AANEKVPQMQSKEHLL 143
                 3334577777777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                 ---TTEEEEEEETTEEEE.EEEEEEE CS
      eIF2_C  24 klkkkEvLmlniGsastg.gvvtsvk 48 
                 k k+ E+L+ +i s+ tg g+v +vk
  AJA91958.1 272 KKKNYEPLITEIVSLGTGaGTVDNVK 297
                 55777899999999877636777776 PP

  == domain 3  score: 83.5 bits;  conditional E-value: 4.6e-27
                 EEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEEEEEE CS
      eIF2_C   4 eieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiGwGei 86 
                 +++++l++  vg+ +++k+++++ +E+L lniG+a   g+vt+vk+  ++v+L++P+c  +++++a+sRr+  rWrLiG G+i
  AJA91958.1 337 KLKVSLFDSAVGSASNEKIAPINMGEMLRLNIGTAPIPGKVTKVKETDIEVTLRRPACLFEKSNVAISRRIADRWRLIGAGII 419
                 57899****************************************************************************87 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     2e-08   3.9e-05       2     112 ..      23     157 ..      22     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2e-08
                 EEEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEE....ETTEE.........................EEEEECGGCSSHHHHHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvk....lkgke.........................ielvDtpGliegaseekglgk 68 
                 ++ +G+   GK++Li+altg+ ++  s++   g T+ + +   +        +                         + +vD pG  e      +l  
  AJA91958.1  23 IGTAGHVDHGKTSLIQALTGKwTSVHSQELkrGITIRVGYSDAAfykcP---DcepptnystspkcpnckqegelsrvVSFVDSPG-HE------SLMA 111
                 7889****************96443344332377777777776643331...15556666677777788888888888********.44......6777 PP

                 HHHHHHC.TSEEEEEEETTTTCSHHHH..HHHHHHHHH.TTSEEEEEE CS
    MMR_HSR1  69 aflalee.adlillvvdaseeklkpld..eeleellee.akkplilvl 112
                 ++l+    +d ++l+v a+ ek+ +++  e+l +l+     k++++v 
  AJA91958.1 112 NMLSGSAlMDGAILLVAAN-EKVPQMQskEHLLALQ-TlGIKQIVVVQ 157
                 7776665579999999877.5454443113333332.21233344444 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.1     1e+04      13      24 ..      52      61 ..      51      65 .. 0.77
   2 !   20.8   0.4   1.9e-07   0.00038       1      62 [.     244     310 ..     244     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.1
                 EETTEEEEEECT CS
  GTP_EFTU_D2 13 lkkGdevrilgn 24
                 lk+G ++r+   
   AJA91958.1 52 LKRGITIRV--G 61
                 899999999..3 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.9e-07
                  EEEEEEEEEESEEETTEEEEEEC.TCTTSEE....EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke....ivtrissletfhededeavaganaGvivaikg 62 
                  G+v++g++ +G+++ Gde++i + +  +kk+     +t+i sl t  + +d + +g+ + +++++++
   AJA91958.1 244 GGVIGGSLTEGQFNIGDEIEIKPgLLNEKKKnyepLITEIVSLGTGAGTVDNVKPGGLVAIGTKLDP 310
                  89********************9988878889*****************************999865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.055   1.1e+02     105     137 ..      26      55 ..      12      58 .. 0.74
   2 !   15.9   0.2   4.5e-06     0.009      14      99 ..     118     209 ..      94     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.055
                  ECSTTSSHHHHHHHHCTT-----S--------- CS
  RsgA_GTPase 105 vGqSGvGKStLinallpelelktgevseklgrG 137
                  +G+   GK++Li al+++    t+  s++l+rG
   AJA91958.1  26 AGHVDHGKTSLIQALTGK---WTSVHSQELKRG 55 
                  455557**********98...555556666665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.5e-06
                  ES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
  RsgA_GTPase  14 aNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsaktkegleelkellkd 99 
                  a +d ++++v+++ +++ + + +  L+++++ gi ++v+v nK+Dl++ +e      +++++ + ++a+  +v+ vsa+ + +l++l   ++ 
   AJA91958.1 118 ALMDGAILLVAAN-EKVPQMQSKEHLLALQTLGIkQIVVVQNKVDLITYKEamsnysDISKFIKGTNAAKSPVIPVSAQANLNLDALIYSIET 209
                  6679999999999.777777788888899999995677788*******999999888888899999999999*******99999999877766 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.7e-05     0.035      57     100 ..     152     207 ..     146     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                   + ++v NK+Dli+++e  + +++            + ++++Sa+ +lnld+L   i
    AJA91958.1 152 QIVVVQNKVDLITYKEAMSNYSDiskfikgtnaakSPVIPVSAQANLNLDALIYSI 207
                   567899*****99988776666456788899988668999************8776 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0024       4.7       2      27 ..      22      47 ..      21      58 .. 0.88
   2 ?    4.7   0.2      0.01        20      96     154 ..     142     205 ..      89     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                EEEEEESTTSSHHHHHHHHHTTSEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkv 27
                ++ ++G  + Gkt+l+ altg+ ++v
  AJA91958.1 22 NIGTAGHVDHGKTSLIQALTGKWTSV 47
                577899***************87766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.01
                 HHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEEEBTTTTBTHHHHHH CS
      FeoB_N  96 yLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg......vpvvktsakkkegieellk 154
                 +L lq l ++ ++v++ n++d ++ k+   + + +s+ ++       pv+++sa+ + ++++l+ 
  AJA91958.1 142 LLALQTLGIK-QIVVVQNKVDLITYKEAMSNYSDISKFIKgtnaakSPVIPVSAQANLNLDALIY 205
                 4555665554.577888******9999999999998877433333379******99999999875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.4e-05      0.19      42      95 ..      38      91 ..      21      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                HHHHHHHHHHHCC.TTTT-EEEEEEE--E.EEETTTS-EEECHHHHHS-TTTSSS CS
        HypA 42 eaLefafellaegtvlegaeLeieevpvk.vrCreCgkefeleekalrCpkCgsa 95
                +aL+  ++ ++++++ +g ++++   ++  ++C +C+  ++ ++ + +Cp+C+++
  AJA91958.1 38 QALTGKWTSVHSQELKRGITIRVGYSDAAfYKCPDCEPPTNYST-SPKCPNCKQE 91
                57888999999999999999999866655169*****8888554.479****987 PP

>> ILEI  Interleukin-like EMT inducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00039      0.78      27      77 ..     106     158 ..      87     168 .. 0.81
   2 ?   -0.7   0.0         1     2e+03      35      55 ..     293     311 ..     290     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
        ILEI  27 eskrlveflk..sipdgsiVlvavkdeassnlsdearkaleslGskkiknlgf 77 
                 + + ++++l   ++ dg i+lva ++  ++  s+e   al++lG k+i  +++
  AJA91958.1 106 HESLMANMLSgsALMDGAILLVAANEKVPQMQSKEHLLALQTLGIKQIVVVQN 158
                 455889999876788**************999**************9988855 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
        ILEI  35 lksipdgsiVlvavkdeassn 55 
                 ++++++g +V++ +k ++  n
  AJA91958.1 293 VDNVKPGGLVAIGTKLDP--N 311
                 7899**********9988..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2828.06
//
Query:       AJA91959.1  [L=508]
Description: putative cytochrome c oxidase, subunit I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.5e-128  429.3  63.1   1.8e-128  429.1  63.1    1.0  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.1  63.1    1e-132  1.8e-128       2     432 .]      23     463 ..      22     463 .. 0.98

  Alignments for each domain:
  == domain 1  score: 429.1 bits;  conditional E-value: 1e-132
                 HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT......-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHHHHHHHHHHHHHHHHHH CS
        COX1   2 igllylilalvlllvggllgllirlqlafp......dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprlnalsfwlvvlgvvlll 94 
                 +gllyli++l+++++gg+l+ll+r++l+ p      d+ tyn+++t+Hg+++iflf++p + +fgnylvp++++ +d+a p+lna++fw+++ +++l++
  AJA91959.1  23 VGLLYLITSLAFMFMGGALALLLRVELFSPgvqiiaDSMTYNRIFTVHGTTLIFLFILPSASAFGNYLVPIMVRFKDMAYPKLNAVAFWMIPPAGALIW 121
                 899*************************9988888888************************************************************* PP

                 HHHHCSS-STTTTTTTC........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHC CS
        COX1  95 lsllgaattgwteYapls.......evdlwllglllvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrsl 186
                 l++   a+  w++Y+ +s       + d+w++gl +++vss+lg+inf+vti+k + p + ++k+pl++wa+l+ ++++l+a+p +a+all+ll+dr  
  AJA91959.1 122 LGF---ADFTWYAYPTYSvvsapgpAADMWIFGLKILGVSSILGSINFVVTIMKCKHPDLPLSKMPLLAWAYLTSSLITLVAVPTFAAALLMLLTDRLG 217
                 ***...9*********99********************************************************************************9 PP

                 T.-SSSC...E-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHH CS
        COX1 187 g.kffsp...gdplldqhlfWffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavP 281
                    ff+p   gdp+ +qhlfWf+ HpeVyil++pa+g +y+i+p+f+++p+fs++  v+af l+++++f  waHH++ tg++ + k++++v +l+ +  
  AJA91959.1 218 AsGFFNPamgGDPIAYQHLFWFTFHPEVYILVIPAIGFMYEIFPRFSRKPIFSHSSGVAAFTLLTIVGFASWAHHMYATGMSFTEKTVFMVGTLAAVPA 316
                 99***999******************************************************************************************* PP

                 HHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHHHHHH CS
        COX1 282 sglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserlaklhf 380
                 s++++fn+lat+w+g+i+f tp+++++g + lf+ +G+ Gv++++ ++++++h++ywvv+HfHl ++g+++f++++++yy +p +tgrm++e ++k+hf
  AJA91959.1 317 SAMHTFNFLATMWGGRIKFATPIMWAVGGIALFFSAGAGGVVNSAMPLDFITHDSYWVVGHFHLFVMGTILFGTVGFVYYFFPYVTGRMYNEAMGKIHF 415
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
        COX1 381 wllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                 +l f+G+vl+f+++hilGl+gmprr++dy++     pe+  +n++ +ig+++
  AJA91959.1 416 ILSFVGTVLVFFTQHILGLFGMPRRIYDYPA----IPEWVQMNIIISIGAFI 463
                 *****************************54....79************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3231.07
//
Query:       AJA91960.1  [L=220]
Description: hypothetical protein T478_0357 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1511.53
//
Query:       AJA91961.1  [L=100]
Description: putative nitrogen regulatory protein P-II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-05   23.9   0.2    6.6e-05   23.5   0.2    1.3  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   3.7e-09   6.6e-05      11      77 ..      19      78 ..      14      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.7e-09
                HHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHH CS
        P-II 11 eevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiika 77
                ++v e L++ +++g+t+ ev+G G +      +rg+  ++e  + vk+e+v+++e+++ vve i ++
  AJA91961.1 19 KNVIEILKNHDITGYTTYEVEGNGAKG-----LRGQGFKNE--KNVKIEVVMREEKLSGVVEDISRT 78
                67999*****************99988.....889999888..99******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 729.07
//
Query:       AJA91962.1  [L=582]
Description: oxidoreductase, short chain dehydrogenase/reductase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-37  127.6   0.0    1.3e-31  109.6   0.0    3.1  3  adh_short        short chain dehydrogenase
    6.7e-34  117.5   0.0    9.1e-25   87.6   0.0    3.7  3  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.1e-12   46.4   0.0    1.2e-09   38.3   0.0    2.7  3  KR               KR domain
     0.0011   18.1   0.2     0.0025   17.0   0.2    1.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0023   17.4   0.0     0.0074   15.8   0.0    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.025   14.0   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.015   15.2   0.2      0.042   13.8   0.2    1.7  1  Thioredoxin_15   Thioredoxin-like domain
      0.026   13.7   1.6       0.19   10.9   0.3    2.2  2  DUF4899          Domain of unknown function (DUF4899)
      0.027   14.3   3.4      0.028   14.3   0.2    2.3  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.06   13.9   0.3       0.39   11.3   0.2    2.5  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.13   12.3   0.4         11    6.2   0.0    3.0  3  PHB_acc_N        PHB/PHA accumulation regulator DNA-binding d


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   8.1e-35   1.3e-31       1     185 [.       6     202 ..       6     209 .. 0.88
   2 ?   -1.1   0.1      0.65   1.1e+03      39      67 ..     338     365 ..     322     375 .. 0.71
   3 !   14.1   0.0   1.4e-05     0.024      39     135 ..     386     493 ..     365     498 .. 0.84

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 8.1e-35
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.......TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--S CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.......gakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsg 91 
                 kvvl+tG + GIG  +ak+++++Ga+vv+++r++e+l  + + l +        g   ++  vDv+d+++v +++++ +++  ++dv+vnNAG+   ++
  AJA91962.1   6 KVVLITGSGTGIGMTVAKKFVENGASVVILGRRKEPLDSTSEMLTKIineknskGFVKIFSGVDVSDEKSVTEMFDALKNEGINIDVIVNNAGVsGPVT 104
                 89*********************************998777666655533333233478889********************************66677 PP

                 SGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG......TSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSS CS
   adh_short  92 pfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag......kvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdT 184
                  f +   e++++++++ ltg+f+++ ++l+ m+  ++G+I+++s   +      + p+    +Y+As +a + l+++++ el ++gi  ++ +PG+v +
  AJA91962.1 105 CFPHAPLEDFRSTVDIHLTGTFWTSVQALKVMK--EGGKIITISTFFAeerpleQRPYRFRGPYTASQGAKNRLVEAMSWELTEKGIISIGTNPGPVHS 201
                 8999***************************98..99********987322222457788899*********************************998 PP

                 H CS
   adh_short 185 d 185
                 d
  AJA91962.1 202 D 202
                 7 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.65
                 HHHHHHHHT..TSEEEEEE-TTTSHHHHHHH CS
   adh_short  39 evakelkee..gakalaiqvDvtdreeveal 67 
                 e++k+      ++k+ ++++D td+e+++++
  AJA91962.1 338 ETVKQ---YdySSKIAVLTIDATDEEDAKKA 365
                 34444...33478999999999999999887 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.4e-05
                 HHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSHHHHHHH..........HHHHTHHHHHHHHHHHHHHHH CS
   adh_short  39 evakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsgpfselseeewerv..........ievNltgvflltravlpamlk 125
                 ++ ke+++  g+k++   +D ++ ee+ + +++a k  g ++v+++ +G     ++  els +ew+++          ++ N +g+f    +  p + k
  AJA91962.1 386 KCSKEIQDSiGNKFHSHVIDFSNNEEITRWFNTA-KSKGDIEVFIHITGKvPTISKLTELSRSEWDELtdkfinipatVSQNAMGIFVPNGSEDPRLFK 483
                 5678888888899*********************.566***********977789999*********98888777777778888888888888888889 PP

                 CTTEEEEEEE CS
   adh_short 126 qssGrIvnvs 135
                   +GrIv ++
  AJA91962.1 484 DAKGRIVIIG 493
                 9999999985 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   5.6e-28   9.1e-25       4     177 ..      15     202 ..      12     233 .. 0.83
   2 ?    4.8   0.0     0.011        18     178     228 ..     269     321 ..     245     324 .. 0.83
   3 !   20.6   0.0   1.6e-07   0.00027       7     121 ..     365     475 ..     364     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 5.6e-28
                   TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT...SE..E...EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH- CS
  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelg...ae..v...lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpflets 91 
                    gIG  +Ak++ e+Ga+vv+  +++e  +++ e l++ ++   ++  v     +DV+de++v++++++++++  ++D++vnnag++ +  + f +++
    AJA91962.1  15 TGIGMTVAKKFVENGASVVILGRRKEPlDSTSEMLTKIINeknSKgfVkifSGVDVSDEKSVTEMFDALKNEGINIDVIVNNAGVSGP-VTCFPHAP 110
                   7*********************9999855444444443442224464366789***********************************.9999**** PP

                   HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGT.SBSTTTT.....HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCT CS
  adh_short_C2  92 reefdraldvnlyslfllakaalplmkeggsivnlssvgae.rvvpnyn.....aygaaKaalealtrylAvelgpkgiRvNavspgpikTl 177
                    e+f+ ++d+ l+++f ++ +al++mkegg+i+++s + ae r +++        y+a+ +a + l+ ++  el +kgi      pgp++ +
    AJA91962.1 111 LEDFRSTVDIHLTGTFWTSVQALKVMKEGGKIITISTFFAEeRPLEQRPyrfrgPYTASQGAKNRLVEAMSWELTEKGIISIGTNPGPVHSD 202
                   ***********************************87755514455543345569************************8888888888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                   GGGGSTT.HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGG.GTT--SEEEE CS
  adh_short_C2 178 aasgikg.fdelleelearaplgrlgtpeevaeaalfLasde.asyitGqtlv 228
                   + +++++ +++++++   ++  +++ ++++va ++l L  d+ a+  +G+++ 
    AJA91962.1 269 LLNKVQSiAEKIQKNTSTMIADQQFLSQDQVATTVLTLSDDQqAKILNGKIIP 321
                   5555555468899999999********************98615667888775 PP

  == domain 3  score: 20.6 bits;  conditional E-value: 1.6e-07
                   HHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHH CS
  adh_short_C2   7 GraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldv 101
                   +++iA  ++++G + ++   +++     +e+++++g+++    +D +++e+++++++++++k g + ++++  g +p+  ++++e+sr+e+d+  d 
    AJA91962.1 365 AEEIATNVQANGGQAICFI-SDKC---SKEIQDSIGNKFhsHVIDFSNNEEITRWFNTAKSK-GDIEVFIHITGKVPT-ISKLTELSRSEWDELTDK 455
                   5788999999998865554.4444...4899999999976899***************9998.9*************9.999***********9998 PP

                   HTHHHHHHHHHHHHHCTSCC CS
  adh_short_C2 102 nlyslfllakaalplmkegg 121
                    ++  + +++ a+ ++ ++g
    AJA91962.1 456 FINIPATVSQNAMGIFVPNG 475
                   88777777777777666665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   7.5e-13   1.2e-09       2     107 ..       7     116 ..       6     131 .. 0.74
   2 ?   -2.4   0.0       2.3   3.7e+03      52      71 ..     346     365 ..     334     381 .. 0.75
   3 ?    5.0   0.0     0.012        20      46     108 ..     389     452 ..     365     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 7.5e-13
                 EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHH...HHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE------.--- CS
          KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedsk...aliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlr.dkl 96 
                 ++litG   g+G+++a+  +e+ga+ ++l  R+++ d++s+   + i+e +++g    +  +Dvsd+++v+++++++k+e+ +i  +++ Agv+   + 
  AJA91962.1   7 VVLITGSGTGIGMTVAKKFVENGASVVILGRRKEPLDSTSEmltKIINEKNSKGFVKIFSGVDVSDEKSVTEMFDALKNEGINIDVIVNNAGVSGpVTC 105
                 579********************986665555554445544111345555555665566679*******************************873344 PP

                 TTT--HHHHHH CS
          KR  97 leemtaedleq 107
                 + +   ed+++
  AJA91962.1 106 FPHAPLEDFRS 116
                 55555555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                 T-EEEE----TT-HHHHHHH CS
          KR  52 gaevevvaaDvsdkdaveal 71 
                   ++ v+ +D +d+++ +++
  AJA91962.1 346 SSKIAVLTIDATDEEDAKKA 365
                 56889999999999888776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.012
                 HHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE------.---TTT--HHHHHHH CS
          KR  46 aeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlr.dklleemtaedleqv 108
                 +e++++ g + +   +D s++++++++++++k++ + i+  ih  g +   ++l+e++ ++++++
  AJA91962.1 389 KEIQDSiGNKFHSHVIDFSNNEEITRWFNTAKSK-GDIEVFIHITGKVPtISKLTELSRSEWDEL 452
                 5666655999*********************955.59******9986542678888888888775 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.5e-06    0.0025       1      78 [.       8      85 ..       8     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE.....E--TT-HHHHHHHTT..T- CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkvei.vpvigdvrdkerlekaleelkv 78
                     vl+tG+g  iG ++ ++++++ ++ +il  r+E  l++ ++ l++ +++k+ k ++ +    dv d++++++++++lk 
       AJA91962.1  8 VLITGSGTGIGMTVAKKFVENGASVVILGRRKEP-LDSTSEMLTKIINEKNSKGFVkIFSGVDVSDEKSVTEMFDALKN 85
                     89******************99887777777775.5555555555555555554430334469*********9997664 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.6e-06    0.0074       1     188 [.       8     211 ..       8     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.6e-06
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...............EEEE--TT-HHHHHHHHHH...H..T-SEEEE--S---HHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...............elveldltdrsalerlfke...e..qpdavihlAavggvaa 79 
                 +l+tG    iG  ++k++ e+g  v+ l r+++   + ++                   +  +d+ d+++++++f+    e  ++d++++ A+v+g+ +
  AJA91962.1   8 VLITGSGTGIGMTVAKKFVENGASVVILGRRKEPLDSTSE--MltkiineknskgfvkIFSGVDVSDEKSVTEMFDAlknEgiNIDVIVNNAGVSGPVT 104
                 79**********************9999999554433333..24578**********************9998887522233579********887766 PP

                 HH.HSHHHHHHHHTHHHHHHHHHHHHHTCT......EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESE CS
   Epimerase  80 ss.edpadfieknlqgtlnlleaarkagvk......rllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfn 171
                  +   p + +++++ + l+   + + + +k      +++ +s+   + +  +      +++ p++ + pY a+  a  +lvea+  +   + ii + +n
  AJA91962.1 105 CFpHAPLEDFRSTVDIHLTGTFWTSVQALKvmkeggKIITIST--FFAEERP------LEQRPYRFRGPYTASQGAKNRLVEAMSWELTEKGIISIGTN 195
                 6525567777766655554333333222222245558888888..6664444......66668999999999999999999988877755555555555 PP

                 EESTTS-TTSTTSHHHH CS
   Epimerase 172 lyGprngegevsrvipa 188
                   Gp + ++  + v+p+
  AJA91962.1 196 P-GPVHSDRIYKTVYPK 211
                 4.555444445555555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05     0.025       1     166 [.       9     179 ..       9     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-T.T.HHHHHCTTT...TTGCCEE.EEE--TT-HHHHHHHHHHH.....T-SEEEE--S---H CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfn.t.griehlakdpkeeleenlk.lhkgDltDssslerllaev.....qpdevynLAAqshV 88 
                    LiTG    iG  +a++++e+g  v+++ rr++ ++ t + + ++ +++  + ++ +k +  +D++D++s++++++       ++d ++n A+ s  
     AJA91962.1   9 LITGSGTGIGMTVAKKFVENGASVVILGRRKEPLDsTsEMLTKIINEK--NSKGFVKiFSGVDVSDEKSVTEMFDALknegiNIDVIVNNAGVSGP 102
                    89997666*******************999977651313444444333..234445536778************8753334489999999999975 PP

                    HHHT.TSH....HHHHHHHTHHHHHH.HHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHH CS
  GDP_Man_Dehyd  89 dvsf.ekP....eytaevnvlGtlrL.LeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvn 166
                     + f + P      t+++ ++Gt+   ++a + +  ++  +++ +St   +   +e    E+ p++ r PY a+  +++ +v++
     AJA91962.1 103 VTCFpHAPledfRSTVDIHLTGTFWTsVQALKVM--KEGGKIITISTF--F---AEERPLEQRPYRFRGPYTASQGAKNRLVEA 179
                    5444244421114577777777764324444333..345677777773..2...333334777777777777777777666665 PP

>> Thioredoxin_15  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.6e-05     0.042      74     157 ..     245     320 ..     233     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                     THHHHHHHHHTGGGGCT-SSHHHHHHHHH............-------HH......HHHHHHHHHH.HTT--TT-EEEEETTEEE CS
  Thioredoxin_15  74 sslissalsaalkklknlealefleklleeeteellvsgmdkdafekelnaeeakdylkalqkflr.vlglepgqnavilNGRvv 157
                     +++i+  ++aa +kl+++e++   ++ll+      +v+ + ++  ++ +++  a++++ ++ ++++ vl l   q+a ilNG+++
      AJA91962.1 245 EDTIKNGIKAAAEKLGKQEST--FTNLLN------KVQSIAEKIQKN-TSTMIADQQFLSQDQVATtVLTLSDDQQAKILNGKII 320
                     455677788888877777766..455555......344444444444.4457777778888888888*****************9 PP

>> DUF4899  Domain of unknown function (DUF4899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.081   1.3e+02     146     192 ..      46      91 ..      32      99 .. 0.87
   2 ?   10.9   0.3   0.00012      0.19     140     253 ..     290     405 ..     254     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.081
     DUF4899 146 aevflelqedfeedkvkeilkRaDlkdlpevfPliDPinGktiaelD 192
                  e +++  ++ +++++++i++  D+ d   v  + D ++ + i ++D
  AJA91962.1  46 SEMLTKIINEKNSKGFVKIFSGVDVSDEKSVTEMFDALKNEGI-NID 91 
                 57788999999*************************9999887.455 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
     DUF4899 140 tyeelsaevflelqedfeedkvkeilkRaDlkdlpevfPliDPinG..ktiaelDvgdkiyvvilnvgkeenleklkelypkkfsedgnvvplegklis 236
                 + + ls  ++ ++   +++d+ ++il+ + +     ++P+   i+   +t++++D   ki v+ ++ ++ee  +k  e+  +   + g+ + + +   s
  AJA91962.1 290 DQQFLSQDQVATTVLTLSDDQQAKILNGKIIPGDRVFYPVRSHITSvpETVKQYDYSSKIAVLTIDATDEEDAKKAEEIATNVQANGGQAICFISDKCS 388
                 55667888888888899999999999999999999999*****997447******************************999999999*********** PP

     DUF4899 237 kelvktkkgelylikvd 253
                 ke+  +  ++++   +d
  AJA91962.1 389 KEIQDSIGNKFHSHVID 405
                 **977666666555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   1.7e-05     0.028       2      59 ..       8      66 ..       7      99 .. 0.77
   2 ?   -0.1   0.3      0.47   7.6e+02      22      72 ..     235     285 ..     227     300 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                EEEE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHH CS
     3HCDH_N  2 vaviGaGt.mGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeee 59
                v + G+Gt +G  +a+ f+++g +Vv++ +++e l++  e+++k +++  +kg +k  +
  AJA91962.1  8 VLITGSGTgIGMTVAKKFVENGASVVILGRRKEPLDSTSEMLTKIINEKNSKGFVKIFS 66
                5678999889******************************************9998333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.47
                 T-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES- CS
     3HCDH_N  22 gleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttd 72 
                 +  V l+  +e++++++ ++++++l k+++      ++v++++++i+ +t+
  AJA91962.1 235 KEIVGLLGEDEDTIKNGIKAAAEKLGKQESTFTNLLNKVQSIAEKIQKNTS 285
                 555667777777777777777777777655555445666666666665444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00024      0.39       2      52 ..       8      59 ..       7      79 .. 0.79
   2 ?   -1.3   0.0         2   3.3e+03      38      57 ..      71      90 ..      62      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                EEEECSSH.HHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHH CS
   Pyr_redox  2 vvvvGgGy.iglElAgalaelgkkVtvversdkllrllDeeaskilqeklek 52
                v++ G+G+ ig+ +A+ + e g++V ++ r++++l    e++ ki+ ek +k
  AJA91962.1  8 VLITGSGTgIGMTVAKKFVENGASVVILGRRKEPLDSTSEMLTKIINEKNSK 59
                678888866**************************66666666666666555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                SSHHHHHHHHHHHHHTTEEE CS
   Pyr_redox 38 lDeeaskilqeklekngiev 57
                 De+  +++ + l+++gi++
  AJA91962.1 71 SDEKSVTEMFDALKNEGINI 90
                57777888999999997664 PP

>> PHB_acc_N  PHB/PHA accumulation regulator DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0065        11      25      60 ..      23      59 ..      11      60 .. 0.80
   2 ?   -2.1   0.2       2.6   4.3e+03      22      40 ..     274     292 ..     271     306 .. 0.72
   3 ?    2.7   0.0     0.085   1.4e+02      23      47 ..     390     414 ..     387     419 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0065
   PHB_acc_N 25 aelvregeevkVvDaktg.eDiTrsillqiileeekk 60
                +++v++g +v ++  + +  D T+++l++ii e+++k
  AJA91962.1 23 KKFVENGASVVILGRRKEpLDSTSEMLTKIINEKNSK 59
                678888888888876544269************9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
   PHB_acc_N  22 ediaelvregeevkVvDak 40 
                 + iae ++++++  + D++
  AJA91962.1 274 QSIAEKIQKNTSTMIADQQ 292
                 7899999999999999986 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.085
   PHB_acc_N  23 diaelvregeevkVvDaktgeDiTr 47 
                 +i++ + ++ + +V+D  ++e+iTr
  AJA91962.1 390 EIQDSIGNKFHSHVIDFSNNEEITR 414
                 7888899999999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      767  (0.0427799); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 3956.87
//
Query:       AJA91963.1  [L=138]
Description: RNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-22   80.5   4.1    1.4e-22   80.2   4.1    1.1  1  RNA_binding      RNA binding
  ------ inclusion threshold ------
      0.053   13.1   0.0      0.073   12.7   0.0    1.1  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
       0.11   12.2   0.0       0.24   11.1   0.0    1.6  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   4.1   2.3e-26   1.4e-22       1     118 [.       4     119 ..       4     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.3e-26
                  EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEEEEHHH CS
  RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekgklylrldKQa 98 
                  +++++ ++haTE+e+kV e l+n ++ e++e+++ee++Gh++npi++++ +l++k a+++++ + +++++ee++ + + +e+ v+ ++ l lr++KQ+
   AJA91963.1   4 EVKINLILHATENEKKVFEELENNFQIEQSEFQVEEVSGHFNNPILLISSKLKRKTAQNFISLFFSKMKKEEFDDVFNYVEDYVT-SSGLNLRISKQK 100
                  5899**********************9999****************************************************999.9*********** PP

                  HHTT---BESSSSEEEEEEE CS
  RNA_binding  99 aylgklslvegddvIkvkik 118
                  ++ g l+l +++d Ik+ i+
   AJA91963.1 101 LMSGILAL-SREDTIKINIS 119
                  ********.5699***9997 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05     0.073     166     228 ..      19      81 ..      12      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                     HHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHH---SHHHHHHHH CS
  Phosphonate-bd 166 daledlvaegpedkdelrviassppipndpvvvrkelseelkekiqdallslaeteegkklle 228
                      ++e+l+++ +++++e++v ++s  ++n++++++++l+ ++ ++  ++++s  + ee  +++ 
      AJA91963.1  19 KVFEELENNFQIEQSEFQVEEVSGHFNNPILLISSKLKRKTAQNFISLFFSKMKKEEFDDVFN 81 
                     6789999999999*******************************9999999999888888775 PP

>> Glyco_transf_7C  N-terminal domain of galactosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.1e-05      0.24       8      35 ..      90     117 ..      86     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
  Glyco_transf_7C   8 dkfgyklpyekyfgGvlalrkedfekiN 35 
                      + ++ +++++k+++G+lal++ed +kiN
       AJA91963.1  90 SGLNLRISKQKLMSGILALSREDTIKIN 117
                      5678899********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1022.05
//
Query:       AJA91964.1  [L=422]
Description: beta-Casp domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-15   56.1   0.1    6.4e-15   54.8   0.1    1.7  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
    8.3e-14   51.8   0.0    1.5e-13   51.0   0.0    1.4  1  Beta-Casp        Beta-Casp domain
    1.9e-11   43.8   0.0    4.8e-11   42.5   0.0    1.8  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    3.5e-11   43.5   0.0    2.7e-08   34.1   0.0    2.2  2  Lactamase_B      Metallo-beta-lactamase superfamily
    2.2e-07   30.6   0.0    4.6e-07   29.6   0.0    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
    0.00027   20.8   0.0      0.001   19.0   0.0    2.0  1  Lactamase_B_3    Beta-lactamase superfamily domain
     0.0035   16.6   0.0     0.0077   15.5   0.0    1.6  1  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.1   2.5e-18   6.4e-15       2      61 ..     353     413 ..     352     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
       RMMBL   2 ipvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfi 61 
                 ++vka+++++ fSgHad+++l e+i+ lk  + ++ vHG+ e++ ++a+ ++e +g ++++
  AJA91964.1 353 LNVKAEVKQFQFSGHADRDSLFEMIKNLKGNPkIMTVHGDDESCTRFAEEIHERFGFEAHA 413
                 68****************************999******************9999*99996 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   5.7e-17   1.5e-13      22     110 .]     244     340 ..     229     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.7e-17
                 -EEEEE-HHHHHHHHHGGGGGG.................E-SHH....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---T CS
   Beta-Casp  22 lpiyldsplaskatevYkeyae.................veakslewmeskkeelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqae 103
                  +i++d+ +a k+ ev  +y+e                 v      + +++k   +  ++p+v+++  gml gG ++++l++l  + +n + lv+yq e
  AJA91964.1 244 HKIIMDG-MALKVNEVLLKYPEylrnpeifkdviekvvsV-----RDHNERK---RALSEPCVVISPAGMLVGGNAVYYLQELSFNDKNGIALVSYQGE 333
                 58999*9.********999999*99**9999987554222.....2233333...34679*************************************** PP

                 TSHHHHH CS
   Beta-Casp 104 gTlgrkl 110
                 gT+g+kl
  AJA91964.1 334 GTPGKKL 340
                 ****997 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   1.9e-14   4.8e-11       3     175 ..      20     177 ..      18     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.9e-14
  Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpeds 98 
                    + d++++LlD G+   k +    + +l+    ++d ++++ha l+h G+ + l+++       n++vy+t p++ L +++++d ++      +++s
     AJA91964.1  20 NCDGTNFLLDYGVMFGKPRGAPPTYPLHVKPRDIDSVIITHAHLDHSGCVPSLFVS------GNCNVYGTAPTFDLSKLLIQDMIKI-----EKNS 104
                    678999999999997777666667777777789***************87666654......59*******************9774.....4677 PP

  Lactamase_B_6  99 eeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLngaal 175
                    +++ + +id+++ k k + ++ k++  +     ++   ++Gh++GG+   ++++ +k+ Y  d+n +  ++L  a+l
     AJA91964.1 105 HSFGVPEIDNMMAKSKIIGFKEKITRGN----ASFELRSSGHVIGGSTVLVESKNKKLFYTGDINLRGSRLLPPADL 177
                    88999*****************987665....567779***************************999999887776 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.1e-11   2.7e-08      14      69 ..      22      77 ..       9     102 .. 0.87
   2 !    7.4   0.0    0.0016         4     128     162 ..     141     175 ..     126     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.1e-11
                 TTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHC CS
  Lactamase_B 14 dggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatd 69
                 dg+++L D G+   ++r a   + l++kp+d+d vi+TH+HlDH G ++ l    +
   AJA91964.1 22 DGTNFLLDYGVMFGKPRGAPPTYPLHVKPRDIDSVIITHAHLDHSGCVPSLFVSGN 77
                 8999****************9**************************998865555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                  TTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
  Lactamase_B 128 gpghghghgvveygggkvlftGDallagetgridl 162
                  g++ g++ + ve++++k+ +tGD  l+g++++ + 
   AJA91964.1 141 GHVIGGSTVLVESKNKKLFYTGDINLRGSRLLPPA 175
                  78999*********************999998887 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.8e-10   4.6e-07       1     174 [.      24     199 ..      24     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.8e-10
                    SEEEES--TTHHHH..HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH...HCCTTCGHHHCHTTTTEEEEEE- CS
  Lactamase_B_2   1 rriLiDagpdlrqq..alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla...vleanfvylaleeepavnvheld 91 
                    +++L+D g  + ++  a ++  P +   ++++id V++thaH DH   +++l      + ++y+++ + +    l + ++ + ++ +    v e+d
     AJA91964.1  24 TNFLLDYGVMFGKPrgAPPTY-PLH--VKPRDIDSVIITHAHLDHSGCVPSLFV--SGNCNVYGTAPTFDlskLLIQDMIKIEKNSH-SFGVPEID 113
                    678888888887775334443.554..55679**************88999988..34589****9887744456666666666666.66666666 PP

                    TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S-SSTTHHHH CS
  Lactamase_B_2  92 wgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadllllditayeddemir 174
                      +  +    g++ ++t  + + + r   +      +++e+++k+++y+gD +       + ++  +g +d+++ + t+ ++++m r
     AJA91964.1 114 NMMAKSK-IIGFKEKITRGNASFELRSSGHVIGGSTVLVESKNKKLFYTGDINLRGsrllPPADLDIGEMDMVITESTYSQENQMPR 199
                    3333222.23455555544444444333333344447778*************6663444345578999999999999988888876 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.9e-07     0.001       6     114 ..      13     164 ..      12     188 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.9e-07
  Lactamase_B_3   6 ghnsflletagarilvDPf.........kanlgyeppaeeaDlvlisqaledHahletlkql.................................. 58 
                    g ++f ++ +g++ l+D++          ++  +  +++++D v+i++a+ dH    +   +                                  
     AJA91964.1  13 GRSAFQVNCDGTNFLLDYGvmfgkprgaPPTYPLHVKPRDIDSVIITHAHLDHSGCVPSLFVsgncnvygtaptfdlsklliqdmikieknshsfg 108
                    8899***************7777765532266666666***************8766555554444444444444444444444444333333333 PP

  Lactamase_B_3  59 .aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhl 114
                      e+ +++++ + + +++   r+ a+ + ++ g++ g+ +  l+e+++ ++++ G++
     AJA91964.1 109 vPEIDNMMAKSKIIGFKEKITRGNASFELRSSGHVIGG-STVLVESKNKKLFYTGDI 164
                    22222223333334444444444444445555555553.555566666666666665 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     3e-06    0.0077      56     185 ..      48     172 ..      17     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-06
  Beta_lactamase3  56 vkaenidkifvts.....snslgifFlkkdvpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeidierlkrnvkfiryneliyfdd 144
                      vk+ +id +++t+     s  +  +F+  + ++Y T p +   +l  +++ +++ ++         ++    +i+++  + k+i ++e i   +
       AJA91964.1  48 VKPRDIDSVIITHahldhSGCVPSLFVSGNCNVYGTAPTFDLSKLLIQDMIKIEKNS---------HSFGVPEIDNMMAKSKIIGFKEKITRGN 132
                      67889999999862222245677799************9987777776666654332.........23344567777788889*********** PP

  Beta_lactamase3 145 ltieakaagtflGWvnyllevekkkilayisslslkkklsl 185
                       + e +++g  +G ++ l+e ++kk l y+  + l+++  l
       AJA91964.1 133 ASFELRSSGHVIGGSTVLVESKNKK-LFYTGDINLRGSRLL 172
                      *************************.999999988776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3096.44
//
Query:       AJA91965.1  [L=464]
Description: cysteine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.2e-121  404.9   0.4   3.8e-121  404.1   0.4    1.2  1  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
      1e-12   48.3   1.5    2.3e-12   47.2   0.3    2.3  3  DALR_2          DALR domain
    3.2e-10   39.3   0.4    0.00021   20.1   0.4    2.4  2  tRNA-synt_1g    tRNA synthetases class I (M)
    7.7e-08   31.0   1.3    8.6e-06   24.3   0.0    3.3  4  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    3.1e-07   29.6   0.3     0.0053   15.7   0.0    2.2  2  tRNA-synt_1f    tRNA synthetases class I (K)
     0.0025   17.5   0.5      0.016   14.9   0.5    2.4  1  UVR             UvrB/uvrC motif
  ------ inclusion threshold ------
      0.023   14.7   0.5       0.11   12.5   0.1    2.3  3  Lig_C           Ligase Pab1020 C-terminal region
       0.21   11.5   5.8       0.99    9.3   0.1    2.6  2  DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.1   0.4  1.7e-124  3.8e-121       8     298 ..      18     306 ..      12     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.1 bits;  conditional E-value: 1.7e-124
                   TEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB--BGGGG CS
  tRNA-synt_1e   8 kkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptleprvsek 104
                   +kv +Y+CG+tvyd+sh+GhaR++++fD lrr+l+a g +v+++qn+tD+dDkii+ra+e+++s + l+ k+i+ +++d + Ln++++t  p+++e+
    AJA91965.1  18 DKVRIYLCGVTVYDQSHIGHARTVIVFDTLRRFLEANGTQVELIQNFTDVDDKIINRAKEQGESASGLSTKYIQTYFEDSDRLNIRRATNYPKATEH 114
                   68*********************************************************************************************** PP

                   HHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHH CS
  tRNA-synt_1e 105 vdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmas 201
                   +d++i+l+++l++k  aY+++ + vyf vsk+++Ygklsk+++e+le+ga++ev e+k+++ DfaLWk s e+ p+w+sPwgkGRPGWhieCs+m+ 
    AJA91965.1 115 IDDMINLIQNLVDKESAYVSK-NGVYFRVSKFSKYGKLSKKKTEDLESGARIEVDESKESPLDFALWKFSDEQ-PNWESPWGKGRPGWHIECSAMSI 209
                   ********************9.77*********************************************9887.*********************** PP

                   HHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
  tRNA-synt_1e 202 kllgseidihsGGiDLafPhhenelaqseaafdkqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeellee 298
                   k+lg++++ih+GG DL+fPhhene+aqse+ + +q++k+++h+g+++i+gekmsks++n+ +i++vl+++ p+++Rl+ +s hy +++d++e+ll+e
    AJA91965.1 210 KYLGKNFEIHGGGRDLIFPHHENEIAQSESFTSEQFAKIWMHAGMITINGEKMSKSVGNVKSINHVLESWGPNVVRLFCISGHYSKPIDYTEDLLKE 306
                   **********************************************************************************************986 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.7   1.3e+04      11      28 ..     107     124 ..     107     136 .. 0.70
   2 !   47.2   0.3     1e-15   2.3e-12       1      57 [.     343     402 ..     343     410 .. 0.77
   3 ?   -2.5   0.0       3.4   7.7e+03      19      34 ..     411     426 ..     407     443 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.7
                 -HHHHHHHHHHHHHHHHH CS
      DALR_2  11 NTaeAiavlFelakeiNr 28 
                 N ++A  ++ ++++ i  
  AJA91965.1 107 NYPKATEHIDDMINLIQN 124
                 678899999999988876 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 1e-15
                 HHHHHHTBT--HHHHHHHHHHHHHHHHH...HHHTT-HHHHHHHHHHHHHHHGGGT-.S-S CS
      DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNr...alkeedkaaasalkallrelaevLGl.lqe 57 
                 kF +a++DDFNT  +++ +F ++k+iN+   ++k ++k a +al  +l+ + evLG+  q 
  AJA91965.1 343 KFDAALNDDFNTSLGLSIFFNMIKTINSlaaDEKISKKIAVQAL-PVLEYMLEVLGIeIQT 402
                 79**************************6422222233333444.99**********6554 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.4
                 HHHHHHHHHHHHHTT- CS
      DALR_2  19 lFelakeiNralkeed 34 
                 +Fel+++  +  +e++
  AJA91965.1 411 VFELINKRETLREEKQ 426
                 6666655444222222 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   9.6e-08   0.00021      12     115 ..      31     133 ..      27     157 .. 0.82
   2 !   16.9   0.0     9e-07     0.002     313     365 ..     247     298 ..     184     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.6e-08
                   S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---.SEEEETTSHHHHHHHHHHHHHH CS
  tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisf.dkygrttseehkelvqeifkkl 107
                   ++ H+Gh+++vi  D + R+  ++g++v  +        +i  +A+++g +++ l +k+ +++ e+ ++lni   ++y ++t++ +   + +++++l
    AJA91965.1  31 DQSHIGHARTVIVFDTLRRFLEANGTQVELIQNFTDVDDKIINRAKEQGESASGLSTKYIQTYFEDSDRLNIRRaTNYPKATEHIDD--MINLIQNL 125
                   578****************************99888899*********************************752678877765443..34555555 PP

                   HHTT-EEE CS
  tRNA-synt_1g 108 kekgliye 115
                    +k+  y 
    AJA91965.1 126 VDKESAYV 133
                   55555554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9e-07
                   S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EE CS
  tRNA-synt_1g 313 kkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDld 365
                   k  +  +++t++g+K+SkS g+v  ++++le+  ++++R + ++ +  +k +d
    AJA91965.1 247 KIWMHAGMITINGEKMSKSVGNVKSINHVLESWGPNVVRLFCIS-GHYSKPID 298
                   33455699*******************************99876.33344444 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.012        26      37      65 ..      32      60 ..       9      67 .. 0.90
   2 !   24.3   0.0   3.9e-09   8.6e-06     523     598 ..     222     296 ..     214     300 .. 0.83
   3 ?   -1.5   0.0      0.25   5.5e+02     239     284 ..     364     409 ..     349     413 .. 0.86
   4 ?    0.0   0.2     0.085   1.9e+02     108     142 ..     426     461 ..     394     464 .] 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.012
  tRNA-synt_1 37 slHiGhalaktlkdivirykrmkGkevly 65
                 + HiGha + ++ d++ r+ + +G +v+ 
   AJA91965.1 32 QSHIGHARTVIVFDTLRRFLEANGTQVEL 60
                 67**********************99975 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.9e-09
  tRNA-synt_1 523 GlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrd 598
                  G D i+   ++ i +s  +t  e f ++ +h+ ++  +G KmSKs+gNv + ++v+++ g +++Rl+ i+ ++++ 
   AJA91965.1 222 GRDLIFPHHENEIAQSESFTS-EQFAKIWMHAGMITINGEKMSKSVGNVKSINHVLESWGPNVVRLFCISGHYSKP 296
                  566666666666666666654.5699*****99999*******************************999888765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.25
  tRNA-synt_1 239 llkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvd 284
                  ++k++     ++ki +++  + L  +e+ l + + +i+ ++d+ ++
   AJA91965.1 364 MIKTINSLAADEKISKKIAVQALPVLEYMLEVLGIEIQTVSDEEIE 409
                  677777788999****************************999775 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.085
  tRNA-synt_1 108 kaeyaeeirkqvkrlGvs.vDfdreylTldkeleea 142
                  + e a++ir+q++ lG+s +D++++ l ++ke  ++
   AJA91965.1 426 QFEEADKIRDQIAGLGISlIDHKNKTLWMKKEAIKS 461
                  347899**********86479999999999987766 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   3.1e-05     0.069       9      73 ..       5      69 ..       1      92 [. 0.82
   2 !   15.7   0.0   2.4e-06    0.0053     273     340 ..     254     319 ..     184     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
  tRNA-synt_1f  9 eklieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDg 73
                  + l++++ k+ + + +  +   G+++  + HiG +r v+  d ++r l++ g +v+li    d+D 
    AJA91965.1  5 DTLTNQK-KELEfSDKVRIYLCGVTVYDQSHIGHARTVIVFDTLRRFLEANGTQVELIQNFTDVDD 69
                  5566444.444535555566799************************************9999995 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.4e-06
  tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                   +i+++g+ kms+S Gnv +++ +le   p+v+r+++++ +  k ++ + d  + + +    ++e  y+
    AJA91965.1 254 MITINGE-KMSKSVGNVKSINHVLESWGPNVVRLFCISGHYSKPIDYTED-LLKENLIRLRQIETCYY 319
                   5666666.****************************99888888887777.55555555566666655 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   7.3e-06     0.016      11      33 ..     418     440 ..     413     441 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-06
         UVR  11 meeAaenedFEkAAklRDqinal 33 
                  e + e+ +FE+A k+RDqi+ l
  AJA91965.1 418 RETLREEKQFEEADKIRDQIAGL 440
                 555557889***********876 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.6     1e+04      80     104 ..      47      71 ..      37      83 .. 0.56
   2 ?   12.5   0.1   4.8e-05      0.11      40      97 ..     354     406 ..     336     418 .. 0.77
   3 ?   -2.2   0.0       1.8   3.9e+03      20      48 ..     418     446 ..     411     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
                 HHHHHHCTT--EEEEEEE...TTEEE CS
       Lig_C  80 llehLrrlgvkaeveekeke.dgelv 104
                 l ++L+  g ++e+ ++ ++ d++ +
  AJA91965.1  47 LRRFLEANGTQVELIQNFTDvDDK-I 71 
                 555555555555555555442332.2 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.8e-05
                 HHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHHHHHHCTT--EEEEEEE CS
       Lig_C  40 keLGesiLepmvetikkvkeeekvkeefrvrfkdeenieellehLrrlgvkaeveeke 97 
                   LG si+  m++ti++ +++ek+++++ v+     ++  l+  L+ lg++++  ++e
  AJA91965.1 354 TSLGLSIFFNMIKTINSLAADEKISKKIAVQ-----ALPVLEYMLEVLGIEIQTVSDE 406
                 57************************99998.....5555555566666666666665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                 HHHHHHHHH--SHHHHHHHHHHHHHHHHH CS
       Lig_C  20 ReafqavefeeseeelrerakeLGesiLe 48 
                 Re ++   + e+ +++r+ +  LG s+++
  AJA91965.1 418 RETLREEKQFEEADKIRDQIAGLGISLID 446
                 55566666667778888888888888875 PP

>> DNA_pol3_a_NII  DNA polymerase III polC-type N-terminus II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00044      0.99       3      56 ..     108     161 ..     106     166 .. 0.93
   2 ?    3.2   1.9     0.035        79      35      98 ..     365     434 ..     363     441 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
  DNA_pol3_a_NII   3 weeiveelskkspslksllkkqepevegnkliikvpneiiaealkkkkldklle 56 
                     ++++ e++++ ++++++l++k + +v+ n + + v++   + +l+kkk + l++
      AJA91965.1 108 YPKATEHIDDMINLIQNLVDKESAYVSKNGVYFRVSKFSKYGKLSKKKTEDLES 161
                     8899*******************************************9987765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.035
  DNA_pol3_a_NII  35 ikvpneiiaealkkkkldklleeyikfgFgklkidvevdedesseeei......eefeeqkeeeeekaik 98 
                     ik+ n+  a+   +kk+  ++  ++++++  l i+++   de+ e         e ++e+k+ ee+ +i+
      AJA91965.1 365 IKTINSLAADEKISKKIAVQALPVLEYMLEVLGIEIQTVSDEEIESVFelinkrETLREEKQFEEADKIR 434
                     5666777777777777777777777777775555555555555555442256656666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3310.78
//
Query:       AJA91966.1  [L=724]
Description: AAA family ATPase, CDC48 subfamily [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-90  300.2   0.0    2.1e-48  164.1   0.0    2.8  2  AAA              ATPase family associated with various cellul
    5.3e-30  103.0   2.3    1.8e-14   53.3   0.5    2.6  2  AAA_lid_3        AAA+ lid domain
    6.4e-26   90.4   1.4    2.1e-25   88.7   0.6    2.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.5e-15   57.3   0.0    1.2e-08   34.9   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.5e-13   49.4   0.0    2.8e-08   34.1   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.7e-12   48.0   0.2     0.0018   18.7   0.0    4.4  3  AAA_16           AAA ATPase domain
      4e-11   43.1   0.0    6.8e-06   26.1   0.0    2.5  2  AAA_14           AAA domain
    1.3e-10   41.6   0.0    0.00062   19.9   0.0    2.5  2  AAA_33           AAA domain
    3.1e-10   40.5   0.2     0.0052   17.1   0.0    4.2  4  AAA_22           AAA domain
    4.7e-10   39.6   0.3    0.00038   20.5   0.0    4.2  2  AAA_5            AAA domain (dynein-related subfamily)
    9.6e-10   38.8   0.1    0.00089   19.2   0.0    3.8  3  ATPase_2         ATPase domain predominantly from Archaea
    2.2e-09   37.2   0.1      0.093   12.3   0.0    4.3  4  AAA_25           AAA domain
    4.4e-09   36.7   0.0     0.0017   18.7   0.0    2.6  2  RNA_helicase     RNA helicase
    1.1e-08   34.8   0.1    6.2e-08   32.3   0.1    2.2  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    7.2e-08   33.0   0.3     0.0048   17.4   0.0    2.8  2  ABC_tran         ABC transporter
    1.9e-07   31.6   0.0      0.018   15.6   0.0    2.9  2  AAA_18           AAA domain
    3.2e-07   30.7   0.0      0.033   14.4   0.0    2.5  2  AAA_28           AAA domain
    4.7e-07   29.4   0.4      0.017   14.5   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.3e-07   29.5   0.0      0.051   13.3   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
    8.5e-07   29.1   0.7      0.056   13.4   0.0    3.8  4  Rad17            Rad17 P-loop domain
    1.4e-06   28.2   0.0      0.033   13.9   0.0    3.4  3  AAA_24           AAA domain
    2.7e-06   27.4   0.2       0.23   11.4   0.1    3.4  3  NACHT            NACHT domain
      4e-06   27.0   0.0      0.058   13.5   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
    1.3e-05   24.6   0.1       0.07   12.3   0.0    3.2  3  TIP49            TIP49 P-loop domain
      2e-05   24.1   0.7       0.32   10.3   0.0    3.5  4  ATPase           KaiC
    5.3e-05   23.2   0.0       0.22   11.6   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    5.4e-05   22.6   0.0      0.043   13.1   0.0    2.5  2  Zeta_toxin       Zeta toxin
    7.7e-05   22.5   0.0        0.1   12.3   0.0    2.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00023   20.7   0.0       0.28   10.7   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    0.00035   21.0   0.1        1.4    9.3   0.0    2.8  2  AAA_17           AAA domain
      0.001   18.3   0.0       0.64    9.1   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
     0.0014   18.3   0.0        1.7    8.3   0.0    3.1  2  Sigma54_activat  Sigma-54 interaction domain
     0.0017   17.9   0.3        3.7    7.0   0.0    3.4  3  PhoH             PhoH-like protein
     0.0022   17.5   0.1      0.011   15.2   0.2    1.9  2  UFD1             Ubiquitin fusion degradation protein UFD1
     0.0025   16.9   0.0        1.8    7.6   0.1    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
      0.003   17.0   0.0          2    7.8   0.0    3.2  3  SRPRB            Signal recognition particle receptor beta su
     0.0045   16.8   0.0        2.8    7.8   0.0    3.2  2  AAA_3            ATPase family associated with various cellul
     0.0048   16.1   0.1        2.1    7.5   0.0    2.4  2  NB-ARC           NB-ARC domain
      0.005   16.1   0.2        7.1    5.8   0.0    3.4  3  KAP_NTPase       KAP family P-loop domain
     0.0058   16.5   0.0        2.6    7.8   0.0    2.7  3  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.1        1.8    8.6   0.0    2.7  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.017   13.9   0.2        6.2    5.5   0.0    2.6  3  Adeno_IVa2       Adenovirus IVa2 protein
       0.05   12.8   0.0        2.2    7.4   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.053   13.3   0.0         11    5.7   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.23   11.8   0.8         28    5.0   0.0    2.8  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   5.3e-51   2.1e-48       1     131 [.     217     346 ..     217     347 .. 0.98
   2 !  133.0   0.0   2.1e-41   8.3e-39       2     130 ..     491     618 ..     490     620 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 5.3e-51
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                 +llyGppG+GKTllak +a+e+++++++i+g+e+++ky ge+e+k+r++fkeake++ psi+fiDEida+a++r+++  ++e+rvv+qLl+ +dg++++
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDARMFSINGPEIMNKYYGETEAKLRDIFKEAKENS-PSIIFIDEIDAIAPKREEAYGDVEKRVVAQLLALMDGLTDR 314
                 69******************************************************9.****************************************7 PP

                 SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA 100 eskvivigatnrpdkldpallr.gRfdrkieie 131
                  ++v+v+gatnrpd++dpal+r gRfdr++ei+
  AJA91966.1 315 -GNVVVLGATNRPDSVDPALRRpGRFDREMEIS 346
                 .66**************************9986 PP

  == domain 2  score: 133.0 bits;  conditional E-value: 2.1e-41
                 EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkk 99 
                 llyGppG+GKT+la+a+a+e+g +++ + g+e+lsk+vgesek ire+f++ak+++ p+++++DE+d+lak +  ++  + +e++++q+lte+++ ++ 
  AJA91966.1 491 LLYGPPGCGKTILARALATESGGNMILVRGPEILSKWVGESEKAIREIFRKAKASS-PCVIIFDELDSLAKMKnGEEGGGIGENILSQMLTEMEEGTT- 587
                 9******************************************************9.***************955668899*****************. PP

                 SSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
         AAA 100 eskvivigatnrpdkldpallr.gRfdrkiei 130
                  s+v++ig+tnrpd +d+ +lr gR+d  +++
  AJA91966.1 588 -SRVVIIGITNRPDLIDSSMLRtGRLDLNVFV 618
                 .59************************98876 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.1e-15   4.4e-13       1      41 [.     369     409 ..     369     413 .. 0.93
   2 !   53.3   0.5   4.4e-17   1.8e-14       1      43 [.     642     684 ..     642     686 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.1e-15
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                 dv+lk LA++ +Gy+GAD+++lcreAa++ +rr ++ei+ e
  AJA91966.1 369 DVNLKSLAAELHGYTGADMKSLCREAAIRSIRRYLPEIDLE 409
                 9*********************************9998765 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 4.4e-17
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                 dvdl+e+  +T+ ySGADla+lcreAa +A++ + keit +df
  AJA91966.1 642 DVDLNEISVATQSYSGADLASLCREAAVEAMQNNSKEITSKDF 684
                 9*****************************************9 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.6   5.4e-28   2.1e-25       1      84 [.       9      92 ..       9      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 5.4e-28
                CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
     CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                ++rV ea+q+d g++++ri p++m+ l++ pgdv++i  kr+T+aivwp +++++ +++Ir+dg tRkn+gv + d V++ k++
  AJA91966.1  9 QMRVGEAKQRDIGKKRARIGPDAMDYLQVTPGDVIQINAKRSTCAIVWPTDEDEKYPDTIRIDGQTRKNLGVALSDVVEINKVT 92
                69***************************************************99**************************986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     3e-11   1.2e-08      34     105 ..     215     293 ..     208     335 .. 0.80
   2 !   19.6   0.0   1.5e-06    0.0006      34      69 ..     488     523 ..     461     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3e-11
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevly 105
                   +llyGpPG Gkt lak++a+e ++++ +  gP +      e ++ l  ++++ +e+   ++fidei  ++++ ee  y
  AJA91966.1 215 SGILLYGPPGCGKTLLAKVLASESDARMFSINGPEImnkyygETEAKLRDIFKEAKENspSIIFIDEIDAIAPKREEA-Y 293
                 569*******************************993322222345666777776665336***********999986.4 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.5e-06
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                    llyGpPG Gkt la+ +a+e g ++    gP +
  AJA91966.1 488 KGALLYGPPGCGKTILARALATESGGNMILVRGPEI 523
                 5679**************************999987 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     7e-11   2.8e-08       2     105 ..     213     310 ..     212     316 .. 0.91
   2 !   12.4   0.0   0.00032      0.13       7     108 ..     491     587 ..     486     603 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7e-11
                 ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHH CS
       AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqr 97 
                 p + ill gp g+Gkt+lak la+  ++    ++  ++  e++     + + + +   ++  ++a+e+   i+++DEid i+pk e++  dv +  V+ 
  AJA91966.1 213 PHSGILLYGPPGCGKTLLAKVLASESDA----RMFSINGPEIMN----KYYGETEAKLRDIFKEAKENSpsIIFIDEIDAIAPKrEEAYGDVEKR-VVA 302
                 567799********************96....************....99999999999999999999999*************99999999876.667 PP

                 HHHHHHH- CS
       AAA_2  98 dLLqileg 105
                  LL +++g
  AJA91966.1 303 QLLALMDG 310
                 78889987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00032
                 EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEEETGGG----.---------HHHHHHHHH CS
       AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivllDEidKihpk.essgadvSregVqrdLLq 101
                 ll gp g+Gkt+la+ala         ++i +   e+l      + v + + a   + ++++     ++ +DE+d  ++  + ++    +e+++  +L 
  AJA91966.1 491 LLYGPPGCGKTILARALATESGG----NMILVRGPEILS-----KWVGESEKAIREIFRKAKASspcVIIFDELDSLAKMkNGEEGGGIGENILSQMLT 580
                 788****************9984....999999999999.....55555444444444444444478***********976555666668999999999 PP

                 HHH--EE CS
       AAA_2 102 ileggtl 108
                  +e+gt 
  AJA91966.1 581 EMEEGTT 587
                 9998875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.6e-06    0.0018      25     135 ..     215     316 ..     204     320 .. 0.55
   2 !   17.3   0.0   1.2e-05    0.0047      25      56 ..     488     518 ..     479     530 .. 0.82
   3 ?    4.7   0.0     0.092        37     122     148 ..     534     559 ..     530     592 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.6e-06
      AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllell 123
                 + +ll+G++G+GK+ l++ l+ +  ++ ++ ++g    +     y+  ++a  r +++++ +++   +    + +++++ +    e+ g+ ++r+ ++l
  AJA91966.1 215 SGILLYGPPGCGKTLLAKVLASESDAR-MFSINGPEIMN----KYYGETEAKLR-DIFKEAKEN---SPSIIFIDEIDAIAPKREEAYGDVEKRVVAQL 304
                 789**************9999765555.33355555555....33332222213.444444444...23333333333333333333344447777777 PP

      AAA_16 124 krllallsrder 135
                  +l++ l+ ++ 
  AJA91966.1 305 LALMDGLTDRGN 316
                 777766665444 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.2e-05
      AAA_16  25 elvllsGesGvGKsslvrellralekdggifl 56 
                    ll+G++G+GK+ l+r+l+++  ++ +i++
  AJA91966.1 488 KGALLYGPPGCGKTILARALATESGGN-MILV 518
                 778******************987776.4444 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.092
      AAA_16 122 llkrllallsrderplvlvlDdlqwad 148
                 ++++++++++  ++p v+++D+l+ + 
  AJA91966.1 534 AIREIFRKAKA-SSPCVIIFDELDSLA 559
                 67888999999.999********9665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.7e-08   6.8e-06       5     103 ..     217     325 ..     214     346 .. 0.80
   2 !   14.2   0.0   8.3e-05     0.033       6      77 ..     491     559 ..     487     594 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.7e-08
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev............pewekalkslvd.e 89 
                 +++ G+  +GKT l+k l++e+     +++ in  +  +k + ++e kl ++++e  ke+  +++f+DEi  +            +++   l  l+d  
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESD---ARMFSINGPEIMNKYYGETEaKLRDIFKEA-KENSPSIIFIDEIDAIapkreeaygdveKRVVAQLLALMDgL 311
                 6899***************9999...9*********99988887764666667665.56699**********999999999999977777788888742 PP

      AAA_14  90 gknldvivtGSnsk 103
                 +++++v+v G  + 
  AJA91966.1 312 TDRGNVVVLGATNR 325
                 25678888887765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.3e-05
      AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                 ++ G+  +GKT l++ l+ e+     +++ +   +   k   ++ek +++i++k+k++   ++++DE   + 
  AJA91966.1 491 LLYGPPGCGKTILARALATESG---GNMILVRGPEILSKWVGESEKAIREIFRKAKASSPCVIIFDELDSLA 559
                 789***************9999...9*******99999998888878877777766678999*****98775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.6e-06   0.00062       2      80 ..     217     325 ..     217     367 .. 0.83
   2 !   19.1   0.0   2.8e-06    0.0011       3      46 ..     491     536 ..     490     562 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.6e-06
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvldrlyqilnelarkalsag 70 
                 +ll G+pG+GK+ la+ l+ + +  ++ ++ ++++++++g+ + +++                             y +v++r+ ++l +l +    +g
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDarMFSINGPEIMNKYYGETEAKLRdifkeakenspsiifideidaiapkreeAYGDVEKRVVAQLLALMDGLTDRG 315
                 6789****************99999********999999955555556666667777778888888888888888889999999999999998888888 PP

      AAA_33  71 rnvildatnl 80 
                 + v+l atn+
  AJA91966.1 316 NVVVLGATNR 325
                 8888899986 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.8e-06
      AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                 ll G+pG+GK+ la+ l+ + g  ++l++ ++++++ +g+ ++ ++
  AJA91966.1 491 LLYGPPGCGKTILARALATESGgnMILVRGPEILSKWVGESEKAIR 536
                 578*****************************99999887666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-05    0.0052       7      59 ..     216     268 ..     211     274 .. 0.75
   2 ?    2.4   0.0      0.44   1.7e+02      87     116 ..     267     308 ..     252     325 .. 0.60
   3 !   12.4   0.0   0.00035      0.14       8      28 ..     490     510 ..     485     519 .. 0.89
   4 ?    4.0   0.0      0.14        58      82     105 ..     535     562 ..     528     601 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-05
      AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                  ++++G++G+GKT+l++ l+++ d++ +  + +pe++ +++   + +++d+++e
  AJA91966.1 216 GILLYGPPGCGKTLLAKVLASESDARMFSIN-GPEIMnKYYGETEAKLRDIFKE 268
                 589*******************986655554.6666666666666677777766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.44
      AAA_22  87 rarav..ielliiDEaqhlr..s........eealeeLrsll 116
                 ++++   ++++ iDE++ +   +        ++++ +L  l+
  AJA91966.1 267 KEAKEnsPSIIFIDEIDAIApkReeaygdveKRVVAQLLALM 308
                 333335568*********987533344444455555555555 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00035
      AAA_22   8 lvvtGesGtGKTtllrrlleq 28 
                  +++G++G+GKT l+r l+ +
  AJA91966.1 490 ALLYGPPGCGKTILARALATE 510
                 589*************99865 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.14
      AAA_22  82 leqalrarav..ielliiDEaqhlr..s 105
                 +++ +r++++  + ++i DE + l   +
  AJA91966.1 535 IREIFRKAKAssPCVIIFDELDSLAkmK 562
                 44444555555669*********96441 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   9.4e-07   0.00038       2      80 ..     217     288 ..     216     336 .. 0.73
   2 !   13.8   0.1   0.00011     0.043       3      32 ..     491     520 ..     489     607 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.4e-07
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--HH CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraese 80 
                 +lL GppG+gK+ la+ la+   ++++ +++++ +++           g+t+ +   + ++a+  +++i+++DE++ + ++
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDARMFSINGPEIMNKY------Y---GETEAKLRDIFKEAKenSPSIIFIDEIDAIAPK 288
                 89*****************************9966543......3...45555667777777778999******9987765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00011
                 EEE--SSSSHHHHHHHGGGGBS--EEEEE- CS
       AAA_5   3 lLvGppGtgKselaerlaaalnreveyvql 32 
                 lL GppG+gK+ la+ la   + ++  v +
  AJA91966.1 491 LLYGPPGCGKTILARALATESGGNMILVRG 520
                 8****************9877666666655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.2e-06   0.00089      18      83 ..     212     281 ..     204     320 .. 0.70
   2 !    9.1   0.0    0.0028       1.1      24      43 ..     491     510 ..     482     518 .. 0.85
   3 ?    5.5   0.0     0.036        14     103     136 ..     532     564 ..     516     596 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.2e-06
    ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........g 83 
                 ep + +++YGp g+GKt L k +++++    + +++ i+  e+ ++++ e+  e + ++ +++a+           
  AJA91966.1 212 EPHSGILLYGPPGCGKTLLAKVLASES----DARMFSINGPEIMNKYYGET--EAKLRDIFKEAKenspsiifidE 281
                 6777899**************999998....4699***************9..66767766666644433333331 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
    ATPase_2  24 fiYGpegsGKtaLlkeiien 43 
                 ++YGp g+GKt L + ++++
  AJA91966.1 491 LLYGPPGCGKTILARALATE 510
                 79***********9988766 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.036
    ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqklidlgln 136
                 +kai ++++k k         +ii+Del  l +++  
  AJA91966.1 532 EKAIREIFRKAK----AsspCVIIFDELDSLAKMKNG 564
                 455555555555....44459***********77754 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00023     0.093      18      54 ..     199     235 ..     186     238 .. 0.78
   2 !    7.7   0.1     0.006       2.4     127     176 ..     259     308 ..     249     323 .. 0.87
   3 !   10.2   0.0     0.001       0.4      36      55 ..     490     509 ..     466     512 .. 0.89
   4 ?    0.7   0.0      0.82   3.3e+02     128     158 ..     533     563 ..     525     594 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
      AAA_25  18 pppprrwlvkgllpagelallaGapgtGKttlaldla 54 
                 p+++++  v+  +  ++ +ll+G+pg+GKt la  la
  AJA91966.1 199 PLRHPELFVRLGIEPHSGILLYGPPGCGKTLLAKVLA 235
                 5566666667556778999*************98887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.006
      AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                 +a+++++ ++++e + +  + iD ++++ +  e++  dv +++v++l  + 
  AJA91966.1 259 EAKLRDIFKEAKE-NSPSIIFIDEIDAIAPKREEAYGDVeKRVVAQLLALM 308
                 567889999****.88**********************9999999997765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.001
      AAA_25  36 allaGapgtGKttlaldlal 55 
                 all+G+pg+GKt la  la 
  AJA91966.1 490 ALLYGPPGCGKTILARALAT 509
                 79*************99885 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.82
      AAA_25 128 advdaleaaieevegvrlvviDplsralgg.d 158
                  +++++ +++++   + ++++D l+++    +
  AJA91966.1 533 KAIREIFRKAKA-SSPCVIIFDELDSLAKMkN 563
                 6799999*****.78*****999998766533 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   4.3e-06    0.0017       1      68 [.     217     275 ..     217     292 .. 0.71
   2 !   15.3   0.0   5.1e-05      0.02       2      45 ..     491     540 ..     490     566 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.3e-06
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                   i+lyGp+g+GK++lak La++   ++        +s  +  +++++Y g++     D+ +  +e++ps
    AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDARM--------FS-INGPEIMNKYYGETEAKLRDIFKEAKENSPS 275
                   789**************766554333........22.3567777777777777777777777665555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.1e-05
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.....klkkkdsvys.rnpeddfwd 45 
                   +lyGp+g+GK+ la+ La++  +++      ++ +++v    ++  +++ 
    AJA91966.1 491 LLYGPPGCGKTILARALATESGGNMilvrgPEILSKWVGEsEKAIREIFR 540
                   69****************99988776666644444555443444445554 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       4.4   1.7e+03      19      30 ..      37      48 ..      35      71 .. 0.88
   2 !   32.3   0.1   1.6e-10   6.2e-08       3      58 ..     111     166 ..     109     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.4
                E-TTEEEEECCT CS
     CDC48_2 19 vtkGdlvvfefk 30
                vt+Gd+++++ k
  AJA91966.1 37 VTPGDVIQINAK 48
                89*****99876 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 1.6e-10
                 SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEE CS
     CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielg 58 
                 d ++ + +k+++ g p+++ d + ++ +g+++++++ +++Pkg+v+i +tT  ++ 
  AJA91966.1 111 DKEFTDFVKNRLKGLPLSQSDEISVMILGNAMDFKIEKISPKGIVRIERTTNLTIL 166
                 6777789********************************************99886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.2e-05    0.0048       4      67 ..     207     268 ..     206     323 .. 0.77
   2 !   12.7   0.1   0.00035      0.14       6      67 ..     482     541 ..     479     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-05
                 EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                 v l +++ + + + G+ G+GK+ L+k+la +++  + +i  +g ++ ++   +++++++ +++e
  AJA91966.1 207 VRLGIEPHSGILLYGPPGCGKTLLAKVLASESDARMFSI--NGPEIMNKYYGETEAKLRDIFKE 268
                 5688999999*********************99988777..77777666666666666666666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00035
                 EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                 + +k+ +   + G+ G+GK+ L+++la ++      il++g ++ ++   +++k i+ ++ +
  AJA91966.1 482 MGIKPPKGALLYGPPGCGKTILARALATESG--GNMILVRGPEILSKWVGESEKAIREIFRK 541
                 56777777889****************9975..45566778888887777777777777666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.6e-05     0.018       1      25 [.     217     259 ..     217     320 .. 0.71
   2 !   12.9   0.0    0.0003      0.12       2      24 ..     491     514 ..     491     587 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                 Ill G+pG+GKt lak L+++  +                   
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESdARmfsingpeimnkyygetE 259
                 99****************8774222344444444444444443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0003
      AAA_18   2 lltGtpGvGKttlakeLskrl.gf 24 
                 ll G+pG+GKt la++L+ +  g+
  AJA91966.1 491 LLYGPPGCGKTILARALATESgGN 514
                 589**************8875333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   8.3e-05     0.033       2      49 ..     217     269 ..     216     305 .. 0.76
   2 !   13.7   0.0   0.00014     0.056       4      32 ..     492     525 ..     490     553 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.3e-05
      AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpwv 49 
                 i + G++++GKT l++ La++     +++  pE++ +++ e  ak +d+ +++
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASEsdarMFSINgPEIMNKYYGETEAKLRDIFKEA 269
                 7899***************5543325555589999999988888888766655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00014
      AAA_28   4 itGgestGKTtlleaLaar...gypvv..pEaar 32 
                 + G++++GKT l++aLa +   ++  v  pE+  
  AJA91966.1 492 LYGPPGCGKTILARALATEsggNMILVrgPEILS 525
                 78***************77654333334555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.2e-05     0.017      25      43 ..     217     235 ..     208     240 .. 0.89
   2 !   12.4   0.1   0.00019     0.075      26      43 ..     491     508 ..     487     510 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +ll+GppG+GKt+lak l+
    AJA91966.1 217 ILLYGPPGCGKTLLAKVLA 235
                   89**************986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00019
  Mg_chelatase  26 llvGppGsGKtmlakrlp 43 
                   ll+GppG+GKt+la++l+
    AJA91966.1 491 LLYGPPGCGKTILARALA 508
                   89*************986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00013     0.051      44      71 ..     211     238 ..     203     292 .. 0.87
   2 !   13.3   0.0   0.00013     0.051      49      82 ..     489     519 ..     482     566 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                 ie + +i+l Gp+G GK+ la  l+ e 
  AJA91966.1 211 IEPHSGILLYGPPGCGKTLLAKVLASES 238
                 677999****************999875 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00013
   IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvr 82 
                 + +l Gp+G GK+ la al++e    g +++ vr
  AJA91966.1 489 GALLYGPPGCGKTILARALATES---GGNMILVR 519
                 6789***************8764...44444444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00014     0.056      44      74 ..     213     243 ..     207     273 .. 0.77
   2 ?   -1.6   0.0       5.5   2.2e+03     140     177 ..     249     284 ..     245     291 .. 0.69
   3 !    9.8   0.1    0.0017      0.69      49      74 ..     491     516 ..     482     555 .. 0.80
   4 ?    1.8   0.0      0.48   1.9e+02     140     183 ..     522     563 ..     513     566 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
       Rad17  44 kkriLLisGPsGCgkstvvkvLskelgiklr 74 
                 ++  +L+ GP+GCgk+   kvL+ e   ++ 
  AJA91966.1 213 PHSGILLYGPPGCGKTLLAKVLASESDARMF 243
                 56668999***************99776654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
       Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteies 177
                 ++ nk+y+++  +lr++ +++   s +   i+ i ei+ 
  AJA91966.1 249 EIMNKYYGETeAKLRDIFKEAKENSPS---IIFIDEIDA 284
                 566888888866788887776554433...666677765 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0017
       Rad17  49 LisGPsGCgkstvvkvLskelgiklr 74 
                 L+ GP+GCgk+   + L+ e g +++
  AJA91966.1 491 LLYGPPGCGKTILARALATESGGNMI 516
                 899***************99987766 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.48
       Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteieslegdnn 183
                 ++ +k+ ++s +a+re+ rk+  ss +   +++  e++sl    n
  AJA91966.1 522 EILSKWVGESeKAIREIFRKAKASSPC---VIIFDELDSLAKMKN 563
                 5667888887799*******9999988...999999999876655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   8.2e-05     0.033       5      77 ..     217     285 ..     215     325 .. 0.78
   2 !    9.8   0.0    0.0015       0.6       6      32 ..     491     510 ..     487     565 .. 0.69
   3 ?   -0.8   0.0       2.7   1.1e+03      80     119 ..     663     703 ..     658     719 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-05
      AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                 il+yGp+g GKT lak l  + ++ ++ +++   ++ ++ +   e+ ++++d ++e +++ +  ++++iD id +
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLasESDARMFSING--PEIMNKYYG--ETEAKLRDIFKEAKENSP--SIIFIDEIDAI 285
                 89**************997766666666666..222222222..266788888888877777..88999999876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
      AAA_24   6 liyGpsgiGKTtlakelgpkplfidte 32 
                 l+yGp+g GKT la+ l        te
  AJA91966.1 491 LLYGPPGCGKTILARAL-------ATE 510
                 89************998.......333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.7
      AAA_24  80 lclaev.irqnekaeskedkgdgkGygelaeefrrllkklq 119
                 lc++ +   ++++ +++++k +++G +++++ +++ +++ +
  AJA91966.1 663 LCREAAvEAMQNNSKEITSKDFAAGLKRIRPSITKEVETWY 703
                 55554436666666677888888888888777777666533 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0012      0.48       3      23 ..     217     237 ..     215     242 .. 0.89
   2 !   11.4   0.1   0.00058      0.23       4      23 ..     491     510 ..     489     515 .. 0.90
   3 ?    1.3   0.0      0.73   2.9e+02      64     109 ..     530     579 ..     521     618 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l G++G+GKT L++ la++
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASE 237
                 7899************99986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00058
                 EEEC-TTTCHHHHHHHHHHH CS
       NACHT   4 ilqGeaGsGKTtLlqklala 23 
                 +l G++G+GKT+L++ la++
  AJA91966.1 491 LLYGPPGCGKTILARALATE 510
                 689**************986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.73
                 S--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............H CS
       NACHT  64 epaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlL 109
                 e++++++e +   ++     ++i+D lD l++  +       +++ + ++L
  AJA91966.1 530 ESEKAIRE-IFRKAKASSPCVIIFDELDSLAKMKNGeegggIGENILSQML 579
                 55555555.333345556678999999999875544433333333333333 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0013      0.51      21      80 ..     214     284 ..     211     291 .. 0.64
   2 !   13.5   0.0   0.00015     0.058      25     118 ..     491     605 ..     487     609 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
                      SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..........HHHHHHT...TTSEEEEEE-TT CS
  Sigma54_activ_2  21 klpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..........ldlleqa...kggtLylkdiad 80 
                      ++ ++l G++G+gk+l A++L+++s     +f ++ +  ++           d++++a   ++ ++++ +i+ 
       AJA91966.1 214 HSGILLYGPPGCGKTLLAKVLASESDA--RMFSINGPEIMNkyygeteaklRDIFKEAkenSPSIIFIDEIDA 284
                      56789****************988765..44444444433333333344446666665444556666666665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                      EEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT--HHHHHHHHHHHHH..........H CS
  Sigma54_activ_2  25 fltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleqa...kggtLylkdiadlskaeqkeLlellak..........a 96 
                      +l G++G+gk++ Ar+L+ +sg+++ +++  +  +            +++ +a   ++ ++++ ++++l k++  e  + + +          +
       AJA91966.1 491 LLYGPPGCGKTILARALATESGGNMILVRGPEILS-KwvgesekaiREIFRKAkasSPCVIIFDELDSLAKMKNGEEGGGIGEnilsqmltemE 583
                      799*******************9887765433332.123334444477777755558999999***9999998877666666656666666666 PP

                      TTTT-EEEEEEEE-TTT..--- CS
  Sigma54_activ_2  97 eksslrlVstsskdleqlleag 118
                      e+  +r+V ++ ++ + l++++
       AJA91966.1 584 EGTTSRVVIIGITNRPDLIDSS 605
                      6888888888888877777665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.1   1.6e+03     166     186 ..      32      52 ..      20      67 .. 0.77
   2 !    8.3   0.0     0.003       1.2      52     101 ..     216     263 ..     208     288 .. 0.86
   3 !   12.3   0.0   0.00018      0.07      51     106 ..     488     542 ..     475     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.1
                 HHHHT--TT-EEEEETTT--E CS
       TIP49 166 llkekvkegDviviekesGkv 186
                 ++  +v+ gDvi+i++++ ++
  AJA91966.1  32 MDYLQVTPGDVIQINAKRSTC 52 
                 556689999999999887655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltq 101
                 ++Ll Gp+g Gkt la  ++ e   d    +++g e+       te+ ++
  AJA91966.1 216 GILLYGPPGCGKTLLAKVLASES--DARMFSINGPEIMNKYYGETEAKLR 263
                 79***************999985..5677899999999998888887544 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00018
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
       TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                 ++ Ll Gp+g Gkt la a++ e g ++  + + g e+ s  v  +e ++ + +rk+
  AJA91966.1 488 KGALLYGPPGCGKTILARALATESGGNM--ILVRGPEILSKWVGESEkAIREIFRKA 542
                 788********************99765..6789*******9999885688899997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00081      0.32      14      37 ..     209     232 ..     182     242 .. 0.85
   2 ?   -0.4   0.0       1.6   6.2e+02     107     149 ..     258     306 ..     235     314 .. 0.62
   3 !    9.3   0.0    0.0016      0.64      13      40 ..     481     508 ..     474     518 .. 0.82
   4 ?   -2.6   0.0         7   2.8e+03     109     154 ..     533     585 ..     517     604 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
      ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                  Gi   + +l++G pG+GKt++a+
  AJA91966.1 209 LGIEPHSGILLYGPPGCGKTLLAK 232
                 68999999**************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
      ATPase 107 lieelaeaikeika...krvviDsitglayeeke...avaReilrqlvr 149
                   ++l+++ ke k+   + + iD i+++a + +e   +v ++ + ql+ 
  AJA91966.1 258 TEAKLRDIFKEAKEnspSIIFIDEIDAIAPKREEaygDVEKRVVAQLLA 306
                 4456666666666544488999999999333333011234445555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0016
      ATPase  13 kgGipegrvvlitGepGtGKtifalqFl 40 
                 k Gi   +  l++G pG+GKti+a   +
  AJA91966.1 481 KMGIKPPKGALLYGPPGCGKTILARALA 508
                 6788888899*************98665 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 7
      ATPase 109 eelaeaikeika...krvviDsitgl....ayeekeavaReilrqlvrvlkkl 154
                 + ++e+ ++ ka     ++ D +++l    + ee      +il q+++++++ 
  AJA91966.1 533 KAIREIFRKAKAsspCVIIFDELDSLakmkNGEEGGGIGENILSQMLTEMEEG 585
                 55666666666643223333555555200222233334455666666666554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00054      0.22      19      62 ..     214     257 ..     187     282 .. 0.81
   2 !    8.6   0.0    0.0043       1.7      22      45 ..     490     513 ..     467     522 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00054
                 TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE. CS
        TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYele 62 
                 ++ ilL+G+ G+GKT l++ la++ + +  +++ P   ++++Y  e
  AJA91966.1 214 HSGILLYGPPGCGKTLLAKVLASESDARmfSINGP--EIMNKYYGE 257
                 3459*******************999987888888..688888654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                 EEEEESTTSSHHHHHHHHHHHTT- CS
        TsaE  22 ilLeGdLGaGKTtlvrglakalgv 45 
                  lL+G+ G+GKT l+r+la + g 
  AJA91966.1 490 ALLYGPPGCGKTILARALATESGG 513
                 79****************998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0      0.01       4.1      19      45 ..     217     241 ..     211     258 .. 0.84
   2 !   13.1   0.0   0.00011     0.043      14      50 ..     485     519 ..     474     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.01
  Zeta_toxin  19 illgGqpGAGKselaellkdelerqgn 45 
                 ill G pG+GK+ la+ l+ e   + +
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASES--DAR 241
                 7899**************9998..444 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00011
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                 + Pk  ll G pG+GK+ la++l++e   +gn++ + 
  AJA91966.1 485 KPPKGALLYGPPGCGKTILARALATES--GGNMILVR 519
                 679999********************8..9**99875 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       4.2       4      71 ..     220     282 ..     217     287 .. 0.70
   2 !   12.3   0.0   0.00026       0.1       5      71 ..     494     555 ..     491     560 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
  Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                       G pGcGK+ l + l+++s  + +++n p  e+ ++   +++++    ++++ ++        i+++DE+
       AJA91966.1 220 YGPPGCGKTLLAKVLASESdaRMFSINGP--EIMNKYYGETEAKLRDIFKEAKENSP-----SIIFIDEI 282
                      588*******9999999988666655555..67777666666666666666555442.....48888886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
  Viral_helicase1   5 GvpGcGKStlirkllrts...liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      G pGcGK+ l r l+ +s   +il+ +    e+l++++ ++++   + ++++  +  +     ++i+DE 
       AJA91966.1 494 GPPGCGKTILARALATESggnMILVRG---PEILSKWVGESEKAIREIFRKAKASSPC-----VIIFDEL 555
                      77*************999975554333...57******88888877877776665543.....7999995 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0007      0.28      25      63 ..     206     244 ..     202     293 .. 0.85
   2 !    7.0   0.0    0.0094       3.7      27      55 ..     481     509 ..     466     518 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0007
       AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekyl 63 
                 +++l ++ +  +ll+Gp G+GKt+++k l ++ d + ++
  AJA91966.1 206 FVRLGIEPHSGILLYGPPGCGKTLLAKVLASESDARMFS 244
                 66777888999****************999988866555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
       AAA_7  27 elllknkkpvllvGptGtGKtviikdllk 55 
                 ++ +k  k  ll+Gp G+GKt++++ l +
  AJA91966.1 481 KMGIKPPKGALLYGPPGCGKTILARALAT 509
                 5566777889************9988654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0036       1.4       1      31 [.     220     251 ..     220     297 .. 0.71
   2 !    8.8   0.1    0.0052       2.1       1      52 [.     493     545 ..     493     587 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0036
                 EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllr 31 
                 +G+PG+GK+ +++ l+ + +  ++s  G  ++
  AJA91966.1 220 YGPPGCGKTLLAKVLASESDARMFSInGPEIM 251
                 7***************9999888876554444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0052
                 EE-TTSSHHHHHHHHHHHHTEEE.EEHHHHHHHHHHTTTSHSSHHHHCTSHHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfth.lsaGdllreeakrgglakardemrklple 52 
                 +G+PG+GK+ +++ l+ + g  + l  G  + +    ++ +  r+ +rk++ +
  AJA91966.1 493 YGPPGCGKTILARALATESGGNMiLVRGPEILSKWVGESEKAIREIFRKAKAS 545
                 7**************99885333033444444444434334455556665555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0085       3.4      53     116 ..     214     282 ..     204     327 .. 0.67
   2 !    9.1   0.0    0.0016      0.64      29     102 ..     454     538 ..     443     619 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0085
      DUF815  53 annvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelp.klvellr..erperfilfvDDL 116
                  + +LL+G  G+GK  l k l +e  ++   +   e+ ++   e + kl ++ +  +++   i+f+D +
  AJA91966.1 214 HSGILLYGPPGCGKTLLAKVLASESDARMFSIngPEIMNKYYGETEaKLRDIFKeaKENSPSIIFIDEI 282
                 5679*****************999988884441146665554433313333333112334567788764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
      DUF815  29 dLvgidkqkealvent.......eqfleg..lpannvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvell 102
                 d+ g+++ k+ l++n        e+f +   +p + +LL+G  G+GK  l +al +e   +   +r  e+  + + e +k ++++
  AJA91966.1 454 DVGGLEESKHILQDNLivamndpEKFSKMgiKPPKGALLYGPPGCGKTILARALATESGGNMilVRGPEILSKWVGESEKAIREI 538
                 555666666666655422222223443322267889*******************998887755555666666665544444333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0042       1.7      23      48 ..     215     240 ..     206     292 .. 0.86
   2 ?    6.1   0.0      0.02         8      21      46 ..     486     511 ..     471     518 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                      S-EEEECSTTSSHHHHHHHHHHHSTT CS
  Sigma54_activat  23 lsvlitGesGtGKellaraiheaskr 48 
                      + +l+ G  G+GK+lla+ + ++s+ 
       AJA91966.1 215 SGILLYGPPGCGKTLLAKVLASESDA 240
                      679****************9887763 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                      SSS-EEEECSTTSSHHHHHHHHHHHS CS
  Sigma54_activat  21 tdlsvlitGesGtGKellaraiheas 46 
                       +   l+ G  G+GK++lara+ ++s
       AJA91966.1 486 PPKGALLYGPPGCGKTILARALATES 511
                      556789**************997765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0092       3.7      22      41 ..     217     236 ..     207     242 .. 0.84
   2 ?   -1.6   0.0         4   1.6e+03      69     105 ..     414     450 ..     405     456 .. 0.85
   3 ?    6.6   0.0     0.012       4.7      24      42 ..     492     510 ..     477     519 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0092
                 EEEE--TTSSTTHHHHHHHH CS
        PhoH  22 vfaiGpaGtGKtylavalav 41 
                 +   Gp G+GKt+la +la 
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLAS 236
                 6789***********99885 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                 ---------TTTHHHHHHHTTTS-TTCHHHHHHTTSE CS
        PhoH  69 pgdleekvdpylrplydaLkdllgaekvekllekgki 105
                 p+++ + +++ l  +yda++ ++ ++  e ++e++ki
  AJA91966.1 414 PTKVLQSMEVKLIDFYDAMHGVIPTAMREFYVERSKI 450
                 666778899999999********99999999999988 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                 EE--TTSSTTHHHHHHHHH CS
        PhoH  24 aiGpaGtGKtylavalave 42 
                   Gp G+GKt la ala e
  AJA91966.1 492 LYGPPGCGKTILARALATE 510
                 68************99976 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.7   6.9e+02     124     145 ..      30      51 ..       9      60 .. 0.71
   2 !   15.2   0.2   2.9e-05     0.011      77     164 ..      74     160 ..      43     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
        UFD1 124 aLrnfatLtkgdvieikyndkv 145
                    ++  +t gdvi+i+ ++++
  AJA91966.1  30 DAMDYLQVTPGDVIQINAKRST 51 
                 5556777888888888876655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.9e-05
        UFD1  77 mmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvyelkvlevkpesavsiiet 164
                   +nlg+  +d+vei++v+ + +k+v+l p   +    ++   + +++L+    L++ d i++    + +++k+ ++ p+  v i  t
  AJA91966.1  74 TRKNLGVALSDVVEINKVTAKPAKSVTLTPIADQVTVDKEFTDFVKNRLKGL-PLSQSDEISVMILGNAMDFKIEKISPKGIVRIERT 160
                 56899999***********************9999999999********986.59************************998888655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0077       3.1     117     137 ..     217     237 ..     209     246 .. 0.87
   2 !    7.6   0.1    0.0045       1.8     118     136 ..     491     509 ..     482     514 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0077
   Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                 +++yGp+ +Gkt la+ +a  
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASE 237
                 89**************99875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0045
   Parvo_NS1 118 wfyGpantGktnlaeaIak 136
                 ++yGp+ +Gkt+la+a+a+
  AJA91966.1 491 LLYGPPGCGKTILARALAT 509
                 68***************97 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.55   2.2e+02     134     178 ..     107     150 ..      82     153 .. 0.76
   2 !    7.8   0.0    0.0051         2       6      48 ..     217     259 ..     213     266 .. 0.75
   3 ?    3.5   0.0       0.1        41       7      28 ..     491     512 ..     487     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.55
                 HHHHHHHHHHHHHCHHHHHH------T....T--------GGGSS CS
       SRPRB 134 kdaLEkElnkiierrskalkeldeeedksavlakkgkdFkfdqle 178
                 +  ++kE +  +++r k l    ++++ s+ +  ++ dFk +++ 
  AJA91966.1 107 QVTVDKEFTDFVKNRLKGLPLS-QSDEISVMILGNAMDFKIEKIS 150
                 445799*********9999987.6677788888999****99885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0051
                 EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GG CS
       SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekg 48 
                 +ll G+  +GKT+l + L ++s  + + S+  +++ +k+ +e +
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDAR-MFSInGPEIMNKYYGETE 259
                 89**********9999888877655.556658888888855544 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                 EEE-STTSSHHHHHHHHHHSS- CS
       SRPRB   7 llvGlsdsGKTslftrLttdsv 28 
                 ll G+  +GKT l   L t+s 
  AJA91966.1 491 LLYGPPGCGKTILARALATESG 512
                 899*************999865 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.007       2.8       2      30 ..     217     245 ..     216     300 .. 0.85
   2 ?    5.4   0.0      0.04        16       3      24 ..     491     512 ..     489     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.007
       AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                 +ll g PG +ktll+k la+  d+++  i
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASESDARMFSI 245
                 7999***************9988876555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.04
       AAA_3   3 llegvPGlaktllvkalakald 24 
                 ll g PG +kt+l++ala+  +
  AJA91966.1 491 LLYGPPGCGKTILARALATESG 512
                 8999*************98765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0053       2.1      23      44 ..     217     238 ..     207     244 .. 0.83
   2 ?    5.9   0.1     0.016       6.3      25      41 ..     492     508 ..     487     513 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0053
                 EEEEESTTSSHHHHHHHHCCSH CS
      NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                 + l+G +G+GKt lak   ++s
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASES 238
                 679***********99877765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.016
                 EEESTTSSHHHHHHHHC CS
      NB-ARC  25 lvGmgGvGKttlakqil 41 
                 l+G +G+GKt+la+   
  AJA91966.1 492 LYGPPGCGKTILARALA 508
                 89**********99765 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.12        47      19      44 ..     213     238 ..     199     245 .. 0.81
   2 ?    5.8   0.0     0.018       7.1     140     189 ..     241     289 ..     230     301 .. 0.82
   3 ?    3.1   0.0      0.11        45     156     186 ..     530     559 ..     455     563 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
  KAP_NTPase  19 tpivvgLygkWGsGKssllnkledel 44 
                 + + + Lyg+ G+GK+ l + l +e 
  AJA91966.1 213 PHSGILLYGPPGCGKTLLAKVLASES 238
                 666799************99998875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
  KAP_NTPase 140 raaklkeeaplkklqteveelladmektLdalqkrlVvviDdLDrcetee 189
                 r++  +  + + k   e e++l d++k+ ++ +++ +++iD++D + +++
  AJA91966.1 241 RMFSINGPEIMNKYYGETEAKLRDIFKEAKE-NSPSIIFIDEIDAIAPKR 289
                 5666666777777778889999999999999.************988776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.11
  KAP_NTPase 156 eveelladmektLdalqkrlVvviDdLDrce 186
                 e e+ + +++++ +a +++ V++ D+LD++ 
  AJA91966.1 530 ESEKAIREIFRKAKA-SSPCVIIFDELDSLA 559
                 556677778888877.9999********986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.033        13      20      37 ..     217     234 ..     206     273 .. 0.80
   2 !    7.8   0.0    0.0065       2.6      18      72 ..     488     540 ..     474     558 .. 0.75
   3 ?   -2.7   0.0       9.8   3.9e+03     109     182 ..     665     707 ..     619     719 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
      AAA_11  20 tliqGPPGtgKTktivel 37 
                  l+ GPPG+gKT     l
  AJA91966.1 217 ILLYGPPGCGKTLLAKVL 234
                 5899********554444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0065
      AAA_11  18 eitliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDelle 72 
                 + +l+ GPPG+gKT    +l  +       ++   ++p+iL    ++S++A+ e+  
  AJA91966.1 488 KGALLYGPPGCGKTILARALATES----GGNMILVRGPEILSkwVGESEKAIREIFR 540
                 45899*********9998888887....45667777777764336666666666655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.8
      AAA_11 109 leekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerkelskele 182
                  e  ve+ +++++                               + +++++++ l++ r  ++ke++++ ++++
  AJA91966.1 665 REAAVEAMQNNSK-------------------------------EITSKDFAAGLKRIRPSITKEVETWYEKIK 707
                 3333333333333...............................222233333333334444444444444444 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.14        54      16      45 ..     410     439 ..     405     456 .. 0.80
   2 ?    8.6   0.0    0.0046       1.8      26      48 ..     676     698 ..     665     702 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.14
      Vps4_C  16 wmdipsdkllePpvtlkDflkalkkarptV 45 
                  ++ip++ l   +v+l Df +a++ + pt 
  AJA91966.1 410 TEKIPTKVLQSMEVKLIDFYDAMHGVIPTA 439
                 567888888888***********9999985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
      Vps4_C  26 ePpvtlkDflkalkkarptVske 48 
                   ++t kDf + lk+ rp+++ke
  AJA91966.1 676 SKEITSKDFAAGLKRIRPSITKE 698
                 569*****************986 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.017       6.9      81     109 ..     207     236 ..     177     244 .. 0.74
   2 ?    5.5   0.0     0.016       6.2      83     108 ..     482     508 ..     459     521 .. 0.83
   3 ?   -2.6   0.0       4.4   1.8e+03     186     209 ..     536     558 ..     533     564 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
  Adeno_IVa2  81 lnyglqPviGv.iyGPtGsGksqllrnlis 109
                 + +g +P  G+ +yGP G+Gk+ l + l s
  AJA91966.1 207 VRLGIEPHSGIlLYGPPGCGKTLLAKVLAS 236
                 5678999999846********999888876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
  Adeno_IVa2  83 yglqPviG.viyGPtGsGksqllrnli 108
                 +g +P  G ++yGP G+Gk+ l r+l 
  AJA91966.1 482 MGIKPPKGaLLYGPPGCGKTILARALA 508
                 55555555378*************996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
  Adeno_IVa2 186 knifvkaakrGpvaiildecmekl 209
                 ++if ka +  p +ii+de +++l
  AJA91966.1 536 REIFRKAKASSPCVIIFDE-LDSL 558
                 689***************9.4555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0056       2.2       4      69 ..     217     275 ..     214     301 .. 0.66
   2 ?    2.5   0.0      0.18        70       5      25 ..     491     511 ..     488     522 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0056
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhpl.vlvlrealakkeekkkkkeafeklss 69 
                 +l  G +G GKt+++  l+ e         a ++s N+p+ +++++ + + k  +  +kea e++ s
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASES-------DARMFSINGPEiMNKYYGETEAKL-RDIFKEAKENSPS 275
                 6789***********9999998.......445555555551678888888888.4444444433333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
     DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                 l  G +G GKt+++ +l++e 
  AJA91966.1 491 LLYGPPGCGKTILARALATES 511
                 5689**********9999885 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.029        11       4      24 ..     217     237 ..     214     240 .. 0.89
   2 ?    4.8   0.0     0.056        22       5      24 ..     491     510 ..     488     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
   PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                 ill G+ g+GKt L++ l  e
  AJA91966.1 217 ILLYGPPGCGKTLLAKVLASE 237
                 89**************99865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.056
   PduV-EutP   5 lliGkvgsGKttLtqalkge 24 
                 ll G+ g+GKt L++al  e
  AJA91966.1 491 LLYGPPGCGKTILARALATE 510
                 799*************9875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.071        28      11      28 ..     215     232 ..     210     244 .. 0.81
   2 ?    3.8   0.3      0.17        68      13      28 ..     490     505 ..     484     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.071
      AAA_19  11 kvllvtaGpGtGKTrvlk 28 
                 + +l+ ++pG+GKT + k
  AJA91966.1 215 SGILLYGPPGCGKTLLAK 232
                 56899*********8765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.17
      AAA_19  13 llvtaGpGtGKTrvlk 28 
                  l+ ++pG+GKT + +
  AJA91966.1 490 ALLYGPPGCGKTILAR 505
                 6899********7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.77u 0.28s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 4673.39
//
Query:       AJA91967.1  [L=51]
Description: hypothetical protein T478_1454 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 401.47
//
Query:       AJA91968.1  [L=423]
Description: histidine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-42  143.7   0.0    9.6e-42  143.3   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    7.8e-12   45.5   5.3      2e-11   44.2   5.3    1.8  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      8e-10   38.7   0.4    1.7e-09   37.7   0.4    1.6  1  HGTP_anticodon  Anticodon binding domain
     0.0005   19.6   0.0    0.00085   18.9   0.0    1.4  1  tRNA-synt_2d    tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.66   10.7   2.6        1.2    9.9   0.1    2.6  3  Ground-like     Ground-like domain


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   0.0   2.7e-45   9.6e-42       1     310 []       6     316 ..       6     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 2.7e-45
                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHHHTSS-EEEEEEE CS
  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqvaRiaahrlnrerplRlcYaG 95 
                    g++d+  +e +kie +r+++++++++ G++l  p+ +E + ++++++g   + +++ + D+ +r ++lR D+T+   R+ a   + + p+++  +G
     AJA91968.1   6 GMKDFENMEIQKIEYIRQHFIETANTFGFDLMEPSPIELMSVIEAKSGPTIRdDVYFFNDKGDREVSLRFDFTIGLTRYIAGQKSMKLPAKISAFG 101
                    799***********************************************875899999************************************* PP

                    EEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHHHHHHTT--HHH..HHHHHHHH...HCT-HHHH CS
  tRNA-synt_His  96 svlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvralleaaglsesl..eeallaal...arkdlael 186
                     v+r  + + gr r + Q  +E++G++++e d+E+++   + ++  +g+++++l ++h ++ ++ ++++  se+    +++l+a+   ++k+ +e+
     AJA91968.1 102 GVWRYDEPQKGRYRFFHQWDIEIFGKQNTETDAEIIEFTSKFFS-NLGLENIVLSISHRKITQSYISSIFESENSevISDILRAIdkiQKKSEQEI 196
                    *******************************************6.*****************9988865433322113455555411155666666 PP

                    HHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHHHHHHHH.H-TTEEE-TT--TTTTT--SEEEEEEETT-S.S CS
  tRNA-synt_His 187 kelaaeaglkealrellkal.elygdaevleealealaaapalqaaldeleelaallealak.pevrvtlDlaelrgyeYytGlvFaayaegvg.q 279
                     + ++++g++++++e +  + +l+g+++++ ++   +          +++ el +l+e+l++ + +++++D++ +rg++Yy+G+vF+a+ ++    
     AJA91968.1 197 ISEYEKKGYSKEKLEKIIEFsKLKGSPDEISKKFD-VT-------QFENWTELTSLFESLKNrNVNNIQIDFGIVRGLDYYSGIVFEAFDKNFDiG 284
                    66666677777777777777899999999999854.32.......256788888888888776679**************************8857 PP

                    -SEEEEEECTTTGGGT-.--EEEEEEEEHHHH CS
  tRNA-synt_His 280 aiarGGrYdelgaafgr.arpAtGfsldleal 310
                    a+++GGrYd+l ++fgr    AtG +  +e++
     AJA91968.1 285 ALVGGGRYDNLPSVFGRdDLGATGVAGGVERI 316
                    ***************87255899999888765 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   5.3   5.6e-15     2e-11       1     123 [.      61     279 ..      61     387 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 5.6e-15
                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlgle 97 
                   Y ++d+ dre  L+   + ++++ i  +  +s +LP k+++++ ++R+ ++ ++G  R+r Fhq d ++f++++   + ++++i+ +s++f++lgle
    AJA91968.1  61 YFFNDKGDREVSLRFDFTIGLTRYIAGQ--KSMKLPAKISAFGGVWRYDEP-QKG--RYRFFHQWDIEIFGKQN--TETDAEIIEFTSKFFSNLGLE 150
                   7799999*******************88..9*88*****************.***..****************9..99******************* PP

                   CEEEEEEGTTSC..................................................................................... CS
                   xxxxxxxxxxxx..................................................................................... RF
  tRNA-synt_2b  98 fraiielmsaks..................................................................................... 109
                     ++  + +  +                                                                                     
    AJA91968.1 151 NIVLSISHR--Kitqsyissifesensevisdilraidkiqkkseqeiiseyekkgyskeklekiiefsklkgspdeiskkfdvtqfenwteltslf 245
                   754433322..22345665666666777777777777666666666666555555555555555555555555555555555555555555555555 PP

                   ....................BTTSEEEEEEEEET CS
                   ....................xxxxxxxxxxxxxx RF
  tRNA-synt_2b 110 ....................adykdkkefeavse 123
                                       +dy+   +fea ++
    AJA91968.1 246 eslknrnvnniqidfgivrgLDYYSGIVFEAFDK 279
                   5555555555555555555544444444444444 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.4   4.8e-13   1.7e-09       3      93 ..     335     420 ..     333     421 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.8e-13
                     EEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   3 vviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                      v+ +ne   +++  a+ +a+ Lr++ i +++d s++ ++k+++++ +    f+++vG++el k+ v vr++ +r ++++ ++el+e +k+
      AJA91968.1 335 SVLYVNE---DVKSNAMTIASILRENSIPTDIDLSGRALKKQMEQSTN--SKFVIIVGPDELSKNMVVVRNMSDRTENKILISELLEHVKK 420
                     6899999...899******************************98765..569**********************************9997 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.4e-07   0.00085       9     152 ..       8     147 ..       1     165 [. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                   SCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH...TTS-SSE CS
  tRNA-synt_2d   9 krieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl...ekkkppi 102
                   k+ e+++++ ++ +++++ e+   +gf  +e + +e      ++++ ++   +R  +d++++ +++   ++++ LR   t    r++   ++ k+p+
    AJA91968.1   8 KDFENMEIQKIEYIRQHFIETANTFGFDLMEPSPIE----LMSVIEAKSGPTIR--DDVYFF-NDKG--DREVSLRFDFTIGLTRYIagqKSMKLPA 95 
                   566777888888888888888888888888888883....23344444444444..477777.5555..689***************9988899*** PP

                   EEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHH..HHHHHHHHHHHH CS
  tRNA-synt_2d 103 kiisigrvfRrdavDathlaeFhqveglvvdenvslad..lkgvleellkkl 152
                   ki ++g v+R d+  + +   Fhq +  + +++ + +d  ++ + ++++++l
    AJA91968.1  96 KISAFGGVWRYDEPQKGRYRFFHQWDIEIFGKQNTETDaeIIEFTSKFFSNL 147
                   ************************9998888866544311455555666655 PP

>> Ground-like  Ground-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.7   6.2e+03      25      37 ..     184     196 ..     149     201 .. 0.65
   2 ?   -0.7   0.0      0.64   2.3e+03       7      28 ..     208     229 ..     206     233 .. 0.82
   3 ?    9.9   0.1   0.00033       1.2       8      51 ..     349     392 ..     342     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
  Ground-like  25 skkaiqkaleekf 37 
                     +iqk+ e++ 
   AJA91968.1 184 AIDKIQKKSEQEI 196
                  3345666666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.64
  Ground-like   7 seLkkiie.enmkqssasdskka 28 
                  ++L+kiie  ++ ++s+ +++k+
   AJA91968.1 208 EKLEKIIEfSKL-KGSPDEISKK 229
                  78******8777.8888888875 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00033
  Ground-like   8 eLkkiieenmkqssasdskkaiqkaleekfgssfevicsegdfs 51 
                  ++ +i++en  ++++  s +a++k++e+  +s+f +i+  ++ s
   AJA91968.1 349 TIASILRENSIPTDIDLSGRALKKQMEQSTNSKFVIIVGPDELS 392
                  6678888766699*************************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1306  (0.0728429); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3056.79
//
Query:       AJA91969.1  [L=486]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-06   28.0   0.6    5.8e-06   26.0   0.1    2.2  2  TPR_2          Tetratricopeptide repeat
      4e-06   26.4   3.4    1.6e-05   24.5   0.6    2.4  2  TPR_1          Tetratricopeptide repeat
    1.4e-05   24.9   0.4    1.4e-05   24.9   0.4    1.9  1  TPR_8          Tetratricopeptide repeat
    7.3e-05   23.0   0.0    0.00013   22.2   0.0    1.4  1  TPR_12         Tetratricopeptide repeat
    8.8e-05   22.6   0.0    0.00018   21.5   0.0    1.5  1  Peptidase_M54  Peptidase family M54
    0.00022   21.8   0.0    0.00051   20.6   0.0    1.6  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00093   19.4   0.0     0.0016   18.6   0.0    1.4  1  Reprolysin_5   Metallo-peptidase family M12
     0.0012   18.5   0.0      0.002   17.8   0.0    1.3  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
     0.0018   17.3   0.4     0.0057   15.6   0.0    1.8  2  Peptidase_M66  Peptidase M66
     0.0042   17.2   0.0     0.0088   16.1   0.0    1.5  1  Zincin_1       Zincin-like metallopeptidase
      0.007   16.0   0.9       0.98    9.2   0.3    2.5  2  TPR_11         TPR repeat
     0.0071   16.3   0.1      0.021   14.8   0.0    1.7  2  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
     0.0078   17.0   0.2      0.019   15.7   0.2    1.6  1  DUF3744        ATP-binding cassette cobalt transporter
  ------ inclusion threshold ------
      0.019   13.6   0.1        0.1   11.2   0.0    1.9  2  Metallopep     Putative peptidase family
       0.04   13.8   0.1      0.096   12.5   0.1    1.8  1  Peptidase_M10  Matrixin
      0.067   13.9   0.1       0.29   11.9   0.0    2.0  2  TPR_6          Tetratricopeptide repeat
       0.14   12.0   0.1       0.29   11.1   0.1    1.5  1  TPR_10         Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.8   1.9e+03      11      25 ..     312     326 ..     309     332 .. 0.83
   2 !   26.0   0.1   5.5e-09   5.8e-06       3      34 .]     343     374 ..     341     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.8
       TPR_2  11 yyklgdyeeAleafe 25 
                  +++g y +A++ ++
  AJA91969.1 312 FFEMGLYGDAIKNYK 326
                 578999******997 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 5.5e-09
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 al+ +Gl++++l++ye+ l +fe++ e++Pn+
  AJA91969.1 343 ALNKIGLSLIQLKNYEKSLSYFEQVYEINPNY 374
                 899***************************96 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.18   1.9e+02      11      25 ..     312     326 ..     312     326 .. 0.91
   2 !   24.5   0.6   1.5e-08   1.6e-05       2      34 .]     342     374 ..     341     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                 HHHTT-HHHHHHHHH CS
       TPR_1  11 yfklgkydeAleyye 25 
                 +f++g y +A++ y+
  AJA91969.1 312 FFEMGLYGDAIKNYK 326
                 589**********97 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.5e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +al+ +G+ + +l++y++ l y+e++ e+nPn+
  AJA91969.1 342 NALNKIGLSLIQLKNYEKSLSYFEQVYEINPNY 374
                 599****************************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.4   1.4e-08   1.4e-05       2      34 .]     342     374 ..     341     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-08
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                  a++++g+ +++l++ye++ +y+e++ e++p++
  AJA91969.1 342 NALNKIGLSLIQLKNYEKSLSYFEQVYEINPNY 374
                 5899***************************85 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.2e-07   0.00013      14      75 ..     313     371 ..     309     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-07
      TPR_12  14 rrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                 +++g y +A+++++ ++  a +++    pl++++l+ +g  + +l++ye+ l+++e++++i 
  AJA91969.1 313 FEMGLYGDAIKNYKVVMKNADKIQ---EPLYLNALNKIGLSLIQLKNYEKSLSYFEQVYEIN 371
                 57999999********99998884...568999*************************9985 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.7e-07   0.00018     139     165 ..      89     115 ..      33     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                    HHHHHHHHHHHHHHHHHHTT----S-T CS
  Peptidase_M54 139 eLflervvkevlhelGhlyGLshCked 165
                    + +++ ++k ++he+Gh++GL+h  +d
     AJA91969.1  89 DKWMDGIFKTIIHEMGHTFGLGHYTTD 115
                    447999*****************8774 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.8e-07   0.00051      59     123 ..      42     111 ..       9     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.8e-07
  Reprolysin_3  59 rgqagyDlvhlftarde......sgvgGlAyvgsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                     +++  +  lf+++ e      s+++G    +s+   ++++++++g + +  +  +t++HE+GH fg+ H
    AJA91969.1  42 SVTDDCTITILFRDDPEfsgsllSKTLGAFMRNSIYVYYENQQSIYGDKWMD-GIFKTIIHEMGHTFGLGH 111
                   3577788888888877788888899999855578888887888888886555.455*************** PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0016     140     184 ..      93     134 ..      32     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
  Reprolysin_5 140 atevqvvaHElGHnfGavHDcdsss.......esqsCslsnstepaggryiM 184
                   +  ++++ HE+GH+fG  H  +++        +           +++  +iM
    AJA91969.1  93 DGIFKTIIHEMGHTFGLGHYTTDDNdynrkiaT----------RDQSPPSIM 134
                   4568999************55555222222222..........444444444 PP

>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.9e-06     0.002     135     180 ..      95     142 ..      69     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
  Reprolysin_4 135 eydifAHEiGHtfGaaHdlsdegegl..sskteegsgqtIM.syaseas 180
                    ++++ HE+GHtfG+ H   d+   +    +t ++s  +IM ++a++  
    AJA91969.1  95 IFKTIIHEMGHTFGLGHYTTDDND-YnrKIATRDQSPPSIMfAPAHINP 142
                   36889************9998888.513556689999999967777765 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.4e-06    0.0057     194     215 ..      97     118 ..      85     129 .. 0.77
   2 ?   -1.0   0.1      0.64   6.8e+02      56     110 ..     314     371 ..     296     397 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
  Peptidase_M66 194 gefiHEqGHalGLpHylageaa 215
                    ++ iHE+GH +GL+Hy + +++
     AJA91969.1  97 KTIIHEMGHTFGLGHYTTDDND 118
                    4569***********9877654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
  Peptidase_M66  56 pfylfGandtntkPfs.ktkvideeiakelfqkvpvsklkvsnhp..iqrfdssylvl 110
                    +++l+G    n+k    +   i+e +  + ++k+ +s ++++n++  +++f++ y + 
     AJA91969.1 314 EMGLYGDAIKNYKVVMkNADKIQEPLYLNALNKIGLSLIQLKNYEksLSYFEQVYEIN 371
                    67788887788876541556788999999999*****999999983346788755543 PP

>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.4e-06    0.0088      45      86 ..      70     109 ..      36     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.4e-06
                 GGG--EEEEEHHHHHHH--TT--HHHHHHHHHHHHHHHHHTT CS
    Zincin_1  45 gslpdrivlyrrpllavaetreeleeevretllHEighhfGl 86 
                 + + ++i++y+++ +++   ++++ + + +t++HE+gh fGl
  AJA91969.1  70 AFMRNSIYVYYENQQSI--YGDKWMDGIFKTIIHEMGHTFGL 109
                 456789*******9998..5789*****************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.02        21       3      18 ..     311     326 ..     309     328 .. 0.92
   2 !    9.2   0.3   0.00093      0.98       1      30 [.     348     377 ..     348     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
      TPR_11   3 ayyeqGkyeeAieaYk 18 
                  ++e G y +Ai++Yk
  AJA91969.1 311 RFFEMGLYGDAIKNYK 326
                 69*************8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00093
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30 
                 G  + ++ +ye+++  +++  +++P+++++
  AJA91969.1 348 GLSLIQLKNYEKSLSYFEQVYEINPNYPNI 377
                 677899**********************98 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.9e-05     0.021     127     172 ..      97     138 ..      65     156 .. 0.81
   2 ?   -2.6   0.0       4.1   4.3e+03      12      34 ..     361     391 ..     356     415 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
  Reprolysin_2 127 dvvaHEvGHaFGatHdndgssasegveenaatsvedaggkfiMa.pa 172
                   + + HE+GH+FG  H  +    +++ +++ at   d++  +iM  pa
    AJA91969.1  97 KTIIHEMGHTFGLGHYTTD---DNDYNRKIAT--RDQSPPSIMFaPA 138
                   4578***********9994...4455778888..8889999997666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
  Reprolysin_2  12 lnrvnqiYe........eddinislrlrnea 34 
                   l++ +q+Ye        e+++++s  l +++
    AJA91969.1 361 LSYFEQVYEinpnypniEQNLKTSKSLIQTD 391
                   6778899998888777777777777776544 PP

>> DUF3744  ATP-binding cassette cobalt transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.8e-05     0.019       8      31 ..     334     357 ..     330     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
     DUF3744   8 gIREPLYitaLKkagidltslnql 31 
                  I+EPLY+ aL k g +l +l++ 
  AJA91969.1 334 KIQEPLYLNALNKIGLSLIQLKNY 357
                 6***************99888654 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.5e-05       0.1     318     332 ..      99     113 ..      97     126 .. 0.90
   2 ?   -0.5   0.0      0.33   3.5e+02      74     114 ..     246     288 ..     194     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.5e-05
  Metallopep 318 flHEiGHllglpHqe 332
                 ++HE+GH++gl+H +
  AJA91969.1  99 IIHEMGHTFGLGHYT 113
                 58***********75 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
  Metallopep  74 kesevasseltlnykpleqnppvhlvil..vakdsdgtfdape 114
                 +++   ++++++nyk l+ +++++ +++  +++++++ fd+ +
  AJA91969.1 246 TRDGFFETYMNFNYKSLPGKYSIEFAYIdkIDQSKNLVFDVEQ 288
                 5566668899*****************9444555556666655 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.1e-05     0.096     108     129 ..      94     115 ..      10     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                    EHHHHHHHHHHHHTTBESXSST CS
                    xxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M10 108 slflVaaHEiGHalGLeHssdk 129
                     +f   +HE+GH+ GL H +  
     AJA91969.1  94 GIFKTIIHEMGHTFGLGHYTTD 115
                    378999************7655 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.9   6.3e+03      10      28 ..     312     330 ..     309     332 .. 0.72
   2 ?   11.9   0.0   0.00027      0.29       5      32 ..     346     373 ..     343     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.9
                 HHHHHHHHHHHHHHHHHHH CS
       TPR_6  10 yrklgdtdkAlealerlik 28 
                 ++++g + +A++ ++ + k
  AJA91969.1 312 FFEMGLYGDAIKNYKVVMK 330
                 5677788888888887766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00027
                 HHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   5 klalsyrklgdtdkAlealerlikeYPd 32 
                 k++ls+++l++++k+l ++e++ +  P+
  AJA91969.1 346 KIGLSLIQLKNYEKSLSYFEQVYEINPN 373
                 89******9*************999998 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00027      0.29       2      31 ..     341     370 ..     341     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
      TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                 +++ln ++  l q+++y++++ ++e++++i
  AJA91969.1 341 LNALNKIGLSLIQLKNYEKSLSYFEQVYEI 370
                 689************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3515.16
//
Query:       AJA91970.1  [L=306]
Description: ornithine carbamoyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-53  178.4   0.0    1.3e-52  177.8   0.0    1.3  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    9.8e-51  171.9   0.3    1.6e-50  171.2   0.3    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.8   0.0   1.4e-56   1.3e-52       3     148 .]      10     148 ..       9     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 1.4e-56
                 BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTGGSTTSSCHHHHHHHHHHHT CS
    OTCace_N   3 llsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssvskgrkEsleDtarvlsryv 101
                 +l+l++l+++ei++++dla +lk++ kk k+++ll++ktla++Fe+pStRTrvSfe+++ +lGg++l+ls ++d+qls     r+Es++Dtar+lsryv
  AJA91970.1  10 ILTLDELESKEINNIIDLAIDLKKELKKGKEKPLLQNKTLAMIFEKPSTRTRVSFETGMFQLGGHALTLS-PNDLQLS-----RGESIADTARTLSRYV 102
                 799*******************************************************************.99*****.....78************** PP

                 SEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
    OTCace_N 102 daiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                 +++++R++++++le++a+++s+pviN++ +d +HP+Q+LaDl+ti+e
  AJA91970.1 103 NVVMARVYDHKSLETFARNSSIPVINGL-SDSYHPCQILADLMTIKE 148
                 ****************************.****************97 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.3   1.8e-54   1.6e-50       1     156 [.     154     302 ..     154     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 1.8e-54
                 CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHHHHHHHHCC. CS
      OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekereerlkklkd. 98 
                 k++kia++Gd+ nnv+nsli ++a+l+++++++ P+g+ep+ +v++     + k ++ +++++++++av++aDvv+td++vs+++     +r+kk+ + 
  AJA91970.1 154 KKIKIAWIGDG-NNVCNSLILGCAKLKIQLSVAIPDGYEPEFDVIK-----IGKDAEILEVSDNPAAAVQDADVVMTDTFVSIHN--TNSDRVKKFLPk 244
                 689********.*******************************993.....345579************************9999..455788888877 PP

                 CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
      OTCace  99 yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                 +qv+++l+++akkdai++HcLPakr++Evt++V+d+ +svv+++aeNrlh++kAllv+
  AJA91970.1 245 FQVNQALMNKAKKDAIFMHCLPAKRDQEVTSDVIDGSQSVVWDEAENRLHVQKALLVH 302
                 ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2204.98
//
Query:       AJA91971.1  [L=167]
Description: hypothetical protein T478_1381 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   13.2   2.9      0.036   12.8   2.9    1.1  1  TctA      Tripartite tricarboxylate transporter TctA family


Domain annotation for each model (and alignments):
>> TctA  Tripartite tricarboxylate transporter TctA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.9     2e-06     0.036     328     379 ..      37      88 ..      31      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-06
        TctA 328 allasllianvlllvlgllliklfakllkipkelLlpiilvllvigayalnn 379
                 +l ++++++++++ +l++++i++f+++  +  ++L+ ++l+++v  + ++++
  AJA91971.1  37 FLALGFWVSSIVAAILAVPAIGVFVYFYAVFDNILVGGVLAFVVHFVLLMKS 88 
                 57889***************************************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1239  (0.0691059); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1125.43
//
Query:       AJA91972.1  [L=356]
Description: GTP-binding protein HflX [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-17   62.6   0.7    1.1e-16   61.3   0.7    1.7  1  GTP-bdg_N    GTP-binding GTPase N-terminal
      1e-15   57.8   1.4    1.5e-15   57.2   0.2    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
    4.8e-15   55.9   3.9    4.8e-15   55.9   3.9    2.2  2  GTP-bdg_M    GTP-binding GTPase Middle Region
    9.7e-06   25.6   8.9     0.0017   18.3   0.2    3.0  3  RsgA_GTPase  RsgA GTPase
    2.8e-05   23.7   0.7    2.8e-05   23.7   0.7    2.1  2  FeoB_N       Ferrous iron transport protein B
     0.0019   17.6   3.3      0.006   16.1   3.3    1.8  1  Arf          ADP-ribosylation factor family
     0.0035   16.8   1.3      0.008   15.6   1.3    1.6  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0036   17.8   0.8      0.014   16.0   0.1    2.1  2  ABC_tran     ABC transporter
     0.0038   17.0   2.4       0.11   12.3   2.4    2.5  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0046   17.4   2.3      0.062   13.7   0.2    2.5  2  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.023   14.7   0.2      0.069   13.2   0.0    2.0  2  Dynamin_N    Dynamin family
      0.042   13.5   0.0      0.046   13.4   0.0    1.2  1  CHASE2       CHASE2 domain
      0.061   13.7   4.3       0.24   11.8   4.3    2.0  1  DUF4200      Domain of unknown function (DUF4200)
       0.17   11.4   4.3        1.1    8.8   0.2    2.9  3  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.25   10.9   5.1        2.2    7.8   1.9    2.9  2  GTP_EFTU     Elongation factor Tu GTP binding domain
        2.8    8.0  10.1         14    5.7   0.5    3.4  3  AAA_14       AAA domain


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.7   9.6e-20   1.1e-16       6      88 ..      17      98 ..      12      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 9.6e-20
   GTP-bdg_N  6 EleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLILdIF 88
                E+++L+++a+++v+ ++ +  +  ++++ i + kvee++e++e+ + d+++fd+ L+p+q  +L  +l+++++DR +LIL+IF
  AJA91972.1 17 EAKSLCEAAQYNVLYTIKVD-DLQKRKYGITESKVEELEEKLEKLKPDVIVFDELLKPNQNYSLAAKLKIEIVDRESLILEIF 98
                99************988776.56778899****************************************************** PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.2   4.7e+03      92     106 ..      48      61 ..      11      69 .. 0.45
   2 !   57.2   0.2   1.4e-18   1.5e-15       2     114 .]     186     305 ..     185     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                 HHHHHHHHHHHHTTS CS
    MMR_HSR1  92 pldeeleelleeakk 106
                  + eelee le + k
  AJA91972.1  48 SKVEELEEKLE-KLK 61 
                 12233333332.223 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 1.4e-18
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC....TSEEEEEEETT..TTCSHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee....adlillvvdas..eeklkpld 94 
                 + ++G++ +GK+tL+n ltge+ + s++ +tT++++++r+kl+++   ++Dt+G+i+  +    + +af++  e    +d+illv+d+   +e +k++ 
  AJA91972.1 186 ISLAGYTSAGKTTLFNNLTGETKEKSAELFTTLTTTTRRLKLGREISLITDTVGFIS--KLPAYMIEAFKSTLEelifTDIILLVIDSLddDELMKKKF 282
                 789**************************************887777889****887..55557777777755556668********446533444444 PP

                 HHHHHHHHH...TTSEEEEEEES CS
    MMR_HSR1  95 eeleellee...akkplilvlnk 114
                 +++ ++l e   ++k++i+++nk
  AJA91972.1 283 STCYKTLVElgvERKNMIFLFNK 305
                 55555554477788999999998 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2         3   3.3e+03      55      69 ..      47      61 ..      38      63 .. 0.78
   2 !   55.9   3.9   4.3e-18   4.8e-15       1      79 []     101     178 ..     101     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
                HHHHHHHHHHHHHHH CS
   GTP-bdg_M 55 reriaklkkeLekvk 69
                + ++++l+++Lek+k
  AJA91972.1 47 ESKVEELEEKLEKLK 61
                567888999999886 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 4.3e-18
                 H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX...X....XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
   GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrq.gGgig..trGpGetkleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                 rA+++e+klQV+lAql+y++ r     ke  r+ +Gg +  ++G G++ ++ +   i++r + +kk+Lek  k+r+l+r+ R
  AJA91972.1 101 RASSAESKLQVKLAQLRYERARA----KERVRLaKGGEQpgFMGIGKYDIDAYYDDIKNRGTVIKKKLEKAGKQRALHRQGR 178
                 9**********************....33333323332234**************************************988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.52   5.8e+02      41      85 ..      23      70 ..       4      88 .. 0.61
   2 !   18.3   0.2   1.5e-06    0.0017      94     161 ..     178     240 ..     142     244 .. 0.78
   3 !   11.0   0.3   0.00026      0.29      20     100 ..     267     350 ..     261     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.52
                 HHHHTT-EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TT CS
  RsgA_GTPase 41 laeekgiepvivlnKiDlleeee......eleelkeelealgyevllvsak 85
                 +a + ++       K+D l++++      ++eel+e+le+l  +v++ ++ 
   AJA91972.1 23 EAAQYNVLY---TIKVDDLQKRKygitesKVEELEEKLEKLKPDVIVFDEL 70
                 444444333...335555555555666668999999999998888876654 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.5e-06
                  HHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
  RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                  +++l  kt+ l+G + +GK+tL n+l++e++ k +e+ ++      TTt+++l    e +l+ Dt Gf
   AJA91972.1 178 RDRLGFKTISLAGYTSAGKTTLFNNLTGETKEKSAELFTT-----LTTTTRRLKLGREISLITDTVGF 240
                  556677999********************77777777765.....467777777777789999*9998 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00026
                  EEEEESTTTT--HH...HHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTS.EEEE--TTTHTTHHHHHHHCTTS CS
  RsgA_GTPase  20 livvslkepelsln...lldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgy.evllvsaktkegleelkellkdk 100
                  l++ sl+++el ++   +  + Lv++  ++ +++ ++nK + +++++ + +++++l+  ++ ++l vsa t+++l++lk+ l+++
   AJA91972.1 267 LVIDSLDDDELMKKkfsTCYKTLVELGVERKNMIFLFNKSESIDDKK-FLHVMNNLKIDEVeNCLDVSALTGKNLTDLKQILQKR 350
                  6677888877765411156699*************************.6666666666665157789**************9986 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.65   7.2e+02      90     132 ..       9      52 ..       5      62 .. 0.76
   2 !   23.7   0.7   2.5e-08   2.8e-05       2     154 ..     185     345 ..     184     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.65
                 GHHHHHHHHHH.HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHH CS
      FeoB_N  90 nlernLyLtlq.llelgvpvvlalnmideaekkgieidlkkLse 132
                 n++ n+ L ++ l+e  +  vl   ++d ++k+++ i ++k++e
  AJA91972.1   9 NVNENISLEAKsLCEAAQYNVLYTIKVDDLQKRKYGITESKVEE 52 
                 66777777654277888888999999999999999998776654 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.5e-08
                 EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS.SSSSSHHH..HHHHHHHHCTSSSEEEEEEEGGGHHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs.lsayseee..kvardflleeepdvvvnvvdatnlernLyL 97 
                 t+ l+G   +Gkttlfn+ltg +++ +    +t   ++ +lkl ++   i+D  G  s l ay +e   +  ++++ ++ + +v++ +d  +l ++ + 
  AJA91972.1 185 TISLAGYTSAGKTTLFNNLTGETKEKSAELFTTLTTTTRRLKLGREISLITDTVGFISkLPAYMIEAfkSTLEELIFTDIILLVIDSLDDDELMKKKFS 283
                 799*******************99999888899999999999888888999****85525555555311333444444444567777776777665544 PP

                 HH..HHHHTT...SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHH CS
      FeoB_N  98 tl..qllelg...vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellk 154
                 t+   l+elg   ++++  +n+++ +++k+    +++L+     +++ +sa +++++ +l++
  AJA91972.1 284 TCykTLVELGverKNMIFLFNKSESIDDKKFLHVMNNLKIDEVENCLDVSALTGKNLTDLKQ 345
                 43226889874446899999***999999988778888777777888899999998888876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.3   5.3e-06     0.006      19     171 ..     188     347 ..     174     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                 EEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEE.TTEEEEEEEE-SSGGGGGGGGGGCTT.......ESEEEEEEETT-CTTHHHHH.HHHH CS
         Arf  19 llGLDnaGKtTilkklkleelvt...tvPTigfnveelei.knlkftvwDvGGqeklRplWknYfek.......tdavifvvDsadreRleeak.eeLk 105
                 l G  +aGKtT+ ++l+ e  ++      T+  ++++l+  +++++ +  vG  +kl  +  + f++       td ++ v+Ds d + l++ k +   
  AJA91972.1 188 LAGYTSAGKTTLFNNLTGETKEKsaeLFTTLTTTTRRLKLgREISLITDTVGFISKLPAYMIEAFKStleelifTDIILLVIDSLDDDELMKKKfSTCY 286
                 568899**********8655443233899**********96799999999**99**999988777762333444588889*****99877666536778 PP

                 HHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHHH CS
         Arf 106 alleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeglewl 171
                 + l e  +++  ++ l NK +  ++ +  ++ ++l+++e++     +   +sa++g++l++  + l
  AJA91972.1 287 KTLVELGVERKNMIFLFNKSESIDDKKFLHVMNNLKIDEVE-----NCLDVSALTGKNLTDLKQIL 347
                 888999999999***************************99.....56677788888877766555 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.3   7.1e-06     0.008       5     107 ..     185     293 ..     183     336 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.1e-06
                 EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEE.EETT-.GCCSHHHHHHHHHHGGEEEEEE......EEETTS-HHHHHHH CS
       SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltli.DfPGh.eklrqklleklkaksslkglvf......vvDStidpkevkev 95 
                 ++ l+G + +GKT+lf+ Lt ++++k+     + +++  + + g ++ li D  G   kl   ++e    ks+l  l+f      v+DS  d+  +k+ 
  AJA91972.1 185 TISLAGYTSAGKTTLFNNLTGETKEKSAELFTTLTTTTRRLKLGREISLItDTVGFiSKLPAYMIEA--FKSTLEELIFtdiillVIDSLDDDELMKKK 281
                 6789*****************9999998877766666666678888887768888636888888888..555555555533333377777666666666 PP

                 HHHHHHHHHHHH CS
       SRPRB  96 AEllyeillite 107
                     y+ l++  
  AJA91972.1 282 FSTCYKTLVELG 293
                 666666666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.1   1.3e+03      48      80 ..      37      97 ..      17     135 .. 0.57
   2 !   16.0   0.1   1.2e-05     0.014      12      72 ..     184     242 ..     182     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                EGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH...........................H CS
                xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...........................x RF
    ABC_tran 48 dlkeqeleslrkeigvlpqe.pqlfpeltvren...........................e 80
                dl++++  +++++++ l+++ ++l+p++ v ++                            
  AJA91972.1 37 DLQKRKYGITESKVEELEEKlEKLKPDVIVFDEllkpnqnyslaaklkieivdreslileI 97
                5555555566666666666666666666655555544455555555555544444444441 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.2e-05
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-T CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfp 72 
                 +++ + G + aGK+tL++ l+g++k ++ e+    + +  +++ +l +ei+ ++ +  + +
  AJA91972.1 184 KTISLAGYTSAGKTTLFNNLTGETKEKSAELFTTLTTT--TRRLKLGREISLITDTVGFIS 242
                 578999*******************9999984443333..347777777777777655444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   2.4   9.4e-05      0.11       2     142 ..     184     348 ..     183     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
   PduV-EutP   2 kkilliGkvgsGKttLtqalkg..........eelkYkktqaiefsdev...iDtPGeylenrkly.salivtsae...advialvqdateeesvfppg 83 
                 k i l G + +GKttL ++l+g           +   + t  +++  e+    Dt G   +   ++ +a+++t  e   +d+i lv d+ + ++++ ++
  AJA91972.1 184 KTISLAGYTSAGKTTLFNNLTGetkeksaelfTT-LTTTTRRLKLGREIsliTDTVGFISKLPAYMiEAFKSTLEElifTDIILLVIDSLDDDELMKKK 281
                 678899**************99777766333211.1234455555444333279999655555554234444433333379******999998888888 PP

   PduV-EutP  84 fasvf.........nkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellkyle 142
                 f+++          +k++i +  k +   d+++   v + Lk   +e+   vsa++ +++ +l++ l+
  AJA91972.1 282 FSTCYktlvelgveRKNMIFLFNKSESI-DDKKFLHVMNNLKIDEVENCLDVSALTGKNLTDLKQILQ 348
                 8776522223333358888889999999.66666778999***********************99997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   5.5e-05     0.062      15      67 ..      18      70 ..      15     113 .. 0.91
   2 ?    3.4   0.2     0.088        98       3      52 ..     188     254 ..     186     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                HHHHHHHHTHEE.EEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETG CS
         AAA 15 akavakelgvef.leisgsellskyvgesekkirelfkeakekakpsilfiDEi 67
                ak++++ ++ ++ ++i++ +l +   g +e+k++el +++++ + p ++++DE+
  AJA91972.1 18 AKSLCEAAQYNVlYTIKVDDLQKRKYGITESKVEELEEKLEKLK-PDVIVFDEL 70
                8999***99887699*******999***************9998.********8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.088
                 EESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS...............STTHHHHHHHHHHHH CS
         AAA   3 lyGppGtGKTllakavakelg...vefleisgsellsk...............yvgesekkirelfke 52 
                 l G    GKT+l + +  e++   +e++++  ++ +                 ++++ ++ + e fk+
  AJA91972.1 188 LAGYTSAGKTTLFNNLTGETKeksAELFTTLTTTTR-RlklgreislitdtvgFISKLPAYMIEAFKS 254
                 677788899999999999986333333333222222.1224444444555455555555555555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.1   4.6e+03      59      76 ..     140     157 ..      82     171 .. 0.55
   2 ?   13.2   0.0   6.2e-05     0.069       1      37 [.     186     222 ..     186     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                 T-EB--CHHHHHHHHHHH CS
   Dynamin_N  59 ekkledfsevreeieket 76 
                     +d++++ + i+++ 
  AJA91972.1 140 GIGKYDIDAYYDDIKNRG 157
                 334455555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.2e-05
                 EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EE CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrple 37 
                 i + G +S+GK+++ n+L+ge    + +  tT ++++
  AJA91972.1 186 ISLAGYTSAGKTTLFNNLTGETKEKSAELFTTLTTTT 222
                 567899***************9777777777666654 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.046      39      84 ..      33     106 ..      13     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
      CHASE2  39 IDeeslaegrwpwsravlarllerLeaagakaiglDilfsepeey............................d 84 
                 I  ++l++ ++ ++ +++ +l e+Le+ ++ +i++D l++++++y                            +
  AJA91972.1  33 IKVDDLQKRKYGITESKVEELEEKLEKLKPDVIVFDELLKPNQNYslaaklkieivdreslileifenrassaE 106
                 444558765677999************************99997766555555555543333333333333332 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.3   0.00021      0.24      24      95 ..      41     112 ..      23     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
     DUF4200  24 rleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkse 95 
                 r+    +++ eele+k ++l+ d++ fd+ lk n++ +  a  k+e+  ++    e   +++ +  ++l+ +
  AJA91972.1  41 RKYGITESKVEELEEKLEKLKPDVIVFDELLKPNQNYSLAAKLKIEIVDRESLILEIFENRASSAESKLQVK 112
                 4445667899*******************************9999987776654443333333333333333 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   1.5e+03     102     125 ..      68      99 ..      38     118 .. 0.61
   2 ?    8.8   0.2   0.00098       1.1       3      26 ..     186     209 ..     184     216 .. 0.78
   3 ?    3.3   0.2      0.05        56      86     164 ..     233     320 ..     210     332 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                 T...SHHHHHCCCECEEEEEEETTTH...... CS
        cobW 102 t...eeelksdltldavvavvDaknl.....e 125
                     +++ + +l ++ ++ +vD + l     e
  AJA91972.1  68 DellKPNQNYSLAAKLKIEIVDRESLileifE 99 
                 33434445556666777777777666665442 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00098
                 EEEEESTTCCHHHHHHHHHCT--S CS
        cobW   3 tvltGflGsGKTtLlnhllenrag 26 
                 + l+G+  +GKTtL n+l+ ++++
  AJA91972.1 186 ISLAGYTSAGKTTLFNNLTGETKE 209
                 6799**************944433 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.05
                 EEEEECTTTT..HHHHHTT..SHHHHHCCCECEEEEEEETTTH........CCHCCHHHHHHHHHHTSSEE.EEE-HHHHCHC..HHHHHH CS
        cobW  86 iliEttGlae..Papvaft..eeelksdltldavvavvDaknl.......eaeeekieekaedqlaaadll.vlnKtDlldeealleklee 164
                 ++  t+G  +  Pa + ++  +++l++ +  d+++ v+D+  l       ++ ++  ++++e +++  +++ ++nK + +d+++ l+++++
  AJA91972.1 233 LITDTVGFISklPAYM-IEafKSTLEELIFTDIILLVIDS--LdddelmkKKFSTCYKTLVELGVERKNMIfLFNKSESIDDKKFLHVMNN 320
                 5677888444014444.33469999999999********9..4346666555566666777778887777625699999999866566654 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.57   6.4e+02     128     157 ..      31      60 ..       4     166 .. 0.70
   2 ?    7.8   1.9     0.002       2.2       6     144 ..     186     319 ..     183     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.57
                 EEESCGSTHHHHHHHHHHHHHHHHHHHHHH CS
    GTP_EFTU 128 fiNKmDrlkaelkeiveevkqklsrkeekl 157
                    K+D l+++   i e   ++l++k ekl
  AJA91972.1  31 YTIKVDDLQKRKYGITESKVEELEEKLEKL 60 
                 444888887776666666666665553322 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                 EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT CS
    GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdav 104
                 i+++g + +GKtTL  +L+ +t++ s    +  ++ ++ t+     r i+  + ++ +   +k   + +      + F + + + l  +D+ +lv+d+ 
  AJA91972.1 186 ISLAGYTSAGKTTLFNNLTGETKEKSA---ELFTTLTTTTRRLKLGREISLITDTVGFI--SKLPAYMI------EAFKS-TLEELIFTDIILLVIDSL 272
                 677888999*********977777665...33345566677777777777766666666..33333322......34433.334455666666666666 PP

                 TB...STHHHHHHHHHHHHTTTE...EEEEEESCGST.HHHHHHHHH CS
    GTP_EFTU 105 eG...vepqteevlrlalkegvp...iivfiNKmDrl.kaelkeive 144
                 ++   ++ +  +  + + ++gv+   +i++ NK   + ++++ ++ +
  AJA91972.1 273 DDdelMKKKFSTCYKTLVELGVErknMIFLFNKSESIdDKKFLHVMN 319
                 55555555555555555555555555666666666665555555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.013        14      29      73 ..      25      70 ..       2     120 .. 0.80
   2 ?    4.9   1.9     0.023        26       4      40 ..     185     220 ..     183     313 .. 0.59
   3 ?    1.4   0.8      0.27     3e+02      38      71 ..     272     303 ..     250     355 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
      AAA_14 29 kkesily.inldderdkkladpekllelileklkeekktylflDEi 73
                 + ++ly i++dd +++k+  +e+  e++ ekl++ k  ++++DE 
  AJA91972.1 25 AQYNVLYtIKVDDLQKRKYGITESKVEELEEKLEKLKPDVIVFDEL 70
                344555527999999999998887788888887777999******7 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldd 40 
                  + + G   +GKTtl ++l  e   +k+  l+ +l +
  AJA91972.1 185 TISLAGYTSAGKTTLFNNLTGETK-EKSAELFTTLTT 220
                 677889999**********98888.333333333333 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.27
      AAA_14  38 ldderdkkladpekllelilek.lkeekktylflD 71 
                 ldd+++  ++++++ ++ + e+ +  e+k+++fl 
  AJA91972.1 272 LDDDELM-KKKFSTCYKTLVELgV--ERKNMIFLF 303
                 3333332.3334455555555533..244444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2442.38
//
Query:       AJA91973.1  [L=322]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-16   58.2  10.8    4.5e-06   26.2   0.4    4.7  4  TPR_1            Tetratricopeptide repeat
      3e-12   45.6   6.5     0.0005   20.0   0.3    4.4  4  TPR_2            Tetratricopeptide repeat
    5.3e-09   35.8  10.8    0.00065   19.9   0.2    3.6  3  TPR_17           Tetratricopeptide repeat
      4e-08   32.8   5.2      0.051   13.8   0.1    4.7  4  TPR_8            Tetratricopeptide repeat
    4.9e-07   29.9   0.1    0.00042   20.5   0.1    3.0  2  TPR_12           Tetratricopeptide repeat
    7.3e-06   25.6   8.9      0.035   13.8   0.0    4.0  4  TPR_11           TPR repeat
    6.2e-05   23.1   0.0    0.00028   21.0   0.0    2.0  2  TPR_9            Tetratricopeptide repeat
     0.0003   21.4   0.0     0.0026   18.3   0.0    2.3  1  Peptidase_C39_2  Peptidase_C39 like family
    0.00046   20.8   0.0        4.2    8.4   0.0    3.4  3  TPR_14           Tetratricopeptide repeat
     0.0026   18.3   0.9        1.9    9.0   0.0    2.8  3  TPR_19           Tetratricopeptide repeat
     0.0048   16.8   0.8       0.22   11.7   0.0    3.3  3  TPR_7            Tetratricopeptide repeat
     0.0074   16.9   0.0        8.1    7.2   0.0    3.0  3  TPR_16           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.6   0.2       0.63   10.0   0.0    3.2  3  TPR_10           Tetratricopeptide repeat
      0.013   15.5   0.0      0.027   14.5   0.0    1.4  1  Peptidase_C70    Papain-like cysteine protease AvrRpt2


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00011      0.15      13      34 .]     186     207 ..     184     207 .. 0.88
   2 !    6.1   0.4     0.008        10      17      34 .]     223     240 ..     208     240 .. 0.80
   3 !   26.2   0.4   3.5e-09   4.5e-06       2      33 ..     242     273 ..     241     274 .. 0.94
   4 !   17.8   0.1   1.6e-06     0.002       3      30 ..     278     305 ..     277     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                 HTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  13 klgkydeAleyyekALelnPnn 34 
                  +++ +e  +  ekA+elnPnn
  AJA91973.1 186 LQKQTKETTDSLEKAIELNPNN 207
                 68888899999**********8 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.008
                 HHHHHHHHHHHHHHSTTH CS
       TPR_1  17 ydeAleyyekALelnPnn 34 
                   e++ yyek Le n+n+
  AJA91973.1 223 NPECVSYYEKSLEKNENC 240
                 458999*********996 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 3.5e-09
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                  a+ +lGn y+k++++d+ ++ y +A+e+n++
  AJA91973.1 242 LAYRGLGNFYLKNQEFDKSEKNYTRAIEINES 273
                 5999**************************85 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 1.6e-06
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALel 30 
                 +++n+G++ ++++k d+A ++y+  ++ 
  AJA91973.1 278 IYKNRGYVRQQQNKIDDAKQDYQNYIKF 305
                 69*********************98876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0051       6.5      23      34 .]     196     207 ..     187     207 .. 0.91
   2 ?    5.7   0.1     0.014        18      15      33 ..     221     239 ..     218     240 .. 0.85
   3 !   20.0   0.3   3.9e-07    0.0005       3      32 ..     243     272 ..     241     274 .. 0.94
   4 !   13.5   0.0   4.5e-05     0.058       3      33 ..     278     308 ..     277     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0051
       TPR_2  23 afekAleldPnn 34 
                  +ekA+el+Pnn
  AJA91973.1 196 SLEKAIELNPNN 207
                 689********8 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
       TPR_2  15 gdyeeAleafekAleldPn 33 
                 ++  e++ ++ek+le ++n
  AJA91973.1 221 QNNPECVSYYEKSLEKNEN 239
                 6778999*********998 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.9e-07
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                 a+  lG+ y+k++++++ ++ + +A+e+++
  AJA91973.1 243 AYRGLGNFYLKNQEFDKSEKNYTRAIEINE 272
                 899*************************96 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 4.5e-05
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                 ++ n+G++  ++++ ++A+++++  ++  Pn
  AJA91973.1 278 IYKNRGYVRQQQNKIDDAKQDYQNYIKFTPN 308
                 588***********************99998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   5.1e-07   0.00065       2      29 ..     197     224 ..     196     225 .. 0.91
   2 !   12.1   1.0   0.00015      0.19       1      33 [.     229     261 ..     229     262 .. 0.93
   3 !    9.3   0.0    0.0012       1.5       2      34 .]     264     297 ..     263     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.1e-07
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdl 29 
                 ++ka+el+Pnn+ a+++L+ +l +++++
  AJA91973.1 197 LEKAIELNPNNSTALCLLGGILNEQNNP 224
                 59*****************999988876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +y+k+le++ n   ay  L++++lkn ++++ +
  AJA91973.1 229 YYEKSLEKNENCYLAYRGLGNFYLKNQEFDKSE 261
                 6*************************9998866 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0012
      TPR_17   2 ylkaleld.PnnadaynnLAelllknGdlmtArq 34 
                 y++a+e++     + y n++++  ++++ ++A+q
  AJA91973.1 264 YTRAIEINeSRFGPIYKNRGYVRQQQNKIDDAKQ 297
                 99*****85669********************97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0064       8.2      22      34 .]     195     207 ..     185     207 .. 0.83
   2 ?    2.7   0.1      0.14   1.8e+02       5      29 ..     212     235 ..     208     240 .. 0.66
   3 !   13.8   0.1     4e-05     0.051       7      32 ..     247     272 ..     243     274 .. 0.93
   4 !    8.4   0.0    0.0022       2.8       4      33 ..     279     308 ..     276     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0064
                 HHHHHHHHHHHH. CS
       TPR_8  22 eyyekaleldpdn 34 
                  ++eka+el+p+n
  AJA91973.1 195 DSLEKAIELNPNN 207
                 689********97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                 HHHHHHHHHTT-HHHHHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                 ++lg i+ ++++  e ++yyek le
  AJA91973.1 212 CLLGGILNEQNNP-ECVSYYEKSLE 235
                 5555555555555.58999999998 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4e-05
                 HHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                 lg+ ylk ++++++++ y +a+e+++
  AJA91973.1 247 LGNFYLKNQEFDKSEKNYTRAIEINE 272
                 89**********************97 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0022
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                 y n g++ +++++++ Ak+ y+ +++  p+
  AJA91973.1 279 YKNRGYVRQQQNKIDDAKQDYQNYIKFTPN 308
                 55899********************99886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.017        21       4      31 ..     209     235 ..     206     241 .. 0.85
   2 !   20.5   0.1   3.3e-07   0.00042       5      69 ..     243     300 ..     239     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
      TPR_12   4 talnnlaavlrrlgrydeAlellekale 31 
                 tal  l+ +l+++ +  e+ +++ek+le
  AJA91973.1 209 TALCLLGGILNEQNN-PECVSYYEKSLE 235
                 677789999999999.9********998 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.3e-07
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69 
                 a++ l++++++ +++d++++++ +a+ei ++ +Gp       ++ n g + +++++ ++A + ++
  AJA91973.1 243 AYRGLGNFYLKNQEFDKSEKNYTRAIEINESRFGP-------IYKNRGYVRQQQNKIDDAKQDYQ 300
                 6778**************************99999.......88999999999999999988776 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.8e-05     0.035      16      36 ..     196     216 ..     187     222 .. 0.87
   2 ?    3.9   0.3     0.033        42      17      41 ..     230     254 ..     223     255 .. 0.91
   3 !    9.9   0.7   0.00046      0.59       1      41 [.     248     289 ..     248     290 .. 0.82
   4 !    5.8   0.8    0.0085        11       1      26 [.     283     308 ..     283     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
      TPR_11  16 aYkkAlkldPdnaeayynLGl 36 
                 +++kA++l+P+n +a++ LG 
  AJA91973.1 196 SLEKAIELNPNNSTALCLLGG 216
                 689****************95 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.033
      TPR_11  17 YkkAlkldPdnaeayynLGlayykq 41 
                 Y+k l+ +++   ay +LG+ y+k+
  AJA91973.1 230 YEKSLEKNENCYLAYRGLGNFYLKN 254
                 9999999999999*********998 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00046
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnae.ayynLGlayykq 41 
                 G+ y + ++++++ ++Y +A++++++    +y n+G++ ++q
  AJA91973.1 248 GNFYLKNQEFDKSEKNYTRAIEINESRFGpIYKNRGYVRQQQ 289
                 8999********************987753666777766665 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0085
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPd 26 
                 G++  +q+k+++A ++Y++ +k++P+
  AJA91973.1 283 GYVRQQQNKIDDAKQDYQNYIKFTPN 308
                 566679*****************998 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.7   2.1e+03      49      65 ..     194     210 ..     189     214 .. 0.82
   2 !   21.0   0.0   2.2e-07   0.00028       4      73 .]     250     320 ..     247     320 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
       TPR_9  49 ladLeaylalapdapda 65 
                  + Le +++l+p++ +a
  AJA91973.1 194 TDSLEKAIELNPNNSTA 210
                 5789********99887 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.2e-07
       TPR_9   4 iaireedweralavverllllaPddpeerr.dRGlllaqlGclsaAladLeaylalapdapdaeairaqLn 73 
                  ++ ++++++  + + r + ++  + + ++  RG +++q++ +  A +d + y+  +p+a d+ +i+ +Ln
  AJA91973.1 250 FYLKNQEFDKSEKNYTRAIEINESRFGPIYkNRGYVRQQQNKIDDAKQDYQNYIKFTPNAKDRGMIERALN 320
                 67788888888888888888888888776538***********************************9997 PP

>> Peptidase_C39_2  Peptidase_C39 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     2e-06    0.0026      12     137 ..      17     117 ..       6     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
  Peptidase_C39_2  12 lpngCeptslamvlsylgkkvtqnelakelktnssgdpntgfvgnitdksglgvynepivklaekyglkvsdtrgssieevkkeidagkPvvvs 105
                      + n C p s+  v +y+++++  +e ++ + +++           ++   g+ +      +lae+ gl  s + +ssi e+k+ id g+P +v+
       AJA91973.1  17 NDNICLPLSINAVAKYWNIDLPISEANEIASKYA----------GMN---GSILIEG--INLAERHGL-SSLIIHSSIPELKQVIDMGIPPIVI 94 
                      8899***************977777655555554..........222...3333333..478999998.88999******************** PP

  Peptidase_C39_2 106 vttfkplndgeikftssgHlvvitGYdekgkr 137
                      +     +          +H+ +i+GYd+k+k+
       AJA91973.1  95 LP----G-----LHDVVQHASIISGYDDKEKT 117
                      *4....3.....45669***********9854 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0071       9.1      15      42 ..     188     215 ..     184     217 .. 0.86
   2 !    8.4   0.0    0.0033       4.2       3      32 ..     243     272 ..     241     276 .. 0.91
   3 ?    0.1   0.0       1.5     2e+03       8      33 ..     283     308 ..     278     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0071
      TPR_14  15 GdpdeAiallrralalaPddaeawllla 42 
                  +++e  + l++a++l+P++ +a+ ll+
  AJA91973.1 188 KQTKETTDSLEKAIELNPNNSTALCLLG 215
                 677778899**************99886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
      TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                 a++ l+ ++l ++++d++++ + ra++ + 
  AJA91973.1 243 AYRGLGNFYLKNQEFDKSEKNYTRAIEINE 272
                 6889**********************9875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.5
      TPR_14   8 aeallalGdpdeAiallrralalaPd 33 
                 + +  ++ + d+A + ++ +++  P+
  AJA91973.1 283 GYVRQQQNKIDDAKQDYQNYIKFTPN 308
                 5666678889*******999999886 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0085        11       6      42 ..     189     225 ..     186     225 .. 0.85
   2 !    9.0   0.0    0.0015       1.9      12      46 ..     228     262 ..     227     273 .. 0.88
   3 ?   -2.4   0.1       5.6   7.1e+03      37      46 ..     288     297 ..     287     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqld 42 
                 +  e  + le+a++ +p+n+ a+ lL  +l ++++++
  AJA91973.1 189 QTKETTDSLEKAIELNPNNSTALCLLGGILNEQNNPE 225
                 556666779*****************99999999875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
      TPR_19  12 alleqalqedpknaearllLAeallalgqldeAea 46 
                 +++e+ l+++ +   a  +L + +l++ ++d+ e+
  AJA91973.1 228 SYYEKSLEKNENCYLAYRGLGNFYLKNQEFDKSEK 262
                 689****************************9887 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.6
      TPR_19  37 algqldeAea 46 
                 +++ +d+A++
  AJA91973.1 288 QQNKIDDAKQ 297
                 5677777765 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.23     3e+02      19      27 ..     227     235 ..     210     240 .. 0.63
   2 !   11.7   0.0   0.00017      0.22       2      34 ..     244     276 ..     243     278 .. 0.88
   3 ?   -2.0   0.1         4   5.1e+03       4      21 ..     281     298 ..     279     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
       TPR_7  19 ielyeqsLa 27 
                 +++ye+sL+
  AJA91973.1 227 VSYYEKSLE 235
                 789999664 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00017
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                 +  L++ y + +++++ ++ y++++++ ++ ++
  AJA91973.1 244 YRGLGNFYLKNQEFDKSEKNYTRAIEINESRFG 276
                 6679*******************9998888776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4
       TPR_7   4 nLarlysrlGdyeeAiel 21 
                 n + +++++++ ++A + 
  AJA91973.1 281 NRGYVRQQQNKIDDAKQD 298
                 677888999999988655 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.72   9.3e+02      20      50 ..     197     224 ..     195     225 .. 0.88
   2 !    7.2   0.0    0.0064       8.1      19      62 ..     229     269 ..     227     274 .. 0.81
   3 ?    5.0   0.0     0.031        40       3      25 ..     282     304 ..     280     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.72
      TPR_16  20 leaalkrdpssPdaaeAllllgdaalrqgrl 50 
                 le a++++   P +  Al llg ++ +q++ 
  AJA91973.1 197 LEKAIELN---PNNSTALCLLGGILNEQNNP 224
                 78999***...************99999875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0064
      TPR_16  19 aleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                 ++e  l+++     ++ A+ +lg+ +l+++++++ +  y +a++
  AJA91973.1 229 YYEKSLEKN---ENCYLAYRGLGNFYLKNQEFDKSEKNYTRAIE 269
                 577788888...88999999999999999999999877777764 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.031
      TPR_16   3 laraalragdyddAaaaleaalk 25 
                 +++ + ++++ ddA   ++ ++k
  AJA91973.1 282 RGYVRQQQNKIDDAKQDYQNYIK 304
                 688999*************9998 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.9   1.1e+03      18      30 ..     223     235 ..     209     238 .. 0.65
   2 ?   10.0   0.0    0.0005      0.63       5      38 ..     244     277 ..     242     281 .. 0.92
   3 ?    1.3   0.1      0.28   3.5e+02       7      26 ..     281     300 ..     278     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.9
      TPR_10  18 ydeAealleeala 30 
                   e + ++e++l+
  AJA91973.1 223 NPECVSYYEKSLE 235
                 4566667777765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0005
      TPR_10   5 lnNLanalrqrgrydeAealleealairrrllGp 38 
                 +  L+n + + +++d++e+ + +a++i +  +Gp
  AJA91973.1 244 YRGLGNFYLKNQEFDKSEKNYTRAIEINESRFGP 277
                 667*************************999986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.28
      TPR_10   7 NLanalrqrgrydeAealle 26 
                 N + + +q+++ d+A ++++
  AJA91973.1 281 NRGYVRQQQNKIDDAKQDYQ 300
                 5677779********99986 PP

>> Peptidase_C70  Papain-like cysteine protease AvrRpt2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.1e-05     0.027      16     131 ..      17     127 ..       6     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
  Peptidase_C70  16 aatgCwaaslsmiasyleqksidpselaalvdkwslmdeglngeekialaeklGlveevpeppqsyeieklvklLraggPlivaiaspgdvvgHvi 111
                    + + C + s++ +a y++   +  se+++   k ++  +g    e i+lae++Gl +++       +i +l ++++ g+P iv      dvv H++
     AJA91973.1  17 NDNICLPLSINAVAKYWN-IDLPISEANEIASK-YAGMNGSILIEGINLAERHGL-SSLIIHS---SIPELKQVIDMGIPPIVILPGLHDVVQHAS 106
                    568899999999999999.44555555555555.33344545678899*******.5555555...59************99999899999***** PP

  Peptidase_C70 112 VltGidedgavivh.DPesga 131
                    ++ G d   + i+h  Pe+++
     AJA91973.1 107 IISGYDDKEKTIFHyVPEQKP 127
                    *****9888855551366554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2187.43
//
Query:       AJA91974.1  [L=629]
Description: KH/beta-lactamase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-24   84.4   0.0    1.2e-23   83.5   0.0    1.4  1  Beta-Casp      Beta-Casp domain
    9.7e-21   73.5   1.1    2.3e-20   72.3   1.1    1.7  1  KH_7           KH domain
    8.3e-14   51.3   0.0    2.1e-13   50.0   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    5.2e-13   48.9   0.0    1.2e-12   47.7   0.0    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      6e-13   49.2   0.4    1.4e-11   44.7   0.4    2.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    3.6e-11   43.0   0.0      1e-10   41.4   0.0    1.8  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0028   17.6   0.0      0.018   15.0   0.1    2.3  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   4.5e-27   1.2e-23       1     109 [.     413     537 ..     413     538 .. 0.81

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 4.5e-27
                 HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...................E-SHH....HHHH..HH...............HS-SS CS
   Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae...................veakslewmeskkeeln...............sskgp 65 
                 aqel++++++++k+++   ++ p+++ + ++++at+++++++e                   +               +               ++++p
  AJA91974.1 413 AQELMMVIDKYMKSGQ--LIESPVFMEG-MIQEATAIHEAHPEylerslkqkiletddnpfdS---------------EyftniehadgrdeplREDTP 493
                 7************966..5678******.************9977777666666655555431...............0333444444555555779** PP

                 EEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
   Beta-Casp  66 kvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                 ++++a+sgmlegG++ e++++++++p+n +++v+yq++gTlgr+
  AJA91974.1 494 CIVIATSGMLEGGPVLEYFRNFAPNPKNKILFVSYQVNGTLGRR 537
                 ******************************************97 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   1.1     9e-24   2.3e-20       9      68 .]       2      61 ..       1      61 [. 0.97

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 9e-24
        KH_7  9 ekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                ++i +++Pk++++t++++EGP +++Yt+ p++++en+++i++l+++++kRiviR+D++++
  AJA91974.1  2 ATILTSIPKDANVTKIDYEGPRIALYTDKPRFLMENNEIISNLVNQIKKRIVIRTDEKIR 61
                57999****************************************************986 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   8.3e-17   2.1e-13       2      62 .]     557     620 ..     556     620 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 8.3e-17
       RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                 + +++  e+++ fSgH+d+n+l+ ++++l+p+   v ++HGe+++ + l +++++ + + +++P
  AJA91974.1 557 VTINCGTEKLEgFSGHSDYNQLMSYVQRLRPKLrrVLVNHGERRKSQNLSSAINRMYRVTTHYP 620
                 6799******************************99999**************99989999998 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   4.6e-16   1.2e-12       2     175 ..     190     358 ..     189     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 4.6e-16
  Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalk..elekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllg 94 
                    L+  + k+L+D+G++      ++a    ++ ++ ++++d+i++ ha l+h G +++l      k++ + p+y+t p+  + ++  ld+++ +g++g
     AJA91974.1 190 LTTPDSKVLIDCGVNPGARTPSEAYPrlDWANIsLDELDAIVIGHAHLDHTGFLPVLT-----KYGYRGPIYCTEPTLPMMNLIQLDAIKVAGAQG 280
                    666789*********76444444433114555448*****************655444.....57899************************9998 PP

  Lactamase_B_6  95 pedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGG..tiWkiskesekivYavdwnhakeshLngaal 175
                     + +      d+++++++ + l Y   ++++    ++ ++  naGh lG   + ++i ++ ++ vY  d+   k  +L++a++
     AJA91974.1 281 RTPMY--AERDVHQIMKQTIGLSYGTVTDISP---DIKLVLANAGHILGSasCHFHIGNGDHNFVYSGDIKYGKSMLLESADT 358
                    87654..679***************9999985...6888889*******7336899***************999999999865 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.4   5.6e-15   1.4e-11       3     162 ..     182     356 ..     180     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 5.6e-15
                  CCSSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH CS
  Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll 97 
                   ++ +++l++++++ +LiD+G+ + a    +   +l  + + ++++da+++ H+HlDH+G l+ l++     ++++ e +  + +    da    g+ 
   AJA91974.1 182 QVGRSCMLLTTPDSKVLIDCGVNPGARTPSEaypRLDWANISLDELDAIVIGHAHLDHTGFLPVLTKYGYRGPIYCTEPTLPMMNLIQLDAIKVAGAQ 279
                  67889***********************999*********************************************************9999999999 PP

                  ............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
  Lactamase_B  98 ............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                               +    ++    +  + + +   ++  + ++ g+ ++h+++++g+ +++++GD  +  + ++ + 
   AJA91974.1 280 grtpmyaerdvhQIMKQTIGLSYGTVTDISPDIKLVLANAGHILGSASCHFHIGNGDHNFVYSGDIKYGKSMLLESA 356
                  *******9998844444445555555555555566778889999*********************999776666555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   4.1e-14     1e-10       3     167 ..     197     373 ..     195     392 .. 0.69
   2 ?   -3.2   0.0       1.9   4.9e+03     158     194 ..     555     588 ..     547     595 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.1e-14
                    EEES--TT..HHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.....HCCTTCGHHHCHTT...TTEEE CS
  Lactamase_B_2   3 iLiDagpd..lrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.....vleanfvylaleee...pavnv 87 
                    +LiD+g +   r + + a  +   +  +l+++da+++ haH DH+  l+ l + ++ + p+y+++ +l      +l+a  v+ a+++    ++ +v
     AJA91974.1 197 VLIDCGVNpgARTP-SEAYPRLDwANISLDELDAIVIGHAHLDHTGFLPVLTK-YGYRGPIYCTEPTLPmmnliQLDAIKVAGAQGRTpmyAERDV 290
                    9*****99767777.44444445888999****************66666666.44558*****99999666663333333333333355544444 PP

                    EEE-.......TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---....HHHHHHHCT-SEEEEE-S-S CS
  Lactamase_B_2  88 held.......wgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip....eeigerlggadllllditay 167
                    h++         g+ +++  ++  i+++ a+ ++        +  + + i++g+++++y+gD +y +    e++++r+  ++ ll++ t+ 
     AJA91974.1 291 HQIMkqtiglsYGTVTDIS-PD--IKLVLANAGHIL-----GSASCHFHIGNGDHNFVYSGDIKYGKsmllESADTRFPRVETLLVESTYG 373
                    4444333333355555555.46..566666666666.....448999********************777667779999999999998854 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                    SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSS CS
  Lactamase_B_2 158 dllllditayeddemirhmgHltpeeaveaaadlgak 194
                    +++ ++++  + +      gH++ ++ +  +++l++k
     AJA91974.1 555 EVVTINCGTEKLEG---FSGHSDYNQLMSYVQRLRPK 588
                    55555555333333...46999999999999999876 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   6.8e-06     0.018       5      50 ..     183     240 ..     182     369 .. 0.74
   2 ?   -2.4   0.0       1.5   3.9e+03     129     158 ..     554     589 ..     550     589 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
  Lactamase_B_3   5 lghnsflletagarilvDPfkanlgyeppa.............eeaDlvlisqaledHa 50 
                    +g +++ll+t++ ++l+D +  n g + p              +e D+++i +a+ dH 
     AJA91974.1 183 VGRSCMLLTTPDSKVLIDCGV-NPGARTPSeayprldwanislDELDAIVIGHAHLDHT 240
                    589***************884.333333334466788889999***************7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
  Lactamase_B_3 129 vDvvltPvgg......pltlgqeealelakrLkpkl 158
                    v+vv ++ g       +  ++ ++ + +++rL+pkl
     AJA91974.1 554 VEVVTINCGTeklegfSGHSDYNQLMSYVQRLRPKL 589
                    666666666655655545678889999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4318.09
//
Query:       AJA91975.1  [L=425]
Description: glutamate-1-semialdehyde-2,1-aminomutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-71  240.4   0.0    3.6e-71  240.0   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    9.3e-07   28.3   0.0    1.2e-06   28.0   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.0   0.0     4e-75   3.6e-71       9     383 ..      29     399 ..      22     414 .. 0.92

  Alignments for each domain:
  == domain 1  score: 240.0 bits;  conditional E-value: 4e-75
                  SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHH CS
  Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKl 106
                   ++++++++G+ l+d+dg++++D+  ++ +++lGh   +++ av++q++k ++     + ++  ++l++ +++ +p  + kv ++n+G+eA++tA++l
   AJA91975.1  29 YPFFVKRSQGSSLWDEDGNQFVDFCNGYGALLLGHTRKEIITAVSNQMKKGTLYT---TPTALEIELSKLIINNFPS-MKKVRTMNTGAEATMTAIRL 122
                  4699***********************************************8888...777788899999******9.******************** PP

                  HHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHH..CHTCCCEEEEEE-SCE CS
  Aminotran_3 107 arkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleeleale..kkkkdevaAvivEpiq 202
                  ar        t+k+kii+f+g++HG   + l  +gs    ++++  +  +   +  + + v+++n+         + +le    k+++va++ivEp+ 
   AJA91975.1 123 ARG------FTKKKKIIKFEGCYHGAYDTVLVKAGS-GSAHNGISISDGGLDEVSRN-TLVVPYND---------IDELEktLSKNKDVAGLIVEPVL 203
                  ***......***************************.99999*****9******999.6999***9.........555554357899*********** PP

                  TTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-H CS
  Aminotran_3 203 gegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnp 295
                  +++G v ++++fl+ lr+++++ d+ li+DEv  Gf  +  G   A +++g++pD++tl+Kal++G+++sav +++e+m+ l+p++   ++sT++Gnp
   AJA91975.1 204 ANMGLVLPEKNFLKDLRKITNQFDIPLIFDEVVNGFriSEGG---AQQKFGIKPDITTLGKALGNGFTISAVGGKNEIMNLLSPDGkvyQASTYAGNP 298
                  ************************************767777...***************************************99999********* PP

                  HHHHHHHHHHHHHHH..TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE-EEETT CS
  Aminotran_3 296 lacavalavleiiee..ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvlilsaGd 379
                  +  a+a+ ++++i++  +kl  + ++  +++ ++  +l+ +y+  +++ +   m+ i ++ +++v +            ++++++++++G+ + ++  
   AJA91975.1 299 ISVAAAISSIKTINKikNKLYPKLERYCKIMVDEIDDLATDYKIPHTINSIASMFQI-FFTNQKVIDyktskksstkkfHKLFTNLLKNGIFTAPSQY 395
                  *************99889***************************************.6666665556888999999998899999999999888776 PP

                  TEEE CS
  Aminotran_3 380 nvir 383
                  +++ 
   AJA91975.1 396 ETVF 399
                  6665 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.3e-10   1.2e-06     108     339 ..     157     397 ..      57     415 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.3e-10
                    HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HH.HHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHH CS
  Aminotran_1_2 108 nilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatle.eleklldlakkynlllfvDeaYagfvfgsldava 202
                    n++ +s+g + +++ +      +d+++le+ l+++    k + +++ve +  + G v++++  l++l +++++  + l++De+  gf   + +a++
     AJA91975.1 157 NGISISDGGLDEVSRNTLVVPYNDIDELEKTLSKN----KDVAGLIVEPVLANMGLVLPEKnFLKDLRKITNQFDIPLIFDEVVNGFRISEGGAQQ 248
                    55555555555555444444468**********93....3568************998865268999999*******************9888877 PP

                    HHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHS. CS
  Aminotran_1_2 203 tranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLael. 295
                      +++++++      +l+Ka+G  G+ + ++ g+ ++ + l      +   + ++ ++ +aa+  + ++++   ++   +l++  k ++de+++l 
     AJA91975.1 249 -KFGIKPDIT-----TLGKALG-NGFTISAVGGKNEIMNLLSPDGKVYQAsTYAGNPISVAAAISSIKTINkIKNKLYPKLERYCKIMVDEIDDLa 337
                    .999999988.....*******.7****************999999998856667888888888888888734456778999999*******999* PP

                    ...TEEEECCS.CSSEEEEEETHH.............CHHHHHHHHHHTCTEEEEEGGGGT CS
  Aminotran_1_2 296 ...glkvlasq.sgmflltdlsae.............takelskkLleevgvyvtpgtsft 339
                        ++++++  + mf +  ++++             + ++l+  Ll++ g+   p ++ t
     AJA91975.1 338 tdyKIPHTINSiASMFQIFFTNQKvidyktskksstkKFHKLFTNLLKN-GIFTAPSQYET 397
                    *9*********89999999999999999976665444444444448888.88777755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2771.43
//
Query:       AJA91976.1  [L=142]
Description: hypothetical protein T478_1489 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.6   0.3      0.035   14.0   0.3    1.3  1  DUF86     Protein of unknown function DUF86
      0.026   14.6   0.5        0.1   12.7   0.5    1.8  1  ENTH      ENTH domain
      0.048   13.8   0.3      0.077   13.1   0.3    1.4  1  DUF4145   Domain of unknown function (DUF4145)


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   5.8e-06     0.035      27      92 ..      32      95 ..      12     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC.HHHHHHHTTSS-HHHHHHHHHHHCCHHHHHT- CS
       DUF86 27 ydavernlqvigEaaidiakhlakklgikkpgdy.ifeilaekgviaeepeepwrkmiglRNrLvHg 92
                +  +er l+ i E  ++i ++++++   +++  y  f il+++g ++ + +++ r +++ RNr  H+
  AJA91976.1 32 QVCIERILEKILEKKFNIHADVLDD---GQFMWYqKFLILEKSGKLKGNVKKNARLINQIRNRFSHR 95
                55699****************8887...78888889****************************997 PP

>> ENTH  ENTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.7e-05       0.1      15     110 ..       6     109 ..       3     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                 SSSS--HHHHHHHHHHTTSHHHHHHHHHHHHHHH.......HH--GGGHHHHHHHHHHHHHHHHHS-HHHHHHHHHTHHHHHGG.GG---.B-TTS-B- CS
        ENTH  15 dpwGpsnkllteiarltyskkelseiisvitkrL.......qnnkgkewrsvlKaLtlieYLlknGseqvidwlkenisiiktl.sefky.ideegkde 104
                  +w ps+k+l++i ++ +s +el  + +v  +r+       + n +  ++     +   ++L+ + s +   ++k+n  +i+++ ++f++ +++++k  
  AJA91976.1   6 AKWAPSKKELEKILEADNS-HELFLVGQVCIERIlekilekKFNIHADVLDDGQFMWYQKFLILEKSGKLKGNVKKNARLINQIrNRFSHrLKPDEKAI 103
                 58**************999.8999999988888866665533355555555566888899999999999999999999999999889999888888888 PP

                 HHHHHH CS
        ENTH 105 glniRk 110
                  ++iR+
  AJA91976.1 104 ENQIRE 109
                 888997 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.3e-05     0.077      20      78 ..      37     101 ..      13     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
     DUF4145  20 raLEkllkdkgiakgkdL.......knkiealvekgvipeklkelldairviGNdgaHelkditke 78 
                 r+LEk+l +k  ++   L       ++k   l + g ++ ++k++++ i  i+N+ +H+lk   ++
  AJA91976.1  37 RILEKILEKKFNIHADVLddgqfmwYQKFLILEKSGKLKGNVKKNARLINQIRNRFSHRLK-PDEK 101
                 788888888886665545666667799999999*************************954.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1035.01
//
Query:       AJA91977.1  [L=44]
Description: hypothetical protein T478_1103 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 327.63
//
Query:       AJA91978.1  [L=94]
Description: hypothetical protein T478_0852 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   12.8   0.0      0.065   12.5   0.0    1.1  1  7tm_1     7 transmembrane receptor (rhodopsin family)


Domain annotation for each model (and alignments):
>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.6e-06     0.065      16      43 ..       7      34 ..       4      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-06
                CSHHHHHHHHHHHHHHHHHHHCHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       7tm_1 16 rtstnyfilsLaiaDlllgllvlpfaiv 43
                ++++ +f+ sLa+a ++lg+lv pf+  
  AJA91978.1  7 QKYAIVFLGSLAVAGIILGTLVFPFWNF 34
                667789********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 710.23
//
Query:       AJA91979.1  [L=46]
Description: hypothetical protein T478_0591 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       174  (0.00970495); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 365.79
//
Query:       AJA91980.1  [L=109]
Description: hypothetical protein T478_0312 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.018   14.9   0.1       0.19   11.5   0.0    2.0  2  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.013   2.4e+02     132     163 ..       8      39 ..       5      43 .. 0.78
   2 ?   11.5   0.0   1.1e-05      0.19     141     165 ..      61      85 ..      58      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.013
                     HHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HH CS
  DNA_pol3_delta 132 kkwiqkraqelglkiekealelLlelvennls 163
                      +++q+ +qel++ ++++ l++ ++++ ++++
      AJA91980.1   8 LQKLQNDVQELQKGLQPDHLSFWYQKIISDTK 39 
                     57889999999999999999888887766665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.1e-05
                     HTT-EE-HHHHHHHHHHHTT-HHHH CS
  DNA_pol3_delta 141 elglkiekealelLlelvennlsai 165
                     + +l+i+k a+ +++++vennls++
      AJA91980.1  61 KFNLDISKRAVRYFIIAVENNLSQM 85 
                     579*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 785.75
//
Query:       AJA91981.1  [L=94]
Description: hypothetical protein T478_0817 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.3   0.2       0.15   11.9   0.2    1.7  1  PetG      Cytochrome B6-F complex subunit 5


Domain annotation for each model (and alignments):
>> PetG  Cytochrome B6-F complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   8.3e-06      0.15      10      33 ..      45      68 ..      43      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-06
        PetG 10 VLGLvpVTlaGLFvaAYlQYkRgn 33
                V GL++  ++GL vaA  Q k gn
  AJA91981.1 45 VFGLIMGQILGLGVAALAQMKGGN 68
                99******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 722.63
//
Query:       AJA91982.1  [L=272]
Description: aspartate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-32  109.8   0.1    1.4e-31  108.7   0.1    1.6  1  DUF108         Domain of unknown function DUF108
    1.4e-14   54.7   0.1    2.5e-14   53.9   0.1    1.4  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
    0.00011   22.3   0.0    0.00023   21.3   0.0    1.6  1  DapB_N         Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.012   16.4   0.0      0.051   14.4   0.0    2.0  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
      0.024   15.2   0.1       0.06   13.9   0.1    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
       0.14   12.2   0.0       0.25   11.3   0.0    1.6  1  ADH_zinc_N     Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> DUF108  Domain of unknown function DUF108
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.1   4.7e-35   1.4e-31       2      89 .]     170     257 ..     169     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 4.7e-35
                 SS-EEEEEEEHHHHHHHSTTS-CHHHHHHHHHH.CCGEEEEEEEETT-SSEEEEEEEEETTEEEEEEEEE-EETTEEEEEHHHHHHHH CS
      DUF108   2 teptvlFeGsareaikkfPknvNvaaalaLaalgfdrvkvelvadpnldkniheieveGsfgefslevenkpspenPktsalaalsvi 89 
                 +ep ++FeG+a+ea+++fPkn+Nv+a l++ +lg +++ v+++adpn +kn+hei+++G+fg++++++en+p+++nP+ts la ls+i
  AJA91982.1 170 NEPSTIFEGTASEAVRLFPKNINVSALLSISGLGSHETIVKIIADPNTTKNTHEITARGKFGQITTKIENVPDSDNPRTSRLAILSAI 257
                 799**********************************************************************************986 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   8.4e-18   2.5e-14       1     117 []       8     122 ..       8     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.4e-18
                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHHHTTEEEE-S--CGGG- CS
  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaLkagkdvvtankgalad 96 
                    G+G iG++++ +++ +   i+++l  + d+d+++s   +++l+++++  +   l++   +d+vVE+as++av + +l++L++ kd+v+++ gal d
     AJA91982.1   8 GCGSIGTQIAIAIDTGI--IPAKLTHIFDEDKEKSVSLASKLKNKPEIVENVHLLSSNPVDLVVEAASQDAVSDNALSILQNRKDLVIMSSGALLD 101
                    9************9999..5***********8888889999999998888888888788************************************* PP

                    HHHHHHHTSSSTTS--.EE-G CS
  NAD_binding_3  97 ealyeeLreaaeangakiyve 117
                    e  +e + +a ++ ++++y++
     AJA91982.1 102 ESVFEIISDACKELKKTVYLP 122
                    **********99999999986 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.8e-08   0.00023       2     116 ..       3     116 ..       2     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.8e-08
                 EEEEETTTSHHHHHHHHHHHH.STTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEEEE-S-HHHHHHHHHHHHHTT-EEEE-- CS
      DapB_N   2 kvavvGasGrmGkevvkavee.aedlelvaavdrkeselegkdagellglgklgvavtddleevlek.advliDFTtpeavlenlklalekgvklViGT 98 
                 +++++G+ G +G++++ a+++    ++l+  +d+++     ++  +l+++ k++ ++ ++++ +  + +d +++  + +av +n+  +l+++++lVi +
  AJA91982.1   3 RIGLLGC-GSIGTQIAIAIDTgIIPAKLTHIFDEDK-----EKSVSLASKLKNKPEIVENVHLLSSNpVDLVVEAASQDAVSDNALSILQNRKDLVIMS 95 
                 799****.***********99557899999999998.....455567777799999999999999999******************************* PP

                 SS-..-HHHHHHHHHHTTT.S CS
      DapB_N  99 TGl..seeelaeleelakk.i 116
                  G   +e+  + +++++k+  
  AJA91982.1  96 SGAllDESVFEIISDACKElK 116
                 997668888888888888754 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.051       2      89 ..       3      91 ..       2      94 .. 0.85
   2 ?   -1.6   0.0       1.5   4.6e+03      43      81 ..     188     225 ..     169     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                  EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE..EESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EE CS
  GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve..aysdleelladpeidavivatpngtheelakaaleagkhv 89
                  r+++ G+G ig++ + ++      +++++++d+d+e++  +a +++ +   ++++  l+++p +d+v+ a   +   + a+ +l++ k++
    AJA91982.1  3 RIGLLGCGSIGTQIAIAIDTGIIPAKLTHIFDEDKEKSVSLASKLKNKpeIVENVHLLSSNP-VDLVVEAASQDAVSDNALSILQNRKDL 91
                  89************99999999999****************999999987888888888877.999988888888888888888877765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                   HHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHH CS
  GFO_IDH_MocA  43 aesfgveaysdleelladpeidavivatpngtheelaka 81 
                    ++ +v+a  +++ l +++   + i+a pn+t + +++ 
    AJA91982.1 188 PKNINVSALLSISGLGSHE-TIVKIIADPNTTKNTHEIT 225
                   5555555555555555544.3345677778777777765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     2e-05      0.06       1      74 [.       3      77 ..       3      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedv 74
                   +ig++G+G++g  +a  ++ +g  p +++ + + ++ek  +la++l+ k + v+n  +++    d vv a    +v
     AJA91982.1  3 RIGLLGCGSIGTQIAI-AIDTGIIPAKLTHIFDEDKEKSVSLASKLKNKPEIVENVHLLSsnPVDLVVEAASQDAV 77
                   79*************9.99999*888888899***************99999999888873334555555555555 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.3e-05      0.25      42      90 ..      48      96 ..       8     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.3e-05
                TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC CS
  ADH_zinc_N 42 kea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGg 90
                k++ ++ve ++ l   ++vd+v+e++ + a+ ++al++l+ +  lv++  
  AJA91982.1 48 KNKpEIVENVHLLS-SNPVDLVVEAASQDAVSDNALSILQNRKDLVIMSS 96
                55567899999888.89***********************9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2154.37
//
Query:       AJA91983.1  [L=237]
Description: N-acetylglucosaminylphosphatidylinositol deacetylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-30  106.2   0.0    2.4e-30  105.8   0.0    1.2  1  PIG-L            GlcNAc-PI de-N-acetylase
  ------ inclusion threshold ------
      0.033   13.7   0.1      0.094   12.2   0.0    1.8  1  QueC             Queuosine biosynthesis protein QueC
      0.053   13.5   0.5       0.55   10.3   0.1    2.2  2  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.22   11.7   0.6        2.8    8.2   0.0    2.7  3  DUF3782          Protein of unknown function (DUF3782)
       0.27   10.9   4.4       0.44   10.2   4.4    1.4  1  SpoIISA_toxin    Toxin SpoIISA, type II toxin-antitoxin syste


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   6.7e-34   2.4e-30       1     130 [.       4     143 ..       4     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 6.7e-34
                 EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH.............-HHHHHHHHHHHHHHHHCTE..EEEEECCCBTT-STTS CS
       PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleek.............eelaeiRekEaraaakhlgvadedvffldfpDgslesy 86 
                 l+++AHpDDe+l++ggti+kl++++++vkiv++ +G a++++ + ++              ++  e+ +k a++aak+lgv  +d++fl++pD++++++
  AJA91983.1   4 LIIVAHPDDEVLGMGGTIKKLTKNKNQVKIVIMATGVAARRSINFKNSsnyditenqqkiiKKQIETIKKHAQKAAKILGV--SDIEFLGYPDNEMDTV 100
                 79**********************************666555555555556666666777744444468899999******..**************** PP

                 -CHHHHHHHHHHHHHH--SEEEEE-TTTTH-HHHHHHHHHHHHH CS
       PIG-L  87 dedellddlaklieryrPdvvltldpegddhpDHtavasaavaa 130
                 ++ el++ ++k+i++y+P++v+t+ p +  ++DH+++++a+ +a
  AJA91983.1 101 SNLELTKSVEKIIQNYKPEIVYTHTPFDV-NVDHVSCYNAVLTA 143
                 *****************************.**********9987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.6e-05     0.094     117     147 ..      80     110 ..      68     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                 EEE---S-STT--GGGSHHHHHHHHHHHHHH CS
        QueC 117 iiiGvneedfsgYPDcrdefvkalnkalnlg 147
                  i+Gv+  +f gYPD+++++v++l+ + ++ 
  AJA91983.1  80 KILGVSDIEFLGYPDNEMDTVSNLELTKSVE 110
                 468******************9998776655 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.064   2.3e+02      17      45 ..      21      46 ..       2      83 .. 0.48
   2 ?   10.3   0.1   0.00015      0.55      37      88 ..      79     131 ..      67     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.064
  Glyco_trans_4_2 17 akeLakrgyeVhvitpkkgakdeleaegi 45
                     +k+L k+  +V+++++ +g      +  i
       AJA91983.1 21 IKKLTKNKNQVKIVIMATGV---AARRSI 46
                     77788888888888775542...222222 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00015
  Glyco_trans_4_2  37 kdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahyakpygl 88 
                       ++l   +i++   +++  +++++l +  ++ k+i+  kP +v++h++ ++++
       AJA91983.1  79 AKILGVSDIEFLGYPDNEMDTVSNLELTkSVEKIIQNYKPEIVYTHTPFDVNV 131
                      4555566666666676666699999965499****************998875 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.1   1.1e+04      17      33 ..      21      37 ..      17      40 .. 0.65
   2 ?    0.4   0.2       0.2   7.1e+02       7      31 ..      58      82 ..      52      84 .. 0.71
   3 ?    8.2   0.0   0.00077       2.8      28      49 ..     207     228 ..     180     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.1
     DUF3782 17 leelekeieklertiga 33
                +++l+k+ ++++  i a
  AJA91983.1 21 IKKLTKNKNQVKIVIMA 37
                66677766776666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.2
     DUF3782  7 eeeeeetkedleelekeieklerti 31
                e++++ +k+++e ++k+ +k  +++
  AJA91983.1 58 ENQQKIIKKQIETIKKHAQKAAKIL 82
                4457778889998888877776655 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00077
     DUF3782  28 ertigaLGaRWGlvsEeafReg 49 
                  ++++++G RWG vs  ++ e+
  AJA91983.1 207 PKALQSIGNRWGTVSGFSVAEA 228
                 57899********997666665 PP

>> SpoIISA_toxin  Toxin SpoIISA, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.4   0.00012      0.44      66     178 ..      30     143 ..      19     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-EEEE......ESSHHHHHHHHHHHHHHHHHTTTSEE CS
  SpoIISA_toxin  66 ilaviiifiDlavlltpsikklgkaelekdiektikenekvlkanlrrvetftellqnesihvy....eeygskeayieglkkllksyadkfeisv 157
                    ++ ++i+++ +a   + ++k   +++++++ +k+ik+  +++k++ +++ +   +   e    y    ++  s  + +++++k++++y     i  
     AJA91983.1  30 QVKIVIMATGVAARRSINFKNSSNYDITENQQKIIKKQIETIKKHAQKAAKILGVSDIEFL-GYpdneMDTVSNLELTKSVEKIIQNYKPE--IVY 122
                    55566777788888999*******************************9988877555444.4469888899999*************655..888 PP

                    EEEE-SSHHHHHHHHTTSS-H CS
  SpoIISA_toxin 158 sivpfevkeekdelleaieqq 178
                      +pf+v+ +  + ++a+   
     AJA91983.1 123 THTPFDVNVDHVSCYNAVLTA 143
                    888888886666655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1514  (0.0844442); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1750.02
//
Query:       AJA91984.1  [L=199]
Description: hypothetical protein T478_0784 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1562.11
//
Query:       AJA91985.1  [L=197]
Description: hypothetical protein T478_1500 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00022   21.1   0.1    0.00052   19.9   0.1    1.7  1  HTH_Crp_2    Crp-like helix-turn-helix domain
    0.00031   20.6   0.0    0.00072   19.4   0.0    1.6  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0049   17.3   0.1     0.0079   16.7   0.1    1.3  1  HTH_27       Winged helix DNA-binding domain
     0.0074   16.2   0.0      0.013   15.3   0.0    1.5  1  MarR_2       MarR family
  ------ inclusion threshold ------
      0.027   14.7   0.8       0.05   13.8   0.5    1.5  1  DUF4330      Domain of unknown function (DUF4330)
      0.041   13.8   0.1      0.067   13.1   0.1    1.4  1  HTH_12       Ribonuclease R winged-helix domain
      0.084   12.8   1.3       0.15   11.9   1.3    1.4  1  MadM         Malonate/sodium symporter MadM subunit
      0.091   12.4   0.0        0.2   11.3   0.0    1.6  1  Crp          Bacterial regulatory proteins, crp family
      0.094   12.8   0.0       0.18   11.9   0.0    1.4  1  HTH_20       Helix-turn-helix domain
       0.11   12.5   0.0       0.22   11.6   0.0    1.5  1  S10_plectin  Plectin/S10 domain


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.9e-07   0.00052      31      54 ..     141     164 ..     125     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                 TTSSHHHHHHHHHHHHHTTSEEET CS
   HTH_Crp_2  31 lGltretvsrilseLkreglisrg 54 
                 lG +re++sr++++++++gl++r+
  AJA91985.1 141 LGKSREHISRTMKKMSDDGLVQRN 164
                 899*******************75 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     4e-07   0.00072      15      64 ..     124     174 ..     120     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4e-07
                 HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
        TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYra 64 
                 l L++  + t ++i   lg +r  + +++++++d GlV+r+   +p+ Y+ 
  AJA91985.1 124 LRLITDRSRTSRDIQITLGKSREHISRTMKKMSDDGLVQRNTnAKPYSYSI 174
                 567888999*******************************99445999975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.4e-06    0.0079       8      68 .]     123     178 ..     121     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-06
      HTH_27   8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                 vL+li   +r  + +d+  +l  +  his  +kk+   GLv+r+   ++ ++  +++T  G
  AJA91985.1 123 VLRLIT--DRSRTSRDIQITLGKSREHISRTMKKMSDDGLVQRN---TNAKPYSYSITQNG 178
                 899999..999999***************************888...77799999999766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.5e-06     0.013      10      56 ..     123     166 ..     110     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.5e-06
                 HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
      MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                 vL  + +r +   t +++  +lg s+  +sr+ k++++ GLv+r ++
  AJA91985.1 123 VLRLITDRSR---TSRDIQITLGKSREHISRTMKKMSDDGLVQRNTN 166
                 7777777875...9999999************************987 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   2.8e-05      0.05      14     114 ..       3     115 ..       2     146 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
     DUF4330  14 vnilDllail.vilavivgiflkpgts..gsvaqaeaaatkpve.........vdvvvrglevpeelakvkegektniiirnqPagdveikdvkvlprk 100
                 v i Dl +i  +ila i g+f+++++s  +s+++ ++++++  e         +d+ ++  +++ e ++  ++   ni+++ +   +v  k+v+v p +
  AJA91985.1   3 VEIPDLDVIFgLILAFIGGLFTLFVYSklKSISASNEQTKQDSErlefyerqlIDLKIKLDAIDLENLSFSQETPQNIVKNEEKPVQVVEKQVQVVPEQ 101
                 566799999999*********999888566665555544444447889989999999999999777777545555555553333344444699999999 PP

     DUF4330 101 vvvpqpdGkvkale 114
                 v+vp++  +  +++
  AJA91985.1 102 VPVPARVERTPNMS 115
                 98866544444333 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.7e-05     0.067      33      66 .]     146     182 ..     121     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
      HTH_12  33 ravRyrLrkleergltrrvgya...greltEkGleeL 66 
                 + + + ++k+ ++gl++r+ +a      +t  Gl+ L
  AJA91985.1 146 EHISRTMKKMSDDGLVQRNTNAkpySYSITQNGLSRL 182
                 445789****************666678999999865 PP

>> MadM  Malonate/sodium symporter MadM subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.3   8.4e-05      0.15      45      59 .]      10      24 ..       8      24 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
        MadM 45 IllGLvlAYiGGvvT 59
                +++GL+lA+iGG++T
  AJA91985.1 10 VIFGLILAFIGGLFT 24
                699**********98 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011       0.2      12      31 ..     141     160 ..     136     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                 HTS-HHHHHHHHHHHHHTTS CS
         Crp  12 lGlTrETVSRlLtrLrekGL 31 
                 lG +rE +SR++++   +GL
  AJA91985.1 141 LGKSREHISRTMKKMSDDGL 160
                 899************99998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.8e-05      0.18      15      56 ..     123     163 ..     122     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.8e-05
                 HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20  15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56 
                 +lr++ +++ +t  ++  +l+ s+  +s+ ++++++ gLv +
  AJA91985.1 123 VLRLI-TDRSRTSRDIQITLGKSREHISRTMKKMSDDGLVQR 163
                 89999.9********************************976 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.22      39      88 ..     147     196 ..     120     197 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                  HHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHHHXXXXSXHHHH CS
  S10_plectin  39 qvikalqSLksrgyvkeqfaWrhyYytLtneGieylreylhlpeeivPat 88 
                  ++ ++++ +++ g+v+++ + + y y +t++G++ l      p++i P+t
   AJA91985.1 147 HISRTMKKMSDDGLVQRNTNAKPYSYSITQNGLSRLSGSGGTPQTIAPQT 196
                  67789*******************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1529.56
//
Query:       AJA91986.1  [L=57]
Description: hypothetical protein T478_0616 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 429.99
//
Query:       AJA91987.1  [L=707]
Description: MG2 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-18   66.7   0.0      4e-05   24.0   0.0    5.2  5  MG2         MG2 domain
    1.5e-06   27.9   6.6       0.45   10.4   0.0    6.3  6  FlgD_ig     FlgD Ig-like domain
    0.00018   21.7   1.1        1.2    9.4   0.0    5.2  5  Gmad2       Immunoglobulin-like domain of bacterial spore ger
    0.00043   20.5   7.8       0.35   11.2   0.1    5.6  6  Big_6       Bacterial Ig domain
  ------ inclusion threshold ------
        1.1    9.3   6.1        7.2    6.7   0.2    5.1  6  Big_1       Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.23   8.2e+02      28      88 ..     273     332 ..     264     338 .. 0.78
   2 !   16.2   0.0     3e-06     0.011      28      93 ..     363     425 ..     357     428 .. 0.86
   3 ?   -1.5   0.0      0.98   3.5e+03      44      85 ..     485     508 ..     451     519 .. 0.53
   4 !   18.3   0.0   6.5e-07    0.0023      36      95 ..     556     613 ..     530     621 .. 0.86
   5 !   24.0   0.0   1.1e-08     4e-05      33      95 ..     645     705 ..     616     706 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                 CSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT- CS
         MG2  28 lqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaees 88 
                 + + +++ l++t +d +g+     +++ + +g   ++  ++ +  lG  s+e+ +d+++++
  AJA91987.1 273 GMATPNTTLTITSKDNNGNILAIDTIQVRFDGKWTYDNLISPELDLGMISIEI-DDGKGKA 332
                 45566789999999999999999999888888899999999999999999999.5555544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3e-06
                 CSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEEE CS
         MG2  28 lqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeeslssgs 93 
                 +++++++++++ i+d+ + e+++ ++   e+g++++++++p+++  G+y +++    ++++++ ++
  AJA91987.1 363 GTAIPNQEMSIIIEDAINTEIFSRTVSVGESGLVNFNVEIPRGSVEGTYILSA---FQGNESGITT 425
                 5678899*********************************************9...4555544444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.98
                 TSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECST CS
         MG2  44 dgkevkelplatdetggaesefalpeaaklGeysvelsadsa 85 
                 dgkev++ + ++                + G++++++   ++
  AJA91987.1 485 DGKEVYKIKSND---------------LPNGSFTLNA---KR 508
                 333333333333...............4556666665...44 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 6.5e-07
                 EEEEEE-TTSSEEEEEEEEE-CTTEEEE.EEE--TT--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2  36 lkltirdpdgkevkelplatdetggaes.efalpeaaklGeysvelsadsaeeslssgsfr 95 
                 l +ti+d++gk +k+ +  +d +g++++ +f++p +a  G+++v++   + +++    +f+
  AJA91987.1 556 LDITISDSNGKIIKKIETFSDRFGVFKVdNFRIPLDATVGKWNVNA---KSGGNFKDVEFS 613
                 679**********************87626****************...555555555555 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 1.1e-08
                 -.EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECSTTT-EEEEEEE CS
         MG2  33 k.lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsaeeslssgsfr 95 
                   + ++++i d++g +++el ++++++g + + +++p++ + Gey++++   +++ s +s++f 
  AJA91987.1 645 LsATVTIKIFDSEGIKIDELNITAKSNGEYLTMWQIPADLESGEYEMTA---DDGASNTSTKFT 705
                 24689********************************************...777777777775 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.086   3.1e+02      12      37 ..     267     293 ..     257     308 .. 0.75
   2 ?   -0.6   0.0      0.35   1.2e+03      26      42 ..     322     338 ..     313     342 .. 0.86
   3 !    6.3   0.1    0.0024       8.6       8      53 ..     353     399 ..     347     411 .. 0.88
   4 ?   -0.2   0.0      0.26   9.4e+02      33      53 ..     485     505 ..     477     525 .. 0.84
   5 !    6.0   0.0    0.0029        10      26      50 ..     557     581 ..     534     584 .. 0.80
   6 !   10.4   0.0   0.00013      0.45      21      73 ..     645     693 ..     627     698 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.086
                 EEEEEE..ESSSEEEEEEEE-SS--EE CS
     FlgD_ig  12 aplgve.lpeaadevtvtikDasGevV 37 
                 + ++++ ++++ +++t+t kD +G++ 
  AJA91987.1 267 DVITLDgMATPNTTLTITSKDNNGNIL 293
                 456677788899999999999999975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.35
                 EEEEE-SS--EEEEEEE CS
     FlgD_ig  26 tvtikDasGevVrtidl 42 
                 +++i D++G+  r++++
  AJA91987.1 322 SIEIDDGKGKALRNVEV 338
                 799********999876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0024
                 SS--EEEEEE..ESSSEEEEEEEE-SS--EEEEEEEEESSSEEEEEE CS
     FlgD_ig   8 gdgeaplgve.lpeaadevtvtikDasGevVrtidlgaqsaGvvsft 53 
                  ++++++++e  + + +e ++ i+Da ++++ + ++   ++G v+f+
  AJA91987.1 353 IEAGESITFEgTAIPNQEMSIIIEDAINTEIFSRTVSVGESGLVNFN 399
                 57778999**99*******************8888888899999987 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.26
                 S--EEEEEEEEESSSEEEEEE CS
     FlgD_ig  33 sGevVrtidlgaqsaGvvsft 53 
                  G++V++i+  + + G+++++
  AJA91987.1 485 DGKEVYKIKSNDLPNGSFTLN 505
                 588899999999998888765 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.0029
                 EEEEE-SS--EEEEEEEEESSSEEE CS
     FlgD_ig  26 tvtikDasGevVrtidlgaqsaGvv 50 
                  +ti D++G+++++i+  +   Gv+
  AJA91987.1 557 DITISDSNGKIIKKIETFSDRFGVF 581
                 89*************9766666655 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.00013
                 SSEEEEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEEE CS
     FlgD_ig  21 aadevtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvkv 73 
                  + +vt++i D++G  ++ ++ +a+s G++   W    +    l++G+Y  ++
  AJA91987.1 645 LSATVTIKIFDSEGIKIDELNITAKSNGEYLTMWQ-IPA---DLESGEYEMTA 693
                 56789*************************99998.333...37777777665 PP

>> Gmad2  Immunoglobulin-like domain of bacterial spore germination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.031   1.1e+02      18      77 ..      31      91 ..      26      98 .. 0.74
   2 ?    0.4   0.0      0.22   7.9e+02      29      50 ..     115     136 ..     106     144 .. 0.79
   3 ?    0.8   0.1      0.16   5.7e+02      15      79 ..     357     417 ..     344     422 .. 0.65
   4 ?   -1.0   0.0      0.58   2.1e+03      17      50 ..     543     576 ..     528     593 .. 0.76
   5 !    9.4   0.0   0.00034       1.2      17      71 ..     636     687 ..     628     696 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.031
       Gmad2 18 kvsGkarvFEatvnvrlrddagevla.egfvtAdegapkfgdFeatvefkapepgkgtlev 77
                kv G+++ FE ++ ++l+ + g+ ++ ++     +g  +f  F+++    ++++++g++++
  AJA91987.1 31 KVIGVSTGFEDSTILELKNNRGNTASiDTVRIWLSGENEFKSFKTENGWMGKNTPQGVIVF 91
                799********************99855444445555667777666666666666666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
       Gmad2  29 tvnvrlrddagevlaegfvtAd 50 
                 ++n++  d++ge+++ +++t +
  AJA91987.1 115 VINWKALDSKGEIISSASTTVT 136
                 68999**********7777644 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
       Gmad2  15 spvkvsGkarvFEatvnvrlrddagevlaegfvtAdegapkfgdFeatvefkape.pgkgtlevye 79 
                 ++++++G+a+  + ++++ ++d+ ++ +  + v+ +e   + ++F+++++    + +g+++l +++
  AJA91987.1 357 ESITFEGTAIPNQ-EMSIIIEDAINTEIFSRTVSVGES--GLVNFNVEIPRG--SvEGTYILSAFQ 417
                 3555555555544.577888888888888776664443..566666665544..448888888776 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.58
       Gmad2  17 vkvsGkarvFEatvnvrlrddagevlaegfvtAd 50 
                 + + G+  +    + +++ d++g+++++  + +d
  AJA91987.1 543 ILILGSTGAINVLLDITISDSNGKIIKKIETFSD 576
                 556666666666788999*******998777655 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00034
       Gmad2  17 vkvsGkarvFEatvnvrlrddagevlaegfvtAdegapkfgdFeatvefkapepg 71 
                 +++sG+     atv++++ d++g  + e ++tA+++ +    ++   +++   +g
  AJA91987.1 636 LNISGSGARLSATVTIKIFDSEGIKIDELNITAKSNGEYLTMWQIPADLE---SG 687
                 789*********************************99999999888877...44 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   4.4e+03      30      74 ..     143     186 ..     117     194 .. 0.65
   2 ?    1.0   0.0      0.15   5.3e+02      38      73 ..     197     233 ..     191     237 .. 0.81
   3 !    6.0   0.1    0.0042        15      16      37 ..     270     293 ..     259     342 .. 0.65
   4 ?    1.0   0.1      0.14     5e+02      19      62 ..     363     412 ..     349     428 .. 0.64
   5 ?   -2.2   0.0       1.4   5.2e+03      26      50 ..     557     583 ..     549     589 .. 0.72
   6 !   11.2   0.1   9.8e-05      0.35      16      79 ..     637     706 ..     627     707 .] 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
       Big_6  30 kdadgtvlgtgtadadGeFsvtlepaqangetlsvvatDaagntS 74 
                  +++ ++ + +t++++ +F++   ++ a ++ ++vv +D   n+S
  AJA91987.1 143 NKPELNQPKIVTIKESSNFRFIP-EKPASNSYFRVVGEDFVPNQS 186
                 44455566677778888888754.455667778888887777777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
       Big_6  38 gtgtadadGe..FsvtlepaqangetlsvvatDaagnt 73 
                  ++++d+dG+  F+ +l pa  n+e+ + v+ D+ gn+
  AJA91987.1 197 ESVKVDSDGKilFTSKL-PAILNDERTEFVLRDSGGNE 233
                 67899999986677777.577999***********997 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0042
       Big_6  16 tltGkaeagatVtv..kdadgtvl 37 
                 tl G a +++t+t+  kd++g++l
  AJA91987.1 270 TLDGMATPNTTLTItsKDNNGNIL 293
                 355666667766663233344444 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.14
       Big_6  19 Gkaeagat..Vtvkdadgtvl..gtgtadadG..eFsvtlepaqangetl 62 
                 G+a ++ +  + + da +t++   t+ ++++G  +F+v+++   ++g+ +
  AJA91987.1 363 GTAIPNQEmsIIIEDAINTEIfsRTVSVGESGlvNFNVEIPRGSVEGTYI 412
                 66666554115667887777745667779999778999998877777543 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.4
       Big_6  26 tVtvkdadgtvlgtgta..dadGeFsv 50 
                  +t++d++g+++++     d  G F+v
  AJA91987.1 557 DITISDSNGKIIKKIETfsDRFGVFKV 583
                 589999999999765433366666665 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 9.8e-05
       Big_6  16 tltGkae.agatVtv..kdadgtvlgtg..tadadGeFsvtl.epaqangetlsvvatDaagntSdaatv 79 
                  ++G++    atVt+   d++g  + +   ta+++Ge+      pa  +  + +++a D a ntS++ t+
  AJA91987.1 637 NISGSGArLSATVTIkiFDSEGIKIDELniTAKSNGEYLTMWqIPADLESGEYEMTADDGASNTSTKFTI 706
                 57787651467777722577777775445599******87652467788889**************9887 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         1   3.7e+03      30      40 ..     120     134 ..      99     139 .. 0.48
   2 ?    6.7   0.2     0.002       7.2       7      31 ..     279     303 ..     276     312 .. 0.85
   3 ?   -2.3   0.0       1.2   4.5e+03      12      26 ..     324     338 ..     320     342 .. 0.82
   4 ?   -1.5   0.0      0.73   2.6e+03       8      22 ..     555     569 ..     550     572 .. 0.76
   5 ?   -2.7   0.0       1.8   6.3e+03      25      42 ..     609     625 ..     608     628 .. 0.67
   6 ?    0.2   0.0      0.22   7.9e+02       7      33 ..     647     673 ..     645     702 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
       Big_1  30 vsg..gals..assg 40 
                 + +  g ++  as++
  AJA91987.1 120 ALDskGEIIssASTT 134
                 322233333233333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.002
       Big_1   7 ntltatvkDangnpvagatVtfsvs 31 
                 +tlt+t kD+ngn +a  t+ ++ +
  AJA91987.1 279 TTLTITSKDNNGNILAIDTIQVRFD 303
                 79************99888777665 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
       Big_1  12 tvkDangnpvagatV 26 
                  + D +g+++ +++V
  AJA91987.1 324 EIDDGKGKALRNVEV 338
                 567999******999 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.73
       Big_1   8 tltatvkDangnpva 22 
                  l +t+ D+ng+ ++
  AJA91987.1 555 LLDITISDSNGKIIK 569
                 567889999998875 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.8
       Big_1  25 tVtfsvsggalsassgtT 42 
                  V fsvsg+++ + +  T
  AJA91987.1 609 DVEFSVSGENN-ELQIFT 625
                 599***99665.445555 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.22
       Big_1   7 ntltatvkDangnpvagatVtfsvsgg 33 
                 +t+t+ + D++g  +   ++t +++g+
  AJA91987.1 647 ATVTIKIFDSEGIKIDELNITAKSNGE 673
                 799999999999999999999998884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 4406.21
//
Query:       AJA91988.1  [L=276]
Description: ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-35  120.4   0.1    1.2e-34  119.7   0.1    1.4  1  ABC_tran         ABC transporter
    4.5e-05   23.9   0.0    0.00013   22.4   0.0    1.8  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    6.6e-05   22.2   0.9    8.5e-05   21.9   0.9    1.1  1  G-alpha          G-protein alpha subunit
    7.5e-05   23.2   0.0    0.00011   22.6   0.0    1.4  1  AAA_16           AAA ATPase domain
    9.3e-05   22.0   1.6    0.00019   21.0   1.6    1.5  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00012   22.3   0.9     0.0013   19.0   0.9    2.1  1  AAA_22           AAA domain
    0.00013   22.0   0.1    0.00031   20.7   0.1    1.7  1  RsgA_GTPase      RsgA GTPase
    0.00026   20.9   0.2       0.39   10.5   0.1    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00055   19.6   0.0      0.001   18.8   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00089   18.0   1.8      0.076   11.7   0.2    2.1  2  AAA_13           AAA domain
     0.0013   18.1   0.0     0.0026   17.1   0.0    1.5  1  Zeta_toxin       Zeta toxin
     0.0021   18.2   1.0     0.0051   16.9   0.4    2.0  2  DUF87            Helicase HerA, central domain
     0.0091   15.1   0.1       0.02   13.9   0.0    1.7  1  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.018   14.2   0.3      0.055   12.7   0.1    1.8  2  NB-ARC           NB-ARC domain
       0.02   14.6   0.0      0.039   13.7   0.0    1.5  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.025   15.0   0.2       0.15   12.4   0.2    2.4  2  RNA_helicase     RNA helicase
      0.026   14.4   0.1       0.29   11.0   0.0    2.5  3  APS_kinase       Adenylylsulphate kinase
      0.026   13.9   1.9        1.3    8.4   0.2    2.9  3  TniB             Bacterial TniB protein
      0.043   14.4   0.1       0.19   12.3   0.1    2.0  2  AAA_18           AAA domain
      0.046   14.2   3.0      0.095   13.2   3.0    1.8  1  AAA_23           AAA domain
      0.059   13.1   0.0       0.18   11.5   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
      0.065   12.2   0.0       0.11   11.5   0.0    1.3  1  DUF3987          Protein of unknown function (DUF3987)
      0.089   12.5   0.2        0.4   10.4   0.0    1.9  2  AAA_30           AAA domain
      0.091   12.7   0.0       0.19   11.6   0.0    1.6  1  NACHT            NACHT domain
       0.13   12.2   0.0       0.37   10.8   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.2   1.0        9.1    6.4   0.1    2.4  2  z-alpha          Adenosine deaminase z-alpha domain
        0.2   11.6   2.7       0.59   10.0   0.0    2.4  2  NTPase_1         NTPase
       0.21   12.0   3.4        2.5    8.5   3.4    2.4  1  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.1   1.9e-37   1.2e-34       2     136 ..      32     183 ..      31     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 1.9e-37
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS..--S-TTSBHHHH..............HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxxxxxxxx..............xxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqe..pqlfpeltvren..............esd 82 
                 + v+++lk+ge++ai G++G+GKSt++kl+++  kp++G+i  ++k++k+  +el+++r + +++ q+  ++++p++t+ +               e++
  AJA91988.1  32 DAVNFSLKQGEILAIAGQSGSGKSTIAKLILRAIKPDSGKIFHNEKEIKDnsDELKKFRMKCQMIYQDpyDSINPRMTISDIvsepleihnlgtkdERK 130
                 679**************************************999******999***************999********999***********998888 PP

                 TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +++ + l+k++l+  +++++k++p+ LSgGq+qrv++ara++ +p+++++DEp 
  AJA91988.1 131 QRVIETLQKVKLEP-AEEIAKKHPHMLSGGQRQRVVIARAIVVEPEIIIADEPV 183
                 8999999***9999.99999*********************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     2e-07   0.00013       1      33 [.     235     267 ..     235     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-07
   oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd 33 
                 +E+g+++k++++p + YTkaL+++v ++d+++ 
  AJA91988.1 235 MEIGTIEKVLSNPENSYTKALIAAVSEPDPKNL 267
                 7****************************9987 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.9   1.3e-07   8.5e-05       7     165 ..      25     225 ..      19     246 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                 XXXXXXXXXXXXXE..EEEEEEEESTTSSHHHHHHHHHHHCS--....--HHHH.HCCHH..........HHHHHHHHHHHHHHHHHHHTT........ CS
     G-alpha   7 idkslkaerkarkkkrevkllllGqseSGKsTilkqlkllykkg....fseeel.atwra..........viqlnivrsiktilealesleselsesf. 89 
                 +++ + a+  +++ k+   l + Gqs+SGKsTi k + +  k+     f++e+  +   +          +i++  ++si+  + + +  ++     + 
  AJA91988.1  25 SNEVIAADAVNFSLKQGEILAIAGQSGSGKSTIAKLILRAIKPDsgkiFHNEKEiKDNSDelkkfrmkcqMIYQDPYDSINPRMTISDIVSE-----Pl 118
                 55556666555554334448899**********99998777776788877773223322245555556667777777777643333333222.....02 PP

                 ...............HHHC-SS-SCCCS-HCHHHH....................HHCCHHC...............-HCHHHHHHHHCCSHHHHHHHC CS
     G-alpha  90 ...............elqelkerldplkkveasliaklssateee..........qeiefnp...............raevgedikaLwndpgiqelye 148
                                 +   k +l+p  ++ +++ + ls++++++                +               rae+ e +k++ ++ +i+++y 
  AJA91988.1 119 eihnlgtkderkqrvIETLQKVKLEPAEEIAKKHPHMLSGGQRQRvviaraivveP-----EiiiadepvsmldvsiRAEILELMKEIQKENNISMIYI 212
                 33444443333332244444444555555555555555555555599996666652.....03334467777778888899999999999999999986 PP

                 CGCCTT--TTHHHHHCT CS
     G-alpha 149 rrnkiklednaeyFldd 165
                    ++     a+ F d+
  AJA91988.1 213 TH-DLA---TAKHFADN 225
                 44.332...34445444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.7e-07   0.00011      23      62 ..      40      80 ..      29     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-07
      AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggiflrgkcdq 62
                ++e++ + G+sG+GKs++++ +lra++ d g if ++k  +
  AJA91988.1 40 QGEILAIAGQSGSGKSTIAKLILRAIKPDsGKIFHNEKEIK 80
                4489************************9434553333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   1.6   2.9e-07   0.00019      25     207 ..      42     224 ..      30     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
                 SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkev 123
                 ++ ai G+ GSGKs +   il  +  +s k + +ek    i+ ++++ +  + + +++++++ ++    +++++is  v++  e  + +  k+ +k+ v
  AJA91988.1  42 EILAIAGQSGSGKSTIAKLILRAIKPDSGKIFHNEKE---IKDNSDELKKFRMKCQMIYQDPYDS---INPRMTISDIVSEPLE-IHNLGTKDERKQRV 133
                 5779****************99999999977776653...5543444444444556666666665...6888999988887777.8999********** PP

                 HHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-SC CS
                 xxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 124 sellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekadk 207
                  e l+++++++          +LSgG+++ v +a  +    v+p  + + De  + LD + ++++ el+k  +k++n  +i i+++  + ++   
  AJA91988.1 134 IETLQKVKLEPAeeiakkhphMLSGGQRQRVVIARAI---VVEP-EIIIADEPVSMLDVSIRAEILELMKeiQKENNISMIYITHDLATAKHFAD 224
                 **********9999*************9966655432...2444.57899********************4445556888999998777766544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.9     2e-06    0.0013       4     128 ..      40     212 ..      37     218 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-06
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfvtlpsst.sskdllrellralgl 66 
                 +  il++ G+sG+GK+t ++ +l+  + +                                        ++             + +d+ +e l++ +l
  AJA91988.1  40 QGEILAIAGQSGSGKSTIAKLILRAIKPD----SgkifhnekeikdnsdelkkfrmkcqmiyqdpydsiNP-----------RmTISDIVSEPLEIHNL 123
                 6789********************97533....23344666777777777777764444433333333311...........12333333333333333 PP

      AAA_22  67 elka.....................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                 ++k+                     + +  + l   + ++ + ara    +e++i DE    l+   ++e+le  +++++  + ++++i++
  AJA91988.1 124 GTKDerkqrvietlqkvklepaeeiAKKHPHMLSgGQRQRVVIARAIvvePEIIIADEPVSmLDvsiRAEILELMKEIQK--ENNISMIYI 212
                 33335555555555555554666655555555554455555555554999999999998886768555999999999999..999999987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   4.8e-07   0.00031      68     130 ..       8      72 ..       1      94 [. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.8e-07
                  HHHHHHHTTSEEEE--.TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
  RsgA_GTPase  68 lkeelealgyevllvs.aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                  +++ +++++ + ++ s +++  ++++++  lk+ ++ +++GqSG GKSt+ + +l   +   g++
   AJA91988.1   8 IENLTKKFQKKNFFSSdSNEVIAADAVNFSLKQgEILAIAGQSGSGKSTIAKLILRAIKPDSGKI 72 
                  44444444444444440455588999*****999****************999988766666665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0     0.002       1.3       2      55 ..      44      78 ..      43      97 .. 0.69
   2 !   10.5   0.1   0.00061      0.39     259     299 ..     175     216 ..      99     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.002
      AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                 ++ G  gsGKS++ +++  +                   i+ ++++++ +++e
  AJA91988.1 44 LAIAGQSGSGKSTIAKLILRA-------------------IKPDSGKIFHNEKE 78
                5799**************554...................34444444444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00061
      AAA_21 259 sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                  +++ DEp + L+ ++ +++lel+ke ++ n++  i  TH+ 
  AJA91988.1 175 EIIIADEPVSMLDVSIRAEILELMKEIQKeNNISMIYITHDL 216
                 67777*******************888888**********96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.6e-06     0.001      15      39 ..      34      58 ..      26      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
      AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                  +++++ ++  ++G+sGsGKST+ 
  AJA91988.1 34 VNFSLKQGEILAIAGQSGSGKSTIA 58
                55667755599************96 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0068       4.3      21     103 ..      46     139 ..      37     163 .. 0.65
   2 !   11.7   0.2   0.00012     0.076     526     581 ..     173     226 ..     164     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0068
      AAA_13  21 iYGwNGaGKTtLSrllrslelgetepkfangsieitnge......eldirVfNrdFveenls...eq..gelkpvftLGeesiekqekieklkk 103
                 i G+ G+GK+t+++l+    +    + f n++ +  n++       +  +++ + +   n +    +  +e   +  LG ++  kq+ ie+l+k
  AJA91988.1  46 IAGQSGSGKSTIAKLILRAIKPDSGKIFHNEKEIKDNSDelkkfrMKCQMIYQDPYDSINPRmtiSDivSEPLEIHNLGTKDERKQRVIETLQK 139
                 55899**********9888777777777777443333322333325555778766633322222313447777788888888888888888776 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
      AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                 + +i++ D PvS LD  +   +  l+k+   k+++++ ++i TH l   k + +n+
  AJA91988.1 173 EPEIIIADEPVSMLDVSIRAEILELMKEIQ-KENNISMIYI-THDLATAKHFADNI 226
                 789*************************97.8888888877.***99999888775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     4e-06    0.0026      17      44 ..      42      69 ..      27     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
  Zeta_toxin 17 klillgGqpGAGKselaellkdelerqg 44
                 ++ ++Gq+G+GKs++a+l+ +++++++
  AJA91988.1 42 EILAIAGQSGSGKSTIAKLILRAIKPDS 69
                57789****************9998444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4     8e-06    0.0051      26      48 ..      44      66 ..      26      74 .. 0.87
   2 ?   -2.0   0.0         5   3.2e+03     159     169 ..     124     134 ..      74     156 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8e-06
       DUF87 26 lAilgsTGsGKSntvavLleell 48
                lAi g++GsGKS+ ++++l+ + 
  AJA91988.1 44 LAIAGQSGSGKSTIAKLILRAIK 66
                79*****************9887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5
       DUF87 159 klknqaiarll 169
                   k++ ++r++
  AJA91988.1 124 GTKDERKQRVI 134
                 22333333333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.2e-05      0.02     110     164 ..      22      76 ..       5     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
       T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                  + +++   a++++ ++++  ++ ++G  gsGK+t++  +l  i+ ++ +i   E
  AJA91988.1  22 SSDSNEVIAADAVNFSLKQGEILAIAGQSGSGKSTIAKLILRAIKPDSGKIFHNE 76 
                 455555556777888888888888*********************9999998766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.5e-05     0.055      21      43 ..      42      64 ..      32      75 .. 0.87
   2 ?   -2.2   0.0       2.8   1.8e+03     214     249 ..      76     111 ..      69     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.5e-05
                EEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                 ++a+ G  G+GK+t+ak il+ 
  AJA91988.1 42 EILAIAGQSGSGKSTIAKLILRA 64
                599***************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                 CCHHHHHHHHHHCTGCCTS--SSSSSSSHHHHHHHH CS
      NB-ARC 214 veewkkvlekleskllevekstskslesvasilqls 249
                 ++e k  +++l++ +++ +++ ++ ++s+   + +s
  AJA91988.1  76 EKEIKDNSDELKKFRMKCQMIYQDPYDSINPRMTIS 111
                 567777788888888888888888888888777665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.2e-05     0.039       1      24 [.      43      66 ..      43     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-05
         PRK  1 vIgvagsSGaGkttvarklekifg 24
                ++++ag+SG+Gk+t+a+ +  +++
  AJA91988.1 43 ILAIAGQSGSGKSTIAKLILRAIK 66
                689**************9988876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00024      0.15       3      29 ..      46      72 ..      44     121 .. 0.73
   2 ?   -1.6   0.0       5.7   3.7e+03      38      55 ..     150     167 ..     131     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklk 29
                  + G+sg GKSt+ak + +a+  +++++
    AJA91988.1 46 IAGQSGSGKSTIAKLILRAIKPDSGKI 72
                  78*************999999555332 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.7
  RNA_helicase  38 npeddfwdgYtgqevvvi 55 
                   ++   +++g ++q vv+ 
    AJA91988.1 150 KKHPHMLSGGQRQRVVIA 167
                   455566677777777765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046      0.29       2      26 ..      41      65 ..      40      74 .. 0.84
   2 ?   -1.9   0.0       4.1   2.7e+03     100     145 ..     205     248 ..     180     252 .. 0.60
   3 ?   -0.0   0.0       1.1   7.2e+02     106     125 ..     251     270 ..     241     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                -EEEEEESSTTSSHHHHHHHHHHHH CS
  APS_kinase  2 gvvvwltGlsgsGKstianalekkL 26
                g ++ ++G sgsGKstia+ + +++
  AJA91988.1 41 GEILAIAGQSGSGKSTIAKLILRAI 65
                678899************9987765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                 TEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----S CS
  APS_kinase 100 lkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPe 145
                  ++  +++  +l+++++     l    ++G++ e+  i++   +Pe
  AJA91988.1 205 NNISMIYITHDLATAKHFADNILIL--KSGKVMEIGTIEKVLSNPE 248
                 4666666666666665544444433..3456666666666666665 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.1
                 EEE--HHHHHHHTTTSHHHH CS
  APS_kinase 106 fvdtplevceerDpkglYkk 125
                 + ++ ++  +e Dpk lYk+
  AJA91988.1 251 YTKALIAAVSEPDPKNLYKE 270
                 667778888999******96 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.044        28      38      58 ..      44      64 ..      37     100 .. 0.85
   2 ?   -2.3   0.0       3.9   2.5e+03     127     142 ..     119     134 ..     104     143 .. 0.60
   3 ?    8.4   0.2     0.002       1.3     115     161 ..     169     213 ..     146     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.044
        TniB 38 lllvGdsnnGKtmivekFarl 58
                l ++G+s  GK++i++   r 
  AJA91988.1 44 LAIAGQSGSGKSTIAKLILRA 64
                789***********9876655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
        TniB 127 Eihnllagsarkqref 142
                 Eihnl +   rkqr +
  AJA91988.1 119 EIHNLGTKDERKQRVI 134
                 5555555555554432 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.002
        TniB 115 lrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvG 161
                    ++++++i DE  ++l   ++ + e+l+++k ++ e +i+++++ 
  AJA91988.1 169 AIVVEPEIIIADEPVSML--DVSIRAEILELMKEIQKENNISMIYIT 213
                 4457899***********..677789*****************9875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0003      0.19       2      22 ..      45      65 ..      44     137 .. 0.73
   2 ?   -0.6   0.0       2.9   1.9e+03      61      69 ..     195     203 ..     141     253 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
      AAA_18  2 lltGtpGvGKttlakeLskrl 22
                +++G +G+GK+t+ak + +  
  AJA91988.1 45 AIAGQSGSGKSTIAKLILRAI 65
                599************995553 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.9
      AAA_18  61 ldaleenss 69 
                 l++++e+ +
  AJA91988.1 195 LELMKEIQK 203
                 333333322 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.0   0.00015     0.095      17      74 ..      36      88 ..       6     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
      AAA_23 17 F...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay 74
                F      + +I G+ G+GK+Ti   i  a   ++        +++++++ ei+++ +  + 
  AJA91988.1 36 FslkQGEILAIAGQSGSGKSTIAKLILRAIKPDS--------GKIFHNEKEIKDNSDELKK 88
                3444446889*************99998886542........3455666665555333333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.18      24      51 ..      43      70 ..      21      86 .. 0.76
   2 ?   -2.9   0.0       7.7   4.9e+03     116     143 ..     234     261 ..     232     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                     -EEEECSTTSSHHHHHHHHHHHSTTTTS CS
  Sigma54_activat 24 svlitGesGtGKellaraiheaskrkek 51
                      + i G+sG+GK+++a++i +a k +++
       AJA91988.1 43 ILAIAGQSGSGKSTIAKLILRAIKPDSG 70
                     34599**************998776655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.7
                      HHHHSEEESBTSSSEEE--EEEEEEESS CS
  Sigma54_activat 116 vlqegevervGsskeikvdvriiaatne 143
                      v++ g++e+v s+ e + +  +iaa +e
       AJA91988.1 234 VMEIGTIEKVLSNPENSYTKALIAAVSE 261
                      7788888888888888888888888765 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.11      39      87 ..      44      91 ..      37     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
     DUF3987 39 tlvvapsGerKSpvdklvlrpleeieaelreeyeeelkeyeaekkawea 87
                ++++++sG++KS+++kl+lr++++   +++ + e+e+k+++ e k++++
  AJA91988.1 44 LAIAGQSGSGKSTIAKLILRAIKPDSGKIFHN-EKEIKDNSDELKKFRM 91
                5799*******************987777764.5566666666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00062       0.4       9      45 ..      33      68 ..      31      79 .. 0.78
   2 ?   -0.5   0.1       1.4   8.7e+02      83     114 ..     168     200 ..     123     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
      AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaa 45
                av+  l++g+ + ++ G  G+GK+t+ k + +a++ +
  AJA91988.1 33 AVNFSLKQGE-ILAIAGQSGSGKSTIAKLILRAIKPD 68
                5555566665.999***************98887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
      AAA_30  83 rarlepgtllivDE.agmvdtkqlaallkaaek 114
                 ra + + +++i DE ++m+d +  a++l+ +++
  AJA91988.1 168 RAIVVEPEIIIADEpVSMLDVSIRAEILELMKE 200
                 344455588999997789998877777776655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.19       3      25 ..      44      66 ..      42     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                EEEEC-TTTCHHHHHHHHHHHHC CS
       NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                +++ G++GsGK+t ++ + +a++
  AJA91988.1 44 LAIAGQSGSGKSTIAKLILRAIK 66
                789*************9999887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00057      0.37       4      26 ..      46      69 ..      43      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00057
                EE--SSSSHHHHHHHGGGGB.S-- CS
       AAA_5  4 LvGppGtgKselaerlaaal.nre 26
                + G++G+gKs++a+ +++a+  ++
  AJA91988.1 46 IAGQSGSGKSTIAKLILRAIkPDS 69
                67*****************96444 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.014       9.1       3      28 ..     127     151 ..     125     153 .. 0.91
   2 ?    4.1   0.1     0.076        49       6      51 ..     191     234 ..     187     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                 HHHHHHHHHHHHHC-TTCECCHHHHH CS
     z-alpha   3 qeqaekilelLeelgekkaatalale 28 
                  e +++++e L+++   ++a ++a++
  AJA91988.1 127 DERKQRVIETLQKVK-LEPAEEIAKK 151
                 5889***********.*******996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.076
                 HHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSE CS
     z-alpha   6 aekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkv 51 
                    ilel++e+  ++    +  + +L t k+ +  +L+   ++gkv
  AJA91988.1 191 RAEILELMKEIQKENNISMIYITHDLATAKHFADNILI--LKSGKV 234
                 668*********999999************99999996..566666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00092      0.59       3      25 ..      45      67 ..      43      73 .. 0.88
   2 ?    0.9   0.8      0.58   3.7e+02      88     155 ..     165     237 ..     129     249 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00092
                EEE--TTSSHHHHHHHHHHHH.. CS
    NTPase_1  3 fiTGppGvGKtTlvkkvlellks 25
                +i G++G+GK+T+ k +l+++k 
  AJA91988.1 45 AIAGQSGSGKSTIAKLILRAIKP 67
                799***************99975 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.58
                 HHHHHH.HHH-EEEE--.-STTGGG-.HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
    NTPase_1  88 alrkal.seadviviDE.iGkmElks.kkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfev 155
                 ++ +a+  e+++i+ DE +  + +++ +++ e ++e+ k ++  ++ + h     +++ ++i   k +kv+e+
  AJA91988.1 165 VIARAIvVEPEIIIADEpVSMLDVSIrAEILELMKEIQKeNNISMIYITHDLAtAKHFADNILILKSGKVMEI 237
                 4455554778888888844444555423566677777775555566666665567777777777777777766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.4    0.0039       2.5       3     111 ..      46     215 ..      44     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0039
                 EESSTTSSHHHHHHHHHHHHTHE...................EEEEETTTCSSS............................................. CS
         AAA   3 lyGppGtGKTllakavakelgve...................fleisgsellsk............................................. 37 
                 + G  G GK+++ak + + ++ +                    +++++  + ++                                             
  AJA91988.1  46 IAGQSGSGKSTIAKLILRAIKPDsgkifhnekeikdnsdelkKFRMKCQMIYQDpydsinprmtisdivsepleihnlgtkderkqrvietlqkvklep 144
                 689****************85322222233333333444443444444444433566666666666666667777777777777777777777777777 PP

                 .........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
         AAA  38 .........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                          ++  + ++ r ++++a   + p i++ DE  ++   +          + +++l+ +++ +k+ +++ +i +t++
  AJA91988.1 145 aeeiakkhpHMLSGGQRQRVVIARAIVVE-PEIIIADEPVSMLDVS----------IRAEILELMKEIQKE-NNISMIYITHD 215
                 77777777766666667777776666665.7777777777777666..........677777777777774.45777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1702.87
//
Query:       AJA91989.1  [L=210]
Description: V-type ATPase, D subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-45  154.7   4.0      3e-45  154.5   4.0    1.0  1  ATP-synt_D      ATP synthase subunit D
  ------ inclusion threshold ------
      0.013   15.7   0.4      0.053   13.8   0.0    2.2  3  PerC            PerC transcriptional activator
      0.048   13.9   0.0       0.16   12.3   0.0    1.8  1  Peptidase_M3_N  Oligopeptidase F
      0.074   13.5   1.9       0.19   12.3   0.9    2.0  2  TFIIS_M         Transcription factor S-II (TFIIS), central do
       0.22   11.8   4.8        2.1    8.6   0.7    2.2  2  RNA_binding     RNA binding


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   4.0   8.3e-49     3e-45       1     196 []      13     204 ..      13     204 .. 0.97

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 8.3e-49
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS-SEEEEEEBTTSEEEEEE CS
  ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvvkvelktenvaGVkvpvfe 99 
                 eL + k+  ++a+ ++++L++Kr++L++ + e+++e++++r  + e l+++y+s+ e +++ g  +++s++++++   +v++ve+ ++ v+ V++pv++
  AJA91989.1  13 ELFKYKRSSQVATMVQKILDDKRKVLLKNIEEMIAEAQKTRGGIWEPLQDIYQSVNESYLSLGVGTVDSVAQSTP---AVMEVESDVKRVVDVTIPVLS 108
                 68899*******************************************************999*****9999555...68******************* PP

                 E-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_D 100 leeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvkk 196
                 ++e k++++ +yg+++t+a++d+ ++ +++ll+++ ++a++e+s+ +L+++++kt++  NaLe+v+IP++++ +++I   L+E+ereef+rlkkvk+
  AJA91989.1 109 VTE-KDTKSIPYGFADTNASIDRGAKLIKDLLPKICKAAEYENSIFSLAKALEKTQKLLNALENVIIPQYKQRVRFILATLEEREREEFARLKKVKA 204
                 *88.67889**************************************************************************************95 PP

>> PerC  PerC transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.053      25      80 ..      24      80 ..      10      87 .. 0.86
   2 ?   -1.8   0.0         1   3.7e+03      53      72 ..      86     105 ..      81     115 .. 0.63
   3 ?   -3.1   0.1       2.8     1e+04      22      43 ..     180     201 ..     176     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
        PerC 25 evmvlletdaeRklvalkRaeClrkasrpplp.alnlseikkavdrtykelGlatvs 80
                  mv+   d +Rk++++   e +++a+++       l +i ++v++ y  lG++tv+
  AJA91989.1 24 ATMVQKILDDKRKVLLKNIEEMIAEAQKTRGGiWEPLQDIYQSVNESYLSLGVGTVD 80
                4577777899*******************9996788*****************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
        PerC  53 pplpalnlseikkavdrtyk 72 
                 +p      s++k+ vd t  
  AJA91989.1  86 TPAVMEVESDVKRVVDVTIP 105
                 55555555788888877655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.8
        PerC  22 RWaevmvlletdaeRklvalkR 43 
                 R  +++  le+ ++ +++ lk+
  AJA91989.1 180 RVRFILATLEEREREEFARLKK 201
                 5556666666555555555554 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.16      20      62 ..      20      62 ..       9      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
  Peptidase_M3_N 20 laeyrfyleeilrqkphtLseeeEklLaelsevggaawnifsd 62
                     ++ + + ++il+ k  +L ++ E+++ae++++ g  w+ ++d
      AJA91989.1 20 SSQVATMVQKILDDKRKVLLKNIEEMIAEAQKTRGGIWEPLQD 62
                    566778899****************************987765 PP

>> TFIIS_M  Transcription factor S-II (TFIIS), central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.34   1.2e+03       7      23 ..      34      50 ..       8      97 .. 0.69
   2 ?   12.3   0.9   5.2e-05      0.19       6      71 ..     130     197 ..     125     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.34
                HHHHHHHHTT---...- CS
     TFIIS_M  7 crelLaealeedsseae 23
                 r++L++ +ee++ ea+
  AJA91989.1 34 KRKVLLKNIEEMIAEAQ 50
                35555555555554444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                 HHHHHHHHHTT---...-.--THHHHHHHHHHH..HHHHT------HHHHHHHHHHHHHS-TT-HHHH CS
     TFIIS_M   6 kcrelLaealeedsseaeeeedveelaaeiEea..lfekekkstdkkykqkvrslvfNLkdkkNpeLr 71 
                 + ++l+ + l ++++ ae e+++ +la+++E+   l +  ++ +  +ykq+vr +++ L  ++  e++
  AJA91989.1 130 RGAKLIKDLLPKICKAAEYENSIFSLAKALEKTqkLLNALENVIIPQYKQRVRFILATLEEREREEFA 197
                 557888889999998877788**********9976566445556699************877766655 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0078        28      41      89 ..       3      51 ..       2      53 .. 0.74
   2 ?    8.6   0.7   0.00059       2.1      39     102 ..     146     207 ..     128     210 .] 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0078
                 CC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSE CS
  RNA_binding 41 ygnpitileaelekkkakkvlkkllellreeeikeLlkeleervdekgk 89
                 +g+++t  ++el k k    + ++++++ ++++k+Llk++ee++ e +k
   AJA91989.1  3 FGQNVTATKIELFKYKRSSQVATMVQKILDDKRKVLLKNIEEMIAEAQK 51
                 6778888888888877755555666666667779********9987765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00059
                  -CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHHHCCHCCB-TTSEEEEEEEHHHHHTT CS
  RNA_binding  39 Ghygnpitileaelekkka.kkvlkkllellreeeikeLlkeleervdekgklylrldKQaaylg 102
                    y+n+i  l   lek ++ +++l++++    +++++ +l +lee   ++ + + rl K +a ++
   AJA91989.1 146 AEYENSIFSLAKALEKTQKlLNALENVIIPQYKQRVRFILATLEE---REREEFARLKKVKASME 207
                  569999999999999999999999999999999999999999999...57777889988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1417  (0.079034); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1553.19
//
Query:       AJA91990.1  [L=381]
Description: phosphoribosylaminoimidazole carboxylase, ATPase subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-61  205.3   0.3      8e-61  204.6   0.3    1.3  1  ATP-grasp        ATP-grasp domain
    2.5e-13   49.5   0.1    5.3e-13   48.4   0.1    1.5  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    2.7e-08   33.6   0.7    7.7e-08   32.1   0.7    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.7e-05   23.8   0.3    5.5e-05   22.7   0.3    1.5  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    3.5e-05   23.5   1.1    6.3e-05   22.6   0.8    1.7  2  RimK             RimK-like ATP-grasp domain
    0.00017   21.7   0.6    0.00032   20.8   0.6    1.5  1  ATP-grasp_3      ATP-grasp domain
    0.00061   19.6   0.3     0.0013   18.5   0.3    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
  ------ inclusion threshold ------
      0.019   14.5   0.0      0.035   13.6   0.0    1.4  1  DUF1297          Domain of unknown function (DUF1297)
      0.049   13.9   0.6       0.29   11.4   0.0    2.6  3  TrkA_N           TrkA-N domain
      0.053   12.9   0.0       0.13   11.6   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.6   0.3   4.5e-64     8e-61       1     171 []     110     280 ..     110     280 .. 0.99

  Alignments for each domain:
  == domain 1  score: 204.6 bits;  conditional E-value: 4.5e-64
                 HHTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEEETTC-EEE--EEEEE CS
   ATP-grasp   1 leklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvrsaeGetafypvvetv 99 
                 l+k+g++v++f  +e+keel+++++++glp+++K+rr +ydG+G++ ++s++++++al+ +++++++vE+fv+fekE+sv+++r+++Ge+++ypvve++
  AJA91990.1 110 LQKNGIAVAEFEKIENKEELNQMIDKMGLPLLLKTRRDAYDGRGNYKINSKSEIDDALDLFSGKTLMVEKFVKFEKEVSVIAARNTKGEISTYPVVENI 208
                 5899*********************************************************************************************** PP

                 EETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS--GGGGGHHHHB CS
   ATP-grasp 100 qedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpHnsGhvtldaa 171
                 +e++ilr+ +ap +vse+  k+ae+ia+k +e L g+Gvf++E+Fv++d+e+l+nE+apR+HnsGh tl+++
  AJA91990.1 209 HENNILRTTIAPGRVSETVRKEAEKIAEKTMEVLHGAGVFGIEMFVTSDDEILINEIAPRVHNSGHHTLQSC 280
                 **********************************************************************98 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   2.9e-16   5.3e-13       1      53 [.     306     360 ..     306     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.9e-16
      PurK_C   1 avMvNlLGedaeeklee..llaipgahlHlYgKeearpgRKmGHitvvgdsaeel 53 
                 ++M+N+LG ++++++ +   ++ +++hl +YgK e++p+RK+GH+++v+ ++  +
  AJA91990.1 306 TIMYNILGPKTFQGEYNvlFKKQDNIHLKMYGKLESKPQRKIGHVNIVDVENRGM 360
                 79*********9777776688999999999******************9877655 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.7   4.3e-11   7.7e-08       2     173 ..     110     266 ..     109     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.3e-11
                      HHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSS.TTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETS CS
  Dala_Dala_lig_C   2 lkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareG.SSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgne 94 
                      l+++G++v++++ +e++e  +++       ++++g+p++ K  r      G  k++s++e+ +a++      ++ +vE++++  e ev+v+   
       AJA91990.1 110 LQKNGIAVAEFEKIENKEELNQM-------IDKMGLPLLLKTRRDAyDGRGNYKINSKSEIDDALDLF--SGKTLMVEKFVKF-EKEVSVIA-- 191
                      78999999999999887766555.......99*********988762568***************965..46789******86.66899998.. PP

                      SCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
  Dala_Dala_lig_C  95 klevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                           + gei +   + ++++ ++    +   p ++++ v+++ +++a k+ ++l+++G+  + +f+t+++ei++nE+ 
       AJA91990.1 192 --ARNTKGEISTYPVVENIHENNI--LRTTIAPGRVSETVRKEAEKIAEKTMEVLHGAGVFGIEMFVTSDDEILINEIA 266
                      ..3344566666666666777775..4566789********************************************95 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   3.1e-08   5.5e-05       1     190 [.     102     281 ..     102     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.1e-08
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEET.TCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaa.fglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEv 97 
                  Dk   k+ l+k ++ v++ ++   e+ ee  ++ +++g P ++k+   +  G+G   +++++e+ +++          f+ k+++vek++k  ke+ v
   AJA91990.1 102 DKLLQKQFLQKNGIAVAEFEKI--ENKEELNQMIDKMGLPLLLKTRrDAYDGRGNYKINSKSEIDDALDL--------FSGKTLMVEKFVKFEKEVSV 189
                  7778889999999999998888..********************9625899************9998765........55677*************** PP

                  EEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CC..HHHHHHH CS
  CPSase_L_D2  98 evlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsve..salaeka 190
                     r +kg + t    en+ +       ++AP + +++  r++ ++ a k+++ ++  g   +e  + + ++e+ + E+ +R+  +  ++l ++ 
   AJA91990.1 190 IAARNTKGEISTYPVVENIHENNIL-RTTIAPGR-VSETVRKEAEKIAEKTMEVLHGAGVFGIEMFVTS-DDEILINEIAPRVHNSghHTLQSCN 281
                  **********999999998766333.34678876.5677777777777777777777777789*99997.99***********876336666655 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.8   3.5e-08   6.3e-05       2     164 ..     101     266 ..     100     284 .. 0.75
   2 ?   -3.9   0.0       4.8   8.5e+03      40      65 ..     303     331 ..     300     337 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.5e-08
                 H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTT.T--EEEEE-SHHHHHHHHHH.GGG--EEEEE--SS-SEEE.EEEEETT CS
        RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegs.qGikvvlakkeqklkqvlea.lkeailvqeyieeaenedi.Rvlvvdd 97 
                 +dKl+  + L k++i v +++ ++++e+++++i+k+  + P+++K+      G +    + + ++ + l+    ++++v ++++++++  +      ++
  AJA91990.1 101 QDKLLQKQFLQKNGIAVAEFEKIENKEELNQMIDKM--GLPLLLKTRRDAyDGRGNYKINSKSEIDDALDLfSGKTLMVEKFVKFEKEVSViAARNTKG 197
                 69*********************************9..69*****976541577777777778888888875567889******998743302223334 PP

                 EEEE..EEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHC.T-SEEEEEEE.EETTEEEEEEEE CS
        RimK  98 evva..alrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakam.elvvaGvDll.rakrgllvlEvn 164
                 e+ +   ++ + ++   R+ +  G v+e   + +e +++A k  +++ ++ v G++++  +++++l+ E+ 
  AJA91990.1 198 EISTypVVENIHENNILRTTIAPGRVSET--VRKEAEKIAEKTMEVLhGAGVFGIEMFvTSDDEILINEIA 266
                 43221134555556679*********996..679999***99888652789*****651566667777775 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.8
                 -SSEEEEE-TTT...T--EEEEE-SHHHH CS
        RimK  40 rfPvvvKsvegs...qGikvvlakkeqkl 65 
                 ++P+++ ++ g    qG + vl kk++++
  AJA91990.1 303 KTPTIMYNILGPktfQGEYNVLFKKQDNI 331
                 67888888876323378888888888876 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.6   1.8e-07   0.00032       2     159 ..     101     270 ..     100     272 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                  TSHHHHHHHHTTT.S---..........-EESS--........SSSEEEEE.SS-------B--SS--TTE...........EEEE---S.EEEEEEE CS
  ATP-grasp_3   2 sdKlktykkLkeagvkvP......tkleaeeleee........ekklvvKp.rdGaggesvrvveekeeaeaaieeve....lvqefieG.kplSvsl 79 
                  +dKl   ++L+++g+ v       +       +ee          +l +K  rd+ +g ++ +++ k e + a++  +    +v +f++  k++Sv +
   AJA91990.1 101 QDKLLQKQFLQKNGIAVAefekieN-------KEElnqmidkmGLPLLLKTrRDAYDGRGNYKINSKSEIDDALDLFSgktlMVEKFVKFeKEVSVIA 191
                  7999999999999999995533321.......2222224444466777775268999****999999988877776667777999***9615677776 PP

                  EE.SS.SEEEEEEEEEEEET....TEEEEEEES----H..HHHHHHHHHHHHTTSTT--EEEEEEE.EESS.SEEEEEEESS-- CS
  ATP-grasp_3  80 lsdge.kvlvlavnrqliekaekefvyaGnvtpietel..keevvelaeevvekleglaGyvGvDl.vlkdeepyviEvNPRlt 159
                    +++ ++++  v +++ e+    ++ +  ++p ++++  ++e++++ae+++e l   aG++G+++ v +d+e+ + E+ PR+ 
   AJA91990.1 192 ARNTKgEISTYPVVENIHEN----NILRTTIAPGRVSEtvRKEAEKIAEKTMEVL-HGAGVFGIEMfVTSDDEILINEIAPRVH 270
                  66554134444444544444....6666677777766666999************.889*****96266779999*******86 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   7.4e-07    0.0013       2     101 ..     102     194 ..     101     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.4e-07
                 BHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-G.GGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---.SEEEEEEE CS
      GARS_A   2 sKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadgla.agKgvivakseeealkavkeilekkkfGeagekvviEelle.GeEvslla 98 
                 +K   k++l+k gi  ae+e++++ ee++++i++++ +   +K  + a  g+g +  +s++e  +a+ ++++       g+++++E++++  +Evs++a
  AJA91990.1 102 DKLLQKQFLQKNGIAVAEFEKIENKEELNQMIDKMGLPL-LLKTRRDAyDGRGNYKINSKSEIDDAL-DLFS-------GKTLMVEKFVKfEKEVSVIA 191
                 68889*********************************9.888877663588888777766643333.3443.......68888999888345888887 PP

                 EEC CS
      GARS_A  99 lvd 101
                   +
  AJA91990.1 192 ARN 194
                 655 PP

>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05     0.035      97     154 ..     226     281 ..     205     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                 HHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--C CS
     DUF1297  97 kvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegsp 154
                 +v + +ek+ e++ ++++    G F++++ vt+d e+++ ++++R+  +   ++++ +
  AJA91990.1 226 TVRKEAEKIAEKTMEVLHG--AGVFGIEMFVTSDDEILINEIAPRVHNSGHHTLQSCN 281
                 5667788888888887773..7************************977666665444 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.29       3      58 ..       7      62 ..       5      68 .. 0.82
   2 ?   -2.5   0.0       3.4   6.1e+03      41      63 ..      96     118 ..      80     120 .. 0.72
   3 ?   -1.2   0.0       1.3   2.3e+03      40      59 ..     237     246 ..     197     292 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                EES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHT CS
      TrkA_N  3 iiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelreeglevvvgdatdeevLeea 58
                iiG G++G+ l+e  ++ +  ++++v d   e++   ++ g++ +++d  de++++++
  AJA91990.1  7 IIGGGQLGMMLTEAAQNlDDiSKIIVLDPT-ENCPA-AKVGAQQIIADFKDEDAIKKL 62
                9****************8776446666665.45555.5799************99986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                 TSEEEES-TTSHHHHHHTTGGGE CS
      TrkA_N  41 glevvvgdatdeevLeeagieka 63 
                  l++++    ++++L++ gi+ a
  AJA91990.1  96 TLRIIQDKLLQKQFLQKNGIAVA 118
                 45677888888888888888765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                 TTSEEEES-TTSHHHHHHTT CS
      TrkA_N  40 eglevvvgdatdeevLeeag 59 
                 + +ev++           ag
  AJA91990.1 237 KTMEVLH----------GAG 246
                 4444444..........333 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.1e-05      0.13      36      96 ..       2      70 ..       1      78 [. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.1e-05
                  TSEEEEES-SHHHHHHHHHHHHTT-..EEEEESSSHHHHH...CHHHHTC...EECSHHHHHHH-SEEE CS
  2-Hacid_dh_C 36 gktvGiiGlGrIGqavakrlkafgm..kviaydrskkkee...eeeelgv...elvsleellaesDivs 96
                   kt+GiiG G++G  + + ++ ++   k+i+ d++++  +    +++  +   + + +++l + sDi++
    AJA91990.1  2 SKTLGIIGGGQLGMMLTEAAQNLDDisKIIVLDPTENCPAakvGAQQIIAdfkDEDAIKKLSELSDIIT 70
                  59*******************998556********9844333322222220113345666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2787.51
//
Query:       AJA91991.1  [L=886]
Description: pyruvate, phosphate dikinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-83  278.9   0.2    7.9e-83  277.9   0.2    1.5  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.3e-55  189.0   0.3    2.6e-32  112.4   0.0    3.7  4  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.2e-23   81.8   0.1    6.4e-23   80.3   0.1    1.9  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
      0.029   14.6   0.1        0.1   12.8   0.0    1.9  2  DUF968           Protein of unknown function (DUF968)
      0.041   13.5   0.3      0.041   13.5   0.3    2.5  3  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
       0.13   12.8   0.0       0.69   10.4   0.0    2.2  2  EF-hand_12       EF-hand fold domain
       0.19   12.0   4.3        8.7    6.7   0.0    4.2  4  GCR1_C           Transcriptional activator of glycolytic enzy


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.9   0.2   3.1e-86   7.9e-83       4     292 ..     521     874 ..     518     876 .. 0.96

  Alignments for each domain:
  == domain 1  score: 277.9 bits;  conditional E-value: 3.1e-86
                      STSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH....................HHHHHHHHHHHTTT CS
  PEP-utilizers_C   4 sgklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee....................qaeaykkvleamng 77 
                      +++++t+l+++++ k++ + aN+dtp++a+ a++ ga+GiGL+RtE++f++++++  + e                    q++++ ++l+am+g
       AJA91991.1 521 TKDFQTILSWAQNTKQLGIRANADTPDAAKLARQYGAQGIGLCRTERMFNESDRIGLFVEmimaesqeernkvlkklqelQKSDFIGILKAMEG 614
                      57899*************************************************9999999********************************* PP

                      SEEEEEXXXSSCCGGSGGC.......................HHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC.......EEEEE CS
  PEP-utilizers_C  78 rpvvvRtlDiggdkelpel.......................keepeevNPmlGfRgirlglsepelfetqlrAllrasaag.......kleim 141
                        v++R+lD++ +++lp+                         +e++e NPm+G+Rg+r+++++pe++++q+ A+++a+a+        k +im
       AJA91991.1 615 YKVTIRLLDPPLHEFLPNPeelkdrmnkendkskktqrvldrARELAEINPMMGHRGVRVAITYPEIYKMQITAVFEAAAELtkkkvnaKPQIM 708
                      *****************98899********************999***********************************6557888889**** PP

                      ESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC....HHHH...... CS
  PEP-utilizers_C 142 lPmvasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee....vakl...... 225
                      +P v s+ el+  k+i   vk+e+e++ +kkk k+++G+M+Ev++a l+ d+la  ++FfS+GtNDLtQ +++ +R+++e    + ++      
       AJA91991.1 709 IPQVGSLAELNYIKSIYDDVKKEIEQK-YKKKFKINFGTMLEVVRACLTSDELADTAEFFSFGTNDLTQAVFSFSREDAEgkflPEYMekelle 801
                      *************************99.****************************************************88875555888999 PP

                      SXTTTCHHCCCHHHHHHHHHHCC......XEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCT CS
  PEP-utilizers_C 226 ydplepavlrlikevikaaeekg......lkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqv 292
                        p++  + +++++++k+  ++g      l++giCGe++gdp+++++++ + + ++S+s++++p+a  a+aq+
       AJA91991.1 802 TSPFQSIDVNGVGHLMKIGIRQGrdikkdLEIGICGEHGGDPNSIKFCHSANVSYVSASPHRIPIAIVAAAQA 874
                      99*********************9999999***********************************99999887 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   7.1e-13   1.8e-09       3      40 ..      20      56 ..      18      59 .. 0.93
   2 !  112.4   0.0     1e-35   2.6e-32      76     226 ..      58     300 ..      55     307 .. 0.93
   3 !   36.0   0.1   1.8e-12   4.6e-09     270     327 ..     305     360 ..     292     361 .. 0.89
   4 ?   -2.2   0.1      0.77     2e+03     274     292 ..     726     744 ..     637     749 .. 0.64

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 7.1e-13
      PPDK_N  3 lvGGKganLaellneagipvPpgfaitadafrefleen 40
                l+GGKga+L+e+ +++++pvPpgf+it++++++++e++
  AJA91991.1 20 LLGGKGAGLSEM-TRLKLPVPPGFTITTEVCNKYYENG 56
                89**********.77*******************9986 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 1e-35
      PPDK_N  76 elPeeleeaikeayeelgkkfgde......elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle............................... 137
                 +lP+++  a+++ + +++kk g++      +l+v+VRS+      +  s++G++dt+Ln+g +e+++e                               
  AJA91991.1  58 KLPKDVMPAVMKNILKMEKKTGKKwnstknPLLVSVRSG------AAISMPGMMDTILNLGLNEKTVEgfavqtknprfswdsyrrfiqlfgkvvfgvn 150
                 6788888777777777777777776665888********......99**************************************************** PP

      PPDK_N 138 .........................................................aikavfaSlfnerAilYrkekgldhe.evalavvvqkmvnsd 178
                                                                          ai+avf+S++ erA++Yr+++g++++   ++av+v  mv+++
  AJA91991.1 151 dekfdhvldsakskqgvtddsklnveslkkivkeykkicenhtkrkfpdtpneqlglAIEAVFRSWMGERAVVYREKNGITKDiANGTAVNVVTMVFGN 249
                 ********************************************************************************9753568************ PP

      PPDK_N 179 lg...asGVafsldpetG...fkdevlinasyGlGeaVVaGrvtpdefvvekst 226
                 +g   a+GV+f+++  +G    ++e+l na   +Ge+VVaG +t  ++ + k++
  AJA91991.1 250 MGddsATGVVFTRNGHNGkreIEGEYLTNA---QGEDVVAGVRTGKNVELLKKE 300
                 ******************888899******...***********9988877766 PP

  == domain 3  score: 36.0 bits;  conditional E-value: 1.8e-12
      PPDK_N 270 veeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetleee 327
                  +eL +  +k+ekh+++p+diEf+i+  +gk+yllQ+R  +    + +k+  ++ +e+
  AJA91991.1 305 HKELSNACEKLEKHFREPQDIEFTIE--QGKFYLLQTRTAKMSAGALVKTSVDMVKEK 360
                 689***********************..**************9999999999988875 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.77
      PPDK_N 274 aeiakkiekhygtpmdiEf 292
                 ++++k+ie++y++ + i f
  AJA91991.1 726 DDVKKEIEQKYKKKFKINF 744
                 5677888888888887777 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.1   2.5e-26   6.4e-23       4      73 .]     425     506 ..     422     506 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 2.5e-26
                    S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.............HH--TEEEEEETTTT CS
  PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati............elkegdlitvDgstG 73 
                    ++vIL+++et+p+d++++  a+Gi+t+ GG+ SHaAiv+r++g+P++vg+ e++i            ++ke++++++Dgs G
     AJA91991.1 425 KKVILIRKETKPEDVPAFFSAEGILTSLGGKSSHAAIVSRGMGKPCIVGCAELKInyenntctangiTVKENEMVSIDGSVG 506
                    56*****************************************************************************977 PP

>> DUF968  Protein of unknown function (DUF968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     4e-05       0.1      54     152 ..      66     166 ..      50     191 .. 0.81
   2 ?   -2.6   0.0       2.1   5.3e+03       6      34 ..     713     741 ..     711     763 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
      DUF968  54 svlrrllelpklevrgvsr..esnivaaqsdarevlkklakpvlkLkvdpeppasymakPkekrfesekylqfvkkqPCvccgkraddphhlighGeGk 150
                  v++ +l+++k+  ++ +   +  +v  +s a + +  + + +l+L +++ + + +  + k+ rf ++ y +f++    v+ g + ++  h++   + k
  AJA91991.1  66 AVMKNILKMEKKTGKKWNStkNPLLVSVRSGAAISMPGMMDTILNLGLNEKTVEGFAVQTKNPRFSWDSYRRFIQLFGKVVFGVNDEKFDHVLDSAKSK 164
                 4667788887776555443114444555888889999999***********************************999999998888888888777766 PP

      DUF968 151 mG 152
                  G
  AJA91991.1 165 QG 166
                 66 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
      DUF968   6 ealaesnlikfiasvirvaLaldsseelt 34 
                  +lae n+ik i + ++++++++ +++++
  AJA91991.1 713 GSLAELNYIKSIYDDVKKEIEQKYKKKFK 741
                 57888888888888888887755444333 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.5   6.5e+03      43     222 ..      51      77 ..      44     100 .. 0.57
   2 ?    0.5   0.5      0.15   3.8e+02     198     248 ..     290     345 ..     275     362 .. 0.67
   3 ?   13.5   0.3   1.6e-05     0.041     128     213 ..     579     664 ..     571     697 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
    PEARLI-4  43 kkneepveLpdesqsftlaeiskmkglktyeikeelqsvlsesyvsvgkYkvrasvsttLqaildKhGDiasnsKLqslatrsyyLetLasvvlELqst 141
                 k +e++ +Lp++     +++i km                                                                           
  AJA91991.1  51 KYYENGRKLPKDVMPAVMKNILKM--------------------------------------------------------------------------- 74 
                 445555555555555555555555........................................................................... PP

    PEARLI-4 142 plkkLkesrvkEmvavvkDlEsvkikvgWlrsvleEiveavkyydeqetavvEKevkerdvllkkqEmekqekelaekEKe 222
                                                                                               EK+
  AJA91991.1  75 ------------------------------------------------------------------------------EKK 77 
                 ..............................................................................443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
    PEARLI-4 198 kerdvllkkqEmekqekelaek.EKeikevre....kvtemaaklgelemkrarle 248
                 + ++v l k+Em k++kel +  EK  k +re    + t  ++k+  l+++ a++ 
  AJA91991.1 290 TGKNVELLKKEMPKSHKELSNAcEKLEKHFREpqdiEFTIEQGKFYLLQTRTAKMS 345
                 5678999999****999998643666666665221234445566666666666665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.6e-05
    PEARLI-4 128 LetLasvvlELqstplkkLkesrvkEmvavvkDlEsvkikvgWlrsvleEiveavkyydeqetavvEKevkerdvllkkqEmekqe 213
                 +e++ +  +E ++ +lkkL+e +  + + ++k +E  k+ +  l + l+E++   +   +  + +++K +k ++vl +  E+ +++
  AJA91991.1 579 VEMIMAESQEERNKVLKKLQELQKSDFIGILKAMEGYKVTIRLLDPPLHEFLPNPEELKDRMNKENDKSKKTQRVLDRARELAEIN 664
                 6788888899999*********************************************999999*****99999999988887766 PP

>> EF-hand_12  EF-hand fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.3     6e+03       8      38 ..     255     285 ..     253     308 .. 0.80
   2 ?   10.4   0.0   0.00027      0.69      54      91 ..     715     752 ..     685     753 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
  EF-hand_12   8 aaGkLlkkeafedkeeipWelfanilhkhll 38 
                 a G++++++  ++k ei  e + n   + ++
  AJA91991.1 255 ATGVVFTRNGHNGKREIEGEYLTNAQGEDVV 285
                 7889999999999999999999987766655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
  EF-hand_12  54 sfefeyiqkkffgnkssvskkevdefWskfGkilqtlr 91 
                   e++yi++ + + k+++++k  ++f   fG +l+ +r
  AJA91991.1 715 LAELNYIKSIYDDVKKEIEQKYKKKFKINFGTMLEVVR 752
                 4699******************************9886 PP

>> GCR1_C  Transcriptional activator of glycolytic enzymes
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0034       8.7      11      43 ..      46      87 ..      42      96 .. 0.80
   2 ?    0.7   0.0      0.27   6.8e+02      52      66 ..     179     193 ..     168     205 .. 0.81
   3 ?    2.4   0.0     0.079     2e+02      44      78 ..     565     599 ..     539     600 .. 0.80
   4 ?   -2.6   0.2       2.8   7.2e+03      28      38 ..     730     740 ..     722     743 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
      GCR1_C 11 edlwnEykeglngkps.........ikslekkygkrWrkdsk 43
                ++++n y+e  ++ p+         i ++ekk gk+W ++++
  AJA91991.1 46 TEVCNKYYENGRKLPKdvmpavmknILKMEKKTGKKWNSTKN 87
                5889999998887776777888888************97766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
      GCR1_C  52 kkiidfierlieeeg 66 
                 kki++++++++e+++
  AJA91991.1 179 KKIVKEYKKICENHT 193
                 889999999998843 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.079
      GCR1_C  44 esklfsrRkkiidfierlieeegitreeavkilee 78 
                  +++f++  +i  f+e ++ e + +r++++k+l+e
  AJA91991.1 565 TERMFNESDRIGLFVEMIMAESQEERNKVLKKLQE 599
                 478999999**********************9987 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.8
      GCR1_C  28 kslekkygkrW 38 
                 k++e+ky+k++
  AJA91991.1 730 KEIEQKYKKKF 740
                 34455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 6041.54
//
Query:       AJA91992.1  [L=194]
Description: hypothetical protein T478_1274 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1231  (0.0686597); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1525.85
//
Query:       AJA91993.1  [L=504]
Description: putative tRNA-guanine(15) transglycosylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-64  215.8   0.0    1.3e-63  215.3   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
    6.1e-10   39.2   1.2    1.3e-09   38.1   1.2    1.5  1  DUF5591   Domain of unknown function (DUF5591)


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.3   0.0   1.5e-67   1.3e-63       3     349 ..      11     333 ..       8     334 .. 0.95

  Alignments for each domain:
  == domain 1  score: 215.3 bits;  conditional E-value: 1.5e-67
                 EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-SHHHHHHHEEEESSEEEEE CS
         TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsggfqvfslkkiteegvsfq 101
                 +R+G l+++hg+ietP f+pv  ++  +++ ++++k e+g +++++n+y++++r +e+   + +g+hk++++d++i+tdsgg+qv++            
  AJA91993.1  11 GRIGVLHTNHGKIETPSFVPV-IHPVKQTIPAKKIK-EIGFDVVITNAYITMKRLEEKA--RKNGIHKIIKYDSSIMTDSGGYQVLE------------ 93 
                 8********************.9999999******5.9***********9986655555..788********************886............ PP

                 -TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH....SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE- CS
         TGT 102 sridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah....qalfgivqGglyedlreesaeelakrdfdgyaig 196
                   + G+ v ++p  + ++  ++  D +++ld+++    skk++++ v+ Tl+  +  ++++    q+++g++qG+ +++l ++s +el++++++++a+g
  AJA91993.1  94 --Y-GE-VDVKPPAMAKFEMDIMTDFAIPLDKPTGFGLSKKQAKEYVDHTLKVCKTTIRNKknngQIWIGPIQGSEHPELVKRSTNELINMGYQMLALG 188
                 ..4.99.***************************************************777799899******************************** PP

                 S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH CS
         TGT 197 G.lsvge..ekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCkn 292
                 + ++++e  e++ l e++ a+++++p++ p +l+G+g+P ++  avalG+D fd++ ++++a+++r++t++g+ +l++ +y     p     +C + ++
  AJA91993.1 189 SpVEFMEsyEYKLLAEMIIAAKKNIPTSIPLHLFGAGHPLTIPLAVALGCDTFDSASYMLYAKHDRVITEDGTRRLQELEYF----P----FDCEVSSR 279
                 *9*****88899*********************************************************************9....8....89****99 PP

                 -BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
         TGT 293 ytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                 y++++l  ++k+++   +  +++ Nl+ ++ +++r+++aI+eg+++e+  + ar+++
  AJA91993.1 280 YKPKELLAMKKEER---TDQIALFNLYSIKAEVDRVKQAIREGRLWEYTMKKARAHP 333
                 *********99999...999*****************************99999887 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   1.2   1.4e-13   1.3e-09       1     119 [.     374     487 ..     374     502 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.4e-13
                 X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------------HHHHHHHHHHHHH CS
     DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiavtgewseeeiefvaellak 99 
                 ++r++e v++ ++ +  kk++v+    + kP  +s  ++k++++ k++   v+ + ++  lG++P e+  v+Pa++Y +    e++ e+  +  e+ + 
  AJA91993.1 374 IRRYHEYVKK-FRTK--KKIVVITKDPMIKPVFTSYDYKKLRRKFKDA-DLVQFCNYNPFLGIIPIEISDVFPASHYVMSRK-EFEPEKFPTFLEVWNV 467
                 789*****96.8877..7****************************99.79**************************88877.8*********9**999 PP

                 HHHHHT-SEEEE---THHHH CS
     DUF5591 100 ylektkyekviahleeeyre 119
                 +++k+k+++v +  ++++ +
  AJA91993.1 468 FFSKNKFDSVYLPKNDSFLQ 487
                 99999999998776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2986.65
//
Query:       AJA91994.1  [L=205]
Description: putative ribosomal protein S2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-21   76.1   0.1    6.6e-12   45.1   0.6    2.1  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   4.3e-11   7.7e-07       4      95 ..      17     105 ..      14     108 .. 0.87
   2 !   45.1   0.6   3.7e-16   6.6e-12     149     212 ..     114     177 ..     111     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.3e-11
  Ribosomal_S2   4 agvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrangyyvnerWlgGtLTN 95 
                   +g+ +G  t   +++m+p+I  +  +g +++d++ tla+++ a+k  +++ +  +k++  + k+ a   +++ ++ +++  +  r+++GtLTN
    AJA91994.1  17 TGIRVG--TDMKTKSMRPFITSASpEGLYMLDIDITLAKIKSAAKWASGFDM--KKVIVCSGKEYATTPIEKFVELTGASPMLRRFMPGTLTN 105
                   556666..4556899******76648*********************99865..678889999****************************** PP

  == domain 2  score: 45.1 bits;  conditional E-value: 3.7e-16
  Ribosomal_S2 149 PdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                   P+l+++ dp+ +  a+ Ea+++gipvi+i +tn  ++++d +IpaN+   +++  i+ +la+ i
    AJA91994.1 114 PQLIIISDPEVDGQAIIEATNAGIPVIGISNTNNVTSNLDLIIPANNRGRKALATIYWLLAREI 177
                   9***********************************************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1274.68
//
Query:       AJA91995.1  [L=76]
Description: hypothetical protein T478_0007 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.1   0.3      0.052   13.1   0.3    1.6  1  RecR      RecR protein


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.9e-06     0.052      10      29 ..       2      21 ..       1      28 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-06
                HHHHHH-EE-TTT--EESSS CS
        RecR 10 qeakekvrhCsrCgnlteed 29
                + +ke+++ Cs+C+ ++ +d
  AJA91995.1  2 VGLKEDMGTCSICRKISATD 21
                5689************7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.33s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 466.99
//
Query:       AJA91996.1  [L=107]
Description: transcription factor S [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-18   65.3   6.4    3.1e-18   65.3   6.4    2.9  3  TFIIS_C         Transcription factor S-II (TFIIS)
     0.0054   16.6   8.8       0.17   11.8   5.7    3.0  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
      0.012   15.5   1.8      0.012   15.5   1.8    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.027   14.4   1.4      0.027   14.4   1.4    3.7  4  zinc_ribbon_4   zinc-ribbon domain
      0.029   14.4   1.4      0.029   14.4   1.4    2.6  2  DZR             Double zinc ribbon
      0.079   12.5   0.3      0.079   12.5   0.3    3.1  3  zf_C2H2_10      C2H2 type zinc-finger
       0.11   12.1   3.7        4.4    7.0   0.8    2.5  2  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
       0.12   12.8   5.7      0.082   13.4   2.3    2.2  2  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
       0.12   12.6  11.8       0.16   12.2   2.3    2.4  2  IBR             IBR domain, a half RING-finger domain
       0.35   10.2   7.1        5.4    6.4   3.6    3.0  3  zf-TFIIB        Transcription factor zinc-finger
       0.41   10.4   4.4       0.31   10.7   0.6    2.3  2  Baculo_LEF5_C   Baculoviridae late expression factor 5 C-term
       0.61   10.3  10.7       0.16   12.1   1.8    2.8  2  zf-C3HC4_4      zinc finger of C3HC4-type, RING
        1.6    8.7   6.9         49    4.0   3.7    3.1  2  Nudix_N_2       Nudix N-terminal
        2.4    7.9   8.9        9.1    6.1   2.3    2.7  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        3.8    7.7   7.6       0.78    9.9   3.2    2.1  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        4.5    7.6  14.5        3.3    8.0   1.6    3.5  3  C1_4            TFIIH C1-like domain
        4.9    7.2   8.4        1.6    8.7   1.0    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
        5.1    7.1  13.6        7.3    6.7   3.2    3.0  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        6.4    6.4  14.2        1.6    8.3   4.5    3.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
        6.5    6.3  10.0        4.1    7.0   0.1    3.4  4  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.59   5.3e+02       2       8 ..       3       9 ..       2      12 .. 0.79
   2 !    6.3   0.9    0.0096       8.6      26      36 ..      17      27 ..       9      30 .. 0.71
   3 !   65.3   6.4   3.4e-21   3.1e-18       2      39 .]      65     104 ..      64     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.59
     TFIIS_C 2 kCpkCgs 8
                Cp C+ 
  AJA91996.1 3 FCPTCDV 9
               5999985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0096
     TFIIS_C 26 tvfykCtkCgh 36
                t  ++C kC++
  AJA91996.1 17 TSVFTCPKCNY 27
                66677777776 PP

  == domain 3  score: 65.3 bits;  conditional E-value: 3.4e-21
     TFIIS_C   2 kCpk..CgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                  C++  C+++ea++++lQtRsaDEp+t f++CtkC+h+Wr
  AJA91996.1  65 NCENkdCDHNEAVWWMLQTRSADEPTTQFFRCTKCQHTWR 104
                 698778*********************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   5.7   0.00018      0.17       1      31 [.       1      29 [.       1      30 [. 0.79
   2 ?    4.0   0.0      0.05        45      10      28 ..      80     100 ..      80     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                    EEBESTTTSBEEEEECSCCCEEEESSSS-EE CS
  RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYee 31
                    +kFCp+C   L  ++  ++  f C +C Y e
      AJA91996.1  1 MKFCPTCDVRLKKDSNTSV--FTCPKCNYTE 29
                    9*******87755555555..99******76 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.05
                     BEEEEECSCCCE..EEESSSS CS
  RNA_POL_M_15KD  10 lLlpkedkegkn..feCrqCg 28 
                     +L  ++++e +   f C +C+
      AJA91996.1  80 MLQTRSADEPTTqfFRCTKCQ 100
                     566667777766799*****8 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.8   1.4e-05     0.012      30      55 ..       3      28 ..       2      30 .. 0.93
   2 ?    3.9   1.8     0.055        49      41      56 ..      88     103 ..      64     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                     C+ C  ++k++ ++ +f+Cp+C+++
      AJA91996.1  3 FCPTCDVRLKKDSNTSVFTCPKCNYT 28
                    5**********************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.055
  OrfB_Zn_ribbon  41 alsgrtfkCpnCgfea 56 
                     +++++ f+C++C++++
      AJA91996.1  88 EPTTQFFRCTKCQHTW 103
                     567889*******987 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.5   1.4e+03       5       8 ..       4       7 ..       3      10 .. 0.65
   2 ?    5.8   0.1     0.015        13       4       9 ..      21      26 ..      14      28 .. 0.63
   3 ?   -0.1   0.2         1   9.1e+02       1       7 [.      62      68 ..      62      68 .. 0.89
   4 ?   14.4   1.4     3e-05     0.027      26      36 .]      94     104 ..      88     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.5
  zinc_ribbon_4 5 CpsC 8
                  Cp C
     AJA91996.1 4 CPTC 7
                  6666 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
  zinc_ribbon_4  4 tCpsCk 9 
                   tCp+C+
     AJA91996.1 21 TCPKCN 26
                   555554 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1
  zinc_ribbon_4  1 MkitCps 7 
                   M i C++
     AJA91996.1 62 MEINCEN 68
                   99***96 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 3e-05
  zinc_ribbon_4  26 vrCskCghvFr 36 
                     rC+kC+h++r
     AJA91996.1  94 FRCTKCQHTWR 104
                    69********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.4   3.2e-05     0.029      13      36 ..       2      27 ..       1      33 [. 0.88
   2 ?    1.1   2.5      0.47   4.2e+02      30      37 ..      95     102 ..      60     107 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
         DZR 13 rfCseCgtklkavaa..edrCpsCge 36
                +fC++C  +lk+ ++    +Cp+C++
  AJA91996.1  2 KFCPTCDVRLKKDSNtsVFTCPKCNY 27
                8*********9877788999****97 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.47
         DZR  30 rCpsCgek 37 
                 rC +C++ 
  AJA91996.1  95 RCTKCQHT 102
                 56666654 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.59   5.3e+02       5       9 ..       4       8 ..       2      11 .. 0.81
   2 ?   12.5   0.3   8.8e-05     0.079       3      11 ..      20      28 ..      19      30 .. 0.90
   3 ?    2.2   0.3      0.15   1.3e+02       3      10 ..      94     101 ..      93     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.59
  zf_C2H2_10 5 CPKCq 9
               CP C 
  AJA91996.1 4 CPTCD 8
               ****7 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.8e-05
  zf_C2H2_10  3 fsCPKCqek 11
                f CPKC++ 
  AJA91996.1 20 FTCPKCNYT 28
                99*****95 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.15
  zf_C2H2_10   3 fsCPKCqe 10 
                 f C KCq 
  AJA91996.1  94 FRCTKCQH 101
                 78****96 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8    0.0049       4.4       5      25 ..       2      26 ..       1      29 [. 0.80
   2 ?    5.3   0.1     0.016        14      17      26 ..      92     101 ..      89     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0049
  Zn_ribbon_17  5 ksCayCelavkg....rvvlcgvCe 25
                  k C  C++++k+    +v+ c++C+
    AJA91996.1  2 KFCPTCDVRLKKdsntSVFTCPKCN 26
                  679*******9844446899****7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
  Zn_ribbon_17  17 rvvlcgvCeH 26 
                   +++ c++C+H
    AJA91996.1  92 QFFRCTKCQH 101
                   6899****** PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.3   9.1e-05     0.082       1      65 [.       4      72 ..       4      74 .. 0.77
   2 ?   -0.2   0.1       1.6   1.4e+03      13      17 ..      96     100 ..      84     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-05
    zf-C4pol  1 ClvCk......eklkkalCkkCrsdkqesllkllsrlkelekklneletvCqsCaqgsleeevkCdsrdCp 65
                C +C+      ++++   C kC+  +    ++++s  +e+e+ +  le+   +  ++ +++e++C+++dC 
  AJA91996.1  4 CPTCDvrlkkdSNTSVFTCPKCNYTEGGPKIEKQSVSQETESDFLVLEENEGK--DVLPTMEINCENKDCD 72
                999996665543444899****87777779999999999***99999875332..345569*********6 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
    zf-C4pol  13 CkkCr 17 
                 C+kC+
  AJA91996.1  96 CTKCQ 100
                 55554 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.3   0.00018      0.16      19      46 ..       2      27 ..       1      28 [. 0.85
   2 ?    5.4   2.1     0.023        21      20      47 ..      65     102 ..      50     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
         IBR 19 kwCprpdCeaiieksegcksvtCskCgf 46
                k Cp   C+  ++k+++++  tC+kC++
  AJA91996.1  2 KFCP--TCDVRLKKDSNTSVFTCPKCNY 27
                79**..9**8888888888899****98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
         IBR  20 wCprpdCeaii........ekseg..cks.vtCskCgfe 47 
                 +C ++dC++          ++ ++  + +  +C+kC++ 
  AJA91996.1  65 NCENKDCDHNEavwwmlqtRSADEptT-QfFRCTKCQHT 102
                 688888884433466665422222433.25789999986 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.6     0.006       5.4       2      25 ..       4      25 ..       3      26 .. 0.83
   2 ?    3.7   0.8     0.042        38       2       6 ..      22      26 ..      21      39 .. 0.82
   3 ?    3.2   0.1     0.062        55      21      26 ..      95     100 ..      83     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.006
    zf-TFIIB  2 CPkCqdeleeserggveidyCpqC 25
                CP+C + l++   ++  +++Cp+C
  AJA91996.1  4 CPTCDVRLKK--DSNTSVFTCPKC 25
                ******9995..456779999999 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.042
    zf-TFIIB  2 CPkCq 6 
                CPkC+
  AJA91996.1 22 CPKCN 26
                9***8 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.062
    zf-TFIIB  21 yCpqCr 26 
                 +C++C+
  AJA91996.1  95 RCTKCQ 100
                 555554 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.54   4.9e+02      36      41 ..      21      26 ..      17      27 .. 0.83
   2 ?   10.7   0.6   0.00035      0.31      11      41 ..      69     100 ..      65     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.54
  Baculo_LEF5_C 36 yCskCg 41
                   +C kC+
     AJA91996.1 21 TCPKCN 26
                   7****9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
  Baculo_LEF5_C  11 kqClHdfv.tiEiQnRagDEivsfvryCskCg 41 
                    k C H+       Q+R+ DE       C kC 
     AJA91996.1  69 KDCDHNEAvWWMLQTRSADEPTTQFFRCTKCQ 100
                    5577755525568*******9998899****5 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.8   0.00018      0.16      19      42 .]       2      25 ..       1      25 [. 0.96
   2 ?    2.3   1.8      0.22     2e+02      13      42 .]      63      99 ..      60      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
  zf-C3HC4_4 19 sfClsCisslqkepdgeqllCplC 42
                 fC +C  +l k+++ + ++Cp C
  AJA91996.1  2 KFCPTCDVRLKKDSNTSVFTCPKC 25
                6***************99****** PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
  zf-C3HC4_4 13 sleCGhsfClsCisslqkepdgeq.......llCplC 42
                 ++C+   C +    +++ +  +        ++C+ C
  AJA91996.1 63 EINCENKDCDHNEAVWWMLQTRSAdepttqfFRCTKC 99
                6777777776666666655443333445556889888 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.7     0.055        49       1      30 [.       2      27 ..       2      29 .. 0.70
   2 ?    3.3   0.1     0.086        78      23      31 ..      94     102 ..      81     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.055
                -B-TTT--B-EEE--TT-SS-EEEETTTTE CS
   Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgt 30
                kFC+ C  +    + ++ n   ++Cp+C++
  AJA91996.1  2 KFCPTCDVR----LKKDSNTSVFTCPKCNY 27
                899999655....44555777788888887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.086
                 EEETTTTEE CS
   Nudix_N_2  23 lvCpaCgti 31 
                 ++C++C+++
  AJA91996.1  94 FRCTKCQHT 102
                 57****985 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.3      0.01       9.1      37      52 ..      12      27 ..       3      29 .. 0.78
   2 ?    5.4   0.6     0.016        15      38      52 ..      87     101 ..      63     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.01
  zinc_ribbon_10 37 keeleevkyrCpkCga 52
                    k+++++  + CpkC+ 
      AJA91996.1 12 KKDSNTSVFTCPKCNY 27
                    67788889******97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.016
  zinc_ribbon_10  38 eeleevkyrCpkCga 52 
                     +e+++  +rC kC++
      AJA91996.1  87 DEPTTQFFRCTKCQH 101
                     45556679*****98 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.2   0.00087      0.78      18      39 ..       4      25 ..       2      26 .. 0.93
   2 ?   -2.0   0.1       4.8   4.3e+03      18      21 ..      96      99 ..      89     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
  Auto_anti-p27 18 CpvCgvPLmrdrkggkvyCvaC 39
                   Cp+C v L +d ++    C+ C
     AJA91996.1  4 CPTCDVRLKKDSNTSVFTCPKC 25
                   ***********99999****** PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
  Auto_anti-p27 18 CpvC 21
                   C +C
     AJA91996.1 96 CTKC 99
                   5555 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   4.1      0.11     1e+02      18      32 ..      12      26 ..       1      28 [. 0.69
   2 ?   -0.1   0.1       1.3   1.1e+03      14      30 ..      52      68 ..      36      78 .. 0.66
   3 ?    8.0   1.6    0.0036       3.3      17      34 ..      85     102 ..      71     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
        C1_4 18 deeltssryrCekCk 32
                ++ + +s+++C+kC+
  AJA91996.1 12 KKDSNTSVFTCPKCN 26
                345678999****97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
        C1_4 14 kkkkdeeltssryrCek 30
                +++ ++ l ++  +Ce+
  AJA91996.1 52 ENEGKDVLPTMEINCEN 68
                45555556667777764 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0036
        C1_4  17 kdeeltssryrCekCknd 34 
                 + +e t+ ++rC kC+++
  AJA91996.1  85 SADEPTTQFFRCTKCQHT 102
                 45678999********97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.0    0.0018       1.6      72      94 ..       3      27 ..       1      44 [. 0.84
   2 ?    3.0   1.2      0.11        97      70      81 ..      93     104 ..      60     107 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                EETTTS-EEECHHH..HHS-TTTSS CS
        HypA 72 rCreCgkefeleek..alrCpkCgs 94
                 C +C+ + +++++   ++CpkC+ 
  AJA91996.1  3 FCPTCDVRLKKDSNtsVFTCPKCNY 27
                5*****999988744678*****86 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                 EEEETTTS-EEE CS
        HypA  70 kvrCreCgkefe 81 
                  +rC++C+++++
  AJA91996.1  93 FFRCTKCQHTWR 104
                 467888888775 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.2    0.0082       7.3      21      45 ..       4      27 ..       2      28 .. 0.71
   2 ?    6.0   0.4     0.013        11      19      27 ..      20      28 ..      15      32 .. 0.80
   3 ?    4.3   2.8     0.043        39      35      46 .]      91     102 ..      69     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0082
  Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrk 45
                   CP C +r k    +t  +f C +C++
     AJA91996.1  4 CPTCDVRlKK-DSNT-SVFTCPKCNY 27
                   9999988544.4444.5999999987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
  Zn_Tnp_IS1595 19 fvCPhCgsr 27
                   f+CP+C ++
     AJA91996.1 20 FTCPKCNYT 28
                   89****875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.043
  Zn_Tnp_IS1595  35 rglfqCkeCrkq 46 
                     + f+C +C+++
     AJA91996.1  91 TQFFRCTKCQHT 102
                    589******995 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.5    0.0018       1.6       3      25 ..       4      25 ..       3      46 .. 0.90
   2 ?    3.2   1.4     0.071        63      15      25 ..      89      99 ..      65     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                  ETTTTCEECHEETSTTCEEESSS CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdC 25
                  CP C  + l  D ++  ++C++C
    AJA91996.1  4 CPTCDVR-LKKDSNTSVFTCPKC 25
                  *****97.8************** PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.071
                  TSTTCEEESSS CS
  TF_Zn_Ribbon 15 pergelvCtdC 25
                  p +  ++Ct+C
    AJA91996.1 89 PTTQFFRCTKC 99
                  4555569**99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0046       4.1       2      16 ..       1      15 [.       1      17 [. 0.72
   2 ?    4.2   0.5     0.034        31       4       9 ..      21      26 ..      18      27 .. 0.75
   3 ?   -2.2   0.0       3.5   3.1e+03      15      19 ..      62      66 ..      55      68 .. 0.57
   4 ?   -0.6   0.2       1.1   9.6e+02      19      23 ..      96     100 ..      94     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
  zf-ribbon_3  2 tvrCPnCGa.plssdd 16
                 +++CP C+  + ++d 
   AJA91996.1  1 MKFCPTCDVrL-KKDS 15
                 799****8744.6665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
  zf-ribbon_3  4 rCPnCG 9 
                 +CP+C+
   AJA91996.1 21 TCPKCN 26
                 688885 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.5
  zf-ribbon_3 15 ddnvC 19
                   ++C
   AJA91996.1 62 MEINC 66
                 45667 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.1
  zf-ribbon_3  19 CpyCG 23 
                  C++C+
   AJA91996.1  96 CTKCQ 100
                  88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 640.28
//
Query:       AJA91997.1  [L=406]
Description: asparagine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-34  117.6   0.0    1.2e-33  117.3   0.0    1.0  1  Asn_synthase   Asparagine synthase
    2.4e-07   30.1   0.1    4.7e-07   29.2   0.1    1.4  1  NAD_synthase   NAD synthase
    0.00025   20.9   0.0    0.00043   20.1   0.0    1.3  1  ATP_bind_3     PP-loop family
     0.0014   17.5   0.0     0.0023   16.8   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
     0.0016   18.0   0.0     0.0026   17.3   0.0    1.3  1  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.0   3.3e-37   1.2e-33      13     355 .]      62     392 ..      59     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 3.3e-37
  Asn_synthase  13 rlradvpvGalLSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhleepfadrsaiply 108
                   ++    ++++ LSGG+DS+l+ +l+++  +  ++ + si+f + + de+k a ++a+ +  +ht + l++   l++lp++i+++  pf+d     +y
    AJA91997.1  62 QTFDKQKICIALSGGVDSTLVLSLLRKIKPdIEIEALSIKF-ANSVDETKNASKIADTFDANHTIINLEN--YLSELPKAISMIKLPFWDLH---WY 152
                   56677899*********************98789*******.99******************97766666..89***************988...77 PP

  Asn_synthase 109 llsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklplarslrasllarklrklaellelaeardleelaelyrlkasdsae....... 198
                   +++++  +  +k + sG+G+DElfgGY+++yk+ ls  +e            s+  +k+++ +e+ e   + ++  ++++ ++k++ s++       
    AJA91997.1 153 YVAKAS-QPISKFLVSGDGGDELFGGYTFRYKKFLSLTNET-----------SSPLEKTKAYLECHE---RDRVSDQEDIFTKKSNFSWNliheqli 234
                   777777.77799****************9999885554333...........333444444444444...444444456666666666667888888 PP

  Asn_synthase 199 .aelegedelhrelyldlktllpgdllrk.DrasmahglEaRvPflDhrlvevalrlppelklrg..gieKyiLRealegylPeeileRpKegfsap 291
                       ++ + l+++++ d++  l ++      r+  +  + + +P l ++l+  a  +p+e+k+++  +i+K  LR +l++  +++++  +K gf++ 
    AJA91997.1 235 pYFDNSLSNLEQIFLADYNGKLLYNFNPVnSRIINSLEMNLLTPILNDDLILSAPHIPIEYKYDEitNIGKIPLRSILKKNGHDSLVSSEKLGFNVN 331
                   888899999*********9999999888779999999999********************************************************8 PP

  Asn_synthase 292 vgewklkgelrelaeellsdsrlakeglldreaveelleeheagkrnesrqlwslllsleawle 355
                   + +  +k   + l++e lsdsr  k g++++e ++++++++e    ++ ++   +l ++e w++
    AJA91997.1 332 TINL-WKSHGHSLCKEFLSDSRVVKDGWINNEWIQKHIDSPEL-DVKYVNKFLGIL-AFEIWYR 392
                   7777.567899***************************99999.666777777777.9999975 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   1.3e-10   4.7e-07       3      88 ..      51     135 ..      49     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.3e-10
                   HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHH CS
  NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivraf 88 
                   +++++ +++++++ + +++ + lSGGvDS+lv  l +k+  + ++ al + +  +s +++++a ++a+ ++ + + i+++++++ +
    AJA91997.1  51 KSICKNIEQKLQTFDKQKICIALSGGVDSTLVLSLLRKIKPDIEIEALSI-KFANSVDETKNASKIADTFDANHTIINLENYLSEL 135
                   57899***********************************99999****9.88899999*********************998765 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-07   0.00043       1      58 [.      68     124 ..      68     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                 EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT CS
  ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckkln 58 
                 k+++A+SgG+DS++ l ll k k    i++ a+ + +  + +e+k+ +++  ++ +++ 
  AJA91997.1  68 KICIALSGGVDSTLVLSLLRKIKP--DIEIEALSIKFANSvDETKNASKIADTFDANHT 124
                 589*******************88..578888888888874455555555544444443 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.4e-07    0.0023       1      56 [.      67     123 ..      67     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.4e-07
  tRNA_Me_trans   1 kkvvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaer 56 
                    +k+++alSgGVDS++++ ll++     e++++ +k+ ++ de++ + ++ +d+ da++
     AJA91997.1  67 QKICIALSGGVDSTLVLSLLRKIKpdIEIEALSIKFANSVDETK-NASKIADTFDANH 123
                    5899****************998722456677778777777777.6666677777665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.2e-07    0.0026       3      62 ..      70     129 ..      68     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.2e-07
                 EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
        QueC   3 vvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62 
                  + lSGG+DSt vl l +k     e+eal++++ +    e++ a+kia++++  +h+i++l+
  AJA91997.1  70 CIALSGGVDSTLVLSLLRKIKpdIEIEALSIKFANS-VDETKNASKIADTFDA-NHTIINLE 129
                 5789*********99887655337999******875.568999**********.99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2153.02
//
Query:       AJA91998.1  [L=365]
Description: peptidase, M50 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-12   44.9  15.4    6.4e-07   28.9   0.6    2.8  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.11   12.7   0.0        0.3   11.3   0.0    1.7  1  DUF5056        Domain of unknown function (DUF5056)
       0.12   12.9   0.1       0.21   12.1   0.1    1.3  1  DUF3698        Protein of unknown function (DUF3698)


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   8.9   1.1e-07   0.00066       4     109 ..     130     214 ..     127     256 .. 0.81
   2 !   28.9   0.6   1.1e-10   6.4e-07     188     226 ..     256     294 ..     223     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-07
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp......LGGyVkmageepeeelseeeakaflkkspwqrllivlA 93 
                     +l+ ++ vHE GH+++Ak++++k                   ++Y+i+ +p      +G++++ ++   +++                 + i++A
     AJA91998.1 130 WALLGILGVHEAGHLFAAKWHKIKT-----------------TWPYFIPGIPivgiptFGAFIQSRSLTVNRD---------------ILFDIAVA 193
                    6899999*****************9.................6799999999999999******999996666...............8899**** PP

                    XXXXXXXXXXXXXXX.....- CS
                    xxxxxxxxxxxxxxx.....x RF
  Peptidase_M50  94 Gplanfilailvfvv.....p 109
                    Gp+a++++a++v+++     p
     AJA91998.1 194 GPIAGLVVAVVVVIFgawtsP 214
                    ************999555551 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 1.1e-10
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleai 226
                    + s++ ++a++++ +++lNLlP ++LDGgh+ + +l + 
     AJA91998.1 256 IMSPIMFAAWLGFLITFLNLLPAWQLDGGHMSRVILGQK 294
                    458999*************************99998765 PP

>> DUF5056  Domain of unknown function (DUF5056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05       0.3      19      60 ..      61     105 ..      45     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
     DUF5056  19 nGFsrr.VmrrlPer..skrlariwtavcavlavvLFvvldGlel 60 
                 +G+ +  V+ ++P++   ++l++ wt  ++ +a v  v++dG+  
  AJA91998.1  61 EGYRHMvVVSKMPKQkkRRWLSKSWTPRIMFAATVAMVLIDGFYR 105
                 56655416789**9966679**********************964 PP

>> DUF3698  Protein of unknown function (DUF3698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.6e-05      0.21      19      98 ..      21     104 ..       5     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
     DUF3698  19 eeadalktpeilfevGdYktenycleqGleel....kvaikdfkqklkekLksieeedlfeDkeWsprvlfalvlrkylyqafl 98 
                 + +  l  ++ +fe  d+k +   l+q le       +  + +++ +     ++++++ +  k W+pr++fa  +   l + f+
  AJA91998.1  21 DREIGLVKMQFYFEDQDFKEKFVRLTQELETNnllcTLEKEGYRHMVVVSKMPKQKKRRWLSKSWTPRIMFAATVAMVLIDGFY 104
                 4555566778888888888888888888877644433333344444444667888899999999******98554444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2457.41
//
Query:       AJA91999.1  [L=146]
Description: PF04027 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-44  150.0   0.1    3.9e-44  149.8   0.1    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.1   2.2e-48   3.9e-44       3     132 ..      15     145 ..      13     146 .] 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 2.2e-48
                 EE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE--TT-----SSEEEEESSS---TTEE CS
      DUF371   3 arGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGspkltlenerdlvvRkSdyvddrTl 101
                 ++GH++v + h++Tleitkdd+lt++gdCI+gv++  ++ dl++++k+++++ e++i++t+++g+ + +i+g+Gspkltl++ +d+v+RkS ++++rT+
  AJA91999.1  15 FTGHKEVLSLHEKTLEITKDDSLTSQGDCIVGVNSGISCIDLPDKMKKKIQNPESKIRFTIKAGKFSFKIQGHGSPKLTLKHVSDIVLRKSAFTCSRTI 113
                 78************************************************************************************************* PP

                 EBS-S--GGGS-HHHHHHHHT.T-EEEEEEEE CS
      DUF371 102 lvkadkaaadldrelveaLkk.gaeltvelev 132
                 ++++dka++d++r++v+ L++ +++ ++ +ev
  AJA91999.1 114 AINCDKASSDIPRDFVHLLQNpQTKGKMIIEV 145
                 *********************88898888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1081.55
//
Query:       AJA92000.1  [L=199]
Description: tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-43  147.8   0.0    2.6e-43  147.6   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   1.4e-47   2.6e-43       4     179 .]      19     188 ..      16     188 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 1.4e-47
                     HTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEEE..E-TS-HHHHTTTT CS
  Sua5_yciO_yrdC   4 rkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlllkrskeklpkevapglk 98 
                     ++G+i+ +pt+tvYg++cd+ ++++++r++e+K+r+ +k +++l  s ++l+k++e  ++  a k+ e+fwPG +tlll+ +ke +++++ ++++
      AJA92000.1  19 ENGEIIGFPTDTVYGIGCDPFKKDSITRIFELKKRDGEKKFPILGISKDELEKIVE--FNSDAEKISEKFWPGQVTLLLPIRKE-ISEKI-ENNG 109
                     68*****************************************************8..**********************8666.99999.78** PP

                     EEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS---EEEETTSSTSSECEXX CS
  Sua5_yciO_yrdC  99 tvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvdstVvdltegkpkilRrG 179
                     +++vr+P ++ ++ +l++++ +++ TSan+sge+si+d +e++ +l  +v+ ++dgg i  + +st++d+++g++ki+R+G
      AJA92000.1 110 KLAVRVPGNKCILSILKQCK-LIIGTSANISGEKSILDSNEFKIKLP-EVNTLVDGGTIVSEGESTIIDFINGELKIIREG 188
                     ******************96.9***********************97.5689***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1503.23
//
Query:       AJA92001.1  [L=500]
Description: putative acetyl-CoA carboxylase, biotin carboxylase subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-69  233.9   0.1      2e-69  233.3   0.1    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    7.1e-46  155.3   0.0    1.3e-45  154.5   0.0    1.4  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    1.6e-33  115.1   0.0    3.2e-33  114.0   0.0    1.6  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    4.9e-11   42.5   0.1    1.2e-10   41.3   0.1    1.5  2  ATP-grasp        ATP-grasp domain
    3.6e-09   36.5   0.2    1.1e-08   34.9   0.2    1.7  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      8e-08   32.5   0.1      2e-07   31.2   0.1    1.7  2  ATP-grasp_3      ATP-grasp domain
    1.5e-07   31.2   0.0    7.6e-07   28.9   0.0    2.0  1  RimK             RimK-like ATP-grasp domain
    0.00022   20.9   0.1    0.00042   19.9   0.1    1.5  1  ATP-grasp_4      ATP-grasp domain
  ------ inclusion threshold ------
      0.027   13.7   0.0       0.11   11.8   0.0    1.9  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
      0.045   13.5   0.0      0.079   12.7   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.051   12.5   0.0      0.084   11.8   0.0    1.2  1  DUF3182          Protein of unknown function (DUF3182)
      0.098   12.4   0.0       0.26   11.0   0.0    1.7  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.1   1.3e-72     2e-69       1     209 [.     115     322 ..     115     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 1.3e-72
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEve 98 
                  Dk + k+a+ k++vp+vp+s+++v+++++a +ia+eigyPv++k+ +g+GG+G r+++n++el++ + + ++e+ aa g++ + vek+l++ ++iE++
   AJA92001.1 115 DKMRCKAAMLKADVPTVPGSPGIVDDAQQAEKIANEIGYPVLLKSVYGGGGRGIRLVTNDKELQDGFDTVTSESIAAVGKSAIIVEKFLEKTRHIEYQ 212
                  8999********************************************************************************************** PP

                  EEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HH CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlv 196
                  + rD++gn+++++ere+s+q+r+qk+ie  Ps+ +++++r++++e  vk++++v++++ gt efl    ++e+y+iE+N+Rl+ve++++e++ Gld v
   AJA92001.1 213 MCRDKHGNAVHLFERECSIQRRNQKLIEQTPSPIVDQAKREEIGELVVKAAEAVDYTNLGTAEFLRAD-NGEFYFIEINARLQVEHPISEMVSGLDFV 309
                  ****************************************************************9886.***************************** PP

                  HHHHHHHTT--GC CS
  CPSase_L_D2 197 keaakialgekLe 209
                  k ++ ia+ge+L+
   AJA92001.1 310 KLQLDIANGETLP 322
                  ***********97 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.0   8.5e-49   1.3e-45       1     110 []       1     110 [.       1     110 [. 0.99

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 8.5e-49
                    ---EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE--SSTTTT-HHHHHHHH CS
  Biotin_carb_N   1 kikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpGyGflsEnaefaeave 96 
                    +i+kvlianrGeiA+r+++++++lgi+tvavys+ed nslhv++ade++ +g+a++++sYln eki++++ +sg+da+hpGyGflsEn++fa+++e
     AJA92001.1   1 MIEKVLIANRGEIALRVMKTCKTLGIKTVAVYSDEDVNSLHVKTADESYYIGEAAPAKSYLNQEKILEVMLSSGTDAIHPGYGFLSENDDFARLCE 96 
                    799********************************************************************************************* PP

                    HTT-EESSS-HHHH CS
  Biotin_carb_N  97 eagivfiGPsaeal 110
                    +++i+fiGPsa+++
     AJA92001.1  97 KNNINFIGPSADSM 110
                    **********9987 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   2.2e-36   3.2e-33       1     107 [.     336     442 ..     336     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 2.2e-36
                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS-BSHHHHHHHHH-HHH CS
  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvktnieflrailedeef 96 
                    e+RinaEd   +f+ps+G v ++++p+gp+vR+d+ ++ g +vsp+yDsl+aKl+++g+t +e   ++ +aL++++i+Gv+t i+++++il++ee+
     AJA92001.1 336 ECRINAEDTFLDFAPSTGPVPYVTIPSGPNVRCDTYLYPGCTVSPFYDSLMAKLCTWGPTFDESRVKMLNALNDFDIQGVETSIPLYKTILNSEEY 431
                    8*********************************************************************************************** PP

                    HHT---TTTCC CS
  Biotin_carb_C  97 akgeldtkfle 107
                    ++g+l+t+fl+
     AJA92001.1 432 KNGQLSTDFLK 442
                    *********97 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.8   7.2e+03     124     146 ..      12      34 ..       7      41 .. 0.76
   2 !   41.3   0.1   7.8e-14   1.2e-10      14     159 ..     138     292 ..     127     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.8
                 HHHHHHHHHHTSSEEEEEEEEEE CS
   ATP-grasp 124 eiakkiveeLggvGvfavElFvl 146
                 eia +++++   +G+ +v ++  
  AJA92001.1  12 EIALRVMKTCKTLGIKTVAVYSD 34 
                 67888899999999988877765 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 7.8e-14
                 ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEETTC-.EEE--EEEEEEETT CS
   ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsaeGe.tafypvvetvqedg 103
                 v++++++e++a+e+g+pv++K ++ g  G+G  +v ++++l++ ++++        ++  +ivE+f + ++ +   + r+++G+ ++ ++    +q+++
  AJA92001.1 138 VDDAQQAEKIANEIGYPVLLK-SVYGGGGRGIRLVTNDKELQDGFDTVtsesiaavGKSAIIVEKFLEKTRHIEYQMCRDKHGNaVHLFERECSIQRRN 235
                 78899****************.888999***************999999999999999*************************9678899999999998 PP

                 EEEEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
   ATP-grasp 104 ilrlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                    +   p+++ ++ + +++ e++ k++e++++  + + E+   ++ge ++ E+  R
  AJA92001.1 236 QKLIEQTPSPIVDQaKREEIGELVVKAAEAVDYTNLGTAEFLRADNGEFYFIEINAR 292
                 8888888888755538899*****************************999999887 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.2   7.1e-12   1.1e-08      26     174 ..     142     291 ..     134     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7.1e-12
                      HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHH......HHTT-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS- CS
  Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaiee......afkydekvlvEeai.egreievavlgneklevsevgeivvkkgfyd 112
                      +  ek+ +e+gypv+ K++  G   G+  v++ +el++ +++      a+   + ++vE+++ ++r ie  +  + + ++ ++ e+  +  + +
       AJA92001.1 142 QQAEKIANEIGYPVLLKSVYGGGGRGIRLVTNDKELQDGFDTvtsesiAAVGKSAIIVEKFLeKTRHIEYQMCRDKHGNAVHLFERECS--IQR 233
                      46799********************************988762212223345689*******99**********888888888777654..556 PP

                      HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
  Dala_Dala_lig_C 113 yeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                       ++k +    + +    ++++++e+i el++ka +a+d + l+   f+  ++ge+++ E+N 
       AJA92001.1 234 RNQKLI----EQTPSPIVDQAKREEIGELVVKAAEAVDYTNLGTAEFLRADNGEFYFIEINA 291
                      777776....3333345789999**************************************6 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.8   7.2e+03      94     120 ..      40      66 ..      34      71 .. 0.68
   2 !   31.2   0.1   1.4e-10     2e-07       1     159 [.     113     294 ..     113     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.8
                  EEEET....TEEEEEEES----H.HHHH CS
  ATP-grasp_3  94 qliekaekefvyaGnvtpietel.keev 120
                   ++++  +e  y G+ +p++  l +e++
   AJA92001.1  40 LHVKT-ADESYYIGEAAPAKSYLnQEKI 66 
                  55544.5558899999999988744554 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.4e-10
                  HTSHHHHHHHHTTT.S-.--...........-EE.SS--SSSEEEEESS-------B--SS--TTE...................EEEE---.SEEEE CS
  ATP-grasp_3   1 asdKlktykkLkeagvk.vP.......tkleaee.leeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefie.GkplS 76 
                  + dK+++  ++ +a v+ vP       +  +ae+ ++e  +++ +K ++G+gg ++r+v +++e++  +++v+            +v +f+e  +++ 
   AJA92001.1 113 CGDKMRCKAAMLKADVPtVPgspgivdDAQQAEKiANEIGYPVLLKSVYGGGGRGIRLVTNDKELQDGFDTVTsesiaavgksaiIVEKFLEkTRHIE 210
                  789999999888886662469999998444444415566***************************999998899999******999****8457788 PP

                  EEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEESS-- CS
  ATP-grasp_3  77 vsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvGvDlvlkd.eepyviEvNPRlt 159
                   ++  d++ + v  + r+   +++++       +pi  +  +ee+ el+ ++ e++ +   +   +++ +d +e y+iE+N+Rl+
   AJA92001.1 211 YQMCRDKHGNAVHLFERECSIQRRNQKLIEQTPSPIVDQAkREEIGELVVKAAEAV-DYTNLGTAEFLRADnGEFYFIEINARLQ 294
                  88888888888888888877776666666666677665544899999999999999.888888889**999899*********97 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.1e-10   7.6e-07       3     179 ..     115     307 ..     113     314 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.1e-10
                 -HHHHHHHHHHTT---.-.-EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.GGG--........EEEEE--SS-SEEE CS
        RimK   3 dKlkslklLakakikv.p.ntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.lkeai........lvqeyieeaenedi 90 
                 dK+++ + ++ka++++ p    ++ d ++aek+ ++i  + Pv++Ksv+g  G ++ l  + ++l++ +++ + e+i        +v +++e++    i
  AJA92001.1 115 DKMRCKAAMLKADVPTvPgSPGIVDDAQQAEKIANEI--GYPVLLKSVYGGGGRGIRLVTNDKELQDGFDTvTSESIaavgksaiIVEKFLEKTRH--I 209
                 9***********987523256899999******9999..6**************************99998744455555555559****998765..5 PP

                 EEEEETTEEEEEEEEE--SSS-.---TTTT-EEEE----H....HHHHHHHHHHHHCT-SEEEEE.EEEETTE.EEEEEEESS--SHH..HHHHHT-- CS
        RimK  91 RvlvvddevvaalrrvskeGdF.RsnlhrGgvaeklqlse....eekelAikaakamelvvaGvD.llrakrg.llvlEvnsspglek..iektlgid 179
                    +  d+   a++   +e    R n ++  ++    +++    e  el +kaa+a++   +G    lra++g ++++E+n+  ++e+  +e+ +g+d
  AJA92001.1 210 EYQMCRDKHGNAVHLFERECSIqRRNQKLIEQTPSPIVDQakreEIGELVVKAAEAVDYTNLGTAeFLRADNGeFYFIEINARLQVEHpiSEMVSGLD 307
                 5556677777777777777664378888777776655554111145589**************9889999886479*******999863356666655 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.8e-07   0.00042       1     151 [.     151     292 ..     151     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
  ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGe.EfavdayfdeeGepvilnilkkefaseedvsdr 97 
                  i +Pv +K + g + +G++ + n++e+++ ++++ +e          ++v ++ ++vE+++e +  +   +  d++G++v  +++++e + ++  ++ 
   AJA92001.1 151 IGYPVLLKSVYGGGGRGIRLVTNDKELQDGFDTVTSE--------SIAAVGKSAIIVEKFLEKTrHIEYQMCRDKHGNAV--HLFERECSIQRRNQKL 238
                  579*******************************987........344588999*******9752567889999999987..678999999999999* PP

  ATP-grasp_4  98 lyvtsakviee.tlealeellkevnallglknfpvHiElrvsedgkiipiEvnpl 151
                  +  t++ ++ + + e++ el+ ++++++  +n  + +E+   ++g+ + iE+n++
   AJA92001.1 239 IEQTPSPIVDQaKREEIGELVVKAAEAVDYTNLGT-AEFLRADNGEFYFIEINAR 292
                  *99*9999976257899*************99987.78888889*********95 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     7e-05      0.11      15      84 ..     109     176 ..      97     199 .. 0.72
   2 ?   -1.3   0.0      0.67     1e+03     227     269 ..     254     296 ..     252     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
  ATPgrasp_ST  15 efplvddKlkfkelalraglk.vpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitered 84 
                   + l  dK+ +k  +l+a ++ vp   g+++   +++++e++ +e+   v++K ++g gG+Gi+ +t++++
   AJA92001.1 109 SMNLCGDKMRCKAAMLKADVPtVPGSPGIVD---DAQQAEKIANEIGYPVLLKSVYGGGGRGIRLVTNDKE 176
                  456889***9999988877642677666665...5555555566663349***************998654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.67
  ATPgrasp_ST 227 evlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                  e+ el++kaae + +  +    +  +++++ + +E+Nar  ++
   AJA92001.1 254 EIGELVVKAAEAVDYTNLGTAEFLRADNGEFYFIEINARLQVE 296
                  5667888888866666666667777889999*******96654 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.3e-05     0.079      44     120 ..     250     327 ..     214     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
  ATPgrasp_Ter  44 ekdeelielaerlaeefgldglvnvQv.rededgpkLLEiNpRasGGlgys.alaGvnlpylalklllgleteeveepe 120
                    k+ee+ el+ + ae++  + l    + r d+++ + +EiN+R +    +s +++G+++++l l+ + g et   ++ +
    AJA92001.1 250 AKREEIGELVVKAAEAVDYTNLGTAEFlRADNGEFYFIEINARLQVEHPISeMVSGLDFVKLQLDIANG-ETLPFKQSD 327
                   4567777777777777777777766652666666*************99984568************99.555544444 PP

>> DUF3182  Protein of unknown function (DUF3182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05     0.084     123     185 ..     139     205 ..     136     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
     DUF3182 123 edarraaarllkeg.kvRlKeveatgGrgQrvvedaaeldaaLaaldeeelaaeG...lVlEedlee 185
                 +da++a +   + g +v lK+v++ gGrg r v++ +el++  +++ +e++aa G   +++E+ le+
  AJA92001.1 139 DDAQQAEKIANEIGyPVLLKSVYGGGGRGIRLVTNDKELQDGFDTVTSESIAAVGksaIIVEKFLEK 205
                 56777666665554489********************************999988555677777765 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.26       2      90 ..     115     204 ..     114     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                 BHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE--- CS
      GARS_A   2 sKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelle 90 
                 +K   k+ + ka++pt   +   ++d+++a+++ +e + ++  +K++   +g+g+ ++++ +e  +  + + ++      ++ +++E++le
  AJA92001.1 115 DKMRCKAAMLKADVPTVpgSPGIVDDAQQAEKIANEIGYPV-LLKSVYGGGGRGIRLVTNDKELQDGFDTVTSESIAAVGKSAIIVEKFLE 204
                 677789999999999985567799*****************.9*****************************9999999999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 3186.17
//
Query:       AJA92002.1  [L=104]
Description: hypothetical protein T478_0805 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.006   16.2   0.2     0.0066   16.0   0.2    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
  ------ inclusion threshold ------
      0.067   13.4   0.5      0.098   12.9   0.5    1.2  1  FISNA            Fish-specific NACHT associated domain
       0.22   11.7   1.1        0.7   10.1   0.1    1.9  2  DUF4330          Domain of unknown function (DUF4330)


Domain annotation for each model (and alignments):
>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.1e-06    0.0066      68     133 ..      35      99 ..       8     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
  GNAT_acetyltran  68 rfilvpqseeweelieeilgeklkkitryaikkeeeafdkekLeklaeslpeeyelkkideelyee 133
                        + v+++++  + ie++++++l   +  a++++++++  + L+++a + + eyel++i+++ly  
       AJA92002.1  35 ITMEVQNNNSVMQEIESCIEQNLAGQSSVALNSFNTNMLLT-LKEAAMETNDEYELEQIKQKLYTL 99 
                      4556899999*********************9887777667.*********************975 PP

>> FISNA  Fish-specific NACHT associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   1.6e-05     0.098       4      55 ..      44      96 ..      42     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
       FISNA  4 sLkkkferifegiakagektlLnsiYTeLyitege.sgevneeHEvlqiekas 55
                s++++ e+  e++   ++++ Lns  T++++t +e   e n+e E+ qi+++ 
  AJA92002.1 44 SVMQEIESCIEQNLAGQSSVALNSFNTNMLLTLKEaAMETNDEYELEQIKQKL 96
                56777788888888889**************98884678**********8765 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4     0.061   3.7e+02      25      54 ..       9      36 ..       5      55 .. 0.46
   2 ?   10.1   0.1   0.00012       0.7     100     144 ..      51      94 ..      25      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.061
     DUF4330 25 ilavivgiflkpgtsgsvaqaeaaatkpve 54
                i+av++ +f +  +    +q++ + ++p++
  AJA92002.1  9 IIAVAIIGFSSSAYF--FSQTTITIESPIT 36
                333333333322222..1232222233333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
     DUF4330 100 kvvvpqpdGkvkaledepylkdllvtlegkakitedglvlggqkv 144
                 +   ++  G+  ++ +  +++++l+tl++ a  t+d++ l++ k 
  AJA92002.1  51 SCIEQNLAGQSSVALN-SFNTNMLLTLKEAAMETNDEYELEQIKQ 94 
                 4455666788888888.9********************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1479  (0.0824921); expected 358.6 (0.02)
Passed bias filter:                      726  (0.0404931); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 675.17
//
Query:       AJA92003.1  [L=532]
Description: methylmalonyl-CoA mutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     5e-215  714.9   0.9   5.7e-215  714.7   0.9    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase
  ------ inclusion threshold ------
      0.038   12.5   0.3      0.056   11.9   0.3    1.2  1  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
      0.081   13.2   0.0       0.24   11.6   0.0    1.7  2  HigB_toxin     HigB_toxin, RelE-like toxic component of a tox


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.7   0.9  9.5e-219  5.7e-215       2     513 .]      16     524 ..      15     524 .. 0.99

  Alignments for each domain:
  == domain 1  score: 714.7 bits;  conditional E-value: 9.5e-219
  MM_CoA_mutase   2 TaegievkplYtaedleekklgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvafdlptlrgyDsdhpraege 97 
                    T + i++kp+Y+++   ++   ++ PG+fPftRG+++ myr+r Wt+rqyagf++a+++n+ryk  Le+Gqtg+s+afdlpt++g+D+d p+aege
     AJA92003.1  16 TDSSIPIKPFYQKSTK-KR--PKEEPGKFPFTRGIHQGMYRDRFWTMRQYAGFGDAAQSNKRYKFMLEKGQTGISMAFDLPTQIGHDPDAPQAEGE 108
                    8999********9995.43..4479*********************************************************************** PP

  MM_CoA_mutase  98 vGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgtiqnDiLkellargtyiyppepslrliadiieyaake 193
                    vGk+Gv+i+sl+dm+t+++gi+l kvs+smtina+a +lla y+a+ e+qg + ++l+gt qnDiLke++ar+tyiyppeps+r+i+d+i y+a+e
     AJA92003.1 109 VGKVGVSISSLKDMQTVFNGIELGKVSTSMTINATASTLLAYYIAVGESQGFSSKQLRGTTQNDILKEYIARNTYIYPPEPSMRIIGDMIGYCATE 204
                    ************************************************************************************************ PP

  MM_CoA_mutase 194 vpkfntisvsgyhireaGatavqElAftladGveYvralleaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklr 289
                    vp+++++s+sgyhireaG++avqE+Aft+a++++Y++++l++Gl++defaprlsFff ++ +ffeeiAk+R+aR+++a+i+ke+f+ak+eksl+l+
     AJA92003.1 205 VPQWYPVSISGYHIREAGSNAVQEIAFTIANAIQYIETCLAQGLKIDEFAPRLSFFFCCTIEFFEEIAKFRVARKVYAKILKERFHAKNEKSLQLK 300
                    ************************************************************************************************ PP

  MM_CoA_mutase 290 vhaqTsgvsltaqdpyvNilRttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawk 385
                    +h+qTsg sltaq+p +Ni+R++++++aAvlggtqslhtns DealalPte+sa+iA++tq+i+a Esg++k+vDP++GS+y+E+L de++e+ w+
     AJA92003.1 301 FHTQTSGESLTAQQPDNNIVRVAMQTMAAVLGGTQSLHTNSRDEALALPTEESAKIALRTQQIVASESGITKTVDPMAGSHYLEELCDEIEEQTWA 396
                    ************************************************************************************************ PP

  MM_CoA_mutase 386 lfqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealraerdeaavkaaLaalgea 481
                    ++++i+++GG lkaie+G++q+ei+++a+r +k++++ ++v+vGvNkf  +e e + ++l+id+++ ++q ++++alr++rd+++ ++aL++l++a
     AJA92003.1 397 YLKKIDKMGGSLKAIEKGFFQAEIRQNAYRIKKEVDDSSRVLVGVNKF-VDEVEAKQKLLRIDDSLGRKQEKAIKALRKSRDNKKTDSALSKLQAA 491
                    ************************************************.889999***************************************** PP

  MM_CoA_mutase 482 arse.nllaraveaaralatlGeisdaleevfg 513
                    a+++ nl++ +v++++ +at Geis++l+evfg
     AJA92003.1 492 ADTDqNLMPFIVNSVKTYATTGEISNTLREVFG 524
                    **889**************************98 PP

>> Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   9.4e-06     0.056     186     362 ..     232     415 ..     224     439 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-06
  Met_asp_mut_E 186 sisiavaiiEallaaeqGvksitvg....ygqvgnlvqDvaalraleelaeeylkk.f.gyedvvvttvlhqwmGg...fPqdeakafgvislgaa 272
                    +i++a++ iE+ la    + +++      +  + ++  ++a  r+ ++++ + lk+ f + ++  +   +h++  g     q+  +    +++ ++
     AJA92003.1 232 TIANAIQYIETCLAQGLKIDEFAPRlsffFCCTIEFFEEIAKFRVARKVYAKILKErFhAKNEKSLQLKFHTQTSGeslTAQQPDNNIVRVAMQTM 327
                    688888888888886555555544300003444456788999999999998888763314456778888998888766444555555666788999 PP

  Met_asp_mut_E 273 vaalakatkvivKtphEalgvptkeanaaglratkqvlnlledqkleeteeleeekelikketraildkvle.lgdGDvavgavrafeaGv 362
                    +a+l++++ + + + +Eal  pt+e+   +lr+ + v   +++  +++t +  + ++ +++   +i +++   l + D + g ++a+e+G 
     AJA92003.1 328 AAVLGGTQSLHTNSRDEALALPTEESAKIALRTQQIV---ASESGITKTVDPMAGSHYLEELCDEIEEQTWAyLKKIDKMGGSLKAIEKGF 415
                    **************************99999977666...444444444444444444444444444443331233344455666666665 PP

>> HigB_toxin  HigB_toxin, RelE-like toxic component of a toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   0.0         3   1.8e+04      31      41 ..     117     127 ..     114     129 .. 0.56
   2 ?   11.6   0.0     4e-05      0.24       4      49 ..     382     427 ..     380     436 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 3
                 EE-SSTEEEEE CS
  HigB_toxin  31 davgnnrvvFn 41 
                 + +++  +vFn
  AJA92003.1 117 SSLKDMQTVFN 127
                 44455555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4e-05
                 HHHHHHHHHHHS--SSHHHHHHH-TT-EE-SSTEEEEEETTTTEEE CS
  HigB_toxin   4 aleawykevkkaewksladvkqtfpsadavgnnrvvFnIkgNkyRL 49 
                  le++++e+++++w+ l+++ ++  s++a+++ ++  +I++N yR+
  AJA92003.1 382 YLEELCDEIEEQTWAYLKKIDKMGGSLKAIEKGFFQAEIRQNAYRI 427
                 5899*****************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3772.83
//
Query:       AJA92004.1  [L=72]
Description: hypothetical protein T478_1151 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.4   2.5       0.02   15.2   2.5    1.1  1  DUF2628          Protein of unknown function (DUF2628)
      0.042   14.1   0.0      0.049   13.9   0.0    1.2  1  Glycophorin_A    Glycophorin A
      0.064   13.3   3.4      0.075   13.1   3.4    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.13   12.0   3.0       0.15   11.9   3.0    1.1  1  DUF2427          Domain of unknown function (DUF2427)
        7.1    6.3  12.5        5.8    6.6   3.2    2.2  2  DUF3149          Protein of unknown function (DUF3149)


Domain annotation for each model (and alignments):
>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.5   5.7e-06      0.02      23      69 ..      12      61 ..       4      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
     DUF2628 23 sfnvwAfffgfiwLlyrklwlkalvllviavavsvvlavl...gfsdavr 69
                 ++ +A+ff + +Ll+   w + ++ l i ++v+ vl ++   g+++a++
  AJA92004.1 12 FVSCIAAFFVYAYLLMLSEWSPIVLQLTILMVVGGVLGIVswiGYQMATT 61
                56789*****************************9999998888888775 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.4e-05     0.049      53      93 ..      29      69 ..      22      72 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                   SSSS-TTHHHHHHHHHHHHHHHHHHHHHHHHTHSXXXXXXX CS
  Glycophorin_A 53 hdFselvitliifgvmAgvigtillisYlirRliKKssvdv 93
                    ++s  v+ l i+ v+ gv+g++  i Y +     K+s+ +
     AJA92004.1 29 SEWSPIVLQLTILMVVGGVLGIVSWIGYQMATTAAKPSSLI 69
                   578999***********************999999988765 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.4   2.1e-05     0.075      44      99 ..       8      66 ..       6      71 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
  Phage_holin_3_6 44 gvlallalllllvalalala.alwlaali...vaavllvlagvlalvglkklkkakplpe 99
                     gv+ +++ +++++  a++l    w   ++   +  v+  + g++ ++g++ +  a+ +p 
       AJA92004.1  8 GVFIFVSCIAAFFVYAYLLMlSEWSPIVLqltILMVVGGVLGIVSWIGYQMATTAA-KPS 66
                     78888888888888876664334444444200223333333555555655444433.354 PP

>> DUF2427  Domain of unknown function (DUF2427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.0   4.2e-05      0.15      15      72 ..       4      60 ..       1      68 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
     DUF2427 15 ksalwvHiilmtlalvvvyPvalvLslaksrwylpvqivnlvlavlglllghiykgst 72
                ++ + v+i++  +a+++vy   l+Ls   s + l + i+ +v  vlg+++ + y+ +t
  AJA92004.1  4 RKSMGVFIFVSCIAAFFVYAYLLMLSEW-SPIVLQLTILMVVGGVLGIVSWIGYQMAT 60
                677899***************9999976.78899999999999999999998887665 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.2    0.0016       5.8      13      31 ..       6      24 ..       5      26 .. 0.90
   2 ?    5.2   1.9    0.0046        17      12      27 ..      39      54 ..      36      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0016
     DUF3149 13 SliVIvftigmgaffiryF 31
                S++V +f+ +++aff+  +
  AJA92004.1  6 SMGVFIFVSCIAAFFVYAY 24
                9**************9665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0046
     DUF3149 12 lSliVIvftigmgaff 27
                 +l+V   ++g+++++
  AJA92004.1 39 TILMVVGGVLGIVSWI 54
                589***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 543.01
//
Query:       AJA92005.1  [L=706]
Description: hydantoinase/oxoprolinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-57  195.0   4.2    1.6e-57  195.0   4.2    2.2  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    3.2e-20   72.6   8.2      5e-19   68.7   4.5    2.8  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
    1.6e-05   23.7   3.2     0.0029   16.3   0.5    2.3  2  MutL            MutL protein
    0.00012   21.7   5.5     0.0031   17.0   1.7    2.9  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
    0.00061   19.4   0.7     0.0023   17.6   0.7    2.0  1  FGGY_N          FGGY family of carbohydrate kinases, N-termin
  ------ inclusion threshold ------
      0.035   14.5   0.1       0.48   10.8   0.0    2.8  3  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.055   1.7e+02      82     103 ..       8      29 ..       2      78 .. 0.77
   2 !  195.0   4.2   5.3e-61   1.6e-57       1     289 [.     196     502 ..     196     504 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.055
  Hydantoinase_A  82 ItfDmGGTstDvslikdgevev 103
                     I++D+GGT t++++++  + e+
      AJA92005.1   8 IGIDVGGTFTKAIALDIVSGEI 29 
                     899********99876444444 PP

  == domain 2  score: 195.0 bits;  conditional E-value: 5.3e-61
  Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekkvItfDmGGTstDvsl 95 
                     rt ta++nA + p+  +  + ve+++++ g++a+lm+m++dGg++s+d++r kp+ t+lSGPaa+v+ga     + + ++ I++++GGTst ++ 
      AJA92005.1 196 RTLTAAINASVLPKTVQVGNFVEEAIRETGVTAPLMIMKGDGGVTSMDTFRTKPILTVLSGPAASVAGALL---YLKITNGIFVEVGGTSTNICI 287
                     899********************************************************************...888899*************** PP

  Hydantoinase_A  96 ikdgevevsleteiagvkvrlpaldirtvgagGgsilvvdeggklrvgpesagadpgp...............................acyrkG 159
                     ik+g++e+++ t+ +++++ ++++d+r +g++Ggs++ v+ ++++ vgp+sa++++                                  c+++ 
      AJA92005.1 288 IKNGKPEIRYVTI-KNHPTCIRSMDVRVLGVAGGSMVQVKSNTVVGVGPRSAHIAGLKyscyasmddlstgeiifvkpkpndieeyvaiKCKNET 381
                     **********999.***********************99*****************999*****************************8888888 PP

  Hydantoinase_A 160 gteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaq 254
                       ++t T+a++ LGr+++ d++       ++d  +a+ a+e l+k+l+++  +vA  il+ a+ ++ n++ k+++e  l+++++ lv+ GG++ +
      AJA92005.1 382 Y-AITNTCAANALGRIPEGDYS-------YSDPATAKFALEILGKKLGVSGAQVALSILQNASYDITNEITKIIKEFELEKSKVKLVGGGGGASV 468
                     8.********************.......9***************************************************************** PP

  Hydantoinase_A 255 haaalaeelgvkkvivppyagvlsalGmalAdvre 289
                     +a+ +ae+l ++ +    ya+v+s +G+a ++++e
      AJA92005.1 469 LAPFVAEQLQLQ-YDKADYAEVISSIGVASSMMQE 502
                     **********97.5666677*********998776 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   4.5   1.7e-22     5e-19       1     175 [.       7     175 ..       7     177 .. 0.83
   2 !    4.3   0.1    0.0096        29       2      20 ..     274     292 ..     273     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 1.7e-22
  Hydant_A_N   1 rigIDvGGTfTDavaldeke.eevavlKllst...pdavaegirealeevleesiprtskidvvrmGTTvatNallerkgervaLittkgfrdlleigr 95 
                 rigIDvGGTfT a+ald  + e + +  +++t   ++ v+ gi+++l+++l+es+++ ++i+ + ++TT+a+Nalle + ++v+++ +   ++   +  
  AJA92005.1   7 RIGIDVGGTFTKAIALDIVSgEILSASTIPTThtaERGVSAGIVSVLSDLLKESQIKLDEIEIIAHSTTQAINALLESDTAKVGIVAMGVGPEKSDVI- 104
                 79***************887566777788888999999************************************************999888777555. PP

  Hydant_A_N  96 qnrpdlfelrikkplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiavvllhSylnpehElrvaeiar 175
                  +r +l     ++  +  ++ ++ + r     +    +  +ev  a+k+lk++g++ i+ + ++ +  p++E+ + e a 
  AJA92005.1 105 -KRTNL-----RDAKINHDNDIKSSHRFL---DTSHLITDSEVSTAIKELKDDGAKVIVATEAFGVDDPSNEQFIMEHAT 175
                 .33344.....333444444444444433...344556789********************************9998776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0096
  Hydant_A_N   2 igIDvGGTfTDavaldeke 20 
                 i++ vGGT T ++++++++
  AJA92005.1 274 IFVEVGGTSTNICIIKNGK 292
                 799************9775 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   9.8e-07    0.0029       4      59 ..      10      66 ..       8     100 .. 0.80
   2 !    7.7   0.1   0.00038       1.1     228     281 ..     257     306 ..     231     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.8e-07
        MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee.edvleGleealeeleeklgkt..e 59
                iD+G t+Tk++++d    ++++l  +  pTt  + + v  G+ ++l++l ++ + +  e
  AJA92005.1 10 IDVGGTFTKAIALDIV--SGEILSASTIPTTHTAeRGVSAGIVSVLSDLLKESQIKldE 66
                8**************5..5************998899***********99985533541 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00038
        MutL 228 PaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspekekvllk.lpep 281
                 PaA + ++ l  +     + + + v+vGG++T++  + +g+pe++ v++k  p+ 
  AJA92005.1 257 PAASVAGALLYLK-----ITNGIFVEVGGTSTNICIIKNGKPEIRYVTIKnHPTC 306
                 5555555544444.....668899********************99999944443 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.7     1e-06    0.0031       1      67 [.       8      72 ..       8     295 .. 0.83
   2 !    5.4   0.1    0.0037        11     186     244 ..     423     481 ..     407     496 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                 EEEEE-SSEEEEEEEE.TTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE.. CS
  BcrAD_BadFG  1 vGiDgGsTttkavlmd.ekgevlgrgitnsanlesvrfeaaekvleealtealerageeeadieetyl 67
                 +GiD+G+T tka+ +d  +ge+l  + t ++  +++r  ++   ++ +l+++l++++ + ++ie ++ 
   AJA92005.1  8 IGIDVGGTFTKAIALDiVSGEIL-SASTIPTTHTAER--GVSAGIVSVLSDLLKESQIKLDEIEIIAH 72
                 7***************7778855.5666666666555..899********************887644 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0037
                  HTT--HHHHHHHHHHHHHHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHH CS
  BcrAD_BadFG 186 sggekaedIlaglhraialrvialisrsggvtdevtltGGvakneaavkelrklvkeny 244
                  sg ++a +Il+++  +i   + ++i++++ ++ +v l+GG   ++ +   + + ++ +y
   AJA92005.1 423 SGAQVALSILQNASYDITNEITKIIKEFELEKSKVKLVGGGGGASVLAPFVAEQLQLQY 481
                  5667899********************************97777666655555555555 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   7.6e-07    0.0023       3      91 ..       8      88 ..       6      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.6e-07
                EEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-EEEEETTTEE CS
      FGGY_N  3 lglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreglvllDkndkp 91
                +g+D+G+t+tkai+ld   g+++++++++ +   +      +    + + + +++  +l++++i+ ++i+ I+ s+ +   +ll+ ++  
  AJA92005.1  8 IGIDVGGTFTKAIALDiVSGEILSASTIPTTHTAE------RG---VSAGIVSVLSDLLKESQIKLDEIEIIAHSTTQAINALLESDTAK 88
                89**********************99998776554......33...33467788888899999999999999999988888888877754 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.77   2.3e+03      14      47 ..      54      85 ..      50      97 .. 0.81
   2 ?   -2.2   0.0       1.9   5.7e+03      19      51 ..     122     150 ..     112     155 .. 0.59
   3 ?   10.8   0.0   0.00016      0.48      23      79 ..     426     481 ..     408     491 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.77
  GHMP_kinases_C 14 gellnlsqrselkavvgilppeleellealselG 47
                     +ll +sq   ++++++i+  + +++++al+e +
      AJA92005.1 54 SDLLKESQI--KLDEIEIIAHSTTQAINALLESD 85
                    678888888..8999999999999***9998887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
  GHMP_kinases_C  19 lsqrselkavvgilppeleellealselGalga 51 
                     +s+r  l + + i   e+ +++++l++ G   a
      AJA92005.1 122 SSHR-FLDTSHLITDSEVSTAIKELKDDG---A 150
                     3333.344466677777777777777777...4 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00016
  GHMP_kinases_C  23 s......elkavvgilppeleelleal.selGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                     +      ++      ++ e++++++++ +e     +kl G GgG++v a f     aeq++++ 
      AJA92005.1 426 QvalsilQN--ASYDITNEITKIIKEFeLEKS--KVKLVGGGGGASVLAPF----VAEQLQLQY 481
                     444454444..667777888999999856666..***************99....666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 4645.07
//
Query:       AJA92006.1  [L=39]
Description: hypothetical protein T478_0299 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 301.35
//
Query:       AJA92007.1  [L=369]
Description: cobalamin biosynthesis protein CbiD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-90  302.9   4.2    2.3e-90  302.3   4.2    1.3  1  CbiD      CbiD
  ------ inclusion threshold ------
      0.033   14.5   0.1       0.84   10.1   0.1    2.7  2  Ret2_MD   RNA editing 3' terminal uridylyl transferase 2 midd
      0.061   13.3   2.2       0.29   11.2   0.1    2.5  2  DUF3042   Protein of unknown function (DUF3042)


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.3   4.2   3.9e-94   2.3e-90       1     252 []      11     271 ..      11     271 .. 0.99

  Alignments for each domain:
  == domain 1  score: 302.3 bits;  conditional E-value: 3.9e-94
        CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeivaeve.....eeieiegGeGvGrv 92 
                 lr+G+TtGscA+A++ka +l +++++++e+++i lpk ++l+i+i++++ ++++  ++vikd+GddpDvT+gaei+++ve     +eiei+gGeGvGrv
  AJA92007.1  11 LRTGFTTGSCATASSKAGVLSIINQKEIEKIDIILPKRTRLDIQINSCQFTKNSakCSVIKDGGDDPDVTHGAEIFVDVEltdkiGEIEIDGGEGVGRV 109
                 69************************************************888899*****************************88************ PP

        CbiD  93 tkpgLevevgeaAInpvprkmieenveevleea..kegvevtisvpeGeelAkkTlNprlGivgGiSiLGTtGivepmSeeallesireelkvaaaegl 189
                 tkpgL +e+g+aAInp+p+kmi env+ev +e   k+g++vt+svp+G+el +kT Npr+Gi+gGiSiLGT+Giv p+S++++ ++ir+++ v  + + 
  AJA92007.1 110 TKPGLGLEIGSAAINPTPKKMILENVKEVGNELleKNGIKVTVSVPKGKELGTKTDNPRIGIMGGISILGTSGIVIPYSTASFAAAIRQQIAVVSSMND 208
                 ******************************9989999************************************************************** PP

        CbiD 190 kelvlvtGnkgeklakkklglpeealvkvsnfvgealeeaaekgvkkvllvghiGKlvKlagG 252
                 + +vl+tG ++e++a++ ++lp+++++++++f g++++++a+k++kk +++g+iGKl+K+a+G
  AJA92007.1 209 DYVVLTTGGRSEDFAREIIELPDHSFIQMGDFSGYTIKQCARKELKKAYVAGFIGKLAKMAAG 271
                 *************************************************************99 PP

>> Ret2_MD  RNA editing 3' terminal uridylyl transferase 2 middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.071   4.3e+02      61      89 ..     198     228 ..     180     235 .. 0.70
   2 ?   10.1   0.1   0.00014      0.84      25      79 ..     309     363 ..     292     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.071
     Ret2_MD  61 qaieaigllP.dGkiltkgmr.edytrdvld 89 
                 q i  ++ +  d ++lt g r ed+ r++++
  AJA92007.1 198 QQIAVVSSMNdDYVVLTTGGRsEDFAREIIE 228
                 45555555541567787766559****9875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
     Ret2_MD  25 eleyiaeklgrenvegiyverttyGcriaiqvsskeqaieaigllPdGkiltkgm 79 
                    ++ e + +++v+g + + t   c+  +q s  +  +e i +  dGk+l++++
  AJA92007.1 309 TARNVQEIIMEDKVDGFFDQITNETCKQMMQHSEGKIPVEVILFDFDGKVLSRTK 363
                 55667777889****************************************9975 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.9e-05      0.29       1      34 [.       8      41 ..       8      44 .. 0.92
   2 ?    1.0   0.4     0.074   4.4e+02       5      24 ..     254     273 ..     250     279 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.9e-05
     DUF3042  1 mkkFlkGflvGvlatiaavagavfvfKkkviePi 34
                +kk  +Gf +G+ at++  ag++ ++ +k ie i
  AJA92007.1  8 KKKLRTGFTTGSCATASSKAGVLSIINQKEIEKI 41
                58999*********************99999876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.074
     DUF3042   5 lkGflvGvlatiaavagavf 24 
                  k +++G ++ +a +a+ v 
  AJA92007.1 254 KKAYVAGFIGKLAKMAAGVK 273
                 55567777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2552.38
//
Query:       AJA92008.1  [L=245]
Description: exosome complex exonuclease 1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-36  126.3   0.0    1.4e-36  125.9   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    8.1e-13   48.2   0.1    1.8e-12   47.1   0.1    1.6  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
       0.15   11.8   0.5        3.1    7.6   0.0    2.9  3  Kazal_3     Kazal-type serine protease inhibitor domain


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9   0.0   2.3e-40   1.4e-36       1     132 []      25     154 ..      25     154 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 2.3e-40
                 EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-CCGCCTCE CS
    RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsillekkpkst 99 
                 e R+++i+ gvl++anGSay+e+Gd+k+l++v+gp+ ++p+ ++d+ +g l +++ +apf+ ger++   ps++e+e+s+++++al+p ++l+++p++ 
  AJA92008.1  25 ETRKVTIKAGVLKNANGSAYIEFGDNKILVGVYGPRDVHPKHMSDTDTGILRCRYHMAPFSVGERKN-PAPSRREVEISKVIKEALEPAVMLKEFPRTA 122
                 67************************************99999766679****************65.79***************************** PP

                 EEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
    RNase_PH 100 ididitvlssdggslldalinaaslALadagip 132
                 +d++++vl++dg ++  a+ ++as+ALadagip
  AJA92008.1 123 VDVFMEVLQADG-GTRCAALTGASVALADAGIP 154
                 ************.*******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1     3e-16   1.8e-12       1      66 [.     157     221 ..     157     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3e-16
                 S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
  RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                 ++v++++ gk  d ++lD ++eE++ +++dl++ +  + +++tl++++g  l++e+ +++ie++ +
  AJA92008.1 157 DLVAGCAAGKAADAVILDVNNEEDQAGQADLPIGYMPNLKKITLLQLDGV-LTPEEYKQCIEIGID 221
                 589***********************************************.************987 PP

>> Kazal_3  Kazal-type serine protease inhibitor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.15   8.8e+02      35      43 ..      16      24 ..      13      28 .. 0.82
   2 ?    7.6   0.0   0.00053       3.1      21      38 ..      61      78 ..      51      83 .. 0.84
   3 ?   -0.6   0.2      0.19   1.1e+03       3      19 ..     211     227 ..     210     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.15
     Kazal_3 35 lrCrGesvs 43
                 rC G +v+
  AJA92008.1 16 IRCDGRKVN 24
                59*****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00053
     Kazal_3 21 kaaeqtMtECeaGllrCr 38
                ++ ++ M++ ++G+lrCr
  AJA92008.1 61 DVHPKHMSDTDTGILRCR 78
                567899***********8 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.19
     Kazal_3   3 easeCeeeGisvCvevn 19 
                 e ++C e Gi  C +v 
  AJA92008.1 211 EYKQCIEIGIDGCNQVY 227
                 67899999999997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1884.64
//
Query:       AJA92009.1  [L=289]
Description: agmatinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-69  234.5   0.0    2.1e-69  234.1   0.0    1.0  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.1   0.0   1.2e-73   2.1e-69       5     275 ..      28     281 ..      25     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 234.1 bits;  conditional E-value: 1.2e-73
                 EEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTTCEEEEEESSGGGHHHHHHH CS
    Arginase   5 llGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilkagklpivlGGDHsialgilra 102
                 l+G+Pfd++ s++pG+rfGP+air+a +++e    + +e gv le+++i dlg+++ t+   +++++ + ++++e+ +  ++ i+lGG+Hs+++g++ +
  AJA92009.1  28 LFGIPFDSTHSYKPGCRFGPDAIRDAFNNIEI---FMPEFGVdLEQVNIKDLGNMEHTV-VAQNMIDMVRKTTSELKDTSNQLIILGGEHSLTYGSYLS 122
                 89*****************************8...4444555577************97.55569******************************8875 PP

                 HHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTT CS
    Arginase 103 laekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdneeyelakelgirvitmreidelglkavveeilervgaee 201
                     y+k+ g + fDAH+Dlr+++  g+++sh+ ++rr++ee+ +  ++++++G r++ +ee e++ e +i++i++ ei++ +  +++e++ e+++   
  AJA92009.1 123 ----YPKDTGYVVFDAHYDLRDEY-AGTKLSHAAYLRRIVEERGP--ENIIHVGARAFVKEELEFLTENNIKTISDSEIRDGNGPKLLEQLTEKFE--- 211
                 ....567899**************.9**************87665..7******************99*************9999**********6... PP

                 SEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHH CS
    Arginase 202 dpvylSfDiDvlDpavaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvr 275
                  ++y+S+D+DvlDpa+aPG+G pe+ G+t+rel++++  l++ +++ +aD+vE+nP +d+ + +t++laarl+ 
  AJA92009.1 212 -NLYVSIDLDVLDPAFAPGVGNPEAIGITSRELHDMIVSLKD-KKIKAADIVELNPMFDN-G-STSSLAARLIS 281
                 .7***************************************9.99**************9.5.8********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2170.44
//
Query:       AJA92010.1  [L=160]
Description: ferritin-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-19   69.2   4.1    4.2e-19   68.9   4.1    1.0  1  Ferritin      Ferritin-like domain
    0.00037   20.7   0.7    0.00049   20.3   0.7    1.3  1  Ferritin_2    Ferritin-like domain
    0.00067   20.1   5.4     0.0037   17.7   5.4    1.9  1  Rubrerythrin  Rubrerythrin


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   4.1     7e-23   4.2e-19       1     140 [.      16     158 ..      16     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 7e-23
                 HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH....C-SSSS....CS.SHHHHHHHHHH CS
    Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee....ieapke....fg.sveevleaale 90 
                 i+ L ++ a e+ a ++ +++  y++g g+     f  e+a +e+eha+k+a r+ +lG++++ ++++++e         +     + +++++le ale
  AJA92010.1  16 IEMLKKAYALEMSAFHYWFYIDQYAEGLGFLHS-DFYSESANDELEHAKKVALRLDQLGAKATDNPQDWAEvsglG----NlepgKHvTLRNALEYALE 109
                 6889**************************986.9999*********************************66650....44445444*********** PP

                 HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin  91 hekkvteslrelielaeeegDpatadfledfleeqeeheweleallekle 140
                  e++++++++el+  ++ + D+ t++++ d++ ++ + e+++e++l+kle
  AJA92010.1 110 FERTAIAHYNELASSTQGK-DHITYHLALDLVSDEAKDEQDIEDILDKLE 158
                 *****************96.***************************996 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.7   8.2e-08   0.00049       3     127 ..      16     147 ..      14     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-08
  Ferritin_2   3 vdiLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaale..Gaaavakptfdf........afdpfadeksflalaav 91 
                 +++L+ A++lE  + +++ +  + +    +++l     +++ e a++e +H++  +  l   Ga+a ++p+           +  +  + ++ l+ a  
  AJA92010.1  16 IEMLKKAYALEMSAFHYWFYIDQ-Y----AEGLGFLHSDFYSESANDELEHAKKVALRLDqlGAKATDNPQDWAevsglgnlEPGKHVTLRNALEYALE 109
                 66778888888766655444433.3....6888889999**************999999999****9988531134445543777777899******** PP

  Ferritin_2  92 lEdvgvsAYlgaapllsnke..lltaaasIlsvEArHa 127
                 +E+++++ Y+  a   + k+    ++a+ ++s+EA+  
  AJA92010.1 110 FERTAIAHYNELASSTQGKDhiTYHLALDLVSDEAKDE 147
                 **************999888557889*********865 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   5.4   6.2e-07    0.0037       1     115 [.      17     130 ..      17     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-07
                   HHHHHHHHHHHHHHHHHHHHHHCHHTT-HHH.HHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG.GHHHHHHHHHHHHHHH CS
  Rubrerythrin   1 eiLekAiagEssarrlYkelaekakegypqi.aelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl.ttaknLeeaiegayae 95 
                   e+L+kA+a E sa+ ++ ++ + a+ g++ + + ++ e A +E eHak+++  l++l  +     + + + ++      +  ++  L++a+e a + 
    AJA92010.1  17 EMLKKAYALEMSAFHYWFYIDQYAE-GLGFLhSDFYSESANDELEHAKKVALRLDQLGAKAT--DNPQDWAEVSGLGNLEpGKHVTLRNALEYALEF 110
                   79************98877777777.66665257889*******************999888..455555555544444315566999********* PP

                   HHCHHHHHHHHHHHTTSHHH CS
  Rubrerythrin  96 eeemyrfyeelaekegneea 115
                   e++++ +y+ela+ ++ +++
    AJA92010.1 111 ERTAIAHYNELASSTQGKDH 130
                   ************98876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1168.37
//
Query:       AJA92011.1  [L=126]
Description: hypothetical protein T478_0691 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.4   0.0       0.32   11.3   0.0    1.9  2  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.8e-05      0.32      32      61 ..      41      70 ..      25      74 .. 0.82
   2 ?   -2.0   0.0      0.24   4.2e+03      84      94 ..      76      86 ..      71      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                ETT-.SEEEEEEEEEEE-SSS-EEEEGGGE CS
     DUF4352 32 qpdaggeflivdvtvkNkgkealtvnssqf 61
                +++++  f +++v+++N+g+++lt  +++f
  AJA92011.1 41 TKEKQSLFIMARVSLENTGSKPLTNVELNF 70
                4577889****************9877776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.24
                --EEEE-TT-E CS
     DUF4352 84 lflgtlnpGkk 94
                  lgtl+pG++
  AJA92011.1 76 IYLGTLKPGQS 86
                67899***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 898.98
//
Query:       AJA92012.1  [L=51]
Description: hypothetical protein T478_0295 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 380.18
//
Query:       AJA92013.1  [L=447]
Description: cobyrinic acid a,c-diamide synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-43  148.7   0.0    2.2e-43  148.2   0.0    1.3  1  GATase_3     CobB/CobQ-like glutamine amidotransferase domain
      3e-19   69.4   0.2    1.5e-17   63.9   0.1    2.7  3  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.5e-16   58.7   2.3    1.1e-09   38.4   0.0    3.4  4  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.011   15.0   0.1      0.025   13.9   0.1    1.5  1  CTP_synth_N  CTP synthase N-terminus
       0.02   14.4   0.0      0.035   13.5   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.082   12.5   0.8       0.28   10.8   0.1    2.0  2  SRP54        SRP54-type protein, GTPase domain
       0.11   12.4   0.1       0.55   10.1   0.0    2.2  3  MobB         Molybdopterin guanine dinucleotide synthesis pro


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.2   0.0   8.4e-47   2.2e-43       2     195 ..     246     435 ..     245     436 .. 0.90

  Alignments for each domain:
  == domain 1  score: 148.2 bits;  conditional E-value: 8.4e-47
    GATase_3   2 iavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegv 98 
                 ia++ ++++++y+  ++++L++e+++  +f+p++d+++++ +dl++l+Gg+++i +  l+++s+++++ik+ ae+g+p++++CGGl++L ++i+  ++ 
  AJA92013.1 246 IAIALDNSFNFYYhdNIEALRREGAKIKFFSPISDKKIPN-CDLIYLGGGFPEILASSLEKNSSMKKSIKNNAEDGTPIYAECGGLMYLTNSITYGHK- 342
                 99************************************76.****************************************************97553. PP

    GATase_3  99 egeageveglglLdietefekekltgqvegevel...aaegeevkGyEiHsGrtilkekakpllkvkv.ggnng.ekdGavkksedgnvlGtYlHglfd 192
                      +++++gl+d++t ++k+ +++ +eg+++     ++  +++++E+H+++ i+ +k +++l   + g++++ +kd + +     n++++Y H+ fd
  AJA92013.1 343 -----KSKMVGLFDVDTMMTKKMTLNYTEGKINSnclISKPRNFRAHEFHYSKIINVPKDSKFLYDLKiGEGISsHKDALTEY----NTVASYCHLYFD 432
                 .....7***************88888889998879976677***********9888776655554434577777899999977....***********9 PP

    GATase_3 193 nrn 195
                 + +
  AJA92013.1 433 SAK 435
                 976 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.1   5.7e-21   1.5e-17       1     125 [.       6     189 ..       6     193 .. 0.91
   2 ?   -0.8   0.0      0.57   1.4e+03      58     113 ..     226     279 ..     196     287 .. 0.61
   3 ?    2.1   0.0     0.073   1.9e+02      17      54 ..     334     371 ..     331     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 5.7e-21
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 ++ia+ ++GvGKT+++ +++  l++rg+ V++++++p+    ++l   ++ + +                                             
  AJA92013.1   6 LVIAGSTSGVGKTSITSAIIYGLKKRGFSVQPFKVGPDYIDPSYLSSISKTETKnldvwlmgqqeliqsftrnsssdisiiegvmgyydgfggnsnlas 104
                 589***********************************8888874333333333677899999999999****************************** PP

                 ................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                 ................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 ................dlkrllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                 d+++ +++++a   ++ ++    +i g++ln+++++++e+l ++al+ l    ++p++gvip++ +v  +++r+
  AJA92013.1 105 thhvatllkspvililDASKTSRSIAATALGFTKFhknSRISGIILNKIGSKKHENLCRSALASL----KIPIIGVIPKNPSV-NLESRH 189
                 **************************999999999999**************************9....8***********99.666666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.57
                 CCCHHHHHHCHCHHHH....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE CS
                 xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  58 rllellealgkkkall..lkiagvvlnrvdgeneetllkealeelkqrygvpvlgvip 113
                 +   +le+++ +k+++  + ia  ++n ++    ++  +eal+++ +  +++++  i+
  AJA92013.1 226 KATSSLEKIKPVKPKKpkISIAIALDNSFNFY--YHDNIEALRREGA--KIKFFSPIS 279
                 34445555655555557788888888888754..5555666666554..666666555 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.073
                 HHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  17 anLaralarrglrVllvDaDpqannlaileglendiep 54 
                 +n++++  ++ + V l+D+D++++  ++l  +e++i+ 
  AJA92013.1 334 TNSITYGHKKSKMVGLFDVDTMMTKKMTLNYTEGKINS 371
                 566677778889999*******9999988888877776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   1.4e-06    0.0037       3      36 ..       6      39 ..       4      42 .. 0.93
   2 !   38.4   0.0   4.3e-13   1.1e-09      82     195 ..      66     184 ..      42     187 .. 0.78
   3 ?   -1.1   0.0      0.57   1.5e+03      38      72 ..     208     242 ..     194     252 .. 0.76
   4 ?   -0.7   0.0      0.41     1e+03      22      41 ..     262     281 ..     262     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
      AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36
                ++++g + gvGKT+++ ++++ lk++g++v+ fK
  AJA92013.1  6 LVIAGSTSGVGKTSITSAIIYGLKKRGFSVQPFK 39
                89**************************998776 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 4.3e-13
      AAA_26  82 egedidlekivkelekdadivvVEGagglgvp..itee.llnadiaknlgapvilVarg..glgtinqllltiealrqknvrvlGvilNkvrnp...en 172
                 +g++  ++++  + +  +di ++EG+ g+ ++   +++ +++  +a+ l++pvil++ +  ++++i++++l    +++ n r+ G+ilNk+ ++   + 
  AJA92013.1  66 MGQQELIQSF--TRNSSSDISIIEGVMGYYDGfgGNSNlASTHHVATLLKSPVILILDAskTSRSIAATALGFTKFHK-NSRISGIILNKIGSKkheNL 161
                 4555556666..677899********999987445777789999************9994344679999999988887.89*********877744346 PP

      AAA_26 173 vetlekksgipvlGvvPylpdle 195
                  +++ ++ +ip++Gv+P +p+++
  AJA92013.1 162 CRSALASLKIPIIGVIPKNPSVN 184
                 788888999**********9976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.57
      AAA_26  38 iqtgieededselikellgldqtyelpeplalsap 72 
                 ++++i++  d +li+++++++++ e ++p+  ++p
  AJA92013.1 208 LSKEISDYLDFDLIEKICKATSSLEKIKPVKPKKP 242
                 55555566699999999999999999999976655 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.41
      AAA_26  22 vralkrkgvkvgyfKPiqtg 41 
                 ++al+r+g+k+++f Pi+ +
  AJA92013.1 262 IEALRREGAKIKFFSPISDK 281
                 57999***********9875 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   9.8e-06     0.025       4      56 ..       6      57 ..       5      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.8e-06
                 EEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC-- CS
  CTP_synth_N  4 lvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGE 56
                 lv  G +Sg+Gk  i++++   lk+rg++v+  k+ P   +d++ ls++ + E
   AJA92013.1  6 LVIAGSTSGVGKTSITSAIIYGLKKRGFSVQPFKVGPD-YIDPSYLSSISKTE 57
                 688899******************************94.37899888887766 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.4e-05     0.035     161     246 ..     129     214 ..     114     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
   Fer4_NifH 161 iakgiekyaksgg.vrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkile 246
                 ia++   ++k ++  r++G+i n+   +++++l +   ++l+++++ v+P++  v+  e r+  +i   ++++  ++ ++l+++i +
  AJA92013.1 129 IAATALGFTKFHKnSRISGIILNKIGSKKHENLCRSALASLKIPIIGVIPKNPSVNL-ESRHLGLIPVREQKQLHNKIKQLSKEISD 214
                 55555566666655799******888888899999999****************986.55777788888888888999999988876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.35     9e+02       9      32 ..      12      35 ..       5      36 .. 0.77
   2 ?   10.8   0.1   0.00011      0.28     115     171 ..     114     174 ..     100     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                STTSSHHHHHHHHHHHHHHTTS-E CS
       SRP54  9 lqGaGKTttlaKLaallkkegkkv 32
                + G+GKT+ ++ +   lkk+g +v
  AJA92013.1 12 TSGVGKTSITSAIIYGLKKRGFSV 35
                46******9999998888888765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                 SEEEEEEETTBHTHHHH.HH...HHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EE CS
       SRP54 115 devllvldattgqeavk.qa...kaFkeavgitgviltklDgdakgGaalsiaaelklPik 171
                   v+l+lda+  +  ++ +a   ++F+++  i+g+il k+ ++ +     s+ a+lk+Pi+
  AJA92013.1 114 SPVILILDASKTSRSIAaTAlgfTKFHKNSRISGIILNKIGSKKHENLCRSALASLKIPII 174
                 56899999987776666233333799******************99999999999999996 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00022      0.55       4      34 ..       8      39 ..       5      47 .. 0.84
   2 ?   -3.8   0.0       4.4   1.1e+04      81      98 ..      71      88 ..      66      89 .. 0.69
   3 ?   -1.7   0.0      0.99   2.5e+03      72     101 ..     196     226 ..     186     248 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
        MobB  4 ivg.ksgsGKTtLleklipelkarglrvgtiK 34
                i+g +sg GKT++ + +i  lk+rg++v   K
  AJA92013.1  8 IAGsTSGVGKTSITSAIIYGLKKRGFSVQPFK 39
                554159********************998666 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.4
        MobB 81 leellarlsevDlvlvEG 98
                l + ++r s+ D+ ++EG
  AJA92013.1 71 LIQSFTRNSSSDISIIEG 88
                455556666799999998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.99
        MobB  72 keleeaelsleellarlse.vDlvlvEGfkk 101
                 +e+++ + ++++l + +s+ +D+ l+E   k
  AJA92013.1 196 REQKQLHNKIKQLSKEISDyLDFDLIEKICK 226
                 4545556677888888855688888886544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3100.86
//
Query:       AJA92014.1  [L=316]
Description: glycosyltransferases group 1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-27   94.5   0.3    1.6e-24   86.4   0.1    2.2  2  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-18   67.3   0.0    2.9e-18   66.6   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
      2e-11   44.1   0.0    2.4e-10   40.7   0.0    2.2  2  Glyco_trans_1_2  Glycosyl transferases group 1
    6.6e-10   39.3   0.1    2.8e-06   27.4   0.0    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
    5.1e-06   27.0   0.0     0.0032   17.9   0.0    2.2  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0012   18.9   0.1     0.0024   17.9   0.1    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0071   15.2   0.1       0.01   14.8   0.1    1.2  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0079   15.6   0.6      0.033   13.6   0.2    1.8  1  eIF-6            eIF-6 family
  ------ inclusion threshold ------
      0.037   14.0   0.2      0.075   13.0   0.1    1.5  2  Helicase_IV_N    DNA helicase IV / RNA helicase N terminal


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0011       2.1      13      39 ..     164     190 ..     153     196 .. 0.82
   2 !   86.4   0.1   7.9e-28   1.6e-24      68     170 ..     188     290 ..     185     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                      TT-EEEEEESS-TTTTTHHHHHHHHHC CS
  Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafal 39 
                      + k+ i +vgr ++eKg+d l +a  +
       AJA92014.1 164 KIKNQIAYVGRDSREKGIDILKEAESE 190
                      56899****************999665 PP

  == domain 2  score: 86.4 bits;  conditional E-value: 7.9e-28
                      HHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHH CS
  Glycos_transf_1  68 elelsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeel 161
                      e e++ nv +    s+e+ ++++k+++i+v+ps++E++++++ EA+++++pvi +n+gg++e++k++etG++v+p+n+ +la+ai++ll+d+e+
       AJA92014.1 188 ESEINGNVVYCTDRSWEEAMHIIKSSSIVVVPSRMESLPTTVKEAFYLNVPVIGTNVGGIPELIKNNETGIIVPPENPSELAQAINELLSDREK 281
                      5678899999999999****************************************************************************** PP

                      HHHHHHHHH CS
  Glycos_transf_1 162 rerlgenar 170
                      +e+l  n+ 
       AJA92014.1 282 SEKLATNGN 290
                      *****9985 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.5e-21   2.9e-18      27     134 .]     165     278 ..     154     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.5e-21
                      HH.HHEEEEEES---.....HHHHHHHT.T-T.TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..T CS
  Glyco_trans_1_4  27 lrkkdvrlvivGdgprp...eeleelaa.gleerveftGfv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..g 110
                      ++    ++  vG+++r+   + l+ +a+ +++ +v+++  +  e+   ++++++++v+Ps  e+++ ++ Ea+ + +pv+ t+vggi+e++  +
       AJA92014.1 165 IK---NQIAYVGRDSREkgiDILK-EAEsEINGNVVYCTDRswEEAMHIIKSSSIVVVPSrmESLPTTVKEAFYLNVPVIGTNVGGIPELIknN 254
                      33...3588899665443554444.44347777866666666999***************999****************************988 PP

                      TSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4 111 engllvppgdpealaeailrLled 134
                      e+g++vpp++p++la+ai +Ll+d
       AJA92014.1 255 ETGIIVPPENPSELAQAINELLSD 278
                      **********************98 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.32   6.4e+02      59      79 ..     102     120 ..      92     132 .. 0.84
   2 !   40.7   0.0   1.2e-13   2.4e-10       1      86 [.     215     302 ..     215     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.32
  Glyco_trans_1_2  59 llanpeerraiaeaarervla 79 
                      l  + +  ++ia++a+ +vl+
       AJA92014.1 102 L--HSKSVSSIAKNAQSQVLQ 120
                      4..888999**********98 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 1.2e-13
  Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                      iv+ psr es+ + + Ea   +++++ +   g++el+++++++i++   ++ ela++i++ll+++e+ +++a+++  +v+++ t+d  
       AJA92014.1 215 IVVVPSRMESLPTTVKEAFYLNVPVIGTNVGGIPELIKNNETGIIVPpeNPSELAQAINELLSDREKSEKLATNGNTFVKNNMTWDVI 302
                      67889********************************************************************************965 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.3    0.0005      0.99       2      22 ..      12      32 ..      11      35 .. 0.95
   2 !   27.4   0.0   1.4e-09   2.8e-06      50     168 ..      42     153 ..      34     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
  Glyco_transf_4  2 GGverhvleLaraLarrGheV 22
                    GG++ h+  La++L ++GheV
      AJA92014.1 12 GGIGGHAAMLAEQLTKNGHEV 32
                    9*******************9 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.4e-09
  Glyco_transf_4  50 llkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeat 144
                     +++    s+a l++l+ +++re +D+vH  + +++ +a+ +++   g++ Vl+vHg + +     ++k  s ++++   ++l++ d++++ S+at
      AJA92014.1  42 IKNMKNPSFAVLSSLKSMFDREFYDIVHGFNIPSA-YAMKYAK---GKKKVLSVHGVFSDQVDTLHSKSVSSIAKNAQSQVLQWPDKLTTDSKAT 132
                     55556667888999*****************7776.7777777...9***********988888899999999999999**************** PP

  Glyco_transf_4 145 adelrerygvppekitVipnGvDl 168
                     ++ ++e+++++    + +p + D+
      AJA92014.1 133 QKLYKEKFDIE---FEYLPSPLDT 153
                     ******99987...4666666665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0041       8.1       1      21 [.      12      32 ..      12      34 .. 0.96
   2 !   17.9   0.0   1.6e-06    0.0032      58     144 ..      51     136 ..      37     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
  Glyco_trans_4_4  1 gGigryvaelaraLaarGheV 21
                     gGig ++a+la++L + GheV
       AJA92014.1 12 GGIGGHAAMLAEQLTKNGHEV 32
                     8*******************9 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.6e-06
  Glyco_trans_4_4  58 aalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeel 144
                      a l  l++++  +re +d+vh +++++++a++ a+ ++++  v+ ++++ ++   s  v ++++ +++ +l+  d +++ s a  +++
       AJA92014.1  51 AVLSSLKSMF--DREFYDIVHGFNIPSAYAMKYAKGKKKVLSVHGVFSDQVDTLhSKSVSSIAKNAQSQVLQWPDKLTTDSKATQKLY 136
                      5567889999..9**********************66688888888877777666899999******************999887766 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.2e-06    0.0024      47     114 ..      32      97 ..      16     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
  Glyco_trans_4_2  47 vhrl...kvdrkg.pleylk.afklkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkf 114
                      v+++    +++k  +   ++ + +lk++++++ +D+vh +++++ +++ + a   +g ++ vlsv+G  v+++
       AJA92014.1  32 VKKMettHIPIKNmKNPSFAvLSSLKSMFDREFYDIVHGFNIPS-AYAMKYA---KG-KKKVLSVHG--VFSD 97 
                      44441113345555777778456******************998.4555554...55.6778****5..5554 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     5e-06      0.01     235     337 ..     187     296 ..     153     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
                  HHHH-T.TEEEE----HHHHHHHHHC-SEEEES-....H.HHHHHHHHCT--EEESSSS-S-THHHHTTSEEE.-T.T-HHHHHHHHHHHCT-..--. CS
  Epimerase_2 235 eleele.nvtlieplgyldflsllknaklvltdS....g.GiqeEapslgvpvvnlReeteRpegveagtnvl.vg.tdkeeIvaaleklledkkele 324
                  + +e++ nv  ++    ++ ++++k++ +v+  S      +  +Ea++l+vpv+   + +  pe +++++  + v+ ++++e+ +a+++ll+d+++ e
   AJA92014.1 187 AESEINgNVVYCTDRSWEEAMHIIKSSSIVVVPSrmesLpTTVKEAFYLNVPVIGT-NVGGIPELIKNNETGIiVPpENPSELAQAINELLSDREKSE 283
                  33444247777777778888888888888886554442355567**********99.99*******98876555763789*************99999 PP

                  .....--TT-SS- CS
  Epimerase_2 325 kmanaknpYgdGk 337
                  k+a + n + + +
   AJA92014.1 284 KLATNGNTFVKNN 296
                  9999999998765 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   1.7e-05     0.033      18     105 ..     213     296 ..     206     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                 SSEEEE-TTS-HH.HHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHHH---EEE--SS--HHHHEEE-S CS
       eIF-6  18 nkyalvpegveee.fvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkeslkleverleekltAlGNvilaND 105
                  ++++vp  +e+  ++ + +  L+v+v+ t+++g++    l+  N+ g++vp    +e  ++++e l+++  + +ekl   GN+++ N+
  AJA92014.1 213 SSIVVVPSRMESLpTTVKEAFYLNVPVIGTNVGGIP---ELIKNNETGIIVPPENPSELAQAINELLSDR--EKSEKLATNGNTFVKNN 296
                 567888888665544444445688999999999976...899***********99999999999986554..46779999999999997 PP

>> Helicase_IV_N  DNA helicase IV / RNA helicase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   8.8e+03     100     115 ..      22      37 ..      18      51 .. 0.60
   2 ?   13.0   0.1   3.8e-05     0.075      62     128 ..      84     155 ..      77     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
  Helicase_IV_N 100 advlqkkeeeieefvq 115
                    a++l+k ++e++++++
     AJA92014.1  22 AEQLTKNGHEVKKMET 37 
                    5566666666655554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.8e-05
  Helicase_IV_N  62 keqkvvrlhGlpweetqqfaqtllssyqqWskeqvqaladvlqkkeeeieefvqqq.....kylstsevanl 128
                     ++kv ++hG+  ++++ ++ + +ss+ + +++qv +  d+l++  + ++++ +++     +yl+++  +++
     AJA92014.1  84 GKKKVLSVHGVFSDQVDTLHSKSVSSIAKNAQSQVLQWPDKLTTDSKATQKLYKEKfdiefEYLPSPLDTTM 155
                    4589***********************************************999988888888877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2291.99
//
Query:       AJA92015.1  [L=115]
Description: hypothetical protein T478_1004 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0024   17.7   0.2     0.0037   17.0   0.2    1.4  1  DUF4364   Domain of unknown function (DUF4364)
     0.0041   17.1   0.4     0.0063   16.5   0.4    1.4  1  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   4.1e-07    0.0037      23      74 ..      65     110 ..      41     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.1e-07
     DUF4364  23 eiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74 
                 +i +++ ++nY+++       ve ++ie+e+  ++ +y+iT+kG+ +lelf 
  AJA92015.1  65 KIRMKKSFLNYLHF------CVEYKFIEKERVGSNVIYTITDKGRVMLELFT 110
                 45556666666555......5899*************************995 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4     7e-07    0.0063      34      69 ..      70     109 ..      43     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7e-07
      HTH_45  34 kllnkYLdmLvekgli....kkskekYvlTekGlellekl 69 
                 k + +YL++ ve ++i      s+  Y++T+kG+ +le +
  AJA92015.1  70 KSFLNYLHFCVEYKFIekerVGSNVIYTITDKGRVMLELF 109
                 56889***********6544447899********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 905.59
//
Query:       AJA92016.1  [L=380]
Description: geranylgeranyl reductase family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00011   22.4   0.7    0.00056   20.1   0.2    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00024   20.5   0.1       0.11   11.7   0.2    2.6  2  FAD_binding_3   FAD binding domain
    0.00058   19.2   0.2        0.9    8.7   0.0    2.5  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00077   20.0   1.5        1.1    9.9   0.0    3.1  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0013   19.0   0.2     0.0071   16.7   0.0    2.2  2  Ntox1           Putative RNase-like toxin, toxin_1
     0.0019   17.4   0.8     0.0033   16.6   0.8    1.4  1  FAD_binding_2   FAD binding domain
     0.0019   17.6   0.2     0.0076   15.6   0.1    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
      0.003   17.2   1.3      0.034   13.7   0.9    2.0  2  DAO             FAD dependent oxidoreductase
     0.0041   16.4   1.0       0.01   15.1   0.2    2.0  2  Thi4            Thi4 family
     0.0095   14.7   0.1       0.02   13.6   0.1    1.5  1  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.023   13.8   0.0        2.5    7.1   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
      0.039   12.8   0.9          3    6.6   0.0    2.9  3  Trp_halogenase  Tryptophan halogenase
      0.087   12.5   0.1       0.19   11.4   0.1    1.5  1  SWI2_SNF2       SWI2/SNF2 ATPase
       0.13   11.5   0.1       0.22   10.8   0.1    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   4.4e-07   0.00056       1      46 [.       6      57 ..       6      68 .. 0.71
   2 ?   -0.8   0.0       1.5   1.9e+03       5      19 ..     268     285 ..     262     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                   EE--SHHHHHHHHHHHCCTEEEEEE-SS......SSSSGGG-EECETTCEEC CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr......drlGGraasyevpgvrvd 46
                   + G+ +sGl+aA+++ak+g++vl+le +      +++GG ++ + +++  +d
     AJA92016.1  6 VAGGSISGLLAAREIAKDGHSVLVLEEGfevgspEHCGGLVSENALKELGID 57
                   569***********************98333333444455555555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                    SHHHHHHHHHHHCC...T CS
  NAD_binding_8   5 GlsGlvaAylLaka...g 19 
                    G++G +a +++++a   g
     AJA92016.1 268 GMAGILAGRAISEAiktG 285
                    999999999999864443 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   8.7e-05      0.11       3     164 ..       3     144 ..       1     187 [. 0.81
   2 !    5.8   0.0    0.0053       6.7     284     337 ..     244     296 ..     238     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.7e-05
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHHCHHCST- CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsdtpkaradlelessper 98 
                    d ++ G++ +Gl++a++ ++ G +v+++e   +       +gl ++  + l++lG++ + +  +++ e  +++  +          +++++s+ ++
     AJA92016.1   3 DAVVAGGSISGLLAAREIAKDGHSVLVLEEGFEVGSPEHCGGLVSE--NALKELGIDPSPKTFDSKIECAKIFSPKG--------KEITINSKRQK 88 
                    78999***********************986555444455555444..57999999999999998888877777777........66677799999 PP

                    CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GT CS
  FAD_binding_3  99 vtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGg 164
                    + v++  el++  + +a+  g+++  kt ++      e+++ ++r ++ g   ++++k+ + + G+
     AJA92016.1  89 IIVINRRELDKQAARQARDNGAEISVKTSFQ------EKIHNTIRTSN-G---NIECKFFIDCRGV 144
                    99999*****999999999999999999999......67777777663.3...4688888888886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
                    TTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHH CS
  FAD_binding_3 284 grvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtYeee 337
                    +   ++GDAa    Pt++ G+ +  +  +  ++++ +++k +++++ L  Ye++
     AJA92016.1 244 EDTVIVGDAAGQAKPTTAGGIFSCGMAGILAGRAISEAIK-TGNSSSLMNYEKQ 296
                    55679****************9999999999*********.9999999999976 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0012       1.5       2      31 ..       3      36 ..       2      61 .. 0.75
   2 !    8.7   0.0    0.0007       0.9     155     238 ..      67     145 ..      66     167 .. 0.83
   3 ?   -2.8   0.0       2.2   2.8e+03     174     203 ..     286     315 ..     262     338 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                 SEEEE--SHHHHHHHHHHHHHTS-EEEEE....T CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve....l 31
                 d vv Gg + Gl aa+++a+ g+ v+++e     
   AJA92016.1  3 DAVVAGGSISGLLAAREIAKDGHSVLVLEegfeV 36
                 78999*******************9999644443 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0007
                  HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvr 238
                  +E+A  ++  gke+t+   r+++     +el ++++++ +++G e+ ++ts++e + n+     + +++  i+++  + + Gv+
   AJA92016.1  67 IECAKIFSPKGKEITINSKRQKIIVINRRELDKQAARQARDNGAEISVKTSFQEKIHNT-----IRTSNGNIECKFFIDCRGVS 145
                  69*********************977779999999999999999999999998877666.....45555558888888887775 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.2
                  SSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 174 rdrllraldkelsaaleealekeGvevklg 203
                  ++  l +++k++++   +++ek++ + k  
   AJA92016.1 286 NSSSLMNYEKQWRDKFGKEFEKQNLARKIL 315
                  444445788888888888888887766555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0066       8.5       2      55 ..       4      56 ..       3      58 .. 0.78
   2 !    9.9   0.0   0.00084       1.1      12      64 ..      67     119 ..      65     131 .. 0.87
   3 ?   -0.0   0.0       1.1   1.4e+03       7      54 ..     262     309 ..     262     340 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0066
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHH.HHHHHHTTE CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskil.qeklekngi 55
                +vv Gg+ +gl +A ++a+ g++V v+e + ++    +e ++ ++ ++ l+++gi
  AJA92016.1  4 AVVAGGSISGLLAAREIAKDGHSVLVLEEGFEVG--SPEHCGGLVsENALKELGI 56
                69**************************998888..5555555552333455566 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00084
                 HHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEE CS
   Pyr_redox  12 lElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkve 64 
                 +E+A++++  gk++t+   + k+     +e+ k  +++ ++ng e+  +t+ +
  AJA92016.1  67 IECAKIFSPKGKEITINSKRQKIIVINRRELDKQAARQARDNGAEISVKTSFQ 119
                 79**********************88888999999999999988887777655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.1
                 SSHHHHHHHHHHHHTT.SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTT CS
   Pyr_redox   7 gGyiglElAgalaelg.kkVtvversdkllrllDeeaskilqeklekng 54 
                 gG   + +Ag+la  + ++     +s+ l+ +++++ ++ + +++ek++
  AJA92016.1 262 GGIFSCGMAGILAGRAiSEAIKTGNSSSLM-NYEKQWRDKFGKEFEKQN 309
                 566667777777555532333333333333.555555555555555554 PP

>> Ntox1  Putative RNase-like toxin, toxin_1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.5e-06    0.0071       7      66 ..      16      76 ..      12     119 .. 0.79
   2 ?   -0.8   0.0       1.5     2e+03      47      77 ..     298     328 ..     290     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.5e-06
       Ntox1  7 aekkpadgghdvvvtpdGvekCsppPCPvlrveY.kkelaaddelkeeneevealRkldak 66
                a+++ a +gh v v ++G+e  sp  C  l  e   kel+ d+  k    ++e  +   +k
  AJA92016.1 16 AAREIAKDGHSVLVLEEGFEVGSPEHCGGLVSENaLKELGIDPSPKTFDSKIECAKIFSPK 76
                899************************9887665169999999988888888877666555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
       Ntox1  47 ddelkeeneevealRkldaklaadeaakLiq 77 
                  d++ +e e+ +  Rk+ a+l+ d  +kL +
  AJA92016.1 298 RDKFGKEFEKQNLARKILARLDNDTVNKLFN 328
                 4678888899899999999999999999876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   2.6e-06    0.0033       1      36 [.       3      38 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                   D++V G+ ++GL AA e+a+ G++v+v+e ++e+g+
     AJA92016.1  3 DAVVAGGSISGLLAAREIAKDGHSVLVLEEGFEVGS 38
                   89******************************9987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.9e-06    0.0076       1      35 [.       3      37 ..       3      63 .. 0.82
   2 ?   -1.2   0.0      0.74   9.5e+02     124     148 ..     127     147 ..      76     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                  D vV GG ++G+ AA   a+ G +vl++ee   +G
    AJA92016.1  3 DAVVAGGSISGLLAAREIAKDGHSVLVLEEGFEVG 37
                  779**************************864333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.74
  FAD_oxidored 124 tveskegrktirAkvfiDATgdGdl 148
                   ++     + +i++k+fiD+ g   l
    AJA92016.1 127 RT----SNGNIECKFFIDCRGVSRL 147
                   22....3678999999999776555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.9   2.7e-05     0.034       1      43 [.       3      45 ..       3      55 .. 0.84
   2 ?    1.2   0.0      0.17   2.2e+02     144     203 ..      93     145 ..      90     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgl 43
                d v+ GG i Gl +A+e a+ g  V++le g ++g  +  + +gl
  AJA92016.1  3 DAVVAGGSISGLLAAREIAKDGhsVLVLEEGFEVG--SPEHCGGL 45
                789******************99********7766..55555555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                 EHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEEEECTEEEEEEEEEEE--GGG CS
         DAO 144 dpakltaalaraaealGveilegtevtg.leeedgkvwgverttpgendaadavVnaaGaw 203
                 + ++l +  ar+a+++G+ei  +t  ++ +        ++ rt++g++ +++  + + G+ 
  AJA92016.1  93 NRRELDKQAARQARDNGAEISVKTSFQEkI------HNTI-RTSNGNI-ECKFFIDCRGVS 145
                 66777788999*********9997666633......4566.4444654.347788888865 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   8.1e-06      0.01      19      63 ..       3      46 ..       1      54 [. 0.91
   2 ?   -1.1   0.0      0.73   9.3e+02      13      26 ..     239     254 ..     236     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.1e-06
                EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTT CS
        Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGql 63
                D v+ G+  sGL aa+ +ak+ +  v++le+   +G     GG +
  AJA92016.1  3 DAVVAGGSISGLLAAREIAKD-GHSVLVLEEGFEVGSPEHCGGLV 46
                8999*****************.**************999999976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.73
                 HHHTEEEEEEE-..-S CS
        Thi4  13 lkyaesDvvivG..aG 26 
                  +++e D vivG  aG
  AJA92016.1 239 KNFVEEDTVIVGdaAG 254
                 6899******994444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.5e-05      0.02       2      36 ..       3      37 ..       2      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 d +v Gg  +Gl+aA ++ak g++Vl+le++ ++g
   AJA92016.1  3 DAVVAGGSISGLLAAREIAKDGHSVLVLEEGFEVG 37
                 7899*************************998887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.002       2.5       1     145 [.       3     148 ..       3     164 .. 0.76
   2 ?    4.6   0.0     0.011        14     244     339 ..     231     327 ..     227     332 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.002
  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.....leecvehsWsgtivylddgkkillg...raYgrvsskr 88 
                    D vv G+   gl+ A ++  ak g +v+++e + ++  p        +++l++       +  + + + + +  ++gk+i+++    +   +++++
     AJA92016.1   3 DAVVAGGSISGLLAAREI--AKDGHSVLVLEEGFEVGSPEHCGGLVSENALKElgidpSPKTFDSKIECAKIFSPKGKEITINskrQKIIVINRRE 96 
                    77999999*****99999..*************999655555777777777775545556889999999999999999999997655666789999 PP

  Lycopene_cycl  89 lkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                    l ++ +++  +ng++     v+   +e+  + ++ +++g +i++++ +d rg+ +l 
     AJA92016.1  97 LDKQAARQARDNGAEIS---VKTSFQEKI-HNTIRTSNG-NIECKFFIDCRGVSRLA 148
                    99999999998888764...333333444.456666665.69999999999977665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
  Lycopene_cycl 244 Pvtlggslprleqk.vlaiGaaaglvhPaT.GYsvarslaeapllasaiaaalres.....slsarawatlwprerkrqreffrllglalllkldi 332
                    P+   g+++++ ++ ++ +G aag  +P+T G  +   +a   l   ai++a ++        ++++w+++ ++e  +q      l +++l +ld+
     AJA92016.1 231 PIWIKGPIKNFVEEdTVIVGDAAGQAKPTTaGGIFSCGMA-GILAGRAISEAIKTGnssslMNYEKQWRDKFGKEFEKQ-----NLARKILARLDN 320
                    666678888877766999***********94444444333.22244677777765432223333334444443333332.....455666666666 PP

  Lycopene_cycl 333 egrrrfl 339
                    +  ++++
     AJA92016.1 321 DTVNKLF 327
                    6666655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.054        69       3      32 ..       5      31 ..       3      47 .. 0.89
   2 ?    6.6   0.0    0.0024         3     177     213 ..     112     148 ..      92     185 .. 0.75
   3 ?    1.1   0.0      0.11   1.4e+02     308     337 ..     236     265 ..     204     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.054
                    EEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
  Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlve 32
                    v++GG ++G laA  +ak +   ++v+++e
      AJA92016.1  5 VVAGGSISGLLAAREIAKDG---HSVLVLE 31
                    89***************999...7788877 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                     EEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-II CS
  Trp_halogenase 177 vevqldedgrveslrledgreveadlfiDcsGfrgll 213
                      +v++  ++++++   ++  ++e  +fiDc G  +l 
      AJA92016.1 112 ISVKTSFQEKIHNTIRTSNGNIECKFFIDCRGVSRLA 148
                     456666688887766666666***********98775 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                     EEES-SEETTEEE-CCCTEE--CCCS-HHH CS
  Trp_halogenase 308 GrrkqawvknvvalGlasgfvePlestsih 337
                     G  k++ ++++v +G+a+g   P  + +i 
      AJA92016.1 236 GPIKNFVEEDTVIVGDAAGQAKPTTAGGIF 265
                     567889999**************9999886 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00014      0.19      48      97 ..      85     133 ..      61     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
   SWI2_SNF2  48 knpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeLkellekeseki 97 
                 k++k ++v+ R++LdkQ ++++++ g e +++++ ++++++++++++++i
  AJA92016.1  85 KRQK-IIVINRRELDKQAARQARDNGAEISVKTSFQEKIHNTIRTSNGNI 133
                 4455.5667899**************999999999******998777776 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00017      0.22       1      27 [.      11      37 ..      11      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                   HHHHHHHHHHHHTTEEEEEEESSSSSB CS
  Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvG 27
                   ++GL aAr+ +  G++V+vlE    vG
     AJA92016.1 11 ISGLLAAREIAKDGHSVLVLEEGFEVG 37
                   8********************876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2800.64
//
Query:       AJA92017.1  [L=451]
Description: threonine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-47  161.7   0.0    3.9e-47  161.1   0.0    1.2  1  PALP         Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.37   10.3   1.8       0.43   10.1   0.4    1.9  2  zf-ribbon_3  zinc-ribbon domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.0   4.4e-51   3.9e-47      21     294 .]     118     426 ..     103     426 .. 0.93

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 4.4e-51
                 CCE...EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHH CS
        PALP  21 gvp...lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadas.pekvallrllGaevvevggdydeav 115
                 g +   + +  E+ np+gSfKd+g++ ++++ k   gak +++as+GN+ +++ + aa  ++++ +++p++   p+k+ +  ++G ++v+v+g++d+a 
  AJA92017.1 118 GLDnenVVFQPEGYNPSGSFKDNGMSAAVTHGKMM-GAKKIICASTGNTSASAGMFAANENMECDVYIPDGQIaPGKLSQAYQFGTQMVKVNGNFDDAF 215
                 44444599***********************9999.***********************************9978************************ PP

                 HHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S. CS
        PALP 116 aaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrr 207
                  +  e+a+e +g y v++  np +ieg++ti +  le l+ ++pd++v p G  g+ + +++ l+e    ++ +  +r+ +++++g+++l++ + +g  
  AJA92017.1 216 TKSLEAAEE-PGSYTVNSV-NPFRIEGQKTIPYRALEYLNwEVPDWLVYPGGALGNTSSCGKSLMElyewGWIKkiPRIAVINASGANTLYQLF-NGIF 311
                 **99*****.*********.9*********************************************9988666688******************.5555 PP

                 SS..B...........................SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHH CS
        PALP 208 vtvpvs..........................dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klr 277
                 ++ +                            +t a+++++g  s+ ++ +++l+ +++ + +v+d+e+l++m  +   +g  +e +s+a++a++ klr
  AJA92017.1 312 DEEKLRwnegapnfelirrfydemskdenlkpKTKATAIQIGkpSNVAKGLRALEFTNGIVEEVTDKEMLDGMSVVG-LNGFDCEMASGASVAGIkKLR 409
                 555544778888999999999999999**************9888888899**************************.********************* PP

                 HHHCCTTCEEEEEEE-B CS
        PALP 278 eagelkegdrvvviltg 294
                 ++g +k++d+vv iltg
  AJA92017.1 410 DKGVIKKDDKVVGILTG 426
                 ***************98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   4.7e-05      0.43       6      22 ..      16      34 ..      16      38 .. 0.92
   2 ?   -2.5   0.0      0.43   3.8e+03       7      10 ..     272     275 ..     271     277 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.7e-05
  zf-ribbon_3  6 PnCGa.p.lssddnvCpyC 22
                 PnCG+   ++s +++C +C
   AJA92017.1 16 PNCGKtYsIKSLAIKCDSC 34
                 9****977*********** PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.43
  zf-ribbon_3   7 nCGa 10 
                  +CG+
   AJA92017.1 272 SCGK 275
                  6776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3356.73
//
Query:       AJA92018.1  [L=271]
Description: ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-27   97.2   0.0    2.5e-27   96.0   0.0    1.6  2  ABC_tran   ABC transporter
    1.8e-14   54.2   0.1    6.2e-08   32.8   0.0    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    8.5e-06   25.4   0.3     0.0095   15.4   0.1    2.2  2  SMC_N      RecF/RecN/SMC N terminal domain
    2.2e-05   25.1   2.4    6.3e-05   23.6   2.4    2.0  1  AAA_23     AAA domain
    0.00036   20.4   0.4      0.042   13.6   0.0    2.3  2  AAA_15     AAA ATPase domain
     0.0004   20.8   0.4       0.43   11.0   0.1    2.3  2  AAA        ATPase family associated with various cellular act
     0.0021   17.7   0.0     0.0042   16.8   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
     0.0048   16.3   0.1       0.28   10.6   0.1    2.2  2  TniB       Bacterial TniB protein
     0.0057   16.4   0.1       0.77    9.5   0.0    2.2  2  IstB_IS21  IstB-like ATP binding protein
     0.0057   16.3   0.0      0.012   15.2   0.0    1.5  1  AAA_27     AAA domain
  ------ inclusion threshold ------
      0.018   15.1   0.4      0.038   14.1   0.4    1.9  1  MMR_HSR1   50S ribosome-binding GTPase
       0.04   13.1   0.3       0.16   11.1   0.0    1.9  2  NB-ARC     NB-ARC domain
      0.051   13.8   0.1       0.29   11.4   0.0    2.0  2  AAA_22     AAA domain
      0.068   13.4   0.0          3    8.2   0.0    2.3  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
       0.09   12.8   0.2        6.9    6.7   0.0    2.4  2  AAA_14     AAA domain
       0.14   11.8   0.1       0.14   11.8   0.1    1.9  2  cobW       CobW/HypB/UreG, nucleotide-binding domain
       0.15   12.5   0.0       0.68   10.3   0.0    1.8  2  AAA_16     AAA ATPase domain
        0.4    9.2   5.8       0.65    8.6   0.2    2.1  2  AAA_13     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   2.5e-30   2.5e-27       1     137 []      22     186 ..      22     186 .. 0.91
   2 ?   -2.2   0.0       5.4   5.4e+03      40      68 ..     209     235 ..     194     265 .. 0.56

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 2.5e-30
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB..HHHH.................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.................. RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt..vren.................. 79 
                 ++n+s++++eg +++ivG+nGaGK+tL+++++gl +  +G+++l g +  +   +s    ig++pq+ ++ p+    v++                   
  AJA92018.1  22 VDNISFDVQEGDCLGIVGPNGAGKTTLFRAILGLQS-FSGNMKLFGYENPK--YSSIIPLIGYVPQKVTFEPNFPatVYDVvsmgiisekrivqgakli 117
                 58********************************87.69999998655544..6899999*******99999873225555****************** PP

                 ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                + ++++++al+++gl+ l+++++     +LSgG+ qrv +a+al+k+p ll+lDEp a
  AJA92018.1 118 qecgccwnrvyqsikKNEDKVTQALHTVGLESLRNRRI----GELSGGELQRVFIAKALVKDPLLLILDEPVA 186
                 *************9988999******************....*****************************75 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.4
                 EEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  40 Geilldgkdlkeqeleslrkeigvlpqep 68 
                  +i + ++dl+   ++++ ++++++ ++ 
  AJA92018.1 209 ITIIWSSHDLDA--ISKYANRVACMNKKL 235
                 344445555555..555555555555553 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.3e-11   6.2e-08       3      83 ..      36      99 ..      34     119 .. 0.75
   2 !   19.7   0.0     6e-07    0.0006     222     299 ..     143     218 ..     124     222 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.3e-11
      AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83
                +++GpNg+GK++L++a+ +l+                 ++++  +l+   +p++++ + ++  + q+v ++ ++     +v
  AJA92018.1 36 GIVGPNGAGKTTLFRAILGLQ-----------------SFSGNMKLFGYENPKYSSIIPLIGYVPQKVTFEPNFPATVYDV 99
                69******************9.................6677777777777777777777777777777777776666666 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6e-07
      AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                 +++  ++ +++ + elS G ++  +++ al  ++    ll++DEp ++ + + +++++ ++  ++++n++ +i ++H+ 
  AJA92018.1 143 HTVGLESLRNRRIGELSGGELQRVFIAKALVKDP---LLLILDEPVASVDVESQTKFYNVIkTINEQNKITIIWSSHDL 218
                 444456667788999*****99999999999999...89**********************86777799********96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   9.6e-06    0.0095      26      52 ..      34      57 ..      12      64 .. 0.75
   2 !    8.2   0.0    0.0015       1.5     136     203 ..     157     222 ..      99     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                EEEEEESTTSSHHHHHHHHHHHCTT.T CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 26 ftaivGpNGSGKsnlldAilFvLGers 52
                   ivGpNG+GK+ l+ Ai   LG +s
  AJA92018.1 34 CLGIVGPNGAGKTTLFRAI---LGLQS 57
                567****************...66655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                 CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
       SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemle 203
                 +LSgGe + v     +A   vk   l +lDe  a  D +  +k+ +++k+ +++    +i  s++ + ++
  AJA92018.1 157 ELSGGELQRVF----IAKALVKDPLLLILDEPVASVDVESQTKFYNVIKTINEQnkITIIWSSHDLDAIS 222
                 79999976443....3445567777899*********************766651144455566555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   2.4   6.3e-08   6.3e-05       7      39 ..      19      52 ..      13     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.3e-08
      AAA_23  7 frsfrdqeidF.skgltlItGpNGaGKTTildAi 39
                f   ++ ++d  +     I+GpNGaGKTT+++Ai
  AJA92018.1 19 FPAVDNISFDVqEGDCLGIVGPNGAGKTTLFRAI 52
                555555556666557889***************9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   4.2e-05     0.042       9      49 ..      17      58 ..      12     141 .. 0.83
   2 ?    5.1   0.0     0.015        15     322     365 ..     174     217 ..     163     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
      AAA_15  9 kNFRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnn 49
                 NF + ++++ d++e     ++G+N++GK+++ +a+  + + 
  AJA92018.1 17 DNFPAVDNISFDVQEGdCLGIVGPNGAGKTTLFRAILGLQSF 58
                68999999888888878999***************9766554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
      AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                 +++ +l+++EP a+   + q+ +++ +k + ++nk  +i ++H 
  AJA92018.1 174 KDPLLLILDEPVASVDVESQTKFYNVIKTINEQNKITIIWSSHD 217
                 5899******************************9999999996 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00043      0.43       3      20 ..      37      54 ..      35      87 .. 0.86
   2 !    8.1   0.1    0.0033       3.3      59     130 ..     176     237 ..     125     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                EESSTTSSHHHHHHHHHH CS
         AAA  3 lyGppGtGKTllakavak 20
                ++Gp G GKT+l +a+  
  AJA92018.1 37 IVGPNGAGKTTLFRAILG 54
                68*************986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0033
                 SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
         AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkiei 130
                 p  l++DE  a +  +           + +++++++  ++ ++k+++i  +++ d +++   r   +++k+++
  AJA92018.1 176 PLLLILDEPVASVDVE----------SQTKFYNVIKTINE-QNKITIIWSSHDLDAISKYANRvACMNKKLFF 237
                 6666666655554444..........7999********99.578***************99999999988876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.3e-06    0.0042       8      43 ..      15      53 ..      12      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
      AAA_29  8 NWgtfdg.htieidlkg..atlltGpsGsGKSTllDAiq 43
                N   f     i++d+++     ++Gp+G+GK+Tl+ Ai 
  AJA92018.1 15 NYDNFPAvDNISFDVQEgdCLGIVGPNGAGKTTLFRAIL 53
                5555555566666666555788************98875 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.037        37      36      53 ..      33      50 ..      27      61 .. 0.86
   2 !   10.6   0.1   0.00028      0.28     122     158 ..     178     212 ..     130     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.037
        TniB 36 pnlllvGdsnnGKtmive 53
                 +l +vG+   GKt++++
  AJA92018.1 33 DCLGIVGPNGAGKTTLFR 50
                6899***********987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00028
        TniB 122 vLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                 +Li+DE   + +  +++q +f n++k+++++ ki+i+
  AJA92018.1 178 LLILDEP--VASVDVESQTKFYNVIKTINEQNKITII 212
                 8999996..556699********************98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00078      0.77      44      71 ..      29      57 ..      15      68 .. 0.79
   2 ?    4.8   0.0     0.022        22     105     145 ..     171     211 ..     157     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00078
   IstB_IS21 44 iekkenivllGpsGvGKshlaia.lgvea 71
                +++ +++ ++Gp G+GK+ l  a lg + 
  AJA92018.1 29 VQEGDCLGIVGPNGAGKTTLFRAiLGLQS 57
                77899*************99877346665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
   IstB_IS21 105 rllkv.dllilDdlgllpldqaeaellfeviekryerrsiii 145
                 +l+k   llilD+  +  +d ++++++++vi+   e++ i i
  AJA92018.1 171 ALVKDpLLLILDE-PVASVDVESQTKFYNVIKTINEQNKITI 211
                 4555415778887.578899999*********9999877644 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.012      18      49 ..      24      55 ..      14      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
      AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                +++f+ +e d   i+GpN AGK+t++rAi  l
  AJA92018.1 24 NISFDVQEGDCLGIVGPNGAGKTTLFRAILGL 55
                46777778888889**************9876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   3.8e-05     0.038       2      28 ..      35      61 ..      34     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-05
                EEEEESTTSSHHHHHHHHHTSTEEESS CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsd 28
                 +ivG   +GK+tL++a++g ++  ++
  AJA92018.1 35 LGIVGPNGAGKTTLFRAILGLQSFSGN 61
                58****************996555544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.16      21      41 ..      33      53 ..      22      65 .. 0.84
   2 ?   -0.1   0.1      0.43   4.2e+02      95     117 ..     167     189 ..     114     263 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                EEEEEEESTTSSHHHHHHHHC CS
      NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                + +++vG  G GKttl++ il
  AJA92018.1 33 DCLGIVGPNGAGKTTLFRAIL 53
                489**************9997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                 HHHHHCCCTTEEEEEEEE-SHHH CS
      NB-ARC  95 klvrlLltkrfllvlDDVweeed 117
                  + ++L +   ll+lD  + ++d
  AJA92018.1 167 FIAKALVKDPLLLILDEPVASVD 189
                 34555555555555554333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.29       6      26 ..      33      53 ..      29      77 .. 0.87
   2 ?   -0.2   0.0       1.1   1.1e+03      75      99 ..     155     183 ..     121     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
      AAA_22  6 gilvvtGesGtGKTtllrrll 26
                 +l ++G+ G+GKTtl r +l
  AJA92018.1 33 DCLGIVGPNGAGKTTLFRAIL 53
                6888************99876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
      AAA_22  75 seell.ealeqalrarav...ielliiDE 99 
                   el    l++ + a+a    + lli+DE
  AJA92018.1 155 IGELSgGELQRVFIAKALvkdPLLLILDE 183
                 44444455555555555556667888887 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0     0.003         3      26      86 ..     151     198 ..     132     202 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.003
     SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                  +r++g+lSGGe q ++    a al           +++ l++LDE  +++D es+++  +
  AJA92018.1 151 RNRRIGELSGGELQRVFI---AKAL----------VKDPLLLILDEPVASVDVESQTKFYN 198
                 678888888888865442...2222..........23466777777777777777766655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0069       6.9       4      23 ..      34      53 ..      31      76 .. 0.84
   2 ?    4.0   0.1     0.047        47      34     101 ..     143     216 ..     126     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0069
      AAA_14  4 ilvitGaRrvGKTtllkqli 23
                 l i+G+  +GKTtl + ++
  AJA92018.1 34 CLGIVGPNGAGKTTLFRAIL 53
                5789***********98775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.047
      AAA_14  34 lyinldderdkkladpe..kllelilek.lkeekktylflDEiqev......pewekalkslvdegknldvivtGSn 101
                   + l++ r++++ + +  +l +++ +k l + +  +l+lDE   +      +++++++k + +++ ++ +i   S+
  AJA92018.1 143 HTVGLESLRNRRIGELSggELQRVFIAKaLVK-DPLLLILDEPVASvdvesqTKFYNVIKTINEQN-KITII-WSSH 216
                 45556666665555444557788888874444.7899*****777656666677888888877766.54444.4444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00014      0.14       3      21 ..      35      53 ..      33      64 .. 0.83
   2 ?   -0.6   0.3      0.86   8.6e+02      56      97 ..     116     177 ..     102     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                EEEEESTTCCHHHHHHHHH CS
        cobW  3 tvltGflGsGKTtLlnhll 21
                ++++G+ G+GKTtL +++l
  AJA92018.1 35 LGIVGPNGAGKTTLFRAIL 53
                689*************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.86
                 ETTTTECCHCTT-HHHHHHHHHHHH......................TT-SEEEEEECTTTTHH CS
        cobW  56 lenGciCctlredllkelealeere......................erldviliEttGlaePa 97 
                 l + c Cc   + + +++++ e++                       ++l++++i +  + +P 
  AJA92018.1 116 LIQECGCCW--NRVYQSIKKNEDKVtqalhtvgleslrnrrigelsgGELQRVFIAKALVKDPL 177
                 555577776..22333333322222223344455555555555555555555555444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00068      0.68      25      45 ..      33      53 ..      24      89 .. 0.79
   2 ?   -0.3   0.0       1.3   1.2e+03     123     143 ..     163     183 ..     121     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00068
      AAA_16 25 elvllsGesGvGKsslvrell 45
                 ++ ++G+ G GK++l r++l
  AJA92018.1 33 DCLGIVGPNGAGKTTLFRAIL 53
                57889************9997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
      AAA_16 123 lkrll.allsrderplvlvlDd 143
                 l+r + a++   ++pl+l+lD+
  AJA92018.1 163 LQRVFiAKALV-KDPLLLILDE 183
                 44444455555.6679999996 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00065      0.65      21      41 ..      37      57 ..      36      74 .. 0.85
   2 ?    2.8   1.4     0.036        36     528     594 ..     177     246 ..     165     270 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00065
      AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                i G NGaGKTtL r++  l++
  AJA92018.1 37 IVGPNGAGKTTLFRAILGLQS 57
                569***********9988865 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.036
      AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntkr.....krkkkeesfyl 594
                    ++D Pv S D +s+   ++ ik+    +++   ++ + H l+   +  +++         ++++e+f+ 
  AJA92018.1 177 LLLILDEPVASVDVESQTKFYNVIKTIN--EQNKITIIWSSHDLDAISKYANRVACmnkklFFHGEKEKFFS 246
                 56789********************996..555556888999999888888866532111122334455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2020.95
//
Query:       AJA92019.1  [L=56]
Description: hypothetical protein T478_1410 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 413.03
//
Query:       AJA92020.1  [L=58]
Description: 4-oxalocrotonate tautomerase family enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-18   65.0   0.1    4.4e-18   64.9   0.1    1.0  1  Tautomerase    Tautomerase enzyme
    2.4e-09   37.2   0.0    2.5e-09   37.1   0.0    1.0  1  Tautomerase_2  Tautomerase enzyme
  ------ inclusion threshold ------
      0.049   13.9   0.0      0.049   13.9   0.0    1.0  1  Tautomerase_3  Putative oxalocrotonate tautomerase enzyme


Domain annotation for each model (and alignments):
>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.1   7.4e-22   4.4e-18       1      55 [.       2      56 ..       2      58 .] 0.98

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7.4e-22
                 -EEEEEESTCS-HHHHHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEEETTE CS
  Tautomerase  1 PfvnIklvegrsaeqKaeLaervTealvealgaprsaivVvieEvpaenwgvgge 55
                 P+v+++l  grs+eqK+e+a++vT+++ve+l+ +++ + Vv++E p+enw+++g+
   AJA92020.1  2 PYVHVSLYPGRSEEQKQEFAKAVTDSAVEILKTKKEHVIVVFDENPKENWFLAGD 56
                 9****************************************************97 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   4.1e-13   2.5e-09      31      79 ..       3      51 ..       1      54 [. 0.96

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.1e-13
                   EEEEEEES---HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-GGGE CS
  Tautomerase_2 31 vieitlsegRseeqKkaLyralaerlaaklgirpeDvfivlvenpkedW 79
                   +++++l  gRseeqK+++ +a+++   + l  ++e+v++v+ enpke+W
     AJA92020.1  3 YVHVSLYPGRSEEQKQEFAKAVTDSAVEILKTKKEHVIVVFDENPKENW 51
                   799999******************************************* PP

>> Tautomerase_3  Putative oxalocrotonate tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.2e-06     0.049      14      57 ..      13      57 ..       1      58 [] 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.2e-06
                   -HHHHHHHHHHHHHHHHHT.T--GGG-EEEEEE--TTSEEETTEE CS
  Tautomerase_3 14 tkeekealakkiteiYtsv.glPaFyvnvlFieieaedffvGges 57
                   ++e+k+++ak++t+  +++ +  +  v v+F e ++e+ f +g++
     AJA92020.1 13 SEEQKQEFAKAVTDSAVEIlKTKKEHVIVVFDENPKENWFLAGDQ 57
                   578999*******9999988999999***********99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 394.22
//
Query:       AJA92021.1  [L=337]
Description: winged helix-turn-helix DNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-53  177.8   0.0    5.9e-30  103.3   0.0    2.7  3  AsnC_trans_reg2  AsnC-like ligand binding domain
    7.5e-10   38.5   0.0    4.4e-05   23.2   0.0    2.4  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      2e-05   24.1   0.4     0.0012   18.3   0.3    3.1  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0072   15.8   0.0       0.19   11.3   0.0    2.5  2  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.023   14.7   0.0        7.1    6.7   0.0    3.3  2  AsnC_trans_reg   Lrp/AsnC ligand binding domain
      0.025   14.4   0.1       0.13   12.1   0.0    2.0  2  LexA_DNA_bind    LexA DNA binding domain
      0.044   13.6   0.0        4.9    7.0   0.0    2.7  2  HTH_10           HTH DNA binding domain
      0.048   13.8   0.0         14    5.8   0.0    2.8  2  DUF2250          Uncharacterized protein conserved in archaea
      0.049   13.7   0.0        5.9    7.0   0.0    2.8  2  DUF3791          Protein of unknown function (DUF3791)
      0.059   13.1   0.0       0.26   11.0   0.0    2.2  2  Sigma70_r4_2     Sigma-70, region 4
      0.075   13.1   0.0       0.15   12.2   0.0    1.4  1  FeoC             FeoC like transcriptional regulator
      0.085   12.3   0.0         12    5.4   0.0    2.4  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.12   12.2   0.9         18    5.2   0.0    3.3  3  IF2_N            Translation initiation factor IF-2, N-termin


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.9   1.4e+04      54      77 ..      35      58 ..      33      60 .. 0.68
   2 !   71.7   0.0   2.9e-23     4e-20       1      82 []      61     141 ..      61     141 .. 0.99
   3 !  103.3   0.0   4.3e-33   5.9e-30       2      82 .]     233     317 ..     232     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.9
  AsnC_trans_reg2 54 eeveevlaeiaaatgledyevLps 77
                     +ev+++l++++++  l+++  ++ 
       AJA92021.1 35 DEVKSRLKKMKEKGVLRQLSAIFD 58
                     678888888888777766666665 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 2.9e-23
  AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                      klG++ ++lva++++++++e+va +++++p+v+H+YeR++++nl+f+++++  ++++  l++ ++  g++++++Lp+++ fK
       AJA92021.1  61 KLGYT-SSLVAMEIDNSKLEQVALIINKHPGVSHNYERKHQFNLWFTLAVPPGSDLKYELDKFSKLDGIKKVRMLPTLQLFK 141
                      79***.*************************************************************************999 PP

  == domain 3  score: 103.3 bits;  conditional E-value: 4.3e-33
  AsnC_trans_reg2   2 lGfkanalvawkvpeerveevaevvaelpevtHcYeR....ewpynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                      +Gf+an++++wkvpe+r+ +v+e++ ++p+v+HcYeR    +wpyn++ m+h++s +e ++v+++i++++++e+y++L+s refK
       AJA92021.1 233 AGFTANGMIVWKVPEDRISKVGEKLGAFPQVSHCYERpvypDWPYNVFSMIHCKSISEANQVASDIQEQINVEEYKILFSSREFK 317
                      8************************************88888******************************************9 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   3.2e-08   4.4e-05       1      42 []       1      45 [.       1      45 [. 0.97
   2 !   13.0   0.0   5.1e-05      0.07       5      40 ..     176     214 ..     174     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.2e-08
  HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrLe 42
                   + eiD  IL+++q       +++ e+A++  +S+++v  R+++++
     AJA92021.1  1 MEEIDNEILNEIQWTfplVPRPFDEIAKKFSISPDEVKSRLKKMK 45
                   779****************************************95 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5.1e-05
  HTH_AsnC-type   5 DrkILeaLqed...aRisyaeLAervGlSestvlrRvrr 40 
                    D+  ++ Lq+d     +++   A ++G++e++v +R+r 
     AJA92021.1 176 DKEFIRQLQKDfeiVDRPFLNAANELGITEEEVFERLRH 214
                    6667999*****************************996 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   8.9e-07    0.0012       2      48 .]       2      51 ..       1      51 [. 0.80
   2 ?   -0.1   0.0      0.52   7.1e+02      24      46 ..     198     220 ..     197     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.9e-07
      HTH_24  2 detdrkILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                 e+d +IL+++q+       +  e+A++  +Sp  v+ rlk+++e+G+++
  AJA92021.1  2 EEIDNEILNEIQWtfpLVPRPFDEIAKKFSISPDEVKSRLKKMKEKGVLR 51
                57777777777776333335788************************985 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.52
      HTH_24  24 AerlglSpstvnrrlkrLeeeGl 46 
                 A +lg++   v +rl+  e+ G+
  AJA92021.1 198 ANELGITEEEVFERLRHYEKIGV 220
                 789*************9999886 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00014      0.19      14      44 ..      13      44 ..       9      47 .. 0.85
   2 ?    1.6   0.0      0.15   2.1e+02      25      37 ..     196     208 ..     176     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                HHHH.TTT--HHHHHHHHTS-HHHHHHHHHHH CS
  Sigma70_r4 14 elrf.geglTleEIgerlgiSrerVrqiekrA 44
                +  f + ++++ EI++++ iS   V++++k+ 
  AJA92021.1 13 QWTFpLVPRPFDEIAKKFSISPDEVKSRLKKM 44
                5566677899*******************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                 HHHHHHTS-HHHH CS
  Sigma70_r4  25 EIgerlgiSrerV 37 
                   +++lgi++e V
  AJA92021.1 196 NAANELGITEEEV 208
                 57999****9987 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.048        66       3      71 ..      71     135 ..      69     138 .. 0.83
   2 ?    6.7   0.0    0.0051       7.1      11      68 ..     248     308 ..     243     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.048
                     EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71 
                     +++++++   le+++  + ++p V + y     +++ +  +v+   +l   l++ +++l+g+++++ + 
      AJA92021.1  71 MEIDNSK---LEQVALIINKHPGVSHNYERKHQFNLWFTLAVPPGSDLKYELDK-FSKLDGIKKVRMLP 135
                     5677677...999999999*****999999999999999999999999888777.99999999998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0051
                     THHHHHHHHHHTSTTEEEEEE..ESS..SSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEE CS
  AsnC_trans_reg  11 eqleefeealaelpeVvecyr..vtG..dydyllkvvvrdlealerflreklaslpgvarte 68 
                     + + ++ e+l ++p+V +cy   v    +y+ +  ++++++ + +++ ++ +++  +v++++
      AJA92021.1 248 DRISKVGEKLGAFPQVSHCYErpVYPdwPYNVFSMIHCKSISEANQVASD-IQEQINVEEYK 308
                     5688999*************733333223444445555555555555555.55555555555 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.1e-05      0.13      29      58 ..      24      52 ..      19      55 .. 0.90
   2 ?   -1.1   0.0       1.2   1.6e+03      32      58 ..     198     223 ..     196     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.1e-05
                   HHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
  LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyier 58
                    eia+++ ++ p  v+++Lk+++ KG+++ 
     AJA92021.1 24 DEIAKKFSIS-PDEVKSRLKKMKEKGVLRQ 52
                   599****997.****************985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                    HHHHTS-.HHHHHHHHHHHHHTTSEE- CS
  LexA_DNA_bind  32 aralglkSpsaveehLkaLerKGyier 58 
                    a++lg++  + v e+L+  e+ G+++r
     AJA92021.1 198 ANELGIT-EEEVFERLRHYEKIGVMRR 223
                    5678888.7889999999999999987 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0036       4.9      27      50 ..      24      47 ..      21      49 .. 0.93
   2 ?    3.5   0.0     0.045        62      30      48 ..     198     216 ..     195     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0036
      HTH_10 27 keLAkelGIskstlsehLrkaesk 50
                +e+Ak++ Is+  ++ +L+k ++k
  AJA92021.1 24 DEIAKKFSISPDEVKSRLKKMKEK 47
                79*****************99887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.045
      HTH_10  30 AkelGIskstlsehLrkae 48 
                 A+elGI++  + e+Lr  e
  AJA92021.1 198 ANELGITEEEVFERLRHYE 216
                 89**************876 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.01        14      28      55 ..      26      53 ..      24      58 .. 0.90
   2 ?    4.8   0.0     0.023        31      27      56 ..     196     225 ..     175     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
     DUF2250 28 iakeleipleevrellkkLeelGLlerv 55
                iak++ i+  ev++ lkk++e G l + 
  AJA92021.1 26 IAKKFSISPDEVKSRLKKMKEKGVLRQL 53
                899********************99875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.023
     DUF2250  27 siakeleipleevrellkkLeelGLlerve 56 
                 + a+el i  eev e l++ e++G + r  
  AJA92021.1 196 NAANELGITEEEVFERLRHYEKIGVMRRFA 225
                 568899******************998864 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.049        67       9      29 ..      25      45 ..      24      52 .. 0.90
   2 ?    7.0   0.0    0.0043       5.9      10      31 ..     197     218 ..     195     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.049
     DUF3791  9 eyarklglsgkevykllkksg 29
                e a+k+++s++ev  +lkk++
  AJA92021.1 25 EIAKKFSISPDEVKSRLKKMK 45
                689**********99999875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0043
     DUF3791  10 yarklglsgkevykllkksgvl 31 
                  a++lg++ +ev+++l+++  +
  AJA92021.1 197 AANELGITEEEVFERLRHYEKI 218
                 79***************99755 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00019      0.26      29      52 ..      23      46 ..      21      47 .. 0.88
   2 ?   -3.3   0.0       5.3   7.4e+03      23      40 ..      72      89 ..      68      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                  HHHHHHHHT--HHHHHHHHHHHHH CS
  Sigma70_r4_2 29 ykEIAellgisegtVksrlsRArk 52
                   +EIA+++ is+  Vksrl++ ++
    AJA92021.1 23 FDEIAKKFSISPDEVKSRLKKMKE 46
                  68*****************98665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.3
                  HTS---HHHHHHHHT--H CS
  Sigma70_r4_2 23 yleglsykEIAellgise 40
                  ++++++ +++A +++ ++
    AJA92021.1 72 EIDNSKLEQVALIINKHP 89
                  678899999999998766 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00011      0.15      17      48 ..      23      54 ..      22      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
        FeoC 17 lkeLsrhfkaspealeamLeqwvrkGrvekva 48
                ++e++++f++sp+ +++ L  +  kG ++++ 
  AJA92021.1 23 FDEIAKKFSISPDEVKSRLKKMKEKGVLRQLS 54
                689***********************999875 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0089        12      28      49 ..      21      42 ..      19      43 .. 0.92
   2 ?    4.3   0.0      0.02        27      27      51 ..     192     215 ..     188     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0089
  HTH_Tnp_ISL3 28 rsvkavArqlgvSwtTVwrild 49
                  r++ ++A+ + +S++ V+ +l+
    AJA92021.1 21 RPFDEIAKKFSISPDEVKSRLK 42
                  5999**************9986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
  HTH_Tnp_ISL3  27 srsvkavArqlgvSwtTVwrildry 51 
                   + ++  +A++lg+++  V  +l++y
    AJA92021.1 192 R-PFLNAANELGITEEEVFERLRHY 215
                   4.9999*************999998 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.045        62       8      28 ..      25      44 ..      24      54 .. 0.84
   2 ?   -1.6   0.0       1.8   2.4e+03      18      29 ..     177     186 ..     172     190 .. 0.75
   3 ?    5.2   0.0     0.013        18      10      31 ..     198     221 ..     198     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.045
       IF2_N  8 eLAkeLgvkskevikkLfkel 28
                e+Ak+  +++ ev  +L+k +
  AJA92021.1 25 EIAKKFSISPDEVKSRLKK-M 44
                9************999944.5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
       IF2_N  18 kevikkLfkelG 29 
                 ke i++L + + 
  AJA92021.1 177 KEFIRQL-Q-KD 186
                 999*999.5.44 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
       IF2_N  10 AkeLgvkskevikkLfkel...Gie 31 
                 A+eLg++ +ev ++L + +   G++
  AJA92021.1 198 ANELGITEEEVFERLRH-YekiGVM 221
                 89*************76.5455655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2024.33
//
Query:       AJA92022.1  [L=181]
Description: transferase hexapeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-08   33.8   9.9    0.00012   21.7   4.6    3.8  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    5.5e-07   29.2   6.7      0.005   16.6   4.7    3.6  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0036        32      19      34 ..      65      80 ..      63      81 .. 0.74
   2 !    8.4   0.0    0.0002       1.8      21      33 ..      89     101 ..      88     104 .. 0.68
   3 !   21.7   4.6   1.3e-08   0.00012       3      35 ..     127     159 ..     125     160 .. 0.94
   4 ?   -1.5   0.1      0.28   2.5e+03      14      20 ..     167     173 ..     164     175 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0036
                TEEE-TTEEEETTEEE CS
     Hexapep 19 nVkIGdnvkIgagvvi 34
                +V IG++++  ++v i
  AJA92022.1 65 GVNIGKHCHFNPYVLI 80
                6778888888887776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0002
                 EE-TTEEEETTEE CS
     Hexapep  21 kIGdnvkIgagvv 33 
                 +IGdnv++g+++ 
  AJA92022.1  89 TIGDNVTLGSFSM 101
                 6777777777765 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.3e-08
                 EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                  I s+++I p+a+i  +V+IG+n++I +g+v++
  AJA92022.1 127 NIKSGAVINPGAIITLGVTIGKNSIISSGCVVT 159
                 699****************************98 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.28
                 EEEETTE CS
     Hexapep  14 aviggnV 20 
                 +v+g+++
  AJA92022.1 167 VVVGNPA 173
                 4555555 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.057   5.1e+02       2       8 ..      66      72 ..      57      74 .. 0.72
   2 !    8.9   0.0   0.00014       1.2       2      14 ..      88     100 ..      88     102 .. 0.85
   3 ?    2.2   0.1     0.018   1.6e+02      18      33 ..     126     141 ..     123     142 .. 0.88
   4 !   16.6   4.7   5.6e-07     0.005      12      34 .]     136     160 ..     131     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.057
                EEE-TT- CS
   Hexapep_2  2 viIGdnC 8 
                v IG+ C
  AJA92022.1 66 VNIGKHC 72
                4455555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00014
                 EEE-TT-EE-TT- CS
   Hexapep_2   2 viIGdnCliGana 14 
                 ++IGdn+ +G+++
  AJA92022.1  88 ITIGDNVTLGSFS 100
                 6899999999987 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.018
                 EEE-TT-EE-TT-EE- CS
   Hexapep_2  18 vslGdncvvgaGvvit 33 
                 +++  ++v+ +G +it
  AJA92022.1 126 INIKSGAVINPGAIIT 141
                 88999*******9998 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 5.6e-07
                 TT-EE..SEEE-TT-EE-TT-EE-S CS
   Hexapep_2  12 anagi..GvslGdncvvgaGvvita 34 
                 + a+i  Gv++G+n+++++G+v+t+
  AJA92022.1 136 PGAIItlGVTIGKNSIISSGCVVTQ 160
                 5788889****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1251.61
//
Query:       AJA92023.1  [L=206]
Description: Kae1-associated kinase Bud32 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-13   51.1   0.6    1.3e-13   50.9   0.6    1.2  1  Pkinase         Protein kinase domain
    2.1e-09   37.1   0.2    1.3e-07   31.2   0.2    2.1  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    9.5e-07   28.4   0.1    1.8e-06   27.5   0.0    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
    2.9e-06   27.0   0.0    3.9e-06   26.6   0.0    1.2  1  RIO1            RIO1 family
    2.7e-05   24.2   0.0      0.029   14.3   0.0    2.1  2  APH             Phosphotransferase enzyme family
    0.00014   21.6   0.7    0.00018   21.2   0.7    1.4  1  WaaY            Lipopolysaccharide core biosynthesis protein 
     0.0032   16.3   0.1     0.0036   16.1   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase
     0.0069   15.7   0.0     0.0097   15.2   0.0    1.3  1  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.032   13.8   0.1      0.078   12.6   0.1    1.7  2  Choline_kinase  Choline/ethanolamine kinase
      0.035   14.1   0.5        0.7    9.8   0.0    2.3  2  Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in pol
        0.1   11.9   0.1       0.13   11.5   0.1    1.2  1  EcKinase        Ecdysteroid kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.6   8.2e-17   1.3e-13       9     152 ..       6     145 ..       1     170 [. 0.87

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 8.2e-17
                 EESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH......HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHH CS
     Pkinase   9 eGsfGkVykaveketgkivAvKkikkekakkkke......kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeak 101
                 +G+ + Vy     ++gk+ ++K+ k++k ++ +       ++++rE +++  +k+  i + +  f + +++ + ++yv+g+    l+++   ++++ + 
  AJA92023.1   6 KGAEADVYLSS--WNGKKSVLKIRKEKKYRNPRLderirkQRTIREAQLISDVKSFGISTPLIHFVDYKKFSIYMQYVNGK----LIRD---MDDKSIP 95 
                 67777788766..78888888888777766654455777899******************99999**************77....6664...8899*** PP

                 HHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
     Pkinase 102 kiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                 k++ qi + +  lH++gi+H Dl ++N+++  +++l ++DFGla++ e+  
  AJA92023.1  96 KVCLQIGKIVGNLHKNGIMHGDLTTSNFILT-QKNLFLIDFGLANRTEKPD 145
                 *******************************.999**********998865 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   8.2e-11   1.3e-07     121     207 .]      95     177 ..       5     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 8.2e-11
         Kdo 121 rallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl..kielteadweallraY 207
                  +   ++g+++ +lh+ g++H+dl   n+ l q++     + liD+  a++   +  +   dL+  k  ++  + ++ e+ w++++++Y
  AJA92023.1  95 PKVCLQIGKIVGNLHKNGIMHGDLTTSNFILTQKN-----LFLIDFGLANRTE-KPDDHAVDLRLFKEILNsaHANVMEKSWKNFVSGY 177
                 455668**************************997.....*******988766.777888999988888778888999*********99 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.1e-09   1.8e-06       6     158 ..       3     146 ..       1     154 [. 0.69

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.1e-09
                  EEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH.HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBH CS
  Pkinase_Tyr   6 klGeGafGkVvegtlkgekekkevkVavKtlkeeateee.keelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltl 102
                   l +Ga ++V+  +++g+k+  +++   K  + + +e+  k++ ++ea++++++k   i   l   ++ ++  i ++yv         + k  + ++ 
   AJA92023.1   3 ILKKGAEADVYLSSWNGKKSVLKIRKEKKYRNPRLDERIrKQRTIREAQLISDVKSFGISTPLIHFVDYKKFSIYMQYV---------NGKLIRDMDD 91 
                  6788999999999999555555554444444444443322555666666666666666655555555566666666665.........4444444566 PP

                  HHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
  Pkinase_Tyr 103 kdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                  k++ +++lq+ k +  L+++ ++H dl++ N +l+++++  + DfGLa+++ek d+
   AJA92023.1  92 KSIPKVCLQIGKIVGNLHKNGIMHGDLTTSNFILTQKNLF-LIDFGLANRTEKPDD 146
                  68999******************************77766.55*****99966554 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.4e-09   3.9e-06      46     159 ..      37     145 ..      11     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.4e-09
                 -HHHHHHHHHHHHHHHHHHHHHTT--S-..-EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT CS
        RIO1  46 nprklvklwaekEfrnLkrleeagvpvP..kpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded 142
                    ++ k  + +E + ++ +++ g++ P  + +++k+  + m++++  g     ++d++ ++ + ++  ++ + +  l  ++g+ H+DL   N +++++
  AJA92023.1  37 LDERIRKQRTIREAQLISDVKSFGISTPliHFVDYKKFSIYMQYVN--GKL---IRDMD-DKSIPKVCLQIGKIVGNLH-KNGIMHGDLTTSNFILTQK 128
                 334566677889****************4456899***********..655...55555.5568899999988666665.9****************** PP

                 EEEE--GTTEEETTSTT CS
        RIO1 143 kvviIDvsQaveldhpn 159
                 ++++ID++ a  +++p+
  AJA92023.1 129 NLFLIDFGLANRTEKPD 145
                 *******9888887775 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0012       1.9       5     107 ..       4     110 ..       1     112 [. 0.81
   2 !   14.3   0.0   1.8e-05     0.029     167     196 ..     112     138 ..     110     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                 E--.SSCEEEEEEETT--EEEEE.....E-TTS-HHHHH.....HHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHH CS
         APH   5 lsggasnrtylvttpagryvlrr.....npparaaeeir.....revallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpe 93 
                 l+ ga+ ++yl  + +++ vl++     ++ +r++e+ir     re++l   +   g+++P ++       ++   +  ++yv g+ +++ ++++ +p+
  AJA92023.1   4 LKKGAEADVYLSSWNGKKSVLKIrkekkYRNPRLDERIRkqrtiREAQLISDVKSFGISTPLIHF-----VDYKKFSIYMQYVNGKLIRD-MDDKSIPK 96 
                 77899999999999999999999666663333678888766556777777777777779*99999.....566667999***********.9******* PP

                 HHHHHHHHHCCHHC CS
         APH  94 llealgeflaalhq 107
                 ++ ++g   ++lh 
  AJA92023.1  97 VCLQIGKIVGNLHK 110
                 ************96 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                 EEE-SS-SGGGEEEC..TTEEEEE---TT- CS
         APH 167 vllHgDlhpgNllvdpddgrvtGviDfeda 196
                 +++HgDl + N++++ +++ +  +iDf++a
  AJA92023.1 112 GIMHGDLTTSNFILT-QKNLF--LIDFGLA 138
                 79*************.88898..*****98 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.7   1.1e-07   0.00018     116     180 ..      72     137 ..       1     166 [. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
        WaaY 116 kvyimiieyiegielvdmpeid.devkakikqsieklhqlgmvsgdphrgnfivkkdevriidlsg 180
                 k + + ++y++g  + dm + +  +v  +i + + +lh+ g++ gd    nfi+ ++++ +id+  
  AJA92023.1  72 KKFSIYMQYVNGKLIRDMDDKSiPKVCLQIGKIVGNLHKNGIMHGDLTTSNFILTQKNLFLIDFGL 137
                 5677889***********9865358999***********************************853 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.2e-06    0.0036     310     370 ..      96     149 ..       6     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
  Pkinase_fungal 310 ealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesg 370
                     +++ +  k+  +L+ k gi+H D  + N ++t      +++ +LiD+ la  +++++ +++
      AJA92023.1  96 KVCLQIGKIVGNLH-KNGIMHGDLTTSNFILT------QKNLFLIDFGLANRTEKPDDHAV 149
                     55556666777999.*****************......8899*********9999888876 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     6e-06    0.0097     149     189 ..      97     136 ..      68     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
  Kinase-like 149 lTlqlirlaanLqakglvhgkftvdnllldekgglmlggft 189
                  + lq+ +++ nL+++g++hg++t  n++l +k  l+l +f+
   AJA92023.1  97 VCLQIGKIVGNLHKNGIMHGDLTTSNFILTQK-NLFLIDFG 136
                  4568999**********************998.57777775 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.55     9e+02      50      80 ..      79     110 ..      46     114 .. 0.75
   2 ?   12.6   0.1   4.8e-05     0.078     145     173 ..     113     137 ..      81     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.55
                     E--TCEE-.-TTGGGCHHHHHHHHHHHHHHTT CS
  Choline_kinase  50 efiesrtl.stedlrepeiskkiAkklaelHs 80 
                     ++++++ + + +d + p++  +i+k +++lH+
      AJA92023.1  79 QYVNGKLIrDMDDKSIPKVCLQIGKIVGNLHK 110
                     78888776245666678888999999999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.8e-05
                     EEEE-S--SGGGEEE.-CTTEEEE--GTT CS
  Choline_kinase 145 vvfcHnDlqegNillnkeekklvlIDFEY 173
                     +   H Dl  +N++l  ++k+l+lIDF  
      AJA92023.1 113 I--MHGDLTTSNFIL--TQKNLFLIDFGL 137
                     3..5***********..**********65 PP

>> Kinase-PolyVal  Serine/Threonine/Tyrosine Kinase found in polyvalent proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00043       0.7      28      57 ..       3      35 ..       1      41 [. 0.81
   2 ?    2.2   0.1     0.098   1.6e+02     130     153 ..     111     134 ..     107     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
  Kinase-PolyVal 28 ylseGaEqkVYl..kddk.sViKlndaiyyasw 57
                     l++GaE++VYl   ++k sV+K+++ ++y ++
      AJA92023.1  3 ILKKGAEADVYLssWNGKkSVLKIRKEKKYRNP 35
                    5789********7645556******99988765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.098
  Kinase-PolyVal 130 lgliledlhdeNVltkdgtlyfID 153
                      g++  dl   N +  +++l++ID
      AJA92023.1 111 NGIMHGDLTTSNFILTQKNLFLID 134
                     6788889****************9 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     8e-05      0.13     215     285 ..     111     181 ..      70     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-05
    EcKinase 215 nvlnHGDlwvnNimfkydeegepedvilvDFQlsryg....SpalDLlyf..lytsteeelrkekfdellriYhesL 285
                 n ++HGDl ++N+++  +      ++ l+DF l++ +      a+DL  f  ++ s++ ++ ++++++++  Y++s 
  AJA92023.1 111 NGIMHGDLTTSNFILTQK------NLFLIDFGLANRTekpdDHAVDLRLFkeILNSAHANVMEKSWKNFVSGYQSSV 181
                 6799***********664......79******997642111579**99888899*****************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1532.64
//
Query:       AJA92024.1  [L=234]
Description: zinc- or iron-chelating domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-09   36.0   0.0    1.8e-08   35.0   0.0    1.6  1  CxxCxxCC  Putative zinc- or iron-chelating domain


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     1e-12   1.8e-08       4      73 ..      64     172 ..      61     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1e-12
    CxxCxxCC   4 e..CgaCCk.elkvklteedlerlkaaevaeeeeeskkiak..................................adgrCvfldeetklCkiYeeRpki 65 
                    C++CC  + +  lt +dl ++ + ++ +++ e  k ++                                  ++  C+fl++e + C i+  Rp +
  AJA92024.1  64 WpdCHNCCDrQGRLPLTSDDLIQIGQGMKYQKTSEFVKQETlvathdeptpsggfsvmtnvslkrktdeteaddgTHISCRFLNGE-GGCGIHPTRPGV 161
                 445******666788999999998555553333333333236899****************************99999********.6*********** PP

    CxxCxxCC  66 crlfpas...e 73 
                 c l+p+s   +
  AJA92024.1 162 CYLYPFStwaQ 172
                 ******85541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1838.29
//
Query:       AJA92025.1  [L=181]
Description: NUDIX domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-13   48.9   0.0    8.6e-13   48.5   0.0    1.3  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   4.8e-17   8.6e-13       4     107 ..      27     132 ..      24     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.8e-17
                 EEEEEEEEETTSEEEEEEES...SSSTTTEESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.....EEEEEEEEEEEEC CS
       NUDIX   4 ravgvvllnekgevLlvrrs...kkpfpgWelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapydgpygd.....eheilyvfleeve 93 
                 ++v ++++ e  ++L+++     +++  + ++PgGk+ + + ++ ++A+RE++EEtG+++e  +++g+l+ +++ +  ++                ++ 
  AJA92025.1  27 ASVLIIIFAESPKILMIKKPitmNHHGGEIAFPGGKISDEDnDLLDTALRETKEETGITVEREKIIGQLEPVTTLNSGFTIlpfvcI--------LDKI 117
                 68999******99*******97444444478*******9999****************999999**998888877666553222220........3333 PP

                 SGCSST.STTTEEEE CS
       NUDIX  94 gelepn.denevsev 107
                 ++l pn + +e+ e+
  AJA92025.1 118 ENLMPNsEVDEFLEI 132
                 333333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1455.93
//
Query:       AJA92026.1  [L=102]
Description: ribosomal protein S10 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-22   78.5   0.0    3.8e-22   78.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.19   12.0   0.0    1.1  1  CTX_RstB       CTX phage RstB protein


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   4.2e-26   3.8e-22       1      97 [.       6      99 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 4.2e-26
                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHHHS-...S---SS-EEEE CS
  Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidtllkllqlnlpegVsvev 97
                   ri+l+S++   L  ++++i+ + k++g+kvkgp plP kr+ v ++ksp++  +++ e++e+r+h+R+id+ +a+++ i++l++   l++p+ V +e+
     AJA92026.1  6 RIKLTSTSLLKLGGVCDEIMGIGKKTGVKVKGPTPLPVKRLNVVTRKSPCGSgTETYEKWEMRMHRRIIDL-NADDKAIRQLMR---LKIPDDVYIEL 99
                   8**********************************************************************.7***********...*******9986 PP

>> CTX_RstB  CTX phage RstB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.1e-05      0.19       4      77 ..      24     101 ..      23     102 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
    CTX_RstB   4 vigvelseGvskkspkPYdiaklfylvparswkkdk..gnieavGldkkeiamqsnpellrklkglelp..vlveLel 77 
                 ++g+ +  Gv  k p P  +++l+++   +   ++   ++  ++ + ++ i+++ +++ +r+l  l++p  v +eL+l
  AJA92026.1  24 IMGIGKKTGVKVKGPTPLPVKRLNVVTRKSPCGSGTetYEKWEMRMHRRIIDLNADDKAIRQLMRLKIPddVYIELSL 101
                 67899999***************999876555444400444457789999*******************777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 770.83
//
Query:       AJA92027.1  [L=224]
Description: 3,4-dihydroxy-2-butanone-4-phosphate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-59  199.5   0.0    4.2e-59  199.3   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
    0.00077   18.1   0.1     0.0013   17.3   0.0    1.4  2  PAF-AH_p_II    Platelet-activating factor acetylhydrolase, is


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   4.7e-63   4.2e-59       2     191 ..       5     219 ..       4     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 4.7e-63
                    HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S....................STT-- CS
  DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene....................dkhkt 77 
                    +a+++lk+G+fv+++D++ rene d+++aAe+vtpe++  m++ha+Gl+c+a++++ a++L+L++m++                          + 
     AJA92027.1   5 SALSSLKQGEFVMIHDSDGRENEIDMVVAAEFVTPEHIVRMRKHAGGLLCLAIDNSLAEKLQLKYMHN--MlsasneldeeskkmimgtapYGDHP 98 
                    6999**************************************************************95..444667799999*******9945569 PP

                    -BB--EEESST-SSS-SHHHHHHHHHHHH-..T.....T--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TT.SC CS
  DHBP_synthase  78 aftvsvdaaegttTGIsaaDRalTirklad..p.....kakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicellndd.gt 165
                    +f++s++++ +t TGI+++DRalTi+++    +     +  ++ f++PGhv +l+a++g + +R+ghTE++v La+la+l+p+ +ice+++++  +
     AJA92027.1  99 TFSISINHK-QTYTGITDRDRALTIKEMSTlyKnenpkQYFNSTFKTPGHVPLLIASNGLLSSRTGHTEMSVYLAQLANLSPITAICEMMDSEtYS 193
                    ********9.9****************99976334443334599**********************************************988677 PP

                    B-BHHHHHHHHHHHT-EEEEHHHHHH CS
  DHBP_synthase 166 marrdeleefakkhglkiitiedlie 191
                    +++ d++e++ak++ +++i +++l+e
     AJA92027.1 194 ALSVDKAEKYAKENAIPFIDGKELLE 219
                    ***********************987 PP

>> PAF-AH_p_II  Platelet-activating factor acetylhydrolase, isoform II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.17   1.6e+03     322     364 ..      36      83 ..      30      87 .. 0.56
   2 !   17.3   0.0   1.5e-07    0.0013      76     145 ..     124     196 ..      99     224 .] 0.67

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.17
                  GSS-HHHHHHTTSS-.....SS-HHHHHHHHHHHHHHHHHHHHT--SS CS
  PAF-AH_p_II 322 fvlgkligkvlklkg.....eidpeealdiankaslaFLqkhldlkkd 364
                  fv+++ i ++ k  g      id ++a +++ k + + L    +l+++
   AJA92027.1  36 FVTPEHIVRMRKHAGgllclAIDNSLAEKLQLKYMHNMLSASNELDEE 83 
                  677777777766644222224566666666666555555555555554 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.5e-07
                  H.HHHHTT-EEEEEET--B--SS-EEEEEEE--TT--TTTT...HHHHHHHHHTT-EEEEE---SS-SSEEEE CS
  PAF-AH_p_II  76 lfkllvgslrlpvkknellktkekyPlivFsHGLgafRtlY...salcielAskGfvvaavEHrDesAaatyv 145
                   +++l+ + +   + n+++kt++  Pl++ s GL ++Rt     s +  +lA    + a  E  D     +  
   AJA92027.1 124 EMSTLYKNENPKQYFNSTFKTPGHVPLLIASNGLLSSRTGHtemSVYLAQLANLSPITAICEMMDSETYSALS 196
                  346788888888999***********************97711145555666677777777777765544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1466.51
//
Query:       AJA92028.1  [L=95]
Description: hypothetical protein T478_0013 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 674.37
//
Query:       AJA92029.1  [L=117]
Description: alpha-NAC protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-14   53.3   4.5    9.3e-14   51.2   3.8    1.9  2  NAC       NAC domain
     0.0071   16.1   0.6      0.011   15.6   0.6    1.3  1  UBA_4     UBA-like domain
  ------ inclusion threshold ------
        0.1   12.2   0.1       0.18   11.4   0.1    1.3  1  DMA       DMRTA motif
       0.12   12.1   0.9        9.6    6.0   0.0    2.7  3  ScdA_N    Domain of Unknown function (DUF542)
       0.43   10.6   0.2       0.43   10.6   0.2    2.1  2  UBA       UBA/TS-N domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   3.8   2.6e-17   9.3e-14       2      51 ..      11      63 ..      10      70 .. 0.91
   2 ?    0.9   0.0      0.13   4.7e+02      21      41 ..      73      95 ..      72     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 2.6e-17
         NAC  2 kKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvf 51
                +++r+++ k+g+  +e+++++eV+i++++ k++++++P V+  k + s +++v+
  AJA92029.1 11 RQMRRMMDKMGMdmEEVNNVQEVIIKTDK-KEIIISKPAVTemKTKDSSIFQVV 63
                89***************************.***********88888899**998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.13
         NAC 21 eVtirksdgkvlvfdnPkVq..k 41
                eV i+ +++  l+ +++ V   +
  AJA92029.1 73 EVQIFSDEDISLICQQANVDeeA 95
                899**999999999999997543 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6     3e-06     0.011       4      33 ..      82     111 ..      79     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-06
       UBA_4   4 iaqFqaiTGadeekArqlLeannWdLerAi 33 
                 i+  ++ +++dee A+  L+ +++dL rAi
  AJA92029.1  82 ISLICQQANVDEEAAKNALQECDGDLARAI 111
                 5555666789*******************9 PP

>> DMA  DMRTA motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.2e-05      0.18      23      34 ..     100     111 ..      97     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
         DMA  23 LqrCkGDVvqAI 34 
                 Lq C+GD+ +AI
  AJA92029.1 100 LQECDGDLARAI 111
                 9**********9 PP

>> ScdA_N  Domain of Unknown function (DUF542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0027       9.6      29      49 ..       8      28 ..       8      32 .. 0.94
   2 ?   -1.3   0.0      0.48   1.7e+03       5      15 ..      59      69 ..      55      83 .. 0.59
   3 ?    3.6   0.4     0.015        52      34      54 ..      82     102 ..      79     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0027
      ScdA_N 29 gGkvsLaeAckekgidleevl 49
                gG++++++ + + g+d+eev 
  AJA92029.1  8 GGNRQMRRMMDKMGMDMEEVN 28
                8******************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.48
      ScdA_N  5 vGeivaelpra 15
                + ++va+ ++ 
  AJA92029.1 59 IFQVVADSYEE 69
                55666666543 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.015
      ScdA_N  34 LaeAckekgidleevlaeLea 54 
                 ++  c+++++d+e+  ++L++
  AJA92029.1  82 ISLICQQANVDEEAAKNALQE 102
                 6678*********99999987 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.8      0.34   1.2e+03      12      19 ..      20      27 ..      12      30 .. 0.88
   2 ?   10.6   0.2   0.00012      0.43      15      34 ..      92     111 ..      92     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.34
                TTS-HHHH CS
         UBA 12 MGFdreev 19
                MG+d eev
  AJA92029.1 20 MGMDMEEV 27
                9**99998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                 -HHHHHHHHHHTTTSHHHHH CS
         UBA  15 dreevveALratgnNeErAv 34 
                 d+e+++ AL  +++++ rA+
  AJA92029.1  92 DEEAAKNALQECDGDLARAI 111
                 799****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 871.23
//
Query:       AJA92030.1  [L=440]
Description: transporter, CPA2 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-54  184.2  54.6      4e-54  183.9  54.6    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
      0.037   14.2   0.2      0.037   14.2   0.2    4.7  5  Spore_YabQ      Spore cortex protein YabQ (Spore_YabQ)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9  54.6   4.5e-58     4e-54       6     380 ..      44     427 ..      41     429 .. 0.85

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 4.5e-58
                     HHHHHHHH..H.HHHTTSXHHHHHHHHHHHHTTTTTS.......................HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHH CS
  Na_H_Exchanger   6 llallvgl..l.arrlklpeivgliiaGlllGpsglglieps..................eedlevlselglilllFlaGleldlrelrknlksi 79 
                     ++++l+g+  l + ++++p i+g+++aG+l+Gp  + + +                       l+v++e+g+illlF +G+e++++++r+ +k +
      AJA92030.1  44 VIMILAGIvtLaFFKIRQPLIIGYLFAGMLIGPLSPIWTSFLpesgsgdhggtsvgilsdIAALNVFAEIGVILLLFVIGIEFPFAKIRSIGKVA 138
                     34445555445599999********************65555667788888888888887799******************************** PP

                     HHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSS CS
  Na_H_Exchanger  80 lllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalakeeagget 174
                     + ++ lg+++t+++  + ++   +lg+ + +al+++a+ls++++++++++l+e+g+++++  +l+lg+++++D++av+l+a+l ++a   ag+++
      AJA92030.1 139 IGVGSLGLFLTLIA-VFYAS--TLLGLGFMDALFISAALSISSTAIIVKVLEEAGKIKKESSILVLGILIVEDVIAVILIASLESIA--LAGTVS 228
                     ***********999.44444..37899***********************************************************9..444444 PP

                     STSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.CTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
  Na_H_Exchanger 175 slllllliflvvavgglllglvigwllrlitrft.dddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfregl 268
                       +++ ++++  ++++ ++ + i  +++l+ +++  ++re+ +l vl ++++ alla ++g+s ++gaflaG++++e++ ++ +s+ l+s +++ 
      AJA92030.1 229 IEGAVTVVVVATILIVGTFTVGIRTVPKLVDKVAsAENREILLLSVLGVCFGYALLANVVGLSVAIGAFLAGVLVAESKSAE-VSKILSSPIKDM 322
                     444444444444445555566666678888888888****************************************999999.8888666666** PP

                     HHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCC.CCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTC CS
  Na_H_Exchanger 269 fnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiig.fgglqrgavalalaalgpalgllarelyalliv 362
                     f+ +fFv+vG+ +d++ l   ++ ++++l+++++ + +++ + +l   l++ ++  +l  + ++g++rg+++++++ +g ++g+ ++ l++l+ +
      AJA92030.1 323 FVAIFFVSVGALMDVSQL---ENYIFIALALIAIAMGMKFGGNMLGNILMRQPRGKSLRSAfTLGAPRGEFSIVIIKVGVDAGVVSAFLFPLIGI 414
                     **************7777...5555555555555556*************999999998887899****************************** PP

                     STSXHHHHHHHHHHHHHH CS
  Na_H_Exchanger 363 vvlftvlvqGlslkpllk 380
                     + ++t +     ++p+l 
      AJA92030.1 415 ISIITAF-----ITPFLV 427
                     *******.....666664 PP

>> Spore_YabQ  Spore cortex protein YabQ (Spore_YabQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   4.2e-06     0.037      32      69 ..      38      75 ..      24      82 .. 0.93
   2 ?   -3.0   3.6      0.99   8.9e+03      12      45 ..     145     176 ..     113     184 .. 0.63
   3 ?   -2.7   1.1       0.8   7.2e+03      62      62 ..     288     288 ..     269     303 .. 0.51
   4 ?    0.3   0.5     0.094   8.4e+02      41      71 ..     323     353 ..     316     359 .. 0.64
   5 ?   -1.4   0.1      0.32   2.9e+03       7      24 ..     402     419 ..     399     432 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-06
  Spore_YabQ 32 fieDilfwllaallvflfllrinygelrlylflgillG 69
                f++D+   ++ a +v l++++i +  + +ylf+g+l+G
  AJA92030.1 38 FVTDLAVIMILAGIVTLAFFKIRQPLIIGYLFAGMLIG 75
                79***********************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.99
  Spore_YabQ  12 llydlf.rilrrllkhkkvltfieDilfwllaall 45 
                  l+ ++  ++ +      +  +++D lf  +a  +
  AJA92030.1 145 GLFLTLiAVFYAS---TLLGLGFMDALFISAALSI 176
                 3333330222222...3345777888887777665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.8
  Spore_YabQ  62 l 62 
                 +
  AJA92030.1 288 V 288
                 2 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.094
  Spore_YabQ  41 laallvflfllrinygelrlylflgillGal 71 
                 ++a+++ ++   +   +l  y+f++++l a+
  AJA92030.1 323 FVAIFFVSVGALMDVSQLENYIFIALALIAI 353
                 4455555555555556677777777766554 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.32
  Spore_YabQ   7 Giilgllydlfrilrrll 24 
                 G++ ++l+ l++i+  + 
  AJA92030.1 402 GVVSAFLFPLIGIISIIT 419
                 788888888887776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2567.32
//
Query:       AJA92031.1  [L=188]
Description: PF04919 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-45  154.0   0.9    4.3e-45  153.9   0.9    1.0  1  DUF655          Protein of unknown function (DUF655)
     0.0042   17.3   0.6      0.075   13.3   0.1    2.7  3  HHH_3           Helix-hairpin-helix motif
     0.0073   16.6   0.0       0.14   12.5   0.0    2.2  2  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.9   7.2e-49   4.3e-45       2     181 .]      12     187 ..      11     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 7.2e-49
                 --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GGGS-HHHHHHHHHHHHHHHHTTHHH CS
      DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisyedLtdvaraeLpdvvekivkekEdr 100
                 ee+a+vLD+ + G+++  +   r+  +v alge++ltLle+  l e ++++ ++++igk+ ++k++++  ++ ye+++d+a++eL +vv  iv+++E r
  AJA92031.1  12 EEYAYVLDFSTRGRSKTVR--GREGVIVTALGEERLTLLEVLGLDESEFEIGEKIYIGKEGRTKVQSVLGKLDYEQISDSAQTELTNVVSTIVTNNEIR 108
                 89***********999886..7999************************************************************************** PP

                 HHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHHHHHHHHHHHHH-TTSS--SS-- CS
      DUF655 101 fveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpaeilverileEiedktekYylFve 181
                 fv++ n+a+p+t R H+Lel+pg+gk +++ i++e ++++Fe +ed+++r  g+k+p++ l +ri+eEi+++ ++++lFv+
  AJA92031.1 109 FVNYINNAQPLTPRKHSLELIPGIGKTYLKVIIDEINKKKFENYEDLESRA-GIKEPVNHLSKRIIEEISGE-TQFRLFVK 187
                 **************************************************9.6******************9.89999985 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.067     4e+02      44      58 ..      45      59 ..      42      62 .. 0.87
   2 ?   -3.9   0.0       2.9   1.7e+04      51      61 ..      77      87 ..      76      88 .. 0.77
   3 !   13.3   0.1   1.3e-05     0.075      14      54 ..     124     163 ..     120     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.067
       HHH_3 44 eeLlkvkglgpktfe 58
                  Ll+v gl++  fe
  AJA92031.1 45 LTLLEVLGLDESEFE 59
                579********9998 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.9
       HHH_3 51 glgpktfeqla 61
                +lg+  +eq+ 
  AJA92031.1 77 VLGKLDYEQIS 87
                58888999986 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 1.3e-05
       HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgp 54 
                   L+ +pG+g+++ k I++  +k+ +f++ e+L +  g+++
  AJA92031.1 124 HSLELIPGIGKTYLKVIIDEINKK-KFENYEDLESRAGIKE 163
                 56999****************555.**********999975 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.049   2.9e+02      34      68 ..      47      78 ..      42      87 .. 0.88
   2 !   12.5   0.0   2.4e-05      0.14       3      42 ..     125     163 ..     123     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.049
  Transposase_20 34 laayaGlapvenqSGkkkrrgriskrGnrrlRraL 68
                    l   +Gl+ +e++ G+k     i k G+ +++++L
      AJA92031.1 47 LLEVLGLDESEFEIGEKIY---IGKEGRTKVQSVL 78
                    67789***********998...9999999999998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
  Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlap 42 
                      Le ipGiG++   +++ ei++ ++f++ ++l + aG+  
      AJA92031.1 125 SLELIPGIGKTYLKVIIDEINK-KKFENYEDLESRAGIKE 163
                     5888****************99.6*************963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1347.62
//
Query:       AJA92032.1  [L=219]
Description: formyl transferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-12   45.6   0.0    8.2e-12   45.2   0.0    1.2  1  Formyl_trans_N  Formyl transferase
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.028   14.6   0.0    1.4  1  Formyl_trans_C  Formyl transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0   9.1e-16   8.2e-12      68     155 ..      32     117 ..      11     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 9.1e-16
                     CHHHHHHHHCTT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE CS
  Formyl_trans_N  68 eeelaeelkelkadlivlagymkllpkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkve 155
                     ++   +++k  ++ +i  + ++  +p+e+v+ ++  ++  H + LP+f+G ++iq  +++G+++t +t + ++e++D G+i++qk + 
      AJA92032.1  32 KQLTYNSIKRINPSIIFFPDWSWKVPEEIVRNFK--CVCFHEAPLPKFRGGSPIQNQILRGKTKTKTTAFIMNEKIDAGNIILQKDLS 117
                     45556789999********************996..699*********************************************9876 PP

>> Formyl_trans_C  Formyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.2e-06     0.028       3      50 ..     161     210 ..     160     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                     -GGGGB--T.TSBHHHHHHHHHHT-.TS--EEEEETTEEEEEEEEEEE-S CS
  Formyl_trans_C   3 kkedgridw.nqsaeeihnlvrgls.pwPgayttlngkrvkllkaevvse 50 
                     k+ed++++  n++ + +++ +r l  p+P+ay+ + +kr+   ka   ++
      AJA92032.1 161 KPEDSELKNlNHTKKYLYDFIRMLEdPYPNAYMKIGKKRLIFKKAFYNNN 210
                     57888887779**************9***********9998777755544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1667.57
//
Query:       AJA92033.1  [L=191]
Description: tRNA-intron endonuclease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-18   64.4   0.1    1.6e-17   63.3   0.1    1.5  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
      5e-12   45.3   0.6    2.9e-09   36.5   0.1    2.3  2  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.1   1.8e-21   1.6e-17       3      85 .]      85     168 ..      83     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.8e-21
                    HHHHHHHHHHHTT-EEEECGGGTSSEEEE.TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
  tRNA_int_endo   3 lkyavyrdLrekGyvvrsGlkFGadFrvY.qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85 
                    +++  yrdLr+kGyvv++G+ F +dFrvY +++ +++ +++l++ ++e+++ ++ +l ++++ ++++ K+ i+a++++ g++ y
     AJA92033.1  85 TRFLLYRDLRTKGYVVKDGFGFDSDFRVYeKGNYGKKDAKFLIFAFNEGTQQKIGKLYKNIQEITQMGKEPIIAVIERRGEIIY 168
                    68999************************88889**********************************************9987 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   3.2e-13   2.9e-09       3      66 ..      11      72 ..       9      73 .. 0.86
   2 !    7.2   0.0   0.00045         4      20      42 ..     111     132 ..     106     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.2e-13
                     EEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
  tRNA_int_endo_N  3 geLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                     +++ +++ +v +  + ++++ ++++G+ l +++L+L+ +E+lYLl+++kle++k ++ + f+el
       AJA92033.1 11 AKFIDEKTIVLN-PKMQNILTERGFGE-LQNNTLVLDSFETLYLLYNNKLELKKVNKNIIFDEL 72
                     677788888887.66667777788***.**************************9999999998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00045
                      HHHHTTT-SEECCTSSEEEEHHH CS
  tRNA_int_endo_N  20 rlyekgfYGkplidepLqLslvE 42 
                      r+yekg YGk ++ + L  ++ E
       AJA92033.1 111 RVYEKGNYGK-KDAKFLIFAFNE 132
                      79********.***999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1526.56
//
Query:       AJA92034.1  [L=103]
Description: 50S ribosomal protein L12P [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-14   54.3  18.1    1.7e-14   54.1  18.1    1.1  1  Ribosomal_60s   60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.072   12.4   4.1      0.082   12.3   4.1    1.1  1  PPR_long        Pentacotripeptide-repeat region of PRORP
       0.08   12.9   0.3       0.12   12.4   0.3    1.3  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1  18.1   2.9e-18   1.7e-14       1      88 []      16     102 ..      16     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.9e-18
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XX--SS--.STTT CS
  Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeee.EeedddmG.fgLF 88 
                    e++++n+++v+ka g+ev++a+vk+lv++l++++ie++++++  +   +aaaaa+aa aaa+ ++++ekk+e++ e  ee  ++G  +LF
     AJA92034.1  16 EVNEANVTSVVKATGAEVNEAQVKALVASLADVNIEDAIKAAPVA---VAAAAAPAADAAAGGDEKKEKKAEPPSEkQEEAAMEGlSSLF 102
                    689***************************************755...678888888888888888888888888533444488999998 PP

>> PPR_long  Pentacotripeptide-repeat region of PRORP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.1   1.4e-05     0.082      84     162 ..      13      90 ..       2      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                 TT----HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-S---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT----HHH CS
    PPR_long  84 kgvspnEatvtalarlaaakedgdlafelvkemekagvsPrLRsyaPaLaayckagdadkaleveehlkasgveleEae 162
                  + + nEa vt++++   a+ +  +  +lv++++ ++++  +++ aP+ +a   a  ad a+  +e+ ++++  + E++
  AJA92034.1  13 LEKEVNEANVTSVVKATGAEVNEAQVKALVASLADVNIEDAIKA-APVAVAAAAAPAADAAAGGDEKKEKKAEPPSEKQ 90 
                 345789*********************************99997.8999999999999999999999888776666655 PP

>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3     2e-05      0.12       2      26 ..      16      40 ..      15      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                    --EEEEEEEEEE---SSSSEEEEEE CS
  Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrv 26
                    e+ +A+V+ v++ tG +++  qV+ 
      AJA92034.1 16 EVNEANVTSVVKATGAEVNEAQVKA 40
                    7899*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 728.14
//
Query:       AJA92035.1  [L=330]
Description: CAAX protease self-immunity [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-15   54.9   5.0    8.2e-15   54.9   5.0    2.7  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   4.5      0.75   1.3e+04      40      55 ..      15      30 ..       2     143 .. 0.69
   2 !   54.9   5.0   4.6e-19   8.2e-15       7      91 ..     156     271 ..     151     272 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.75
                HHHHHHHHHHHCSGGG CS
        CPBP 40 ailissilFglaHlpn 55
                  ++ s++Fgl+ +  
  AJA92035.1 15 FSALMSVIFGLMIVSF 30
                5556666666654443 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 4.6e-19
                 HHHHHHHHHHHHHHHHHTTCHHHH.........................HHHH.S-....HHHHHHHHHHHHHCSGGG.....HHHHHHHHHHHHHHHH CS
        CPBP   7 vfllalllapllEEllfRglllql.........................lqergss....tlailissilFglaHlpn.....gpsvllaalaGlvlgy 71 
                 +++l + lap++EE++fR +l+                           l+ +       +  i+i +i+Fg+aH++      +  +l a++ G++lg+
  AJA92035.1 156 ILFLQISLAPITEEIGFRLILIGIplfliyshkssikffikslwspysnLHVY--DskkaIGLIVIVGIFFGVAHVISgepwtTGKILQASVGGIILGW 252
                 67788899*************55555555555555555544443333333333..0345699****************997753349************ PP

                 HHHHTT-HHHHHHHHHHHHH CS
        CPBP  72 lylktgsllaaillHallnl 91 
                 +y ++g l+aai+lH+++n+
  AJA92035.1 253 VYFRYG-LAAAIILHWATNY 271
                 ******.************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2536.93
//
Query:       AJA92036.1  [L=217]
Description: siroheme synthase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-16   61.2   0.2      6e-16   58.8   0.0    2.0  2  NAD_binding_7   Putative NAD(P)-binding
    0.00053   20.1   0.7    0.00053   20.1   0.7    2.1  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
     0.0012   18.2   0.7     0.0027   17.1   0.7    1.5  1  Sirohm_synth_M  Sirohaem biosynthesis protein central
     0.0043   17.3   0.1      0.014   15.6   0.0    1.9  2  TrkA_N          TrkA-N domain
     0.0099   15.2   0.0      0.017   14.5   0.0    1.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.036   13.6   0.4      0.064   12.8   0.1    1.6  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
        0.1   13.2   1.1        2.7    8.6   0.0    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.12   12.9   0.0        0.2   12.1   0.0    1.4  1  XdhC_C          XdhC Rossmann domain
       0.16   11.3   1.9        2.7    7.3   0.1    2.6  3  Peripla_BP_1    Periplasmic binding proteins and sugar bindin
        1.5    8.9   6.2       0.77    9.8   1.9    2.1  2  DUF3793         Protein of unknown function (DUF3793)


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   3.3e-19     6e-16       3     100 ..       5     111 ..       3     115 .. 0.84
   2 ?    0.4   0.1       0.5   8.9e+02      22      39 ..     161     178 ..     116     216 .. 0.56

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 3.3e-19
  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeelekd..legad..lviaatddrelneriaeaakarrilv 89 
                    l+l++k+v+++G+G+ A+++++ l ++g+k++v+ ++ ++e+      ++++l+++++ +   l++++  lvia t+d +ln++i+++ak+ +il 
     AJA92036.1   5 LHLNEKTVIIIGAGNEALKRIKLLESEGCKIIVIGEKPNSEITklsqkKKITLKKTKITSMlfLKKYKpfLVIASTTDSSLNQKIVQTAKKMKILS 100
                    6799*********************************744444455556677777777666565555455************************** PP

  NAD_binding_7  90 nvadkpelcdf 100
                     ++d+p+ +d+
     AJA92036.1 101 YASDSPDSSDI 111
                    *******9997 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.5
  NAD_binding_7  22 kvrklleagakvtvvape 39 
                    k++k+++++ k ++++++
     AJA92036.1 161 KIQKFARTESKKHILTQT 178
                    333333333333333333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   2.9e-07   0.00053       9      77 ..       6      72 ..       1     113 [. 0.72
   2 ?   -2.0   0.0         2   3.5e+03      81      93 ..     127     139 ..     100     157 .. 0.61
   3 ?   -0.7   0.0      0.78   1.4e+03      80      95 ..     165     180 ..     132     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                  ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-S CS
  Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaead 77
                  +l+ek+v++iGaG+ a + +k L ++g+k +v+     +   +l ++ k + ++ +k++++   l+++ 
    AJA92036.1  6 HLNEKTVIIIGAGNEALKRIKLLESEGCKIIVIGEKPNSEITKLSQKKKIT-LKKTKITSML-FLKKYK 72
                  699**************************9999888899999998887444.7777777776.444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                   E-SSSSS-SB-HH CS
  Shikimate_DH  81 sataseepileke 93 
                   ++t+ ++pi+ k+
    AJA92036.1 127 ISTSGSSPIMAKK 139
                   4666666666654 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.78
                   EE-SSSSS-SB-HHHH CS
  Shikimate_DH  80 isataseepilekeev 95 
                   ++ t s+++il++ e 
    AJA92036.1 165 FARTESKKHILTQTER 180
                   2334444444444333 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.7   1.5e-06    0.0027       5      22 ..     124     141 ..     122     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
  Sirohm_synth_M   5 QIaiSTnGksPrLAaliR 22 
                     ++ iST G+sP +A++i+
      AJA92036.1 124 KVGISTSGSSPIMAKKIK 141
                     689**************8 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   7.9e-06     0.014       1      93 [.      12      99 ..      12     124 .. 0.79
   2 ?   -1.5   0.0       1.6   2.9e+03      30      46 ..     189     206 ..     162     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.9e-06
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESSH.HHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEE CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkde.erveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkii 93
                +iiiG+G+ + + ++ L++ g+k ++vi  ++ + + +l++++ ++  +   t+  +L++ +     +via t d   n  +v++ak+     ki 
  AJA92036.1 12 VIIIGAGNEALKRIKLLESeGCK-IIVIGEKPnSEITKLSQKKkITLKKTKITSMLFLKKYK---PFLVIASTTDSSLNQKIVQTAKK----MKIL 99
                79*****************7775.9999777734577776666599999*******999975...46999999999**********97....3344 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                 SHHHHHHHHHTT.SEEEE CS
      TrkA_N  30 deerveelreeg.levvv 46 
                 +++rv+el ++g +++++
  AJA92036.1 189 NDKRVKELLKDGkYKAIQ 206
                 567777777666677766 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   9.5e-06     0.017      33      76 ..       6      48 ..       2     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.5e-06
                  -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHH CS
  2-Hacid_dh_C 33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeee 76
                   l++ktv iiG+G+ + + +k+l++ g+k+i++  ++++e  ++
    AJA92036.1  6 HLNEKTVIIIGAGNEALKRIKLLESEGCKIIVIGEKPNSEI-TK 48
                  5899*******************************999665.22 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.6e-05     0.064       2      53 ..       7      59 ..       6     127 .. 0.69
   2 ?   -1.6   0.0         1   1.8e+03      43      43 ..     151     151 ..      93     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.6e-05
                HHTS-EEEES-SHHHHHHHHHHHHTT--EE.EEE-TT-HHHHHHHHTT-EEEE CS
        IlvN  2 lkgkkiaviGyGsqGhaqalnlrdsgldvv.vglregsksvkkAkeegfevlt 53
                l++k++ +iG G+ +  + + l   g++++ +g + +s+ +k  +++ ++ ++
  AJA92036.1  7 LNEKTVIIIGAGNEALKRIKLLESEGCKIIvIGEKPNSEITKLSQKKKITLKK 59
                899************************97527899999877766666554443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                 H CS
        IlvN  43 k 43 
                 +
  AJA92036.1 151 N 151
                 2 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0015       2.7       2      35 ..      12      45 ..      11      65 .. 0.85
   2 ?    2.4   0.2      0.13   2.3e+02      36      67 ..     138     169 ..     129     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                v+++G+G+ +l   + l   g+k+ v+  +++  
  AJA92036.1 12 VIIIGAGNEALKRIKLLESEGCKIIVIGEKPNSE 45
                89*************************9988755 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.13
                 TTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
   Pyr_redox  36 rllDeeaskilqeklekngievllntkveeie 67 
                 +++  +++k lq++++++ ie++  +k ++ e
  AJA92036.1 138 KKIKSKTEKCLQKNISDQDIELIKIQKFARTE 169
                 5666788999************9888777766 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011       0.2       1      66 [.      12      95 ..      12     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE...................-EEEE--S-HHHHHHHHHHHSS CS
      XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade...................tavvvlthdhklDaealeaalr 66
                ++i+Gag+ a + ++l+++ g++++v+ ++++  + +++ ++++                     v++ t d +l ++++++a +
  AJA92036.1 12 VIIIGAGNEALKRIKLLESEGCKIIVIGEKPN-SEITKLSQKKKitlkktkitsmlflkkykpFLVIASTTDSSLNQKIVQTAKK 95
                69*****************************8.4566666555577777888899999999877788889999999999998875 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0015       2.7      35      78 ..      11      52 ..       6      63 .. 0.84
   2 ?   -1.3   0.0      0.66   1.2e+03      60      84 ..      75     100 ..      57     112 .. 0.72
   3 ?    2.6   0.1     0.041        74      20      48 ..     145     173 ..     142     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
                  EEEE-SSHHHHHHHHHHHHHTT-SEEEEE-S-GGHHHHHHHHHH CS
  Peripla_BP_1 35 lllaageeedlakaidllkakgidgliiatsdtsfdditakaes 78
                  +++ +g +++++k+i+ll+++g + ++i+   +s  +it+  ++
    AJA92036.1 11 TVIIIGAGNEALKRIKLLESEGCKIIVIGEKPNS--EITKLSQK 52
                  688899999********************88888..88887666 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.66
                   EEEE-S-GG..HHHHHHHHHHT-EEEE CS
  Peripla_BP_1  60 liiatsdts..fdditakaesgipvia 84 
                   l+ia+ ++s    +i++ a++ ++++ 
    AJA92036.1  75 LVIASTTDSslNQKIVQTAKK-MKILS 100
                   677855555366778888887.77764 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.041
                   HHHHHHHHHHHTEEEEEEE-SSHHHHHHH CS
  Peripla_BP_1  20 vkgitkaakehgvdvlllaageeedlaka 48 
                    k+++k  +++++++++++ +   + +k 
    AJA92036.1 145 EKCLQKNISDQDIELIKIQKFARTESKKH 173
                   589****************9988877744 PP

>> DUF3793  Protein of unknown function (DUF3793)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.2   3.6e+02      37      74 ..      34      71 ..      20     109 .. 0.45
   2 ?    9.8   1.9   0.00043      0.77      30      89 ..     156     213 ..     116     217 .] 0.68

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.2
     DUF3793 37 slkvlkekekkalilvyreekLeeylsdeevrefLkkl 74
                +++v+ ek ++ +  + +++k++ +  + +   fLkk+
  AJA92036.1 34 KIIVIGEKPNSEITKLSQKKKITLKKTKITSMLFLKKY 71
                44444444444444444444433222222222222222 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00043
     DUF3793  30 lleekgislkvlkekekkalilvyreekLeeylsdeevrefLkklgYesesleelleeLk 89 
                  +e  +i+ +  +e++k++l    r++ L e ++d++v+e+Lk+  Y++  ++++++++ 
  AJA92036.1 156 DIELIKIQKFARTESKKHILTQTERKKFLYELMNDKRVKELLKDGKYKA--IQTTIKKMV 213
                 2333333333345567777777889999*******************87..777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1632.32
//
Query:       AJA92037.1  [L=292]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0003   20.9   0.0    0.00081   19.5   0.0    1.8  1  Cupredoxin_1  Cupredoxin-like domain
     0.0066   16.9   0.0      0.026   15.0   0.0    2.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.1e-08   0.00081      16     104 .]      23     127 ..       8     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-08
  Cupredoxin_1  16 a..aaaektveitvkdg...........gfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftc 92 
                   a  a ae++++ tv++             f P+++++  g    +++ n+d+ +++ ++         ++ +  +++g+++t   ++l++GeY+++c
    AJA92037.1  23 ApgAFAEHSMNATVENAmgsstpgcepdCFIPATVTIGVGG--MVTFANNDSAAHTSTAGTpadgpsgVWDSSLVMMGAAYTT--PALEAGEYPYFC 115
                   34433333333333333346677666657888888888887..7899*******9999988899**************99994..78********** PP

  Cupredoxin_1  93 dmhmdakGkliV 104
                     h+ ++G +iV
    AJA92037.1 116 MVHPWMEGLVIV 127
                   ****99****98 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.9e-06     0.026      14      99 .]      52     128 ..      50     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                  EESSEEEEETTEEEEEEEESSSSBEEEEET..TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldk..dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  F ++++t+  g  vtf n+++ +H     +  dg p+gv ++ + +         G ++++   eag+Y +fC  H    M+g v+ve
   AJA92037.1  52 FIPATVTIGVGGMVTFANNDSAAHTSTAGTpaDG-PSGVWDSSLVM--------MGAAYTTPALEAGEYPYFCMVHP--WMEGLVIVE 128
                  88999******************98766555455.56665555555........4999999999*************..69****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2273.47
//
Query:       AJA92038.1  [L=332]
Description: putative transcription initiation factor IIB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-20   72.2   5.1    9.4e-11   41.6   0.2    2.3  2  TFIIB           Transcription factor TFIIB repeat
      3e-05   23.4   1.9    3.8e-05   23.1   0.3    1.9  2  TF_Zn_Ribbon    TFIIB zinc-binding
    8.7e-05   22.8   0.6      0.031   14.6   0.1    2.6  2  Rrf2            Transcriptional regulator
     0.0026   17.8   0.2      0.059   13.4   0.1    2.2  2  RB_B            Retinoblastoma-associated protein B domain
     0.0027   17.5   0.0      0.065   13.1   0.0    2.5  2  HTH_IclR        IclR helix-turn-helix domain
     0.0093   15.5   0.6        3.7    7.2   0.1    2.6  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.011   15.6   0.8       0.34   10.9   0.5    3.0  3  HTH_6           Helix-turn-helix domain, rpiR family
      0.012   15.4   0.4       0.06   13.1   0.1    2.1  2  Cyclin_N        Cyclin, N-terminal domain
      0.017   15.0   0.1          8    6.4   0.0    2.4  2  MarR_2          MarR family
      0.021   14.7   0.2        1.7    8.6   0.0    2.5  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.028   13.9   0.0        5.1    6.7   0.0    2.5  2  Sigma70_r4      Sigma-70, region 4
      0.038   14.0   0.1        9.4    6.3   0.0    2.4  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.067   13.3   0.4          8    6.6   0.1    2.9  2  HTH_3           Helix-turn-helix
      0.085   12.8   0.3       0.72    9.9   0.1    2.4  2  HTH_37          Helix-turn-helix domain
       0.14   12.7   0.5         20    5.7   0.0    2.8  2  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.18   11.9   2.3        5.2    7.1   0.3    2.5  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.41   10.4   2.3        0.8    9.5   2.3    1.4  1  Ribosomal_S27e  Ribosomal protein S27
       0.98    9.4   4.6        1.3    9.0   0.1    3.3  5  HTH_11          HTH domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.2   9.4e-14   9.4e-11       6      70 ..     132     196 ..     128     197 .. 0.94
   2 !   32.3   1.0   7.5e-11   7.5e-08       1      71 []     221     291 ..     221     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9.4e-14
                 HHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
       TFIIB   6 daleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                 ++l L++   ++A ++++++l++k+  Grs   i++Ac+y  cr  ++ rt +++++ ++ +  +
  AJA92038.1 132 AKLSLSDAAVEQAAYIYRKTLAKKIGRGRSIPVILSACVYASCRFTNTPRTIQDVAEATNLRRTS 196
                 689*****************************************************999877665 PP

  == domain 2  score: 32.3 bits;  conditional E-value: 7.5e-11
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i+r+  +++  ek +++A + + +a e  +++G+ p ++aA+++y+A+  +++k +q+ +s+ +++s +ti
  AJA92038.1 221 ITRITTEVGATEKTKRDAIKFLIKAEELMITSGKNPVAMAATVVYLAAITNGEKVSQTQVSKAANISSVTI 291
                 788889999999********************************************************998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.9   1.9e+03      14      23 ..       4      13 ..       3      14 .. 0.85
   2 !   23.1   0.3   3.9e-08   3.8e-05       5      39 ..      16      50 ..      15      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                  ETSTTCEEES CS
  TF_Zn_Ribbon 14 DpergelvCt 23
                  D e+++++C 
    AJA92038.1  4 DSESNDHICN 13
                  8999*****6 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 3.9e-08
                  TTTCEECHEETSTTCEEESSSSBEEEECCCCCCCH CS
  TF_Zn_Ribbon  5 nCgstnlveDpergelvCtdCGlVlednsidegpe 39
                  +C+   lv+D  +ge+ C++CG V+  n ++ gpe
    AJA92038.1 16 KCKDVLLVTDSTTGEVMCSSCGQVVSQNMAELGPE 50
                  699999********************999988887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.018        18      11      51 ..     166     206 ..     160     208 .. 0.85
   2 !   14.6   0.1   3.1e-05     0.031      12      54 ..     261     303 ..     249     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                 HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHH CS
        Rrf2  11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrk 51 
                 l a +y + + +++p +++++ae +n+ ++ + +i ++L +
  AJA92038.1 166 LSACVYASCRFTNTPRTIQDVAEATNLRRTSIHRIYRMLVR 206
                 5666777777788899**********************986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.1e-05
                 HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
        Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkagl 54 
                  +++yLa+  ++e+vs +++++  nis + ++ + +kL+ a++
  AJA92038.1 261 ATVVYLAAITNGEKVSQTQVSKAANISSVTIRNLCKKLKDAKI 303
                 45789999999999*************************9976 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   5.9e-05     0.059      11      97 ..     121     205 ..     117     242 .. 0.79
   2 ?    2.1   0.0      0.19   1.9e+02       7      26 ..     281     300 ..     277     323 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.9e-05
        RB_B  11 klaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvyrsvl 97 
                 + a + l+ L ++L+ls+   e++  + +++l++  ++ + R +  il ++vY+ ++ t++ ++ +++ +a + + ++ +++yr  +
  AJA92038.1 121 QKAFTLLEGLKAKLSLSDAAVEQAAYIYRKTLAK--KIGRGRSIPVILSACVYASCRFTNTPRTIQDVAEATNLRRTSIHRIYRMLV 205
                 5677778889999999998888877788888875..5779*******************************9999999999998654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
        RB_B   7 rkvyklaavrlrdLcerLkl 26 
                  k  ++++v +r+Lc++Lk 
  AJA92038.1 281 SKAANISSVTIRNLCKKLKD 300
                 6788999***********53 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   6.5e-05     0.065      20      44 ..     182     206 ..     176     207 .. 0.87
   2 ?    1.4   0.0      0.29   2.9e+02      17      44 ..     273     300 ..     266     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.5e-05
                 BHHHHHHHHTS-HHHHHHHHHHHHH CS
    HTH_IclR  20 tlselArrtglpkStvhRlLqtLve 44 
                 t++++A++t l +++ hR+ + Lv+
  AJA92038.1 182 TIQDVAEATNLRRTSIHRIYRMLVR 206
                 79*****************999997 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                 SS-BHHHHHHHHTS-HHHHHHHHHHHHH CS
    HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLve 44 
                 + ++ +++++++ ++  t ++l++ L  
  AJA92038.1 273 EKVSQTQVSKAANISSVTIRNLCKKLKD 300
                 447899*****************99976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0086       8.5      19      44 ..     182     207 ..     179     207 .. 0.94
   2 !    7.2   0.1    0.0037       3.7      11      44 ..     268     301 ..     266     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0086
      HTH_24  19 sqreLAerlglSpstvnrrlkrLeee 44 
                 +++++Ae+++l ++ ++r  + L+++
  AJA92038.1 182 TIQDVAEATNLRRTSIHRIYRMLVRD 207
                 899********************986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0037
      HTH_24  11 lLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                 ++    + sq++++++ ++S+ t++   k+L+++
  AJA92038.1 268 AITNGEKVSQTQVSKAANISSVTIRNLCKKLKDA 301
                 56666679***********************986 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.39   3.9e+02      36      58 ..     182     204 ..     177     206 .. 0.88
   2 ?   -2.2   0.0       4.3   4.3e+03      18      46 ..     235     263 ..     222     270 .. 0.78
   3 ?   10.9   0.5   0.00034      0.34      33      58 ..     273     298 ..     263     302 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.39
                 -HHHHHHHTT--HHHHHHHH--- CS
       HTH_6  36 sikalAkaaavSeativrfakkL 58 
                 +i+++A+a +  + +i r+ + L
  AJA92038.1 182 TIQDVAEATNLRRTSIHRIYRML 204
                 89**************9998765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                 HHHHHHHHHH-S---TT--HHHHHHHTT- CS
       HTH_6  18 ekkiaeyilaspdkaielsikalAkaaav 46 
                  +  ++++ +  + +i ++ + +A aa v
  AJA92038.1 235 KRDAIKFLIKAEELMITSGKNPVAMAATV 263
                 55668888899999999999999988876 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00034
                 TT--HHHHHHHTT--HHHHHHHH--- CS
       HTH_6  33 ielsikalAkaaavSeativrfakkL 58 
                  ++s  +++kaa++S  ti  ++kkL
  AJA92038.1 273 EKVSQTQVSKAANISSVTIRNLCKKL 298
                 678999*******************9 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.1e-05      0.06      31     122 ..     120     208 ..      94     213 .. 0.81
   2 ?    0.0   0.0      0.66   6.5e+02      54      87 ..     237     270 ..     215     315 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                 HHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHT CS
    Cyclin_N  31 RailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetL 122
                  + + + l  + +k++l+   +  a+ ++ + l+kk+ + + +  +  +c++ ++++ ++ p +++d++ +t+   +++ i ++ r +++ L
  AJA92038.1 120 MQKAFTLLEGLKAKLSLSDAAVEQAAYIYRKTLAKKIGRGRSIPVILSACVYASCRFTNT-PRTIQDVAEATN--LRRTSIHRIYRMLVRDL 208
                 3557888999***********************************************999.9******99986..55666666666666555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.66
                 HHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH CS
    Cyclin_N  54 lavnyldRflskksvpkdklqlvgatcLllAaKv 87 
                  a+++l +  +  +++ ++   ++at ++lAa +
  AJA92038.1 237 DAIKFLIKAEELMITSGKNPVAMAATVVYLAAIT 270
                 3333333333333333444444455555555544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.01        10      22      46 ..     181     205 ..     173     207 .. 0.85
   2 ?    6.4   0.0    0.0081         8      10      49 ..     265     302 ..     260     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.01
                 EEHHHHHHHHTSSHHHHHHHHHHHH CS
      MarR_2  22 ltvgelarrlglsksavsrilkrLv 46 
                  t++++a++++l + +++ri + Lv
  AJA92038.1 181 RTIQDVAEATNLRRTSIHRIYRMLV 205
                 49*****************987666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0081
                 HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
      MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaG 49 
                  Laa+ +++   ++++++ ++ ++s  ++ +++k+L +a 
  AJA92038.1 265 YLAAITNGEK--VSQTQVSKAANISSVTIRNLCKKLKDAK 302
                 5999999999..************************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0017       1.7      20      47 ..     178     205 ..     170     207 .. 0.89
   2 ?    3.4   0.1     0.071        71      13      49 ..     264     301 ..     262     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                 HCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
        TrmB  20 lgpatadeiaeelgvprskvYevLrsLe 47 
                 + p t++++ae++++ r+++ ++ r L+
  AJA92038.1 178 NTPRTIQDVAEATNLRRTSIHRIYRMLV 205
                 6799****************99988887 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.071
                 HCHHHHHHC.CCHHCHHCCCTTSSCHCHHHHHHHHHHC CS
        TrmB  13 vYlaLlklg.patadeiaeelgvprskvYevLrsLedk 49 
                 vYla +++g + + ++++++++++  ++ +  ++L+d+
  AJA92038.1 264 VYLAAITNGeKVSQTQVSKAANISSVTIRNLCKKLKDA 301
                 6776665540557789**************99999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.025        25      15      42 ..     174     202 ..     173     208 .. 0.87
   2 ?    6.7   0.0    0.0051       5.1      12      42 ..     263     296 ..     260     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                 HHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  15 lrf.geglTleEIgerlgiSrerVrqiek 42 
                 +rf   ++T ++++e  ++ r  +++i +
  AJA92038.1 174 CRFtNTPRTIQDVAEATNLRRTSIHRIYR 202
                 588899*************9999999987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0051
                 HHHHHH...TTT--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4  12 vlelrf...geglTleEIgerlgiSrerVrqiek 42 
                 v++l     ge+ ++ ++++  +iS  ++r + k
  AJA92038.1 263 VVYLAAitnGEKVSQTQVSKAANISSVTIRNLCK 296
                 6667667889********************9866 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.021        21      21      47 ..     180     206 ..     165     208 .. 0.86
   2 ?    6.3   0.0    0.0094       9.4      21      53 ..     274     307 ..     258     319 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.021
                 EHHHHHHHHHTTSSHHHHHHHHHHHHH CS
   HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkr 47 
                 p t ++ A+  +l+r ++ ri + L r
  AJA92038.1 180 PRTIQDVAEATNLRRTSIHRIYRMLVR 206
                 67889****************998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0094
                 EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
   HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r 53 
                 +++q++ +   +++ +t+  + ++Lk++++ s  
  AJA92038.1 274 KVSQTQVSKAANISSVTIRNLCKKLKDAKIASfS 307
                 689*************************998743 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.066        65      11      29 ..     182     200 ..     181     210 .. 0.91
   2 ?    6.6   0.1    0.0081         8       9      31 ..     274     296 ..     265     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.066
                 HHHHHHHHHTSSHHHHHHH CS
       HTH_3  11 sqeeLAeklGvsrstisri 29 
                 +++++Ae++++ r++i ri
  AJA92038.1 182 TIQDVAEATNLRRTSIHRI 200
                 789*************987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0081
                 THHHHHHHHHHTSSHHHHHHHHT CS
       HTH_3   9 glsqeeLAeklGvsrstisriEn 31 
                 + sq+++++++++s  ti+++ +
  AJA92038.1 274 KVSQTQVSKAANISSVTIRNLCK 296
                 689***************98865 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.91   9.1e+02      53      69 ..     189     205 ..     177     213 .. 0.60
   2 ?    9.9   0.1   0.00072      0.72      13      68 ..     256     315 ..     242     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.91
                 TT--TT--HHHHHHHHH CS
      HTH_37  53 rgklsrfsldkLlnllt 69 
                   +l+r s+++  ++l+
  AJA92038.1 189 ATNLRRTSIHRIYRMLV 205
                 33555666666666555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00072
                 HHHHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHH....HHTT--TT--HHHHHHHH CS
      HTH_37  13 lkaKaqlalaiaeliekrelsqseaaqllgiaqPkvsr....llrgklsrfsldkLlnll 68 
                   a+a+ +  +a++  +++ sq+++ ++ +i+   + +    l+++k+ +fs  kL +++
  AJA92038.1 256 PVAMAATVVYLAAITNGEKVSQTQVSKAANISSVTIRNlckkLKDAKIASFSNPKLTKVV 315
                 4589999999**********************9998762222577788888877777766 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.02        20      12      40 ..     182     210 ..     181     214 .. 0.87
   2 ?    3.9   0.1     0.076        75      10      33 ..     274     297 ..     269     303 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
      HTH_26  12 tkseLargtgisaatlsrlvkgkpervsl 40 
                 t++++a++t++ +++++r++ + ++ ++l
  AJA92038.1 182 TIQDVAEATNLRRTSIHRIYRMLVRDLDL 210
                 6799****************987776665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.076
      HTH_26  10 gitkseLargtgisaatlsrlvkg 33 
                 ++++++++++++is+ t+ +l+k+
  AJA92038.1 274 KVSQTQVSKAANISSVTIRNLCKK 297
                 5699****************9985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0052       5.2      51      83 ..      11      43 ..       6      67 .. 0.82
   2 ?    4.1   0.1     0.046        46      21      50 ..     216     245 ..     198     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                HHCC.TTTT-EEEEEEE--EEEETTTS-EEECH CS
        HypA 51 laegtvlegaeLeieevpvkvrCreCgkefele 83
                +++++ +++  L  +++  +v+C++Cg+ ++++
  AJA92038.1 11 ICNNSKCKDVLLVTDSTTGEVMCSSCGQVVSQN 43
                5667778999999**************998865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.046
                 TT..EEEEEEEEEETTCT--HHHHHHHHHH CS
        HypA  21 aaarkvtkvkvevGelsgvepeaLefafel 50 
                 + ++ +t+++ evG+ ++ + +a++f  ++
  AJA92038.1 216 NPVSFITRITTEVGATEKTKRDAIKFLIKA 245
                 567789******************998775 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.3   0.00081       0.8      12      38 ..      16      42 ..      12      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00081
                    TTS-EEEEESS-SS-EEESSSTCEEEE CS
  Ribosomal_S27e 12 dCenetvvFshaatvvkCisCgkvLve 38
                    +C++   v ++    v+C sCg+v+ +
      AJA92038.1 16 KCKDVLLVTDSTTGEVMCSSCGQVVSQ 42
                    799999999***************976 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         6     6e+03      10      26 ..      82      98 ..      79     100 .. 0.73
   2 ?   -2.7   0.0       5.9   5.9e+03      21      33 ..     130     142 ..     128     144 .. 0.83
   3 ?   -1.1   0.1       1.9   1.9e+03      15      34 ..     180     199 ..     176     199 .. 0.84
   4 ?   -1.7   0.0       2.8   2.8e+03       3      18 ..     236     252 ..     234     254 .. 0.76
   5 ?    9.0   0.1    0.0013       1.3      12      42 ..     271     301 ..     264     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6
      HTH_11 10 leargpisgeeLAeeLn 26
                 +++++ +g+ L+ e++
  AJA92038.1 82 QQSDKDATGKNLSGEMK 98
                56777899999987765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.9
      HTH_11  21 LAeeLnvSrrtvr 33 
                 L+ +L++S ++v 
  AJA92038.1 130 LKAKLSLSDAAVE 142
                 78899***99995 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
      HTH_11  15 pisgeeLAeeLnvSrrtvrr 34 
                 p ++++ Ae +n+ r+ ++r
  AJA92038.1 180 PRTIQDVAEATNLRRTSIHR 199
                 5799999*****99999997 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 2.8
      HTH_11   3 lqilelLleargp.isg 18 
                 ++ +++L++a++  i++
  AJA92038.1 236 RDAIKFLIKAEELmITS 252
                 67889999998877775 PP

  == domain 5  score: 9.0 bits;  conditional E-value: 0.0013
      HTH_11  12 argpisgeeLAeeLnvSrrtvrrdIkaLeel 42 
                 + +++s  + ++  n+S  t+r+ +k+L+++
  AJA92038.1 271 NGEKVSQTQVSKAANISSVTIRNLCKKLKDA 301
                 55669999999*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2623.47
//
Query:       AJA92039.1  [L=112]
Description: ATP synthase subunit C [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-16   58.1  17.4    8.1e-16   58.1  17.4    1.9  2  ATP-synt_C   ATP synthase subunit C
  ------ inclusion threshold ------
       0.28   11.1   0.6       0.38   10.7   0.6    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.1   8.9e+02      34      50 ..      14      30 ..       5      34 .. 0.66
   2 !   58.1  17.4     9e-20   8.1e-16       1      60 []      50     109 ..      50     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                HHHHHHHHHHHHHHHHH CS
  ATP-synt_C 34 klftksliilafaeaia 50
                ++f  ++i ++f + ++
  AJA92039.1 14 SIFLLAVIAVSFTGLTG 30
                56666667777766555 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 9e-20
                 HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                 +gagla Gl+a+g+Gig G +gsag+  + +np l++k++i+++++e+ia+yg+++++i+
  AJA92039.1  50 IGAGLAFGLAAMGAGIGLGYVGSAGLAVITENPALQSKVFIFIGMVESIAIYGIVMMFII 109
                 7**********************************************************8 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   4.3e-05      0.38       1      41 [.      10      48 ..      10      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
  Trypan_PARP  1 maprslyllaillfsanlfagvgfaaaaegpedkgltkggk 41
                 m p s++lla++  s   ++gv  a aae+ ++ g   g k
   AJA92039.1 10 MRPLSIFLLAVIAVSFTGLTGV--AHAAEEDASSGSGDGSK 48
                 7899********9997777666..55667777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 683.67
//
Query:       AJA92040.1  [L=322]
Description: acetohydroxy acid isomeroreductase, catalytic domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-62  209.6   0.1    3.2e-62  209.1   0.1    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.5e-31  108.8   0.0    1.7e-31  108.6   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    6.5e-09   36.1   0.1      1e-08   35.5   0.1    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
      4e-05   23.3   0.5    9.7e-05   22.0   0.2    1.8  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00093   19.7   0.0      0.002   18.6   0.0    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.027   14.6   0.8      0.044   13.8   0.1    1.7  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      0.046   13.0   0.0       0.14   11.4   0.0    1.7  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.052   13.9   2.4       0.13   12.6   2.4    1.8  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.1   0.1   1.4e-65   3.2e-62       1     178 []     111     291 ..     111     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 1.4e-65
                   HHHHHHHHTTHHHHHHHHHTTCC...HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SE CS
  2-Hacid_dh_C   1 lalllallrrlaeadeevregew...ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDi 94 
                   ++l+l++lrr++e+d+ +r+++w       +++g+e+sgkt+GiiG+GrIG++va++++++gm++i+++r++ +++ e+ l++++vs + l+++sDi
    AJA92040.1 111 IGLILDVLRRISEGDRIIRNKKWnqiFGAYDYTGTEVSGKTIGIIGMGRIGREVARKANGLGMNIIYHNRKPISKRIENMLKAKYVSENMLYKNSDI 207
                   589********************76666669******************************************9999999999************** PP

                   EEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
  2-Hacid_dh_C  95 vslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpedspllelpnviltPHia 178
                   +slh+p++++t+hl+n++ ++kmkk+++liNt+RG++v+e+ L++aL +++i+ga++Dv+e+ep++++spll+l+nv+l PH++
    AJA92040.1 208 ISLHVPYNNDTHHLMNSKIFKKMKKTSFLINTSRGKIVNEKQLVNALMKKEIQGAGMDVYESEPVKRNSPLLKLENVVLAPHVG 291
                   **********************************************************************************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.0   7.7e-35   1.7e-31       1     132 [.       7     321 ..       7     322 .] 0.98

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 7.7e-35
                 EEEEST.CHHHHHHHHHTTEEEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh   1 vlileplreeelellkeegvevevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgyste 96 
                 vl++++l++++l+ lk+ +++v+++    ++++++l++k+k++d+l+++  + +++ev+++ ++Lkvi++++vG+D++D++ ak +Gi++  +p++ t+
  AJA92040.1   7 VLVTRRLHTSALDELKR-KCNVSLHIgkiPIPKKNLIDKIKNMDGLVCHPYDTIDKEVIKNSKNLKVISTFSVGFDHIDVNFAKSQGIKIGYTPEVLTN 104
                 79999************.5588877777*********************************************************************** PP

                 HHHHHH............................................................................................. CS
                 xxxxxx............................................................................................. RF
  2-Hacid_dh  97 svAElt............................................................................................. 102
                 ++AElt                                                                                             
  AJA92040.1 105 ATAELTiglildvlrrisegdriirnkkwnqifgaydytgtevsgktigiigmgrigrevarkanglgmniiyhnrkpiskrienmlkakyvsenmlyk 203
                 *************************************************************************************************** PP

                 ........................................................................................T-BHHHHHHHH CS
                 ........................................................................................xxxxxxxxxxx RF
  2-Hacid_dh 103 ........................................................................................aaTeeaqenia 113
                                                                                                         ++T+e+++++ 
  AJA92040.1 204 nsdiislhvpynndthhlmnskifkkmkktsflintsrgkivnekqlvnalmkkeiqgagmdvyesepvkrnspllklenvvlaphvgSSTNETRQKMS 302
                 *************************************************************************************************** PP

                 HHHHHHHHHHHTTCCGTTB CS
                 xxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh 114 eeaaenlvaflkgespana 132
                 +++a nl+ +l+g+++ + 
  AJA92040.1 303 DITARNLILALEGKKLLYS 321
                 *************998765 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   4.6e-12     1e-08       1     116 [.     151     266 ..     151     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.6e-12
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHH.HHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---H CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesie.elvasldvvitmvkagkavdevieg.llealkkgdilidgstssp 94 
                    +ig+iG+G +G++ a++    g++++ +nr++  + + +++ +ka +  e  l ++ d++ + v+ ++++ +++++ +++++kk ++li++s  ++
     AJA92040.1 151 TIGIIGMGRIGREVARKANGLGMNIIYHNRKP--ISKRIENMLKAKYVSEnMLYKNSDIISLHVPYNNDTHHLMNSkIFKKMKKTSFLINTSRGKI 244
                    59***************************994..44555555444444441577888******************99******************* PP

                    HHHHHHHHHHHHTT-EEEEEEE CS
  NAD_binding_2  95 edtrelakelkekglkfldaPV 116
                     + ++l ++l +k+++  ++ V
     AJA92040.1 245 VNEKQLVNALMKKEIQGAGMDV 266
                    ************9998777655 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.92   2.1e+03      85     105 ..      64      84 ..      52     114 .. 0.66
   2 !   22.0   0.2   4.3e-08   9.7e-05       3     102 ..     148     248 ..     146     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.92
                 --TT-EEEESSSHHHHTTSS- CS
        IlvN  85 lkegkalafahGfnihfglik 105
                 +k+ k l+  + f++ f+ i+
  AJA92040.1  64 IKNSKNLKVISTFSVGFDHID 84 
                 445555555555555555554 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 4.3e-08
                 HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHH..HHHT-SEEEE-S-HHH.HHHHHHHHTGGG--TT-EEE.ESSSH CS
        IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvae..avkkadvvmiliPDel.qkevyeeeiepnlkegkala.fahGf 97 
                 +gk+i +iG+G  G+  a++    g+++++ +r+     +k  e+ ++ + v+e  + k++d++ + +P +   +++++++i +++k+ + l   + G 
  AJA92040.1 148 SGKTIGIIGMGRIGREVARKANGLGMNIIYHNRKPI---SKRIENMLKAKYVSEnmLYKNSDIISLHVPYNNdTHHLMNSKIFKKMKKTSFLInTSRGK 243
                 79***************************9988766...44445555555554422789**********765167899*********999764155565 PP

                 HHHTT CS
        IlvN  98 nihfg 102
                  ++ +
  AJA92040.1 244 IVNEK 248
                 55555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   9.1e-07     0.002       1      92 [.     151     237 ..     151     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.1e-07
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH..HHHHHHHCGHHHHTTSEEE CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkped..veevlselakdalkgklvi 92 
                    +igiiG+G++g+ +a+++   g    +i+   +r+p + + +++ l  k++ v+ + + +++d++ l v++++  ++ + s+++k+ +k +++i
     AJA92040.1 151 TIGIIGMGRIGREVARKANGLG---MNII-YHNRKPIS-KRIENML--KAKYVSENMLYKNSDIISLHVPYNNdtHHLMNSKIFKKMKKTSFLI 237
                    69********************...9999.54777642.3444444..455566899999*******999875112223334456656666555 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       3.6   8.1e+03      90     123 ..      57      90 ..      44      96 .. 0.66
   2 ?   13.8   0.1     2e-05     0.044      19     123 ..     145     256 ..     136     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                    SSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHT CS
  AdoHcyase_NAD  90 diitlehlkkmkddaivcniGhfdseidvaalea 123
                    d i +e +k+ k+  +++        idv+  ++
     AJA92040.1  57 DTIDKEVIKNSKNLKVISTFSVGFDHIDVNFAKS 90 
                    5566666777777766666655555666665555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2e-05
                    S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-S....SSSSSB-HHHHCCS-TTEEEEE-. CS
  AdoHcyase_NAD  19 vllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvttt....Gnkdiitlehlkkmkddaivcni. 109
                    + ++Gk++ ++G G +G+  a+  +glG  +i  +  Pi+     m   + v  + + k++di+         ++ +++++ +kkmk+++ + n  
     AJA92040.1 145 TEVSGKTIGIIGMGRIGREVARKANGLGMNIIYHNRKPISKRIENMLKAKYVSENMLYKNSDIISLHVpynnDTHHLMNSKIFKKMKKTSFLINTs 240
                    5689***********************************9988888888888888999999998543311113456899999******99998863 PP

                    .SSTTTTBT.HHHHHT CS
  AdoHcyase_NAD 110 .Ghfdseid.vaalea 123
                     G   +e + v+al++
     AJA92040.1 241 rGKIVNEKQlVNALMK 256
                    3555555552344544 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.2e-05      0.14      26      78 ..     147     210 ..     141     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
                  B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE...........H CS
  AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev...........l 78 
                  v+  ++ +iG G  G + ++ a+glg ++  ++ +p  ++  + l+ak+v+            l
   AJA92040.1 147 VSGKTIGIIGMGRIGREVARKANGLGMNIIYHNRKPISKRIENMLKAKYVSEnmlyknsdiisL 210
                  5556788**********************99999998888777799997765443333333330 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.4   5.8e-05      0.13       2      46 ..     151     194 ..     150     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-05
                 EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-HHHHHHHHHEE CS
     Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdletlayllkyD 46 
                  ++i G+GRIGr v+r++     ++++  n+    + ++ +lk  
  AJA92040.1 151 TIGIIGMGRIGREVARKANG-LGMNIIYHNRKPISKRIENMLKAK 194
                 59**************9863.355565555554445555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2252.65
//
Query:       AJA92041.1  [L=130]
Description: ribosomal protein S8 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-23   80.7   0.1    9.6e-23   80.5   0.1    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.1   5.3e-27   9.6e-23       2     127 .]       6     130 .]       5     130 .] 0.87

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 5.3e-27
                   HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEECCC...CCCEEEEE-BSSS-SBSSSEEEE-SBTTC--EE-CCC---CGG CS
  Ribosomal_S8   2 piadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeveeek...kkkikielkynkkkksvikklkrvskpgrrvYakvkelpkvln 94 
                    +a+++ +i N e+++k e+ v p+sk+ +++l+ Lk+ Gyikd+e +e++   k ki++  k++k  +++i+   +v+k       +++ lp++ +
    AJA92041.1   6 VLANLFVTIYNTEARRKGECVVlPTSKIGTNVLETLKKDGYIKDYERTEDNrggKYKINLIAKITK--CGAISPRFKVKKDEYL-EWEKQYLPSFNR 99 
                   689**************999999************************8444455555888888888..*****99999986554.355677888876 PP

                   GTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
  Ribosomal_S8  95 glGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                     G++iv+T++Gvm+++eA +k++GG ++ yv+
    AJA92041.1 100 --GMLIVTTNQGVMSHHEAANKGLGGFLVGYVY 130
                   ..67****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1010.97
//
Query:       AJA92042.1  [L=252]
Description: ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-53  182.1   0.1    1.7e-53  181.9   0.1    1.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0029   16.9   0.1     0.0042   16.4   0.1    1.2  1  DUF2075      Uncharacterized conserved protein (DUF2075)
      0.003   18.0   0.0     0.0068   16.8   0.0    1.5  2  AAA_16       AAA ATPase domain
     0.0056   17.2   0.0     0.0083   16.7   0.0    1.3  1  AAA_18       AAA domain
  ------ inclusion threshold ------
      0.011   15.2   0.4        1.5    8.4   0.0    2.9  3  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.076   12.6   0.4        2.4    7.8   0.1    2.2  2  SRP54        SRP54-type protein, GTPase domain
      0.079   12.2   0.0       0.17   11.1   0.0    1.5  1  Zeta_toxin   Zeta toxin
      0.079   12.7   0.9         11    5.7   0.0    3.0  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
      0.091   13.0   0.0       0.15   12.4   0.0    1.5  1  AAA_22       AAA domain
      0.091   12.5   0.1       0.14   11.8   0.1    1.3  1  AAA_30       AAA domain
       0.12   12.2   0.5         12    5.8   0.0    3.2  3  RsgA_GTPase  RsgA GTPase
       0.13   12.0   0.0       0.17   11.5   0.0    1.2  1  AAA_24       AAA domain
       0.17   11.8   0.2       0.75    9.7   0.1    2.0  2  NTPase_1     NTPase


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.1   1.2e-56   1.7e-53       1     238 [.       6     243 ..       6     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 1.2e-56
  ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldwldeelekeeddyllfDtP 99 
                 v+G+aG+GK+ +++++ e++ ++ + + ++NLDP++ +lpY++++d+r++++++++me+++lg+ng+l++a +++++++d++++e +  + dyl++DtP
  AJA92042.1   6 VTGTAGAGKSLLTSKIKEYYAKNATFPITLNLDPGVASLPYSPDIDVRDYVDVNSLMEQYELGSNGSLIMANDLIATKIDDIQKEADTINPDYLIVDTP 104
                 89************************************************************************************66699******** PP

  ATP_bind_1 100 GQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.eky 197
                 GQielf +++s+  +v+++e   + + ++L+D +++++p++f+s +l++ s+ lrl+lP+v+v++k+Dl++ekl++ l +     +l++ l  e  + +
  AJA92042.1 105 GQIELFAYRQSGPFFVQNFE-AEEKMNLFLFDGTMVSTPSNFVSLMLLSTSIRLRLGLPTVNVITKTDLIEEKLQQVLSWSGTDSKLEADLAGEVnGDT 202
                 ********************.588899********************************************99*9*****9866666655444435999 PP

  ATP_bind_1 198 kklaeaiaelleefalvlrflplssekeesiedllslidea 238
                  +l +++  +++  + +++++p+s+ +++++ +l s++  +
  AJA92042.1 203 FSLVSDMLTSINRNDFQQDLIPVSNATGDGMVNLQSALSRT 243
                 99********************************9988765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     3e-06    0.0042       2      25 ..       2      25 ..       1      42 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
     DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                +v++VtG aG+GK+++ +++   +
  AJA92042.1  2 KVIFVTGTAGAGKSLLTSKIKEYY 25
                79***************9997665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.9e-06    0.0068      26      73 ..       3      50 ..       2     107 .. 0.78
   2 ?   -2.2   0.0       3.4   4.7e+03     105     105 ..     194     194 ..     146     247 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.9e-06
      AAA_16 26 lvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysala 73
                +++++G +G GKs l  ++++++ k+ + f ++ + d   +++pys+ +
  AJA92042.1  3 VIFVTGTAGAGKSLLTSKIKEYYAKN-ATFpITLNLDPGVASLPYSPDI 50
                589*****************999999.8888999999998899995533 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
      AAA_16 105 l 105
                 l
  AJA92042.1 194 L 194
                 2 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.1e-06    0.0083       1      81 [.       4     103 ..       4     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.1e-06
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                 I++tGt+G+GK+ l+  +++   ++                     + +rd++  n l + ++    + s+++  d  +  +d +++ ++   +++ l+
  AJA92042.1   4 IFVTGTAGAGKSLLTSKIKEYYaKNatfpitlnldpgvaslpyspDIDVRDYVDVNSLMEQYELG-SNGSLIMANDLIATKIDDIQKEAD-TINPDYLI 100
                 99****************77643446778899999999999999999999999999888888888.888888888887777777777665.56666766 PP

      AAA_18  79 idg 81 
                 +d 
  AJA92042.1 101 VDT 103
                 664 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.3   4.2e+02       6      28 ..       4      26 ..       1      31 [. 0.81
   2 ?    2.7   0.0     0.056        78      57      82 ..      83     108 ..      75     115 .. 0.75
   3 ?    8.4   0.0    0.0011       1.5     119     190 ..     157     242 ..     149     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                EEEEESTTSSHHHHHHHHHHHTT CS
    GTP_EFTU  6 igiighvDhGKtTLtdrLlyktg 28
                i + g   +GK+ Lt ++ ++  
  AJA92042.1  4 IFVTGTAGAGKSLLTSKIKEYYA 26
                67889999*******99977655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.056
                 SCEEEEEETTCSSEEEEEEEESSSGG CS
    GTP_EFTU  57 ksaaisleketkkylinliDtPGHvd 82 
                 k+  i+ e++t +  + ++DtPG ++
  AJA92042.1  83 KIDDIQKEADTINPDYLIVDTPGQIE 108
                 45555555678889999******875 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0011
                 HHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH..................HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHH CS
    GTP_EFTU 119 lkegvpiivfiNKmDrlkaelkeiveevkqklsrk..................eeklekygekgekevpvvfgSalkgegvktllealve 190
                 l++g+p++ +i+K D ++++l+++ +   ++ + +                   ++++   +    +  ++++S  +g+g+ +l +al +
  AJA92042.1 157 LRLGLPTVNVITKTDLIEEKLQQVLSWSGTDSKLEadlagevngdtfslvsdmLTSINRNDF----QQDLIPVSNATGDGMVNLQSALSR 242
                 578999***************99988766555333557777877777776443333333333....556888888888888877777655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0017       2.4       2      30 ..       2      30 ..       1      38 [. 0.86
   2 ?    2.8   0.0     0.056        78      73      95 ..      84     107 ..      68     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0017
                EEEEEEESTTSSHHHHHHHHHHHHHHTTS CS
       SRP54  2 nvillvGlqGaGKTttlaKLaallkkegk 30
                +vi + G+ GaGK   ++K+ +++ k+++
  AJA92042.1  2 KVIFVTGTAGAGKSLLTSKIKEYYAKNAT 30
                6999********************99854 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.056
                 HHHH.HHHHHTTSSEEEEEE--SS CS
       SRP54  73 keav.ekakeekidvvlvDTaGrl 95 
                  + + ++a+  + d+++vDT G+ 
  AJA92042.1  84 IDDIqKEADTINPDYLIVDTPGQI 107
                 4444045666789********986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.17      17      43 ..       2      29 ..       2      40 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
  Zeta_toxin 17 klillgGqpGAGKselaellkdele.rq 43
                k+i++ G  GAGKs l +++k++ + ++
  AJA92042.1  2 KVIFVTGTAGAGKSLLTSKIKEYYAkNA 29
                689******************9986333 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0083        11       1      23 [.       1      23 [.       1      34 [. 0.90
   2 ?    4.3   0.1     0.023        32      81     111 ..     152     180 ..      79     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0083
   PduV-EutP  1 mkkilliGkvgsGKttLtqalkg 23
                mk i++ G+ g+GK  Lt ++k+
  AJA92042.1  1 MKVIFVTGTAGAGKSLLTSKIKE 23
                899999*************9987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.023
   PduV-EutP  81 ppgfasvfnkeviGiitkidlaedeenieav 111
                 + +++  +  +++ +itk+dl   ee++++v
  AJA92042.1 152 STSIRLRLGLPTVNVITKTDLI--EEKLQQV 180
                 4445555566889999999999..6666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.15       7      30 ..       3      26 ..       1     102 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
      AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                +++vtG +G+GK++l  +++e + 
  AJA92042.1  3 VIFVTGTAGAGKSLLTSKIKEYYA 26
                799**************9999874 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0001      0.14      20      45 ..       3      28 ..       1      42 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
      AAA_30 20 vavltGpAGtGKttalkalreaweaa 45
                v ++tG AG+GK+ + ++++e ++++
  AJA92042.1  3 VIFVTGTAGAGKSLLTSKIKEYYAKN 28
                7799*****************99987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0086        12     100     121 ..       2      23 ..       1      41 [. 0.77
   2 ?    0.0   0.0       0.5   6.9e+02     150     161 ..      95     106 ..      87     110 .. 0.78
   3 ?    2.3   0.1     0.098   1.4e+02      47      65 ..     161     180 ..     144     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0086
                  SEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                  k++++ G  G+GKS L  ++++
   AJA92042.1   2 KVIFVTGTAGAGKSLLTSKIKE 23 
                  577899**********999987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.5
                  TTTEEEESS-SS CS
  RsgA_GTPase 150 aegglliDtPGf 161
                  + + l++DtPG 
   AJA92042.1  95 NPDYLIVDTPGQ 106
                  55779******5 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.098
                  -EEEEEEE-GGG--HHH.HH CS
  RsgA_GTPase  47 iepvivlnKiDlleeee.el 65 
                  ++ v v++K+Dl+ee+  ++
   AJA92042.1 161 LPTVNVITKTDLIEEKLqQV 180
                  55667999999999886333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.17       4      76 ..       3     106 ..       1     115 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
      AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel........................aaeladyktlvi 71 
                  i+++G +g+GK+ l +++          p+ ++++ G++sl      d++ + d+ + +++                         +a+  + + l++
  AJA92042.1   3 VIFVTGTAGAGKSLLTSKIkeyyaknATFPITLNLDPGVASLPYSPDIDVRDYVDVNSLMEQYelgsngslimandliatkiddiqkEADTINPDYLIV 101
                 699**************9999999877889999********9999999888555555554444555777777777777777777755333333466777 PP

      AAA_24  72 Dtide 76 
                 Dt ++
  AJA92042.1 102 DTPGQ 106
                 77665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00054      0.75       2      23 ..       4      25 ..       3      32 .. 0.88
   2 ?   -1.0   0.0         1   1.4e+03      94     111 ..      94     111 ..      65     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                EEEE--TTSSHHHHHHHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                +f+TG  G GK+ l +k+ e  
  AJA92042.1  4 IFVTGTAGAGKSLLTSKIKEYY 25
                8*****************9876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1
                 HHH-EEEE---STTGGG- CS
    NTPase_1  94 seadviviDEiGkmElks 111
                  ++d +++D  G++El++
  AJA92042.1  94 INPDYLIVDTPGQIELFA 111
                 456699999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1779.63
//
Query:       AJA92043.1  [L=373]
Description: putative DNA primase small subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.9   0.1    8.9e-17   61.7   0.1    2.0  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.025   14.9   0.0    1.6  1  MutS_IV        MutS family domain IV
      0.094   12.9   0.5         13    6.0   0.0    2.7  2  zf-Dof         Dof domain, zinc finger
       0.35   10.9   4.8       0.59   10.2   4.3    1.7  1  HypA           Hydrogenase/urease nickel incorporation, metal
        1.4    8.9   3.6       0.66   10.0   0.8    1.9  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
        7.2    6.7  10.8        7.2    6.7   4.6    2.7  2  zinc_ribbon_6  Zinc-ribbon
          8    6.0   8.3        1.1    8.8   3.5    2.1  2  zf-ribbon_3    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.1   3.5e-20   8.9e-17      14     175 ..     139     309 ..      94     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 3.5e-20
                    --HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH.............................. CS
  DNA_primase_S  14 atvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnlyrplhpflsrs.mlkivkpvveeiile 106
                    ++ c  c k+ ++ v +l++ l++d+g++  +i+  fsg+ GfH++v++ +  + +++era+i +y+ +      +++ +  ++++   + +  + 
     AJA92043.1 139 TLTCSDCIKSSKDEVNKLNQILTDDLGINedNIKTFFSGNEGFHIYVPKSEYESVGSKERAEISDYIMFR-G---SIPETfGFRKFNMNKSSLPKF 230
                    678**************************************************************98884.3...344443444444445555555 PP

                    ........HCHHHHCT--------..........................-----------------....--------- CS
  DNA_primase_S 107 eqdpf...eikkllrllpdkslrekkkw........eakedivlvllyprldeqvtkgikhllkapfcihgktgnvcvpl 175
                    ++  +     k+l  + +++ + + + +            +++++++ +++d +vt++i++ +++p++i+ k+g +++ +
     AJA92043.1 231 DDAGWngrLAKHLYGTKSNRPKIS-QEVisggyalfQKNLEDFRDSIGIKIDPNVTQDIHRIFRLPGSINSKSGLTKIFV 309
                    667787777777777777777777.55567777787777889*******************************9887765 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.8e-06     0.025      13      58 ..     146     193 ..     141     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.8e-06
                 HHHHHHHHHHHHCCCCCCCT-..TTBEECCCSSSEEEEEE-TCCCTTT CS
     MutS_IV  13 leelekeleeleekereklgi..kslkveynkvlGyylevtrseakkv 58 
                 ++  ++e ++l++ ++ +lgi  +++k+ +++  G+++ v++se+++v
  AJA92043.1 146 IKSSKDEVNKLNQILTDDLGIneDNIKTFFSGNEGFHIYVPKSEYESV 193
                 6788999*************************************9998 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.018        46       4      16 ..     125     137 ..     122     141 .. 0.84
   2 ?    6.0   0.0    0.0051        13       5      31 ..     334     361 ..     330     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.018
      zf-Dof   4 lkCprCestntkF 16 
                  +Cp C+st+  F
  AJA92043.1 125 ESCPNCQSTKLSF 137
                 68******98877 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0051
      zf-Dof   5 kCprCes.tntkFcYyNNyslsqPRyfC 31 
                 +Cp   s ++ kF  +NN+++s P+++ 
  AJA92043.1 334 NCPIEFSlKKKKFGPFNNEQVSVPKFAA 361
                 666554515679*************974 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.3   0.00023      0.59      68     100 ..     109     138 ..      75     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                 --EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
        HypA  68 pvkvrCreCgkefeleekalrCpkCgsadveiv 100
                 +  ++C++C++  +l+   ++Cp+C+s++++++
  AJA92043.1 109 NTIIKCSDCNEISQLN---ESCPNCQSTKLSFI 138
                 56799*****888877...46******998765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1         2     5e+03      39      44 ..     113     118 ..     109     119 .. 0.76
   2 ?   10.0   0.8   0.00026      0.66      21      43 ..     127     145 ..     123     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
  Zn_Tnp_IS1595  39 qCkeCr 44 
                    +C++C+
     AJA92043.1 113 KCSDCN 118
                    788886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
  Zn_Tnp_IS1595  21 CPhCgsrkayriktrglfqCkeC 43 
                    CP+C+s+k+ +i+      C++C
     AJA92043.1 127 CPNCQSTKLSFITL----TCSDC 145
                    ************95....99999 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.6    0.0028       7.2      13      55 ..      95     132 ..      83     134 .. 0.79
   2 ?   -0.0   3.9      0.36   9.2e+02      26      40 ..     136     150 ..     125     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
  zinc_ribbon_6  13 eiaeqpmpeeyknkkvkilCnDCekksevkfhvlglkCkeCgS 55 
                     i+++ + +e  +  + i C DC++ s+         C +C+S
     AJA92043.1  95 DIDAKDLRKEHPKDNTIIKCSDCNEISQL-----NESCPNCQS 132
                    5777778888888999********99985.....467777776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.36
  zinc_ribbon_6  26 kkvkilCnDCekkse 40 
                    + ++ +C DC k+s+
     AJA92043.1 136 SFITLTCSDCIKSSK 150
                    456778999988876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.5   0.00042       1.1       3      23 ..     112     131 ..     112     133 .. 0.93
   2 ?   -3.6   0.2       3.4   8.6e+03       4       8 ..     141     145 ..     139     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00042
  zf-ribbon_3   3 vrCPnCGaplssddnvCpyCG 23 
                  ++C+ C+++ s     Cp+C+
   AJA92043.1 112 IKCSDCNEI-SQLNESCPNCQ 131
                  68*******.**********7 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.4
  zf-ribbon_3   4 rCPnC 8  
                  +C+ C
   AJA92043.1 141 TCSDC 145
                  56655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2598.37
//
Query:       AJA92044.1  [L=163]
Description: acetolactate synthase, small subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-22   78.9   5.4    2.5e-21   75.6   0.4    2.3  2  ALS_ss_C  Small subunit of acetolactate synthase
    3.5e-16   58.7   0.1    7.6e-16   57.6   0.1    1.6  2  ACT       ACT domain
    2.1e-14   53.1   0.1    5.1e-14   51.8   0.1    1.7  1  ACT_5     ACT domain
    2.3e-06   28.1   1.1    4.5e-06   27.2   1.1    1.4  1  ACT_4     ACT domain
     0.0058   16.5   0.1      0.018   14.9   0.1    1.8  2  NIL       NIL domain
  ------ inclusion threshold ------
      0.017   14.7   2.0      0.021   14.4   2.0    1.2  1  ComR_TPR  ComR tetratricopeptide
      0.093   13.5   0.4       0.15   12.8   0.4    1.2  1  CppA_C    CppA C-terminal


Domain annotation for each model (and alignments):
>> ALS_ss_C  Small subunit of acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.6    0.0063        16      32      65 ..      42      76 ..       8      76 .. 0.80
   2 !   75.6   0.4   9.9e-25   2.5e-21       1      73 [.      85     158 ..      85     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0063
                EETTEEEEEEEE-HHHHHHHHHHS-.GGGEEEEEE CS
    ALS_ss_C 32 vspdsliieltgteekidaliellk.pfgilevvR 65
                 + + ++i   g+e++i+++++ l+  +  +ev R
  AJA92044.1 42 KKYSRMTITTIGDEKQITQIVKQLDkMIDTIEVRR 76
                5556799*****************72555888765 PP

  == domain 2  score: 75.6 bits;  conditional E-value: 9.9e-25
                 EEEEEEEEE.-S.CHHHHHHHHHHHTT-EEEEEETTEEEEEEEE-HHHHHHHHHHS-GGGEEEEEEEEEEEEES CS
    ALS_ss_C   1 RElaLiKVkaek.eerseileiaeifrakivdvspdsliieltgteekidaliellkpfgilevvRtGrvAleR 73 
                 REl+++K+k++k e+  ei+++a++++ak+ d +++s+i+e+t t+++i a+ el k+fgi+e++RtG++AleR
  AJA92044.1  85 RELVMFKIKVSKpEDSMEINKLASAYSAKTHDAKKESIIVEMTATPHQISAFEELAKKFGIKEMARTGITALER 158
                 9*********9956***********************************************************9 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.1     3e-19   7.6e-16       2      64 ..       5      67 ..       4      70 .. 0.96
   2 ?   -3.3   0.0       3.3   8.4e+03      45      52 ..     122     129 ..     111     141 .. 0.52

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3e-19
                EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
         ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64
                +l++ v+++PG+L++v+ ++  r++Nidsi+++ +edk  ++++++ ++de+++ +++++l k
  AJA92044.1  5 ILSIKVENKPGILFKVTHLFRSRNFNIDSISVGVTEDKKYSRMTITTIGDEKQITQIVKQLDK 67
                799**********************************************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.3
                 EEEEEEEH CS
         ACT  45 fvvivvde 52 
                 ++v+ + +
  AJA92044.1 122 IIVEMTAT 129
                 33333333 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.1     2e-17   5.1e-14       2      62 .]      13      74 ..      12      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2e-17
       ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvelLsnQleKLidVlkV 62
                +pg+L +v+ ++r r F+++s+++  ted++++r+++t  + e+ ++++++Ql+K+id ++V
  AJA92044.1 13 KPGILFKVTHLFRSRNFNIDSISVGVTEDKKYSRMTITTIGdEKQITQIVKQLDKMIDTIEV 74
                79********************************************************8876 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   1.1   1.8e-09   4.5e-06       9      80 .]       6      76 ..       4      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.8e-09
       ACT_4  9 leveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVisVeR 80
                l++++e+++g+L ++t ++ + + ni s+++  ++++++ +++it  + d +++++++++L ++ + i+V+R
  AJA92044.1  6 LSIKVENKPGILFKVTHLFRSRNFNIDSISVGVTEDKKYSRMTIT-TIGDEKQITQIVKQLDKMIDTIEVRR 76
                799*******************************99999999999.8***********************99 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   6.9e-06     0.018      27      70 ..      28      71 ..      16      74 .. 0.86
   2 ?   -1.8   0.0       1.1   2.8e+03      47      68 ..     123     144 ..     121     146 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.9e-06
                EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHTT-E CS
         NIL 27 evnIlqGsveriqgtpfGqlvielsgsqesiaaalqylrkrnvd 70
                ++nI + sv+   ++++ +++i+  g++++i+++++ l k   +
  AJA92044.1 28 NFNIDSISVGVTEDKKYSRMTITTIGDEKQITQIVKQLDKMIDT 71
                577777799999************************99986555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                 EEEEES-HHHHHHHHHHHHHTT CS
         NIL  47 vielsgsqesiaaalqylrkrn 68 
                 ++e++ ++++i a  + ++k +
  AJA92044.1 123 IVEMTATPHQISAFEELAKKFG 144
                 6777777777777766666654 PP

>> ComR_TPR  ComR tetratricopeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   2.0     8e-06     0.021     107     184 ..      51     128 ..      38     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                 HHH..HHHHHHHHHHHHHTTTS-GGGHHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHT--TTHHHHHHHHH CS
    ComR_TPR 107 klfdkklfeklvekllnqeesleeedlfllrdvllsaltvllklkeyeklekllkvlnkimektqdfqkkpivlmlew 184
                 ++ d+k++ ++v++l + ++++e  +l + ++v+ +++  ++k+ ++e+ +++ k +    +kt+d +k  i++ + +
  AJA92044.1  51 TIGDEKQITQIVKQLDKMIDTIEVRRLDVNNSVYRELVMFKIKVSKPEDSMEINKLASAYSAKTHDAKKESIIVEMTA 128
                 56699*****************************************************************99998876 PP

>> CppA_C  CppA C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   5.8e-05      0.15       3      92 ..      28     124 ..      27     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
      CppA_C   3 dFeveslelnvadkeeseafy.ekllglklp......leldfseaegedLavetdevwdLeiLkfkvdkdfd...laqLkekleekgekvyldkkekvl 91 
                 +F+++s+++ v ++++ ++    ++ ++k +      l+  +   e + L v++ +  +L + k+kv+k  d   +++L++  ++   k++  kke+++
  AJA92044.1  28 NFNIDSISVGVTEDKKYSRMTiTTIGDEKQItqivkqLDKMIDTIEVRRLDVNNSVYRELVMFKIKVSKPEDsmeINKLASAYSA---KTHDAKKESII 123
                 7**********988877666505555555556666556677889999********************986551115555555555...67777777777 PP

      CppA_C  92 v 92 
                 v
  AJA92044.1 124 V 124
                 5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1421  (0.0792571); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1121.30
//
Query:       AJA92045.1  [L=171]
Description: hypothetical protein T478_1281 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1332.67
//
Query:       AJA92046.1  [L=100]
Description: hypothetical protein T478_0738 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.8   0.0     0.0029   17.4   0.0    1.2  1  DUF35_N   Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.6e-07    0.0029      11      33 ..       8      30 ..       2      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-07
     DUF35_N 11 gqrCpdCGtvqfPPravCphCgs 33
                +++C +C+  ++PP  +C  C+ 
  AJA92046.1  8 ISYCEKCDEKIWPPNEICHVCFN 30
                789******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 786.19
//
Query:       AJA92047.1  [L=180]
Description: hypothetical protein T478_0727 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   12.3   5.2          1   10.0   5.2    2.2  1  ING       Inhibitor of growth proteins N-terminal histone-bin


Domain annotation for each model (and alignments):
>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.2   5.8e-05         1      30      86 ..      93     151 ..       7     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.8e-05
                 HHHHHHHHHHHHHHHH..TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
         ING  30 vqellkeidskiekfl..kngslqknekeeelsriqeelkeaqelldeKiqlaqqaldl 86 
                 ++el+k++d+ i  f+  ++ s+q ne+ +e+++iq++ +++  +++e ++++q+a+ +
  AJA92047.1  93 LEELRKNNDNAIVIFFakTSDSMQINERIQEIKKIQKKDSNIWIISKEIMNISQSAYAI 151
                 6789999999999999*9999**********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1430.46
//
Query:       AJA92048.1  [L=327]
Description: putative universal archaeal protein Kae1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-78  263.5   0.0    3.1e-78  263.2   0.0    1.0  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.2   0.0   1.7e-82   3.1e-78       5     270 ..      30     294 ..      26     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 263.2 bits;  conditional E-value: 1.7e-82
                    EEEEEEEEE....S.SSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHHHHHHCCHC CS
  Peptidase_M22   5 nvvasqkelhakyG.GvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhleahalaarl 99 
                    +v + +k   ++ G G++P++asr+H e+  ++++++l+ea+++++dld Ia++ gPGl+++LrvG+ +A+ l+  +++P+++Vnh ++h++ ++l
     AJA92048.1  30 DVRKIYK---PPEGeGIHPREASRHHIENSSSVLKQCLDEAKIKINDLDMIAYAGGPGLGPCLRVGAVVARSLSSYYDIPIYPVNHAIGHIELGKL 122
                    4444444...77789********************************************************************************9 PP

                    TSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST CS
  Peptidase_M22 100 eekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklakeg.kkiefprplkgldfsfsGlktavlkelek 194
                     ++ ++P+vllvsGght++++ ++gr +++getld+ +g+ ld+++r lg+  p g kie+la++  +++++p+++kg+d+sfsGl +a+ + ++k
     AJA92048.1 123 LTGAKNPLVLLVSGGHTMILAFSSGRWRVFGETLDITLGQLLDQFGRSLGFASPCGRKIEELANKStNYVDLPYVVKGNDVSFSGLLSAAKQSTSK 218
                    9999******************99******************************************889********************9999966 PP

                    THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
  Peptidase_M22 195 evedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamia 270
                     v+d ++s+qe+++++++e teral+ ++++e++i+GGvaankrL ++le+++++ ++k+++ pl+y  d + +ia
     AJA92048.1 219 GVQDACYSLQETAFAMIAEATERALAFTRKNEIMIVGGVAANKRLSSMLEDVCKRQKAKFFVVPLNYAGDCGSQIA 294
                    7******************************************************99*************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2039.68
//
Query:       AJA92049.1  [L=50]
Description: hypothetical protein T478_0881 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 380.32
//
Query:       AJA92050.1  [L=218]
Description: hypothetical protein T478_1482 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.048   13.4   0.0    1.4  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-06     0.048       3      64 ..     152     213 ..     150     214 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-06
                 EEEEEEEEE-S-..---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHH CS
       ACT_7   3 edgwiklsvvgs.glpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLh 64 
                 ++g +k++v  + g+  + + ++a +++ L  +gI +     t++  +i+ +eed+ kA+e L+
  AJA92050.1 152 NSGLAKIKVAVPeGH--SRSDVMAFVTEILHYNGIDMADALfTQDGLVIVLKEEDAPKAYEKLR 213
                 578899999999566..699******************9999******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1579.32
//
Query:       AJA92051.1  [L=381]
Description: aminotransferase, class V [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-62  209.1   0.0    1.1e-61  208.8   0.0    1.1  1  Aminotran_5    Aminotransferase class-V
    0.00088   18.5   0.0     0.0018   17.5   0.0    1.4  2  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.8   0.0   1.3e-65   1.1e-61       2     370 ..      16     373 ..      15     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 208.8 bits;  conditional E-value: 1.3e-65
                  EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEE..ETTS CS
  Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivv..teae 97 
                  yl +a  +  p++ ++a+++++ dy+  +     + +  ++   e++r+ +a++++ +  +eii t++ t++in+va+++  +++++ +iv+  +e e
   AJA92051.1  16 YLNNASVSVMPKTSIEAMKQFLIDYSEMG-PDSPESEIFIKGLWEKTRTSIAKVVKCNP-DEIIITQSVTDGINIVANGM--KFENDSNIVIrgGEHE 109
                  99*********************999998.4444444556678899************7.********************..699******9445899 PP

                  HGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS.---HHHHTESE CS
  Aminotran_5  98 hhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghi.pidvkklgvDf 194
                  hhan  pw +l    +++v+ +p++e+g    ++l+k l+ektklva++h    +G i pv+eigk ++k+++ +++D aq+vg i ++d++++g+Df
   AJA92051.1 110 HHANYFPWLKLG--GKIDVRSLPVNENGGFGNSDLKKVLDEKTKLVALSHGLYNSGLILPVKEIGKELQKENVPYFLDTAQTVGCIgEFDFADTGCDF 205
                  ***********9..77*******************************************************************98649********** PP

                  EEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_5 195 lafsghK.llgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerl 291
                  ++f g K l+gP G+Gv y+++e    lep  +gge+ e+ +  e t++e p +f+aG  n +g+ g++  + +le++g ++i++h  +l++   +++
   AJA92051.1 206 MSFNGSKwLCGPMGTGVFYCKRESSDLLEPSNIGGETAETNENGELTYKELPDRFQAGFRNYVGLAGMESSVTFLENLGWNNIRNHIISLSNLFIDEI 303
                  ************************************************************************************************** PP

                  CTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHH CS
  Aminotran_5 292 kslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdr 370
                   ++ + r++ p+++ +r+sivsf +++ ++e++++ L+++gI +   +            + ++R+S +iynt++e+ +
   AJA92051.1 304 GKISESRVFCPEDESERTSIVSFEIEKQDPEKIVSELAQKGIIIAKREIYE---------KPVLRISPHIYNTKDEILN 373
                  ********************************************9866666.........7899***********9976 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     2e-07    0.0018      51     207 ..      63     206 ..      51     219 .. 0.83
   2 ?   -3.2   0.0      0.39   3.5e+03     316     348 ..     332     362 ..     286     375 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-07
                    HHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE....EEEEEBEETTTTEE-HHHHHHHHTTH CS
  Aminotran_1_2  51 ealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgge....vvryplyseedfhldlealeealkea 142
                    + +ak ++       +++ +++ ++  + +i++++  +k++ +++i++    ++++ n++ + ++     v++ p++  e+ +    +l++ l+e 
     AJA92051.1  63 TSIAKVVK------CNPD-EIIITQSVTDGINIVANGMKFENDSNIVIRGGEHEHHANYFPWLKLGgkidVRSLPVN--ENGGFGNSDLKKVLDE- 148
                    45555555......8899.89999998888888888888*********************99765441125555544..88899999********. PP

                    HCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGS CS
  Aminotran_1_2 143 pegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat.ranv 207
                         ktk++++     ++G +++ +e+ k     +k n+  f+D a  +++ g+ d++ t + ++
     AJA92051.1 149 -----KTKLVALSHGLYNSGLILPVKEIGKE---LQKENVPYFLDTAQTVGCIGEFDFADTgCDFM 206
                    .....*******999999**********888...8889****************999988865544 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.39
                    CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC CS
  Aminotran_1_2 316 takelskkLleevgvyvtpgtsftvpgrlRitv 348
                    + +++  +L+++ g+++ + +++++p  lRi++
     AJA92051.1 332 DPEKIVSELAQK-GIIIAKREIYEKPV-LRISP 362
                    334455557777.77777755555554.78776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2612.86
//
Query:       AJA92052.1  [L=95]
Description: hypothetical protein T478_0527 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 664.68
//
Query:       AJA92053.1  [L=171]
Description: GINS complex protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-07   29.9   1.4    7.9e-07   29.5   1.4    1.1  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   1.4   4.4e-11   7.9e-07       2     108 ..      45     148 ..      44     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.4e-11
                 EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTSSSSTTTTTTHHHHHHH.HHHHHT...HCHHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS- CS
        Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetkssdlpslpphflelavk.llelard..ldelkrllrdllevRlakirkfaenledaagggg 97 
                 ++P W+a++L+ +  v +++++++++ + ++++ed  ++ +l +l +hf+      + +l+     d+  ++l++l+++R  ki  +a++ + ++    
  AJA92053.1  45 NIPRWVADILESEKHVILHEQDMIKELKQAKVKEDIADEDTLATLDKHFYIKLHAyMKKLE-TvdFDKAESMLNQLVRIRQGKIVRLADSSKLTS---- 138
                 79********999999999999887777788888888888889999999855533133333.35699*************************999.... PP

                 TCCHCCS-HHH CS
        Sld5  98 gellsglseeE 108
                  +l s+ls eE
  AJA92053.1 139 -DLSSKLSVEE 148
                 .9999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1232.84
//
Query:       AJA92054.1  [L=74]
Description: hypothetical protein T478_0756 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.068   12.9   0.4      0.077   12.7   0.4    1.1  1  FimH_man-bind  FimH, mannose binding


Domain annotation for each model (and alignments):
>> FimH_man-bind  FimH, mannose binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   4.3e-06     0.077       8      38 ..      25      56 ..      19      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-06
                   EE.TTSEEEEEEE---SBEETTSEEEEEGGGT CS
  FimH_man-bind  8 qi.igsgsanvyvnLepsvevgqnLvvDLsqq 38
                   +i i +g a++ v L++s++   n+v+DL + 
     AJA92054.1 25 DImIVTGRADISVILNSSIDEINNVVIDLKNV 56
                   555899***********************864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 541.23
//
Query:       AJA92055.1  [L=686]
Description: V-type H(+)-translocating pyrophosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     3e-218  726.6  47.7   3.6e-218  726.4  47.7    1.0  1  H_PPase   Inorganic H+ pyrophosphatase


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.4  47.7    2e-222  3.6e-218       3     650 .]      23     676 ..      21     676 .. 0.97

  Alignments for each domain:
  == domain 1  score: 726.4 bits;  conditional E-value: 2e-222
                 HHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
     H_PPase   3 allfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllallsvltaiaflvGallSalagyigmkvavranvrtakaar 101
                 ++++a + + +v k++ gt++m+ei+ea++ ga+afl+r++++i+ +++ l v++ +  +++    iaf vGa+lSa+ag+i++kv+v+a vr+a+a+ 
  AJA92055.1  23 SFAVAGIYTGWVAKQNPGTKQMQEISEAVRIGAAAFLRREMRIIIPIAIGLSVIIGF--FIGDSNGIAFAVGATLSAVAGFISLKVTVKAAVRAAHATG 119
                 6778889999***********************************************..567799********************************** PP

                 HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-EE-HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TTH CS
     H_PPase 102 kslkkalkvafrsGavmgllvvglallgvsllllllkaaalelekllellvgfglGaslvalfarvgGGiytKaADvGaDLvGKveagipEDdprnpav 200
                 ++l k+++++fr+Ga +gl+v ++al   ++l++++ +        + +++g g+Gasl+alf r+gGGi+tKaAD+GaDLvGKvea+ipEDdprnpa+
  AJA92055.1 120 SGLGKTFAITFRGGATVGLAVPAMALAATAILYMIYPN--------PITIAGIGIGASLIALFIRIGGGIFTKAADMGADLVGKVEANIPEDDPRNPAT 210
                 **************************************........999************************************************** PP

                 HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH....SHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHHHHHHH CS
     H_PPase 201 iADnvGDnvGDvaGmgADlfesyvasivaamvlg...aavklvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsvvlval 296
                 iADnvGDnvGD aGmg+D++esy+++i+a+++++    + + +++p+l+ a g++asiig++++       s+k ++++k L+ +++vsa+++++l ++
  AJA92055.1 211 IADNVGDNVGDAAGMGSDVYESYIVTILASLLIAaliGSPENFAYPILIGASGLVASIIGTATI------GSRKITDVMKPLNISFYVSAAIAIALNFV 303
                 **********************************66438999********************99......2345679*****************99999 PP

                 HHH-S..-TTTTSHHHHHHHHHHHHHHHHHHHHHHHH-TTSHHHHHHHHHGGG-HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHH........... CS
     H_PPase 297 lslll..keaaalklflavlvGlvagllivllteyytsteykpvkeiaeasetGaatniisGlavgmestvlpvlviavaillsylla........... 382
                 +++++  ++  a++lf a+++G+++  +i+++t+yyt+ ++kpv ei+e+++ G a   + G+  g++st   ++++++ai++s++++           
  AJA92055.1 304 FTQIIlgDTPIAYALFGATVIGVILVPVIQKITDYYTNANSKPVVEISESAKWGYASLTLMGIIKGLQSTGPFMIALVAAIIVSFAITsaaapegtdpl 402
                 999777866788999************************************************************************888999999999 PP

                 ..HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT......HHCS-- CS
     H_PPase 383 ..glygialaavgmLstlgitlavdayGPiaDNAggiaemseleeevreitdklDavGNttkAitKgfaigsAalaalaLfaaylee......aklekv 473
                   g++g++l+a++mLs++gi+l++da+GPiaDNAggi+em+e+ ee r+itd++DavGNttkA+tKgfai+sAalaala+++a+  e      + + + 
  AJA92055.1 403 lyGIFGTSLTAMAMLSLAGIVLSIDAFGPIADNAGGIVEMTEMGEENRKITDEIDAVGNTTKAVTKGFAIASAALAALAMIQAFQFEashyfqDMVIDY 501
                 999**********************************************************************************99898887667889 PP

                 BTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTTSS---HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHH CS
     H_PPase 474 dllnpevlvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgilegkekpdykkcveistkaalkemilpgllavlapivvglllgaealag 572
                  l+np+v+vgll+G++++f++++  ++ V +aA+++v evrrqfke+p+il+gk+kpdy+kcv+++t a++ e+++ + +av+api+vg+llg++a+ag
  AJA92055.1 502 GLSNPSVIVGLLVGGLIPFIITGQLISGVERAAKKMVYEVRRQFKEDPEILTGKSKPDYAKCVDVATIASIGELWKSASIAVAAPIIVGILLGPSAVAG 600
                 9************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTT.SSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHH CS
     H_PPase 573 llagalvsgvllAifmanaGgawDNAKkyiEegelggkgseahkaaVvGDtVGDPfKDtagpslniliklmsivslvi 650
                 ll+ga+vsg++lA  +an+GgawDNAKk+iE    g+kg+e+hk aVvGD +GDP+KDtagp+ln +ikl++++++v+
  AJA92055.1 601 LLMGAVVSGIFLAYHLANTGGAWDNAKKLIEM--KGEKGTEEHKVAVVGDIIGDPYKDTAGPALNTVIKLLNTIAIVF 676
                 *******************************9..699***************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 4526.73
//
Query:       AJA92056.1  [L=102]
Description: Rieske [2Fe-2S] domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-17   62.2   0.0    3.8e-17   62.0   0.0    1.0  1  Rieske    Rieske [2Fe-2S] domain
    1.4e-09   37.8   0.0    1.7e-09   37.6   0.0    1.0  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   4.2e-21   3.8e-17       2      88 ..       4      89 ..       3      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.2e-21
                EEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHHEEEE CS
      Rieske  2 wvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprplaty 88
                w++++ ++++ +g++ ++++ +++l++ +  +g+++A++ +CtH+ a ls+g ++e+  l+Cp+H ++++  dGk ++ Pa+++l+ty
  AJA92056.1  4 WIKACSTDNLGQGEMFSFDHNEKKLLLTNM-NGKIFATDRTCTHADADLSTGFLTEN-GLTCPLHLSVFNmDDGKPQNPPAENSLQTY 89
                9****************************6.***********************777.9**************************998 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.9e-13   1.7e-09       2     103 ..       4     100 ..       3     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.9e-13
                 EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS.-TTSB-BEE-EEESTS CS
    Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle.deevslkvypvrvedg 99 
                 w++ c++++l +++      ++k+ +l  + +++++A+d +++ +  + ls G++ ++     +++Pl+ ++f++++G+ ++  +e sl++y+++++d+
  AJA92056.1   4 WIKACSTDNLGQGEMFSFDHNEKKLLLTNM-NGKIFATDRTCTHA-DADLSTGFLTEN----GLTCPLHLSVFNMDDGKPQNpPAENSLQTYRTKIQDN 96 
                 ***********9999999999999988888.*************5.788******998....689***************9944569************ PP

                 EEEE CS
    Rieske_2 100 kvev 103
                 ++ +
  AJA92056.1  97 NILI 100
                 *988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 697.45
//
Query:       AJA92057.1  [L=325]
Description: PhoU domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-11   42.9   3.9    2.1e-10   40.9   1.7    2.4  2  PhoU            PhoU domain
    7.5e-06   25.8   0.1    1.9e-05   24.4   0.1    1.7  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.083   12.6   0.0       0.24   11.2   0.0    1.8  1  DUF2080         Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.7   3.6e-14   2.1e-10       1      88 [.     138     228 ..     138     229 .. 0.89
   2 ?    1.6   0.0     0.065   3.9e+02      13      31 ..     254     273 ..     249     315 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3.6e-14
                 HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH..HHHHH..HHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae..dlrel..lsllriardlERigDhavniaer 88 
                 l+rm++i++ m+ d++++le++d+  ++ + +rd ei+r ++++ r +   ++ +  la   +l+ +  l+++ +a+ lE  gD +v++ae+
  AJA92057.1 138 LKRMSSIALGMFTDVVSSLESGDKTNLETISNRDAEINRQYFLLVRLIRSTIM-DTRLAGifNLENIdiLDYRIAANTLEIAGDTVVELAES 228
                 78******************************************999666665.67777788676655499*******************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.065
                 HHHHHHHHCT-HHHH.HHHH CS
        PhoU  13 ddalealeekdtela.revi 31 
                 +++++++ ++d+ la +++ 
  AJA92057.1 254 SKSIDSFISNDRSLAiNAIT 273
                 68899999999999966663 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   3.2e-09   1.9e-05       1      39 [.       9      47 ..       9      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.2e-09
                    EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCC CS
  MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilr 39
                    +k+G+s  v++Pke+ +++++++ + ve+e++ + + +r
      AJA92057.1  9 QKIGSSILVSLPKEWIDANNLDKTNQVEIETNQNNLSIR 47
                    699***************************998855554 PP

>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     4e-05      0.24      16      38 ..       2      24 ..       1      25 [. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4e-05
     DUF2080 16 pffegkVkpfGnSAkvsiPkeyl 38
                 +f ++  ++G+S  vs+Pke++
  AJA92057.1  2 TTFTRRLQKIGSSILVSLPKEWI 24
                58*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2440.64
//
Query:       AJA92058.1  [L=271]
Description: NAD(+)/NADH kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-33  115.4   0.3    3.9e-33  114.9   0.3    1.2  1  NAD_kinase  ATP-NAD kinase
      0.005   16.4   0.0     0.0086   15.7   0.0    1.4  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.3   4.3e-37   3.9e-33      47     291 ..      28     257 ..       5     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 4.3e-37
                 --HHHHTTTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEES.SS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEE CS
  NAD_kinase  47 aaefrsevisvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvna.Gvkgfltefepeaaaellekllegeirvekrevl 144
                  ++++ +v ++++  ++ +   ++le+f + + dl++++GGDGT+l+++r l++ e P+l++n+ G+ g l+e++ ++++ + +++ +++i ++kr+++
  AJA92058.1  28 LIAKKIKVYTIAPVSVSGAEKVESLEEFSKIKLDLVVTLGGDGTTLRAFRNLRN-ETPILTINVgGNRGILSEITLDDFDDAVTAIGKDDIWLDKRTRV 125
                 444555555555555666699999*****************************7.*********8999*****************************99 PP

                 EEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EE CS
  NAD_kinase 145 davimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiV 243
                  a+ + ++           + +lne+++ r++ ++ +e+e++ ++  + ++ +dg+i+stP Gst++s+s Ggpl++ +++ ++i+p+ P  +   + V
  AJA92058.1 126 VASCNGEEF----------SPALNEIYVNRKNLTKTAEFEIKFQNDTV-KQKMDGVIISTPSGSTGHSFSIGGPLLHESLDVLIITPVAPVHRLPSI-V 212
                 866555544..........457*********************98776.6789*************************************9887664.5 PP

                 E-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
  NAD_kinase 244 vssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                 v++++ ++  ++  +++ +++d +     ++++ +++ + +k++ ++r
  AJA92058.1 213 VPDEK-IE--INCSHDCNIVMDAQMIKSSEFDQKITIKKFKKQAVFVR 257
                 55544.44..3378*************************999999998 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.6e-07    0.0086      22      88 ..      24      88 ..       6     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-07
                CHHHHHHCTC.EEEEEE--.STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEE CS
    DAGK_cat 22 vrelleeagv.eleliete.epgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgii 88
                + ++l  +++  +++  ++ +  +  e ++e ++ + dl+v +GGDGt   ++  l +    ++p+ +i
  AJA92058.1 24 ISKKLIAKKIkVYTIAPVSvSGAEKVESLEEFSKIKLDLVVTLGGDGTTLRAFRNLRN----ETPILTI 88
                4444444444234444444222223455677777788***********9999998888....4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1906.03
//
Query:       AJA92059.1  [L=344]
Description: S-methyl-5-thioribose-1-phosphate isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-88  296.4   1.2    2.1e-88  296.2   1.2    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.2   1.2   1.2e-92   2.1e-88       2     280 ..      45     329 ..      44     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.2 bits;  conditional E-value: 1.2e-92
                 S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeadekigdi 100
                 vrG+pai+++++ +l+ +  ++++++ ++L++++++a + L ++rPtav+l + ++ +++     ++ s+v+e+kk+++ ++k++++e+ ++++ +g++
  AJA92059.1  45 VRGAPAIGVSGAFGLALASLQSDATEKNDLISYMENAKKILFETRPTAVNLAWGLDKIME---VANEASSVEEIKKNVVAHAKKMAEEDIQINMTMGKN 140
                 89**********************************************************...5699******************************** PP

                 HHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEET CS
       IF-2B 101 aaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrile 189
                 +++l++d+dti+T+cn+++        +l+v+ra ++++k++kVi++E+rP  qG rlta eL+++gi+v li+d+av+y m +  vdk+ivGAdril+
  AJA92059.1 141 GSQLFNDNDTIMTHCNAGAlatvgygtALGVIRATKDSGKNIKVIATETRPIQQGsRLTAFELKHDGIDVSLIPDTAVGYSMANgLVDKIIVGADRILR 239
                 *************************************************************************************************** PP

                 TSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEE CS
       IF-2B 190 nGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvl 280
                  G ++nkiGT+++A +A++++ip++v+a++++f+ + ++ ed++ie r+  e++ i ++++a+  ++v+npafD+tPpelI +iITe+Gv 
  AJA92059.1 240 TGHVYNKIGTYQVATMANQHEIPFYVAAPLSTFDMK-SNPEDVIIEQRKGSEVTGIGDKKTAPDGINVINPAFDMTPPELIAGIITEKGVA 329
                 ************************************.78888999********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2372.77
//
Query:       AJA92060.1  [L=308]
Description: hypothetical protein T478_0227 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-05   23.0   2.8      0.068   13.4   0.0    2.3  2  CARDB     CARDB


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.8e-06     0.068       8      78 ..      33     110 ..      30     118 .. 0.86
   2 !    9.2   0.7   7.7e-05       1.4       4      83 ..     147     229 ..     144     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-06
                 EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S..-S-CEE CS
       CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtte..ategev 78 
                 +++ p+++ ++++++i++ ++N+G ++ +++ ++l+  ++       +++ +++L +++s   ++ ++++  ateg++
  AJA92060.1  33 EIVHPDSVLNERTFSISFLIQNNGWESKQNIILKLTNPDDAFtpvaeEKIRIEELTSSSSFGTTLDYVVHkdATEGTH 110
                 56789999****************************9998888999889999*******9999999888866666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.7e-05
                 EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
       CARDB   4 LtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtltvv 83 
                  ++ +t++p++ f+++e++i++t++ + +++ +++++++++ + +    +  +++sL+ ++ +t+s+   t+    + e+t+ v+
  AJA92060.1 147 IVI-ETITPESIFAKSEFSIQATITSN-DIDLEDITLEIIAPDIEFrgdTFYKLSSLEKQTPYTISAELITPveNVTTEYTIPVK 229
                 566.999*****************988.9************9999988777789*****************97666677775444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2053.86
//
Query:       AJA92061.1  [L=126]
Description: hypothetical protein T478_0548 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 920.24
//
Query:       AJA92062.1  [L=139]
Description: hypothetical protein T478_0305 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.01   16.0   0.2      0.026   14.7   0.2    1.6  2  Lectin_like  Lectin like domain


Domain annotation for each model (and alignments):
>> Lectin_like  Lectin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.041   7.3e+02      69      88 ..       8      26 ..       4      29 .. 0.82
   2 ?   14.7   0.2   1.5e-06     0.026      51     133 ..      25     106 ..      18     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.041
  Lectin_like 69 aasgtlkyaGYytvdldkpv 88
                   +g++ + G+  ++++++v
   AJA92062.1  8 R-EGKMPKPGFKSITISEQV 26
                 3.89**********999987 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-06
  Lectin_like  51 yvykdfenekplsnklklaasgtlkyaGYytvdldkpvelkagk...kfavvvkittpgskypvaiEynveeysskasandGesYi 133
                  +vy++f +  + ++++ + ++g  + aGY+t  l+++  + ++k   k+a  +++ + + +  v + +n++++ +++  ++Ge Y 
   AJA92062.1  25 QVYEKFYDVYEKNKEKLT-MKGVNSFAGYITYMLEDS--MLKDKtfaKYAPKLELMSIE-DDRVILKNNIQNRIAEVVFQRGELYC 106
                  689999999655555555.5**************994..44444011556666666644.45566677999999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 986.59
//
Query:       AJA92063.1  [L=144]
Description: acetyltransferase (GNAT) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-15   54.9   0.1    9.2e-15   54.7   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.7e-08   32.8   0.1    8.2e-08   32.5   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.8e-06   28.6   0.1    4.4e-06   27.3   0.0    1.8  2  Acetyltransf_5   Acetyltransferase (GNAT) domain
    2.9e-06   27.6   0.1    4.4e-06   27.0   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   13.8   0.0       0.11   12.5   0.0    1.7  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.062   13.3   0.0       0.12   12.3   0.0    1.6  1  Nitrate_red_del  Nitrate reductase delta subunit


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   3.1e-18   9.2e-15      21     127 .]      37     144 .]      17     144 .] 0.90

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3.1e-18
  Acetyltransf_10  21 alrerieegealllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                      +l ++  ++++ +++ ++g++i G +++ + ++  +++++++ +++r + +gk+ + +++e+++++g + ++ +++    ++fY+k+GF++ g+
       AJA92063.1  37 ELFDKN-DENCDHFLIFDGKEITGSVRIlSMEKvaKLERMAILKDFRTKNYGKNCIFQLKEYYSEHGFS-HIILDSIYSVREFYKKCGFTEEGD 128
                      444443.899999*************998777789*******************************999.************************ PP

  Acetyltransf_10 112 eqeenGirfvpMekel 127
                      ++++ Gi +++M ++l
       AJA92063.1 129 VFQRVGIDHIRMSLTL 144
                      ************9875 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   2.7e-11   8.2e-08      14     117 .]      29     123 ..      14     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.7e-11
                     HHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHH CS
  Acetyltransf_1  14 ppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaa 108
                      + + + +e f +   +e++ ++++ ++ e+ G +++l        va +e++a+ +++r k++G+  + +l e+  e+g+  i l+   +    
      AJA92063.1  29 NELGISKQELFDKN--DENCDHFLIFDGKEITGSVRILSMEK----VAKLERMAILKDFRTKNYGKNCIFQLKEYYSEHGFSHIILDSIYS---V 114
                     44444444554444..57777777888899*****9999988....*************************************9**44444...5 PP

                     HHHHHHTTE CS
  Acetyltransf_1 109 irlYeklGF 117
                     +++Y+k+GF
      AJA92063.1 115 REFYKKCGF 123
                     ****88**9 PP

>> Acetyltransf_5  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.5e-09   4.4e-06       1      68 [.      22      83 ..      22     109 .. 0.88
   2 ?   -3.6   0.0         6   1.8e+04       6      16 ..     117     127 ..     113     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.5e-09
  Acetyltransf_5  1 LRyevFreemgaegeaaapeldiDefDavcdhllvideaeevVGtyRllrpdeaerlegfysesefdl 68
                    +R+ vF +e+g ++++      +D+ D+ cdh+l+ d +e + G +R+l+ ++ ++le++   + f+ 
      AJA92063.1 22 IRETVFTNELGISKQE-----LFDKNDENCDHFLIFDGKE-ITGSVRILSMEKVAKLERMAILKDFRT 83
                    69***********999.....79**************999.*********999998888877777764 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6
  Acetyltransf_5   6 Freemgaegea 16 
                     F++++g+++e 
      AJA92063.1 117 FYKKCGFTEEG 127
                     77777777665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   1.5e-09   4.4e-06       3      76 .]      46     125 ..      44     125 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.5e-09
                     EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHH.HHTT....SEEEEEEEEETHH.HHHHHHHHTTEEE CS
  Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLl.eaae....kgiileqlelnae.kaikfYeklGFee 76 
                     + +f++ d+++i G +++   +  a ++r+a+++++r k +G+  + +++e    +g+   +  l++    ++fY+k+GF+e
      AJA92063.1  46 CDHFLIFDGKEITGSVRILSMEkvAKLERMAILKDFRTKNYGKNCIfQLKEyyseHGFS--HIILDSIySVREFYKKCGFTE 125
                     5566688999999*999888889999999****************94442244445522..222322222355*******86 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.8e-05      0.11       7      63 ..      13      67 ..      10     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                    GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEE CS
  Acetyltransf_9  7 eedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallple 63
                    ++ + ++ ++ +++F  e       +e f+k  e+ ++++++d+ e+ g++++l++e
      AJA92063.1 13 DKAFSHIRDIRETVFTNELGIS--KQELFDKNDENCDHFLIFDGKEITGSVRILSME 67
                    678999*************986..468999999999*****************9987 PP

>> Nitrate_red_del  Nitrate reductase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05      0.12      59      94 ..     105     142 ..      83     144 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
  Nitrate_red_del  59 llfgestlevrefyrqaglevaeefnep..pDHlaveL 94 
                      ++  +s + vrefy+++g++++ ++++    DH+ + L
       AJA92063.1 105 HIILDSIYSVREFYKKCGFTEEGDVFQRvgIDHIRMSL 142
                      555567789***********99999998889**98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1005.29
//
Query:       AJA92064.1  [L=38]
Description: hypothetical protein T478_1414 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00076   19.3   0.7    0.00093   19.0   0.7    1.1  1  Rad50_zn_hook   Rad50 zinc hook motif
  ------ inclusion threshold ------
      0.022   14.6   0.6      0.028   14.3   0.6    1.2  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.023   14.4   0.3      0.023   14.4   0.3    1.4  2  zinc_ribbon_2   zinc-ribbon domain
       0.11   10.8   0.4       0.11   10.8   0.4    1.0  1  DUF530          Protein of unknown function (DUF530)


Domain annotation for each model (and alignments):
>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.7   2.1e-07   0.00093      21      39 ..       8      26 ..       3      27 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-07
                   E-TTT--EE-HHHHHHHHH CS
  Rad50_zn_hook 21 cCPlCgReldeehrseLik 39
                    CP CgR+l  ++rseL+k
     AJA92064.1  8 ECPKCGRKLKAHSRSELAK 26
                   6****************87 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   6.2e-06     0.028       7      27 ..       9      27 ..       8      29 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.2e-06
  Zn_ribbon_SprT  7 CtgCgreythhlsirrhnYrC 27
                    C+ Cgr+ ++h+++  ++  C
      AJA92064.1  9 CPKCGRKLKAHSRSELAK--C 27
                    **************9888..7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   5.2e-06     0.023       2      12 ..       9      19 ..       8      22 .. 0.83
   2 ?   -3.0   0.0       1.5   6.7e+03       1       2 [.      26      27 ..      25      28 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-06
  zinc_ribbon_2  2 CpnCGaelqdn 12
                   Cp+CG++l+  
     AJA92064.1  9 CPKCGRKLKAH 19
                   99***999865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
  zinc_ribbon_2  1 fC 2 
                   +C
     AJA92064.1 26 KC 27
                   34 PP

>> DUF530  Protein of unknown function (DUF530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   2.5e-05      0.11     121     150 ..       2      30 ..       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.5e-05
      DUF530 121 eeyaelkCksCekkyklseleleskkCecg 150
                  +y++++C +C++k+k +  + e +kC++ 
  AJA92064.1   2 SKYMNMECPKCGRKLKAHS-RSELAKCSLK 30 
                 5799*************99.5688899875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 267.73
//
Query:       AJA92065.1  [L=219]
Description: hypothetical protein T478_0436 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1565.53
//
Query:       AJA92066.1  [L=68]
Description: hypothetical protein T478_0774 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 449.72
//
Query:       AJA92067.1  [L=171]
Description: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-10   39.0   1.9    1.4e-09   38.1   0.8    1.7  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    8.3e-09   36.0   0.7    9.8e-06   26.0   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    8.2e-05   22.7   0.2     0.0026   17.8   0.2    2.4  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.024   14.7   1.8      0.024   14.7   0.5    1.6  2  HAD_2        Haloacid dehalogenase-like hydrolase
        0.1   12.5   0.0       0.21   11.5   0.0    1.6  1  HA1          Hemagglutinin I
       0.11   12.9   0.0        2.6    8.4   0.0    2.4  1  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.24   7.3e+02       1      28 [.      15      41 ..      15      50 .. 0.74
   2 !   38.1   0.8   4.6e-13   1.4e-09     163     250 ..      63     150 ..      51     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.24
                 EEEEIIIIIS-TTS---HHHHHHHHHHH CS
  Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklk 28
                 +++D+DG L ++++++  +t e +kk++
   AJA92067.1 15 VVTDVDGVL-TDGGRYFSSTGELLKKFH 41
                 689****76.666666777888887776 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 4.6e-13
                  HHCTTTEEEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTH CS
  Hydrolase_3 163 sklnklltitssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedG 250
                  ++++k ++ +  s ++ ++++    K + lk ++ +++ ++ e++ +GD+ NDi++L+++g++    ++  +vkk+ dyv+k+   +G
   AJA92067.1  63 KETSKITKSWAKSMNITKVYSGAKIKEEKLKSICDFFDTTPIEMAFIGDDVNDINLLKKVGISASPSDGISQVKKMVDYVCKNSGGNG 150
                  4444444667777778889999999********************************************************9987776 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.5   0.00076       2.3       1      16 [.      12      27 ..      12      44 .. 0.84
   2 !   26.0   0.0   3.3e-09   9.8e-06     126     210 .]      47     123 ..      40     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00076
                SSEEEEESBTTTBCHH CS
                xxxxxxxxxxxxxxxx RF
   Hydrolase  1 iktvvfDkdGTLttge 16
                ik+vv D+dG+Lt+g 
  AJA92067.1 12 IKLVVTDVDGVLTDGG 27
                89************97 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 3.3e-09
                 HHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 126 avasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet...vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                 av+ L +++i++++lt   ++  ++ a+ ++           i++    ak + e ++ +++ +   p e+a++GD vnD+  l+++g
  AJA92067.1  47 AVNLLLRNNIKTIILTKETSKITKSWAKSMN-----------ITKvysGAKIKEEKLKSICDFFDTTPIEMAFIGDDVNDINLLKKVG 123
                 67778899***********************...........5555778999*************99***************999876 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   8.8e-07    0.0026       1      51 [.      15      76 ..      15      94 .. 0.88
   2 ?    2.4   0.0     0.057   1.7e+02      50      78 ..     118     146 ..     113     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.8e-07
                 EEEESTTTSEETTEE-TTHHHHHHHHHHTT...........-EEEEEE---SS-HHHHHHHH CS
  Hydrolase_6  1 flfDidGvLwrgdkaipgaaealnalraag...........kpvvllTNnsskseeeyakkl 51
                 +++D+dGvL +g++ +    e+l+ ++ +            +++++lT ++sk  ++ ak +
   AJA92067.1 15 VVTDVDGVLTDGGRYFSSTGELLKKFHVRDgmavnlllrnnIKTIILTKETSKITKSWAKSM 76
                 699************************99889*********99*****99999888887766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.057
                  HHHHTT----GGGEEEHHHHHHHHHHHHS CS
  Hydrolase_6  50 kleklgvditeeqvvtsataaaeylkkrk 78 
                   l+k+g+++++++ ++  + +++y++k+ 
   AJA92067.1 118 LLKKVGISASPSDGISQVKKMVDYVCKNS 146
                  5899*********************9954 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.69   2.1e+03       3      16 ..      17      30 ..      15      48 .. 0.69
   2 ?   14.7   0.5   8.2e-06     0.024      88     174 ..      48     125 ..      28     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.69
       HAD_2  3 FDlDgTlldteeli 16
                 D+Dg+l d   + 
  AJA92067.1 17 TDVDGVLTDGGRYF 30
                59999999976654 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.2e-06
       HAD_2  88 LeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagik 174
                 ++ L ++++k  i T ++++ +++  + ++i    ++++++ +++++K     ++ +++ +++++ e+ ++GD  +Di   kk+gi 
  AJA92067.1  48 VNLLLRNNIKTIILTKETSKITKSWAKSMNI----TKVYSGAKIKEEK-----LKSICDFFDTTPIEMAFIGDDVNDINLLKKVGIS 125
                 56677999*********************96....89999***99998.....999**************************99996 PP

>> HA1  Hemagglutinin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.9e-05      0.21      24      55 ..      46      77 ..      40     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
         HA1 24 itrylfiqgrdlpviltdeksklpqswavgvn 55
                ++  l+++     +ilt e sk+ +swa  +n
  AJA92067.1 46 MAVNLLLRNNIKTIILTKETSKITKSWAKSMN 77
                55567777777789**************9887 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00085       2.6      87     188 .]      44     120 ..      27     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00085
         HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlp 185
                 d +a+ ll    ++++++++++   + +++ +++ ++    +        +++g          +e+k++++ +  +    +i+   + ++GD ++D+ 
  AJA92067.1  44 DGMAVNLLL---RNNIKTIILTKETSKITKSWAKSMN----ITK------VYSGA-------KIKEEKLKSICD--FFDTTPIE---MAFIGDDVNDIN 117
                 456666666...9999999999999999999999999....666......55555.......556677777777..55555554...789999999999 PP

         HAD 186 llr 188
                 ll+
  AJA92067.1 118 LLK 120
                 886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1212.39
//
Query:       AJA92068.1  [L=199]
Description: glutamine amidotransferase, class I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-53  178.9   0.1    9.6e-53  178.8   0.1    1.0  1  GATase         Glutamine amidotransferase class-I
    2.7e-10   40.4   0.2    4.5e-10   39.7   0.2    1.4  1  Peptidase_C26  Peptidase C26
    0.00022   21.1   0.2    0.00051   19.9   0.2    1.7  1  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.074   12.9   0.1       0.15   11.8   0.0    1.5  2  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.1   2.2e-56   9.6e-53       2     189 ..       5     192 ..       4     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 2.2e-56
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTS.HHHHHHH.THHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpida.saeeile.llknpdgilvsgGpgspg....vegkieaikearenkiPiLGICLGmQllaiefgrkvvk 94 
                 +iDnyds+++n++++l elgv+ +vv++d+ +++   + +++n+d+i++s+Gpg+p      + + ++i+e+   k+PiLG+CLG+Q ++  fg+kvv+
  AJA92068.1   5 IIDNYDSFVYNIAQRLGELGVTSDVVRNDKvTIS---DiENSNYDAIIISPGPGTPDderyFGICKKVITEIGP-KKPILGVCLGHQGIISCFGGKVVN 99 
                 89***************************63333...3369****************88888888888888888.************************ PP

                 EECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
      GATase  95 ekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnflik 189
                 +  +  hg+t+++++++++l++g kn+++++++H+++ ++  + p+ l++ta+ edd+e+m++ +k++ + gvQFHPEs++t eg++++ nf+ k
  AJA92068.1 100 AD-NIRHGKTSQVKHTDESLFEGVKNPFRATRYHSLVGQK-TIIPNSLKITAVAEDDGEVMGVSHKEYLIEGVQFHPESILTDEGSKIFSNFIKK 192
                 *9.9***********************************8.*************************************************99765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   9.9e-14   4.5e-10     101     216 .]      72     175 ..      39     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.9e-14
  Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike..laeelrveAvae.D 193
                    ++  ++Pilg+C+G+q +   +GG+++++ +      +h       ++ +vk + +sl++ + +   ++ + +H+   ++  + ++l+++Avae D
     AJA92068.1  72 EIGPKKPILGVCLGHQGIISCFGGKVVNADN-----IRH------GKTSQVKHTDESLFEGVKN--PFRATRYHSLVGQKtiIPNSLKITAVAEdD 154
                    57789*******************9987655.....334......4456788999999999866..8999999998877767899*********77 PP

  Peptidase_C26 194 gviEaieseeakafvlgvQwHPE 216
                    g +  ++++e  + + gvQ+HPE
     AJA92068.1 155 GEVMGVSHKE--YLIEGVQFHPE 175
                    7777776666..99********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   1.1e-07   0.00051     106     187 ..     108     194 ..      25     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-07
                 -SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEE..EEECTTEEEEEEETTEE..EESS-GG..GSTTHCHHHHHHHHHHC CS
         SNO 106 GrqvdsfekeldfknliekftavfiraPvieeilddeavkv..lyeldgeivvakqkkil..atsfhPe..laeddirvhdyfveevv 187
                   qv+  + e  f++++++f a+   + v ++ + +++ k+  + e dge++++  k++l  ++ fhPe  l++++ ++   f+++v+
  AJA92068.1 108 TSQVKH-TDESLFEGVKNPFRATRYHSLVGQKTIIPNSLKItaVAEDDGEVMGVSHKEYLieGVQFHPEsiLTDEGSKIFSNFIKKVE 194
                 445544.44455889999999999999999988878776662257888*******9988844689****999*************997 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.15      52     108 ..      35      90 ..      21      98 .. 0.84
   2 ?   -3.1   0.0       1.3     6e+03      27      47 ..     144     164 ..     139     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                 EEGGGCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHH CS
   DJ-1_PfpI  52 aslddvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLa 108
                 ++++d+++++yDa+++  G   p++ r    + + v +    +k++  +C g q  +
  AJA92068.1  35 VTISDIENSNYDAIIISPGPGTPDDERYF-GICKKVITEIGPKKPILGVCLGHQGII 90 
                 5799************9999988888865.6777777777899*********98766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                 TEEEEEEESSTSEEEETTSEE CS
   DJ-1_PfpI  27 gikvdvvsvdkeevkgsrGlk 47 
                 ++k+++v  d++ev g ++ +
  AJA92068.1 144 SLKITAVAEDDGEVMGVSHKE 164
                 578888888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1424.14
//
Query:       AJA92069.1  [L=268]
Description: 3' exoribonuclease family, domain 1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.5e-23   81.3   0.0    1.9e-22   80.2   0.0    1.6  2  RNase_PH    3' exoribonuclease family, domain 1
    1.4e-15   57.1   0.2    3.2e-15   55.9   0.2    1.6  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   0.0   2.2e-26   1.9e-22       2     132 .]      33     167 ..      32     167 .. 0.93
   2 ?   -2.2   0.0      0.61   5.5e+03      64      64 ..     234     234 ..     194     267 .. 0.57

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.2e-26
                 EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-C....... CS
    RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsill....... 92 
                  R+l+i +gv+++a+GSa+ +lGdt+v+a+v+++ e  p++++ d  +g l +  e+ p+a ++++  g p+   +el+r+ +r +r+s++l       
  AJA92069.1  33 PRKLTIDIGVIPKAEGSARARLGDTEVVAGVKVQPER-PFPDTgD--KGMLICTAEILPIAHPSAET-GPPQPPVVELARVTDRGIRESGMLdmkqlvl 127
                 59********************************986.8999766..578***************55.9**********************99999999 PP

                 .CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
    RNase_PH  93 .ekkpkstididitvlssdggslldalinaaslALadagip 132
                  + k+   + +d  v+++dg +l+da++ a+++A+  ++ip
  AJA92069.1 128 eKDKSVIGVFCDNAVTDHDG-NLFDACSYASTAAINACKIP 167
                 7667779999**********.***************99998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.61
                 - CS
    RNase_PH  64 e 64 
                 +
  AJA92069.1 234 Q 234
                 0 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.2   3.6e-19   3.2e-15       2      65 ..     191     254 ..     190     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 3.6e-19
                 --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHH CS
  RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAk 65 
                 ++++vt++k+d+ +++Dpt eE +++++++t++ +++++vv+l+k g+ ++++e+l+++ e++ 
  AJA92069.1 191 LPVSVTMAKIDNFIIVDPTIEEWAIMDARITITTNSDGNVVALQKGGSDGFTQEELIKCSEMSI 254
                 89**************************************9999999999*********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2034.94
//
Query:       AJA92070.1  [L=80]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-10   40.7   0.1    1.9e-10   40.6   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1     1e-14   1.9e-10       1      70 [.       6      72 ..       6      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1e-14
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                    vl+++e g+    e ++ +l++++ ++e++ + G yd+++kv +++++ +++ +  k+++++ +++t t+
      AJA92070.1  6 VLINCELGS---EEHIISELKTFDDIEEVHGTFGAYDIIAKVSSESVDKIRETITWKIRKIEKIRSTLTL 72
                    789999999...9******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 637.20
//
Query:       AJA92071.1  [L=284]
Description: shikimate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-10   39.0   0.9    1.2e-09   38.3   0.2    1.7  2  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0083   16.5   0.0      0.022   15.1   0.0    1.8  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.078   13.2   1.1        3.2    8.0   0.0    2.2  2  ArlS_N          ArlS sensor domain
      0.089   12.9   0.1       0.16   12.0   0.1    1.4  1  Trans_coact     Phage late-transcription coactivator


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   9.3e+03      48      58 ..      19      29 ..      11      32 .. 0.55
   2 !   38.3   0.2   2.6e-13   1.2e-09       2      65 ..      78     145 ..      77     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                    HHHHHHHHSHH CS
  GHMP_kinases_N 48 laqggngsggD 58
                    ++++g++ g+D
      AJA92071.1 19 AVGKGSTLGID 29
                    34555566666 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.6e-13
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHH.HHHHHS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDv.aasvyG 65 
                     + +ks+iP+g GL SS+A++ a+v+  ++++g+ +++   +kl+++   +  +  ++  D+ +a+ +G
      AJA92071.1  78 LDFKSNIPTGYGLKSSSAISSAVVLSCAKAFGKTMSDeeiLKLGAKTSIQTKVSITGAYDDaCACHFG 145
                     6789***************************9997333589999999988887888888884566555 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.9e-06     0.022      39      77 ..     225     260 ..     182     264 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-06
  GHMP_kinases_C  39 llealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                     l+  l+e Gal a +sG   Gp++ a++ d+ + ++v+ 
      AJA92071.1 225 LIMRLMEKGALCATISGN--GPSIMAIA-DRKNKSRVQK 260
                     555678************..*******9.6666566665 PP

>> ArlS_N  ArlS sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.012        55      19      62 ..      34      77 ..      28      91 .. 0.79
   2 ?    8.0   0.0   0.00072       3.2      36      99 ..     219     281 ..     181     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.012
      ArlS_N 19 evttyleekklslteeelqesdsllekinekdqtirildkdgke 62
                ++ t  e k++++t+e+ ++s  l++k++e+ +   ild+ + e
  AJA92071.1 34 TTLTKKEGKGIHITSENKTISSRLINKLIENMIPKKILDNTKLE 77
                4445556667779******************9988888887655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00072
      ArlS_N  36 lqesdsllekinekdqtirildkdgkevlevsndspeikftvpfekvkkkeieevkingdkllv 99 
                 l++  +l+ +++ek  + + +  +g  ++ ++++ +++ ++++f+   + +i+ ++in++k++v
  AJA92071.1 219 LNSEPNLIMRLMEKGALCATISGNGPSIMAIADRKNKSRVQKEFSG-LDGKIMISNINNKKAYV 281
                 4577899999**********************************99.**************998 PP

>> Trans_coact  Phage late-transcription coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.7e-05      0.16      18      61 ..      30      73 ..      16      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
  Trans_coact 18 sYlEAvlewceendieeeqvpklIskpLkeKikaEAielnllkp 61
                 ++ E++l+  e ++i++++ +k+Is+ L+ K+ ++ i +++l +
   AJA92071.1 30 TFVETTLTKKEGKGIHITSENKTISSRLINKLIENMIPKKILDN 73
                 7889999999**********************999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2364.74
//
Query:       AJA92072.1  [L=283]
Description: B12 binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-10   41.0   0.0    2.5e-10   40.4   0.0    1.3  1  B12-binding    B12 binding domain
    1.4e-07   31.8   0.0    2.2e-07   31.2   0.0    1.3  1  B12-binding_2  B12 binding domain
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.95    9.8   0.0    2.1  2  OKR_DC_1_N     Orn/Lys/Arg decarboxylase, N-terminal domain
        1.9    8.8   5.5        5.2    7.3   0.7    3.4  3  SAC3           Leucine permease transcriptional regulator hel


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   5.7e-14   2.5e-10       2      92 ..     165     255 ..     164     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.7e-14
  B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahps 92 
                  k++l+t  g+ h+lG +vl  +l  +gf   +l   +++e +++ i+  kpd++ +S++l  +++  +++v+ ++++ +++++++GG +++
   AJA92072.1 165 KIVLTTPVGEDHNLGCNVLDSFLVSKGFTTFNLSPSTPAESLIEFIKTAKPDALIVSITLEDNIRSGQRMVKKIHEAYKKLPIFIGGLAFT 255
                  7999***********************************************************************************9866 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   4.9e-11   2.2e-07       7      73 ..      82     151 ..      69     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.9e-11
  B12-binding_2   7 waivhgdkegieelidealaqgsa...avdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavah 73 
                     ++     eg  +++ e  ++  +   ++++++ ++ p+m e+G l+ +g+l+++ ++ ++++ ++ v++
     AJA92072.1  82 TKLFSSLTEGSLKDTMEIYTAFVSsntLDQFYERIMTPVMAEIGYLWSEGKLSIATEHVASNIAHSLVKV 151
                    444444444444444444422212456************************************9998876 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.23     1e+03      26      59 ..      45      82 ..      40      86 .. 0.82
   2 ?    9.8   0.0   0.00021      0.95      28      68 ..     205     249 ..     178     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.23
  OKR_DC_1_N 26 tdDllsvieqnsriaavvlsvd....deaaelldeire 59
                 dD+ +  +++++i++++l+      +++++l++++r 
  AJA92072.1 45 RDDIPAEFREDAKINSFLLQNTpkdrEKREKLIEQLRT 82
                57788888999999999999889888888899998886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00021
  OKR_DC_1_N  28 Dllsvieqnsriaavvlsvd.....deaaelldeirernedlPvFl 68 
                  l+++i++ ++ +a+++s+       + + ++++i+e  ++lP+F+
  AJA92072.1 205 SLIEFIKT-AKPDALIVSITledniRSGQRMVKKIHEAYKKLPIFI 249
                 34445554.778999***999999999999***************8 PP

>> SAC3  Leucine permease transcriptional regulator helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.75   3.4e+03      27      43 ..      23      39 ..      16      40 .. 0.73
   2 ?    7.3   0.7    0.0012       5.2      21      48 ..      63      87 ..      55     118 .. 0.82
   3 ?    1.2   0.1     0.095   4.3e+02       8      35 ..     135     162 ..     133     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.75
                HHH...HHHHHHHHHHH CS
        SAC3 27 eenrknerkqiIdsLse 43
                +++rk+ r++ I+ L+e
  AJA92072.1 23 DKERKTSRQETIKYLGE 39
                44558899999999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0012
                HHHHHHHHH...HHHHHHHHHHHHHHHH CS
        SAC3 21 lknllkeenrknerkqiIdsLseeLydA 48
                l+n  k+++   +r+++I++L + L++ 
  AJA92072.1 63 LQNTPKDRE---KREKLIEQLRTKLFSS 87
                566666666...**************96 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.095
                 HHHHHHHHHHHHHHHHHHHHHH...HHH CS
        SAC3   8 iiqdvVdselekilknllkeenrknerk 35 
                 i ++ V s++   l +++ +enrk +++
  AJA92072.1 135 IATEHVASNIAHSLVKVIADENRKSKKD 162
                 6778899999999999999999777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2061.07
//
Query:       AJA92073.1  [L=513]
Description: pyridoxal-phosphate dependent protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-21   76.3   0.1    3.9e-20   72.5   0.0    2.7  2  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   2.2e-24   3.9e-20      23     190 ..      61     286 ..      52     365 .. 0.74
   2 ?   -3.3   0.0      0.26   4.6e+03      49      71 ..     454     475 ..     426     484 .. 0.49

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 2.2e-24
                 EEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H........................... CS
        PALP  23 plflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGlkvtivvpadasp........................... 91 
                 +++ K +++  tgS+K+R a+++++++  +   t+++tv+ea+sGN g+al + ++ +G+ ++ +v+++  +                           
  AJA92073.1  61 KVYGKFDGTLLTGSIKVRPAVNIIHDAITTgkiTSGTTVIEATSGNFGIALGLLSK-IGVTAIALVSRKLQEgvfkelrngnirimdldmdicpapgme 158
                 399***********************7777799**********************9.********9999996555555555566666666666666666 PP

                 .............HHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH............STTCEE--TTTSHHHHHH.HHTHHHHHHHHTT......TTE CS
        PALP  92 .............ekvallrllGaevvevggdydeavaaaaelaae............gegaylvsqfdnptvieg.ygtiglEileqlg......gkp 158
                                + ++ +lG e +     +d+  a +++l+a+            +++ +   q+dn +++++  + +g Ei +ql       +++
  AJA92073.1 159 skqdelvakataaNVRSQMIELGFEPET----FDNNIADIETLLAKkdiinlakflakIYNLFCPEQYDNDLNVDAhRTVTGVEIDQQLHengeslENF 253
                 6644333333333333444444444444....44444444433333455555666666******************9999*****99998888666666 PP

                 EEEEEE-SSSHHHHHHHHHHHHHSTT..-EEEEE CS
        PALP 159 davvvpvGgGgliaGiaaglkerrpd..vrvigv 190
                 + +v++ G+Gg+ +G+++++ e+ ++  v+vi+ 
  AJA92073.1 254 N-IVCTFGTGGTSGGLSRYFDEKYGKkgVHVIFP 286
                 6.********************888867888764 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.26
                 HHTTTTTSEEEEEBSSHHHHHHH CS
        PALP  49 lkegtgaktvveassGNhgralA 71 
                 l+e  ++k ++++ +G + + +A
  AJA92073.1 454 LQES-QGKSLMVCMAGRTSLMAA 475
                 2222.444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3702.53
//
Query:       AJA92074.1  [L=476]
Description: preprotein translocase, SecY subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-60  204.0  16.3    3.9e-60  203.7  16.3    1.1  1  SecY             SecY translocase
    8.3e-12   44.7   1.9    2.6e-11   43.2   0.6    2.6  2  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
       0.08   13.3   4.0       0.95    9.9   0.1    2.9  2  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7  16.3   6.5e-64   3.9e-60       1     306 []      79     454 ..      79     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 6.5e-64
                 BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH.HHHHHHHHHHHHHHHHHHHHH CS
        SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg.......lalllivlqltagtvllmwLgEqi 89 
                 s+++LGI+P++t ++++qLl ++     ++lk +  ++++r  ++++t+++t ++++ +++++a+++        ++l +++ ql+ ++v++m+L+E i
  AJA92074.1  79 SLVELGIGPIVTGGLLMQLLrGS-----DILKfDFkNPAERGVFQTATKLVTYIVIVAESIVYAIAVYgpgitepTVLYILIGQLMGASVIVMFLDETI 172
                 899*****************999.....777776669*************************99766679****977899999**************** PP

                 HH.HSSTTHHHHHHHHHHHHHHC.CHSS................-HHHH.........SS.....THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBST CS
        SecY  90 te.kGiGnGisllifagivarlp.kals................gliel.........ale...gilallllllvtllvillvvyveeaerripvqyak 158
                 ++ +G+G+Gis++i+ag+++++  + +s                g   +         a     + l+ ++ l++t  +++++vy + ++++ip+ ++k
  AJA92074.1 173 QKgWGLGSGISIFIMAGVAQQILwSLFSpmpagdggavgvfpfiG---QmaaygdvadA-IfrsNQLPSIFGLFLTAGILAILVYTQGMKVEIPIVSTK 267
                 ***********************7777777777666665544441...04434544431.0457889*******************************6 PP

                 T....S.S-EEEEETTCCCSCHHHHHHHHHHHHHCCCCS.........................................TCCCS.......THHHHHH CS
        SecY 159 rgrkggqssylPlklnyagviPiIfassllalpstiaqfl........................................lalls.......psvlyvv 210
                     +g   ++P+k++y ++iP+I+as+l a   +i q++                                        l   +         v yv+
  AJA92074.1 268 Y---RGFAATYPIKMMYVSNIPVILASALTANAVFIGQMFwsqfnprnnnvflnilaefdptapssptggivyfitpprgL---DiaaqdplRAVGYVI 360
                 5...499************************87777777767777777777777777777777777777766666665552...133333433344888 PP

                 HHHHHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
        SecY 211 lyvlliifFayfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                 ++v+++i+F  +++e+  ++pk+ a+nl + + ++pg+r + k++++ L+++++ +t+iG+++l+lia ++d+lg   +g  +g ++L+ V + ++++
  AJA92074.1 361 FMVAIVIVFGRLWVELGgLSPKKAAQNLLDADVQVPGFRrSNKPIETLLNRYIPSVTIIGSAILGLIAGVSDVLGV--FG--TGIGILLSVDILINYY 454
                 88888888********************************************************************..87..9**********99986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.6   4.3e-15   2.6e-11       1      35 []      45      78 ..      45      78 .. 0.98
   2 ?   -1.5   0.0      0.39   2.3e+03       1      23 [.     335     353 ..     335     355 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.3e-15
                     HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
  Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                     ++Ylv++q+PL+G + +  +D++++ R+ifAs++G
       AJA92074.1 45 VIYLVMGQTPLFGAT-APEFDFLAFARVIFASAQG 78
                     8*************9.99****************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.39
                      HHHHHHCCSB-TT--SSS-TCCH CS
  Plug_translocon   1 llYlvlsqiPLyGissssssDpf 23 
                      ++Y++   +P  G++  + +Dp+
       AJA92074.1 335 IVYFI---TPPRGLD-IAAQDPL 353
                      78999...8888888.5578886 PP

>> Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0     0.023   1.4e+02      11      52 ..     124     164 ..     118     195 .. 0.79
   2 ?    9.9   0.1   0.00016      0.95      17      63 ..     394     440 ..     388     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.023
  Phage_holin_5_1  11 mtflvvvtpvfvqaikktelvpskwlptv.silvgailgalat 52 
                      +t++v+v+  +v ai      p    ptv  il+g ++ga   
       AJA92074.1 124 VTYIVIVAESIVYAIAV--YGPGITEPTVlYILIGQLMGASVI 164
                      68999999999999965..56888899984699*****99543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00016
  Phage_holin_5_1  17 vtpvfvqaikktelvpskwlptvsilvgailgalatsldgsgslatm 63 
                        p f ++ k  e +  +++p+v+i+  ailg +a + d  g + t 
       AJA92074.1 394 QVPGFRRSNKPIETLLNRYIPSVTIIGSAILGLIAGVSDVLGVFGTG 440
                      56888899999999*********************999988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3592.30
//
Query:       AJA92075.1  [L=170]
Description: biotin-requiring enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   60.0   5.1    1.5e-16   60.0   5.1    2.2  2  Biotin_lipoyl    Biotin-requiring enzyme
    3.3e-12   46.0  11.4    2.9e-08   33.4   0.2    3.3  3  Biotin_lipoyl_2  Biotin-lipoyl like
    2.4e-05   23.7   0.5      0.098   11.9   0.1    2.2  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    5.5e-05   23.8   1.3       0.34   11.6   0.1    2.8  3  HlyD_3           HlyD family secretion protein
    0.00026   21.0   1.7      0.092   12.8   0.1    3.0  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
     0.0019   18.1   1.7     0.0019   18.1   1.7    2.4  2  GCV_H            Glycine cleavage H-protein
  ------ inclusion threshold ------
      0.011   15.6   6.4       0.16   11.8   0.4    3.2  3  PASTA            PASTA domain
      0.029   14.3   0.2      0.029   14.3   0.2    2.1  2  DUF2118          Uncharacterized protein conserved in archaea
      0.032   14.6   1.0       0.11   12.9   0.2    2.2  2  PCC_BT           Propionyl-coenzyme A carboxylase BT domain
      0.054   13.0   0.6      0.081   12.4   0.6    1.3  1  DUF3114          Protein of unknown function (DUF3114)
       0.42   10.8   2.9         13    6.1   0.0    3.1  3  Peptidase_M23    Peptidase family M23


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.0      0.19     3e+02      18      58 ..       2      40 ..       1      47 [. 0.68
   2 !   60.0   5.1   9.3e-20   1.5e-16       9      73 .]     110     169 ..     102     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                   SESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESS CS
  Biotin_lipoyl 18 evlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilv 58
                   +++v++ d+V  g++l  ++ +  +++   +++ +v++il+
     AJA92075.1  2 KYKVQDSDEVVDGEILEKLSKDEYKIK--IKDNEYVVKILH 40
                   688999999999999998887744444..444446666665 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 9.3e-20
                    EEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
  Biotin_lipoyl   9 GesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                    G+     vv++ v++G +Vk+g++++++e+mKm++ ++a+k+G+vk i++keG++v+ +d++a i
     AJA92075.1 110 GK-----VVSIDVEDGAEVKKGDTVCTLESMKMQVAVKAQKDGIVKGIKIKEGNSVNKNDVIADI 169
                    33.....5669***************************************************987 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.031        50      17      43 ..       4      30 ..       2      37 .. 0.88
   2 !   33.4   0.2   1.8e-11   2.9e-08       4      43 ..     103     142 ..     100     145 .. 0.92
   3 !   17.7   2.2   1.4e-06    0.0024       2      33 ..     138     169 ..     137     170 .] 0.94

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.031
  Biotin_lipoyl_2 17 nVkdGqrVkaGdvLaelDsralqlala 43
                      V+d ++V  G +L  l +++++ +++
       AJA92075.1  4 KVQDSDEVVDGEILEKLSKDEYKIKIK 30
                     699999***************998775 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.8e-11
  Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralqlala 43 
                      ++ ++++G+V+++ V+dG +Vk+Gd+  +l+s + q+a++
       AJA92075.1 103 TLRSQIPGKVVSIDVEDGAEVKKGDTVCTLESMKMQVAVK 142
                      7889********************************9986 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.4e-06
  Biotin_lipoyl_2   2 vvsIaapvsGrVaqlnVkdGqrVkaGdvLael 33 
                      +v ++a+ +G V+ + +k+G  V++ dv+a +
       AJA92075.1 138 QVAVKAQKDGIVKGIKIKEGNSVNKNDVIADI 169
                      5899*************************988 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   9.9e-05      0.16     108     142 ..     101     135 ..      80     137 .. 0.76
   2 !   11.9   0.1     6e-05     0.098     105     139 ..     135     169 ..     133     170 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.9e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlftiadl 142
                 + t++++i G V++ +v +G  v++gdt+ t+ ++
  AJA92075.1 101 QSTLRSQIPGKVVSIDVEDGAEVKKGDTVCTLESM 135
                 56778888888888888888888888888777654 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 105 vqktvtvkapisGvVteknvreGqyvqpgdtlfti 139
                 ++ +v vka+ +G+V   ++ eG+ v+++d+++ i
  AJA92075.1 135 MKMQVAVKAQKDGIVKGIKIKEGNSVNKNDVIADI 169
                 677899************************99887 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   2.8e+03      26      31 ..      34      39 ..       5      81 .. 0.57
   2 !   11.4   0.1   0.00024      0.39       1      33 [.     103     135 ..     103     144 .. 0.83
   3 !   11.6   0.1   0.00021      0.34       2      30 ..     141     169 ..     140     170 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
      HlyD_3 26 elleii 31
                 +++i+
  AJA92075.1 34 YVVKIL 39
                244444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
      HlyD_3   1 tlrApvdGvvvelnveegevvqagdelleiipp 33 
                 tlr+ + G+vv+++ve g  v +gd++ ++   
  AJA92075.1 103 TLRSQIPGKVVSIDVEDGAEVKKGDTVCTLESM 135
                 79*************************998754 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00021
      HlyD_3   2 lrApvdGvvvelnveegevvqagdellei 30 
                 ++A  dG+v+ ++++eg+ v+++d+++ i
  AJA92075.1 141 VKAQKDGIVKGIKIKEGNSVNKNDVIADI 169
                 89************************987 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2     2e+03      50      66 ..       3      19 ..       1      36 [. 0.72
   2 !   12.8   0.1   5.6e-05     0.092      44      68 ..     109     133 ..      98     141 .. 0.84
   3 !    6.4   0.1    0.0055         9      46      68 ..     148     170 .]     135     170 .] 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                ESS-TT-EEETTEEEEE CS
   QRPTase_N 50 llvkDGervekgdvlle 66
                ++v+D ++v  g++l +
  AJA92075.1  3 YKVQDSDEVVDGEILEK 19
                56777777777777644 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.6e-05
                 TTTEEEESS-TT-EEETTEEEEEEE CS
   QRPTase_N  44 pglevellvkDGervekgdvlleie 68 
                 pg  v++ v+DG++v+kgd+++++e
  AJA92075.1 109 PGKVVSIDVEDGAEVKKGDTVCTLE 133
                 788899****************998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0055
                 TEEEESS-TT-EEETTEEEEEEE CS
   QRPTase_N  46 levellvkDGervekgdvlleie 68 
                 +   +++k+G++v+k+dv++ ie
  AJA92075.1 148 IVKGIKIKEGNSVNKNDVIADIE 170
                 5555899*************986 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.85   1.4e+03      96     112 ..      25      42 ..       4      51 .. 0.64
   2 !   18.1   1.7   1.2e-06    0.0019      21      73 ..     100     151 ..      81     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.85
                 EEEEES-GGGGGG.SEEH CS
       GCV_H  96 iklklsnleelee.Llsa 112
                 +k+k++++e + + L + 
  AJA92075.1  25 YKIKIKDNEYVVKiLHTD 42 
                 467777777666644444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.2e-06
                 EE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
       GCV_H  21 GitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73 
                 G + +  +  g+vv++++ e+g++vkkg+++ ++Es K+   v a+ +G v  
  AJA92075.1 100 GQSTLRSQIPGKVVSIDV-EDGAEVKKGDTVCTLESMKMQVAVKAQKDGIVKG 151
                 556666677799*****9.68***************************99864 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.53   8.6e+02       9      25 ..      20      36 ..      15      46 .. 0.75
   2 ?   11.8   0.4    0.0001      0.16      37      57 ..     109     129 ..      99     129 .. 0.93
   3 ?    5.2   0.1     0.011        19      31      57 ..     140     166 ..     131     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.53
                SBHHHHHHHHHHTT--C CS
       PASTA  9 msvdeAkatLkalGlki 25
                +s+de+k  +k+++  +
  AJA92075.1 20 LSKDEYKIKIKDNEYVV 36
                68899999999888744 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                 TTBEEEECS-TTSEECTTS-E CS
       PASTA  37 eGtVisQsPeaGtevskgskv 57 
                 +G+V+s ++e G+ev+kg++v
  AJA92075.1 109 PGKVVSIDVEDGAEVKKGDTV 129
                 7******************98 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.011
                 ECTCCGTTBEEEECS-TTSEECTTS-E CS
       PASTA  31 tsddvpeGtVisQsPeaGtevskgskv 57 
                  ++ + +G V +  +++G +v+k++ +
  AJA92075.1 140 AVKAQKDGIVKGIKIKEGNSVNKNDVI 166
                 5677899****************9977 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.3      0.47   7.6e+02      13      59 ..      22      64 ..      10      79 .. 0.64
   2 ?   14.3   0.2   1.8e-05     0.029      86     136 ..     106     155 ..      98     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.47
     DUF2118 13 seeevevileeeeevekfadkveekklkgkvvYeelldeivdvleek 59
                ++ e+++ ++++e v+k++  +++ + +  v+ +e ++++  v  ++
  AJA92075.1 22 KD-EYKIKIKDNEYVVKILHTDSNVMEF--VLNNE-FHSVRYVDSQT 64
                33.7888888888888888877766633..33333.55544444444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
     DUF2118  86 ipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikee 136
                  ++ g +v++ v+ G +v++gdt+  + + k +v  ++a+++g+V  ik +
  AJA92075.1 106 SQIPGKVVSIDVEDGAEVKKGDTVCTLESMKMQV-AVKAQKDGIVKGIKIK 155
                 56778999**************************.69********877655 PP

>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   6.6e-05      0.11      31      79 ..      31      90 ..       9     108 .. 0.72
   2 ?   -0.5   0.0       0.9   1.5e+03      33      53 ..     127     147 ..     101     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
      PCC_BT 31 ekdwvvtvdgedet..........vtvk.veeaadevevkvdgksvkvssdwklgqplir 79
                 +++vv +  +d +          ++v+ v+ +++e+ + vdg+s++v+++ +l + +++
  AJA92075.1 31 DNEYVVKILHTDSNvmefvlnnefHSVRyVDSQTSEMNFIVDGSSMSVNMNSHLDDIVFK 90
                556666665543333333333333788845788889999999999999999999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.9
      PCC_BT  33 dwvvtvdgedetvtvkveeaa 53 
                 d v t++  + +v vk ++++
  AJA92075.1 127 DTVCTLESMKMQVAVKAQKDG 147
                 334444444455555554444 PP

>> DUF3114  Protein of unknown function (DUF3114)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6     5e-05     0.081     149     206 ..      19      76 ..       3      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-05
     DUF3114 149 KialkdnkviypdgaislNlKill..dfhsEFildseGnFlnelDaekatkngiiNGaSf 206
                 K++  + k+  +d+++   +Kil   ++ +EF+l++e + +  +D+++++ n i+ G+S 
  AJA92075.1  19 KLSKDEYKIKIKDNEY--VVKILHtdSNVMEFVLNNEFHSVRYVDSQTSEMNFIVDGSSM 76 
                 5443344444454444..456766558899****************************96 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.8     3e+03      34      46 ..      33      45 ..      11      63 .. 0.59
   2 ?    6.1   0.0     0.008        13      54      76 ..     114     136 ..      99     144 .. 0.84
   3 ?    3.7   0.1     0.043        70      53      72 ..     150     169 ..     143     170 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                   EEEEEEEECTCEE CS
  Peptidase_M23 34 Gnvviidhgdgys 46
                     vv i h+d  +
     AJA92075.1 33 EYVVKILHTDSNV 45
                   4566666655433 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.008
                    EESS-TTEEE-TTCEEEEEBSTS CS
  Peptidase_M23  54 kisvkegqkVkaGqvIGtvgstg 76 
                    +i+v+ g +Vk+G+++ t  s +
     AJA92075.1 114 SIDVEDGAEVKKGDTVCTLESMK 136
                    788*************9987655 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.043
                    SEESS-TTEEE-TTCEEEEE CS
  Peptidase_M23  53 skisvkegqkVkaGqvIGtv 72 
                    + i++keg  V++ +vI+ +
     AJA92075.1 150 KGIKIKEGNSVNKNDVIADI 169
                    56899************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1340.16
//
Query:       AJA92076.1  [L=345]
Description: diphthine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-16   60.5   0.0    3.4e-16   59.8   0.0    1.4  1  TP_methylase    Tetrapyrrole (Corrin/Porphyrin) Methylases
    4.7e-15   55.4   0.5    2.2e-14   53.3   0.3    2.1  2  DUF357          Protein of unknown function (DUF357)
  ------ inclusion threshold ------
        0.1   12.7   0.2       0.33   11.0   0.2    1.8  1  EFP             Elongation factor P (EF-P) OB domain
       0.11   12.3   0.0       0.41   10.5   0.0    1.8  2  Ala_racemase_C  Alanine racemase, C-terminal domain
       0.16   12.1   0.0       0.39   10.8   0.0    1.6  1  Antirestrict    Antirestriction protein


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   9.6e-20   3.4e-16       1     212 [.       1     220 [.       1     221 [. 0.76

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 9.6e-20
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaealaealragkdVvllvsGDPlvygtg 96 
                   +l+++G+G+ +   l+  +l+++k+a++v+ +    ++ + d  ++  +le+  g e +++ +   e+ +e+l  a +++   vl++ GDP++++t+
    AJA92076.1   1 MLWFIGLGISGISELSNSTLEVIKNAEIVYLES--FTSPISDTEKK--QLEDISGGEFKTAKRWlVEDGNEILENAKNRK--TVLISYGDPYIATTH 91 
                   699**************************9888..77777654333..23333333322222223444444444444443..9************** PP

  TP_methylase  97 selvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallangdtlvllkapr.k.....laelaelL..... 180
                    el +++ +   +ie+++i   s++++++  +g++ ++ g+vl+++   +++ ++  + +e+ll ++++++ll+  + k     +++++ lL     
    AJA92076.1  92 LELKTRAIR--DDIETRTIHSSSIVSSLIGEVGLHYYKVGKVLTIMndPKSMITPYNTIFENLLGKTHSVILLEYNEdKsffldPKDALSLLlntek 186
                   ****87777..89*********************************9877777788899**************777744787774444444444444 PP

  TP_methylase 181 ..kealyddttpvavveragtedervvrgtleel 212
                      +++  ++t ++v++r+g++ ++++ g+++ l
    AJA92076.1 187 tqNRKVISEETFAIVASRIGKDSQKIISGNISNL 220
                   42333677788****************9999865 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.47   1.7e+03      20      49 ..      43      73 ..      30      84 .. 0.58
   2 !   53.3   0.3   6.1e-18   2.2e-14       1      71 [.     273     339 ..     273     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.47
                TS---HHHHHHHHHHHHHH.HHHHHHHHTT- CS
      DUF357 20 esplgeaaeevlemaesYl.eDakyflekgd 49
                +++l++      + a+++l eD+++ le+ +
  AJA92076.1 43 KKQLEDISGGEFKTAKRWLvEDGNEILENAK 73
                4555555544444444443366666666544 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 6.1e-18
                 HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS CS
      DUF357   1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlg 71 
                 +Y+++++eal+++k   +  ++l+ ++e+vl +a+ Y+ Da+ fl++g+ + A+ s+ Ya G++Da++ ++
  AJA92076.1 273 KYVPMVREALAEIK---PHYENLK-EYEDVLINAKLYIDDAENFLKEGKKEYAVLSIGYADGLVDALRIAK 339
                 7*************...4444444.88****************************************9986 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   9.2e-05      0.33      18      46 ..     292     322 ..     289     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                 TTT--EEEEEHHHH.TTGCGG--TT-E.EEE CS
         EFP  18 netYeqielpkeql.gdaakfLkEgme.vtv 46 
                  + Ye + ++++    da++fLkEg + + v
  AJA92076.1 292 LKEYEDVLINAKLYiDDAENFLKEGKKeYAV 322
                 578*********6615666*****9765555 PP

>> Ala_racemase_C  Alanine racemase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.88   3.1e+03      18      31 ..      78      91 ..      67      97 .. 0.72
   2 ?   10.5   0.0   0.00011      0.41      27      49 ..     313     335 ..     307     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.88
                    SEESGGGSEE-SSS CS
  Ala_racemase_C 18 egvgYgatyvaerd 31
                      ++Yg  y+a+ +
      AJA92076.1 78 VLISYGDPYIATTH 91
                    45899999998876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                     E-SSSEEEEEES--GGGTCGGGG CS
  Ala_racemase_C  27 vaerdtriavvpiGYaDGlpral 49 
                       e +++ av++iGYaDGl  al
      AJA92076.1 313 LKEGKKEYAVLSIGYADGLVDAL 335
                     56778899**********98766 PP

>> Antirestrict  Antirestriction protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.39      14      53 ..     166     205 ..     162     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
  Antirestrict  14 sngglymaPesderlrlvvkengfegevSadAaGiivtll 53 
                   +++ +++ P+ + +l l+ +++++++ +S++++ i+++ +
    AJA92076.1 166 EDKSFFLDPKDALSLLLNTEKTQNRKVISEETFAIVASRI 205
                   6899********************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2748.53
//
Query:       AJA92077.1  [L=468]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-89  300.5   0.0    1.6e-89  299.9   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    4.2e-31  107.8   8.3    6.6e-31  107.2   8.3    1.3  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.9   0.0   1.8e-93   1.6e-89       2     270 ..       3     280 ..       2     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 299.9 bits;  conditional E-value: 1.8e-93
                 EEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESS....S. CS
                 xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
      GatB_N   2 viGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqke....ep 95 
                 +iGlEiH+ql++ +sKlF+ ++++  + epn+++++v+++lPG+lP+ln++ave+a ++alalnc+  e++ f RKnyfypdlpk++Qitq +    ++
  AJA92077.1   3 KIGLEIHCQLTKlESKLFCPCKANYREFEPNHNICPVCMGLPGSLPRLNQKAVESATSIALALNCQTPEKIAFFRKNYFYPDLPKNFQITQLNvygdMS 101
                 8*********988*********8766669**************************************************************75444367 PP

                 SEEEEEEEE.TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEE CS
                 xxxxxxxxx.xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N  96 lakeGslel.ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvS 189
                 +  eG++++  kk++i+ri+lEeD ++ ++    ++++ +lvd+nRaG+pL+Eivt+pd+++p+++r +++ l +ll+ lgv++ ++ eG++R+D NvS
  AJA92077.1 102 VGGEGYVDVeGKKIKIRRIQLEEDPGRLIYegasDRTKITLVDYNRAGTPLVEIVTDPDFENPRQVRIFLNILSDLLENLGVAEPGL-EGAMRADGNVS 199
                 8899999997799****************9888767789************************************************.7********** PP

                 ECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 190 vreeekgeeegtrvEiKnlnslksiekaieyeierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleisee 270
                 ++        g++vEiKn+ s++ +eka+++e +rq +l         eTr++d++++ tvs Rskee +dYryf e d+p ++i+++
  AJA92077.1 200 IEG-------GNKVEIKNIGSFHDLEKALHFELTRQQSLSerdidivMETRHWDDRRKITVSSRSKEEDQDYRYFLENDIPWVKIEQS 280
                 **4.......49***************************9*********************************************987 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   8.3   7.4e-35   6.6e-31       1     148 []     322     466 ..     322     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 7.4e-35
                 HHHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHH CS
   GatB_Yqey   1 dffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklve 99 
                 ++fe++ +e  +ak +an ++++++g +  ++++ ++ k+t ++l +l++ i+ ++I+ ++ak  l+e++++gk+ + i++e++L q+sd++e+ +++ 
  AJA92077.1 322 QLFENAYSEQ-NAKDIANLITTDVIGFIDTKEKQQTS-KITSKHLSDLIDAINAKTITRNSAKVALQEIVKSGKDTKLILQEMDLGQVSDSSEIDAIIS 418
                 6899999997.******************99998888.8************************************************************ PP

                 HHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
   GatB_Yqey 100 eviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                 ++++ +++av d k+++e  ++flvG+vM+ktkGkadp ++ el+k+kL
  AJA92077.1 419 QIFEDEKQAVIDAKERPE-TVNFLVGKVMQKTKGKADPVKTLELIKSKL 466
                 *****************6.99**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3430.93
//
Query:       AJA92078.1  [L=187]
Description: hypothetical protein T478_0658 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1336.97
//
Query:       AJA92079.1  [L=46]
Description: hypothetical protein T478_0333 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 351.82
//
Query:       AJA92080.1  [L=507]
Description: GMP synthase (glutamine-hydrolyzing) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-43  147.2   0.0      7e-43  146.6   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
      8e-34  115.6   0.1    2.6e-33  113.9   0.1    1.9  2  GMP_synt_C     GMP synthase C terminal domain
    4.1e-12   45.7   0.2    2.8e-06   26.6   0.0    2.2  2  NAD_synthase   NAD synthase
    1.1e-07   31.8   0.1      4e-07   30.0   0.1    2.0  1  Peptidase_C26  Peptidase C26
    0.00041   19.2   0.0     0.0023   16.8   0.0    1.9  2  tRNA_Me_trans  tRNA methyl transferase
     0.0014   18.3   0.0      0.033   13.8   0.0    2.2  2  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.029   14.4   0.0      0.048   13.7   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
       0.21   11.1   0.0        4.4    6.7   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   3.1e-46     7e-43       1     189 [.       5     185 ..       5     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 3.1e-46
                 EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEE CS
      GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgrkvvkekeke 99 
                 +++D+++++++ ++++++e+ v+ e+vp+d s ee +  ++np+gi++sgGp s++ e +++  +e+++ ++P+LGIC+G+Ql++++fg+kv +++ ke
  AJA92080.1   5 VVLDFGSQYSHLICRRIREFSVYAELVPYDISPEELQ--KMNPKGIIFSGGPSSVYNEDAPKPDEELFNFDLPLLGICYGHQLIVNKFGGKVKRAN-KE 100
                 589*****************************99995..79****************************************************999.56 PP

                 EEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
      GATase 100 hhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnflik 189
                 +      +++ +++ll g +++++++++H++e+++    p+++ev++++e++ + ++i + ++ ++g+QFHPE+++t++g+ +l+nf+++
  AJA92080.1 101 YGSSLLSMDK-NSGLLDGIGESIRAWMSHGDEAEE---IPSNFEVIGHTENS-HAAAIANIDRTVFGIQFHPEVVHTERGTDILKNFVLN 185
                 5555555555.88**********************...***********998.79999999999***********************876 PP

>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       5.5   1.2e+04      57      78 ..     351     372 ..     345     373 .. 0.77
   2 !  113.9   0.1   1.2e-36   2.6e-33       1      91 [.     415     505 ..     415     506 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 5.5
                 -HHHHHHHHHHHHHHSTT---E CS
  GMP_synt_C  57 pyevLekissrivnevkgvnrv 78 
                 + ++Le + +   +ev++v+r+
  AJA92080.1 351 NLKILEPLRELYKDEVRDVARI 372
                 5567777777778899999998 PP

  == domain 2  score: 113.9 bits;  conditional E-value: 1.2e-36
                 CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
  GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditskPpatiE 91 
                 eel +ag+y+k+wQa+a++ + k+vGv gd+R+y+ +v++R+v+s Damtad+++lp  vLekis+ri+ne+++v+ v y i+skPpatiE
  AJA92080.1 415 EELWDAGVYDKVWQAYAAVGDDKAVGVVGDERKYGRIVTVRVVDSIDAMTADWTRLPNGVLEKISNRITNEIDEVTWVSYVISSKPPATIE 505
                 68899*************************************************************************************9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.2e-09   2.8e-06       6      84 ..     196     276 ..     193     298 .. 0.77
   2 !   16.8   0.1   1.2e-06    0.0028     148     177 ..     355     384 ..     352     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                   HHHHHHHHHHCTT..SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHH CS
  NAD_synthase   6 vdflkeyvkkaga..kgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpi 84 
                   + f+++ vk+      +v+ G+SGG+DS+++a l  ka+g+ + +++ +  +    +e++e   ++ +n++++++ +d ++ 
    AJA92080.1 196 EGFVEKTVKEISEieGNVLCGVSGGIDSTVAALLIHKAIGDRQ-TGVFVDnGLLRLDESKEIEDMFKNNFSLNFHRVDSSEQ 276
                   56899999987655345677*******************7655.67777757778888888888888999999998886665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.2e-06
                   BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                   l+p+ el+K ev++ a+ l+vPe++lk++P
    AJA92080.1 355 LEPLRELYKDEVRDVARILGVPEKLLKRHP 384
                   68**************************99 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1   1.8e-10     4e-07     103     216 .]      71     168 ..      11     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.8e-10
  Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaeelrveAvaeDgviEa 198
                    + ++P+lgiC G+ql+   +GG++ ++ +e            +  s  ++++k+s l + +g e+i+    H    +e+ ++++v+ ++e     a
     AJA92080.1  71 NFDLPLLGICYGHQLIVNKFGGKVKRANKE------------Y-GSSLLSMDKNSGLLDGIG-ESIRAWMSHGDEAEEIPSNFEVIGHTENSHAAA 152
                    5579******************98766553............3.4778999**999999999.9******************************** PP

  Peptidase_C26 199 ieseeakafvlgvQwHPE 216
                    i  +++  +v+g+Q+HPE
     AJA92080.1 153 IANIDR--TVFGIQFHPE 168
                    *99994..6********9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-06    0.0023       2      34 ..     212     245 ..     211     271 .. 0.84
   2 ?   -0.2   0.0      0.15   3.4e+02     164     184 ..     354     374 ..     349     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeq.gyevigvflkl 34 
                    +v++++SgG+DS+vaa+l++++ g   +gvf+ +
     AJA92080.1 212 NVLCGVSGGIDSTVAALLIHKAiGDRQTGVFVDN 245
                    79*****************997357788998876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
  tRNA_Me_trans 164 llfPlgeltKeevrkiAkeag 184
                    +l Pl el K+evr++A+  g
     AJA92080.1 354 ILEPLRELYKDEVRDVARILG 374
                    5669************98665 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.5e-05     0.033       3      39 ..     210     247 ..     208     307 .. 0.80
   2 ?    2.2   0.0     0.051   1.1e+02     134     161 ..     348     375 ..     339     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
        ThiI   3 qgkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknep 39 
                 +g+vl+ +SgGiDS Vaa l+ k  G r   v+++n +
  AJA92080.1 210 EGNVLCGVSGGIDSTVAALLIHKAiGDRQTGVFVDNGL 247
                 699***************99876435555555555555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.051
        ThiI 134 avvnllilrPLigldKeeiiklAkeigt 161
                 +  nl il+PL  l K+e+ ++A+ +g 
  AJA92080.1 348 EWLNLKILEPLRELYKDEVRDVARILGV 375
                 56799******************99885 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.048       5      76 ..     216     289 ..     212     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                  E--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB.-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-T CS
  PAPS_reduct   5 svsgGkdslVllhLalkafkpv.pvvfvdtghe.fpetiefvdeleeryglrlkvyepeeevaekinaekhgss 76 
                   vsgG+ds+V   L+ ka  ++ + vfvd g    +e  e  d +++++ l+++ +++ e++  k++  + +++
   AJA92080.1 216 GVSGGIDSTVAALLIHKAIGDRqTGVFVDNGLLrLDESKEIEDMFKNNFSLNFHRVDSSEQFLSKLKGITDPEQ 289
                  68*******************6379*****97525777777777788889998888888888888777776665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.002       4.4       3      22 ..     214     233 ..     212     285 .. 0.81
   2 ?    2.0   0.0     0.057   1.3e+02     144     177 ..     336     377 ..     316     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.002
                 EEE--SSHHHHHHHHHHHHH CS
        QueC   3 vvllSGGlDSttvlalakke 22 
                 ++ +SGG+DSt++++l +k+
  AJA92080.1 214 LCGVSGGIDSTVAALLIHKA 233
                 6779********99888775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.057
                 HHHH........HTS--EEE-TTTT--HHHHHHHHHHTTHHH CS
        QueC 144 lnlg........edkkieieaPlidlsKaeivklgkelgvpl 177
                 +  +        e+ +++i  Pl +l K e+  ++  lgvp 
  AJA92080.1 336 VIKShhnvgglpEWLNLKILEPLRELYKDEVRDVARILGVPE 377
                 3333344446668899*******************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3756.66
//
Query:       AJA92081.1  [L=412]
Description: HD domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.6   0.2    3.8e-16   59.4   0.2    1.7  1  HD        HD domain
     0.0041   16.9   0.9      0.023   14.4   0.0    2.2  2  HD_2      HD containing hydrolase-like enzyme
     0.0069   16.1   0.0       0.04   13.6   0.0    2.0  2  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.024   14.1   0.0    1.4  1  HDOD      HDOD domain
      0.032   14.1   0.4      0.032   14.1   0.4    2.1  3  PIN_8     PIN like domain
      0.076   13.4   5.6        3.8    7.9   0.5    2.8  2  NusA_N    NusA N-terminal domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.2   1.3e-19   3.8e-16       1     121 [.      54     173 ..      54     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 1.3e-19
                 HHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHH.HHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH CS
          HD   1 rleHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekk.eeefekflaHekvgaeilrevekrlgldledvaklirehheswe 93 
                 r+eHsl+V+++a++ + +l+       +d + ++laaLlHDiG+gpf++ fe+  ++++++   He++g ei+ ++         ++ ++i++ ++++ 
  AJA92081.1  54 RFEHSLGVMHIAGMAGTSLASkkqmpGTDIDDIRLAALLHDIGHGPFSHLFEEVlQKKKRI--THEQIGKEIILKS---------EIGDIISKTTDKKK 141
                 79***************************************************96544555..9***********9.........56666666666666 PP

                 HHHHH....HHHHCCTSCHHHHHHHHHHHHHH CS
          HD  94 gkkrp....rglaerqlslearivklaDrlaa 121
                 ++       ++  e ++++ a+ ++ +D+l +
  AJA92081.1 142 INRLAvgegSKQFENEIISGALSADMMDYLLR 173
                 55434443237777888888888888888876 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.9e-06     0.023       3      68 ..      31      97 ..      29     173 .. 0.77
   2 ?    0.6   0.2      0.14   4.2e+02     137     177 ..     295     338 ..     248     342 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.9e-06
        HD_2  3 fallsrlkyieRwalmrntreenvaeHslevaliahalal.ienkkfggkldaerlallalyHDasE 68
                f+ l+r+k ++   l +   +++  eHsl v  ia + ++ +++kk     d++ + l+al+HD+  
  AJA92081.1 31 FQRLRRIKQLSGAHLTYPGAQHTRFEHSLGVMHIAGMAGTsLASKKQMPGTDIDDIRLAALLHDIGH 97
                667788888888889999999***************99987888887779**************865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.14
        HD_2 137 alikcleelka.gnkeF.eeakkeieeklkel.elpevdyFlee 177
                  l kc+ e++  g k F +++ k+ ++ +++  +l e ++F+++
  AJA92081.1 295 KLFKCVFEKTIsGKKTFgKNTLKQFRADIAKKsKLAENQIFIDT 338
                 57899888775155558345678888888776369999999876 PP

>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.4e-05      0.04       4     116 ..      55     168 ..      53     173 .. 0.85
   2 ?   -1.4   0.0      0.54   1.6e+03      44      60 ..     185     200 ..     176     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                 HHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT--S--HHHHHHCT-HHHHHCCC...SSHHHHHHHHHHHHHHTSGGG-TTTTS-HHH. CS
    PDEase_I   4 frHAadVlqalfyllkkeklkeeltpleilalliaalcHDvdHpGtnNsFlvnskselailYnd...esvLEnhHlalafqllkkeecnifknlskee. 98 
                 f H++ V+++  +  ++   k+++   +i  + +aal HD++H  ++  F+   +++  i +++   e +L +   +++ + + k++ n ++     e 
  AJA92081.1  55 FEHSLGVMHIAGMAGTSLASKKQMPGTDIDDIRLAALLHDIGHGPFSHLFEEVLQKKKRITHEQigkEIILKSEIGDIISKTTDKKKINRLAVG---Eg 150
                 78*******************9999999999*******************99999999888887664668888888888888888877777666...44 PP

                 HHHHHHHHHHHHHTTSGG CS
    PDEase_I  99 ykelrkliielIlaTdma 116
                  k++++ ii+  l+ dm 
  AJA92081.1 151 SKQFENEIISGALSADMM 168
                 788888888888888886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.54
                 TT--S--HHHHHHCT-H CS
    PDEase_I  44 vdHpGtnNsFlvnskse 60 
                 +dH+  +NsF+v  + +
  AJA92081.1 185 IDHNRITNSFEVYKN-K 200
                 8999999*9999654.3 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.1e-06     0.024     103     151 ..      66     116 ..      34     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.1e-06
                 HHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHH CS
        HDOD 103 Alvarelaeelgledp..eeaflaGLLhdiGklvllsllpeeleellekva 151
                 +++ + la++ +++ +  +++ la+LLhdiG   + +l++e l++  + ++
  AJA92081.1  66 GMAGTSLASKKQMPGTdiDDIRLAALLHDIGHGPFSHLFEEVLQKKKRITH 116
                 444566777776666456**********************99998766443 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.72   2.2e+03     137     165 ..     128     157 ..     100     167 .. 0.47
   2 ?   -2.8   0.0       1.5   4.6e+03      95     110 ..     186     201 ..     141     215 .. 0.68
   3 ?   14.1   0.4   1.1e-05     0.032      23     112 ..     238     338 ..     225     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
       PIN_8 137 llegkigealskeel.eelvkegekRyenk 165
                  +++ i++  +k+++ + +v eg k +en+
  AJA92081.1 128 EIGDIISKTTDKKKInRLAVGEGSKQFENE 157
                 223334445555555333445555555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
       PIN_8  95 lrkelkkqleelkeel 110
                  ++++ +++e +k++l
  AJA92081.1 186 DHNRITNSFEVYKNKL 201
                 3667777777777777 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.1e-05
       PIN_8  23 llkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkald.........teelrkelkkqleelkeel.. 110
                 ll+++   +d+l ++   a+E++++ +++i ++ +++ ++++el+++kk a++ ++++l k+  +k+++          +++r+++ k+ + +++++  
  AJA92081.1 238 LLEAMSLADDHLGLSSMNAQEYVKQTDDTILEKLTSLPETNSELKAAKKIANDYQDRKLFKCVFEKTISgkktfgkntLKQFRADIAKKSKLAENQIfi 336
                 6778888899******************************************99999999999999999877777777777777777777777777755 PP

       PIN_8 111 ka 112
                  +
  AJA92081.1 337 DT 338
                 33 PP

>> NusA_N  NusA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.2    0.0024       7.1      64     110 ..     106     153 ..     100     160 .. 0.79
   2 ?    7.9   0.5    0.0013       3.8      13     119 ..     152     331 ..     149     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                 S-S-TTTEEEHHHH.HCCSTT--TTBEEEEE----SSCCHCHHHHHHH CS
      NusA_N  64 evedpekeIsleea.kkidpkikvGdtveeevtpkdfgriaaqtakqv 110
                 ev +++k I+ e+  k+i  k ++Gd++++  ++k+++r+a+ +  + 
  AJA92081.1 106 EVLQKKKRITHEQIgKEIILKSEIGDIISKTTDKKKINRLAVGEGSKQ 153
                 4556778899999955699999********9999******98765555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
                 S---HHHHHHHHHHHHHHHHHCC.T-SS.S-EEEEE-TTT--EEEEEEEEEESS-S........................................... CS
      NusA_N  13 kgiskevviealeeaLakaykkn.yged.enveveidretgeikvyskktVveeve........................................... 66 
                 k+ + e++  al + +   + ++ y ++ e+++++ +r t+ ++vy++k   ++                                             
  AJA92081.1 152 KQFENEIISGALSADMMDYLLRDgYFTGaEHAKIDHNRITNSFEVYKNKLALQSSAlvnfetmmisrfqmfkavyfhktvragevmlleamsladdhlg 250
                 56667777777777777777776555664669*****************99954223446667777888888888888888999999999999888888 PP

                 .......................-TTTEEEHHHHHCCSTT--...TTBEEEE.E-.---SSCCHCHHHHHHHHHHHHHHHC CS
      NusA_N  67 .......................dpekeIsleeakkidpkik...vGdtvee.ev.tpkdfgriaaqtakqvivqkireae 119
                                         pe++ +l+ akki  +++   + + v e  +  +k fg+ + ++++  i++k + ae
  AJA92081.1 251 lssmnaqeyvkqtddtilekltsLPETNSELKAAKKIANDYQdrkLFKCVFEkTIsGKKTFGKNTLKQFRADIAKKSKLAE 331
                 888888888888888887777777778888888888866664222555555534465688888888888888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3156.77
//
Query:       AJA92082.1  [L=88]
Description: hypothetical protein T478_0651 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.039   14.1   4.3       0.11   12.6   4.3    1.7  1  Zn-ribbon_8  Zinc ribbon domain
       0.12   12.5   1.0       0.15   12.1   1.0    1.1  1  HypA         Hydrogenase/urease nickel incorporation, metallo


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.3   1.2e-05      0.11       6      40 .]      62      87 ..      58      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
  Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevrrvi 40
                 Y+C  C+++++++          CP+Cgs+++r i
   AJA92082.1 62 YECLVCHKVYNARE---------CPRCGSTMKRAI 87
                 99999999999554.........*********976 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   1.6e-05      0.15      69      96 ..      60      83 ..      54      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                -EEEETTTS-EEECHHHHHS-TTTSSS- CS
        HypA 69 vkvrCreCgkefeleekalrCpkCgsad 96
                +k++C +C+k ++ +    +Cp+Cgs+ 
  AJA92082.1 60 IKYECLVCHKVYNAR----ECPRCGSTM 83
                6899*****999965....7*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 695.66
//
Query:       AJA92083.1  [L=344]
Description: putative 3-isopropylmalate/3-methylmalate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-80  271.5   0.1    1.3e-80  271.2   0.1    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.2   0.1     7e-85   1.3e-80       1     348 []       4     334 ..       4     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 271.2 bits;  conditional E-value: 7e-85
                 EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS....SSS-HHHHHHHHHSSEEEEEE---.CSSSSSSHHHHHHHHHHHTTE CS
      Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg....eplpeetleaikeadvvllgavgt.pkekevrpengLlaLrkeldl 94 
                 k+a+++gdgiGpe+v+a++ +lk+ +    l+ e+  +d+G ++ ++ g    + +pe t+  ++e d+  +g+++t pk++  r+    ++Lr++++l
  AJA92083.1   4 KVAIMKGDGIGPEIVDAMTGILKECN----LQSEMVFCDAGSEQWEKNGskdaSYIPESTMTTLEEVDACFKGPTTTiPKPGAPRSVA--VTLRQKFEL 96 
                 699**********************9....4445677889999988888666678*******************99856788888888..99******* PP

                 EEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHH CS
      Iso_dh  95 fanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlkss 193
                 fan+rpvk f   k  +p ++     vd+v++Re+t+g+Y g e++ ++      +a+ + ++s+++ +r++  a++ A+k + +kv++++K+n+lk++
  AJA92083.1  97 FANIRPVKTF---KRLTPNRN-----VDFVCFREATEGLYTGVETQLNED-----TAIAIRKISRKGCSRFMDSALDWAKKYELNKVVAITKRNILKKT 182
                 **********...67788885.....9*******************9997.....7******************************************* PP

                 H.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGS..EEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S- CS
      Iso_dh 194 e.lwrkiveevaeeeypdielehqlvDsaamqlvkspkqfd..VivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaN 289
                 + l+ ++ve+ ++  +p++el++ ++D++a+qlv +p+qf+  V+v +Nlf Di+S +a+ +vGs+Gl+ S+++g k  a+fEa+HGsap + g++k+N
  AJA92083.1 183 DgLFFEEVEKSVK-SFPNMELQEIYIDNMAQQLVINPEQFNnsVLVSTNLFMDIISELASGIVGSIGLIYSSNMG-KDYAMFEAAHGSAPSFKGQNKVN 279
                 ************9.*************************9999********************************.68********************* PP

                 THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
      Iso_dh 290 piavilSaalmLryslgleeaAdkiekAvekvlea.givTkDlageaakevstsefgdav 348
                 p+a++l+ a m  y lg+ +  d+i +A ++ +++ ++vT D++gea    +t+++ +++
  AJA92083.1 280 PTATVLAGAWMADY-LGERDIRDAIFSATDQIINEgKYVTFDIGGEA----TTTQMSEKI 334
                 **************.********************899********9....777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2481.16
//
Query:       AJA92084.1  [L=309]
Description: aspartate carbamoyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-42  144.8   0.0    3.5e-42  143.9   0.0    1.4  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    5.4e-30  104.5   0.0    8.6e-30  103.9   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
  ------ inclusion threshold ------
      0.016   15.4   0.4        1.9    8.8   0.0    2.5  2  DUF2149   Uncharacterized conserved protein (DUF2149)


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   5.8e-46   3.5e-42       2     147 ..      12     151 ..      11     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 5.8e-46
                 -BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTGGSTTSSCHHHHHHHHHHH CS
    OTCace_N   2 hllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssvskgrkEsleDtarvlsry 100
                 +++s++dlsk+++ee++++ +e+ e + +e+++++++gktl+ lF+epStRTr+Sf++A++ lGg+   + +a    +ssv+kg  Esl+Dt+r++s+y
  AJA92084.1  12 DIISIRDLSKDNLEEIYSKTNEIIEMK-AEERREIARGKTLGYLFFEPSTRTRLSFQSAMALLGGTSFGIADA---TSSSVQKG--ESLADTVRIMSGY 104
                 689********************9876.58999*************************************966...56899***..************* PP

                 TSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
    OTCace_N 101 vdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                 +daiv+Rh+  g+   +  a+ +s p+iNag+g++eHPtQa+ Dl+ti+
  AJA92084.1 105 TDAIVLRHSldGS--SKFAAEVSSKPIINAGSGTEEHPTQAIQDLYTIK 151
                 *********8766..66668999************************97 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.0   1.4e-33   8.6e-30       1     156 [.     158     306 ..     158     307 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.4e-33
                 CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHH...HHHHH CS
      OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekere...erlkk 95 
                 +g++i +vGd k+++++ sl+++l+ ++++v+l++P++l+   +   ++k+     + s+t +e+l e +++ Dv+y ++++     ker+   e++ k
  AJA92084.1 158 DGKNIGIVGDlKYGRTVYSLLYGLSNYDVNVHLISPESLKIRSDSTYNLKE-----NLSYTESENLDEYIEDLDVLYVTRIQ-----KERFpdeEEYVK 246
                 599***********************************9997777655555.....6899**********************.....666666688888 PP

                 HCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
      OTCace  96 lkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                 +k+ y + +++++++k+d i+lH+LP  r +E++++V++s+++ +f+qae++ +t++A+l l
  AJA92084.1 247 VKGsYVIGQDVVNKMKDDSILLHPLP--RIDEISTDVDSSKQAKYFQQAEYGKFTRAAILSL 306
                 8888**********************..9******************************987 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00032       1.9      30      79 ..       7      54 ..       1      61 [. 0.86
   2 ?    4.5   0.1    0.0071        42      55      89 ..     140     175 ..     119     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00032
     DUF2149 30 ellsseedvtvvkkpgkekmeiivkegeelkkakesaekasgkGerlGta 79
                ++   ++d+  +++ +k+++e i+ +++e+ ++k +++ +  +G+ lG  
  AJA92084.1  7 NFS--QNDIISIRDLSKDNLEEIYSKTNEIIEMKAEERREIARGKTLGYL 54
                333..6899999999********************************975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0071
     DUF2149  55 egeelkk.akesaekasgkGerlGtayrlkdGkliy 89 
                 +++ +++ ++ ++e ++ +G+++G++  lk G+++y
  AJA92084.1 140 PTQAIQDlYTIKKELGKIDGKNIGIVGDLKYGRTVY 175
                 467888888999999999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2238.39
//
Query:       AJA92085.1  [L=176]
Description: SNARE-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-21   77.5   6.7    1.2e-21   77.4   5.3    1.7  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.041   7.3e+02      62      90 ..      18      46 ..       5      61 .. 0.64
   2 !   77.4   5.3   6.8e-26   1.2e-21       2     119 ..      37     165 ..      33     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
  SNARE_assoc 62 lverygflallllrllpivPrdlvnyvaG 90
                 ++    fla+ll  ++p +P+ +v  +aG
   AJA92085.1 18 YLYTGVFLAALLETIIPPIPTMAVFPTAG 46
                 33344555666666666666665555554 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 6.8e-26
  SNARE_assoc   2 PsevllvaaGvlf........glllgtlvtslgallGaslayllgrylgr....kalrrkllsekrvkalerlverygflallllrllpivPrdlvny 87 
                  P+ ++  +aG+++          +l  +v  lga++G+++ yl++ +lgr    ++l++  +sek+++++er++e+yg +a+l++r++p++ r ++++
   AJA92085.1  37 PTMAVFPTAGFIAsqnglsvaEAVLLGIVGGLGASIGSTVIYLIALKLGRtallRYLGKFRISEKKLEKVERWFEKYGDKAVLFGRMVPVF-REMISV 133
                  555556667777766655555666699999***********************************************************98.****** PP

  SNARE_assoc  88 vaGltrvsfkrFflatfiGsipwalvyaylGs 119
                  +aGl+++s+k+F+++t++Gs  w +  +++G+
   AJA92085.1 134 PAGLLKMSVKKFLAYTILGSCSWGVTMVLIGY 165
                  ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1310.59
//
Query:       AJA92086.1  [L=330]
Description: dTDP-glucose 4,6-dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-76  256.0   0.2    6.7e-76  255.8   0.2    1.0  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    2.9e-55  187.4   0.0    3.8e-55  187.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      6e-19   68.1   0.5    7.9e-19   67.7   0.5    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.2e-14   51.6   0.0    1.2e-13   50.9   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    4.5e-12   45.7   0.4    5.1e-11   42.2   0.4    2.2  1  NAD_binding_4    Male sterility protein
    6.6e-12   45.2   0.1    3.5e-11   42.8   0.1    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.7e-05   24.8   0.0    0.00016   21.6   0.0    2.0  2  NAD_binding_10   NAD(P)H-binding
     0.0012   19.2   0.4     0.0036   17.6   0.0    2.0  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.039   13.4   0.3       0.14   11.6   0.3    1.8  1  adh_short        short chain dehydrogenase
       0.11   12.5   0.0       0.18   11.7   0.0    1.3  1  KR               KR domain


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.8   0.2   3.7e-79   6.7e-76       1     332 []       4     302 ..       4     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 255.8 bits;  conditional E-value: 3.7e-79
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    L+TG+ GfiGs+++ ++l+++ +vh++ + +++++ ++ ++l++    e+++n++++kg++++++ +e+ + ++  d+v+n+AA+s+Vd+s++++ 
     AJA92086.1   4 LVTGGLGFIGSNFILKILNENNDVHIT-NVDAELDGSNRKNLQN---LENSNNYEFFKGNISNKKLMEEQITKC--DAVVNFAAESFVDRSINDAN 93 
                    9***********************975.6666667777777764...345789****************99987..9******************* PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf 192
                     ++  n+ G++++L++i +    +k+r++q+St+Ev+G+++    tE+t+f+P sPYaa+K++a+ i+ +y  +++  ++++++ n+++pr+   f
     AJA92086.1  94 PFLVSNIRGAFTILDIITK----QKKRMIQISTDEVFGSLSTGTATEQTKFNPSSPYAATKAAAELIINSYSTTFDSDVIITRCTNNYGPRQ---F 182
                    *****************76....568*****************************************************************6...* PP

                    CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTG CS
  GDP_Man_Dehyd 193 vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgk 288
                     +++i+++++ + ++k +++++Gn++++Rdw +v+D+++a+ l+l ++k       +ge+++v   +e++++ ++k+i   ++            k
     AJA92086.1 183 AEKLIPKTIMLAYQNK-KIPIYGNGKNVRDWIYVDDHCDAVSLALFNGK-------KGESYNVSAYNEINNITIVKKILDIMD------------K 258
                    *********9988877.7889************************9998.......8*******************9976532............2 PP

                    GCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
  GDP_Man_Dehyd 289 vvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                     +  ++++ +rpg++ ++ +d +k+ +eL Wk k +f+++++++
     AJA92086.1 259 SEDLIEFVEDRPGHDFRYSMDSQKISTELKWKTKLNFKDGLEKT 302
                    33468899********************************9986 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.0   2.1e-58   3.8e-55       2     240 ..       4     237 ..       3     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 2.1e-58
                 EEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHT CS
   Epimerase   2 lVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknl 92 
                 lVtG+ GfiGs+++ ++l+++  ++++++d + ++sn+++l++l      e+ ++++ +++ +e+ +   ++dav+++Aa++ v++s++d++ f+ +n+
  AJA92086.1   4 LVTGGLGFIGSNFILKILNENndVHITNVDAELDGSNRKNLQNLensnnyEFFKGNISNKKLMEEQIT--KCDAVVNFAAESFVDRSINDANPFLVSNI 100
                 9************9999999956668899999999999999999*********************999..9**************************** PP

                 HHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHH CS
   Epimerase  93 qgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalir 191
                 +g+ ++l+ + k++  r++++s++ev+G   +   +e+t   +++p+spYaa+K+a+e ++ +y  +++ ++ii+r++n+yGpr   ++ +++ip+ i 
  AJA92086.1 101 RGAFTILDIITKQKK-RMIQISTDEVFGSLSTGTATEQT---KFNPSSPYAATKAAAELIINSYSTTFDSDVIITRCTNNYGPR---QFAEKLIPKTIM 192
                 ***********9999.************99995477777...******************************************...99********** PP

                 HHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
   Epimerase 192 kilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                  ++++k ++ ++g+g+++Rd++yv+D+++a+ l+l +   g+kge yn+
  AJA92086.1 193 LAYQNK-KIPIYGNGKNVRDWIYVDDHCDAVSLALFN---GKKGESYNV 237
                 ******.******************************...9999****8 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.5   4.4e-22   7.9e-19       1     228 [.       4     225 ..       4     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 4.4e-22
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegvdvvihlaslvdvagklte.deimkvnvkG 95 
                 +vtGg GF+G++ + +++++++  ++  +D + + + +++l+++++ +   + +g + +k+ +ee + + d+v+  a+ + v   +++ + +   n++G
  AJA92086.1   4 LVTGGLGFIGSNFILKILNENNDVHITNVDAELDGSNRKNLQNLENSNnyeFFKGNISNKKLMEEQITKCDAVVNFAAESFVDRSINDaNPFLVSNIRG 102
                 69*******************977777788666655555555444444444**************************999998866551667888**** PP

   3Beta_HSD  96 TrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kllvpl 192
                   ++l+  +k+  ++++  S+ ev g       +  g  +++ + +++++y+ +Ka aE  ++++  +t+     ++T   R +  yG+++  ++l p 
  AJA92086.1 103 AFTILDIITKQK-KRMIQISTDEVFGS------LSTGTATEQTKFNPSSPYAATKAAAEL-IINSYSTTFDSD-VIIT---RCTNNYGPRQfaEKLIPK 189
                 ******998877.88999***999998......77777788888999*********9995.556666455544.4555...88999***9644667777 PP

   3Beta_HSD 193 lkqlaklglalfkigdeevlsdrvYvgNvawahilA 228
                    la +++++  +g+ +++ d++Yv+   +a  lA
  AJA92086.1 190 TIMLAYQNKKIPIYGNGKNVRDWIYVDDHCDAVSLA 225
                 777777777*****************9988888777 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   6.6e-17   1.2e-13       1     154 [.       1     179 [.       1     203 [. 0.79

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 6.6e-17
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.T--TTSHHHHHHHH....................HHH--SEEEE------HHHHHHSHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.eldltdaeavaell....................keakpdvvvnaAAytavDkaEseeeaay 75 
                    m++lvtG+ G +Gs+ + ++ +e+ +v+ ++ + eld ++++++++l                     + +k+d+vvn AA   vD+  ++ +   
     AJA92086.1   1 MRLLVTGGLGFIGSNFILKILNENNDVHITNVDaELDGSNRKNLQNLEnsnnyeffkgnisnkklmeeQITKCDAVVNFAAESFVDRSINDANPFL 96 
                    89*************8877777776777776555555555555555555555555555555555555444569*********************** PP

                    HHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-S....SEEEEEE-SEESS CS
  RmlD_sub_bind  76 avnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagk....kalivRtswvyge 154
                      n +++ ++ +  ++ +  +i++StD VF    +   +e+ + +P + Y++tK+a E  +++++     +++i R +  yg 
     AJA92086.1  97 VSNIRGAFTILDIITKQKKRMIQISTDEVFGSLSTGTATEQTKFNPSSPYAATKAAAELIINSYSTtfdsDVIITRCTNNYGP 179
                    *************************************************************9965412225677777777765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.4   2.8e-14   5.1e-11       1     256 [.       5     221 ..       5     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.8e-14
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+ GF+G+ ++ k+L+++++v+i+  v         + l +   +k+l++ ++   +++ ++ +G++s+++l      ++e + ++d++++ aA
     AJA92086.1   5 VTGGLGFIGSNFILKILNENNDVHITN-V--------DAEL-DGSNRKNLQNLEN---SNNYEFFKGNISNKKL------MEEQITKCDAVVNFAA 81 
                    7********************855543.2........2333.3334445555555...788999******9985......77778999******** PP

                    S-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHH CS
  NAD_binding_4  97 tvnfdepyke...llrvNveGtrevlelakklkklkvllhvST.ayvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvr 188
                       +d+++++   +l  N++G+  +l++ +k   +k ++++ST  ++   ++g                 + +++++ + +  Y  +Ka+aE +++
     AJA92086.1  82 ESFVDRSINDanpFLVSNIRGAFTILDIITKQ--KKRMIQISTdEVFGSLSTG-----------------TATEQTKFNPSSPYAATKAAAELIIN 158
                    **999988884446789************955..456******5555555554.................56888999****************** PP

                    HHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB---TT--EEEHHHHHHH CS
  NAD_binding_4 189 earrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgdkeavldlvpvDyvana 256
                    +++   +  v+i R+++ +g     ++ ++ l++++++ +++ +++p i+g+ ++v d++ vD  ++a
     AJA92086.1 159 SYSTTFDSDVIITRCTNNYGPR---QFAEK-LIPKTIMLAYQNKKIP-IYGNGKNVRDWIYVDDHCDA 221
                    *****9*********9988833...33444.47999**********9.99999999999999977776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   1.9e-14   3.5e-11       1     267 [.       3     271 ..       3     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.9e-14
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-.HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerd.ElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlv 93 
                      +lvtG+ G iGs+++ +il+++   + + + d El   + +k+l++  ++++++++     g++ +k+ +e+ ++  k+d+v++ AA   V   
       AJA92086.1   3 LLVTGGLGFIGSNFILKILNENND-VHITNVDaELDG-SNRKNLQNLENSNNYEFF----KGNISNKKLMEEQIT--KCDAVVNFAAESFVDRS 88 
                      59*****************98765.555444404443.334445555555556555....8**************..***************99 PP

                      HHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT CS
  Polysacc_synt_2  94 eenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlg 173
                       + +   +  N+ g+ +++++ +++  k+++ iStD                 nP + + atK++ae+++ +++++    ++ ++++R  N  g
       AJA92086.1  89 INDANPFLVSNIRGAFTILDIITKQ-KKRMIQISTDEVfgslstgtateqtkFNPSSPYAATKAAAELIINSYSTTF---DSDVIITRCTNNYG 178
                      999999*************987665.599*******8522222222233333589999***********99999888...7899999*999999 PP

                      GTT...SSHHHHHHHHHTTSSEEES.-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE-- CS
  Polysacc_synt_2 174 SrG...SviplFkkqikeggpvtvT.dpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitG 263
                       r     +ip+      +++++++  + + +R ++ +++ ++ v  al ++k+ge + + + + ++ + ++k+++++++++e+      i+++ 
       AJA92086.1 179 PRQfaeKLIPKTIMLAYQNKKIPIYgNGKNVRDWIYVDDHCDAVSLALFNGKKGESYNVSAYNEINNITIVKKILDIMDKSED-----LIEFVE 267
                      98533379999999999*******6266899************************9988888889888999999899876544.....466776 PP

                      --TT CS
  Polysacc_synt_2 264 lRpG 267
                       RpG
       AJA92086.1 268 DRPG 271
                      7776 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   8.8e-08   0.00016       1     134 [.       7     159 ..       7     172 .. 0.70
   2 ?    0.7   0.0      0.23   4.1e+02      59      88 ..     217     259 ..     198     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.8e-08
                     TTTSHHHHHHHHHHHHC-.T-EEEEE.....ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHH............ CS
  NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtal.....vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeeg............ 77 
                     G+ G +G+  + ++l+++ ++++t +       n + l++le++++ e ++g++++++ ++e ++ +daVv  ++ +  d+ +            
      AJA92086.1   7 GGLGFIGSNFILKILNENnDVHITNVdaeldGSNRKNLQNLENSNNYEFFKGNISNKKLMEEQITKCDAVVNFAAESFVDRSIndanpflvsnir 101
                     7778899988888888876555444421111346889999**99*************************98888555443333444556766667 PP

                     .HHHHHHHHHHCT--EEEEEEETTTTSGCG.CHHHHHHHHCCHHHHHHHHHHHHHHHHS CS
  NAD_binding_10  78 .aknivdaakeagvkRfvlvsaigvgdevp.gefgewnkellkaylaakraaeellras 134
                      a +i+d   + + kR++ +s+  v  +   g+  e +k + ++ +aa +aa+el+ +s
      AJA92086.1 102 gAFTILDIITK-QKKRMIQISTDEVFGSLStGTATEQTKFNPSSPYAATKAAAELIINS 159
                     79999998876.569*******8886543304444444545666666666666666554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.23
                     TT-SEEEES---TCC....HHHH...........HHHHHHHHHHC CS
  NAD_binding_10  59 kgadaVvsalggggk....deeg...........aknivdaakea 88 
                     +++daV  al +g+k    +  +           +k+i+d ++++
      AJA92086.1 217 DHCDAVSLALFNGKKgesyN--VsayneinnitiVKKILDIMDKS 259
                     689******96666644441..14445556667799999988875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     2e-06    0.0036       2      78 ..       4      81 ..       3      91 .. 0.82
   2 ?   -2.3   0.0       2.8   4.9e+03      51      81 ..     134     164 ..     105     175 .. 0.50
   3 ?   -3.3   0.0       5.6     1e+04      44      65 ..     243     264 ..     233     269 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                     EEE--.SHHHHHHHHHHH.CTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
  Sacchrp_dh_NADP  2 liiGa.GsvGqavaella.rhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnlsp 78
                     l+ G+ G++G+ ++ +++ +++dv  +it +d ++++ ++   +   ++ + e+ + +++n++  +++ +++ d+vvn + 
       AJA92086.1  4 LVTGGlGFIGSNFILKILnENNDV--HITNVDAELDGSNRKNLQNleNSNNYEFFKGNISNKKL-MEEQITKCDAVVNFAA 81
                     566777****97766655055666..*********9988877776789999************8.*************886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                      EEE--TTTHHHHHHHHHTTSSEEEE-SSGGG CS
  Sacchrp_dh_NADP  51 aialdaenyeavLaallkegdlvvnlsppis 81 
                      a++ ++ n+++  aa  + ++l++n    ++
       AJA92086.1 134 ATEQTKFNPSSPYAATKAAAELIINSYSTTF 164
                      3344444444422233333466666555554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.6
                      HTTTCEEEEE--TTTHHHHHHH CS
  Sacchrp_dh_NADP  44 algvrfeaialdaenyeavLaa 65 
                      ++++++ ++ ld++++++ L +
       AJA92086.1 243 INNITIVKKILDIMDKSEDLIE 264
                      3566666666777776665555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   7.9e-05      0.14       4     163 ..       4     160 ..       2     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.9e-05
                 EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHH CS
   adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseee 100
                 lvtG+ + IG ++  ++++e+ +v +++  +e      k+l+++  ++++ ++++++++++ +e+ + k+       d++vn A+     +f + s ++
  AJA92086.1   4 LVTGGLGFIGSNFILKILNENNDVHITNVDAELDGSNRKNLQNLenSNNYEFFKGNISNKKLMEEQITKC-------DAVVNFAAE----SFVDRSIND 91 
                 8*************************99999988889999998887899*********877776666555.......999999998....688888899 PP

                 HHHHHHHHTHHHHHHHHHHHHH...HH....HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHH CS
   adh_short 101 wervievNltgvflltravlpa...ml....kqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrsl 163
                  +  +  N+ g+f +   ++++   m+    ++  G+   ++  + + +++  ++Y+A+Kaa + +++s 
  AJA92086.1  92 ANPFLVSNIRGAFTILDIITKQkkrMIqistDEVFGS-LSTGTATEQTKFNPSSPYAATKAAAELIINSY 160
                 9999999999999999999988666773333333333.24444555677778899999999988777665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.9e-05      0.18       4      77 ..       4      75 ..       2      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
          KR  4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77
                l+tGGlG +G  ++  ++++    h+  +  +a+ d ++++++++le+   + e+++  +s+k+ +e+ +++++a
  AJA92086.1  4 LVTGGLGFIGSNFILKILNENnDVHITNV--DAELDGSNRKNLQNLEN-SNNYEFFKGNISNKKLMEEQITKCDA 75
                9**********999888877525555555..55589999999****98.56899*************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2173.16
//
Query:       AJA92087.1  [L=172]
Description: co-chaperone GrpE [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-36  124.0   3.9    5.4e-36  123.8   3.9    1.0  1  GrpE      GrpE
  ------ inclusion threshold ------
      0.026   12.5   1.0      0.029   12.4   1.0    1.1  1  Prominin  Prominin
       0.28   11.9   2.6        2.8    8.8   1.0    2.9  2  M         M protein repeat
       0.34   11.0   4.6       0.41   10.7   4.2    1.3  1  UPF0242   Uncharacterised protein family (UPF0242) N-terminus


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   3.9   1.2e-39   5.4e-36       4     166 .]      12     171 ..       5     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 1.2e-39
                 ...CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHHHHHHHHHH CS
        GrpE   4 eeeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeekslleGvemtlkql 102
                 +ee++e+ d+  + + + ++le+e  +lk+k++r+la+++nl++rt+ e+++  +++  +++ +++++++++ ra +s  ++e+++    G+  + k++
  AJA92087.1  12 NEENNELIDNPGKTDDQTKKLEEENSDLKDKWQRALADYQNLERRTQVEISQRVSSKTNDLLLNFINIYEDFVRAENSL-SKEKID--TSGIIAVIKNM 107
                 5667777778888888999**********************************************************75.444444..89********* PP

                 HHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEEE CS
        GrpE 103 lkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVsk 166
                 ++ L+++++++i++ ge FDp+lheavs+v dd+ +egt+ ++v+kGY  +  +l+p++V+Vsk
  AJA92087.1 108 ENLLAENNIKPIDAIGEIFDPQLHEAVSMVVDDTLDEGTITQEVSKGYISGKAILKPSKVIVSK 171
                 **************************************************************97 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   6.4e-06     0.029     666     748 ..      15      97 ..       4     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.4e-06
    Prominin 666 vlplessvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinneskklldrileqfeeYidwvieevtenvgk 748
                 + +l  +  k   ++kkl+eensdl+++ ++ la  +++e   + ++s+ ++++++ ll  + +++e++++  ++ ++e++ +
  AJA92087.1  15 NNELIDNPGKTDDQTKKLEEENSDLKDKWQRALADYQNLERRTQVEISQRVSSKTNDLLLNFINIYEDFVRAENSLSKEKIDT 97 
                 55666667788899********************************************************9999888888865 PP

>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   0.00063       2.8       1      16 [.      27      42 ..      27      45 .. 0.88
   2 ?    1.1   0.0       0.2   9.2e+02       8      16 ..      48      56 ..      47      59 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00063
           M  1 eakkeLEaelqeLeee 16
                ++ k+LE e+++L+ +
  AJA92087.1 27 DQTKKLEEENSDLKDK 42
                589**********976 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
           M  8 aelqeLeee 16
                a++q+Le+ 
  AJA92087.1 48 ADYQNLERR 56
                678888765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.2   9.2e-05      0.41      94     147 ..      11      64 ..       4      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.2e-05
     UPF0242  94 lqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaek 147
                  +ee++eL ++  + + + ++l+een  L+ k + + +d+++l +  + ++ ++
  AJA92087.1  11 TNEENNELIDNPGKTDDQTKKLEEENSDLKDKWQRALADYQNLERRTQVEISQR 64 
                 579999************************************999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1244  (0.0693848); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1207.01
//
Query:       AJA92088.1  [L=42]
Description: hypothetical protein T478_0812 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 314.16
//
Query:       AJA92089.1  [L=706]
Description: ATP-grasp domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-65  221.0   0.3    1.9e-65  220.4   0.3    1.3  1  ATP-grasp_5      ATP-grasp domain
    1.7e-48  163.9   0.2    4.6e-48  162.5   0.2    1.8  1  Succ_CoA_lig     Succinyl-CoA ligase like flavodoxin domain
    1.5e-25   90.0   0.2    6.7e-25   87.8   0.1    2.2  2  CoA_binding_2    CoA binding domain
    3.6e-09   37.2   0.2    1.5e-08   35.2   0.2    2.2  1  CoA_binding      CoA binding domain
      4e-07   29.8   2.6    4.5e-07   29.6   0.8    2.0  2  ATP-grasp_2      ATP-grasp domain
     0.0014   18.4   1.1       0.93    9.2   0.0    3.8  4  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
  ------ inclusion threshold ------
      0.031   13.8   0.0      0.068   12.7   0.0    1.5  1  ATP-grasp        ATP-grasp domain
      0.035   13.7   1.7        1.1    8.8   0.1    3.2  4  Peripla_BP_4     Periplasmic binding protein domain
      0.054   12.8   0.5       0.19   11.0   0.0    1.9  2  Hydantoinase_A   Hydantoinase/oxoprolinase
       0.15   12.3   0.1       0.46   10.8   0.1    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.4   0.3   1.1e-68   1.9e-65       4     222 .]      13     231 ..      10     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 1.1e-68
  ATP-grasp_5   4 aegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvl 101
                  + + ++ te+ +k +l+ yg++v+ + la+sa+ea++ a+++g+p v+K+vsp+ilhKtdvgGv++++++ ++v+++++++  r+++ +++  ++g+l
   AJA92089.1  13 NTDHKVITEESSKTILKKYGVKVPGFALAKSADEAAKQAKKLGFPLVMKVVSPQILHKTDVGGVKVGIDNVADVKKTFNDMYGRLSK-KKGVDVKGIL 109
                  5678899******************************************************************************77.7899****** PP

  ATP-grasp_5 102 VqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvd.lpeI 198
                  +++m+++gg+Elivg+++Dp+FGp+i+ GlGG+ +ev+kdva+++ p+++++a+++++++k skllkg+rg++++d++ +++ lv++ ++ v+ + +I
   AJA92089.1 110 LEKMVPKGGVELIVGIQNDPQFGPMIMAGLGGVMTEVFKDVAFRMLPITTSDAKSMLNELKGSKLLKGFRGSAPIDTNMVAKALVQIGKIGVEnANYI 207
                  ****999***********************************************************************************7763788* PP

  ATP-grasp_5 199 reldinPllveeegvvalDarirl 222
                  +++d nP++v+++  +++Da+i l
   AJA92089.1 208 NSIDFNPVIVYPKSYFVVDAKIIL 231
                  *********************975 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.5   0.2   2.6e-51   4.6e-48       2     137 ..     404     539 ..     403     540 .. 0.97

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 2.6e-51
  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark..kpvvvlksGrseaga 96 
                   G++a++sqSG++++++l++a    +g+sk++s+Gn++dvd+ad++ y a+dp+tkvi+ly+E+++dgrkf+++a+r+ ++  kpv+++ksGr++aga
    AJA92089.1 404 GNVAFFSQSGTMGISMLESADL--FGLSKMISFGNRSDVDEADMIWYAANDPQTKVIGLYVEGFGDGRKFINTAKRVMKEkkKPVIIWKSGRTAAGA 498
                   99*****************997..7****************************************************96657*************** PP

  Succ_CoA_lig  97 raaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                   ++aashtg+l gs+a++  af+qaG++ vds +el+ ++++
    AJA92089.1 499 KQAASHTGSLGGSNAMIMGAFKQAGIISVDSYQELVGVLKA 539
                   ************************************99987 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.5   4.5e+03      79     107 ..      32      60 ..      19      63 .. 0.73
   2 !   87.8   0.1   3.7e-28   6.7e-25       1     113 [.     257     381 ..     257     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.5
                    --SEEEE-TT---HHHHHHHHHTT-EEE. CS
  CoA_binding_2  79 gakavwlqpgsedeeaaelaeeagirvvg 107
                    g+k+  + ++   +eaa++a++ g ++v+
     AJA92089.1  32 GVKVPGFALAKSADEAAKQAKKLGFPLVM 60 
                    56666666777889999999999888876 PP

  == domain 2  score: 87.8 bits;  conditional E-value: 3.7e-28
                    --EEEET--S-TTSHHHHHHHHHHH...HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT..... CS
  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle...hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpg..... 88 
                    +++a+vGas++pgk g+ vl+ l +   +g +v+p+npk+++ilg k+y+sl++ +e+vdlv+v++  +a+ +i+k ++++g+  v++ +g     
     AJA92089.1 257 KSVALVGASATPGKIGNSVLDALGKqdyKG-KVFPINPKQKKILGIKCYPSLDAIKEKVDLVVVCVDLSACGPIMKTCAKKGIHNVVIVSGggkel 351
                    799********************9978777.9*********************857**************************************** PP

                    .....---HHHHHHHHHTT-EEE.ES-HHH CS
  CoA_binding_2  89 .....sedeeaaelaeeagirvvgdrCilv 113
                         + ++e+ el  +++irv+g++Ci++
     AJA92089.1 352 ggdraAMEAEVKELSLKHKIRVIGPNCIGM 381
                    ****99999*******************97 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.2   8.3e-12   1.5e-08       3      94 ..     256     345 ..     254     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 8.3e-12
                  TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEES CS
  CoA_binding   3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviit 94 
                  +++v+++Ga+ + ++++ ++ +   k   k +vf++np+   +++lg+++y+s+d ++ek  vd  v++v   ++  +++ ++++gi  +vi++
   AJA92089.1 256 PKSVALVGASATPGKIGnSVLDALGKQDYKgKVFPINPK--QKKILGIKCYPSLDAIKEK--VDLVVVCVDLSACGPIMKTCAKKGIHNVVIVS 345
                  689**************99999999999*99********..*******************..*****************************987 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.8   2.5e-10   4.5e-07       3     102 ..      20     115 ..      18     150 .. 0.81
   2 ?   -2.1   0.0       1.3   2.4e+03     160     194 ..     227     261 ..     190     263 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 2.5e-10
                  -HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSE..EEEE--SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEE CS
  ATP-grasp_2   3 hEyqakeilakygvkvpegevaesaeeaeeaakklgekel..vvKaQvlaGGRGKagGvkl.vkskeeakeaakellgkelvtkqtgkeGkkvekvlv 97 
                   E ++k il+kygvkvp +++a+sa+ea+++akklg   +  vv  Q+l   +   gGvk+ ++++ ++k++ +++ g   +     k+G  v+ +l+
   AJA92089.1  20 TEESSKTILKKYGVKVPGFALAKSADEAAKQAKKLGFPLVmkVVSPQILH--KTDVGGVKVgIDNVADVKKTFNDMYGRLSK-----KKGVDVKGILL 110
                  67789*******************************87532278889996..5677****9678899**********97555.....89999999999 PP

                  EE--- CS
  ATP-grasp_2  98 eeald 102
                  e++++
   AJA92089.1 111 EKMVP 115
                  99875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                  HHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEE CS
  ATP-grasp_2 160 reiakklglekelvkkaakiikklyklfveldatl 194
                   +i+ + +l+k++++ka+ +i+ + k f+ +   l
   AJA92089.1 227 AKIILNKELKKNSISKAKPVIASMEKFFTPKSVAL 261
                  57888899999999999999999999998776665 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.2   5.7e+03      24      44 ..      40      60 ..      37      67 .. 0.81
   2 ?    1.4   0.0      0.14   2.5e+02      13      59 ..     340     389 ..     336     408 .. 0.71
   3 ?    3.5   0.1     0.031        56       1      32 [.     472     503 ..     472     547 .. 0.77
   4 !    9.2   0.0   0.00052      0.93       4      46 ..     648     687 ..     645     694 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.2
                  HTTGHHHHHHHHHHHT-EEEE CS
  TPP_enzyme_M 24 rsgaseelrelaeklgiPvvt 44
                   ++ ++e+++ a+klg+P v 
    AJA92089.1 40 LAKSADEAAKQAKKLGFPLVM 60
                  567889999999999999875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                   SEEEEE-CH....HCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTE CS
  TPP_enzyme_M  13 rpvilvGgg....varsgaseelrelaeklgiPvvttlmgkgvipedhply 59 
                   ++vi+ Ggg     +r+  ++e++el+ k++i v+  +++ g+++  + l 
    AJA92089.1 340 NVVIVSGGGkelgGDRAAMEAEVKELSLKHKIRVIG-PNCIGMFNAANRLD 389
                   67788887533327788899************9974.56666666666554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.031
                   HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHH CS
  TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelr 32 
                   i+ a   +k++k+pvi+  +g   +ga++++ 
    AJA92089.1 472 INTAKRVMKEKKKPVIIWKSGRTAAGAKQAAS 503
                   56788899*********999999999988765 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00052
                   HHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEG CS
  TPP_enzyme_M   4 aaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttl 46 
                   +a+l k++k+p++  G+g      +e++ +l+ek ++Pv++ l
    AJA92089.1 648 LAALSKKKKKPILCGGNGGP---YTEKMIKLIEKNNVPVFQDL 687
                   45555666666666666665...9***************9866 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.068       2      35 ..      29      62 ..      28      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEE CS
   ATP-grasp  2 eklglpvprflaveskeeleeaaeelglpvvvKa 35
                +k g++vp f++++s++e+ + a++lg+p+v+K 
  AJA92089.1 29 KKYGVKVPGFALAKSADEAAKQAKKLGFPLVMKV 62
                789*****************************94 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       4.8   8.7e+03     115     137 ..     109     130 ..     102     145 .. 0.81
   2 ?   -3.0   0.0       2.5   4.4e+03     175     212 ..     250     289 ..     247     293 .. 0.71
   3 ?    8.8   0.1   0.00061       1.1      50      88 ..     308     345 ..     307     360 .. 0.81
   4 ?    2.2   0.0     0.061   1.1e+02     174     247 ..     616     695 ..     586     702 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.8
                   HHHHCTTH.EEEEEETSCCCHHH CS
  Peripla_BP_4 115 laeklggkkgkvvilaGspgdpn 137
                   l+ek+  k g v ++ G ++dp+
    AJA92089.1 109 LLEKMVPK-GGVELIVGIQNDPQ 130
                   56777777.99999999998875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                   HHHHHHTTT..ECEEEESSCCHHHCHHHHHHHTTTTSTEE CS
  Peripla_BP_4 175 lealltanp..ldgilaandgmaegalealeaaglagkvv 212
                   +e+++t+++  l+g  a+ + ++  +l+al +++++gkv+
    AJA92089.1 250 MEKFFTPKSvaLVGASATPGKIGNSVLDALGKQDYKGKVF 289
                   7788886643455555555666667999999999999975 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00061
                   HHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEEST CS
  Peripla_BP_4  50 daiakgvdgiivapvdstalapalkkakaaGIpVvafds 88 
                   dai+ +vd+++v  vd +a  p++k+++++GI  v++ s
    AJA92089.1 308 DAIKEKVDLVVVC-VDLSACGPIMKTCAKKGIHNVVIVS 345
                   699*****88777.999***************7555544 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.061
                   HHHHHHH.TT.T..ECEEEESSCCHHHCHHHHHHHTTTTST.EE...EEEES-HHHHHHHHHTTSSEEEEE--HHHHHHHHH CS
  Peripla_BP_4 174 aleallt.an.p..ldgilaandgmaegalealeaaglagk.vv...vtgqDatpealeaikdGtidatvaqdpyelgyaav 247
                    le++l+ +n +  + +++  +d   e ++++l+a  +++k ++     g  +t++++++i++ ++   v+qd + + +aa 
    AJA92089.1 616 VLEQFLAdKNiDiaMPWFVFQDDPLEETIVDYLAALSKKKKkPIlcgGNGGPYTEKMIKLIEKNNVP--VFQDLRTWVAAAS 695
                   6788888766566666777788888889999999977644425554555555677888888888876..7777776666655 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.19     161     204 ..     155     198 ..     148     209 .. 0.92
   2 ?   -3.9   0.1       3.6   6.4e+03     245     276 ..     342     373 ..     334     385 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
  Hydantoinase_A 161 teltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelak 204
                      ++t++Da+ +L++l+ +++l+g  g  ++d +++ +a+ +++k
      AJA92089.1 155 LPITTSDAKSMLNELKGSKLLKGFRGSAPIDTNMVAKALVQIGK 198
                     589*************************************9987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.6
  Hydantoinase_A 245 lvvfGGaGaqhaaalaeelgvkkvivppyagv 276
                     ++v GG+ ++   ++a e +vk+   ++   v
      AJA92089.1 342 VIVSGGGKELGGDRAAMEAEVKELSLKHKIRV 373
                     34445555777788888888888777766555 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00025      0.46      59      97 ..     304     341 ..     269     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                      HHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHHHT-EEE CS
  Sacchrp_dh_NADP  59 yeavLaallkegdlvvnlsppissldvlkaCietgvhyv 97 
                      y++ L+a+ ++ dlvv ++      +++k+C+++g+h v
       AJA92089.1 304 YPS-LDAIKEKVDLVVVCVDLSACGPIMKTCAKKGIHNV 341
                      777.88877778************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4910.36
//
Query:       AJA92090.1  [L=93]
Description: hypothetical protein T478_0843 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 661.05
//
Query:       AJA92091.1  [L=57]
Description: hypothetical protein T478_0422 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0053   16.8   0.2     0.0059   16.7   0.2    1.1  1  ADIP          Afadin- and alpha -actinin-Binding
  ------ inclusion threshold ------
      0.021   14.6   0.8      0.038   13.8   0.8    1.5  1  DivIC         Septum formation initiator
      0.033   13.5   0.1      0.033   13.5   0.1    1.0  1  CorA          CorA-like Mg2+ transporter protein
      0.047   14.0   0.3      0.054   13.8   0.3    1.1  1  CCDC-167      Coiled-coil domain-containing protein 167
      0.074   13.3   0.1      0.087   13.1   0.1    1.2  1  ABC_tran_CTD  ABC transporter C-terminal domain
       0.08   13.0   2.4       0.17   11.9   2.4    1.7  1  DUF1192       Protein of unknown function (DUF1192)
       0.11   11.4   0.2       0.12   11.2   0.2    1.0  1  DUF3375       Protein of unknown function (DUF3375)


Domain annotation for each model (and alignments):
>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   2.3e-06    0.0059     111     145 ..      13      47 ..       8      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
        ADIP 111 lknekeelqrlknalqqiktqyahelkkkdreiek 145
                 + ++ +e++ l+n ++ ik+++++el ++++++ k
  AJA92091.1  13 IEKLEDEIATLRNEIDVIKNAFRNELARHEVKMIK 47 
                 56789**************************9976 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   1.5e-05     0.038      39      71 ..      12      49 ..       6      57 .] 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                HHHHHHHHHCC-XX.....XXXXXXXXXXXXXXXXXXX CS
       DivIC 39 eneeLeaevkdLks.....dedyieerARselglvkpg 71
                ++e+Le+e++ L++       ++  e AR e  ++k+g
  AJA92091.1 12 RIEKLEDEIATLRNeidviKNAFRNELARHEVKMIKKG 49
                55666666666665333334666679999999999998 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.3e-05     0.033     195     229 ..       7      41 ..       1      48 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
        CorA 195 rdlldelerllemlealrerleslqdtyssllser 229
                  +++d++e+l++++ +lr+ ++++++++ + l+ +
  AJA92091.1   7 GTVYDRIEKLEDEIATLRNEIDVIKNAFRNELARH 41 
                 579*************************9998865 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.1e-05     0.054       2      34 ..       9      41 ..       8      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
    CCDC-167  2 vaseIdkleeklascrerLeaverrlrkeelse 34
                v   I+kle+++a +r++++ + +  r+e   +
  AJA92091.1  9 VYDRIEKLEDEIATLRNEIDVIKNAFRNELARH 41
                7789*******************9999876555 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.4e-05     0.087       9      31 ..      12      34 ..       8      52 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
  ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleael 31
                  ++e+le+eI+ L +ei  + +++
    AJA92091.1 12 RIEKLEDEIATLRNEIDVIKNAF 34
                  35666666666666666666555 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.4   6.8e-05      0.17      27      44 ..      11      28 ..       8      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.8e-05
     DUF1192 27 erIalLeaEIaRleaaia 44
                +rI++Le+EIa l+++i+
  AJA92091.1 11 DRIEKLEDEIATLRNEID 28
                688889999988888886 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.8e-05      0.12     138     170 ..      11      43 ..       4      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
     DUF3375 138 eRlaeLeaeiaeidaeidrlrageveelddeqv 170
                  R+++Le eia +++eid +++  ++el + +v
  AJA92091.1  11 DRIEKLEDEIATLRNEIDVIKNAFRNELARHEV 43 
                 6********************999998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1082  (0.0603492); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 413.70
//
Query:       AJA92092.1  [L=61]
Description: ribosomal protein S27a [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-20   73.0   5.9    1.8e-20   72.8   5.9    1.1  1  Ribosomal_S27    Ribosomal protein S27a
     0.0044   17.0   1.7     0.0049   16.8   1.7    1.1  1  Cytochrome_C7    Cytochrome c7 and related cytochrome c
     0.0044   16.9   1.9        1.7    8.6   0.1    2.2  2  Nudix_N_2        Nudix N-terminal
     0.0055   16.4   0.5     0.0083   15.9   0.5    1.2  1  Ephrin_rec_like  Putative ephrin-receptor like
  ------ inclusion threshold ------
      0.013   15.5   0.8      0.014   15.4   0.8    1.1  1  DUF1451          Zinc-ribbon containing domain
      0.015   15.5   2.9      0.025   14.7   2.9    1.4  1  Ribosomal_L37e   Ribosomal protein L37e
      0.024   14.9   1.6      0.028   14.6   1.6    1.2  1  IBR              IBR domain, a half RING-finger domain
      0.028   14.4   1.0      0.037   14.0   1.0    1.3  1  NCD3G            Nine Cysteines Domain of family 3 GPCR
      0.092   12.8   2.9       0.21   11.6   2.9    1.6  1  DZR              Double zinc ribbon
        1.5    9.0   7.1        4.3    7.5   7.0    1.7  1  PknG_rubred      Protein kinase G rubredoxin domain
        4.1    7.5   8.5         96    3.1   7.9    2.2  2  YhfH             YhfH-like protein


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   5.9   1.1e-23   1.8e-20       1      45 []      15      57 ..      15      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.1e-23
                   SSSSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
  Ribosomal_S27  1 vlkyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                   v +yYkvd+ +kv+r rk C r CG+GvfM+ehk+R++CGkCg T
     AJA92092.1 15 VSQYYKVDN-DKVSRERKTCVR-CGKGVFMSEHKNRRTCGKCGDT 57
                   679******.9***********.*******************976 PP

>> Cytochrome_C7  Cytochrome c7 and related cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.7     3e-06    0.0049      33      71 ..      16      54 ..       3      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
  Cytochrome_C7 33 aemekgkskkaevesltCgaCHdgknafsvakkaeCakC 71
                   ++++k   +k++ e +tC  C +g ++++++++++C+kC
     AJA92092.1 16 SQYYKVDNDKVSRERKTCVRCGKGVFMSEHKNRRTCGKC 54
                   44444455555666688********************** PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.2    0.0015       2.4      19      29 ..      27      37 ..      18      38 .. 0.88
   2 !    8.6   0.1    0.0011       1.7      18      30 ..      44      56 ..      40      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                SS-EEEETTTT CS
   Nudix_N_2 19 nreRlvCpaCg 29
                +reR +C +Cg
  AJA92092.1 27 SRERKTCVRCG 37
                69********9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                -SS-EEEETTTTE CS
   Nudix_N_2 18 DnreRlvCpaCgt 30
                +++ R +C +Cg 
  AJA92092.1 44 EHKNRRTCGKCGD 56
                7899*******95 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   5.1e-06    0.0083       6      34 ..      28      57 ..      25      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
  Ephrin_rec_like  6 tgletCipCprgtYqn.eegqlsClaCPlg 34
                      + +tC  C +g + +    +++C +C+++
       AJA92092.1 28 RERKTCVRCGKGVFMSeHKNRRTCGKCGDT 57
                     5679**********995566789****976 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.8   8.7e-06     0.014     112     143 ..      28      59 ..      13      61 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.7e-06
     DUF1451 112 lGtlvCekCgkelalkkteeippCpkCgateF 143
                   + +C +Cgk + +++ ++  +C kCg teF
  AJA92092.1  28 RERKTCVRCGKGVFMSEHKNRRTCGKCGDTEF 59 
                 55679*************************** PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.9   1.5e-05     0.025      17      38 ..      31      55 ..      24      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
  Ribosomal_L37e 17 ilCrrCgkrsy...hvqkktCascG 38
                     +C rCgk  +   h +++tC++cG
      AJA92092.1 31 KTCVRCGKGVFmseHKNRRTCGKCG 55
                    57******999666778889****9 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.6   1.7e-05     0.028      14      46 ..      26      56 ..      14      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
         IBR 14 sdpnlkwCprpdCeaiieksegcksvtCskCgf 46
                 ++++k C    C++ +  se++++ tC kCg 
  AJA92092.1 26 VSRERKTCV--RCGKGVFMSEHKNRRTCGKCGD 56
                36679****..9**********9999*****94 PP

>> NCD3G  Nine Cysteines Domain of family 3 GPCR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   2.3e-05     0.037      27      50 ..      32      58 ..      14      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
       NCD3G 27 dCvpCpege.is..tdseeCtkCpede 50
                +Cv+C +g  +s  ++  +C kC ++e
  AJA92092.1 32 TCVRCGKGVfMSehKNRRTCGKCGDTE 58
                5********6675449*******9876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.9   0.00013      0.21       9      35 ..      27      55 ..      12      58 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
         DZR  9 ppdarfCseCgtklkavaa..edrCpsCg 35
                + + ++C +Cg+ +   ++   ++C +Cg
  AJA92092.1 27 SRERKTCVRCGKGVFMSEHknRRTCGKCG 55
                45556666666664333334466666666 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.0    0.0026       4.3      84     121 ..      22      55 ..      18      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
                  CSS---GGG-B-TTT--B-S---SS----SEEE-TTT- CS
  PknG_rubred  84 tnpvvpEskRfCwrCGrpvGRsekerkgaseGtCpkCg 121
                  +n  v+  +++C rCG+ v  se++++     tC kCg
   AJA92092.1  22 DNDKVSRERKTCVRCGKGVFMSEHKNR----RTCGKCG 55 
                  67889999***********99987654....3566666 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   7.9     0.059        96      13      25 ..      30      44 ..      28      54 .. 0.71
   2 ?    1.4   2.7      0.19   3.2e+02      14      21 ..      49      56 ..      44      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.059
        YhfH 13 kKkCteCGke..ieE 25
                 K+C+ CGk   + E
  AJA92092.1 30 RKTCVRCGKGvfMSE 44
                6*******9755555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
        YhfH 14 KkCteCGk 21
                 +C +CG+
  AJA92092.1 49 RTCGKCGD 56
                58999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 444.88
//
Query:       AJA92093.1  [L=42]
Description: hypothetical protein T478_1148 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0028   18.4   0.2     0.0036   18.0   0.2    1.2  1  zf-C2H2_4    C2H2-type zinc finger
     0.0037   17.6   0.1     0.0041   17.4   0.1    1.1  1  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.037   14.3   0.1      0.047   14.0   0.1    1.2  1  zf-Di19      Drought induced 19 protein (Di19), zinc-binding
      0.042   12.4   0.0      0.042   12.4   0.0    1.0  1  DUF629       Protein of unknown function (DUF629)
      0.073   12.2   0.1      0.073   12.2   0.1    1.0  1  Actin_micro  Putative actin-like family
      0.082   13.4   0.2       0.12   12.9   0.2    1.3  1  zf-C2H2      Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   1.2e-06    0.0036       2      24 .]       3      25 ..       2      25 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                 C++Cg+ F s  ++l+H+   H
  AJA92093.1  3 NCSVCGEKFDSDIRFLNHMMEKH 25
                5********99999*****9988 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.4e-06    0.0041       2      31 ..       4      33 ..       3      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
   zf-C2H2_2  2 Clfcekkskeveellehmskkhgffipere 31
                C +c +k+++  + l+hm++khgf  p+ +
  AJA92093.1  4 CSVCGEKFDSDIRFLNHMMEKHGFRNPNID 33
                99*****999999***********988654 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.047       4      26 ..       3      26 ..       1      32 [. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
     zf-Di19  4 tCPyCgkelt.vkeLveHvedeHr 26
                +C  Cg++++ + ++++H++++H 
  AJA92093.1  3 NCSVCGEKFDsDIRFLNHMMEKHG 26
                566666665413466666666665 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05     0.042      58      81 ..       3      26 ..       1      37 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
      DUF629 58 vCrtCsekfsdaeeckqHlvqeHv 81
                 C  C ekf +   +++H++++H 
  AJA92093.1  3 NCSVCGEKFDSDIRFLNHMMEKHG 26
                6**********************6 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.4e-05     0.073     227     251 ..       3      28 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
  Actin_micro 227 sCkvCdvkfev.ekiseHllkkHiik 251
                  +C+vC+ kf++  ++ +H+++kH + 
   AJA92093.1   3 NCSVCGEKFDSdIRFLNHMMEKHGFR 28 
                  7**********99**********874 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   4.1e-05      0.12       3      23 .]       4      25 ..       2      25 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                ETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  3 CpdCgksFkrksnLkrHirt.H 23
                C++Cg++F +   + +H++  H
  AJA92093.1  4 CSVCGEKFDSDIRFLNHMMEkH 25
                ******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 293.81
//
Query:       AJA92094.1  [L=290]
Description: carbohydrate kinase, PfkB domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-09   37.9   0.0    1.8e-09   37.3   0.0    1.3  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.27   11.3   0.1    1.6  1  WD40_3        WD domain, G-beta repeat
       0.13   11.7   0.0       0.19   11.1   0.0    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     3e-13   1.8e-09     105     293 ..      77     261 ..      59     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 3e-13
                 EEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES...EECTTSHHHHHHHHHHHHHHTTE....EEEEECESSSHH....HHHHHHHHHCTESEEEEEHH CS
        PfkB 105 ivfnrgaaadltkeeleededlleeadllyisg...llsselpeavleelaeaaknggt....fdpnlldplgaq....fkeallellaladllkpnee 192
                 + + ++++    +     +e+ + + d++  +    ++s+++ e +le+ ++++++ ++        l+++ + +     k + l+ l  ++++k+n +
  AJA92094.1  77 FRIELNDSDRKLF-----VENMCDKIDFIDNDDdgtIISPVFDEISLETYSQIKNSDNFtfldPQGFLREKNS-NnevsLKNTTLD-LTNVNAIKMNPD 168
                 5555555555555.....4566667777776666678888888888888888888888776322333344444.358766777777.459********* PP

                 HHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHT CS
        PfkB 193 ElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvq 291
                 El altg ++   ++ +++l+k    g++ v+ t  ke +l+v kd+ +    +pk +  DttG GD f++ f+   l++k++  al fa  +A+ +++
  AJA92094.1 169 ELFALTGLTG---HDGIKQLQK---LGIEYVIYTNKKEISLLV-KDKLYT-IFLPKMTLTDTTGIGDIFCSTFTCTMLKEKDFLWALSFAGGAAQSALE 259
                 *********4...677888888...79********99999999.665555.5559***********************************999998887 PP

                 SS CS
        PfkB 292 kk 293
                 +k
  AJA92094.1 260 SK 261
                 76 PP

>> WD40_3  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.5e-05      0.27      11      41 ..      86     116 ..      82     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
      WD40_3  11 kklfpnpsGtrlvfiDekgdgfvynPvseel 41 
                 +klf+++ + ++ fiD++ dg + +Pv +e+
  AJA92094.1  86 RKLFVENMCDKIDFIDNDDDGTIISPVFDEI 116
                 799************************9986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.2e-05      0.19     148     235 ..     182     262 ..     148     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                   HHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHH.CG CS
  Phos_pyr_kin 148 akkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaik.ea 235
                    k+l+klg ++V+ + ++     +    +l++++  +++  ++++ ++t G G+ + s  ++ + k+++   A++ A    ++a++ +a
    AJA92094.1 182 IKQLQKLGIEYVIYTNKK-----EI--SLLVKDKL-YTIFLPKMTLTDTTGIGDIFCSTFTCTMLKEKDFLWALSFAGGAAQSALEsKA 262
                   678899999999976665.....23..56776665.555555666699*************************9999999999888444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2122.83
//
Query:       AJA92095.1  [L=600]
Description: nitrite/sulfite reductase, 4Fe-4S iron-sulfur cluster-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-41  140.2   0.0    3.4e-30  104.7   0.0    2.3  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
    9.6e-32  108.7   0.0    3.8e-16   58.7   0.0    2.8  3  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 


Domain annotation for each model (and alignments):
>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   3.8e-34   3.4e-30       2     153 ..     132     284 ..     131     289 .. 0.91
   2 !   33.2   0.0   3.6e-12   3.2e-08       7     142 ..     413     545 ..     409     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 3.8e-34
                 SSSCCCCCCSTCCCTBSS-SS-THHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE...EEEEEE--B-SSSTC-TC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
     NIR_SIR   2 ganlrnvtlcpgaglceeallDttelakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei...gfnilvGGglgrthgakk 97 
                 g+++rnv+++p +g+c+++++D+t++a ai + +  ++  + lPrKfK+++++c++  +  ++ D+gl++  ++   +   gf+i++GGglg++   + 
  AJA92095.1 132 GNTVRNVMCSPLSGVCKDEIFDATPYAMAIAKFMLRNPICQGLPRKFKFNFTCCEKHGM-IRIVDVGLLPQIQEIDGEkrkGFKIFLGGGLGNRSFVGH 229
                 899***************************************************87655.6677*****977642222355****************** PP

                 EEEEEEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHHHHHHHHHHH.HH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
     NIR_SIR  98 tsarlgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverlGvekFrekv.ee 153
                 ++    f+p e++l++  a+++++++ gdrkn  + R++ylv++lG+ekF + v +e
  AJA92095.1 230 ELE--DFTPVEDLLYTSMAVIRIFDRMGDRKNLSRNRMRYLVNDLGWEKFQNLVlKE 284
                 ***..6**********************************************99554 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 3.6e-12
                 CCCCSTCCCTBSS-SS-THHHHHHHH.HHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEETTCEE...EEEEEE--B-SSSTC-TCEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
     NIR_SIR   7 nvtlcpgaglceeallDttelakaie.delepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkdekei...gfnilvGGglgrthgakktsar 101
                 + ++c g++ c  al+++  lak+++ + le +++e +  r   i++sgcpn c+++++  ig++g    ++      +++ +GG++ ++ + + ++ar
  AJA92095.1 413 SAVGCSGTTSCNLALTNSHRLAKEVQrKFLELNFDEDDDLRDSTIKISGCPNSCGQHQIATIGFYGGGGRHGTDmfpNYTMSLGGKFDEDSMLGHHTAR 511
                 6789**********************555677888888899************************9888777777889********************9 PP

                 EEEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     NIR_SIR 102 lgfvpeeevlevveaivevyrdhgdrknrkkeRlkylverl 142
                    vp + +++v+ +i+e+++    ++++    l ++++r+
  AJA92095.1 512 ---VPVKRIIPVILKIIELFK----ENKQPDDTLSKWIDRV 545
                 ...79999*************....9999888999999885 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.26   2.3e+03      13      30 ..      31      49 ..      21      60 .. 0.68
   2 !   58.7   0.0   4.2e-20   3.8e-16       6      66 ..      60     120 ..      55     123 .. 0.93
   3 !   46.8   0.0   2.1e-16   1.9e-12       2      68 ..     334     400 ..     333     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.26
  NIR_SIR_ferr 13 rlrvp.nGritaeqlrala 30
                  ++++   G+i+++++r+++
    AJA92095.1 31 TVKLFrQGKIDPDMFRRFR 49
                  555554699****999876 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 4.2e-20
  NIR_SIR_ferr   6 gkgyymvrlrvpnGritaeqlraladiaekygsgeirlTtrQnlqlhgvpeedleeileeL 66 
                    + y+mvr++vp+G+i + ql+++a+++e y++g ++++tr n+qlh+v  ed+ ei++ L
    AJA92095.1  60 TDDYAMVRIKVPAGQIYPYQLEKIAQLSEMYSIGSAHFSTRENIQLHWVILEDVSEIMQSL 120
                   46789*****************************************************988 PP

  == domain 3  score: 46.8 bits;  conditional E-value: 2.1e-16
  NIR_SIR_ferr   2 kqkdgkgyymvrlrvpnGritaeqlraladiaekyg.sgeirlTtrQnlqlhgvpeedleeileeLae 68 
                   kq +  g+++v + +++G+ita qlr +a+i+++y+ +g  r    Qn+++++v+++dl+ i+++L e
    AJA92095.1 334 KQSQ-SGFNSVFIGLEAGDITANQLRSVAEIIRDYSaEGFGRNGFSQNIVIRYVHDDDLKSIYSRLIE 400
                   4566.89*****************************66999***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4257.27
//
Query:       AJA92096.1  [L=323]
Description: cobalamin biosynthesis protein CobD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.1e-87  290.9   0.0      1e-86  290.6   0.0    1.1  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
       0.34   11.3   6.9       0.21   12.0   1.8    2.8  2  DUF4199    Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.6   0.0   1.2e-90     1e-86       3     273 ..      11     292 ..       9     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 290.6 bits;  conditional E-value: 1.2e-90
   CobD_Cbib   3 lAlllDlllgdprrllhPvvligklisalekrl.r.kakkerlaGvllalllvllallvalllllla...laall.......glvlealllkltlalrs 89 
                 +A+llDll+gdp++++hP ++ig li+ +++r+ + +++ e+l G++++l+ v+++++v+ +l + +   +   +        +++ ++l+k+t+a++ 
  AJA92096.1  11 FAILLDLLFGDPKNRFHPTAWIGILIGNITTRMkNeNHNLEKLGGIFIVLIPVCISIVVLSGLDYSIdliS---VeslsiliSIITGIVLFKMTIAIKG 106
                 79*******************************53335678899999999999999999999988666531...123444556678899********** PP

   CobD_Cbib  90 Lleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflllglpgalaykavnTlDsmvGYkneryedfGwaaA 187
                 +++++ +v++++ k+dl++aR+++smiV+R+t++ld+++i++ ++Es++EN++Dg+++P+fyf+++glpga++y++vnT+DsmvGYk++ ++++Gw+ A
  AJA92096.1 107 MERHALAVLDSIqKNDLTQARTNLSMIVKRNTKNLDKNHILSGTLESLSENIVDGITGPMFYFAIFGLPGAFVYRIVNTVDSMVGYKTQMFKNLGWFGA 205
                 ************559************************************************************************************ PP

   CobD_Cbib 188 rlDDllnyiPARltalllala.........aalriarrdarkhpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieral 273
                  +D +lnyiP+Rlt+l+++l          ++++i++rd++k++SpN+g+p+aa+Agalg ++++ ++Y lg+ e          +++ ++++ a+
  AJA92096.1 206 NCDNVLNYIPSRLTGLTIVLGsmllghdwkNCYEIFKRDGKKTDSPNAGYPMAAFAGALGTKFEKLEHYsLGTGEY---------EITSKKVKDAI 292
                 ********************545555556677*************************************7774333.........34445555555 PP

>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.8   2.4e-05      0.21      79     167 ..      85     181 ..      29     181 .. 0.81
   2 ?    0.2   0.2     0.099   8.8e+02     146     164 ..     294     312 ..     260     320 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
     DUF4199  79 vagllsavfqyiyfn.fidpdfienyiaeilekleeakeesaeeenaemseeeikeale...sls....piiv.alqsflgnliiGlilsliiAlilk 167
                 ++ l+s+++ +++f+  i    +e+++ ++l++++++  ++a   n +m  +  ++ l+    ls    +++  ++ +++g +++ +i++l+ A++ +
  AJA92096.1  85 LSILISIITGIVLFKmTIAIKGMERHALAVLDSIQKNDLTQA-RTNLSMIVKRNTKNLDknhILSgtleSLSEnIVDGITGPMFYFAIFGLPGAFVYR 181
                 5678888888888885667788*********99997765555.45555666655665555552224454555559*******************9976 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.099
     DUF4199 146 qsflgnliiGlilsliiAl 164
                  + +++l++  i+s++i l
  AJA92096.1 294 LMKVTSLLFFGIVSIPIIL 312
                 3334445555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2336.40
//
Query:       AJA92097.1  [L=55]
Description: cysteine-rich CWC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.026   14.9  12.1       0.11   13.0  12.1    1.9  1  Cys_rich_CWC  Cysteine-rich CWC
      0.027   14.4   0.6      0.027   14.4   0.6    2.3  2  DM            DM DNA binding domain
       0.12   12.3   0.2       0.12   12.3   0.2    2.1  2  Flavi_propep  Flavivirus polyprotein propeptide
          6    7.1   9.4    1.5e+02    2.6   9.4    2.1  1  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Cys_rich_CWC  Cysteine-rich CWC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  12.1   2.4e-05      0.11       1      49 [.       5      44 ..       5      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
  Cys_rich_CWC  1 CplCgqanqCameagedisdCwCakqalsdkllqllsqrakaClCeaCl 49
                  C  Cg ++ C+ + +    +CwC + +  +  +++    +k+ClC++Cl
    AJA92097.1  5 CAECGDNFSCEND-I----SCWCGDFP--KLSKNE--IDDKDCLCRSCL 44
                  99********854.3....5***8765..333333..379********8 PP

>> DM  DM DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.8     0.064   2.9e+02       3       9 ..       3       9 ..       1      16 [. 0.79
   2 ?   14.4   0.6     6e-06     0.027      27      43 ..      36      52 ..      30      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.064
          DM 3 pkCarCr 9
               +kCa C 
  AJA92097.1 3 KKCAECG 9
               6899885 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6e-06
          DM 27 kdCsCekCslveerqkv 43
                kdC C  C lv+ r+++
  AJA92097.1 36 KDCLCRSCLLVRYRKRI 52
                79************998 PP

>> Flavi_propep  Flavivirus polyprotein propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   4.2      0.03   1.4e+02      46      63 ..       3      22 ..       1      25 [. 0.62
   2 ?   12.3   0.2   2.8e-05      0.12      48      66 ..      25      43 ..      23      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.03
  Flavi_propep 46 ykcprls..eeepddvdcwc 63
                   kc +        +d+ cwc
    AJA92097.1  3 KKCAECGdnFSCENDISCWC 22
                  566665532234589***** PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.8e-05
  Flavi_propep 48 cprlseeepddvdcwcyav 66
                   p+ls++e dd dc c + 
    AJA92097.1 25 FPKLSKNEIDDKDCLCRSC 43
                  59**************875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   9.4     0.033   1.5e+02       8      40 .]       5      52 ..       3      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
  Zn-ribbon_8  8 CeeCghefe.............vlqsis.dapltaCPeCgs.evrrvi 40
                 C eCg  f              +l +   d+++  C +C   + r++i
   AJA92097.1  5 CAECGDNFScendiscwcgdfpKLSKNEiDDKDCLCRSCLLvRYRKRI 52
                 77777777777777777777769999996666666****877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 393.51
//
Query:       AJA92098.1  [L=52]
Description: hypothetical protein T478_0819 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 401.27
//
Query:       AJA92099.1  [L=544]
Description: ferrous iron transport protein B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-15   55.3   0.1    8.5e-15   54.6   0.1    1.3  1  FeoB_N       Ferrous iron transport protein B
    1.3e-13   51.0   0.3    2.3e-13   50.2   0.3    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    6.6e-07   29.6  19.9    1.2e-05   25.6   1.8    3.1  3  Gate         Nucleoside recognition
    1.2e-06   28.0   0.5    2.3e-06   27.1   0.5    1.4  1  AIG1         AIG1 family
     0.0014   18.4   0.1     0.0023   17.7   0.1    1.3  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0022   18.1   2.9      0.014   15.5   0.1    2.3  2  Dynamin_N    Dynamin family
  ------ inclusion threshold ------
      0.012   15.8   0.5      0.036   14.3   0.2    2.1  2  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.035   13.5   0.1      0.068   12.6   0.1    1.5  1  SRPRB        Signal recognition particle receptor beta subuni
      0.047   14.0   0.0       0.11   12.8   0.0    1.6  1  AAA_22       AAA domain
      0.047   13.6   1.4       0.15   12.0   0.1    2.3  3  RsgA_GTPase  RsgA GTPase
      0.057   13.9   0.0      0.099   13.2   0.0    1.5  1  ABC_tran     ABC transporter
       0.06   12.9   1.1       0.14   11.8   0.0    2.1  2  Saf_2TM      SAVED-fused 2TM effector domain
      0.061   12.9   0.1       0.11   12.1   0.1    1.4  1  Ras          Ras family
       0.14   11.9   0.1       0.23   11.2   0.1    1.3  1  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   6.6e-18   8.5e-15       2     148 ..       9     146 ..       8     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 6.6e-18
                 EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatnlernLyLtlq 100
                 +++++G+  vGk+ l+ +ltg++ + +N+ G tv k++     +++++++vD PGi  +++ se  k+a + ++    d ++ vv a+n++ ++  +l 
  AJA92099.1   9 KIIVIGKEGVGKSQLISSLTGKYAESSNFKGSTVSKESY----NNDKFSFVDTPGI-VFDSDSETTKIAISSIH--GNDSILLVVSAANIDDDIEYFLP 100
                 6899******************************99875....456*********9.478899999***99997..5689******************* PP

                 HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
      FeoB_N 101 llelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                 l+  ++ ++++ n +d  ++k+ ++ l+kL++ L++p+ ++ a++ ++
  AJA92099.1 101 LIKNKKGMIIVTN-WDRFNSKNEDM-LEKLQQDLKIPITALDARRITE 146
                 ****999999988.68888777766.689**********999988665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.3   1.8e-16   2.3e-13       1     113 [.       9     113 ..       9     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.8e-16
                 EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHH CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeelee 99 
                 +++++G+  vGKS Li++ltg+ a+ s+++g T   + ++     +++ +vDtpG++  +s+++  + a+ ++   d illvv+a+ + ++++ e +  
  AJA92099.1   9 KIIVIGKEGVGKSQLISSLTGKYAESSNFKGSTVSKESYNN----DKFSFVDTPGIVF-DSDSETTKIAISSIHGNDSILLVVSAA-N-IDDDIEYFLP 100
                 589*******************************9999954....58********664.45566677788877778*******966.4.6666555555 PP

                 HHHHTTSEEEEEEE CS
    MMR_HSR1 100 lleeakkplilvln 113
                 l+ ++kk +i+v n
  AJA92099.1 101 LI-KNKKGMIIVTN 113
                 54.47777888876 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.9     5e+03       6      38 ..     187     219 ..     183     231 .. 0.62
   2 !   25.6   1.8     9e-09   1.2e-05       3     108 ..     254     347 ..     252     351 .. 0.84
   3 !   11.7   6.5   0.00018      0.23       2     110 ..     413     511 ..     412     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.9
        Gate   6 piillasiliwflssssllgrigkllepvfapl 38 
                  +i l+++l   + s   + ++g l+ p+++ l
  AJA92099.1 187 VLIGLVLLLAPAILSVIGANYFGELIHPIISEL 219
                 555555555555555555677788888887764 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9e-09
        Gate   3 kagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpksalafllfvllytpcvat 101
                  a p++++  +++++ +s++ll+r + ++ p+++++g   +++ ++ +++gf+   ++v+++++ +       + +  t+ + ++++ f++ ++  +++
  AJA92099.1 254 WATPVVVIYALVLGIYKSTGLLDRTSLAIHPLVKKIG--VSGRDVTRIVMGFG---CNVPAVISSR-------SCSSCTRGTTVSAISFGSACSYQFSA 340
                 689**********************************..**************...******9998.......55556666666777777777766666 PP

        Gate 102 lavivre 108
                  +++++ 
  AJA92099.1 341 SIAVFSA 347
                 6666665 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00018
        Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtpksalafllfvllyt...p 97 
                 + a+pi+l ++++ +++s ++++++++  ++ +++ +   l+  a+ ++++g + k  ++ +l+++          +  +  sa+  l  v l+    p
  AJA92099.1 413 KMALPIFLGITFVASIISWTGIIDYFAVEIGFLMKFFN--LPEDASLAIIFGSIRKD-GLLLLAEP----------NLVGSLSAIQILTGVYLAGtllP 498
                 7899********************************99..**************555.66666677..........56666666655555544444559 PP

        Gate  98 cvatlavivrelg 110
                 c+ t+ +++re++
  AJA92099.1 499 CIVTFLTVIREMS 511
                 *****99999986 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.5   1.8e-09   2.3e-06       2     110 ..       9     105 ..       8     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                 EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SC.CCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHH CS
        AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPgl.fdlsvsadkiskeivrclllseegihalllvlslgrftee 99 
                 +i+++Gk g+GkS  + s+ gk a +s++      k ++ ++++ ++ k + +DTPg+ fd+++++ ki  +       s +g + +llv+s+ +++++
  AJA92099.1   9 KIIVIGKEGVGKSQLISSLTGKYAESSNF------KGSTVSKESYNNDKFSFVDTPGIvFDSDSETTKIAIS-------SIHGNDSILLVVSAANIDDD 94 
                 69**********************99997......445555557788999*******988988877766554.......456999********999988 PP

                 HHHHHHHHHHH CS
        AIG1 100 dekalktlkel 110
                  e  l  +k+ 
  AJA92099.1  95 IEYFLPLIKNK 105
                 77777777764 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.8e-06    0.0023       3     114 ..       9     131 ..       7     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
   PduV-EutP   3 killiGkvgsGKttLtqalkg...eelkYk.ktqaiefsde....viDtPGeylenrklysalivtsae.advialvqdateeesvfppgfasvfnkev 92 
                 ki++iGk g+GK  L  +l+g   e+ ++k +t + e +++    ++DtPG   ++ +  + ++++s+   d i lv++a + +  +   +  + nk+ 
  AJA92099.1   9 KIIVIGKEGVGKSQLISSLTGkyaESSNFKgSTVSKESYNNdkfsFVDTPGIVFDSDSETTKIAISSIHgNDSILLVVSAANIDDDIEYFLPLIKNKKG 107
                 8*******************96653444443466666665433337*********99999999999876279999*99999998888877777888999 PP

   PduV-EutP  93 iGiitkidlae..deenieaveel 114
                 + i+t  d  +  +e+ +e+ ++ 
  AJA92099.1 108 MIIVTNWDRFNskNEDMLEKLQQD 131
                 9999*9998741134445555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.8      0.11   1.4e+02       1      21 [.      10      30 ..      10      37 .. 0.92
   2 !   15.5   0.1   1.1e-05     0.014      93     140 ..      42      90 ..      32     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                EEEEEBTTTTHHHHHHHHHTS CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                i+v+G+   GKS ++ +L+g+
  AJA92099.1 10 IIVIGKEGVGKSQLISSLTGK 30
                89****************997 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.1e-05
                 EEEEETTS-SEEEEE---B-S.SSGTTSHHHHHHHSTTEEEEEEEETTS CS
   Dynamin_N  93 lkilsllvkgltlvDlPGlds.vnkrdqelvkeyikkadiilavtsanh 140
                 +++ s ++++ ++vD+PG+   ++ + ++++ + i+ +d il+v+sa +
  AJA92099.1  42 VSKESYNNDKFSFVDTPGIVFdSDSETTKIAISSIHGNDSILLVVSAAN 90 
                 5677889999********9862666666*******99999999988765 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   2.8e-05     0.036       1      28 [.       9      36 ..       9     113 .. 0.74
   2 ?   -2.7   0.0       5.3   6.8e+03      97     113 ..     511     527 ..     491     531 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.8e-05
                EEEEESSTTSSHHHHHHCHCT-CCC-EE CS
         Roc  1 KvvlvGdsgvGKtsllkrfvedkfseke 28
                K++++G++gvGK+ l+++++ +  ++++
  AJA92099.1  9 KIIVIGKEGVGKSQLISSLTGKYAESSN 36
                9******************976665443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                 HHHHHHHHHCSSS-EEE CS
         Roc  97 eWlkelkkvagkspvil 113
                 +W+  +k v++++++++
  AJA92099.1 511 SWMFAIKMVGKQIIAVV 527
                 79999999998887766 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.3e-05     0.068       2      59 ..       6      60 ..       5     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                ---EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT- CS
       SRPRB  2 skpavllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGh 59
                s+p+++++G    GK  l+  Lt + ++++     + + +++   ++ k+ ++D PG 
  AJA92099.1  6 STPKIIVIGKEGVGKSQLISSLTGKYAESSNFKGSTVSKESY---NNDKFSFVDTPGI 60
                6899******************98877776666566666666...8889999****95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.6e-05      0.11       8     112 ..      10     128 ..       5     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........erpevvfvtlpsst.sskdllrellralglelka.....erlsseellealeqalraravi 92 
                 ++v+G  G+GK+ l+  l+ ++ e ++ +         +++++ fv+ p+   +s++  ++++    +++++     + ++ ++ +e++   +++++  
  AJA92099.1  10 IIVIGKEGVGKSQLISSLTGKYAESSNFKGstvskesyNNDKFSFVDTPGIVfDSDSETTKIAISSIHGNDSillvvSAANIDDDIEYFLPLIKNKKG- 107
                 79********************8877777799999998777777888887776555555555555555555567888888999999999999999887. PP

      AAA_22  93 elliiDEaqhlr..seealeeL 112
                  ++i+ + ++++  +e++le+L
  AJA92099.1 108 -MIIVTNWDRFNskNEDMLEKL 128
                 .999999999985448888888 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011      0.15     102     124 ..      10      32 ..       2      63 .. 0.64
   2 ?   -0.9   0.1       1.1   1.4e+03      17      84 ..      80     141 ..      68     182 .. 0.61
   3 ?   -3.3   0.0       5.5   7.1e+03       3      19 ..     395     411 ..     394     412 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                  EEEECSTTSSHHHHHHHHCTT-- CS
  RsgA_GTPase 102 svlvGqSGvGKStLinallpele 124
                  ++++G+ GvGKS Li +l+++  
   AJA92099.1  10 IIVIGKEGVGKSQLISSLTGKYA 32 
                  5789**************99832 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                  -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--T CS
  RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsa 84 
                  d +l+vvs++  ++  + ++ fL l+++k+   +i+++  D  ++++  + l++  ++l +++++++a
   AJA92099.1  80 DSILLVVSAA--NI-DDDIEYFLPLIKNKK--GMIIVTNWDRFNSKN-EDMLEKLQQDLKIPITALDA 141
                  5556666655..22.345666666665554..466667777777766.44444444455555555544 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.5
                  --S-EETTTTEES--EE CS
  RsgA_GTPase   3 eRknelvrpkvaNvdql 19 
                  +R +++ r++ +N+ q 
   AJA92099.1 395 PRASAIWRESKSNISQF 411
                  899***********986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.8e-05     0.099      12      38 ..       8      34 ..       2     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                SEEEEEESTTSSHHHHHHHHTTSS--S CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 12 ekvaivGenGaGKStLlkllagllkpt 38
                 k+ ++G+ G GKS L++ l+g++   
  AJA92099.1  8 PKIIVIGKEGVGKSQLISSLTGKYAES 34
                57889******************9763 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011      0.14      46     108 ..     326     389 ..     316     398 .. 0.89
   2 ?   -2.7   0.3       3.1     4e+03       7      37 ..     506     535 ..     501     542 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
     Saf_2TM  46 alklaggslevsfssse.ipeivlaiilvigvllivvGavllilryvneakrqskkkvivIEgr 108
                 ++ + g + + +fs s  ++++  +  lvi +l++++   +l+ r v  +k++ k ++ vIEg 
  AJA92099.1 326 SAISFGSACSYQFSASIaVFSASGMPWLVIPFLFFLTATTILYTRIVSRKKNRIKLNMPVIEGQ 389
                 556667778889999988999999**************************************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
     Saf_2TM   7 virklidwlfRkrsaelllft.igvalllail 37 
                 vir+ ++w+f  +  +  ++  ++ +llla +
  AJA92099.1 506 VIRE-MSWMFAIKMVGKQIIAvVAFTLLLA-H 535
                 5555.4677777777766554045555554.4 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.3e-05      0.11       1      38 [.       9      48 ..       9      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.3e-05
                EEEEEESTTSSHHHHHHHHHHSSCSSSCT...TTSSEEEEE CS
         Ras  1 KlvlvGdsavGKtslllrfvkdkFkeeye...sTigvdfyt 38
                K++++G+++vGK+ l+ + + + + e+++   sT+  ++y+
  AJA92099.1  9 KIIVIGKEGVGKSQLISSLTGK-YAESSNfkgSTVSKESYN 48
                89*************9987754.444332122666666655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018      0.23       3      36 ..       8      41 ..       6      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
      AAA_24  3 lkiliyGpsgiGKTtlakelgpkplfidtekGlk 36
                 ki+++G++g+GK+ l+++l+ k +    +kG+ 
  AJA92099.1  8 PKIIVIGKEGVGKSQLISSLTGKYAESSNFKGST 41
                69*****************988877777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3630.32
//
Query:       AJA92100.1  [L=178]
Description: ATP:cob(I)alamin adenosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-53  180.0   0.0    4.3e-53  179.8   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.8   0.0   2.4e-57   4.3e-53       1     163 [.       3     164 ..       3     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 2.4e-57
                      XXXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHH CS
  Cob_adeno_trans   1 iyTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveeleke 94 
                      iyT+tGD+G+Tsl++++rv K+d r+  yG+vDelns ig+a++l  e + e+k+ L +iqn+Lf +g++la+p+ + +k + + e ++ le++
       AJA92100.1   3 IYTKTGDEGKTSLFDNSRVWKSDERILSYGAVDELNSSIGVALSL--ELDPEIKDILIKIQNDLFIVGSDLANPKMSDKKIRTSPEMITFLEQK 94 
                      9******************************************54..45789**********************8888898999999******* PP

                      HHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHHHH CS
  Cob_adeno_trans  95 ideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvlarv 163
                      +d le +l+pl+sfilpgg+ +a+ lh+ Rt+ RraE +vv+l+++e +++++  ylNRLSDl+f+lar 
       AJA92100.1  95 MDLLEPQLEPLTSFILPGGTLLASILHLSRTISRRAETHVVALSRNEeINKDAAIYLNRLSDLMFILARS 164
                      ********************************************988899******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1491.37
//
Query:       AJA92101.1  [L=320]
Description: transcription factor TFIIB repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-19   69.9   1.8    8.4e-09   35.4   0.1    2.4  2  TFIIB          Transcription factor TFIIB repeat
    4.6e-05   22.9   5.0    4.6e-05   22.9   5.0    2.4  2  TF_Zn_Ribbon   TFIIB zinc-binding
  ------ inclusion threshold ------
      0.084   13.0   0.0       0.21   11.7   0.0    1.7  1  Cyclin_C       Cyclin, C-terminal domain
        1.2    9.2   5.0         19    5.3   0.1    2.8  3  Zn_Tnp_IS91    Transposase zinc-binding domain
        1.5    8.9   8.8       0.55   10.3   0.6    2.9  2  DZR            Double zinc ribbon


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.2   7.7e-12   2.7e-08       2      62 ..     125     186 ..     124     189 .. 0.92
   2 !   35.4   0.1   2.3e-12   8.4e-09       9      71 .]     231     296 ..     224     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 7.7e-12
                 HHHHHHTT--HHHHHHHHHHHHHHTTSTT.TTSGCTTHHHTTHHHHHHTTTTSS--HHHHHH CS
       TFIIB   2 krfadaleLpekVadaAkelaklaleekv.lkGrspagiaAAclyiAcrkeevkrtqkeiss 62 
                 ++ +    Lp+ V + A  +++    +++ +kG+s  +i  A++y+Ac++++  r++ ei++
  AJA92101.1 125 SETCVSCSLPKNVVETASMIYRSLDGKNIeVKGKSVVSITIAVVYMACKQCGIVRSLDEICK 186
                 56688889***************99999879*****************************96 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 2.3e-12
                 T--H...HHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   9 eLpe...kVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 +L +    V++ A e+a ++ +++++ G+ p+gia+A ly+ + + + +  q+++s v+ ++e+ti
  AJA92101.1 231 NLTKtdvRVERLALEIAAKTETKNITDGKAPNGIASAYLYVSSVLLGQNVLQRDVSTVSGITEVTI 296
                 44444448********************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   5.0   1.3e-08   4.6e-05       3      41 ..      10      47 ..       9      49 .. 0.94
   2 ?    0.7   0.4       0.1   3.7e+02      22      28 ..     172     178 ..     169     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.3e-08
                  ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHH CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewr 41
                  C +C+s+ ++ D  +ge +C+ CG V++++ +d gpe  
    AJA92101.1 10 CTECKSP-VIDDIHNGERICSGCGIVVDEQMADMGPETK 47
                  9*****8.89**************************965 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
                   ESSSSBE CS
  TF_Zn_Ribbon  22 CtdCGlV 28 
                   C+ CG V
    AJA92101.1 172 CKQCGIV 178
                   7777766 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.9e-05      0.21      43      91 ..     260     308 ..     216     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.9e-05
                 -HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHHH CS
    Cyclin_C  43 ppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilells 91 
                  p  iA+a l++++  l+++  ++ +  ++g+++  +++ v+ il+ ++
  AJA92101.1 260 APNGIASAYLYVSSVLLGQNVLQRDVSTVSGITEVTIRNRVKEILSTHK 308
                 67889****************************************9994 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7    0.0085        31      39      72 ..       7      40 ..       5      46 .. 0.88
   2 ?   -2.0   0.0         1   3.7e+03      32      46 ..     118     132 ..      92     140 .. 0.64
   3 ?    5.3   0.1    0.0054        19      39      81 ..     169     211 ..     162     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0085
  Zn_Tnp_IS91 39 ryeCeeCghekivyfsCksrhCpsCqkkateewl 72
                 + +C+eC++  i     ++r C+ C+    e+++
   AJA92101.1  7 QSCCTECKSPVIDDIHNGERICSGCGIVVDEQMA 40
                 568***********************98888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
  Zn_Tnp_IS91  32 taalGfaryeCeeCg 46 
                  t+ lG     C +C+
   AJA92101.1 118 TNVLGKISETCVSCS 132
                  444666666676665 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0054
  Zn_Tnp_IS91  39 ryeCeeCghekivyfsCksrhCpsCqkkateewlekqqeellp 81 
                   ++C++Cg  + +   Ck+   p+  k +t+  ++  ++ +l+
   AJA92101.1 169 YMACKQCGIVRSLDEICKNVCAPKDVKAKTKLAAKYYRNLVLE 211
                  578****************999998888887777666666665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00015      0.55       1      23 [.      10      36 ..       6      69 .. 0.71
   2 ?    1.3   2.1       0.1   3.7e+02      14      38 ..     127     179 ..     104     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
         DZR  1 CpqCgee....lppdarfCseCgtklk 23
                C +C+++    ++++ r Cs Cg  ++
  AJA92101.1 10 CTECKSPviddIHNGERICSGCGIVVD 36
                555555555555555555555554444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
         DZR  14 fCseCgtklkavaa............................edrCpsCgekv 38 
                 +C  C  + + v++                              +C +Cg   
  AJA92101.1 127 TCVSCSLPKNVVETasmiyrsldgknievkgksvvsitiavvYMACKQCGIVR 179
                 55555555433333445555555555555555555555556556677776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2477.68
//
Query:       AJA92102.1  [L=555]
Description: putative ribulose-phosphate 3-epimerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-53  178.7   0.2    1.3e-52  178.1   0.2    1.2  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
    2.7e-44  151.5   0.5    5.3e-43  147.3   0.5    2.1  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    2.7e-06   26.8   0.0    0.00054   19.3   0.0    2.4  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    4.1e-05   22.7   0.0      7e-05   21.9   0.0    1.3  1  E1_dh            Dehydrogenase E1 component
    9.6e-05   22.2   0.0    0.00023   21.0   0.0    1.6  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00013   21.0   0.7    0.00059   18.7   0.7    2.1  1  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.1   0.2   4.2e-56   1.3e-52       2     198 .]     293     492 ..     292     492 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 4.2e-56
                     EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT-SEEEEE-S..T-TTH CS
  Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeagasiisvHaE..alehl 94 
                     iapS+++ d+++l++evk+ ++  ad++H+DvmDg+fvpN t+  + +++lr+lt +p+d HLm++e+ r ++++++ag++i++vHaE  + +  
      AJA92102.1 293 IAPSIIAGDMTNLKNEVKRCDDGRADYIHLDVMDGQFVPNSTFDHTKIKELRPLTVIPFDTHLMINEPVRQIQNYIDAGSDIVTVHAEvcDESSF 387
                     9***************************************************************************************6666677 PP

                     HHHHHHHHHTTSEEEEEE-TT--G.GGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT- CS
  Ribul_P_3_epim  95 krtiqeikeaGakaglvlnpatpl.ealeyllekldlvllmsvePgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeaga 188
                      ++   +k++ + +gl++np t + ++ ++++++ld +++msv Pg++GQk+i+++ ek k++   ++e+++   ie+DGGv+ldni q  ++ga
      AJA92102.1 388 GEIHDLLKSNKVGVGLAINPDTSMpDWSKKFISSLDQIIVMSVVPGKSGQKYIENTHEKTKNLMINLKENGFAGYIEADGGVTLDNIGQCFADGA 482
                     899999****************99456689***************************************************************** PP

                     -EEEESHHHH CS
  Ribul_P_3_epim 189 dvlVagsavf 198
                      v+V gsa++
      AJA92102.1 483 RVFVGGSAII 492
                     ********95 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.3   0.5   1.8e-46   5.3e-43       6     262 ..      12     274 ..       8     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 1.8e-46
                      HHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-SS- CS
  Transketolase_N   6 vnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsledlksfrqlgsktpGhP 99 
                      v + R L++   + a+sGhPG ++++a+i   +f ++lk +P++p+w dRD+ +Ls Ghas  l+s + + Gy ++ ++l  +rq+gsk  GhP
       AJA92102.1  12 VLQARKLVIRGTSIAGSGHPGGSFSMAEIMGCIFYNHLKFDPKNPEWEDRDKLILSKGHASPGLFSNMAVAGY-FEESQLDTLRQFGSKLQGHP 104
                      55678999999999***********************************************************.56799*************** PP

                      -TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGG CS
  Transketolase_N 100 elghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGetei 193
                      +  + +gve   G LG G++ ++g ala k           d  d +++ ++gDg   eG   ea+  a++ ++++L  + D n i  d  te+
       AJA92102.1 105 D-LKCPGVEFCGGSLGIGLSYSIGNALAAKL----------DQKDTHIFTVMGDGESDEGQVWEAAMTAAKYNVDNLTLILDRNFIQQDSYTEK 187
                      *.689*******************9987653..........3457899************************************9976665554 PP

                      T-......-S-.............HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTSTTTTTSGGGTSS- CS
  Transketolase_N 194 sf......ted.............vakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygspakagtedvhGap 262
                       +      + d             + ++++++gW+vie  dg+ +e+i++a+++ak++k  Ps+i  rt+ G +    +++ + hG +
       AJA92102.1 188 IMpldeslDGDelsemwkdasrwkTGDKWRSFGWNVIE-VDGHRIEQISDALNRAKSVKGMPSIIIARTIKGKAVEHMEDNPQWHGKA 274
                      321111111111111111112222457999*******9.799*********************************9999999999976 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.8e-07   0.00054     110     180 ..     115     189 ..       6     213 .. 0.77
   2 !    5.4   0.0     0.003         9     235     269 ..     217     251 ..     197     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
  DXP_synthase_N 110 agHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnni.gelkkkllvilNdN...emsisknvG 180
                      g  +  +s++ G a a++l+++++++ +v+GDg    G  +ea  ++ + + ++l +il  N   + s+++++ 
      AJA92102.1 115 GGSLGIGLSYSIGNALAAKLDQKDTHIFTVMGDGESDEGQVWEAAMTAaKYNVDNLTLILDRNfiqQDSYTEKIM 189
                     45556789***********************************85555166678999999988333345555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.003
  DXP_synthase_N 235 eelgfkYlGpidGhdleelikvleevkklkg.pvll 269
                     +++g + +  +dGh +e++ ++l+++k++kg p ++
      AJA92102.1 217 RSFGWNVI-EVDGHRIEQISDALNRAKSVKGmPSII 251
                     55566555.69*****************98756665 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.4e-08     7e-05      91     152 ..     108     167 ..      80     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.4e-08
                 BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT- CS
       E1_dh  91 ekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwkl 152
                 + ++++ gg+  +g+      G alaak ++k++  ++++GDg + +G+v+ea+  aa +++
  AJA92102.1 108 CPGVEFCGGSLGIGLS--YSIGNALAAKLDQKDTHIFTVMGDGESDEGQVWEAAMTAAKYNV 167
                 6677888888888888..55699******************************999887765 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   7.7e-08   0.00023      30     148 ..     122     247 ..     110     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.7e-08
                   TTTHHHHHHHHHHHSTTSEEEEEEEHHH..HHHTGGGHHHHHHTT-.SEEEEEEE-SBCCCHHHH......HHHHTCCTTTTSBB.BS----HHHHH CS
  TPP_enzyme_C  30 mGyglpaAiGaklakpdrevvaivGDGg..flmilqelatavrrnl.pitvvvlnNegygmtggq......qepfggkrksgpagkdlkpvdfakla 117
                   + y+++ A++akl ++d +++ ++GDG        ++ +ta+++n+ ++t+++  N + +    +      ++   ++ + ++  kd    +     
    AJA92102.1 122 LSYSIGNALAAKLDQKDTHIFTVMGDGEsdEGQVWEAAMTAAKYNVdNLTLILDRNFIQQDSYTEkimpldESL--DGDELSEMWKDASRWKTGDKW 216
                   335555555556557799*********8445667999*********7777777778877766666656643222..33333444458899999999* PP

                   HHTTSEEEEESSH.HHHHHHHHHHHHCSSSE CS
  TPP_enzyme_C 118 ealGakgarvekadveeleealkealekkgp 148
                   +++G +++ v+ + +e++ +al +a + kg+
    AJA92102.1 217 RSFGWNVIEVDGHRIEQISDALNRAKSVKGM 247
                   *************************966653 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.7     2e-07   0.00059     124     176 ..     100     156 ..      86     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2e-07
       XFP_N 124 ipshvaaetPGsiheGGelGyalshayG....avldnPdlivacvvGdGeaetGPla 176
                 +  h   + PG    GG lG  ls+++G    a ld+ d  +++v+GdGe++ G + 
  AJA92102.1 100 LQGHPDLKCPGVEFCGGSLGIGLSYSIGnalaAKLDQKDTHIFTVMGDGESDEGQVW 156
                 56788888999999*****9888887773333678*****************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3844.97
//
Query:       AJA92103.1  [L=165]
Description: ribosomal-protein-alanine acetyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-16   60.8   0.0    1.8e-16   60.5   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.3e-09   37.0   0.3    6.5e-09   36.1   0.1    1.5  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.6e-09   36.6   0.3    5.9e-09   35.9   0.3    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.9e-08   34.2   0.1    1.4e-07   31.4   0.0    2.0  2  FR47             FR47-like protein
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.061   13.0   0.0    2.1  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
      0.026   15.2   0.0      0.034   14.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.031   14.4   0.0       0.06   13.4   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.039   14.1   0.0      0.061   13.5   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
      0.058   13.5   0.5      0.083   13.0   0.5    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   8.8e-20   1.8e-16       5     117 .]      25     141 ..      14     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 8.8e-20
                     HHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT CS
  Acetyltransf_1   5 vellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipd.......ekggvayieslaVspeyrgkGlGsaLlealeeraree 92 
                     +e+ +++ +++++d ++e         +e +lvae+d + +G+i+++              +++++ s+aV +e rg+G G+ L++++ + ++e+
      AJA92103.1  25 MEINMKTLPEHYSDYFYESLLAE---APEAFLVAEKDSQYVGYIMCKTEFGfsnfkklGFVKKGHVVSVAVLEEQRGNGFGKILVNEAFKGVKEK 116
                     55666666666666666665555...6669999***********9999999**9*9998889********************************* PP

                     TESEEEEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  93 gikkivlaveedndaairlYeklGF 117
                     ++++++l+v+ +n+ a++lY+ lG+
      AJA92103.1 117 QCDEMYLEVRCSNTEAVKLYQDLGM 141
                     ********************77995 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         6   1.2e+04      67      71 ..      39      43 ..      19      44 .. 0.60
   2 !   36.1   0.1   3.2e-12   6.5e-09       3      73 ..      50     140 ..      48     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6
                    HHHHH CS
  Acetyltransf_7 67 kfYek 71
                     fYe+
      AJA92103.1 39 YFYES 43
                    38887 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 3.2e-12
                     EEEEEEEETTEEEEEEEEEEES.............TCTEE...EEE-GGGTTSSHHHHHHHH.....TTSEEEEEEEEE....THHHHHHHHHHT CS
  Acetyltransf_7   3 gevfVaeddgkivGfialslld.............aeitr...laVdpeyrgkGiGraLlea.....aekgiileqlel....naekaikfYekl 72 
                     + ++Vae+d + vG+i ++ +              +   +   +aV++e rg+G G+ L++      +ek++   + +l    ++++a+k+Y+ l
      AJA92103.1  50 EAFLVAEKDSQYVGYIMCKTEFgfsnfkklgfvkkG---HvvsVAVLEEQRGNGFGKILVNEafkgvKEKQCD--EMYLevrcSNTEAVKLYQDL 139
                     6799**********9998888899998887775544...1456*****************9523333113333..223332445559******99 PP

                     T CS
  Acetyltransf_7  73 G 73 
                     G
      AJA92103.1 140 G 140
                     8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.3   2.9e-12   5.9e-09      22     109 ..      40     144 ..      25     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.9e-12
  Acetyltransf_10  22 lreri.eegealllvaeeggkivGvielrdgs..............hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                      ++e + +e    +lvae++ + vG+i  +++               h+  ++V +e+rg+G gk L++++ + +++++  +  l+v+ s+ +av
       AJA92103.1  40 FYESLlAEAPEAFLVAEKDSQYVGYIMCKTEFgfsnfkklgfvkkgHVVSVAVLEEQRGNGFGKILVNEAFKGVKEKQCDEmYLEVRCSNtEAV 133
                      4444446777889*************777766799999***********************************999999999*****9999*** PP

  Acetyltransf_10  99 pfYeklGFkav 109
                      ++Y+ lG+   
       AJA92103.1 134 KLYQDLGMDIK 144
                      *******9755 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.13   2.5e+02      50      80 ..      54      84 ..       4      88 .. 0.71
   2 !   31.4   0.0     7e-11   1.4e-07      22      78 ..      85     142 ..      82     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                HHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
        FR47 50 iaergktvllvvvasNtpsirlyeklGfeki 80
                +ae++ + + ++  + +   + ++klGf k 
  AJA92103.1 54 VAEKDSQYVGYIMCKTEFGFSNFKKLGFVKK 84
                4556666666777777777778999999875 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 7e-11
                 SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-E CS
        FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfe 78 
                 g + ++ vl+e r+ G+g+ lv++  k++ e + +++ l v+ sNt++ +ly+ lG  
  AJA92103.1  85 GHVVSVAVLEEQRGNGFGKILVNEAFKGVKEkQCDEMYLEVRCSNTEAVKLYQDLGMD 142
                 78899**************************666888999***************975 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05     0.061      20     139 ..      26     143 ..      23     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                     HHH-----HHHHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT CS
  Acetyltransf_8  20 ewweeagtleevrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHllig.eaeargkglttallralvhylfadpr 113
                     e+ +++ +++  +++++ l a+     l+++ d + vgy+ +    e   +++++      G  + ++  +e+rg g+++ l+++  + + ++ +
      AJA92103.1  26 EINMKTLPEHYSDYFYESLLAEAPEAFLVAEKDSQYVGYIMCK--TEFGFSNFKKLGFVKKGHVVSVAvLEEQRGNGFGKILVNEAFKGVKEK-Q 117
                     5666667767777777777777777777777777777777773..44444566666666666666666457799*********9999998766.9 PP

                     --EEEE--BTT-HHHHHHHHHTT-EE CS
  Acetyltransf_8 114 trrvvvEPdvrNerairllekaGfek 139
                     ++ + +E + +N++a++l++ +G+  
      AJA92103.1 118 CDEMYLEVRCSNTEAVKLYQDLGMDI 143
                     **********************9875 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.7e-05     0.034      39     137 ..      43     141 ..      11     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
  Acetyltransf_3  39 ewlera....waeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSi 129
                     ++l++a    + +e++++ +g++++  +t + G+ ++ +l    +   ++  + ++ +g+G+++  v+ + + + +e + ++++ ++  +N+  +
      AJA92103.1  43 SLLAEApeafLVAEKDSQYVGYIMC--KT-EFGFSNFKKLGFVKKGHVVSVAVLEEQRGNGFGKILVNEAFKGV-KEKQCDEMYLEVRCSNTEAV 133
                     2222222222223334444556665..33.356666666666655477788888999*****************.7777**************** PP

  Acetyltransf_3 130 rvleklGf 137
                     ++++ lG+
      AJA92103.1 134 KLYQDLGM 141
                     *******9 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05      0.06      42     106 ..      50     117 ..      13     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                     SEEEEEEETTEEEEEEEE.EEEEEEE.TT.EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT CS
  Acetyltransf_9  42 srvlgaedngelvgqlal.lplelnv.pG.ktlkaagvtgVavapehrgrgvlskLlaraleemreeg 106
                     + +l+ae++ + vg +++ + + ++       +k + v++Vav  e+rg+g+ + L+++a++ ++e++
      AJA92103.1  50 EAFLVAEKDSQYVGYIMCkTEFGFSNfKKlGFVKKGHVVSVAVLEEQRGNGFGKILVNEAFKGVKEKQ 117
                     577777777787776665334444331445667889**************************999875 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.1e-05     0.061      27      57 ..      87     117 ..      61     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
  Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaalddareeg 57 
                      +  + V ee rG G++k Lv++a++ ++e++
       AJA92103.1  87 VVSVAVLEEQRGNGFGKILVNEAFKGVKEKQ 117
                      5567899*****************9999875 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   4.1e-05     0.083      51     153 ..      51     160 ..      26     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
  Acetyltransf_4  51 vflvae.sdrivGy......aylgqfkkr.akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelv 137
                      flvae + + vGy      +  ++fkk    ++   +sv +  + ++ +g g+ l++   +  ke    +++ e+  +n++++++++ lG ++ 
      AJA92103.1  51 AFLVAEkDSQYVGYimckteFGFSNFKKLgFVKKGHVVSVAVL-EEQRGNGFGKILVNEAFKGVKEKQCDEMYLEVRCSNTEAVKLYQDLGMDIK 144
                     5888888888999822222223456777754455556788887.57999****99**************************************** PP

  Acetyltransf_4 138 gifkkcikkngrwiDm 153
                     +++k ++ ++   + m
      AJA92103.1 145 QRLKSYYRDGEDAYMM 160
                     *****99998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1184.47
//
Query:       AJA92104.1  [L=439]
Description: PF08489 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-36  125.0   0.0    5.5e-36  123.2   0.0    1.9  2  DUF1743         Domain of unknown function (DUF1743)
     0.0067   16.3   4.5      0.013   15.4   4.5    1.4  1  C1_1            Phorbol esters/diacylglycerol binding domain 
  ------ inclusion threshold ------
       0.12   12.2   2.0       0.52   10.2   2.0    2.0  1  MCM_OB          MCM OB domain
       0.62   10.0   3.2        1.3    9.0   3.2    1.5  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.57   2.6e+03      69     102 ..      50      89 ..      35     100 .. 0.75
   2 !  123.2   0.0   1.2e-39   5.5e-36       1     116 []     142     255 ..     142     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                 -STTSS......EEEEEEES-HHHHHHHHHCSEE..S-EE CS
     DUF1743  69 Phtpdp......vlfGirgedpeallkaakeilskeeese 102
                 P+ p +      v   i  ++pe++++ +k+  ++++ ++
  AJA92104.1  50 PNIPWKtrgngaVGIKISTSNPEKIKNLVKKFVKQYSDVK 89 
                 5555555555556666788899999999999999888776 PP

  == domain 2  score: 123.2 bits;  conditional E-value: 1.2e-39
                 TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEEES-HHHHHHHHHCSEE.. CS
     DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGirgedpeallkaakeilske 98 
                 g+g++GAt ++g+n++  d tyEll+Yr+++++g +r++d+++v+e++ektyp+tf+++D ++++v+l+Ph+pdpv++G+rged  +l++a k+i+  +
  AJA92104.1 142 GQGLVGATSVIGYNFK--DQTYELLSYRKSSQFGkKRSIDKSKVKEMQEKTYPNTFNSFDSKKNKVLLMPHGPDPVFYGVRGEDSSTLISASKMIKP-K 237
                 789**********776..79*****************************************************************************.8 PP

                 S-EECEEEEEESTTS-TT CS
     DUF1743  99 eeseemavfrtnqgtdah 116
                 e+   +++f++nqgt +h
  AJA92104.1 238 EKLAGYLIFKSNQGTGDH 255
                 99999**********998 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   4.5   2.9e-06     0.013      11      36 ..     358     384 ..     351     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                 --B-TTT-SB--S.SSS-EEEETTT-- CS
        C1_1  11 ptfCkhCgeflwg.kekqglkCswCkl 36 
                   fCk+C+++++  +  qg++C  Ck 
  AJA92104.1 358 NPFCKKCKKSMKSkGKNQGFQCVKCKK 384
                 569********887999********96 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0   0.00012      0.52      10      64 ..     319     369 ..     310     403 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                 TTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH- CS
      MCM_OB  10 igklvkveGivtrasevkpklkkavfeckkcgktveveleePrkCeekeCeskdp 64 
                 ig ++kv G + +as+++p++ ++ f      + ++ +l++P+ C  k+C+++ +
  AJA92104.1 319 IGDMIKVGGGIRKASKTHPRILNIEFIQVLKLE-KKSKLTNPF-C--KKCKKSMK 369
                 899******************999887655444.4458999*9.8..67774332 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.2   0.00029       1.3       3      28 ..     360     383 ..     359     389 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                     BESTTTSBEEEEECSCCCEEEESSSS CS
  RNA_POL_M_15KD   3 FCpkCgNlLlpkedkegknfeCrqCg 28 
                     FC kC+  + +k++  g  f C +C+
      AJA92104.1 360 FCKKCKKSMKSKGKNQG--FQCVKCK 383
                     *****************..99****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3019.67
//
Query:       AJA92105.1  [L=1125]
Description: DNA polymerase II, large subunit DP2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1023.8   0.0          0 1023.3   0.0    1.2  1  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
          2    8.5  14.7        6.2    6.9   0.1    2.8  2  zinc-ribbons_6  zinc-ribbons


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.3   0.0         0         0       1     863 [.      19     873 ..      19     874 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1023.3 bits;  conditional E-value: 0
    PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeiaegkvgeae.skeeavdkavrta 98 
                 eY+e+l+k++ + +e+a++a+s+ ld +  +E ++A dla+Rv+k+++i+ +a  +rel +++++e++al ++keia gk+++ + s e+++d+avr++
  AJA92105.1  19 EYYEELSKQVYKEFETAADAKSTLLDSSGIIEPKIAFDLAERVAKMHDID-IATPLRELLDKTGKENAALIMSKEIALGKYQSSDaSLEDRLDHAVRVG 116
                 6************************************************9.***************************999876626789********* PP

    PolC_DP2  99 lalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDyvrkklgldrykpr..eeeieRyveEielYer..vaslqyspsd 193
                 la++tegv++APl+Gi+++kik+n+dg+eyl+v+ aGP+RsaGGt++a+++L+aD+vr+++gl++y++   ++e+ R+veE+++Ye+   +s+q+++sd
  AJA92105.1 117 LAIVTEGVTIAPLQGISEIKIKNNKDGSEYLSVSIAGPMRSAGGTESAVTMLIADHVRRAVGLEKYQADcfDDETGRFVEELRIYESeaKQSFQFHVSD 215
                 *******************************************************************9888***************977789******* PP

    PolC_DP2 194 eeirlivknipveidGeatedeevsgyrdlervetnrvRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkeky 292
                 ++i+++++n+pve++Ge t+  ev ++r++ r++t+rvRGG+l+vl++G++ ++kK++k++++++legWewl+e++ a    +k+e+ ++    ++ek 
  AJA92105.1 216 DDIKTVISNLPVELEGEGTDPDEVVNHRNMTRIKTDRVRGGALRVLNDGLIGRSKKLLKRIEQYNLEGWEWLHEIQGA---VQKGESGDD----ASEKR 307
                 **************************************************************************9999...444444444....678** PP

    PolC_DP2 293 lrdliaGRpvlshpsrkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveealeikke 391
                 ++++i+GR+vls+p+++GGfRLrYGR++ntg+a++g+hP   e+ld+ +avGtq+k+++P K+a+v+ vds+e+P+v+lk G+vv+i+d+e+ ++ik++
  AJA92105.1 308 MKEVITGRSVLSMPNKTGGFRLRYGRACNTGFASVGLHPVIAEILDHTIAVGTQIKLDKPSKGATVAFVDSLETPIVRLKGGEVVKIQDTEHGIQIKHD 406
                 *************************************************************************************************** PP

    PolC_DP2 392 veeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee.....kpsaeealelseeldvpLhPkytylwhdisveelekLaeavaekk 485
                 +e+il+lG+iL+++G+flenn++L+p++ vee wi+ l+++ +k++ +      +p+  ea+ ls+el++pLhPk+ y+w+ i++eel+++++ + +++
  AJA92105.1 407 IEKILHLGDILITFGDFLENNAELIPTPMVEEVWIEYLKAKLSKNDVRLefltkTPTFVEAILLSKELKIPLHPKFLYYWNFITTEELKQITSPILKSE 505
                 ***************************************8888776554789989****************************************9988 PP

    PolC_DP2 486 kleeeklvleleeevkeiLekllvehkvkeekivieea.lallkslgldleeeklekeeekdalelvnelsglevrekaptrigaRmGRPeKskeRkmk 583
                     +++  ++e + k+i+e+ +++hkv+++ki+i+     +l+ l + ++   l+  +++++lel+++ +g+e+++k + +ig+R+GRPeK+++R mk
  AJA92105.1 506 ----NEI--HYEISKKQIFENAGIPHKVSDDKIIISGIdVQILNHLIFGNS---LDFGSSSSVLELLSKNTGIEIKNKFSKSIGVRIGRPEKAAPRLMK 595
                 ....334..4455668*******************5441446677766555...33346679************************************* PP

    PolC_DP2 584 pavhvLfpigeaggkrrsvkeaakkkgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkelleka 682
                 p+vhvLfp+ e+gg +r++ +a++k+++   ++++r+C++C+  ++ + C++Cg+kt++ + C+ c+ e e+ +cekc+++a+  + k++ lk+ l +a
  AJA92105.1 596 PPVHVLFPVAEKGGITRDILKASAKSESFFSNLNNRRCDNCNIPSIGIICTKCGKKTTKYYICRICKDELETPHCEKCKRDANGFSYKQFPLKQSLISA 694
                 ************************89999********************************************************************** PP

    PolC_DP2 683 leklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGkplesedqivelkvq 781
                 +eklg+  ++++ +kgv++l+++ekipEpleKg++R++ ++svfkdgtvR+D+t+ plthf+ ++ig++v+++++lGY++D++G+ +++++q++elk+q
  AJA92105.1 695 QEKLGI--RAKSPFKGVEQLINQEKIPEPLEKGLIRQNFGLSVFKDGTVRFDATNSPLTHFKLSWIGTTVDQIKNLGYEKDVNGNSITNDEQLIELKMQ 791
                 ******..67999************************************************************************************** PP

    PolC_DP2 782 DivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRR 863
                 D++++ ++a+yl++v+k++D +L+k++g + fYn+++++dL+G+lviglaPHts+g+ gR+iG+tk++v++a P++H+akRR
  AJA92105.1 792 DVIIPLESAQYLVNVSKYIDFELQKFFGKQSFYNLKNTQDLLGHLVIGLAPHTSVGITGRLIGYTKTHVCFASPIWHSAKRR 873
                 *********************************************************************************9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  10.4     0.015   1.4e+02      17      45 ..     643     673 ..     629     681 .. 0.66
   2 ?    6.9   0.1   0.00069       6.2      13      36 ..    1038    1061 ..    1026    1080 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                     EE-TTT--EEEEEEE-SSS-S---E..EEET CS
  zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqelev..lkaC 45 
                     + C +C ++ +k  +C  C++ele+  +++C
      AJA92105.1 643 IICTKCGKKTTKYYICRICKDELETphCEKC 673
                     5677777777777777777777774223334 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00069
                      -SSEEE-TTT--EEEEEEE-SSS- CS
  zinc-ribbons_6   13 rgeqyhCeaCqedlkkealCpeCe 36  
                       +++++C aC +++++ +l ++C 
      AJA92105.1 1038 AKQKFRCTACGAKYRRMPLLQKCT 1061
                      4689***********999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.43
# Mc/sec: 7843.99
//
Query:       AJA92106.1  [L=77]
Description: putative sulfurtransferase TusA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-21   74.7   0.0    4.1e-21   74.6   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.016   15.0   0.0    1.3  1  DUF2249   Uncharacterized conserved protein (DUF2249)


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   4.6e-25   4.1e-21       1      70 []       6      75 ..       6      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 4.6e-25
                EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEEE CS
        TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivirk 70
                ++lD+rGl CP P +++  +l k++ g+vl vladdpaa+ di  +++ +ghelv  ++++   +++i+k
  AJA92106.1  6 KTLDVRGLYCPSPAMQTVVELSKMQVGQVLLVLADDPAAEDDITDLCRTRGHELVQLNKNGSDLEFTIKK 75
                69******************************************************************98 PP

>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-06     0.016       1      34 [.       7      40 ..       7      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
     DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvnd 34
                tlDvR+l  p +  ++  ++++++ G++l++++d
  AJA92106.1  7 TLDVRGLYCPSPAMQTVVELSKMQVGQVLLVLAD 40
                79*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 593.17
//
Query:       AJA92107.1  [L=70]
Description: ribosomal protein L24e-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-20   71.2   3.6    6.4e-20   71.2   3.6    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
     0.0053   16.2   0.3       0.01   15.3   0.3    1.4  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
     0.0066   16.4   1.2      0.012   15.5   1.2    1.5  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
       0.03   14.7   0.0      0.034   14.5   0.0    1.1  1  NosL            NosL
       0.07   13.3   5.3        5.2    7.3   0.1    3.0  3  DUF2256         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   3.6   1.8e-23   6.4e-20       3      57 ..       8      63 ..       6      70 .] 0.88

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.8e-23
                    X-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-X CS
  Ribosomal_L24e  3 tekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRr 57
                    ++ CsF+++++ +G+G++fv+nDg+v+ F+s+Kc ++++  kr Prk kWT++y +
      AJA92107.1  8 VKPCSFCDRPVAKGTGTMFVKNDGTVLWFCSAKCkKNYMTLKRDPRKFKWTNKYVK 63
                    578*******************************5555678***********9955 PP

>> zf-FLZ  zinc-finger of the FCS-type, C2-C2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.9e-06      0.01      14      50 ..       9      48 ..       5      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
      zf-FLZ 14 saCflCkkkLgegkDiymYrGdka...FCSeeCRqqqiel 50
                + C++C +  ++g  +   + d     FCS+ C ++ ++l
  AJA92107.1  9 KPCSFCDRPVAKGTGTMFVKNDGTvlwFCSAKCKKNYMTL 48
                67************8877777765567*********9976 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   3.4e-06     0.012       4      41 .]       9      45 ..       6      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
      zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41
                k+C+fC +    ++  t  + ndg v  FCS  C++ Y
  AJA92107.1  9 KPCSFCDRPVAKGT-GTMFVKNDGTVLWFCSAKCKKNY 45
                79********8888.6889***************9987 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.6e-06     0.034      23      62 ..      21      62 ..       9      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.6e-06
        NosL 23 pkgqifyededepakFcstrdlfafllepeerk..eikaiyv 62
                  g++f+++++++++Fcs+++  +++  +++++  + ++ yv
  AJA92107.1 21 GTGTMFVKNDGTVLWFCSAKCKKNYMTLKRDPRkfKWTNKYV 62
                46899***99***************99998877345555565 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0015       5.2       7      17 ..       8      18 ..       4      21 .. 0.84
   2 ?    6.2   0.1    0.0031        11      32      40 .]      36      44 ..      30      44 .. 0.87
   3 ?    1.3   0.3      0.11   3.8e+02      15      23 ..      53      61 ..      52      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
     DUF2256  7 sKiCavCgrpf 17
                 K+C  C rp 
  AJA92107.1  8 VKPCSFCDRPV 18
                69*******97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
     DUF2256 32 yCSerCrrn 40
                +CS +C++n
  AJA92107.1 36 FCSAKCKKN 44
                7*****986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.11
     DUF2256 15 rpftwRkkW 23
                r+f+w  k+
  AJA92107.1 53 RKFKWTNKY 61
                89***9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 500.81
//
Query:       AJA92108.1  [L=195]
Description: ribosomal protein L31e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-16   59.9   0.4    5.1e-16   58.7   0.4    1.6  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.4   2.9e-20   5.1e-16       5      72 ..       7      73 ..       4      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.9e-20
  Ribosomal_L31e  5 reytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsr 72
                    r ytI + k + + + ++ra rA+++i++fa+k+m+t++ +id ++   +w+kg+r++p++irv++++
      AJA92108.1  7 RVYTIPLGKVLLS-QSQHRAVRAINMIREFARKHMKTQEIKIDEEVAHLIWSKGVRSPPRKIRVKMTK 73
                    7899998888765.77899*********************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1671  (0.093201); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 1241.93
//
Query:       AJA92109.1  [L=154]
Description: putative pantetheine-phosphate adenylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-15   55.9   0.0    5.8e-15   55.7   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.032   14.1   0.5      0.085   12.7   0.2    1.9  2  FAD_syn          FAD synthetase
       0.13   12.3   0.1        4.4    7.4   0.0    2.1  2  DpaA_N           Dipicolinate synthase subunit A N-terminal d


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   9.7e-19   5.8e-15       2     142 ..       7     142 ..       6     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 9.7e-19
                      EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH......HHHHHTTTTEEEEE CS
  CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltr......evlkklkpdklylv 88 
                      +gGtFD+iH GH  l+e+a +  e+ +i+g++sde   k + k   + e+R e+le+++++   ++ + +e+ +        + + ++d  +lv
       AJA92109.1   7 LGGTFDIIHVGHVGLIEKAVSISEK-IIIGLTSDEFISKHGkKINNNFEQRFENLEKMIHE--NFPNCSFEIAKldddfgPAVIEGNVD--ALV 95 
                      69***********************.**************64888899**********554..4799******999999999999999*..*** PP

                      EEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
  CTP_transf_like  89 igadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                      +++++ ++ +  ++ ++     ++ ++ +p       +k + + + iSst+ir+
       AJA92109.1  96 VSEETRKKGDILNASRKERNLTPVEIITIP-------MKLASDGKRISSTRIRN 142
                      *****9998778888888888888888888.......****************7 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.4e-05     0.085      13      35 ..       9      31 ..       4      62 .. 0.91
   2 ?   -1.1   0.0      0.27   1.6e+03     139     158 .]     119     139 ..      94     139 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
     FAD_syn 13 GnFDGvHlGHqallkkaveaake 35
                G FD +H+GH  l++kav+++++
  AJA92109.1  9 GTFDIIHVGHVGLIEKAVSISEK 31
                89****************99875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
     FAD_syn 139 fevevvp.kveleeekissta 158
                 +e+ ++p k+  ++++isst+
  AJA92109.1 119 VEIITIPmKLASDGKRISSTR 139
                 444444414578888999885 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.017     1e+02      45      91 ..      22      72 ..      10      86 .. 0.73
   2 ?    7.4   0.0   0.00074       4.4      31      71 ..      98     138 ..      85     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.017
                GGS-GGG-SEEE--TT....-BETTTEE-BSS-SS-EE-HHHHHTS-TT-E CS
      DpaA_N 45 leealedadviilPvp....gtkdggeintpfseeklsleelleklkkgql 91
                +e+a++ ++ ii  ++    ++k+g++in +f+++  +le+++++  +++ 
  AJA92109.1 22 IEKAVSISEKIIIGLTsdefISKHGKKINNNFEQRFENLEKMIHENFPNCS 72
                56666666666666654444689999****999999999999887776665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00074
                 TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BS CS
      DpaA_N  31 eleekiegvekaesleealedadviilPvpgtkdggeintp 71 
                 e+++k  ++ +a+  e  l  +++i  P+ + +dg++i+++
  AJA92109.1  98 EETRKKGDILNASRKERNLTPVEIITIPMKLASDGKRISST 138
                 677788889999999999********************983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1177.74
//
Query:       AJA92110.1  [L=646]
Description: excinuclease ABC, B subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-29  101.5   3.5    2.3e-29  101.4   1.0    2.5  3  UvrB_inter   UvrB interaction domain
    4.1e-21   74.5   4.9      1e-20   73.3   4.9    1.7  1  UvrB         Ultra-violet resistance protein B
    8.8e-19   67.9   0.8    4.3e-18   65.7   0.1    2.6  3  Helicase_C   Helicase conserved C-terminal domain
    1.2e-07   31.9   0.1    1.2e-07   31.9   0.1    3.0  4  ResIII       Type III restriction enzyme, res subunit
    2.9e-07   30.4   0.4    9.6e-05   22.2   0.1    3.4  3  DEAD         DEAD/DEAH box helicase
    2.9e-06   26.8   1.3    2.9e-06   26.8   1.3    2.7  2  UVR          UvrB/uvrC motif
  ------ inclusion threshold ------
      0.022   14.7   0.7      0.073   13.0   0.0    2.2  2  Microtub_bd  Microtubule binding
      0.046   14.2   0.9        1.9    8.9   0.0    3.3  3  AAA          ATPase family associated with various cellular a
      0.058   13.1   0.0        0.3   10.8   0.0    2.1  2  AAA_30       AAA domain
      0.061   13.5   0.0        7.5    6.8   0.0    2.6  2  Rhomboid_N   Cytoplasmic N-terminal domain of rhomboid serine
      0.093   12.9   0.0       0.31   11.2   0.0    1.9  2  AAA_33       AAA domain
       0.13   12.6   0.4         18    5.7   0.1    2.7  2  AAA_19       AAA domain


Domain annotation for each model (and alignments):
>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   1.0   1.6e-32   2.3e-29       1      91 []     157     246 ..     157     246 .. 0.98
   2 ?   -3.7   0.0       9.5   1.4e+04      50      67 ..     366     383 ..     346     400 .. 0.65
   3 ?   -2.6   0.0       4.2   6.3e+03      53      76 ..     462     485 ..     456     491 .. 0.69

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.6e-32
  UvrB_inter   1 lelkvgqkidreellrkLvelqYerndvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgkslekleeitifPakhf 91 
                 ++lk++++i+r+e+++kL+++ Yerndvel +G+Frv+Gdt++++pa+ ++ +iri++fgdeie+i+++d ++ +++++le+++ifPakh+
  AJA92110.1 157 ITLKKNEEIARNEIIKKLINARYERNDVELIPGNFRVKGDTIDVIPAY-SQDIIRISLFGDEIERITILDNVSLDIKKQLESFKIFPAKHY 246
                 689*********************************************.5****************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.5
  UvrB_inter  50 eevairieffgdeiesir 67 
                 +++++++e f+++++ + 
  AJA92110.1 366 DNRPLKFEEFEKKLKDVI 383
                 566666666666666554 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.2
  UvrB_inter  53 airieffgdeiesireidpltgks 76 
                  +r+     eie +++ + + +  
  AJA92110.1 462 EVRVRYLHSEIEGLQRTELIRQLR 485
                 577777788888887777666655 PP

>> UvrB  Ultra-violet resistance protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   4.9   6.8e-24     1e-20       1      42 [.     544     585 ..     544     586 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 6.8e-24
                 EE-SS--HHHHHHHHHHHHHHHHHHHHHHHHT------XXXX CS
        UvrB   1 lYADkiTdSMkkAideTerRReiQeaYNeehgItPktikKki 42 
                 +YAD+iT+SMk Ai+eTerRRe+Q++YN+e++I+Pkti+K+i
  AJA92110.1 544 MYADNITKSMKSAIAETERRREKQIEYNNENKIIPKTIIKSI 585
                 9***************************************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.9     1e+04      14      33 ..      53      77 ..      43      97 .. 0.57
   2 ?   -2.1   0.0       3.2   4.8e+03      45      75 ..     223     252 ..     185     259 .. 0.68
   3 !   65.7   0.1   2.9e-21   4.3e-18       6     110 ..     427     537 ..     422     538 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.9
                TTTSEEEEEESSHH...HHHH..HH CS
  Helicase_C 14 eeggkilifvntid...rlek..vk 33
                + g+++li++++++   +l++   +
  AJA92110.1 53 NTGKNALIISHNKTlaaQLYSelKQ 77
                4566777777777743322223223 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                 EEST.TSTHHHHHHHHHHHHTTSSSEEEESGG CS
  Helicase_C  45 vlhg.elpqnereeileqfnkgesdvLiatdv 75 
                 +l+  +l  ++++e+++ f ++  ++Lia d+
  AJA92110.1 223 ILDNvSLDIKKQLESFKIFPAK--HYLIAKDI 252
                 4443367777788888888653..47887775 PP

  == domain 3  score: 65.7 bits;  conditional E-value: 2.9e-21
                 HHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.....SSH CS
  Helicase_C   6 llell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.....rnv 97 
                 l++++ ++ ++++++l+ + t++++e+ +++l +kk+++v +lh+e++  +r e ++q + ge+dvL+  + + +G+dip+v+lV ++d++     rn 
  AJA92110.1 427 LIKEVsNRAKKNERTLVTTLTKRMAEDlADYL-SKKEVRVRYLHSEIEGLQRTELIRQLRLGEFDVLVGINLLREGLDIPEVSLVAILDADkegflRNN 524
                 55555578899************999877888.6667******************************************************88888889 PP

                 HHHHHHHTTSSST CS
  Helicase_C  98 tsyiqriGRtgRa 110
                 ts+iq  GR++R 
  AJA92110.1 525 TSLIQTFGRAARN 537
                 ************6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   7.8e-11   1.2e-07       7      96 ..      15      95 ..       9     174 .. 0.74
   2 ?    0.6   0.0      0.32   4.9e+02     130     144 ..     322     336 ..     221     391 .. 0.70
   3 ?   -2.8   0.0       3.5   5.3e+03      97     113 ..     432     448 ..     394     490 .. 0.64
   4 ?   -2.7   0.5       3.4   5.1e+03     109     109 ..     579     579 ..     533     639 .. 0.55

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 7.8e-11
                HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B-- CS
      ResIII  7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka 96
                 Q +ai++l+e  k   + +  +   TG+GKT++ a++i++  k     ++l++ ++k+l  q+++e+k+f+++++  +g +vs   + +
  AJA92110.1 15 DQPQAIDDLVEGSK--TKMNQTLLGVTGSGKTFTVANVIANTGK-----NALIISHNKTLAAQLYSELKQFFPKNN--VGYFVSYYDYYQ 95
                699*******9986..5556666788***************999.....8***********************986..343333332222 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                 TTT-SEEEEETGGGT CS
      ResIII 130 rdrfdviiiDEaHrl 144
                  +++ +++iDE+H +
  AJA92110.1 322 YGKEFLLVIDESHVT 336
                 334449999999965 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.5
                 .......-SEEEEEHHH CS
      ResIII  97 kekdstnkkilvttiqs 113
                 ++++++n + lvtt  +
  AJA92110.1 432 SNRAKKNERTLVTTLTK 448
                 34444445555554443 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.4
                 E CS
      ResIII 109 t 109
                  
  AJA92110.1 579 K 579
                 1 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   6.4e-08   9.6e-05       3      75 ..      15      83 ..      13     148 .. 0.78
   2 ?    1.2   0.0      0.19   2.8e+02     125     170 ..     328     390 ..     322     395 .. 0.54
   3 ?    2.7   0.1     0.065        98      36     103 ..     428     494 ..     419     512 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.4e-08
                HHHHHHHHHHTT....CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  3 iQaeaiplilgg....gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                 Q +ai+ +++g     +  + + TGsGKT   +  +         +tg+ ali++  + La q +++lk+f+ + +
  AJA92110.1 15 DQPQAIDDLVEGsktkMNQTLLGVTGSGKTFTVANVIA--------NTGKNALIISHNKTLAAQLYSELKQFFPKNN 83
                588888888866333345668899******99554444........7999**********************98543 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                 EEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTT................SEEEEEESSBS CS
                 xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxx RF
        DEAD 125 lVlDEadrlldq...gfsdfinrilnqlpqitcdgklq................rqvivlSATlp 170
                 lV+DE +  l q    ++ + +r  + ++    + + +                + vi++SAT+ 
  AJA92110.1 328 LVIDESHVTLPQlhgMYKGDFSRKKSLID-YGFRLP-SafdnrplkfeefekklKDVIFVSATPG 390
                 78888887777755544444444333331.111112.1344555556666655555888888876 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.065
                 HHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHHHTT.CSEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
        DEAD  36 lqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskldng.vdivvg 103
                 +++v++ + k++ ++l+ + t+ +ae+ ++ l+k     ++r+l + i+g ++++ +++l+ g  d++vg
  AJA92110.1 428 IKEVSN-RAKKNERTLVTTLTKRMAEDLADYLSKKEV--RVRYLhSEIEGLQRTELIRQLRLGeFDVLVG 494
                 666665.777788999999999999999998866544..5666668899999999999999666999998 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.1   4.6e+03      25      33 ..     263     271 ..     262     271 .. 0.86
   2 !   26.8   1.3   1.9e-09   2.9e-06       3      36 .]     606     639 ..     604     639 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.1
         UVR  25 klRDqinal 33 
                 +l+D++++l
  AJA92110.1 263 ELKDRLSRL 271
                 799**9987 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.9e-09
         UVR   3 likeLeeemeeAaenedFEkAAklRDqinalkkq 36 
                 +  e+e +m+  ae++dFE A k+RD+i++++k+
  AJA92110.1 606 QKIEIETQMKVFAEDLDFENAIKCRDKIKRIEKE 639
                 56799***************************85 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05     0.073      81     123 ..      30      70 ..       4      90 .. 0.71
   2 ?   -2.0   0.1       2.1   3.1e+03     108     136 ..     547     575 ..     536     592 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                  T--EEEEEEES................ST-HCHHHHHHHHHHC CS
  Microtub_bd  81 gynvcifaygqTGsGKtyTmegeeeeagmipraveeifetise 123
                  ++n ++  +g TGsGKt+T+ +  +++g++  ++++  + +++
   AJA92110.1  30 KMNQTL--LGVTGSGKTFTVANVIANTGKNALIISHNKTLAAQ 70 
                  444444..688***********666666655555544444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                  ST-HCHHHHHHHHHHCCTSCCCCEEEEEE CS
  Microtub_bd 108 gmipraveeifetiselkekgwkyeielq 136
                  ++i++++++ + ++++++ek+++y+ e +
   AJA92110.1 547 DNITKSMKSAIAETERRREKQIEYNNENK 575
                  45566666666666666666666665544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0013       1.9       3      35 ..      35      67 ..      34     136 .. 0.81
   2 ?    0.9   0.1      0.39   5.8e+02      82     112 ..     420     450 ..     410     468 .. 0.63
   3 ?   -0.4   0.0      0.95   1.4e+03      42      79 ..     523     562 ..     501     574 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
         AAA  3 lyGppGtGKTllakavakelgvefleisgsell 35
                l G  G GKT ++  v+ ++g + l is  + l
  AJA92110.1 35 LLGVTGSGKTFTVANVIANTGKNALIISHNKTL 67
                789*****************9999999988887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                 HHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
         AAA  82 eervvnqLlteldgvkkkeskvivigatnrp 112
                 ++  ++ L++e+++  kk+++++v + t+r+
  AJA92110.1 420 SQGQMDDLIKEVSNRAKKNERTLVTTLTKRM 450
                 4455666666666666666666666666663 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.95
                 HHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH.TTCCC CS
         AAA  42 sekkirelfkeakeka.kpsilfiDEidalaksr.sgses 79 
                 ++ ++ ++f +a +++ +++i+  D+i + +ks   ++e+
  AJA92110.1 523 NNTSLIQTFGRAARNSqGKVIMYADNITKSMKSAiAETER 562
                 4555667777766666567999999999998888533322 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002       0.3       5      66 ..      15      75 ..      13     113 .. 0.78
   2 ?   -1.5   0.0       1.2   1.8e+03      46      68 ..     438     460 ..     424     508 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
      AAA_30  5 eQaaavealltsgd..rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66
                +Q +a++ l+++++  + ++l G+ G+GKt++++    ++++ g++ ++++++++ A++L  el
  AJA92110.1 15 DQPQAIDDLVEGSKtkMNQTLLGVTGSGKTFTVAN---VIANTGKNALIISHNKTLAAQLYSEL 75
                788899888876541156899**********9765...56667777888888888888887665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
      AAA_30  46 ggrviglAptgkaAkvLaeelgi 68 
                 ++r ++ + t+++A++La+ l  
  AJA92110.1 438 NERTLVTTLTKRMAEDLADYLSK 460
                 46788888999999999875543 PP

>> Rhomboid_N  Cytoplasmic N-terminal domain of rhomboid serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.044        65      34      57 ..      54      79 ..      43      83 .. 0.80
   2 ?    6.8   0.0     0.005       7.5       4      33 ..     442     471 ..     440     481 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.044
  Rhomboid_N 34 egvq.lwle.deeqlaqveaeleeFl 57
                +g+  l+++ +++ +aq+ +el++F 
  AJA92110.1 54 TGKNaLIIShNKTLAAQLYSELKQFF 79
                4555577766***************6 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.005
  Rhomboid_N   4 LlslenpraaqafidYlrsqgiklelrsee 33 
                 L++    r+a  + dYl+++++ +++ ++e
  AJA92110.1 442 LVTTLTKRMAEDLADYLSKKEVRVRYLHSE 471
                 6666678***************99987765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021      0.31       5      78 ..      36     139 ..      34     167 .. 0.59
   2 ?   -3.8   0.0       8.9   1.3e+04      35      61 ..     429     453 ..     424     462 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
      AAA_33   5 vGlpGsGKstlaerllkklg..avllssdtlrr.rlfgtdqq..skt..........................dytrvldrlyq.ilnelarkalsagr 71 
                  G+ GsGK++ + ++++++g  a ++s ++ +  +l+ + +q  +k+                          + t++++++ + +l   a+ +l +g 
  AJA92110.1  36 LGVTGSGKTFTVANVIANTGknALIISHNKTLAaQLYSELKQffPKNnvgyfvsyydyyqpesympqtdtyieKDTQINEKIEKmRL--EATAMLLSGE 132
                 69**************9999*999999998444355554433222223444444444444444444444333333334433333133..3334566666 PP

      AAA_33  72 nvildat 78 
                 ++i+ +t
  AJA92110.1 133 PTIIVST 139
                 6666666 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.9
      AAA_33  35 rrlfgtdqqsktdytrvldrlyqilne 61 
                 + + ++ +++  ++t v++ ++++ ++
  AJA92110.1 429 KEVSNRAKKN--ERTLVTTLTKRMAED 453
                 5555433332..233344444444333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.012        18      12      36 ..      32      56 ..      21      72 .. 0.81
   2 ?    4.4   0.0     0.029        43      34      75 ..     431     471 ..     408     614 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
      AAA_19 12 vllvtaGpGtGKTrvlkhivallve 36
                +  +++  G+GKT ++  ++a   +
  AJA92110.1 32 NQTLLGVTGSGKTFTVANVIANTGK 56
                5678999**********99997765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
      AAA_19  34 lvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                 + ++   k e+ l+ ++t+r a+ l++ l++ +++ + +H+ 
  AJA92110.1 431 VSNRA-KKNERTLVTTLTKRMAEDLADYLSKKEVRVRYLHSE 471
                 33333.34499****************998877776666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1444  (0.0805399); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4738.17
//
Query:       AJA92111.1  [L=128]
Description: hypothetical protein T478_1214 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.8   0.0       0.16   13.4   0.0    1.3  1  DUF393    Protein of unknown function, DUF393


Domain annotation for each model (and alignments):
>> DUF393  Protein of unknown function, DUF393
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06      0.16       2      75 ..      11      81 ..      10      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
      DUF393  2 lyDgeCplCnravqflerrdrkgrirfadlqsasgkallkelgidaeqldslllvieagrvysgsdAaleiara 75
                +yD++C +C ++++++  + + g++r++   ++ g ++    +i ++++ ++++ i+++++y g +A++ +++a
  AJA92111.1 11 IYDDKCYVCIKFAKLMNFLAK-GKLRMIGHYTEFGGKIR--KEILEDDALEMFWFIDKETAYGGRAAIIPLLSA 81
                8***************99965.89**9999888887744..4444566666665599999****9999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 924.10
//
Query:       AJA92112.1  [L=622]
Description: putative type 2 DNA topoisomerase 6 subunit B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-57  193.0   0.0    4.4e-57  192.4   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
      8e-10   39.2   0.0    1.7e-09   38.2   0.0    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    3.1e-05   23.8   0.0    7.8e-05   22.5   0.0    1.6  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0029   16.4   0.0     0.0071   15.1   0.0    1.6  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
     0.0053   17.1   0.1          2    8.8   0.0    2.5  2  Ribosomal_S13   Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4   0.0   1.2e-60   4.4e-57       1     158 [.     415     571 ..     415     572 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 1.2e-60
  Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvitkavksinwkrYkle 95 
                     P+ +cl+p+g+e +ekg++++++p+f+a+v+r++++y+g pf+vE+giayGG++ +++ ++++RfaNr+PLlydeg+dv++k+vk+ +w+rYk++
      AJA92112.1 415 PDPTCLAPLGAEPLEKGIQRRFEPDFMAVVQRTASAYSGFPFVVEMGIAYGGKI-ETRGTTVYRFANRIPLLYDEGSDVVLKVVKDADWNRYKVK 508
                     899*************************************************99.567889********************************** PP

  Topo-VIb_trans  96 qpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeeke 158
                     +++ p++++ h++st+vP+k++gKe++ad +eieke++lalq + rkL+ y+skk +++ +k+
      AJA92112.1 509 SDSAPFIIVSHICSTRVPYKTVGKENVADRPEIEKELRLALQFLSRKLSGYMSKKGQAEAAKK 571
                     ********************************************************9998876 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   4.7e-13   1.7e-09       4     111 ..      30     149 ..      27     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.7e-13
                 HHHHHHHHHHHHHHHHHHSTTT...EEEEEEEE...EE...TEEEEEEEESSSSSTTHHHTGTCS.TTCH...HCSTCHTSTSSSHHHHHHHH.HHHHT CS
   HATPase_c   4 krLrqiisnlvdNavkfatkag...eieveika...se...ddlvisveDnGiGipkedlkklfe.kfsq...ddstkrggggtGlGlsivkk.lvelm 88 
                 + L+ +++++v+N++++  ++g   +i+ +ika   ++   +++ ++v+DnG+Gip +++++ f+  ++      +++rg +g G  ++i    ++   
  AJA92112.1  30 RSLYTAVREFVENSLDACDHSGilpNIHMTIKAvdpEKpdpKQYILTVKDNGPGIPSKHVPLAFGtVLYGskfGLKQARGMFGLGATMAILYGqIT--T 126
                 67999***********94444444477888888766115568*******************88876444445545666777777777777777344..5 PP

                 TTEEEEEEETTTEEEEEEEEESS CS
   HATPase_c  89 gGeiwvesepgrGttftftlple 111
                 +  ++v+s+ ++ t+f f+++l+
  AJA92112.1 127 NKPVKVKSNADGKTRFDFEMKLD 149
                 889***************99987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   2.2e-08   7.8e-05       3     106 ..      32     151 ..      30     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.2e-08
  HATPase_c_3   3 lekAlaelvdNsldAdaen.......vkievn...knrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGiGlklAsl....slg 85 
                  l++A+ e+v+NsldA  ++        +i++    k + k+  ++++D+G G++ + +  a+ ++   sk     ++ +G +G+G  +A+l       
   AJA92112.1  32 LYTAVREFVENSLDACDHSgilpnihMTIKAVdpeKPDPKQYILTVKDNGPGIPSKHVPLAFgTVLYGSKFG--LKQARGMFGLGATMAILygqiTTN 127
                  578*************9999**99775555543322224457789*************99874688888885..58999******8888762222345 PP

  HATPase_c_3  86 kkltvitkkegess...tltldvd 106
                  k ++v + ++g++    +++ld++
   AJA92112.1 128 KPVKVKSNADGKTRfdfEMKLDIQ 151
                  566777777777665444444444 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     2e-06    0.0071     180     237 ..     350     408 ..     331     424 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-06
                 HHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHH CS
        FbpA 180 ellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqe 237
                 +l ++ + ++l+++L k+fq ++p+ a e ++ a++++et++ ++++++l +l +alq+
  AJA92112.1 350 QLANTvQGESLTHFLTKRFQRVGPTAALEFCKFAKFKPETRVGNMTDQELVKLSDALQT 408
                 444446789***********************************************997 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.9     0.011        38      32     104 ..     241     315 ..     236     317 .. 0.83
   2 !    8.8   0.0   0.00056         2      20      66 ..     368     414 ..     352     419 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
  Ribosomal_S13  32 lkkadvdedkrigelteeeiekieeivenkaqy.kipnwi.nrqkdikdGkdshvvendlrrklredieRlkkir 104
                    ++++ vd++ +i +++++ iek+++++   +q+   ++++    k  k+      v   l + l++d e+l++ir
     AJA92112.1 241 IRRMLVDTHYQIPNVDDKMIEKVRKELGMSKQKfTYNEIMkKTEKKWKSLTRPVRVVIALMSFLEADFEKLQRIR 315
                    5677899******************99876554144555557788999999999999999999999999999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00056
  Ribosomal_S13  20 ikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqyki 66 
                     + +G ++a + +k a+ + ++r+g++t++e+ k+ + ++    +++
     AJA92112.1 368 FQRVGPTAALEFCKFAKFKPETRVGNMTDQELVKLSDALQTYEGFRS 414
                    6779*********************************9998666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4398.37
//
Query:       AJA92113.1  [L=468]
Description: fumarase C C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-84  284.5   0.3    1.4e-84  284.2   0.3    1.1  1  Lyase_1         Lyase
    4.3e-13   49.4   0.0    1.4e-12   47.8   0.0    2.0  1  FumaraseC_C     Fumarase C C-terminus
  ------ inclusion threshold ------
       0.12   12.6   1.9       0.12   12.6   0.2    1.9  2  ToxN_toxin      Toxin ToxN, type III toxin-antitoxin system
       0.14   12.0   2.4       0.18   11.7   0.2    2.3  2  Chordopox_A30L  Chordopoxvirus A30L protein
       0.14   12.2   0.2       0.51   10.4   0.1    2.0  2  DUF3929         Protein of unknown function (DUF3929)


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   0.3   3.8e-88   1.4e-84       1     312 []      26     355 ..      26     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 3.8e-88
                 CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHH CS
     Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnev 90 
                 g ++ +ad+++g ft r++ ++ +++   +      ++++k++aa an+++    k++   i+ka+d++l+ gk+ dqfv++  + g+gta+nmn+nev
  AJA92113.1  26 GPVKIPADAYYGPFTGRAIKQYNVTGRPSHhnlikSFVMIKRSAAVANMKTkainKKQGTIIVKACDKILS-GKHIDQFVVDMVNSGAGTAFNMNTNEV 123
                 56789********************8887789999****************9998888999**********.*************************** PP

                 HH....HHTT........HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHH CS
     Lyase_1  91 ig....ellg........ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayae 177
                 i     +  g        e ++pnd+v+++qSsnD++pTa+++a+  + +e ++p +++Li+++++kak+f +  k+GrThl dA Pvtlg e++ay++
  AJA92113.1 124 ITnvalK--GlgkkqgqyEFLHPNDHVNMSQSSNDTYPTAMHMAILFSFKE-MIPVIDKLIKSINKKAKQFSKYKKLGRTHLMDALPVTLGSEFAAYVT 219
                 **76441..36688889999*****************************66.*********************************************** PP

                 HHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.T CS
     Lyase_1 178 alerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.a 274
                  l++ r+++  ++ ++l +++ ggtavgtg+n+ + + ++v+ el++v++l   ++++   a++++  v+++++alk++a++L k+++D+rl++sg+ a
  AJA92113.1 220 SLTNARNQIIASQ-KELEQVALGGTAVGTGANTPRGYRKAVIIELSRVSKLSlKPQKDMQYALQSKFPVANASSALKNFAIELGKVSNDVRLMASGPiA 317
                 ***********99.7777888888****************************889999999************************************** PP

                 SSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
     Lyase_1 275 glvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                 gl el +++  +GSSiMPgKvNP  +E ++++++ v+G
  AJA92113.1 318 GLSELGIPAVHAGSSIMPGKVNPSLAECMNMICFSVIG 355
                 ************************************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   3.8e-16   1.4e-12       1      47 [.     421     467 ..     421     468 .] 0.96

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.8e-16
                  GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT CS
  FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldell 47 
                  +VT L+p+IGY k+a + ke lk+gkt+re+v+ ++l+t++e+  ll
   AJA92113.1 421 IVTLLTPKIGYLKSADLFKESLKTGKTIRELVVSKKLMTNKEVSSLL 467
                  8****************************************998776 PP

>> ToxN_toxin  Toxin ToxN, type III toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.5   9.1e+03     110     127 ..      73      90 ..      57      96 .. 0.59
   2 ?   12.6   0.2   3.4e-05      0.12      78     108 ..     167     197 ..     133     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
  ToxN_toxin 110 qkelkfinknkekilkka 127
                 +   k ink++ +i+ ka
  AJA92113.1  73 NMKTKAINKKQGTIIVKA 90 
                 334445555555554443 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.4e-05
  ToxN_toxin  78 alnlnnMiPvpdevleeldinkeekekykdL 108
                    +++MiPv d+ ++ ++ + ++ +kyk+L
  AJA92113.1 167 LFSFKEMIPVIDKLIKSINKKAKQFSKYKKL 197
                 4589*******************999***98 PP

>> Chordopox_A30L  Chordopoxvirus A30L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.83     3e+03      38      49 ..      71      82 ..      62      84 .. 0.78
   2 ?   11.7   0.2   4.9e-05      0.18      25      55 ..     163     193 ..     147     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.83
  Chordopox_A30L 38 qINlkvleinKK 49
                      N+k  +inKK
      AJA92113.1 71 VANMKTKAINKK 82
                    569999999999 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.9e-05
  Chordopox_A30L  25 faatlsvikElisqINlkvleinKKsKKnsr 55 
                       a+l   kE+i  I   + +inKK K  s+
      AJA92113.1 163 HMAILFSFKEMIPVIDKLIKSINKKAKQFSK 193
                     56899999*******************8776 PP

>> DUF3929  Protein of unknown function (DUF3929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00014      0.51      35      57 ..      72      95 ..      61      98 .. 0.80
   2 ?   -2.3   0.0       1.3   4.7e+03      29      40 ..     453     464 ..     442     466 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
     DUF3929 35 dnrevtaid.kqGtlisiacediv 57
                 n +  ai+ kqGt+i  ac+ i+
  AJA92113.1 72 ANMKTKAINkKQGTIIVKACDKIL 95
                57777888636**********996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
     DUF3929  29 vknrvtdnrevt 40 
                 v ++++ n+ev 
  AJA92113.1 453 VSKKLMTNKEVS 464
                 566777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3362.60
//
Query:       AJA92114.1  [L=239]
Description: adenylylsulfate reductase, thioredoxin dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-39  136.1   0.0    1.5e-39  135.8   0.0    1.1  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   8.4e-44   1.5e-39       4     174 .]      36     209 ..      33     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 8.4e-44
                  EE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC.....HHHHHHTHHHHHHHHH CS
  PAPS_reduct   4 vsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee.....aaeriaKveplkkaLe 96 
                   + s+G++++++++++ k++ + +++ ++tg+  +et + ++++e+ry+ +++   p+ ++ ek+++ek    +y +      ++ i+Kv+p++k L 
   AJA92114.1  36 KASSFGAEDAAIIDMMFKINSDSRLFTLETGRLPKETFDAIEQVEQRYNTKIEKLYPDPNEVEKMIEEKGLNCFYDSienrkLCCGIRKVHPMNKMLA 133
                  578******************************************************************88888888999999*************** PP

                  CTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-CCCCTT-SS--BCTTB-S CS
  PAPS_reduct  97 kldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynpLydqgfrsiGcvpctga 174
                   ld   ++tG+R d++++r+  +++eide   + ++v+Pl+nWt  + w+y++++n pyn+L dqg+ siGc pct++
   AJA92114.1 134 TLD--GWITGLRNDQNQNRSGASMLEIDEMHGNIVKVNPLVNWTFDETWDYVKSNNCPYNKLLDQGYPSIGCEPCTRP 209
                  **9..***********************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1783.33
//
Query:       AJA92115.1  [L=39]
Description: hypothetical protein T478_0250 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-06   28.0   1.4      2e-06   28.0   1.4    1.4  2  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.4   1.1e-10     2e-06      40      58 ..       1      19 [.       1      20 [. 0.91
   2 ?   -2.5   0.0      0.38   6.8e+03      19      25 ..      25      31 ..      22      37 .. 0.52

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-10
                --SHHHHHHHHTB--THHH CS
   RNA_pol_N 40 lkryCCrrmllthvdliek 58
                ++ryCCrrmllt+v++i++
  AJA92115.1  1 MERYCCRRMLLTTVETIQQ 19
                58**************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.38
                HHHHHHH CS
   RNA_pol_N 19 eeylell 25
                e+++++ 
  AJA92115.1 25 EAMHKRN 31
                4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 289.96
//
Query:       AJA92116.1  [L=567]
Description: carbamoyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-89  300.2   0.2    3.4e-89  299.8   0.2    1.1  1  Carbam_trans_N  Carbamoyltransferase N-terminus
    2.4e-74  248.5   0.0    7.1e-74  247.0   0.0    1.7  2  Carbam_trans_C  Carbamoyltransferase C-terminus
    0.00053   19.8   0.0      0.046   13.4   0.0    2.3  2  Peptidase_M22   Glycoprotease family
     0.0033   17.0   0.0     0.0059   16.1   0.0    1.4  1  Sua5_yciO_yrdC  Telomere recombination


Domain annotation for each model (and alignments):
>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.8   0.2   7.6e-93   3.4e-89       3     337 ..       4     339 ..       2     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 299.8 bits;  conditional E-value: 7.6e-93
  Carbam_trans_N   3 lGikltlflHDgavalvddgklvaaveeErltrikrdqklpklkaidyaleeagvelsdiDqivfdeidgeiesqlkekyveeaaerlkeliqgk 97 
                     lGi+   ++HD+a+al++dg +vaaveeEr++r+k d+++p+  ai+++l+eag+++sdi  ++f++++   +++l ++y++ a+++l ++ + +
      AJA92116.1   4 LGIS--CYYHDSAAALLKDGVVVAAVEEERFSRKKFDDDYPR-MAIEWCLKEAGISPSDIKSVAFYDKPVLKFERLLDNYIAVAPRGLYSFLNTM 95 
                     89**..8***********************************.9*************************************************** PP

  Carbam_trans_N  98 slllleklylkkilekllvekvdrkdvslyeHhlsHaaSaystSpFakkeklvlcldgdGdiaprllaveketelkikslvsfsesiGhlYaaat 192
                      ++l+ +l++k   e++ + k +  ++++ eHh+sHaa a++tS F  +e+++l++dg+G++ ++++   k++   +   + +++s+G+ Y+a+t
      AJA92116.1  96 PKWLHSRLWTKS--EIKKSLKGFTGEILFPEHHMSHAAHAFYTSQF--EESAILTVDGVGEWSTTSFGHAKNNTINLTHDIRWPHSLGLFYSAFT 186
                     ************..999999**************************..*********************************************** PP

  Carbam_trans_N 193 eylGfkknsdegKlmalaayGkpk..eriveelyellkkagyrinl.....ennieiskkkvhdffeasalrlkearek..dedlaAsiqvflEr 278
                     ++lGf +n++e+Klm+la+yGkpk  ++i+ +l +++++++ ++ +     + +  +++ k+ ++f+    r+k+++++  + d+ As q++lE+
      AJA92116.1 187 YFLGFRVNEGEYKLMGLASYGKPKyyDEIIHNLVDIKDDGSIHLDMsyfafTYDKVMTNEKFSKLFGIEP-RKKNEKAEqiHFDIGASAQKVLED 280
                     **************************************998888887888889999**********9766.333333331255************ PP

  Carbam_trans_N 279 lvvevlnivyeklkirnLclaGGvalNiklNsallesglFedvwvqPaanDsGsAiGAA 337
                     ++++++n+vye+ +++nLc+ GGvalN ++N ++l++g F++++v+P ++D+GsA+G A
      AJA92116.1 281 ILLKMVNHVYENSNSKNLCIGGGVALNGVANYRILKEGHFDNIHVPPSPGDAGSAVGCA 339
                     *********************************************************98 PP

>> Carbam_trans_C  Carbamoyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.45     2e+03      80     110 ..     251     281 ..     233     299 .. 0.70
   2 !  247.0   0.0   1.6e-77   7.1e-74       1     170 []     400     567 .]     400     567 .] 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.45
  Carbam_trans_C  80 vakvkeekreeipavtHvDgtaRvqtvkkea 110
                     ++ ++++k++e ++ +H+D  a +q v ++ 
      AJA92116.1 251 LFGIEPRKKNEKAEQIHFDIGASAQKVLEDI 281
                     5566777788888889999999999997764 PP

  == domain 2  score: 247.0 bits;  conditional E-value: 1.6e-77
  Carbam_trans_C   1 aellaegkvvgwfqgrmEfGpRALGnRSiladprkeemkeklnekikkResfrPfApsvleeeaeeyfeeekespymllvakvkeekreeipavt 95 
                     a+l+++g++vgw+q++mE+GpRALG RSiladprk+emk+ lnekik+ResfrPfAps+lee+++eyf+ ++ spyml+v++vk+   e+ipavt
      AJA92116.1 400 AKLISDGNIVGWYQDKMEWGPRALGCRSILADPRKAEMKDILNEKIKHRESFRPFAPSILEEYVSEYFDIDRISPYMLMVVPVKK--PEKIPAVT 492
                     789******************************************************************9999***********7..589***** PP

  Carbam_trans_C  96 HvDgtaRvqtvkkeanpryhelleafekltgvpvllNTSfNvrgepivetpedalelflkteldalvlgdllvek 170
                     HvDgt R+qtv++eanp y++l+++f k tgvpv++NTS+Nv+gepiv+tpe+a++++ kt++d+lv+g++lv+k
      AJA92116.1 493 HVDGTGRLQTVHREANPLYYDLIKEFYKITGVPVVINTSMNVMGEPIVHTPEQAYQMIVKTDMDYLVMGNYLVKK 567
                     ************************************************************************987 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0083        37      36      60 ..      45      69 ..      43      69 .. 0.87
   2 !   13.4   0.0     1e-05     0.046     189     238 ..     259     309 ..     181     328 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0083
                   HHHHHHHHHTSTGGGEEEEEEEEES CS
  Peptidase_M22 36 lieealaeaglsledldaIavtkgP 60
                   +ie +l+eag+s++d++ +a+  +P
     AJA92116.1 45 AIEWCLKEAGISPSDIKSVAFYDKP 69
                   68899***************96655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1e-05
                    HHHHSTT......HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHH CS
  Peptidase_M22 189 lkeleke......vedlaasfqeavvdhlvekteralklpkakelvilGGvaankr 238
                          +        d+ as q+   d l +++ +++++ ++k+l+i+GGva n  
     AJA92116.1 259 K-----NekaeqiHFDIGASAQKVLEDILLKMVNHVYENSNSKNLCIGGGVALNGV 309
                    2.....133445678********99999************************9976 PP

>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-06    0.0059     106     155 ..     507     562 ..     461     567 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-06
                     SSHHHHHHHHHCTS-.....EEEEES-STTS-S-SSHHHHHHH.C-TTSECB-SS- CS
  Sua5_yciO_yrdC 106 dtplarlLlealgep.....lvaTSanlsgepsitdaeeveee.lgeivdlildgg 155
                     ++pl ++L++++ +      ++ TS n+ gep++ ++e++++  ++  +d+++ g+
      AJA92116.1 507 ANPLYYDLIKEFYKItgvpvVINTSMNVMGEPIVHTPEQAYQMiVKTDMDYLVMGN 562
                     6889999999887666777999********************96688899998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3706.71
//
Query:       AJA92117.1  [L=198]
Description: hypothetical protein T478_1201 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1361.26
//
Query:       AJA92118.1  [L=123]
Description: hypothetical protein T478_0574 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   17.1   1.1        0.4   11.3   1.1    2.3  1  PepSY     Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.1   2.3e-05       0.4       8      62 ..      25     100 ..      22     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                 HHHHHHHSTTE.EEEEEEEEEE.TTEEEEEEE.EE.........EE.TTEEEEEE..........EETTT--EEEE CS
       PepSY   8 laiAlaavpgk.iieieleded.dgrlvYeve.lst........aepegpeyevf..........iDAkTGkvlkk 62 
                 ++iA+++vp+k +++  +  +d d+  vY v+  ++        ++ + + y+v+          +D +TGkvl+ 
  AJA92118.1  25 KEIAKKFVPKKgEVTSSYMHRDmDEEEVYDVDrAIDadgnpvlqEKAKLTLYDVEyklsgmnvvpVDKNTGKVLDE 100
                 6899999885554444444444588888888877766766666544444445555556666666799999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 886.63
//
Query:       AJA92119.1  [L=205]
Description: histidine phosphatase superfamily (branch 1) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-48  165.0   0.0    1.8e-48  164.9   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.9   0.0   9.8e-53   1.8e-48       1     192 [.       2     194 ..       2     196 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.9 bits;  conditional E-value: 9.8e-53
                 EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGGS----GGGTT-B.HHHHHH.. CS
  His_Phos_1   1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegLrEidfGdweglttaeiaeeyp 98 
                 ++++RHG+ e+n++++  ++   + Lte+GreqAe+++e +++ +i+aiysSp+ Ra+qTae+++++++l+++ d++L E+d+G++   +++ei e++ 
  AJA92119.1   2 IIFLRHGQAENNTKKIlAGRTPGINLTEQGREQAEQAGEMIKSLNISAIYSSPIDRAMQTAEIVGKHCNLKPISDDRLIELDMGKFTMVPYNEIFEKHG 100
                 79**************7777789**************************************************************************** PP

                 HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHHHHHHHT--GGGGGGB---TT-EEEEEE-SS-EEEEEEE CS
  His_Phos_1  99 eeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvirallarllglpleelrrleldnaslsvlefdeggwrlvrln 192
                 + + ++ +++ + + +g Es+ +v++Rv ++++ ++++h++e+v++V+H  +i+a++ ++l l++e l +l ++nasl+++++d+++  l ++n
  AJA92119.1 101 NVFLKFYEGSLEISHNGVESFSEVQKRVFDIVDFVKNEHKDENVVLVTHMDPIKAMIGKVLSLKPEILFQLIVANASLNIFKYDDQNYYLSSIN 194
                 **************************************************************************************99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1484.70
//
Query:       AJA92120.1  [L=219]
Description: hypothetical protein T478_0597 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.23   11.3   0.1    1.5  1  Replicase  Replicase family
       0.17   11.7   0.1          2    8.2   0.0    2.2  2  DUF4035    Protein of unknown function (DUF4035)


Domain annotation for each model (and alignments):
>> Replicase  Replicase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.6e-05      0.23      30      92 ..     154     214 ..     151     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
   Replicase  30 iDkpdallrwedaklpkPnlivknpknghahllyaletpvattenarskplrylkavkealae 92 
                 +D+ + l +  d   ++P++  ++ +n h h +y++  +  ++ + +  p+ yl+ +k+ +++
  AJA92120.1 154 LDDVKKLKKLCDRFYKNPKINLEDIQNAHIHSVYLI--NTDKGFAKELDPELYLQMTKQLMKQ 214
                 7888889899999999********************..6667777889999999999998876 PP

>> DUF4035  Protein of unknown function (DUF4035)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.041   3.7e+02      14      32 ..     109     124 ..     108     132 .. 0.83
   2 ?    8.2   0.0   0.00023         2      13      30 ..     176     192 ..     174     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.041
     DUF4035  14 DyrtAqishllaminrdsk 32 
                 Dy +A i++ +a   r sk
  AJA92120.1 109 DYYAARIVSKIA---RYSK 124
                 9********998...5555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00023
     DUF4035  13 eDyrtAqishllaminrd 30 
                 eD++ A+i h++++in d
  AJA92120.1 176 EDIQNAHI-HSVYLINTD 192
                 8*******.88898**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1609.73
//
Query:       AJA92121.1  [L=168]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 6 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-23   82.4  11.5    3.7e-23   81.9  11.5    1.2  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.37   10.9   0.1       0.37   10.9   0.1    3.2  4  YrhC         YrhC-like protein


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9  11.5   4.1e-27   3.7e-23       1     144 []      16     157 ..      16     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 4.1e-27
                  HHHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHHHHHHHHHHHTT--.... CS
  Oxidored_q3   1 gallvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaalligllllallllllless 98 
                  +a++++ ++++vy  ++L+ ++ gvag++++l+ +F+a++q+ vYvG i+vl+lF++ml+++ e   ++   ++  +a++ ++l+ ++ l ++++  s
   AJA92121.1  16 SAIAALEMRSLVYGSIALMGTLGGVAGFYVMLDSPFVAMFQLAVYVGSIAVLILFTVMLVKR-ELIFKKIEDPKRKFAGIGLMLITILALGAIIMD-S 111
                  5889999****************************************************844.333444444455555555555555555666555.4 PP

                  ..--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
  Oxidored_q3  99 ssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                    ++ ++ +d+ + ++ig  ++t+y+ +++l++l+L   ++ga+vl
   AJA92121.1 112 GIKTITTDSDPVDFREIGGDFLTYYWPALILMALILAGSVMGALVL 157
                  444566788999*******************************997 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.33     3e+03      50      60 ..       6      16 ..       2      35 .. 0.55
   2 ?    1.4   0.4     0.038   3.4e+02      38      66 ..      55      83 ..      45      85 .. 0.81
   3 ?   10.9   0.1   4.1e-05      0.37       4      39 ..      81     117 ..      78     120 .. 0.88
   4 ?   -0.4   0.0      0.14   1.3e+03      43      59 ..     143     159 ..     131     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.33
        YrhC 50 fLllaflflrr 60
                fL++++l +  
  AJA92121.1  6 FLAISVLTIGS 16
                44444433322 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.038
        YrhC 38 lkksillgaivvfLllaflflrrskkyqk 66
                ++ ++ +g i+v++l+ +++++r ++++k
  AJA92121.1 55 FQLAVYVGSIAVLILFTVMLVKRELIFKK 83
                56677889999999999999999888776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 4.1e-05
        YrhC   4 kkkveDYkr.FafvLLalsaFLyiGlviPseaketlk 39 
                  kk+eD kr Fa + L l++ L +G++i +++++t+ 
  AJA92121.1  81 FKKIEDPKRkFAGIGLMLITILALGAIIMDSGIKTIT 117
                 5899999866******************999998875 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.14
        YrhC  43 llgaivvfLllaflflr 59 
                 + ++ ++ +++a++++r
  AJA92121.1 143 MALILAGSVMGALVLAR 159
                 44444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1123.03
//
Query:       AJA92122.1  [L=337]
Description: ATPase, AAA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-64  214.9   0.0    5.2e-64  214.0   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    7.2e-21   73.8   0.1    1.4e-20   72.9   0.1    1.4  1  AAA_lid_2        AAA lid domain
    1.7e-15   57.2   0.0    3.2e-15   56.3   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    6.6e-08   31.9   0.0    1.7e-07   30.6   0.0    1.7  1  MCM              MCM P-loop domain
    5.4e-06   26.2   0.3    8.7e-05   22.3   0.1    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00016   21.5   0.1     0.0011   18.7   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
    0.00031   20.2   0.3      0.018   14.4   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00047   20.6   0.3     0.0024   18.3   0.0    2.4  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.055   13.8   1.9        8.6    6.7   0.3    3.2  3  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.0   0.0   2.6e-67   5.2e-64       1     130 [.      58     187 ..      58     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 214.0 bits;  conditional E-value: 2.6e-67
       AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsalleameerqvtvegethk 99 
                 hvllegvPGlakt++v +l+k+l+++f riqftpdllP+di+Gt+++++k+++f ++kGpvf+nl+ladeinrappk+qsalleam+erqv+++g+t++
  AJA92122.1  58 HVLLEGVPGLAKTKMVDTLSKTLGANFCRIQFTPDLLPADITGTKIYDNKNEKFVTEKGPVFSNLILADEINRAPPKVQSALLEAMQERQVSIHGDTFE 156
                 9************************************************************************************************** PP

       AAA_3 100 lpepflvlatqnPieqeGtyplpeaqldrfl 130
                 +++pflvlatqnPie+eGty lpeaq+drf 
  AJA92122.1 157 IEKPFLVLATQNPIESEGTYRLPEAQIDRFA 187
                 ******************************7 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.1   7.1e-24   1.4e-20       7      73 .]     263     330 ..     259     330 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.1e-24
   AAA_lid_2   7 laielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeiveei 73 
                  +ie+g+s+r a++ l+ aA+A+A+l+gr +V+p+D+k +a+ VL+HR++   e+eaeg+t+++i+++i
  AJA92122.1 263 DMIEFGASPR-ASIWLILAAKAHALLAGRGFVIPDDIKSIAHDVLRHRIIltFEAEAEGNTSDAIIDKI 330
                 689*******.****************************************99************9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   1.6e-18   3.2e-15       1     138 []      58     186 ..      58     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.6e-18
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE.. CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllle 97 
                 +vlL G pG +K+++++ l++ l++++  +q+t d+ ++d++g   ++  n++ + +++p+      + +++ DE++ra+++v+++Ll  + er++++ 
  AJA92122.1  58 HVLLEGVPGLAKTKMVDTLSKTLGANFCRIQFTPDLLPADITGTKIYDnkNEKFVTEKGPVF-----SNLILADEINRAPPKVQSALLEAMQERQVSIH 151
                 79*****************************************9999955666666788888.....99****************************99 PP

                 -SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
       AAA_5  98 eggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                   ++++ + +      f v+at np +  +  +l +a ++Rf
  AJA92122.1 152 GDTFEIEK-P------FLVLATQNPIEsEGTYRLPEAQIDRF 186
                 99999955.5......***********888889999999998 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   8.6e-11   1.7e-07      48     176 ..      47     172 ..      11     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 8.6e-11
                 BSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHH CS
         MCM  48 ledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhE 143
                 ++  + + +d +vll g pg+aK++++ +++k++  a++  ++ +     a++t +   d+++++fv+e G +      +++ De+++   + +sal+E
  AJA92122.1  47 KKLVIAMMADGHVLLEGVPGLAKTKMVDTLSKTL-GANFCRIQFTPDllpADITGTKIYDNKNEKFVTEKGPVFSN---LILADEINRAPPKVQSALLE 141
                 33345688999*******************9776.55666666654323399*******************98864...899***************** PP

                 HHHHSEEEEESSSCEEEEE--EEEEEEE--SSS CS
         MCM 144 amEqqtisiaKaGivatLnartsvlaAanpkag 176
                 am + ++si     +  ++    vla  np+++
  AJA92122.1 142 AMQERQVSIHGD--TFEIEKPFLVLATQNPIES 172
                 *********844..5778888888888888843 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   4.4e-08   8.7e-05      10     115 ..      40     150 ..      33     155 .. 0.73
   2 ?   -1.7   0.0       1.1   2.1e+03      99     142 ..     230     273 ..     214     277 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.4e-08
      RuvB_N  10 igqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaa..lltnleek..........dvlfideihr 95 
                 +gqe+v +kl i++ a         hvll G PGl kt +   ++k lg+++ +i  +P l  ++d+++  +  n +ek          ++++ dei r
  AJA92122.1  40 VGQEEVIKKLVIAMMA-------DGHVLLEGVPGLAKTKMVDTLSKTLGANFcRIQFTPDLL-PADITGtkIYDNKNEKfvtekgpvfsNLILADEINR 130
                 7888888888887765.......47*************************964778888875.5566542234343332111122222267889***** PP

      RuvB_N  96 lsraveevlysamedfrldi 115
                   ++v+  l  am++ ++ i
  AJA92122.1 131 APPKVQSALLEAMQERQVSI 150
                 *************9999877 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
      RuvB_N  99 aveevlysamedfrldivigkGpsarsikldlpkftlvgattra 142
                  v+ +      + ++  +++  ++ ++  l+l+ +   ga+ ra
  AJA92122.1 230 FVQKIYADEKIEEYVSAIVDATRNPKNYDLELEDMIEFGASPRA 273
                 44444333222333566677777777777777777777777665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.4e-07    0.0011      96     147 ..     122     172 ..      36     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.4e-07
                      EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HHH CS
  Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedlee 147
                       ++ Dei++ p+++Q+ Ll+++qe++v+  G++ ei+  + ++ at++ +e+
       AJA92122.1 122 LILADEINRAPPKVQSALLEAMQERQVSIHGDTFEIEKPF-LVLATQNPIES 172
                      5677*****************************9998776.55667666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   9.2e-06     0.018       4      46 ..      38      80 ..      35      86 .. 0.91
   2 ?    3.5   0.0      0.02        39     110     161 ..     123     172 ..     118     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.2e-06
  Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsll 46
                   ++Gqee  + l ia     ++ll G pG  Kt +   l++ l
    AJA92122.1 38 VIVGQEEVIKKLVIAMMADGHVLLEGVPGLAKTKMVDTLSKTL 80
                  589*******************************999998766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.02
  Mg_chelatase 110 LfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc 161
                   ++ DE+     kv  +L e +++++v+i+  + ++e p  f ++a+ Np  +
    AJA92122.1 123 ILADEINRAPPKVQSALLEAMQERQVSIHGDTFEIEKP--FLVLATQNPIES 172
                   5679************************9988887766..888899999765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.9   3.7e+03      50      74 ..      18      42 ..       6      55 .. 0.53
   2 !   18.3   0.0   1.2e-06    0.0024       1     125 [.      59     187 ..      59     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                HHHHHHTSTSEEEEEETGGGHHHHH CS
         AAA 50 fkeakekakpsilfiDEidalaksr 74
                 ++ k  ak+   ++DE+ +++  +
  AJA92122.1 18 TEQSKVYAKQIMTIVDEVQKVIVGQ 42
                3333433333444556666655444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.2e-06
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHH.HHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvges.ekkirelfkeakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteld 94 
                 vll G pG  KT ++  + k+lg++f++i+  ++ll  ++ g +  ++ +e f    ek       ++ DEi +  ++            +++Ll++++
  AJA92122.1  59 VLLEGVPGLAKTKMVDTLSKTLGANFCRIQFtPDLLpADITGTKiYDNKNEKFV--TEKGpvFSNLILADEINRAPPKV-----------QSALLEAMQ 144
                 79***************************9636777544444331222233332..2222333489********98888...........********* PP

                 HTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSS CS
         AAA  95 gvkkk........eskvivigatnr.....pdkldpallrgRfd 125
                 + + +        e++++v+++ n        +l++a + +Rf 
  AJA92122.1 145 ERQVSihgdtfeiEKPFLVLATQNPiesegTYRLPEAQI-DRFA 187
                 **9999999999977788888877644333444555555.6665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0043       8.6      94     126 ..      17      50 ..       2      55 .. 0.75
   2 ?    2.7   0.1     0.074   1.5e+02       7      34 ..      53      80 ..      47      88 .. 0.83
   3 ?    2.5   0.0     0.083   1.6e+02      99     137 ..     117     153 ..      96     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
      AAA_19  94 aeeekklqeee.llivDEfqdvdelqyrLlkall 126
                  +e++k+ +++ + ivDE+q v   q +++k+l+
  AJA92122.1  17 LTEQSKVYAKQiMTIVDEVQKVIVGQEEVIKKLV 50 
                 34555665666699*********99999999986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.074
      AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                 ++++++l+ + pG  KT+++ +  + l
  AJA92122.1 53 MMADGHVLLEGVPGLAKTKMVDTLSKTL 80
                677899**************99887766 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.083
      AAA_19  99 klqeeellivDEfqdvd.elqyrLlkallgekkklllvGD 137
                 ++   +l++ DE+     ++q +Ll+a+  e++ + + GD
  AJA92122.1 117 PV-FSNLILADEINRAPpKVQSALLEAMQ-ERQ-VSIHGD 153
                 44.456999********99*********9.444.666676 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2133.43
//
Query:       AJA92123.1  [L=112]
Description: hypothetical protein T478_0779 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00023   21.2   0.0    0.00035   20.6   0.0    1.3  1  HTH_20          Helix-turn-helix domain
    0.00064   19.5   0.4     0.0019   18.1   0.1    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0032   17.3   0.2     0.0038   17.1   0.2    1.1  1  TFIIE_alpha     TFIIE alpha subunit
     0.0087   15.9   0.0      0.011   15.5   0.0    1.2  1  DUF742          Protein of unknown function (DUF742)
  ------ inclusion threshold ------
      0.021   14.3   0.3      0.027   13.9   0.3    1.5  1  DUF3839         Protein of unknown function (DUF3839)
      0.037   13.9   0.1      0.042   13.7   0.1    1.1  1  DUF2806         Protein of unknown function (DUF2806)
      0.098   11.9   0.0        0.1   11.8   0.0    1.0  1  SdiA-regulated  SdiA-regulated


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.3e-07   0.00035       2      56 ..      18      71 ..      17      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                HHHHHHS-.HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20  2 qiaeALah.PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                +++e La+ ++R+ i++ +  ++g ta+el e   ++ +++++ +  Lee  L++v
  AJA92123.1 18 KVIEMLADaESRAIIFSII--RKGKTAAELSEKHKIPLSSVYKKISDLEELTLIHV 71
                68899***9**********..******************************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.55   1.4e+03      29      46 ..       2      19 ..       1      22 [. 0.77
   2 !   18.1   0.1   7.3e-07    0.0019      20      54 ..      37      71 ..      23      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.55
                CCCTTSSCHCHHHHHHHH CS
        TrmB 29 aeelgvprskvYevLrsL 46
                a+++ +p+ k Y+v ++ 
  AJA92123.1  2 AKRVTLPQLKKYDVTQKV 19
                678888999999998876 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 7.3e-07
                HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
        TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                ++ +ta e++e+ ++p s+vY+ ++ Le+  l+++
  AJA92123.1 37 RKGKTAAELSEKHKIPLSSVYKKISDLEELTLIHV 71
                6889************************9988876 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.5e-06    0.0038       4      82 ..      17      94 ..      14     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                 HHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHC CS
  TFIIE_alpha  4 kevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklv 82
                 + v+   ++ e   +++++++kg+++  +l+++ ki l  + k + +L e  l+ +  ++  ek+ +   +r   + + 
   AJA92123.1 17 QKVIEMLADAESRAIIFSIIRKGKTAA-ELSEKHKIPLSSVYKKISDLEELTLIHVDSWQISEKGRRFKVYRSRIKDAE 94
                 789999999***************886.6****************************9999888887777776655554 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.5e-06     0.011      43      93 ..      27      77 ..      10      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
      DUF742 43 pehrailrLcreplsVaelaAelklPvgvvrvLlsdLldaglltvrapvtd 93
                + ++ i  ++r+ ++ ael+ + k+P++ v   +sdL +  l++v   ++ 
  AJA92123.1 27 ESRAIIFSIIRKGKTAAELSEKHKIPLSSVYKKISDLEELTLIHVDSWQIS 77
                344556789999*******************************99876665 PP

>> DUF3839  Protein of unknown function (DUF3839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   1.1e-05     0.027     144     178 ..      66     100 ..       6     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
     DUF3839 144 vslvakcvweirdkdrrgkvwneqikptaselkkt 178
                 ++l+    w+i +k rr kv++ +ik +  ++kk 
  AJA92123.1  66 LTLIHVDSWQISEKGRRFKVYRSRIKDAEISIKKP 100
                 56777788***********************9996 PP

>> DUF2806  Protein of unknown function (DUF2806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.042     110     166 ..      19      79 ..       7     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
     DUF2806 110 slklllgfrkkaglfdlfkkakqqelnlskfgls....ysslltLeelgllhaselesgel 166
                   ++l + +++a +f++++k k+     +k++++    y+++  Leel l+h+++ + +e 
  AJA92123.1  19 VIEMLADAESRAIIFSIIRKGKTAAELSEKHKIPlssvYKKISDLEELTLIHVDSWQISEK 79 
                 467899999************************94444556678**********9887765 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05       0.1      31     114 ..      26     109 ..       3     112 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
  SdiA-regulated  31 dpdtktLfavtnkpeelveLskeGevlrriplkgfkdpEaveylgdgrlaivdE.reqalvvvkvdadtksldaadlkklelglk 114
                      +++  +f+++ k ++  eLs++ ++  +   k ++d E ++ ++ ++ +i++  r+ ++++ ++++++ s++  +  +l+l ++
      AJA92123.1  26 AESRAIIFSIIRKGKTAAELSEKHKIPLSSVYKKISDLEELTLIHVDSWQISEKgRRFKVYRSRIKDAEISIKKPE-ASLTLTPN 109
                     5677889********************************************9753556777777766655555544.44555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 807.85
//
Query:       AJA92124.1  [L=132]
Description: ribosomal protein S19 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-28   96.0   0.2    1.2e-27   95.6   0.2    1.2  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
       0.18   11.0   0.1       0.22   10.7   0.1    1.1  1  Peptidase_M56  BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.2   1.3e-31   1.2e-27       1      81 []      34     115 ..      34     115 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 1.3e-31
                    .HHHSS.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
  Ribosomal_S19   1 rslkkg.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81 
                    rslk+g +  +++l++++++ak+ k+k++ikth+Rd +IlP m+g t++V++Gk+f p+ i  emvGh++gE+++T+k+v+h
     AJA92124.1  34 RSLKRGlSDNKKKLIAEIKEAKEGKNKNPIKTHQRDLIILPYMIGTTINVFDGKEFKPIGIGAEMVGHYIGEYAITNKRVNH 115
                    89****99***************9********************************************************99 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   2.5e-05      0.22     122     177 ..      25      80 ..      22      84 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.5e-05
  Peptidase_M56 122 aallvlkkrfvrklgklraeelkea...LkeakeemqlkrnikirlsssidsPavlgll 177
                    +all+ ++r  r+l++  ++++k++   +keake ++ k++ik    + i  P ++g  
     AJA92124.1  25 FALLNSRQR--RSLKRGLSDNKKKLiaeIKEAKEGKN-KNPIKTHQRDLIILPYMIGTT 80 
                    688999988..55555555555555000555555555.999***************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 929.54
//
Query:       AJA92125.1  [L=628]
Description: arginine--tRNA ligase, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-31  106.7   0.5    4.5e-29  101.0   0.0    2.4  2  DALR_1           DALR anticodon binding domain
    3.9e-26   91.8   7.4    8.1e-20   71.1   2.0    2.2  2  tRNA-synt_1d     tRNA synthetases class I (R)
    7.8e-15   55.2   0.1    2.3e-14   53.7   0.1    1.9  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
     0.0063   15.5   0.2      0.024   13.5   0.1    2.0  2  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0079   15.6   0.8      0.022   14.1   0.2    1.8  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
  ------ inclusion threshold ------
      0.031   13.0   2.6       0.15   10.8   0.1    2.5  2  tRNA-synt_1g     tRNA synthetases class I (M)
          6    7.5   7.5        4.3    8.0   0.1    3.1  2  DUF3800          Protein of unknown function (DUF3800)


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.029        74      22      66 ..     208     249 ..     199     270 .. 0.78
   2 !  101.0   0.0   1.8e-32   4.5e-29       1     119 []     512     628 .]     512     628 .] 0.95

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.029
                 CCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHH CS
      DALR_1  22 leeealalleeeeekeLlkalaqfpevleeaaeelephklaeyly 66 
                 + e++++   ee+  e+lk++ +  ++++++a++ + ++l e+l+
  AJA92125.1 208 Y-ETDKQ--LEEKRHEILKQIEDSSSTISKMAQTITRKVLDEQLK 249
                 2.23333..589********************9988777666665 PP

  == domain 2  score: 101.0 bits;  conditional E-value: 1.8e-32
                 HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTSTTSCTHHH.HHHHHHHHH CS
      DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkervlkeeeeelaaaRLaLvka 99 
                 +qy++aR++ il+k e++ + + +  ++l ++e ek+L+k++a f   +++++++++p+++a+y y+La tf++fY++++vlk+e +el +aRL Lv +
  AJA92125.1 512 IQYSYARASRILEKTETKPNFD-SGFELL-SSEYEKNLIKKIAMFDVQVNDSVNNFSPKVIAKYSYDLAVTFSSFYEHVKVLKSETPELLNARLCLVVS 608
                 7************999888555.555555.8******************************************************************** PP

                 HHHHHHHHHHHTT----S-- CS
      DALR_1 100 vrqvLangLdlLGieapekm 119
                  +++L++ L+lLGi+ape+m
  AJA92125.1 609 FQKTLKSSLSLLGIDAPERM 628
                 *******************9 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   2.0   3.2e-23   8.1e-20       9     223 ..     106     328 ..      97     348 .. 0.81
   2 !   23.8   0.4   7.3e-09   1.9e-05     208     337 ..     347     486 ..     333     495 .. 0.76

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 3.2e-23
                   TTTT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHT.TTTTTS-----SC..CCHHH CS
  tRNA-synt_1d   9 krklqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkq.dekllqeqelqdL..eafyk 102
                   ++  +   ++++k+vv+++s n  k +hvGh+r  i+Gd vs++l    +dv  ln+v D G q   +i+++ + +  ++  ++++ ++   +++y+
    AJA92125.1 106 ENYGSLDIGHNEKIVVEHTSVNPNKALHVGHIRNVILGDIVSKILRKGNFDVKVLNYVDDSGLQVADIIVGFTELGfSQEPPENEKFDHYcgDTVYV 202
                   444467889*************************************************************999875133334555666653368*** PP

                   HHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC..CCCCCHHHHHHHHHCTT-EEECT.....TCEE CS
  tRNA-synt_1d 103 eakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGes..lykeslneivkelkkkglvkesd.....Galv 191
                   ++  +y+++ +++e+ +++++++++    i k+ + ++  +  e+ k+  +l v+      es  ++ +  ++i ++lk ++ +k ++     G  v
    AJA92125.1 203 KTTEKYETDKQLEEKRHEILKQIEDSSSTISKMAQTITRKVLDEQLKTVWNLGVFYDClNFESqiIHSKLWDKIFEKLKSENQIKYEEtgdnaGCWV 299
                   **************************************999999999********96567788845666668899****999887543211113344 PP

                   EEECCCTSSCCEECC-TTS-B-HHHHHHHHHH CS
  tRNA-synt_1d 192 vfldefgkrlgvvvqksDGgylytttDiaaak 223
                   +  +  g+    ++++s+G  +y ++Di  a 
    AJA92125.1 300 IPAE--GED-DKILVRSNGVATYIAKDIPYAA 328
                   4444..554.679999***********97654 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 7.3e-09
                   TTS-B-HHHH..HHHHHHHHHHTT--SEEEEEEECCC...HHHHHHHHHHHHCTT.SST...TTSEEEE...EEE--EE-TTSSBSBCSSSTC-BHH CS
  tRNA-synt_1d 208 sDGgylyttt..Diaaakerkeelkadkvlyvidsrq...slhlqqiflilkkig.yvp...eskdleh...anfGmvlgkdkkkfktrkGetvkLa 292
                   ++  +ly+tt  +i+   + k +l  +kv+ vid+rq   ++ ++ + +  k  g y     es++l     +++G+ +  +  +++ rkG  v+ +
    AJA92125.1 347 KNSQTLYETTldEISDHDDDKLNLSGNKVITVIDNRQirlQKIVSGLMAKFKEEGaYTHlgyESVTLSAdtvKSLGLSVDGESAQMSGRKGLYVNAD 443
                   5567788876546888899999**************9332222333344444433443211167777542226789999899999************ PP

                   HHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCC CS
  tRNA-synt_1d 293 dlLdealeralqlikeknkdkvlqadelekvaeavgvgaikyaDl 337
                   ++L+   +r  +  k +n++  l+  ele++a+ v+vg+i+y+ +
    AJA92125.1 444 TVLETLTKRVYDESKSRNEN--LSESELENIANIVAVGTIRYEMI 486
                   ************88888888..9******************9865 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1     9e-18   2.3e-14       4      84 ..       7      89 ..       4      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9e-18
                     HHHHHHHHHHHH.SS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.EEEEE CS
  Arg_tRNA_synt_N  4 keaiaealkkaa.gadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGFiNff 84
                      e i+++ +++   ++ +++ +++e+ ++p fGD+ +nva+ l+k+lkk+P+ei +e+ +  + ++i  i++ve    G++Nf 
       AJA92125.1  7 LENIRKETSEILdSQNYDPVTFSVES-AKPGFGDITCNVAFLLSKQLKKSPQEISKELSKLYKFDDIpqIKNVESHASGYLNFN 89
                     56677777777765678899999*96.*********************************888887777**************7 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   9.5e-06     0.024      23      70 ..     117     165 ..     101     168 .. 0.85
   2 ?   -3.0   0.0         1   2.6e+03     267     310 ..     349     396 ..     340     403 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-06
  tRNA-synt_1f  23 devvve.sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDd 70 
                   +++vve + + p   +H+G +r+v+ +d+v + lrk   +v+++ ++Dd
    AJA92125.1 117 EKIVVEhTSVNPNKALHVGHIRNVILGDIVSKILRKGNFDVKVLNYVDD 165
                   455554378889999*********************************9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1
  tRNA-synt_1f 267 ekvvYelillkgge....kmssSkGnvltledwlevaepevlrflilr 310
                    +  Ye  l++  +    k+  S  +v+t+ d  ++  +++++ l+++
    AJA92125.1 349 SQTLYETTLDEISDhdddKLNLSGNKVITVIDNRQIRLQKIVSGLMAK 396
                   555666554443333334999999999999999999998888888877 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   8.7e-06     0.022      20      56 ..     129     165 ..     111     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-06
                   TS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB- CS
  tRNA-synt_1e  20 ydashlGhaRslvafDilrrilqalgYdvqfvqnvtD 56 
                     a h+Gh R+++  Di+ +il++ ++dv+ ++ v D
    AJA92125.1 129 NKALHVGHIRNVILGDIVSKILRKGNFDVKVLNYVDD 165
                   5689*************************98776655 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.9e-05      0.15      10      52 ..     128     170 ..     119     173 .. 0.87
   2 ?    1.5   0.5     0.038        98      63     117 ..     236     290 ..     196     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.9e-05
                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHH CS
  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpi 52 
                   +n +lH+Gh+++vi +Di+++  r+ + +v  +   D  G ++
    AJA92125.1 128 PNKALHVGHIRNVILGDIVSKILRKGNFDVKVLNYVDDSGLQV 170
                   6999***********************9999988888888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.038
                   HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEE CS
  tRNA-synt_1g  63 peelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekgliyeke 117
                   ++ +++kv +e+ ++  +l++ +d  +  ++  h++l  +if+klk++++i+ +e
    AJA92125.1 236 AQTITRKVLDEQLKTVWNLGVFYDCLNFESQIIHSKLWDKIFEKLKSENQIKYEE 290
                   5566677777777888889999999999999999999999999999999998665 PP

>> DUF3800  Protein of unknown function (DUF3800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0017       4.3      76     116 ..     101     177 ..       5     179 .. 0.56
   2 ?    0.2   3.3      0.43   1.1e+03      28      88 ..     209     286 ..     183     565 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
     DUF3800  76 dk......kkkkekakkeleilld............................................esvkfvdSkesrglQlADlvaga 116
                 +                      +                                             +vk  +  +  glQ+AD+++g+
  AJA92125.1 101 NSslqenyG--------------SldighnekivvehtsvnpnkalhvghirnvilgdivskilrkgnFDVKVLNYVDDSGLQVADIIVGF 177
                 112222220..............022333344444445555556666677777777778888888888999999999***********996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
     DUF3800  28 eeikkleekikelkkky............................................krlleriakflkkndliksdeesdesilivldkkkkke 82 
                 e+ k+leek +e+ k+                                             +                            ++dk ++k 
  AJA92125.1 209 ETDKQLEEKRHEILKQIedssstiskmaqtitrkvldeqlktvwnlgvfydclnfesqiihS---------------------------KLWDKIFEKL 280
                 35667777777777777777444433333333333333333333333333333333333332...........................3333322222 PP

     DUF3800  83 kakkel 88 
                 k ++++
  AJA92125.1 281 KSENQI 286
                 222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1296  (0.0722851); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3469.32
//
Query:       AJA92126.1  [L=152]
Description: peptide-methionine (S)-S-oxide reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-64  215.0   4.4    6.1e-64  214.8   4.4    1.0  1  PMSR      Peptide methionine sulfoxide reductase
  ------ inclusion threshold ------
      0.097   12.5   0.1        1.5    8.8   0.3    2.2  2  Vsr       DNA mismatch endonuclease Vsr
       0.12   12.8   0.1        1.5    9.4   0.0    2.5  3  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.8   4.4     1e-67   6.1e-64       1     147 [.       3     151 ..       3     152 .] 0.98

  Alignments for each domain:
  == domain 1  score: 214.8 bits;  conditional E-value: 1e-67
                 EEEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT-SSEETTEESGGG--EEEESS CS
        PMSR   1 eavlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDptqlnrqgnDvGtqYrsaiyytn 99 
                 +a++a+GCFW ve++f+k++Gv st+vGY+gG+t+nptYe+vc+++tghaEa++v+ydp+++s+++l+++ff +h+pt++n+qg DvG qYrsai+++n
  AJA92126.1   3 KATFAAGCFWHVEEVFSKTDGVKSTAVGYTGGHTDNPTYEDVCTDRTGHAEAIQVEYDPNEISYSDLVKVFFANHNPTTANKQGPDVGIQYRSAIFCHN 101
                 589************************************************************************************************ PP

                 CCHHHHHHHHHHHHHTT..HTTSSS---EEEEG-SEEE--CCCTTHHHH- CS
        PMSR 100 eeqkevaeevleelqkk..kalkkkivteieplkefykaeeyHqqYlekn 147
                 eeq+++a+ev+eel+ +  k+++++ivtei+p+++fy+aeeyHq+Y+ekn
  AJA92126.1 102 EEQEKTAKEVKEELNPSahKTFGNDIVTEIKPASKFYRAEEYHQKYFEKN 151
                 **************99988999**************************98 PP

>> Vsr  DNA mismatch endonuclease Vsr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00024       1.5      59      70 ..       4      15 ..       1      18 [. 0.83
   2 ?    1.1   0.0     0.059   3.5e+02      49      64 ..      87     101 ..      78     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00024
                EEEEE-TTTTT- CS
         Vsr 59 vvFvhGcFWHgh 70
                + F  GcFWH +
  AJA92126.1  4 ATFAAGCFWHVE 15
                6899******76 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                 -SEEEGGGTEEEEEE- CS
         Vsr  49 PDvvlkkykvvvFvhG 64 
                 PDv + +y+ ++F h 
  AJA92126.1  87 PDVGI-QYRSAIFCHN 101
                 78776.699****995 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00024       1.5      10      31 ..       8      29 ..       5      35 .. 0.89
   2 ?    0.0   0.0       0.2   1.2e+03      39      54 ..      56      71 ..      52      73 .. 0.85
   3 ?   -1.6   0.0      0.66     4e+03      42      43 ..     115     116 ..      98     136 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
         HMA 10 agCaakvekvLselpgVesvkv 31
                agC  +ve+v+s+ +gV+s  v
  AJA92126.1  8 AGCFWHVEEVFSKTDGVKSTAV 29
                7999*************99876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.2
         HMA 39 tVegdaestklrkiie 54
                +Ve+d+ +++++++++
  AJA92126.1 56 QVEYDPNEISYSDLVK 71
                79*****999999886 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.66
         HMA  42 gd 43 
                 ++
  AJA92126.1 115 LN 116
                 23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1096.58
//
Query:       AJA92127.1  [L=403]
Description: glycosyltransferase-like protein, family 2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-29  102.1   0.0    3.8e-29  101.7   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.7e-17   64.1   0.0    2.4e-17   63.6   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.5e-12   47.3   0.0    2.3e-12   46.7   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    6.3e-12   45.6   0.1    8.2e-12   45.2   0.1    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00052   20.5   0.0    0.00092   19.7   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.095   12.6   0.0       0.31   10.9   0.0    1.9  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      0.096   12.3   0.1       0.21   11.3   0.1    1.5  1  VasI             Type VI secretion system VasI, EvfG, VC_A011
       0.55   10.1   4.0       0.11   12.3   0.4    1.8  2  VIT1             VIT family
        2.7    7.8   5.9       0.78    9.5   1.4    2.3  2  Sarcolipin       Sarcolipin


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.0   1.9e-32   3.8e-29       1     170 []      55     228 ..      55     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.9e-32
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSE CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak...edprvrvirreenv.GkagalnaglraatgdyilflDaDd 90 
                      sv+ p+ Nee+ + ++le l +q +y++feii +DD+S+D+t ei+e+++k   +  +v    ++e++ Gk  a ++g+r+atg+++lf DaD+
       AJA92127.1  55 SVILPARNEEEFISKCLETLGSQ-DYENFEIIAIDDSSEDKTGEIIEKFSKensKIIHVSAKEKPEKWmGKNWACMEGFRKATGEILLFTDADT 147
                      8**********************.***************************75555555556788999************************** PP

                      EE-TTHHHHHHHHHHH.TTCE.EEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHCH CS
  Glycos_transf_2  91 epdpdwleklvealekdgadv.vlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealeell 170
                       ++++ +   v +l+ ++ d+  +  r r+ +  ++i+ +   ++    y   + ++ k ++ ++ gs+++++r+++ee++
       AJA92127.1 148 KFKKNVITLAVSHLQSENLDAlTVIPRLRCIDTITKITLPMLSTFLHSRYSALNVNNPKKKVGYFFGSFFVIKRKVYEEIG 228
                      ****************987751566778888888889988888**********************************9985 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.2e-20   2.4e-17       1     206 [.      52     259 ..      52     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.2e-20
  Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllv 94 
                      p  ++v+ p+ nee+ + ++le l +q+y ++e++ ++d s+++t e +e + ++ +++ ++v  +++     gk +a  e++r ++++++l+ 
       AJA92127.1  52 PK-VSVILPARNEEEFISKCLETLGSQDYENFEIIAIDDSSEDKTGEIIEKFSKENSKI-IHVSAKEKPEKWMGKNWACMEGFRKATGEILLFT 143
                      55.9************************************************9999997.9988888877999********************* PP

  Glyco_tranf_2_3  95 DdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl....vsalgalefaerhlrflaarralgvltlnGsgslirrevlkelegldp.lfl 183
                      D+Dt   ++++  ++  +++++ +a+++  +l+  +t     +++   +++  r+    +    ++v ++ Gs+++i r+v++e++++ + +  
       AJA92127.1 144 DADTKFKKNVITLAVSHLQSENLDALTVIPRLRCIDTItkitLPM-LSTFLHSRYSALNVNNPKKKVGYFFGSFFVIKRKVYEEIGTHEKvKQE 236
                      ******************************999766553332333.3336666666666666666798889***************999999** PP

  Glyco_tranf_2_3 184 ltdDyelglrlrragfrtayvpg 206
                      + +D  lg   ++ g+  ++v g
       AJA92127.1 237 IIEDGALGKITKESGYALKMVRG 259
                      ****9999999998888777655 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   1.2e-15   2.3e-12       9     148 ..     115     259 ..     106     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-15
  Glyco_transf_21   9 sgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa.kl....sg 97 
                      +++p++   K+++++ ++++a  ++l++ D+d+ +k++ ++  + +l++++   +t +p+    +++++     + ++l+ +++a ++    ++
       AJA92127.1 115 KEKPEKWMGKNWACMEGFRKATGEILLFTDADTKFKKNVITLAVSHLQSENLDALTVIPRLRCIDTITKITLPMLSTFLHSRYSAlNVnnpkKK 208
                      356667777*********************************************************9998888888988888888766555569 PP

  Glyco_transf_21  98 lgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspa 148
                      +g  +G++ +++r++ e+iG  e++++e+ eD algk+ ++ G+ + +++ 
       AJA92127.1 209 VGYFFGSFFVIKRKVYEEIGTHEKVKQEIIEDGALGKITKESGYALKMVRG 259
                      9*******************************************9999876 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.1   4.1e-15   8.2e-12       1     184 [.      55     232 ..      55     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 4.1e-15
  Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv...ylkdeddkayslaaarNrGaskaesdlvlFlDaD 91 
                      sv++p r++ee   i   +    ++  e++e+i +dd S +k+ e ++++ + n ++   + k++++k  ++  a   G+ ka ++++lF DaD
       AJA92127.1  55 SVILPARNEEEF--ISKCLETLGSQDYENFEIIAIDDSSEDKTGEIIEKFSKENSKIihvSAKEKPEKWMGKNWACMEGFRKATGEILLFTDAD 146
                      688888887765..99999666666559************************9986544478999999************************** PP

  Glyco_tranf_2_2  92 cfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapssssilinrraflevGGyDEr 184
                        +  +    ++ l+ +   +en da+ v+p    ++  +++   +   + +sr    +l + ++  k     +s ++i+r+ + e+G + E+
       AJA92127.1 147 TKFKKN----VITLAVSHLQSENLDALTVIPRLRCIDTITKITLPMLSTFLHSRYS--ALNVNNPKKKVGYFFGSFFVIKRKVYEEIGTH-EK 232
                      855444....345556677789********************************98..89999*9999777789**********999865.44 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.6e-07   0.00092       1      81 [.      61     146 ..      61     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.6e-07
  Glyco_tranf_2_4   1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkel..pevkllhvdksyederrqvellkalla..ryaeadwvlvvDaD 81 
                      rne++++ ++l+ + + ++++  i+ +d+ s+D+t +i+++   ++ k++hv  + +  + ++    a+++  r a ++ +l+ DaD
       AJA92127.1  61 RNEEEFISKCLETLGSQDYENfeIIAIDDSSEDKTGEIIEKFskENSKIIHVSAKEK-PEKWMGKNWACMEgfRKATGEILLFTDAD 146
                      8*****************98655999*************996336677887776543.44555555555553345677889999888 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.31       2     184 ..     140     318 ..     139     342 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
  Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgp.vl.v.mnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdg 92 
                       l+ DaDt    +++ +++++l+s + ++++ +  l + +   +++  +  +f   + +++  v +  ++v  ++Gs +++ r++ +e+g+ + 
       AJA92127.1 140 LLFTDADTKFKKNVITLAVSHLQSENLDALTVIpRLrCiDTITKITLPMLSTFLH-SRYSALNVNNPKKKVGYFFGSFFVIKRKVYEEIGTHEK 232
                      5788*******************99999888552333224566666666666654.5567888876667788899******************* PP

  Glyco_trans_2_3  93 dessvsEDfdmglrlqrkGyrvrfvpes.lvkekspltlraalrQrkRwayGceleklillvrllgylgsllwsalplhlallllfsllalal 184
                        + + ED  +g    + Gy + +v ++ l+    +++ +  ++  kR +         l+++++  +  ++++ l+++++  +l +++++a+
       AJA92127.1 233 VKQEIIEDGALGKITKESGYALKMVRGEhLIEALYSRSAKEMWNGLKRLMVP-------LYHQSSSTAVGVFFAVLFILFMPIPLLGYSIIAF 318
                      ********99999999999999999988554444555555555555555555.......3455555566666666666666677777666443 PP

>> VasI  Type VI secretion system VasI, EvfG, VC_A0118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.21      29     102 ..     112     192 ..     100     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
        VasI  29 vakensaekWq....raieqekerdsksvvllvksdeenkkaavlltapalelks...prpvLmlsCidnitrlei.alpka 102
                 v++++++ekW     + +e   +++  +  l +++d+++kk+ ++l++  l++++      +  l+Cid it++ + +l ++
  AJA92127.1 112 VSAKEKPEKWMgknwACMEGF-RKATGEILLFTDADTKFKKNVITLAVSHLQSENldaLTVIPRLRCIDTITKITLpMLSTF 192
                 444445555531110223333.3345556667778888888888888888888887755555679*********99544444 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3       3.6   7.1e+03     175     190 ..      13      28 ..       6      38 .. 0.51
   2 ?   12.3   0.4   5.7e-05      0.11     130     188 ..     287     349 ..     218     380 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
        VIT1 175 lalllfGavkalltgs 190
                 ++++l+G++ a+l+ +
  AJA92127.1  13 FTVILVGVFLAWLSLL 28 
                 3344444444444433 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.7e-05
        VIT1 130 elasplkaAlssalsfliGgliPllpylfve....svglalvvsiavtllalllfGavkallt 188
                 ++ s+   ++  a++f+++  iPll y +++       + l++s+++++++++   ++ a+++
  AJA92127.1 287 HQSSSTAVGVFFAVLFILFMPIPLLGYSIIAfepnISFTTLLISAIISTITIFSASIMEAKMG 349
                 23567789*******************887766655888999999999999999999998887 PP

>> Sarcolipin  Sarcolipin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   0.00039      0.78      12      24 ..      13      25 ..       7      33 .. 0.81
   2 ?   -1.6   0.2       1.1   2.2e+03      10      20 ..     322     332 ..     318     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00039
  Sarcolipin 12 FTvVLITViLmWL 24
                FTv+L+ V L WL
  AJA92127.1 13 FTVILVGVFLAWL 25
                9***********9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
  Sarcolipin  10 lNFTvVLITVi 20 
                 + FT  LI  i
  AJA92127.1 322 ISFTTLLISAI 332
                 67*****9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2576.30
//
Query:       AJA92128.1  [L=136]
Description: scavenger mRNA decapping enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-24   85.5   1.0      4e-24   85.2   1.0    1.1  1  HIT       HIT domain
    9.7e-15   55.1   0.8    1.3e-14   54.6   0.8    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0025   17.7   0.2     0.0031   17.4   0.2    1.3  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   1.0   6.7e-28     4e-24       2      97 ..      11     104 ..      10     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 6.7e-28
                 GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-T CS
         HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprre 97 
                 keip++++yedd+++ fld +p a+gh+Lvipkkh ++++dl+ +  +kl+ +v k+  ++     + ++ v+i ng+++gq+++h+H+H+ipr++
  AJA92128.1  11 KEIPTKILYEDDDTMSFLDAFPVAKGHTLVIPKKHHAKIQDLPSDVNQKLFNTVHKMTPKVDS--LQGSTLVAIHNGKDSGQEIPHVHVHLIPRSN 104
                 79************************************************************9..34688899********************975 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.8   2.2e-18   1.3e-14       2     103 ..       3     103 ..       2     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.2e-18
                 -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT--S-S--EEEE CS
      DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyqPsvyhlHlHvi 100
                 ++f++++ +++p++++yed++++ + D+ p ak h lvipk++ ++++dL ++  + l + ++k+   +++   +     +  g    + + h+H+H+i
  AJA92128.1   3 CIFCKIVTKEIPTKILYEDDDTMSFLDAFPVAKGHTLVIPKKHHAKIQDLPSDVNQKLFNTVHKMTPKVDSLQ-GSTLVAIHNGKDSGQEIPHVHVHLI 100
                 9*************************************************88888888888888888886655.568899******************9 PP

                 E.. CS
      DcpS_C 101 sld 103
                   +
  AJA92128.1 101 PRS 103
                 755 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   5.2e-07    0.0031      42     111 ..      31     104 ..       2     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.2e-07
                 S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHHH.TT--EEEEEE-...SSS-----EEEEE--H CS
    CwfJ_C_1  42 gpLssgHvliipieHisallsldeevldeirkfrkalvkmykk.qdkdavvfEis...sersvHlaiqvipvpk 111
                  p ++gH l+ip +H ++ + l+ +v + + +  + ++   ++ q++ +v   +     ++ +H+++++ip ++
  AJA92128.1  31 FPVAKGHTLVIPKKHHAKIQDLPSDVNQKLFNTVHKMTPKVDSlQGSTLVAIHNGkdsGQEIPHVHVHLIPRSN 104
                 5779*************************9877666665555516666666666556677889******99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 849.02
//
Query:       AJA92129.1  [L=74]
Description: hypothetical protein T478_0573 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0023   17.7   0.2     0.0031   17.3   0.2    1.2  1  COX14     Cytochrome oxidase c assembly


Domain annotation for each model (and alignments):
>> COX14  Cytochrome oxidase c assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   1.7e-07    0.0031      20      54 ..      31      62 ..      30      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.7e-07
       COX14 20 tLiGvTlyaggllvytvysygkynrkqkaeliere 54
                ++iG T++ +++l+yt+y+ +++n  +k     re
  AJA92129.1 31 SCIGYTIVVSLGLAYTIYRVLTRNMSKKG---RRE 62
                8********************99987776...444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.71
# Mc/sec: 312.32
//
Query:       AJA92130.1  [L=331]
Description: DHHA1 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-16   59.6   0.5    4.2e-16   59.6   0.5    2.0  3  DHHA1     DHHA1 domain
    0.00061   20.0   1.0     0.0012   19.0   1.0    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.2     1e+04      80     102 ..       7      30 ..       2      34 .. 0.63
   2 ?   -2.5   0.0      0.71   6.4e+03      41      65 ..     106     130 ..      92     142 .. 0.45
   3 !   59.6   0.5   4.7e-20   4.2e-16      23     136 ..     211     327 ..     202     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                 CT.EEEEEEEESSHSS-HHHHHHH CS
       DHHA1  80 gd.kvkvsarskkdgvdagelake 102
                 ++  v vs r   dg++ ++l+k+
  AJA92130.1   7 KSkIVCVSHREDCDGISSAALIKQ 30 
                 344667777777778888888887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.71
                 EEEEEECHCCHHHHHHHHHHHHHHT CS
       DHHA1  41 kvlvaevgeewdagalgiaadklks 65 
                 k + ++v ++++  a  ++ d  k+
  AJA92130.1 106 KKIKVNVVHDTNECASVQVYDTYKK 130
                 2222222233444444444444444 PP

  == domain 3  score: 59.6 bits;  conditional E-value: 4.7e-20
                 HHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECT..EEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE CS
       DHHA1  23 aklkaeellekaeevk...gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegd..kvkvsarskkd.gvdagelakeaaaklgggGGGH 114
                 a+l+ e+l + + +vk   + k  + ++  e+      +a++ ++    + + + +++ke+ d   ++vs+r +k+ ++++g l++++ +++gg+GGGH
  AJA92130.1 211 AQLQVEKLASVVAKVKknmKLKKNLGYM--EITDSGASGAVNFVLG--LSgKDVGVAYKERVDygVYAVSVRGSKQcKIHLGRLINKITTEVGGSGGGH 305
                 5556666666666666545666666666..5555566778999999..888***********************99*********************** PP

                 TCEEEEEEEHCHHHHHHHHHHH CS
       DHHA1 115 dlAaGagipaekleealealee 136
                 d A+Ga+ip++k+ ++l+ l++
  AJA92130.1 306 DKACGASIPKNKITKFLNTLNS 327
                 ******************9986 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.0   1.4e-07    0.0012       5      98 ..      12     141 ..       9     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-07
                 E-ECSSSHHHHHHHHHHHH..............................CECS--TCGGCGCCH......HCCCSEEEEEEE-S---S....S---SS- CS
                 xxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxx....xxxxxxx RF
         DHH   5 vghknpDtDsigSaialan..............................llvDhneksqavege......akeeaedviiiDHHrlge....efetlap 63 
                 +  ++ D+D+i Sa ++++                               ++D + +++ +++       ++++ +++  +DHH l +    +++++ +
  AJA92130.1  12 CVSHREDCDGISSAALIKQafggetiltdypgmmddmeplrndeslkelYICDLGLNKKNECDFvellthLRKRSVKISYLDHHDLDRkiinQLKKI-K 109
                 345667*******9999987777777777777666666666666666666999999988888879999999***************98888655666.6 PP

                 -EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         DHH  64 ilflnepvgstaeivaelleekkeeiskeiaelll 98 
                 + +++ +  +++  v++ +++k ++   + a++ +
  AJA92130.1 110 VNVVHDTNECASVQVYDTYKKKLDD---HAAFIAA 141
                 7888899999999999998764444...5555332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2638.87
//
Query:       AJA92131.1  [L=128]
Description: 50S ribosomal protein L7Ae [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-25   89.1   0.1    1.4e-25   88.9   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.041   12.9   0.0      0.048   12.7   0.0    1.0  1  PAD             Protein-arginine deiminase (PAD)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.1   1.5e-29   1.4e-25       3      93 ..      19     109 ..      17     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 1.5e-29
                     HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEEEEESTTTHH CS
  Ribosomal_L7Ae   3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsalaikdegdskd 93 
                     i e+l++++ +gk+v+G++e+tka+erg  kl+i+Aedvep+e +++l+ +c+e++  y +v+sk+eLG+++g  ++++a+ai + gd++ 
      AJA92131.1  19 ILEALRVSATSGKVVRGTNEATKAIERGISKLIIIAEDVEPPEVVAHLPLICEEQKAAYAFVPSKQELGKALGIDVTSAAAAILESGDASH 109
                     568999*********************************************************************************9875 PP

>> PAD  Protein-arginine deiminase (PAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.4e-06     0.048     137     226 ..      16     106 ..      12     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-06
                 E--SEEETTEEETT--EEEEE..ESSTT--SS-.HHHHHTGTT--EEEE-TTBSS--CCCTEEEEE-SSTTSEEEEEEEHHHHHHHHHHCC CS
         PAD 137 viPPvtvkgkeYplGriliGkhssslpearsmt.dfLeaqevqapvelesdWLlvghvdefltFvPakdkkgfrlllaspsaclellrekk 226
                 v+P +++ +++   G+++ G+++++   +r ++  ++ a+ v++p  +    L+ ++ +    FvP+k++ g +l ++ +sa+ ++l++ +
  AJA92131.1  16 VSPILEALRVSATSGKVVRGTNEATKAIERGISkLIIIAEDVEPPEVVAHLPLICEEQKAAYAFVPSKQELGKALGIDVTSAAAAILESGD 106
                 6788899999999*******98877777777874567899**********************************************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1002.81
//
Query:       AJA92132.1  [L=108]
Description: hypothetical protein T478_0117 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 825.21
//
Query:       AJA92133.1  [L=150]
Description: JAB1/Mov34/MPN/PAD-1 ubiquitin protease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-21   74.6   0.0    6.1e-21   74.4   0.0    1.1  1  Prok-JAB     Prokaryotic homologs of the JAB domain
    0.00054   19.9   0.1     0.0009   19.2   0.1    1.4  1  RadC         RadC-like JAB domain
    0.00076   19.5   0.1     0.0012   18.8   0.1    1.4  1  JAB          JAB1/Mov34/MPN/PAD-1 ubiquitin protease
     0.0081   16.5   0.2      0.015   15.6   0.2    1.4  1  Toxin-JAB1   JAB-like toxin  1
  ------ inclusion threshold ------
      0.048   14.0   0.0      0.067   13.5   0.0    1.3  1  tRNA_bind_3  tRNA-binding domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.7e-24   6.1e-21       6     114 ..      29     136 ..      24     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.7e-24
    Prok-JAB   6 salvaharrahpeEtcGlllgke..seseevivvplvnewsn..rfeipdpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarvka 100
                 ++l++ a++++p E c++l+g+e  +++ + ++v  +n++++   f+i +p+  + +++ +a e ++e+v+i+HSHp+++a+PSetD + ++ +  + +
  AJA92133.1  29 EELAKYAEAEKPYESCAILVGNEtdENWTVKEIVLTENTTKSevMFTI-SPDKEFEVDQ-KAKESNMEIVCIFHSHPESEAQPSETDKKFMRVN--PFP 123
                 78999******************5555555555555555555******.*********9.********************************97..245 PP

    Prok-JAB 101 lliivgdkaeelra 114
                 ++i+ g k++e+++
  AJA92133.1 124 WIIYSG-KTKEMNC 136
                 555555.4666655 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.5e-07    0.0009      19      89 ..      40     118 ..      22     120 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.5e-07
                 TS-EEEEEEE-TTSBEEEEEEE..EESTT-...GGGCSHH...HHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHH CS
        RadC  19 eqEefvvllLdsknrliadeel..seGtln...stlvdpr...evfkealklnAaavilaHnhPsgdlepSeeDieltk 89 
                 + E +++l+ ++  +  + +e+  +e t++     +++p    ev ++a ++n + v ++H hP+ +++pSe D+++++
  AJA92133.1  40 PYESCAILVGNETDENWTVKEIvlTENTTKsevMFTISPDkefEVDQKAKESNMEIVCIFHSHPESEAQPSETDKKFMR 118
                 3477777777766555544444444444442222223333333788999999***********************9986 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.3e-07    0.0012      19     107 ..      34     115 ..      15     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-07
                 HHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTTSEEEEEEEESSSS-SS--HHHHH CS
         JAB  19 halrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgrervvGWYhshpditvwlsevdvr 107
                 +a+ ++    e + +l+G   d+ +  + +++ ++  ++++   ++s+d+e+   +   +k+   ++++v  +hshp+ ++++se d +
  AJA92133.1  34 YAEAEKPY--ESCAILVGNETDE-NWTVKEIVLTENTTKSEVMFTISPDKEFEVDQ--KAKE--SNMEIVCIFHSHPESEAQPSETDKK 115
                 44455555..7778999999999.999************************54433..3333..459************9999998855 PP

>> Toxin-JAB1  JAB-like toxin  1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   4.2e-06     0.015      19      86 .]      55     116 ..      48     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
  Toxin-JAB1  19 n.tkvEwslagvgengkkglvvsTsheknsvsgtyllskllkagytireliHsHpdggtkkpsdaDkgf 86 
                 n t  E+ l+    ++++ + +s ++e + +      +k ++ +++i    HsHp+ + ++ps+ Dk+f
  AJA92133.1  55 NwTVKEIVLTENTTKSEVMFTISPDKEFEVD------QKAKESNMEIVCIFHSHPE-SEAQPSETDKKF 116
                 4456666666666666666666666666555......6777777777777******.9999*****986 PP

>> tRNA_bind_3  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05     0.067      32      59 ..      18      45 ..       6      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                 -------HHHHHHHHHHHHS---TCCCH CS
  tRNA_bind_3 32 eadqalneqdwreLagFAfahrPleasl 59
                 +++  l+e+d +eLa +A+a +P+e++ 
   AJA92133.1 18 NKSIILSEKDKEELAKYAEAEKPYESCA 45
                 67789********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1171.17
//
Query:       AJA92134.1  [L=209]
Description: TIGR00153 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-22   79.6   7.5    2.3e-22   79.4   7.5    1.1  1  PhoU_div  Protein of unknown function DUF47
     0.0077   15.4   0.2      0.014   14.5   0.2    1.5  1  AIP3      Actin interacting protein 3
  ------ inclusion threshold ------
      0.052   14.0   0.9        4.5    7.7   0.2    2.4  2  DUF5406   Family of unknown function (DUF5406)


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   7.5   3.9e-26   2.3e-22      13     213 ..      19     206 ..       3     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 3.9e-26
    PhoU_div  13 lqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtlrkvefpee 111
                 l ++++k +e+++ + el+ +  ++d      ++  ise+E eAD ++r+i  +l+k +++P dRed+ ++++++D+i+d +  i+ +   +k+    +
  AJA92134.1  19 LENLAKKAVEASDAVLELMDDPTNKD------KIAHISEIETEADVLTRDIFSELNKTFITPLDREDMQRVASKIDDIIDFMDGIGARFASYKI---TK 108
                 34556677888888888888888866......8999*********************************************************6...55 PP

    PhoU_div 112 lkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvadrisi 210
                   +   ++++ + +a ++++ ++ +l  + +  l   +   + + +E+ iD+l+r  i +lf+ +d   p++++ l++i+e +e  sdr  dvad ++ 
  AJA92134.1 109 SPPHTKQMAEELAKATREVEYMVGKLGNVKNPKLMI-EHCRNTSVIEHVIDDLYRLAISELFESND---PIKIIKLKDIYETMETASDRCVDVADVVED 203
                 5789999*******************9877777774.88999999******************766...**************************9998 PP

    PhoU_div 211 ill 213
                 i+l
  AJA92134.1 204 IVL 206
                 876 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   2.3e-06     0.014     197     258 ..      77     138 ..       4     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        AIP3 197 seesdklvtkvddLqDlvedlrkDVvqRgvrpskkqlesvakeikkakkelkkleeyiktek 258
                  e+ +++ +k+dd+ D ++ +    ++ +++ s+ + +++a+e++ka+ e++ +  ++ ++k
  AJA92134.1  77 REDMQRVASKIDDIIDFMDGIGARFASYKITKSPPHTKQMAEELAKATREVEYMVGKLGNVK 138
                 36899*************************************************99988877 PP

>> DUF5406  Family of unknown function (DUF5406)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2   0.00075       4.5      42     106 ..       8      72 ..       2      75 .. 0.89
   2 ?    4.7   0.0    0.0066        40      35      76 ..     146     186 ..     120     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00075
     DUF5406  42 lsldvedayeklerlgqklsdetyalkllgeddegkewleailindkkdeletedewdaLsemlv 106
                 ++++++++ + le+l +k  + + a+  l +d   k++++ i   +++ ++ t d +++L++  +
  AJA92134.1   8 VKSNEKELLTILENLAKKAVEASDAVLELMDDPTNKDKIAHISEIETEADVLTRDIFSELNKTFI 72 
                 66788889999***************999999999999*999999***************98776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0066
     DUF5406  35 nCtgldvlsldvedayeklerlgqklsdetyalkllgeddeg 76 
                  C+   v++  ++d+y  l   +   s+++++++ l +  e 
  AJA92134.1 146 HCRNTSVIEHVIDDLYR-LAISELFESNDPIKIIKLKDIYET 186
                 59999***********9.9999************99654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1128  (0.0629148); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1507.47
//
Query:       AJA92135.1  [L=156]
Description: hypothetical protein T478_0836 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   63.9   0.0    1.7e-17   63.1   0.0    1.4  1  PUA       PUA domain
     0.0077   16.5   0.1      0.012   15.8   0.1    1.4  1  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
        5.1    6.8   7.6         32    4.3   0.6    3.3  3  SH3_1     SH3 domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   2.9e-21   1.7e-17       1      73 [.      72     144 ..      72     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.9e-21
                 CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
         PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                 ++v+vd gAvk+ ++ga+L+ pG+ ++ + f+++d+V iv e  ++++avG++ ++s+el  +++g + ++ ++
  AJA92135.1  72 PYVQVDMGAVKFMCKGANLMRPGIKKFSE-FSKDDIVCIVEESqNKFLAVGKSIVDSSELDNMDKGEVLKNLHY 144
                 689*************************9.************769*************************9998 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     2e-06     0.012      10      67 ..      81     142 ..      73     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-06
     UPF0113  10 klFLY.GrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivvknl 67 
                  +F++ G ++++ +i+k++e  k+  v++V   ++++l++Gk++ d+      +++ v+knl
  AJA92135.1  81 VKFMCkGANLMRPGIKKFSEFSKDDIVCIVEESQNKFLAVGKSIVDSseLdNMDKGEVLKNL 142
                 4454438899***********************************99863356666677776 PP

>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.6    0.0053        32      11      30 ..      38      57 ..      36      58 .. 0.90
   2 ?    2.6   0.1     0.017     1e+02      16      29 ..     101     114 ..     100     116 .. 0.88
   3 ?    2.5   0.1     0.019   1.1e+02      11      32 ..     127     150 ..     125     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0053
                TTBXEBSTTEEEEEEEECSS CS
       SH3_1 11 sdELsfkkGDviivleksed 30
                +dE+++  G++i++l+ +++
  AJA92135.1 38 DDEIQLITGNEIKILKIKDE 57
                79*************99887 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.017
                 BSTTEEEEEEEECS CS
       SH3_1  16 fkkGDviivlekse 29 
                 f k+D++ ++e+s 
  AJA92135.1 101 FSKDDIVCIVEESQ 114
                 99*********986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.019
                 TTBX.EBSTTEEEEEEEECSS.SE CS
       SH3_1  11 sdEL.sfkkGDviivleksed.gW 32 
                 s+EL ++ kG+v+++l+   d  W
  AJA92135.1 127 SSELdNMDKGEVLKNLHYISDkAW 150
                 66663489*******998777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1108.29
//
Query:       AJA92136.1  [L=352]
Description: cobalamin biosynthesis protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-33  112.2   0.2    1.5e-32  111.5   0.2    1.4  1  CbiG_N         Cobalamin synthesis G N-terminal
    1.3e-26   93.4   0.1    4.1e-26   91.8   0.0    1.8  2  CbiG_C         Cobalamin synthesis G C-terminus
    4.6e-12   45.9   0.0    1.4e-11   44.3   0.0    1.8  2  CbiG_mid       Cobalamin biosynthesis central region
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.24   11.7   0.0    2.2  3  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.2   3.3e-36   1.5e-32       5      82 .]      55     132 ..      51     132 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 3.3e-36
                 HHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XXXXX. CS
      CbiG_N   5 elfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviTtatd 82 
                 +lfke+d++++++++G+v+Rl+ap++kdKktDpaV+v+d++++fvis+lsGhlggAnel++eia+ +ga+ viTta d
  AJA92136.1  55 NLFKENDGIICLFSLGAVIRLLAPHIKDKKTDPAVIVIDDNANFVISVLSGHLGGANELSNEIAEKMGATSVITTAAD 132
                 78**************************************************************************97 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.85   3.8e+03      78      97 ..     115     134 ..     105     173 .. 0.67
   2 !   91.8   0.0   9.1e-30   4.1e-26       1     116 []     231     348 ..     231     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.85
                 CHHHCCCSSS-HHHHHHHHH CS
      CbiG_C  78 efvkkevGvpsVaEaaAlla 97 
                 + +++++G +sV   aA + 
  AJA92136.1 115 NEIAEKMGATSVITTAADVN 134
                 55566777777766666543 PP

  == domain 2  score: 91.8 bits;  conditional E-value: 9.1e-30
                 EEEEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT-CHHHCCCSSS-HHHHHHHHHC. CS
      CbiG_C   1 lvvGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnpsefvkkevGvpsVaEaaAllaa. 98 
                 lv+GiG + +t++e+i + ++e+le++gl+++++a++ +i++ +d  gl+el +++++p++++++eeLa+++ pnps++v++  G+ sV+EaaA+  + 
  AJA92136.1 231 LVIGIGLHWDTPKETILNGVNETLEKYGLKQNKIARFVSIKKDKDVIGLIELGKEMNIPVEYIDREELATISAPNPSKTVQAFEGTASVSEAAAIKSSq 329
                 79*********************************************************************************************8864 PP

                 .EECSCEEEE.TTEEEEEE CS
      CbiG_C  99 arllvpKqak.ggvTvAia 116
                 ++l+v+Kq+   + TvAia
  AJA92136.1 330 GELIVEKQKFpPNLTVAIA 348
                 6******87799******8 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.95   4.3e+03      42      62 ..      41      72 ..      35      97 .. 0.54
   2 !   44.3   0.0   3.2e-15   1.4e-11       1      77 [.     137     219 ..     137     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.95
    CbiG_mid 42 egterlertlpehvdveyke...........k 62
                + + + e+t  ++v++++++            
  AJA92136.1 41 KIQWYDESTTQKIVNLFKENdgiiclfslgaV 72
                44445567777777777764355555555440 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3.2e-15
    CbiG_mid   1 palDilgrpfGwriegegaltevsaalvngepvavlqdvrlegterlertlpehvdveyke........kaliwitprqlrfsee 77 
                 +a+D++g++fGw+i++++++t++sa +vn+e+++v+q  +  ++e+ + + pe  + + +         k  ++it+ +++ +++
  AJA92136.1 137 IAVDLVGKEFGWKIHDDSNVTRISAFMVNKEQIGVFQ--NAGQKEWWKGKMPENITFFSNVldlknsdsKGYLIITNDEIKDEDV 219
                 69***********************************..4555555555566665555553577788889999999888877655 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   5.7e+03      44      67 ..      40      64 ..      35      68 .. 0.57
   2 ?   11.7   0.0   5.3e-05      0.24      20      58 ..     266     302 ..     247     307 .. 0.72
   3 ?   -3.4   0.0       2.7   1.2e+04       3      15 ..     314     326 ..     314     339 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
  SpoU_sub_bind 44 ikvelvdkekLdklsg.tanHQGvv 67
                    k+++ d+   +k+++  +  +G++
     AJA92136.1 40 EKIQWYDESTTQKIVNlFKENDGII 64
                   5566666666666666544445555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.3e-05
  SpoU_sub_bind  20 kllvtegradkrleellklakkrgikvelvdkekLdkls 58 
                    + +v+ + +dk++  l++l k+ +i+ve++d+e+L ++s
     AJA92136.1 266 R-FVSIK-KDKDVIGLIELGKEMNIPVEYIDREELATIS 302
                    3.33333.47888899********************998 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.7
  SpoU_sub_bind   3 yGlhaVleaLksg 15 
                    +G+ +V ea + +
     AJA92136.1 314 EGTASVSEAAAIK 326
                    6888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2432.87
//
Query:       AJA92137.1  [L=380]
Description: hypothetical protein T478_1097 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2497.54
//
Query:       AJA92138.1  [L=487]
Description: hypothetical protein T478_0287 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-05   23.4   0.0     0.0058   15.8   0.0    2.1  2  FAD_binding_2   FAD binding domain
     0.0034   16.7   0.9        1.9    7.7   0.1    2.6  2  FAD_binding_3   FAD binding domain
     0.0035   16.6   0.3        2.3    7.4   0.0    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0091   15.6   1.7       0.19   11.3   0.0    2.1  2  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.013   14.1   0.0       0.13   10.7   0.0    2.1  2  GDI             GDP dissociation inhibitor
      0.023   13.6   0.0       0.26   10.1   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
        2.4    7.4   5.0         24    4.1   5.0    2.2  1  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0028       7.3       1      20 [.       7      26 ..       7      43 .. 0.81
   2 !   15.8   0.0   2.3e-06    0.0058      89     203 ..      60     172 ..      56     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                   SEEEE--SHHHHHHHHHHHH CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaae 20
                   DviV G+Gl G  AA +++ 
     AJA92138.1  7 DVIVAGGGLTGTIAAQAISY 26
                   9**************98765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.3e-06
                    HHHHHHHHHHT.T----BCCTS...SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEE CS
  FAD_binding_2  89 apeavdeLeel.gvpfsrtedg...pvdvrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavve 180
                    ++eavd+++e   +p++r ++    + +v  +   ++t  +++d a      + + ++l +   e+ +k+gv+f ++ ++  Li+++++v+G+  +
     AJA92138.1  60 SKEAVDFMTERiKIPWTR-PEIehdVKGVMAFSPDKET-AIPFDGAG----YMLNRQKLPEIQNERTKKMGVEFNFEVALSGLIYDGQQVVGVQGT 149
                    689999999999999999.3331234455555555555.55665555....599****************************************** PP

                    ETTTTCEEEEEESEEEE-----G CS
  FAD_binding_2 181 npesgrevrirakavvlatgGfg 203
                    + ++++  + +ak vv+a g  +
     AJA92138.1 150 DNKTKQPYKKTAKLVVDAMGITS 172
                    65555555655666666655444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1   0.00073       1.9       2      37 ..       6      44 ..       5      52 .. 0.74
   2 !    7.1   0.1    0.0011       2.8     112     182 ..     117     188 ..     102     337 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00073
                   EEEEEE--SHHHHHHHHHHHHTTHH...EEEEESSSSSC CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvr...vvlvekrsttv 37
                   +dV++ G+G++G ++a+  s +  +    + v++  +t 
     AJA92138.1  6 YDVIVAGGGLTGTIAAQAISYYSKQnlrILSVDRNPETL 44
                   79***************9998876643344556666555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                    HHHHHHHTEEETCSEEEECCEECCCCCCCE.EEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEE CS
  FAD_binding_3 112 vehaeerglqvrfktevesleqdeegvtae.vrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetv 182
                     e+ ++ g++++f+  + +l  d+++v  +  +d++t + ++ +ak +v a G  S+ r+ l  + + e+++
     AJA92138.1 117 NERTKKMGVEFNFEVALSGLIYDGQQVVGVqGTDNKTKQPYKKTAKLVVDAMGITSKLRNGLQNSTKVEKEI 188
                    56677889**************999987651569999999********************999888888766 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0009       2.3     144     203 ..       7      69 ..       2      84 .. 0.80
   2 !    6.8   0.3    0.0013       3.4     185     251 ..     112     185 ..     105     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0009
                  EEEEES-SHHHHHHHHH...HHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                  xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 144 rivvvGgGyiGvElAaa...laklgkevtlveardrllraldkelsaaleealekeGvevklg 203
                  +++v GgG++G+  A+a   ++k + ++  v+++++ l++ +  ++ ++ +a  ke v+++++
   AJA92138.1   7 DVIVAGGGLTGTIAAQAisyYSKQNLRILSVDRNPETLPGRKGGAGWTCGDACSKEAVDFMTE 69 
                  68999*********9994444555558888999999998888888888888888888888765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0013
                  HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE.....EEESEEEE-S-EEES-HHCS.HCCT-E CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.....xxxxxxxxxxxxxxxxxxxx.xxxxxx RF
  Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngekle.vvledgee.....idadlvvvavGvrpstelle.eklgle 251
                  l ++ +e+ +k+Gve+ ++     ++ +g+++  v+ +d+++       a+lvv a G++ + +    ++ ++e
   AJA92138.1 112 LPEIQNERTKKMGVEFNFEVALSGLIYDGQQVVgVQGTDNKTkqpykKTAKLVVDAMGITSKLRNGLqNSTKVE 185
                  567788999999**************999944446666666667777999********9887544224555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.8      0.03        76       1      30 [.       7      41 ..       7      56 .. 0.74
   2 !   11.3   0.0   7.4e-05      0.19     156     270 ..     120     249 ..     101     290 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.03
                EEEEECTSHHHHHHHHHHHHTT.....EEEEESSS CS
         DAO  1 dvviiGGGiiGlstAyeLarrg.....Vtllekgd 30
                dv++ GGG +G  +A + +        ++ +++++
  AJA92138.1  7 DVIVAGGGLTGTIAAQAISYYSkqnlrILSVDRNP 41
                8*************998854322347788777775 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.4e-05
                 HHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEEE....EEEEEEE--GGGHH...HHHTT.......CTT.TSEEEEEEEEEEEEEECCTHSTG CS
         DAO 156 aealGveilegtevtgleeedgkvwgve...rttpgend....aadavVnaaGawsd...llgll.......kel.dlpispvrgqvlvlkplseklvs 236
                  ++ Gve+ ++    gl  ++ +v+gv+   ++t+   +    +a+ vV a+G+ s+       l       ke+ +  ++ +  +++ ++p +e l++
  AJA92138.1 120 TKKMGVEFNFEVALSGLIYDGQQVVGVQgtdNKTK---QpykkTAKLVVDAMGITSKlrnG---LqnstkveKEIdRTDVETTGRHIMYFEPGKEDLSE 212
                 67889999999999998556688999976553332...223335677********985432...22223333333335555555555555887775544 PP

                 SGCSEEEEE......EEETTTTEEEEEETTSEEEEEESSE CS
         DAO 237 paailpvpe......tdddgrgvyvtprkdgrvlvGgtad 270
                  ++ +           + +g++  v+p +d++v +G   +
  AJA92138.1 213 FDPDY---CiihldqDIAPGGYGWVFPKADNKVNIGLGVE 249
                 43333...23346668888999999999999999988763 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.1e-05      0.13       2      37 ..       3      41 ..       2      46 .. 0.84
   2 ?    0.7   0.0     0.058   1.5e+02     244     280 ..     101     137 ..      95     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.1e-05
                XXEECEEEE--SHHHHHHHHHHHHTT-...-EEEE-SSS CS
         GDI  2 deeydvivlGtGlkecilsGllsvdgk...kvlhldrnd 37
                + +ydviv G Gl+  i +  +s++ k   ++l +drn+
  AJA92138.1  3 ETDYDVIVAGGGLTGTIAAQAISYYSKqnlRILSVDRNP 41
                679****************99988766333689999996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.058
                 TT-EEETS--ECEEEE-TTS-EEEEEETTEEEEECEE CS
         GDI 244 yGGtymlnkpvdevvldedgkvvGvkseeevakakkv 280
                  G  ymln++    + +e +k +Gv+ + eva +  +
  AJA92138.1 101 DGAGYMLNRQKLPEIQNERTKKMGVEFNFEVALSGLI 137
                 5889****99999999999******999999876554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001      0.26       1      32 [.       7      38 ..       7      49 .. 0.91
   2 ?    1.0   0.0     0.058   1.5e+02     148     216 ..     104     177 ..      84     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                    +++++GGG  G +aA a++ + k++l+++ v+
      AJA92138.1  7 DVIVAGGGLTGTIAAQAISYYSKQNLRILSVD 38
                    699*******************999*999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.058
                     EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.....S-EEE-SEEEE-SGGG-IIIII CS
  Trp_halogenase 148 AyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled.....greveadlfiDcsGfrgllieq 216
                     +y l+++++ ++ ++  ++ Gv+       +  + +  +v +++ +d       +  a l++D+ G  ++l + 
      AJA92138.1 104 GYMLNRQKLPEIQNERTKKMGVEFNFEVALSGLIYDGQQVVGVQGTDnktkqPYKKTAKLVVDAMGITSKLRNG 177
                     6889999999999999999999999999999999999999999999855544345689**********999765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.0    0.0092        24       1     142 [.       7     167 ..       7     172 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0092
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaA...araGakvlLveergv.lGGlltsglvatdignkaeeqvvtgiareflerlrq.rggarlkkrskwn.......... 82 
                   Dv+V GGg+ G++AA a     ++  + l v++++  l G   ++  ++ +g        +  ++ ++er++   +  +++ + k +          
    AJA92138.1   7 DVIVAGGGLTGTIAAQAIsyySKQNLRILSVDRNPEtLPGRKGGA--GWTCGDA----CSKEAVDFMTERIKIpWTRPEIEHDVKGVmafspdketa 97 
                   9*************9875222456666666665543133332222..2333322....111112222222211111111111111101111222223 PP

  FAD_oxidored  83 ........tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDA 142
                           + + + + ++ +e  ++ gv+  ++  l++ + +g+++ +v+  +++ +  ++ +Ak+++DA
    AJA92138.1  98 ipfdgagyMLNRQKLPEIQNERTKKMGVEFNFEVALSGLIYDGQQVVGVQGTDNKtKqPYKKTAKLVVDA 167
                   3334445566666666666666666666666666666666666666666666666555666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3039.42
//
Query:       AJA92139.1  [L=44]
Description: hypothetical protein T478_0005 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0025   17.6   4.7     0.0025   17.6   4.7    1.4  1  Ephrin_rec_like  Putative ephrin-receptor like


Domain annotation for each model (and alignments):
>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   4.7   1.4e-07    0.0025       9      38 ..       4      32 ..       2      41 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-07
  Ephrin_rec_like  9 etCipCprgtYqneegqlsClaCPlgtttk 38
                      +Ci+C +g++ + +g+ +C++C +  t+ 
       AJA92139.1  4 MKCIECGIGFFSADGGN-KCSKCRPSVTQG 32
                     69**********99887.7****7443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 348.75
//
Query:       AJA92140.1  [L=82]
Description: hypothetical protein T478_0537 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.046   14.4   0.7      0.053   14.2   0.7    1.1  1  Polo_box_3  Polo box domain


Domain annotation for each model (and alignments):
>> Polo_box_3  Polo box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7     3e-06     0.053      19      73 ..      17      71 ..      12      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-06
                EEETTS-EEEEETTE.EEEE-TTT--EEE-----------TCCHHHHHHHHHHHH CS
  Polo_box_3 19 klmEnGdlRikfrdsrlivrkkgskevqvsiddkrkeevsdeelskvkevysyll 73
                 +mEn ++   + ++++i+  k+ +e  ++++ ++ke v++ + sk ++v+s l 
  AJA92140.1 17 EIMENEKFYHCVFKEKVILVFKDHQEFLNCFEIEEKEIVEQIKSSKDEDVHSILE 71
                69*****96554455588888999*******************999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1523  (0.0849462); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 610.26
//
Query:       AJA92141.1  [L=190]
Description: phosphoribosylaminoimidazole carboxylase, catalytic subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-57  193.3   0.2    2.2e-57  192.8   0.2    1.2  1  AIRC          AIR carboxylase
     0.0037   16.9   0.0     0.0069   16.0   0.0    1.4  1  PrpR_N        Propionate catabolism activator
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.024   14.5   0.1    1.5  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.8   0.2   3.6e-61   2.2e-57       2     144 ..       8     164 ..       7     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 3.6e-61
                 EEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE-.............. CS
        AIRC   2 VgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvk.............. 86 
                 VgiimGS+sD ++m++aaeil+++++++e +++Sahrtpe+l eya++ae++++kviIagAGgaahLpg++as+tt+PVigvP+               
  AJA92141.1   8 VGIIMGSSSDSRIMHGAAEILDSFSIPHEDQIISAHRTPERLNEYAKHAEKSKFKVIIAGAGGAAHLPGMIASHTTIPVIGVPIMvyndkqmkktdknk 106
                 9***********************************************************************************988888888777654 PP

                 -STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHH CS
        AIRC  87 skalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyree 144
                  +a+ gldsllSi +mP+g pv++v+++ka nA+++A++il+++++e+++kl++++ +
  AJA92141.1 107 YSAFGGLDSLLSISEMPTGSPVVAVGVNKASNAGIYALKILGNSYPEIKTKLKKHKFD 164
                 359**************************************************98855 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-06    0.0069      12      58 ..      44      94 ..      35     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
      PrpR_N 12 gdleeavelakeleaegvdviiSrGgtae....llrkhvsvPVveikvsgy 58
                 + e+  e+ak++e+ +++vii++ g a+    ++ +h+ +PV+ +++ +y
  AJA92141.1 44 RTPERLNEYAKHAEKSKFKVIIAGAGGAAhlpgMIASHTTIPVIGVPIMVY 94
                556677789*************9877776455589************9887 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     4e-06     0.024      34     108 ..      28     101 ..      10     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
                   EE-CCS-TCHHHHHCH.T..THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHHHHHH-SSEEEECHHHH..HHHHHH CS
  Asp_Glu_race  34 lndsaipdrteaieeesgddpvl.klleaakkLekagadaiviaCnTahavadelqkkikiPvlgiveat..aealka 108
                   l + +ip+  + i+++    +++ +l e ak+ ek++ ++i+  +  a  +   ++++++iPv+g++ ++   +++k+
    AJA92141.1  28 LDSFSIPHEDQIISAH----RTPeRLNEYAKHAEKSKFKVIIAGAGGAAHLPGMIASHTTIPVIGVPIMVynDKQMKK 101
                   5555667556666444....3455************************99999999*********9999955335555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1377.30
//
Query:       AJA92142.1  [L=387]
Description: PF04412 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-112  376.6   0.0   1.4e-112  376.4   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)
     0.0027   17.4   1.7        2.3    8.0   0.2    3.4  3  DUF2963   Protein of unknown function (DUF2963)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.4   0.0  1.6e-116  1.4e-112       1     401 []       1     383 [.       1     383 [. 0.97

  Alignments for each domain:
  == domain 1  score: 376.4 bits;  conditional E-value: 1.6e-116
      DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnpigvdlerweel.gvdeefa 98 
                 m+Lt+ee++ lnG++Ge+lq+a +ilva+Ge+++Ae+L+p+++ah+sgv+y+tigd g +fl+el+ k+a+v+v++t+np+g+d ++++e+ ++d+ef+
  AJA92142.1   1 MELTSEEKDALNGKHGETLQIAYRILVATGEATDAEKLIPIKWAHLSGVNYNTIGDSGEQFLRELS-KDARVKVKATVNPMGIDFDHISEFnHIDDEFV 98 
                 9****************************************************************9.9***********************67****** PP

      DUF521  99 ekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTnreggpsalaaAitGrtpeyGlhldenRkptvlveveaesedea 197
                 +kq +i + y ++Gve+tf+Ctpy + + p+k+++++++ES+a+++aNS+ G +Tn+e+++sala+AitG+ p+  l  +en    +++++++++ +e 
  AJA92142.1  99 KKQASIRDSYIRMGVEPTFSCTPYDIFDLPEKNTQVSFAESNAAIFANSLGGLKTNKESAFSALASAITGKSPYSDLR-KENITTPMTIRMKMDNPSEL 196
                 **************************************************************************9987.67777778999999999*** PP

      DUF521 198 dygalGylvGkkvgeriPvlkglekpsedelKalgAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlval 296
                 d+g+lG+++Gk  g+    ++g+++p+++ +Kal+  +++sg++a f +++   e            k ek+++ ke+++e+++el  ++ ek d+++l
  AJA92142.1 197 DFGMLGFFAGKV-GDTSVNISGVSQPNRRSCKALCGGMGTSGTCAKFQFVDNEDE------------KSEKVDFGKEEMNEIFDEL--NTAEKGDVITL 280
                 **********86.6666779*****************************998888............5799***************..999999***** PP

      DUF521 297 GcPhlsleElrelaellkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkvalgs 395
                 G+P+l leE+ +l+++l  k+k+ ++++++++sr+v+e+a+ l++++++e+aG+++lsd+C++++pli+++e+++v tnS K a+Yl++ tgv+v l+ 
  AJA92142.1 281 GSPQLGLEEISDLSKML--KGKSFQKRCMIFCSRAVQEQARTLDYINEIERAGGEILSDCCTCLTPLIDTNETDAVTTNSIKGAYYLKNSTGVDVNLKP 377
                 *****************..99999*************************************************************************** PP

      DUF521 396 leecve 401
                 l++++e
  AJA92142.1 378 LSKIIE 383
                 ***996 PP

>> DUF2963  Protein of unknown function (DUF2963)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.0    0.0072        65      15      42 ..      66      92 ..      52     102 .. 0.74
   2 !    3.3   0.0    0.0075        67      28      41 ..     315     328 ..     312     337 .. 0.80
   3 !    8.0   0.2   0.00026       2.3      11      31 ..     348     368 ..     345     373 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0072
     DUF2963 15 npqtgkkiKrtnYqedGktinsIeeyDd 42
                +++   k+K+t   + G++ + I e+++
  AJA92142.1 66 SKDARVKVKATVN-PMGIDFDHISEFNH 92
                5555667777765.88***********4 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0075
     DUF2963  28 qedGktinsIeeyD 41 
                 qe ++t+++I+e+ 
  AJA92142.1 315 QEQARTLDYINEIE 328
                 78899*******97 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00026
     DUF2963  11 ideYnpqtgkkiKrtnYqedG 31 
                 ++e++ +t ++iK  +Y ++ 
  AJA92142.1 348 TNETDAVTTNSIKGAYYLKNS 368
                 68***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2851.48
//
Query:       AJA92143.1  [L=268]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-11   42.9   0.2     0.0016   18.2   0.0    3.3  3  TPR_1            Tetratricopeptide repeat
    1.7e-10   40.2   0.0      0.015   15.4   0.0    3.4  3  TPR_2            Tetratricopeptide repeat
    2.5e-08   34.3   0.3    5.5e-06   26.8   0.2    2.3  2  TPR_19           Tetratricopeptide repeat
    3.4e-08   33.1   0.5      0.087   13.1   0.0    3.5  3  TPR_8            Tetratricopeptide repeat
    6.6e-08   32.5   0.0       0.18   11.9   0.0    3.3  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    3.9e-07   30.3   0.1    0.00076   19.7   0.0    2.5  2  TPR_12           Tetratricopeptide repeat
    4.8e-07   30.1   0.0      0.022   15.5   0.0    3.3  3  TPR_14           Tetratricopeptide repeat
      3e-06   27.2   0.3       0.18   12.2   0.1    3.4  3  TPR_17           Tetratricopeptide repeat
    4.3e-06   26.8   0.0     0.0099   16.0   0.0    2.2  2  TPR_9            Tetratricopeptide repeat
    0.00017   22.2   0.0     0.0072   17.0   0.0    2.2  2  TPR_16           Tetratricopeptide repeat
     0.0027   18.2   0.1        1.4    9.4   0.0    2.4  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0056   15.7   0.1       0.26   10.2   0.0    2.0  2  NARP1            NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.017   14.9   0.2       0.11   12.3   0.0    2.1  2  Peptidase_C39    Peptidase C39 family
      0.027   14.7   0.3      0.079   13.2   0.1    2.0  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      0.097   12.6   0.1      0.097   12.6   0.1    2.3  3  DUF4919          Domain of unknown function (DUF4919)
       0.11   12.9   0.3        7.5    7.0   0.0    2.3  2  TPR_20           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00063      0.71      12      34 .]      46      68 ..      43      68 .. 0.89
   2 !   11.3   0.0   0.00022      0.24       2      33 ..      70     101 ..      69     102 .. 0.96
   3 !   18.2   0.0   1.4e-06    0.0016       3      34 .]     105     136 ..     104     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00063
                HHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 12 fklgkydeAleyyekALelnPnn 34
                   +++ eA+ y +k Le +P+n
  AJA92143.1 46 VAEKRFSEAIIYLDKILEQEPDN 68
                5679*****************98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                 kal n++ ++ +lg++ + l   +k+Le +P+
  AJA92143.1  70 KALTNKAGLLAQLGNFSKSLSLSNKVLEMDPD 101
                 79*****************************8 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.4e-06
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 al n++ a+  l++y++  e + k L ++P+n
  AJA92143.1 105 ALTNKAIALKMLNEYEKSFEVFTKILIIDPDN 136
                 89****************************98 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   8.7e-05     0.098       4      34 .]      38      68 ..      35      68 .. 0.90
   2 !    8.3   0.0    0.0025       2.8       2      33 ..      70     101 ..      69     102 .. 0.93
   3 !   15.4   0.0   1.3e-05     0.015       3      34 .]     105     136 ..     104     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
       TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                +  +  a+ + +++ eA+ +++k le +P+n
  AJA92143.1 38 WESISAALVAEKRFSEAIIYLDKILEQEPDN 68
                6667889999*******************98 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                 +al n + ++++lg++ + l + +k+le dP+
  AJA92143.1  70 KALTNKAGLLAQLGNFSKSLSLSNKVLEMDPD 101
                 57889999***********************7 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.3e-05
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 al n + a+  l++ye+  e f k l +dP+n
  AJA92143.1 105 ALTNKAIALKMLNEYEKSFEVFTKILIIDPDN 136
                 78899*************************98 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   4.9e-09   5.5e-06       1      64 [.      45     106 ..      45     109 .. 0.94
   2 !   13.0   0.0   9.9e-05      0.11      15      67 ..      93     145 ..      89     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.9e-09
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                 l+ae+++ eA+ +l ++l+++p+n+ a+ + A +l +lg++ +   l ++++e+dpd  r+++L
  AJA92143.1  45 LVAEKRFSEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSLSLSNKVLEMDPD--RLSAL 106
                 6899*****************************************************..66665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.9e-05
      TPR_19  15 eqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                  ++l+ dp+ + a+ + A+al  l+++++  ++  +++  dpd++ +++++A 
  AJA92143.1  93 NKVLEMDPDRLSALTNKAIALKMLNEYEKSFEVFTKILIIDPDNEKIKQARAS 145
                 5799***************************************9999988886 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0032       3.6       9      34 .]      43      68 ..      38      68 .. 0.86
   2 !   13.1   0.0   7.8e-05     0.087       2      33 ..      70     101 ..      69     102 .. 0.95
   3 !    8.5   0.0    0.0023       2.6       2      34 .]     104     136 ..     103     136 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0032
                HHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  9 siylklgdyeeAkeyyekaleldpdn 34
                 ++   +++ eA+ y+ k le +pdn
  AJA92143.1 43 AALVAEKRFSEAIIYLDKILEQEPDN 68
                5677889**************99986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.8e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +a+ n++ ++ +lg++ ++ +  +k+le+dpd
  AJA92143.1  70 KALTNKAGLLAQLGNFSKSLSLSNKVLEMDPD 101
                 7999***************************8 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0023
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +a+ n++ +++ l++ye++ e++ k l +dpdn
  AJA92143.1 104 SALTNKAIALKMLNEYEKSFEVFTKILIIDPDN 136
                 5889999999*****************999996 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00016      0.18      15      38 ..      49      72 ..      41      74 .. 0.88
   2 !    8.8   0.0    0.0015       1.7      13      38 ..      81     106 ..      79     110 .. 0.91
   3 !    8.0   0.0    0.0026       2.9       8      38 ..     110     140 ..     108     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                T-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPenrQaq 38
                +++seA  y+d +Le EP+n  a+
  AJA92143.1 49 KRFSEAIIYLDKILEQEPDNLKAL 72
                789*****************9886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                 HHT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaq 38 
                  lg++s+++ + + +Le++P+   a+
  AJA92143.1  81 QLGNFSKSLSLSNKVLEMDPDRLSAL 106
                 69*******************98886 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0026
                 HHHHHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenrQaq 38 
                 A++   l eY+++ +    +L i+P+n+  +
  AJA92143.1 110 AIALKMLNEYEKSFEVFTKILIIDPDNEKIK 140
                 66777799*******************8665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.013      11      76 ..      43     100 ..      38     101 .. 0.88
   2 !   19.7   0.0   6.8e-07   0.00076       4      72 ..      70     130 ..      67     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
      TPR_12  11 avlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 a+l + +r+ eA+ +l+k le+      pd+   + +l n + l+ +lg++ + l+l +++l++++
  AJA92143.1  43 AALVAEKRFSEAIIYLDKILEQE-----PDN---LKALTNKAGLLAQLGNFSKSLSLSNKVLEMDP 100
                 6778899999*********9999.....998...779999999999*****************975 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.8e-07
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                 +al+n a +l++lg++ ++l+l +k+le+      pd+   +++l n ++++ +l++ye+  e +++ l
  AJA92143.1  70 KALTNKAGLLAQLGNFSKSLSLSNKVLEMD-----PDR---LSALTNKAIALKMLNEYEKSFEVFTKIL 130
                 6899**************************.....996...99*******************9999866 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-05     0.022       8      42 ..      42      76 ..      36      78 .. 0.89
   2 ?    7.0   0.0     0.011        12       8      42 ..      76     110 ..      71     112 .. 0.91
   3 ?    5.4   0.0     0.035        40       8      42 ..     110     144 ..     109     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-05
      TPR_14  8 aeallalGdpdeAiallrralalaPddaeawllla 42
                 +al a  ++ eAi +l+++l++ Pd++ a++  a
  AJA92143.1 42 SAALVAEKRFSEAIIYLDKILEQEPDNLKALTNKA 76
                578999**********************9998765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                 a +l++lG++ +++ l +++l+ +Pd + a++  a
  AJA92143.1  76 AGLLAQLGNFSKSLSLSNKVLEMDPDRLSALTNKA 110
                 67899**********************99998766 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.035
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeawllla 42 
                 a al  l +++++ +++ ++l  +Pd++ +  + a
  AJA92143.1 110 AIALKMLNEYEKSFEVFTKILIIDPDNEKIKQARA 144
                 67899999*******************99988776 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00016      0.18       2      29 ..      58      85 ..      57      89 .. 0.90
   2 !    9.7   0.0    0.0011       1.2       4      31 ..      94     121 ..      92     124 .. 0.93
   3 ?    1.2   0.0      0.55   6.1e+02       2      24 ..     126     148 ..     125     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdl 29
                + k le++P+n +a++n+A ll+++G++
  AJA92143.1 58 LDKILEQEPDNLKALTNKAGLLAQLGNF 85
                5799*********************986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
      TPR_17   4 kaleldPnnadaynnLAelllknGdlmt 31 
                 k+le dP+   a++n+A +l++++++++
  AJA92143.1  94 KVLEMDPDRLSALTNKAIALKMLNEYEK 121
                 89**********************9986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.55
      TPR_17   2 ylkaleldPnnadaynnLAelll 24 
                 ++k l +dP+n +  + +A ll+
  AJA92143.1 126 FTKILIIDPDNEKIKQARASLLS 148
                 6788999****999888988887 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.8e-06    0.0099       3      49 ..      43      89 ..      41      91 .. 0.93
   2 !    9.3   0.0    0.0011       1.3      17      71 ..      91     145 ..      86     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-06
       TPR_9  3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAl 49
                a++  e+++++a+ +++ +l   Pd    +   + llaqlG++s+ l
  AJA92143.1 43 AALVAEKRFSEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSL 89
                67889**************************************9865 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
       TPR_9  17 vverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                  ++ +l ++Pd+ + +   +++l  l+ +++  + +   l ++pd++ + ++ra 
  AJA92143.1  91 LSNKVLEMDPDRLSALTNKAIALKMLNEYEKSFEVFTKILIIDPDNEKIKQARAS 145
                 5678999*******************************************99986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.17     2e+02      43      66 ..      44      67 ..      38      68 .. 0.77
   2 !   17.0   0.0   6.4e-06    0.0072       2      67 ..      74     136 ..      73     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
      TPR_16 43 aalrqgrlaeAaalyraalraapd 66
                a+ + +r+ eA+ ++++ l++ pd
  AJA92143.1 44 ALVAEKRFSEAIIYLDKILEQEPD 67
                444779999***999999988777 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.4e-06
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                 ++a +++++g++ + + + + +l++d   Pd+  Al +++ a+  ++++++  +++ + l  +pd+
  AJA92143.1  74 NKAGLLAQLGNFSKSLSLSNKVLEMD---PDRLSALTNKAIALKMLNEYEKSFEVFTKILIIDPDN 136
                 6799**********************...***********************************98 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0013       1.4      80     127 ..      46      93 ..      38      99 .. 0.87
   2 ?    6.3   0.0     0.011        13      77     115 ..     111     149 ..      99     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                      HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHH CS
  Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRn 127
                      ++e+ +  a+  l+++++++p+n +a + ka  l qlg++++s    n
       AJA92143.1  46 VAEKRFSEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSLSLSN 93 
                      577788889999*****************************9987766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                      HHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH CS
  Alkyl_sulf_dimr  77 kealkegdyrwaaellnhlvfadpenaeakelkadaleq 115
                       +    ++y+ + e+  +++  dp+n++ k+++a+ l +
       AJA92143.1 111 IALKMLNEYEKSFEVFTKILIIDPDNEKIKQARASLLSE 149
                      444556799*************************99976 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00023      0.26     209     256 ..      52      99 ..      45     102 .. 0.86
   2 ?    4.2   0.1     0.015        17      36      82 ..     101     147 ..      99     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                 HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
       NARP1 209 ekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                 ++A+ y+dk +e++p  +   ++Ka +l + G+++k  ++ ++  ++D
  AJA92143.1  52 SEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSLSLSNKVLEMD 99 
                 589999999999999999999999999999999999999999998888 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                 -HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
       NARP1  36 DklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                 D+l+ +++ka  l  L+++e++ ++++++l   p+n+k  ++    +
  AJA92143.1 101 DRLSALTNKAIALKMLNEYEKSFEVFTKILIIDPDNEKIKQARASLL 147
                 89999*******************************98765544444 PP

>> Peptidase_C39  Peptidase C39 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.6e-05      0.11      42     117 ..      74     146 ..      57     150 .. 0.79
   2 ?    0.4   0.0      0.47   5.2e+02      77     121 ..     151     195 ..     141     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.6e-05
  Peptidase_C39  42 eeGlslsgLkkaakklglkakaikadlkelkelklpaIah..wdgklkHfvvvekikkkkvliadPakgkiklskeef 117
                    ++   l +L + +k+l l+ k++++d ++l+ l+ +aIa    ++ +k f v       k+li+dP + kik  ++++
     AJA92143.1  74 NKAGLLAQLGNFSKSLSLSNKVLEMDPDRLSALTNKAIALkmLNEYEKSFEVF-----TKILIIDPDNEKIKQARASL 146
                    4444578999*****************************97666666666555.....56899999999998877766 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
  Peptidase_C39  77 paIahwdgklkHfvvvekikkkkvliadPakgkiklskeefekew 121
                    p I  +d  ++  v+v   +k++ lia  + +++++  ++f ++w
     AJA92143.1 151 PTISTNDSMYDVHVLVVVRDKDENLIAVTESNNARYLPSKFTEKW 195
                    667766666666666666677777888888888888889999988 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.1e-05     0.079       3      79 ..      49     126 ..      47     129 .. 0.88
   2 ?   -3.0   0.0       8.2   9.1e+03      15      28 ..     175     187 ..     173     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                 +++ +Ai++++++l++e+++++++  +A  l ++g++ + + l +k  + ++  l ++  +A +l  L++ye+   ++
  AJA92143.1  49 KRFSEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSLSLSNKVlEMDPDRLSALTNKAIALKMLNEYEKSFEVF 126
                 6889*******************************************8888888888888888888888888766655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.2
                 HH.HHH--HHHHHH CS
      ANAPC3  15 llaaetespedayl 28 
                 l  a tes++++yl
  AJA92143.1 175 LI-AVTESNNARYL 187
                 66.78999999997 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.7e-05     0.097      56     118 ..      36      96 ..      25      99 .. 0.86
   2 ?    3.6   0.0     0.052        58      74     113 ..      86     125 ..      83     132 .. 0.84
   3 ?   -2.9   0.3       5.1   5.7e+03      14      33 ..     207     226 ..     198     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-05
     DUF4919  56 ekleelkldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrln 118
                 +++e  + +   + e+ + e+i +  ++l+++P +lk+l++ a  + +lg+ +++ ++s+++ 
  AJA92143.1  36 KEWE--SISAALVAEKRFSEAIIYLDKILEQEPDNLKALTNKAGLLAQLGNFSKSLSLSNKVL 96 
                 4554..357888999************************************999999998875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.052
     DUF4919  74 keiislaeealkknPfdlkqlnllayaykalgkkeeakiy 113
                  + +sl++++l+ +P  l +l++ a+a+k l++ e++ ++
  AJA92143.1  86 SKSLSLSNKVLEMDPDRLSALTNKAIALKMLNEYEKSFEV 125
                 5667899*************************99886555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.1
     DUF4919  14 YpkLmeryqanDttLteedy 33 
                 Y++  e +q+++t+L+++d+
  AJA92143.1 207 YENGYEIFQKENTMLSNDDH 226
                 66666677888888888876 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.055        62      11      42 ..      58      89 ..      48      94 .. 0.86
   2 ?    7.0   0.0    0.0067       7.5      13      65 ..      94     147 ..      86     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.055
      TPR_20 11 leaalaanpddldarldlAlallaagryeeAl 42
                l++ l+++pd+l+a  + A +l++ g+  ++l
  AJA92143.1 58 LDKILEQEPDNLKALTNKAGLLAQLGNFSKSL 89
                77789*******************99988876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0067
      TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleilkrdrkw.eddaarkqll 65 
                 + l+ +pd l a  + A al + ++ye+++e + +il  d +  + ++ar  ll
  AJA92143.1  94 KVLEMDPDRLSALTNKAIALKMLNEYEKSFEVFTKILIIDPDNeKIKQARASLL 147
                 557899********************************9987625578888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1802.84
//
Query:       AJA92144.1  [L=65]
Description: hypothetical protein T478_0786 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.042   13.8   0.1      0.049   13.6   0.1    1.1  1  DUF1815      Domain of unknown function (DUF1815)
      0.051   13.6   0.0      0.051   13.6   0.0    1.1  1  Lum_binding  Lumazine binding domain


Domain annotation for each model (and alignments):
>> DUF1815  Domain of unknown function (DUF1815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.4e-06     0.049      10      57 ..      11      57 ..       5      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-06
     DUF1815 10 slvkdlvlslqalaislekrGvlascytcgde.aesasfvvdlgdghlv 57
                sl++d++l+ +   + l    +  scy+c ++  ++ s+ ++  d + v
  AJA92144.1 11 SLIQDFILKTEP--VFLTSDAHEMSCYVCKKGiHDGVSLTAKTLDSKNV 57
                678898877665..67889999********9967789998887777655 PP

>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.7e-06     0.051      24      55 ..      27      53 ..       5      65 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
                 TEESGGGGG..TTT-EEEETTEEEEEEEEEE. CS
  Lum_binding 24 ielpelakylvekGdsiavnGvcLTVvteeve 55
                  +++e++ y+++kG    ++Gv+LT  t  ++
   AJA92144.1 27 SDAHEMSCYVCKKG---IHDGVSLTAKT--LD 53
                 33348999******...8********74..23 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 484.28
//
Query:       AJA92145.1  [L=361]
Description: luciferase-like monooxygenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-54  183.6   0.0    8.1e-54  183.2   0.0    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.0   4.5e-58   8.1e-54      24     314 .]      21     331 ..       6     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 4.5e-58
  Bac_luciferase  24 ylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpavee 114
                     +++    +a++ G++++w ++h ++p+ +     d++++la +aa+T++++lgt+vt +++rhP ++A +  tLd+ls+GR  lg+g+g++++  
      AJA92145.1  21 QILTACSLADKTGYHSIWYMDHSNVPQWSnaivNDPWVMLAGIAAVTNNVELGTCVTDALRRHPSNIALASITLDRLSKGRGTLGIGAGEAQNL- 114
                     56667789*****************99989****************************************************************. PP

  Bac_luciferase 115 rrfGvdhderyarlrEfvevlrrlwrg...eevdfeGeffsvkgalllprpgqgp.iPvyvaaaspaglelaarhadglllageppeeaaelier 205
                     + f +++d+++  ++E ++v++ l  +   ++ ++eG+++++ +a+l+ +++ +p +P+y+a+++p++l+++++++dg+l+ g +pe  +++ ++
      AJA92145.1 115 KEFNIPFDKPVSKFEEQLQVIKHLYDSdpdNRKTWEGKYYQLTEACLQAKSVRQPhVPIYMASGGPRTLKMTGKYGDGWLPIGYTPELFEDHKNQ 209
                     8899*********************55884555*********999999999998889**************************999999999999 PP

  Bac_luciferase 206 lragaaeagrdpa...dirvgisltvivadteeeAraearaliagldfyaldsegagreaeaa..........eiqeeedanlwagaadavpdel 287
                     +     e gr+ +   d++ ++ + v+  d++e  +a++++ i+ + f+++  + +g ++               +++ +  ++++aa+ +pd++
      AJA92145.1 210 IVDSMNENGRTEEekqDFQMALDIDVYFSDDAETSWAKMKEAIKVSLFKPEVLRVHGLKDIEGfdfkkyfteySMSNQDWIVKMREAATTIPDKI 304
                     9999999***999999***********************99996666666666666666555544444422222233344445588889999999 PP

  Bac_luciferase 288 vaatalvGtpeqvaerlaayaeagvde 314
                      ++ + vGtp++v+e ++ + +agv++
      AJA92145.1 305 ARSSVGVGTPDDVIEVFEKFLKAGVNH 331
                     999999******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2496.00
//
Query:       AJA92146.1  [L=533]
Description: hypothetical protein T478_0512 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00025   20.7   3.6        1.8    8.1   0.0    4.6  4  SGL       SMP-30/Gluconolactonase/LRE-like region
     0.0087   16.1   0.1       0.72   10.0   0.0    3.1  2  NHL       NHL repeat
  ------ inclusion threshold ------
      0.074   13.3   6.2         18    6.0   0.1    4.6  4  Reg_prop  Two component regulator propeller
      0.076   13.7   1.1       0.17   12.6   1.1    1.5  1  FliD_N    Flagellar hook-associated protein 2 N-terminus


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.4    0.0027        12      92     163 ..      89     158 ..      87     168 .. 0.78
   2 ?    2.9   0.0     0.016        71     146     203 ..     185     240 ..     179     259 .. 0.76
   3 !    8.1   0.0   0.00041       1.8     176     219 ..     276     319 ..     268     330 .. 0.86
   4 ?    0.4   0.0     0.087   3.9e+02     171     212 ..     382     428 ..     349     447 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0027
         SGL  92 vvdpdGrlwfGtmgdeeakgeevgalyrldpdgklervldd.ltipNGlawspdgktlYlaDsltrkiwaydv 163
                 +v+pdG++wf   + ++ ++     +  + ++ + e++ d+  t++ G+  s+dg+  Y +D   ++iw++d 
  AJA92146.1  89 KVAPDGNVWFVESNVGQIAKF--NPMSEIFTEFENELWPDGaRTMSWGMDYSSDGTMWY-TDGSFDTIWRFDT 158
                 788899999988888887777..677777777677888877357899999999997777.9999999999997 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.016
         SGL 146 ktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwg 203
                 + ++++D +  ki+ +d++ +  +++    +a +++       +a+D+e+n+w + w 
  AJA92146.1 185 SNIIVNDFTGSKITFFDLSHNIDEIEYSSIVAPIPNSF--TGDFAIDSENNLWYTNWV 240
                 55667777788888888888888888888888887775..3349**********9994 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00041
         SGL 176 fadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGkliee 219
                 ++d++++  +  Gl vD+++nvw+   +++   +fdp+ +  ++
  AJA92146.1 276 VYDFPTDLTTANGLSVDENDNVWIVDTSSSFFFKFDPEEETFTK 319
                 688899998899**************************876655 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.087
         SGL 171 snrrvfadlkkge....gepDGlavDa.eGnvwvAvwgggkvvrfdp 212
                 s+   +ad++++     g+   +  Da  +++w + w+++k+ ++d+
  AJA92146.1 382 SKNPNWADCEDKSnsncGVAQIFGFDAiGDKIWFTEWAENKIGVVDT 428
                 33334444444443333333333345545555555555555555555 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.037   1.7e+02       3      28 .]      84     109 ..      83     109 .. 0.90
   2 !   10.0   0.0   0.00016      0.72       4      24 ..     286     306 ..     283     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.037
                 SEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL   3 yPhGvavdsnGdiyVaDsenhrvqvF 28 
                 +P  + v ++G+++  +s+  ++ +F
  AJA92146.1  84 QPLAIKVAPDGNVWFVESNVGQIAKF 109
                 788999********999999999988 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                 EEEEEEETTTEEEEEECCCTE CS
         NHL   4 PhGvavdsnGdiyVaDsenhr 24 
                 ++G++vd n+++++ D+ ++ 
  AJA92146.1 286 ANGLSVDENDNVWIVDTSSSF 306
                 68**************88765 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.024   1.1e+02       9      20 ..      87      98 ..      82      99 .. 0.85
   2 ?   -1.3   0.3      0.95   4.2e+03      13      19 ..     138     144 ..     132     145 .. 0.85
   3 ?    6.0   0.1     0.004        18       4      19 ..     219     235 ..     217     239 .. 0.85
   4 ?    2.9   0.1      0.04   1.8e+02       8      20 ..     287     299 ..     283     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                EEEE-TTSCEEE CS
    Reg_prop  9 aileDsdGrlWv 20
                ai   +dG++W+
  AJA92146.1 87 AIKVAPDGNVWF 98
                677889*****8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.95
                 -TTSCEE CS
    Reg_prop  13 DsdGrlW 19 
                  sdG++W
  AJA92146.1 138 SSDGTMW 144
                 68***** PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.004
                 SSCEE.EEEE-TTSCEE CS
    Reg_prop   4 snnvt.aileDsdGrlW 19 
                  n++t +++ Ds+++lW
  AJA92146.1 219 PNSFTgDFAIDSENNLW 235
                 577888*********** PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.04
                 EEEEE-TTSCEEE CS
    Reg_prop   8 taileDsdGrlWv 20 
                 + +  D + ++W+
  AJA92146.1 287 NGLSVDENDNVWI 299
                 57889*******9 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.1   3.7e-05      0.17      27      88 ..     440     512 ..     434     524 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                 XXXXXXXHHHHHHHHHHHHHHHHHH..........HHHXX.GGGGGXEEEEECSTTTEEEEEETTS-SEEEEE CS
      FliD_N  27 ktklewkqsayrelnsklsnlksal..........salsk.sstfsakkatssdesvvtatassgaaagsysi 88 
                  ++++ k+ + ++++ +++nl+++           sa++k s+ + +   tssde +v++tas+ a +g y++
  AJA92146.1 440 TESITLKKGEPQTISLNINNLSNTDkinfnfahtaSAVTKsSDLLVSHDFTSSDEIIVSVTASEIAISGDYKL 512
                 566677777778888888888883333333333223445545555677999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3570.41
//
Query:       AJA92147.1  [L=94]
Description: hypothetical protein T478_0376 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.2   2.1         13    6.4   0.1    2.7  2  KID       KID repeat


Domain annotation for each model (and alignments):
>> KID  KID repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4    0.0012        22       3       9 ..      51      57 ..      50      59 .. 0.85
   2 ?    6.4   0.1   0.00071        13       2       9 ..      68      75 ..      67      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0012
         KID  3 DsVEKNL 9 
                D VEKN 
  AJA92147.1 51 DDVEKNI 57
                89****7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00071
         KID  2 IDsVEKNL 9 
                ID+  KNL
  AJA92147.1 68 IDTLQKNL 75
                9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 682.97
//
Query:       AJA92148.1  [L=420]
Description: serine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-39  133.3   0.9    8.8e-39  133.3   0.9    1.7  3  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.4e-23   83.2   8.0    1.4e-23   83.2   8.0    1.8  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.09   13.3   2.3       0.19   12.2   2.3    1.5  1  FlgN          FlgN protein
       0.54   10.5   4.1          5    7.3   0.0    2.8  3  I_LWEQ        I/LWEQ domain
          1    9.7   6.5       0.42   10.9   3.4    2.0  2  BLOC1_2       Biogenesis of lysosome-related organelles compl


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7   6.2e+03      42      42 ..      54      54 ..      15     100 .. 0.59
   2 ?   -2.8   0.0       1.5   5.4e+03      78     104 ..      83     109 ..      74     157 .. 0.68
   3 !  133.3   0.9   2.4e-42   8.8e-39       2     179 .]     218     398 ..     216     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                  E CS
                  x RF
  tRNA-synt_2b 42 i 42
                  +
    AJA92148.1 54 M 54
                  1 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                   HHHHHHHHHHHHHHHHTT.SCEEEEEE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  78 dslrdlikaisriferlglefraiiel 104
                   d+l++l k++++ +++l ++   ++++
    AJA92148.1  83 DELENLRKTVDENYHNLSFSIPNLVHD 109
                   677888888888888887765555444 PP

  == domain 3  score: 133.3 bits;  conditional E-value: 2.4e-42
                   EEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHT CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   2 kledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferl 94 
                   k++d   +++ L+ t+e+++++++ de+l   ++Pl+++ i++++R+E+     d++G++Rv++F++ ++++f+ +++++++ +++ik +++++++l
    AJA92148.1 218 KVQD---EDLFLIGTSEHAIASMYYDEILEGSKIPLRYASISPCFRREAGahgkDQKGIFRVHQFEKIEQFIFCRPEESWEEHEKMIKNTEEFYQQL 311
                   5544...58******************888777****************778999****************************************** PP

                   T.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.SEEEEEEEEEE.EEHHHHHHHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxx RF
  tRNA-synt_2b  95 glefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.reksvimicaa.igveRllsaileqn 179
                    +++r ++++ +++    ++++++ea++  +++++ei++++++ +++s+rl++++ ++ n   k  ++++ + +++eR++ aile+n
    AJA92148.1 312 EIPYRLMLLSSGDMGKVSAKTYDIEAWMAGQNAYREIVSCSNCIDYQSRRLKIRFREKSNeDTKYIHTLNSTlVAIERTMVAILENN 398
                   *****99999888888999************************************88777478999******999**********98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   8.0   3.8e-27   1.4e-23       1     108 []       1     107 [.       1     107 [. 0.99
   2 ?   -2.8   0.1         2   7.2e+03      50      87 ..     368     381 ..     358     400 .. 0.49

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 3.8e-27
                   ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                   MLD+k+ir+ pe++k+ lk R + + d++++lel++ r+e++ + +el+++rN++s +Ig+ kk+++da+el+ e+ +++++l++le+  k+++++ 
    AJA92148.1   1 MLDPKIIRDKPELIKQMLKDR-AVEFDFEKMLELNNTRKEMMMQSDELKQKRNQMSVKIGSEKKAGNDASELLREMGDISKKLDELENLRKTVDENY 96 
                   *********************.799************************************************************************ PP

                   HHHHCTS---- CS
  Seryl_tRNA_N  98 eklllaiPNip 108
                   ++l  +iPN++
    AJA92148.1  97 HNLSFSIPNLV 107
                   *********85 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                   HHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
  Seryl_tRNA_N  50 aerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                   +++Ne +k I+                         l+
    AJA92148.1 368 EKSNEDTKYIHT------------------------LN 381
                   333333333332........................22 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.3   5.4e-05      0.19      30      99 ..      16      95 ..      12     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                HHHHTT....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--.SCHHHHHHHHCT.....TCCHHHHHHHHHHHHH CS
        FlgN 30 eaLkag....dieaLeelleekqellekleqleqkrakllaelgls.aeeatlsellak.....eedeelkelwqelkel 99
                ++Lk++    d e++ el++  +e + + ++l+qkr ++  ++g + +     sell++     ++ +el++l++ ++e 
  AJA92148.1 16 QMLKDRavefDFEKMLELNNTRKEMMMQSDELKQKRNQMSVKIGSEkKAGNDASELLREmgdisKKLDELENLRKTVDEN 95
                56777777779***********************************9899999999997777776667777776666655 PP

>> I_LWEQ  I/LWEQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.9     0.096   3.4e+02     106     135 ..      22      51 ..       7      58 .. 0.79
   2 ?   -0.9   0.0      0.49   1.8e+03      68      89 ..      79     100 ..      72     122 .. 0.77
   3 ?    7.3   0.0    0.0014         5      30      94 ..     336     400 ..     332     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.096
      I_LWEQ 106 eeeldisklslvqakrqemeaqvkilklek 135
                 + e+d++k+ + + +r+em  q++ lk ++
  AJA92148.1  22 AVEFDFEKMLELNNTRKEMMMQSDELKQKR 51 
                 347899999999999999999999988876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.49
      I_LWEQ  68 skslkrLeaaskaVkkatkelv 89 
                 sk+l++Le+  k V +  ++l 
  AJA92148.1  79 SKKLDELENLRKTVDENYHNLS 100
                 7888889999999888888876 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0014
      I_LWEQ  30 davvqgkakeeeLivaakevaastaqLvvasrvKadknskslkrLeaaskaVkkatkelvkavke 94 
                 +a + g+++  e++++++ +  +  +L +  r K++++ k  + L+++  a+++++ +++++ ++
  AJA92148.1 336 EAWMAGQNAYREIVSCSNCIDYQSRRLKIRFREKSNEDTKYIHTLNSTLVAIERTMVAILENNQT 400
                 6788999*****************************************99999998888877665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.4   0.00012      0.42      24      90 ..      32      98 ..      20     102 .. 0.88
   2 ?   -2.7   0.1       2.1   7.5e+03      26      39 ..     298     311 ..     291     315 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
     BLOC1_2 24 lLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90
                 L++  ++++ + ++lk++ +++++k+   ++  +  +++l+++ +i k+++eLe++ + +De   +
  AJA92148.1 32 ELNNTRKEMMMQSDELKQKRNQMSVKIGSEKKAGNDASELLREMGDISKKLDELENLRKTVDENYHN 98
                46777788899999*******************************************9999987665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
     BLOC1_2  26 eklNeaasekykkl 39 
                 ek+ ++++e y++l
  AJA92148.1 298 EKMIKNTEEFYQQL 311
                 33333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1409  (0.0785878); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3058.91
//
Query:       AJA92149.1  [L=694]
Description: AAA ATPase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-25   89.5   4.7    3.5e-25   89.5   4.7    2.3  2  AAA_15    AAA ATPase domain
    3.2e-15   56.7  10.5    9.9e-15   55.1   6.5    3.0  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0023   18.2   0.4       0.41   10.9   0.1    3.4  2  AAA_22    AAA domain
      0.004   17.7   8.4      0.004   17.7   8.4    3.4  2  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.1      0.011   16.3   0.1    2.8  3  ABC_tran  ABC transporter
      0.013   15.1   0.1      0.098   12.2   0.0    2.1  2  AAA_27    AAA domain
      0.015   15.1   0.0      0.037   13.8   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.038   13.4   0.0          6    6.2   0.0    2.7  2  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   4.7   1.5e-28   3.5e-25       1     369 []       1     419 [.       1     419 [. 0.56
   2 ?   -4.4   9.4       5.3   1.2e+04      92     256 ..     548     671 ..     487     693 .. 0.36

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.5e-28
      AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......................kkvikiekedleifenisesk 75 
                 M+++k++ + +R++ d  ei + + l  ++G+N sGK++il+al l+ + + + +                       +    ++ ++++  ++     
  AJA92149.1   1 MRLRKFRARAYRCIHDsGEIRVGD-LAAFVGRNESGKTTILQALTLLNKDQ-PVSdldlcdemtedlkqevrlaegefD----LNHNEIRLIKE----- 88 
                 99**************99******.*******************7776644.444666777666555555555533331....22222222222..... PP

      AAA_15  76 dikIdvef................aek....ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeek 154
                                         +++    ++ +++++++++++ ++ ++  +k+ s l+++ +  ++kl+        +   +  ++ e + ++  +
  AJA92149.1  89 -------TfpsipeikkikifrtnKNPipqyDFGDVEISEAENSGLNSWENFREKFLSFLDTIPNHVQIKLD------TGFFQGQAPETEEMFRNEMAE 174
                 .......23444444444435544222434555666666666666666665555555555555555555554......222222222222222222222 PP

      AAA_15 155 lekekeelkidkedlkklikkleeslkkee....................................elknvlksaiiklllisakRnvsdedsek.kss 216
                      ++l++   d   +i++++++  +++                                     ++nv  ++++k ++ ++   ++de+++  + +
  AJA92149.1 175 F---GNNLQVLAADEPQVIEEWNKISDENDsnfqsllvgttekmalenfidsnlhprfvyfsdykkIIGNVNLNEYRKERTSPSIEFSEDEFDKAdTVD 270
                 2...22233333333333333333333333333555566666664444444444444544444444555555555555555555555555444331334 PP

      AAA_15 217 llgklkekileealqekleeelteklkeiqeklkeidkklaeelk.......kilkkkidkik.kfnykgkkneeieik.......ddeelplnknGsG 300
                 +l+ l e  +ee       ee +   +++ + l++ +k l+e+l+                    +  +++++  + i+         +   ln++  G
  AJA92149.1 271 NLFYLAELDVEE------LEEAKNSPSQLIKLLNTCSKRLTEKLNpawkgdpI---------HvELRLNPNNVMSVVISdvhkdgtVTNTGLLNRRAEG 354
                 444444444444......34444444444444444444444444433323331.........2233344444444444477776666677789****** PP

      AAA_15 301 vqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                 ++ ++++i+  +   ++   e k +ill++EP  +LHp +q+ + +llk+la +n  Qv++ THSp++i
  AJA92149.1 355 FKWTFSFIVNFAAETQR--AELKEAILLLDEPARNLHPTQQRGISDLLKSLAGSN--QVLYATHSPYMI 419
                 *****999876666665..7999********************************..***********8 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 5.3
      AAA_15  92 yektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvl 190
                   +            l+ ++ s+++++++++k+k                                               ++ +e ++  e+ l  v 
  AJA92149.1 548 SAQ------------LIANEFSKTQTIFFEEKTK----------------------------------------------ALQSIEDYMITEDYLYAVN 588
                 111............2222222222222222222..............................................2222222222222233333 PP

      AAA_15 191 ksaiiklllisakRnvsdedsekkssllgklkekileealqekl..................eeelteklkeiqeklkeidkkl 256
                 +  +ikl+    ++  +++    ++s +++ +++i+ee  ++                    +ee    ++++++k++ ++  +
  AJA92149.1 589 QTYAIKLRKEGYVNLTEQDIQSRNKSGIIESLNSIWEEHRED-GweefdseevaryicekiaIEEADFLSDKTKDKFRSLYRLI 671
                 333333333333333333333333333333333333332211.12333333333333333332233333333333333333333 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   6.5   4.4e-18   9.9e-15       1     302 [.      25     419 ..      25     420 .. 0.83
   2 ?   -1.7   0.1      0.86   1.9e+03     103     156 ..     519     572 ..     434     631 .. 0.61

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.4e-18
      AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqveeklssvetllesgll 99 
                 l++++G+N sGK+++L+al ll         +++        + +     + d +++++++  ef+++++++r + +   s+               ++
  AJA92149.1  25 LAAFVGRNESGKTTILQALTLLN-------KDQP------VSDLDLCDEMTEDLKQEVRLAEGEFDLNHNEIRLIKETFPSIP--------------EI 96 
                 5789******************3.......3333......337777889999999****************************..............55 PP

      AAA_21 100 ldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveie 198
                 ++ ++ +  ++ +p+++  ++ +s+ ++  l+  e ++++f ++l+ i+++    +l        + g+++ +a +  ++ ++++++   +   l+ +e
  AJA92149.1  97 KKIKIFRTNKNPIPQYDFGDVEISEAENSGLNSWENFREKFLSFLDTIPNHVQI-KL--------DTGFFQGQAPETEEMFRNEMAEFGNNLQVLAADE 186
                 555555555555555555555566666666666666677777777777776664.33........6777777777777777777777666666666666 PP

      AAA_21 199 lsdlgegeeliasvderlrer.............................................................................. 219
                 ++ ++e + +i ++++ + ++                                                                              
  AJA92149.1 187 PQVIEEWN-KISDENDSNFQSllvgttekmalenfidsnlhprfvyfsdykkiignvnlneyrkertspsiefsedefdkadtvdnlfylaeldveele 284
                 66665444.333334444444577888888899999999************************************************************ PP

      AAA_21 220 ..............................................gvvflengdgqelparel...SdGtkrllalltallralkkg....sllliDE 265
                                                                v+  +++dg  ++   l    +G+k  + +++ +++  + +    ++ll+DE
  AJA92149.1 285 eaknspsqlikllntcskrlteklnpawkgdpihvelrlnpnnvmsVVISDVHKDGTVTNTGLLnrrAEGFKWTFSFIVNFAAETQRAelkeAILLLDE 383
                 *********************************************9999999999999999999***********99999999998889999******* PP

      AAA_21 266 pEngLHPkllrrllellkelsrngaQviltTHSplll 302
                 p  +LHP  +r + +llk+l+    Qv+ +THSp+ +
  AJA92149.1 384 PARNLHPTQQRGISDLLKSLAG-SNQVLYATHSPYMI 419
                 ********************99.***********975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.86
      AAA_21 103 rsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawslll 156
                 ++l+   ++ + ++++++++++ ++   + ++ ++++f+k+ t +++++ ++l+
  AJA92149.1 519 SVLPLSIFYRNHGYNTFVLLDNTEESKEISAQLIANEFSKTQTIFFEEKTKALQ 572
                 333333344444444444444444444444444444444444444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00018      0.41      11     132 ..      29     213 ..      21     216 .. 0.72
   2 ?    0.9   0.0      0.23   5.1e+02      93     118 ..     646     670 ..     580     687 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
      AAA_22  11 tGesGtGKTtllrrlleqldeeakaee...........................................................erpevvfvtlpss 50 
                 +G   +GKTt l+ l+  ++ ++  +                                                             ++e+ + + +++
  AJA92149.1  29 VGRNESGKTTILQALTLLNKDQPVSDLdlcdemtedlkqevrlaegefdlnhneirliketfpsipeikkikifrtnknpipqydfGDVEISEAENSGL 127
                 566666666666666666654444444666666666666666666666666666666666666666666666777666666555444555556677777 PP

      AAA_22  51 tsskdllrellralglelka.............erlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpe 132
                 +s++++++++l++l+   ++             ++ ++e +++ +++  ++ +v   l  DE q +   e ++++   ++ +++++q +LvGt+e
  AJA92149.1 128 NSWENFREKFLSFLDTIPNHvqikldtgffqgqAPETEEMFRNEMAEFGNNLQV---LAADEPQVI---EEWNKI---SDENDSNFQSLLVGTTE 213
                 7**************99999************6666666666********9977...*******99...777777...5556899*******985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
      AAA_22  93 elliiDEaqhlrseealeeLrsllnl 118
                 e + i+Ea++l s++   ++rsl+ l
  AJA92149.1 646 EKIAIEEADFL-SDKTKDKFRSLYRL 670
                 55789999999.75555555555543 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   8.4   1.8e-06     0.004      20     194 ..      24     299 ..       8     309 .. 0.67
   2 ?   -2.8   5.0       3.3   7.4e+03     134     172 ..     600     681 ..     515     692 .. 0.42

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
      AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrks..................grgfeksdveiese....gkvkay..veltfenkdgry........ 86 
                  l +++G N++GKTTil+A++l    ++   s+ +                  + +++++++++ +e       +++  +++  +nk+           
  AJA92149.1  24 DLAAFVGRNESGKTTILQALTLLNKDQP--VSDLDlcdemtedlkqevrlaegEFDLNHNEIRLIKEtfpsI--PEIkkIKIFRTNKNP-Ipqydfgdv 117
                 57899****************9877764..344445678888888888887744477788888776677442..333224443333333.357777777 PP

      AAA_23  87 ....................................................................trsiererelskkkgkttkkaklellei.de 116
                                                                                       ++ +e +++++++++  ++ l ++++  +
  AJA92149.1 118 eiseaensglnswenfrekflsfldtipnhvqikldtgffqgqapeteemfrnemaefgnnlqvlaadEPQVIEEWNKISDENDSNFQSLLVGTTEkMA 216
                 777888888889999999999999999999999999999999999999999999999999999999886666677777777666666665544433488 PP

      AAA_23 117 leqfisellgskkiil.nlilflgqerfeefelkdkkerleelekeleeledekkllekl....eqekekekeleeleeelee 194
                 le+fi+++l+ ++  + ++  ++g  + +e ++++++  +e  e+e++++ ++++l+       e+++e ++  ++l + l++
  AJA92149.1 217 LENFIDSNLHPRFVYFsDYKKIIGNVNLNEYRKERTSPSIEFSEDEFDKADTVDNLFYLAeldvEELEEAKNSPSQLIKLLNT 299
                 99999999888888443666777777766666666666666666666666666664333322333333333333333333333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.3
      AAA_23 134 lilflgqer...........................................feefelkdkkerleelekeleeledekkll 172
                 ++ +  q+                                            ++ f+  ++k++ ++l + + e   +++ l
  AJA92149.1 600 YVNLTEQDIqsrnksgiieslnsiweehredgweefdseevaryicekiaieEADFLSDKTKDKFRSLYRLIAERIRQQQNL 681
                 1111111111111111122222222222222233333333333333333444444455666666666666666655555544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.1   4.8e-06     0.011       7      38 ..      19      50 ..      15     189 .. 0.80
   2 ?   -1.1   0.1       1.1   2.5e+03     126     136 ..     375     385 ..     373     386 .. 0.84
   3 ?   -2.7   0.0       3.4   7.5e+03      39      74 ..     598     627 ..     591     687 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                EEETTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpt 38
                +++ g + a+vG+n +GK+t+l++l+ l k++
  AJA92149.1 19 EIRVGDLAAFVGRNESGKTTILQALTLLNKDQ 50
                6888999******************9887764 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                 TSSEEEEESTT CS
                 xxxxxxxxxxx RF
    ABC_tran 126 kpkllllDEpt 136
                 k  +lllDEp 
  AJA92149.1 375 KEAILLLDEPA 385
                 5689******6 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.4
                 EEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  39 eGeilldgkdlkeqeleslrkeigvlpqepqlfpel 74 
                 eG ++l ++d+++      r+++g+++  +++++e+
  AJA92149.1 598 EGYVNLTEQDIQS------RNKSGIIESLNSIWEEH 627
                 5556555555555......33333333333333333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.4e-05     0.098       1      48 [.       1      45 [.       1      47 [. 0.74
   2 ?   -0.2   0.0      0.28   6.2e+02     108     137 ..     653     682 ..     648     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
      AAA_27  1 MrlerLdLeryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisd 48
                Mrl++++ ++y  + d+ +++ +    dl   +G NE+GK+t+l+A++ 
  AJA92149.1  1 MRLRKFRARAYRCIHDSgEIRVG----DLAAFVGRNESGKTTILQALTL 45
                66666666666666665345554....89999**************975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
      AAA_27 108 aallggldretFealFgLdherLreGGeal 137
                 a++l   ++++F++l+ L +er+r+  + +
  AJA92149.1 653 ADFLSDKTKDKFRSLYRLIAERIRQQQNLM 682
                 6799999****************9965554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05     0.037      20      45 ..      21      46 ..      14      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
      AAA_29 20 dlkgatlltGpsGsGKSTllDAiqal 45
                ++ +   ++G+++sGK+T+l A++ l
  AJA92149.1 21 RVGDLAAFVGRNESGKTTILQALTLL 46
                44567899*************99865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0027         6      26      45 ..      25      44 ..       2      73 .. 0.83
   2 ?    4.2   0.0     0.011        26     159     202 ..     376     419 ..     358     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                EEEEEESTTSSHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxx RF
       SMC_N 26 ftaivGpNGSGKsnlldAil 45
                + a vG+N SGK+ +l+A+ 
  AJA92149.1 25 LAAFVGRNESGKTTILQALT 44
                6789**************94 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.011
                 -SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 159 aplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                 +++ llDe + +L  ++ + +++llk+   + Q++  +++  m+
  AJA92149.1 376 EAILLLDEPARNLHPTQQRGISDLLKSLAGSNQVLYATHSPYMI 419
                 57899**********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4551.58
//
Query:       AJA92150.1  [L=279]
Description: hypothetical protein T478_0080 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.6   0.2       0.73   10.3   0.0    2.1  2  DUF3980   Domain of unknown function (DUF3980)


Domain annotation for each model (and alignments):
>> DUF3980  Domain of unknown function (DUF3980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   4.1e-05      0.73       5      48 ..       5      48 ..       2      60 .. 0.89
   2 ?   -0.7   0.0      0.12   2.1e+03      77      87 .]     267     277 ..     253     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.1e-05
     DUF3980  5 tlylsikilkimsviyligsilmafstgpfihnlgfdeisisgs 48
                +++  +k +ki+  +  i +il a+    f   + fd++s+   
  AJA92150.1  5 SSFSKLKNMKILLAVVGIAAILAALDVVEFYMPMEFDDMSVNRH 48
                56778999********************************9765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.12
     DUF3980  77 lvetvikiyek 87 
                 lv+t ++iyek
  AJA92150.1 267 LVKTTVNIYEK 277
                 899******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2149.79
//
Query:       AJA92151.1  [L=142]
Description: hypothetical protein T478_1456 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1054.88
//
Query:       AJA92152.1  [L=149]
Description: hypothetical protein T478_1008 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.48    8.8  13.6       0.53    8.6  13.6    1.0  1  WDCP            WD repeat and coiled-coil-containing protein 
        1.1    8.1   6.9        1.6    7.6   6.9    1.1  1  Etmic-2         Microneme protein Etmic-2
        2.7    6.4   5.5          3    6.3   5.5    1.0  1  FUSC            Fusaric acid resistance protein family
        2.7    7.4   6.0        3.4    7.1   6.0    1.3  1  Allexi_40kDa    Allexivirus 40kDa protein
        4.9    6.5  14.7       0.52    9.7   2.0    2.4  2  DUF3482         Domain of unknown function (DUF3482)


Domain annotation for each model (and alignments):
>> WDCP  WD repeat and coiled-coil-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  13.6   0.00015      0.53     488     605 ..       2     124 ..       1     135 [. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00015
        WDCP 488 seksgrkLieeiks.leqsplss.vvdlseka.ssessvaletldaepvnrsaalasasstsdes.srpe.spkvekkknlekekeaeqlskelerlse 581
                 seks+ +L+ e ++ + q+  s+ + + ++ + s+e   ++   +ae+v++ aa +++ s++ ++ s  e ++k e  ++++k ++  ql ke+ +l+e
  AJA92152.1   2 SEKSREELLLEYEKeYLQRLASEgKLKADDVQkSEEVRNEMTVEEAEKVQADAAAQVQASSAAKNqSEDEqKKKEEFDNEVAKIRKELQLLKEMATLTE 100
                 5667777777777424444333313333343446666666666777888877777665554444303333033334567888999999*********** PP

        WDCP 582 kltevqqsLseltdllqngkkssp 605
                 +l+ +++ L   ++ +  +kk+ p
  AJA92152.1 101 ELESLKKDLKRPSKRKATKKKAAP 124
                 *********999999888888765 PP

>> Etmic-2  Microneme protein Etmic-2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.9   0.00044       1.6     330     375 ..      22      68 ..      17      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00044
     Etmic-2 330 aeegdv.aqdaqqsagaqqeaevqevgepqqeaaaaeqgssaaesdt 375
                 a eg + a+d q+s   ++e  v+e  + q +aaa  q ssaa+ ++
  AJA92152.1  22 ASEGKLkADDVQKSEEVRNEMTVEEAEKVQADAAAQVQASSAAKNQS 68 
                 4556543899*********************************8755 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.5   0.00083         3     251     332 ..      48     119 ..      12     139 .. 0.46

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00083
        FUSC 251 aavpelaallaelaal.eaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaaar 332
                 + v+  a+  a+++a  +a++++e+++++ ++++ +++++r++l+        ll ++a+l +el  l ++l++++++ a+ +
  AJA92152.1  48 EKVQ--ADAAAQVQASsAAKNQSEDEQKKKEEFDNEVAKIRKELQ--------LLKEMATLTEELESLKKDLKRPSKRKAT-K 119
                 1111..111111111122344444444445555555555555555........5555555555555555555555554444.2 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.0   0.00094       3.4      76     161 ..      51     137 ..      13     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00094
  Allexi_40kDa  76 qttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelssse.tsesegPsssptkassaeaa 161
                   q+   +++++++ + ++  d+ k++e+  ++ a+  ++ +llk+++++ ++le+l++ l++ s+ + t++++ P+   tk+++a+++
    AJA92152.1  51 QADAAAQVQASSAAKNQSEDEQKKKEEFDNEVAKIRKELQLLKEMATLTEELESLKKDLKRPSKRKaTKKKAAPKRKATKKKAAPKR 137
                   445556666666666666677677777777777778889999999999999999999998877655155556688777766665543 PP

>> DUF3482  Domain of unknown function (DUF3482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.9    0.0054        19     236     291 ..      27      81 ..       8      83 .. 0.78
   2 ?    9.7   2.0   0.00014      0.52      14      58 ..      77     120 ..      73     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0054
     DUF3482 236 rdaielsseeakewtseklpeelkklekkarahpewssln.akadeeeakrqeliea 291
                  +a ++++ e+   ++e+  ee +k+++ a a+ + ss + +++++e++k++e+ ++
  AJA92152.1  27 LKADDVQKSEE--VRNEMTVEEAEKVQADAAAQVQASSAAkNQSEDEQKKKEEFDNE 81 
                 44555555555..789999*******************9978888888888888766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
     DUF3482  14 eFDavaaefeeelrLyesLatLleekreaLqrliealeeqrqarr 58 
                 eFD+  a++++el+L++++atL ee  e L++ +++  +++++ +
  AJA92152.1  77 EFDNEVAKIRKELQLLKEMATLTEE-LESLKKDLKRPSKRKATKK 120
                 8**********************99.4555555554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3907  (0.217915); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 904.98
//
Query:       AJA92153.1  [L=347]
Description: putative sugar O-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.31   10.9   0.0    1.8  1  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.7e-05      0.31      19      55 ..     169     209 ..     149     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.7e-05
  Methyltransf_23  19 k.lraggrvLdiGcGtGillevlrengf...svtgvDlspe 55 
                      + l++ ++ L++G+G G +  ++++n+    +++++D+ p+
       AJA92153.1 169 RsLNKLQSFLEVGPGFGVNIHLIEQNFSnfkKFIVIDIVPN 209
                      2478889******************8644469******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2388.84
//
Query:       AJA92154.1  [L=230]
Description: creatininase family amidohydrolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-52  178.0   0.0    2.7e-52  177.6   0.0    1.0  1  Creatininase  Creatinine amidohydrolase
  ------ inclusion threshold ------
      0.016   15.7   0.1      0.036   14.6   0.1    1.6  1  DUF4473       Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.6   0.0     3e-56   2.7e-52       7     239 ..      10     224 ..       7     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 177.6 bits;  conditional E-value: 3e-56
  Creatininase   7 eveea.lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTislspetliavlrdileslarhGfrr 102
                   +++++ ++++++ai+PvGs+EqHGphlp++tD+ i+++++ r  +k++   ++lPt++yG+s+eh  f + +s++++tl ++l di+ sl+++G+ r
    AJA92154.1  10 DLRKRiKQKKQIAIIPVGSIEQHGPHLPISTDSDIVTEISLRFSKKID--GILLPTINYGISDEHFPFFN-LSVKKSTLSKMLDDICGSLIKNGISR 103
                   6777768899************************************99..78*************99876.************************** PP

  Creatininase 103 ivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg 199
                   i+++ngH gn + lk + r+ ++   ++ v        l    +++ +         +++  HAg +EtS+mla+  + V+m++a+++ +++  +++
    AJA92154.1 104 ILIINGHYGNLDSLKDFERKKKKSR-KIKV--------LS---YWKYM---------DREFDHAGNVETSIMLAIS-KNVKMNNAKKGFQTDGMSKQ 178
                   *******************766666.3321........22...22222.........23889*************6.68********9999888888 PP

  Creatininase 200 ......vstaedaeelspsGvlGdpskataekGealleaaveelae 239
                            ++++ +++ +Gv+Gdp+k++a+ G+++++++v++l++
    AJA92154.1 179 eiskinKLAQKSFPKVTGNGVWGDPTKSSAKLGRKIINEVVNNLVK 224
                   9****999999*******************************9986 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1     4e-06     0.036       6      51 ..     165     217 ..     162     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
     DUF4473   6 eakaeLvaaGlsekaadglvkiaekfksefaka..........kgdkeaakkafek 51 
                 +ak+ ++  G+s++ + ++ k+a+k   +f+k+          k++++ ++k++++
  AJA92154.1 165 NAKKGFQTDGMSKQEISKINKLAQK---SFPKVtgngvwgdptKSSAKLGRKIINE 217
                 689999*******************...9999966667666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1719.51
//
Query:       AJA92155.1  [L=226]
Description: phosphoribosylformylglycinamidine synthase I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-41  142.5   0.0    2.7e-41  141.4   0.0    1.5  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
    1.2e-08   34.8   0.0    3.7e-08   33.2   0.0    1.8  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    3.3e-08   33.5   0.0    7.5e-08   32.4   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    4.8e-07   29.7   0.0    7.5e-07   29.1   0.0    1.3  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0071   16.1   0.0      0.017   14.9   0.0    1.6  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   7.6e-45   2.7e-41       3     256 ..       2     218 ..       1     221 [. 0.87

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 7.6e-45
    GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklrealekflnredtlaLGiCnGfq 101
                 kv +++++G+n++++m + +++      +   +   +++   +d+  ++lpGGfsygD l +g ++a     ++ + ++++k+ ++ +  +LG+CnGfq
  AJA92155.1   2 KVGVIVFPGSNCDRDMHHVLTDVF----NLNAEFYWHEKNLPSDIDAVVLPGGFSYGDRLRAGVIAA-----HSPIISDVKKLSEK-GIPILGVCNGFQ 90 
                 899****************98753....33333345556667899******************9999.....5667899***9999.************ PP

    GATase_5 102 lLvklglvpggeieeaeksptltrNksgrfesrlvsv.vvsekspsvflkgme.glslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteey 198
                 +Lv+ gl+pg           l +N+s +f ++++++ v ++k+p     +++ ++ +p+a GeGr  + ++e+l++l++n+q+++ Y ++        
  AJA92155.1  91 ILVESGLLPG----------VLLKNESLNFMCEWTNLiVNNNKTPFTNKLELNqKIPIPIANGEGRYFV-DDETLSQLKKNNQIVFSYENK-------- 170
                 **********..........8****************7777788888887775599999**********.999***************999........ PP

    GATase_5 199 plNPNgSpegiagitspdGRvlalmpHpervveavqksiipeeeeeevspwlrlFena 256
                     NgS+++iag+++ dG v+++mpHper+ e+  ++ i++      +p   +Fe+ 
  AJA92155.1 171 ---VNGSVSQIAGVCNSDGNVVGMMPHPERAAEKAINQ-IDH------KPSSLIFESL 218
                 ...8******************************9999.542......5666777665 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     1e-11   3.7e-08      31      90 ..      33      94 ..       3     102 .. 0.86
   2 ?   -1.5   0.0      0.44   1.6e+03     155     186 ..     161     192 ..     151     195 .. 0.57

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1e-11
    GATase_3 31 plkdeslgedadlvilpGgkdtiqdla...llresgldeaikeaaeaggpvlgiCGGlqmLGe 90
                  ++++l++d+d+v+lpGg+++ ++l    +++ s +  ++k+++e+g+p+lg+C G+q+L e
  AJA92155.1 33 W-HEKNLPSDIDAVVLPGGFSYGDRLRagvIAAHSPIISDVKKLSEKGIPILGVCNGFQILVE 94
                4.7899**************9877775222688999*************************77 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
    GATase_3 155 akpllkvkvggnng...ekdGavkksedgnvlGtY 186
                  +  + ++++ n g   +  G+   ++dgnv+G  
  AJA92155.1 161 NQIVFSYENKVN-GsvsQIAGVC--NSDGNVVGMM 192
                 444444433222.2345777888..6688888865 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.1e-11   7.5e-08      29     173 ..      34     197 ..      17     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.1e-11
                 TTSHHHHHHH.THHSTSEEEEEEESSCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE...EEECEEEEEEEEEEEETTT.. CS
      GATase  29 idasaeeile.llknpdgilvsgGpgspg.........vegkieaikearenkiPiLGICLGmQllaiefgrkvv...kekekehhggtmrlgddet.. 112
                 ++       + l +++d+++++gG+ +               i+ +k++ e++iPiLG+C G+Q+l+++   + v   +e+ + +  +t  + ++++  
  AJA92155.1  34 HE-------KnLPSDIDAVVLPGGFSYGDrlragviaaHSPIISDVKKLSEKGIPILGVCNGFQILVESGLLPGVllkNESLNFMCEWTNLIVNNNKtp 125
                 22.......2246789*********98888866665433344555678888****************98766444344333233444555555444456 PP

                 ....CGGTTTTSEEEEEEEEEEEEESG...CHHHTT..EEEEEEEETTE...EEEEEEEETTTEEEESSBTTS CS
      GATase 113 ....allyglknevierhrHryevnpk...elepag..levtaksedde...elmeiiekknpfvgvQFHPEs 173
                      +l+++ +  i+    ry v+++   + ++++  ++++ +++ ++   +++++ + + ++vg+  HPE 
  AJA92155.1 126 ftnkLELNQKIPIPIANGEGRYFVDDEtlsQ-LKKNnqIVFSYENKVNGsvsQIAGVCNSDGNVVGMMPHPER 197
                 6654333444344455556667777666743.33331245555554444565666666666677777777775 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.1e-10   7.5e-07      59     115 ..      39     100 ..      12     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.1e-10
                 CCG-SEEEE--BHHHHHHHHT.....SHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTT CS
   DJ-1_PfpI  59 aaeyDalvlpGGragperlre.....nekvvelvkefaekgklvaaICagpqlLaaagvlkg 115
                 +++ Da+vlpGG +  +rlr+     ++ +++ vk+  ekg ++  +C g q+L++ g+l+g
  AJA92155.1  39 PSDIDAVVLPGGFSYGDRLRAgviaaHSPIISDVKKLSEKGIPILGVCNGFQILVESGLLPG 100
                 5689**************986222225688999**************************987 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.2   7.9e+03      57      67 ..      40      50 ..      36      52 .. 0.84
   2 !   14.9   0.0   4.7e-06     0.017      99     121 ..      73      94 ..      65     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
  Peptidase_C26 57 dkldgllltGg 67
                   + +d+++l+Gg
     AJA92155.1 40 SDIDAVVLPGG 50
                   5799******8 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.7e-06
  Peptidase_C26  99 raalergvPilgiCrGlqllnva 121
                    ++  e+g+Pilg+C G+q+l v 
     AJA92155.1  73 KKLSEKGIPILGVCNGFQIL-VE 94 
                    667899*************9.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1805.73
//
Query:       AJA92156.1  [L=96]
Description: hypothetical protein T478_0505 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1763  (0.0983323); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 802.78
//
Query:       AJA92157.1  [L=471]
Description: hypothetical protein T478_0679 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.9   2.4      0.062   13.6   2.4    1.7  1  CDT1      DNA replication factor CDT1 like
          5    7.4   8.6       0.45   10.8   1.8    2.6  4  MRP-S23   Mitochondrial ribosomal protein S23


Domain annotation for each model (and alignments):
>> CDT1  DNA replication factor CDT1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.4   6.9e-06     0.062      32     106 ..     186     279 ..     167     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.9e-06
        CDT1  32 akvkkaVermsrksfeekhLaqiktvyPeayklkqekqlkefgssgkakaskyelviePnleddl...................kvsaseaetd 106
                 + v+k++ + + ++ + +h++ +  v P+a+ +  +++++ f +s k+ + ++   + P l  d+                   k++ s+++++
  AJA92157.1 186 RAVSKEISNPLSSNLDVQHVRDLRDVSPNAFDFTPQQEMQMFRESVKNTSFDVVGALMPRLMVDEswfepestaqtnsnmknieKQNISQSMVE 279
                 679999999999**********************999899996666666577777888987777768888877655544444442233333333 PP

>> MRP-S23  Mitochondrial ribosomal protein S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8     5e-05      0.45      67     120 ..     247     300 ..     216     307 .. 0.76
   2 ?   -2.2   0.0      0.51   4.6e+03      93     107 ..     341     356 ..     329     381 .. 0.71
   3 ?   -1.4   0.1       0.3   2.7e+03      81     110 ..     359     388 ..     341     407 .. 0.57
   4 ?   -1.6   0.2      0.35   3.1e+03      83     122 ..     422     461 ..     381     466 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5e-05
     MRP-S23  67 evrakfykqygkgseavdllkekkkstcqrfvekyqelkkkeeldeeelfeeae 120
                 +v +++++ + + +++ +  + +k++ +q +ve++++ ++k++++ee+lf+e+ 
  AJA92157.1 247 MVDESWFEPESTAQTNSNMKNIEKQNISQSMVESQKQEEQKKQVEEEKLFQETS 300
                 566677877777777888888888999************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.51
     MRP-S23  93 tcqrfvekyqelkk.k 107
                 tcq  +++y++ +k +
  AJA92157.1 341 TCQVIIRHYRNSQKtH 356
                 6999999999888733 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.3
     MRP-S23  81 eavdllkekkkstcqrfvekyqelkkkeel 110
                 +++  +k+++ ++ + ++++ ++l +++++
  AJA92157.1 359 SITIESKNNYLTEVESLLTHATSLYRQNNI 388
                 334445555555566666666666554444 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.35
     MRP-S23  83 vdllkekkkstcqrfvekyqelkkkeeldeeelfeeaeka 122
                 ++ +++++ks  ++ ++    ++  +++++++ fe+   +
  AJA92157.1 422 MKRFDSHEKSLVEESLRLSDMIEFAKHIEKDNKFEQIITE 461
                 4455555555555555555555556666677777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2142  (0.119471); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 3352.13
//
Query:       AJA92158.1  [L=73]
Description: archaeal histone A2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-11   43.8   0.2    2.7e-11   43.6   0.2    1.1  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    5.6e-05   23.5   0.0    5.9e-05   23.4   0.0    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    9.2e-05   22.5   0.1     0.0001   22.4   0.1    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    0.00011   22.6   0.1    0.00018   21.8   0.1    1.4  1  CENP-S         CENP-S protein
     0.0043   17.1   0.0      0.005   16.9   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.018   15.0   0.0    1.1  1  Bromo_TP       Bromodomain associated
      0.031   14.4   0.5       0.04   14.1   0.5    1.2  1  TAF            TATA box binding protein associated factor (TA
      0.032   14.3   0.0      0.033   14.2   0.0    1.1  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
       0.12   12.9   0.1       0.15   12.6   0.1    1.1  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.2   1.3e-14   2.7e-11       6      64 ..       9      66 ..       5      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.3e-14
                   HHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
  CBFD_NFYB_HMF  6 arvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                   +++ +I+k++ +a ++++++ e + +++e    e+a+ A++  k+++rKt+kae++klA
     AJA92158.1  9 SAMYRILKKA-GADRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLA 66
                   5678******.**********************************************98 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0     3e-08   5.9e-05      82     129 ..      21      68 ..       6      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3e-08
                 XEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
     Histone  82 lrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                  r+s e+ + l  +lE++ +e++++A  + kha R+T+ ++D++lA++
  AJA92158.1  21 DRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLAAK 68 
                 5899999999************************************97 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     5e-08    0.0001      24      80 ..      17      73 .]       5      73 .] 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5e-08
    CENP-T_C 24 sgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkrqrkv 80
                ++   +++ e+ + l +++++    +++      kHagRKt++++Dv l  k+ +k+
  AJA92158.1 17 KAGADRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLAAKSSGKI 73
                45778999999999999999999999999999****************999988776 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   9.2e-08   0.00018      52      73 ..      49      70 ..      34      73 .] 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.2e-08
      CENP-S 52 FakHAkRstittdDvlLlaRrn 73
                  kHA+R+t++++Dv+L a+ +
  AJA92158.1 49 MGKHAGRKTVKAEDVKLAAKSS 70
                569***************9865 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06     0.005       9      69 ..       9      69 ..       3      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
  TFIID-31kDa  9 rlihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqs 69
                 + +  iL++ g + ++++  + L  +     +++ ++A  + +ha++k+v+++dv+lA +s
   AJA92158.1  9 SAMYRILKKAGADRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLAAKS 69
                 5678899***************************************************876 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     9e-06     0.018      14      67 ..      13      66 ..       4      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9e-06
                HHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHH CS
    Bromo_TP 14 qileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvlt 67
                 il++aG d++ ++  E L+ ++++   e+++ a     hagR +++ +Dv l+
  AJA92158.1 13 RILKKAGADRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLA 66
                589******************************99999*************875 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5     2e-05      0.04      16      64 ..      18      66 ..       6      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH CS
         TAF 16 lGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsA 64
                 G   +sde a++L   +e    ei+++a+   +h+ R++  ++Dv  A
  AJA92158.1 18 AGADRVSDESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLA 66
                67788999999999999998889***********************877 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.033      22      63 ..      25      66 ..       9      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                 HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXX CS
  TFIID-18kDa 22 qetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfl 63
                 +e+++ l  ++++  ie+ ++a++++k+ g++ ++ ED++ +
   AJA92158.1 25 DESAEELRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLA 66
                 677778888888889***********************9865 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.6e-05      0.15      14      61 ..      20      66 ..       9      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                 SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHH CS
  TFIID_20kDa 14 setkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlh 61
                 ++ + de  e+ L ++ +d   ++ k a+ + kh   +++ + D++l 
   AJA92158.1 20 ADRVSDESAEE-LRRVLEDIGIEIAKNAVDMGKHAGRKTVKAEDVKLA 66
                 55555555555.78999999999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 535.62
//
Query:       AJA92159.1  [L=1042]
Description: helicase C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-12   45.9   0.0    3.3e-11   43.5   0.0    2.3  2  Helicase_C       Helicase conserved C-terminal domain
    3.9e-08   33.2   0.0    4.1e-05   23.4   0.0    2.8  2  DEAD             DEAD/DEAH box helicase
    0.00022   21.3   4.8       0.02   14.9   0.0    3.2  3  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.11   11.9   0.1       0.18   11.3   0.1    1.2  1  IcmF-related     Intracellular multiplication and human macro
       0.22   11.6   5.8       0.86    9.7   1.2    2.6  2  DZR              Double zinc ribbon
       0.38   10.9  10.5        3.5    7.8   0.3    3.9  3  Zn-ribbon_8      Zinc ribbon domain
       0.76   10.2   5.7        8.4    6.9   0.7    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
          1    9.4   3.9         25    4.9   0.4    3.4  4  RNHCP            RNHCP domain
          2    8.4  10.4       0.28   11.1   0.6    3.2  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
        2.3    8.3   9.1        4.3    7.4   0.5    2.5  2  zinc-ribbons_6   zinc-ribbons
        3.1    8.1   7.7        0.2   12.0   0.4    2.5  3  zf-LITAF-like    LITAF-like zinc ribbon domain
        3.7    7.6   7.4        6.6    6.8   0.3    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8   5.7e+03      14      48 ..     447     490 ..     438     496 .. 0.57
   2 !   43.5   0.0   2.2e-14   3.3e-11      48     111 .]     804     867 ..     781     867 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                 TTTSEEEEEESSHH....HHHH...HHHH..HHHT..TSTEEEEST CS
  Helicase_C  14 eeggkilifvntid....rlek...vkll..lekk..gikvavlhg 48 
                  +g  +li  +t+     +      v+++  l+k+  +i++ +++g
  AJA92159.1 447 LDGTSTLITFPTKAlnaaQ--FndmVRYFyhLNKRgiEISIGYYTG 490
                 5666777777777764332..1335678755444445555555555 PP

  == domain 2  score: 43.5 bits;  conditional E-value: 2.2e-14
                 TTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
  Helicase_C  48 gelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                 g+ + +e  + l+q  k+e dvLi+t+v+++G+d+p++n +++f++p +  ++ q +GRt+R++
  AJA92159.1 804 GRNTRKELFDLLSQVEKNELDVLITTSVLGQGVDFPNINIMHFFGVPNSFVELAQVAGRTARGN 867
                 5556666668899999**********************************************85 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.7e-08   4.1e-05       6      75 ..     407     477 ..     398     497 .. 0.74
   2 !    6.6   0.0     0.004       5.9     119     170 ..     630     682 ..     608     687 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.7e-08
                 HHHHHHH..TTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                 xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   6 eaiplil..gggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                 + i+ +l  +   ++v+a+T sGK+l+f +  +  + +t ++ +g+ +li  Pt++L   ++n++ +++ +++
  AJA92159.1 407 KFIKKLLnkESSPFIVRAPTDSGKSLVFYVCSV--IHKTfNELDGTSTLITFPTKALNAAQFNDMVRYFYHLN 477
                 233444444446899************877655..44445699999******************999998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.004
                 CTTEEEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                 xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 119 lsqvrflVlDEadrlldq...gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                  s+ +++V+DE+++l+      f+ f++  l+ +++++  ++   q +  +AT+ 
  AJA92159.1 630 HSNPSLIVFDEVHTLSGTsgnLFGHFLSL-LKVTNEKYGITN-AIQHLGATATIA 682
                 67889**********99844344444444.344433333333.345888888886 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.9         5   7.5e+03      45     122 ..      97     193 ..      94     214 .. 0.52
   2 !   14.9   0.0   1.3e-05      0.02       3      81 ..     396     476 ..     395     544 .. 0.82
   3 !    7.0   0.0    0.0036       5.4     122     169 ..     622     681 ..     597     683 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5
                 HHHH-S.....-EEEEESSHHHHHHHH...HHGGGGTGG..........GEEEESSS-B--.......-SEEEEEHHHHHHTH................ CS
      ResIII  45 ierllkkgkeekflflvprkslleqtl...eefkkflseayke......igkkvsgdkkkakekdstnkkilvttiqsldadseee............e 122
                 i++ ++++ e +f fl p ++ +++++    +++k  +  ++e      ++ ++sg+++k+  + ++  ++ +t  +s+ + +++e            e
  AJA92159.1  97 IKSTKENKIETNFSFLRPILKNVKKMEeveINYQKSGKGLVTEnrlnstQSISISGKEHKQ--GIEDVQNFSFTGNESIESLLSKEklipieipkienE 193
                 5555555555566666666666666553333343333333333444444444455555555..666666777777777776665555555555555440 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.3e-05
                 EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH..HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
      ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva..aklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                 el++ Q eai+++++kl +k+   +++ ++T +GK+lv   +++i + +++ +   +l+  p+k+l     +++ +++   
  AJA92159.1 396 ELYKFQFEAIQKFIKKLLNKESSPFIVRAPTDSGKSLVFyvCSVIHKTFNELDGTSTLITFPTKALNAAQFNDMVRYFYHL 476
                 57899************999999***************978899*********99***********988888776665544 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0036
                 .....HHHTTT-SEEEEETGGGTTS.T...........TTHHH.HHT-...--SEEEEEESS- CS
      ResIII 122 eeeseellrdrfdviiiDEaHrlgakk...........swrei.lekf...keavllglTATp 169
                 + +++++ +++  +i++DE+H l++ +           +   + +ek+   ++   lg TAT+
  AJA92159.1 622 DMDNKTKFHSNPSLIVFDEVHTLSGTSgnlfghflsllK---VtNEKYgitNAIQHLGATATI 681
                 3334444555555**********9973455554443332...221111222335567777775 PP

>> IcmF-related  Intracellular multiplication and human macrophage-killing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00012      0.18     228     285 ..     932     993 ..     921    1000 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
  IcmF-related 228 eeddWVlgdltes....sseaspeqlakelrelYftdYaae..WqafLndlrvkpfaslaqave 285
                   +++  V+++++ +    ++  ++ + +k+l++ Y++d ++   W+++Ln+l+v+++ +++qa +
    AJA92159.1 932 NDS-TVMNSSK-AfeafDKMIESGEFEKDLTKIYKKDWVKDegWKEILNQLQVQAYMKVKQASS 993
                   444.6888222.2345557788899**************7555*************99999975 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.052        78      14      36 ..     519     547 ..     507     551 .. 0.64
   2 ?    9.7   1.2   0.00057      0.86      12      44 ..     592     629 ..     585     632 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.052
         DZR  14 fCseCgtklkavaa......edrCpsCge 36 
                  C++C++k   v++        +C sC+e
  AJA92159.1 519 KCPKCKEKKIIVEKindfrlIPKCASCDE 547
                 47777666433334445666666777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
         DZR  12 arfCseCgtk....lkavaa.....edrCpsCgekvdpearf 44 
                 ++ C++C+      l    +      ++C +C++++d++++f
  AJA92159.1 592 SKRCPKCNLVqpliL----KnqndeIHKCKNCQTDMDNKTKF 629
                 788999997745443....23356899************998 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.15   2.2e+02      26      34 ..     516     525 ..     506     529 .. 0.69
   2 ?    7.8   0.3    0.0024       3.5       7      30 ..     541     564 ..     535     565 .. 0.77
   3 ?    4.6   1.5     0.025        37       7      35 ..     594     622 ..     592     627 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
  Zn-ribbon_8  26 lta.CPeCgs 34 
                  l+  CP+C++
   AJA92159.1 516 LIRkCPKCKE 525
                  5666****86 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0024
  Zn-ribbon_8   7 rCeeCghefe.vlqsisdaplta.CP 30 
                  +C +C+++fe v++++s+   +  CP
   AJA92159.1 541 KCASCDEKFEfVFVTSSE--VEWyCP 564
                  6*********88887664..444598 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.025
  Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgse 35 
                  rC +C+    +l   +++++++ C++C+ +
   AJA92159.1 594 RCPKCN-LVQPLILKNQNDEIHkCKNCQTD 622
                  8*****.8888887778888888****875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4      0.02        29       4      31 ..     518     545 ..     516     558 .. 0.81
   2 ?    6.9   0.7    0.0056       8.4       4      36 ..     593     621 ..     591     634 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.02
  Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyC 31 
                        CP C++++++++  +    i +c +C
       AJA92159.1 518 RKCPKCKEKKIIVEKINDFRLIPKCASC 545
                      57**********9999888885555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0056
  Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyCadCga 36 
                      k CP C+  + l+  +++++       C++C  
       AJA92159.1 593 KRCPKCNLVQPLILKNQNDE----IHKCKNCQT 621
                      89*****************9....99*****98 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       9.8   1.5e+04      49      79 ..     111     141 ..     102     146 .. 0.73
   2 ?    3.3   0.0     0.055        83      41      76 ..     494     527 ..     488     539 .. 0.80
   3 ?   -0.2   0.1      0.69     1e+03      55      74 ..     528     547 ..     526     552 .. 0.83
   4 ?    4.9   0.4     0.017        25      65      88 ..     612     635 ..     583     637 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9.8
       RNHCP  49 lmepiavevkkkkewvivhrCekCgelkknr 79 
                  ++pi  +vkk +e+ i ++ +  g +++nr
  AJA92159.1 111 FLRPILKNVKKMEEVEINYQKSGKGLVTENR 141
                 5778878888888888888777666666666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.055
       RNHCP  41 draseCkglmepiavevkkkkewvivhrCekCgelk 76 
                 d   + +++++p +v+   ++ + ++ +C kC+e k
  AJA92159.1 494 DGDIDPNAILRPASVS--GEEPLNLIRKCPKCKEKK 527
                 6666677889999987..67999*********9865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.69
       RNHCP  55 vevkkkkewvivhrCekCge 74 
                 + v+k +++ ++ +C++C+e
  AJA92159.1 528 IIVEKINDFRLIPKCASCDE 547
                 5567788999********87 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.017
       RNHCP  65 ivhrCekCgelkknrvakddneel 88 
                  +h+C++C++   n+++  +n +l
  AJA92159.1 612 EIHKCKNCQTDMDNKTKFHSNPSL 635
                 389*****9999999887777655 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       5.3     8e+03       5      18 ..     211     224 ..     209     227 .. 0.82
   2 ?    2.0   1.0      0.13     2e+02      11      51 ..     522     565 ..     519     569 .. 0.89
   3 ?   11.1   0.6   0.00019      0.28      27      57 ..     591     624 ..     587     627 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.3
  OrfB_Zn_ribbon   5 keqleykakeyGik 18 
                     k+ +e kak+ G +
      AJA92159.1 211 KKAIEIKAKKLGGE 224
                     789******99976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.13
  OrfB_Zn_ribbon  11 kakeyGikveevnpayTSktCseCgsknke...alsgrtfkCpn 51 
                     k+ke+ i ve++n +    +C+ C +k +    + s+ +++Cp+
      AJA92159.1 522 KCKEKKIIVEKINDFRLIPKCASCDEKFEFvfvTSSEVEWYCPS 565
                     89999999999999999999****99999999999999999985 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00019
  OrfB_Zn_ribbon  27 TSktCseCgsknke...alsgrtfkCpnCgfead 57 
                     +Sk+C++C  ++     +++++ +kC+nC++ +d
      AJA92159.1 591 SSKRCPKCNLVQPLilkNQNDEIHKCKNCQTDMD 624
                     9*********999999999**********99877 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5    0.0029       4.3      18      53 ..     519     564 ..     510     566 .. 0.78
   2 ?    4.0   2.7     0.033        49       2      29 ..     594     626 ..     593     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0029
                     E-TTT--.........EEEEEEE-SSS-S---EE.EETTEEEE--T CS
  zinc-ribbons_6  18 hCeaCqe.........dlkkealCpeCeqelevl.kaCgavdyfCn 53 
                     +C +C+e         d++  + C  C+++ e++    + v+++C 
      AJA92159.1 519 KCPKCKEkkiivekinDFRLIPKCASCDEKFEFVfVTSSEVEWYCP 564
                     6888888888888888999999999999999854156666777775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.033
                     --SSS-..S--E.E-S..SEEE-TTT--EEEEE CS
  zinc-ribbons_6   2 kCpeCq..qele.krg..eqyhCeaCqedlkke 29 
                      Cp+C+  q+l  k++  e  +C++Cq+d++++
      AJA92159.1 594 RCPKCNlvQPLIlKNQndEIHKCKNCQTDMDNK 626
                     5999985556654332447788****9998765 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.98   1.5e+03      58      64 ..     519     525 ..     514     529 .. 0.69
   2 ?   -3.2   0.2       7.2   1.1e+04      49      60 ..     553     564 ..     541     565 .. 0.60
   3 ?   12.0   0.4   0.00013       0.2      40      64 ..     597     621 ..     574     626 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.98
  zf-LITAF-like  58 yCpnCga 64 
                    +Cp+C++
     AJA92159.1 519 KCPKCKE 525
                    6777764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.2
  zf-LITAF-like  49 vdslkdvehyCp 60 
                    + +  +ve yCp
     AJA92159.1 553 FVTSSEVEWYCP 564
                    444566777777 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00013
  zf-LITAF-like  40 llccliPfcvdslkdvehyCpnCga 64 
                     + ++ P+++++ +d +h+C+nC++
     AJA92159.1 597 KCNLVQPLILKNQNDEIHKCKNCQT 621
                    222445*****************97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.4     0.051        77      19      44 ..     518     546 ..     512     548 .. 0.71
   2 ?    6.8   0.3    0.0044       6.6      19      45 ..     593     621 ..     578     622 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.051
  Zn_Tnp_IS1595  19 fvCPhCgsr..kayrikt.rglfqCkeCr 44 
                    + CP+C+ +   + +i++ r   +C++C 
     AJA92159.1 518 RKCPKCKEKkiIVEKINDfRLIPKCASCD 546
                    57*****9944344555566666888885 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0044
  Zn_Tnp_IS1595  19 fvCPhCgsrkayrikt..rglfqCkeCrk 45 
                     +CP+C   ++  +k+   + ++Ck C++
     AJA92159.1 593 KRCPKCNLVQPLILKNqnDEIHKCKNCQT 621
                    57*****998888888889********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1042 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 6584.85
//
Query:       AJA92160.1  [L=150]
Description: hypothetical protein T478_1317 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1082.00
//
Query:       AJA92161.1  [L=363]
Description: oxidoreductase, CzcO family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-94  314.8   0.1    7.9e-94  314.3   0.1    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-15   57.7   0.2    3.1e-14   52.9   0.2    3.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-10   40.2   0.1      0.037   12.7   0.0    4.0  5  HI0933_like    HI0933-like protein
    7.4e-10   38.5   0.0    2.5e-07   30.2   0.0    2.2  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    2.6e-09   37.5   3.7      0.016   15.7   0.4    4.1  4  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   25.2   0.0       0.98    8.9   0.0    3.4  3  DAO            FAD dependent oxidoreductase
    1.3e-05   25.4   0.5      0.042   14.1   0.1    2.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.1e-05   23.2   0.2        1.8    7.6   0.0    3.9  4  GIDA           Glucose inhibited division protein A
    3.7e-05   23.1   0.1     0.0011   18.3   0.3    2.6  3  FAD_binding_3  FAD binding domain
    4.9e-05   23.4   0.5          1    9.3   0.0    3.4  2  NAD_binding_9  FAD-NAD(P)-binding
     0.0021   17.2   0.0        7.5    5.5   0.0    3.3  3  FAD_binding_2  FAD binding domain
     0.0094   15.2   0.2       0.28   10.4   0.2    2.2  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.078   13.2   0.5         12    6.2   0.0    2.7  2  TrkA_N         TrkA-N domain
      0.094   12.0   0.1         14    4.9   0.0    2.3  2  FAD_oxidored   FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.3   0.1   6.2e-97   7.9e-94       1     305 []       5     303 ..       5     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 314.3 bits;  conditional E-value: 6.2e-97
  Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypkemtfispsftsekleipdlnaiseetspafslkeeklsrkealeYlrevaksfelpi 98 
                  +++GaGP G+++ i l+k+g+ ++++l+++n+g s+ ++pk+m++++psf s+ ++++dlnai+ +tspa++l++e++s++e++ Yl+++a++f+lpi
   AJA92161.1   5 VVVGAGPSGIGVSIILQKMGV-KFTVLDRNNVGSSFLKWPKQMKLLTPSFFSNTFKMIDLNAITYDTSPALTLQTEHPSGQEYAAYLKKLAEHFKLPI 101
                  79*******************.7*************************************************************************** PP

  Pyr_redox_3  99 klfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrg 196
                  + +++V sv+k+++ f+++t+k+++++k+v++A+Gef++P+ +++pG++ +++h+s ++++++++g+++ V+Gg++S++D+A++l+++ ++V +++++
   AJA92161.1 102 QGNTNVDSVTKNGDVFTIKTNKGEIKTKYVVWAAGEFQYPKIHSFPGSK-YCTHNSLITNWENVEGDEFFVVGGYESGMDTAINLAARKKRVLIIDKD 198
                  ************************************************9.************************************************ PP

  Pyr_redox_3 197 seiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteete 294
                  + +++e+ dps +++p++++rl+++ + + i++++  +v ++++++ ey + te+ kk+++k++++latG+k +ls++k  lf++ edg+ +l++ +e
   AJA92161.1 199 NLLNSEDIDPSRTISPYTKDRLRKVNTDNLIEFHTG-KVIRVEKENDEYVIFTEK-KKLRSKTKPILATGFKGSLSLIK-GLFDW-EDGKAQLNSYDE 292
                  ************************999899**9999.899999999***999998.99********************9.*****.************ PP

  Pyr_redox_3 295 etnvpglflaG 305
                  +t++pgl++ G
   AJA92161.1 293 STKTPGLYVTG 303
                  *********98 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.2   2.4e-17   3.1e-14       4     277 ..       5     305 ..       3     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.4e-17
                  EEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHC.HHHHHHHHHHHHH............................HHHHCHHHHCCCCHC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx............................xxxxxxxxxxxxxxx RF
  Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlvelegtclnggcllsk.allgvaedaeias............................evvkklnqgielllg 72 
                  vv+G+Gp G+ +++ l++ g+k t++++++    +  ++++ +ll  + + ++++                              +kkl ++++l  +
   AJA92161.1   5 VVVGAGPSGIGVSIILQKMGVKFTVLDRNNVGSSFLKWPKQmKLLTPSFFSNTFKmidlnaitydtspaltlqtehpsgqeyaAYLKKLAEHFKLPIQ 102
                  9*************************844444444444444255555555555668889999999*******99998888888444555555444433 PP

                  ..CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---.E.EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT- CS
                  ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  73 ..eevvkidpgkkkvklekkkegdeekiaydklvlAtG.s.sprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgk 166
                    ++v ++ ++  +v   k++   + +i+ +++v A G +  p++   pG  ++++++ + +++ e ++     + + vvGg   G+++A+ la  +k
   AJA92161.1 103 gnTNVDSVTKNG-DVFTIKTN---KGEIKTKYVVWAAGeFqYPKIHSFPGS-KYCTHN-SLITNWENVEG----DEFFVVGGYESGMDTAINLAARKK 190
                  324477775555.55554444...448***********63478888999*9.777777.66666666543....5678******************** PP

                  EEEEEESSSSSS........TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEE.EE-S-EEES-HHCSHCCT-EEEE CS
                  xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 167 evtlveardrll........raldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlv.vvavGvrpstelleeklglelde 254
                  +v +++  d+ll        r+  +  +++l+++ +++ +e+++g+++ +++++++  e v+ ++++++  ++  ++a+G++ s +l+  k    + e
   AJA92161.1 191 RVLIIDK-DNLLnsedidpsRTISPYTKDRLRKVNTDNLIEFHTGKVI-RVEKEND--EyVIFTEKKKLRSKTKpILATGFKGSLSLI--KGLFDW-E 281
                  9998877.66665744444445556666666666677789********.9999998..5577777777776664499********997..677777.* PP

                  TTEEE--TTSBES.STTEEE-GGG CS
                  xxxxxxxxxxxxx.xxxxxxxxxx RF
  Pyr_redox_2 255 rggivvdeflrtn.vpgiyaiGDv 277
                  +g+ + +++ +++  pg+y+ G +
   AJA92161.1 282 DGKAQLNSYDESTkTPGLYVTGPM 305
                  **********7655******9965 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   5.5e-05     0.071       2      33 ..       3      34 ..       2      41 .. 0.90
   2 !   12.7   0.0   2.9e-05     0.037     110     172 ..      85     145 ..      52     154 .. 0.82
   3 !   10.4   0.0   0.00015      0.19       4      33 ..     170     199 ..     167     203 .. 0.91
   4 ?   -2.6   0.0       1.3   1.7e+03     131     163 ..     235     266 ..     218     269 .. 0.65
   5 ?   -1.9   0.0      0.83   1.1e+03     371     386 ..     292     307 ..     288     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                 + +v+G+G++G+  +i ++k g + ++l++++
   AJA92161.1  3 EAVVVGAGPSGIGVSIILQKMGVKFTVLDRNN 34
                 579**************************985 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.9e-05
                  HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGGT- CS
  HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPklGs 172
                  +    l+k +++ +  ++ +t+v sv+k+ d  f++kt +++e++++++v A G   +Pk+ s
   AJA92161.1  85 EYAAYLKKLAEHFKLPIQGNTNVDSVTKNGDV-FTIKT-NKGEIKTKYVVWAAGEFQYPKIHS 145
                  55567777888889999*********887777.*****.9*******************9855 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00015
                  EEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
  HI0933_like   4 iviGgGaAGlmaAisaakrgkrVlllekak 33 
                   v+Gg  +G+ +Ai++a+r+krVl+++k +
   AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLIIDKDN 199
                  79*************************986 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1.3
                  -EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
  HI0933_like 131 evksvekeedgkfrvktkseeeleadklvlAtG 163
                  +v +veke+d+ + + t++++  + +k +lAtG
   AJA92161.1 235 KVIRVEKENDE-YVIFTEKKKLRSKTKPILATG 266
                  56678888888.666664666666677888888 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 0.83
                  BBTTSTTEEE-GGGBS CS
  HI0933_like 371 eskkvpgLffaGEvlD 386
                  es k+pgL+++G +l 
   AJA92161.1 292 ESTKTPGLYVTGPMLQ 307
                  7899********9996 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0031         4       3      37 ..       2      34 ..       1      60 [. 0.84
   2 !   30.2   0.0     2e-10   2.5e-07      86     217 ..      74     192 ..      68     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0031
  K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqp 37
                 l+ + +G+Gps +++ i l+++   +k  +l+r++
   AJA92161.1  2 LEAVVVGAGPSGIGVSIILQKMG--VKFTVLDRNN 34
                 56799*****************9..9999999975 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 2e-10
  K_oxygenase  86 lnletflpsRkefedYlrWvasqleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseyle 183
                  l+l+t++ps +e++ Yl+  a++++  ++ +++v++v+ + +    ++t+++     ++ e++++ +v + G   + P++   + g++ ++H+s +++
   AJA92161.1  74 LTLQTEHPSGQEYAAYLKKLAEHFKLPIQGNTNVDSVTKNGD----VFTIKT-----NKGEIKTKYVVWAAGEF-QYPKIHS-FPGSKYCTHNSLITN 160
                  56899********************99***********9995....8****9.....6789*********9965.5688766.777899999999988 PP

  K_oxygenase 184 rkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                   +  + +++++ VvG+  S+ + + +l++r+k+v
   AJA92161.1 161 WE--NVEGDEFFVVGGYESGMDTAINLAARKKRV 192
                  87..89**********************998754 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   1.3e-05     0.016       2      32 ..       4      34 ..       3      37 .. 0.94
   2 ?    3.4   0.0     0.091   1.2e+02      42      78 ..      86     121 ..      79     125 .. 0.74
   3 !   15.1   0.0     2e-05     0.026       3      72 ..     170     245 ..     168     253 .. 0.73
   4 ?    0.7   0.0      0.62   7.9e+02      15      32 ..     324     345 ..     322     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversd 32
                +vvvG+G +g+ +  +l+++g k tv++r++
  AJA92161.1  4 AVVVGAGPSGIGVSIILQKMGVKFTVLDRNN 34
                79*************************9975 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                 HHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
   Pyr_redox  42 askilqeklekngievllntkveeiegsedgvesvkl 78 
                  +++l++  e+ +  +  nt+v ++++++d v ++k+
  AJA92161.1  86 YAAYLKKLAEHFKLPIQGNTNVDSVTKNGD-VFTIKT 121
                 555666666666999999999999999999.655666 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2e-05
                 EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSS..HHHHHHHHHHHHHT....TEEEECSEEEEEEEEETTS CS
   Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkll.rllD..eeaskilqeklekn....gievllntkveeiegsedg 72 
                  vvGg  +g++ A +la+ +k+V +++  + l    +D  +++s +++++l+k      ie+++++++ ++e+++d+
  AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLIIDKDNLLNsEDIDpsRTISPYTKDRLRKVntdnLIEFHTGKVI-RVEKENDE 245
                 69*********************888766555555555333677788999987645547999998654.56656554 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.62
                 HHHHHHTT....SEEEEEESSS CS
   Pyr_redox  15 Agalaelg....kkVtvversd 32 
                 A +++++g    k+Vtv+e  +
  AJA92161.1 324 AVVANNIGiklsKDVTVIEQYK 345
                 5556666666659999999755 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0029       3.7       2      33 ..       4      36 ..       3      42 .. 0.89
   2 !    8.9   0.0   0.00077      0.98     147     201 ..      85     136 ..      70     151 .. 0.79
   3 ?    4.9   0.0     0.012        16       4      33 ..     171     202 ..     168     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0029
                EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
         DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                 v++G+G  G+++   L++ g   t+l+++  +g
  AJA92161.1  4 AVVVGAGPSGIGVSIILQKMGvkFTVLDRN-NVG 36
                69***************88899*******9.555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00077
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--G CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaG 201
                 +++a+l + ae     i  +t+v ++  ++g+v ++  +t+ ge+++ ++vV aaG
  AJA92161.1  85 EYAAYLKKLAEHFKLPIQGNTNVDSV-TKNGDVFTI--KTNkGEIKT-KYVVWAAG 136
                 456666666666678899*******9.557899***..666688654.88*****9 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.012
                 EECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
         DAO   4 iiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                 ++GG   G+ tA  La+r+  V++++k++ + 
  AJA92161.1 171 VVGGYESGMDTAINLAARKkrVLIIDKDNLLN 202
                 7777778999******99779******97765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   3.2e-05     0.042       1      29 [.       6      34 ..       6      37 .. 0.95
   2 !    8.8   0.0    0.0015       1.9       1      29 [.     171     199 ..     171     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                   +vGaG sG      L+k g++ ++l++++
     AJA92161.1  6 VVGAGPSGIGVSIILQKMGVKFTVLDRNN 34
                   8*************************986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                    +vG+  sG+ +A  La ++++vl+++k +
     AJA92161.1 171 VVGGYESGMDTAINLAARKKRVLIIDKDN 199
                    799999********************976 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0014       1.8       3      28 ..       5      30 ..       3      48 .. 0.87
   2 !    5.0   0.0    0.0086        11      97     157 ..      86     144 ..      52     161 .. 0.77
   3 ?    1.7   0.0     0.083   1.1e+02       3      28 ..     170     195 ..     168     211 .. 0.85
   4 ?    4.0   0.0     0.017        21      97     157 ..     215     273 ..     210     296 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                EEE-SSHHHHHHHHHHHHTT--EEEE CS
        GIDA  3 iViGgGhAGceAAlaaarlGakvlLi 28
                +V+G+G +G+  ++ + ++G+k + +
  AJA92161.1  5 VVVGAGPSGIGVSIILQKMGVKFTVL 30
                8********************97665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0086
                 HHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEE CS
        GIDA  97 yskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkih 157
                 y++++ +kl ++ +l i  ++  + +++++ v  ++t++ge ik+k vv a+G f   kih
  AJA92161.1  86 YAAYL-KKLAEHFKLPIQGNTNVDSVTKNGDVFTIKTNKGE-IKTKYVVWAAGEFQYPKIH 144
                 55444.456777899998776555558899***99999986.899*********9988887 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.083
                 EEE-SSHHHHHHHHHHHHTT--EEEE CS
        GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                  V+Gg  +G+  A+++a +  +vl+i
  AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLII 195
                 69*********************998 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.017
                 HHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEE CS
        GIDA  97 yskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkih 157
                 y k+  +k+++ + +e  +++v +++  e+   ++ te+++  ++ + ++atG    + + 
  AJA92161.1 215 YTKDRLRKVNTDNLIEFHTGKVIRVEK-ENDEYVIFTEKKKLRSKTKPILATGF-KGSLSL 273
                 555666788889999999****99955.5555566677777667779******6.333333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   8.8e-07    0.0011       3      34 ..       3      34 ..       1      41 [. 0.91
   2 ?   -1.0   0.0      0.64   8.2e+02     107     159 ..      86     132 ..      55     137 .. 0.76
   3 ?    1.1   0.0      0.14   1.8e+02       5      34 ..     170     199 ..     168     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.8e-07
                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                   + ++VGaGp+G+  + +L++ Gv+ +++++ +
     AJA92161.1  3 EAVVVGAGPSGIGVSIILQKMGVKFTVLDRNN 34
                   678**************************987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
                    HHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEE CS
  FAD_binding_3 107 leriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlv 159
                       +L + ae   l ++ +t+v s++++++  t +  +       +++ kY+v
     AJA92161.1  86 YAAYLKKLAEHFKLPIQGNTNVDSVTKNGDVFTIKTNKG------EIKTKYVV 132
                    456788888889999999999999999988755444433......35666666 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                    EEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                     +VG+  +G+ +a  L+ +  rv++++k +
     AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLIIDKDN 199
                    59*****************9*******976 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.4    0.0022       2.8       1      46 [.       5      45 ..       5     138 .. 0.53
   2 !    9.3   0.0    0.0008         1      88     154 ..     204     266 ..     185     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdq 46
                   ++vGaGp+G+ v   L +       ++ t+ d+++ g+     ++q
     AJA92161.1  5 VVVGAGPSGIGVSIILQKM-----GVKFTVLDRNNVGSSFLKWPKQ 45
                   6899999999998766555.....6888999998888544444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0008
  NAD_binding_9  88 ddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                    +d  p + ++ Y +d+++++  +      +e+h+++v+++e+++d++ + +++++     + +LA+G
     AJA92161.1 204 EDIDPSRTISPYTKDRLRKVNTDN----LIEFHTGKVIRVEKENDEYVIFTEKKKLRSKTKPILATG 266
                    555566677778888888876433....69****************988777777667777888888 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0093        12       2      33 ..       4      35 ..       3      42 .. 0.89
   2 ?    2.8   0.0     0.038        49     135     204 ..      78     140 ..      53     167 .. 0.78
   3 !    5.5   0.0    0.0059       7.5       4      35 ..     171     202 ..     168     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0093
                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                   ++V+G+G +G   ++ +++ G k +v++  ++
     AJA92161.1  4 AVVVGAGPSGIGVSIILQKMGVKFTVLDRNNV 35
                   79************************998876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.038
                    ....HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
  FAD_binding_2 135 etlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                    ++  +g++ +a l + a++ ++ +q +t++d+++      +G+v++ +++++  +i+ k vv a+g f+ 
     AJA92161.1  78 TEHPSGQEYAAYLKKLAEHFKLPIQGNTNVDSVTK-----NGDVFTIKTNKG--EIKTKYVVWAAGEFQY 140
                    466799999999999999999************77.....666677444444..5678999999999985 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0059
                    EE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
  FAD_binding_2   4 ViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                    V+G+  +G+  A+++a + ++v++++k +  +
     AJA92161.1 171 VVGGYESGMDTAINLAARKKRVLIIDKDNLLN 202
                    8899999********************87655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00022      0.28      20      50 ..       4      33 ..       1      38 [. 0.90
   2 ?    2.5   0.0     0.057        74      10      49 ..     159     197 ..     150     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                EEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4 20 vvivGaGssGLtaayylakkpdlkvailers 50
                 v+vGaG+sG+  + +l k  ++k ++l+r+
  AJA92161.1  4 AVVVGAGPSGIGVSIILQKM-GVKFTVLDRN 33
                69***************999.******9985 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                 HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
        Thi4  10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                 +++ +    +  +vG+  sG+ +a  la + + +v+i+++
  AJA92161.1 159 TNWENVEGDEFFVVGGYESGMDTAINLAAR-KKRVLIIDK 197
                 5677766777899***************99.889999976 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.032        41       2      30 ..       5      33 ..       4      38 .. 0.89
   2 ?    6.2   0.0    0.0096        12       2      31 ..     170     199 ..     169     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.032
                EEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
      TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                +++G+G  G  +   L++ g  +++v d++
  AJA92161.1  5 VVVGAGPSGIGVSIILQKmGV-KFTVLDRN 33
                8*****************666.6*****98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0096
                 EEES-SHHHHHHHHHHHHTTEEEEEEESSH CS
      TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkde 31 
                  ++G  + G+  a +L +++k+v++idkd 
  AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLIIDKDN 199
                 699***************8878******95 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.013        17       3      32 ..       5      34 ..       3      36 .. 0.92
   2 ?    4.9   0.0     0.011        14       3      33 ..     170     200 ..     168     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
  FAD_oxidored  3 vVvGGgpaGvaAAiaAaraGakvlLveerg 32
                  vVvG+gp+G+   i   ++G k  ++++++
    AJA92161.1  5 VVVGAGPSGIGVSIILQKMGVKFTVLDRNN 34
                  9********************999999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
  FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                    VvGG  +G+  Ai  a + ++vl++++++ 
    AJA92161.1 170 FVVGGYESGMDTAINLAARKKRVLIIDKDNL 200
                   59*************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2443.52
//
Query:       AJA92162.1  [L=365]
Description: chorismate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.8e-132  438.6   0.6   1.1e-131  438.4   0.6    1.0  1  Chorismate_synt  Chorismate synthase
  ------ inclusion threshold ------
      0.076   12.8   0.0       0.11   12.2   0.0    1.2  1  BCIP             p21-C-terminal region-binding protein


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.4   0.6  1.3e-135  1.1e-131       3     327 .]      13     356 ..      11     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 438.4 bits;  conditional E-value: 1.3e-135
                      EEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS-..SSSSSTSBE-TT CS
  Chorismate_synt   3 vttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdqrskdyeeikevpRpg 96 
                      +t+fGeShgk +gav+dg+paglel+e+diqk Ld R+pgqs ++tqrkE D veil+G+f+g+t+G+pi+++i+Nkdq+s  ye++++ +Rpg
       AJA92162.1  13 LTSFGESHGKCIGAVLDGCPAGLELEEKDIQKMLDLRKPGQSLVSTQRKEGDVVEILTGTFRGYTTGAPITMVIWNKDQKSIAYEKLRTEMRPG 106
                      799******************************************************************************************* PP

                      STCHHHHHHC.-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHT.TTEEEEEEEEEETTE...........CHHHHHTT-BS-CCCHHHHHHHHH CS
  Chorismate_synt  97 HADltyalkY.girdlrgggrsSaReTaarvaaGavakklLke.lgieivayvssigei...........ekeaenpvrcpdeeaaeemeeaie 177
                      H+D+ + +kY +++d+rgggr+S+R Ta++v+ Ga+a+klLk+ +g+e  +y+++ig+i           ++  +n+vrcp++++a++m+++i 
       AJA92162.1 107 HSDYPAYMKYkKFNDHRGGGRFSGRLTATHVMGGAIARKLLKDtIGVETNSYTTQIGKIkmkkaaakkefRSIYTNEVRCPEKNTAQKMKSVIL 200
                      ******************************************978************8888888887665434789****************** PP

                      HHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEETTGGGGGGSBHHHHS--EEEE......SS-TTTTEETTEEBSS CS
  Chorismate_synt 178 eakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgveiGsGfeaaelkGseanDeivlr......ktnnaGGieGGisnGe 265
                      +a+k+gdslGg++e +++++p+GlGep+f +l+++++ka++sipAvkg+e+GsGf+++e+ Gse+nD++v++      k+nn+GGi+GGisnG+
       AJA92162.1 201 DARKKGDSLGGIIESITTNLPVGLGEPIFGSLESDISKAIFSIPAVKGIEFGSGFAGSEKFGSENNDAYVMKggkvstKSNNSGGILGGISNGM 294
                      **********************************************************************44555567**************** PP

                      -EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
  Chorismate_synt 266 pivvrvavKpipsiakeqktvdletkeevelevkgrhDpcvvpravvvveamvalvladall 327
                      pi++r+a+Kp +si++ q++vd+++k++++l+v grhDpcvvpra +vv+++val++ad++l
       AJA92162.1 295 PITIRIAFKPASSISQIQQSVDIKKKKSIKLQVGGRHDPCVVPRAPPVVDSLVALTIADHAL 356
                      ***********************************************************987 PP

>> BCIP  p21-C-terminal region-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.3e-05      0.11      80     145 ..     172     240 ..     159     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
        BCIP  80 cikqlkeyllekakksass.kkklkk.lLss.skdkkvglliseRliNiPvevvpplykmLleeiewaq 145
                 + k++++  +++++  +++ ++k+k+ +L++ +k  ++g +i     N+Pv +  p++ +L ++i++a 
  AJA92162.1 172 AKKEFRSIYTNEVRCPEKNtAQKMKSvILDArKKGDSLGGIIESITTNLPVGLGEPIFGSLESDISKAI 240
                 4555666665555544444488888867776657789*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2445.96
//
Query:       AJA92163.1  [L=92]
Description: double-stranded DNA-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-22   77.5   0.6      9e-22   77.5   0.6    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.6     5e-26     9e-22      28     106 ..      11      89 ..       2      92 .] 0.91

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 5e-26
                 --SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS---XXXXX CS
  dsDNA_bind  28 qqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvaekkketki 106
                 q +e++ +++k  +L+q+L++eAr RL+++++vkp+ a++ven+L+ la++G+  s++t++qLk++L + ++ kk+ ki
  AJA92163.1  11 QPNEDQINAQKDMLLKQLLSSEARLRLNNVKMVKPDLANMVENYLLGLASQGRSPSQITDDQLKQILLSAQQPKKDFKI 89 
                 344455899***************************************************************9999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 702.41
//
Query:       AJA92164.1  [L=39]
Description: hypothetical protein T478_0624 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00017   20.2   0.5    0.00017   20.2   0.5    1.0  1  DUF4503         Domain of unknown function (DUF4503)
     0.0018   18.2   4.1      0.023   14.6   4.1    2.1  1  zinc_ribbon_4   zinc-ribbon domain
     0.0024   17.9   1.7      0.033   14.3   0.6    2.1  2  Zn-ribbon_8     Zinc ribbon domain
     0.0051   16.5   4.8      0.014   15.1   4.8    1.7  1  zinc_ribbon_5   zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.1   0.5      0.025   14.2   0.5    1.5  1  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
      0.014   15.4   2.5      0.018   15.0   2.5    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.02   14.9   3.0       0.02   14.9   3.0    2.0  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.029   14.3   0.2      0.035   14.0   0.2    1.2  1  UBZ_FAAP20      Ubiquitin-binding zinc-finger
       0.04   13.9   1.6      0.079   13.0   1.7    1.5  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.051   13.1   3.0       0.09   12.3   3.0    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.076   12.9   1.4      0.076   13.0   1.4    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.12   12.4   1.9       0.13   12.3   0.4    1.7  2  DUF1451         Zinc-ribbon containing domain
       0.14   11.6   7.2       0.78    9.2   0.9    2.8  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.5   1.2e-07   0.00017     276     311 ..       3      38 ..       1      39 [] 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
     DUF4503 276 tafsWPvCdrCgsekleqspedrgafsCgsCssvvt 311
                 +a + P+C +Cgs+k+e+ + d  +++C sC++++t
  AJA92164.1   3 SARACPICPECGSKKFERLDGDGVKVRCLSCKKIIT 38 
                 56678***************************9986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.1   1.7e-05     0.023       5      36 .]      10      38 ..       9      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
  zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCghvFr 36
                   Cp+C++k     e+l ++gvkvrC  C+++++
     AJA92164.1 10 CPECGSK---KFERLDGDGVKVRCLSCKKIIT 38
                   8888877...55789*************9985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.6   2.4e-05     0.033      25      39 ..       6      21 ..       1      21 [. 0.75
   2 ?    3.2   0.0     0.072     1e+02       7      14 ..      29      36 ..      24      39 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
  Zn-ribbon_8 25 pltaCPeCgs.evrrv 39
                 + + CPeCgs + +r+
   AJA92164.1  6 ACPICPECGSkKFERL 21
                 4456******999996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.072
  Zn-ribbon_8  7 rCeeCghe 14
                 rC +C++ 
   AJA92164.1 29 RCLSCKKI 36
                 89999875 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   4.8     1e-05     0.014       5      36 ..      10      38 ..       7      39 .] 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
  zinc_ribbon_5  5 CpdCdtk.FklvdsklKksgkkVrCakCaevFd 36
                   Cp+C++k F      l   g+kVrC  C ++ +
     AJA92164.1 10 CPECGSKkFER----LDGDGVKVRCLSCKKIIT 38
                   *****973633....33458********99965 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   1.8e-05     0.025       5      20 ..       8      23 ..       5      23 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
     zf-RRN7  5 ppCgvCgcrsftlddG 20
                p+C++Cg++ f   dG
  AJA92164.1  8 PICPECGSKKFERLDG 23
                79*********98555 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.5   1.3e-05     0.018      19      45 ..       8      35 ..       2      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
  Zn_Tnp_IS1595 19 fvCPhCgsrkayrikt.rglfqCkeCrk 45
                   ++CP Cgs+k+ r+ +   + +C +C+k
     AJA92164.1  8 PICPECGSKKFERLDGdGVKVRCLSCKK 35
                   89************99755678888886 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   3.0   1.4e-05      0.02       2      20 ..      10      30 ..       9      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
  DNA_ligase_ZBD  2 CPvCGsavv.Reeg.eaiyRC 20
                    CP+CGs+   R +g ++  RC
      AJA92164.1 10 CPECGSKKFeRLDGdGVKVRC 30
                    ******987697753888*** PP

>> UBZ_FAAP20  Ubiquitin-binding zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.6e-05     0.035       2      29 ..       5      32 ..       4      35 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
  UBZ_FAAP20  2 rsCPmCqkefaprlsqLDiDsHLAqCLa 29
                r CP+C +  + ++  LD D+   +CL+
  AJA92164.1  5 RACPICPECGSKKFERLDGDGVKVRCLS 32
                68*******************9999998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.7   5.7e-05     0.079      88     109 ..       9      30 ..       1      33 [. 0.83
   2 ?    2.3   0.1      0.12   1.7e+02      69      79 ..      26      36 ..      25      38 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                 S-TTTSSS-EEEEESSSEEEEE CS
        HypA  88 rCpkCgsadveivsGeellvks 109
                  Cp+Cgs+++e ++G++++v+ 
  AJA92164.1   9 ICPECGSKKFERLDGDGVKVRC 30 
                 6*****************9975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                -EEEETTTS-E CS
        HypA 69 vkvrCreCgke 79
                vkvrC +C+k 
  AJA92164.1 26 VKVRCLSCKKI 36
                68999999875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.0   6.5e-05      0.09       2      25 ..       9      33 ..       8      35 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                  EETTTTCEEC.HEETSTTCEEESSS CS
  TF_Zn_Ribbon  2 kCPnCgstnl.veDpergelvCtdC 25
                  +CP+Cgs+++  +D +   ++C +C
    AJA92164.1  9 ICPECGSKKFeRLDGDGVKVRCLSC 33
                  6******997355666667777777 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.4   5.5e-05     0.076      30      54 ..       9      35 ..       1      38 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
  OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgf 54
                     C+eCgsk+ e  + +g +++C +C+ 
      AJA92164.1  9 ICPECGSKKFErlDGDGVKVRCLSCKK 35
                    7********997777777889999975 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   9.6e-05      0.13     128     145 ..       3      20 ..       1      22 [. 0.85
   2 ?   -0.2   0.1      0.66   9.1e+02     114     124 ..      27      37 ..      24      39 .] 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.6e-05
     DUF1451 128 kteeippCpkCgateFrR 145
                 +++  p Cp+Cg+++F+R
  AJA92164.1   3 SARACPICPECGSKKFER 20 
                 6778899**********9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.66
     DUF1451 114 tlvCekCgkel 124
                 +++C +C+k +
  AJA92164.1  27 KVRCLSCKKII 37 
                 56788888765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.7    0.0032       4.5      18      24 ..       9      15 ..       3      17 .. 0.70
   2 ?    9.2   0.9   0.00057      0.78       5      10 ..      10      15 ..       9      20 .. 0.66
   3 ?    4.9   0.1     0.013        18       2      13 ..      27      38 ..      26      39 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0032
  zf-ribbon_3 18 vCpyCGt 24
                 +Cp CG+
   AJA92164.1  9 ICPECGS 15
                 5666665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00057
  zf-ribbon_3  5 CPnCGa 10
                 CP+CG+
   AJA92164.1 10 CPECGS 15
                 666666 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
  zf-ribbon_3  2 tvrCPnCGapls 13
                 +vrC +C+++++
   AJA92164.1 27 KVRCLSCKKIIT 38
                 699*****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 289.38
//
Query:       AJA92165.1  [L=123]
Description: hypothetical protein T478_0866 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.3   0.0        7.3    6.6   0.0    2.1  2  Tube      Tail tubular protein


Domain annotation for each model (and alignments):
>> Tube  Tail tubular protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00041       7.3      71     105 ..      36      72 ..      13      82 .. 0.74
   2 ?    5.0   0.0    0.0013        23      82     106 ..      84     109 ..      75     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00041
        Tube  71 cLavl..alkessidvtlrggrlydrdnhtfkldsai 105
                  L+    + +++  +v+++gg++ d+ n ++ l+  i
  AJA92165.1  36 ILKTSghFGSKKVTKVEWQGGKIADTLNADTVLNDLI 72 
                 34444657889999**************999986655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0013
        Tube  82 idvtlrggrlydrdnhtfklds.aie 106
                 id t +g r+y +++++f++++ +++
  AJA92165.1  84 IDPTSKGVRIYGKWKNSFEFNVsKVQ 109
                 6667899*************541454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 901.87
//
Query:       AJA92166.1  [L=356]
Description: glutamyl-tRNAGlu reductase, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-27   93.6   0.0    1.6e-26   92.9   0.0    1.3  1  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    8.7e-19   68.0   0.7    1.6e-18   67.1   0.2    1.8  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.052   14.0   0.0       0.13   12.7   0.0    1.6  1  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   2.6e-30   1.6e-26       3     146 .]      13     175 ..      12     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.6e-30
     GlutR_N   3 inhktapvelreklafseee.lkellkeleekvkeaviLsTCNRtEiylsaeeee................easeellellaevs.............l 71 
                 +++k++p++ + ++af++ + +++++k++  +v+e++i++T  R+Ei+++++ e+                +          +++              
  AJA92166.1  13 VTFKNVPLHSLARFAFKDVAaATDAFKKI-PGVEECIIIQTSSRVEIFTVSNLETddstdarrpegkgliiN----------QMKetwqensnieqidI 100
                 689*************8776588899998.699***************755555545556666554443331..........22112222223333337 PP

     GlutR_N  72 eelkeklyvlegeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                 ++++++l+v++++++  Hl+r+a+GLdS+v+G ++++  +k+++e ak+ g++gk+L++lf++ i+ a ++r +t
  AJA92166.1 101 DHFDQTLEVFKDDDVYLHLLRLACGLDSIVVGKEEVFDEIKKSIENAKKSGASGKILNKLFDSIIRLANSIRGST 175
                 7777******************************************************************99766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.83     5e+03      77      97 ..      46      66 ..      29      75 .. 0.75
   2 !   67.1   0.2   2.7e-22   1.6e-18       4     133 ..     193     318 ..     190     323 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.83
                  SEEEE-SSSSS-SB-HHHHHC CS
  Shikimate_DH 77 dvvisataseepilekeevee 97
                  + +i+ t+s+  i++ +++e 
    AJA92166.1 46 ECIIIQTSSRVEIFTVSNLET 66
                  567888888888888877765 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 2.7e-22
                   HHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHCCHH CS
  Shikimate_DH   4 kkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeeveealk 100
                   ++k++  ++kkvlliG+Ge a  vak L +k++    v+  ++era+++ + l g+    l++ ++ +  +++d++i+at +  ++++ e ++ ++k
    AJA92166.1 193 EEKVGLDAKKKVLLIGTGESAAMVAKTLGQKEIS-FSVTSKDMERAANFSQLLCGT---PLEFADVLTGFDKFDIIIVATTADYFLIDLETIKLVMK 285
                   5666655789***********************9.******************999...9************************************* PP

                   H.S..EEEEE--SS-SB-TTGGGSTTCCCEEHH CS
  Shikimate_DH 101 krkkplllvDiavPRdvepevaeledvrlytvD 133
                   ++kk +l++Di+ PR ve+ + el  ++l   D
    AJA92166.1 286 EKKKGTLILDISEPRAVEETIMELPRIKLLFRD 318
                   *99*********************999987655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.2e-05      0.13       7      70 ..     201     269 ..     199     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeele..elvklaeeelekd...legadlviaatd 70 
                    +kkvl++G Ge Aa  +++l +++    v +++++++++  +l+  ++ e+ +    ++++d++i+at+
     AJA92166.1 201 KKKVLLIGTGESAAMVAKTLGQKEISFSVTSKDMERAANfsQLLCGTPLEFADVltgFDKFDIIIVATT 269
                    69*******************************843333435555456666555222666778887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2463.74
//
Query:       AJA92167.1  [L=181]
Description: hypothetical protein T478_1468 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1378.11
//
Query:       AJA92168.1  [L=379]
Description: PF04123 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.6e-94  314.7   9.5      1e-93  314.5   9.5    1.0  1  DUF373     Domain of unknown function (DUF373)
  ------ inclusion threshold ------
      0.068   13.3   0.4       0.35   11.0   0.4    2.2  1  SPC12      Microsomal signal peptidase 12 kDa subunit (SPC12)
        2.2    8.8   6.3        3.6    8.1   0.2    2.6  2  DUF4231    Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  314.5   9.5   1.7e-97     1e-93       1     316 [.      18     337 ..      18     366 .. 0.88

  Alignments for each domain:
  == domain 1  score: 314.5 bits;  conditional E-value: 1.7e-97
      DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgveadrkiaeqldevlsklead 99 
                 k+Lv+cvDrDdD+grkag+ tPvvGr+ +++aa++lal+dPeD+D+N++f a+k+y++L ++g +vevavvtG ek+gv+ad+ki ++++++l+k++a+
  AJA92168.1  18 KLLVICVDRDDDVGRKAGIATPVVGRDSCINAAQRLALEDPEDADSNSIFYAVKTYEDLVSKGYNVEVAVVTGVEKRGVQADEKIVSEIRSILEKFSAN 116
                 68************************************************************************************************* PP

      DUF373 100 saivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrktiLvplGlllliyalllllglpelalaiillllGlylll 194
                 +a++VsDG++De+v+p+iq+ v+v+sv+rVv++ sr+iE++y+++    k++++d+ ++k++L+++G+llli ++ +++g+++ ++a+++ +lG+++l+
  AJA92168.1 117 GAVIVSDGEDDEMVIPVIQNVVPVVSVQRVVMQVSRTIEHSYAVFgkflKMVVYDKTYSKFFLGVPGILLLIGGIGTVVGYTAEIFAVLVSILGGAFLI 215
                 **********************************************999************************************************** PP

      DUF373 195 rGfgldelleelleklkesleegritfvtyvvallllligiisgyislesvss...asvssglltlila..fiygavewlalailtaslgkiideylkr 288
                 r+f++d+++    +++ +++ +g i++++ v++++l+l ++ +g+++++s       + s++l ++i++  f++g++++l++++ t+s+g +i+++l+r
  AJA92168.1 216 RAFDIDKSW----SNWTKATPTGFIRIFALVTGIILILASVPAGIANIDSQLFengLDFSQSLSNQIVVgqFLQGLFPFLWMGLGTISAGILISNWLNR 310
                 *******66....6******************************999776554678677777777777777**************************99 PP

      DUF373 289 eekdiarllllpflvlaiglvlygasay 316
                 + k+i+ +l +++l  ai+  + ++++ 
  AJA92168.1 311 KLKHISDVLRIIVL-AAIYPTAAQFTNI 337
                 97777555533332.2333333333333 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   5.8e-05      0.35      16      50 ..     184     218 ..     181     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.8e-05
       SPC12  16 ilvlsaviafivGyitqdlkltlyillagvvltll 50 
                 il+l++ i+ +vGy ++ + +++ il++++++ ++
  AJA92168.1 184 ILLLIGGIGTVVGYTAEIFAVLVSILGGAFLIRAF 218
                 89999***********************9998776 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.6     0.033     2e+02      27      64 ..     202     246 ..     184     260 .. 0.78
   2 ?    8.1   0.2    0.0006       3.6       9      72 ..     311     372 ..     304     372 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.033
     DUF4231  27 lgallpilvs.......sklgagvsvlkiltallsalvailaale 64 
                 +++l++il         +++++ ++++k+++++   + a++++++
  AJA92168.1 202 FAVLVSILGGaflirafDIDKSWSNWTKATPTGFIRIFALVTGII 246
                 445555555577777777788889999999999999999988876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0006
     DUF4231   9 kasrakrrfrllrlitivlgallpilvs..sklg.agvsvlkiltallsalvailaaleeffryker 72 
                 k ++     r     +ivl+a+ p+++    +l   ++s++ i ++l++a++++++a   f+ry++r
  AJA92168.1 311 KLKHISDVLR-----IIVLAAIYPTAAQftNILTtNDSSFTLIPPLLAGAAITLISATLLFRRYRKR 372
                 4444444444.....7999999999999994444044555556678899999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2733.41
//
Query:       AJA92169.1  [L=304]
Description: branched-chain-amino-acid transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-48  165.2   0.0    2.4e-48  165.0   0.0    1.0  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.0   0.0   1.3e-52   2.4e-48       2     223 .]      35     264 ..      34     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.0 bits;  conditional E-value: 1.3e-52
  Aminotran_4   2 lfEtmrvy....ngeiffldeHleRLrksaellglelpfdeeelrkileelleannsen.grlrllvsrgggglg.aatsepsvavyvsalppgpese 93 
                  +fE++r+y      +if+ldeH+ R+r+s +  ++ l+f+ +e++ ++  l ++n+ +  +++r++++ g+ g++   t+++  + ++ ++p+g    
   AJA92169.1  35 IFEGIRAYwngeELNIFRLDEHIRRFRNSGKFYDITLRFSNKEIKDAVINLCKKNKIKTsCYIRPFYFVGQYGINlHVTKKAPTHAVIFCFPFGDLFN 132
                  7*****9995555567*******************************************9***********8888999999999999999***99999 PP

  Aminotran_4  94 ke.lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvdedgnvtEgstsNvfivkggelitPplssgiLpGitrrallelakalg 189
                  k+ +++++s++ + +  s+ ++aK    yl+++la + ak+r++de++l+d+++ v+E+   N+fivk+++litPplss+ L+Gitr+++le ak  +
   AJA92169.1 133 KNgITACISKWKKFNDSSTPTQAKMGGnYLNSILATQDAKKRKFDEAILLDKNNKVSEAPGENIFIVKNNTLITPPLSSSALDGITRKSILEFAKIIK 230
                  99**********************9877*******************************************************************99* PP

  Aminotran_4 190 leveereitlkdleeadeafltntlrgvlpvrsi 223
                  ++ + rei+ ++l++ade+flt+t+++++pv +i
   AJA92169.1 231 IKTKIREISKDELKKADEVFLTGTAAEITPVIKI 264
                  *******************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2096.48
//
Query:       AJA92170.1  [L=179]
Description: hemerythrin HHE cation-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-08   35.1   0.4    4.7e-08   33.7   0.1    1.7  2  Hemerythrin  Hemerythrin HHE cation binding domain
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.24   11.5   0.1    1.4  1  SUIM_assoc   Unstructured region C-term to UIM in Ataxin3


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   5.3e-12   4.7e-08       3     124 ..       4     129 ..       2     135 .. 0.83
   2 ?   -0.9   0.0      0.26   2.4e+03       9      75 ..     144     164 ..     138     175 .. 0.47

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.3e-12
                  HHHHHHHHHHHHHHHHHH.HHHHHHHHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHHHHHHHHHHHHHHHHHHHHCHT CS
  Hemerythrin   3 vealdeeHralrallerl.raladaaaevhga...lrklaelldelvdeleaHhaaEEellfPlledrpggravldvlereHdeirelleelrellkg 96 
                   e+l+ eH+ +++l + +  ++ +  a+++ +   ++k+  l++e+ d    H+++EE  +fP ++  ++   ++++l  eH+  r +++ + + lk 
   AJA92170.1   4 SEFLRNEHQDILRLEKVItKSYKALYAGADIPfsdIDKINFLIAEFLDS--VHFTREEGSYFPCVASYDHLNKEIRELLIEHEFSRNIARSISKNLKL 99 
                  5789************9955555556666666899*************8..9**************99999999999999999999999999999999 PP

                  CGGSTCHHHHH....HHHHHHHHHHHHHHHHH CS
  Hemerythrin  97 leepsaaafae....lleeladllreHiakEe 124
                  ++e+++    e     l ++ + l eH+++Ee
   AJA92170.1 100 WKEGQDKR--EpvarFLSVYSTFLIEHMKREE 129
                  99333322..23356999999**********9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.26
                  HHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH.CCC.HHHHHH CS
  Hemerythrin   9 eHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlledrpggravldv 75 
                  e ++++++++ ++a+a++                                              + +
   AJA92170.1 144 EEQEMFEQFQSISAIAEK----------------------------------------------VTS 164
                  333444444444444444..............................................333 PP

>> SUIM_assoc  Unstructured region C-term to UIM in Ataxin3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.7e-05      0.24      20      55 ..     125     163 ..     121     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
  SUIM_assoc  20 rkrreaYFEKqeqq...qqqqqqqqdppgqlshprekpt 55 
                  kr ea+FEK e++   +++ q   ++ + +s + ek t
  AJA92170.1 125 MKREEAFFEKAENEilsKEEEQEMFEQFQSISAIAEKVT 163
                 59********55551113444444455556667777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1349.29
//
Query:       AJA92171.1  [L=249]
Description: NDP-hexose 2,3-dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-66  222.4   0.0    4.5e-66  222.2   0.0    1.0  1  Hexose_dehydrat  NDP-hexose 2,3-dehydratase
  ------ inclusion threshold ------
      0.018   15.1   0.8      0.026   14.6   0.8    1.3  1  Cnd1             non-SMC mitotic condensation complex subunit


Domain annotation for each model (and alignments):
>> Hexose_dehydrat  NDP-hexose 2,3-dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.0     5e-70   4.5e-66       3     204 .]      43     249 .]      41     249 .] 0.96

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 5e-70
  Hexose_dehydrat   3 evlswlterraaeeleveriplaelkgWsleedt.niahesgrfFsVegveveae.erev..eeWtqPlieqpeigilgllvkeidgvlhfLvq 92 
                       v++w++++r+++++ ve+i  ++l++W+++++t n++hesg fF+V+gv+ +   +rev  + WtqP+i+++  gilg+l+k+i+g +h+L+q
       AJA92171.1  43 YVIEWFNKKREESDMIVEEIGVNDLDKWNVDSNTgNVKHESGGFFQVIGVKASNTfDREVgkKGWTQPMIAKNPGGILGILMKRINGIPHYLLQ 136
                      5899***********************************************9998866663367****************************** PP

  Hexose_dehydrat  93 akaEpGnldlveLsPTvqatrsnytkahkgrkppyldefleaerervlvdvlqSEeGgrFyrkrnrnliveveedve.elpddfrWltlgqlke 185
                      akaEpGn+++++LsPT+qat+sn  kah+g+kp + ++f+e+++ ++++ ++qSE+GgrFy k+n n+ivev+ed   e+pd f+W+tl q+k+
       AJA92171.1 137 AKAEPGNIGKLQLSPTLQATTSNLLKAHGGSKPLFAEYFNEENNLNIIYAKWQSEDGGRFYLKSNYNMIVEVTEDKDlEIPDSFIWVTLYQIKQ 230
                      ************************************************************************7777778*************** PP

  Hexose_dehydrat 186 LlrednlvnvqaRsllscl 204
                      L++ +n v  ++R ++s l
       AJA92171.1 231 LMKIENFVGPHVRGIISYL 249
                      ****************976 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8   2.9e-06     0.026      84     141 ..       5      62 ..       1      80 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-06
        Cnd1  84 eiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaeslvekl 141
                 ei+   en+ y+l +d+is++++ l+++  ++qi+ l+++++  +k+++e +++ve +
  AJA92171.1   5 EIKVILENNEYELDSDTISRIQTMLESIRDDNQINKLDYVIEWFNKKREESDMIVEEI 62 
                 6666656889*********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1827.32
//
Query:       AJA92172.1  [L=500]
Description: DEAD/DEAH box helicase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-22   79.4   0.3    2.3e-22   79.4   0.3    2.4  3  Helicase_C    Helicase conserved C-terminal domain
    3.1e-22   79.4   0.0    6.7e-22   78.3   0.0    1.5  1  ResIII        Type III restriction enzyme, res subunit
    9.9e-18   64.5   0.6    6.1e-17   61.9   0.1    2.1  2  DEAD          DEAD/DEAH box helicase
    0.00017   21.6   0.0    0.00081   19.4   0.0    2.1  2  Flavi_DEAD    Flavivirus DEAD domain
     0.0034   16.8   0.0      0.007   15.7   0.0    1.4  1  DUF3638       Protein of unknown function (DUF3638)
     0.0044   17.2   0.0      0.059   13.5   0.1    2.3  2  Helicase_C_2  Helicase C-terminal domain
  ------ inclusion threshold ------
      0.011   16.1   0.0       0.04   14.2   0.0    2.0  2  AAA_19        AAA domain
      0.012   14.9   0.0      0.019   14.2   0.0    1.3  1  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.02   14.6   0.0      0.046   13.4   0.0    1.5  1  SWI2_SNF2     SWI2/SNF2 ATPase
      0.042   13.6   0.0       0.12   12.1   0.0    1.8  2  AAA_30        AAA domain
      0.044   13.6   0.0        3.6    7.3   0.0    2.4  2  AAA_11        AAA domain
      0.063   12.9   0.6       0.33   10.5   0.6    2.0  1  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3   3.5e+03      79      96 ..     125     142 ..      48     147 .. 0.61
   2 !   79.4   0.3   1.6e-25   2.3e-22       5     110 ..     337     445 ..     333     446 .. 0.91
   3 ?   -3.2   0.0       6.9     1e+04      21      49 ..     454     479 ..     450     490 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
                 SSTSTTESEEEESSSSSS CS
  Helicase_C  79 GidipkvnlVinfdlprn 96 
                  idi++ +lVi+ ++ r 
  AJA92172.1 125 MIDIDQFSLVIFDEAHRA 142
                 467777777776665555 PP

  == domain 2  score: 79.4 bits;  conditional E-value: 1.6e-25
                 HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTT.....STHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHH CS
  Helicase_C   5 allellkleeeggkilifvntidrlekvklllekkgikvavlhge.....lpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvt 98 
                  l +++  +++++k+lif+ ++d+++ ++  l+k gi++ +l g+     l+q++++e++++f++g ++vL+at+v+e+G+di +vnlVi++d   +  
  AJA92172.1 337 ELQKII--SSVNDKVLIFTSYRDSVNVINDTLQKMGINSEILIGKagetgLKQQKQIETVQRFRDGLTKVLVATRVGEEGLDISEVNLVIFYDNVPSSI 433
                 566666..7899***********997645556777*********999999************************************************* PP

                 HHHHHHTTSSST CS
  Helicase_C  99 syiqriGRtgRa 110
                 +++qr+GRtgR 
  AJA92172.1 434 RFVQRKGRTGRK 445
                 ***********5 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.9
                 EEESSHHHHHHHHHHHHHTTSTEEEESTT CS
  Helicase_C  21 ifvntidrlekvklllekkgikvavlhge 49 
                 i   tid+++   +   +++ik+a+l g+
  AJA92172.1 454 IAKDTIDQVY---YHIGQRKIKSAKLMGD 479
                 4444555553...4445667888888885 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   4.5e-25   6.7e-22       3     170 ..      17     169 ..      14     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 4.5e-25
                 EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
      ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekds 101
                 elr+yQ +  ++        ++++ l++++TG GKT +a+++++++l+++k   +l+l+p++ l++q  + +k+ l  +     ++v+g+  ++k+k+s
  AJA92172.1  17 ELRDYQVNLANEA-------KNENSLVVLPTGLGKTTIALQIMAHVLSQNK-GGVLLLAPTRVLVNQHFDFLKENLLLD---DIGIVTGEDLINKRKKS 104
                 5666666555554.......58899**********************9855.5**************999998888876...68999999999978888 PP

                 ..-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---.SEEEEEESS-S CS
      ResIII 102 tnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfke.avllglTATpe 170
                   ++++ +t +   +d+     e++  + d+f ++i+DEaHr+ ++ +++ i+++fke +++lg+TAT++
  AJA92172.1 105 WMNSVVCATPEITRNDL-----ERNMIDIDQFSLVIFDEAHRAVGDYAYTGIARHFKEkSLILGMTATLP 169
                 88888888888888888.....99*********************99*********87699*******86 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   4.1e-20   6.1e-17      10     174 ..      28     174 ..      19     176 .. 0.78
   2 ?    0.8   0.1      0.25   3.7e+02      37     105 ..     339     409 ..     231     425 .. 0.71

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.1e-20
                 HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  10 lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrl 108
                 ++ ++++ lv  +TG GKT+++l  + + +    ++++  +l+++Ptr L++q+++ lk+ +         i++g++  ++++k      +v +tp+  
  AJA92172.1  28 EA-KNENSLVVLPTGLGKTTIALQIMAHVL----SQNKGGVLLLAPTRVLVNQHFDFLKENLLL---DDIGIVTGEDLINKRKKS-WMNSVVCATPEIT 117
                 44.47899*************988888666....467778*******************99993...444455665554555544.45899******** PP

                 HHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
        DEAD 109 ddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kdvk 174
                  + l+++ ++++q++++++DEa+r   +     i    +++       k+++ ++ ++ATlp ++vk
  AJA92172.1 118 RNDLERNMIDIDQFSLVIFDEAHRAVGDYAYTGIA---RHF-------KEKSLILGMTATLPsEKVK 174
                 ***************************95555555...566.......33345*********88887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                 HHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHHHHHH...HTT.CSEEEEEH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxx.xxxxxxxx RF
        DEAD  37 qivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardqlskl...dng.vdivvgtp 105
                 q++++   + + k+li +  r  ++ + ++l+k++ + ++ +  +  +g ++++q++++   + g ++++v+t 
  AJA92172.1 339 QKIIS---SVNDKVLIFTSYRDSVNVINDTLQKMGINSEILIGkAGETGLKQQKQIETVqrfRDGlTKVLVATR 409
                 44433...334688888888888888888888888864422221222344444555544222333666776664 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.4e-07   0.00081       5     139 ..      32     171 ..      12     177 .. 0.72
   2 ?   -1.4   0.0       1.3     2e+03      15      61 ..     328     374 ..     317     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.4e-07
                 -EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS......-EEE-------------SEEEEEHHH.HHHHHHH..T---- CS
  Flavi_DEAD   5 kltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkgl......evryktsavkeektgrelvdvmchat.ftkrlls..pvrkk 94 
                 +  ++ l  G Gkt   l  + +   +++   l+LaPtrv ++   + lk+        +   ++++ +++++  +  v+c +  +t++ l+   +   
  AJA92172.1  32 ENSLVVLPTGLGKTTIALQIMAHVLSQNKGGVLLLAPTRVLVNQHFDFLKENlllddiGIVTGEDLI-NKRKKSWMNSVVCATPeITRNDLErnMIDID 129
                 55566677799***99998888888888889999*******99866665543111100444444555.6777777778888654367777875456788 PP

                 --SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT- CS
  Flavi_DEAD  95 nyeliimDeahflDPasiaarGyletkaeegeaalilltatPPGt 139
                 ++ l+i Deah       a  G++++ +e+    ++ +tat P +
  AJA92172.1 130 QFSLVIFDEAHRAV-GDYAYTGIARHFKEKS--LILGMTATLPSE 171
                 9**********764.4567888877766554..666799998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                 S-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE- CS
  Flavi_DEAD  15 aGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkglevryk 61 
                 +G  +  lpel k   + + + l+ +  r  ++ +++ l+++ ++++
  AJA92172.1 328 QGIEHSKLPELQKIISSVNDKVLIFTSYRDSVNVINDTLQKMGINSE 374
                 56678889999999999999999999999999999999999999875 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.7e-06     0.007      20      92 ..      15      84 ..      11      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
     DUF3638 20 niliReeQaevAkemispssgensvlQLnmGeGKssvIvPivaaaladgk.kLvrvivlkpllkqmaqlLvskL 92
                +i +R+ Q++ A+e     ++ens++ L  G GK+++ + i+a +l+++k  ++ +  ++ l++q +++L+++L
  AJA92172.1 15 SIELRDYQVNLANEA----KNENSLVVLPTGLGKTTIALQIMAHVLSQNKgGVLLLAPTRVLVNQHFDFLKENL 84
                577888888888765....579************************977736667777889999*999999877 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.31   4.7e+02       3      42 ..      54      93 ..      52     116 .. 0.79
   2 !   13.5   0.1   3.9e-05     0.059       2      83 ..     339     420 ..     338     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
  Helicase_C_2  3 ellevvpggvlvffpSyklleevverlkeeleskkieifv 42
                  ++l++ +ggvl++ p   l+++ +++lke+l  ++i i++
    AJA92172.1 54 HVLSQNKGGVLLLAPTRVLVNQHFDFLKENLLLDDIGIVT 93
                  5778899**********************99877776554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.9e-05
  Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeeleskkieifvee....keesrekvleeykekkkkgaillavcrGklsEGidfsdd 83 
                    +++++v+++vl+f++  + ++ + ++l++ + +++i i +      k++++ ++++++++  + +++l+a+      EG+d+s+ 
    AJA92172.1 339 QKIISSVNDKVLIFTSYRDSVNVINDTLQKMGINSEILIGKAGetglKQQKQIETVQRFRD--GLTKVLVATR--VGEEGLDISEV 420
                   68999********9988889999999*******9999888766778999999999******..*********9..5579**99964 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05      0.04       5      52 ..      26      70 ..      22     162 .. 0.79
   2 ?   -2.2   0.0       3.1   4.7e+03      35      69 ..     339     381 ..     326     432 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
      AAA_19  5 vealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftg 52
                ++++k+++ lv+ + G GKT++  +i+a+++++++     +ll+a+t+
  AJA92172.1 26 ANEAKNENSLVVLPTGLGKTTIALQIMAHVLSQNK---GGVLLLAPTR 70
                458899999********************999995...589*****98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
      AAA_19  35 velggvkpeeillvaftgrAakelrerlaalgae........a 69 
                 +++ +   +++l+ +  + +++ +++ l+++g +         
  AJA92172.1 339 QKIISSVNDKVLIFTSYRDSVNVINDTLQKMGINseiligkaG 381
                 4444444578888888888888888888777766444444440 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05     0.019      11     102 ..      41     144 ..      38     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
     DUF2075  11 GtGKtvvllnllaeleddeeertavylsvNhplvl....vlrealakke......ekkkkkeafeklssfinnlsef...kkaeekkeepkedvvivDE 96 
                 G GKt ++l+++a +  ++++  + +l   + lv+     l+e+l  ++      e+   k++ + ++s++ ++ e    + + ++ + +++ +vi+DE
  AJA92172.1  41 GLGKTTIALQIMAHV-LSQNKGGVLLLAPTRVLVNqhfdFLKENLLLDDigivtgEDLINKRKKSWMNSVVCATPEItrnDLERNMIDIDQFSLVIFDE 138
                 88***********99.33333333333333333332222677777666678776633344444444445554444445545566677899********* PP

     DUF2075  97 Ahrllt 102
                 Ahr+  
  AJA92172.1 139 AHRAVG 144
                 ***976 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-05     0.046      19     161 ..      32     172 ..      19     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
   SWI2_SNF2  19 kgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeLkelleke.sekiifttiqKfeeeekeklevl 116
                 ++ ++   +G GK+   + +++ +l+  +++  v+++   + L +Q ++ +++    +   + ++++L ++ +k+  ++++++t +  +++ +   +++
  AJA92172.1  32 ENSLVVLPTGLGKTTIALQIMAHVLS--QNKGGVLLLAPTRVLVNQHFDFLKENLLLDDIGIVTGEDLINKRKKSwMNSVVCATPEITRNDLE--RNMI 126
                 55556666788887777666666665..46677777777777888888888877666666788888888888666677777777666655433..3566 PP

   SWI2_SNF2 117 sereniivlvDEaHRsqygelakklrkalpnaa.figFTGTPilkk 161
                 + ++  +v++DEaHR   +   + + +++++ + ++g+T T  ++k
  AJA92172.1 127 DIDQFSLVIFDEAHRAVGDYAYTGIARHFKEKSlILGMTATLPSEK 172
                 667777***********99999999999987651569999944444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.9e-05      0.12       3      61 ..      19      75 ..      17     149 .. 0.64
   2 ?   -2.5   0.0       2.3   3.4e+03     138     170 ..     378     409 ..     352     419 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
      AAA_30  3 naeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkv 61
                ++ Q ++++++ +++   ++++ p G GKtt+  ++ ++++ +++g v++lApt    ++
  AJA92172.1 19 RDYQVNLANEAKNEN---SLVVLPTGLGKTTIALQImAHVLSQNKGGVLLLAPTRVLVNQ 75
                566777777766555...577779999***9765553888888899********887665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
      AAA_30 138 rdlveaagigtaeLtevvRqkeseeraaalalr 170
                  +  e+   ++ ++++v+R+++    ++  a r
  AJA92172.1 378 GKAGETGLKQQKQIETVQRFRD-GLTKVLVATR 409
                 5554444556777888888865.4555555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.027        41       5      66 ..      21      72 ..      17      94 .. 0.70
   2 ?    7.3   0.0    0.0024       3.6     197     231 ..     108     144 ..      95     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.027
      AAA_11  5 sqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaA 66
                 q +  ++a +e+  +l+  P G gKT+  +++++++ls+        +k  +L+ ap+ + 
  AJA92172.1 21 YQVNLANEAKNEN--SLVVLPTGLGKTTIALQIMAHVLSQ--------NKGGVLLLAPTRVL 72
                5666666666666..6899999**********99999654........34444444444443 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0024
      AAA_11 197 eivltTlsgagsklleklak..kfdvviIDEAaqavE 231
                 ++v++T  +  ++l +++ +  +f +vi DEA +av 
  AJA92172.1 108 SVVCATPEITRNDLERNMIDidQFSLVIFDEAHRAVG 144
                 79*******9999888888788**********99985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.6   0.00022      0.33      36      61 ..      34      59 ..      29     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
      AAA_25 36 allaGapgtGKttlaldlalavatGk 61
                +l++ ++g GKtt+al+++++v++  
  AJA92172.1 34 SLVVLPTGLGKTTIALQIMAHVLSQN 59
                5566689***************9433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3619.39
//
Query:       AJA92173.1  [L=194]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   52.3   2.2      4e-06   26.5   0.1    5.2  5  TPR_2            Tetratricopeptide repeat
    2.5e-12   46.1   4.8    3.9e-08   32.8   0.3    4.4  4  TPR_1            Tetratricopeptide repeat
    5.1e-12   45.3   2.5      0.068   13.6   0.0    4.4  4  TPR_17           Tetratricopeptide repeat
    1.6e-10   41.4   0.0    0.00089   19.7   0.0    3.3  3  TPR_19           Tetratricopeptide repeat
    1.2e-09   37.6   6.8     0.0022   18.1   0.2    4.5  4  TPR_8            Tetratricopeptide repeat
    4.1e-09   36.5   0.1        1.5    9.6   0.0    5.1  5  TPR_6            Tetratricopeptide repeat
    7.5e-08   32.3   0.5       0.04   14.0   0.0    4.1  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    5.5e-07   30.1   0.0    9.5e-05   23.0   0.0    2.5  2  TPR_16           Tetratricopeptide repeat
    8.7e-07   29.3   0.0       0.62   11.0   0.0    4.2  5  TPR_14           Tetratricopeptide repeat
      2e-06   27.4   0.8      0.036   13.7   0.2    3.4  3  TPR_11           TPR repeat
    9.5e-05   22.6   2.0     0.0051   17.0   0.1    2.9  3  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    0.00028   19.9   0.8      0.076   11.9   0.1    2.1  2  NARP1            NMDA receptor-regulated protein 1
     0.0029   17.6   0.9       0.57   10.1   0.2    2.3  2  DUF4919          Domain of unknown function (DUF4919)
     0.0036   17.2   0.0        3.7    7.8   0.0    3.4  3  TPR_7            Tetratricopeptide repeat
     0.0044   17.3   0.1        6.7    7.1   0.0    3.4  3  TPR_12           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.11   12.9   0.0    2.1  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.013   15.0   1.0       0.36   10.2   0.0    2.0  2  Coatomer_E       Coatomer epsilon subunit
       0.04   13.8   0.0        5.6    7.0   0.0    3.5  4  TPR_10           Tetratricopeptide repeat
      0.096   12.9   0.0        6.8    7.0   0.0    2.5  2  Virulence_fact   Virulence factor
       0.11   12.7   0.4       0.11   12.7   0.4    2.3  2  USP8_dimer       USP8 dimerisation domain
       0.21   11.8   0.0       0.86    9.8   0.0    1.9  2  TPR_9            Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00035       0.3       6      34 .]       5      33 ..       4      33 .. 0.94
   2 !   26.5   0.1   4.7e-09     4e-06       3      34 .]      36      67 ..      34      67 .. 0.96
   3 ?    5.1   0.0     0.033        28      12      33 ..      79     100 ..      76     101 .. 0.92
   4 ?    1.0   0.0      0.68   5.8e+02      10      34 .]     111     135 ..     110     135 .. 0.85
   5 ?    3.6   0.0       0.1        85       2      19 ..     137     154 ..     136     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
       TPR_2  6 nlGlayyklgdyeeAleafekAleldPnn 34
                n G+ ++  +++++A++ ++  l  +P+n
  AJA92173.1  5 NEGNRLFLEKKFQDAIKKYNIILDKEPDN 33
                7899*******************999997 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 4.7e-09
       TPR_2  3 alynlGlayyklgdyeeAleafekAleldPnn 34
                al+n G+++ kl++y +Al +++k l+++Pn+
  AJA92173.1 36 ALNNKGYSLSKLKKYSDALVCYDKFLQINPND 67
                89****************************97 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.033
       TPR_2  12 yklgdyeeAleafekAleldPn 33 
                 +k g++ +A+  +++ l+ +P+
  AJA92173.1  79 RKTGEFHKAVGICDELLKNNPD 100
                 799******************7 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.68
       TPR_2  10 ayyklgdyeeAleafekAleldPnn 34 
                 ++ kl++++e    + k   ++P+n
  AJA92173.1 111 ILKKLNRFAESNTICMKLADIYPEN 135
                 688999**99999999999999986 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.1
       TPR_2   2 ealynlGlayyklgdyee 19 
                 e+ly+++   +klg+ e+
  AJA92173.1 137 EVLYEMASNFLKLGNKEQ 154
                 789************997 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.017        14      11      34 .]      10      33 ..       4      33 .. 0.86
   2 !   32.8   0.3   4.5e-11   3.9e-08       3      34 .]      36      67 ..      35      67 .. 0.97
   3 ?    5.6   0.0     0.018        15       4      33 ..      71     100 ..      69     101 .. 0.90
   4 ?    0.1   0.1      0.94     8e+02       2      19 ..     137     154 ..     136     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                HHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 11 yfklgkydeAleyyekALelnPnn 34
                +f  +k+++A++ y+  L  +P+n
  AJA92173.1 10 LFLEKKFQDAIKKYNIILDKEPDN 33
                6889**********9999999987 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 4.5e-11
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                al+n+G+ + kl+ky +Al +y+k L++nPn+
  AJA92173.1 36 ALNNKGYSLSKLKKYSDALVCYDKFLQINPND 67
                89****************************97 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.018
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                 l n+  +++k g++ +A+  +++ L+ nP+
  AJA92173.1  71 LINKISLFRKTGEFHKAVGICDELLKNNPD 100
                 6788899************99999999997 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.94
                 HHHHHHHHHHHHTT-HHH CS
       TPR_1   2 kalynlGnayfklgkyde 19 
                 ++ly ++  ++klg+ ++
  AJA92173.1 137 EVLYEMASNFLKLGNKEQ 154
                 57899999999***9875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   0.00013      0.11       6      32 ..      27      53 ..      22      54 .. 0.92
   2 !   13.6   0.0   7.9e-05     0.068       1      32 [.      56      87 ..      56      89 .. 0.94
   3 ?    4.2   0.0     0.077        66       2      30 ..      91     119 ..      90     121 .. 0.87
   4 !   11.5   0.0   0.00038      0.32       2      30 ..     125     153 ..     124     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
      TPR_17  6 leldPnnadaynnLAelllknGdlmtA 32
                l+++P+n  a+nn+++ l+k++++ +A
  AJA92173.1 27 LDKEPDNLIALNNKGYSLSKLKKYSDA 53
                7899*******************9888 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.9e-05
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtA 32
                +y k+l+++Pn+  ++ n+  l++k G++ +A
  AJA92173.1 56 CYDKFLQINPNDKTVLINKISLFRKTGEFHKA 87
                8***********************99999888 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.077
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlm 30 
                 + + l+++P+   a++ + ++l+k+++++
  AJA92173.1  91 CDELLKNNPDEIIALYHKLRILKKLNRFA 119
                 7789************9999999998876 PP

  == domain 4  score: 11.5 bits;  conditional E-value: 0.00038
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlm 30 
                 + k ++++P n ++++++A  +lk+G+++
  AJA92173.1 125 CMKLADIYPENGEVLYEMASNFLKLGNKE 153
                 78999******************999976 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   6.1e-05     0.052       2      59 ..      11      68 ..      10      71 .. 0.94
   2 !   19.7   0.0     1e-06   0.00089       5      64 ..      48     109 ..      44     115 .. 0.90
   3 !   12.7   0.0   0.00016      0.13      16      57 ..     127     168 ..     112     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdda 59
                + e+++++A++ +  +l+++p+n+ a+ +    l +l+ + +A  + d+ ++ +p+d 
  AJA92173.1 11 FLEKKFQDAIKKYNIILDKEPDNLIALNNKGYSLSKLKKYSDALVCYDKFLQINPNDK 68
                67899********************************************999999986 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1e-06
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd..aryasL 64 
                 ++y +Al  + + lq +p++  ++++ + +  ++g++ +A  ++d+l++ +pd+  a y++L
  AJA92173.1  48 KKYSDALVCYDKFLQINPNDKTVLINKISLFRKTGEFHKAVGICDELLKNNPDEiiALYHKL 109
                 57999************************************************544666655 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00016
      TPR_19  16 qalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 ++ + +p+n+e+++ +A   l+lg+ ++  +lL+++ ++ p+
  AJA92173.1 127 KLADIYPENGEVLYEMASNFLKLGNKEQFFNLLQKAVNALPN 168
                 56789***********************99999999999887 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   2.5e-06    0.0022       3      34 .]      36      67 ..      35      67 .. 0.96
   2 ?    2.0   0.0      0.36   3.1e+02      10      33 ..      77     100 ..      73     101 .. 0.89
   3 !    9.8   0.1    0.0012      0.98       3      34 .]     104     135 ..     102     135 .. 0.94
   4 !    8.4   0.1    0.0032       2.7       2      29 ..     137     164 ..     136     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34
                a++n+g+ ++kl++y  A  +y k l+++p++
  AJA92173.1 36 ALNNKGYSLSKLKKYSDALVCYDKFLQINPND 67
                689***************************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.36
                 HHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  10 iylklgdyeeAkeyyekaleldpd 33 
                 + +k+g++++A+  + + l+ +pd
  AJA92173.1  77 LFRKTGEFHKAVGICDELLKNNPD 100
                 6789********999999999997 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 a+y++ +i++kl+++ e+   ++k  ++ p+n
  AJA92173.1 104 ALYHKLRILKKLNRFAESNTICMKLADIYPEN 135
                 79*************************99986 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0032
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekale 29 
                 e++y ++s  lklg++e+    ++ka+ 
  AJA92173.1 137 EVLYEMASNFLKLGNKEQFFNLLQKAVN 164
                 789***********************86 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.08        68      12      33 .]      13      33 ..       7      33 .. 0.83
   2 !    9.6   0.0    0.0018       1.5       7      32 ..      41      66 ..      36      67 .. 0.92
   3 !    7.7   0.0    0.0072       6.2      10      32 ..      78     100 ..      75     101 .. 0.88
   4 ?    1.7   0.0      0.58   4.9e+02      10      32 ..     112     134 ..     104     135 .. 0.84
   5 ?    6.5   0.0     0.017        15       1      31 [.     137     167 ..     137     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.08
                HHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6 12 klgdtdkAlealerlikeYPdS 33
                + ++ ++A++ ++ ++++ Pd+
  AJA92173.1 13 E-KKFQDAIKKYNIILDKEPDN 33
                3.4999**************95 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                HHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  7 alsyrklgdtdkAlealerlikeYPd 32
                ++s+ kl+++++Al  ++++++  P+
  AJA92173.1 41 GYSLSKLKKYSDALVCYDKFLQINPN 66
                88999999****************98 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0072
                 HHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                 +rk+g+  kA+ + ++l+k+ Pd
  AJA92173.1  78 FRKTGEFHKAVGICDELLKNNPD 100
                 56699*****************8 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.58
                 HHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  10 yrklgdtdkAlealerlikeYPd 32 
                 ++kl++ +++ ++  +l + YP+
  AJA92173.1 112 LKKLNRFAESNTICMKLADIYPE 134
                 566789999999999*******7 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.017
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlikeYP 31 
                 ++ly +a  ++klg++++   +l++ ++  P
  AJA92173.1 137 EVLYEMASNFLKLGNKEQFFNLLQKAVNALP 167
                 68**********99***99999999888766 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.028        24      15      35 ..      14      34 ..      13      38 .. 0.86
   2 !   14.0   0.0   4.6e-05      0.04      12      35 ..      45      68 ..      41      71 .. 0.91
   3 !    7.8   0.0     0.004       3.4      13      33 ..      80     100 ..      79     102 .. 0.94
   4 ?   -0.1   0.0       1.2     1e+03      13      37 ..     114     138 ..     113     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.028
                T-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPenr 35
                +++++A +  + +L +EP+n 
  AJA92173.1 14 KKFQDAIKKYNIILDKEPDNL 34
                578899999***********7 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.6e-05
                HHHT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 12 yklgeYseArryvdalLeiEPenr 35
                 kl++Ys+A+ + d +L+i P+ +
  AJA92173.1 45 SKLKKYSDALVCYDKFLQINPNDK 68
                59*******************976 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.004
                 HHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                 k ge+ +A   +d lL+  P+
  AJA92173.1  80 KTGEFHKAVGICDELLKNNPD 100
                 88****************997 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.2
                 HHT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                 kl ++ e+   +  l  i Pen  +
  AJA92173.1 114 KLNRFAESNTICMKLADIYPENGEV 138
                 8899999999999999999999765 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-07   9.5e-05       4      67 ..       7      67 ..       4      68 .. 0.88
   2 ?    5.0   0.0     0.047        41       6      52 ..      77     120 ..      72     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-07
      TPR_16  4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                ++ ++  ++++dA++ +++ l++    Pd+  Al+++g ++ +++ + +A+  y++ l+  p++
  AJA92173.1  7 GNRLFLEKKFQDAIKKYNIILDKE---PDNLIALNNKGYSLSKLKKYSDALVCYDKFLQINPND 67
                566666789***************...***********************98888888888775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.047
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52 
                 ++++ g++ +A+   +++lk++   Pd   Al+++ +++ +++r+ae
  AJA92173.1  77 LFRKTGEFHKAVGICDELLKNN---PDEIIALYHKLRILKKLNRFAE 120
                 56788899999999999*****...**********999999999998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.038        32      15      38 ..      14      37 ..       7      43 .. 0.84
   2 ?    5.5   0.0     0.045        38      11      40 ..      44      73 ..      40      77 .. 0.85
   3 !   11.0   0.0   0.00072      0.62      10      42 ..      77     109 ..      74     112 .. 0.86
   4 ?    2.6   0.0      0.36   3.1e+02       3      42 ..     104     143 ..     102     145 .. 0.87
   5 ?    1.7   0.0      0.71   6.1e+02       2      32 ..     137     167 ..     136     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.038
      TPR_14 15 GdpdeAiallrralalaPddaeaw 38
                 ++++Ai+ ++ +l++ Pd++ a+
  AJA92173.1 14 KKFQDAIKKYNIILDKEPDNLIAL 37
                6799***************98765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.045
      TPR_14 11 llalGdpdeAiallrralalaPddaeawll 40
                l  l ++ +A+ ++++ l+ +P+d ++++ 
  AJA92173.1 44 LSKLKKYSDALVCYDKFLQINPNDKTVLIN 73
                66788999****************998865 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00072
      TPR_14  10 allalGdpdeAiallrralalaPddaeawllla 42 
                 +++  G++ +A+ +++++l+ +Pd+  a+++  
  AJA92173.1  77 LFRKTGEFHKAVGICDELLKNNPDEIIALYHKL 109
                 67889*******************998887765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.36
      TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                 al+  +++l  l +++e+ +++ ++ + +P++ e+++++a
  AJA92173.1 104 ALYHKLRILKKLNRFAESNTICMKLADIYPENGEVLYEMA 143
                 5677788999999999999999999999******999998 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.71
      TPR_14   2 eallalaeallalGdpdeAiallrralalaP 32 
                 e+l+++a+ +l lG+ ++  +ll++a+ + P
  AJA92173.1 137 EVLYEMASNFLKLGNKEQFFNLLQKAVNALP 167
                 578999999*******999999999986665 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   4.2e-05     0.036       1      40 [.       7      46 ..       7      48 .. 0.94
   2 !   11.7   0.0   0.00019      0.16       2      27 ..      42      67 ..      41      73 .. 0.85
   3 ?   -1.0   0.0       1.7   1.4e+03      28      40 ..     129     141 ..     124     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
      TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                G+ ++   k+ +Ai++Y+  l+  Pdn  a++n G+ + k
  AJA92173.1  7 GNRLFLEKKFQDAIKKYNIILDKEPDNLIALNNKGYSLSK 46
                99*********************************98766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
      TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdn 27
                + + ++ ky +A+ +Y k l+++P++
  AJA92173.1 42 YSLSKLKKYSDALVCYDKFLQINPND 67
                5666789*****************98 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.7
      TPR_11  28 aeayynLGlayyk 40 
                 a++y + G+++y+
  AJA92173.1 129 ADIYPENGEVLYE 141
                 4555555555554 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.3   0.00095      0.81      33      81 ..      10      59 ..       7      60 .. 0.93
   2 !   17.0   0.1   5.9e-06    0.0051       4      74 ..      49     120 ..      48     128 .. 0.87
   3 ?    0.6   0.0      0.76   6.5e+02      20      50 ..     133     164 ..     122     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                HHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3 33 lylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81
                l+l ++++ A++ ++   ++++ +l ++  ++ +l kLkky +A+ +++k
  AJA92173.1 10 LFLEKKFQDAIKKYNIIlDKEPDNLIALNNKGYSLSKLKKYSDALVCYDK 59
                8999*********99999999************************99887 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.9e-06
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74 
                 +y +A+ ++++ l+ ++++   +  +   + ++g++++A  +++++ k n+  + ++y + + l kL+++ e
  AJA92173.1  49 KYSDALVCYDKFLQINPNDKTVLINKISLFRKTGEFHKAVGICDELlKNNPDEIIALYHKLRILKKLNRFAE 120
                 799**********5555555556667999**************************************99988 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.76
                 H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.S CS
      ANAPC3  20 tespedayllAlclylngqykrAyellrka.k 50 
                 +e+ e +y  A  ++++g+ ++ ++ll+ka +
  AJA92173.1 133 PENGEVLYEMASNFLKLGNKEQFFNLLQKAvN 164
                 45555567778888888888888888888755 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0029       2.4      19      71 ..      15      67 ..       8      71 .. 0.89
   2 !   11.9   0.1   8.9e-05     0.076       8     104 ..      72     167 ..      68     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                HHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
       NARP1 19 kleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71
                k ++A+++ +   ++  D+l  +++k+  l kL+++++A   y + l+ np++
  AJA92173.1 15 KFQDAIKKYNIILDKEPDNLIALNNKGYSLSKLKKYSDALVCYDKFLQINPND 67
                567788888888888899********************************986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.9e-05
                 HHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHH.HHHHHHHT..SSS-HHHHHHHHHHTTTS-T CS
       NARP1   8 LyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskY.yeglekakklskedeeallalydelaekyp 104
                 + k+++++++g+  +A+   +e  k+  D++  +  k ++l kL+r++e++++  +L +  pen +  ye   + +kl ++  e+  +l++++++++p
  AJA92173.1  72 INKISLFRKTGEFHKAVGICDELLKNNPDEIIALYHKLRILKKLNRFAESNTICMKLADIYPENGEVlYEMASNFLKLGNK--EQFFNLLQKAVNALP 167
                 5688999*********************************************************87515555555554444..666666666665554 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00066      0.57      68     120 ..      11      63 ..       1      66 [. 0.90
   2 !    6.3   0.0    0.0098       8.4      69     120 ..      80     131 ..      61     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00066
     DUF4919  68 lseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                   e++++++i+  + +l+k+P +l +ln+  y++++l+k + a   ++++ ++
  AJA92173.1  11 FLEKKFQDAIKKYNIILDKEPDNLIALNNKGYSLSKLKKYSDALVCYDKFLQI 63 
                 56899**************************************9999999876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0098
     DUF4919  69 seeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkl 120
                 ++ e+++++ +  e+lk+nP ++ +l+  + ++k+l++  e++ +  +l+ +
  AJA92173.1  80 KTGEFHKAVGICDELLKNNPDEIIALYHKLRILKKLNRFAESNTICMKLADI 131
                 5678999999***************************999999988888776 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       4.1   3.5e+03      14      22 ..      15      23 ..      13      33 .. 0.76
   2 ?    5.3   0.0     0.028        24       1      28 [.      36      63 ..      36      69 .. 0.88
   3 !    7.8   0.0    0.0043       3.7       7      32 ..      76      99 ..      71     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.1
       TPR_7 14 dyeeAiely 22
                ++++Ai+ y
  AJA92173.1 15 KFQDAIKKY 23
                6899*9988 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLal 28
                aL+n +   s+l +y++A+ +y + L++
  AJA92173.1 36 ALNNKGYSLSKLKKYSDALVCYDKFLQI 63
                799*******************997655 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0043
       TPR_7  7 rlysrlGdyeeAielyeqsLaltkdp 32
                +l+++ G++ +A++++ +   l + p
  AJA92173.1 76 SLFRKTGEFHKAVGICDE--LLKNNP 99
                5899************99..666555 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0079       6.7       4      32 ..      35      63 ..      32      70 .. 0.84
   2 ?    4.7   0.0     0.044        37      26      64 ..      84     121 ..      68     134 .. 0.79
   3 ?    2.9   0.0      0.15   1.3e+02      12      74 ..     111     165 ..     100     168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0079
      TPR_12  4 talnnlaavlrrlgrydeAlellekalei 32
                +alnn +  l +l++y +Al +++k l+i
  AJA92173.1 35 IALNNKGYSLSKLKKYSDALVCYDKFLQI 63
                68889999999999999999999987776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
      TPR_12  26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeA 64 
                 ++ka+ i+ +ll +++p+++++l+   r++ +l+r++e 
  AJA92173.1  84 FHKAVGICDELL-KNNPDEIIALYHKLRILKKLNRFAES 121
                 677777776665.78888888888888888888888875 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
      TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                 +l +l r++e+ +++ k  +i+     p++    ++l+ ++  +++lg+ e+  +ll++a+++
  AJA92173.1 111 ILKKLNRFAESNTICMKLADIY-----PEN---GEVLYEMASNFLKLGNKEQFFNLLQKAVNA 165
                 5667778888888888888888.....444...556777777777777777666666666655 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.11      44     124 ..      28     123 ..      12     132 .. 0.84
   2 ?    1.2   0.0      0.54   4.6e+02      70     104 ..     137     173 ..     126     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                      -S-GGGTS---HHHHHHHHHHHTT...............SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
  Alkyl_sulf_dimr  44 dgnPanLnplppeekakrlvelmG...............gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                      d +P nL  l+++  +   ++  +               ++  +++k++  +k g+++ a+ +++ l+ ++p++  a   k ++l++l ++aes
       AJA92173.1  28 DKEPDNLIALNNKGYSLSKLKKYSdalvcydkflqinpnDKTVLINKISLFRKTGEFHKAVGICDELLKNNPDEIIALYHKLRILKKLNRFAES 121
                      77777777777777665555555556667888888888899999999**********************************************9 PP

                      HH CS
  Alkyl_sulf_dimr 123 at 124
                       t
       AJA92173.1 122 NT 123
                      86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.54
                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT..-HH CS
  Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpe..nae 104
                      e + e+a++ lk g+ +   +ll+++v a p+  n++
       AJA92173.1 137 EVLYEMASNFLKLGNKEQFFNLLQKAVNALPNlkNKS 173
                      5678999999999999999999999999966522332 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042      0.36     181     250 ..      14      83 ..      12      89 .. 0.93
   2 ?    3.0   0.1     0.067        58     188     230 ..     123     165 ..     108     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT- CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgk 250
                 +k+qdA   ++ + +k + + + ln k     +l++y +A     + L+ +++d+ +LiN + +  ++g 
  AJA92173.1  14 KKFQDAIKKYNIILDKEPDNLIALNNKGYSLSKLKKYSDALVCYDKFLQINPNDKTVLINKISLFRKTGE 83 
                 5899**********************************************************99988885 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.067
                 HHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
  Coatomer_E 188 yifqelsekykstplllngkAvvslllgryeeAeslLkeaLdk 230
                  i   l++ y+++  +l  +A   l+lg+ e+  +lL++a + 
  AJA92173.1 123 TICMKLADIYPENGEVLYEMASNFLKLGNKEQFFNLLQKAVNA 165
                 5677899*******************************99986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0066       5.6       4      27 ..      36      59 ..      34      64 .. 0.88
   2 ?   -0.4   0.0       1.3   1.1e+03      16      36 ..      82      95 ..      77     101 .. 0.57
   3 ?   -2.9   0.0       8.2     7e+03      11      22 ..     111     122 ..     110     131 .. 0.76
   4 ?    1.9   0.0      0.25   2.2e+02      14      30 ..     148     164 ..     139     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0066
      TPR_10  4 slnNLanalrqrgrydeAeallee 27
                +lnN +  l+++++y +A+  +++
  AJA92173.1 36 ALNNKGYSLSKLKKYSDALVCYDK 59
                89*****************99887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
      TPR_10 16 grydeAealleealairrrll 36
                g++++A       + i+ +ll
  AJA92173.1 82 GEFHKA-------VGICDELL 95
                555555.......55555555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8.2
      TPR_10  11 alrqrgrydeAe 22 
                 +l +++r++e+ 
  AJA92173.1 111 ILKKLNRFAESN 122
                 678899999875 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.25
      TPR_10  14 qrgrydeAealleeala 30 
                 ++g+ ++  +ll++a++
  AJA92173.1 148 KLGNKEQFFNLLQKAVN 164
                 6899***********97 PP

>> Virulence_fact  Virulence factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.008       6.8      16      43 ..       5      36 ..       1      43 [. 0.83
   2 ?    3.4   0.0      0.11        90      45      77 ..      79     111 ..      65     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.008
  Virulence_fact 16 eeearveLperFeqAidraam....asdnyia 43
                    +e +r  L+++F++Ai++ +     + dn+ia
      AJA92173.1  5 NEGNRLFLEKKFQDAIKKYNIildkEPDNLIA 36
                    678999***********998888777777776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
  Virulence_fact  45 rkwaeqgvrygdleeiaeevaeeleaaYpeerL 77 
                     rk+ e++++ g  +e  ++  +e+ a Y + r+
      AJA92173.1  79 RKTGEFHKAVGICDELLKNNPDEIIALYHKLRI 111
                     888999**********************99886 PP

>> USP8_dimer  USP8 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.3   1.1e+03      75     104 ..      14      47 ..       8      54 .. 0.62
   2 ?   12.7   0.4   0.00013      0.11      10      76 ..     110     174 ..      98     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
  USP8_dimer  75 sdykekkasvkellgdkkankvildk....lekL 104
                 +++++  ++++++l ++ +n ++l++    l kL
  AJA92173.1  14 KKFQDAIKKYNIILDKEPDNLIALNNkgysLSKL 47 
                 4566666777777777766666665544444444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
  USP8_dimer  10 ssledLkkladklkkdkknksikrllrsaeklfkkAeeyrlegdeEkAYvlymkylnllelIrkksd 76 
                   l++L+  a+++  ++  k  +++ +++e l+++A++  + g++E+ + l+ k +n l  +++ks+
  AJA92173.1 110 RILKKLNRFAESN--TICMKLADIYPENGEVLYEMASNFLKLGNKEQFFNLLQKAVNALPNLKNKSK 174
                 4566777766663..56666667799*******************************9977777764 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     0.001      0.86       4      65 ..       9      70 ..       7      75 .. 0.92
   2 ?   -0.7   0.0       1.9   1.6e+03      10      29 ..      83     102 ..      76     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.001
       TPR_9  4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                ++  e++++ a++ ++ +l   Pd    +   G  l +l  +s Al + + +l+++p++ ++
  AJA92173.1  9 RLFLEKKFQDAIKKYNIILDKEPDNLIALNNKGYSLSKLKKYSDALVCYDKFLQINPNDKTV 70
                56668999*************************************************99876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
       TPR_9  10 dweralavverllllaPddp 29 
                 ++ +a  +++ ll  +Pd++
  AJA92173.1  83 EFHKAVGICDELLKNNPDEI 102
                 56778888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1359.75
//
Query:       AJA92174.1  [L=245]
Description: putative orotidine 5'-phosphate decarboxylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-23   82.3   0.0    4.5e-23   82.0   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   2.5e-27   4.5e-23       4     223 ..      18     237 ..      15     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.5e-27
                 EEEE-SSSH.....HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEEGTGH CS
   OMPdecase   4 clalDvata.....relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsarikewadivtvhavaG 97 
                 +la D++ +      + l+  + + ++ + +K++  l+ + + ++ + k+ + a++ g   ++D+K+ DIGnt     +        + d+v+v++ +G
  AJA92174.1  18 ILANDYDPKtpnieSKTLKNMKLLSDYLCGIKINFHLLLQLD-KKQISKINKVAHDSGLQCIADIKLNDIGNTNIITTE---NLWNMGFDAVIVNPIMG 112
                 566666665566667889999999******************.66899999999999*****************99998...678************** PP

                 HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH...H..SHHHHHHHHHHHHHHHTTESEEECCCHTH......HHHHH.TTCSCEEEHHHTTEEEE CS
   OMPdecase  98 kasvkalaeaaekwgnrgllilaqmsskgnlmlqe...k..gytqacveaarehkaedfvmGfvaqetln......ateed.addfihltpgigleqgg 184
                 k+s+k l+e   k + +g++ l+ ms +++    e   k  +  q++++   + + +  v+G+++++t +      +  ++   ++  + pgi      
  AJA92174.1 113 KKSLKNLVELSHKKN-KGVISLCHMSAPEAKLSYEleiKnrSKNQQLYQLFLDWALSTHVDGIIVGATYPkiisycK--KSvRGKLSLFSPGI------ 202
                 *************96.9*************988888553789999999999999999***********995443211..11334555555555...... PP

                 ECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
   OMPdecase 185 dgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                    g q   p k+++  g+d++ivGR Il++++p ++++
  AJA92174.1 203 ---GTQGGSPSKAKK-LGSDYLIVGRTILNSKNPLKTTK 237
                 ...555555566655.68****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1701.47
//
Query:       AJA92175.1  [L=240]
Description: precorrin-2 C(20)-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-53  181.7   0.0    1.9e-53  181.5   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.0   1.1e-57   1.9e-53       2     212 ..       4     222 ..       3     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1.1e-57
  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeel.....eleapmgkekepleeayeeiaealaealragkdVvllvs 87 
                   l+++GvGpGdp+llTv+A++a+++ad +++++s+      al+ +  l+++ +     +l +pm+k+k+ le++++e+++++ae++ +gk+Vv+l+ 
    AJA92175.1   4 LTGIGVGPGDPDLLTVKAVKAIQNADTIMCPASKedrpsiALSVVDSLIDKSKnqeivKLIFPMTKDKDILEAHWKENSKIMAEKVLSGKNVVYLTV 100
                   89**************************9999667767888888888888877999***************************************** PP

  TP_methylase  88 GDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkaprklaelaelLkea. 183
                   GDP++y+t+++++++++++++++++ viPG+ s+ + a+++g++++eg e++s++ p+++  + + ++++++n + lv+lk++r +++++el +e+ 
    AJA92175.1 101 GDPYLYSTWIYMHREISQNHPEMKINVIPGIVSMFTFASKVGVSIAEGAEKVSII-PSCY--DLSSVKEIAKNSEVLVFLKDGRYFDQVIELVRESg 194
                   *******************************************************.9999..**********************************8 PP

  TP_methylase 184 lyddttpvavveragtedervvrgtleel 212
                   ++dd    a+++++gt++e +++ +l+++
    AJA92175.1 195 FPDDS-IFAIGQDLGTDKEIIRKLRLGDV 222
                   88866.****************9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1751.96
//
Query:       AJA92176.1  [L=258]
Description: D-aminoacyl-tRNA deacylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-62  211.1   0.0    3.6e-62  209.5   0.0    1.6  2  tRNA_deacylase  D-aminoacyl-tRNA deacylase


Domain annotation for each model (and alignments):
>> tRNA_deacylase  D-aminoacyl-tRNA deacylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0     0.063   1.1e+03     146     162 ..      10      26 ..       4      46 .. 0.68
   2 !  209.5   0.0     2e-66   3.6e-62       3     205 .]      55     256 ..      53     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.063
                     EEEEEEE-GGGGGG--H CS
  tRNA_deacylase 146 vavGhilskyaleelke 162
                      a Gh ++k+  +++++
      AJA92176.1  10 DAAGHNMAKHISQNMEK 26 
                     45678888877776665 PP

  == domain 2  score: 209.5 bits;  conditional E-value: 2e-66
                     ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS-----S-EEEEEEEESHHH CS
  tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGPtelkvPslFvEiGSteee 97 
                      d+d ++flS+H++esg+ +LT+H tGn++ea++GG+ +ela+++P+l+k++l++l + +e+ ++fe+t+EatHHGPt+lk+Ps+FvEiG+t+ +
      AJA92176.1  55 YDYDGFVFLSKHAAESGTLALTCHSTGNFNEAKFGGNAKELAIPYPNLQKKYLKTLWENRESFSDFEITIEATHHGPTHLKKPSIFVEIGTTDLQ 149
                     6899******************************************************************************************* PP

                     HT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGGGGG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHH CS
  tRNA_deacylase  98 WkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskyaleelkeevikqaleksegadvalidkkslkseqkea 192
                     W+de+ ++ va++vle+le+ +++ + ++++GG+HY+++ftk +l  ++a+G +++k+ale l+ +++++++++++ga++al+d+ksl ++qk++
      AJA92176.1 150 WNDEQLCSSVAQLVLETLEKPSDSHPFAICFGGTHYSEKFTKELLFGKYALGTVMPKHALEFLNPDLFEHIITQNNGAEAALLDWKSL-GKQKQT 243
                     **************************************************************************************99.899999 PP

                     HHHHHHHHT-EEE CS
  tRNA_deacylase 193 ieelleelgievl 205
                     +++ll+ +++ev+
      AJA92176.1 244 LIDLLSTTKLEVI 256
                     *****99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1847.65
//
Query:       AJA92177.1  [L=458]
Description: signal recognition particle-docking protein FtsY [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-70  234.3   1.9    1.2e-69  233.9   1.9    1.2  1  SRP54            SRP54-type protein, GTPase domain
    1.3e-10   41.3   3.8      4e-10   39.8   3.8    1.9  1  SRP54_N          SRP54-type protein, helical bundle domain
    1.1e-07   31.8   0.1    1.6e-07   31.3   0.1    1.2  1  AAA_30           AAA domain
    3.2e-06   26.8   0.8    5.7e-06   26.0   0.8    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    5.2e-05   22.6   0.1    9.2e-05   21.8   0.1    1.3  1  Zeta_toxin       Zeta toxin
     0.0002   21.4   0.7     0.0064   16.5   0.5    2.9  2  B12-binding      B12 binding domain
    0.00022   21.5   0.0    0.00098   19.4   0.0    2.0  1  AAA_22           AAA domain
     0.0008   19.6   0.1     0.0018   18.4   0.0    1.6  1  AAA_33           AAA domain
      0.003   17.1   1.2     0.0034   16.9   0.1    1.5  2  KdpD             Osmosensitive K+ channel His kinase sensor d
     0.0036   17.6   0.1     0.0062   16.9   0.1    1.4  1  AAA_19           AAA domain
     0.0043   17.0   1.0       0.23   11.4   1.0    2.4  1  NTPase_1         NTPase
      0.007   16.1   0.2       0.11   12.2   0.1    2.7  3  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
     0.0073   15.5   0.2      0.011   14.9   0.2    1.2  1  PIF1             PIF1-like helicase
  ------ inclusion threshold ------
      0.012   16.1   0.2      0.035   14.5   0.1    1.9  1  AAA              ATPase family associated with various cellul
      0.013   15.3   0.1       0.17   11.6   0.0    2.1  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.014   15.0   0.0      0.072   12.8   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.015   15.5   0.0      0.027   14.7   0.0    1.4  1  AAA_28           AAA domain
      0.018   15.5   0.2      0.052   14.1   0.1    1.7  1  ABC_tran         ABC transporter
      0.018   14.3   0.1      0.029   13.6   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.019   15.4   0.1       0.05   14.0   0.1    1.7  1  AAA_17           AAA domain
      0.023   14.2   0.2       0.08   12.5   0.2    1.9  1  AAA_7            P-loop containing dynein motor region
       0.03   14.2   0.2      0.068   13.0   0.2    1.5  1  TK               Thymidine kinase
      0.032   14.1   0.5       0.12   12.3   0.2    2.0  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.035   14.5   0.0       0.06   13.7   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.038   14.0   1.6      0.045   13.8   0.2    1.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.039   14.0   0.0       0.12   12.4   0.0    1.8  1  AAA_14           AAA domain
      0.041   13.1   0.0      0.075   12.2   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.046   13.4   0.0      0.096   12.4   0.0    1.4  1  AAA_24           AAA domain
      0.062   13.2   0.0       0.16   11.9   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
      0.071   13.1   0.2       0.46   10.4   0.0    2.2  2  SPOUT_MTase      Predicted SPOUT methyltransferase
       0.11   12.5   0.9       0.28   11.1   0.9    1.8  1  ResIII           Type III restriction enzyme, res subunit
       0.12   12.4 104.1       0.15   12.0  56.6    2.5  2  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
       0.42   10.7   3.2       0.38   10.9   0.8    2.2  2  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.9   1.9   2.3e-72   1.2e-69       2     195 ..     106     299 ..     105     300 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.9 bits;  conditional E-value: 2.3e-72
                 EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHH CS
       SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndke 100
                  +i++vG++G+GKTt+laK+a++lk+e+ +v+++aaDt+Ra+A+eQL++++++l+ ++i+++ ++dpaavak+av  a+++k+d+vlvDTaGr+q+ ++
  AJA92177.1 106 FIIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGAIEQLREHTNRLNLKIIAQNYGSDPAAVAKDAVLYAQSHKVDCVLVDTAGRMQTSSN 204
                 799************************************************************************************************ PP

                 HHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
       SRP54 101 lmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                 lme+++ki kvv+pd +++v d+++g+++v+qa++F+++v+++  iltk D+da+gGaalsi++ + +Pi+++gvG++++d+ +f++++++++++
  AJA92177.1 205 LMEQIAKITKVVNPDMKIFVGDSLAGNDTVNQAREFHKQVKFDCSILTKSDADARGGAALSIVKVTSSPIIYVGVGQEYDDIVKFSKKTFLENVF 299
                 ******************************************************************************************99876 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   3.8   7.4e-13     4e-10       1      75 []       5      76 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 7.4e-13
                HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
     SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                L+k +++a +++s+ + ++e+d+e++l ele  Lle+DV+ +v +++ +++k+k +g +++ +k+ +++ vk++L
  AJA92177.1  5 LKKAFSNASTGFSE-KDLNEKDIEDVLFELEINLLESDVATEVIDSIKDSLKEKIIG-SRV-EKKNIQNFVKQSL 76
                34455555555433.45****************************************.777.9999**9999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   2.9e-10   1.6e-07      19     124 ..     106     226 ..      86     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.9e-10
      AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa...eelg.ieastiakllkrlk.............grarlepgtllivDEagmv 100
                  + v +G  GtGKtt+l+++++++++++++v+++A     A +++   e+++ ++ + ia+                     a+ ++ ++++vD ag +
  AJA92177.1 106 FIIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGAIEqlrEHTNrLNLKIIAQN----YgsdpaavakdavlY-AQSHKVDCVLVDTAGRM 199
                 467899**********************9999988887777666611143332222222222....134446666776642.345566*********99 PP

      AAA_30 101 ..dtkqlaallkaaekag.akvilvGD 124
                   +++ +++++k+ +  +    i+vGD
  AJA92177.1 200 qtSSNLMEQIAKITKVVNpDMKIFVGD 226
                 566667888887777654444568888 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.8     1e-08   5.7e-06       2     152 ..     107     256 ..     106     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1e-08
                 EEEEEESTTCCHHHHHHHHHCT--SS-EEEEES..S-SSCHCCCCCCHCCCT.....EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEEECT.T CS
        cobW   2 vtvltGflGsGKTtLlnhllenraglklavivN..efgevsiDaellretgve....ivelenGciCctlredllkelealeereerldviliEttG.l 93 
                 ++v++G  G+GKTt l ++ +  +++k  v++   + +  +  ++l ++t+      i+  + G  + ++++d++       ++++++d++l+ t G +
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAaaDTYRAGAIEQLREHTN-RlnlkIIAQNYGSDPAAVAKDAVLY-----AQSHKVDCVLVDTAGrM 199
                 6899****************8888888887775115555444444443332.23566999999**999999988754.....34458**********66 PP

                 TTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
        cobW  94 aePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                  +   ++ +  ++++ ++ d++++v D+ +  +++ ++++++++q+++ d+ +l+K D 
  AJA92177.1 200 QTSSNLMEQIAKITKVVNPDMKIFVGDSLAG-NDTVNQAREFHKQVKF-DCSILTKSDA 256
                 66677788899*****************776.8999**********98.9999999996 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.7e-07   9.2e-05       8     118 ..      96     210 ..      91     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
  Zeta_toxin   8 kk.ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe.lhPeyeeilka.dpkkaseltqkdaselvekllqeaiengyniiveg 102
                 ++  +s+++P +i+ +G  G GK++ ++++++ l+ ++ +vv   +D++R+  + + +e+ +  + k  +++  +d   +++ ++ +a +++++ ++  
  AJA92177.1  96 INeKKSSNQPFIIVFVGINGTGKTTSLAKVANMLKnEKFSVVIAAADTYRAgAIEQLREHTNRlNLKIIAQNYGSDPAAVAKDAVLYAQSHKVDCVLVD 194
                 3334589***************************966667777789****8568888888887688889999999999****************88777 PP

  Zeta_toxin 103 tlrspdvvkklaealk 118
                 t    ++ ++l+e+++
  AJA92177.1 195 TAGRMQTSSNLMEQIA 210
                 7777777777766655 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.79   4.3e+02      24      89 ..      54     113 ..      38     120 .. 0.82
   2 !   16.5   0.5   1.2e-05    0.0064      10      87 ..     115     225 ..     106     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.79
  B12-binding  24 lrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGa 89 
                  l++     +++g  ve+++i + +++   +++  ++  ++   + k+ ++++k+ +  +++v+ G+
   AJA92177.1  54 LKE-----KIIGSRVEKKNIQNFVKQSLIEFISETF-DNAGQIDLKDRINEKKSSNQPFIIVFVGI 113
                  444.....7999999999999999999999999999.99999999999999999988888888775 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
  B12-binding  10 gdlhplGlavlaaalrdagfeVqllganven...............................edivaairaekpdvvglSal..ltsqleavkelvel 74 
                  g   +  la +a++l+++ f+V++  a++                                 +d v  ++++k+d+v++ +   ++++ + ++++++ 
   AJA92177.1 115 GTGKTTSLAKVANMLKNEKFSVVIAAADTYRagaieqlrehtnrlnlkiiaqnygsdpaavaKDAVLYAQSHKVDCVLVDTAgrMQTSSNLMEQIAKI 212
                  55666778889999999999888885555555556666666777777777777888888899999999***********77667************** PP

  B12-binding  75 lkrirprvkvvvG 87 
                   k ++p++k++vG
   AJA92177.1 213 TKVVNPDMKIFVG 225
                  ************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.8e-06   0.00098       7     115 ..     107     212 ..     102     228 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-06
      AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.....erlsseellealeqalraravielliiDEa 100
                 i+v +G  GtGKTt+l+++++ l++e      + +   v ++++t ++   ++l + +++ + +     ++ +  ++ +    ++++++v  ++++D a
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNE------KFS--VVIAAADTYRAGAIEQLREHTNRLNLKiiaqnYGSDPAAVAKDAVLYAQSHKV-DCVLVDTA 196
                 7899*******************644......333..33333333333334444444443333344444445555555444455555555.78888888 PP

      AAA_22 101 qhlr.seealeeLrsl 115
                  ++  s +++e++ ++
  AJA92177.1 197 GRMQtSSNLMEQIAKI 212
                 8886545555555443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-06    0.0018       2      79 ..     108     196 ..     107     248 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
      AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdqqskt.......dytrvldrlyqilnelarkalsagrnvildatn 79 
                 +++vG +G+GK+t + ++++ l+     +v+ + dt+r    ++ +++++         ++  ++  +  ++ +  a+s++ +++l  t 
  AJA92177.1 108 IVFVGINGTGKTTSLAKVANMLKnekfsVVIAAADTYRAGAIEQLREHTNrlnlkiiA-QNYGSDPAAVAKDAVLYAQSHKVDCVLVDTA 196
                 89***************98888888897777788999885555444444433343321.2222334446677777888999998887773 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       8.6   4.7e+03     122     144 ..      42      65 ..      21      79 .. 0.54
   2 !   16.9   0.1   6.3e-06    0.0034       7      96 ..     109     201 ..     106     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.6
        KdpD 122 vnvqhleslndvve.kitgvrvre 144
                 v  + ++s++d ++ ki g rv++
  AJA92177.1  42 VATEVIDSIKDSLKeKIIGSRVEK 65 
                 444445555554433444444444 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.3e-06
        KdpD   7 iflGaapGvGktyamLeeaqelkeegvdvviglvethgrketeallegleviprkeveyk.gkeleeldldaila...rkpevvlvDelahtna 96 
                 +f+G ++G Gkt ++ + a+ lk+e   vvi++ +t +   +e+l e+ + ++ k ++++ g+    +  da+l    +k + vlvD  +  ++
  AJA92177.1 109 VFVG-INGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGAIEQLREHTNRLNLKIIAQNyGSDPAAVAKDAVLYaqsHKVDCVLVDTAGRMQT 201
                 5666.58*********************************************999876543778888999999963225667899998776654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.1e-05    0.0062      12      69 ..     106     174 ..      94     257 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
      AAA_19  12 vllv.taGpGtGKTrvlkhivallvelggvkpeeillvaftgr..Aakelrerlaalgae...........a 69 
                  ++v ++  GtGKT+ l ++ ++l++++      ++++a t r  A ++lre ++ l+++           a
  AJA92177.1 106 FIIVfVGINGTGKTTSLAKVANMLKNEKF---SVVIAAADTYRagAIEQLREHTNRLNLKiiaqnygsdpaA 174
                 444415668*********99999999984...4566666677622689******988888433333333320 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   1.0   0.00042      0.23       4      31 ..     110     137 ..     107     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                 EE--TTSSHHHHHHHHHHHH...GGGEE CS
    NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvg 31 
                   G  G+GKtT + kv+++lk++ ++v 
  AJA92177.1 110 FVGINGTGKTTSLAKVANMLKNEKFSVV 137
                 56889*****************999874 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0002      0.11       2      48 ..     123     169 ..     122     187 .. 0.90
   2 ?   -1.6   0.0       3.7     2e+03      16      37 ..     222     243 ..     207     251 .. 0.62
   3 ?    0.1   0.0       1.1   6.2e+02       4      26 ..     263     285 ..     261     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                   HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG CS
  TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmg 48 
                   +k+a++lk+ k  v+++   + r+ga e+lre  ++l++ ++ +  g
    AJA92177.1 123 AKVANMLKNEKFSVVIAAADTYRAGAIEQLREHTNRLNLKIIAQNYG 169
                   79************************************999876655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.7
                   EEE-CHHCHTTGHHHHHHHHHH CS
  TPP_enzyme_M  16 ilvGggvarsgaseelrelaek 37 
                   i+vG   a +++ +++re+ ++
    AJA92177.1 222 IFVGDSLAGNDTVNQAREFHKQ 243
                   5555555555555555555544 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                   HHHHHHH-SSEEEEE-CHHCHTT CS
  TPP_enzyme_M   4 aaellkaakrpvilvGggvarsg 26 
                   a++++k  + p+i+vG g  +++
    AJA92177.1 263 ALSIVKVTSSPIIYVGVGQEYDD 285
                   6778888999******9987554 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.1e-05     0.011       6     125 ..      89     212 ..      86     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                 HHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHH..HHHTSCCCHHHHHC CS
        PIF1   6 QkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestc..kikrgsklaellkk 102
                 Q    d+i e  +++++ ++ + G  GtgKt  + ++ ++l++e+  v+  A     a  +e+ r    r ++ + +++  +   +++++  l  + +k
  AJA92177.1  89 QIDLKDRINEKKSSNQPFIIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGAIEQLREHTNRLNLKIIAQNYGSDpaAVAKDAVLYAQSHK 187
                 66777899999999******************************9999999988888999999888888888887766654333489999999999999 PP

                 -SEEEEECGGGSB..HHHHHHHHHH CS
        PIF1 103 tsliiwDEapmve..recfealdrt 125
                 ++ +++D a  ++   +++e++ ++
  AJA92177.1 188 VDCVLVDTAGRMQtsSNLMEQIAKI 212
                 9999999886543114555655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.4e-05     0.035       2      34 ..     109     143 ..     108     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-05
                 EEESSTTSSHHHHHHHHHHHHTHE.E.EEEETTTC CS
         AAA   2 llyGppGtGKTllakavakelgve.f.leisgsel 34 
                 +++G  GtGKT+    va+ l+ e f + i +++ 
  AJA92177.1 109 VFVGINGTGKTTSLAKVANMLKNEkFsVVIAAADT 143
                 799******************74412233333333 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.49   2.7e+02       3      31 ..     114     142 ..      92     148 .. 0.84
   2 ?   11.6   0.0   0.00032      0.17      97     158 ..     182     244 ..     170     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.49
      CLP1_P   3 kdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                 + +GK+T  +  +N++ +++ ++v+  +D
  AJA92177.1 114 NGTGKTTSLAKVANMLKNEKFSVVIAAAD 142
                 57899999999999999988888877666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00032
      CLP1_P  97 enkkakasgliIntpGwvkglg..aellleliealepdvvvvldqeellnelkrdlplskvkvv 158
                   +++k ++++++t G ++     +e + +++++++pd+ ++++++   n+  ++++ ++ k v
  AJA92177.1 182 YAQSHKVDCVLVDTAGRMQTSSnlMEQIAKITKVVNPDMKIFVGDSLAGNDTVNQAR-EFHKQV 244
                 55788999**********9774357********************999999999998.544444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.8   1.5e+03      54      84 ..      31      59 ..      19      63 .. 0.76
   2 ?   12.8   0.0   0.00013     0.072       3      29 ..     112     138 ..     110     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.8
                     HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEE CS
  Thymidylate_kin 54 eqteallfaadriehleekikpalkqgktvi 84
                      + e +l+  d++ ++ ++ik +lk++  +i
       AJA92177.1 31 FELEINLLESDVATEVIDSIKDSLKEK--II 59
                     445788999999999*******99994..44 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00013
                      ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
  Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                      G++G+GKtt ++++++ lk+e+ +vv+
       AJA92177.1 112 GINGTGKTTSLAKVANMLKNEKFSVVI 138
                      9********************998665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.9e-05     0.027       2      51 ..     108     160 ..     107     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-05
      AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaareileeklakgedalpwved 51 
                 iv++G  +tGKTt l++ a++    +++vv  aa ++     ++ +++ +   +
  AJA92177.1 108 IVFVGINGTGKTTSLAKVANMlkneKFSVVIAAADTYRAGAIEQLREHTNRL-N 160
                 9**************9999666666899997777777666666666655543.2 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   9.5e-05     0.052      13      74 ..     107     174 ..      99     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.5e-05
                 EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG......B-HHHCCHCEEEE-SS--S-TTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke......qeleslrkeigvlpqepqlfpel 74 
                 ++++vG nG+GK+t l+ +a++lk+++ ++ +  +d+ +       +++  r +++++ q+   +p  
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRagaieqLREHTNRLNLKIIAQNYGSDPAA 174
                 6899***********************99988877777776665344445555667777776666666 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.3e-05     0.029       4     109 ..     108     208 ..     105     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrllt 102
                 ++  G  GtGKt  l ++++ l   ++e+ +v++      ++   e+l++++++ + k  ++++ s   ++   k+a   +++ k+d+v+vD A r+ t
  AJA92177.1 108 IVFVGINGTGKTTSLAKVANML---KNEKFSVVIAAADTYRAGAIEQLREHTNRLNLKIIAQNYGSDPAAVA--KDAVLYAQSHKVDCVLVDTAGRMQT 201
                 5556999**************9...88889999999999999999999888844444444444444444444..888899******************* PP

     DUF2075 103 ksdqaek 109
                 +s+  e+
  AJA92177.1 202 SSNLMEQ 208
                 7776444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   9.3e-05      0.05       1     108 [.     111     224 ..     111     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.3e-05
                 EE-TTSSHHHHHHHHHHHH...TEEE.EEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSE..EEEEE-SEEEETTEEEESS CS
      AAA_17   1 lGgPGsGKgtqceklveky...gfth.lsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkg..vlvdghprikeqagfldgl 92 
                 +G+ G GK+t ++k++  +   +f++ + a d  r+ a ++    ++r +++   ++   +  + a++++  ++++k   vlvd+  r+++++ +++++
  AJA92177.1 111 VGINGTGKTTSLAKVANMLkneKFSVvIAAADTYRAGAIEQLReHTNRLNLKIIAQNYGSDPAAVAKDAVLYAQSHKVdcVLVDTAGRMQTSSNLMEQI 209
                 79**************88755566641577899998776663324556666667777777777788887766553333359********9999988887 PP

                 HHHHHHHH..SEEEEE CS
      AAA_17  93 pkevleelkpdaiill 108
                  k + + ++pd+ i++
  AJA92177.1 210 AK-ITKVVNPDMKIFV 224
                 75.7788899887776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00015      0.08      35      66 ..     107     138 ..      95     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
       AAA_7  35 pvllvGptGtGKtviikdllkkldkekylslt 66 
                  +++vG  GtGKt+ + ++ + l++ek+++++
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNEKFSVVI 138
                 4789***********************99875 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   0.00013     0.068       5     107 ..     109     216 ..     106     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
          TK   5 lilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRyseg.kvvthd...gisleak...ksktssleeikeeleeedvdvvlvDEaqFfeqdivel 96 
                 + +g   +GK+t+L + +++++  +++vv+  a    R ++  ++  h    ++++ a+   ++ ++ +++ +  +++++vd+vlvD a  ++    +l
  AJA92177.1 109 VFVGINGTGKTTSLAKVANMLKNEKFSVVIAAA-DTYRAGAIeQLREHTnrlNLKIIAQnygSDPAAVAKDAVLYAQSHKVDCVLVDTAGRMQ-TSSNL 205
                 56666678**************99999877654.4445554335555541114444444456667777777777788889********99888.77788 PP

          TK  97 seklanegkiv 107
                 +e++a+  k+v
  AJA92177.1 206 MEQIAKITKVV 216
                 88888776665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00022      0.12       1      30 [.     107     136 ..     107     142 .. 0.92
   2 ?   -1.0   0.0       2.8   1.5e+03      54      96 ..     145     193 ..     139     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
        MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                 ++ +vg +g+GKTt l k+ ++lk+++++v
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNEKFSV 136
                 689**********************99988 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.8
        MobB  54 kAGAkevlvaskerlal..ikel...eeaelsleell.arlsevDlvlv 96 
                 +AGA e l ++ +rl l  i +    + a ++ + +l a+ ++vD vlv
  AJA92177.1 145 RAGAIEQLREHTNRLNLkiIAQNygsDPAAVAKDAVLyAQSHKVDCVLV 193
                 5888888888888776543444455322222222222033345999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00011      0.06      18      78 ..      99     153 ..      89     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
      AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalar 78 
                 + +s++p +++++G  G+GK++ + ++++ l+ +++ ++ + +d ++     +  +++l r
  AJA92177.1  99 KKSSNQPFIIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYR-----AGAIEQL-R 153
                 567788899*******************9999888777777777772.....2255555.3 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       4.7   2.6e+03      76     101 ..      55      80 ..      17     106 .. 0.54
   2 ?   13.8   0.2   8.3e-05     0.045       9      70 ..     115     216 ..     107     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.7
                 EEEEEEEEESS...-TTCHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  76 iagvvlnrvdgeneetllkealeelk 101
                    ++  rv+++n ++  k++l e +
  AJA92177.1  55 KEKIIGSRVEKKNIQNFVKQSLIEFI 80 
                 34455555555555555555554443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.3e-05
                 TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..........................................CCHCCCHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................................xxxxxxxxxxx RF
        CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..........................................dlkrllellea 65 
                 G+GKTt +a+ a  l+++++ V+   aD+ +  +  +e+l++  ++                                          + + l e +++
  AJA92177.1 115 GTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGA--IEQLREHTNRlnlkiiaqnygsdpaavakdavlyaqshkvdcvlvdtagrmqTSSNLMEQIAK 211
                 9***********************9999984332..344444444477777777777777777777777777777777777777655544444555555 PP

                 HCHCH CS
                 xxxxx RF
        CbiA  66 lgkkk 70 
                 + k++
  AJA92177.1 212 ITKVV 216
                 55443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00022      0.12       4     103 ..     107     230 ..     104     246 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd...kkladpe.....kllelileklke................ekktylflDEiqevpe 78 
                 i+v +G+  +GKTt l ++++ l  +k s++  + d+ r    +   + +      +l++i +++ +                +k  +++ D + ++++
  AJA92177.1 107 IIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAgaiE---QLRehtnrLNLKIIAQNY-GsdpaavakdavlyaqsHKVDCVLVDTAGRMQT 201
                 7899****************887766666666677776664431...222111211223333332.134556666666666666666777776655555 PP

      AAA_14  79 wekalkslvd....egknldvivtGSnsk 103
                  ++ + ++ +     +++++++v  S+++
  AJA92177.1 202 SSNLMEQIAKitkvVNPDMKIFVGDSLAG 230
                 55444444443223225667776666665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014     0.075      11      54 ..      95     137 ..      89     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                 HHHC.TTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEE CS
      NB-ARC  11 kLle.kdelqslvvalvGmgGvGKttlakqilnksdevegrFdsv 54 
                 +  e k + q +++ +vG  G GKtt ++++ n     +++F +v
  AJA92177.1  95 RINEkKSSNQPFIIVFVGINGTGKTTSLAKVANM--LKNEKFSVV 137
                 444424566778***************9999998..445566655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018     0.096       5      78 ..     108     200 ..     105     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
      AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel......................aaeladyktlviDtidele 78 
                 i+ +G +g+GKTt++++    + ++  ek +  + a++  ++ ++e++++  + l                      +a+ ++ + + +Dt++ + 
  AJA92177.1 108 IVFVGINGTGKTTSLAKV---ANMLKNEKFSVVIAAADTYRAGAIEQLREHTNRLnlkiiaqnygsdpaavakdavlYAQSHKVDCVLVDTAGRMQ 200
                 7889**************...667777775567888887778799999999999999999999****************************99874 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.16       1      50 [.     104     153 ..     104     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                 S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
  APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                 +++++ + G+ g+GK+t   +++++L++++ sv++   d+ R g  ++L 
  AJA92177.1 104 QPFIIVFVGINGTGKTTSLAKVANMLKNEKFSVVIAAADTYRAGAIEQLR 153
                 5899************************************9999887775 PP

>> SPOUT_MTase  Predicted SPOUT methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       2.5   1.4e+03      25      71 ..      66     109 ..      47     154 .. 0.44
   2 ?   10.4   0.0   0.00085      0.46      58     116 ..     179     237 ..     142     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.5
                  HHHTTT-EEEEEEE......---S-HHHHHHHHHHT--.....TT-EEEE CS
  SPOUT_MTase  25 krlkkyakleiiel..kkekksekeeekakekegeril.kklkkkayvil 71 
                  k +++++k ++ie+  +    +  ++ ++  k  +ri  kk +++ ++i+
   AJA92177.1  66 KNIQNFVKQSLIEFisE----TFDNAGQIDLK--DRINeKKSSNQPFIIV 109
                  45555666666665211....11111111111..1222111112222222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00085
                  T--....TT-EEEEE-TTSEE--HHHHHHHHHHHHHHT-.-EEEEE--TT---GGGGGG CS
  SPOUT_MTase  58 rilkklkkkayvillderGkelsSeelakkleklaeegkselvfvIGGsdGlseevkkr 116
                  ++l + ++k  ++l+d  G++ +S +l ++++k+++  + ++ +++G s   +++v ++
   AJA92177.1 179 AVLYAQSHKVDCVLVDTAGRMQTSSNLMEQIAKITKVVNPDMKIFVGDSLAGNDTVNQA 237
                  555556677789************************9999*******998766666655 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00052      0.28       7      62 ..      88     139 ..      44     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                 HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEES CS
      ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvp 62 
                  Q++  +++ ek +s++   ++++   GtGKT  +ak++  l+++    kf +++ 
  AJA92177.1  88 GQIDLKDRINEKKSSNQPFIIVFVGINGTGKTTSLAKVANMLKNE----KFSVVIA 139
                 4555555666666668999999****************9999996....5544443 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  56.6   0.00028      0.15      58     111 ..     314     368 ..     291     370 .. 0.58
   2 ?    8.5  61.8    0.0034       1.9      58     113 ..     353     411 ..     353     422 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
  Trypan_PARP  58 dpepep.epepepepepepepepete.peeepepepepepepepepepepepepep 111
                  +pepep  +epepepepepepepe+   e+ep+pep  e epepepepepepepep
   AJA92177.1 314 KPEPEPvVEEPEPEPEPEPEPEPEPVvEEPEPKPEPVVE-EPEPEPEPEPEPEPEP 368
                  445554212344444444444443320334444444444.7778888888888887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0034
  Trypan_PARP  58 dpepepepepepepepe.pepepetepeeepepepepepepepep...epepepepepga 113
                  +pepepepepepepep  pepepe++pe+   +epepepepepep   epe+epepe  a
   AJA92177.1 353 EPEPEPEPEPEPEPEPFvPEPEPEPKPEPVV-EEPEPEPEPEPEPvveEPESEPEPEDDA 411
                  4666666666666666567777777777653.3455555555554444788888888776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       5.8   3.1e+03      73      87 ..      37      55 ..      15     100 .. 0.63
   2 ?   10.9   0.8    0.0007      0.38       2      95 ..     108     239 ..     107     256 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.8
                HHCTSEEEEEEETT....T CS
    MMR_HSR1 73 leeadlillvvdas....e 87
                l e+d++  v+d+     +
  AJA92177.1 37 LLESDVATEVIDSIkdslK 55
                4457777777773333321 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0007
                 EEEEESTTSSHHHHHHHHHT.................STEEESSSTTSSSSEEEEEEEETTEE......................EEEEECGGCSSHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltg.................ekaivsdkpgtTrdinegrvklkgke......................ielvDtpGliegas 61 
                 +++vG   +GK+t + +  +                 ++  +++    T   n + ++    +                      ++lvDt+G ++++s
  AJA92177.1 108 IVFVGINGTGKTTSLAKVANmlknekfsvviaaadtyRAGAIEQLREHTNRLNLKIIAQ---NygsdpaavakdavlyaqshkvdCVLVDTAGRMQTSS 203
                 78999999999999999887666665655555443222334455555555555555552...13334555555556666666666********555222 PP

                 HHHHHHHHHHHHHCTSEEEEEEETT..TTCSHHHHH CS
    MMR_HSR1  62 eekglgkaflaleeadlillvvdas..eeklkplde 95 
                 +  +   ++ ++ + d+ ++v d+   ++++++ +e
  AJA92177.1 204 NLMEQIAKITKVVNPDMKIFVGDSLagNDTVNQARE 239
                 222444444445557999999994454334444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 2960.42
//
Query:       AJA92178.1  [L=148]
Description: hypothetical protein T478_1108 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.036   13.9   0.0    1.5  1  FlgD_ig   FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-06     0.036      49      75 ..     104     130 ..      95     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-06
                 EEEEEE-SB-TTS-B--SEEEEEEEEE CS
     FlgD_ig  49 vvsftWdGtdndGnkladGaYtvkvta 75 
                 +v+f Wd  +n+G +  +G+Y+++ +a
  AJA92178.1 104 DVTFVWDQIKNNGDQILEGTYKITSKA 130
                 69*********************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1167.25
//
Query:       AJA92179.1  [L=281]
Description: cyclopropane-fatty-acyl-phospholipid synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-08   35.1   0.0    2.8e-08   34.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.9e-05   23.5   0.0    5.7e-05   22.6   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0011   18.8   0.0     0.0031   17.4   0.0    1.8  1  Methyltransf_8   Hypothetical methyltransferase
     0.0017   19.0   0.0     0.0029   18.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
     0.0078   16.1   0.0      0.023   14.6   0.0    1.8  2  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.053   14.3   0.0      0.096   13.4   0.0    1.4  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   9.5e-12   2.8e-08       2      96 .]      77     167 ..      76     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 9.5e-12
                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEE CS
  Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllv 95 
                      dvG+G    a+ +    +++  + +s   ++ ++ +++e+ + ++ + ++a+ lpf ++s D v++ e+ +h++   ++++e  RvLk +G+l+
       AJA92179.1  77 DVGSGILGPAKIWN---SQYPSLQISSVNVNFSQLASVEPSN-ISKLNSTARMLPFSNSSLDRVIALESAQHFKPIGDFFSESNRVLKDDGILA 166
                      78888888888888...5666777777777777777777775.66799********************************************98 PP

                      E CS
  Methyltransf_11  96 i 96 
                      i
       AJA92179.1 167 I 167
                      6 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.9e-08   5.7e-05      41     248 ..      48     246 ..      43     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.9e-08
                 --HH..HHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHH.HHHHTS-SSS-EEEEES-GGG-----SEEEEES CS
        CMAS  41 mtLe..eAqlaKldlileklelkpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklak.krvdeldlerkvevklldyedldekvdrvvsvg 135
                 +tL+  +Aq++ ++++ + +++   + + d+G G  + ++   ++y   ++ ++ +   q + ++  ++ +l    + + ++l +   +  +drv++++
  AJA92179.1  48 TTLHpvDAQKRLCEMMSDMAQISSAEIIADVGSGILGPAKIWNSQYpSLQISSVNVNFSQLASVEpSNISKL----NSTARMLPFS--NSSLDRVIALE 140
                 455433688888888999999999999999998865544444444422344444444444333331222222....3445555555..3589******* PP

                 -GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCCHHHHHHTSTTS---BHHHHHHHHHHTT-EEEEEEE-HHHHHHHHHHHHHHHH CS
        CMAS 136 afehvgkenydtffkklkkllkedGllllhtitslhkkelaerglklkfidkeiFPgGelpsieeieeeiseagftvvdveslrahYakTLkaWaealq 234
                   +h++     +ff++ +++lk+dG+l++   t++++++l++ g+  kf+        e  s ++i++eis++gf++++ ++++++ ++ L +++ +  
  AJA92179.1 141 SAQHFKP--IGDFFSESNRVLKDDGILAIAIPTATENSNLSNLGIL-KFTWS-----SEHYSQKNIVNEISKNGFEIIESNEIGKNIYSPLAEYYLNNR 231
                 ****975..78******************99999999999988865.66654.....46789999********************99999976653332 PP

                 .HTHHHHHHHSHHHH CS
        CMAS 235 .enkdeaialvseev 248
                  e ++++ + +s+ v
  AJA92179.1 232 dELQKKILSRYSKYV 246
                 033333333344444 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     1e-06    0.0031      62     157 ..      61     168 ..      37     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-06
                     HHHHHHCTS-TTS-EEEES-T...T-HHHHH--S-..EEEEE.....SS-SSTTEEE...S-TTS-S--TT-EEEEEEES---.SS-HHHHHHHH CS
  Methyltransf_8  62 viirklkkkkdnlvvadlGcG...eakiaeavrekekvrsfd.....lvavnervva...cdlakvPledesvdvavfclslm.gtnladflkea 144
                     +++ ++ +  +  ++ad+G G    aki +++  + ++ s++     l++v++  ++      + +P  ++s d ++   s    + + df  e 
      AJA92179.1  61 EMMSDMAQISSAEIIADVGSGilgPAKIWNSQYPSLQISSVNvnfsqLASVEPSNISklnSTARMLPFSNSSLDRVIALESAQhFKPIGDFFSES 155
                     45566668888999*****8533389**99998888888876211124555544333111233568********9999888751578******** PP

                     HHHEEEEEEEEEE CS
  Methyltransf_8 145 nrvlkvGGllkva 157
                     nrvlk  G+l +a
      AJA92179.1 156 NRVLKDDGILAIA 168
                     ***********98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   9.8e-07    0.0029      44      97 .]     112     163 ..      75     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.8e-07
                      TTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
  Methyltransf_25  44 egl.nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                      e + n++ ++  a+ lpf ++s D v++  + +h++   + ++++e  rvLk++G
       AJA92179.1 112 E-PsNISKLNSTARMLPFSNSSLDRVIALESAQHFK--PIGDFFSESNRVLKDDG 163
                      2.248999999*****************88899998..588************99 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.38   1.1e+03     129     149 ..       7      27 ..       4      32 .. 0.86
   2 !   14.6   0.0   7.6e-06     0.023      44     164 ..     105     211 ..      14     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.38
  Methyltransf_23 129 llldwlylvpagrhisffsar 149
                      +ll w++ +++++++++++a 
       AJA92179.1   7 DLLLWTFRRNENDVVKLYDAL 27 
                      6789**************975 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7.6e-06
  Methyltransf_23  44 gfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylv 137
                      + +++ v++s +            k +  +   ++++ + d +++ e+  h+++    ++  ++ lk++G l +  p+a    +++ l++l + 
       AJA92179.1 105 FSQLASVEPSNI-----------SKLNSTARMLPFSNSSLDRVIALESAQHFKPIGDFFSESNRVLKDDGILAIAIPTA---TENSNLSNLGIL 184
                      335555666532...........233333345566889***************************************75...578888899999 PP

  Methyltransf_23 138 pagrhi.sffsarslkelleeaGlevve 164
                      +  +++   +s +++ +   ++G+e++e
       AJA92179.1 185 KF-TWSsEHYSQKNIVNEISKNGFEIIE 211
                      88.677689999**************98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.096      41      99 .]     109     165 ..      86     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
  Methyltransf_12  41 akrennnnnnvelealdlldldgg........ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                      a+ e+ n ++++                    ss D v+a++  +h+k+i +++++  ++Lk++G+l
       AJA92179.1 109 ASVEPSNISKLNS----------TarmlpfsnSSLDRVIALESAQHFKPIGDFFSESNRVLKDDGIL 165
                      3333333334444..........1444445568********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2154.75
//
Query:       AJA92180.1  [L=167]
Description: hypothetical protein T478_0566 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-28   99.3   0.0    1.4e-28   98.8   0.0    1.2  1  DUF192    Uncharacterized ACR, COG1430
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.031   14.1   0.0    1.3  1  Ph1570    Ph1570 protein


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.8   0.0   1.6e-32   1.4e-28       2      95 ..      51     163 ..      50     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 1.6e-32
                 EEEEE-SHHHHHHTTTT--..---TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT.........-........ECEEEEEETT CS
      DUF192   2 tvevAdteeerarGLmgre..slpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq.........s........vryvLElpaG 81 
                 +v +Adt+  r+rGLm  +   l++d+gmlfvfd++ ++s+wMkn+++ Ldii++d++g++++ie++++p+         +        ++yvLE+ +G
  AJA92180.1  51 EVYLADTDPRRMRGLMWENesFLSDDKGMLFVFDEPGTRSMWMKNMQFHLDIIWFDKNGSVIAIEKNVPPCitpmevmscKsvgvsadnAQYVLEMTSG 149
                 7899************96522699***********************************************98776665505666666799******** PP

                 HHHHHT--TT-EEE CS
      DUF192  82 aakklgikpGdrle 95 
                 +++k+ i++ ++le
  AJA92180.1 150 YVDKHSINENSKLE 163
                 *********99986 PP

>> Ph1570  Ph1570 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.4e-06     0.031     120     154 ..      63      97 ..      46      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-06
      Ph1570 120 dgllvlgknflldekgrlfvfnkpsvrelilkyik 154
                  gl+     fl d+kg lfvf+ p  r + +k ++
  AJA92180.1  63 RGLMWENESFLSDDKGMLFVFDEPGTRSMWMKNMQ 97 
                 577777889********************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1025.63
//
Query:       AJA92181.1  [L=227]
Description: hypothetical protein T478_0720 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.029   14.0  12.4      0.056   13.0  12.4    1.5  1  Snf7          Snf7
      0.032   13.8   0.9      0.043   13.4   0.9    1.2  1  Exonuc_VII_L  Exonuclease VII, large subunit
      0.096   12.3   0.8       0.16   11.6   0.8    1.3  1  DUF2026       Protein of unknown function (DUF2026)


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  12.4   9.4e-06     0.056       2     117 ..      46     163 ..      45     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.4e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
        Snf7   2 airsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkk 100
                 a+++L++++ kl   +++l++k +    ++ +  k++n++ a+ ++ ++ +++k  + ++n + ++eqv+  + + +   +v+ ++    + +k  +  
  AJA92181.1  46 AQKRLQQQIVKLGETEQKLKQKDSMFMDKIVEATKTNNQAYAKMYATELAEIRKNNKTVSNAKLSMEQVQIRLNTVSELGDVVVTLSPCMSLIKGLSTS 144
                 6789*****************************************************************************999999999999999777 PP

                 T..CCHHHHHHHHHHHHHH CS
        Snf7 101 v..didkidklmdeiedqm 117
                 +   ++++ + m++++ ++
  AJA92181.1 145 LggMMPEVAESMQDLSSML 163
                 6334678888888777665 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.9   7.2e-06     0.043     174     273 ..      39     145 ..      11     171 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-06
  Exonuc_VII_L 174 lasrlkspeellerkrqrldeleerleralkkq....lkkkrerleelkerlk...ekleekkerlkklkerlelleekkerleeleeklealsplk 263
                   l++rl  ++++l+++  +l e+e++l+++ +      +++ +++ + +++ +    ++++++++++++ k ++e+++ + ++++el + + +lsp  
    AJA92181.1  39 LKNRLDVAQKRLQQQIVKLGETEQKLKQKDSMFmdkiVEATKTNNQAYAKMYAtelAEIRKNNKTVSNAKLSMEQVQIRLNTVSELGDVVVTLSPCM 135
                   3444444555555555555555555555322222222333333333333222234456777777777776677788888899999999999999999 PP

  Exonuc_VII_L 264 vLkrGyaivr 273
                    L +G +   
    AJA92181.1 136 SLIKGLSTSL 145
                   9999988765 PP

>> DUF2026  Protein of unknown function (DUF2026)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   2.6e-05      0.16     109     194 ..      41     121 ..      25     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                 ..G-----BEEEEGGG--SSTT---STT-EEEEE-HHHHHHHTTTGGG-HHHHHHHHHHHHH---TTS--.-SEEEEE-TTS-EEEE CS
     DUF2026 109 ydllvpakmfqkkldsmaesindlkksGDffldpdlevteellkklakslalkdlaevcaeWfrkpPkkm.easisikdadgklnkv 194
                   l v +k +q+++ ++ e+ ++lk++   f+d  +e+t++  + +ak +  ++lae+ ++      k + +a++s+++ + +ln+v
  AJA92181.1  41 NRLDVAQKRLQQQIVKLGETEQKLKQKDSMFMDKIVEATKTNNQAYAK-MYATELAEIRKN-----NKTVsNAKLSMEQVQIRLNTV 121
                 5678999********************************998887765.566788888543.....333313455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1760  (0.098165); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1368.12
//
Query:       AJA92182.1  [L=129]
Description: hypothetical protein T478_1349 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 797.45
//
Query:       AJA92183.1  [L=81]
Description: LSM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-17   62.4   2.1    2.6e-17   62.2   2.1    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.035   14.0   0.1    1.6  1  Gemin7    Gem-associated protein 7 (Gemin7)
      0.025   14.2   0.0      0.033   13.8   0.0    1.2  1  Hfq       Hfq protein
      0.071   13.2   0.1      0.072   13.2   0.1    1.0  1  Tim44     Tim44-like domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   2.1   5.9e-21   2.6e-17       2      66 ..      13      76 ..      12      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 5.9e-21
                HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
         LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                 l+k ++k+v+v+lkn+ e++G++k++D +mNl+++++ee +++k ++ k  + ++RGnn+++i 
  AJA92183.1 13 TLQKNVKKTVIVRLKNEVEYKGKMKNVDSYMNLIMTEAEELVDGK-TVGKFARAILRGNNVLFIK 76
                6999***************************************99.*****************97 PP

>> Gemin7  Gem-associated protein 7 (Gemin7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.8e-06     0.035      11      75 ..       8      76 ..       3      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-06
      Gemin7 11 erfLrslkalvgkpveftllektevsaefkgvdideenflVe..nLq..TplGtikeAllRssDiisis 75
                +r L +l++ v+k v + l +++e +++ k vd  ++ ++ e  +L     +G+ ++A+lR + ++ i+
  AJA92183.1  8 KRPLTTLQKNVKKTVIVRLKNEVEYKGKMKNVDSYMNLIMTEaeELVdgKTVGKFARAILRGNNVLFIK 76
                58899****************************999888765225643246899**********99886 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.4e-06     0.033       6      45 ..      11      51 ..       8      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-06
                HHHHHHC.T-EEEEEETTS-EEEEEEEEE-SSEEEEEETTE CS
         Hfq  6 Lnqlrke.kipvtifLvnGiklkGviksfDnftvlLesdgk 45
                L +l+k+ k +v++ L n +  kG++k  D+++ l+ ++++
  AJA92183.1 11 LTTLQKNvKKTVIVRLKNEVEYKGKMKNVDSYMNLIMTEAE 51
                56666663678**********************99977764 PP

>> Tim44  Tim44-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.6e-05     0.072      33      96 ..       4      68 ..       1      79 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                HHHHHT-HHHHHHHB-HHHHHHHHHHHHHH.HHTT-EE--EEEEEEEEEEEEEEEETTEEEEEEE CS
       Tim44 33 eayakgDletLrkllteevyeefkaeiker.akqgltldaellgirevdlkeakiegdtavltvr 96
                +  ak+ l tL+k++ + v+ ++k+e++ + +++++ +  +l+  +  +l ++k+ g+ a++++r
  AJA92183.1  4 TTAAKRPLTTLQKNVKKTVIVRLKNEVEYKgKMKNVDSYMNLIMTEAEELVDGKTVGKFARAILR 68
                566788899*********************999999999999999999********999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 552.19
//
Query:       AJA92184.1  [L=325]
Description: ATP phosphoribosyltransferase HisG [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-42  144.5   0.0    3.6e-42  144.0   0.0    1.2  1  HisG       ATP phosphoribosyltransferase
    6.3e-16   58.3   0.0    1.6e-15   57.0   0.0    1.6  1  HisG_C     HisG, C-terminal domain
  ------ inclusion threshold ------
      0.066   13.2   0.1       0.15   12.0   0.1    1.7  1  PTCB-BRCT  twin BRCT domain


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   6.1e-46   3.6e-42       1     158 [.      50     235 ..      50     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 6.1e-46
                 -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG......TT.-.EEEEES-HHHHHHHHHHT........ CS
        HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdl.....ved.kgkriaTsypnlakkyfeek........ 85 
                 r+++ip +V +g +d+GitGkD+++E+k  ++v+ lldL++gk klv+a+p++ ++k+ +++     + + k +r  ++y + a+k++++         
  AJA92184.1  50 RPQEIPNLVSDGLYDVGITGKDWINETK--SDVDPLLDLEYGKIKLVIAIPDTLKFKNFDQMiaeyaK-KkKILRLSSEYLTNASKFIKSCksykkafg 145
                 89************************74..57***************************998655432.2466789************99967777777 PP

                 ...............T-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHH.S..HHHHHHHHHHH CS
        HisG  86 ...............glkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslk.k..kekieellerl 158
                                + +v+i+ + G++Ea+p+ + +DaI+D++etG+TL++ngLk+i+t+++ssa+Liank+slk k  +eki ++++ +
  AJA92184.1 146 nkdpmiitpwmrvgtNKNVQIHLSFGATEAKPPED-VDAIMDVTETGTTLKQNGLKIIDTVMKSSAHLIANKQSLKdKnkREKIFDIVTLM 235
                 777777777776666559****************7.9***************************************545445777777665 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   2.6e-19   1.6e-15       2      69 ..     242     308 ..     241     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.6e-19
                 TTEEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEEE CS
      HisG_C   2 rkyvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlvl 69 
                 +ky  l +n+++++l+++lk lP+l++PTvspl+++gwv V++v+ ++++ ++i++L+++ A++I+v 
  AJA92184.1 242 KKYLHLYLNIKENNLKKLLKELPSLKKPTVSPLSEKGWVGVNTVILKTDFHKLIPKLRKI-AQGIVVH 308
                 5788999*****************************************************.****995 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.6e-05      0.15      18      45 ..     192     219 ..     185     242 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                 HHHHHTT-EEESSEETT-SEEEECSS-C CS
   PTCB-BRCT  18 klieamGaeyskdltksvTHLicksgeG 45 
                 ++++++G ++ ++++ks  HLi+++ + 
  AJA92184.1 192 TTLKQNGLKIIDTVMKSSAHLIANKQSL 219
                 6789*******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2162.57
//
Query:       AJA92185.1  [L=260]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1810.05
//
Query:       AJA92186.1  [L=254]
Description: putative coenzyme F420-0:L-glutamate ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-44  151.2   0.1    4.6e-44  150.6   0.1    1.2  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.1   2.5e-48   4.6e-44      19     244 .]      25     224 ..      18     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 2.5e-48
                  CCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H..................HHHHHHHHTEEEEEE-...S-EEEE. CS
  F420_ligase  19 esvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsliLkalakatrkvevvlsepsdevgn...qlideky 113
                  + +k++++ +++gDi+v+++k++++++g+++++e+ ++ e+A++ia+k+ +++                   +++e+v +e+++++g    + +    
   AJA92186.1  25 NIIKSSKVVIKEGDILVISSKFISNSQGRILEIEKSRVCEEAKKIAKKF-NTNE------------------KFMEIVYRESDKILGGvagFAMAT-- 101
                  3344557889***************************************.7777..................9**************966433333.. PP

                  ......TTS-EEEGGG-B-TTS-TTEEE---S-HHHHHHHHHHHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B- CS
  F420_ligase 114 tdevlvklGllgsnagidesnveegllkllPedpdksaeeikkklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkel 211
                          G+l+ nagid+sn +++ ++l P++pdk+aee+k+++  +++ +v+++i   D++  + + ++++vai+++g+e+++dlrg+kdldg++l
   AJA92186.1 102 ------TNGILAPNAGIDKSNSKGTKIILYPNEPDKFAEELKRRIFLELKLHVGIII--VDSRLMPARIGTTGVAIACAGIEPTKDLRGEKDLDGNPL 191
                  ......57*************************************************..*************************************** PP

                  S--EEEHHHHHHHHHHHHC-SSSS---EEEEES CS
  F420_ligase 212 gttpravtdelgsladLvsGsadegtPvvlvrg 244
                  ++t +a +d+l+s+a+  +G++d+  P+++vr+
   AJA92186.1 192 KVTFQATADNLASIANHKMGEGDDLHPIAIVRD 224
                  *******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1922.69
//
Query:       AJA92187.1  [L=143]
Description: ribosomal protein L14p/L23e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-33  113.9   1.0    5.4e-33  113.7   1.0    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   1.0     3e-37   5.4e-33       2     122 .]      23     143 .]      22     143 .] 0.94

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 3e-37
                    .CSS-EEE--SSSSBSEEEEEEETT-.--....-EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEESS-EEEEB-TTS-B CS
  Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggkkr....kaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfddnaaVllnkkgep 93 
                    i +++r+ +aDNsgak +e+++v ++k+r    +aasvGd + v+vkk+     + +++++ av++r+k  v+r++G+ ++f+dna Vl++ +ge+
     AJA92187.1  23 IPVGARIVCADNSGAKIIEIVNVHQHKTRtsrlPAASVGDFCNVVVKKGPA---ELRKQIHGAVIIRQKYAVHRPNGVRVQFEDNAGVLITPEGEM 115
                    678899******************9994445569************99988...89**************************************** PP

                    SS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
  Ribosomal_L14  94 lGtrifgpvarelrekkflkivslApevl 122
                    +Gt i+gpva+e+ ek ++++++lA++v+
     AJA92187.1 116 KGTDIKGPVASEVTEK-WPRVANLAKMVV 143
                    ***************9.*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1031.44
//
Query:       AJA92188.1  [L=132]
Description: ribosomal protein L32 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-33  113.2   0.1      9e-33  112.9   0.1    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.1     5e-37     9e-33       2     108 .]      19     124 ..      18     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 5e-37
                     -----TTTTT-TTS-SS------TT-TTTTT.-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EEEE-TTS-HHHHHHH CS
  Ribosomal_L32e   2 kkFirhqsdryvklkeswrkprGidnrvrrr.fkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaaeiahsVsskkrkei 95 
                     ++Fir +s+ryv+l++ wrkp+G+dn++r++  +g++ ++k+GYg+pk   gl+psG+++ lVhn+++Le+l+++++   ++ +hsV++kkr+ei
      AJA92188.1  19 PEFIRPESWRYVRLESGWRKPKGMDNHQRKQkSRGRPGLVKVGYGTPKIALGLHPSGYTDNLVHNANDLENLNPKED--GIRFGHSVGAKKRREI 111
                     89**************************9862679******************************************..**************** PP

                     HHHHHHTT-EBSS CS
  Ribosomal_L32e  96 verAaelgikVtN 108
                     ++ A e ++kV+N
      AJA92188.1 112 MKIALEKKFKVFN 124
                     ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 917.82
//
Query:       AJA92189.1  [L=230]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.2   11.7   0.3        0.2   11.7   0.3    2.9  3  AA_permease_C  C-terminus of AA_permease
        1.1    9.0   3.1       0.59    9.9   0.2    2.0  2  NCE101         Non-classical export protein 1
        2.2    8.5   8.8       0.35   11.1   1.3    2.3  2  DUF2878        Protein of unknown function (DUF2878)


Domain annotation for each model (and alignments):
>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   3.4e-05       0.2      27      48 ..       9      30 ..       4      33 .. 0.87
   2 ?   -1.9   0.7      0.63   3.8e+03      29      40 ..      43      54 ..      37      61 .. 0.52
   3 ?   -2.1   0.1      0.71   4.2e+03      27      42 ..     161     176 ..     157     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
  AA_permease_C 27 ltwirfgvwmliglliYflYgi 48
                   l +i f++ ++ig++ Y++Y+ 
     AJA92189.1  9 LNLIGFIIGIIIGVFAYVGYKN 30
                   67899***************86 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
  AA_permease_C 29 wirfgvwmligl 40
                   +i +g+   i  
     AJA92189.1 43 FIAIGIGFGIIW 54
                   444444444433 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.71
  AA_permease_C  27 ltwirfgvwmliglli 42 
                    l++  f++w  + ++ 
     AJA92189.1 161 LAFGEFIAWYSLVFPE 176
                    5566677777665554 PP

>> NCE101  Non-classical export protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   9.9e-05      0.59      10      25 ..      15      30 ..      14      35 .. 0.88
   2 ?   -3.1   0.2       1.1   6.5e+03      11      18 ..     152     159 ..     151     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.9e-05
      NCE101 10 lLaifiGvaaYylyEk 25
                +++i+iGv+aY  y +
  AJA92189.1 15 IIGIIIGVFAYVGYKN 30
                69*********99976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
      NCE101  11 LaifiGva 18 
                 La+ +G+a
  AJA92189.1 152 LAVGTGLA 159
                 89999985 PP

>> DUF2878  Protein of unknown function (DUF2878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   1.1     0.058   3.5e+02     109     148 ..      11      49 ..       4      59 .. 0.60
   2 ?   11.1   1.3   5.8e-05      0.35      92     152 ..     112     172 ..     107     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.058
     DUF2878 109 llaallgavggplsYlaGaklgavtlglpllltllilalv 148
                 l+ +++g ++g+++Y++  + g       l++++++++++
  AJA92189.1  11 LIGFIIGIIIGVFAYVGYKNTGSPV-LFRLTIAFIAIGIG 49 
                 4578889999999987544444433.33333345555544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.8e-05
     DUF2878  92 lfaltlnhslawlrkrpllaallgavggplsYlaGaklgavtlglpllltllilalvWavl 152
                 lfal++    + +r+ ++++++ ga+   +s+l G + ga+++g +l+l+++  ++ W  l
  AJA92189.1 112 LFALSAMNIEHIIRSFSFILLVYGAIETFVSFLEGKQKGALAVGTGLALLAFGEFIAWYSL 172
                 5777777778889999******************************************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1603.25
//
Query:       AJA92190.1  [L=365]
Description: histidinol-phosphate transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-57  194.6   0.0    3.3e-57  194.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.035   12.6   0.1      0.055   12.0   0.1    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   0.0   3.7e-61   3.3e-57       2     362 ..      30     356 ..      29     357 .. 0.93

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 3.7e-61
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    ++i+++sn ++ +      p v+k  k+   + ++++ y++++ +  l+++l  f g      l+++ +++ g+Ga++li  +  ++ +n+++++l
     AJA92190.1  30 KIIDFSSNVNPLG----CHPGVKKYLKK---QLNQIHVYPDSE-STRLRSNLKWFTG------LNTS-QILIGNGATELIYNFCSAF-VNKKTKVL 109
                    79***********....88888888877...999*********.*************......9999.*******************.9******* PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                    +p pt+++y+++++ sgg+v+++++    + ++d+ ++++++ +       + v+++++p+NPtG +++++  ek++++a+k+  l+fvDe++ ++
     AJA92190.1 110 IPCPTFSEYEKAVEFSGGKVISFKTL---NLNVDFSKFLTKIPT-------KGVVFICNPNNPTGEILSKKNMEKIVKTAEKKSSLVFVDETFIEL 195
                    ************************66...99*********9986.......479****************************************** PP

                    BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelr 289
                    v +s    +++ +++ + nl+i++s+ K+fGlaG+R+Gy lg++++++ l++++ p+++  ++q a++aal  ++    +le+++q ++k+  +l 
     AJA92190.1 196 VPDSN--PSLVKTLKSYENLFILRSFTKSFGLAGLRIGYGLGSKKIIEVLQRVKIPWNVNYIAQMAASAALCYSD----FLEKSQQNIKKEYSFLI 285
                    ***55..3669****************************************************************....89*************** PP

                    HHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
  Aminotran_1_2 290 deLael.glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                    ++L ++  l++++s ++++l+    ++  k+l+kkLl++ +++v+ ++ f    ++ +Ri v   ++ +++ l+ea
     AJA92190.1 286 NALSKIdWLSYYPSSTNFILIKTKINS--KKLQKKLLKK-NILVRDCSTFCGldENYIRIAV--KNRIQNKLLLEA 356
                    ******667899999999999877777..9*********.*****98887667********9..777777777776 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.1e-06     0.055     137     177 ..     150     193 ..     102     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-06
                      TEEEEEEESS-TTTT---...-HHHHHHHHHHTT-EEEEEGTTT CS
  Cys_Met_Meta_PP 137 ntklvylEtptnpllkvv...DiekiaklakkagvlvvvDntfa 177
                         +v++  p np+ +++    +eki+k+a k++ lv+vD tf+
       AJA92190.1 150 TKGVVFICNPNNPTGEILskkNMEKIVKTAEKKSSLVFVDETFI 193
                      33489********98886333899*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2649.20
//
Query:       AJA92191.1  [L=634]
Description: fibronectin-binding protein A, N-terminal [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-50  171.2   2.3    4.2e-50  170.8   2.3    1.1  1  FbpA        Fibronectin-binding protein A N-terminus (FbpA)
    1.4e-21   77.2   0.1    1.1e-20   74.3   0.0    2.3  2  NFACT-R_1   NFACT protein RNA binding domain
      1e-05   25.4   1.1     0.0023   17.9   0.0    3.1  3  H2TH        Formamidopyrimidine-DNA glycosylase H2TH domain
  ------ inclusion threshold ------
      0.079   12.7   2.1       0.36   10.5   2.4    2.0  2  Fungal_KA1  Fungal kinase associated-1 domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   2.3   9.5e-54   4.2e-50      24     417 ..      27     412 ..       5     427 .. 0.84

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 9.5e-54
                 EEEEETTEEEEEEEETTEEEE.EEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXG CS
        FbpA  24 iyqpekdelvltlranrgrhk.LllsahpsyarihltekpkenpkeppnFcmlLRkyLkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimg 121
                 i   ++++l ++l+  ++    L++s       + +t+ +k ++ ep+  +  LR  L  a++++ieq+g +Ri  +++++      e+e tLivE +g
  AJA92191.1  27 IWGINRNSLLFKLHHPTKPDImLMVSS----IGMWITD-KKIETIEPNKMLRRLRSDLLRAKLTKIEQIGTERIAYFTFTNF-----EKEFTLIVEFFG 115
                 555666777777774444433244444....3444444.455899*************************************.....************ PP

                 GGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH.... CS
        FbpA 122 rhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsa 220
                 + +NiiL++ee+kI+++++ +  +   +R++  g +Y +Pp+ d+++ l++++ e+f+el+  ++  + k++ + + Gl + ++ee+++  g+d++++ 
  AJA92191.1 116 D-GNIILCNEERKILALLHSIDVR---HRQLRVGLEYSPPPE-DGVDVLNLTK-ESFRELF--STSGIGKTIGRGL-GLPKKYVEEIIRLSGIDPKKPS 205
                 *.*******************999...9*************9.**********.******5..5679*********.********************** PP

                 ...........HHHHHHHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHHH CS
        FbpA 221 kelseedlerlyealqelleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekkl 319
                 +e+++e++e+lye +++ l++++++   p ++++++   + ++++++  ++l+ +++ds++e ld  ++++      e+ +s ++    +++e lek+l
  AJA92191.1 206 NEVTNEEFEALYEIITSTLSKVTQGPHDPSVIIEDD-VHDAYPIRFSD-DNLNAKKVDSFNEGLDIVFTEEIL----EKGKSLFSSPADKKIESLEKTL 298
                 *******************************99986.77777777776.68999**************98665....5555566666666677777777 PP

                 HHHHHHHHCCGGH.HHHHCCHH-----------------------.--...............---------------HHHHHHHHHHHHHHHHHHHHH CS
        FbpA 320 kklekelekaeka.enyrligelltaylyaikkgmsevelenyydege...............evtIpLdprkspsenAqkyfkkykKlkraveaveeq 402
                  ++++ ++   ++ +++  +++ll+++ +a + +  +  + n ++e++               e +I++dp+ s +  A k+f++ kK k av+ +e++
  AJA92191.1 299 TEQKNAINVVLEKsKTIAEVANLLFTMTSAGQHDIRNEMITNSLKEKNaeiisekgvpymkinESKIQIDPDSSLPTIASKLFDESKKQKGAVKSIEKL 397
                 77777776654333777889999**99999999999999999999844589999****9999999********************************** PP

                 HHHHHHHHHHHHHHH CS
        FbpA 403 ieetkeeleylesve 417
                 +++t+++le+  ++ 
  AJA92191.1 398 MKKTESKLEKTIEKG 412
                 ********9876655 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.32   1.4e+03      57     108 ..     366     422 ..     320     423 .. 0.56
   2 !   74.3   0.0   2.4e-24   1.1e-20       2     109 .]     433     542 ..     432     542 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.32
   NFACT-R_1  57 eeipeelleeaaqlakanSia.gnklssvdvvy.vpasnlsktap...ldtGsvgfk 108
                 +  p+++l  +a    ++S++ +  ++s++  +    s l+kt +   +++G+vgfk
  AJA92191.1 366 QIDPDSSLPTIASKLFDESKKqKGAVKSIEKLMkKTESKLEKTIEkgeIAKGAVGFK 422
                 333445566666666666666544444544333044567777766777888888886 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 2.4e-24
   NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnklssvdvvyvpasnlsktap 99 
                 ++wF +sd++l ++G+D+++n  +i+kyle++d +fh+++++s++ +l+  e+e  e+ + +lee+a+ +++ S+a +     ++ ++v++++++k ap
  AJA92191.1 433 YRWFYTSDEVLAVGGRDSSSNSAIIRKYLEKNDKVFHAEVHGSPFFLLK-GEDE--ELLPLSLEEVAHATVCFSRAwQISAYGMSSFWVNPDQVKKGAP 528
                 68***********************************************.4444..79999****************99999***************** PP

   NFACT-R_1 100 ....ldtGsvgfkg 109
                     +++G+++++g
  AJA92191.1 529 tgqsMAKGAFMING 542
                 ***********986 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.2e-07    0.0023      40      80 ..     186     226 ..     180     232 .. 0.91
   2 !    4.5   0.1    0.0078        35      10      73 ..     289     353 ..     284     362 .. 0.84
   3 ?   -2.1   0.1      0.87   3.9e+03      65      85 ..     392     412 ..     382     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.2e-07
                 -HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHH CS
        H2TH  40 GNiyadEvLfrakihPerlakslskeelellhqeikevlke 80 
                    y++E++  ++i+P+++++++++ee+e+l++ i+++l +
  AJA92191.1 186 PKKYVEEIIRLSGIDPKKPSNEVTNEEFEALYEIITSTLSK 226
                 467***********************************987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0078
                 S-HHHHHHHHHT--SBHHHHHHCTTTSCS--HH.HHHHHHHHTT--TTSBGGGS-HHHHHHHHHH CS
        H2TH  10 ftvdalaerlkkkkrkiktlLLDqklvaGlGNi.yadEvLfrakihPerlakslskeelellhqe 73 
                  ++++l++ l+++k++i  +L   k++a + N+ +   +  ++ i  e+  +sl+++++e + ++
  AJA92191.1 289 KKIESLEKTLTEQKNAINVVLEKSKTIAEVANLlFTMTSAGQHDIRNEMITNSLKEKNAEIISEK 353
                 577899**************************725567778899999999999999999888765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.87
                 HHHHHHHHHHHHHHHHHHHTT CS
        H2TH  65 eelellhqeikevlkeaielg 85 
                 +++e l++++ + l++ ie g
  AJA92191.1 392 KSIEKLMKKTESKLEKTIEKG 412
                 567888888888899988854 PP

>> Fungal_KA1  Fungal kinase associated-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.4   8.1e-05      0.36      15     113 ..     301     407 ..     280     409 .. 0.81
   2 ?   -2.8   0.0       1.1     5e+03      63      84 ..     544     577 ..     542     605 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.1e-05
  Fungal_KA1  15 atkvlktslskkelrqelaklLreWkkyGlkdvksdkesntitgkvsseN..........ilslksvkFeieiisvseh..klSlvrftkekGsassfr 101
                 +++ +++ l+k+++  e+a+lL   ++ G +d++    +++it +++++N          ++++ + k++i   s +     +   + +k+kG+ +s++
  AJA92191.1 301 QKNAINVVLEKSKTIAEVANLLFTMTSAGQHDIR----NEMITNSLKEKNaeiisekgvpYMKINESKIQIDPDSSLPTiaSKLFDESKKQKGAVKSIE 395
                 347899999*************999999977776....567888888888888888899999999999998887777665444455789********** PP

  Fungal_KA1 102 klvkeiekvlrk 113
                 kl+k+ e+ l+k
  AJA92191.1 396 KLMKKTESKLEK 407
                 *******99987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
  Fungal_KA1  63 eNilslksvkFeieiisvseh............k 84 
                 +N++++ s+k+++ i+++ e+            k
  AJA92191.1 544 RNFIKVSSLKLAVGIFKQDEDyllvcgppepikK 577
                 6888999999999999998765555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4428.03
//
Query:       AJA92192.1  [L=266]
Description: KR domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-59  198.8   0.7    7.8e-59  198.4   0.7    1.1  1  adh_short        short chain dehydrogenase
      5e-42  144.1   0.2      6e-42  143.8   0.2    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.1e-18   67.7   0.3    1.5e-18   67.3   0.3    1.2  1  KR               KR domain
    2.6e-06   26.8   0.4      4e-06   26.2   0.4    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.2e-05   23.3   0.1     0.0001   22.6   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0003   20.7   0.2    0.00054   19.8   0.2    1.3  1  DFP              DNA / pantothenate metabolism flavoprotein
    0.00056   19.8   0.3      0.002   18.1   0.1    1.8  2  NAD_binding_10   NAD(P)H-binding
     0.0012   18.4   0.1     0.0016   17.9   0.1    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0015   18.0   0.0     0.0039   16.6   0.0    1.7  1  DUF1776          Fungal family of unknown function (DUF1776)
      0.002   18.0   1.6     0.0033   17.3   1.6    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
       0.03   14.2   0.6      0.068   13.0   0.3    1.6  2  Pox_J1           Poxvirus J1 protein
      0.032   14.3   1.1      0.058   13.5   1.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.049   12.6   0.2      0.067   12.1   0.2    1.1  1  Adenylsucc_synt  Adenylosuccinate synthetase
      0.057   12.8   0.1      0.077   12.4   0.1    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.071   12.5   0.1       0.13   11.6   0.1    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.11   12.9   1.5       0.22   12.0   0.9    1.8  2  NAD_binding_7    Putative NAD(P)-binding
       0.14   12.1   0.0       0.25   11.2   0.0    1.4  1  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
       0.15   11.8   0.4       0.22   11.2   0.4    1.2  1  Wax2_C           WAX2 C-terminal domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.7   7.8e-62   7.8e-59       1     187 [.       6     192 ..       6     197 .. 0.99

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 7.8e-62
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kvv++tGassGIG a a+++ak+Ga++v+v+r++ekle+va++l + ++k l+  +Dv+d+++v+++ ek+++ + k+d+LvnNAG    g+++els e
  AJA92192.1   6 KVVVITGASSGIGEAAAEQFAKRGANLVLVARRKEKLEQVAQKLSKYSTKTLIQVCDVSDKQQVKEMSEKVIETFSKIDILVNNAGFVIYGKVEELSIE 104
                 89************************************************************************************************* PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdma 187
                 ++e+ +++N++g++++t+ +lp++lkq+sG+ vnv+Sv g  +v+g a+Y+A+K+a+ g+++ l++el+ t++ v++v P +v+T + 
  AJA92192.1 105 DIESQMQTNYFGTINCTKYFLPHFLKQNSGHMVNVASVGGSFGVPGIASYCATKFAMLGFSEGLHHELHGTNVGVTVVSPIMVRTSLF 192
                 *************************************************************************************875 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.8   0.2     6e-45     6e-42       1     188 [.      12     200 ..      12     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 143.8 bits;  conditional E-value: 6e-45
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsree 94 
                   Ga sgIG+a+A+++a++Ga++vl+ +++e+ ++ +++l ++++++  +  cDV+d++qv+++ e+v e+f k+Dilvnnag++    g+++e+s e+
    AJA92192.1  12 GASSGIGEAAAEQFAKRGANLVLVARRKEKlEQVAQKL-SKYSTKtlIQVCDVSDKQQVKEMSEKVIETFSKIDILVNNAGFVIY--GKVEELSIED 105
                   899**************************955555555.5566554559************************************..********** PP

                   HHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHH CS
  adh_short_C2  95 fdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdel 188
                   ++  +++n  ++++++k++lp  +k++ g +vn++svg++ +vp+ + y+a+K a+ +++  l +el   ++ v +vsp +++T + ++ + f+++
    AJA92192.1 106 IESQMQTNYFGTINCTKYFLPhFLKQNsGHMVNVASVGGSFGVPGIASYCATKFAMLGFSEGLHHELHGTNVGVTVVSPIMVRTSLFDHPS-FKNF 200
                   *********************6444447********************************************************9976544.4444 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.3   1.5e-21   1.5e-18       3     159 ..       8     164 ..       6     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.5e-21
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 ++itG+  g+G + a++ a++ga +lvl++R+   +e+ ++  ++l+++ ++  +  +Dvsdk++v+++ e++ +++++i   ++ Ag++  +++ee++
  AJA92192.1   8 VVITGASSGIGEAAAEQFAKRGA-NLVLVARR---KEKLEQVAQKLSKYSTKTLIQVCDVSDKQQVKEMSEKVIETFSKIDILVNNAGFVIYGKVEELS 102
                 79********************8.69999999...456666889******************************************************* PP

                 HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDal 159
                  ed+e+ ++    G+ n  +++ +    ++  ++v ++S++g +g +g a+Y a+   + ++
  AJA92192.1 103 IEDIESQMQTNYFGTINCTKYFLPhflkQNSGHMVNVASVGGSFGVPGIASYCATKFAMLGF 164
                 *******************9998777779999*********************987665555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.4     4e-09     4e-06       1     113 [.       8     122 ..       8     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4e-09
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.......T-SEEEE------ CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel.....kvdvvfhaAAlKh 89 
                      v++tGa+  iG++  +q++k+ ++ +++  r+E kl +++++l+ ++++k+l ++    ++dv dk++++++ e++     k+d++++ A +  
       AJA92192.1   8 VVITGASSGIGEAAAEQFAKRGANLVLVARRKE-KLEQVAQKLS-KYSTKTL-IQ----VCDVSDKQQVKEMSEKVietfsKIDILVNNAGFVI 94 
                      79*****************99987666666665.8999**9995.4444444.45....99*****9998776653222247899999998766 PP

                      HHHHHHSHHH....HHHHHHHHHHHHHH CS
  Polysacc_synt_2  90 VPlveenple....aiktNvlgtenvie 113
                         vee  +e     ++tN +gt n+ +
       AJA92192.1  95 YGKVEELSIEdiesQMQTNYFGTINCTK 122
                      6666665444111156788888888765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     1e-07    0.0001       1      84 [.       8      97 ..       8     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-07
                     EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTS.......SEEEE-SSGGGHHH CS
  Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkeg.......dlvvnlsppissld 84
                     v+i Ga  ++G+a+ae  a+++    +++++ r kekle++a+k+   +++  ++ +d++++++ ++++ ++        d++vn ++ +   +
       AJA92192.1  8 VVITGAsSGIGEAAAEQFAKRGA---NLVLVARRKEKLEQVAQKLskYSTKTLIQVCDVSDKQQ-VKEMSEKVietfskiDILVNNAGFVIYGK 97
                     78999999*************97...59**************9998888999999********9.99998887888888899999888775555 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   5.4e-07   0.00054      20      91 ..       7      91 ..       4     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.4e-07
                TEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-.SS--..........-TT-EEEE-...-SHHHHHHHHHHHHTT-SEEEE--- CS
         DFP 20 VRfisNrSSGkmGyalAeaaaarGaeVtlvsgpv.slet..........pegvevvkv...esaeemleaveealkeadivimaAA 91
                V +i+  SSG  G a Ae++a+rGa+  lv+    +le+          ++ ++v +v   ++++em e+v e++++ di++  A 
  AJA92192.1  7 VVVITGASSG-IGEAAAEQFAKRGANLVLVARRKeKLEQvaqklskystKTLIQVCDVsdkQQVKEMSEKVIETFSKIDILVNNAG 91
                7789******.69*****************99853666444455555433345555552225678999**************9985 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     2e-06     0.002       1      57 [.      12      72 ..      12      91 .. 0.78
   2 ?   -0.8   0.0       1.2   1.2e+03     162     180 ..     203     221 ..     169     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT....TTCEEEE.--TT-CCHHHHH CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleae....eglevve.gdvtdvedlaea 57
                    GA+ ++G +++++ ++rg  ++++++R++ekl++++++    +  ++++  dv+d+++++e 
      AJA92192.1 12 GASSGIGEAAAEQFAKRG-ANLVLVARRKEKLEQVAQKlskySTKTLIQvCDVSDKQQVKEM 72
                    9****************5.*************998844321233344443788888877765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                     S----EEEHHHHHHHHHHH CS
  NAD_binding_10 162 pfkggsisradVAdvlvav 180
                       +g s s ++VA++++++
      AJA92192.1 203 FATGISLSADSVANAIIKA 221
                     3356688999999999887 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.6e-06    0.0016       1      98 [.       8     120 ..       8     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHH....HHHHHHH.T-SEEEE--S.---HHH...HHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsal....erlfkee.qpdavihlAa.vggvaa...sse 82 
                 +++tGa+  iG a +++++++g +++ ++r++++ ++   +++         +  +d+ d++++    e++++++ ++d+ ++ A+ v   ++   s+e
  AJA92192.1   8 VVITGASSGIGEAAAEQFAKRGANLVLVARRKEKLEQV--AQKlskystktLIQVCDVSDKQQVkemsEKVIETFsKIDILVNNAGfVIYGKVeelSIE 104
                 68**********************99999984433332..22257899*97667799999996611113455555689999998887755544112555 PP

                 SHHHHHHHHTHHHHHH CS
   Epimerase  83 dpadfieknlqgtlnl 98 
                 d +  +++n  gt n 
  AJA92192.1 105 DIESQMQTNYFGTINC 120
                 6666666666666665 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.9e-06    0.0039      96     194 ..      85     181 ..       4     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
     DUF1776  96 ilvPslsy.ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphnidvt 193
                 ilv +  +  +g +e+++++ ++s+++++ + +i  ++ +lp++ +   q++  +v  +s+  s  +p  a    +  a+  + e L++el   n+ vt
  AJA92192.1  85 ILVNNAGFvIYGKVEELSIEDIESQMQTNYFGTINCTKYFLPHFLK---QNSGHMVNVASVGGSFGVPGIASYCATKFAMLGFSEGLHHELHGTNVGVT 180
                 78888889899*********************************98...88999999999************9****************9998888877 PP

     DUF1776 194 q 194
                  
  AJA92192.1 181 V 181
                 5 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.6   3.4e-06    0.0033       9      91 ..      16     102 ..       7     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                 CCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH.HHHCCTTTTSS-.HHHHCCCHHC.EEEES-HHHHH.C-SEEEE-S-SSHH CS
     3HCDH_N   9 tmGagiaavfasagleVvlvdiseealekalekiek.sleklvekgklk.eeeveaalar.isfttdleeav.dadlviEavvEnle 91 
                  +G+  a++fa++g + vlv +++e+le++++k++k s++ l++   ++ +++v+++ ++ i++ ++++ +v +a +vi   vE+l+
  AJA92192.1  16 GIGEAAAEQFAKRGANLVLVARRKEKLEQVAQKLSKySTKTLIQVCDVSdKQQVKEMSEKvIETFSKIDILVnNAGFVIYGKVEELS 102
                 489*******************************99888888888888744555555544267889999999999999987777766 PP

>> Pox_J1  Poxvirus J1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   6.8e-05     0.068      45     101 ..      32      89 ..      28     114 .. 0.88
   2 ?   -2.1   0.0       3.2   3.2e+03       4      20 ..     121     137 ..     118     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-05
      Pox_J1  45 LallirskdkLeaiGylYeplsee.fraliefrdlkelkklfnrallkveeekvkvdk 101
                 L+l+ r k+kLe++       s + + ++++++d++++k++ +++   +++  + v++
  AJA92192.1  32 LVLVARRKEKLEQVAQKLSKYSTKtLIQVCDVSDKQQVKEMSEKVIETFSKIDILVNN 89 
                 78999*************9999886899****************99988887777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
      Pox_J1   4 ekylLtlFleddesFfk 20 
                 +ky L  Fl+++++ + 
  AJA92192.1 121 TKYFLPHFLKQNSGHMV 137
                 69********9998765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   5.8e-05     0.058      10      64 ..       3      55 ..       1     107 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                  .TT-EEEEES-SH.HHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEE CS
  Shikimate_DH 10 lkekkvlliGaGe.maelvakhLlakgvkkvvvaNRtlerakelaeelkgeeieal 64
                  +k+k v++ Ga   ++e +a++++++g++ +v + R  e+ +++a++l+++++  +
    AJA92192.1  3 FKNKVVVITGASSgIGEAAAEQFAKRGAN-LVLVARRKEKLEQVAQKLSKYST--K 55
                  67888999999763788888999999998.66666778999999999966532..2 PP

>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   6.7e-05     0.067     127     202 ..      13      91 ..       4     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                      --TTHHHHHHHHHTT---BGGGGGS.HHHHHHHHHHHHHHTHHHHHHT.....T-----HHHHHHHHHHHHGGGEE-HH CS
  Adenylsucc_synt 127 TkkGiGpayadkvarrgirvgdlld.eeeleeklekllelknkllekldk..eeleveelleellkyaerlkpyvvdtv 202
                        +GiG+a a+++a+rg ++  +++ +e+le+  +kl ++ +k+l ++ +  ++ +v+e+ e++ +  ++++ +v ++ 
       AJA92192.1  13 ASSGIGEAAAEQFAKRGANLVLVARrKEKLEQVAQKLSKYSTKTLIQVCDvsDKQQVKEMSEKVIETFSKIDILVNNAG 91 
                      678*****************99996467799999999999998888875456555666777777776666665565555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.8e-05     0.077       2     108 ..      10     119 ..       9     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH.....T-SEEEE--S---...H. CS
  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev.....qpdevynLAAqsh...V. 88 
                    iTG +  iG   ae++ ++g + + + rr++++     e++a++ + +++++  +  +D++D+++++++ ++v     ++d  +n A+      V 
     AJA92192.1  10 ITGASSGIGEAAAEQFAKRGANLVLVARRKEKL-----EQVAQKLS-KYSTKTLIQVCDVSDKQQVKEMSEKVietfsKIDILVNNAGFVIygkVe 99 
                    9****9*****************9999998774.....34443332.34567778889********999888766666778778877764322241 PP

                    HHHTTSHHHHHHHHTHHHHH CS
  GDP_Man_Dehyd  89 dvsfekPeytaevnvlGtlr 108
                    + s+e+ e  +++n  Gt++
     AJA92192.1 100 ELSIEDIESQMQTNYFGTIN 119
                    34777778888888877776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00013      0.13      34      94 ..       3      63 ..       1      90 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                  GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SE CS
  2-Hacid_dh_C 34 lsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDi 94
                   ++k v i G+ + IG+a+a+ +++ g++++ + r+k+k e + ++++++ s ++l++ +D+
    AJA92192.1  3 FKNKVVVITGASSgIGEAAAEQFAKRGANLVLVARRKEKLE-QVAQKLSKYSTKTLIQVCDV 63
                  67899999998644******************999988666.55557788999999999996 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   0.00022      0.22       4      92 ..       2      90 ..       1      98 [. 0.68
   2 ?   -2.2   0.0       5.8   5.8e+03      32      40 ..     178     186 ..     171     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
  NAD_binding_7  4 dlkgkkvlvvGgG.evAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneriaeaakarrilvnva 92
                   d+k+k v++ G+   +++  ++++++ ga++++va + ke+le+  +  +++  k l ++  v    + +e++e++ e+  +  ilvn a
     AJA92192.1  2 DFKNKVVVITGASsGIGEAAAEQFAKRGANLVLVARR-KEKLEQVAQKLSKYSTKTLIQVCDVSDKQQVKEMSEKVIETFSKIDILVNNA 90
                   899999****986269*********************.3333332222222223333333334444444677777888887788888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.8
  NAD_binding_7  32 kvtvvapev 40 
                     vtvv+p +
     AJA92192.1 178 GVTVVSPIM 186
                    578888765 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.25     138     186 ..       7      53 ..       1      75 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
  TP_methylase 138 vlsvllpglakeeereleallangdtlvllkapr.klaelaelLkealyd 186
                   v+ + + +++ ++e+  e+++++g +lvl+ +++ kl+++a+ L+++   
    AJA92192.1   7 VVVI-TGASSGIGEAAAEQFAKRGANLVLVARRKeKLEQVAQKLSKY--S 53 
                   3333.5888999******************999989********998..2 PP

>> Wax2_C  WAX2 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00022      0.22       1      58 [.       8      67 ..       8      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
      Wax2_C  1 vlltgklskvaraialaLcergvkvlvl..skeeyeklkkelpeelqknlvlskkasskv 58
                v++tg++s +++a a + ++rg + +++  +ke+ e++ ++l++ ++k+l+++ + s k 
  AJA92192.1  8 VVITGASSGIGEAAAEQFAKRGANLVLVarRKEKLEQVAQKLSKYSTKTLIQVCDVSDKQ 67
                799********************988887899********************99865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1538  (0.0857828); expected 358.6 (0.02)
Passed bias filter:                     1006  (0.0561102); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 1859.55
//
Query:       AJA92193.1  [L=275]
Description: nicotinate-nucleotide diphosphorylase (carboxylating) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-52  177.6   2.8    1.7e-52  177.6   2.8    1.4  2  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal
    1.3e-25   89.3   0.3    3.2e-25   88.0   0.2    1.8  2  QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.062   13.4   0.0    1.6  1  Ufm1       Ubiquitin fold modifier 1 protein
      0.032   13.6   0.1      0.057   12.7   0.1    1.4  1  TMP-TENI   Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   6.6e+03     103     135 ..      53      83 ..      30      84 .. 0.54
   2 !  177.6   2.8   3.8e-56   1.7e-52       1     169 []     104     273 ..     104     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                 EEEEES--HHHHHHHHHHHHHHSTTSEEEEESS CS
   QRPTase_C 103 iimLDnfsveelkkaveelkeknkrvlievSGg 135
                 i  L +++++ lk+  +  ++k ++ ++e SG+
  AJA92193.1  53 IFALKKCKTKILKQDGK--TAKPNQTILELSGN 83 
                 44444444444444444..22333366666666 PP

  == domain 2  score: 177.6 bits;  conditional E-value: 3.8e-56
                 HHHHHHHHHHHHHCT..SSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHH CS
   QRPTase_C   1 iAtltarmveaaksa..kvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdkevkievevesleeleevl 97 
                 iAt+t+++++ +ks+  k ++++TRkt+Pglr ++k Av+iGGg++hr++L++m++ikdnh+a+ +si+e+++++++  +k   ie+eve+  ++   +
  AJA92193.1 104 IATQTNSLKKLVKSTgsKSKVFATRKTAPGLRFFDKEAVKIGGGEKHRMNLNEMIMIKDNHLAVQKSIEEILRKAKKTRGK---IEIEVETSSDAILCA 199
                 9**************99**********************************************************998854...677777788888899 PP

                 HHT-SEEEEES--HHHHHHHHHHHHHHSTT..SEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
   QRPTase_C  98 eaeadiimLDnfsveelkkaveelkeknkr..vlievSGgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                 +++adiimLDnfs++++kk++++l+e + r  v++e+SG ++ +n+++ya++++d+isvg++t+sv  +D+sl+
  AJA92193.1 200 KMGADIIMLDNFSPTQIKKTMKKLTELKLRnkVILEASGRINSKNITKYAETNIDMISVGSITNSVDGIDLSLE 273
                 99**********************99888888****************************************95 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.2   7.2e-29   3.2e-25       2      89 .]      18     102 ..      17     102 .. 0.97
   2 ?   -3.6   0.0       2.6   1.2e+04      61      71 ..     230     240 ..     224     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 7.2e-29
                 TT--HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
   QRPTase_N   2 grgDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                  +gD+t+   +++++k+ a+ii++ee vvaG+++a+e+f l  ++++++l++DG+++++++++le++Gna ++l++ER+aLnll+r++
  AJA92193.1  18 AKGDITS--KLLKKQKIVARIITREETVVAGTKYAKEIFALK-KCKTKILKQDGKTAKPNQTILELSGNAGDILTCERTALNLLSRMC 102
                 68*****..88899**************************99.********************************************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
                 TEEEEEEEEEH CS
   QRPTase_N  61 gdvlleieGna 71 
                 ++v+le++G++
  AJA92193.1 230 NKVILEASGRI 240
                 78999999986 PP

>> Ufm1  Ubiquitin fold modifier 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.062      24      63 ..      40      79 ..      29      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
        Ufm1 24 eapftavlkfaaeeFkvpaatsaiitndGvginpqqtagn 63
                e  + a  k+a e F +++ ++ i+++dG    p+qt+++
  AJA92193.1 40 EETVVAGTKYAKEIFALKKCKTKILKQDGKTAKPNQTILE 79
                55567888*****************************987 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.3e-05     0.057      73     178 ..     159     259 ..     149     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
    TMP-TENI  73 gadgvHlgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevleag 171
                  ++  Hl  ++   + +r+  + +  i + v++ ++a   +++gad i++  + pT+ Kk       ++l+el+ + ++ + a G i+ +n+ + +e++
  AJA92193.1 159 MIKDNHLAVQKSIEEILRKAKKTRGKIEIEVETSSDAILCAKMGADIIMLDNFSPTQIKKTM-----KKLTELKLRNKVILEASGRINSKNITKYAETN 252
                 55556666666666777777778888888999999************************986.....66777777777778899*************** PP

    TMP-TENI 172 adgvavv 178
                 +d+++v 
  AJA92193.1 253 IDMISVG 259
                 ****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2162.26
//
Query:       AJA92194.1  [L=141]
Description: polyketide cyclase/dehydrase and lipid transport [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-11   43.1   0.0    5.2e-11   43.0   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.021   13.6   0.1      0.021   13.6   0.1    1.1  1  FbpA             Fibronectin-binding protein A N-terminus (Fb


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   5.8e-15   5.2e-11       3     141 ..       5     140 ..       3     141 .] 0.87

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.8e-15
                      EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEE.CCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSEEEEEEEE CS
  Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvr.vggrgtvreelvevdpegrllsyrivkpvpvanyvatwtvt 95 
                      +v++sv i+ + ek+w  +s  +++  W ++ ++++  g + +++g+++ ++   g ++v+e +v + p +  +sy +v+ +p++ y at++++
       AJA92194.1   5 SVKKSVIIQTDLEKAWTKISKIAKLD-WLQGQKSTKFLGDKKTGVGAKRLISfEDG-SKVEEHVVGWKP-KEYFSYIAVSGLPLEAYHATISIE 95 
                      7999**********************.***99999866523333477788887777.99**********.******99899************* PP

                      ECCET.EEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  96 pdggg.trvtwtgefdagplggpfekpaaakavkgdleagLerLkar 141
                         +   +vtw+  f+a   +g f++  + +++  ++ ++L++L+++
       AJA92194.1  96 KNKTKsVKVTWESYFAAKTTKGEFDE--FVEFLSNFYAQSLKNLREE 140
                      ***88567*****9998788888843..458*************987 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.4e-06     0.021     246     295 ..      87     137 ..      13     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-06
                 ..XXEE.....XSSSEESSXXTTXX..SSXXXXSXHHHHHHHHTTTXXX-- CS
        FbpA 246 kfepqlvlkeekpeefsvvplksls.elekesfdslsealdeyYakkaerd 295
                 +++ ++ ++++k+++++v+++++   +++k +fd++ e l ++Ya+ +++ 
  AJA92194.1  87 AYHATISIEKNKTKSVKVTWESYFAaKTTKGEFDEFVEFLSNFYAQSLKNL 137
                 67778889999*********9999999999***************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1061.22
//
Query:       AJA92195.1  [L=246]
Description: amino acid kinase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-28   98.4   0.0    5.4e-28   98.2   0.0    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.0     3e-32   5.4e-28       3     241 .]       2     223 ..       1     223 [. 0.91

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 3e-32
                 EEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHH CS
   AA_kinase   3 vVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdalaslgerlvaalla 95 
                 + +KlGGs++t+ke+      + +++++++i ++   ++++++VhGggs+++  + + ++++ ++++     t+ +   v++  +++ l+++++++ ++
  AJA92195.1   2 ILIKLGGSIITNKEKplsprrKTINNILKEIGKI---KEPVILVHGGGSYGHYWSVK-YDMHTKPAK-----TSPKGVAVVK-NSMVELNKIILDSAVK 90 
                 89********************************...999*****************.********9.....6777666666.**************** PP

                 TTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCC CS
   AA_kinase  96 aglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvp 194
                 + ++++ l++ ++   ++ +         + ++ +i+e+ ++g  p++ g++    +++++++s+D+i + +A+ l+++  +++ +VdGVy++   k  
  AJA92195.1  91 NKVNSYCLPPTDFMKGNKSI---------RSKILTINEIAKSGLTPITFGDALWFGQKKSYILSGDVIMTTIAKVLKPRLSLFVLNVDGVYSDLKTK-- 178
                 ***********999666666.........89999*****************9888888899******************************887544.. PP

                 TTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 195 darllpeisvdeaee.saselatgGmkvkhpaalaaarrggipvvItn 241
                   +l++  + ++ +  ++  ++tgGm  k+ +a ++a+ g  +v+ +n
  AJA92195.1 179 --KLIHDFKKETPKIqENVMDVTGGMTRKITEANKMAKAG-LKVFFVN 223
                 ..7999997666666667779*******************.9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1945.62
//
Query:       AJA92196.1  [L=165]
Description: copper-binding protein, plastocyanin/azurin family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-06   27.5   0.0      5e-06   26.9   0.0    1.3  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.049   13.7   0.0      0.076   13.1   0.0    1.5  1  Cupredoxin_1  Cupredoxin-like domain
      0.057   13.2   1.9       0.11   12.2   1.8    1.5  1  DUF4448       Protein of unknown function (DUF4448)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.4e-10     5e-06      13      98 ..      71     160 ..      61     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.4e-10
                  EEESSEEEEETT..EEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE.....SSEE..EEEEETTTTTTTSEEEEEE CS
  Copper-bind  13 qFetkeitvkkg..ekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd.....eagt..YkffCsPHaaagMkgkvtv 98 
                  ++ +k+i+v+ +  +kv +vn++ ++H v  d+  +++  d    + + +  +  +G++++  f+        +   +++C PH    M g+++v
   AJA92196.1  71 NYMPKKIQVQLTidNKVRWVNQDEIPHTVTPDSYDLDEITDPYSGEFG-SIGVLMPGDEYEFLFTkappnG--AkvITYHCHPHP--WMTGTIEV 160
                  68899999886543899**************99555555555555554.445999**********876433..245*********..69****98 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.076      29      90 ..      69     131 ..      19     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpG.eYef 90 
                   ++ + P+ki+v+     k++++n+d+ p++++ ++ + ++  +p +     i  l pG eYef
    AJA92196.1  69 KDNYMPKKIQVQLTIDNKVRWVNQDEIPHTVTPDSYDLDEITDPYSGEFGSIGVLMPGdEYEF 131
                   459**************************9998887776666666555555555777755666 PP

>> DUF4448  Protein of unknown function (DUF4448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   1.9e-05      0.11      44     103 ..      27      84 ..      18     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
     DUF4448  44 iTWdprfFdekenekVkihlsyvkestkekglkksffssdwlpnsdGfypltvdeewlkg 103
                 iTW+++++  +en+kV +    ++ + ++ +  + +  s + + +d ++p +++ ++  +
  AJA92196.1  27 ITWYTSYWLPEENQKVFVDEHILNPDGETVV--NIIMGSATPEQKDNYMPKKIQVQLTID 84 
                 9*******99********9999999987755..445666666666666666666555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1287.52
//
Query:       AJA92197.1  [L=593]
Description: oligoendopeptidase, pepF/M3 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-43  147.9   0.2    1.4e-42  146.5   0.2    1.7  1  Peptidase_M3    Peptidase family M3
    0.00057   20.1   1.6     0.0073   16.6   0.0    3.3  4  Peptidase_M3_N  Oligopeptidase F
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.038   13.9   0.0    1.6  1  Peptidase_M78   IrrE N-terminal-like domain
      0.058   13.2   0.9       0.22   11.4   0.0    2.3  2  Tho1_MOS11_C    Tho1/MOS11 C-terminal domain
      0.083   13.0   0.1       0.35   11.0   0.0    2.2  2  MIT             MIT (microtubule interacting and transport) d


Domain annotation for each model (and alignments):
>> Peptidase_M3  Peptidase family M3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.2   3.9e-46   1.4e-42       2     456 ..     201     580 ..     200     582 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 3.9e-46
                   HHC-S-HHHHHHHHHHHCTTTCCSS..THHHHHHHHHHHHHHHH.HHHTT-SSHHHHHHTTSTT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Peptidase_M3   2 lkespdrelRkeayeashskaaeqrntlensklleellklrael.Akllgyesyaelaledkmaknpetvldfleelvkklrpllekelkllkelkk 97 
                   l +++++++R++ay+ + +k+++++      +++++++ + +++  +++g+++ ++ +     ++ +++  d++ e+ kk++p+++k+++++++   
    AJA92197.1 201 LVRNKNPKVREAAYKSLLTKYQDNKGVI--GQIYQNIVLNWKNEgIDMRGFKDPISIQNIS--NDVDDKTIDVMLEVCKKNAPVFQKYFQQKAK--- 290
                   56799***************99877666..7777777776666679***************..*******************************... PP

                   HCCT-SSS--CCCHHHHHHHHHCCCCS.--CCCCGGG-BHHHHHHCHHHHHHHHHTEEEEEETTS..--SSTT-EEEEEEET.TT-EEEEEEEEEEC CS
  Peptidase_M3  98 kelglegelqpwDvaYYsekqreekyd.ldqeelkeyfpletvleGllelfeeLfGikfveekdakgevwhedVrkleVvdeilsegligeiylDly 193
                    + g++ +l+ +D+           y+  +++++++++++++ ++           + +     +  + +++     ++ +    + + +e+ +D+ 
    AJA92197.1 291 -RVGVK-KLRRYDL-----------YApSKKSAAERNYTFDQGTK-----------LVLD----S-LNRFSP-----KIAEY--ASRVFNENHIDYS 351
                   .99999.*******...........9955566678899*******...........4443....2.467777.....55555..555559999**** PP

                   --TTS-SS-EEEEEE--BTTS-B--EEEEEEEEE---BTTS--B--HHHHHHHHHHHHHHHHHHC--BSSGGGSTT-S-CCCCCHHHHHHHHGGGSH CS
  Peptidase_M3 194 erkgKrggAasfglvksredgtrqlpviylllNftkpsskkPsLLtldevetLfHEfGHsmHsllsrteysnvsgtnvpidfvElpSqlmEnlltep 290
                    r gKr+gA++++  +        +  +++l+N+t+         + ++v+tL+HE+GH++Hs+ ++++       + p+ ++E +S+  E ll ++
    AJA92197.1 352 LRHGKRDGAFCSTPLP--------YITPFVLINYTG---------KSRDVFTLAHEIGHAVHSVAASEKSIL--VSDAPLPLAETASTYSELLLYDN 429
                   ****************........699*********.........9**********************9755..5599999**********999886 PP

                   HHHHCC-B-TTT--B--HHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHCTT-TCCGHH....HHHHHHHHHHCTTSCTTBTTSSGGGC-CCCHTSS- CS
  Peptidase_M3 291 evlkslskhyetgeaipeelleklikaknvnaalellrqlvfaafdqelHeeaeeeqilkkdlletyaelrkkflglpvapdeasqasFghlfahgY 387
                    + +++  ++ ++++++ ++++++         +++ rq +f+ f+ e H++++++ +  +d++++y++  k+ +g + +  e +    + +  h+Y
    AJA92197.1 430 IS-SQI--SDGEKASMLSDKIDDFY--------ATIGRQSFFTLFEIEAHKQIANSITV-DDISNIYRKNLKEQFGNSIDISEDFGIEWSCIP-HFY 513
                   55.555..4788999**********........**********************8765.59*************************988884.*** PP

                   TTTTCHHHHHHHH..HHHHHHCCHHCCTT-..CCHHHHHHHHTTTTTTSS-HHHHHHCCCSS---SHHHHHHC CS
  Peptidase_M3 388 aanYYsylyaevl..aldifekffeedpln..retGeryrkeiLsrGgskdplellkkflgrepsadallkal 456
                   ++++Y+y y+ +   a+++f+ +++e+  +  +    +++++iLs+Ggs++p +llk+ + +  +++ ++  +
    AJA92197.1 514 HSPFYCYSYSFGNllAVSLFQIYKNEG--DdfV----STYTDILSAGGSQKPEKLLKEHGLDISKSKFWQSGF 580
                   ******999977667**********98..3358....9***************************99998765 PP

>> Peptidase_M3_N  Oligopeptidase F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.1   3.8e+03      11      35 ..      16      39 ..      14      45 .. 0.73
   2 ?   -0.3   0.2      0.38   1.4e+03       7      63 ..      28      85 ..      24      89 .. 0.66
   3 ?   -0.9   0.0      0.58   2.1e+03      32      58 ..      81     107 ..      79     109 .. 0.84
   4 !   16.6   0.0     2e-06    0.0073       4      65 ..     119     177 ..     118     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
  Peptidase_M3_N 11 eellkeepelaeyrfyleeilrqkp 35
                    + l+k+ p  + + + ++ei +q +
      AJA92197.1 16 DDLVKN-PTRQTFDKKIKEIQKQSE 39
                    667774.888888888888888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
  Peptidase_M3_N  7 eekleellkeepelaeyrfyleeilrqkph.tLseeeEklLaelsevggaawnifsdl 63
                    ++k++e+ k+++++a+ +  l+  +  k+  +L  e E +  + s++gg a  +fs+ 
      AJA92197.1 28 DKKIKEIQKQSEKFAKNKSQLKPNMSSKKFlQLLHEIEDITEKSSKIGGYAGLKFSED 85
                    5677788887788887777777555555532677777777777777777776666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.58
  Peptidase_M3_N  32 rqkphtLseeeEklLaelsevggaawn 58 
                     ++ + t s+e  +lL+  s+ g++ +n
      AJA92197.1  81 KFSEDTQSDEATALLNRISQFGSTIQN 107
                     566778899999**********99877 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 2e-06
  Peptidase_M3_N   4 aldeekleellkeepelaeyrfyleeilrqkphtLseeeEklLaelsevggaawnifsdltn 65 
                     ++de+  ++l+k+  el++y   l+  +  +++ L+e eEk+++ l ++g +a  + +d  +
      AJA92197.1 119 QVDEKNARRLIKDAGELSDY---LRYKRLVAKYALTEPEEKIINTLDVTGISALVKIYDKIT 177
                     689999******99999999...99999**********************999776666554 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.1e-05     0.038      27      56 ..     369     397 ..     344     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
  Peptidase_M78  27 etkvivlnsnhsptrqrftlaHElgHlllh 56 
                     t+++++n    + r  ftlaHE+gH+++ 
     AJA92197.1 369 ITPFVLINYT-GKSRDVFTLAHEIGHAVHS 397
                    5788888877.889************9976 PP

>> Tho1_MOS11_C  Tho1/MOS11 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5      0.83     3e+03      19      29 ..      38      48 ..      28      57 .. 0.72
   2 ?   11.4   0.0     6e-05      0.22      21      48 ..      81     107 ..      80     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.83
  Tho1_MOS11_C 19 akKFgqeeeai 29
                  ++KF+++++++
    AJA92197.1 38 SEKFAKNKSQL 48
                  57888888775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6e-05
  Tho1_MOS11_C  21 KFgqeeeaidelekqleRieKFGvdlnt 48 
                   KF+++ ++ de++  l+Ri  FG + ++
    AJA92197.1  81 KFSEDTQS-DEATALLNRISQFGSTIQN 107
                   9*999999.**************66655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.8e-05      0.35      21      62 ..       2      40 ..       1      43 [. 0.92
   2 ?   -2.4   0.1       1.4   5.2e+03      32      53 ..     196     218 ..     194     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.8e-05
         MIT 21 eeAlelYkealelLlqalkekneerrellrekieeYleRaee 62
                ++A+++Yk+++  L  ++k  n  +r+++ +ki+e ++  e+
  AJA92197.1  2 KDAVQKYKNGIWDLDDLVK--N-PTRQTFDKKIKEIQKQSEK 40
                68****************9..8.99**********9998886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
         MIT  32 elLlqalkekneerrel.lreki 53 
                 e L++++++kn++ re+ +++ +
  AJA92197.1 196 EQLTTLVRNKNPKVREAaYKSLL 218
                 66788888788877765144444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4071.19
//
Query:       AJA92198.1  [L=253]
Description: 3-hydroxybutyryl-CoA dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-69  231.8   0.8    8.6e-69  231.6   0.8    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    8.7e-41  140.5   0.3    1.2e-39  136.7   0.3    1.9  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.032   14.5   0.1    1.5  1  DUF4362   Domain of unknown function (DUF4362)


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.6   0.8   1.4e-72   8.6e-69       3     245 ..       9     252 ..       7     253 .] 0.99

  Alignments for each domain:
  == domain 1  score: 231.6 bits;  conditional E-value: 1.4e-72
                 ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHHHHHHSSSEEEEEE-SEEE CS
       ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeekakqallkeevlelwtklytvpkpviaavnGaai 100
                  +gv+v+k+nrP+++Na++  +  E+i  +e+l++d sv+++vLtG gdkaF+aGad++ m + +  + +++ +  +e    + +v kp+iaavnG+a+
  AJA92198.1   9 DEGVCVVKINRPTKLNAMNIDVAREIISTFEQLDKDDSVKVIVLTGeGDKAFSAGADIEYMSKISADESEVYAKLGQEVTATVENVSKPTIAAVNGFAL 107
                 78**************************************************************9999******************************* PP

                 THHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHH CS
       ECH_1 101 gGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalr 199
                 gGG+e+a+ cDi+ia++na+ g++e+ +G+ pg ggtq+l+r+vG +kA+e++++gk i+a+ea+++Glv++vvp e l+ee +++a+ +a+++ +a+r
  AJA92198.1 108 GGGCEVAMSCDIRIASENARMGQPEVTIGIPPGWGGTQRLMRIVGIAKAKELVYTGKMIKAAEAKEIGLVNNVVPLESLMEEVMSMAKTIASNATLAVR 206
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHTCSH CS
       ECH_1 200 qlkealnakledalaeqleaeaklfestfskddikeGlqaflEkrk 245
                 + k a+n+  +  l ++l +e     + fs  d+++ +  f+ k k
  AJA92198.1 207 MSKTAINKGRNADLDTGLGVELLAWRNCFSDPDREKRMVDFVNKSK 252
                 ******************************************9987 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   0.3     2e-43   1.2e-39       2     195 ..      13     203 ..      12     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 2e-43
                 EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHHHHHC-SS-EEEEE-BEEET CS
       ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklnyliatypkpvvalmdGivmG 100
                  v+++nrp +lNa++ +++r++ +++++ +kdd+vk++vl+g+g+kaf+AG D++ + +   ++++    + +   ++ +++++++kp++a ++G+++G
  AJA92198.1  13 CVVKINRPTKLNAMNIDVAREIISTFEQLDKDDSVKVIVLTGEGDKAFSAGADIEYMSKISADESE---VYAKLGQEVTATVENVSKPTIAAVNGFALG 108
                 6899****************************************************9998888664...4999999*********************** PP

                 HHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HHHHHHTTS--EE--GGGHHHHHHHHHTT........ CS
       ECH_2 101 gGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkgadalaaglathyvpseklealeeaLaelessdeeav 195
                 gG+ +++++ +r+++e++++  PE++IG+ P  Gg+  L r+ g + ++ l  TG+ +k+a+a ++gl +++vp e+l +   ++a++  s+ +++
  AJA92198.1 109 GGCEVAMSCDIRIASENARMGQPEVTIGIPPGWGGTQRLMRIVGiAKAKELVYTGKMIKAAEAKEIGLVNNVVPLESLMEEVMSMAKTIASN-ATL 203
                 *****************************************988799***************************998866555555543332.222 PP

>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.3e-06     0.032       9      46 ..      23      61 ..      17      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-06
     DUF4362  9 veisNvdklekFienveq.kkkdkirivsyTeeGdpile 46
                ++ +N+d   + i  +eq  k+d ++++ +T eGd  ++
  AJA92198.1 23 LNAMNIDVAREIISTFEQlDKDDSVKVIVLTGEGDKAFS 61
                4679************9835679************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1832.01
//
Query:       AJA92199.1  [L=336]
Description: GHMP kinase C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-09   38.0   0.0    3.7e-09   36.8   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal
    1.7e-05   25.0   0.1    2.9e-05   24.2   0.1    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.033   14.4   0.0        4.4    7.5   0.0    2.5  2  DUF3861         Domain of Unknown Function with PDB structure


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   6.2e-13   3.7e-09       3      81 ..     236     313 ..     234     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.2e-13
  GHMP_kinases_C   3 ealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                      al+++dl+l+ ++l +s+  ++k+  gi +p +++++++  +lGa + k++GaGgG+ +++ + +k++ ++++r +++
      AJA92199.1 236 TALRKNDLNLFQDILKQSWIEKKKYASGITNPKIDAIIKKGFSLGAGAMKVTGAGGGGHLYMYA-EKSKHKRIIRNMSK 313
                     6899************99999999***************************************9.99999****99976 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   4.9e-09   2.9e-05       2      66 .]      94     161 ..      93     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.9e-09
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                     i i +++  g+GLGSS++la+ +v  +  + ++++++   a+la+++     + n + +D +as++Gg
      AJA92199.1  94 IFICTDVSAGSGLGSSSSLATNIVNVISTMKNKKWSKnkiAMLAYKISTSNLKWNIGKQDEFASAFGG 161
                     666789999**********************9999554789999999988888999*********998 PP

>> DUF3861  Domain of Unknown Function with PDB structure (DUF3861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00073       4.4      52      83 ..      29      60 ..      18      63 .. 0.87
   2 ?    3.7   0.3     0.011        67       4      77 ..     171     249 ..     166     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00073
     DUF3861 52 aalavglkLlgevmlknrknplFaelrpafre 83
                 ++++++ L + v+ k+r++ l++ + p f +
  AJA92199.1 29 YSICTSINLYTYVIAKKRNDNLLQGFSPDFAS 60
                5688999*********************9976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.011
     DUF3861   4 ritveeleda..dgeeseekpleFeaenhdDilkiv.erlkkkedldadeaaalavglkLlgevmlknrknp..lFael 77 
                 ++tv++++ +    +e e+++l F ++n+    +i+ e+lk+ ++ ++++ +al     L  e+  + rkn   lF+++
  AJA92199.1 171 KVTVTPVKLNksTRNEIEKNSLLFFIGNRKPSYDILsEQLKNINKNKSETINALHKVKELTLEMYTALRKNDlnLFQDI 249
                 68899888773244455556***********999984567777777788877777666677777666666665567766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2427.40
//
Query:       AJA92200.1  [L=269]
Description: uroporphyrinogen-III synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-44  151.5   0.0    2.6e-44  151.3   0.0    1.0  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.3   0.0   1.4e-48   2.6e-44       2     230 ..      21     258 ..      20     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.3 bits;  conditional E-value: 1.4e-48
                 HHHHHHHHTTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHH...HTT---HHHHHCSEEESSHHHHHHHHHTT---SEE CS
        HEM4   2 elaealearGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealk...reeedvkalaslkvaavGpaTaraLeelglrvdlv 97 
                 e+ +++ ++ a+p+ lP+ie +  + ++ ++++l +++++++d+ +f+S++av+ l+e  k   + ee+  a+ ++ v+avGp+T++aLe+ ++rv+++
  AJA92200.1  21 EFIQLITKHNATPITLPTIELVS-KGEKIVDDFLTSVKTENPDYSVFMSSKAVKLLIESSKkisKFEELRLAITNTIVIAVGPKTKEALENENIRVSHM 118
                 7899*******************.99999********************************9999999999999************************* PP

                 -..SSSHHHHGGGS-.---E.EEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEE..EE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HH. CS
        HEM4  98 pseegtaegLaeelaeslag.krvlllrgeiarddlaegLeergaevdevevYet..vpaeeepeelkealkagevdavvftSpstvrnllellkdeg. 192
                 p   ++++g+ e++ + +a  k+v+++r+  + + l+e Le+ g+e+ e+ +Y+    +++ +  e++ ++ +++vd+++ftS+s+vr+++e+++++  
  AJA92200.1 119 PT-RYSSVGVGEVFTKLNAVgKKVIVPRSGASTPFLKELLEKIGLEIIELYLYDVcaFRDTTQWNEFRSLFSKNSVDGIIFTSASSVRAFFEIMTKDFe 216
                 *9.************96665599********************************9888888*********************************9989 PP

                 .....HHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHH CS
        HEM4 193 .....delkevkvaaiGptTaealkklglkvdvvaeeptaegl 230
                      ++l+++kv+aiGp Ta++lkk+ +++ ++a+ +t+ g 
  AJA92200.1 217 hsqllENLQKTKVIAIGPFTADELKKFDVQN-IIADVHTVAGS 258
                 *******************************.9**99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1881.31
//
Query:       AJA92201.1  [L=164]
Description: hypothetical protein T478_1445 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.8   0.0       0.11   13.0   0.0    1.6  1  LEA_2     Late embryogenesis abundant protein
       0.12   11.9   0.2        5.2    6.6   0.0    2.1  2  GXGXG     GXGXG motif


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05      0.11       4      34 ..      64      94 ..      62     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                EEESSSS-EEEEEEEEEEEESSSEEEEEEEC CS
       LEA_2  4 vrNPNsfgvrydgleldlsyngqrlasgtsp 34
                v NP +++v++  ++++l+++g ++++gt +
  AJA92201.1 64 VANPGEVTVTVPVITYQLYADGSQIGQGTYS 94
                89************************76543 PP

>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00058       5.2     154     185 ..      18      46 ..      12      56 .. 0.67
   2 ?    3.6   0.0    0.0048        43      72     101 ..     117     145 ..      83     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00058
                 T--EEEEEEE-SSSTHHHHB-TTT-EEEES-S CS
       GXGXG 154 GmsgGiayvldedekfekklnkelvelekved 185
                 Gm+gGi+y  + d++   +l ++++el++ve 
  AJA92201.1  18 GMMGGIVYYASLDND---DLSMATIELQSVEL 46 
                 9*******9977766...55555555555443 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0048
                 EEEEE--TT-SS-GGGSB-S-SSTTTT--S CS
       GXGXG  72 kivikpskeskfkaeeniivGnvvlygatg 101
                 k++i  s+  + +  ++ii G ++ y+atg
  AJA92201.1 117 KLTIVMSD-INKTVYDKIISGQTIQYSATG 145
                 55555555.55677899**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1152.69
//
Query:       AJA92202.1  [L=141]
Description: Raf-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-28   99.0   0.0    3.5e-28   98.6   0.0    1.2  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   1.9e-32   3.5e-28       2     132 .]      17     139 ..      16     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.9e-32
                 --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCT.TEEEEEEEEEETTSSEE-TTC.EE-B-TTSSCCCCS---B--STTS..EEEEEEEE CS
         PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvse.tflHwvvtnipasvtslpega.vqgknslgeesesgYlgpcPpkgdgkHrYvflly 96 
                 +pkk+  + en +P++s++  p+ t ++al++ DpDa    +  +lHw+++         +e + v+gk+++ e   +gY+gp+Pp+g   H+Yvf+ y
  AJA92202.1  17 IPKKFgyKFENEEPNISFNRPPSSTTTLALIMDDPDAMGAVGkVWLHWLQYHNL------TESSpVEGKTDFDE---IGYGGPAPPDGR--HTYVFKAY 104
                 8999866777888************************6344434******9654......2333489******9...************..******** PP

                 EESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
         PBP  97 aldvealdlkagftraelgaaiaghvlakatlagnY 132
                 ald+e  +lk+gf+++el+ a++gh++a+a+l+g++
  AJA92202.1 105 ALDTEL-ELKEGFSKQELEDAMKGHIIAEAKLTGTF 139
                 *****5.89*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1054.73
//
Query:       AJA92203.1  [L=253]
Description: ribosomal protein L11 methyltransferase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-10   40.4   0.0    3.3e-10   40.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    4.7e-10   39.3   0.5    2.3e-08   33.8   0.5    2.1  1  DOT1             Histone methylation protein DOT1
    5.3e-10   39.9   0.0      1e-09   39.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.5e-07   32.0   0.0    2.5e-07   31.2   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00017   21.1   0.1    0.00028   20.4   0.1    1.4  1  Methyltransf_4   Putative methyltransferase
    0.00018   21.0   0.1    0.00025   20.6   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00041   21.1   0.0    0.00065   20.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0006   19.0   0.0    0.00074   18.7   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00076   19.3   0.0     0.0011   18.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0013   18.1   0.1     0.0018   17.6   0.1    1.1  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
     0.0033   16.9   0.1     0.0056   16.1   0.1    1.4  1  TehB             Tellurite resistance protein TehB
     0.0038   16.6   0.1     0.0053   16.1   0.1    1.2  1  GidB             rRNA small subunit methyltransferase G
  ------ inclusion threshold ------
      0.018   14.6   0.1      0.034   13.7   0.1    1.3  1  MTS              Methyltransferase small domain
      0.019   14.3   0.0      0.025   13.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.044   13.4   0.0      0.058   13.0   0.0    1.1  1  Spb1_C           Spb1 C-terminal domain
      0.052   12.9   0.1      0.076   12.3   0.1    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.081   12.2   0.0       0.12   11.7   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
      0.087   12.7   0.0       0.11   12.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.098   12.5   0.1       0.43   10.4   0.0    2.0  2  DUF5362          Family of unknown function (DUF5362)


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   3.5e-13   3.3e-10       3     103 ..      38     130 ..      36     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.5e-13
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkilee 96 
                      ++ +++ lG+G+G+ ++ + +e +  ++ +GiD+se++i+lA+++  + +++n+++ ++d+ ++e  ++d   D+il+   +++   +++  e+
       AJA92203.1  38 QNDTFYHLGSGNGTSLKIARQEFN-VKNAIGIDNSEKMISLAKKMINEENISNIKVIEQDVRKAE--FKD--ADVILCW--FMDAEVLESLVEK 124
                      5677888*******9999997765.5779************************************..998..****994..4444444444444 PP

  Methyltransf_31  97 iervlkp 103
                       ++ lk+
       AJA92203.1 125 -FQKLKN 130
                      .344444 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.5   2.5e-11   2.3e-08      28     156 ..      24     136 ..      17     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.5e-11
                 HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEESS-STT-HHHHHHGGG-SEE CS
        DOT1  28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefirksFvenekveeiieeadvi 126
                 p+ + e+ +  +l+++d+F+ LGSG G     a  e+++k+++G++ +++  +la+k+ +e          + ++i+ i+++  + e      ++advi
  AJA92203.1  24 PDTIREICKFADLGQNDTFYHLGSGNGTSLKIARQEFNVKNAIGIDNSEKMISLAKKMINEE---------NISNIKVIEQDVRKAE-----FKDADVI 108
                 6788999999*********************************************9987764.........4566777766655544.....4789*** PP

                 EE--TT--HHHHHHHHHHHTT--TT-EEEE CS
        DOT1 127 lvNNfaFdaelnkqlkellqdlkegtkiis 156
                 l   +  dae+ ++l e +q+lk+g +ii+
  AJA92203.1 109 LC--WFMDAEVLESLVEKFQKLKNGVRIIT 136
                 97..788**********************8 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.1e-12     1e-09       4      78 ..      45     119 ..      43     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.1e-12
                      ET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GGGSS CS
  Methyltransf_25   4 lGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lhhls 78 
                      lG G+G+ ++ + ++++ ++ +g+D se+m+  a++ ++ee++ n++++++d+++ +f+d   D+++++++  ++l+
       AJA92203.1  45 LGSGNGTSLKIARQEFNVKNAIGIDNSEKMISLAKKMINEENIsNIKVIEQDVRKAEFKD--ADVILCWFMdAEVLE 119
                      89*****99999999999***********************99****************9..9*****977555543 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   2.7e-10   2.5e-07       3      74 ..      45     121 ..      43     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.7e-10
                      ET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES....-CCC- CS
  Methyltransf_11   3 vGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvsse....vlhhv 74 
                      +G+G+G  ++   + +  ++ +g+D s++m+ lak+ ++ee++ +++++++d++k  f+d   D++++ +    vl+ +
       AJA92203.1  45 LGSGNGTSLKIARQEFnvKNAIGIDNSEKMISLAKKMINEENIsNIKVIEQDVRKAEFKD--ADVILCWFmdaeVLESL 121
                      8************88889***********************99*****************..78887765333344444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.9e-07   0.00028       3      60 ..      40      97 ..      38     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.9e-07
                    EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
  Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgda 60
                     ++  +G+G+G++l    +++  kn +Gi+ ++k++  + k i++++++N++++++d 
      AJA92203.1 40 DTFYHLGSGNGTSLKIARQEFNVKNAIGIDNSEKMISLAKKMINEENISNIKVIEQDV 97
                    578889******998888888999*******************************996 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.6e-07   0.00025     163     252 ..      40     130 ..      32     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.6e-07
        PrmA 163 eevlDvGtGSGi.LaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvivaNIL.aevlielaedikklvke 252
                 +++  +G G G  L ia + ++ k+++++D  e  ++ ak+ ++  ++++   +  ++++ k   + advi++  + aevl +l+e+++kl k+
  AJA92203.1  40 DTFYHLGSGNGTsLKIARQEFNVKNAIGIDNSEKMISLAKKMINEENISNIKVI--EQDVRKaeFKDADVILCWFMdAEVLESLVEKFQKL-KN 130
                 5666789999866**********************************9996634..444443336789*****99889********98775.44 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.9e-07   0.00065       3      74 ..      45     112 ..      43     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.9e-07
  Methyltransf_12   3 iGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasn 74 
                      +G+G+G+ l+  ++++  ++ +g+D s+++i  ak+ +++++  n +++e +++ ++     +  D++++ +
       AJA92203.1  45 LGSGNGTSLKIARQEFNVKNAIGIDNSEKMISLAKKMINEENISNIKVIEQDVRKAEF----KDADVILCWF 112
                      8******************************777777666666555555555555443....499***9864 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.9e-07   0.00074      14      93 ..      22     105 ..      15     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.9e-07
                 --HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGHHHHHH CS
      RrnaAD  14 knkkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls..kdeklkvvhqDflkfetpee 93 
                 + + +i eI + ++l +++t + +g+G G   ++  + +  k+   + + e+++ l +k ++  + +++kv++qD+ k+e++  
  AJA92203.1  22 IPPDTIREICKFADLGQNDTFYHLGSGNGTSLKIARQEFnvKNAIGIDNSEKMISLAKKMINeeNISNIKVIEQDVRKAEFKDA 105
                 567899***********************888887666679******************99987889**************984 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0011      59     160 ..      24     122 ..       4     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                 HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSBBSS--H CS
        PCMT  59 phmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaaapeiPe 157
                 p ++  ++++ +l + +    +GsG G    +  + ++ k  +++i+ ++++++ ak+ +++++++n++v++ D rk   e+   d+i+      e+ e
  AJA92203.1  24 PDTIREICKFADLGQNDTFYHLGSGNGTSLKIARQEFNVKN-AIGIDNSEKMISLAKKMINEENISNIKVIEQDVRKA--EFKDADVILCWFMDAEVLE 119
                 56777788999999999999********9999999999887.9*******************************9984..4444466766666666666 PP

                 HHH CS
        PCMT 158 ali 160
                 +l+
  AJA92203.1 120 SLV 122
                 665 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.9e-06    0.0018      37     122 ..      41     123 ..      32     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
       Rsm22  37 slldvgegpgtalwaaselweeleevlvidaseelleiskelaadapelkeaalrrsvirealeleeadLviisyvLleledesre 122
                 ++ ++g+g gt+l +a + ++ +++++ id se++ +++k+++++ +  + +  +++v   ++e+++ad++ + ++  e+ ++  e
  AJA92203.1  41 TFYHLGSGNGTSLKIARQEFN-VKNAIGIDNSEKMISLAKKMINEENISNIKVIEQDVR--KAEFKDADVILCWFMDAEVLESLVE 123
                 6889**************996.78999*************9998776666665666665..799*********9987777665444 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.9e-06    0.0056      36     124 ..      44     129 ..      26     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-06
                 EES-TTSHHHHHHHHTT-EEEE...EES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-GGGHHHHHHHHHHTE CS
        TehB  36 dlgcgqgrnslylsllgydvta...wdknensiafleeikekenlknistalydineaklderydfilstvvlmfleaeripsiienmqect 124
                  lg g+g  sl ++ + ++v+    +d+ e+ i+  +++++ en++ni+    d+ +a++++  d il      f++ae + s++e +q+  
  AJA92203.1  44 HLGSGNG-TSLKIARQEFNVKNaigIDNSEKMISLAKKMINEENISNIKVIEQDVRKAEFKD-ADVILC----WFMDAEVLESLVEKFQKLK 129
                 6899999.59*********9853337999******************************976.577764....6889999999999888764 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.6e-06    0.0053      51     121 ..      41     110 ..      25     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.6e-06
                 .EEEETSTTTTTHHHHHHH-TTSE...EEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCCTTTTT-EEEEEE CS
        GidB  51 kviDvGsGaGlPGipLaiarpelk...ltLleslekkiaFLeevkeelklenveivearaeekqeeekydvvts 121
                 ++  +GsG+G     L+iar+e +    + ++ +ek i+  +++++e +++n++++e+++ +  e ++ dv+++
  AJA92203.1  41 TFYHLGSGNGT---SLKIARQEFNvknAIGIDNSEKMISLAKKMINEENISNIKVIEQDVRK-AEFKDADVILC 110
                 48899****86...7999999887444567********************************.89999999998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.6e-05     0.034      36     103 ..      43     110 ..      33     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                 EEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE CS
         MTS  36 lDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivs 103
                   lG+G+G  ++++a+++ +++    +d++ + + +ak+ +++++++ ++v+++dv ++   k+ d+i++
  AJA92203.1  43 YHLGSGNGT-SLKIARQEFNVKnAIGIDNSEKMISLAKKMINEENISnIKVIEQDVRKAEF-KDADVILC 110
                 569*****7.6666666666655889*******************999********99998.99999987 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.7e-05     0.025      51     117 ..      27      94 ..      18     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                 HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEE CS
        CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevk 117
                 ++ i++ ++l + +t   +G G G+ ++ a ++++v + +g+  S++   lakk+++e+++++ + ++
  AJA92203.1  27 IREICKFADLGQNDTFYHLGSGNGTSLKIARQEFNVkNAIGIDNSEKMISLAKKMINEENISNIKVIE 94 
                 678899999***************************4589******************9988765433 PP

>> Spb1_C  Spb1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.058      34      80 ..      68     116 ..      39     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
      Spb1_C  34 ilta.ealalaqqlatgkktke.dlidegfnryafndkdgLPeWFldDE 80 
                 i +  + ++la++++++++ ++ ++i++   +  f+d d +  WF+d E
  AJA92203.1  68 IDNSeKMISLAKKMINEENISNiKVIEQDVRKAEFKDADVILCWFMDAE 116
                 444404569******99987777************************98 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.1e-05     0.076      62     115 ..      52     105 ..      29     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
                      HHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T CS
  Ubie_methyltran  62 afklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedd 115
                      ++k++++  +  + +++D +e+m++ ++k ++ee  +ni+ +  +  + +f+d 
       AJA92203.1  52 SLKIARQEFNVKNAIGIDNSEKMISLAKKMINEENISNIKVIEQDVRKAEFKDA 105
                      45555555555577899**********************************994 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.12      53     132 ..      29     109 ..      20     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                     HHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-H.HHHHHHHHHS-----TTEEEEES-TTTS-----SEEE CS
  Methyltransf_2  53 kvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlp.eVveaAkehlsageeervefvgGdffkdslPeaDail 132
                     ++ +  dl +  +++ +G G G  +k + + +   ++i  D + + ++ Ak+ ++ ++ +++++++ d++k +  +aD+il
      AJA92203.1  29 EICKFADLGQNDTFYHLGSGNGTSLKIARQEFNVKNAIGIDNSeKMISLAKKMINEENISNIKVIEQDVRKAEFKDADVIL 109
                     55566678888999************************999863699*******************************875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012      0.11      29      91 ..      45     113 ..      36     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
  Methyltransf_23  29 iGcGtGillevlrengf..svtgvDlspeaveiae................kakkaqkdqfdeqeaaepqgkfdlIvlrev 91 
                      +G G G+ l+++r+++   + +g+D s++++++a+                         +    ++ + +  d+I ++++
       AJA92203.1  45 LGSGNGTSLKIARQEFNvkNAIGIDNSEKMISLAKkmineenisnikvieqD--------V----RKAEFKDADVILCWFM 113
                      699*********9874345999***********9888877655422222221........1....2222346677777654 PP

>> DUF5362  Family of unknown function (DUF5362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.7   2.6e+03      59      77 ..     119     137 ..     113     138 .. 0.81
   2 ?   10.4   0.0   0.00046      0.43      34      74 ..     206     246 ..     204     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.7
     DUF5362  59 eklkealeklakylkilli 77 
                 e+l e ++kl++ ++i+ i
  AJA92203.1 119 ESLVEKFQKLKNGVRIITI 137
                 6778899999999999887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00046
     DUF5362  34 llIivglklfkaakaikealrskseeklkealeklakylki 74 
                 l+Ii +l ++  ak+++ a  ++ + +++ +++ l++y+ i
  AJA92203.1 206 LVIIQALTIWINAKNLGVACGEEIPDSIRSYIAILREYFGI 246
                 89************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1828.92
//
Query:       AJA92204.1  [L=179]
Description: hypothetical protein T478_1415 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-05   24.6   0.0    3.7e-05   24.1   0.0    1.2  1  MG2       MG2 domain
  ------ inclusion threshold ------
      0.036   13.9   0.1      0.058   13.3   0.1    1.3  1  FlgD_ig   FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   4.1e-09   3.7e-05       5      81 ..      33     115 ..      30     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.1e-09
                 EES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEE.......E CS
         MG2   5 ytDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvel.......s 81 
                 + D  +Y  g+ +s+++ +  +++ +     l+++i++p+g +++ + l++d++g +e+ f+l+++   G+y v++       +
  AJA92204.1  33 IDDNFVYSVGDDLSITGWVEYDDAATSDV-LLSVKISNPNGTVISDFFLTSDSNGQFEFPFELSDDDTSGDYLVNImsmcreiH 115
                 55667899999999999998888777665.89******************************************9966665554 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.4e-06     0.058      25      72 ..      63     106 ..      41     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                 EEEEEE-SS--EEEEEEEEESSSEEEEEEE-SB-TTS-B--SEEEEEE CS
     FlgD_ig  25 vtvtikDasGevVrtidlgaqsaGvvsftWdGtdndGnkladGaYtvk 72 
                 ++v+i + +G+v+    l++ s G+++f +   d+d     +G+Y v+
  AJA92204.1  63 LSVKISNPNGTVISDFFLTSDSNGQFEFPFELSDDD----TSGDYLVN 106
                 49*************************998844444....36777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1302.11
//
Query:       AJA92205.1  [L=828]
Description: pentapeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-71  234.8  64.0    5.9e-13   48.2   2.9   11.9 13  Pentapeptide    Pentapeptide repeats (8 copies)
    1.1e-46  156.9  38.5    1.2e-08   34.9   0.3    7.1  9  Pentapeptide_4  Pentapeptide repeats (9 copies)
    2.1e-32  111.0  15.2    6.5e-06   26.2   0.1   10.8 10  Pentapeptide_3  Pentapeptide repeats (9 copies)
    5.9e-05   23.5   0.0     0.0001   22.7   0.0    1.4  1  Lipase_GDSL_2   GDSL-like Lipase/Acylhydrolase family
  ------ inclusion threshold ------
      0.046   14.3   0.7         34    5.0   0.0    3.4  3  SIN1            Stress-activated map kinase interacting prote


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   1.3e-06    0.0048       7      38 ..     416     447 ..     411     447 .. 0.94
   2 !   36.4   3.2   7.8e-13   2.8e-09       1      39 [.     430     468 ..     430     468 .. 0.97
   3 !   42.6   4.4   9.5e-15   3.4e-11       1      39 [.     445     483 ..     445     483 .. 0.96
   4 !   37.1   1.5   4.8e-13   1.7e-09       1      40 []     465     504 ..     465     504 .. 0.96
   5 !   35.2   0.8   1.9e-12   6.9e-09       2      40 .]     506     544 ..     506     544 .. 0.93
   6 !   35.2   0.8   1.8e-12   6.6e-09       2      40 .]     546     584 ..     546     584 .. 0.93
   7 !   25.0   2.0   3.1e-09   1.1e-05       2      39 ..     586     623 ..     586     623 .. 0.97
   8 !   24.4   0.4   4.4e-09   1.6e-05       2      34 ..     601     633 ..     601     636 .. 0.47
   9 !   12.4   0.0   2.6e-05     0.092      13      30 ..     640     657 ..     625     660 .. 0.73
  10 !    4.7   0.1    0.0068        24      26      39 ..     667     680 ..     665     681 .. 0.54
  11 !   14.6   0.1   5.3e-06     0.019       4      24 ..     685     705 ..     683     706 .. 0.73
  12 !   38.4   2.1   1.9e-13   6.8e-10       7      40 .]     758     791 ..     758     791 .. 0.97
  13 !   48.2   2.9   1.6e-16   5.9e-13       1      39 [.     782     820 ..     782     820 .. 0.98

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                   B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   7 nLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                   n+s+ + +++ +  +++t++nls+  Ls+++L
    AJA92205.1 416 NFSNMIIKNSIFDMSDFTSVNLSNVILSNSRL 447
                   9****************************987 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 7.8e-13
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   ++++ +nLs+ +Ls++ l+  n+++Anl+gAdLs++nLs
    AJA92205.1 430 SDFTSVNLSNVILSNSRLYSVNFQNANLIGADLSNSNLS 468
                   69***********************************97 PP

  == domain 3  score: 42.6 bits;  conditional E-value: 9.5e-15
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   ++L+ +n+++anL ga+ls++nL++Anlsg dLs++nLs
    AJA92205.1 445 SRLYSVNFQNANLIGADLSNSNLSYANLSGLDLSDTNLS 483
                   57999********************************97 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 4.8e-13
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   +nLs AnLsg +Ls++nls++ L+gA+ls+++L + n++g
    AJA92205.1 465 SNLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEG 504
                   79************************************98 PP

  == domain 5  score: 35.2 bits;  conditional E-value: 1.9e-12
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   +Ls AnLsg +Ls++nls++ L+gA+ls+++L + n++g
    AJA92205.1 506 DLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEG 544
                   799999999999999999999999999999999999997 PP

  == domain 6  score: 35.2 bits;  conditional E-value: 1.8e-12
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   +Ls AnLsg +Ls++nls++ L+gA+ls+++L + n++g
    AJA92205.1 546 DLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEG 584
                   799999999999999999999999999999999999997 PP

  == domain 7  score: 25.0 bits;  conditional E-value: 3.1e-09
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   +++++nL   ++s  nls +n+ +A+++ ++L+++nLs
    AJA92205.1 586 DFEETNLNYNDFSYKNLSKSNFKEASFYESNLENSNLS 623
                   799*********************************97 PP

  == domain 8  score: 24.4 bits;  conditional E-value: 4.4e-09
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EEC CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLs 34 
                   nLs  n+ +a++ ++nl+++nL+++ +++ dL+
    AJA92205.1 601 NLSKSNFKEASFYESNLENSNLSKSIFINVDLT 633
                   444444444444444444444444444444444 PP

  == domain 9  score: 12.4 bits;  conditional E-value: 2.6e-05
                   CEECCCESEEECT-B-TT CS
  Pentapeptide  13 LsganlsgAnLtgAnlsg 30 
                   L+g++l++A+++++nls+
    AJA92205.1 640 LKGTDLTEAVFSYSNLSN 657
                   667777777777777776 PP

  == domain 10  score: 4.7 bits;  conditional E-value: 0.0068
                   -B-TT-EECCEEEC CS
  Pentapeptide  26 AnlsgAdLsganLs 39 
                   +n++ A++++++Ls
    AJA92205.1 667 TNFNYAKMNESDLS 680
                   55666666666655 PP

  == domain 11  score: 14.6 bits;  conditional E-value: 5.3e-06
                   TT-B-CCSCCEECCCESEEEC CS
  Pentapeptide   4 sgAnLsganLsganlsgAnLt 24 
                   sgA++ +a+++++n+++++++
    AJA92205.1 685 SGAYFGNAKMRDVNFENTDFS 705
                   677777888888888877776 PP

  == domain 12  score: 38.4 bits;  conditional E-value: 1.9e-13
                   B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   7 nLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   n++ a+L++a +++AnL ++++++A+L+ganL+g
    AJA92205.1 758 NFHDADLRNAQFKNANLEYVDFTNANLEGANLEG 791
                   89******************************98 PP

  == domain 13  score: 48.2 bits;  conditional E-value: 1.6e-16
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   AnL+gAnL+ganL+++ + ++nL gAnl+gA+L+ganLs
    AJA92205.1 782 ANLEGANLEGANLKNTYMVNTNLEGANLEGANLEGANLS 820
                   9************************************97 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1   4.1e+03      35      43 ..     136     144 ..     125     175 .. 0.62
   2 !   34.2   1.9     6e-12   2.1e-08      10      75 ..     409     475 ..     406     477 .. 0.92
   3 !   29.3   0.0   1.9e-10   6.9e-07       9      73 ..     463     528 ..     462     532 .. 0.92
   4 !   28.4   0.0   3.7e-10   1.3e-06       6      72 ..     500     567 ..     496     571 .. 0.91
   5 !   25.7   0.0   2.7e-09   9.7e-06       7      68 ..     531     592 ..     522     595 .. 0.59
   6 !   31.5   1.5   4.2e-11   1.5e-07      10      75 ..     569     635 ..     565     636 .. 0.89
   7 !   29.0   3.9   2.6e-10   9.2e-07       7      77 .]     586     660 ..     582     660 .. 0.93
   8 !   21.5   0.9   5.3e-08   0.00019       3      74 ..     635     710 ..     633     716 .. 0.79
   9 !   34.9   0.3   3.5e-12   1.2e-08       1      68 [.     762     819 ..     756     826 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
  Pentapeptide_4  35 nvnFdecnl 43 
                     n+nF++ ++
      AJA92205.1 136 NTNFENFDI 144
                     333333332 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 6e-12
  Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdi 75 
                     n++++n nFs+  ++++ F  +++++vn+++  ls+++++ v++ +a++ g +l+n+n+s   l ++
      AJA92205.1 409 NVDFKNKNFSNMIIKNSIFDMSDFTSVNLSNVILSNSRLYSVNFQNANLIGADLSNSNLSYaNLSGL 475
                     89*********************************************************84367655 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 1.9e-10
  Pentapeptide_4   9 nncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klk 73 
                      n++ls++n+s  +l d+n++e+ l  + +++++l d +f++ dl +a++sg +l+++n+s+  l 
      AJA92205.1 463 SNSNLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEGRDLSYANLSGLDLSDTNLSEtILI 528
                     699*********************************************************763565 PP

  == domain 4  score: 28.4 bits;  conditional E-value: 3.7e-10
  Pentapeptide_4   6 csfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.kl 72 
                       f++ +ls++n+s  +l d+n++e+ l  + +++++l d +f++ dl +a++sg +l+++n+s+  l
      AJA92205.1 500 MNFEGRDLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEGRDLSYANLSGLDLSDTNLSEtIL 567
                     679999*********************************************************76245 PP

  == domain 5  score: 25.7 bits;  conditional E-value: 2.7e-09
  Pentapeptide_4   7 sfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                      + n+kl ++nF+  +l  +n+++ +ls++n++e+ l  +d+++++l +++F+g +++++n+
      AJA92205.1 531 DLSNTKLGDMNFEGRDLSYANLSGLDLSDTNLSETILIGADLSNTKLGDMNFEGRDFEETNL 592
                     34555555566666666666666666666666666666666666666666666666666665 PP

  == domain 6  score: 31.5 bits;  conditional E-value: 4.2e-11
  Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkdi 75 
                     +++lsn+ +   ++++ +F+e++l++  F+  nls+++f e+++ +++++++nl+++ f +  l++i
      AJA92205.1 569 GADLSNTKLGDMNFEGRDFEETNLNYNDFSYKNLSKSNFKEASFYESNLENSNLSKSIFiNVDLTEI 635
                     6899999999999999999999999999***************************999944477765 PP

  == domain 7  score: 29.0 bits;  conditional E-value: 2.6e-10
  Pentapeptide_4   7 sfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkra...sFsgcnlknvnfsd.klkdidF 77 
                      f++++l++ +Fs  +l  +nF+e+ + + n++++nls++ f +vdl+++   s++g +l++++fs   l +i+F
      AJA92205.1 586 DFEETNLNYNDFSYKNLSKSNFKEASFYESNLENSNLSKSIFINVDLTEIknkSLKGTDLTEAVFSYsNLSNIEF 660
                     699********************************************999999************9658999987 PP

  == domain 8  score: 21.5 bits;  conditional E-value: 5.3e-08
  Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFt....ecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsdklkd 74 
                     +++ s+++++l+++ Fs ++l +  F     ++++++++++e++lsd  ++++ + +a    +n++n+ fs  +k+
      AJA92205.1 635 IKNKSLKGTDLTEAVFSYSNLSNIEFPitsyQTNFNYAKMNESDLSDRIISGAYFGNAKMRDVNFENTDFSSRMKT 710
                     67888888888888888888888888522225555999999**************************999765554 PP

  == domain 9  score: 34.9 bits;  conditional E-value: 3.5e-12
  Pentapeptide_4   1 aeftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                     a++++++f+n++l++v+F++a+l+++n+++++l+n+ + ++nl+ +++++++l  a+          +
      AJA92205.1 762 ADLRNAQFKNANLEYVDFTNANLEGANLEGANLKNTYMVNTNLEGANLEGANLEGAN----------L 819
                     234444444444444444444444444444444444444444444444444443333..........3 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   6.1e-06     0.022       4      44 ..     410     447 ..     408     449 .. 0.88
   2 !   16.8   0.0   1.6e-06    0.0058       2      47 ..     443     485 ..     442     486 .. 0.90
   3 !    6.3   0.0    0.0031        11       3      43 ..     489     526 ..     487     531 .. 0.82
   4 !    6.7   0.0    0.0022         8       3      42 ..     529     565 ..     522     571 .. 0.68
   5 ?    3.7   0.0      0.02        71       3      29 ..     569     593 ..     562     601 .. 0.62
   6 !   17.7   0.1     8e-07    0.0029       6      46 ..     597     634 ..     587     636 .. 0.82
   7 ?    1.5   0.1     0.096   3.4e+02      25      35 ..     647     657 ..     637     681 .. 0.48
   8 !   12.6   0.5   3.2e-05      0.11       1      39 [.     669     705 ..     669     707 .. 0.80
   9 !   26.2   0.1   1.8e-09   6.5e-06       5      47 ..     758     797 ..     757     798 .. 0.87
  10 !   23.9   0.0   9.2e-09   3.3e-05       1      44 [.     779     819 ..     779     820 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.1e-06
  Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                     + F++  +F++   +++  F+ +dF+s+++s+++ + ++++
      AJA92205.1 410 VDFKNK-NFSNMIIKNS-IFDMSDFTSVNLSNVILS-NSRL 447
                     679999.9999999999.5**************998.7776 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.6e-06
  Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     s+++++   +F +a+ +ga + sn++++ a++sg   + d+++s++
      AJA92205.1 443 SNSRLYSV-NFQNANLIGA-DLSNSNLSYANLSGLDLS-DTNLSET 485
                     78899999.9*********.9************99999.9999987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0031
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvd 43 
                     ga +s++  + + +F+g  + s a++++ d+s+++ + ++ 
      AJA92205.1 489 GADLSNT-KLGDMNFEGR-DLSYANLSGLDLSDTNLS-ETI 526
                     6778888.9999999999.999999999999999987.665 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0022
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdv 42 
                     ga +s++  + + +F+g  + s a++++ d+s+++ + ++
      AJA92205.1 529 GADLSNT-KLGDMNFEGR-DLSYANLSGLDLSDTNLS-ET 565
                     4556666.6667777777.777777777777777766.54 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.02
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFg 29 
                     ga +s++  + + +F+g  +F++++++
      AJA92205.1 569 GADLSNT-KLGDMNFEGR-DFEETNLN 593
                     4455555.6666666666.66666654 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 8e-07
  Pentapeptide_3   6 FsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                     Fs   ++++++F+ a sF +++++++++s+++F  +vd+++
      AJA92205.1 597 FSYK-NLSKSNFKEA-SFYESNLENSNLSKSIFI-NVDLTE 634
                     4444.566*******.9*****************.***987 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.096
  Pentapeptide_3  25 nadFgsadFsg 35 
                     +a+F+ +++s+
      AJA92205.1 647 EAVFSYSNLSN 657
                     33333333333 PP

  == domain 8  score: 12.6 bits;  conditional E-value: 3.2e-05
  Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFt 39 
                     F+ a +  + d+++   sga +F na +++++F+++ F+
      AJA92205.1 669 FNYAKMNES-DLSDRIISGA-YFGNAKMRDVNFENTDFS 705
                     666667777.7777777888.999*********999997 PP

  == domain 9  score: 26.2 bits;  conditional E-value: 1.8e-09
  Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     nF++a d+r+a F++a + +  dF++a+++ga+ + +++++++
      AJA92205.1 758 NFHDA-DLRNAQFKNA-NLEYVDFTNANLEGANLE-GANLKNT 797
                     68899.9999999999.899999999999999998.9998875 PP

  == domain 10  score: 23.9 bits;  conditional E-value: 9.2e-09
  Pentapeptide_3   1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                     F++an++ga +++ga+ +++ ++ n+++++a+++ga+ + ++++
      AJA92205.1 779 FTNANLEGA-NLEGANLKNT-YMVNTNLEGANLEGANLE-GANL 819
                     99*******.**********.9****************9.8887 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.9e-08    0.0001       1      83 [.     184     267 ..     184     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.9e-08
                    EEESHHHHTCTTBCCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H..HHHHHHHHCTGGG-TSEEEEE--CCCCCTT--HHH CS
  Lipase_GDSL_2   1 alGDSiTaGygadgggrsypaylarllaarl...gldvvnnlgvsGattallrllerlrdllrlkpdlvtiliGtNDlgrgvpaaa 83 
                    a+G S T+G    + ++++pa+l++ +++++     + +n +g+  att +++++    +  +++pd +++  G+ND ++ + ++ 
     AJA92205.1 184 AVGGSTTHGASLVNDDETWPAFLQQIINQKNleiEIQIIN-AGIMAATT-EREFEMISKKIVKFDPDMIIMYDGWNDSYNLPLEQS 267
                    68*******9888******************987777777.********.555555555888***************654433333 PP

>> SIN1  Stress-activated map kinase interacting protein 1 (SIN1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.047   1.7e+02       6      26 ..     479     499 ..     476     513 .. 0.85
   2 ?    2.7   0.0     0.049   1.8e+02       6      26 ..     519     539 ..     516     552 .. 0.86
   3 ?    5.0   0.0    0.0096        34       6      54 ..     559     606 ..     556     649 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.047
        SIN1   6 DtGlcetvlldeDvpktylrk 26 
                 Dt l+et+l+  D++ t+l  
  AJA92205.1 479 DTNLSETILIGADLSNTKLGD 499
                 9*************9998765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
        SIN1   6 DtGlcetvlldeDvpktylrk 26 
                 Dt l+et+l+  D++ t+l  
  AJA92205.1 519 DTNLSETILIGADLSNTKLGD 539
                 9*************9998765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0096
        SIN1   6 DtGlcetvlldeDvpktylrksqeavaedtasalrkpsdtkkvegsggq 54 
                 Dt l+et+l+  D++ t+l  ++ + +  ++ +l+  +d + ++ s+++
  AJA92205.1 559 DTNLSETILIGADLSNTKLGDMNFEGRDFEETNLNY-NDFSYKNLSKSN 606
                 9***************99998887777666666655.333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (828 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.23s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5737.36
//
Query:       AJA92206.1  [L=236]
Description: glycosyltransferase, group 2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-25   88.8   0.1      1e-24   87.2   0.0    1.7  2  Glycos_transf_2  Glycosyl transferase family 2
    5.2e-11   42.9   0.0    1.1e-10   41.8   0.0    1.4  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    3.3e-06   26.8   0.5    5.6e-06   26.0   0.3    1.4  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0012   19.4   0.0     0.0033   17.9   0.0    1.9  2  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   2.3e-28     1e-24       1     164 [.      10     170 ..      10     176 .. 0.93
   2 ?   -1.0   0.0       0.3   1.3e+03     111     134 ..     191     217 ..     181     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 2.3e-28
                      EEEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE CS
  Glycos_transf_2   1 svviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdep 92 
                      s++ p+yNee+ l+++++  ++    +   +eii+v +gStD+t +i+++++k++  + v+++ee  G+ +a+++g++ a+g++++ lD D+  
       AJA92206.1  10 SIILPAYNEENGLEKCVNETIKTvnSENISYEIIIVENGSTDNTYKIAQQISKNFNFISVVHLEEP-GFENAIRNGFKLAKGELVAHLDVDLST 102
                      8********999999999999999999***************************************.*************************** PP

                      -TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEH CS
  Glycos_transf_2  93 dpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrre 164
                      d  ++++l+ ++++  +d v g+r+   ++ ++   +++      ++    ++ lk ++ ++ +++++++++
       AJA92206.1 103 DMSHFKELLSHAKN--YDFVTGSRYLDLSSAKRTFGRLF--LSKAFNSLLINFLLKSKIKDNNCGFRIIKKN 170
                      ************99..777****************9998..7888888888888888888888888888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.3
                      EEEEEEEEEECCCCCCCHC-SS...EE CS
  Glycos_transf_2 111 vvlgqrprifgetdeiernkrv...ge 134
                      +v++qr  +++++++ ++++++   ++
       AJA92206.1 191 IVIAQRKGYSVKEFPVKWTENMsdiKF 217
                      788999999999999999888766633 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   2.4e-14   1.1e-10       4     128 ..       9     128 ..       8     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 2.4e-14
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqey...prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllv 94 
                      l+++ p++nee  l+++++++++  +   +++e+++v ++s++ t + a+++ +++    ++vv+ ++ +g+    +a+ ++++ +k++lv+++
       AJA92206.1   9 LSIILPAYNEENGLEKCVNETIKTVNsenISYEIIIVENGSTDNTYKIAQQISKNFNF--ISVVHLEE-PGF---ENAIRNGFKLAKGELVAHL 96 
                      689******************9653322489*************************55..79998877.675...56666************** PP

  Glyco_tranf_2_3  95 DdDtvvePdtlkrllqffltpkvgavgtpvflln 128
                      D D  ++   +k ll  +  +++++v+++++l+ 
       AJA92206.1  97 DVDLSTDMSHFKELLSHA--KNYDFVTGSRYLDL 128
                      ******99999**99998..99******998875 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   1.3e-09   5.6e-06       1     105 [.      10     113 ..      10     121 .. 0.85
   2 ?   -2.6   0.0      0.68   3.1e+03     141     171 ..     120     150 ..     113     151 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-09
  Glyco_tranf_2_2   1 svviplrasee..rhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92 
                      s+++p +++e+  ++ ++e+++  ++  +   e+i+v++gS++++ +  ++i +    +++ + ++  + +a  rN G++ a+++lv  lD+D 
       AJA92206.1  10 SIILPAYNEENglEKCVNETIKTVNSE-NISYEIIIVENGSTDNTYKIAQQISKNFNFISVVHLEEPGFENA-IRN-GFKLAKGELVAHLDVDL 100
                      688899998874456899999888887.7899************999999999999999*9***99999765.566.****************9 PP

  Glyco_tranf_2_2  93 fissDkfekilkl 105
                           +f+ +l+ 
       AJA92206.1 101 STDMSHFKELLSH 113
                      8888888888874 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.68
  Glyco_tranf_2_2 141 tassrvledllaakstlvkffapss.ssilin 171
                      ++ sr l dl  ak t+ + f+ ++ +s+lin
       AJA92206.1 120 VTGSRYL-DLSSAKRTFGRLFLSKAfNSLLIN 150
                      3445666.899999999998888888999997 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.4e-07    0.0033      19      81 ..      39      99 ..      16     121 .. 0.68
   2 ?   -2.3   0.0       1.5   6.9e+03      44      63 ..     191     210 ..     169     222 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.4e-07
  Glyco_tranf_2_4 19 fdrilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                       +i++++n+stD+t++i ++  +   + ++ + e+  +++++++ +    a+++ v+++D+D
       AJA92206.1 39 SYEIIIVENGSTDNTYKIAQQISKNFNFISVVHLEEPGFENAIRNGFKL--AKGELVAHLDVD 99
                     346****************997554433344445555677777777663..357788888877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
  Glyco_tranf_2_4  44 kllhvdksyederrqvellk 63 
                       ++  +k y+ ++++v++ +
       AJA92206.1 191 IVIAQRKGYSVKEFPVKWTE 210
                      33334444444455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1855.99
//
Query:       AJA92207.1  [L=257]
Description: FeS assembly ATPase SufC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-19   70.3   0.0    4.1e-19   69.5   0.0    1.4  1  ABC_tran      ABC transporter
    3.7e-10   39.6   0.6      2e-05   24.2   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    4.6e-09   36.5   0.2     0.0011   18.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00092   18.9   0.0     0.0023   17.6   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.002   18.3   0.0      0.003   17.7   0.0    1.5  1  AAA_33        AAA domain
     0.0088   16.3   0.0       0.41   10.9   0.0    2.3  2  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.2       0.32   11.5   0.0    2.4  2  AAA_18        AAA domain
      0.011   15.5   0.2        1.7    8.3   0.1    2.2  2  AAA_15        AAA ATPase domain
      0.018   14.6   0.0      0.038   13.6   0.0    1.5  1  AAA_27        AAA domain
      0.028   14.0   0.0       0.12   11.9   0.0    1.9  2  AAA_25        AAA domain
      0.033   12.8   1.6       0.24   10.0   0.0    2.1  2  AAA_13        AAA domain
      0.074   12.4   0.1        8.9    5.6   0.0    2.4  2  ATPase        KaiC
      0.094   12.8   0.0       0.28   11.2   0.0    2.0  1  AAA_14        AAA domain
      0.094   13.2   1.9        0.1   13.1   0.3    1.8  2  AAA_23        AAA domain
        0.1   12.6   0.2        2.4    8.1   0.0    2.2  2  MutS_V        MutS domain V
       0.12   12.3   0.0       0.24   11.3   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.13   12.7   0.0        0.9   10.0   0.0    2.1  2  RNA_helicase  RNA helicase
       0.14   12.6   0.1        1.1    9.7   0.0    2.2  2  AAA_17        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.0   4.1e-22   4.1e-19       1     136 [.      19     179 ..      19     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 4.1e-22
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren................. 79 
                 lk v+lk  +ge++ai+G+nG+GKStL  +l+ + k   t+G+illdg+++ e +  e+++k +   +q p+  +++    +                 
  AJA92207.1  19 LKGVNLKTGPGEVHAIMGPNGSGKSTLSYTLLAHPKYevTQGDILLDGESILElTADERAKKGLFLGFQYPTEVSGVGFS-Hflrtsynalskamkgee 116
                 789***************************999766666**************988899999999999999988888444.448889999999988877 PP

                 ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                         e ++ +++ ++++gl e  d   ++  + +SgG+k+r ++ ++ + kpk+ +lDEp 
  AJA92207.1 117 revfitvrEFQNYLKENINSVGLRE--DFLSRYLNEGFSGGEKKRAEVLQMAVLKPKISILDEPD 179
                 7777666666666888888888777..444445569***************************95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   2.9e-05     0.029      25      42 ..      30      47 ..      16      52 .. 0.84
   2 !   24.2   0.1     2e-08     2e-05     136     213 ..     151     225 ..      98     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                SEEEEEESTTSSHHHHHH CS
                xxxxxxxxxxxxxxxxxx RF
       SMC_N 25 sftaivGpNGSGKsnlld 42
                ++ ai+GpNGSGKs l  
  AJA92207.1 30 EVHAIMGPNGSGKSTLSY 47
                5789**********9866 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 2e-08
                 CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtk 213
                  +SgGek+ + + L +A+ k k   + +lDe d+ LD   v+ va+ + + s++ +  ivi++ +++l+  dkl  v  
  AJA92207.1 151 GFSGGEKKRAEV-LQMAVLKPK---ISILDEPDSGLDIDAVQSVAKAISQVSDKdSTTIVITHYARILNFLDKLDHVHV 225
                 6899**997654.777877655...779*********************877655**************9999987765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     1e-05      0.01       2      22 ..      32      50 ..      31     143 .. 0.68
   2 !   18.9   0.0   1.1e-06    0.0011     257     303 .]     169     215 ..     150     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
      AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                 ++ GpNgsGKS+L ++l  l
  AJA92207.1 32 HAIMGPNGSGKSTLSYTL--L 50
                5799***********999..3 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.1e-06
      AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                 k+++ ++DEp++gL+  ++ ++++ +++ s++++  i+ TH   +l+
  AJA92207.1 169 KPKISILDEPDSGLDIDAVQSVAKAISQVSDKDSTTIVITHYARILN 215
                 448889***********************************988876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.3e-06    0.0023      17      38 ..      24      45 ..      17      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
      AAA_29 17 ieidlkgatlltGpsGsGKSTl 38
                ++  + +++ ++Gp+GsGKSTl
  AJA92207.1 24 LKTGPGEVHAIMGPNGSGKSTL 45
                556666699************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     3e-06     0.003       3      33 ..      33      78 ..      31     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3e-06
      AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt...............l 33
                 + G++GsGKstl+  ll++ ++++   d+               +
  AJA92207.1 33 AIMGPNGSGKSTLSYTLLAHPKYEVTQGDIlldgesileltaderA 78
                678***************9999*99999995555555555555550 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00041      0.41       3      26 ..      33      57 ..      31      84 .. 0.82
   2 ?    3.2   0.0     0.094        94      11      30 ..     235     255 ..     233     257 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
      AAA_28  3 vitGgestGKTtlleaLaar.gypv 26
                +i+G+ ++GK+tl+  L a+ +y+v
  AJA92207.1 33 AIMGPNGSGKSTLSYTLLAHpKYEV 57
                79************99999987775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.094
      AAA_28  11 GKTtlleaLaargypvv.pEa 30 
                 G  +l+++L++rgy +v +Ea
  AJA92207.1 235 GDASLAQELEKRGYDWVlEEA 255
                 55689************6664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032      0.32       3      44 ..      34      75 ..      33      84 .. 0.81
   2 ?    2.6   0.1      0.19   1.9e+02      49     114 ..     160     247 ..     103     253 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
      AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                ++G+ G+GK+tl+  L  + ++ v  +d++ ++++ le +++
  AJA92207.1 34 IMGPNGSGKSTLSYTLLAHPKYEVTQGDILLDGESILELTAD 75
                89************9988778888888888888877776666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
      AAA_18  49 skrldedkldklldaleenss................aleegknlvidghlaeleseaakdikk......vvLtaspeelleRlekRg 114
                  ++l++ +l+  +++l+e +s                 +++ ++ ++  h a  +   +k  +        +L+  +  l++ lekRg
  AJA92207.1 160 AEVLQMAVLKPKISILDEPDSgldidavqsvakaisqVSDKDSTTIVITHYARILNFLDKLDHVhvfadgKILKSGDASLAQELEKRG 247
                 4444444444444444444334444444444444444334555555556666666555555552234444444444555555555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0017       1.7      25      83 ..      31      88 ..      21     144 .. 0.60
   2 ?    6.1   0.1    0.0076       7.6     288     364 ..     126     209 ..      90     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
      AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekkn.kkvikiekedleifeniseskdikIdvef 83
                +  + G+N+sGKS++ + l  +   k++    + + + ++ le + ++  +k + + +++
  AJA92207.1 31 VHAIMGPNGSGKSTLSYTL--LAHPKYEVTqGDILLDGESILELTADERAKKGLFLGFQY 88
                66799*********99888..666665554433344444455555566666666666666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0076
      AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeek........nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                  +++l++n n+ G+++ +l  +l + ++ +++k+++        ++i +++EP+  L ++a ++++k++  ++++++  +i+ TH
  AJA92207.1 126 FQNYLKENINSVGLREDFLSRYLNEGFSGGEKKRAEvlqmavlkPKISILDEPDSGLDIDAVQSVAKAISQVSDKDS-TTIVITH 209
                 556666666666666665555555555555222222334444449999****************************9.7888888 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.038       3      43 ..       6      46 ..       4      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
      AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstal 43
                ++ L+++r Gk   + ++++++  ++h i+GpN +GKst+ 
  AJA92207.1  6 IKDLHVTREGKEILKGVNLKTGPGEVHAIMGPNGSGKSTLS 46
                66777777777777889999999****************85 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.12      32      56 ..      28      52 ..      13      71 .. 0.90
   2 ?   -0.8   0.0      0.99   9.9e+02     149     187 ..     185     209 ..     149     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
      AAA_25 32 agelallaGapgtGKttlaldlala 56
                 ge+++++G+ g+GK+tl + l ++
  AJA92207.1 28 PGEVHAIMGPNGSGKSTLSYTLLAH 52
                599***************9999876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.99
      AAA_25 149 Dplsralggdensnsdvgalvealeriarrtgaavllvh 187
                 D               v+++ +a+ +++++   +++++h
  AJA92207.1 185 DA--------------VQSVAKAISQVSDKDSTTIVITH 209
                 22..............34444555554333333333322 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00024      0.24      18      37 ..      31      50 ..      20      83 .. 0.80
   2 ?    1.7   0.6     0.079        79     524     575 ..     167     215 ..     158     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
      AAA_13 18 iNliYGwNGaGKTtLSrllr 37
                +  i G NG+GK+tLS  l 
  AJA92207.1 31 VHAIMGPNGSGKSTLSYTLL 50
                55799***********8765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.079
      AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffk 575
                 + k ki ++D P S LD +++ +v+  i ++    +k +  ++ TH    ++
  AJA92207.1 167 VLKPKISILDEPDSGLDIDAVQSVAKAISQVS---DKDSTTIVITHYARILN 215
                 57999*************************97...66677788899766655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.024        24      19      39 ..      29      49 ..      25      58 .. 0.87
   2 ?    5.6   0.0    0.0089       8.9      42      72 ..     109     139 ..     101     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.024
      ATPase 19 grvvlitGepGtGKtifalqF 39
                g+v  i+G  G+GK++++ + 
  AJA92207.1 29 GEVHAIMGPNGSGKSTLSYTL 49
                57889************9875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0089
      ATPase  42 kgaekygepgvfvtveepaedlrenakslGw 72 
                 + a+k +e+ vf+tv e ++ l+en++s+G 
  AJA92207.1 109 SKAMKGEEREVFITVREFQNYLKENINSVGL 139
                 5567778999******************996 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.28       3      43 ..      30      79 ..      28     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
      AAA_14  3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldderd 43
                ++ +i+G+  +GK+tl ++l+ +            + esil+++ d+  +
  AJA92207.1 30 EVHAIMGPNGSGKSTLSYTLLAHPKyevtqgdilLDGESILELTADERAK 79
                5778**************99877666877777777777777777777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3    0.0001       0.1      21      35 ..      31      45 ..      16      48 .. 0.87
   2 ?   -1.5   0.1         3     3e+03     167     167 ..     135     135 ..      91     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
      AAA_23 21 ltlItGpNGaGKTTi 35
                + +I GpNG+GK+T+
  AJA92207.1 31 VHAIMGPNGSGKSTL 45
                568***********8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
      AAA_23 167 d 167
                 +
  AJA92207.1 135 N 135
                 2 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.15   1.5e+02       3      14 ..      34      45 ..      32      49 .. 0.88
   2 ?    8.1   0.0    0.0024       2.4      69     136 ..     160     226 ..     148     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                EE-STTSSHHHH CS
      MutS_V  3 itGpnmaGksty 14
                i Gpn +Gkst+
  AJA92207.1 34 IMGPNGSGKSTL 45
                88********96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                 HHHHTT--TT.SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEE CS
      MutS_V  69 asilknatek.slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknl 136
                 a++l+ a  k  + ilDE   G  +    ++a+a+ +   + + ++t+  tHy  + +  +kl++v+ +
  AJA92207.1 160 AEVLQMAVLKpKISILDEPDSGLDIDAVQSVAKAISQV--SDKDSTTIVITHYARILNFLDKLDHVHVF 226
                 55666665441456999999999999999999999875..45699***********9999998888755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.24      99     127 ..      29      57 ..       2      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                  TSEEEEECSTTSSHHHHHHHHCTT----- CS
  RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelkt 127
                  +++ +++G+ G GKStL  +ll + + ++
   AJA92207.1  29 GEVHAIMGPNGSGKSTLSYTLLAHPKYEV 57 
                  48999************999988766665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00091       0.9       3      20 ..      34      51 ..      32      63 .. 0.86
   2 ?   -0.3   0.0       1.4   1.4e+03       8      43 ..      94     129 ..      92     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00091
  RNA_helicase  3 lyGpsgeGKStlakeLak 20
                  + Gp+g GKStl+++L +
    AJA92207.1 34 IMGPNGSGKSTLSYTLLA 51
                  79************9765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
  RNA_helicase   8 geGKStlakeLakallkklklkkkdsvysrnpeddf 43 
                   g+G S++ ++  +al+k++k ++++ +++    +++
    AJA92207.1  94 GVGFSHFLRTSYNALSKAMKGEEREVFITVREFQNY 129
                   777788877777888888855555555554444433 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011       1.1       1      32 [.      35      65 ..      35      81 .. 0.85
   2 ?    0.5   0.0      0.78   7.8e+02      58      92 ..     187     220 ..     140     237 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllre 32
                +G+ GsGK+t++ +l  + ++++ + Gd+l +
  AJA92207.1 35 MGPNGSGKSTLSYTLLAHPKYEVTQ-GDILLD 65
                599******************9998.999874 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.78
                 HHHHHHHHHHHH..HSSEEEEEE-SEEEETTEEEESS CS
      AAA_17  58 qkeaaekiaeea..kkkgvlvdghprikeqagfldgl 92 
                  + +a++i + +  ++++++++ ++ri +   fld+l
  AJA92207.1 187 VQSVAKAISQVSdkDSTTIVITHYARILN---FLDKL 220
                 33444444444332455677777777754...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1811.19
//
Query:       AJA92208.1  [L=80]
Description: hypothetical protein T478_0425 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.45   10.5   3.8        2.2    8.3   0.0    2.4  3  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.4      0.01   1.9e+02      49      57 .]       4      12 ..       2      12 .. 0.90
   2 ?   -2.8   0.1      0.34   6.2e+03      34      45 ..      17      28 ..      13      30 .. 0.58
   3 ?    8.3   0.0   0.00012       2.2      13      37 ..      42      66 ..      41      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.01
     DUF4083 49 kiIeLLeKd 57
                +iI+ LeK+
  AJA92208.1  4 RIIKILEKK 12
                8*******6 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.34
     DUF4083 34 aakkkkskeleq 45
                 ++++k ke+  
  AJA92208.1 17 KTENNKTKEIVD 28
                456666666655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00012
     DUF4083 13 vLilllvfsftlfiRrvvsrsaakk 37
                +Li+ l+ sf+   Rrv+ r ++  
  AJA92208.1 42 ILIGRLLNSFYYQHRRVLKRDPTDT 66
                79******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1464  (0.0816554); expected 358.6 (0.02)
Passed bias filter:                      819  (0.0456802); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 542.49
//
Query:       AJA92209.1  [L=228]
Description: MobA-like NTP transferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-31  107.5   0.1    1.2e-30  106.9   0.1    1.4  1  NTP_transferase  Nucleotidyl transferase
    3.6e-14   53.4   0.0      5e-14   53.0   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0003   20.6   0.0     0.0004   20.2   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0026   17.7   0.1     0.0034   17.3   0.1    1.3  1  CTP_transf_3     Cytidylyltransferase
     0.0041   16.9   0.0     0.0051   16.6   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
       0.19   12.2   0.0       0.31   11.6   0.0    1.4  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.1     4e-34   1.2e-30       1     190 [.       2     172 ..       2     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 4e-34
                      EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTH CS
  NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaa 94 
                      ka+ILaGG+G+RL+P+t +++k+l+p+ +k +li+ t++ l + gi+e i++++ ++s l+e+ lk++++fg+e+++++e+ + gt +Av++a+
       AJA92209.1   2 KAIILAGGRGKRLRPITDKIPKPLIPINNK-PLIERTIKYLKKYGITE-IIISSGYKSDLIEKFLKKKKNFGCEISFSIEKTPLGTGGAVKKAL 93 
                      79****************************.*****************.********************************************* PP

                      HHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHH CS
  NTP_transferase  95 elledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeakaselassGiYvfnsevll 188
                      +++++e+    ++vL+gD++++ ++++++kk    aa          +e +t++G + + ++ ++ +f EK +  +   +++ GiY    ++ +
       AJA92209.1  94 RFVDEES----FVVLNGDIVTNIDLKKILKKPNTIAA----------NELKTKFGTMDIRNN-KILKFNEKKDVTD--VWMNPGIYHLSMNIEK 170
                      ****999....8*****************99888777..........899*********995.9*******88877..7999999988766655 PP

                      HH CS
  NTP_transferase 189 fl 190
                      ++
       AJA92209.1 171 II 172
                      55 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.7e-17     5e-14       1      97 [.       3     109 ..       3     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.7e-17
                   EEEEEESS-TTTTT.....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC...TS-EEE-TTS.S-SHHHHHHHHHHHH.SS CS
  NTP_transf_3   1 aviLAGGrSsRmgg.....dKallplggkpllervldalraagvdevvvvggd..eevlaalarl...gvrvvededp.gkgplaslaaalraaada 86 
                   a+iLAGGr++R+       +K+l+p+++kpl+er+++ l++ g+ e++++ g+  + +++ l+++   g+++    ++   g++++++ alr + d+
    AJA92209.1   3 AIILAGGRGKRLRPitdkiPKPLIPINNKPLIERTIKYLKKYGITEIIISSGYksDLIEKFLKKKknfGCEISFSIEKtPLGTGGAVKKALRFV-DE 98 
                   79**********7333458********************************996545555554333338999888666269************9.9* PP

                   SCEEEEETT-T CS
  NTP_transf_3  87 davlvlacDmP 97 
                   + ++vl +D++
    AJA92209.1  99 ESFVVLNGDIV 109
                   *********85 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-07    0.0004       2      63 ..       2      64 ..       1     113 [. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHH CS
        IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqll 63
                 ++i A G+GkR++      pK ++ +++++l+e+t++ l +++  + i+    +   + +e++l
  AJA92209.1  2 KAIILAGGRGKRLRpitDKIPKPLIPINNKPLIERTIKYLKKYGITEIIISSGYKS--DLIEKFL 64
                69**********86332688********************9987666555444333..4555555 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.1e-06    0.0034      15      59 ..      22      67 ..       3     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                  TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES..-HHHHHHHHHT CS
  CTP_transf_3 15 gKnlldlggkpliayvleaalkskafekvivaTD..seeiknvakef 59
                   K+l+++++kpli+++++ ++k +  +++i+++   s+ i+ ++k+ 
    AJA92209.1 22 PKPLIPINNKPLIERTIKYLKKYGI-TEIIISSGykSDLIEKFLKKK 67
                  5*********************776.999**9952245566665554 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0051       8     102 ..      29     119 ..      25     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                      S-TTTHHHHHHHHHHHGGCCEEEEEEEEES-.SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHH CS
  Glycos_transf_2   8 NeektlletlesllaqdpypdfeiivvDDgS.tDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwlekl 100
                      N ++++++t++ l++      ++ i++  g  +D  +++l++  + +  + +   +   G +ga+ ++lr ++ + +++l+ D + + d l+k+
       AJA92209.1  29 NNKPLIERTIKYLKKY----GITEIIISSGYkSDLIEKFLKKKKNFGCEISFSIEKTPLGTGGAVKKALRFVDEESFVVLNGDIVTNID-LKKI 117
                      66799******88887....6666666666559**********999999999999999*************************998885.6666 PP

                      HH CS
  Glycos_transf_2 101 ve 102
                      ++
       AJA92209.1 118 LK 119
                      55 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.31       2      43 ..      29      70 ..      28     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
  Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkelpev 43
                     n ++++++++++++++g+++i++ +  ++D   ++lk+ ++ 
       AJA92209.1 29 NNKPLIERTIKYLKKYGITEIIISSGYKSDLIEKFLKKKKNF 70
                     7889********************************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1642.52
//
Query:       AJA92210.1  [L=120]
Description: hypothetical protein T478_0301 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.3    6.6   8.0        4.7    7.0   0.5    2.3  2  FixP_N    N-terminal domain of cytochrome oxidase-cbb3, FixP


Domain annotation for each model (and alignments):
>> FixP_N  N-terminal domain of cytochrome oxidase-cbb3, FixP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.0   0.00086        15      23      43 ..      43      63 ..      41      67 .. 0.92
   2 ?    7.0   0.5   0.00026       4.7      18      39 ..      62      83 ..      60      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.00086
      FixP_N 23 WlylFyativfavvYlilYpa 43
                Wl +F +t +  +vY  +Yp+
  AJA92210.1 43 WLATFGGTAAGYFVYPWAYPT 63
                ********************7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00026
      FixP_N 18 plPrWWlylFyativfavvYli 39
                p P +   + ++ti+ a++Yl+
  AJA92210.1 62 PTPSGHYAFIVLTIIEAIGYLF 83
                8899999999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 841.64
//
Query:       AJA92211.1  [L=564]
Description: thermosome subunit beta [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.4e-178  591.8  20.1   1.1e-177  591.6  20.1    1.0  1  Cpn60_TCP1       TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.048   13.2   0.0    1.5  1  Ustilago_mating  Ustilago B locus mating-type protein
      0.043   13.7   5.6        1.3    8.9   0.2    2.9  2  Dak2             DAK2 domain
       0.33   11.2   6.8       0.74   10.1   0.9    3.7  4  YbaB_DNA_bd      YbaB/EbfC DNA-binding family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.6  20.1  2.4e-181  1.1e-177       1     489 [.      38     527 ..      38     529 .. 0.99

  Alignments for each domain:
  == domain 1  score: 591.6 bits;  conditional E-value: 2.4e-181
                 HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                 +a+iv t+lGPkGmdKmlv++ g+v++TnDGatilke++++hPaak+lve+++++d+evGDGTt++v+Lag+Lle ae+l+ ++vhpt i++gy+ka  
  AJA92211.1  38 IAEIVHTSLGPKGMDKMLVDSLGDVTITNDGATILKEIDVQHPAAKMLVEISKTTDNEVGDGTTSAVVLAGALLEHAETLVLQDVHPTIIVDGYRKAGR 136
                 79************************************************************************************************* PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTS CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene...keldlgrikvvkieggsledselveGlvldkgvlspdm 195
                 ka e+L++ia ++s +  d+ +Llk+a+ts+++kl++k++e+l++++v+Avk++ e++    ++d++ ikv+k+ ggs++ds++++G+vldk+++++ m
  AJA92211.1 137 KAKEFLDQIADNVSPT--DNGILLKIAKTSMQTKLVRKDSEQLADMIVKAVKAVAEQSgdkFTVDIDDIKVEKKAGGSIKDSKIIQGIVLDKEIVHSGM 233
                 *********8888865..999******************************9999998998899*********************************** PP

                 SCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT CS
  Cpn60_TCP1 196 pkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatG 294
                 pkk+++ k++ll+  Lei ktet++++++s+++++++++++e+k+l+ +++k+i sg+nvv+cqkgidd+a+h+l k+gila+rrvk++dl +lakatG
  AJA92211.1 234 PKKITEGKIALLNAALEINKTETDAKINISNPQQMKAFLDEENKMLKTMVDKVIGSGANVVLCQKGIDDMAQHYLSKAGILAVRRVKESDLSKLAKATG 332
                 *************************************************************************************************** PP

                 --EBSCGGGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
  Cpn60_TCP1 295 atavssledltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                 a++v++l+dl + +lG+a++++e+k++++k++++e++k++k++t+llr+ ++ v+de+er+++d+l vv+ ++e + vv+GGGa e+ +a+k++++aks
  AJA92211.1 333 ARIVTNLDDLFERDLGSASSIQEKKVEEDKWVFVEGCKHPKSVTLLLRAGSQRVVDEVERSVHDSLMVVRDVMELPSVVAGGGAPETFAATKIRSWAKS 431
                 *************************************************************************************************** PP

                 SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
  Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiika 489
                 ++g+eqla+e+fa+ALe+ip +L eNaG+dpi++l++lra++ kgek++gidv +g++ +l++  +++pl+vk+q++++Ateaa++iLrid++i +
  AJA92211.1 432 LQGREQLAAEKFAEALEAIPLALSENAGMDPIDTLTHLRAKQIKGEKWTGIDVMKGKVGNLKSTDIIEPLAVKHQIVSAATEAACMILRIDDVIAT 527
                 **********************************************************************************************86 PP

>> Ustilago_mating  Ustilago B locus mating-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.1e-05     0.048      16      64 ..     314     363 ..     301     370 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
  Ustilago_mating  16 lvrakllasdqsaraiatsdslvgnlddllrenlGrltpvdkeefe.ddw 64 
                      l   ++  sd s  a at   +v+nlddl++ +lG  + ++ ++ e d w
       AJA92211.1 314 LAVRRVKESDLSKLAKATGARIVTNLDDLFERDLGSASSIQEKKVEeDKW 363
                      555678899***************************88887766651556 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.1    0.0026        11      18     136 ..      71     191 ..      62     197 .. 0.68
   2 ?    8.9   0.2   0.00029       1.3      13      96 ..     381     464 ..     378     550 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                 HHHHHHC---SSHHHHHHHHHHHHHHH--..STHHHHHHHHHHHHHHHC........TT---HHHHHHHHHHHHHHHH.---TTSSSTHHHHHHHHHHH CS
        Dak2  18 vlkaleeleeaslaevlkalakallsgag..GtsGvlysqflralakal..ke.keeldaedlaaalkaaleaiqavg.karpgdkTmlDvlrpaveal 110
                 +lk+++   ++ +a++l +++k+  +++g   ts v ++ +l++ a++l  ++ + ++ ++   +a ++a e + +++ +  p d  +l  +++++ + 
  AJA92211.1  71 ILKEIDV--QHPAAKMLVEISKTTDNEVGdgTTSAVVLAGALLEHAETLvlQDvHPTIIVDGYRKAGRKAKEFLDQIAdNVSPTDNGILLKIAKTSMQT 167
                 5555554..5888999999999999998543799************99944444555888889999999999999994335566666655555555555 PP

                 HT............T---HHHHHHHHH CS
        Dak2 111 ekakd.gedlkealekaakaaekgaea 136
                 +      +d +++++ ++ka ++ ae+
  AJA92211.1 168 K---LvRKDSEQLADMIVKAVKAVAEQ 191
                 5...44455555555555555555554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00029
                 HHHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH---TTS CS
        Dak2  13 rgaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavgkarpgd 96 
                 +g++ v++++e+   +sl  v + +    + + gG+  ++ ++ +r+ ak+l+++e+l ae++a+al+a   a+++ ++++p d
  AJA92211.1 381 AGSQRVVDEVERSVHDSLMVVRDVMELPSVVAGGGAPETFAATKIRSWAKSLQGREQLAAEKFAEALEAIPLALSENAGMDPID 464
                 67778888888877777777777777777778889999999999*************************999999888777665 PP

>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.33   1.5e+03      30      49 ..      60      79 ..      57      96 .. 0.79
   2 ?    1.7   0.1     0.069   3.1e+02      38      88 ..      97     147 ..      69     150 .. 0.73
   3 ?   10.1   0.9   0.00017      0.74      45      78 ..     163     195 ..     157     204 .. 0.79
   4 ?   -2.0   0.0      0.96   4.3e+03      33      51 ..     204     222 ..     195     262 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.33
                 TTEEEEEETT--EEEEEE-G CS
  YbaB_DNA_bd 30 glVkVtvngkgevksikIdp 49
                 g V++t +g   +k+i+++ 
   AJA92211.1 60 GDVTITNDGATILKEIDVQH 79
                 77999999999999999854 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.069
                  TT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
  YbaB_DNA_bd  38 gkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaeeemskltg 88 
                  g+g+  ++ +  +ll+  +  +L+d   + + d ++ka ++a+e ++++++
   AJA92211.1  97 GDGTTSAVVLAGALLEHAETLVLQDVHPTIIVDGYRKAGRKAKEFLDQIAD 147
                  555666777778888888888999999999999999999999999988875 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00017
                  EEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHH CS
  YbaB_DNA_bd  45 ikIdpslldpedkemLedlivaAvndAlkkaeee 78 
                   +++ +l+  +d e L+d+iv+Av++  +++ ++
   AJA92211.1 163 TSMQTKLVR-KDSEQLADMIVKAVKAVAEQSGDK 195
                  555666764.679*************99998775 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.96
                  EEEEETT--EEEEEE-GGG CS
  YbaB_DNA_bd  33 kVtvngkgevksikIdpsl 51 
                  kV+ ++ g +k+ kI + +
   AJA92211.1 204 KVEKKAGGSIKDSKIIQGI 222
                  3434444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3953.71
//
Query:       AJA92212.1  [L=278]
Description: methyltransferase FkbM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-18   66.7   0.1    3.7e-18   66.2   0.1    1.2  1  Methyltransf_21  Methyltransferase FkbM domain
    4.7e-08   33.0   0.0    6.6e-08   32.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.3e-07   30.8   0.1    3.7e-07   30.1   0.1    1.3  1  Met_10           Met-10+ like-protein
     0.0012   18.0   0.0     0.0021   17.2   0.0    1.3  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.016   15.0   0.5      0.023   14.4   0.5    1.2  1  Sial-lect-inser  Vibrio cholerae sialidase, lectin insertion
      0.017   14.5   0.1      0.025   14.0   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.032   13.9   0.0      0.055   13.1   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.1   1.4e-21   3.7e-18       1     172 [.      78     236 ..      78     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.4e-21
  Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksggkyfpfavgdtngfstssvlggedary 94 
                      dvGanig   +++ l+++l g++g+v++iEP+p+   +f+ l++n   l  +n+++ +++ ++  ++++  +f+++ ++     +      ++ 
       AJA92212.1  78 DVGANIG---TVTLLASALIGNSGTVYSIEPHPK---TFNYLQEN---LKFNNTNNVVSFNLAIGDKNSTIGFSDKKSDDQNQVT----FSNTN 158
                      9******...6666777899**************...********...******9999988854444666666666666666665....5699* PP

  Methyltransf_21  95 ievpvvtld..sfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefet..elfdeirqflrecgyr 172
                       +vp + ld  ++ e+i    idllkiD  G+E  vL G+++ l++ +  ++ +  +  k+f+t   + +ei+q+lr+++++
       AJA92212.1 159 LTVPLKKLDdlDIQEDI----IDLLKIDSIGFEKFVLLGSKNILEKTRCIQLPISGSYPKFFQTygYEYEEILQILRKHDFE 236
                      *********77777777....*************************99999756666666666699999***********98 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.6e-11   6.6e-08      33     127 ..      30     126 ..      17     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.6e-11
                 GSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEE CS
        PCMT  33 fvpesfkekaYedaplsigynatiSaphmvalalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvi 127
                 f +    +++ +  p  +++n+ i + +++a+   +l+  +k+g+++++vG+  G  t + + l+g++g+v sie  ++  +  ++nlk ++++nv+
  AJA92212.1  30 FFTIRQSHYTLKFFPTALSQNKWINQNYVHAADDPFLQhyIKNGDKIIDVGANIGTVTLLASALIGNSGTVYSIEPHPKTFNYLQENLKFNNTNNVV 126
                 555544555556678899***********************************************************************99999653 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   1.4e-10   3.7e-07      96     154 ..      68     127 ..      55     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 1.4e-10
                 TT--TT-EEEETT-TTTCCHHHC.CHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
      Met_10  96 klveegevVvdvfAGiGpfaipi.akyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                 + +++g+ ++dv A iG  ++ + a  ++  +v++i+  P++++yl+en+k N+ ++vv+
  AJA92212.1  68 HYIKNGDKIIDVGANIGTVTLLAsALIGNSGTVYSIEPHPKTFNYLQENLKFNNTNNVVS 127
                 56899**************986516679*****************************994 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.3e-07    0.0021      66     112 ..      68     114 ..      62     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.3e-07
                  -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH CS
  Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli 112
                   +ik+g+k++ +Ga  Gt     s ++g++g+vy++e  p+++  l 
   AJA92212.1  68 HYIKNGDKIIDVGANIGTVTLLASALIGNSGTVYSIEPHPKTFNYLQ 114
                  689**********************************9999887775 PP

>> Sial-lect-inser  Vibrio cholerae sialidase, lectin insertion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.5   9.1e-06     0.023      27     136 ..      45     158 ..      35     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.1e-06
                      ---TTS-EEEEEEEEEEEES-EEEEEEESSEEEEEEEEE-TTS-EEEEETT--S-EEEE-SHHHHTSEEEEEEEEETTTTEEE..EEETTEEEE CS
  Sial-lect-inser  27 elssqqdWslnaklkivdGaandlqvadGekkfvvtlavdesgnLvanlngesspilirlesenvagFhdvelrydpvtktas..llvDgevia 118
                      +  sq++W  +  +++ d    + ++ +G+k+  v   ++    L   l g+s+++   + + +  ++ + +l+++  ++  s  l + ++  +
       AJA92212.1  45 TALSQNKWINQNYVHAADDPFLQHYIKNGDKIIDVGANIGTVTLLASALIGNSGTVYSIEPHPKTFNYLQENLKFNNTNNVVSfnLAIGDKNST 138
                      556999************************************************************************9977521667666555 PP

                      .EE--EE-S-.EEEEEEE-- CS
  Sial-lect-inser 119 .elsGepssd.kkvlFGnad 136
                        +s + s d ++v+F n++
       AJA92212.1 139 iGFSDKKSDDqNQVTFSNTN 158
                      57887776542799**9997 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   9.8e-06     0.025     154     217 ..      65     130 ..      64     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.8e-06
        PrmA 154 aleklvkegeevlDvGtGSGiLa.iaaakLgak.kvvavDiDevAvkvakeNaelNkveakleval 217
                 +l++++k+g++++DvG+  G  + +a+a++g + +v+ +   + + +  +eN+++N++++ ++ +l
  AJA92212.1  65 FLQHYIKNGDKIIDVGANIGTVTlLASALIGNSgTVYSIEPHPKTFNYLQENLKFNNTNNVVSFNL 130
                 5899*************99877625777777643899*********************99765544 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.055       7      60 ..      71     124 ..      67     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                      -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--S CS
  Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtn 60 
                      +++++i+D+ a  G  T + ++l+ n+gtv+ ++ + +  + ++enlk  + +n
       AJA92212.1  71 KNGDKIIDVGANIGTVTLLASALIGNSGTVYSIEPHPKTFNYLQENLKFNNTNN 124
                      799*******************************************98666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1735.75
//
Query:       AJA92213.1  [L=535]
Description: dolichyl-phosphate-mannose-protein mannosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-08   34.3  16.9    2.4e-08   34.3  16.9    3.2  4  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
       0.11   12.3   0.5       0.42   10.4   0.3    2.1  2  Zds_C     Activator of mitotic machinery Cdc14 phosphatase ac


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3  16.9   2.7e-12   2.4e-08      22     156 ..      91     222 ..      71     225 .. 0.85
   2 ?   -0.0   3.7       0.1     9e+02     102     155 ..     280     335 ..     263     339 .. 0.49
   3 ?   -1.4   2.7      0.26   2.4e+03     117     153 ..     350     385 ..     336     394 .. 0.37
   4 ?   -0.2   0.4      0.11     1e+03      17      41 ..     371     395 ..     364     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.7e-12
       PMT_2  22 lairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkywllagvlfGlgflsKytaal 120
                  a r+ s+++++lti+ +++l +++++++ al++a l  +++ ++  s l+  ++++++l++++l+++l    kn++ y++++ +++ l+  ++y++++
  AJA92213.1  91 NAQRITSVVISSLTIIPIFFLCKKFVSSKYALIGASLFGFSYRLMDNSILGLSESLFLFLISFVLLYSL---SKNST-YFIFSFIFLSLSAIVRYESLI 185
                 46799*********************************************************9999985...79995.********************* PP

       PMT_2 121 lliaallyllis.arrilkekkpylalllalllfspv 156
                 +li+++++++i+ +++++   k+ l +++++l+ +p+
  AJA92213.1 186 FLIPLTIIFFIKfRKQKISYLKFSLFIFIFILILLPI 222
                 *******999996666777777777666666666665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.1
       PMT_2 102 llagvlfGlgflsKytaallliaallyllis..arr.ilkekkpylalllalllfsp 155
                 l++ +   l    K+  ++l++ ++++++ +   +  +l++k +++ l++++ l++p
  AJA92213.1 280 LISFMGTSLFNTLKFLGFVLIP-LFIFFIPTgiYNLiKLRNKDLFYLLIFGIFLIIP 335
                 4444444444444555555555.6664444447444467775555544444444445 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.26
       PMT_2 117 taallliaall..yllisarrilkekkpylalllalllf 153
                   +l++i  ++  y l s  +++++ k+  ++l++ +++
  AJA92213.1 350 LFVLFPIFCAIsvYGLNS-IKKFQKTKF--VVLIITVII 385
                 444444422222222222.112222222..222222222 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.11
       PMT_2  17 fgfselairlvsalagvltilllyl 41 
                 f ++ +++ ++++++ +  ill+y 
  AJA92213.1 371 FQKTKFVVLIITVIILSSIILLIYE 395
                 5667888888888888888888885 PP

>> Zds_C  Activator of mitotic machinery Cdc14 phosphatase activation C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.23   2.1e+03       3      26 ..     346     369 ..     344     371 .. 0.84
   2 ?   10.4   0.3   4.7e-05      0.42      22      51 ..     479     509 ..     477     510 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.23
       Zds_C   3 dvvmydtRfpihvERaiYRlsHlK 26 
                 dv +++  fpi     +Y l  +K
  AJA92213.1 346 DVRYLFVLFPIFCAISVYGLNSIK 369
                 7899999****9999999887766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.7e-05
       Zds_C  22 lsHlKLanprRpLreQVLlSNfM.YsYLnlv 51 
                 l H+ L++  R+L+   Ll N+  YsYL++v
  AJA92213.1 479 LTHIVLTENNRSLFLDKLLKNYQeYSYLEKV 509
                 79*******************966****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3671.45
//
Query:       AJA92214.1  [L=47]
Description: hypothetical protein T478_0363 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0043   17.8   1.0     0.0045   17.7   1.0    1.0  1  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.013   15.6   1.8       0.03   14.3   1.9    1.6  1  DZR             Double zinc ribbon
      0.014   15.0   4.1        1.6    8.5   0.2    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.016   14.9   1.3          3    7.7   0.2    2.4  2  zinc_ribbon_2   zinc-ribbon domain
      0.033   14.0   4.6        1.8    8.4   0.3    2.1  2  zf_C2HC_14      C2HC Zing finger domain
      0.034   14.2   0.8      0.042   13.9   0.8    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.075   13.4   2.2       0.39   11.1   2.2    1.9  1  GFA             Glutathione-dependent formaldehyde-activating
       0.91    9.2   3.2         12    5.6   0.4    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.0     2e-06    0.0045      38      75 ..       4      41 ..       1      44 [. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
  zinc_ribbon_15 38 lacskCkslleaskelgkeiekkessekkeCknCgkev 75
                    ++c kC++++e+++ +++++++++ + k +C +Cg++v
      AJA92214.1  4 AYCVKCRKKVEIQDAEETKLKNGRPAVKGVCGECGTKV 41
                    689********************************987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.9   1.3e-05      0.03      13      38 ..       4      41 ..       1      43 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
         DZR 13 rfCseCgtklkavaa............edrCpsCgekv 38
                 +C +C++k++ + a            + +C +Cg+kv
  AJA92214.1  4 AYCVKCRKKVEIQDAeetklkngrpavKGVCGECGTKV 41
                79*******986666999*****************986 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5   0.00088         2       3      16 ..       6      19 ..       5      25 .. 0.87
   2 ?    8.5   0.2   0.00071       1.6       3      10 ..      34      41 ..      33      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00088
                    -SSS--B----SSS CS
  DNA_RNApol_7kD  3 CgeCgaevslkkgd 16
                    C +C ++v+++  +
      AJA92214.1  6 CVKCRKKVEIQDAE 19
                    9*********9876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00071
                    -SSS--B- CS
  DNA_RNApol_7kD  3 CgeCgaev 10
                    CgeCg++v
      AJA92214.1 34 CGECGTKV 41
                    99999987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0026       5.8       1       9 [.       5      13 ..       2      19 .. 0.74
   2 ?    7.7   0.2    0.0014         3      16      22 ..      34      40 ..      21      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
  zinc_ribbon_2  1 fCpnCGael 9 
                   +C +C +++
     AJA92214.1  5 YCVKCRKKV 13
                   677777776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
  zinc_ribbon_2 16 CpyCGtp 22
                   C +CGt+
     AJA92214.1 34 CGECGTK 40
                   7777776 PP

>> zf_C2HC_14  C2HC Zing finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3   0.00079       1.8       2      16 ..       1      15 [.       1      17 [. 0.88
   2 ?    7.6   0.6    0.0014       3.2       3      15 ..      30      42 ..      29      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00079
  zf_C2HC_14  2 stegnCkgCekqVcL 16
                +te+ C  C+k+V +
  AJA92214.1  1 MTEAYCVKCRKKVEI 15
                68999********86 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
  zf_C2HC_14  3 tegnCkgCekqVc 15
                ++g C +C+++V+
  AJA92214.1 30 VKGVCGECGTKVF 42
                5788*******95 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.8   1.9e-05     0.042      70      99 ..       3      44 ..       1      46 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                EEEETTTS-EEECHHHHH............S-TTTSSS-EEE CS
        HypA 70 kvrCreCgkefeleekal............rCpkCgsadvei 99
                +++C +C+k++e++++++             C++Cg++ ++i
  AJA92214.1  3 EAYCVKCRKKVEIQDAEEtklkngrpavkgVCGECGTKVFRI 44
                689*********886422467999*****9*****9987765 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2   0.00017      0.39      39      61 ..      20      43 ..       1      47 [] 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
         GFA 39 kt.adsgnkvtrsfCpeCgsplys 61
                +t  ++g+++ + +C eCg++++ 
  AJA92214.1 20 ETkLKNGRPAVKGVCGECGTKVFR 43
                2225689**************994 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4    0.0055        12       5      19 ..       6      20 ..       3      20 .. 0.88
   2 ?    4.5   0.1     0.012        26       4      12 ..      33      41 ..      31      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0055
      zf_UBZ  5 CerCgkeipeselqE 19
                C +C k++++ + +E
  AJA92214.1  6 CVKCRKKVEIQDAEE 20
                99*******998876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
      zf_UBZ  4 lCerCgkei 12
                +C +Cg+++
  AJA92214.1 33 VCGECGTKV 41
                7*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 357.86
//
Query:       AJA92215.1  [L=280]
Description: oxidoreductase NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-13   50.1   0.0    5.3e-13   49.6   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
      2e-08   34.5   0.0      3e-08   33.9   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
        0.2   10.9   0.0       0.25   10.6   0.0    1.2  1  Methyltransf_34  Putative SAM-dependent methyltransferase


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   8.8e-17   5.3e-13       2     104 ..     126     248 ..     125     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 8.8e-17
                    EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT......EEEEEEEESSCTT....TSSSEESSHHHHHHHHHHH CS
  NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg......rlkvvavvsreea....gweggkgrvqdalleells 87 
                    i+gGtG+aP++s+ +++ +   dk+++++++G+ + ++l y++ l  l+++  +      ++k+ a+ sr+++     w+g++grv++ l+ ++ +
     AJA92215.1 126 IGGGTGLAPFVSYAQHLHDI-GDKREIIVLHGASYVDELSYKQLLTDLENESIDkgtdkwNFKYRAAISRPQEwfnrAWTGQTGRVEQFLRSKAGE 220
                    89**************9997.99*************************998766667778999999977776433338************999999 PP

                    ...........HSSTTEEEEEECSHHHH CS
  NAD_binding_1  88 ...........lkkeethvyvCGppgMi 104
                               ++k++t++y+CG +g i
     AJA92215.1 221 kspleelvgepITKDNTMFYICGWQGTI 248
                    99*********9***********87765 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     5e-12     3e-08       2      97 ..       7     107 ..       6     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5e-12
                    EEEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC...ETTCCEEEEEE.BSSTTECCEEEEEEE--...TT-HHHHHHHCS-TT-EEEEE CS
  FAD_binding_6   2 lkltekeevsedtrifrfklpsekqklglpvGqhvflrlk...ikgeaviRsYtpissenekGelellvkvy...pgGkmsqaLdelkigdtleik 91 
                    ++lt  + + ed+ ifr+  p++    ++ +Gq++ + ++    +++ v R+Y+++s++++k ++e++++ +     G+++  L ++k g+ ++  
     AJA92215.1   7 ATLTYTQLLKEDLGIFRLV-PEDGVIPDYKPGQFLTIGMPvpgEDNKIVRRAYSIASHPENKKFFEFVIRWVrkpFPGRLTTELFNAKEGSEVSWI 101
                    5778888888999999985.44666679**********9944334556889*********************88778******************* PP

                    EEE-SE CS
  FAD_binding_6  92 GPlGkf 97 
                     P+G++
     AJA92215.1 102 KPTGHL 107
                    ***997 PP

>> Methyltransf_34  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.1e-05      0.25      87     144 ..     115     175 ..      52     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
  Methyltransf_34  87 e...kklkvlciGGGag.aElvalaallrekeeekessssslsltlvDiadWssvvkkLeka 144
                      +   ++ +++ciGGG g a +v+ a  l++   +k++       + vD   +++++++Le++
       AJA92215.1 115 DgepDTRRIVCIGGGTGlAPFVSYAQHLHDI-GDKREIIVLHGASYVDELSYKQLLTDLENE 175
                      04447889*******9767777777777743.333444444456788888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2036.25
//
Query:       AJA92216.1  [L=674]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-08   32.9   0.2    8.7e-07   29.5   0.0    2.6  3  Radical_SAM  Radical SAM superfamily
    4.5e-06   26.7   0.0    8.7e-06   25.8   0.0    1.4  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.04   14.1   0.5       0.75   10.0   0.0    2.8  2  MATH         MATH domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.24   1.4e+03      37      73 ..      48      84 ..      43     114 .. 0.71
   2 !   29.5   0.0   1.5e-10   8.7e-07       4     164 ..     170     331 ..     167     334 .. 0.83
   3 ?   -1.5   0.0      0.49   2.9e+03      85     124 ..     516     557 ..     468     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.24
                 HHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                 xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 37 evkelkaekg.vkevilgggepllypdfvellerlakl 73
                 +++e+k +k+    +i+gg +  l+++  e++++ + +
   AJA92216.1 48 LAREIK-SKDpDTLIIFGGPNFPLDDPSREKWLKQHTE 84
                 677885.5554777888888888888888888777776 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 1.5e-10
                  ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCTEEEEEEECSSCHG...HHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx...xxxx RF
  Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlakla...vpgiritvetngtlpd...eekl 94 
                   rgC++ C+fC  + +  ++ r++++ v + ++e+++++ ++  +k+++l   +  +y   +e+  ++a ++   +  + i v+t     +     k 
   AJA92216.1 170 NRGCPFTCTFCVDGIK--DRSRVYYKEVSRFEKELEYIAtHY-EGKVLTLADLNFGMYNQDIEISNAIANIKekfNYPYYIQVSTGKN--NkpkVLKC 262
                  59************95..********************8444.4**************999999999999988555555555555444..34455667 PP

                  HHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  95 erllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                  +++l+ g   ++ +++++d+e vl +++ ++   +++l+ +++ ++   +  + +i+ lpG ++e++ +++
   AJA92216.1 263 AEILK-GSMSLAASVQSLDKE-VLTKIKrKNIQEDQLLDMTKAGNKMSANTYSEVILALPGDSKEKHMDTV 331
                  78888.569************.9999986777888999999999998877799999*******99988875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.49
                  CSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CT CS
                  xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
  Radical_SAM  85 ngtlpd..eeklerllelgvdrvslgleaaddekvlklmn.rg 124
                  +   +d   +++e++l+   ++ +l  + + +e  ++  + r+
   AJA92216.1 516 SDSIHDevFKIIEEMLKIKNNQAYLQYKDYLNE-LKEFSKlRK 557
                  445555556788888888888888888888887.555555544 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.5e-09   8.7e-06      39     120 ..      17     100 ..       6     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.5e-09
  B12-binding  39 enedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsld...peetleak.lgiddvvvgegedaleal 120
                  +++++++   ++kp +vg+S  + ++ e   el++++k+++p++ +++GG+ + ld    e  l+ +  ++d  ++ge+e+ +  +
   AJA92216.1  17 DPKKFIEWYLSNKPKIVGFSN-YVWNKELSCELAREIKSKDPDTLIIFGGPNFPLDdpsREKWLK-QhTEVDLYIIGEAEESFTKI 100
                  557888888899*********.****************************988776222344444.26999**********99776 PP

>> MATH  MATH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00012      0.75      11      47 ..     231     267 ..     226     312 .. 0.79
   2 ?    0.8   0.1     0.086   5.2e+02       2      29 ..     550     579 ..     549     614 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
        MATH  11 esryskveerfnipWrlkikrkngflglyLrcnkeee 47 
                  +++ ++ e fn+p+++++++ +++   +L+c++  +
  AJA92216.1 231 SNAIANIKEKFNYPYYIQVSTGKNNKPKVLKCAEILK 267
                 5778899*************************99833 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.086
        MATH   2 knfSklk.egesrys.kveerfnipWrlki 29 
                 k+fSkl+ ++  +y+ ++e+ fn+ ++  +
  AJA92216.1 550 KEFSKLRkRNVFDYEkQYESEFNYDFKTLM 579
                 678999877778888899999999888433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4734.60
//
Query:       AJA92217.1  [L=144]
Description: ribosomal protein S6e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-27   95.3   0.5    3.2e-27   95.0   0.5    1.1  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.5   1.8e-31   3.2e-27       1     111 [.       4     109 ..       4     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 1.8e-31
                    -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSSSS-EEEEEE CS
  Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprrkGerkrksv 96 
                    +kl isd + gk+ + e++e +++ l+g  ig e d++++G  l+g +lkitggsdk+G+pm+ ++++  r+r+Llsk gvg + +++G rkrk v
     AJA92217.1   4 FKLTISDVK-GKSITKELKEGDANPLMGLVIGAETDAAIVG--LAG-KLKITGGSDKSGVPMRGDLHGMARKRVLLSK-GVGLQDTEHGLRKRKLV 94 
                    799***987.9******************************..999.79*****************************.***************** PP

                    E-SB--SSEEEEEEE CS
  Ribosomal_S6e  97 rGcivsadisqlnlv 111
                    rG++vs++i q+n++
     AJA92217.1  95 RGNTVSDEIFQVNCK 109
                    *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 929.85
//
Query:       AJA92218.1  [L=38]
Description: hypothetical protein T478_0575 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1624  (0.0905795); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 288.59
//
Query:       AJA92219.1  [L=570]
Description: DEAD/DEAH box helicase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-38  130.5   0.0    8.5e-38  130.0   0.0    1.2  1  SNF2_N      SNF2 family N-terminal domain
    6.4e-12   45.8   2.7    6.3e-11   42.6   0.1    3.1  3  Helicase_C  Helicase conserved C-terminal domain
    0.00025   20.9   0.0     0.0007   19.4   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
        6.9    6.4   9.1        2.7    7.7   4.4    2.4  2  DUF445      Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   1.9e-41   8.5e-38      54     326 ..     123     380 ..     114     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.9e-41
                 TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------E CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydv 152
                 s+ + +LaDemGLGKTvq+la +               k++ ++p+Liv+P  +l++W++eie++++++  +  v ++++ ++ + ++ + + l +yd 
  AJA92219.1 123 SSGNALLADEMGLGKTVQTLAYLS--------------KEKNSFPALIVAPLVTLTNWQREIEKFLKKKGKNGKVIENETPSSTMIRNGKLADLGEYDF 207
                 56688*******************..............334579************************9999999999998888888999999****** PP

                 EEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--....-S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N 153 vittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLs....tsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqr 247
                  i++Y+ l ++         l++v ++ vv+DE + l+++t++ + av++L+     ++r+ l+GTPi n  ++++++++ L+++ +g+++ f + +  
  AJA92219.1 208 YIINYELLHKRL------PDLTKVGIRSVVCDEVQHLRSKTTQKYAAVKELAglesVKYRVGLSGTPIYNRGSEIWPIVDILKPGLLGSFKEFCEYFCY 300
                 *********777......9*******************************98776789*******************************9999998877 PP

                 HHH....HHHHHHHHHH.HTT-STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH....................HHHHH CS
                 xxx....xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      SNF2_N 248 pie....aqaekgrsrL.lqllqrlmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkss 326
                   e       e++r  L +ql + +mlrr k+dv k+l +   ++++ +  + ++k+Y+  l++  kk l   +k +e a+++s
  AJA92219.1 301 VNEkgkaIVLENKRDTLrNQLTKHVMLRRKKSDVLKELKD---KVRYSSPVHADEKFYKAELSKIWKK-LEEEQKYAESAFDKS 380
                 766567633455555561577889**********666655...5666677778899***444444333.333444444444433 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.46   2.1e+03      12      57 ..     147     195 ..     137     217 .. 0.58
   2 ?    1.3   0.1     0.098   4.4e+02       6      34 ..     294     325 ..     290     358 .. 0.69
   3 !   42.6   0.1   1.4e-14   6.3e-11       2     111 .]     398     507 ..     397     507 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.46
                 HTTTTSEEEEEESSHH......HHHHHHHHHHHTTSTEEEESTTSTHHHHHH CS
  Helicase_C  12 leeeggkilifvntid......rlekvklllekkgikvavlhgelpqneree 57 
                 +e++   +li+++ ++      ++   + +l+kkg +  v+  e+p++  ++
  AJA92219.1 147 KEKNSFPALIVAPLVTltnwqrEI---EKFLKKKGKNGKVIENETPSSTMIR 195
                 555555566666666633221244...6666777888888888877766555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.098
                 HHHHHHHTTTTSEEEEEESSHHHHHH...HHH CS
  Helicase_C   6 llellkleeeggkilifvntidrlek...vkl 34 
                 ++e++   +e+gk+++  n++d+l +    ++
  AJA92219.1 294 FCEYFCYVNEKGKAIVLENKRDTLRNqltKHV 325
                 4555557799************8864443222 PP

  == domain 3  score: 42.6 bits;  conditional E-value: 1.4e-14
                 HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTSTTESEEEESSSSSS CS
  Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekk..gikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidipkvnlVinfdlprn 96 
                 kl+++++++ +  e+++ +++f++ +      +ll++ +  +++ a + g  +   r++ +++f+kg+++ ++   +++  Gi+++++++Vi+ +l+++
  AJA92219.1 398 KLKHVVDFVtEIMEIEESVVVFCHHKAIH---SLLHN-NlaQYTPASIIGGQTDVVRQREIDRFQKGQTKlMIAGLRAGNVGINLTNAKYVIFAELDWS 492
                 6777777766777999*********9955...66643.347999999***********************888889*********************** PP

                 HHHHHHHHTTSSSTT CS
  Helicase_C  97 vtsyiqriGRtgRag 111
                 ++   q+ +R +R+g
  AJA92219.1 493 PAIHRQAEDRLHRIG 507
                 *************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.6e-07    0.0007       4     139 ..     113     244 ..     110     271 .. 0.69
   2 ?   -3.1   0.0       1.2   5.6e+03     116     131 ..     475     490 ..     435     506 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-07
                 HHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST....SEEEEE.ETTSSHHHHHHHHHT CS
                 xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx.xxxxxxxxxxxxxxx RF
        DEAD   4 Qaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid....lrvlli.iggvaardqlskldn 96 
                 Q+e ++ ++ + g+ l+a e G GKT   l  +       k+k+   aliv+P+  L++ + ++++kf+k+ +    + ++ +  +   ++ +l++l  
  AJA92219.1 113 QREGLDFLIkSSGNALLADEMGLGKTVQTLAYLS------KEKNSFPALIVAPLVTLTNWQ-REIEKFLKKKGkngkVIENETpSSTMIRNGKLADL-G 203
                 6666665554778*************99776666......79***************9754.66777777544222222221112233334444445.6 PP

                 TCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  97 gvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfs 139
                 ++d+++ + + l++ l    l+   +r +V DE++ l ++  +
  AJA92219.1 204 EYDFYIINYELLHKRLP--DLTKVGIRSVVCDEVQHLRSKTTQ 244
                 6*********9999663..333456799*********999433 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                 SSHCTTEEEEEEETHH CS
                 xxxxxxxxxxxxxxxx RF
        DEAD 116 klnlsqvrflVlDEad 131
                  +nl + +++++ E d
  AJA92219.1 475 GINLTNAKYVIFAELD 490
                 4788888999988877 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.22     1e+03     204     275 ..     143     220 ..      55     252 .. 0.68
   2 ?    7.7   4.4    0.0006       2.7     228     339 ..     311     563 ..     300     566 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.22
      DUF445 204 hllreeedkkvreliadllndpelaakveklkkkklsdlevqeyeealwealkdlllkdlneee......sllreris 275
                  +l++e++ + +  +a l +  +++ ++ek++kkk ++ +v e+e   ++ +++  l+dl e +       ll++r+ 
  AJA92219.1 143 AYLSKEKNSFPALIVAPLVTLTNWQREIEKFLKKKGKNGKVIENETPSSTMIRNGKLADLGEYDfyiinyELLHKRLP 220
                 556666666655666666666678888888888888888887777777777777666666665555555555555555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0006
      DUF445 228 aakveklkkkklsdlevqeyeealwealkdlllkdlneee..sllrerisklleklge......................................... 283
                 ++k ++l++++ ++++ +++++++ ++lkd+++ +       ++ + ++sk+++kl+e                                         
  AJA92219.1 311 ENKRDTLRNQLTKHVMLRRKKSDVLKELKDKVRYSSPVHAdeKFYKAELSKIWKKLEEeqkyaesafdksasyhraieserqaaglaklkhvvdfvtei 409
                 477888999999999999999999999999988776653334666667777777666666666666666666666666666666666666666666666 PP

      DUF445 284 ..............................................................................klaedpklrekln........ 296
                                                                                               +                    
  AJA92219.1 410 meieesvvvfchhkaihsllhnnlaqytpasiiggqtdvvrqreidrfqkgqtklmiaglragnvginltnakyvifaE-----------Ldwspaihr 497
                 6666666666666666666666666666665555555555555555555555555555555555555555555555552...........044444445 PP

      DUF445 297 .......................kflenaaakvlekyrldiskiveetvnafdaeeleelIelivg 339
                                          l +++a++l +++++i++i  ++ ++f+++e  ++I+ ++ 
  AJA92219.1 498 qaedrlhrigqkntvfayylvgkGTLDEHVAEILTDKEFEIDSILDKQGESFENKEKAKMILAQIH 563
                 5557777777777788888899999************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3629.92
//
Query:       AJA92220.1  [L=165]
Description: PF04019 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-35  120.6   0.0    3.9e-35  120.2   0.0    1.1  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   2.2e-39   3.9e-35       1     125 [.      46     164 ..      46     165 .] 0.93

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 2.2e-39
      DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDLavlpaillapegsvvvYG 99 
                 +++ ll++g++P l ivDg+ kRe+ +        e e+ ++++++kN++G+i+ e ++ +k++++++ ++++lVdGEEDL+vlp++l+ape+svv+YG
  AJA92220.1  46 TSELLLEMGLIPLLHIVDGQEKREKRSPP------EIESISTELTIKNNPGEISTESFNLLKTIFDQKPPIRLLVDGEEDLLVLPVCLFAPENSVVMYG 138
                 57889*******************44443......33556899******************************************************** PP

      DUF359 100 qpdeGvvlvkvteeakeeaeellekf 125
                 qp+eG+v+ ++t+e++e+++++++++
  AJA92220.1 139 QPNEGLVIAEITDEVREKVQKIVNQM 164
                 ************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1250.34
//
Query:       AJA92221.1  [L=260]
Description: DNA methylase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-37  129.8   4.8    1.5e-37  129.5   4.8    1.1  1  N6_N4_Mtase      DNA methylase
    4.3e-05   22.9   0.1     0.0034   16.7   0.2    2.1  2  N6_Mtase         N-6 DNA Methylase
     0.0001   22.0   0.0       0.18   11.5   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.026   14.3   0.1      0.053   13.3   0.1    1.7  1  N6-adenineMlase  Probable N6-adenine methyltransferase
      0.067   12.7   0.0       0.71    9.4   0.1    2.1  2  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   4.8   4.2e-41   1.5e-37       1     230 [.      26     244 ..      26     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 4.2e-41
                  EEEEEE--SSSSSCS.....GCCGCCH..........HHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESS CS
  N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeeds..........yeeyleflekvlkevrrvLkddgsifiniddseikkelkaladeifggffllnvivwkkpn 88 
                  +dli+tdpP+ +  + +++ +y+ ++s           e+y++f + +++e+ r+Lk++gs++i+ + ++ k+  +++a ++ g + ++n+i+wk++ 
   AJA92221.1  26 IDLIITDPPFAIDFK-AKKANYNRKSSrviegyneilPENYSQFSYDWISEANRILKESGSMYIFSGWNNLKD--ILIAIDDVG-LTVINHIIWKYQF 119
                  89*************.999999999999******************************************986..666666668.************9 PP

                  STTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHH CS
  N6_N4_Mtase  89 smpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIk 186
                  ++   nk ++ts +  ++v++ +kk+++++     ++ ++ek++  ++       + ++ ed+W   ++ +  +++k       p++ P++++++++ 
   AJA92221.1 120 GVVTKNK-FVTSHYHCLFVCKNPKKRKFYP---FSRYGKNEKSEDGHSL------HYHDKEDVW-EIKREYWTGEDK-----T-PTKLPAEIIKKILM 200
                  9999886.8888888888888888884333...3444444444444444......557899***.333344444444.....3.************** PP

                  HHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
  N6_N4_Mtase 187 lstkkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                   s+kk+div+DpF+GSG  av+ k l+r+f G+ei +ey++ a+
   AJA92221.1 201 YSSKKNDIVFDPFLGSGQVAVVGKMLDRRFCGFEIVKEYYKFAQ 244
                  ****************************************9876 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   9.6e-07    0.0034     100     179 ..       2      86 ..       1      95 [. 0.74
   2 !    4.3   0.0    0.0058        21      30      60 ..     186     219 ..     177     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.6e-07
    N6_Mtase 100 hgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkektlekde...rfrea...vapksnadla..fllhiieslkpkGra 179
                 + i+ +  ki +++ l   k  +++k+d +++ ppf ++ +k k+ + +    r  e+   + p++  +++  ++  +   lk++G +
  AJA92221.1   2 KKIDFN--KIYNKNCLDGMKLIDKNKIDLIITDPPFAID-FKAKKANYNRkssRVIEGyneILPENYSQFSydWISEANRILKESGSM 86 
                 566777..69999***9999999***************9.9444444333111444447886666666666669******99999987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0058
    N6_Mtase  30 TPrevs.klivell..epksgesvyDpacGsggl 60 
                 TP ++  ++i ++l   +k++  v+Dp  Gsg +
  AJA92221.1 186 TPTKLPaEIIKKILmySSKKNDIVFDPFLGSGQV 219
                 56555413333444666677778********976 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   4.9e-05      0.18     108     141 ..      13      45 ..       2      53 .. 0.82
   2 !    8.1   0.0   0.00055         2       6      54 ..     184     231 ..     180     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                 EE--GGG--STTS---EEEE----------HHHH CS
     UPF0020 108 sqadaakLrlkegevdvivtnpPYGerlgskkal 141
                 +++d  kL  +++++d+i+t+pP+ +  ++kka+
  AJA92221.1  13 NCLDGMKLI-DKNKIDLIITDPPFAIDFKAKKAN 45 
                 566777888.7779************99999987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00055
                 SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT-- CS
     UPF0020   6 fngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallgania 54 
                 ++ p++L +++   +++ +   +++  +DP+ GsG +++ + +l ++  
  AJA92221.1 184 DKTPTKLPAEIIKKILMYSSK-KNDIVFDPFLGSGQVAVVGKMLDRRFC 231
                 567888888888888888865.567889*********997777766655 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.5e-05     0.053      83     107 ..      18      44 ..       3     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
  N6-adenineMlase  83 eel..kgkfdviviDPPFlseeclkkl 107
                       +l  k+k+d+i++DPPF  +  +kk+
       AJA92221.1  18 MKLidKNKIDLIITDPPFAIDFKAKKA 44 
                      333579************665555553 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0002      0.71      88     114 ..      16      42 ..       2      64 .. 0.73
   2 ?    1.0   0.0     0.078   2.8e+02     121     137 ..      72      88 ..      63      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                 STTTTSTTS-EEEEEE---STTTCHCH CS
         MTS  88 dvleeveekkfdlivsNPPfhagkate 114
                 d+++ ++++k+dli++ PPf  + +++
  AJA92221.1  16 DGMKLIDKNKIDLIITDPPFAIDFKAK 42 
                 445556699***********8765544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.078
                 HHHHHHHHEEEEEEEEE CS
         MTS 121 liaeAkeaLkegGeLli 137
                  i eA+++Lke+G+++i
  AJA92221.1  72 WISEANRILKESGSMYI 88 
                 6899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1890.73
//
Query:       AJA92222.1  [L=458]
Description: pyridine nucleotide-disulfide oxidoreductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-47  161.1   0.0    4.1e-47  160.8   0.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.1e-15   55.1   1.0    1.7e-10   41.3   1.5    2.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0026   17.4   0.0        1.4    8.4   0.0    3.7  4  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.011   14.8   0.0        1.1    8.2   0.0    2.6  3  GIDA            Glucose inhibited division protein A
      0.075   13.1   0.6       0.16   12.1   0.1    1.9  2  LSM14           Scd6-like Sm domain
      0.096   12.9   0.0         18    5.6   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.11   11.3   0.0        7.4    5.3   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
       0.15   11.1   0.0        4.4    6.2   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   1.8e-50   4.1e-47       2     294 .]       3     350 ..       2     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 1.8e-50
                  SEEEE--SHHHHHHHHHHHH.....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTC CS
                  xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq.....agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgkkkvklekkkegd 94 
                  +++++GgG+AGl++ l+l        +++ tlv +e+++ +++++l++++ g+ e ++i++  ++ l ++ +++ g ++  idp  k v+l  ++e+ 
   AJA92222.1   3 RILILGGGFAGLECCLKLESyfqnnPEIELTLV-SEDNFILFTPMLPQVASGTIETRHIVTP-IRTLIKKTKFYEG-KIKYIDPHGKSVTLYGTNENR 97 
                  899*****************88864599*****.************************9984.4667778999999.999999999************ PP

                  EEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.................SEEEEES-SHHHHHHHHHHHHHT-......... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxx......... RF
  Pyr_redox_2  95 eekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.................krivvvGgGyiGvElAaalaklgk......... 166
                  +  i yd lv+A Gs+++ +g++ v+en +k+  t+++a  l+    +                  +ivvvGgG+ GvE+A++l+++           
   AJA92222.1  98 GMLIHYDFLVVALGSQTNFFGMKDVEENSYKM-NTINDAIILRNRIIDlmeqaenetdpilrkalLKIVVVGGGFAGVETAGELNDFITdvseyypsi 194
                  *************************9999888.99999999999999999999999999***999999****************99966678888888 PP

                  .....EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.......EEE.EEETTSCE............EEESEEEE-S-EEE CS
                  .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx.xxxxxxxx............xxxxxxxxxxxxxx RF
  Pyr_redox_2 167 .....evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.......kle.vvledgee............idadlvvvavGvrp 239
                       +v+lvea +++l++++++l+ +++e+l ++G++v l + v+ ++g++        + e v l+d ++            i  +++v+ +G++p
   AJA92222.1 195 dehdvKVVLVEASTEILNGFPQKLAGFAKEKLVERGIDVILDAGVTSFNGKEVllksnsnS-EkVLLSDSSQqkghaelveinsISSRTLVWTAGITP 291
                  88888999********************************************977666532.245555555588999********************* PP

                  S-HHCSHCCT-EEEETTEEE--TTSBES.STTEEE-GGGC......TECCSS--HHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx......xxxxxxxxxxxxxxxx RF
  Pyr_redox_2 240 stelleeklglelderggivvdeflrtn.vpgiyaiGDva......ggkggpelaqaAvqqG 294
                   + +  +++  ++ ++g+i+v+efl++   p+++aiGD+         k+ p +aq A +++
   AJA92222.1 292 TDLI--KESLFNT-HKGRIKVNEFLQVVeFPEVFAIGDCStfdpelTMKKFPPTAQIAEAHA 350
                  *977..6777777.9***********855***********9998888888888888888776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00046         1       1      43 [.       3      52 ..       3      67 .. 0.73
   2 !   41.3   1.5   7.4e-14   1.7e-10       1      70 [.     163     246 ..     163     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                EEEEECSSHHHHHHHHHH.....HHTTSEEEEEESSSSSS..TTSSHHHH CS
   Pyr_redox  1 kvvvvGgGyiglElAgal.....aelgkkVtvversdkll..rllDeeas 43
                +++++GgG+ glE+   l     ++   + t+v   + +l  ++l++ as
  AJA92222.1  3 RILILGGGFAGLECCLKLesyfqNNPEIELTLVSEDNFILftPMLPQVAS 52
                799***********999954444444567788888777776666665555 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 7.4e-14
                 EEEEECSSHHHHHHHHHH..............HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
   Pyr_redox   1 kvvvvGgGyiglElAgal..............aelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                 k+vvvGgG+ g+E Ag+l               e+  kV +ve+s ++l++++++++   +ekl ++gi+v+l++ v++++g+e
  AJA92222.1 163 KIVVVGGGFAGVETAGELndfitdvseyypsiDEHDVKVVLVEASTEILNGFPQKLAGFAKEKLVERGIDVILDAGVTSFNGKE 246
                 79****************7777777666666666669*******************************************9887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.094   2.1e+02       2      18 ..       4      20 ..       3      41 .. 0.75
   2 ?    0.2   0.0       0.2   4.6e+02     162     207 ..      72     117 ..      51     134 .. 0.68
   3 !    8.4   0.0   0.00063       1.4       1      29 [.     163     207 ..     163     213 .. 0.69
   4 ?    1.4   0.0     0.086   1.9e+02     145     182 ..     215     247 ..     213     302 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.094
                EEEECTSHHHHHHHHHH CS
         DAO  2 vviiGGGiiGlstAyeL 18
                ++i GGG +Gl + + L
  AJA92222.1  4 ILILGGGFAGLECCLKL 20
                99*********888777 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.2
                 EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE--GGGHHHH CS
         DAO 162 eilegtevtgleeedgkvwgve.rttp.gendaadavVnaaGawsdll 207
                 +++eg +++ ++   gk ++++ ++++ g   ++d +V+a G +++++
  AJA92222.1  72 KFYEG-KIKYIDP-HGKSVTLYgTNENrGMLIHYDFLVVALGSQTNFF 117
                 78888.8888844.4565666664444466546688********9966 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00063
                 EEEEECTSHHHHHHHHHH..............HHTT..EEEEESS CS
         DAO   1 dvviiGGGiiGlstAyeL..............arrg..Vtllekg 29 
                 ++v++GGG +G+ tA eL               ++   V+l+e++
  AJA92222.1 163 KIVVVGGGFAGVETAGELndfitdvseyypsiDEHDvkVVLVEAS 207
                 59*************999666655543333322233777777776 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.086
                 HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEE CS
         DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgv 182
                 p+kl+ +  +++ ++G+++++ + vt++   +gk  +v
  AJA92222.1 215 PQKLAGFAKEKLVERGIDVILDAGVTSF---NGK--EV 247
                 67788888888***************99...333..33 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.012        26       2      18 ..       4      20 ..       3      43 .. 0.91
   2 ?   -2.7   0.0       1.1   2.4e+03     246     270 ..      63      86 ..      45     125 .. 0.70
   3 ?    8.2   0.0   0.00051       1.1       1      17 [.     163     179 ..     163     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                EEEE-SSHHHHHHHHHH CS
        GIDA  2 viViGgGhAGceAAlaa 18
                + ++GgG AG+e++l++
  AJA92222.1  4 ILILGGGFAGLECCLKL 20
                789**********9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                 HHHCTCCC-T.T----B--S-CCC- CS
        GIDA 246 iikenlkksaklfegcieelgpryc 270
                  i+  +kk+  ++eg+i+ + p ++
  AJA92222.1  63 PIRTLIKKTK-FYEGKIKYIDPHGK 86 
                 4556666544.77777776666554 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00051
                 CEEEE-SSHHHHHHHHH CS
        GIDA   1 dviViGgGhAGceAAla 17 
                 +++V+GgG AG+e A +
  AJA92222.1 163 KIVVVGGGFAGVETAGE 179
                 699**********9966 PP

>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     7e-05      0.16       7      43 ..      64     121 ..      58     150 .. 0.68
   2 ?   -2.9   0.1       3.5   7.8e+03      62      74 ..     429     441 ..     428     442 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
       LSM14   7 islisksdirYeGilceinledstiaLqn.....................vrsfGteg 43 
                 i   +k+++ YeG+++ i+++ ++++L                          fG+++
  AJA92222.1  64 IRTLIKKTKFYEGKIKYIDPHGKSVTLYGtnenrgmlihydflvvalgsqTNFFGMKD 121
                 6777999********************8756666666666666555555555555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
       LSM14  62 FrgsDikdLevle 74 
                 F   Di+ L++++
  AJA92222.1 429 FFKRDISRLKIIK 441
                 5668******986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.019        42       1      17 [.       6      22 ..       6      36 .. 0.81
   2 ?    5.6   0.0    0.0081        18       1      29 [.     166     208 ..     166     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                   EE--SHHHHHHHHHHHC CS
  NAD_binding_8  1 IvGaGlsGlvaAylLak 17
                   I+G+G++Gl ++  L  
     AJA92222.1  6 ILGGGFAGLECCLKLES 22
                   89*******99988875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0081
                    EE--SHHHHHHHHHHH..............CCTEEEEEE-SSS CS
  NAD_binding_8   1 IvGaGlsGlvaAylLa..............kagfdvlllekrd 29 
                    +vG+G++G  +A +L               +++++v+l+e+++
     AJA92222.1 166 VVGGGFAGVETAGELNdfitdvseyypsidEHDVKVVLVEAST 208
                    8***********9998666666665555544688888888765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0033       7.4       1      35 [.       3      39 ..       3      45 .. 0.88
   2 ?    3.9   0.0    0.0087        19       1      22 [.     163     184 ..     163     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0033
                    EEEEE--SHHHHHHHHHHHHHTTTS..SEEEEEE-SS CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk..levtlvesee 35
                    +i+i+GGG aG      l+ +++++  +e+tlv  ++
      AJA92222.1  3 RILILGGGFAGLECCLKLESYFQNNpeIELTLVSEDN 39
                    69********************999778888887665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0087
                     EEEEE--SHHHHHHHHHHHHHT CS
  Trp_halogenase   1 kivivGGGtaGwlaAaalakal 22 
                     kiv+vGGG aG  +A  l+  +
      AJA92222.1 163 KIVVVGGGFAGVETAGELNDFI 184
                     79**********9999887655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.024        53       2      38 ..       4      43 ..       3      47 .. 0.82
   2 ?    6.2   0.0     0.002       4.4       2      37 ..     164     211 ..     163     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.024
  Lycopene_cycl  2 vvviGaGpAglslAarl...teakpglkvvlieaspsllf 38
                   +++ G+G Agl    +l    +++p+++++l+   + +lf
     AJA92222.1  4 ILILGGGFAGLECCLKLesyFQNNPEIELTLVSEDNFILF 43
                   689********99999877778999999999966655665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.002
  Lycopene_cycl   2 vvviGaGpAglslAarl............teakpglkvvlieaspsll 37 
                    +vv+G+G Ag+  A +l               + ++kvvl+eas ++l
     AJA92222.1 164 IVVVGGGFAGVETAGELndfitdvseyypSIDEHDVKVVLVEASTEIL 211
                    89***************8888777666666678889999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3314.51
//
Query:       AJA92223.1  [L=93]
Description: translation elongation factor aEF-1 beta [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-16   58.3   0.5    7.1e-16   58.2   0.5    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.18   12.1   0.0    1.2  1  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.5   7.9e-20   7.1e-16       2      90 .]       6      88 ..       5      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 7.9e-20
                EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....SEEEEEEEEEE- CS
     EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlVqsveivsfnkl 90
                +++++ P  +e+dle+l +++ks +l++ +++ + + +ep+afGl+ ++ +++ ed +++++ le  ++++eg     V++ e+ +++++
  AJA92223.1  6 LIVKILPTGTEVDLEKLVDEIKS-SLKDdIELLR-HTKEPLAFGLEFIKAEFTLEDAEGKMESLESSVKSVEG-----VSEFEVLNMSRM 88
                689********************.77777****6.**************************************.....*********995 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.18      31      82 ..      15      79 ..       1      84 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
      DUF948 31 aaatieelekqvdpilkevedllakvne.............lledvneklekvdplteavadlge 82
                ++  +e+l +++++ lk+  +ll++++e             +led ++k+e++++ +++v+ ++e
  AJA92223.1 15 TEVDLEKLVDEIKSSLKDDIELLRHTKEplafglefikaefTLEDAEGKMESLESSVKSVEGVSE 79
                555678889999999999999999999999999999999*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 674.58
//
Query:       AJA92224.1  [L=404]
Description: threonine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-68  229.0   0.4    9.1e-68  228.8   0.4    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.16   12.3   1.9       0.34   11.3   1.9    1.6  1  C1_2      C1 domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.8   0.4     1e-71   9.1e-68       3     294 .]      69     373 ..      67     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 228.8 bits;  conditional E-value: 1e-71
                 GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHT CS
        PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrll 100
                  ++g TPlv++++l kelg + l++K++s npt SfKdR a  +++++ke  g + v +as+GN + a+Aa aa+++++++i+ p++  ++k+a+  ++
  AJA92224.1  69 IEAGMTPLVKAEKLGKELGLNnLYIKNDSVNPTFSFKDRPAGVAISKAKEF-GLESVGCASTGNLASATAAHAAKANMPCYIFAPSNIETAKIAQALSY 166
                 67899**********************************************.*********************************************** PP

                 T-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT.TTEEEEEEE-SSSHHHHHHHHHHHH........HSTT-EEEEE CS
        PALP 101 GaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg.gkpdavvvpvGgGgliaGiaaglke........rrpdvrvigv 190
                 Gae + v+g+ydea ++aa++  + +g+ +v+    ++ +eg +t+++E++eql+ ++p++++vp+G+G+++ +i++g+ e        + ++ ++  +
  AJA92224.1 167 GAEYISVDGTYDEANRIAAQIGDR-KGVGVVNINMRSYYVEGSKTLAYEVAEQLDwNVPNHLIVPTGSGAMLNAICKGFEElqsvslldDLSSMHMHCA 264
                 ************************.********************************************************888876655555****** PP

                 EECTTCGGTTCCS..S.SS..B...SSS.CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTT CS
        PALP 191 epegsdalarslragrrvtvpvs..dtiadglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelke 284
                 +p+g++++ ++++++  + + v+  +t a++la+g   +++++++ l+++++ + + +d+e+l+a+ lla++egi++ep++++++ +l k++e g++++
  AJA92224.1 265 QPQGCAPIVDAFDKNVDKVTAVEqpNTVAKSLAIGdpGDGRYVLKRLKQYNGVAKQTNDKEILDAILLLAKTEGIFTEPAGGVSVSVLkKMVEEGKIDK 363
                 ************5543333322256**********9999************************************************************ PP

                 CEEEEEEE-B CS
        PALP 285 gdrvvviltg 294
                 ++++v+ +tg
  AJA92224.1 364 DEPTVCYVTG 373
                 *******998 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.9   3.8e-05      0.34      17      38 ..       4      26 ..       1      33 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
        C1_2 17 esfnCsaCgrkidgff.YsCseC 38
                +  +C+ C+++ +++f Y+C+eC
  AJA92224.1  4 NHLQCRECKKEYEPTFkYICDEC 26
                5679*******888888****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2852.33
//
Query:       AJA92225.1  [L=484]
Description: proline--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-19   68.8   0.0      3e-18   66.4   0.0    2.0  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
      3e-18   65.7   1.2    9.8e-18   64.1   1.2    1.9  1  HGTP_anticodon  Anticodon binding domain
    1.8e-16   60.1   2.2    6.5e-16   58.3   0.7    2.4  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   5.1e-22     3e-18       6     158 ..     106     259 ..      97     278 .. 0.83
   2 ?   -0.3   0.0      0.15     9e+02      57      97 ..     370     414 ..     355     473 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 5.1e-22
                   TTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHT.T.SCE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
  tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlikaisriferl.glefr 99 
                   + +++++L+Pt+e+  + l+ ++ +rs ++LPlk+    t  R E +++++ lR  eF +++g+ +h   ++++ ++ d+++++++  e+   ++  
    AJA92225.1 106 ELGDRLALRPTSETLAYTLFAKW-IRSwRDLPLKINFWNTALRAEIKATKPFLRTSEFLWQEGHTVHVnSEEAEKEVTDILELYKKTVEEElAIP-- 199
                   45899****************99.***888**************************************8899************99887761556.. PP

                   EEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEE CS
                   xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 100 aiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreks 158
                   +i +    ++k + + +++ +e +++  +k++++gt ++lg+++s+ ++++++d++n e  
    AJA92225.1 200 VITGKksEKEKFVGAVYTLTMESLMP-DGKALQMGTSHFLGQNFSKPFELKYADKENVESY 259
                   55555224444477888999999999.9************************998886654 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.15
                   TB-SEEEEEEEEEEES.G...GGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  57 lRvreFhqkdgyvfha.e...aslddslrdlikaisriferlgle 97 
                    R ++ +++d+ + ++ e   ++ld + +d++ ++++i+e+   e
    AJA92225.1 370 ARRHNRQKDDQAITGLvErvvSELDKIHNDMFSDAKKILEDRTSE 414
                   566677777777777754444556666777777777777765544 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   1.2   1.6e-21   9.8e-18       1      92 [.     295     390 ..     295     392 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.6e-21
                     SEEEEESSSS...HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHH CS
  HGTP_anticodon   1 qvvviplnek...aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelvekl 91 
                     qv++ip+      +e++e+  k++ e+L++a irv +d+ ++ ++g+k++e++++gip+++++G+k+lek++vt  +r++r++   ++  lve +
      AJA92225.1 295 QVIIIPIYYSdedKEKIEKISKEIEEKLKDAKIRVQVDNrEQLTPGFKFNEWEMKGIPLRIEIGPKDLEKNQVTFARRHNRQKDDQAITGLVERV 389
                     8999999888888999***********************9999****************************************999998888877 PP

                     H CS
  HGTP_anticodon  92 k 92 
                      
      AJA92225.1 390 V 390
                     5 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.19   1.1e+03      20      38 ..     306     329 ..     283     350 .. 0.74
   2 !   58.3   0.7   1.1e-19   6.5e-16       1      69 []     418     484 .]     418     484 .] 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.19
                 SGHHHHHHHHHHH.....S-EEEE CS
   ProRS-C_1  20 geeecEekIkeet.....gakslc 38 
                 +++e  ekI +e+      ak+++
  AJA92225.1 306 EDKEKIEKISKEIeeklkDAKIRV 329
                 445555555555577777788886 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 1.1e-19
                 HHHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
   ProRS-C_1   1 weefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                 ++efk++lek+++++ap c++++cEe+Ikeet+a +++i  d   +++++kCi c  +++ + lf+r Y
  AJA92225.1 418 YDEFKTELEKGRLIKAPICDNPKCEEEIKEETSADVRVITNDA--KDTSSKCIKCSDQSTIRPLFARGY 484
                 89*************************************9985..6899******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1288  (0.0718389); expected 358.6 (0.02)
Passed bias filter:                      791  (0.0441185); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3436.75
//
Query:       AJA92226.1  [L=403]
Description: hypothetical protein T478_0414 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00069   19.5   7.0    0.00091   19.2   3.6    2.8  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0063   16.7  22.8       0.56   10.5   5.3    5.1  5  DUF948           Bacterial protein of unknown function (DUF94
     0.0074   16.6   1.0     0.0074   16.6   1.0    5.0  4  Syntaxin_2       Syntaxin-like protein
     0.0099   16.0   8.8      0.074   13.2   0.1    3.0  2  Nup54            Nucleoporin complex subunit 54
  ------ inclusion threshold ------
      0.033   14.2   1.1      0.033   14.2   1.1    4.0  5  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.042   13.6   1.8        3.2    7.6   0.1    3.6  3  BRX_N            Transcription factor BRX N-terminal domain
      0.043   13.9  31.0       0.17   11.9   4.6    4.5  4  DUF1664          Protein of unknown function (DUF1664)
      0.047   13.5  28.5       0.15   11.9   4.3    3.9  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        0.1   12.7  17.2        3.7    7.7   0.5    4.9  4  TolA_bind_tri    TolA binding protein trimerisation
        0.4   11.3  15.4       0.74   10.4   0.8    4.2  4  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.51   10.4  22.6         10    6.2   0.9    3.4  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.68   10.1  34.9      0.033   14.4   2.9    3.7  5  Fib_alpha        Fibrinogen alpha/beta chain family
        1.2    9.1  22.4        2.2    8.1   0.4    5.1  7  Sec34            Sec34-like family
        1.3    9.1  31.6      0.054   13.5   5.3    4.2  4  Laminin_II       Laminin Domain II
        1.6    8.6  24.9        3.4    7.5   2.4    3.5  3  PIN_8            PIN like domain
        1.7    7.9  25.3       0.54    9.5   0.5    3.4  3  DUF3450          Protein of unknown function (DUF3450)
        1.8    8.6  19.4       0.62   10.1   1.1    4.5  4  DUF1515          Protein of unknown function (DUF1515)
        2.3    8.9  11.8         49    4.6   0.2    5.2  5  SlyX             SlyX
          6    6.9  12.0        1.8    8.6   0.5    4.2  4  DUF2205          Short coiled-coil protein


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   3.6   9.6e-07   0.00091       2     180 ..      58     263 ..      57     267 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.6e-07
                     HHHCCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHH.......... CS
  Apolipoprotein   2 leesldelkayaeeleeqlaplaqelrdrlskeleelrarl..raeleevrarlepyrdevqeqlgqnleelrqrlapyteelre.......... 84 
                     +++ +++l+  ++++++q +++     d ++++++ l a l   +  e+  ++l  +++e+ +++++  e+  q+  p t+e+ +          
      AJA92226.1  58 MSDMMQSLNLAMSQMQKQAKQM-----DIIEEDTQRLFAGLnqVKVHEQFISKLNKQTEEFDKKIAKINEN--QKTGPKTNEIIKsiaeskasiq 145
                     7888899999999999999988.....77778888887777655678888888888888888888877664..5666777777777777888888 PP

                     .......HHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----...............-----SSSHHHHH CS
  Apolipoprotein  85 .......rlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaph.............aeeveerlssrveel 159
                            ++a +++e++e+++++  + +  l + +e+l+++++ ++ ++ + +++ + +lk+++                 + ++++++++++++
      AJA92226.1 146 nnskmimKIANRVDEVKEKMDKVPTKTEGNLTSQIEELRENIKSITNRTGD-IGKDMSNLKNEIGGIvsnpkissligdgMKTFKSEIEEKISNI 239
                     88888888999********************************99999998.9999999999999985555555555555445555555555555 PP

                     HHTS-T...TSHHHHHS--XXXXX CS
  Apolipoprotein 160 reklee...qaeelrerleanlee 180
                     +   ++    a+e +++ +++++e
      AJA92226.1 240 SNMIDRsdqIASEFHRKTDKVMQE 263
                     555555555666666666666665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.8     0.061        58      40      70 ..      49      79 ..      19      91 .. 0.47
   2 ?    5.7   3.0     0.018        17      19      72 ..      53     115 ..      51     127 .. 0.70
   3 !   10.5   5.3   0.00059      0.56      18      88 ..     134     205 ..     101     206 .. 0.90
   4 ?    5.9   0.3     0.017        16      23      68 ..     238     283 ..     234     290 .. 0.83
   5 ?   -2.0   0.0       4.6   4.3e+03      40      54 ..     307     321 ..     282     333 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.061
      DUF948 40 kqvdpilkevedllakvnelledvneklekv 70
                k+ +++l  + d+++  n  +++++++ +++
  AJA92226.1 49 KDNQKVLVSMSDMMQSLNLAMSQMQKQAKQM 79
                3444444444444444444444444444444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
      DUF948  19 vvllklkktldeaaatieele...kqvdpilkevedllakvne......lledvneklekvdp 72 
                 +vl+++++++++++ ++ +++   kq+d i +++++l a  n+        + +n+++e+ d+
  AJA92226.1  53 KVLVSMSDMMQSLNLAMSQMQkqaKQMDIIEEDTQRLFAGLNQvkvheqFISKLNKQTEEFDK 115
                 689999999999999999999666778888999999999999944444434444444444443 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00059
      DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvne.lledvneklekvdplteavadlgesvseln 88 
                 i+ + + k  +++++++i ++ ++vd++ ++++++ +k++  l+++++e  e+++++t+  +d+g+ +s+l+
  AJA92226.1 134 IKSIAESKASIQNNSKMIMKIANRVDEVKEKMDKVPTKTEGnLTSQIEELRENIKSITNRTGDIGKDMSNLK 205
                 56666778889999999999999999999999999999986599999999****************999986 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.017
      DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvnekle 68 
                 ++++++d+  +   e  +++d++++e++++   +n+  +d ++++ 
  AJA92226.1 238 NISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSSKEVM 283
                 6788899999999999999999999999999999999888877765 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 4.6
      DUF948  40 kqvdpilkevedlla 54 
                 k+v+++  ++++l++
  AJA92226.1 307 KDVEKMASQTTELIN 321
                 445555555555544 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  10.8     0.069        65      10      99 ..      25     126 ..      19     128 .. 0.82
   2 !    6.9   5.7    0.0083       7.8       5      65 ..     103     160 ..      88     167 .. 0.65
   3 !   16.6   1.0   7.8e-06    0.0074       3      86 ..     149     228 ..     147     232 .. 0.78
   4 ?    1.6   5.9      0.37   3.5e+02       1      90 [.     232     327 ..     229     334 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.069
  Syntaxin_2  10 snvstleklvkqLgtk........kdteelreklhelieeinelikktnellkklsqldnsssds....qqklqkekLkkdfkealqeFqkiqrqyaek 96 
                 ++v+t  + +k L+          kd++++  ++ ++++++n   ++++++ k+++ +++ ++      +q   +e   +++++  +eF k   +++e 
  AJA92226.1  25 NKVNTVSESTKALSREikgmakifKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLfaglNQVKVHEQFISKLNKQTEEFDKKIAKINEN 123
                 4455555555555555555566689**********************************999766999999999*****************99999999 PP

  Syntaxin_2  97 ekq 99 
                 +k 
  AJA92226.1 124 QKT 126
                 985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0083
  Syntaxin_2   5 lqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssd 65 
                 ++k+n+++ +++k++ +++   +++++  k +e+i++i e    ++++ k +++++n  + 
  AJA92226.1 103 ISKLNKQTEEFDKKIAKIN---ENQKTGPKTNEIIKSIAESKASIQNNSKMIMKIANRVDE 160
                 4455555555555555555...556666677777777777777777777777777766543 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 7.8e-06
  Syntaxin_2   3 snlqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeF 86 
                 + + ki++ v + +++++++ tk++  +l ++++el+e+i+ + ++t +  k++s+l+n       +++  k+++ + + ++ F
  AJA92226.1 149 KMIMKIANRVDEVKEKMDKVPTKTE-GNLTSQIEELRENIKSITNRTGDIGKDMSNLKNEIG---GIVSNPKISSLIGDGMKTF 228
                 6689******************965.889999999999999999999999999999988763...3555555555555555555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.37
  Syntaxin_2   1 issnlqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldnsssds........qqklqkekLkkdfkealqeFqkiq 90 
                 i++++++i++ +   ++  +  + k  t+++ ++++ +   +n+ + + ++ +  + +l + +s+           +   ek++++ +e+++ F k+ 
  AJA92226.1 232 IEEKISNISNMIDRSDQIASEFHRK--TDKVMQEIQGVKGVTNKASDDSSKEVMAILKLNEYQSSIrmqaeskyGDIKDVEKMASQTTELINLFDKLS 327
                 4455555555555555555555555..66888888888888888888887777666666555543256675554334477788888888887777765 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   5.3     0.077        73      53     124 ..      52     125 ..      19     144 .. 0.80
   2 !   13.2   0.1   7.8e-05     0.074      42     131 ..     148     251 ..     133     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.077
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS CS
       Nup54  53 keisdrleeleqkhqletsvrlekakkrhv..elshRllrllrkleilrsrgyaldaeEeelrarletleaqln 124
                 +++  ++++++q+ +l +s+  ++ak++ +  e ++Rl   l+++++ +++ + l+++ ee  +++ +++++ +
  AJA92226.1  52 QKVLVSMSDMMQSLNLAMSQMQKQAKQMDIieEDTQRLFAGLNQVKVHEQFISKLNKQTEEFDKKIAKINENQK 125
                 577888999999999999988888888875336789999999999999******************99887655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.8e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-..............SS---SSHHHHHHHHHHHHHHHS-H CS
       Nup54  42 qkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsr..............gyaldaeEeelrarletleaqlndp 126
                  k++ +  +r++e++++++++ +k + ++++++e+++ + + +++R+  + + ++ l++               g ++++   e+++++ ++++ +++ 
  AJA92226.1 148 SKMIMKIANRVDEVKEKMDKVPTKTEGNLTSQIEELRENIKSITNRTGDIGKDMSNLKNEiggivsnpkissliGDGMKTFKSEIEEKISNISNMIDRS 246
                 5778888999*********************************************99998777777777777777788899999999999999999876 PP

                 HH.HH CS
       Nup54 127 aqlkg 131
                  q+ +
  AJA92226.1 247 DQIAS 251
                 55443 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7      0.16   1.5e+02      34      82 ..      21      75 ..      17      93 .. 0.61
   2 ?    3.7   5.4     0.064        60      17      83 ..      57     124 ..      41     146 .. 0.64
   3 ?   14.2   1.1   3.6e-05     0.033      23     106 ..     135     213 ..     127     223 .. 0.53
   4 ?    2.1   0.1      0.19   1.8e+02      37      80 ..     226     268 ..     215     321 .. 0.78
   5 ?   -2.6   0.0       5.5   5.2e+03      25      57 ..     295     326 ..     283     334 .. 0.49

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.16
  Baculo_PEP_C 34 aqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalqdt 82
                  +ql + ++++ ++ +als ++k + + +++       ++++++ L+ a+ ++q++
    AJA92226.1 21 SQLFNKVNTVSESTKALSREIKGMAKIFKDnqkvlvSMSDMMQSLNLAMSQMQKQ 75
                  5677777777777777777777755544445555556666666666666666633 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.064
  Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt.........rldtlltnLtdalnalqdtl 83 
                    ++++++++ l  +q+  + a+++d ie+  + l + l+       +         +l++++++ ++++++++++ 
    AJA92226.1  57 SMSDMMQSLNLAMSQM-QKQAKQMDIIEEDTQRLFAGLN-------QvkvheqfisKLNKQTEEFDKKIAKINENQ 124
                   5666666665555555.3334555555555555555555.......4444445677*****************653 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.6e-05
  Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNins 106
                   ++i   +++i  + ++++ +i++++++++e++ ++ ++       +  nLt+++ +l    ++++n+   + ++++nL +++++i s
    AJA92226.1 135 KSIAESKASI-QNNSKMIMKIANRVDEVKEKMDKVPTK-------TEGNLTSQIEELReniKSITNRTGDIGKDMSNLKNEIGGIVS 213
                   4444444444.222333444555555555555554444.......455555555555544445557777777777777777777654 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.19
  Baculo_PEP_C  37 atlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                   +t + +ie++++++s+ + + + +++++++  ++++ + ++ ++
    AJA92226.1 226 KTFKSEIEEKISNISNMIDR-SDQIASEFHRKTDKVMQEIQGVK 268
                   45566777777777777777.66777777777777777766655 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 5.5
  Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksl 57 
                   ir+q  +  ++++ +++++++q ++l + + +l
    AJA92226.1 295 IRMQAESKYGDIK-DVEKMASQTTELINLFDKL 326
                   4444444444443.3344444444444444444 PP

>> BRX_N  Transcription factor BRX N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0034       3.2       7      24 ..      28      45 ..      25      46 .. 0.86
   2 ?    2.1   0.0      0.18   1.7e+02       7      18 ..     128     139 ..     123     139 .. 0.85
   3 ?    0.4   0.0      0.61   5.8e+02      11      18 ..     185     192 ..     176     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0034
       BRX_N  7 kaakEvIKSLTaQLKdMa 24
                +++ E  K+L  ++K Ma
  AJA92226.1 28 NTVSESTKALSREIKGMA 45
                67789************9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
       BRX_N   7 kaakEvIKSLTa 18 
                 + + E+IKS+++
  AJA92226.1 128 PKTNEIIKSIAE 139
                 6788*****985 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
       BRX_N  11 EvIKSLTa 18 
                 E IKS+T+
  AJA92226.1 185 ENIKSITN 192
                 77999997 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.6     0.022        21      47     106 ..      20      79 ..       8      89 .. 0.76
   2 ?    8.8   5.8    0.0016       1.5      51     119 ..     100     167 ..      86     172 .. 0.67
   3 ?   11.9   4.6   0.00018      0.17      46     120 ..     133     211 ..     129     215 .. 0.75
   4 ?    6.7   1.7    0.0074         7      46     104 ..     221     279 ..     215     299 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
     DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                 ++ql +  +++++  + Ls++i+ + k  ++++++  ++++ +++++  +s+++++ +++
  AJA92226.1  20 TSQLFNKVNTVSESTKALSREIKGMAKIFKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQM 79 
                 456666677777778888888888888888888888888888888888888888877776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
     DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                 eq+ ++l+++ +++ ++i++++++++   + ++ei + ++e +  +++ ++ + ++ + v ++++k+++
  AJA92226.1 100 EQFISKLNKQTEEFDKKIAKINENQKTGPK-TNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKMDK 167
                 78999****************999875433.33444455555555555555555555566666666555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00018
     DUF1664  46 vskqleqvseslaatkr...hLssridrvdkkldeq.keiskeikeevtevredlseigedvesvkeavegleskleri 120
                 + k++ + ++s+++  +   ++++r+d+v +k+d++ +++  +++++++e+re++++i +    + + +++l++++  i
  AJA92226.1 133 IIKSIAESKASIQNNSKmimKIANRVDEVKEKMDKVpTKTEGNLTSQIEELRENIKSITNRTGDIGKDMSNLKNEIGGI 211
                 5666777777777665512245678999999999873566778999999999999999999999999999999988766 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0074
     DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                 ++  ++++++++++   ++s+ idr d+   e  + + ++ +e++ v++ +++ ++d++
  AJA92226.1 221 IGDGMKTFKSEIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSS 279
                 55566666666666666666666666666666666666666666666666666666554 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.1   0.00046      0.43      76     164 ..      26     113 ..      23     124 .. 0.87
   2 ?    7.8   3.3    0.0029       2.7     101     159 ..     105     166 ..      91     169 .. 0.47
   3 ?   11.9   4.3   0.00016      0.15      79     148 ..     135     205 ..     129     216 .. 0.85
   4 ?    1.6   3.9      0.22   2.1e+02      90     129 ..     231     270 ..     212     321 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00046
                 HHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  76 EVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                  V ++ e ++  ++ei+ +  +i k+ ++++ s+++  q  + +++++++ ++++  i e ++++ + ++++++  + +s+  +++ + 
  AJA92226.1  26 KVNTVSESTKALSREIKGMA-KIFKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLFAGLNQVKVHEQFISKLNKQTEEF 113
                 578888999999******98.********************************************999999999888887776666554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                 .........HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
   MCPsignal 101 eindsvesleetrqrveegselveetgealkeiveavaev...adlvqeiaaaseeqsasie 159
                 + n+ +e +++   +++e  ++  +t+e +k+i+e+ a++   ++++  ia  ++e  + ++
  AJA92226.1 105 KLNKQTEEFDKKIAKINENQKTGPKTNEIIKSIAESKASIqnnSKMIMKIANRVDEVKEKMD 166
                 33444444455555555555555555555555555444441112344444444444444333 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00016
                 HHHHHHHHHHHHHHHHH..............HHHHHHHHHH.HHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  79 kLAersaqaakeiealiieiqkeindsvesleetrqrveeg.selveetgealkeiveavaevadlvqeia 148
                 k  ++s+ + ++ +++i++i + ++++ e ++++ +++e   ++++ee +e++k+i+++++++ + +++++
  AJA92226.1 135 KSIAESKASIQNNSKMIMKIANRVDEVKEKMDKVPTKTEGNlTSQIEELRENIKSITNRTGDIGKDMSNLK 205
                 444567888888999999*****************99997625689******************9999986 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.22
                 HHHHHH..............HHHHHHHHHHHHHHHHHCCH CS
   MCPsignal  90 eiealiieiqkeindsvesleetrqrveegselveetgea 129
                 eie+ i +i + i++s ++ +e ++++++ +++++  + +
  AJA92226.1 231 EIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGV 270
                 3333333333333333333333333333333333322222 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   5.2       1.3   1.2e+03      36      57 ..      57      78 ..      30      89 .. 0.61
   2 ?    7.7   0.5    0.0039       3.7      13      56 ..      82     125 ..      79     127 .. 0.90
   3 ?    4.7   0.2     0.034        32      15      68 ..     146     207 ..     136     211 .. 0.70
   4 ?    5.8   0.0     0.016        15       2      42 ..     232     272 ..     231     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.3
  TolA_bind_tri 36 eLRGqiEelqyqleqleerQrd 57
                   ++   ++ l+  ++q++++ ++
     AJA92226.1 57 SMSDMMQSLNLAMSQMQKQAKQ 78
                   3333344444444444444443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0039
  TolA_bind_tri  13 learsqlllelqqqlealqqelreLRGqiEelqyqleqleerQr 56 
                    +e  +q l+  ++q++  +q +++L+ q+Ee+  ++ +++e Q+
     AJA92226.1  82 IEEDTQRLFAGLNQVKVHEQFISKLNKQTEEFDKKIAKINENQK 125
                    6667788888999******************************9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.034
  TolA_bind_tri  15 arsqlllelqqqlealqqelre........LRGqiEelqyqleqleerQrdlYldlDerlrk 68 
                    ++s++++++ +++++ ++ +++        L  qiEel+ +++++ +r  d+ +d+ ++ ++
     AJA92226.1 146 NNSKMIMKIANRVDEVKEKMDKvptktegnLTSQIEELRENIKSITNRTGDIGKDMSNLKNE 207
                    55566666666666666666653333333377899999999999999999988888887776 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.016
  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiE 42 
                    +e++++ + ++++ ++q   e +++ ++  qe++  +G + 
     AJA92226.1 232 IEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTN 272
                    7999******************************9999775 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.3    0.0098       9.3      34      96 ..      38     111 ..       3     114 .. 0.65
   2 ?    3.1   3.4      0.14   1.4e+02      50      96 ..      65     111 ..      52     162 .. 0.69
   3 ?   10.4   0.8   0.00079      0.74      22      98 ..     156     242 ..     131     243 .. 0.68
   4 ?    2.0   0.5      0.32     3e+02       6      37 ..     228     273 ..     223     332 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0098
  Syntaxin-6_N  34 s...........tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreevk 96 
                   s            ++++   ++++ ++l+ +  +++   + ++i+e++ ++     ++++ +++f+++++++ +
    AJA92226.1  38 SreikgmakifkDNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLFAGLNQVKVHEQFISKLNKQTE 111
                   122222333333455555556666666666666666666777999******99***************999876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
  Syntaxin-6_N  50 lrsiewdledLeetvriveknpskfkidekelsrrrafveevreevk 96 
                   l+ +  +++   + ++i+e++ ++     ++++ +++f+++++++ +
    AJA92226.1  65 LNLAMSQMQKQAKQMDIIEEDTQRLFAGLNQVKVHEQFISKLNKQTE 111
                   44444444444555567777777777777777777777777776654 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00079
  Syntaxin-6_N  22 rrwerlledtsss..........tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreevkem 98 
                   +r  +++e+ ++           + eel+e  + + +  ++i +d+++L++ ++ + +np+  ++  + +++ ++ +ee  +++++m
    AJA92226.1 156 NRVDEVKEKMDKVptktegnltsQIEELRENIKSITNRTGDIGKDMSNLKNEIGGIVSNPKISSLIGDGMKTFKSEIEEKISNISNM 242
                   233222222222122333334447888888888899999999999999999999999999888888888888888888877777776 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.32
  Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtsss..............tse 37 
                   +k+e++++++++ ++++r  ++ ++ + +              t++
    AJA92226.1 228 FKSEIEEKISNISNMIDRSDQIASEFHRKtdkvmqeiqgvkgvTNK 273
                   5667777777777777777665555444323333344444444333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.6     0.019        18      12     118 ..      22     123 ..      13     126 .. 0.88
   2 ?    4.8   5.6     0.029        27      26     116 ..     108     198 ..     100     208 .. 0.73
   3 ?    6.2   0.9     0.011        10       2      84 ..     235     317 ..     234     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.019
  TPR_MLP1_2  12 slkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselek 110
                 +l ++ +   +  ++l ++++ +a+i k+ q+     lv  ++ +++l+ + +++++  +++  ++++ +++ a l++ + + e+  ++l k+ +e+ k
  AJA92226.1  22 QLFNKVNTVSESTKALSREIKGMAKIFKDNQK----VLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLFAGLNQVKVH-EQFISKLNKQTEEFDK 115
                 566777888899999*****************....*****************************************99875.7778889999999988 PP

  TPR_MLP1_2 111 riedlneq 118
                 +i  +ne 
  AJA92226.1 116 KIAKINEN 123
                 88888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
  TPR_MLP1_2  26 klqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaelee....seesweeqkeelekelselekriedln 116
                 k  e+  k+ +  +e q+       k +e +k++++ ++ +++  + i ++ ++++++k+++++     e ++++q eel+++++++++r  d+ 
  AJA92226.1 108 KQTEEFDKKIAKINENQK----TGPKTNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKMDKvptkTEGNLTSQIEELRENIKSITNRTGDIG 198
                 455555555555555555....56688999******************************99862222577777888888888888888877765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
  TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                 ++++  + i++ ++ ++e  +k  k++++++  +  +++a ++ ++e++   +  +  +++r ++++   +i+++++ a +++
  AJA92226.1 235 KISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSSKEVMAILKLNEYQSSIRMQAESKYGDIKDVEKMASQTT 317
                 788899999****************************************9999999999999999999999999988888776 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  11.6      0.19   1.8e+02      26     123 ..      30     122 ..      10     126 .. 0.66
   2 ?    1.8  12.9      0.26   2.5e+02      28     122 ..      77     169 ..      70     173 .. 0.76
   3 ?   10.2  10.8    0.0007      0.66      26     129 ..     106     205 ..     100     213 .. 0.53
   4 ?   14.4   2.9   3.5e-05     0.033      28     122 ..     171     268 ..     168     278 .. 0.85
   5 ?    4.9   3.5     0.029        27      24     102 ..     223     301 ..     216     329 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                 CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeq 123
                 +++  k ++++++ + + ++++++   ++++++++++  + + qk++k+   +i++ +++l        ++++ +e+ i +L +  e+ ++ki+k+++
  AJA92226.1  30 VSESTKALSREIKGMAKIFKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQ-MDIIEEDTQRLF----AGLNQVKVHEQFISKLNKQTEEFDKKIAKINE 122
                 3444555566666666666666666666666666666666666666663.444444444443....44567888888888998888888888888765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                 CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                 k+   +++d ++l   l++++  ++ +++l k++++  ++  k + +n+++  k ++ ++  i++ k++i+++ + i ++ n +++ ++k+ k  
  AJA92226.1  77 KQMDIIEEDTQRLFAGLNQVKVHEQFISKLNKQTEEFDKKIAKIN-ENQKTGPKTNEIIK-SIAESKASIQNNSKMIMKIANRVDEVKEKMDKVP 169
                 445556777788888888888888888888888877755544444.47777777777777.9999999999999999999999999999999875 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0007
                 CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                 l+k+ ++++k+++k++++ +    +t+e+ + + e k s++++ k   +  n + ++++++++  ++ + +++   s+i++L+++++s  ++  ++ +d
  AJA92226.1 106 LNKQTEEFDKKIAKINENQK-TGPKTNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKMDKVPTKTEGNLT---SQIEELRENIKSITNRTGDIGKD 200
                 67777777777777765522.2333333333344444444444444444466666666666655555555444...55666666666655555544444 PP

                 HHHHH CS
   Fib_alpha 125 idqke 129
                 +++++
  AJA92226.1 201 MSNLK 205
                 44433 PP

  == domain 4  score: 14.4 bits;  conditional E-value: 3.5e-05
                 CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                 k+e +++ ++e+l++++++i+n+t ++ + ++++k+ +    ++ k +      +k +++e+ee+i+++ + id+  +   +     ++  q+iq  +
  AJA92226.1 171 KTEGNLTSQIEELRENIKSITNRTGDIGKDMSNLKNEIGGIVSNPKISsliGDGMKTFKSEIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVK 268
                 788899********************99999999998765444433323358999*********************9999999999999999998766 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.029
                 HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCH.H CS
   Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqe.s 102
                 d +++ +++++++++++ n +++  +  +e ++ + ++++ ++  +  +++  d   k++   l+   ++++ +i  q  s
  AJA92226.1 223 DGMKTFKSEIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKAsDDSSKEVMAILK--LNEYQSSIRMQAeS 301
                 66788888888899999988888888888888777777666665555444433677777777666..66667776666544 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.13   1.2e+02      27      58 ..      21      52 ..      16      66 .. 0.75
   2 ?    4.2   4.3      0.04        37       3      66 ..      70     136 ..      68     145 .. 0.80
   3 ?    6.2   2.2    0.0092       8.6       3      64 ..     104     165 ..      92     171 .. 0.78
   4 ?    8.1   0.4    0.0024       2.2       5      69 ..     137     202 ..     133     207 .. 0.80
   5 ?    6.0   0.1     0.011        10       5      51 ..     158     205 ..     154     229 .. 0.65
   6 ?    3.9   0.1     0.048        45      20      59 ..     230     269 ..     222     278 .. 0.84
   7 ?   -0.0   0.1      0.78   7.4e+02      25      74 ..     277     326 ..     261     332 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
       Sec34 27 eeleekfksvsektsslheaceqlleeqkrle 58
                ++l +k+++vse+t++l+++ + + +  k+ +
  AJA92226.1 21 SQLFNKVNTVSESTKALSREIKGMAKIFKDNQ 52
                67889999999999999999888766555444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.04
       Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvs...ektsslheaceqlleeqkrleelaeeiee 66 
                 +q++++ +++d + e+t+++   L++++   +++s   ++t++++++  ++ e+qk   +++e i++
  AJA92226.1  70 SQMQKQAKQMDIIEEDTQRLFAGLNQVKVHEQFISklnKQTEEFDKKIAKINENQKTGPKTNEIIKS 136
                 7899999999999999999999999887666555422279***********9999987777776664 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0092
       Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                 ++L++++ee+d+ +++++e +++  + +e  ks++e+  s++++++ +++  +r++e++e++
  AJA92226.1 104 SKLNKQTEEFDKKIAKINENQKTGPKTNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKM 165
                 57788888888888888888888888888888888888888888888888888888877765 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0024
       Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsekts.slheaceqlleeqkrleelaeeieekLk 69 
                 + ++++++++  + + ++ + ++e++ek+++v +kt+ +l ++ e+l e+ k++++ + +i ++++
  AJA92226.1 137 IAESKASIQNNSKMIMKIANRVDEVKEKMDKVPTKTEgNLTSQIEELRENIKSITNRTGDIGKDMS 202
                 566777777777888899999999999999999999757999999999999999998888888765 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.011
       Sec34   5 Leskeeecdelleqtd.ealeqLeeleekfksvsektsslheaceqll 51 
                 +++ +e++d++ ++t+ ++ +q+eel+e+ ks++++t ++ +++ +l 
  AJA92226.1 158 VDEVKEKMDKVPTKTEgNLTSQIEELRENIKSITNRTGDIGKDMSNLK 205
                 455556666666666523445666666666666666666666665554 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.048
       Sec34  20 dealeqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                 +e++e+++++++  ++ ++  s++h++++++++e + ++ 
  AJA92226.1 230 SEIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKG 269
                 6789999999999999999999999999999999876665 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.78
       Sec34  25 qLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeel 74 
                 + ++      + +e  ss++ ++e+ + + k++e++a + +e ++ F++l
  AJA92226.1 277 DSSKEVMAILKLNEYQSSIRMQAESKYGDIKDVEKMASQTTELINLFDKL 326
                 55555555556666677777777777777777777777777777777776 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.9     0.048        45      22      95 ..      23      96 ..      16     100 .. 0.67
   2 ?    7.5   9.9    0.0041       3.9      16     100 ..     100     188 ..      93     189 .. 0.72
   3 ?   13.5   5.3   5.7e-05     0.054       1     107 [.     140     251 ..     140     254 .. 0.80
   4 ?    4.0   3.8     0.051        48      14      63 ..     231     280 ..     227     331 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.048
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHH CS
  Laminin_II 22 lsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnisei 95
                l ++++ ++e+ + + r+++ + +  kd +k++++ ++ ++ L+  + q+ ++ k+++  ee  + l + ++++
  AJA92226.1 23 LFNKVNTVSESTKALSREIKGMAKIFKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLFAGLNQV 96
                55666777777777777777777777777777777777777777777777777777666666665555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0041
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH........HHHHHHHHHHHHH CS
  Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.....lsdniseikelIa 100
                 ++ + +l++++e+  +k+ +in++ ++t  k ++  k i++ + s+++  k + ++ +++ e+k++ ++  +     l  +i+e++e I+
  AJA92226.1 100 EQFISKLNKQTEEFDKKIAKINEN-QKTGPKTNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKMDKVPTktegnLTSQIEELRENIK 188
                 455678889999999999999888.7777777777777777777777777777777777777777766543344556*********9886 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 5.7e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGG..GHHHHHHHHHH.....HHHHHHH CS
  Laminin_II   1 skelaaeanetakevleqlaplsqnlentkekls.einrsveetnekvkdankairdArrsvkkLeklapqLld..klkelkqleeasss..lsdnise 94 
                 sk+ +++ ++ + ++ + + +++++++++  k + ++ +++ee  e++k+ ++ + d ++ +++L++++  +++  k+++l     +     + ++is+
  AJA92226.1 140 SKASIQNNSKMIMKIANRVDEVKEKMDKVPTKTEgNLTSQIEELRENIKSITNRTGDIGKDMSNLKNEIGGIVSnpKISSLIGDGMKTFKseIEEKISN 238
                 567777777777777788888888888877776525889999*******************************8557777754444432246******* PP

                 HHHHHHHHHHHHH CS
  Laminin_II  95 ikelIaqARkaAn 107
                 i ++I +  + A+
  AJA92226.1 239 ISNMIDRSDQIAS 251
                 ******9988887 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.051
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63 
                 e++e++ ++s+ +++  + +se++r+ +++ ++++  + +++ A++ ++k
  AJA92226.1 231 EIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSSK 280
                 66777777777777777777777777777777777666666666655554 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  10.0     0.095        90      49     137 ..      52     140 ..       3     148 .. 0.74
   2 ?    3.5   9.7     0.059        55      51     142 ..     102     208 ..      94     241 .. 0.44
   3 ?    7.5   2.4    0.0036       3.4      24      99 ..     233     316 ..     225     350 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.095
       PIN_8  49 esviskekkayedlekeleklkkaaekkleealkkwakkkald......teelrkelkkqleelkeelkaeleelkksskadkeedpilkkleel 137
                 ++v+ + ++ +++l+ ++++++k+a++   ++++++ ++          +e++ ++l+kq+ee+++++     ++++++k+  + ++i k ++e 
  AJA92226.1  52 QKVLVSMSDMMQSLNLAMSQMQKQAKQ--MDIIEEDTQRLFAGlnqvkvHEQFISKLNKQTEEFDKKI----AKINENQKTGPKTNEIIKSIAES 140
                 456666777777777777777777774..223333333333336666677888888888888888888....88888888888889999999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.059
       PIN_8  51 viskekkayedlekeleklkkaaek..kleealkkwakkkald...teelrkelkkqleelkeel...........kaeleelkksskadkee.dpilk 132
                  isk +k++e++ k+++k++++ ++  k++e++k+ a++ka +   ++++  ++ + ++e+ke++             + eel++++k+++++  +i k
  AJA92226.1 102 FISKLNKQTEEFDKKIAKINENQKTgpKTNEIIKSIAESKA-SiqnNSKMIMKIANRVDEVKEKMdkvptktegnlTSQIEELRENIKSITNRtGDIGK 199
                 44455555555555555554444421122222222222222.123444444455555555555552222222333233333333333333322244445 PP

       PIN_8 133 kleellegki 142
                  +++l +++i
  AJA92226.1 200 DMSNL-KNEI 208
                 55544.4444 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0036
       PIN_8  24 lkvlekladrlwvPhqvalEfqrnresvis.......kekkayedlekeleklkkaaekkleealkkwakkkald.teelrkel 99 
                  + + ++++ +  + q+a+Ef+r+ ++v++         +ka +d +ke+ ++ k  e + + +++ ++k+  ++ +e++ +++
  AJA92226.1 233 EEKISNISNMIDRSDQIASEFHRKTDKVMQeiqgvkgVTNKASDDSSKEVMAILKLNEYQSSIRMQAESKYGDIKdVEKMASQT 316
                 455666777777788999999999999988444333333333344444444444444444444444444444444333333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  10.6     0.068        64      33     114 ..      21     104 ..       3     127 .. 0.76
   2 ?    2.5   3.6     0.079        75      25      91 ..     130     197 ..     107     213 .. 0.60
   3 ?    9.5   0.5   0.00058      0.54      14     153 ..     232     370 ..     220     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.068
     DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvplle..kmidrLeqfve 114
                 +q  +k++ +++ ++ l++e++ + +  ++ ++    ++++++s++  ++++++q ++++ ie++ + l+   + ++  eqf+ 
  AJA92226.1  21 SQLFNKVNTVSESTKALSREIKGMAKIFKDNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEEDTQRLFAglNQVKVHEQFIS 104
                 555579999999999999999999999999999999999999999999999999999999999999988751144556666664 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.079
     DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeelesl.evyneqlerlvasqeqeiasleeqieei 91 
                 +++++++ a+s + i++ ++   ++++++ ++ke+ ++  ++ + +l++++++++++i+s++++  +i
  AJA92226.1 130 TNEIIKSIAESKASIQNNSKMIMKIANRVDEVKEKMDKVpTKTEGNLTSQIEELRENIKSITNRTGDI 197
                 44555555555555555555556666666666665555522334456666666666666666665554 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00058
     DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqf 112
                 ++++++++ +   ++ ++a++ ++k dk+ +e q ++   +++++  ++  +   +l+++++s + + +s   +i+++e+++++ + l+ ++ d+L   
  AJA92226.1 232 IEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSSKEVMAILKLNEYQSSIRMQAESKYGDIKDVEKMASQTTELI-NLFDKLSIE 329
                 46788889999999***********************************************************************9987.699999999 PP

     DUF3450 113 veldlPflleeRqarlakLkelmdradvslaekyrrvleay 153
                     +P   e Rq  + k+ +  d+ ++  +e ++   e +
  AJA92226.1 330 TDDKIPLPHEVRQWAVGKILDCADKWELRFSEVLNVMAENL 370
                 99999999999999999998888888888888777776655 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2       0.1        94      30      75 ..       8      53 ..       2      61 .. 0.78
   2 ?    1.9   1.0      0.23   2.1e+02       5      62 ..      29      85 ..      25     100 .. 0.65
   3 ?    2.2   4.0      0.19   1.8e+02      10      56 ..     147     194 ..     101     208 .. 0.48
   4 ?   10.1   1.1   0.00066      0.62      10      64 ..     225     279 ..     189     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
     DUF1515 30 rsdasrakmyrkmdelvervtalegsvvklkaditsvkevtedvkk 75
                + ++++ k   ++ +l ++v+++  s+ +l  +i  + ++ +d +k
  AJA92226.1  8 KKQSAKPKREPNTSQLFNKVNTVSESTKALSREIKGMAKIFKDNQK 53
                44445556667789999*****************999999988776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
     DUF1515  5 gvlqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkad 62
                +v ++++ l +e+k + + +k  +++  +s ++m++ ++  + +++     +  +++d
  AJA92226.1 29 TVSESTKALSREIKGMAKIFK-DNQKVLVSMSDMMQSLNLAMSQMQKQAKQMDIIEED 85
                667777888888888877665.466777777777776666665555555555555554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.19
     DUF1515  10 lgtllaevkelredlkrsedrsda.srakmyrkmdelvervtalegsv 56 
                   +++ ++ +  +++k+  d+  + +  +++ +++el e ++++   +
  AJA92226.1 147 NSKMIMKIANRVDEVKEKMDKVPTkTEGNLTSQIEELRENIKSITNRT 194
                 233333333333333333333222022334444444444444444444 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00066
     DUF1515  10 lgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkadit 64 
                 ++t+++e++e   ++ +  drsd + ++ +rk+d++++ ++ ++g + k  +d +
  AJA92226.1 225 MKTFKSEIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVTNKASDDSS 279
                 6788889999999999999***************************999999854 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.5       0.4   3.8e+02      16      36 ..      59      79 ..      48      89 .. 0.59
   2 ?    4.6   0.2     0.052        49      22      61 ..      93     131 ..      84     134 .. 0.75
   3 ?    0.3   0.1       1.2   1.1e+03      23      44 ..     148     169 ..     135     188 .. 0.50
   4 ?    1.0   0.0      0.71   6.7e+02      31      49 ..     178     196 ..     174     207 .. 0.57
   5 ?    3.2   0.0      0.15   1.4e+02       7      47 ..     231     271 ..     230     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.4
                HHHHHHHHHHHHHHHHHHHHH CS
        SlyX 16 edtieeLndvvaeqqqqidrl 36
                 d++++Ln ++ + q+q +++
  AJA92226.1 59 SDMMQSLNLAMSQMQKQAKQM 79
                345555555555555554443 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.052
                 HHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXX CS
        SlyX  22 Lndvvaeqqqqidrlqrqlrllaerlkeleessgaseaee 61 
                 Ln+v + ++q i++l +q ++  +++++++e+++++++ +
  AJA92226.1  93 LNQVKV-HEQFISKLNKQTEEFDKKIAKINENQKTGPKTN 131
                 565544.566799999999999999999999988777654 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.2
                 HHHHHHHHHHHHHHHHHHHHHH CS
        SlyX  23 ndvvaeqqqqidrlqrqlrlla 44 
                 ++++++ + ++d+ +++++++ 
  AJA92226.1 148 SKMIMKIANRVDEVKEKMDKVP 169
                 3344444444444444444333 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.71
                 HHHHHHHHHHHHHHHT-XX CS
        SlyX  31 qqidrlqrqlrllaerlke 49 
                  qi++l++ ++ +++r  +
  AJA92226.1 178 SQIEELRENIKSITNRTGD 196
                 4555555555555555444 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.15
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
        SlyX   7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                 e+E+k++   ++i++ +++  e +++ d+  ++++ ++   
  AJA92226.1 231 EIEEKISNISNMIDRSDQIASEFHRKTDKVMQEIQGVKGVT 271
                 7999***************99*9999999999999877655 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.8   1.7e+03      20      39 ..      22      41 ..       3      65 .. 0.67
   2 ?   -1.6   0.3         3   2.8e+03      20      28 ..      71      79 ..      56     111 .. 0.56
   3 ?    8.6   0.5    0.0019       1.8      26      49 ..     149     168 ..     125     173 .. 0.72
   4 ?    4.8   0.2     0.029        27      11      52 ..     166     207 ..     164     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.8
     DUF2205 20 rLqqqakeLqssLqaLaerv 39
                +L +++++  +s +aL+  +
  AJA92226.1 22 QLFNKVNTVSESTKALSREI 41
                44455555555555555544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
     DUF2205 20 rLqqqakeL 28
                ++q+qak++
  AJA92226.1 71 QMQKQAKQM 79
                344444433 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0019
     DUF2205  26 keLqssLqaLaervdeVkeehdKL 49 
                 k       ++a+rvdeVke  dK 
  AJA92226.1 149 K----MIMKIANRVDEVKEKMDKV 168
                 3....3578***********9996 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.029
     DUF2205  11 eklerearerLqqqakeLqssLqaLaervdeVkeehdKLese 52 
                 +k+ + +  +L +q++eL +  +++ +r   + ++   L++e
  AJA92226.1 166 DKVPTKTEGNLTSQIEELRENIKSITNRTGDIGKDMSNLKNE 207
                 56666677789*******************999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3041  (0.169613); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 1.00u 0.32s 00:00:01.32 Elapsed: 00:00:00.48
# Mc/sec: 2510.66
//
Query:       AJA92227.1  [L=106]
Description: hypothetical protein T478_0260 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   16.1   1.3      0.044   14.2   0.2    1.9  2  eIF3_N        eIF3 subunit 6 N terminal domain
      0.072   12.0   0.5      0.087   11.8   0.5    1.0  1  Radial_spoke  Radial spokehead-like protein


Domain annotation for each model (and alignments):
>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   4.9e-06     0.044      78     125 ..       3      52 ..       1      57 [. 0.89
   2 ?    1.3   0.1     0.047   4.2e+02     100     119 ..      73      92 ..      52      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-06
      eIF3_N  78 leeleeeaekvlelledeevvsnlrs..dkkqnlefLkeehgitpemida 125
                 ++e  e ++k+l+ + de++ + l +  ++ + +efL+e+++itp+ +d+
  AJA92227.1   3 MNESDEHTQKILDAVFDENISEILAEmeNSPKKCEFLTEKFEITPNDLDE 52 
                 5778899************9999988889999**************9986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.047
      eIF3_N 100 nlrsdkkqnlefLkeehgit 119
                 + + d++++ +++++ h+++
  AJA92227.1  73 EYSVDSEKLAKLMETAHNFE 92 
                 23337777777777777765 PP

>> Radial_spoke  Radial spokehead-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   9.7e-06     0.087      35     127 ..       9     103 ..       5     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.7e-06
  Radial_spoke  35 rpenaldal..eeisrkvkeekfkkkedtlrdesekskeaelaeklrnlfkkeekeeeeeekeeeeeeeetelpnlleeafyfeqaGvgLsreei 127
                   + +++lda+  e+is+ + e + ++k+ ++ +e+ + +  +l ekl  l+++e   +  ++++ e +  +++l +l+e+a++fe+++ gL + + 
    AJA92227.1   9 HTQKILDAVfdENISEILAEMENSPKKCEFLTEKFEITPNDLDEKLSFLMQHEFVGKTGSDSQAEYSVDSEKLAKLMETAHNFENVDAGLAKMDG 103
                   4555554332345666666666666666777777777777888888889999988888888899999999********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 737.66
//
Query:       AJA92228.1  [L=147]
Description: hypothetical protein T478_0417 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1083.98
//
Query:       AJA92229.1  [L=153]
Description: hypothetical protein T478_0073 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.1   0.0      0.061   13.0   0.0    1.1  1  DUF3445   Protein of unknown function (DUF3445)
      0.094   12.8   0.2       0.16   12.1   0.2    1.4  1  TetR_C_2  MAATS-type transcriptional repressor, C-terminal re


Domain annotation for each model (and alignments):
>> DUF3445  Protein of unknown function (DUF3445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.8e-06     0.061      30     110 ..      41     125 ..       5     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.8e-06
     DUF3445  30 ehgekvlavlpeaeaavkElleelveyLparYPqlFelsk..kktlenkvtgetfel..eplevlarlvqeDllillendgeyyl 110
                 +++ ++++  pe ++a+  +   lv++  +rYP++ e +k  +++l+n++  +++e   + l+ + +  q D++  +   +ey++
  AJA92229.1  41 KKRLRTISESPELKEAAAMFAPILVSQAQKRYPMVIEAQKkiEQVLQNSIPAQSLEQdlDTLQKALECRQSDIVKAQDTGREYFM 125
                 33344455559*************************9944444449999988887654348888888899998766666666665 PP

>> TetR_C_2  MAATS-type transcriptional repressor, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.8e-05      0.16      42      80 ..      66     104 ..      57     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
    TetR_C_2  42 avleirkelllaeysrleevlqeciekgllpanldlrra 80 
                 +  + r  ++++ ++++e+vlq++i ++ l ++ld+ + 
  AJA92229.1  66 SQAQKRYPMVIEAQKKIEQVLQNSIPAQSLEQDLDTLQK 104
                 5667788899************************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1157.05
//
Query:       AJA92230.1  [L=922]
Description: DEAD/DEAH box helicase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-37  128.2   0.1    6.1e-37  127.1   0.1    1.6  1  DEAD           DEAD/DEAH box helicase
    9.1e-22   77.5   0.7      7e-19   68.2   0.1    2.9  2  Helicase_C     Helicase conserved C-terminal domain
    5.6e-19   68.7   0.0    3.6e-18   66.0   0.0    2.2  1  DEAD_assoc     DEAD/H associated
    7.1e-15   55.4   0.1    2.6e-14   53.6   0.1    2.0  1  ResIII         Type III restriction enzyme, res subunit
    0.00027   21.2   2.0      0.028   14.7   0.0    3.6  3  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi
    0.00027   21.3   0.1      0.001   19.4   0.1    2.0  1  AAA_19         AAA domain
    0.00044   19.1   0.0    0.00083   18.2   0.0    1.4  1  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.017   15.4   1.1       0.12   12.7   0.2    2.5  2  AAA_22         AAA domain
      0.062   12.7   0.0       0.16   11.4   0.0    1.7  1  PhoH           PhoH-like protein
       0.16   11.4   4.8        0.1   12.1   0.7    2.7  2  UvrD-helicase  UvrD/REP helicase N-terminal domain
       0.18   11.3   0.3       0.31   10.5   0.3    1.3  1  Clc-like       Clc-like


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.1   3.7e-40   6.1e-37       1     170 [.      31     199 ..      31     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 3.7e-40
                 -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH.HTTC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
        DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl.dngv 98 
                 t+iQ+eaip+il+++++l+ a+TGsGKT+++ ip+++++ ++k +++ kal+++P+r+L +++++++ ++ ++ +l+++ i +g++ + +++++ dn +
  AJA92230.1  31 TEIQKEAIPEILEEKNCLIIAPTGSGKTECATIPIFSKLKTRKVSKKIKALYITPLRALNRDVFKRIINYAENENLKIE-IRHGDTSQANRKRIaDNPP 128
                 79*************************************7779*****************************9889998.455666667777772566* PP

                 SEEEEEHHHHHHHH.HCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                 xxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  99 divvgtpgrlddll.stgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                 di+++tp+ l++ll ++++l+ ls+++++++DE+++ll ++++ ++   l++l qi+++  +q + i lSAT+ 
  AJA92230.1 129 DILITTPETLVNLLsQKKHLDaLSDLEWVIIDEVHELLASERGSQLCLSLERL-QIKSK--NQIHRIGLSATVG 199
                 ************9944555779*******************************.66665..4566*******86 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0     0.006       9.7      33      62 ..      96     127 ..      61     138 .. 0.65
   2 !   68.2   0.1   4.3e-22     7e-19       5     106 ..     243     345 ..     239     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.006
                 HHH..HHHTTSTEEEESTTSTHHHHHHHHHHH CS
  Helicase_C  33 kll..lekkgikvavlhgelpqnereeileqf 62 
                 +++   e++++k+ + hg+++q +r++i ++ 
  AJA92230.1  96 RIInyAENENLKIEIRHGDTSQANRKRIADNP 127
                 2224347779*****************99876 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 4.3e-22
                 HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHH CS
  Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiq 102
                 +++e++k+e++++ +l+f+n++ + e+  ++l++k +i+v  +hg+l+ + ree+ +  ++g+s ++++t+ +e G+di +v+lVi+++ pr+v++++q
  AJA92230.1 243 KIIEYIKKEQITSPVLLFTNSRGESERlSSILKQKTSINVELHHGSLSRQVREETEDMLRDGKSGIVVCTSSLELGLDIGSVELVIHYGSPRQVSKFMQ 341
                 57778899***************8887667777777*************************************************************** PP

                 HHTT CS
  Helicase_C 103 riGR 106
                 riGR
  AJA92230.1 342 RIGR 345
                 **** PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   2.2e-21   3.6e-18       1     191 []     583     759 ..     583     759 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.2e-21
  DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellellspd.eleedleaalnase 98 
                 +P+++t+++E+ r  + +  l++hs+fG+++n +l ++l+  l +++ + v+ + + ++i+l+++  +r+    +++++ + +d +++e++  al++ +
  AJA92230.1 583 VPDEKTIVIESHRLPQ-KSVLILHSCFGTKINSTLKVILETLLDASLASRVKSSSDAYRILLSVE--SRFT--KKHITDVFLSDfDINEIMSVALKGKN 676
                 8***********7655.779******************************************664..4653..457778877777************** PP

  DEAD_assoc  99 lfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDlerlaellrriaageirvvevetprpSpfA 191
                  + ++   v ++++   r++           ++ +  +d+ r   d+pl++ea+re +++++Dle+++++++ i++++i+v+ v+++++S +A
  AJA92230.1 677 DVTWKTFCVGKKFGFYDRSDVY---------VKNEIRYDFER-NIDTPLVKEAFRELFHEKFDLEGTQRIIDLIKENKIQVEWVDVDKFSKLA 759
                 *******************988.........66666677655.559********************************************998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.1   1.6e-17   2.6e-14       3     169 ..      29     198 ..      27     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.6e-17
                 EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.. CS
      ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee...kflflvprkslleqtleefkkflseaykeigkkvsgdkkka.. 96 
                 el e Q+eai ++l      ++k+ li ++TG+GKT +a+  i + lk +k +   k+l + p ++l     +++ +++++++  + ++ +gd+ +a  
  AJA92230.1  29 ELTEIQKEAIPEIL------EEKNCLIIAPTGSGKTECATIPIFSKLKTRKVSkkiKALYITPLRALNRDVFKRIINYAENENL-KIEIRHGDTSQAnr 120
                 67889999999998......678999*************55555555555555589*************************987.67788888888877 PP

                 .......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHH.HHT---SEEEEEESS- CS
      ResIII  97 kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swrei.lekfkeavllglTATp 169
                 k+++++  +il+tt ++l + +   +++++    +  + +iiDE+H l a++       s +++ +++ ++  ++gl+AT 
  AJA92230.1 121 KRIADNPPDILITTPETLVNLL---SQKKHLDALSDLEWVIIDEVHELLASErgsqlclSLERLqIKSKNQIHRIGLSATV 198
                 77889999**************...8888888888888************85566667777775555556699*******6 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.08   1.3e+02      16      48 ..      76     110 ..      67     119 .. 0.86
   2 ?   -0.5   0.0      0.93   1.5e+03      19      59 ..     355     396 ..     347     400 .. 0.74
   3 !   14.7   0.0   1.7e-05     0.028      19      67 ..     721     768 ..     715     776 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.08
  SpoU_sub_bind  16 rriekllvtegradkr..leellklakkrgikvel 48 
                    ++i++l++t+ ra +r  ++ ++++a+  + k+e+
     AJA92230.1  76 KKIKALYITPLRALNRdvFKRIINYAENENLKIEI 110
                    56*********77777788********99999985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.93
  SpoU_sub_bind  19 ekllvtegradkr.leellklakkrgikvelvdkekLdklsg 59 
                    + l++te++ d+  ++ +++++k+  i+ +++    Ld l++
     AJA92230.1 355 RGLIITENADDEFeIQAIIERIKEGSIEEQKIHHGSLDVLAH 396
                    568999994444457999999999999888777777777765 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 1.7e-05
  SpoU_sub_bind  19 ekllvtegradkrleellklakkrgikvelvdkekLdklsgtanHQGvv 67 
                    ++l++++    + ++ +++l+k+++i+ve+vd +k+ kl++ +  Q v+
     AJA92230.1 721 RELFHEKF-DLEGTQRIIDLIKENKIQVEWVDVDKFSKLAEPVLDQTVM 768
                    44444444.555558************************9877766665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.3e-07     0.001       1     114 [.      34     165 ..      34     182 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.3e-07
      AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhiv.allvelggvkpeeillvaftgrAakelrerlaalgae...........atTiHrlal......... 77 
                 q+ea+   l+ek++l++a+ G+GKT++ +  + + l+ ++  k  + l +++ +   + + +r+ ++ ++           +                 
  AJA92230.1  34 QKEAIPeILEEKNCLIIAPTGSGKTECATIPIfSKLKTRKVSKKIKALYITPLRALNRDVFKRIINYAENenlkieirhgdT-------Sqanrkriad 125
                 89999669******************98875515555555555567777777766666677777554444667644444330.......2344455555 PP

      AAA_19  78 ......ldfddlltealelleeaeeekklqeeellivDEfqdv 114
                       + +++++   ++ll ++++ + l + e++i+DE+ ++
  AJA92230.1 126 nppdilI-TTPET--LVNLLSQKKHLDALSDLEWVIIDEVHEL 165
                 5554422.22222..3455557677777867779999999876 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.1e-07   0.00083      97     214 ..      78     197 ..      19     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
                 S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T.. CS
                 xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
      SNF2_N  97 gptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns.. 192
                   +L + P  +l +   + i +++++ +l++ + +g++++ ++    ++   +  d++itt ++l +  + +k+ ++l+++ew  v++DE h l  s  
  AJA92230.1  78 IKALYITPLrALNRDVFKRIINYAENENLKIEIRHGDTSQANR----KRIADNPPDILITTPETLVNLLSQKKHLDALSDLEW--VIIDEVHELLASer 170
                 34677788877778888899999******99999998733333....34444567*************9999**********9..9*******999844 PP

                 TSHHHHHHHH--.....-S-EEEE-S- CS
                 xxxxxxxxxxxx.....xxxxxxxxxx RF
      SNF2_N 193 tskaaeavskLs.....tsnrwiltGT 214
                  s++   +++L+     + +r+ l++T
  AJA92230.1 171 GSQLCLSLERLQiksknQIHRIGLSAT 197
                 345544444444333335566666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   7.3e-05      0.12       6     105 ..      45     168 ..      42     194 .. 0.74
   2 ?   -0.4   0.0      0.78   1.3e+03      40     105 ..     277     368 ..     258     387 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
      AAA_22   6 gilvvtGesGtGKTtllrr.lleqldeeakaee.......................erpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                 + +++++++G+GKT ++   ++++l+ ++  ++                       ++ e +++++ ++ +s+  +++++ +  + l + + ++  ll+
  AJA92230.1  45 KNCLIIAPTGSGKTECATIpIFSKLKTRKVSKKikalyitplralnrdvfkriinyAENENLKIEIRHGDTSQANRKRIADNPPDILITTPETLVNLLS 143
                 6689************98535555555544444778899999999999999999999999999999999999999999999999999994444444444 PP

      AAA_22  81 aleqalraravielliiDEaqhlr.s 105
                 +   +l+a ++ e +iiDE++ l  s
  AJA92230.1 144 QKK-HLDALSDLEWVIIDEVHELLaS 168
                 443.45555557**********7543 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.78
      AAA_22  40 pevvfvtlpsstsskdllrellralglelka........................erlsseellealeqalrarav..ielliiDEaqh.lrs 105
                 ++ + v+l +++ s+++++e    l +++++                        ++ + + +++++ +  ++r++  ++l+i ++a+  + +
  AJA92230.1 277 KTSINVELHHGSLSRQVREETEDMLRDGKSGivvctsslelgldigsvelvihygSPRQVSKFMQRIGRSKHDRGDsaRGLIITENADDeF-E 368
                 5556666666666666666666666666666777777777777777777777666777777777777777777777999999999999766.4 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.9e-05      0.16       5      51 ..      30      76 ..      27      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.9e-05
                -SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SE CS
        PhoH  5 ktkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkr 51
                 t+ Qke++  + +++ + +i+p+G+GKt  a+   ++ lk +kv++
  AJA92230.1 30 LTEIQKEAIPEILEEKNCLIIAPTGSGKTECATIPIFSKLKTRKVSK 76
                6788*****************************99999999999876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   6.3e-05       0.1       1      45 [.      30      76 ..      30     389 .. 0.82
   2 ?   -0.4   0.2      0.39   6.4e+02     134     200 ..     762     854 ..     697     880 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.3e-05
                   SSHHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTG CS
  UvrD-helicase  1 lnpeqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiep 45
                   l+++q+eai     ++++l++A  GsGKT   +  i  ++k+++++ 
     AJA92230.1 30 LTEIQKEAIPEilEEKNCLIIAPTGSGKTECATIPIFSKLKTRKVSK 76
                   688999999988899****************9999999999998654 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.39
                    HHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCH...........................HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHC CS
  UvrD-helicase 134 llkelleksaddslnldkkkleklikelsksrnik...........................keelslskskaeelrelvskakekqlspkelk 200
                    +l + + ++++   n+dk+ l k+++ l++ ++ +                            +    +++  e ++ + +k + k+l+p e+k
     AJA92230.1 762 VLDQTVMSYTN-PANIDKEMLLKVKTRLMQTKQRLicvrcglwqqvmtpnqthplrckyckgQQITCTYEYDHELVKIIQKKHQGKKLTPDENK 854
                    33333333333.3555555555554444444443366777777777777777777766666533333333333333333333333333333333 PP

>> Clc-like  Clc-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00019      0.31      39      84 ..     798     844 ..     788     876 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
    Clc-like  39 vqsGLWldCtraek.hvvksqdvdegplhCvYkFdidallvysekle 84 
                 v+ GLW + +++++ h ++ +  +  ++ C+Y +d++ ++++++k +
  AJA92230.1 798 VRCGLWQQVMTPNQtHPLRCKYCKGQQITCTYEYDHELVKIIQKKHQ 844
                 788*****999877699999998888***********9999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (922 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 5942.90
//
Query:       AJA92231.1  [L=491]
Description: DNA polymerase II small subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-22   79.0   0.0    5.4e-22   78.2   0.0    1.3  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    8.7e-13   49.2   0.1    1.7e-12   48.3   0.1    1.3  1  Metallophos      Calcineurin-like phosphoesterase
    1.8e-09   38.0   0.0    4.4e-08   33.5   0.0    2.4  2  Metallophos_2    Calcineurin-like phosphoesterase superfamily
  ------ inclusion threshold ------
      0.094   12.7   0.0        0.3   11.1   0.0    1.8  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   1.2e-25   5.4e-22       2     202 ..     220     416 ..     219     421 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.2e-25
                  EEEES--S-TT----HHHHHHHHHHH....HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTSEEEEE--TTBTT-S- CS
  DNA_pol_E_B   2 vivsglnldndnrsleaLrkiLqgya...peesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesllekttvvlvPgpnDpanst 96 
                  v++s+l++ ++ +  e L+++++ +    p + ++  +++ G ++d      ++ kv   ++ + +d l+++ ++l+++ ++++v+l+ g  D+  + 
   AJA92231.1 220 VFLSDLHVGSKFFMEEELSEFIKWISsadPIARKIRFVVIGGDLIDGVGVFPGQDKVL--DQLTTEDQLQKTFEVLDKIPKHIKVFLISGNHDAGRK- 314
                  7999*****666667889999999988889999*******************999996..8888899999***************************. PP

                  SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG CS
  DNA_pol_E_B  97 vlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdverlrklvktildqrhlaPlaptlrpvswdkddalvle 194
                  +lPq+++p+++ s++    +++ ++ NPs+++ln+v+v+++ ++ ++d+ r++   s    ++ + ++++ l+ rh++P++ +  p+  +  d +v++
   AJA92231.1 315 ALPQPAIPKMYNSELWDR-ENFFMLGNPSMVSLNGVKVLMYHGQSIDDVVRTTPGVSY---DKPAAVMRHFLRARHMSPIYGSRTPIAPETEDMMVID 408
                  **********99998886.67*********************************9999...8************************************ PP

                  ---SEEE- CS
  DNA_pol_E_B 195 plPdvlvl 202
                   +Pd++  
   AJA92231.1 409 DVPDIFHS 416
                  *****865 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   3.8e-16   1.7e-12       4     202 ..     220     420 ..     219     421 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.8e-16
                  EEEESBTB...TTCCTHHHHHHHHHHHH.HHHTTESEEEEESTSSSSS.................HHHHHHHHHHHHHHHH..TSEEEEEC-TTSCHH CS
  Metallophos   4 lvigDlHl...algggqlddllkllddl.lreekpdlvllaGDlvdrg.................dlekellellaalvky..pipvylllGNHegfe 78 
                  ++++DlH+      ++ l++++k+++ + +   k+ +v++ GDl+d+                  +    l++ ++ l k   +i+v+l+ GNH+   
   AJA92231.1 220 VFLSDLHVgskFFMEEELSEFIKWISSAdPIARKIRFVVIGGDLIDGVgvfpgqdkvldqlttedQ----LQKTFEVLDKIpkHIKVFLISGNHD-AG 312
                  689*****888777788888888887777444699************7799988888888854433....44444444443557999********.66 PP

                  H.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSS CS
  Metallophos  79 e.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgs 175
                     l+++   + ++se+w +++ ++ + p+ +  +g +kvl +hG s+++   +    +++++++a+    ++l+               H+ +  ++
   AJA92231.1 313 RkALPQPAIPKMYNSELWDRENFFMLGNPSMVSLNG-VKVLMYHGQSIDD--VVRTTPGVSYDKPAAVM-RHFLRA-------------RHMSPI-YG 392
                  64666666666666*********9999999997777.7999999995555..33333333333333333.666666.............677777.67 PP

                  SCSCCHHHHHHH.HHHTTESEEEEESSS CS
  Metallophos 176 gylfgdealedl.lkkygvdlvisGHtH 202
                  + +   +++ed    +  +d+  sGH+H
   AJA92231.1 393 SRTPIAPETEDMmVIDDVPDIFHSGHVH 420
                  777777777777355555677667***9 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.058   2.6e+02       4      50 ..     138     184 ..     137     193 .. 0.73
   2 !   33.5   0.0   9.8e-12   4.4e-08       5     151 ..     221     443 ..     218     460 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.058
  Metallophos_2   4 aiiSDlHsnldaleavlealkevgvdaiihaGDleeeepe.vleelle 50 
                    ++++D  s +++++  +e+  +  ++ +++ GDl++++ +  ++++ +
     AJA92231.1 138 GLVTDRKSDRNITKITVEDPTSS-MEIVVFEGDLKDAADTlLMDQFAM 184
                    67899999999999999998777.9********933333324444443 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.8e-12
  Metallophos_2   5 iiSDlH........snldaleavlealke..vgvdaiihaGD.......................leeeepevleellelapvlaVrGNnD..... 62 
                    ++SDlH        ++l++  ++++ ++    ++  ++  GD                       l ++++evl+++ +  +v  + GN+D     
     AJA92231.1 221 FLSDLHvgskffmeEELSEFIKWISSADPiaRKIRFVVIGGDlidgvgvfpgqdkvldqlttedqL-QKTFEVLDKIPKHIKVFLISGNHDagrka 315
                    789****977777766666666665555433459999999**777777766666665553322221.23334555555555**********99999 PP

  Metallophos_2  63 ......eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl................................gvkdalaellke...aee 117
                          +++  +++ +++++++   p+     l+g+kvl++Hg+                                  g +  +a+ +++    ++
     AJA92231.1 316 lpqpaiPKMYNSELWDRENFFMLGNPSMVS--LNGVKVLMYHGQSIddvvrttpgvsydkpaavmrhflrarhmspiyGSRTPIAPETEDmmvIDD 409
                    988766555777777777777766665555..55*********977*****************************999555555555555333367 PP

  Metallophos_2 118 gsdvvvcGHtHvpevekeggvlvvnPGsvgeprd 151
                    + d++ +GH H  +++  +gvl+vn G+ +++ d
     AJA92231.1 410 VPDIFHSGHVHFVGLDMYKGVLIVNSGAWQRQTD 443
                    777*************************999854 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.6e-05       0.3       5      46 ..     138     177 ..     135     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                      EEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS CS
  tRNA_anti-codon   5 GrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenl 46 
                      G vt++  +s +++  i+++D t ++++v+f ++ ++ a++l
       AJA92231.1 138 GLVTDR--KSDRNITKITVEDPTSSMEIVVFEGDLKDAADTL 177
                      889999..999*********************7776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3427.43
//
Query:       AJA92232.1  [L=234]
Description: 5,6-dimethylbenzimidazole synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-25   89.7   0.0    4.7e-25   88.6   0.0    1.5  1  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
      0.023   14.3   0.8       0.27   10.8   0.0    2.4  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   5.2e-29   4.7e-25       1     170 []      17     184 ..      17     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 5.2e-29
                     HHH--B--.-B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEE CS
  Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeelklkaqkalagapvli 94 
                     i +Rr +R +F+ ep+ +e+l kil+aa++aPs g +qpw+f++++d ++++k++e+++++  ka +  e+  r +   +  ++ + + +++v +
      AJA92232.1  17 IYSRRDVRsHFTQEPINEETLTKILHAAHHAPSVGFSQPWNFILIKDMKTKEKVKESFQKEHEKASKLVEDPKRSE---YLSLKLEGIMESDVNV 108
                     569******************************************9888887777777777777766666666654...7777788888888888 PP

                     EE..---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
  Nitroreductase  95 vi..vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliavGy 170
                     ++  + t+         +  +  + +++ a+qnl+LaA+a+++g  +++ + ++   +rk l+lp++  +v+ +++G+
      AJA92232.1 109 CVtyDPTKFGPFIIGTTSIPEAGIYSVCGAIQNLWLAARAENIGLGWVSIVSNDV--LRKELNLPEHIVPVAYLCLGH 184
                     88334444445567778888888999999**************************..********7666668888886 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00061       5.5       3      31 ..      14      43 ..      12      45 .. 0.88
   2 ?   10.8   0.0     3e-05      0.27     157     191 ..      34      68 ..      29      84 .. 0.78
   3 ?   -2.2   0.0      0.27   2.4e+03      89     119 ..     140     171 ..     131     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00061
                    HHHHHH--B---.B--S---HHHHHHHHH- CS
  TM1586_NiRdase  3 yeaiekRhsvRk.Ykdealeeelleelkea 31
                    y+ai  R+ vR+ +++e+++ee+l+++ +a
      AJA92232.1 14 YKAIYSRRDVRShFTQEPINEETLTKILHA 43
                    99*********769*********9999765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 3e-05
                     -HHHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
  TM1586_NiRdase 157 pewfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                     +e + +il aa  APs   +qpw f l +d + k 
      AJA92232.1  34 EETLTKILHAAHHAPSVGFSQPWNFILIKDMKTKE 68 
                     57889********************9887654443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.27
                     HHHHHHHHHTT-EEEEES--SST......... CS
  TM1586_NiRdase  89 eqlvLkltalGlgtcWvggtykk.kkakvelk 119
                     ++l L + a+++g  Wv++  +   +++++l+
      AJA92232.1 140 QNLWLAARAENIGLGWVSIVSNDvLRKELNLP 171
                     67889999999999999987776333334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1706.10
//
Query:       AJA92233.1  [L=391]
Description: argininosuccinate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-159  531.0   0.2   2.4e-159  530.8   0.2    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    1.1e-05   25.3   0.0    1.7e-05   24.7   0.0    1.2  1  Asn_synthase     Asparagine synthase
    0.00013   21.6   0.1    0.00029   20.4   0.1    1.6  2  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
       0.12   12.1   0.2       0.34   10.7   0.1    1.8  2  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.8   0.2  5.3e-163  2.4e-159       1     386 [.       6     387 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 530.8 bits;  conditional E-value: 5.3e-163
  Arginosuc_synth   1 vLaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalYedrYllgtalaRPlia 94 
                      +La+sGGlDtsv++k+++++ +++vi+v+vdvGq+ +d +++++ka+klg +k++ +Dak+efv +yifpaikanalY+++Y l+talaRPlia
       AJA92233.1   6 ILAFSGGLDTSVVVKYMQDMHNMDVITVTVDVGQG-DDNNKIAKKAKKLGVKKHYNIDAKKEFVTEYIFPAIKANALYQKKYCLATALARPLIA 98 
                      79*********************************.999******************************************************* PP

  Arginosuc_synth  95 kklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyakekgipvevtkkkpysiDenllgrsieagiLedp 188
                      +k++e+akke  + +ahGc GkGnDqvRf++++rs + +l +iaP+R+++l Re+e+++a+++gi++++   k +siD+nl+gr+ie+g+Le+p
       AJA92233.1  99 HKVLEIAKKEKVSSLAHGCSGKGNDQVRFDNTLRSGS-NLPIIAPIRDMNLDRETELKFANKHGIEIDTVA-KKFSIDQNLWGRAIEGGVLENP 190
                      **********************************998.*****************************9885.55******************** PP

  Arginosuc_synth 189 knappediyeltkdpakapdepeeveiefekGvPvaldgeelsvlelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdl 282
                       n+pp+d++ ++k   + p++p +++i+f kGvP ++dg++l +++lie++n+ ag++GvG +D++edR+vg+ksRe+Ye+paa+ Li+ah+dl
       AJA92233.1 191 FNEPPDDAFIWIKTK-NLPEKPSYLKIKFVKGVPTEVDGKKLPPVKLIEYINKKAGNNGVGIVDHIEDRVVGIKSREVYETPAAICLIEAHSDL 283
                      ************976.5677************************************************************************** PP

  Arginosuc_synth 283 ekltlerevakfkkiveekyaelvYkGlwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGf 376
                      ek++ +++++kfk+ v++++a +vY+Glw +Pl+++ld+fie++q+rvtGtv++kl+kG+v+v+gRes++slY++++a+y ++++fdqk a+Gf
       AJA92233.1 284 EKMVHTKHETKFKTLVDDEWAWMVYSGLWDDPLRKELDQFIEQSQKRVTGTVKLKLHKGNVRVVGRESKYSLYSHDIATYGKDSTFDQKLAKGF 377
                      ********************************************************************************************** PP

  Arginosuc_synth 377 ikihglqakl 386
                      ++++g+q+  
       AJA92233.1 378 VELWGMQSTE 387
                      ******9875 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.8e-09   1.7e-05      24      89 ..       9      73 ..       5     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.8e-09
  Asn_synthase 24 LSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgte.htelvlteeelldalp 89
                  +SGGlD S+++ +++ +++ ++ t++++    + d+    ++ a++lg++ h+++  ++e +++++ 
    AJA92233.1  9 FSGGLDTSVVVKYMQDMHNMDVITVTVDV--GQGDDNNKIAKKAKKLGVKkHYNIDAKKEFVTEYIF 73
                  7****************************..889999999999******988888877776666654 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   6.5e-08   0.00029       1      62 [.       4      64 ..       4      95 .. 0.73
   2 ?   -3.4   0.0       1.2   5.4e+03     147     176 ..     134     163 ..     126     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.5e-08
                EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
        QueC  1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                k+++ +SGGlD ++v+ ++++     v+++t+d gq  ++  ++ +k ak+lgv++h  +d +
  AJA92233.1  4 KSILAFSGGLDTSVVVKYMQDMHnMDVITVTVDVGQGDDN--NKIAKKAKKLGVKKHYNIDAK 64
                57899******999998887765379*********98543..344455788888888877765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.2
                 HHTS--EEE-TT..TT--HHHHHHHHHHTTHH CS
        QueC 147 gedkkieieaPl..idlsKaeivklgkelgvp 176
                 g+  ++ i aP+  ++l+++  +k +++ g++
  AJA92233.1 134 GS--NLPIIAPIrdMNLDRETELKFANKHGIE 163
                 44..6778888844455666667777776655 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   7.5e-05      0.34       2      61 ..       5      61 ..       4      94 .. 0.80
   2 ?   -2.4   0.0      0.76   3.4e+03     136     154 ..      88     106 ..      69     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EE CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikl 61
                 ++A+SgGlD  + ++ ++++++   ++++ ++vd g  +  ++ a+  k+l  k + ++
  AJA92233.1  5 SILAFSGGLDTSVVVKYMQDMHN---MDVITVTVDVGQGDDNNKIAKKAKKLGVKKHYNI 61
                589********999998888855...6999999999988888888888887766665555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.76
                 TTCCEE-CCCT--HHHHHH CS
  ATP_bind_3 136 asirlvRPlLkvskeelee 154
                   + l RPl+ ++  e+ +
  AJA92233.1  88 LATALARPLIAHKVLEIAK 106
                 4567889998876555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2919.78
//
Query:       AJA92234.1  [L=385]
Description: PF04894 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-87  292.0   0.0    7.9e-87  291.5   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    1.2e-34  118.5   0.0    2.1e-34  117.7   0.0    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.5   0.0   8.8e-91   7.9e-87      18     266 ..      21     266 ..      10     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 291.5 bits;  conditional E-value: 8.8e-91
       Nre_N  18 kakkki.sskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklrlslvrgekkvkvkkakedklleeiqelalsekpvd 115
                 ++  +  ss+e++GsspPsvfVG+ygYPkV +gp++pp++gd++ ld+pekwlg+sle+i+++rl+lvrg +k+ +++++  +++e+++ela+s+ ++d
  AJA92234.1  21 SKYANLfSSNEIQGSSPPSVFVGSYGYPKVGIGPMLPPIHGDTTLLDTPEKWLGKSLEEIVNYRLNLVRGVQKTGIEETT-GRFIESLHELAMSSGSID 118
                 3333444899********************************************************************98.****************** PP

       Nre_N 116 vevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvd 214
                 +e+++ k+p++  ++d+  aP+Gp +e++++k + n+++ +++e++++DtdlkAe+av++Ly+sg++++kiq+++S+G++G+  +r+lVPT+WsITA+d
  AJA92234.1 119 SEIKFIKNPTPIPSIDGQNAPFGPLGEIKTAKFSPNSSI-KSIENAYYDTDLKAEDAVMKLYNSGIEISKIQKCFSIGMFGK--NRKLVPTKWSITATD 214
                 ************************************999.69***************************************8..*************** PP

       Nre_N 215 divgkelkkeikdlpeidevevfsgeylgNrflviLaPgkwsfelvEawapg 266
                 +i++++l+++i +++ id++evf+  +lgN f viL+P++w fe+ Eaw+ +
  AJA92234.1 215 QIISNDLMHDILEFDIIDRYEVFRFDHLGNLFSVILFPHRWIFEMQEAWHDK 266
                 *************************************************975 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.7   0.0   2.3e-38   2.1e-34       2     110 .]     277     384 ..     276     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 2.3e-38
       Nre_C   2 gyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevseklklplkkllkkskllke 100
                 +++g ++ ++iaGaY+a +lav e+L+kik+q++v+++rei+p+Y +PvGvWqvRe+vr+a++++p+e++sl+ea++ ++++++++++++l++ ++lk 
  AJA92234.1 277 TAKGIDHPPSIAGAYFAGKLAVTEYLQKIKKQSGVMIFREIQPQYAVPVGVWQVREGVREAMKNNPQEVNSLNEAIALATKRMSISKNEWLAHGDMLKL 375
                 5677788899****************************************************************************************9 PP

       Nre_C 101 lkkqktLddF 110
                 +  q++++dF
  AJA92234.1 376 I-AQTSMSDF 384
                 9.79999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2807.57
//
Query:       AJA92235.1  [L=110]
Description: phosphoribosyl-AMP cyclohydrolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-33  112.5   0.1    7.8e-33  112.1   0.1    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.1   4.3e-37   7.8e-33       2      74 .]      33     105 ..      32     105 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 4.3e-37
                 EEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
      PRA-CH   2 laymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                 lay+nke+le t +tg+ +++Srsr+klW+KGe+Sgn+qkvk+i +DcD+Da+++ ve++g+aCH+g+++CF+
  AJA92235.1  33 LAYTNKESLELTKKTGNSWFWSRSRNKLWMKGEESGNTQKVKKILVDCDSDAIIYLVEPSGPACHLGEDTCFH 105
                 79**********************************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 844.19
//
Query:       AJA92236.1  [L=213]
Description: PqqD family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-17   63.4   0.2    3.3e-17   62.4   0.2    1.5  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.3e-09   38.2   0.0    2.3e-09   37.4   0.0    1.3  1  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
      0.007   16.4   0.3      0.015   15.4   0.1    1.6  2  HemN_C          HemN C-terminal domain
     0.0085   16.0   0.8          4    7.3   0.0    2.2  2  DUF4252         Domain of unknown function (DUF4252)
  ------ inclusion threshold ------
      0.071   13.4   0.1       0.18   12.0   0.1    1.7  1  DUF4777         Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.2   9.1e-21   3.3e-17       2      73 ..       7      79 ..       6      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 9.1e-21
                    HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEEE CS
  FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveVe 73
                    e v++ L++ +DPe ++++v++gl+++id+++ ++V++++t+t+ +c+l e + +d+++ ++++ gv+ v Ve
      AJA92236.1  7 ENVRDSLKKCMDPEVPLSIVDMGLIYGIDVTEnNDVNIKMTMTTKGCPLHETMVDDVKRYAKKVSGVNNVDVE 79
                    679***************************************************************8888887 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   6.4e-13   2.3e-09       5      67 .]     134     196 ..     130     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.4e-13
                 E-SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
        PqqD   5 ldpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                 l+ e  + ++ n+   + Wk+++g+r+v e+v+ +a++++  + ++e+ v ++l+qL+e gl+
  AJA92236.1 134 LANEHEQGFMVNQAIIDFWKSCNGQRKVTELVDMFAQQTGLQRTQVEKEVMQLLKQLHEGGLL 196
                 5555567789999999*******************************************9997 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.6   9.2e+03      46      55 ..     127     136 ..     123     138 .. 0.53
   2 !   15.4   0.1   4.1e-06     0.015      24      55 ..     166     200 ..     165     202 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
      HemN_C  46 qeqGLLeldg 55 
                 qe+G L+l++
  AJA92236.1 127 QEDGSLVLAN 136
                 4555555555 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.1e-06
      HemN_C  24 aafeqrfgld...leellaaaleklqeqGLLeldg 55 
                 + f+q++gl+   +e+++++ l++l+e GLL++ +
  AJA92236.1 166 DMFAQQTGLQrtqVEKEVMQLLKQLHEGGLLVIPN 200
                 579****************************9855 PP

>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2    0.0011       4.1      53      99 ..      57     102 ..      34     116 .. 0.76
   2 !    7.3   0.0    0.0011         4      19      55 ..     155     190 ..     142     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
     DUF4252  53 sklddeeddkelkellkklksikvltte....nkadaeklkkevkkilkkn 99 
                   +      +++k + kk+++++ + +e     + + +k+++e+k+++k+ 
  AJA92236.1  57 ETMV-----DDVKRYAKKVSGVNNVDVEivwdPPWTMDKMSDEAKAMMKTM 102
                 2222.....29********************999************99975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
     DUF4252  19 qsaqaksldklfdkyednenvtsvniskkmlkllskl 55 
                 +++ ++++ +l d ++++ + + +++ k+ ++ll++l
  AJA92236.1 155 CNG-QRKVTELVDMFAQQTGLQRTQVEKEVMQLLKQL 190
                 554.489**************************9886 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.1e-05      0.18      23      57 ..     162     196 ..     160     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
     DUF4777  23 dEivervaerydlseeelkkvVkntLeaAvrhGFl 57 
                  E+v+ +a+ ++l+  +++k+V ++L++ +  G+l
  AJA92236.1 162 TELVDMFAQQTGLQRTQVEKEVMQLLKQLHEGGLL 196
                 69************************987777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1493.28
//
Query:       AJA92237.1  [L=352]
Description: NeuB family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-77  260.8   0.2    1.3e-77  260.5   0.2    1.1  1  NeuB      NeuB family
  ------ inclusion threshold ------
      0.061   13.1   0.0        0.1   12.4   0.0    1.3  1  TraF      F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.5   0.2   1.5e-81   1.3e-77       1     240 [.      39     276 ..      39     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 260.5 bits;  conditional E-value: 1.5e-81
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGG CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSge 99 
                 li++A  +gada+KfQt++ +  v + a  ++y +k+   ++s+ e+++++++s+++   lk+ c+e  ief+stpf+ +++++++++ v+++K+aS+e
  AJA92237.1  39 LIKTASVCGADAIKFQTYDSSVYVEN-AGMSNYLSKKG-ITKSVNEIFDEFSMSYKMLPLLKKICQEYSIEFMSTPFSIKDIHAIDKF-VNIHKLASYE 134
                 799****************9887777.78999988855.778*******************************************998.********** PP

                 TT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SS.SSHHHHHHHHHT--E CS
        NeuB 100 ltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtl.giavaiaAvalGAkv 197
                 ++++p+le++akt+kpvi+StG++tleei+ a++++++  +++l+ll+Cts+YPa+++++nL++i+++k ++++pvG+SDH++  + ++i+Av lGA++
  AJA92237.1 135 INHIPMLEALAKTKKPVIISTGASTLEEINFAIKTMKKFDNNQLCLLQCTSKYPAKINSLNLSVISNFKTKYKIPVGLSDHSTdPLIAPITAVGLGATI 233
                 *********************************************************************************99568899********** PP

                 EEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--T CS
        NeuB 198 iEkHftldrnlegpDhkaSlepeelkelveairnvekalgege 240
                 iEkHftld++legpDh ++l+p elk++v+a+rn   ++g+ +
  AJA92237.1 234 IEKHFTLDKSLEGPDHYFALDPIELKTMVTALRNCVISIGNPV 276
                 ***********************************99999865 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1     143     220 ..      89     164 ..      86     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
        TraF 143 yceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaGllsldele 220
                 ++ +++p l++++++y +e +      + +    ++ v+ +++a ++++++P l +  +  +k v+++ G+ +l+e++
  AJA92237.1  89 MSYKMLPLLKKICQEYSIEFMSTPFSIKDIHA-IDKFVNIHKLASYEINHIPMLEALAKT-KKPVIISTGASTLEEIN 164
                 67899**************9999888888854.4458889999***********999998.9999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2488.24
//
Query:       AJA92238.1  [L=306]
Description: PHP-associated [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-14   51.0   0.0    3.5e-13   49.1   0.0    2.0  2  PHP_C         PHP-associated
  ------ inclusion threshold ------
      0.015   15.6   3.1      0.026   14.8   3.1    1.4  1  PHP           PHP domain
      0.036   14.0   4.3       0.07   13.0   4.3    1.4  1  DUF5621       Domain of unknown function (DUF5621)
      0.057   12.6   1.0      0.092   11.9   1.0    1.3  1  7TM_GPCR_Sri  Serpentine type 7TM GPCR chemoreceptor Sri
       0.17   12.0   2.5         11    6.2   0.2    3.0  2  Sigma70_r1_1  Sigma-70 factor, region 1.1


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.71   2.5e+03      41      53 ..     103     115 ..      93     117 .. 0.76
   2 !   49.1   0.0   9.8e-17   3.5e-13       2      55 ..     153     205 ..     153     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.71
       PHP_C  41 iatpdelleaire 53 
                 + ++de+l+a ++
  AJA92238.1 103 SQSIDEILDAAKS 115
                 45789***99775 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 9.8e-17
       PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegr 55 
                 ++N++A+ fA++++l  ++GSD+H++ ++Gr+ +++ ++ ++ d++l a+++g+
  AJA92238.1 153 YSNKKAEVFAKEHNLLTIAGSDSHVASTIGRCTNLINSE-NNLDDILYAMKKGK 205
                 68**********************************444.447**********8 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.1   7.2e-06     0.026       1     102 [.       8     246 ..       8     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.2e-06
                 EEEE--CCC.........--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHH..HHHHHHHHHHTTTTSEEEEEEE....................... CS
                 xxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
         PHP   1 dlHvHteys.........lldgalsieelvkkakelglkaiaiTDhgnlfgy..vefykaakkkykagikpiiGleayvaddse............... 73 
                 +lH+H  +s           d +++++e ++ka + +l+ + +T h+ l+g+  + +yk+  +k  +++k+   +e++  ++ +               
  AJA92238.1   8 ELHCHNVFSnghvgdlepPFDCNVTVNEQLQKALDSKLDVLFVTNHNTLDGFkqMTDYKNSHEKF-SNVKVYPAVEITTDKEAHvlvyglqeeikssqs 105
                 57777777777666655545678899************************762266677775555.9*********55555554777777777777777 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
         PHP  74 ................................................................................................... 73 
                                                                                                                    
  AJA92238.1 106 ideildaaksqdavtiaphpfslidalrddslkcdlfeifnsanidiysnkkaevfakehnlltiagsdshvastigrctnlinsennlddilyamkkg 204
                 777777777777777766666666666666666666666666666666666666666666666666666666555555555555555555555555555 PP

                 ......................E....E.HHHHHHHHHHHHH CS
                 ............xxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
         PHP  74 ............kerpshltllaknqeG.yknllkllskayl 102
                             +e   hl   ++n ++ +++++k+++ +y+
  AJA92238.1 205 kisiekmeyvtrREVLEHLQYKIENSKEyIDQYVKEFYPKYF 246
                 555555555555555555555555555543444555555555 PP

>> DUF5621  Domain of unknown function (DUF5621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.3   1.9e-05      0.07      13      81 ..     191     263 ..     183     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                 HHHHHHHHHHHHHT.HHHHTSS--S---TTTTTGGGTSTTTTT-SSHHHHHHHHHH-HHHHH.....HHHBTT.. CS
     DUF5621  13 heeRekylksgkkn.klydglpvpraeRslnehlefYvkdselFinqleRELfKilYPktFn.....ylFEknqf 81 
                 +++ ++ l ++kk   +++++    ++R+++ehl++ + +s+ +i q  +E +   Y + Fn     y+F kn f
  AJA92238.1 191 ENNLDDILYAMKKGkISIEKM-EYVTRREVLEHLQYKIENSKEYIDQYVKEFYP-KYFRLFNsmykfYMFTKNSF 263
                 555678899999994445564.567899********************999765.57788887777788888876 PP

>> 7TM_GPCR_Sri  Serpentine type 7TM GPCR chemoreceptor Sri
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   2.6e-05     0.092     152     195 ..     225     270 ..     217     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
  7TM_GPCR_Sri 152 slsslskeeqleyvkenyPeylskfsslenFeiYdln..pwlivvv 195
                   ++++ ske   +yvke yP+y+  f+s+ +F ++++n   w +++ 
    AJA92238.1 225 YKIENSKEYIDQYVKEFYPKYFRLFNSMYKFYMFTKNsfVWDVAFK 270
                   566777888889************************9643433333 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.01        38       7      60 ..     106     158 ..     100     174 .. 0.61
   2 ?    6.2   0.2     0.003        11      18      44 ..     212     239 ..     189     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                   HHHHHHHHHHHSCEEHH....HHHHHGCCSS--HHHHHHHHHHHHCCT-EEE-SS-.. CS
  Sigma70_r1_1   7 vkeLikkgKkkGyLtye....EindaLpddeldseqiediiemLedmgIdvveeaede 60 
                   + e+++ +K++  +t +     + daL dd l+     d++e+++ ++Id++ +++ +
    AJA92238.1 106 IDEILDAAKSQDAVTIAphpfSLIDALRDDSLKC----DLFEIFNSANIDIYSNKK-A 158
                   5555555666666665522222344444333333....678899*******99877.3 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.003
                   SCEEHHHHHHHGC.CSS--HHHHHHHHH CS
  Sigma70_r1_1  18 GyLtyeEindaLp.ddeldseqiediie 44 
                    y+t  E+ ++L+ + e ++e i++ ++
    AJA92238.1 212 EYVTRREVLEHLQyKIENSKEYIDQYVK 239
                   69***********8888999***99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1021  (0.0569468); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2028.21
//
Query:       AJA92239.1  [L=146]
Description: pyridoxamine 5'-phosphate oxidase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-15   57.5   0.0    1.4e-15   57.2   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
     0.0073   16.1   0.0     0.0081   16.0   0.0    1.1  1  DUF447          Protein of unknown function (DUF447)
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.031   13.9   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.4e-19   1.4e-15       1      88 []       4      91 ..       4      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.4e-19
                    HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEEESCHH CS
  Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtaelvsdge 88
                    +d+el+++++ +k++ +ATv+ dG+Pn+sp++ +a  ++ ++vfa  +  ++ +nl +np + + ++d+ ++ g+r++G a+++sdge
      AJA92239.1  4 FDDELKKLVNFQKLGYVATVSSDGTPNLSPKGTIAILDDSRLVFANIRSPKTIENLTNNPSIEINVIDPFSRMGYRFKGLAKILSDGE 91
                    699*****************************888888889*********************************************97 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.4e-06    0.0081       5      56 ..      20      73 ..      19     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                EEEE-TT.-EEEEEEEEEE..SSSEEEEEEETTSHHHHHHHHHSEEEEEE---HH CS
      DUF447  5 vtTksek.rpnaaPiGviv..kgdkvvlrlfkgsrTleNllengelvinvtdDpl 56
                v T s++ +pn++P G i+  ++  +v++  +  +T+eNl++n+ + inv+d p+
  AJA92239.1 20 VATVSSDgTPNLSPKGTIAilDDSRLVFANIRSPKTIENLTNNPSIEINVID-PF 73
                56777788**********9986666777777777****************97.65 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-06     0.031       4      89 ..       6      91 ..       3     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-06
  Pyrid_ox_like  4 kklkelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsGtaevvedra 89
                   ++lk+lv+  k + ++t ++dg+ +  P  t ++ +d +l f   ++ + ++++++++++++ + d+ ++    ++G a++  d +
     AJA92239.1  6 DELKKLVNFQKLGYVATVSSDGTPNLSPKGTIAILDDSRLVFANIRSPKTIENLTNNPSIEINVIDPFSRMGYRFKGLAKILSDGE 91
                   6799**************************************************************99999999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1053.74
//
Query:       AJA92240.1  [L=526]
Description: excinuclease ABC, C subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-48  162.9   0.6    1.4e-47  161.4   0.0    2.0  2  UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
    4.4e-12   46.1   1.8    1.5e-11   44.4   1.8    2.0  1  GIY-YIG     GIY-YIG catalytic domain
    7.9e-10   38.2   0.8      3e-09   36.3   0.8    2.1  1  UVR         UvrB/uvrC motif
  ------ inclusion threshold ------
      0.013   16.1   0.3          2    9.1   0.0    2.7  2  DUF3067     Domain of unknown function (DUF3067)
       0.17   12.0   1.1          5    7.2   0.0    2.5  2  DUF1106     Protein of unknown function (DUF1106)


Domain annotation for each model (and alignments):
>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3         1   3.6e+03     111     147 ..     193     227 ..     178     233 .. 0.50
   2 !  161.4   0.0     4e-51   1.4e-47       2     153 ..     368     515 ..     367     516 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                 ES............SSSEEEE--TT-HHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N 111 aKdkkrktrakaeereeevlelkkssealkllqrird 147
                  K+k++ ++ +  ++ ++ +e +++s+ ++   +ird
  AJA92240.1 193 LKSKQQMKEFT--KKLQKQMEDASDSQQFERAIEIRD 227
                 44333322222..122222444555555555555555 PP

  == domain 2  score: 161.4 bits;  conditional E-value: 4e-51
                 HHTT-SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS--HHHHHHHHHHHHHTTS.....---SEEEESSSHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N   2 ellglkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvkegdDyaamrevlrRrfkrllkefsklPdLiliDGGkgqlnaakevlee 100
                 ++l+l++ p+ iec+DiS+  ++++vgsm  f dgkp+ks yRkfkik+ ++ dD+a+++e++ Rr+ rl ke+s+ PdLi+iDGGkgql+aa ++l+e
  AJA92240.1 368 DILKLPSIPRIIECFDISNHGDEYAVGSMARFVDGKPDKSGYRKFKIKTISGRDDFAMINEIVGRRYWRLRKEKSEFPDLIVIDGGKGQLSAALSALKE 466
                 689************************************************************************************************ PP

                 TT----EEEEES............SSSEEEE--TT-HHHHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  UvrC_HhH_N 101 lglkipvvglaKdkkrktrakaeereeevlelkkssealkllqrirdeaHrfA 153
                 +g++ p v+laK++++    k +++    ++++k+++ +k+lq+irde+Hrf 
  AJA92240.1 467 VGIETPCVSLAKENEEVFIPK-RTK---SIRIAKNKDSIKILQHIRDETHRFG 515
                 ************776654444.333...49**********************7 PP

>> GIY-YIG  GIY-YIG catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   1.8   4.1e-15   1.5e-11       2      78 .]      14      88 ..      13      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.1e-15
                -EEEEEEETTT--EEEEEESSHHHHHHHHHHHHHHT--S-HS.STEEEEEEEE----HHHHHHHHHHHHHHTTSSSS CS
     GIY-YIG  2 ggvYiirskenkliYvGstknlekRlkqHnagkkakytrkkgkkpfeliileifptksealelEkklikkyksnkyn 78
                 g+Y++++ ++++iY+G++knl++R k+++ ++ +  t+ k + + e i +   +++sea  lE   ik+y++ +yn
  AJA92240.1 14 PGIYLMKDSKGEIIYIGKAKNLKNRVKSYFLKNQNYKTQ-KLVSKIEDIEFVLTDNESEAFLLESNMIKRYRP-TYN 88
                59***************************9998655555.47*******************************.998 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.8   8.3e-13     3e-09       1      33 [.     200     232 ..     200     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 8.3e-13
         UVR   1 kklikeLeeemeeAaenedFEkAAklRDqinal 33 
                 k+  k+L+++me A+++++FE+A ++RD + +l
  AJA92240.1 200 KEFTKKLQKQMEDASDSQQFERAIEIRDTLQRL 232
                 6789**************************998 PP

>> DUF3067  Domain of unknown function (DUF3067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.017        62       4      31 ..      76     103 ..      74     109 .. 0.87
   2 ?    9.1   0.0   0.00055         2      37      76 ..     172     211 ..     143     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                 HHHHHHHHSS-EEEEEEEETTEEEEEEE CS
     DUF3067   4 rqlllekwgksyDvqlvrrkeklylqvm 31 
                 ++ +++++  +y+++l+ +++  yl+v 
  AJA92240.1  76 ESNMIKRYRPTYNIELKDQQRYTYLRVT 103
                 566899******************9985 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00055
                 STT-SS-HHHHHHHHHHHHHHHHHHS-HHHHHHHHHH--- CS
     DUF3067  37 qasfplteqeYlehldavaellnelgavdqvrefleetkk 76 
                   +f+  ++eY+++++++ ++l++ +++++++++l+++ +
  AJA92240.1 172 PCEFKSAQKEYVKNISDLESILKSKQQMKEFTKKLQKQME 211
                 457999***********************99999998766 PP

>> DUF1106  Protein of unknown function (DUF1106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6     0.045   1.6e+02      40      86 ..      19      64 ..       7      69 .. 0.69
   2 ?    7.2   0.0    0.0014         5      21      54 ..     247     280 ..     234     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.045
     DUF1106 40 ikcskg.iiylsikvspnnrkhvllynkkeyvfdklkelfpdeaiefs 86
                +k skg iiy+    + +nr + ++ ++++y  +kl      e ief 
  AJA92240.1 19 MKDSKGeIIYIGKAKNLKNRVKSYFLKNQNYKTQKLVS--KIEDIEFV 64
                56777658999888888887777777777887777754..44556665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
     DUF1106  21 eeehsfsilcgrlrgivltikcskgiiylsikvs 54 
                  +e  f i  g+   iv+t++ ++g+i  s k s
  AJA92240.1 247 SDEEYFGIRYGKQDAIVMTFRQTHGVIRDSEKFS 280
                 57889**********************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2051  (0.114396); expected 358.6 (0.02)
Passed bias filter:                      901  (0.0502538); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3572.20
//
Query:       AJA92241.1  [L=78]
Description: phosphopantetheine attachment domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-05   22.9   0.0    9.5e-05   22.7   0.0    1.1  1  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   5.3e-09   9.5e-05       2      63 ..       4      66 ..       3      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.3e-09
  PP-binding  2 klrelvaevlgvpleeidpdtdlfdlG.lDSllavellaaleeefgveiplsdlfehptlael 63
                kl  ++++v++v+   i+++t+  +l   DS ++  ll ++e ef+++++l++ ++ + +++l
  AJA92241.1  4 KLYKIISRVFNVDYNKINDETSPENLEeWDSFNFYVLLDEIENEFNIKFDLDETLDIKKIGDL 66
                7889*************99999998777************************99999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 589.02
//
Query:       AJA92242.1  [L=412]
Description: TIGR00299 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-106  356.4   0.6     2e-106  356.2   0.6    1.0  1  DUF111    Protein of unknown function DUF111


Domain annotation for each model (and alignments):
>> DUF111  Protein of unknown function DUF111
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.2   0.6  1.1e-110    2e-106       1     371 [.      11     398 ..      11     400 .. 0.95

  Alignments for each domain:
  == domain 1  score: 356.2 bits;  conditional E-value: 1.1e-110
      DUF111   1 lyldcs.sGisGDmllgALldlgadkeeleealek.lgl....eeveleiekvkksgisatkvdveeeehehehrslaeieeiie....aaslsekvke 89 
                 l++dc+ +GisGDm+l++L+d+ga+k+++ + +++ +++    +  +l+++kv+k+g sat++ +e  +++ ++r+ +ei+++i+    +++ls+++ke
  AJA92242.1  11 LFIDCQiAGISGDMILSSLVDIGANKSKIIDGIKEsANFlegsTIKKLDFTKVQKKGKSATQLVLE-LDENIHERKGTEIKNCIQlsceKLELSDSAKE 108
                 689***9************************999966668776566899**************995.58888899999**99998877799******** PP

      DUF111  90 kalaiferlaeAeakvhgvpleevhfhEvGavDaivdivgaalaldeLgv..ekvvasplalGsGtvrcahGilPvPaPAvlellkelklkl..geveg 184
                  a + +++l +Ae++vhg + ++vhfhE  ++D++vdivg+a+ald+L++  e++ +s++a+G+Gtv+++hG+ + Pa A++e++k++++ +  g+v++
  AJA92242.1 109 FAENSINTLINAESNVHGENESSVHFHEASSIDTVVDIVGTAIALDDLNLfdEEISCSHVAIGGGTVSFSHGVTSNPAYAITEIFKNSNIVVtgGPVTE 207
                 **************************************************9999***********************************9999999*** PP

      DUF111 185 ElvTPTGaAilaalaeefgslp.amkvekiGyGaGkrdleeipnvlRvlleeeeeelekeevvvletniDDlspevlgyvlerLleaGAlDvfltpilm 282
                 El+TPTGa il +la++++++  +m+++++GyGaG++d++ ++nvl+++ ++++e+le+++v +letn+DD+s+ev+++++e+L+e+GA Dv++t +++
  AJA92242.1 208 ELTTPTGASILVNLASSCKEFFvDMSIDSVGYGAGTKDFDGFANVLKIIQGKSNETLERDSVKILETNLDDVSGEVIANTIEKLMENGAKDVTVTQAIT 306
                 *******************5555**************************************************************************** PP

      DUF111 283 KKgRpavllsvlckeedaeeleellfretttlGvReseverlvlereietvetelg....evrvKvaeevvkvkpEyedvkkiAeetglplke 371
                 KKgRp+ l+sv+c+++++++l ++l++et tlGvR ++ er++++r+i + +++l+    +++ K++ +  ++k E+edvk+i+++ ++++++
  AJA92242.1 307 KKGRPTQLISVICSSQNTNSLLNILISETRTLGVRIRTSERYIVPRKILESDVTLEnqkfTIHYKIS-DSDHFKLEFEDVKSISNALNISFNK 398
                 **************************************************99999978888888888.4789*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2938.24
//
Query:       AJA92243.1  [L=526]
Description: radical SAM enzyme/protein acetyltransferase, ELP3 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-25   87.5   0.4    9.2e-25   86.5   0.4    1.6  1  Radical_SAM_C    Radical_SAM C-terminal domain
    1.9e-21   77.2   0.0    5.1e-21   75.8   0.0    1.7  1  Radical_SAM      Radical SAM superfamily
    5.9e-06   26.2   0.1    1.4e-05   25.0   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0024   18.1   0.0     0.0046   17.2   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.037   14.5   0.0    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
       0.03   14.6   0.2       0.82   10.0   0.0    2.8  2  DUF4777          Domain of unknown function (DUF4777)


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.4   3.1e-28   9.2e-25       1      81 [.     296     376 ..     296     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.1e-28
  Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlreliekrlk 81 
                    pd++K+yp lv+k+T+L+e yk g+ykp+s+ee+++++++ ++++p+++r++R++++i +++++ gp+ +nlr+ ++++l+
     AJA92243.1 296 PDMLKIYPALVLKDTPLYEDYKLGNYKPYSTEEMINVLTESKKIIPKWVRIMRVQREITMDEIVDGPKMGNLRQKVHEELA 376
                    8****************************************************************************9985 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.7e-24   5.1e-21       6     165 ..      91     284 ..      87     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.7e-24
                  EESS--TTTSCCTT.................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC........... CS
                  xxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
  Radical_SAM   6 gCnlrCsfCarpet.................vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla........... 74 
                  + ++rC+fC+ ++                   ++++ + +  +++i++++  + +++   + vi+gg   ++ +d+++   + +  a           
   AJA92243.1  91 CPHGRCTFCPGGTEintpnsytgkepvtlsaIEDNYEPGVQIKRRIEQLIAFG-HDPTkLELVIVGGTFLFMPDDYQRNFIKSCYDAingfesvsled 187
                  44556*******99****************99999999999999999999999.67774666666666666666666666666666699999999999 PP

                  ......CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                  ......xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  75 ......vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                        ++++r++  t +t+pd    ++++ +l++g++rv++g+++++++ v k++nrgh++++v+ +++++++ag k v ++++glp  + ee  ++
   AJA92243.1 188 akrnneKAKMRNVGFTIETKPDycqQKHVDMMLDYGTTRVEIGVQSLTER-VYKIVNRGHNLQQVISSFQIAKDAGYKIVAHMMPGLPTMSPEE--DI 282
                  9999999999**********99999*************************.**************************************99995..66 PP

                  HH CS
                  xx RF
  Radical_SAM 164 le 165
                  ++
   AJA92243.1 283 AD 284
                  65 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   4.7e-09   1.4e-05      62     108 ..     471     517 ..     469     524 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.7e-09
  Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFka 108
                      ++++qGigk+L++++e+ a +d ++++l v ++   +++Y+kl ++ 
       AJA92243.1 471 SFQHQGIGKKLMMEAEKIAATDLSSNKLCVISAVGTREYYKKLNYRI 517
                      58****************98887777******************985 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-06    0.0046      61     117 .]     450     515 ..     389     515 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                     EEEEEEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.TESEE.EEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  61 ayieslaV...........speyrgkGlGsaLlealeeraree.gikki.vlaveedndaairlYeklGF 117
                      ++++l+V             +++++G+G++L+ ++e++a      +k+ v+    + ++++++Y+kl +
      AJA92243.1 450 SIVRELHVfgkaisigeqeEFSFQHQGIGKKLMMEAEKIAATDlSSNKLcVI----SAVGTREYYKKLNY 515
                     45555555555555555444578********************888996555....67899****88876 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.037      35      75 ..     471     516 ..     457     517 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                     GGTTSSHHHHHHH.HTT...SEEEEEEEEE.THH.......HHHHHHHHTTEE CS
  Acetyltransf_7  35 eyrgkGiGraLle.aae...kgiileqlel.nae.......kaikfYeklGFe 75 
                     +++ +GiG++L+  a++   +        l +++        ++++Y+kl ++
      AJA92243.1 471 SFQHQGIGKKLMMeAEKiaaT-------DLsSNKlcvisavGTREYYKKLNYR 516
                     59*********9624222221.......22111123332225567****9997 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00028      0.82      22      51 ..      12      41 ..      10      44 .. 0.90
   2 ?    1.2   0.0      0.15   4.4e+02      14      28 ..     347     361 ..     344     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00028
     DUF4777 22 ldEivervaerydlseeelkkvVkntLeaA 51
                 +Ei er++e+++l+++++k ++k t +++
  AJA92243.1 12 CREICERLSEIENLEKNQIKNEIKETCSKY 41
                69**********************997776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
     DUF4777  14 kvlnrPaTldEiver 28 
                 + ++r +T+dEiv+ 
  AJA92243.1 347 MRVQREITMDEIVDG 361
                 567899*******84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3851.46
//
Query:       AJA92244.1  [L=153]
Description: copper-binding protein, plastocyanin/azurin family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-07   31.9   0.1    3.9e-07   30.4   0.1    1.8  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    0.00042   20.4   0.0    0.00059   19.9   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.38   10.9   2.8       0.35   11.0   0.9    1.9  2  DUF4884       Domain of unknown function (DUF4884)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.1   6.5e-11   3.9e-07       8      98 ..      73     152 ..      66     153 .] 0.86

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.5e-11
                  TTETSEEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind   8 esgdlqFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtv 98 
                  e +dl F + e t+++ge+v fvn + + HNv l  d     + +d + +          e +  +f e g+Y+++C+ H    M+g + +
   AJA92244.1  73 EVDDLCFLPYEKTINAGETVLFVNEDEFEHNVRLRGDPNYLHFPTDVIRQ---------NEYFVYKFYEMGEYQYHCTLHP--WMEGVINI 152
                  567899*****************************999755555555555.........599******************9..58998875 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.8e-08   0.00059      26     102 ..      73     150 ..      43     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.8e-08
  Cupredoxin_1  26 tvkdggfePskievkagekvklkiknkdktpeefesed....lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkl 102
                   +v d  f P + +++age  ++ ++n+d+  +++  +     l++ +++  ++++ +  +  + GeY+++c +h+ ++G++
    AJA92244.1  73 EVDDLCFLPYEKTINAGE--TVLFVNEDEFEHNVRLRGdpnyLHFPTDVIRQNEYFVY-KFYEMGEYQYHCTLHPWMEGVI 150
                   455558999*********..899************999999***99887777777766.66**************999987 PP

>> DUF4884  Domain of unknown function (DUF4884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   8.4e+03      35      43 ..      23      31 ..      22      33 .. 0.79
   2 ?   11.0   0.9   5.9e-05      0.35      18      32 ..     127     141 ..     120     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
     DUF4884 35 DvTsiknDS 43
                DvT  + D+
  AJA92244.1 23 DVTNFETDA 31
                899998886 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.9e-05
     DUF4884  18 VYRFyDmgsYvYFTt 32 
                 VY+Fy+mg+Y Y  t
  AJA92244.1 127 VYKFYEMGEYQYHCT 141
                 9***********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1108.03
//
Query:       AJA92245.1  [L=373]
Description: putative type II DNA topoisomerase VI subunit A [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   50.8   0.1    2.3e-13   49.9   0.1    1.5  1  TP6A_N    Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.085   13.1   0.9       0.15   12.3   0.0    1.9  2  Toprim    Toprim domain
       0.11   12.8   0.0       0.23   11.8   0.0    1.6  1  SPATA48   Spermatogenesis-associated protein 48


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   3.9e-17   2.3e-13       1      61 [.      85     148 ..      85     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3.9e-17
                 HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...GGGS-SSHHHHHHHHHHHHHHHTS-GGGGT CS
      TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...dvelFksQaesdrliddievllgvsReeLn 61 
                 r+f+qll+++ + ++l +e+k++T+Rd+YY+       F++Q+esd++i d+e++l+ +Re++ 
  AJA92245.1  85 RSFTQLLWLAFFANKLTHEKKSSTLRDVYYSsqaFAVDFEDQQESDNIIVDLEAVLSQPREDFF 148
                 68*****************************6654778***********************985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.6       1.3   7.7e+03      44      54 ..      15      27 ..       3      37 .. 0.41
   2 ?   12.3   0.0   2.6e-05      0.15      59      84 ..     242     272 ..     181     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                E..ECTTTHHHHH CS
      Toprim 44 e..eiedkkkvlk 54
                +  +i++ kk ++
  AJA92245.1 15 KkeKIDKSKKLIQ 27
                1122333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.6e-05
                 HHHHHS.....EEEEECSSSHHHHHHHHHHH CS
      Toprim  59 lakrad.....eiilatDpDreGeaiawell 84 
                 l+kr +      ++++tD+D+ Ge+ia+ + 
  AJA92245.1 242 LLKRLHdelglPVVILTDGDVYGEHIAMVIK 272
                 3333333444689**************8776 PP

>> SPATA48  Spermatogenesis-associated protein 48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.23      32      84 ..     141     191 ..     105     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
     SPATA48  32 dnpkediksltkkRsskplytetsrraniPgYtgkvhftathpansnipsttp 84 
                 ++p ed+  ++++Rss   + + +   +iPgY+gk++  ++hp   +i ++  
  AJA92245.1 141 SQPREDFFVFPEERSSI--FGDLTIEYTIPGYEGKTQNLSSHPDGYAIGPSMT 191
                 34555555555555543..556666789**************98877754433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2642.60
//
Query:       AJA92246.1  [L=278]
Description: hypothetical protein T478_0748 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.2   0.9       0.16   12.0   0.2    2.5  3  SLIDE     SLIDE


Domain annotation for each model (and alignments):
>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.07   1.3e+03      52      69 ..      80      97 ..      47     136 .. 0.58
   2 ?   12.0   0.2   8.9e-06      0.16      40      72 ..     133     165 ..     103     190 .. 0.74
   3 ?   -0.7   0.1     0.076   1.4e+03      22      62 ..     176     213 ..     162     218 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.07
       SLIDE 52 yteeeDrfllvllakyGy 69
                y+++eD   + + +++ +
  AJA92246.1 80 YSSDEDLRRIFIKSEIKL 97
                666665433333333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.9e-06
       SLIDE  40 ikyppsnkgkkeyteeeDrfllvllakyGygn..y 72 
                 i+    n+++k y+ee Dr ++  l+++G+++   
  AJA92246.1 133 INA-GGNSESK-YEEESDRLIIEKLNELGFKDmpK 165
                 344.6666666.*****************987442 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.076
       SLIDE  22 ellkkkveqyknplqelkikyppsnkgkkeyteeeDrfllv 62 
                 + l+kk++++ ++ q   i  + ++ ++  + +e D+ l+ 
  AJA92246.1 176 DELAKKIKNMIDDSQPEVIDIQGQK-NQL-F-KELDNLLIE 213
                 5677778877777777777774443.333.3.555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1937.26
//
Query:       AJA92247.1  [L=206]
Description: HD domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-13   50.5   0.9    2.7e-13   50.2   0.2    1.5  2  HD            HD domain
  ------ inclusion threshold ------
      0.088   12.5   0.1        8.8    6.1   0.0    2.3  2  Prok_Ub       Prokaryotic Ubiquitin
       0.14   12.4   1.2        0.4   10.9   0.1    2.4  2  Nuclease_act  Anticodon nuclease activator family
        2.4    8.3   7.9        2.7    8.2   1.9    2.4  2  DUF5636       Family of unknown function (DUF5636)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.2   5.9e-17   2.7e-13       2     121 ..      27     125 ..      26     126 .. 0.90
   2 ?   -3.3   0.0       2.3     1e+04      58      72 ..     179     193 ..     166     201 .. 0.55

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.9e-17
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHTTCCHHHHHHHHH CS
          HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.ledvaklirehheswegkkrpr 99 
                 +eH ++V++ a+++++ +    ++ l+l a LlHDi+k ++           ++ l+ +k +++il+e+   +  d +++++++i++h++s+       
  AJA92247.1  27 FEHVMRVYRNAEKICKTES--GNKKLILSAVLLHDIIKTKNCK---------DSALKSAKLSEKILKENNFHD--DeIKIISNAIKQHSFSKG------ 106
                 79****************9..*******************653.........455678899999999998888..57***************6...... PP

                 HHHCCTSCHHHHHHHHHHHHHH CS
          HD 100 glaerqlslearivklaDrlaa 121
                    + + ++e +i+++ Drl+a
  AJA92247.1 107 ---KIPSTIEGKILQDSDRLDA 125
                 ...57***************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                 HHHHHHHHHHHHHHH CS
          HD  58 aHekvgaeilrevek 72 
                  ++k g  +++++ k
  AJA92247.1 179 MNTKTGKNLAKKRTK 193
                 345555555555554 PP

>> Prok_Ub  Prokaryotic Ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0093        42      10      33 ..      12      35 ..       5      38 .. 0.88
   2 ?    6.1   0.0     0.002       8.8       4      29 ..     130     158 ..     128     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0093
     Prok_Ub 10 kyngirLaDpnpklspeeVrdfYa 33
                k+ +i+La  +p+ + e V+++Y 
  AJA92247.1 12 KIAKIKLAKNDPAHDFEHVMRVYR 35
                5678******************96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.002
     Prok_Ub   4 tlkRvFkyng...irLaDpnpklspeeVr 29 
                 +l RvF++ g     + Dpn  +s + V 
  AJA92247.1 130 GLARVFSFSGsnnRPFYDPNDPFSKNRVL 158
                 689*******99999*****999988886 PP

>> Nuclease_act  Anticodon nuclease activator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     9e-05       0.4       7      18 ..      28      39 ..      24      43 .. 0.85
   2 ?   -1.7   0.2      0.91   4.1e+03       3       7 ..      85      89 ..      84      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9e-05
  Nuclease_act  7 EHvmqFYRnnLK 18
                  EHvm  YRn  K
    AJA92247.1 28 EHVMRVYRNAEK 39
                  9********755 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.91
  Nuclease_act  3 nFHnE 7 
                  nFH +
    AJA92247.1 85 NFHDD 89
                  9**86 PP

>> DUF5636  Family of unknown function (DUF5636)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.019        84      55      96 ..      76     120 ..      26     127 .. 0.65
   2 ?    8.2   1.9    0.0006       2.7      22      61 ..     165     204 ..     152     206 .] 0.62

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.019
                 HHHHHHHHTT--SS-EEECCG----HHHHHH....HHHTT--B-HH CS
     DUF5636  55 fleeweaaagfnkgtsktiskdflskedFqe....llknglllkDs 96 
                 + e++++++ f+  ++k+is+  +++  F +    ++ +g +l+Ds
  AJA92247.1  76 LSEKILKENNFHDDEIKIISN-AIKQHSFSKgkipSTIEGKILQDS 120
                 335678888998899999888.555666666555555556666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0006
                 HHHHHHHHHHHHHHHHHCT--TTS...HHHHHHHHHHHHHHHH CS
     DUF5636  22 lkqlkkLeeeLqkkekefnkkpke...kkksklLrtfleewea 61 
                 l+   +  e+L + ek++n k ++   kk++k+L++fl+e+++
  AJA92247.1 165 LD---HFYEKLLTLEKKMNTKTGKnlaKKRTKILKNFLKELKN 204
                 33...3334555555555555444111666**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1412.96
//
Query:       AJA92248.1  [L=131]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-06   25.9   0.3     0.0066   16.2   0.0    3.1  3  TPR_1       Tetratricopeptide repeat
    0.00016   21.5   0.2       0.44   10.8   0.0    3.1  3  TPR_2       Tetratricopeptide repeat
     0.0029   18.1   0.0       0.69   10.5   0.0    2.4  2  TPR_19      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   15.2   0.6        1.3    8.9   0.2    2.2  3  DUF4919     Domain of unknown function (DUF4919)
      0.024   14.7   3.3        2.9    8.0   0.1    3.2  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
      0.082   12.2   0.3        0.1   11.9   0.3    1.1  1  DUF3638     Protein of unknown function (DUF3638)
      0.095   11.9   0.0       0.21   10.8   0.0    1.4  1  TPR_15      Tetratricopeptide repeat
       0.16   12.9   0.0         54    5.0   0.0    3.0  3  TPR_14      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.01        23      14      22 ..      18      26 ..      15      27 .. 0.86
   2 !   16.2   0.0   2.9e-06    0.0066       3      33 ..      41      71 ..      39      72 .. 0.91
   3 ?    1.3   0.0      0.15   3.4e+02      21      34 .]     104     117 ..      95     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
                TT-HHHHHH CS
       TPR_1 14 lgkydeAle 22
                +g+y++A+e
  AJA92248.1 18 QGEYEKAEE 26
                9******98 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.9e-06
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPn 33
                 l+ +G +y+ l++ ++ l y +++Le nP 
  AJA92248.1 41 FLFIMGSMYYMLNEEEKTLHYLDRVLEMNPY 71
                57789*************************6 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                 HHHHHHHHHHSTTH CS
       TPR_1  21 leyyekALelnPnn 34 
                 +++++k L   P+n
  AJA92248.1 104 IDCCRKILDETPDN 117
                 89****99876665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0082        18      12      26 ..      16      30 ..      13      38 .. 0.82
   2 !   10.8   0.0    0.0002      0.44       2      33 ..      40      71 ..      39      72 .. 0.93
   3 ?    1.6   0.0      0.17   3.8e+02      13      34 .]      96     117 ..      94     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0082
       TPR_2 12 yklgdyeeAleafek 26
                + +g+ye+A+e+ ++
  AJA92248.1 16 ITQGEYEKAEEFGQE 30
                569*******98776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0002
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                + l+ +G  yy l++ e+ l++++++le +P 
  AJA92248.1 40 DFLFIMGSMYYMLNEEEKTLHYLDRVLEMNPY 71
                67999*************************96 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
       TPR_2  13 klgdyeeAleafekAleldPnn 34 
                 k+++++  +++++k l   P+n
  AJA92248.1  96 KQNELNVVIDCCRKILDETPDN 117
                 6667777799*********997 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00031      0.69       1      58 [.      15      72 ..      15      81 .. 0.88
   2 ?    5.4   0.0     0.012        27      36      67 ..      95     126 ..      94     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
      TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                l+ +g y+ A ++ +++ ++  k+++ +  +   ++ l++ ++    Ld+++e++p d
  AJA92248.1 15 LITQGEYEKAEEFGQELEAKFSKDPDFLFIMGSMYYMLNEEEKTLHYLDRVLEMNPYD 72
                678999**********9999999********************999999999999975 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.012
      TPR_19  36 lalgqldeAealLdalpeedpddaryasLlAk 67 
                 l++++l+  ++++ ++++e+pd+ ++++L+  
  AJA92248.1  95 LKQNELNVVIDCCRKILDETPDNFQVRDLITE 126
                 57777777889999**************9876 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0017       3.8      64     118 ..      12      66 ..       5      69 .. 0.91
   2 ?    8.9   0.2   0.00059       1.3      74     121 ..      56     104 ..      49     109 .. 0.78
   3 ?    6.4   0.1    0.0036       8.1      47      88 ..      69     115 ..      66     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0017
     DUF4919  64 dkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrln 118
                  +k +++ e++++ ++++e+ +k+  d+  l+++  +y  l+++e+  +y +r+ 
  AJA92248.1  12 LRKLITQGEYEKAEEFGQELEAKFSKDPDFLFIMGSMYYMLNEEEKTLHYLDRVL 66 
                 57899*****************************************999999875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00059
     DUF4919  74 keiislaeealkknPfdlkqlnllayaykalgkkeeakiy.skrlnkll 121
                 ++ +++  ++l+ nP d++ l l + +y+ + +++e +++ ++ ln ++
  AJA92248.1  56 EKTLHYLDRVLEMNPYDVESLSLKLRVYQFRAENQEDQELkQNELNVVI 104
                 67789999****************9999988877665554155666555 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0036
     DUF4919  47 kpyrvskdeekleel.....kldkkelseeelkeiislaeealkknP 88 
                 +py+v + + kl+       +++ +el+++el+ +i+  +++l++ P
  AJA92248.1  69 NPYDVESLSLKLRVYqfraeNQEDQELKQNELNVVIDCCRKILDETP 115
                 67777777777764456766667788899999999999999999998 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.22     5e+02      14      24 ..      18      28 ..      15      42 .. 0.78
   2 ?    5.4   0.1    0.0083        19      11      41 ..      49      79 ..      39      84 .. 0.81
   3 ?    8.0   0.1    0.0013       2.9      21      46 ..     104     129 ..      88     131 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.22
                HT-HHHHHHHH CS
  Fis1_TPR_C 14 lgeYseArryv 24
                +geY++A ++ 
  AJA92248.1 18 QGEYEKAEEFG 28
                699**998874 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0083
                HHHHT-HHHHHHHHHHHHHHTTS-HHHHHHH CS
  Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPenrQaqsLk 41
                +y l e ++ + y+d++Le+ P     +sLk
  AJA92248.1 49 YYMLNEEEKTLHYLDRVLEMNPYDVESLSLK 79
                67777778999***********998888887 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0013
                 HHHHHHHHHHTTS-HHHHHHHHHHHH CS
  Fis1_TPR_C  21 rryvdalLeiEPenrQaqsLkelied 46 
                   +++ +L   P+n Q+++L + +e+
  AJA92248.1 104 IDCCRKILDETPDNFQVRDLITELES 129
                 579*****************887776 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   4.6e-05       0.1     140     188 ..      75     121 ..      54     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
     DUF3638 140 ilSfkLmglekllskkeekvakelletq.kwldessrdilDEsDellsvk 188
                  lS+kL + +  ++++e    +el + + +++ + +r+ilDE   +++v+
  AJA92248.1  75 SLSLKLRVYQFRAENQE---DQELKQNElNVVIDCCRKILDETPDNFQVR 121
                 58899999998888555...455555554677899************998 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.2e-05      0.21     197     248 ..      22      73 ..      10      78 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.2e-05
      TPR_15 197 aeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdp 248
                 +++ e  ++++a+ ++d++    +++ + +L++++k L+yl + ++ n+ d+
  AJA92248.1  22 EKAEEFGQELEAKFSKDPDFLFIMGSMYYMLNEEEKTLHYLDRVLEMNPYDV 73 
                 4444444445555555555555555555555555555555555555555444 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.024        54      11      41 ..      15      45 ..      11      48 .. 0.86
   2 ?    2.8   0.0      0.13   2.8e+02       6      36 ..      44      74 ..      39      87 .. 0.80
   3 ?    3.1   0.0     0.099   2.2e+02      20      38 ..     103     121 ..      80     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.024
      TPR_14 11 llalGdpdeAiallrralalaPddaeawlll 41
                l ++G++++A++  +++ a++ +d+++++ +
  AJA92248.1 15 LITQGEYEKAEEFGQELEAKFSKDPDFLFIM 45
                5689***************999999888765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
      TPR_14  6 alaeallalGdpdeAiallrralalaPddae 36
                 +++ ++ l + ++ + +l+r+l+ +P d e
  AJA92248.1 44 IMGSMYYMLNEEEKTLHYLDRVLEMNPYDVE 74
                567777778888888889*********9876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.099
      TPR_14  20 AiallrralalaPddaeaw 38 
                  i+++r++l+  Pd+ +++
  AJA92248.1 103 VIDCCRKILDETPDNFQVR 121
                 58899*********98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 926.05
//
Query:       AJA92249.1  [L=336]
Description: homoserine dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-52  177.4   0.3    3.5e-52  176.8   0.3    1.3  1  Homoserine_dh  Homoserine dehydrogenase
    1.7e-08   34.5   0.0    3.2e-08   33.6   0.0    1.6  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
    6.1e-06   26.9   0.0    1.5e-05   25.6   0.0    1.7  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.3   5.9e-56   3.5e-52       1     173 []     156     327 ..     156     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 5.9e-56
                    --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTTT--GGGSEE--STTS- CS
  Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgleveledvevegisklt 96 
                    Pi++  k++l+g++i +++Gilngt+nyilt+m+e g+sf+++l++a+++Gy eaD   D++GlDaa+Kl+ila+ ++g++v++ d+  +gi+k++
     AJA92249.1 156 PILDYAKNSLRGEKILSFQGILNGTTNYILTNMAE-GMSFEDALNDAKSKGYVEADEALDLDGLDAAAKLVILANWIMGMKVTMPDIIKKGIRKVN 250
                    99999*****************************6.999********************************************************* PP

                    HHHHHHHHCTTEEEEEEEEE.CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEES-SSHHHHHHHHHHHHH CS
  Homoserine_dh  97 aedikeakeegkvlklvasa.vearVkpelvpkshplasvkgsenavlvetdrlgelviqGpgaGaepTAsavlsDll 173
                     +dik+a+++g  +kl+as+  e++V+p +++ ++pl+ v+g+ na+++++++ g+ +i G+gaG+ +TAs++l+Dl+
     AJA92249.1 251 TNDIKNAEKNGSAVKLIASCdKELTVSPVEIKINDPLC-VNGTLNAISFTSEHSGTQTIIGRGAGGTETASSILRDLI 327
                    *******************9879**************9.*************************************97 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   5.4e-12   3.2e-08      56     120 ..      34      94 ..       1     117 [. 0.82

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 5.4e-12
                    -EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE- CS
  ELFV_dehydrog  56 akvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyieneeellelkvdilvPc 120
                     ++v+v Ds+G+ yd++Gld+++l ++k++ ++v++y+k    +++ i+++e + ++++d+l+  
     AJA92249.1  34 PRIVGVFDSKGCAYDETGLDLKKLNKIKKQSGTVRNYDK----SIKQISGKEIIENFDADVLIET 94 
                    479***********************************4....6789***9777888***99855 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.6e-09   1.5e-05       1     115 [.       7     146 ..       7     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.6e-09
                    --SHHHHHHHHHHHH---S......SEEEEEEEEESS.EEE-TT.........HHHHHT--CB---HHHHHHHH.........S-EEEEE-S--HH CS
  NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrd.sllskd.........rkallasealtldlddliahl.........dpdvvVEcassea 71 
                    G+G++++++ e+l++ + +      ++ ++v+v d++  + ++          +    ++  ++ + d+ i+++         d+dv++E ++s++
     AJA92249.1   7 GFGVVAQSFSELLESRTHDlyskfgLRPRIVGVFDSKgCAYDETgldlkklnkI---KKQSGTVRNYDKSIKQIsgkeiienfDADVLIETTASNY 99 
                    99*************99999***8878888888888855555559988865441...33334445555555555666677777********99887 PP

                    HH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE CS
  NAD_binding_3  72 va.....elvlkaLkagkdvvtankgaladealyeeLreaaeangakiy 115
                           +++ +a+k++++v+ +nkg la    +  L+e+a+ n++ ++
     AJA92249.1 100 KDaepgmSHIISAMKKKMHVISVNKGPLA--LAFPSLMELANYNQVMLR 146
                    54233338*********************..999999999999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2442.66
//
Query:       AJA92250.1  [L=143]
Description: cupredoxin-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-16   60.1   0.5    4.5e-13   49.1   0.0    2.1  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
    1.1e-06   28.7   0.0    1.4e-06   28.4   0.0    1.2  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.079   12.8   0.5       0.11   12.4   0.1    1.4  1  PRMT5_C       PRMT5 oligomerisation domain


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2   0.00013       0.8       3      19 ..      44      60 ..      42      70 .. 0.86
   2 !   49.1   0.0   7.5e-17   4.5e-13      54     113 ..      73     132 ..      65     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
        COX2  3 ikaiGhqwywsyeytdf 19
                ik  G+qw w++e++d 
  AJA92250.1 44 IKVTGQQWIWTFEHEDG 60
                899**********9985 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 7.5e-17
        COX2  54 tkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssm 113
                 +  ++ +t++dv+hsf +  + v  davpGr+n v+++ +  G f  qc e cG  h  m
  AJA92250.1  73 KAYKFEITSKDVIHSFNIHDYVVLLDAVPGRVNTVWFSPTEAGEFDIQCREYCGLIHYNM 132
                 567899***************************************************988 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.3e-10   1.4e-06      27     104 .]      57     138 ..      36     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.3e-10
  Cupredoxin_1  27 vkdggfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitiaplkpGeYeftcd.....mhmdakGkliV 104
                    +dg+ e  +++v+ g+  k++i+ kd   ++f ++d  +  +  pg  +t++++p ++Ge+++ c+     +h +++G+liV
    AJA92250.1  57 HEDGTKEIGELHVERGKAYKFEITSKD-VIHSFNIHDYVVLLDAVPGRVNTVWFSPTEAGEFDIQCReycglIHYNMRGTLIV 138
                   5677778889*************9887.46*******9999*************************9977766667******9 PP

>> PRMT5_C  PRMT5 oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.8e-05      0.11      39      79 ..      47      89 ..      28     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.8e-05
                SSS-EEEEEEESS-TTSS....-S-EEEEEEEEE-SSEEEEEEE CS
     PRMT5_C 39 sekvkevweFehpneeke...eenersktlefkikekaeihGla 79
                +   + +w+Feh   +ke    + er k  +f+i++k +ih + 
  AJA92250.1 47 TG-QQWIWTFEHEDGTKEigeLHVERGKAYKFEITSKDVIHSFN 89
                33.6889******999998889*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1058.61
//
Query:       AJA92251.1  [L=181]
Description: RNA polymerase Rpb6 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-10   41.1   0.0    2.9e-10   39.9   0.0    1.6  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.6e-14   2.9e-10       5      49 .]     110     160 ..     108     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.6e-14
                   SS--HHHHHHHHHHHHHHH....HT..........SS-SSSSTTCHHHHTT-S-- CS
  RNA_pol_Rpb6   5 kvltrYelvriaakRArQieegesl..........etqkpvviAlrEiaegkipi 49 
                   ++ltr+e++ri ++RA+Q+    sl          ++   ++i ++E++e  ipi
    AJA92251.1 110 PTLTRFEKARIMGARALQL----SLgappfidipvSAATSLDISMKELEERVIPI 160
                   89*****************....88888888888656699*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1267.85
//
Query:       AJA92252.1  [L=103]
Description: hypothetical protein T478_0735 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.019   15.1   1.7      0.051   13.8   1.8    1.6  2  Fib_alpha  Fibrinogen alpha/beta chain family
      0.019   14.4   2.0      0.023   14.1   2.0    1.0  1  FliD_C     Flagellar hook-associated protein 2 C-terminus
       0.02   15.2   0.5      0.026   14.9   0.5    1.1  1  DUF641     Plant protein of unknown function (DUF641)
      0.023   14.8   0.2      0.045   13.9   0.2    1.5  1  GIT1_C     G protein-coupled receptor kinase-interacting prot


Domain annotation for each model (and alignments):
>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.11   5.1e+02      93     111 ..      13      32 ..       3      41 .. 0.60
   2 ?   13.8   1.8   1.1e-05     0.051      43     105 ..      38      99 ..      14     103 .] 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                 HHHHHHCCH.HHHHHHHHHH CS
   Fib_alpha  93 lketidaqe.snirvLqnvl 111
                 +k t+++q+ +++ +L+ ++
  AJA92252.1  13 YKLTLTDQVlNQVDNLKALY 32 
                 55555555555555555544 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                 CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHH CS
   Fib_alpha  43 eleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnir 105
                 + e++++ ++e++  +++i++s+ ++ +  +  d +i+++ k +e++ ++++++i+++ s+i 
  AJA92252.1  38 DPESFEQVSSEISAAINNISESVSPEISDGH-LDGLIQEVFKAVEDKKSEVEKQIKDKDSKIS 99 
                 3355666677777777777777766666665.6************************999996 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.0   5.1e-06     0.023     141     221 ..      16     102 ..      12     103 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-06
                 HHHHHHHHHHHHHHHHHTTTSS........SXSHHHHHHHHHHHHH.....STT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHH CS
      FliD_C 141 kLkkalkenpssveelFsgstsqektv.tsdsglatrlenllksyv.....kssngtlqtasknltkqikdldkkiedldkrletle 221
                 +L++++ ++++++++l++ + +  ++    +s++   ++n+ +s++     +  +g +q+  k +++++++++k+i+d d+++++++
  AJA92252.1  16 TLTDQVLNQVDNLKALYATAAEDPESFeQVSSEISAAINNISESVSpeisdGHLDGLIQEVFKAVEDKKSEVEKQIKDKDSKISKKK 102
                 7999**************986655444134666777777666666697777444488888889999999999999999999999875 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   5.7e-06     0.026      49     110 ..      21     100 ..      16     103 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
      DUF641  49 eLkklselkrlyrkkqkkkas.eaeeseleaeiqe.................qrsllktyeitvkkleaelkakdseiee 110
                  L+++ +lk ly +  ++++s e+ +se++a i++                  +++ k+ e   +++e+++k kds+i++
  AJA92252.1  21 VLNQVDNLKALYATAAEDPESfEQVSSEISAAINNisesvspeisdghldglIQEVFKAVEDKKSEVEKQIKDKDSKISK 100
                 589999*********9999886555666666666667788888999***9999*************************87 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     1e-05     0.045      11      69 ..      17      77 ..      11     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
      GIT1_C 11 kteqitkriqeLlqaaq..eekkesfvpcaerIqsaVqdlvalfpenlseetlrtaLkqLt 69
                 t+q+  ++ +L ++    +e  esf ++++ I +a++++ + ++++ s+ +l   ++++ 
  AJA92252.1 17 LTDQVLNQVDNLKALYAtaAEDPESFEQVSSEISAAINNISESVSPEISDGHLDGLIQEVF 77
                689999999998665542268899*********************9999998887655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1960  (0.10932); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 794.26
//
Query:       AJA92253.1  [L=153]
Description: iron dependent repressor, metal binding/dimerization domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-16   58.1   0.1    1.5e-15   57.2   0.1    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    6.6e-15   54.9   0.0    1.2e-14   54.1   0.0    1.4  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    5.3e-06   26.8   0.1    9.1e-06   26.1   0.1    1.4  1  HTH_27          Winged helix DNA-binding domain
    1.1e-05   25.3   0.0    1.6e-05   24.8   0.0    1.3  1  MarR            MarR family
    1.2e-05   25.1   0.0      2e-05   24.3   0.0    1.3  1  MarR_2          MarR family
    8.4e-05   22.8   0.0    0.00035   20.9   0.1    1.9  2  Rrf2            Transcriptional regulator
     0.0009   19.1   0.1     0.0014   18.5   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.001   19.0   0.0     0.0018   18.2   0.0    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0039   17.0   0.0     0.0077   16.0   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.054   13.6   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.035   14.0   0.1      0.093   12.6   0.0    1.7  2  HTH_5           Bacterial regulatory protein, arsR family
      0.046   13.7   0.0       0.07   13.1   0.0    1.4  1  HTH_45          Winged helix-turn-helix
      0.057   13.5   0.2      0.085   13.0   0.2    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.17   11.9   0.0       0.71    9.9   0.0    1.8  2  NLPC_P60        NlpC/P60 family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.1   1.1e-18   1.5e-15       4      56 ..      17      69 ..      16      72 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 1.1e-18
                    HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
  Fe_dep_repress  4 estEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                    e tE+YL++++ + e+++ vk + +a+rLnv+ +sV +mlkkL++  +v y+k
      AJA92253.1 17 EHTEMYLKAVWHIREKGDDVKISTIAKRLNVRQPSVVQMLKKLAERDLVTYNK 69
                    689************************************************98 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   9.6e-18   1.2e-14       2      69 ..      76     141 ..      76     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 9.6e-18
                    HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
  Fe_dep_repr_C   2 ekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                    ++G+++A +++r+ rlle+++   l++d +e  e ++ +Eh++++++ ++l+ +l+ p+++P+g+ ip
     AJA92253.1  76 DSGEKVASSMIRNSRLLEVLMDSALKIDIDE--EMVCGIEHHMNKQFTDALCIMLKCPSKSPRGRDIP 141
                    58*******************9999998887..**********************************9 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   7.1e-09   9.1e-06       9      49 ..      26      66 ..      20      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.1e-09
      HTH_27  9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                +++ir+ ++ +k++ +++rlnv + +++ +lkkL e++Lv+
  AJA92253.1 26 VWHIREKGDDVKISTIAKRLNVRQPSVVQMLKKLAERDLVT 66
                79**************************************3 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.2e-08   1.6e-05       8      48 ..      25      66 ..      19      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.2e-08
                HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR  8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                +++ ++e+g+  ++s +ak+l+v +++v  +l++L +++l++
  AJA92253.1 25 AVWHIREKGDdVKISTIAKRLNVRQPSVVQMLKKLAERDLVT 66
                67788999988****************************996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.6e-08     2e-05      17      54 ..      31      68 ..      22      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.6e-08
                TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                + g d+ ++ +a+rl++ +++v ++lk+L ++ Lv++ 
  AJA92253.1 31 EKGDDVKISTIAKRLNVRQPSVVQMLKKLAERDLVTYN 68
                4455899****************************986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.7e-07   0.00035       7      67 ..      19      74 ..      16      88 .. 0.79
   2 ?   -0.9   0.0       1.7   2.1e+03       3      21 ..     116     134 ..     115     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
        Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                te+ l+a+ ++ ++ ++  v++++ia+r n+ ++ + ++l+kL++ +lv+     + G++L
  AJA92253.1 19 TEMYLKAVWHIREKGDD--VKISTIAKRLNVRQPSVVQMLKKLAERDLVTYN---KAGVTL 74
                56667777777777774..9*****************************975...355555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                 --HHHHHHHHHHHHHHHSS CS
        Rrf2   3 lsskteyalhallyLakee 21 
                 ++++++ al ++l + +++
  AJA92253.1 116 MNKQFTDALCIMLKCPSKS 134
                 5899999999999875554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.1e-06    0.0014      23      56 ..      36      69 ..      21      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
        TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek 56
                 ++++ia++l+v +++v ++L++L +++lV+ +k
  AJA92253.1 36 VKISTIAKRLNVRQPSVVQMLKKLAERDLVTYNK 69
                57899*************************8766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-06    0.0018      25      61 ..      39      76 ..      27      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES- CS
   HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrr.irild 61
                  +A +l++++ +v ++l++L ++ l++ ++  ++++d
  AJA92253.1 39 STIAKRLNVRQPSVVQMLKKLAERDLVTYNKAgVTLKD 76
                579*************************6533399998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-06    0.0077      12      51 ..      29      68 ..      27      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-06
                -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                ++e + ++++s +A+r+ +  ++v  +L+ L e+ +v+++
  AJA92253.1 29 IREKGDDVKISTIAKRLNVRQPSVVQMLKKLAERDLVTYN 68
                6788999******************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.054      28      58 ..      39      69 ..      32      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                HHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20 28 selaerldlskntlsyHLrvLeeagLvevvr 58
                s +a+rl +++ ++ + L++L+e +Lv+  +
  AJA92253.1 39 STIAKRLNVRQPSVVQMLKKLAERDLVTYNK 69
                78*************************9765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.2e-05     0.093      17      47 .]      37      67 ..      31      67 .. 0.92
   2 ?   -3.3   0.0       6.9   8.8e+03      17      25 ..     108     116 ..     103     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVek 47
                +++ +a+ l++ q+ v + LkkL e +LV++
  AJA92253.1 37 KISTIAKRLNVRQPSVVQMLKKLAERDLVTY 67
                6889*************************86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.9
                 EHHHHHHHH CS
       HTH_5  17 cvcelaeel 25 
                  vc +  ++
  AJA92253.1 108 MVCGIEHHM 116
                 567766554 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05      0.07      20      71 ..      36      87 ..      16      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
      HTH_45 20 akkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelleklke 71
                 k + i ++ n     + ++L++L e++l++ +k   +l + G+++ +++ +
  AJA92253.1 36 VKISTIAKRLNVRQPSVVQMLKKLAERDLVTYNKAGVTLKDSGEKVASSMIR 87
                577899999***********************************99988765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   6.7e-05     0.085       3      67 ..      15      81 ..      13      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
     DUF2250  3 eleedelalkvlkhlkkanvdYa.ksiakeleipleevrellkkLeelGLlerve.gktikrteakl 67
                e e++e++lk + h+++ + d    +iak+l++++  v ++lkkL e  L+++ + g t+k +  k 
  AJA92253.1 15 EAEHTEMYLKAVWHIREKGDDVKiSTIAKRLNVRQPSVVQMLKKLAERDLVTYNKaGVTLKDSGEKV 81
                567889999999999999988762579*************************988567788776665 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00056      0.71      57      94 ..       8      44 ..       6      57 .. 0.88
   2 ?   -0.7   0.0       1.1   1.4e+03      23      38 ..      66      81 ..      58      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                EEEESGTGGESEEEEEEETTEEEEEETTEEEEEETTST CS
    NLPC_P60 57 LvffktkkgisHvgiYlgngkmlhassekvsvsslsek 94
                ++f++t  +++H  +Yl+  +++ ++++ v++s++ ++
  AJA92253.1  8 VLFVGT-AEAEHTEMYLKAVWHIREKGDDVKISTIAKR 44
                678888.99**********************9998765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                HHHTTT----SSHHHH CS
    NLPC_P60 23 afakagielprssgeq 38
                +++kag++l++s ++ 
  AJA92253.1 66 TYNKAGVTLKDSGEKV 81
                5666666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1250.48
//
Query:       AJA92254.1  [L=200]
Description: hypothetical protein T478_0215 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-06   28.8   0.1    1.9e-06   28.1   0.0    1.4  2  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
    1.3e-06   28.7   0.0    1.9e-06   28.2   0.0    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    1.8e-06   28.2   0.0    3.4e-06   27.3   0.0    1.4  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.1e-10   1.9e-06       1      96 [.      12     114 ..      12     152 .. 0.80
   2 ?   -3.3   0.0       1.7     1e+04      53      65 ..     160     172 ..     153     194 .. 0.48

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.1e-10
                 SS-HHHHHHHHH-HHHHHHH.....EEEEEEEE--ST....TEEEEEEETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEEEEEEEEEEE.ETTE CS
       AHSA1   1 dapperVfraltdpellkrW.....ftlteaemdlrp....Ggkfrlrdspdgkefgnegeylevvpperlvytwrledepeeeestvtielee.eggg 89 
                 +ap+++Vf ++ +pe++          +t++ md+++    G +fr+  +  gk+ ++ +e +e v+ e+++ + + +  ++ +++++t e++e  ++ 
  AJA92254.1  12 KAPVDTVFTYFARPEHVSDQmsdkgVGMTVIPMDIKAgmgvGTTFRVIGDFSGKRLEWDCETTEFVRGEKISAK-QIK--GKFKKWEITTEFKElSDNL 107
                 69****************9779999777788888866666699****8889***********************.444..34679*********88888 PP

                 EEEEEEE CS
       AHSA1  90 Trltlth 96 
                 T++ +t 
  AJA92254.1 108 TNVSMTV 114
                 ***9998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                 EEEEETTTEEEEE CS
       AHSA1  53 ylevvpperlvyt 65 
                 y++++ +++l   
  AJA92254.1 160 YITLDAYQKLLAE 172
                 5555555555444 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   3.1e-10   1.9e-06       4     135 ..       5     144 ..       3     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.1e-10
                      EEEEEEESS-HHHHHHHHTTTTGGGGT..-TTEEEEECS.E.STSSSTTTEEEEECCCS.....SEEEEEEEEEETTTTEEEEEEE.SSS-TSE CS
  Polyketide_cyc2   4 vtvsvviaappekVwalvsdfenwprW..hpevarvele.g.gggpargvegtvrvggr.....gtvreelvevdpegrllsyrivkpvpvany 88 
                      v++s++i+ap+++V+ +++ +e+++    + +v  + ++ + + g   gv+ t+rv g          +e +e+   g  +s +   + ++++ 
       AJA92254.1   5 VKKSIDIKAPVDTVFTYFARPEHVSDQmsDKGVGMTVIPmDiKAGM--GVGTTFRVIGDfsgkrLEWDCETTEFVR-GEKISAKQI-KGKFKKW 94 
                      889**********************642344666555443345666..8888999888888844225677777776.555555553.7899999 PP

                      EEEEEEEECCET.EEEEEEEEEEE..E--TT--HHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  89 vatwtvtpdggg.trvtwtgefda..gplggpfekpaaakavkgdleagL 135
                      + t ++++  ++ t+v+ t+++++  gplg  ++k+ +ak  +  le++L
       AJA92254.1  95 EITTEFKELSDNlTNVSMTVDYEMplGPLGNILDKVKFAKSAENGLETAL 144
                      9**********99**********867888777777767666666566555 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   5.7e-10   3.4e-06       1     121 [.      11     134 ..      11     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.7e-10
                     ESS-HHHHHHHHTTTGGCCSCCCCEE.EEEE.SSSEE....E....EEECSTTSSCEEEEEEEEEEETTT.EEECTTCCCCCEEEEEEEECTECC CS
  Polyketide_cyc   1 vpapadqvyalvadvesypeflphcs.svevleeaes.glsa....dlevgfggltesftarvtldppee.itfklvegdfkslegkWtieslpp 88 
                     ++ap+d+v+ + a+ e+ ++ ++     ++v+  + + g+ +    ++   f g + +++ + t+ +  e i  k+++g fk+ e++ ++++l+ 
      AJA92254.1  11 IKAPVDTVFTYFARPEHVSDQMSDKGvGMTVIPMDIKaGMGVgttfRVIGDFSGKRLEWDCETTEFVRGEkISAKQIKGKFKKWEITTEFKELS- 104
                     689***************998885442578877777774444666699999**************999999***********************. PP

                     EEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHH CS
  Polyketide_cyc  89 nsggtrtkvalevdfkfaspllgalvgqvaerv 121
                        ++ t v+++vd+++  ++lg+++ +v   +
      AJA92254.1 105 ---DNLTNVSMTVDYEMPLGPLGNILDKVKFAK 134
                     ...9************99999999998886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1485.63
//
Query:       AJA92255.1  [L=195]
Description: imidazoleglycerol-phosphate dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-47  159.3   1.3    9.4e-47  158.9   1.3    1.1  1  IGPD      Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.021   14.9   0.2       0.15   12.2   0.0    2.3  3  DUF916    Bacterial protein of unknown function (DUF916)


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.9   1.3   1.1e-50   9.4e-47       1     144 []      33     175 ..      33     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.9 bits;  conditional E-value: 1.1e-50
                 ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEEE--SS-EEE--..-SB--TT.- CS
        IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaevaldlsgrpylvleaelkrekigel 99 
                 Tgi+fldh++ ++ kh+ +dl vk+k    + +Hh++ed+gi++G+a+++alg+++gi+Rf +  +pmDealae++ldl +r+y +++ + kr+ki  +
  AJA92255.1  33 TGIKFLDHLIGSFGKHSMMDLVVKAKSRDGI-EHHLIEDTGITIGSAIDKALGNRSGITRFSFSSVPMDEALAETSLDLVKRQYHKITLSTKRTKIEGI 130
                 9*************************88887.79***************************************************************** PP

                 -HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
        IGPD 100 dtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                 + e +e+ff sla++ ++++hv+v++g+n+hh+vea++K++a a+
  AJA92255.1 131 SKEDLEHFFFSLAQNLNCCIHVTVKYGDNDHHKVEAAIKSMAVAI 175
                 ******************************************996 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       0.4   3.6e+03      96     104 ..      14      22 ..       5      39 .. 0.45
   2 ?   12.2   0.0   1.6e-05      0.15      21      96 ..      53     127 ..      46     131 .. 0.84
   3 ?   -0.4   0.0      0.13   1.2e+03      17      50 ..     136     169 ..     128     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.4
      DUF916  96 tvklkikmP 104
                 + +++i+++
  AJA92255.1  14 ETSVSITIN 22 
                 222222222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.6e-05
      DUF916  21 LkvkpgqeqelevkikNssdkeitveitvntAvTndnGvidYskskekkdkslkvslselvkip.keitlpakeskt 96 
                 L vk ++++ +e ++   +d+ it+  ++ +A  n++G+  +s s+   d++l  +  +lvk + ++itl  k +k+
  AJA92255.1  53 LVVKAKSRDGIEHHLI--EDTGITIGSAIDKALGNRSGITRFSFSSVPMDEALAETSLDLVKRQyHKITLSTKRTKI 127
                 5555555555555554..567899********************************9*****999*******99986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.13
      DUF916  17 sYFdLkvkpgqeqelevkikNssdkeitveitvn 50 
                 ++F + ++++ +  ++v++k   +   +ve++++
  AJA92255.1 136 EHFFFSLAQNLNCCIHVTVKYGDNDHHKVEAAIK 169
                 5666666666666677777777777667666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1415.57
//
Query:       AJA92256.1  [L=417]
Description: histidinol dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.6e-132  440.9   2.6   5.2e-132  440.7   2.6    1.0  1  Histidinol_dh   Histidinol dehydrogenase
  ------ inclusion threshold ------
      0.035   14.7   0.1        0.1   13.2   0.1    1.9  1  T_Ag_DNA_bind   Origin of replication binding protein
       0.76    9.6   6.1       0.76    9.6   0.5    2.2  2  SLS             Mitochondrial inner-membrane-bound regulator
        3.1    7.7   6.6        3.3    7.6   2.3    2.2  2  Lipoprotein_20  YfhG lipoprotein


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.7   2.6  1.2e-135  5.2e-132       3     409 .]      17     416 ..      15     416 .. 0.95

  Alignments for each domain:
  == domain 1  score: 440.7 bits;  conditional E-value: 1.2e-135
                    ------HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC----EEEEEECTTEEE CS
  Histidinol_dh   3 rseedseeveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkeseeevketepgvvl 98 
                    r++++s++ ++ v++il+dvr++Gd+a+++y++kF++  k+++lrvs++e   + +k++++  +al+ +a +++k ++   +s   +  ++   + 
     AJA92256.1  17 RRQKTSQKDRKIVQSILDDVRKNGDSAVKKYEQKFNGR-KTTQLRVSKQEA--KNAKITDAEFTALQLSAIRLSKSQRILNKS--LI--QSVKKIS 105
                    7788888999**************************55.468899999987..55679999999*****99999877766644..34..4445567 PP

                    EEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT-SEEEE--HHHHHHHHHH--SSS---SEEE-- CS
  Histidinol_dh  99 gqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagvdeiykvGGaqAiaalAyGtesipkvdkivGP 193
                       ++p+ +vG+Y+PgG+a ypS+++m++++A  Agvk+ivvv+Pp+ dgk++p ++ +a+ +g+ eiykvGGaqAiaalAyGt+sipkvdkivGP
     AJA92256.1 106 DISFVPVPSVGCYIPGGQARYPSSAIMSVITAAEAGVKKIVVVSPPNsDGKIDPMTITVAQNCGA-EIYKVGGAQAIAALAYGTKSIPKVDKIVGP 200
                    8899************************************************************8.8***************************** PP

                    -SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EE CS
  Histidinol_dh 194 GniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsai 289
                    G ++V  AK +vs+e++iDmiaGP+E+ +i D+tadpe+vA+DL+sqaEH +d+ ++++tts++ a++++++++k +++++r++i+++s++k++ i
     AJA92256.1 201 GGKFVSIAKSIVSEETSIDMIAGPTELGIIVDSTADPELVAYDLISQAEHSNDTMCFVITTSKSKATQIQKSLKKIIPNIERSSIVKQSISKNGFI 296
                    ************************************************************************************************ PP

                    EE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHH CS
  Histidinol_dh 290 ilvedleeaielaneyApEHlelqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkel 385
                     ++++ +++ielan++ApEH+el+v+ ++ l +ki+  G +++G+++p s+ DY+ Gtnh+LPT+g+ r+ +glsv dFlk  ++ e++k++l+++
     AJA92256.1 297 AVCKNQKDVIELANKIAPEHMELMVKGAKVLSKKITGPGLVLIGKNTPSSASDYLLGTNHILPTNGFGRTRGGLSVLDFLKLQTTLETKKSELSKI 392
                    ************************************************************************************************ PP

                    HHHHHHHHHHTT-HHHHHHHHHHH CS
  Histidinol_dh 386 aeavetlAeaEgLeaHaeavkvRl 409
                    +++++ l++aEgL++H +av+ Rl
     AJA92256.1 393 SDKLKILTDAEGLPNHYKAVEKRL 416
                    *********************996 PP

>> T_Ag_DNA_bind  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05       0.1       9      42 ..     243     275 ..     237     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
  T_Ag_DNA_bind   9 aylsaaifsnktleafliyttkeKlkeLykklle 42 
                    + +s+a  sn t+ +f+i t+k+K+ +++k+l++
     AJA92256.1 243 DLISQAEHSNDTM-CFVITTSKSKATQIQKSLKK 275
                    56899******98.****************9963 PP

>> SLS  Mitochondrial inner-membrane-bound regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.8     0.021        95      97     166 ..      11      97 ..       1     115 [. 0.74
   2 ?    9.6   0.5   0.00017      0.76      70     102 ..     259     290 ..     249     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.021
         SLS  97 dlsellkl.skvdklkdl.lseelleelgrltntvie...............vs..eddnnknskselkisalgedradlakRlLlwal 166
                 d   +++  +++++ kd+ + + +l+ + +  ++ ++               vs  e++n+k ++ e++  +l+  r  + +R L+ +l
  AJA92256.1  11 D--SFVEArRQKTSQKDRkIVQSILDDVRKNGDSAVKkyeqkfngrkttqlrVSkqEAKNAKITDAEFTALQLSAIRLSKSQRILNKSL 97 
                 3..44444544556678889999999999999999998888888888777775555666677888888888888889999999998888 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
         SLS  70 itAtkstaeyieasineilknittetvdlsell 102
                 it++ks+a++i++s+++i+ ni++ ++  ++ +
  AJA92256.1 259 ITTSKSKATQIQKSLKKIIPNIERSSIV-KQSI 290
                 99***********************999.3333 PP

>> Lipoprotein_20  YfhG lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.3   0.00074       3.3      72     154 ..      20     106 ..      12     110 .. 0.78
   2 ?    1.7   0.1     0.048   2.1e+02     135     159 ..     379     403 ..     371     411 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00074
  Lipoprotein_20  72 eitlaerrkllerlnaysaqfpaslrpllqlWreqqalqlalaeeraryqrlqeesdskld....slreqqaaLeaeLeettrKLen 154
                     ++++++r+ + + l+ ++++  ++++   q +  ++++ql+++++ a+++++ ++  + l+    +l ++q+ L+++L +  +K+ +
      AJA92256.1  20 KTSQKDRKIVQSILDDVRKNGDSAVKKYEQKFNGRKTTQLRVSKQEAKNAKITDAEFTALQlsaiRLSKSQRILNKSLIQSVKKISD 106
                     45566666666679*************************************987755544422334567888899999999888765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.048
  Lipoprotein_20 135 reqqaaLeaeLeettrKLenLtdiE 159
                     +++ ++ ++eL++++ KL+ Ltd E
      AJA92256.1 379 QTTLETKKSELSKISDKLKILTDAE 403
                     3344556789*************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1483  (0.0827152); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2875.35
//
Query:       AJA92257.1  [L=451]
Description: chorismate mutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-60  203.6   0.0      7e-60  203.1   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-10   41.3   1.1    3.3e-10   40.2   1.1    1.7  1  CM_2             Chorismate mutase type II
      5e-07   29.0   0.0    1.7e-06   27.2   0.0    1.8  2  Aminotran_5      Aminotransferase class-V
    9.9e-05   21.8   0.0    0.00032   20.1   0.0    1.8  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0004   19.0   0.0    0.00082   18.0   0.0    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.017   14.4   0.0      0.038   13.3   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
        3.8    7.7   5.3          2    8.5   0.7    2.7  2  bZIP_1           bZIP transcription factor


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.1   0.0   2.7e-63     7e-60       2     356 ..     108     440 ..     107     447 .. 0.95

  Alignments for each domain:
  == domain 1  score: 203.1 bits;  conditional E-value: 2.7e-63
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    ++i L ++e+++     ++ +v+k   e     +++ +ygp +glpe++++la+f++++    ++ e +v v++Ga  +  ++i+ l l+p+dei+
     AJA92257.1 108 KIIHLEVGEPDFQ----PPLNVKKSLSE--VYDKGFGKYGPAKGLPEFRTKLAEFANNNFDAGVNLE-NVMVTPGARFGVFLAITTL-LDPSDEII 195
                    789**********....*********99..88899**********************8888999999.*******************.******** PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                    v +p ++ y +++ +sg++v++++++ e++++ dl+++   ++e       tk+i+++ p+NPtG+++++    +++++ak++nl++++De+Y+  
     AJA92257.1 196 VIEPAWPAYRQCAINSGIKVRSIKTKLENKWEPDLDEISSCINE------NTKMIVLNYPNNPTGKILPKTLQDQIVNIAKENNLYILSDEIYSNY 285
                    ********************************************......99******************************************** PP

                    BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrke 287
                      g+   ++ ++  + e   ++++s+sK+ +++G R+Gy+++++++++ l+kl++  l   s++ q+ ++++l d      +++++ + +++r ++
     AJA92257.1 286 SNGE---WSSILSYNYEKS-IVTQSFSKSHSMTGYRIGYLVSSKDIIEKLTKLQALCLTnvSEPIQYTAMNSLGD------DVTKNTEIMNERLTK 371
                    ***4...555777777777.************************************99999**************......899************ PP

                    HHHHHHHSTEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS.TTEEEEECTTS-HHHH CS
  Aminotran_1_2 288 lrdeLaelglkvlasqsgmflltdlsae.takelskkLleevgvyvtpgtsftv.pgrlRitvAglteeel 356
                    l + ++e +l++++++++m+ + ++++  + ++ls++Ll++ gv++ pg  f+   +++Ri+  +l+ ++l
     AJA92257.1 372 LEEICKEMELEFVKPDGAMYIFARTKNPiNTSDLSEELLNH-GVAIAPGIGFGDyNEFFRISA-CLDIKTL 440
                    **************************999************.******9999999*******9.8887776 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   1.1   1.3e-13   3.3e-10       1      74 [.       8      85 ..       8      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.3e-13
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHH..HH..S-HHHHHHHHHHHHHHHHHHH CS
        CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerlee..ga..ldeeaierifreiisasralq 74
                Rk+I+ i  e+l LL+ R e+a+e+g++K+++g++v +++Re+e+ e +++  ++  +d++++ ++++ ++++s+++q
  AJA92257.1  8 RKKIEVITIEMLSLLKTRTEIAQEIGKIKNQQGMSVSNESREDELRELVKKtcQEinFDSNTALKFLNFLLNESIKVQ 85
                99*************************************************763367*******************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.38   9.7e+02      94     121 ..      88     114 ..      15     133 .. 0.67
   2 !   27.2   0.0   6.7e-10   1.7e-06      47     175 ..     148     279 ..     140     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.38
                  ETTSHGGGTHHHHHHHHHHTEEEEEEEB CS
  Aminotran_5  94 teaehhanlvpwqelakrtgakvkvipl 121
                  t++ h a ++ ++el+ ++g k+ ++++
   AJA92257.1  88 TSNTHLAIFLKAKELE-QQGKKIIHLEV 114
                  4455666666666666.44555555555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 6.7e-10
                  HHHHHHHHHHT-STG.....GGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE..EBETTSCBEGGGHHHH-- CS
  Aminotran_5  47 earekvaelinaese.....eeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi..pldeegeldldeleklln 137
                  e r+k+ae+ n + +     e++++t G+  ++ l++ +l   l+p dei+v e    a +    + a   g+kv+ i  +l++++e dlde+ + +n
   AJA92257.1 148 EFRTKLAEFANNNFDagvnlENVMVTPGARFGVFLAITTL---LDPSDEIIVIEPAWPAYR----QCAINSGIKVRSIktKLENKWEPDLDEISSCIN 238
                  5667777776655442222267899999999*********...***********9999999....66678899999985578999************* PP

                  TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
  Aminotran_5 138 ektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                  e+tk++ ++  +n tG i p    ++i+++ak+++ ++l D
   AJA92257.1 239 ENTKMIVLNYPNNPTGKILPktlQDQIVNIAKENNLYILSD 279
                  *****************998443479********9999988 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-07   0.00032      50     145 ..     179     280 ..     125     357 .. 0.75
   2 ?   -1.2   0.0      0.38   9.9e+02     222     303 ..     339     415 ..     327     418 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                      HHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB--..-H.HHHHHHHHH CS
  DegT_DnrJ_EryC1  50 AlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl...pVhlyGqva..dm.dalkaiaak 136
                      ++ la++ l ++p de+Iv    + a  ++++++g k+  +  + ++ + +d ++i + i+e+tk I+   p +  G++    + d++ +ia++
       AJA92257.1 179 GVFLAITTL-LDPSDEIIVIEPAWPAYRQCAINSGIKVRSIKTKlENKWEPDLDEISSCINENTKMIVlnyPNNPTGKILpkTLqDQIVNIAKE 271
                      455555543.5689***************************9984689*******************94445788899875434489******* PP

                      CT-EEEEE- CS
  DegT_DnrJ_EryC1 137 hglkvieDa 145
                       +l++++D 
       AJA92257.1 272 NNLYILSDE 280
                      *****9995 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                      -BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE CS
  DegT_DnrJ_EryC1 222 lteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegig 303
                      lt+++  i  + ++ l + v++++ei++   ++L+e+ +++el++ k +   a++ +a +++  + ++ ++l e+l ++g++
       AJA92257.1 339 LTNVSEPIQYTAMNSLGDDVTKNTEIMNERLTKLEEICKEMELEFVKPDG--AMYIFA-RTK--NPINTSDLSEELLNHGVA 415
                      44444444555555555555555555555555555555555555444443..333333.333..347888888888888775 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.2e-07   0.00082      78     176 ..     178     282 ..     163     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.2e-07
                      HHHHHHHHTTS-TTEEEEEESTSSHHHHH.HHHHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEEESS-TTTT----...HHHHHHHHHH CS
  Cys_Met_Meta_PP  78 aAiaaailallkaGdeivvsddlYggtqr.llkkvlkklgievkfvdt..sdleelekaikentklvylEtptnpllkvvD...iekiaklakk 165
                        +++ai++ll   dei+v + ++   ++  +++ +k  +i++k  ++   dl+e+ + i+entk++ l  p np+ k++      +i+++ak+
       AJA92257.1 178 FGVFLAITTLLDPSDEIIVIEPAWPAYRQcAINSGIKVRSIKTKLENKwePDLDEISSCINENTKMIVLNYPNNPTGKILPktlQDQIVNIAKE 271
                      567899**************9998765441456666777788888776446889************************975222458******* PP

                      TT-EEEEEGTT CS
  Cys_Met_Meta_PP 166 agvlvvvDntf 176
                      +++ ++ D  +
       AJA92257.1 272 NNLYILSDEIY 282
                      *9999988765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.038      46     167 ..     166     279 ..     136     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                      T-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS--S-TTS-EEEEEEEESSB CS
  Beta_elim_lyase  46 gkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..GkmdlekleaaikevgaheekiklisltvTn 137
                        e ++ +p  + +  +++++ll + +e+iv epa    + +      +g+k+r +k+k +   + dl+++ + i+e      ++k+i+l   n
       AJA92257.1 166 NLENVMVTPGARFGVFLAITTLLDPSDEIIVIEPAWPAYRQCA---INSGIKVRSIKTKLEnkWEPDLDEISSCINE------NTKMIVLNYPN 250
                      55667778888888899999*************9977666664...4577777777766652246788899999988......799******** PP

                      TTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
  Beta_elim_lyase 138 ntagGqvvsleelrevaaiakkygiplhlD 167
                      n   G++++    +++ +iak++++ ++ D
       AJA92257.1 251 NP-TGKILPKTLQDQIVNIAKENNLYILSD 279
                      *5.9********************998877 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.7    0.0008         2      27      62 ..       3      38 ..       1      40 [. 0.94
   2 ?   -0.2   0.3      0.41   1.1e+03      43      61 ..     363     381 ..     356     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0008
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
      bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLksk 62
                eieeL ++ ++++ e+ sL ++  e++ e+ k k++
  AJA92257.1  3 EIEELRKKIEVITIEMLSLLKTRTEIAQEIGKIKNQ 38
                89****************************999986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.41
                 HHHHHHHHHHHHHHHHHHH CS
      bZIP_1  43 ksLkseleelkkevekLks 61 
                 + + ++l +l++ +++++ 
  AJA92257.1 363 EIMNERLTKLEEICKEMEL 381
                 5578999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3082.65
//
Query:       AJA92258.1  [L=64]
Description: hypothetical protein T478_1066 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2073  (0.115623); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 446.22
//
Query:       AJA92259.1  [L=59]
Description: hypothetical protein T478_0993 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.13   12.2   8.4        2.6    8.1   8.8    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.8   0.00014       2.6      21      41 ..       7      29 ..       3      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00014
  OrfB_Zn_ribbon 21 evnpayTSktCseCgsknke..a 41
                    +++ +yTS++C+ C  ++k+  +
      AJA92259.1  7 KISTCYTSTECNSCKIIKKRkfT 29
                    7899**************99541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 450.10
//
Query:       AJA92260.1  [L=938]
Description: excinuclease ABC, A subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-34  118.7   1.0    4.3e-34  116.9   1.0    2.1  1  UvrA_inter       UvrA interaction domain
    2.8e-34  117.8   0.6      4e-32  110.8   0.3    3.2  2  UvrA_DNA-bind    UvrA DNA-binding domain
    3.1e-24   86.0   0.2    3.7e-10   40.5   0.0    4.5  3  ABC_tran         ABC transporter
    1.1e-09   38.1   3.1      0.031   13.7   0.0    4.2  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.9e-08   34.5   1.0       0.12   12.1   0.1    4.7  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.2e-07   32.2   0.0      0.033   14.6   0.0    3.4  3  AAA_16           AAA ATPase domain
    2.7e-07   30.2   0.5      0.039   13.7   0.0    2.7  2  AAA_29           P-loop containing region of AAA domain
      3e-06   27.2   3.2      0.043   13.7   0.1    3.3  3  RsgA_GTPase      RsgA GTPase
    3.1e-05   24.0   0.0       0.19   11.8   0.0    3.7  3  AAA_14           AAA domain
    0.00012   21.4   0.2       0.65    9.1   0.0    3.6  3  NB-ARC           NB-ARC domain
    0.00012   22.4   4.3       0.49   10.7   0.0    4.5  4  AAA_22           AAA domain
    0.00013   22.2   0.2       0.55   10.4   0.0    2.9  2  AAA_33           AAA domain
    0.00014   21.8   0.3       0.77    9.6   0.1    2.6  2  APS_kinase       Adenylylsulphate kinase
    0.00017   22.1   1.1          1    9.9   0.1    4.0  3  AAA_18           AAA domain
    0.00037   20.1   0.1        0.7    9.4   0.0    3.3  3  AAA_25           AAA domain
    0.00048   19.9   0.0      0.058   13.1   0.1    2.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00064   19.1   0.1       0.55    9.5   0.0    2.8  2  ATPase           KaiC
      0.001   18.2   0.1        1.1    8.2   0.0    2.4  2  T2SSE            Type II/IV secretion system protein
     0.0011   18.6   1.3        0.5    9.9   0.3    3.0  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0014   18.5   0.1          1    9.2   0.0    2.6  2  NACHT            NACHT domain
     0.0041   17.2   0.6       0.48   10.5   0.1    3.2  3  MMR_HSR1         50S ribosome-binding GTPase
     0.0078   16.1   4.6       0.83    9.5   0.5    3.6  2  ATPase_2         ATPase domain predominantly from Archaea
      0.009   15.3   0.9        2.9    7.0   0.0    2.6  3  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.015   14.6   0.1        4.1    6.6   0.0    3.1  4  Zeta_toxin       Zeta toxin
      0.016   14.7   0.2        3.5    7.1   0.1    3.1  3  AAA_7            P-loop containing dynein motor region
      0.017   15.5   0.1        7.2    7.1   0.0    3.2  2  RNA_helicase     RNA helicase
      0.018   15.4   0.4      0.018   15.4   0.4    4.0  3  DnaJ_CXXCXGXG    DnaJ central domain
      0.022   14.7   2.5       0.85    9.5   0.1    3.8  4  NTPase_1         NTPase
      0.023   14.3   0.3       0.34   10.4   0.0    2.3  2  Ssu72            Ssu72-like protein
      0.033   13.2   0.0        1.2    8.1   0.0    2.7  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.055   13.2   0.1         17    5.0   0.1    3.0  3  AAA_30           AAA domain
      0.066   13.7   0.1      0.066   13.7   0.1    3.9  3  AAA_23           AAA domain
      0.072   12.8   0.2        2.4    7.8   0.1    2.7  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.14   12.4   0.3         30    4.8   0.0    2.7  2  AAA_28           AAA domain
       0.14   11.8  15.5       0.15   11.8   0.3    4.5  4  AAA_15           AAA ATPase domain
       0.15   11.8   3.7        3.3    7.5   0.3    2.9  2  zinc_ribbon_2    zinc-ribbon domain
       0.18   11.5   4.8         26    4.5   0.0    4.1  4  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> UvrA_inter  UvrA interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.9   1.0   8.9e-37   4.3e-34       1     108 [.     132     240 ..     132     241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 8.9e-37
  UvrA_inter   1 QsveqIvdqilkleegtkllilaPvvrerkgefkkllenlkkkGfvrvriDgeiydlde.dieldknkkhsievvvDrlvvkkeersrlaesvetAlkl 98 
                 Qs+e+I+d+++k  +++k+l+laP+++++kg+++kl+e++kk+G++r r++gei+ l++  ++ld++k h+ie+vvDr++ +k+++sr++e ++tAlk 
  AJA92260.1 132 QSIESITDSVIKEFSQKKVLVLAPLIQRKKGTYEKLFEQMKKDGYSRARVNGEIILLEDeFPKLDRQKWHNIEIVVDRIIASKSDKSRIFEGIQTALKA 230
                 9********************************************************986889************************************ PP

  UvrA_inter  99 geglvivsev 108
                 ++g+v+v+++
  AJA92260.1 231 AKGSVLVASE 240
                 ******9875 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.18        87      77     109 ..      36      68 ..      24      69 .. 0.85
   2 !  110.8   0.3   8.3e-35     4e-32       1     110 []     289     399 ..     289     399 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.18
                    ........---HHHHHHHHHH-------HHHHH CS
  UvrA_DNA-bind  77 rkrsyektfeGvipnlerryreteSeavreele 109
                    ++ + +  f+ +  + +rry e+ S ++r+ le
     AJA92260.1  36 GSGKSTLAFDTIYAEGQRRYVESLSAYARQFLE 68 
                    56677889999******************9887 PP

  == domain 2  score: 110.8 bits;  conditional E-value: 8.3e-35
                    -S----.-----------GGG..TT-HHHHHHHHHHHTTTS------------S-THHHHH----.....................---HHHHHHH CS
  UvrA_DNA-bind   1 DpdlvvpdpslslaegAiapwsskkssyyrqlleavaehygidldtpfkeLpeeqkdilLyGsgeekikveyks..ggrkrsyektfeGvipnler 94 
                    Dpdlv+pd+++s+ +gAi pws + ssy++q l+ v ++y+++l tp+++++ +q +++LyG+++ ++k++y+   + + ++y+  feGv++nl+r
     AJA92260.1 289 DPDLVIPDKTKSILDGAIVPWSGRFSSYRKQELRVVGKKYKFNLMTPMNQMKSKQIKVILYGTED-VMKFSYEAktSDTIWEYTDAFEGVLNNLQR 383
                    9***************************************************************9.788888777799****************** PP

                    HHH-------HHHHHH CS
  UvrA_DNA-bind  95 ryreteSeavreelek 110
                    ++ et+Se+ re+l++
     AJA92260.1 384 KFMETDSESKREWLKQ 399
                    *************985 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.3e-06   0.00064       1      28 [.      16      43 ..      16     152 .. 0.88
   2 !   19.1   0.0     3e-06    0.0015      79     136 ..     424     516 ..     357     517 .. 0.70
   3 !   40.5   0.0   7.6e-13   3.7e-10       1     136 [.     621     857 ..     621     858 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-06
                EEEEEEEEETTSEEEEEESTTSSHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  1 lknvslklkegekvaivGenGaGKStLl 28
                lkn+++++ ++++v+i G +G+GKStL+
  AJA92260.1 16 LKNIDVNIPKNKIVVISGLSGSGKSTLA 43
                79************************95 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3e-06
                 H.................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS..EEEEESTT CS
                 x.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
    ABC_tran  79 n.................................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk..llllDEpt 136
                 n                                 +  +ei++ l+ l++++l+   +++s ++LSgG+ qr+ la  + ++ +  l++lDEpt
  AJA92260.1 424 NsknimevcdlsidssyeffnkleltdteqfiarDILKEIKERLEFLRNVGLNYLSLNRSSATLSGGESQRIRLATQIGSNLTgvLYVLDEPT 516
                 1444444444444444444444544333444444444557777788888888888998999****************9998755599*****9 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 7.6e-13
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHT.TSS--....SEEEE................EETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx....xxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlklla.gllkp....teGei................lldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                 lkn+++++  g ++ ++G +G+GKStL++ ++ + l+     t G                   +d+ ++ +++++     ig ++   +lf+++++ +
  AJA92260.1 621 LKNINVEFPLGFLISVTGVSGSGKSTLINDILlKALSSyfykTTGLPgkhkdvagvenidkiiSIDQSPIGRTPRSNPATYIGAFTPIRELFSNTELSK 719
                 79************************9874430333333433444447778888888888888999999999**************99*******9655 PP

                 H.....................................................................HHHTC...........HHHHHHHSTTGGT CS
                 x.....................................................................xxxxx...........xxxxxxxxxxxxx RF
    ABC_tran  79 n.....................................................................esdee...........iekalsklglkel 97 
                 +                                                                         e           i+k l+++ +++l
  AJA92260.1 720 ErgytpgqfsfnvavgrcfacegdgvkkiemqflsdvyvkcdecngkrynsetlgvmykgkniadilqmtV---EealkffenipaIKKKLETVLDVGL 815
                 56*********************************************999999999988888888775540...2444455556668888888888889 PP

                 TCBGESTTSGGS-HHHHHHHHHHHHHHHT...SSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
    ABC_tran  98 kdtvvksspssLSgGqkqrvalarallkk...pkllllDEpt 136
                    ++++s ++LSgG+ qrv+la  l k+   ++l++lDEpt
  AJA92260.1 816 GYIKLGQSSTTLSGGEAQRVKLASELSKRgtgKTLYILDEPT 857
                 999999999*****************98644479*******9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.011       5.5       9      46 ..      10      48 ..       4      67 .. 0.69
   2 !   10.4   0.0   0.00066      0.32     135     208 ..     229     557 ..     124     562 .. 0.69
   3 ?    4.8   0.4     0.033        16      15      44 ..     621     651 ..     609     659 .. 0.72
   4 !   13.7   0.0   6.3e-05     0.031     125     209 ..     710     899 ..     702     906 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.011
                SETTEECEEEEEET.TSSEEEEEESTTSSHHHH.HHHHHH CS
                xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxx RF
       SMC_N  9 nFksyagktvilpf.sksftaivGpNGSGKsnl.ldAilF 46
                + +  + k++++++ ++++ +i G  GSGKs l +d i +
  AJA92260.1 10 GARHHNLKNIDVNIpKNKIVVISGLSGSGKSTLaFDTI-Y 48
                55555555566655134588999********9834555.5 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00066
                 T.................................................................................................. CS
                 x.................................................................................................. RF
       SMC_N 135 e.................................................................................................. 135
                 +                                                                                                  
  AJA92260.1 229 Kaakgsvlvaseknekifsqnnacphcgitvgeleprtfsfnspfgmcnqcnglgvkmefdpdlvipdktksildgaivpwsgrfssyrkqelrvvgkk 327
                 055555555555555555555555555555556666666666666666666666666666666666666666666666666666666666666666666 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
       SMC_N 136 ................................................................................................... 135
                                                                                                                    
  AJA92260.1 328 ykfnlmtpmnqmkskqikvilygtedvmkfsyeaktsdtiweytdafegvlnnlqrkfmetdseskrewlkqfmrdtpcltcqgrklkpealavkinsk 426
                 666666666666666666666666666667777777777777777777777777777777777777777777777777777777777777777777777 PP

                 ...........................................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                 ...........................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 ...........................................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                                                            +LSgGe + + la    i +     ly+lDe    L ++ 
  AJA92260.1 427 nimevcdlsidssyeffnkleltdteqfiardilkeikerleflrnvglnylslnrssaTLSGGESQRIRLATQ--IGSNLTGVLYVLDEPTIGLHQRD 523
                 777777777778888888888888888888888888888888888888888899999999*****998777766..67777889*************** PP

                 HHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCE CS
                 xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
       SMC_N 176 vkkvaellkekskn.aQfivislreemlekadkl 208
                  +++ + l + ++    +iv+ ++ee+++++d +
  AJA92260.1 524 NARLIKTLSKLRDLgNTVIVVEHDEEIIRNSDWI 557
                 *********999876899********99998765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.033
                 CEEEEEETTSSE.EEEEESTTSSHHHHHHHH CS
                 xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
       SMC_N  15 gktvilpfsksf.taivGpNGSGKsnlldAi 44 
                  k++ ++f  +f  +++G  GSGKs l++ i
  AJA92260.1 621 LKNINVEFPLGFlISVTGVSGSGKSTLINDI 651
                 4556666666652579***********9877 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 6.3e-05
                 HHHHCTT-STT........................................................................................ CS
                 xxxxxxxxxxx........................................................................................ RF
       SMC_N 125 ellesagiske........................................................................................ 135
                 el++++++ske                                                                                        
  AJA92260.1 710 ELFSNTELSKErgytpgqfsfnvavgrcfacegdgvkkiemqflsdvyvkcdecngkrynsetlgvmykgkniadilqmtveealkffenipaikkkle 808
                 555555555555555555555566666666666666666666666666666666666666666666666666666666666666666666666666777 PP

                 .................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEE CS
                 .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 .................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklv 209
                                  +LSgGe + v la  ++  +   + ly+lDe    L ++ v+k+ ++l++  +    +ivi ++ ++++++d ++
  AJA92260.1 809 tvldvglgyiklgqsstTLSGGEAQRVKLASELSK-RGTGKTLYILDEPTTGLHFADVQKLLDVLNRLVNVgNTVIVIEHNMDVIKNSDWII 899
                 777777777777777779************99875.556789************************999876899********999998776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0         2   9.9e+02       2      15 ..      29      42 ..      28      80 .. 0.93
   2 ?   -1.5   0.0       3.5   1.7e+03     121     205 ..     130     216 ..      85     228 .. 0.83
   3 !   12.1   0.1   0.00025      0.12     100     301 ..     392     550 ..     337     552 .. 0.72
   4 ?    4.6   0.1      0.05        24       4      27 ..     636     658 ..     633     707 .. 0.72
   5 !   11.7   0.0   0.00034      0.16     245     294 ..     835     884 ..     804     893 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2
      AAA_21  2 nvliGpNgsGKSnL 15
                 v+ G  gsGKS+L
  AJA92260.1 29 VVISGLSGSGKSTL 42
                6888999*****98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
      AAA_21 121 gvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlgeg 205
                   ++ ++++ sv+++++++++ +l  ++ r+  +++ l +++k+  +++   +    + +++ ++l ++ ++ +  v +++ +++  
  AJA92260.1 130 STQSIESITDSVIKEFSQKKVLVLAPLIQRKKGTYEKLFEQMKKdgYSRARVNGEIILLEDEFPKLDRQKWHNIEIVVDRIIASKSD 216
                 567788999999999999999999999999999999999999988888888888888888888888888888888777777777655 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00025
      AAA_21 100 ldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveie 198
                 +++++l+++ ++ p+  ++   ++++ l+ ++ s+ + + +   ++++++++++l+l        +   ++i++d +++ ke+  + r v+   l  ++
  AJA92260.1 392 SKREWLKQFMRDTPCLTCQGRKLKPEALAVKINSKNIMEVCDLSIDSSYEFFNKLEL--------TDTEQFIARDILKEIKERLEFLRNVGLNYLSLNR 482
                 556666666666777777777777777777777777777777777777777777666........5555555555555555555555555555555555 PP

      AAA_21 199 lsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                  s++                                  lS G  + ++l+t + + l    l+++DEp  gLH +  +rl++ l++l++ g  vi++ H
  AJA92260.1 483 SSAT----------------------------------LSGGESQRIRLATQIGSNLTG-VLYVLDEPTIGLHQRDNARLIKTLSKLRDLGNTVIVVEH 546
                 5555..................................5****9999**********99.9*************8888888888888888888988766 PP

      AAA_21 298 Spll 301
                 + ++
  AJA92260.1 547 DEEI 550
                 6655 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.05
      AAA_21   4 liGpNgsGKSnLLdaldllarldr 27 
                 ++G  gsGKS+L+  + ll+ l +
  AJA92260.1 636 VTGVSGSGKSTLINDI-LLKALSS 658
                 7899*********999.5665533 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00034
      AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                  +l++ l  +    +l+++DEp +gLH + + +ll++l++l + g  vi+
  AJA92260.1 835 VKLASELSKRGTGKTLYILDEPTTGLHFADVQKLLDVLNRLVNVGNTVIV 884
                 47777777777777*********************999998886666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-05     0.033      21      63 ..      23      66 ..      11     237 .. 0.84
   2 !   13.3   0.0   0.00017     0.081      27      53 ..     634     660 ..     628     705 .. 0.82
   3 ?   -1.1   0.0       4.4   2.1e+03     130     165 ..     844     879 ..     746     888 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-05
      AAA_16 21 sgrpelvllsGesGvGKsslv.rellralekdggif..lrgkcdql 63
                 +   +v++sG sG+GKs+l+ ++++   e+++ ++  l++ ++q+
  AJA92260.1 23 IPKNKIVVISGLSGSGKSTLAfDTIYA--EGQRRYVesLSAYARQF 66
                455589***************666664..44445665688888877 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
      AAA_16  27 vllsGesGvGKsslvrellralekdgg 53 
                 + ++G sG+GKs+l++ +l  +  +++
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLKALSSYF 660
                 789************999877766643 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.4
      AAA_16 130 lsrderplvlvlD....dlqwadeaslqllaaLlrllesk 165
                   + ++ ++ +lD          ++ ++ll+ L rl++ +
  AJA92260.1 844 RGT-GK-TLYILDepttG--LHFADVQKLLDVLNRLVNVG 879
                 222.22.44444422222..22223344444444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     8e-05     0.039      16      38 ..      20      42 ..      12      49 .. 0.76
   2 !   13.7   0.1     8e-05     0.039      24      39 ..     633     648 ..     620     658 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-05
      AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                +++i  + +++++G sGsGKSTl
  AJA92260.1 20 DVNIPKNKIVVISGLSGSGKSTL 42
                4556655699************9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8e-05
      AAA_29  24 atlltGpsGsGKSTll 39 
                  + +tG sGsGKSTl+
  AJA92260.1 633 LISVTGVSGSGKSTLI 648
                 5679***********9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00022      0.11      82     116 ..       8      43 ..       1      62 [. 0.81
   2 ?   -2.0   0.0       5.9   2.8e+03      53      84 ..     443     482 ..     433     489 .. 0.83
   3 !   13.7   0.1   8.8e-05     0.043      60     120 ..     593     652 ..     587     670 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                  --TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
  RsgA_GTPase  82 vsaktkegleelkellkd.ktsvlvGqSGvGKStLi 116
                  v+  ++++l+++  ++ + k++v+ G SG GKStL 
   AJA92260.1   8 VRGARHHNLKNIDVNIPKnKIVVISGLSGSGKSTLA 43 
                  5556678899999888777***************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.9
                  EE-GGG--HHH........HHHHHHHHHHHTTSEEEE--T CS
  RsgA_GTPase  53 lnKiDlleeee........eleelkeelealgyevllvsa 84 
                  +nK++l+++e+        e++e  e l+++g++ l ++ 
   AJA92260.1 443 FNKLELTDTEQfiardilkEIKERLEFLRNVGLNYLSLNR 482
                  8999999999999988888888888888888888887765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.8e-05
                  -HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  60 eeeeeleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                  ++++ l ++++++++   ++++  a+ +++l++++ ++    ++ + G SG GKStLin +l
   AJA92260.1 593 KDHN-LIKIEDKIREQKGKIVVKGAQ-ENNLKNINVEFPLgFLISVTGVSGSGKSTLINDIL 652
                  5555.666666666666666655454.78888888888764778899************986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00038      0.19       2      27 ..      26      51 ..      25      82 .. 0.82
   2 ?    6.9   0.0     0.012         6       5      35 ..     634     661 ..     631     684 .. 0.86
   3 ?   -0.1   0.0       1.8   8.8e+02      56      92 ..     841     880 ..     804     889 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
      AAA_14  2 rkilvitGaRrvGKTtllkqlikell 27
                +ki+vi+G+  +GK+tl+++ i+ + 
  AJA92260.1 26 NKIVVISGLSGSGKSTLAFDTIYAEG 51
                89******************998776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesily 35 
                 + +tG+  +GK+tl+++++ + l   +s++y
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLKAL---SSYFY 661
                 679**************998888...66665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.8
      AAA_14  56 ileklkeekktylflDEiqev......pewekalkslvdegkn 92 
                 + ++  + +kt+ +lDE          +++ ++l++lv+ g n
  AJA92260.1 841 LSKR--GTGKTLYILDEPTTGlhfadvQKLLDVLNRLVNVG-N 880
                 3332..25899999999765444444477777777777766.4 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0045       2.2      19      38 ..      25      44 ..      15      59 .. 0.83
   2 ?   -1.3   0.0         2   9.7e+02     151     177 ..     426     452 ..     418     466 .. 0.69
   3 !    9.1   0.0    0.0013      0.65      21      43 ..     632     654 ..     618     662 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0045
                CSEEEEEEESTTSSHHHHHH CS
      NB-ARC 19 qslvvalvGmgGvGKttlak 38
                +  +v ++G  G+GK+tla 
  AJA92260.1 25 KNKIVVISGLSGSGKSTLAF 44
                5679**************85 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                 EEEEEESS--HHHHHHHHHHCCTS-GG CS
      NB-ARC 151 sekievelLekdeawellenkvfekkl 177
                 ++ +ev  L++d ++e++++     + 
  AJA92260.1 426 KNIMEVCDLSIDSSYEFFNKLELTDTE 452
                 67789999**********987655544 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0013
                 EEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC  21 lvvalvGmgGvGKttlakqilnk 43 
                 +++++ G  G+GK+tl+++il k
  AJA92260.1 632 FLISVTGVSGSGKSTLINDILLK 654
                 789***************99866 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1     0.003       1.4       5      37 ..      26      58 ..      24     216 .. 0.80
   2 ?   -1.8   0.0       7.2   3.5e+03     117     133 ..     337     354 ..     327     356 .. 0.78
   3 ?   -0.8   0.1       3.4   1.6e+03      50     103 ..     448     519 ..     430     545 .. 0.61
   4 !   10.7   0.0     0.001      0.49       8      31 ..     634     657 ..     632     682 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
      AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee 37
                 +i+v+ G sG+GK+tl+    +   ++ + e 
  AJA92260.1 26 NKIVVISGLSGSGKSTLAFDTIYAEGQRRYVES 58
                5799*************9666666655555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.2
      AAA_22 117 nl.srkgvqliLvGtpel 133
                 n  ++k++++iL Gt+++
  AJA92260.1 337 NQmKSKQIKVILYGTEDV 354
                 445699********9875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.4
      AAA_22  50 stsskdl.lrellralglelka..................erlsseellealeqalraravielliiDEaqh.l 103
                 +t+ +++ +r++l++++++l+                   ++++s++++ a +  ++ ++v  l ++DE    l
  AJA92260.1 448 LTDTEQFiARDILKEIKERLEFlrnvglnylslnrssatlSGGESQRIRLATQIGSNLTGV--LYVLDEPTIgL 519
                 5544444488888888888888777788888777777775555555555444444444444..88888855545 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.001
      AAA_22   8 lvvtGesGtGKTtllrrlleqlde 31 
                 + vtG sG+GK+tl++ +l ++  
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLKALS 657
                 789*************99988754 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0011      0.55       2      20 ..      29      47 ..      28     103 .. 0.72
   2 !    8.6   0.0    0.0039       1.9       1      19 [.     633     651 ..     633     663 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
      AAA_33  2 vllvGlpGsGKstlaerll 20
                v++ Gl+GsGKstla   +
  AJA92260.1 29 VVISGLSGSGKSTLAFDTI 47
                8999**********96655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0039
      AAA_33   1 lvllvGlpGsGKstlaerl 19 
                 l+ + G++GsGKstl+  +
  AJA92260.1 633 LISVTGVSGSGKSTLINDI 651
                 56789**********9874 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0018      0.89       3      21 ..      27      45 ..      25      58 .. 0.85
   2 !    9.6   0.1    0.0016      0.77       2      38 ..     631     668 ..     630     672 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                EEEEEESSTTSSHHHHHHH CS
  APS_kinase  3 vvvwltGlsgsGKstiana 21
                 +v ++GlsgsGKst+a+ 
  AJA92260.1 27 KIVVISGLSGSGKSTLAFD 45
                6899************974 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
                 -EEEEEESSTTSSHHHHHH.HHHHHHHHTT--EEEEEH CS
  APS_kinase   2 gvvvwltGlsgsGKstian.alekkLvekgisvylLdG 38 
                 g+ + +tG+sgsGKst+ n  l k+L +  ++++ L G
  AJA92260.1 631 GFLISVTGVSGSGKSTLINdILLKALSSYFYKTTGLPG 668
                 678999**********8761567778877788877776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.008       3.9       1      15 [.      29      43 ..      29      64 .. 0.94
   2 ?   -1.8   0.0       8.7   4.2e+03      20      55 ..     583     615 ..     529     625 .. 0.60
   3 !    9.9   0.1    0.0021         1       1      18 [.     634     651 ..     634     695 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.008
      AAA_18  1 IlltGtpGvGKttla 15
                ++++G +G+GK+tla
  AJA92260.1 29 VVISGLSGSGKSTLA 43
                78***********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.7
      AAA_18  20 krlgfgvnlrdvakenglllevdpealdeskrlded 55 
                 ++     + +d++k+++l   +d+   ++ k+++++
  AJA92260.1 583 NH---KSVTGDYLKDHNLIKIEDKIREQKGKIVVKG 615
                 33...3344444444444444444433333444444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0021
      AAA_18   1 IlltGtpGvGKttlakeL 18 
                 I +tG++G+GK+tl + +
  AJA92260.1 634 ISVTGVSGSGKSTLINDI 651
                 679***********9876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0014       0.7      29      53 ..      22      46 ..       9      52 .. 0.86
   2 ?   -3.0   0.0       9.6   4.7e+03     163     188 ..     522     546 ..     520     546 .. 0.86
   3 ?    6.6   0.0     0.011       5.3      31      56 ..     629     654 ..     616     669 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
      AAA_25 29 llpagelallaGapgtGKttlaldl 53
                 +p+++++++ G +g+GK+tla d 
  AJA92260.1 22 NIPKNKIVVISGLSGSGKSTLAFDT 46
                479*******************986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.6
      AAA_25 163 sdvgalvealeriarrtgaavllvhH 188
                 +d ++l++ l ++ r +g +v++v H
  AJA92260.1 522 RDNARLIKTLSKL-RDLGNTVIVVEH 546
                 5778999999999.799999999999 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
      AAA_25  31 pagelallaGapgtGKttlaldlala 56 
                 p+g l+ ++G +g+GK+tl  d+ l+
  AJA92260.1 629 PLGFLISVTGVSGSGKSTLINDILLK 654
                 89*****************9988776 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.072        35       2      18 ..      30      46 ..      29      90 .. 0.76
   2 !   13.1   0.1   0.00012     0.058       2      21 ..     635     654 ..     634     679 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.072
  Viral_helicase1  2 vvhGvpGcGKStlirkl 18
                     v++G  G+GKStl  + 
       AJA92260.1 30 VISGLSGSGKSTLAFDT 46
                     89**********86555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
  Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                       v Gv G+GKStli ++l +
       AJA92260.1 635 SVTGVSGSGKSTLINDILLK 654
                      699**************987 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0011      0.55      16      41 ..      23      48 ..      17      60 .. 0.86
   2 !    6.5   0.0    0.0099       4.8      16      46 ..     628     658 ..     618     664 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
      ATPase 16 ipegrvvlitGepGtGKtifalqFli 41
                ip++++v i+G +G+GK+++a   ++
  AJA92260.1 23 IPKNKIVVISGLSGSGKSTLAFDTIY 48
                89******************977665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0099
      ATPase  16 ipegrvvlitGepGtGKtifalqFlikgaek 46 
                 +p g  + +tG++G+GK+++    l+k +++
  AJA92260.1 628 FPLGFLISVTGVSGSGKSTLINDILLKALSS 658
                 7888899************988877777666 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0023       1.1     108     147 ..       6      44 ..       1      54 [. 0.72
   2 !    7.4   0.0     0.004         2     130     151 ..     632     653 ..     601     660 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
       T2SSE 108 lgaeealkekiaevlrkavrerglilvsGgTgsGKttlly 147
                 l +++a ++++++ +   + +++++++sG  gsGK+tl+ 
  AJA92260.1   6 LKVRGARHHNLKN-IDVNIPKNKIVVISGLSGSGKSTLAF 44 
                 5555555555444.56666799***************974 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
       T2SSE 130 glilvsGgTgsGKttllyallk 151
                  li v+G  gsGK+tl++ +l 
  AJA92260.1 632 FLISVTGVSGSGKSTLINDILL 653
                 5788*************97764 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.019       9.3       2      23 ..      28      49 ..      27      57 .. 0.79
   2 ?   -1.5   0.0       3.4   1.7e+03      38      80 ..     543     584 ..     533     602 .. 0.77
   3 !    9.9   0.3     0.001       0.5       3      23 ..     634     654 ..     632     666 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.019
                EEEEEESTTCCHHHHHHHHHCT CS
        cobW  2 vtvltGflGsGKTtLlnhllen 23
                ++v++G  GsGK+tL   ++  
  AJA92260.1 28 IVVISGLSGSGKSTLAFDTIYA 49
                689************8877744 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                 SCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH CS
        cobW  38 evsiDaellretgveivelenGciCctlredllkelealeere 80 
                  v++D+e++r+++  i++l  G   +  +  +  +l+++++++
  AJA92260.1 543 VVEHDEEIIRNSD-WILDLGPGAGVHGGSVVFEGTLKQILNNH 584
                 5899******995.69999999999998888888888888877 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                 EEEEESTTCCHHHHHHHHHCT CS
        cobW   3 tvltGflGsGKTtLlnhllen 23 
                 + +tG  GsGK+tL+n +l +
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLK 654
                 679**************9944 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.015       7.3       2      18 ..      28      44 ..      27     105 .. 0.83
   2 !    9.2   0.0    0.0021         1       3      28 ..     634     659 ..     633     666 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                CEEEEC-TTTCHHHHHH CS
       NACHT  2 lvilqGeaGsGKTtLlq 18
                +v++ G +GsGK+tL+ 
  AJA92260.1 28 IVVISGLSGSGKSTLAF 44
                699************85 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
                 EEEEC-TTTCHHHHHHHHHHHHCTS- CS
       NACHT   3 vilqGeaGsGKTtLlqklalawaegk 28 
                 + ++G +GsGK+tL+  + l++ +++
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLKALSSY 659
                 6799**************99887666 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       0.2        98       2      15 ..      29      42 ..      28      58 .. 0.90
   2 ?   -2.3   0.0       9.7   4.7e+03      48      84 ..     509     545 ..     475     558 .. 0.61
   3 !   10.5   0.1     0.001      0.48       2      22 ..     634     654 ..     633     687 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.2
                EEEEESTTSSHHHH CS
    MMR_HSR1  2 vaivGrpNvGKStL 15
                v+i G + +GKStL
  AJA92260.1 29 VVISGLSGSGKSTL 42
                7999*********9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.7
                 EEEEECGGCSS.HHHHHHHHHHHHHHHHCTSEEEEEEE CS
    MMR_HSR1  48 ielvDtpGlie.gaseekglgkaflaleeadlillvvd 84 
                 ++++D p  i   ++++ +l k++ +l++    ++vv+
  AJA92260.1 509 LYVLDEPT-IGlHQRDNARLIKTLSKLRDLGNTVIVVE 545
                 55566555.43223334467777776666655666655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.001
                 EEEEESTTSSHHHHHHHHHTS CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                 + + G + +GKStLin ++ +
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLK 654
                 6799*************9864 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.5    0.0017      0.83      15     131 ..      23     196 ..      11     220 .. 0.60
   2 ?    6.1   0.0     0.019         9      22      49 ..     633     660 ..     618     687 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
    ATPase_2  15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............................... 82 
                 + +  n+i++i G  gsGK++L    i    +   yv  ++a  +++++ +d+   + ++ + l+ a+                               
  AJA92260.1  23 IPK--NKIVVISGLSGSGKSTLAFDTIYAEGQR-RYVESLSAYARQFLEMMDKP--DVDSIDGLSPAIsiqqkttsknprstvgttteiydymrllfar 116
                 444..99***************99999888543.34444444444444444444..4444455555555555556666666666677777777777777 PP

    ATPase_2  83 ......................giavpkaeleeilk..eksklvfkaielllekikkkgkk.......iiiiiDelqkli 131
                                        +++++++ +++l     ++  +   e+l+e++kk+g         ii++ De++kl 
  AJA92260.1 117 igiphctncgrkistqsiesitDSVIKEFSQKKVLVlaPLIQRKKGTYEKLFEQMKKDGYSrarvngeIILLEDEFPKLD 196
                 77777777766666666666654444444444444444444444555566666666665555555666666666666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
    ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk 49 
                  + ++G  gsGK++L++ i+ + +++ +
  AJA92260.1 633 LISVTGVSGSGKSTLINDILLKALSSYF 660
                 56799*************9987766554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0059       2.9       2      25 ..      27      50 ..      26      72 .. 0.81
   2 ?   -3.5   0.1       9.3   4.5e+03     120     184 ..     339     401 ..     329     404 .. 0.59
   3 ?    6.1   0.1     0.012       5.8       4      25 ..     634     655 ..     632     678 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0059
     DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                ++v+++G +G+GK+ +++  +++ 
  AJA92260.1 27 KIVVISGLSGSGKSTLAFDTIYAE 50
                799**************9998875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.3
     DUF2075 120 mkrakvvvalvDegQelntgeigteee.lkklakkleveleekvhLksqfRvaaseaviewvdall 184
                 mk +++ v+l++ + +++ + ++++++ + ++++  e  l    +L+++f    se+  ew+++++
  AJA92260.1 339 MKSKQIKVILYGTEDVMKFSYEAKTSDtIWEYTDAFEGVL---NNLQRKFMETDSESKREWLKQFM 401
                 5555677777777777776665555544444444444444...25666666666666666666665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.012
     DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                 + VtGv+G+GK+ + + +l ++
  AJA92260.1 634 ISVTGVSGSGKSTLINDILLKA 655
                 679************9999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0084       4.1      14      39 ..      24      49 ..      13      88 .. 0.78
   2 ?   -3.2   0.0       8.7   4.2e+03      82     123 ..     136     177 ..     131     178 .. 0.77
   3 ?   -2.6   0.0       5.8   2.8e+03      94     107 ..     567     580 ..     564     588 .. 0.80
   4 ?    3.9   0.0     0.057        28      18      37 ..     633     652 ..     619     658 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0084
  Zeta_toxin 14 erPklillgGqpGAGKselaellkde 39
                 + k+++++G +G+GKs+la ++  +
  AJA92260.1 24 PKNKIVVISGLSGSGKSTLAFDTIYA 49
                56789**************9766554 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
  Zeta_toxin  82 elvekllqeaiengyniivegtlrspdvvkklaealkkaGYe 123
                  +++++++e  ++++ ++     r+  + +kl e++kk+GY+
  AJA92260.1 136 SITDSVIKEFSQKKVLVLAPLIQRKKGTYEKLFEQMKKDGYS 177
                 667777777777787777777778888899999999999995 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.8
  Zeta_toxin  94 ngyniivegtlrsp 107
                 +g ++++egtl+++
  AJA92260.1 567 HGGSVVFEGTLKQI 580
                 6789*******976 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.057
  Zeta_toxin  18 lillgGqpGAGKselaellk 37 
                 li + G +G+GKs+l++++ 
  AJA92260.1 633 LISVTGVSGSGKSTLINDIL 652
                 677899**********9886 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.091        44      28      55 ..      21      48 ..      14      65 .. 0.79
   2 ?    7.1   0.1    0.0072       3.5      38      61 ..     636     660 ..     630     667 .. 0.82
   3 ?   -1.1   0.0       2.4   1.2e+03      42      64 ..     844     867 ..     841     895 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.091
       AAA_7 28 lllknkkpvllvGptGtGKtviikdllk 55
                  + ++k v++ G +G+GK++++ d++ 
  AJA92260.1 21 VNIPKNKIVVISGLSGSGKSTLAFDTIY 48
                56778999*************9988544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0072
       AAA_7  38 lvGptGtGKtviikd.llkkldkek 61 
                 ++G +G+GK+++i+d llk+l++  
  AJA92260.1 636 VTGVSGSGKSTLINDiLLKALSSYF 660
                 79*************8888888544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.4
       AAA_7  42 tGtGKtviikd.llkkldkekyls 64 
                  GtGKt++i d  ++ l+  +++ 
  AJA92260.1 844 RGTGKTLYILDePTTGLHFADVQK 867
                 7*******9886666666555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.086        42       1      17 [.      29      45 ..      29      73 .. 0.84
   2 ?    7.1   0.0     0.015       7.2       2      25 ..     635     658 ..     634     680 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.086
  RNA_helicase  1 iwlyGpsgeGKStlake 17
                  ++++G sg GKStla +
    AJA92260.1 29 VVISGLSGSGKSTLAFD 45
                  6899**********987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.015
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkk 25 
                    ++G sg GKStl++++  + l++
    AJA92260.1 635 SVTGVSGSGKSTLINDILLKALSS 658
                   689************965544433 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.5     0.072        35      15      54 ..     250     286 ..     232     290 .. 0.54
   2 ?    1.5   0.1      0.78   3.8e+02      42      50 ..     404     412 ..     388     432 .. 0.67
   3 ?   15.4   0.4   3.7e-05     0.018      15      51 ..     735     767 ..     723     772 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.072
  DnaJ_CXXCXGXG  15 ktCktCkGsG.vvreeqktlgpfvqqsqstCpeCeGtGkvi 54 
                    + C++C+ +  + + ++  ++  +++    C++C+G G  +
     AJA92260.1 250 NACPHCGITVgELEPRT--FS--FNSPFGMCNQCNGLGVKM 286
                    45666654431322222..21..122233677777776544 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.78
  DnaJ_CXXCXGXG  42 stCpeCeGt 50 
                    ++C +C+G+
     AJA92260.1 404 TPCLTCQGR 412
                    344444443 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.7e-05
  DnaJ_CXXCXGXG  15 ktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtG 51 
                     +C +C+G Gv++ e+    +f + +  +C+eC+G+ 
     AJA92260.1 735 GRCFACEGDGVKKIEM----QFLSDVYVKCDECNGKR 767
                    57********644444....36667889*******86 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.29   1.4e+02       2      17 ..      29      44 ..      28      53 .. 0.87
   2 ?   -2.4   0.0       8.2     4e+03     107     159 ..     386     438 ..     385     446 .. 0.73
   3 ?   -1.3   0.1       3.8   1.8e+03     113     155 ..     572     613 ..     569     624 .. 0.70
   4 ?    9.5   0.1    0.0018      0.85       2      32 ..     634     665 ..     633     688 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.29
                EEEE--TTSSHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvk 17
                v+i+G +G+GK+Tl  
  AJA92260.1 29 VVISGLSGSGKSTLAF 44
                799**********975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.2
                 TGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE--TTT CS
    NTPase_1 107 mElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevteen 159
                 mE  s++ +e +++ ++  +p l+   r+  ++al  +i++++ ++v +++ ++
  AJA92260.1 386 METDSESKREWLKQFMRD-TPCLTCQGRKLkPEALAVKINSKNIMEVCDLSIDS 438
                 899999999999998875.45555555555699999999999888888877665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.8
                 HHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE- CS
    NTPase_1 113 kfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfev 155
                 +f+ +++++L+++k v +   + +   ++ ++ire+k +k++ v
  AJA92260.1 572 VFEGTLKQILNNHKSVTGDYLKDHnLIKIEDKIREQK-GKIV-V 613
                 688899999*999999987766654777888999875.5544.3 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0018
                 EEEE--TTSSHHHHHHHHH.HHH...GGGEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvl.ellkssgvkvgG 32 
                 + +TG +G+GK+Tl++ +l ++l+s  +k +G
  AJA92260.1 634 ISVTGVSGSGKSTLINDILlKALSSYFYKTTG 665
                 679************99862556555556555 PP

>> Ssu72  Ssu72-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.54   2.6e+02      54     121 ..     162     230 ..     153     246 .. 0.78
   2 ?   10.4   0.0    0.0007      0.34      15      66 ..     333     384 ..     322     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.54
                 S-HHHHHHHHHHHHHHHHHHTSHHHHHHHHHHH-SS--BGGG---.--SEEEESS...HHHHHHHHHHHHH CS
       Ssu72  54 tsyeeiyedLkskdkelyeanGllkmldrnrkiKkaPerwqeaeekkfdvvitce...ervfdavvedlls 121
                  +ye+++e++k++  +  + nG + +l+ +   K   ++w+++e  ++d +i+      r+f+ +   l++
  AJA92260.1 162 GTYEKLFEQMKKDGYSRARVNGEIILLEDE-FPKLDRQKWHNIEI-VVDRIIASKsdkSRIFEGIQTALKA 230
                 6899******9999999999**99988865.569999*****988.8998887641225777777766655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0007
                 HHHHHHHHHTT-EEEEEE-SSSEEEEESSTTSEEEE-TTS-HHHHHHHHHHH CS
       Ssu72  15 meahkvLkkagfkvkSfGtgsavrLPgpsidkpnvyeFgtsyeeiyedLksk 66 
                 m   +++k++++kv+ +Gt++++++  ++ ++  ++e++ ++e + ++L++k
  AJA92260.1 333 MTPMNQMKSKQIKVILYGTEDVMKFSYEAKTSDTIWEYTDAFEGVLNNLQRK 384
                 55668899*****************************************998 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.23   1.1e+02      21      46 ..      18      43 ..       8      54 .. 0.79
   2 ?    8.1   0.0    0.0024       1.2      31      50 ..     633     652 ..     617     658 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.23
                HHGGG-S-SEEEEEEE-TTSSHHHHH CS
        MeaB 21 rllakaGraqvvGltGvPGaGkstlv 46
                ++  +  + + v + G+ G+Gkstl 
  AJA92260.1 18 NIDVNIPKNKIVVISGLSGSGKSTLA 43
                5555666778999***********85 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
                 EEEEEE-TTSSHHHHHHHHH CS
        MeaB  31 vvGltGvPGaGkstlvealg 50 
                  + +tGv G+Gkstl++ + 
  AJA92260.1 633 LISVTGVSGSGKSTLINDIL 652
                 5889************9875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.063        30      18      34 ..      26      42 ..      21      73 .. 0.86
   2 ?    5.0   0.1     0.036        17      22      39 ..     635     653 ..     631     677 .. 0.78
   3 ?   -2.0   0.0         5   2.4e+03      86     111 ..     845     874 ..     818     885 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
      AAA_30 18 drvavltGpAGtGKtta 34
                ++++v+ G  G+GK+t+
  AJA92260.1 26 NKIVVISGLSGSGKSTL 42
                5699***********97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.036
      AAA_30  22 vltGpAGtGKttalkal.r 39 
                  +tG+ G+GK+t+++ +  
  AJA92260.1 635 SVTGVSGSGKSTLINDIlL 653
                 589**********998744 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5
      AAA_30  86 lepgtllivDEagmv....dtkqlaallka 111
                  + +tl+i DE        d ++l ++l++
  AJA92260.1 845 GTGKTLYILDEPTTGlhfaDVQKLLDVLNR 874
                 234477888875432222244444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00014     0.066       2      35 ..       6      42 ..       5      46 .. 0.86
   2 ?   -2.1   1.9       9.4   4.6e+03     116     143 ..     427     454 ..     337     484 .. 0.42
   3 ?    7.0   0.1     0.015       7.3      21      39 ..     633     651 ..     571     687 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
      AAA_23  2 LkienfrsfrdqeidF...skgltlItGpNGaGKTTi 35
                Lk+++ r ++ ++id    ++++++I+G  G+GK+T+
  AJA92260.1  6 LKVRGARHHNLKNIDVnipKNKIVVISGLSGSGKSTL 42
                788888888777777777999***************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 9.4
      AAA_23 116 eleqfisellgskkiilnlilflgqerf 143
                 +  +  + +++s+++ +n + + + e+f
  AJA92260.1 427 NIMEVCDLSIDSSYEFFNKLELTDTEQF 454
                 1112222233333334444444444432 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.015
      AAA_23  21 ltlItGpNGaGKTTildAi 39 
                 l  +tG  G+GK+T+++ i
  AJA92260.1 633 LISVTGVSGSGKSTLINDI 651
                 66789***********755 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.32   1.6e+02       1      16 [.      28      43 ..      28      70 .. 0.84
   2 ?    7.8   0.1     0.005       2.4       1      19 [.     633     651 ..     633     667 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.32
         PRK  1 vIgvagsSGaGkttva 16
                ++ ++g SG+Gk+t+a
  AJA92260.1 28 IVVISGLSGSGKSTLA 43
                57799*********86 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.005
         PRK   1 vIgvagsSGaGkttvarkl 19 
                 +I+v+g SG+Gk+t+ + +
  AJA92260.1 633 LISVTGVSGSGKSTLINDI 651
                 69************87654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.062        30       2      16 ..      29      43 ..      28      93 .. 0.70
   2 ?    4.6   0.2     0.071        35       2      18 ..     634     650 ..     633     664 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
      AAA_28  2 ivitGgestGKTtll 16
                +vi+G +++GK+tl+
  AJA92260.1 29 VVISGLSGSGKSTLA 43
                8*************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.071
      AAA_28   2 ivitGgestGKTtllea 18 
                 i +tG +++GK+tl++ 
  AJA92260.1 634 ISVTGVSGSGKSTLIND 650
                 779***********976 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   4.6       3.5   1.7e+03      14      40 ..      16      43 ..      14     251 .. 0.88
   2 ?   11.8   0.3   0.00031      0.15     199     369 .]     378     551 ..     295     551 .. 0.59
   3 ?    0.4   0.1      0.89   4.3e+02      25      55 ..     633     674 ..     616     699 .. 0.64
   4 ?    5.5   0.0     0.024        12     319     365 ..     843     888 ..     777     892 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.5
      AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsil 40
                lk++++++ ++ + v+ G  +sGKS+++
  AJA92260.1 16 LKNIDVNIPKNkIVVISGLSGSGKSTLA 43
                6777777777769999*********974 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00031
      AAA_15 199 lisakRnvsdedsekkssllgklkekileealqekl......eeelteklkeiqeklkeid.kklaeelkkilkkkidkikkfnykgkkneeieik... 287
                 l++ +R++ ++dse+k+++l + ++++               ++ + e+l    ++ + ++  +l+ + ++++++k++   +++ +++ + ++eik   
  AJA92260.1 378 LNNLQRKFMETDSESKREWLKQFMRDT--------PcltcqgRKLKPEALAVKINSKNIMEvCDLSIDSSYEFFNKLEL-TDTEQFIARDILKEIKerl 467
                 233344444444444444444443333........02223332222222222222222222123333444556666555.3555556666666666888 PP

      AAA_15 288 ..........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                              + + +  + G ++ + l+++i ++  +       v+++++EP + LH      lik+l +l + ++  vi+  H + ii
  AJA92260.1 468 eflrnvglnyLSLNRSSATLSGGESQRIRLATQIGSNLTG-------VLYVLDEPTIGLHQRDNARLIKTLSKLRDLGN-TVIVVEHDEEII 551
                 8777774444223333334456888888888888888888.......*****************************998.899998988886 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.89
      AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn.............k 55 
                 l  + G  +sGKS++++ + l++  + +++              
  AJA92260.1 633 LISVTGVSGSGKSTLINDI-LLKALS-SYFykttglpgkhkdvA 674
                 666778889*******988.555544.44446777777664441 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.024
      AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                 ++ +   +++++EP + LH    + l + l +l+n ++  vi+  H+
  AJA92260.1 843 KRGTGKTLYILDEPTTGLHFADVQKLLDVLNRLVNVGN-TVIVIEHN 888
                 44566789*****************************9.66665555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3    0.0068       3.3       2      10 ..     122     130 ..     121     133 .. 0.87
   2 ?    4.1   0.3     0.082        40      16      20 ..     252     256 ..     247     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0068
  zinc_ribbon_2   2 CpnCGaelq 10 
                    C+nCG++++
     AJA92260.1 122 CTNCGRKIS 130
                    *******97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.082
  zinc_ribbon_2  16 CpyCG 20 
                    Cp+CG
     AJA92260.1 252 CPHCG 256
                    66665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.053        26       2      20 ..      26      44 ..      25      54 .. 0.86
   2 ?    1.2   0.0      0.52   2.5e+02     110     133 ..     526     549 ..     517     554 .. 0.69
   3 ?    4.1   0.0      0.07        34       6      22 ..     635     651 ..     632     661 .. 0.86
   4 ?   -1.4   0.1       3.2   1.6e+03     110     131 ..     867     888 ..     863     893 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.053
      AAA_24  2 klkiliyGpsgiGKTtlak 20
                ++ ++i G sg+GK+tla 
  AJA92260.1 26 NKIVVISGLSGSGKSTLAF 44
                6678999**********96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.52
      AAA_24 110 efrrllkklqelrknvifiahekt 133
                 +++++l kl++l+++vi++ h ++
  AJA92260.1 526 RLIKTLSKLRDLGNTVIVVEHDEE 549
                 345555666666669999999765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.07
      AAA_24   6 liyGpsgiGKTtlakel 22 
                  ++G sg+GK+tl++ +
  AJA92260.1 635 SVTGVSGSGKSTLINDI 651
                 689**********9876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.2
      AAA_24 110 efrrllkklqelrknvifiahe 131
                 ++ ++l++l +++++vi+i h 
  AJA92260.1 867 KLLDVLNRLVNVGNTVIVIEHN 888
                 56788999999999*****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (938 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.92u 0.27s 00:00:01.19 Elapsed: 00:00:00.49
# Mc/sec: 5810.33
//
Query:       AJA92261.1  [L=462]
Description: dihydroorotase, multifunctional complex type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-19   68.3   0.1    1.9e-15   57.1   0.0    2.5  2  Amidohydro_1  Amidohydrolase family
    1.1e-14   54.9   0.0    1.5e-08   34.6   0.0    2.8  3  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0001      0.92       3      37 ..      52      74 ..      50     132 .. 0.69
   2 !   57.1   0.0   2.1e-19   1.9e-15     127     344 .]     171     441 ..     166     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0001
                  EE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHH CS
  Amidohydro_1  3 lPGlIDaHvHleqsllrgatledwlvppetaaeal 37
                  +PGl+D HvH+  +            +p + a+ +
    AJA92261.1 52 IPGLVDPHVHYGVY------------SPIDQAAIS 74
                  8**********744............222222222 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 2.1e-19
                   CCSHHHHHHHHHHHHHHHTTEEEEEE.......TSSCHHHHHHHHHHTTTEEEETTTTSTCC...HHTTTHCCEEEHCTCEEE.....HH....... CS
  Amidohydro_1 127 pafsdeelkealkeakkrdlpvaiHa.......letkgevedaeaafgetiehgthlevaes...lglldeiklilahgvhlt.....pt....... 201
                   + +++e++++++k a+  + pv +Ha       ++ k e+e           h ++  + es      +++i++i + g  ++     ++       
    AJA92261.1 171 VNVTNELVEKIVKNAASLKCPVLVHAedyqecsCGMKTEKEKN---------HDGLNAWSESrspNFEAKSIQIICEYGRKYDcqiyfVHigsklal 258
                   6789999999999999999999999966333333333333333.........333333333333445556678887777777765554224445666 PP

                   .HHHHHHHHHHHHCEE...HHHHHHHH.................SEHHHHHHHHHHHHTSCEEEEEECT.....................TSSCCG. CS
  Amidohydro_1 202 .eaellkerlkeagva...hcpfsnsi.................lrsgrealrkaldeGvkvglgtDga.....................asgnsl. 255
                    +++  k+++ ++ v    h                         + +++ +++al+++ + ++gtD++                     + g sl 
    AJA92261.1 259 dKIKEEKKKGTKIFVEtcpH---YLTLshetqtgylakvmppirTNNDVQSVWNALQNNEIDTIGTDHVanqlklklggddvwgalagfpGIGTSLp 352
                   66777666655555555553...33334447889999999999999***********************8998888777777766444443333331 PP

                   GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT..............CGGGTTTCTSEEEEEEE CS
  Amidohydro_1 256 nlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi..............laafvglkkdgnvkkvi 338
                    ll e++++               + l+++++++++n Ak++gl+  +Gs+e+G+dAD++++dl++              +  + g++ +g+++k+i
    AJA92261.1 353 ILLSEGINKN------------R-INLNQLVNLTSTNSAKIFGLS-GKGSLEKGYDADITMIDLKKeekvspelfggfsdYLVYDGWNLKGWPVKTI 435
                   2233344444............4.9*******************7.******************4445678899*********************** PP

                   ETTEEE CS
  Amidohydro_1 339 vkGklv 344
                   v+G++v
    AJA92261.1 436 VRGTVV 441
                   ***987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.6e-07    0.0042       4      49 ..      45      89 ..      42     100 .. 0.90
   2 ?   -0.3   0.0     0.063   5.7e+02     230     288 ..     138     201 ..     106     216 .. 0.72
   3 !   34.6   0.0   1.7e-12   1.5e-08     405     472 ..     361     441 ..     325     442 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-07
  Amidohydro_3  4 DakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavr 49
                  + +G++ +PG+vD+H H +g+ + +  +  +++++ ++ gv+t++r
    AJA92261.1 45 NGSGLVSIPGLVDPHVH-YGVYSPIDQAAISESHAAAIGGVTTMIR 89
                  5579999**********.999999999999999***********98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.063
  Amidohydro_3 230 tigavklfadgvlgsrtalltepyf......tgwpdfedealaelvaaadergldvaihaigdaa 288
                   +i ++k+  ++ ++  ++++            ++ +++ e ++++v++a+  +++v +ha +++ 
    AJA92261.1 138 KIISFKIYMNLGGDVGHVYMEMN-PgeekliAAEVNVTNELVEKIVKNAASLKCPVLVHAEDYQE 201
                   55556666665555666665543.135665555556666669*****************998765 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 1.7e-12
  Amidohydro_3 405 deelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear..................vrltvvdGrvv 472
                   ++++ l++++ l+++++Ak++gl+ + G+Le+G+dAD++++d ++  +v p+     +                  +++t+v+G vv
    AJA92261.1 361 KNRINLNQLVNLTSTNSAKIFGLSGK-GSLEKGYDADITMIDlKKEEKVSPE-----LfggfsdylvydgwnlkgwPVKTIVRGTVV 441
                   57899********************8.***************5555555544.....344458889999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3195.85
//
Query:       AJA92262.1  [L=54]
Description: hypothetical protein T478_0953 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 419.55
//
Query:       AJA92263.1  [L=272]
Description: oxidoreductase NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-10   39.5   0.0    2.5e-09   37.8   0.0    1.8  2  NAD_binding_1    Oxidoreductase NAD-binding domain
    5.3e-09   35.7   6.4    1.1e-08   34.7   6.4    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0068   16.7   0.0      0.015   15.6   0.0    1.6  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.048   13.8   0.0       0.11   12.6   0.0    1.7  1  FAD_binding_8    FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.73   3.3e+03      63     100 ..      16      51 ..       1      60 [. 0.66
   2 !   37.8   0.0   5.6e-13   2.5e-09       1     106 [.     109     203 ..     109     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.73
                    ESSCTTTSSSEESSHHHHHHHHHHHHSSTTEEEEEECS CS
  NAD_binding_1  63 vsreeagweggkgrvqdalleellslkkeethvyvCGp 100
                    ++  +++++ ++ + +d+ll ++l+   + +++ + G 
     AJA92263.1  16 EKIIDETPTVRTLYFKDSLLANVLP--GQFAMIWIPGV 51 
                    5556777888888999999888888..77777777775 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 5.6e-13
                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHHHHHHHHHHSSTTEEEE CS
  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqdalleellslkkeethvy 96 
                    +i+gGtG+ P++ +++     +++ ++++++ G +t+++++++e  ++l + +++  ++++v   +e+g+ g+kg+v+d l e+ll+ k++ + +y
     AJA92263.1 109 LIGGGTGLVPLMRLIK---F-SNPSNHITVLMGSQTKNEVFFEETAKKLLEHNSH--EIIPV---TEDGSYGEKGYVTDIL-ENLLE-KNSYDAIY 193
                    79********866554...3.367899**********************666666..78999...77788889*****988.99999.89****** PP

                    EECSHHHHHH CS
  NAD_binding_1  97 vCGppgMika 106
                     CGp+ M+  
     AJA92263.1 194 TCGPELMMYK 203
                    *****99965 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   6.4   2.4e-12   1.1e-08       1      41 [.     220     252 ..     220     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2.4e-12
                      ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
  DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                      e++M+CGvG+C++C+v            +C+dG vFd+d +
       AJA92263.1 220 ERMMKCGVGICGSCCVND--------DLACRDGTVFDGDHL 252
                      89***************9........489*********976 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.4e-06     0.015      30      97 ..      38      99 ..      13     100 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-06
                   --TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS-TT-EEEEEEEE-SE CS
  FAD_binding_6 30 lpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdelkigdtleikGPlGkf 97
                    ++Gq+ ++ ++  +e  +    ++s+en+  +  l v+  + G+ s aL +l +g+++ ++GP+G++
     AJA92263.1 38 VLPGQFAMIWIPGVNE--LPMSVMVSAEND--QAALTVR--KRGESSTALYNLSVGQQIGVRGPYGNA 99
                   5667777777773333..333333444444..4455676..68***********************86 PP

>> FAD_binding_8  FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05      0.11      29      88 ..      37     123 ..      24     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
  FAD_binding_8  29 kykaGqyvyinipslsklfwqsHPFtiasapeddklslvikvksgltkklakkllsssk................................k 88 
                    +  +Gq++ i ip +++l     P +++ ++e+d+  l ++++++ ++ l++  + ++                                  
     AJA92263.1  37 NVLPGQFAMIWIPGVNEL-----PMSVMVSAENDQAALTVRKRGESSTALYNLSVGQQIgvrgpygnafeikngkilligggtglvplmrlI 123
                    5679************99.....**************************9998776633566666655555555555555555555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2013.33
//
Query:       AJA92264.1  [L=744]
Description: AAA family ATPase, CDC48 subfamily [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     7e-100  330.7   0.2    3.1e-49  166.8   0.0    2.6  2  AAA              ATPase family associated with various cellul
    1.6e-29  101.9   0.1    5.9e-29  100.1   0.1    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
      1e-19   70.0   2.0    3.1e-11   42.9   0.0    3.3  2  AAA_lid_3        AAA+ lid domain
    4.6e-16   59.4   0.2      4e-07   30.3   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    4.3e-15   55.8   0.0    7.8e-09   35.5   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      6e-15   56.0   0.1    7.4e-06   26.5   0.0    3.5  2  AAA_16           AAA ATPase domain
      1e-10   41.4   0.1    0.00014   21.2   0.0    2.6  2  TIP49            TIP49 P-loop domain
    4.5e-10   39.9   0.4     0.0026   18.0   0.0    4.1  3  AAA_22           AAA domain
    2.3e-09   37.6   0.0      0.002   18.3   0.0    2.5  2  AAA_33           AAA domain
    2.8e-09   37.1   0.0     0.0013   18.8   0.0    3.1  3  AAA_14           AAA domain
      3e-09   37.0   0.8     0.0012   18.8   0.1    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
      9e-09   35.0   0.1    2.3e-08   33.7   0.1    1.7  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    2.1e-07   30.8   0.0     0.0079   16.0   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    2.5e-07   30.6   0.1      0.052   13.2   0.0    3.3  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-06   28.7   0.0      0.046   14.1   0.0    2.7  2  RNA_helicase     RNA helicase
    1.8e-06   27.5   1.3       0.11   11.8   0.0    3.7  3  ATPase           KaiC
    2.1e-06   27.4   0.0      0.036   13.6   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    3.2e-06   27.7   0.1      0.029   14.9   0.0    3.2  2  AAA_18           AAA domain
    3.4e-06   27.1   0.0     0.0014   18.5   0.0    2.5  2  Bac_DnaA         Bacterial dnaA  protein
    7.3e-06   26.0   0.1       0.19   11.7   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.2e-05   25.1   0.0      0.036   13.8   0.0    2.7  2  AAA_24           AAA domain
    1.4e-05   25.4   0.1      0.027   14.7   0.0    2.7  2  AAA_28           AAA domain
    1.7e-05   24.3   1.2      0.041   13.3   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.8e-05   22.6   0.2       0.36   10.3   0.0    2.4  2  PhoH             PhoH-like protein
    0.00011   21.5   0.1       0.15   11.3   0.0    2.9  2  Zeta_toxin       Zeta toxin
    0.00014   21.9   1.0      0.068   13.1   0.0    4.0  4  ATPase_2         ATPase domain predominantly from Archaea
     0.0002   21.3   0.1        1.7    8.5   0.0    3.5  4  NACHT            NACHT domain
    0.00031   20.0   0.0       0.12   11.6   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    0.00031   21.3   0.0       0.83   10.2   0.0    2.6  2  ABC_tran         ABC transporter
    0.00033   19.9   0.0       0.45    9.7   0.0    2.8  2  NB-ARC           NB-ARC domain
    0.00064   19.5   0.4        1.6    8.4   0.1    2.8  2  AAA_30           AAA domain
    0.00071   19.4   0.0       0.53   10.2   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
      0.001   18.8   0.1        1.2    8.9   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
     0.0016   17.8   0.3        0.4    9.9   0.0    2.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0018   17.4   0.0       0.32   10.1   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0042   16.9   0.8       0.71    9.6   0.0    2.7  3  AAA_11           AAA domain
     0.0069   16.4   0.0        2.2    8.3   0.0    2.7  2  ResIII           Type III restriction enzyme, res subunit
     0.0073   16.4   0.0        2.6    8.2   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0074   16.0   0.1        5.8    6.6   0.0    3.6  3  Guanylate_kin    Guanylate kinase
  ------ inclusion threshold ------
      0.011   15.7   2.5        3.9    7.6   0.5    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
      0.012   15.5   0.4         10    6.0   0.0    3.8  3  NTPase_1         NTPase
      0.015   14.9  10.1        1.4    8.5   0.2    4.5  5  AAA_25           AAA domain
      0.016   15.7   0.6        1.2    9.5   0.0    3.3  2  AAA_17           AAA domain
      0.018   14.8   0.1        3.8    7.3   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.019   14.8   0.0        2.8    7.8   0.0    2.8  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.024   14.0   0.0        6.6    6.1   0.0    2.7  2  TniB             Bacterial TniB protein
      0.026   14.9   2.6        3.6    7.9   0.1    3.7  3  AAA_19           AAA domain
       0.03   14.2   0.0         11    5.9   0.0    3.1  3  Rad17            Rad17 P-loop domain
      0.033   13.3   0.0          8    5.4   0.0    2.3  2  T2SSE            Type II/IV secretion system protein
      0.064   12.6   0.1         13    5.1   0.0    2.5  2  IPT              Isopentenyl transferase
      0.067   12.9   0.0          3    7.5   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.077   11.9   0.0         12    4.6   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.083   12.5   0.0        6.4    6.4   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.16   11.7   0.0         23    4.7   0.0    2.9  3  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.21   11.7   0.1         12    6.0   0.0    2.5  2  Torsin           Torsin


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.0   9.6e-52   3.1e-49       1     131 [.     214     343 ..     214     344 .. 0.98
   2 !  161.4   0.0   4.3e-50   1.4e-47       1     132 []     492     623 ..     492     623 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 9.6e-52
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                 vllyGppGtGKTllakava+e++++f++isg+e++sk+ gese+++re+fkea+eka psi+f+DEid++a++r++ + e+e+rvv+q+l+ +dg++ +
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFISISGPEIMSKFYGESEARLREIFKEAREKA-PSIIFVDEIDSIAPKREEVTGEVERRVVSQMLSLMDGLEAR 311
                 79******************************************************9.****************************************6 PP

                 SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
         AAA 100 eskvivigatnrpdkldpallr.gRfdrkieie 131
                  +kvivi atnrp+ +dpal+r gRfdr+iei+
  AJA92264.1 312 -GKVIVISATNRPNAIDPALRRpGRFDREIEIK 343
                 .77***************************986 PP

  == domain 2  score: 161.4 bits;  conditional E-value: 4.3e-50
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkk 98 
                 +ll+Gp GtGKTl+akava+e++++f+++ g+ellsk+vgese+ ire+fk+a+++a p+++f+DEid++a+ r  g+e+ ++ervv+qLlteldg+++
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSVRGPELLSKWVGESERGIREIFKRARQSA-PCVIFFDEIDSIAPIRgAGGETAVTERVVSQLLTELDGMEN 589
                 69******************************************************9.****************9999********************* PP

                 SSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
         AAA  99 keskvivigatnrpdkldpallr.gRfdrkieiel 132
                   + v+v++atnr d++dpallr gRfd++i+i+l
  AJA92264.1 590 M-HGVVVLAATNRADMIDPALLRpGRFDKIIQIPL 623
                 7.55****************************985 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.1   1.8e-31   5.9e-29       2      84 ..       8      90 ..       7      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.8e-31
                EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE- CS
     CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrkae 84
                L+V ea+ +dvgrg++rid + m+ l+ ++gdv+e++gkr+Tva+++p++p+degkgiIr+dg+ R+n g+ iGd++tV+k++
  AJA92264.1  8 LKVLEAYTRDVGRGVARIDYDSMDTLNASTGDVIELKGKRRTVAKCLPLYPSDEGKGIIRIDGLGRNNSGIAIGDTITVKKIK 90
                9*******************************************************************************986 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   9.6e-14   3.1e-11       2      41 ..     372     411 ..     371     432 .. 0.83
   2 !   23.5   1.3   1.1e-07   3.4e-05       2      44 ..     651     720 ..     650     721 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 9.6e-14
   AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                 v ++++A+ ++Gy+GADl+ lc+eAa+ +lrr ++e++ e
  AJA92264.1 372 VKIEKIAAVSHGYVGADLEYLCKEAAMKCLRRLLPELNLE 411
                 789*****************************77765544 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.1e-07
   AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr..........................gik.eitmedfe 44 
                 +d++++Ae+T+G S AD a++ + A+ l + +                           ++ ++tm++fe
  AJA92264.1 651 IDFDKIAELTDGLSSADVASIANTAVSLVVHEhldnaipdkdlsdeetkkfvdeiekkATDaKVTMKHFE 720
                 8*****************************9956666665555555555555555443333247777776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.2e-09     4e-07       6     107 ..     214     309 ..     211     368 .. 0.90
   2 !   25.4   0.0   3.9e-08   1.3e-05       6     105 ..     492     586 ..     489     592 .. 0.91
   3 ?   -1.8   0.2       9.1     3e+03      73      82 ..     701     710 ..     693     723 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.2e-09
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqrdLLq 101
                 +ll gp g+Gkt+laka+a+  ++    ++i +   e++     + + +++   ++  ++a e+   i+++DEid i+pk e+ + +v r  V+  +L 
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNA----HFISISGPEIMS----KFYGESEARLREIFKEAREKApsIIFVDEIDSIAPKrEEVTGEVERR-VVSQMLS 303
                 5789******************96....************....99999999999999999999999************988888888886.6677889 PP

                 HHH--E CS
       AAA_2 102 ileggt 107
                 +++g +
  AJA92264.1 304 LMDGLE 309
                 999855 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3.9e-08
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----.---------HHHHHHHHH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk.essgadvSregVqrdLLq 101
                 ill gp+g+Gkt++aka+a   ++    +++ +   ell     + + +++ g ++  ++a ++   ++++DEid i+p  +  g+    e V+  LL 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEA----NFVSVRGPELLS----KWVGESERGIREIFKRARQSApcVIFFDEIDSIAPIrGAGGETAVTERVVSQLLT 582
                 7999***************99985....************....999999**************9**************97777777888899999988 PP

                 HHH- CS
       AAA_2 102 ileg 105
                  l+g
  AJA92264.1 583 ELDG 586
                 7776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9.1
                 EEETGGG--- CS
       AAA_2  73 llDEidKihp 82 
                 ++DEi+K + 
  AJA92264.1 701 FVDEIEKKAT 710
                 89****9877 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   2.4e-11   7.8e-09      32     104 ..     210     290 ..     188     332 .. 0.82
   2 !   17.2   0.0     1e-05    0.0033      35      94 ..     491     558 ..     482     565 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.4e-11
      RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                 a   vllyGpPG Gkt lak +a+e ++++ + sgP +      e ++ l  ++++ +ek   ++f+dei  ++++ eev 
  AJA92264.1 210 APKGVLLYGPPGTGKTLLAKAVANESNAHFISISGPEImskfygESEARLREIFKEAREKapSIIFVDEIDSIAPKREEVT 290
                 66779*******************************993333333345566677666554337*************99985 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1e-05
      RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideih 94 
                  +ll+Gp G Gkt +ak +a+e ++++ +  gP l      e ++ +  ++++ +++   v+f dei 
  AJA92264.1 491 GILLHGPSGTGKTLMAKAVATESEANFVSVRGPELlskwvgESERGIREIFKRARQSApcVIFFDEID 558
                 58*******************************87332222334555666655544433366666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.3e-08   7.4e-06      18     139 ..     205     316 ..     199     318 .. 0.71
   2 !   23.7   0.0   1.6e-07   5.1e-05      16     132 ..     481     589 ..     479     596 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.3e-08
      AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawrekleealaavpelagae 115
                 ++    p  vll+G++G+GK+ l++++++   +++++f++    +      +s +      e  lr++  e  e+a    + +++++ +    e++g+ 
  AJA92264.1 205 KLGIEAPKGVLLYGPPGTGKTLLAKAVAN---ESNAHFISISGPEI-----MSKFYGES--EARLREIFKEaREKAPSIIFVDEIDSIAPKREEVTGEV 293
                 555667899*******************7...55577999999999.....44444433..24444444441444455555566666666888888888 PP

      AAA_16 116 asrllellkrllallsrderplvl 139
                 ++r+  ++ +l++ l+ +++ +++
  AJA92264.1 294 ERRVVSQMLSLMDGLEARGK-VIV 316
                 899**999999999999788.444 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.6e-07
      AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelaga 114
                 ++++    p+ +ll+G+sG+GK+ ++++++++ e++   f++ +  +l     +s ++   +r ++ +  +++ +sa    + +++++ +  ++ + g+
  AJA92264.1 481 YDKLGHKMPRGILLHGPSGTGKTLMAKAVATESEAN---FVSVRGPEL-----LSKWVGESER-GIREIFKRARQSAPCVIFFDEIDSIAP-IRGAGGE 569
                 667777889*********************988888...888777777.....4446666634.777777777777677777766665444.5555555 PP

      AAA_16 115 ea..srllellkrllallsr 132
                  a  +r+  +l   l+ +++
  AJA92264.1 570 TAvtERVVSQLLTELDGMEN 589
                 55666666666666665555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.4e-07   0.00014      50     103 ..     211     262 ..     204     311 .. 0.81
   2 !   17.4   0.0   6.3e-06    0.0021      47     103 ..     487     541 ..     483     546 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.4e-07
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqal 103
                  ++vLl Gp+gtGkt la a+++e +   +f+++sg e+ s     +e+ ++++
  AJA92264.1 211 PKGVLLYGPPGTGKTLLAKAVANESN--AHFISISGPEIMSKFYGESEARLREI 262
                 699********************965..89**********99888888754443 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.3e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
       TIP49  47 klaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqal 103
                 k+  r++Ll GpsgtGkt +a a++ e  ++  fv++ g e+ s  v  +e  + + +
  AJA92264.1 487 KMP-RGILLHGPSGTGKTLMAKAVATE--SEANFVSVRGPELLSKWVGESERgIREIF 541
                 454.9********************98..5689**********999988875244445 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     8e-06    0.0026       8      49 ..     214     246 ..     209     317 .. 0.68
   2 !   14.7   0.1   8.7e-05     0.028       8      39 ..     492     514 ..     487     530 .. 0.82
   3 ?    0.4   0.0       2.3   7.4e+02      85     106 ..     543     574 ..     525     603 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                 ++++G++GtGKT+l++ ++++          +++++++  p+
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANES---------NAHFISISGPE 246
                 689*****************98.........55555444333 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 8.7e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeer 39 
                 ++++G+sGtGKT+ ++ ++ +          +
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATES---------E 514
                 79***************99986.........3 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.3
      AAA_22  85 alrarav..ielliiDEaqhlr...s........e 106
                  +r      + ++  DE++ +             e
  AJA92264.1 543 RAR---QsaPCVIFFDEIDSIApirGaggetavtE 574
                 333...34459********9976641444444442 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     6e-06     0.002       2      79 ..     214     321 ..     214     343 .. 0.69
   2 !   16.8   0.0   1.8e-05    0.0058       2      45 ..     492     537 ..     492     602 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6e-06
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvldrlyqilnelarkalsag 70 
                 vll G+pG+GK+ la+ ++++    ++ +s ++++++ +g+ + +++                               +v+ r+  ++  l +   ++g
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNahFISISGPEIMSKFYGESEARLReifkearekapsiifvdeidsiapkreeVTGEVERRVVSQMLSLMDGLEARG 312
                 7899***************999999999*****999999977766665555555555666666666666554433222244444444445555444555 PP

      AAA_33  71 rnvildatn 79 
                 + +++ atn
  AJA92264.1 313 KVIVISATN 321
                 555556665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.8e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsk 45 
                 +ll+G++G+GK+  a+ ++ +    +v ++ ++l+++ +g+ ++ +
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEanFVSVRGPELLSKWVGESERGI 537
                 689****************999988999999999988888655444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     4e-06    0.0013       4      84 ..     213     290 ..     210     320 .. 0.76
   2 !   13.9   0.0   0.00013     0.042       5      77 ..     492     561 ..     489     594 .. 0.78
   3 ?   -0.3   0.1       3.1     1e+03      52      90 ..     684     730 ..     646     736 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4e-06
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqevpewekalk 84 
                  +++ G+  +GKT l+k +++e+     +++ i+  +   k + ++e +l e+++e  +e+  +++f DEi  +   ++ + 
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVANESN---AHFISISGPEIMSKFYGESEaRLREIFKEA-REKAPSIIFVDEIDSIAPKREEVT 290
                 57899***************9988...999999999988866666553555666665.455899*******99855554444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00013
      AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                 +++ G+  +GKT ++k ++ e+     +++ +   +   k   ++e+ +++i+++++++   ++f+DEi  + 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESE---ANFVSVRGPELLSKWVGESERGIREIFKRARQSAPCVIFFDEIDSIA 561
                 6899**************98887...7777777777666666666655666666655568999******9874 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.1
      AAA_14  52 llelilek.lkeekktylflDEiqev........pewekalkslvdeg 90 
                 l+++i +k l++ ++t  f DEi +         +++e+a++++ +++
  AJA92264.1 684 LDNAIPDKdLSD-EETKKFVDEIEKKatdakvtmKHFEEAVRKVREQK 730
                 444555553333.66668999999887777777777777777777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.7e-06    0.0012       1     135 [.     213     331 ..     213     333 .. 0.68
   2 !   13.3   0.1   0.00018      0.06       2      79 ..     492     562 ..     491     611 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-06
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--...HHHHHHHHHHHHSSEE CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae...sevlnsLlslleerrl 94 
                 +vlL GppGtgK+ la+ +a   n+ +  + +++ +++  + g+ e        +  ++ ++ar   ++i+++DE++ +     ev++++ +    + l
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVANESNAHFISISGPEIMSK--FYGESE-------ARLREIFKEARekAPSIIFVDEIDSIApkrEEVTGEVERRVVSQML 302
                 59***********************9999999998865..445544.......3446666677756778999999998872223455555555555555 PP

                 E..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
       AAA_5  95 lleeggelvkaknddllerfrviatanpldrslnelspalr 135
                 +l++g e  ++        + vi ++n+++     ++palr
  AJA92264.1 303 SLMDGLEARGK--------VIVISATNRPN----AIDPALR 331
                 55555444433........66666666666....6666665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00018
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--H CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraes 79 
                 +lL Gp+GtgK+ +a+ +a   +++++ v +++      l+ ++   ++ ++    +++ra +  ++++++DE++ + +
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSVRGPE------LLSKWV--GESERGIREIFKRARQsAPCVIFFDEIDSIAP 562
                 89****************999999999888887......566666..33333344555555557778888888887765 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   6.9e-11   2.3e-08       7      60 ..     110     164 ..     104     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 6.9e-11
                 CHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCC.SCEEECTSCCEEEST CS
     CDC48_2   7 maylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkg.pvgitetTeielgtk 60 
                 + yl +++++ p+ kGd v+++++g+ +++ V +++P+  +v +t +T  ++ +k
  AJA92264.1 110 ERYLADALESVPLIKGDNVMVPYFGGRLTFQVIGVTPAAdAVLVTQKTTFHIAEK 164
                 55***********************************98899******9999876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.4e-05    0.0079      44      74 ..     208     238 ..     200     280 .. 0.87
   2 !   12.3   0.0   0.00033      0.11      49      74 ..     491     516 ..     487     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-05
   IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavra 74 
                 ie+ ++++l Gp+G+GK+ la a++ e  ++
  AJA92264.1 208 IEAPKGVLLYGPPGTGKTLLAKAVANESNAH 238
                 6777899*****************9987655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00033
   IstB_IS21  49 nivllGpsGvGKshlaialgveavra 74 
                 +i+l GpsG+GK+ +a a+++e  ++
  AJA92264.1 491 GILLHGPSGTGKTLMAKAVATESEAN 516
                 689****************9987555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00017     0.054      21      57 ..     210     243 ..     201     326 .. 0.80
   2 !   13.2   0.0   0.00016     0.052      22      52 ..     489     516 ..     482     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                      SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
  Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavn 57 
                       +  vl+ G  GtGK+lla+a+ ++s+   ++f+++ 
       AJA92264.1 210 APKGVLLYGPPGTGKTLLAKAVANESN---AHFISIS 243
                      56789*****************98876...5566655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00016
                      SS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
  Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekp 52 
                      +  +l++G sGtGK+l+a+a+ ++s+   ++
       AJA92264.1 489 PRGILLHGPSGTGKTLMAKAVATESE---AN 516
                      5679****************998876...34 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00014     0.046       1      31 [.     214     244 ..     214     288 .. 0.84
   2 !   11.8   0.0   0.00073      0.24       1      26 [.     492     517 ..     492     556 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00014
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkk 31 
                   ++lyGp+g+GK++lak +a++   ++ +++ 
    AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFISISG 244
                   689**************99999888744444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00073
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                   i+l+Gpsg+GK+++ak +a++ + ++
    AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANF 517
                   689**************988766554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00035      0.11      11      38 ..     202     230 ..     199     252 .. 0.86
   2 ?    2.4   0.1      0.25        83     113     155 ..     264     309 ..     245     325 .. 0.65
   3 !    9.3   0.0     0.002      0.65      15      41 ..     485     511 ..     475     520 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
      ATPase  11 il.kgGipegrvvlitGepGtGKtifalq 38 
                 i+ k Gi   + vl++G pGtGKt++a+ 
  AJA92264.1 202 IFeKLGIEAPKGVLLYGPPGTGKTLLAKA 230
                 665679999999**************985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.25
      ATPase 113 eaikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                 +  +e+  + + +D i+++    +e + +v R+ + q+++ + +l+
  AJA92264.1 264 KEAREKAPSIIFVDEIDSIapkREEVTGEVERRVVSQMLSLMDGLE 309
                 3334444456666666666321555666778999999999887665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
      ATPase  15 GipegrvvlitGepGtGKtifalqFli 41 
                 G  + r +l+ G +GtGKt++a+  + 
  AJA92264.1 485 GHKMPRGILLHGPSGTGKTLMAKAVAT 511
                 55566779*************987655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00011     0.036      28      62 ..     206     239 ..     199     288 .. 0.84
   2 !   10.8   0.0   0.00077      0.25      34      58 ..     490     514 ..     480     522 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
       AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                 l +++ k vll+Gp GtGKt+++k + ++ +  ++
  AJA92264.1 206 LGIEAPKGVLLYGPPGTGKTLLAKAVANESN-AHF 239
                 55778899****************9998887.444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00077
       AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                 + +ll Gp+GtGKt+++k + ++ +
  AJA92264.1 490 RGILLHGPSGTGKTLMAKAVATESE 514
                 679**************99877766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     9e-05     0.029       1      25 [.     214     259 ..     214     332 .. 0.59
   2 !    9.0   0.0     0.006         2       1      22 [.     492     513 ..     492     561 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................g 25 
                 +ll G+pG+GKt lak+++++ +                       
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAhfisisgpeimskfygesearL 259
                 799***************8875335677777755555555553332 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.006
      AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                 Ill G++G+GKt +ak+++ + 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATES 513
                 89***************96653 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.4e-06    0.0014      37     180 ..     214     359 ..     205     384 .. 0.76
   2 ?    5.8   0.0     0.034        11      37      65 ..     492     520 ..     484     531 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.4e-06
                 EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT-HH.........HHHHHHHHHHH CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagkek.........tqeelfhtfna 125
                 +++yg+ G Gkt L ka++ne     ++++ + +++ e ++++    + +  e fke    +  ++ +D+i  +a k +         +  +++ +++ 
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANE-----SNAHFISISGPEIMSKFYGESEARLREIFKEAREkAPSIIFVDEIDSIAPKREevtgeverrVVSQMLSLMDG 307
                 89*************999875.....56777889***********999999999*998762557999*******9885322211111133456777888 PP

                 HHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
    Bac_DnaA 126 lleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                 l   gk +v+s+   P++++    r   rf++   ++i+ pd++ r +il+ + +
  AJA92264.1 308 LEARGKVIVISATNRPNAIDPAL-RRPGRFDR--EIEIKVPDKKGRQEILQIHTR 359
                 8889************9987654.34578887..567777999999999975544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.034
                 EEEE-SSSSSHHHHHHHHHHHHHHHSSSS CS
    Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapel 65 
                 ++++g++G Gkt + ka++ e ++n+ + 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSV 520
                 79*****************9998887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00088      0.29      14      48 ..     206     242 ..     187     256 .. 0.78
   2 !   11.7   0.0   0.00058      0.19      13      49 ..     483     521 ..     475     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00088
                 HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..-- CS
        TsaE  14 lakalgdvilLeGdLGaGKTtlvrglakalgve..ev 48 
                 l+ ++ + +lL+G+ G+GKT l++++a++ + +  ++
  AJA92264.1 206 LGIEAPKGVLLYGPPGTGKTLLAKAVANESNAHfiSI 242
                 333334569******************9987665555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00058
                 HHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
        TsaE  13 klakalgdvilLeGdLGaGKTtlvrglakalgve..evk 49 
                 kl++++ + ilL+G+ G+GKT +++++a + + +  +v+
  AJA92264.1 483 KLGHKMPRGILLHGPSGTGKTLMAKAVATESEANfvSVR 521
                 455555557*******************99877655555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00011     0.036       4      30 ..     213     241 ..     210     290 .. 0.74
   2 !    8.5   0.0    0.0047       1.5       3      22 ..     490     509 ..     488     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
      AAA_24   4 kiliyGpsgiGKTtlakel..gpkplfid 30 
                  +l+yGp+g+GKT lak    + ++ fi 
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVanESNAHFIS 241
                 589**************997766666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0047
      AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                 + il+ Gpsg+GKT +ak  
  AJA92264.1 490 RGILLHGPSGTGKTLMAKAV 509
                 5699************9976 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.2e-05     0.027       2      49 ..     214     266 ..     213     301 .. 0.80
   2 ?    7.8   0.0     0.011       3.6       2      31 ..     492     526 ..     491     551 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.2e-05
      AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileeklakgedalpwv 49 
                 + + G+++tGKT l++a a    a+ +++  pE++ +++ e  a+ +++ +++
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVAnesnAHFISISgPEIMSKFYGESEARLREIFKEA 266
                 6799***************5544446777799999999988888877766654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
      AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaa 31 
                 i + G+++tGKT +++a a +   +++ v  pE  
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATEseaNFVSVrgPELL 526
                 7899***************5544454444455555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00013     0.041      25      42 ..     214     231 ..     206     235 .. 0.90
   2 !    9.2   0.2    0.0022      0.72      25      43 ..     492     510 ..     486     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
  Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                   +ll+GppG+GKt+lak++
    AJA92264.1 214 VLLYGPPGTGKTLLAKAV 231
                   89*************987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                   +ll Gp+G+GKt++ak+++
    AJA92264.1 492 ILLHGPSGTGKTLMAKAVA 510
                   89*************9875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0011      0.36      21      41 ..     213     233 ..     203     240 .. 0.84
   2 !    9.8   0.0    0.0015      0.49      24      42 ..     494     512 ..     486     519 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                 EEEEE--TTSSTTHHHHHHHH CS
        PhoH  21 ivfaiGpaGtGKtylavalav 41 
                  v   Gp GtGKt+la a+a 
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVAN 233
                 57889***********99985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                 EE--TTSSTTHHHHHHHHH CS
        PhoH  24 aiGpaGtGKtylavalave 42 
                   Gp+GtGKt++a a+a e
  AJA92264.1 494 LHGPSGTGKTLMAKAVATE 512
                 68************99976 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00047      0.15      14      50 ..     209     243 ..     200     258 .. 0.86
   2 ?    6.8   0.0     0.011       3.5      14      50 ..     487     521 ..     482     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00047
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                 e Pk +ll G pG GK+ la+++++e   +  ++ ++
  AJA92264.1 209 EAPKGVLLYGPPGTGKTLLAKAVANES--NAHFISIS 243
                 78************************8..77777776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                 + P  ill G +G GK+ +a+++++e   + n+v + 
  AJA92264.1 487 KMPRGILLHGPSGTGKTLMAKAVATES--EANFVSVR 521
                 67889*********************8..88888775 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00021     0.068      20     122 ..     211     317 ..     200     331 .. 0.63
   2 ?    2.1   0.0      0.46   1.5e+02      23      45 ..     492     514 ..     482     521 .. 0.82
   3 ?    1.5   0.0       0.7   2.3e+02     110     225 ..     537     662 ..     518     666 .. 0.61
   4 ?   -1.8   0.4       7.2   2.3e+03      60      89 ..     696     726 ..     676     742 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00021
    ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdk....yviyyialreesiskldefie...eeeekkklekalgiavpkaeleeilkeksklvfkaiellle 111
                  + +++YGp g GKt L k ++++++  ++        ++++ +es+++l+e ++   e+  +  + + + +  p  + ee+  e  + v +++ +l++
  AJA92264.1 211 PKGVLLYGPPGTGKTLLAKAVANESNA-HFisisGPEIMSKFYGESEARLREIFKearEKAPSIIFVDEIDSIAP--KREEVTGEVERRVVSQMLSLMD 306
                 556799*********999999999854.44133312234445555555555544322233333333444433333..3455677888888889999999 PP

    ATPase_2 112 kikkkgkkiii 122
                  ++ +gk i+i
  AJA92264.1 307 GLEARGKVIVI 317
                 99999987776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.46
    ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                 +++ Gp g GKt + k +++++e
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESE 514
                 6789********99998887764 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.7
    ATPase_2 110 lekikkkgkk...iiiiiDelqklidlgln.....gaellvkeLlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnf 200
                 +++i k++++    +i++De+  +  +          e +v++Ll+ ++  +++ h +vv++++    +i+       + gr + i   +l  +  +++
  AJA92264.1 537 IREIFKRARQsapCVIFFDEIDSIAPIRGAggetaVTERVVSQLLTELDG-MENMHGVVVLAATNRADMID---PALLRPGRFDKIIQIPLPDKDGRKM 631
                 56677777777879999****99995544444444456667777777766.67777777777777777776...3334456666644444444444444 PP

    ATPase_2 201 lke.gfkel..eel...skedfeeiyryvGG 225
                 + e  +k++   +     k df++i ++++G
  AJA92264.1 632 VIEiHSKDIplADNnspDKIDFDKIAELTDG 662
                 4331344444422234556666666666666 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 7.2
    ATPase_2  60 esiskldefie.eeeekkklekalgiavpka 89 
                 e+++k+ + ie +  ++k   k++ +av+k+
  AJA92264.1 696 EETKKFVDEIEkKATDAKVTMKHFEEAVRKV 726
                 2222222222221222222222223333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0053       1.7       3      23 ..     214     234 ..     212     238 .. 0.89
   2 ?   -1.4   0.0       5.9   1.9e+03      62     137 ..     252     328 ..     245     356 .. 0.62
   3 !    7.9   0.0    0.0083       2.7       3      23 ..     492     512 ..     490     519 .. 0.89
   4 ?   -0.8   0.0       3.8   1.2e+03      62     111 ..     530     583 ..     521     606 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0053
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 v+l G++G GKT L++ +a +
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANE 234
                 799*************99875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.9
                 CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEECCCHHHHCT CS
       NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrpralrdlee 137
                 + e++a+ +e++++  e + ++ + +D +D ++ + ++   + +++v   + +l+ + l  + ++++++ +++ + +  
  AJA92264.1 252 YGESEARLREIFKEAREKAPSIIF-VDEIDSIAPKREEvtgEVERRVVSQMLSLMDG-LEARGKVIVISATNRPNAIDP 328
                 566777777777777777777776.58888888877778884444444455577777.333444444444444444554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0083
                 EEEEC-TTTCHHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklala 23 
                 ++l+G++G GKT +++ +a++
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATE 512
                 89**************99986 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3.8
                 CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..............HHH CS
       NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq.....kekqpvrtlLse 111
                   e+++ ++e +  ++++    ++ +D +D ++ + g+      +++ v +lL+e
  AJA92264.1 530 VGESERGIRE-IFKRARQSAPCVIFFDEIDSIAPIRGAggetaVTERVVSQLLTE 583
                 5555666666.55677777888899999999999999974444333344444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00036      0.12      54     115 ..     212     278 ..     157     328 .. 0.69
   2 ?    5.9   0.0     0.019       6.1      54      81 ..     490     517 ..     447     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
      DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrli..evek....edlkelpklvellrerperfilfvDD 115
                 + vLL+G  GtGK  l ka+ ne +++ + +   e+      e+ + l +++++ re+    i+fvD 
  AJA92264.1 212 KGVLLYGPPGTGKTLLAKAVANESNAHFISISgpEIMSkfygESEARLREIFKEAREK-APSIIFVDE 278
                 679********************99988655322443300003333444444444332.334666665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
      DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg 81 
                 + +LL G  GtGK  + ka+ +e +++ 
  AJA92264.1 490 RGILLHGPSGTGKTLMAKAVATESEANF 517
                 579*****************99987765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0025      0.83       7      37 ..     207     237 ..     205     330 .. 0.78
   2 ?    8.2   0.0      0.01       3.3      14      37 ..     492     515 ..     484     587 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0025
                 EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                  +++ + v + G+ G+GK+ L+k++a++++ 
  AJA92264.1 207 GIEAPKGVLLYGPPGTGKTLLAKAVANESNA 237
                 677778899*****************99875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.01
                 EEEEESTTSSHHHHHHHHTTSS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  14 vaivGenGaGKStLlkllagllkp 37 
                 + + G++G+GK+ ++k++a +++ 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEA 515
                 5689**************999864 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0014      0.45      22      44 ..     213     235 ..     200     242 .. 0.80
   2 !    6.8   0.0      0.01       3.2      23      44 ..     492     513 ..     479     523 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                 EEEEEESTTSSHHHHHHHHCCSH CS
      NB-ARC  22 vvalvGmgGvGKttlakqilnks 44 
                  v l+G +G GKt lak + n+s
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVANES 235
                 5889***************9995 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.01
                 EEEEESTTSSHHHHHHHHCCSH CS
      NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                 + l+G  G GKt +ak +  +s
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATES 513
                 789***********99998873 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.006       1.9      21      40 ..     214     233 ..     203     244 .. 0.84
   2 !    8.4   0.1    0.0048       1.6      22      45 ..     493     516 ..     485     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.006
      AAA_30  21 avltGpAGtGKttalkalre 40 
                 ++l Gp+GtGKt + ka+++
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVAN 233
                 5789**********999976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0048
      AAA_30  22 vltGpAGtGKttalkalreaweaa 45 
                 +l+Gp GtGKt + ka++   ea+
  AJA92264.1 493 LLHGPSGTGKTLMAKAVATESEAN 516
                 789************998776665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0016      0.53       2      31 ..     214     243 ..     213     321 .. 0.80
   2 ?    6.8   0.0     0.017       5.6       2      31 ..     492     521 ..     491     601 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
       AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                 vll g PG++ktll+ka+a+  +++f  i 
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFISIS 243
                 7999****************9999997764 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
       AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                 +ll+g  G++ktl++ka+a+  +++f  ++
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSVR 521
                 7999****************9999998765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.012       3.8       4      28 ..     217     241 ..     214     245 .. 0.90
   2 !    8.9   0.0    0.0036       1.2       2      27 ..     493     518 ..     492     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                     E-STTSSHHHHHHHHHHHHT-EEEE CS
  Cytidylate_kin   4 DGPagsGKssvaralaeklglkyld 28 
                      GP g+GK  +a+a+a++ ++++++
      AJA92264.1 217 YGPPGTGKTLLAKAVANESNAHFIS 241
                     6********************9987 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0036
                     EEE-STTSSHHHHHHHHHHHHT-EEE CS
  Cytidylate_kin   2 aiDGPagsGKssvaralaeklglkyl 27 
                      + GP+g+GK  +a+a+a++ +++++
      AJA92264.1 493 LLHGPSGTGKTLMAKAVATESEANFV 518
                     578****************9999887 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0012       0.4       4      65 ..     214     268 ..     211     292 .. 0.69
   2 ?    5.5   0.0     0.026       8.5       4      25 ..     492     513 ..     489     542 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
     DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafe 65 
                 vl  G +GtGKt+++ ++++e        +a+++s ++p+++ + + + + +  ++ +kea e
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANES-------NAHFISISGPEIMsKFYGESEARL-REIFKEARE 268
                 6789************999998.......555555555554325555555555.455555544 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.026
     DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                 +l +G +GtGKt+++ ++++e 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATES 513
                 6889***********9999987 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00098      0.32     117     138 ..     214     235 ..     212     239 .. 0.90
   2 ?    4.8   0.0      0.04        13     117     136 ..     492     511 ..     477     517 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00098
   Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                 v++yGp+ tGkt la+a a+ +
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANES 235
                 899**************99865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.04
   Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                 ++++Gp  tGkt +a+a a+
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVAT 511
                 7899*************997 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0022      0.71      17      42 ..     211     236 ..     197     276 .. 0.75
   2 ?    4.6   0.0     0.071        23      20      38 ..     492     510 ..     483     546 .. 0.81
   3 ?   -2.0   0.3       7.6   2.5e+03     123     147 ..     699     723 ..     655     740 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
      AAA_11  17 seitliqGPPGtgKTktivellsqll 42 
                 ++ +l+ GPPGtgKT    ++ ++ +
  AJA92264.1 211 PKGVLLYGPPGTGKTLLAKAVANESN 236
                 556899*********88877777775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.071
      AAA_11  20 tliqGPPGtgKTktivell 38 
                  l++GP GtgKT +  ++ 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVA 510
                 589*********6655554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.6
      AAA_11 123 aqlakeiskeleklakelrafeeee 147
                  + ++ei+k+  + + +++ fee  
  AJA92264.1 699 KKFVDEIEKKATDAKVTMKHFEEAV 723
                 1222222222222222222222221 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.057        19      17      46 ..     204     233 ..     182     283 .. 0.84
   2 !    8.3   0.0    0.0067       2.2      22      47 ..     487     512 ..     459     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.057
                 ......TTSEEEEEESTTSTHHHHHHHHHH CS
      ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklie 46 
                 ekl ++  k +l+  + GtGKTl+a +++ 
  AJA92264.1 204 EKLGIEAPKGVLLYGPPGTGKTLLAKAVAN 233
                 455558899999***********9966655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0067
                 .TTSEEEEEESTTSTHHHHHHHHHHH CS
      ResIII  22 krdkrglikmaTGtGKTlvaaklier 47 
                 k  + +l++ + GtGKTl+a +++ +
  AJA92264.1 487 KMPRGILLHGPSGTGKTLMAKAVATE 512
                 6667889************9666554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0079       2.6      23      47 ..     213     237 ..     204     287 .. 0.75
   2 ?    5.4   0.0     0.056        18      24      47 ..     492     515 ..     485     561 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0079
                      -EEEEEETT--HHHHHHCC--TTS- CS
  Sigma54_activ_2  23 pvfltGekGsgkelvArlLhknsgp 47 
                       v+l G++G+gk+l A++ +++s  
       AJA92264.1 213 GVLLYGPPGTGKTLLAKAVANESNA 237
                      69****************9998754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.056
                      EEEEEETT--HHHHHHCC--TTS- CS
  Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                      ++l G+ G+gk+l+A++ + +s+ 
       AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEA 515
                      799**************9988876 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.11        37       3      31 ..     212     240 ..     210     248 .. 0.84
   2 ?    0.8   0.0         1   3.3e+02      74      95 ..     247     268 ..     235     288 .. 0.78
   3 ?    6.6   0.0     0.018       5.8       3      31 ..     490     518 ..     488     523 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                    SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                    + v l gp g+Gk  l ka+ +e + +f 
     AJA92264.1 212 KGVLLYGPPGTGKTLLAKAVANESNAHFI 240
                    66899***************999998884 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
                    ETTEEEEEEHHHHHHHHHTTSE CS
  Guanylate_kin  74 fsgnlygtsveaieevlekgki 95 
                      ++ yg+s +  +e+++++++
     AJA92264.1 247 IMSKFYGESEARLREIFKEARE 268
                    66899*************9987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.018
                    SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                    r + l gpsg+Gk  + ka+ +e + +f 
     AJA92264.1 490 RGILLHGPSGTGKTLMAKAVATESEANFV 518
                    7799****************999998885 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.023       7.6      18      44 ..     414     440 ..     407     442 .. 0.87
   2 ?    7.6   0.5     0.012       3.9      18      50 ..     704     732 ..     693     740 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
      Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                 +ip++ l +  v+ +Df+kal ++ p+
  AJA92264.1 414 KIPPETLDKLIVNADDFKKALVEVTPS 440
                 59999999*************999987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
      Vps4_C  18 dipsdkllePpvtlkDflkalkkarptVskeDL 50 
                 +i+ +k +  +vt+k+f++a++k+r    ++DL
  AJA92264.1 704 EIE-KKATDAKVTMKHFEEAVRKVRE---QKDL 732
                 555.788889*************994...5555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.032        10       2      32 ..     214     244 ..     213     260 .. 0.83
   2 ?   -0.1   0.1       2.3   7.6e+02      84     120 ..     258     295 ..     248     322 .. 0.72
   3 ?    4.7   0.0      0.08        26       2      32 ..     492     522 ..     491     544 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                 v++ GppG+GKt l k v+++ + + ++++G
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFISISG 244
                 6788*************99987766666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.3
                 HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHH CS
    NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeavee 120
                    e++++a  + + +i +DEi ++  k +++  +ve+
  AJA92264.1 258 RLREIFKEAReKAPSIIFVDEIDSIAPKREEVTGEVER 295
                 55566677773455699999998776666666665554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.08
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                 +++ Gp+G+GKt + k v+ + + + v+v+G
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSVRG 522
                 6889**************9999988888888 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0042       1.4      36      52 ..     214     230 ..     207     235 .. 0.86
   2 ?    2.7   0.0      0.24        79     128     177 ..     257     306 ..     246     325 .. 0.83
   3 ?   -1.9   0.0       6.6   2.2e+03      70     135 ..     310     379 ..     297     383 .. 0.65
   4 ?    6.1   0.4     0.023       7.5      36      55 ..     492     511 ..     485     608 .. 0.63
   5 ?   -0.2   0.2         2   6.4e+02     100     185 ..     627     716 ..     592     719 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0042
      AAA_25  36 allaGapgtGKttlald 52 
                 +ll+G+pgtGKt la  
  AJA92264.1 214 VLLYGPPGTGKTLLAKA 230
                 69***********9965 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.24
      AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                 a ++++ ++++e + +  + +D ++++ +  e+   +v +++v+++ ++ +
  AJA92264.1 257 ARLREIFKEARE-KAPSIIFVDEIDSIAPKREEVTGEVeRRVVSQMLSLMD 306
                 556788899999.78***************999999999999999988876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.6
      AAA_25  70 eqgkVlyvsaEdsedelrrRlravg.eal.......rddarllvldlagveslpLfakdrggtlltadvdalea 135
                  +gkV+++sa ++ + + + lr+ g  ++       + ++r  +l+++++ ++pL++   ++++l+ ++++++a
  AJA92264.1 310 ARGKVIVISATNRPNAIDPALRRPGrFDReieikvpDKKGRQEILQIHTR-NMPLAD---EEQQLPVKIEKIAA 379
                 46788888888888788877777664333557777777888888888775.777754...44445666666655 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.023
      AAA_25  36 allaGapgtGKttlaldlal 55 
                 +ll G++gtGKt +a  +a 
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVAT 511
                 689*********98865554 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2
      AAA_25 100 darllvldlagveslpLfakdrggtl....ltadvdale.aaieeveg..vrlvviDplsralggdensnsdvgalvealeriarrtgaavll 185
                 d+r  v+ ++++ ++pL+++ + +++    +++ +d l  a++ ++++  v lvv   l+ a +    s+++++++v+ +e+  ++t+a v++
  AJA92264.1 627 DGRKMVIEIHSK-DIPLADNNSPDKIdfdkIAELTDGLSsADVASIANtaVSLVVHEHLDNAIPDKDLSDEETKKFVDEIEK--KATDAKVTM 716
                 555566666553.777766666666643333444444421334444445588888888999999988889999999999998..566666655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0038       1.2       1      26 [.     217     242 ..     217     291 .. 0.81
   2 ?    2.6   0.0      0.52   1.7e+02       2      25 ..     496     521 ..     495     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0038
                 EE-TTSSHHHHHHHHHHHHTEEEEEH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                 +G+PG GK+ +++ ++ + + +++s 
  AJA92264.1 217 YGPPGTGKTLLAKAVANESNAHFISI 242
                 7***************9998888876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.52
                 E-TTSSHHHHHHHHHHHH..TEEEEE CS
      AAA_17   2 GgPGsGKgtqceklveky..gfthls 25 
                 G+ G GK+ +++ ++ +   +f  + 
  AJA92264.1 496 GPSGTGKTLMAKAVATESeaNFVSVR 521
                 99*********999977622555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.078        25      21      39 ..     211     228 ..     202     233 .. 0.79
   2 ?    7.3   0.0     0.012       3.8      18      38 ..     487     505 ..     474     511 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.078
      AAA_29  21 lkgatlltGpsGsGKSTll 39 
                 +kg +ll Gp G+GK+ l 
  AJA92264.1 211 PKG-VLLYGPPGTGKTLLA 228
                 467.9**********8765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
      AAA_29  18 eidlkgatlltGpsGsGKSTl 38 
                 ++ ++g +ll GpsG+GK+ +
  AJA92264.1 487 KM-PRG-ILLHGPSGTGKTLM 505
                 44.477.9**********865 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.14        46       4      34 ..     214     244 ..     212     321 .. 0.86
   2 ?    7.8   0.0    0.0086       2.8       4      32 ..     492     520 ..     490     535 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                 EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEH CS
         CPT   4 ilLnGgsssGKsslaralqevldepwlhlgv 34 
                 +lL G + +GK+ la+a+ + +++ ++ +  
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFISISG 244
                 89******************99999998865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0086
                 EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
         CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                 ilL+G s +GK+ +a+a+ + +++ ++ +
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESEANFVSV 520
                 9******************9999999876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.052        17      32      60 ..     208     236 ..     190     245 .. 0.83
   2 ?    6.1   0.0      0.02       6.6      27      58 ..     481     512 ..     465     521 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.052
        TniB  32 rkrmpnlllvGdsnnGKtmivekFarlhp 60 
                  + ++ +ll+G++ +GKt +++  a++ +
  AJA92264.1 208 IEAPKGVLLYGPPGTGKTLLAKAVANESN 236
                 5667899*************998877655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
        TniB  27 leypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                 +++  +k ++ +ll+G+s +GKt +++  a +
  AJA92264.1 481 YDKLGHKMPRGILLHGPSGTGKTLMAKAVATE 512
                 55555566689************999877655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.011       3.6      12      32 ..     213     233 ..     207     273 .. 0.83
   2 ?    3.8   0.0      0.21        68      13      32 ..     492     511 ..     486     526 .. 0.80
   3 ?   -0.4   0.0         4   1.3e+03      22      54 ..     568     602 ..     561     608 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.011
      AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                  +l+ ++pGtGKT + k++ +
  AJA92264.1 213 GVLLYGPPGTGKTLLAKAVAN 233
                 5899*********88776654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.21
      AAA_19  13 llvtaGpGtGKTrvlkhiva 32 
                 +l+ ++ GtGKT + k++ +
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVAT 511
                 789999******98776654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 4
      AAA_19  22 GKTrvlkhivallvelgg..vkpeeillvaftgrA 54 
                 G T v++ +v+ l+ + +  ++++ ++++a t+rA
  AJA92264.1 568 GETAVTERVVSQLLTELDgmENMHGVVVLAATNRA 602
                 7788888888777665431145689999*****99 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.21        68      48      75 ..     214     241 ..     204     249 .. 0.80
   2 ?    0.8   0.0       1.2     4e+02     140     178 ..     246     282 ..     235     288 .. 0.71
   3 ?    5.9   0.0     0.034        11      42      72 ..     486     516 ..     462     558 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.21
       Rad17  48 LLisGPsGCgkstvvkvLskelgiklre 75 
                 +L+ GP+G gk+   k ++ e   +++ 
  AJA92264.1 214 VLLYGPPGTGKTLLAKAVANESNAHFIS 241
                 5789*********999999987776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
       Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                 ++ +kfy++s  +lre+ +++   + a p i+ + ei+s+
  AJA92264.1 246 EIMSKFYGESeARLREIFKEARE-K-A-PSIIFVDEIDSI 282
                 67899**9997899999887633.2.2.446666778765 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.034
       Rad17  42 srkkriLLisGPsGCgkstvvkvLskelgik 72 
                 ++  r +L+ GPsG gk+ + k ++ e   +
  AJA92264.1 486 HKMPRGILLHGPSGTGKTLMAKAVATESEAN 516
                 444456789*********9999998876555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.025         8     129     156 ..     211     238 ..     176     246 .. 0.87
   2 ?    5.2   0.0     0.028       9.2     132     152 ..     492     512 ..     482     521 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.025
       T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                  + +l+ G+ g+GKt l+ a+ +e n++
  AJA92264.1 211 PKGVLLYGPPGTGKTLLAKAVANESNAH 238
                 5678999*************99998877 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
       T2SSE 132 ilvsGgTgsGKttllyallke 152
                 il+ G+ g+GKt ++ a+ +e
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATE 512
                 99************9998776 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.04        13       5      31 ..     215     241 ..     211     244 .. 0.89
   2 ?    4.9   0.0     0.045        15       5      31 ..     493     519 ..     490     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.04
         IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                 l++G+ +tGKt  a ++a+e  a  i+
  AJA92264.1 215 LLYGPPGTGKTLLAKAVANESNAHFIS 241
                 89*****************99888776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.045
         IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                 l++G+ +tGKt +a ++a e  a  ++
  AJA92264.1 493 LLHGPSGTGKTLMAKAVATESEANFVS 519
                 799***************998877765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.23        76       5      71 ..     218     279 ..     214     283 .. 0.63
   2 ?    7.5   0.0    0.0091         3       1      71 [.     492     557 ..     492     562 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.23
  Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      G pG GK+ l + ++++s  + + +++   e+ ++   +++++  + ++++ +++       i+++DE+
       AJA92264.1 218 GPPGTGKTLLAKAVANESnaHFI-SISG-PEIMSKFYGESEARLREIFKEAREKA-----PSIIFVDEI 279
                      78***************884443.3333.35555544555555555555544443.....247777775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0091
  Viral_helicase1   1 ivvhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                      i+ hG  G GK+ + + ++ +s  +++++r   ell++++ ++++   + ++ + +++ +     ++++DE+
       AJA92264.1 492 ILLHGPSGTGKTLMAKAVATESeANFVSVRG-PELLSKWVGESERGIREIFKRARQSAPC-----VIFFDEI 557
                      5789***************999999988888.9*******88888878888877777654.....7999997 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.042        14      59      79 ..     208     228 ..     181     237 .. 0.86
   2 ?    4.6   0.0     0.037        12      59      78 ..     486     505 ..     465     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
  AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                   e+++g+ l+G+ G GKt l 
   AJA92264.1 208 IEAPKGVLLYGPPGTGKTLLA 228
                  579***************985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.037
  AFG1_ATPase  59 vepvrglYlwGgvGrGKtyl 78 
                  ++ +rg+ l+G+ G GKt +
   AJA92264.1 486 HKMPRGILLHGPSGTGKTLM 505
                  6789*************965 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.02       6.4      18      66 ..     215     269 ..     210     326 .. 0.75
   2 ?    3.7   0.0      0.13        42      18      49 ..     493     570 ..     488     608 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                  EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHS CS
                  xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpeg 66 
                  l+ g  g+Gkt ++++++++sn++        i     Ge +  ++e+++e +e+
   AJA92264.1 215 LLYGPPGTGKTLLAKAVANESNAHfisisGpEIMSKFYGESEARLREIFKEAREK 269
                  678999***************9996666523555566888888888888888774 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                  EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE................................................E CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................x RF
  ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg................................................i 49 
                  l+ g +g+Gkt ++++++ +s+++   + v                                                  
   AJA92264.1 493 LLHGPSGTGKTLMAKAVATESEAN--FVSVRgpellskwvgesergireifkrarqsapcviffdeidsiapirgaggeT 570
                  67899***************8666..444444677777755555555555555555555555555555555555544443 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.8   1.9e+03      77     102 ..     126     151 ..     121     193 .. 0.73
   2 ?    4.7   0.0     0.069        23       2      24 ..     212     234 ..     211     239 .. 0.89
   3 ?    3.1   0.0      0.22        73       4      24 ..     492     512 ..     489     516 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.8
   PduV-EutP  77 esvfppgfasvfnkeviGiitkidla 102
                 ++v+ p f   ++ +viG+   +d +
  AJA92264.1 126 DNVMVPYFGGRLTFQVIGVTPAADAV 151
                 67888999999999****98887754 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.069
   PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                 k +ll G+ g+GKt L++a+ +e
  AJA92264.1 212 KGVLLYGPPGTGKTLLAKAVANE 234
                 5699***************9987 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.22
   PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                 ill G++g+GKt +++a+  e
  AJA92264.1 492 ILLHGPSGTGKTLMAKAVATE 512
                 899***********9998765 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.37   1.2e+02      57      76 ..     215     234 ..     205     242 .. 0.86
   2 ?    6.0   0.0     0.038        12      55      75 ..     491     511 ..     480     518 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.37
                 EEEE-TTSSHHHHHHHHHHH CS
      Torsin  57 sfhGwtGtGknfvaeiiaen 76 
                  ++G +GtGk  +a+ +a++
  AJA92264.1 215 LLYGPPGTGKTLLAKAVANE 234
                 5799************9986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.038
                 EEEEEE-TTSSHHHHHHHHHH CS
      Torsin  55 vlsfhGwtGtGknfvaeiiae 75 
                  + +hG +GtGk  +a+ +a 
  AJA92264.1 491 GILLHGPSGTGKTLMAKAVAT 511
                 5779************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              55  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 4811.54
//
Query:       AJA92265.1  [L=327]
Description: polyprenyl synthetase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-71  240.5   0.2    1.8e-71  240.2   0.2    1.1  1  polyprenyl_synt  Polyprenyl synthetase
      8e-05   22.1   0.0    0.00016   21.1   0.0    1.4  1  Terpene_synth_C  Terpene synthase family, metal binding domai
      0.004   16.8   0.1     0.0071   16.0   0.1    1.4  1  HEPPP_synt_1     Heptaprenyl diphosphate synthase (HEPPP synt


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.2   0.2     3e-75   1.8e-71       2     255 ..      27     279 ..      26     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 240.2 bits;  conditional E-value: 3e-75
                      HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHH CS
  polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllaraf 95 
                      ++l++a+ +l+ +gGKrlRp lvl+++++l+ ++   ++a ++a  ve++h+++LvhDDimD++e+R G p+ h++++++lAi++gd+l+++a+
       AJA92265.1  27 KQLYDAAAHLIIHGGKRLRPYLVLKSCKVLGGKQ---SDAIAAASSVEMIHNFTLVHDDIMDNDEMRHGVPTTHNKFDMPLAILAGDVLYSKAY 117
                      567777888888*******************444...89******************************************************* PP

                      HHHHHHH..STT..HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt  96 ellaklf..eks..lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGl 185
                      +++++    +++  ++l+  +s+++++++eGq+ d++ ++  + + +++ ey +++++KTa+lf++++a++a++a+ +++++++l+++g++lG+
       AJA92265.1 118 HTISSKSklSPNhtTQLVTKLSKACVEICEGQVDDVKLAE--NKRIPTEREYIKMIEKKTAVLFEVSCAMGAICAKRKEKDVRNLSSFGRNLGI 209
                      ***977667344469*********************7664..444469****************************9999************** PP

                      HHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHHHTTSSHHHHHHHHHHHHH CS
  polyprenyl_synt 186 aFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlkeilgkkaekeedvkealel 255
                      aFQi DD++ ++gd++v+ Kp+g+Di+egk +lpil a+++a  +++k++ +++gk +++++dv+ a+++
       AJA92265.1 210 AFQITDDLIGIMGDSKVTKKPVGNDIREGKKSLPILLAIRKARGSDKKKILKVFGKSKAAKKDVQTAVNT 279
                      *****************************************************************99986 PP

>> Terpene_synth_C  Terpene synthase family, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.7e-08   0.00016     112     230 ..     111     224 ..     107     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.7e-08
  Terpene_synth_C 112 ilykallntfneledelekeeksdrvskylkeawkelvkaylkeakWreekyvPsfeEylenslvssglpllllaalvgmgdevtkeafewvas 205
                      +ly++ ++t+++   +l++++   +++  l++a+ e+++  +  +k +e+k++P+  Ey+++  ++  +++l+ +++  mg ++ k + + v++
       AJA92265.1 111 VLYSKAYHTISSK-SKLSPNHTT-QLVTKLSKACVEICEGQVDDVKLAENKRIPTEREYIKM--IEKKTAVLFEVSC-AMGAICAKRKEKDVRN 199
                      5799999999987.667885555.66689*******************************98..5556677777777.7888777766799*** PP

  Terpene_synth_C 206 ypklvkalstilRLlnDiasyereq 230
                       +++ + l + + +++D+ ++ +++
       AJA92265.1 200 LSSFGRNLGIAFQITDDLIGIMGDS 224
                      *****************98887654 PP

>> HEPPP_synt_1  Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-06    0.0071      49     132 ..      77     172 ..      47     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
  HEPPP_synt_1  49 ldtHdkvsekkee.....eeeekknrqLtVLAGd.yYSglYYkl.....Laevkdielirllaeaikeinehkik.lYekkeetveellesvkkie 132
                     +Hd + +++e      + ++k +  L +LAGd +YS  Y  +     L+ ++  +l+  l++a  ei+e ++  +  ++++++ +  e +k+ie
    AJA92265.1  77 TLVHDDIMDNDEMrhgvpTTHNKFDMPLAILAGDvLYSKAYHTIsskskLSPNHTTQLVTKLSKACVEICEGQVDdVKLAENKRIPTEREYIKMIE 172
                   4577777765333111112333334579******77*****97644444888899****************9985233334444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2249.87
//
Query:       AJA92266.1  [L=353]
Description: anaphase-promoting complex, cyclosome, subunit 3 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-52  171.3  15.0    3.4e-08   33.0   0.0    8.2  8  TPR_1            Tetratricopeptide repeat
    1.5e-47  155.9   6.8    6.4e-06   25.9   0.0    8.2  8  TPR_2            Tetratricopeptide repeat
    2.3e-37  124.1   9.2    0.00011   22.2   0.1    8.2  8  TPR_8            Tetratricopeptide repeat
    2.7e-36  121.3  11.9    2.6e-05   24.3   0.0    8.5  8  TPR_17           Tetratricopeptide repeat
    3.7e-34  116.9   6.9    6.4e-11   42.4   0.0    6.3  7  TPR_12           Tetratricopeptide repeat
      2e-33  113.8  11.6      5e-09   35.7   0.1    8.1  8  TPR_11           TPR repeat
    2.7e-31  107.9   0.0    2.5e-10   40.8   0.0    5.1  6  TPR_16           Tetratricopeptide repeat
      3e-29   99.2   0.0    3.7e-05   24.2   0.1    7.8  8  TPR_14           Tetratricopeptide repeat
    1.2e-28   99.4   5.8      8e-09   35.9   0.3    5.1  5  TPR_19           Tetratricopeptide repeat
    1.2e-23   83.1   7.6    1.6e-11   44.3   0.0    4.4  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    8.7e-22   75.5   0.1     0.0021   18.0   0.0    7.5  7  TPR_7            Tetratricopeptide repeat
    3.5e-21   74.4   1.2      0.065   13.9   0.0    8.2  8  TPR_6            Tetratricopeptide repeat
    3.8e-17   62.2   0.0    2.4e-06   27.6   0.0    4.8  6  TPR_9            Tetratricopeptide repeat
      1e-13   51.4   7.7     0.0095   16.3   0.0    6.0  7  TPR_20           Tetratricopeptide repeat
    1.7e-12   46.8   4.5    0.00078   19.2   0.0    6.6  7  TPR_10           Tetratricopeptide repeat
    2.6e-10   40.2   9.0     0.0061   16.0   0.1    4.5  5  Coatomer_E       Coatomer epsilon subunit
    4.7e-10   39.4   9.0     0.0054   16.8   0.0    7.1  8  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    9.1e-09   34.8   0.8    3.2e-05   23.1   0.0    2.4  2  ChAPs            ChAPs (Chs5p-Arf1p-binding proteins)
    1.1e-06   28.1   1.1    0.00051   19.3   0.1    3.1  3  TPR_15           Tetratricopeptide repeat
    2.1e-06   28.3   2.0      0.018   15.5   0.0    3.6  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
    8.6e-06   25.8  14.0        1.5    8.8   0.0    5.3  5  DUF4919          Domain of unknown function (DUF4919)
    1.4e-05   25.1   0.1       0.36   10.9   0.0    4.2  4  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
    3.3e-05   23.7   2.7      0.015   15.0   0.0    3.6  3  TPR_21           Tetratricopeptide repeat-like domain
      8e-05   23.1   0.0      0.012   16.1   0.0    3.0  4  BTAD             Bacterial transcriptional activator domain
    9.5e-05   22.5   0.2        3.4    7.7   0.0    4.5  4  DUF3856          Domain of Unknown Function (DUF3856)
    0.00031   21.1   4.7       0.09   13.1   0.1    4.4  4  RPN6_N           26S proteasome regulatory subunit RPN6 N-ter
    0.00047   20.1  11.4       0.41   10.7   0.1    6.1  6  TPR_3            Tetratricopeptide repeat
    0.00053   20.2   0.0        3.9    7.7   0.0    3.4  3  TPR_5            Tetratrico peptide repeat
     0.0014   19.0   0.0       0.39   11.5   0.0    2.8  2  TPR_4            Tetratricopeptide repeat
     0.0015   19.1   0.1         17    6.2   0.0    4.1  3  Sel1             Sel1 repeat
     0.0038   16.0   0.0        1.2    7.8   0.0    2.7  4  PknG_TPR         Protein kinase G tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   14.9  11.9        4.6    6.9   0.1    5.1  5  TOM20_plant      Plant specific mitochondrial import receptor
      0.021   14.3   3.0         12    5.2   0.0    4.3  5  SPO22            Meiosis protein SPO22/ZIP4 like
      0.051   13.2   0.0        1.9    8.2   0.0    2.8  3  HrpB1_HrpK       Bacterial type III secretion protein (HrpB1_
      0.082   12.7   0.3        5.3    6.8   0.1    2.9  2  COP23            Circadian oscillating protein COP23
       0.14   12.4   5.8         40    4.8   0.1    5.3  5  PPR              PPR repeat
       0.77    9.7  13.4       0.52   10.2  11.3    1.7  2  DUF2796          Protein of unknown function (DUF2796)
        1.1    8.4   2.8        1.4    8.1   2.8    1.1  1  Zip              ZIP Zinc transporter
        1.3    8.4  12.0        2.2    7.6  12.0    1.3  1  SelP_N           Selenoprotein P, N terminal region


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.7e-05    0.0078       8      34 .]       8      34 ..       3      34 .. 0.88
   2 !    9.1   0.1    0.0026       1.2      10      33 ..      44      67 ..      37      68 .. 0.86
   3 !   33.0   0.0   7.4e-11   3.4e-08       3      34 .]      71     102 ..      69     102 .. 0.97
   4 !   27.7   0.0   3.3e-09   1.5e-06       2      33 ..     104     135 ..     103     136 .. 0.94
   5 !   25.7   0.0   1.4e-08   6.6e-06       2      30 ..     138     166 ..     137     170 .. 0.92
   6 !   28.3   0.1   2.2e-09     1e-06       2      34 .]     172     204 ..     171     204 .. 0.96
   7 !    9.7   0.0    0.0017      0.78       5      34 .]     209     238 ..     205     238 .. 0.93
   8 !   25.5   0.0   1.7e-08   7.6e-06       2      33 ..     240     271 ..     239     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                G   f+++++++A++ +ek L+ +P+n
  AJA92266.1  8 GIQNFENENFQKAIKLFEKILKSDPDN 34
                5566899******************98 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0026
                HHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1 10 ayfklgkydeAleyyekALelnPn 33
                ++ +lgky+eA+e  e  L+ nPn
  AJA92266.1 44 CLAELGKYNEAIEQLEIFLKKNPN 67
                8999*********88877777777 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 7.4e-11
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 alyn+G +++ + +++eAl+ ++ AL+++P+n
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTALKIDPKN 102
                 9*****************************98 PP

  == domain 4  score: 27.7 bits;  conditional E-value: 3.3e-09
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                 +al+n++n++  lg++d+A+  y++AL+ +P 
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQAEPR 135
                 79**************************9996 PP

  == domain 5  score: 25.7 bits;  conditional E-value: 1.4e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                 ++l+n+G +y  ++k+++A++++e AL  
  AJA92266.1 138 EILNNIGIVYAGQKKHKKAIKFFESALDM 166
                 789************************86 PP

  == domain 6  score: 28.3 bits;  conditional E-value: 2.2e-09
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 ++l+nlGn +++ ++ + A +y+++A++l+Pn+
  AJA92266.1 172 DTLCNLGNSLLEIENNKSAYKYFQQAVKLDPND 204
                 789****************************97 PP

  == domain 7  score: 9.7 bits;  conditional E-value: 0.0017
                 HHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   5 ynlGnayfklgkydeAleyyekALelnPnn 34 
                 ++l+ ++ +l++++ Al  ++k L+ + nn
  AJA92266.1 209 FRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 89*************************998 PP

  == domain 8  score: 25.5 bits;  conditional E-value: 1.7e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                 ++l n+G+ ++ ++ky  A+ +y+k+L+ +P+
  AJA92266.1 240 DVLINKGYSLHLMEKYGRAILCYDKVLKQDPQ 271
                 7899***************************6 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-06    0.0015       5      34 .]       5      34 ..       2      34 .. 0.90
   2 !   13.6   0.1   0.00012     0.056      10      34 .]      44      68 ..      43      68 .. 0.95
   3 !   25.9   0.0   1.4e-08   6.4e-06       3      34 .]      71     102 ..      69     102 .. 0.97
   4 !   23.6   0.0   7.7e-08   3.5e-05       2      34 .]     104     136 ..     103     136 .. 0.94
   5 !   20.2   0.0     9e-07   0.00041       2      32 ..     138     168 ..     137     170 .. 0.91
   6 !   24.2   0.0   4.8e-08   2.2e-05       3      34 .]     173     204 ..     171     204 .. 0.95
   7 ?    6.6   0.0     0.021       9.7       5      34 .]     209     238 ..     205     238 .. 0.88
   8 !   19.3   0.0   1.8e-06   0.00084       2      33 ..     240     271 ..     239     272 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
       TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                 ++G   +++ ++++A+++fek l+ dP+n
  AJA92266.1  5 LEQGIQNFENENFQKAIKLFEKILKSDPDN 34
                567888899*******************98 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00012
       TPR_2 10 ayyklgdyeeAleafekAleldPnn 34
                ++++lg+y+eA+e +e  l+ +Pn+
  AJA92266.1 44 CLAELGKYNEAIEQLEIFLKKNPND 68
                7899*******************97 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 1.4e-08
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 alyn G  +y ++++eeAl+ f+ Al++dP+n
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTALKIDPKN 102
                 89****************************97 PP

  == domain 4  score: 23.6 bits;  conditional E-value: 7.7e-08
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +al+n ++++ +lg++++A++ +++Al+ +P++
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQAEPRD 136
                 689**************************9976 PP

  == domain 5  score: 20.2 bits;  conditional E-value: 9e-07
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                 e+l+n+G +y+ ++++++A+++fe Al    
  AJA92266.1 138 EILNNIGIVYAGQKKHKKAIKFFESALDMQK 168
                 899************************8765 PP

  == domain 6  score: 24.2 bits;  conditional E-value: 4.8e-08
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                  l+nlG+++++  + + A ++f++A++ldPn+
  AJA92266.1 173 TLCNLGNSLLEIENNKSAYKYFQQAVKLDPND 204
                 689***************************97 PP

  == domain 7  score: 6.6 bits;  conditional E-value: 0.021
       TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                 ++l+  + +l+ +e+Al  f+k l+ d nn
  AJA92266.1 209 FRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 78888888999****************997 PP

  == domain 8  score: 19.3 bits;  conditional E-value: 1.8e-06
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                 ++l n G+++  + +y +A+ +++k+l+ dP+
  AJA92266.1 240 DVLINKGYSLHLMEKYGRAILCYDKVLKQDPQ 271
                 6899***************************7 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00093      0.43      13      34 .]      13      34 ..      11      34 .. 0.91
   2 ?    6.5   0.0     0.024        11       9      25 ..      43      59 ..      35      68 .. 0.81
   3 !   21.5   0.0   3.8e-07   0.00018       3      34 .]      71     102 ..      70     102 .. 0.97
   4 !   20.3   0.0   9.3e-07   0.00043       2      33 ..     104     135 ..     103     136 .. 0.94
   5 !   19.0   0.0   2.4e-06    0.0011       2      32 ..     138     168 ..     137     170 .. 0.93
   6 !   22.2   0.1   2.3e-07   0.00011       2      34 .]     172     204 ..     171     204 .. 0.95
   7 ?    6.5   0.0     0.025        12       5      34 .]     209     238 ..     206     238 .. 0.92
   8 !   15.1   0.0   4.2e-05     0.019       2      33 ..     240     271 ..     239     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00093
                HTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8 13 klgdyeeAkeyyekaleldpdn 34
                + +++++A++ +ek l+ dpdn
  AJA92266.1 13 ENENFQKAIKLFEKILKSDPDN 34
                56899***************97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.024
                HHHHHTT-HHHHHHHHH CS
       TPR_8  9 siylklgdyeeAkeyye 25
                s++ +lg+y+eA+e +e
  AJA92266.1 43 SCLAELGKYNEAIEQLE 59
                67899********9887 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 3.8e-07
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 a+yn+g ++ ++ ++eeA  ++  al++dp+n
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTALKIDPKN 102
                 79****************************97 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 9.3e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +a++n+++++  lg+++ A+ +y++al+++p 
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQAEPR 135
                 79**************************9996 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 2.4e-06
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                 e+++n+g +y  ++++++A++++e al++++
  AJA92266.1 138 EILNNIGIVYAGQKKHKKAIKFFESALDMQK 168
                 799************************9986 PP

  == domain 6  score: 22.2 bits;  conditional E-value: 2.3e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 + ++nlg+ +l+ ++ ++A +y+++a++ldp++
  AJA92266.1 172 DTLCNLGNSLLEIENNKSAYKYFQQAVKLDPND 204
                 679****************************96 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.025
                 HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 ++l+ ++ +l+  e A   ++k l+ d++n
  AJA92266.1 209 FRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 6899999********************986 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 4.2e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +++ n+g+ ++ +++y  A+ +y k+l+ dp+
  AJA92266.1 240 DVLINKGYSLHLMEKYGRAILCYDKVLKQDPQ 271
                 6899**************************97 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.8e-06    0.0031       1      34 []      23      56 ..      23      56 .. 0.97
   2 !   21.2   0.0   5.6e-07   0.00026       5      33 ..      61      89 ..      59      90 .. 0.94
   3 !   24.3   0.0   5.6e-08   2.6e-05       2      33 ..      92     123 ..      91     124 .. 0.95
   4 !   17.0   0.0   1.2e-05    0.0054       2      34 .]     126     158 ..     125     158 .. 0.95
   5 ?    7.2   0.0     0.016       7.3       2      31 ..     160     189 ..     159     192 .. 0.83
   6 !   15.5   0.0   3.7e-05     0.017       1      33 [.     193     225 ..     193     226 .. 0.94
   7 !   13.8   0.0   0.00013     0.057       2      33 ..     228     259 ..     227     259 .. 0.94
   8 ?    4.7   0.1       0.1        46       1      28 [.     261     288 ..     261     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.8e-06
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtArq 34
                l++k l+ dP+n++a  n+  +l+++G++ +A++
  AJA92266.1 23 LFEKILKSDPDNPEAIINKTSCLAELGKYNEAIE 56
                79******************************86 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 5.6e-07
      TPR_17  5 aleldPnnadaynnLAelllknGdlmtAr 33
                +l+++Pn+++a++n++++l+   ++++A+
  AJA92266.1 61 FLKKNPNDFVALYNKGTTLYDMDQHEEAL 89
                599***********************996 PP

  == domain 3  score: 24.3 bits;  conditional E-value: 5.6e-08
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +  al++dP+n+ a++n+A++l  +G++++A+
  AJA92266.1  92 FDTALKIDPKNSQALCNKANVLVALGRHDDAI 123
                 789***************************97 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 1.2e-05
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                 y +al+ +P +++ +nn + +++ ++++++A++
  AJA92266.1 126 YNRALQAEPRDVEILNNIGIVYAGQKKHKKAIK 158
                 99*************************999985 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.016
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmt 31 
                 ++ al+  + + d ++nL++ ll++ + + 
  AJA92266.1 160 FESALDMQKGDIDTLCNLGNSLLEIENNKS 189
                 78899999************9997666554 PP

  == domain 6  score: 15.5 bits;  conditional E-value: 3.7e-05
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 ++++a++ldPn++da + LA +  +++ +++A+
  AJA92266.1 193 YFQQAVKLDPNDFDATFRLAITCNNLKMPERAL 225
                 599**********************99999985 PP

  == domain 7  score: 13.8 bits;  conditional E-value: 0.00013
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 + k l++d nn+d++ n+++ l+   ++++A+
  AJA92266.1 228 FNKLLRRDRNNVDVLINKGYSLHLMEKYGRAI 259
                 789*************************9996 PP

  == domain 8  score: 4.7 bits;  conditional E-value: 0.1
      TPR_17   1 lylkaleldPnnadaynnLAelllknGd 28 
                 +y k+l++dP   +a +++ +  +k++d
  AJA92266.1 261 CYDKVLKQDPQEMNAVYYKSKSTAKQND 288
                 8*********999999988875555544 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00029      0.13      10      69 ..       8      59 ..       1      59 [. 0.77
   2 !   20.5   0.0   9.6e-07   0.00044      18      76 ..      50     100 ..      35     101 .. 0.78
   3 !   36.5   0.2   9.9e-12   4.6e-09       5      73 ..      71     131 ..      67     135 .. 0.94
   4 !   42.4   0.0   1.4e-13   6.4e-11       4      76 ..     104     168 ..     101     169 .. 0.94
   5 !   28.8   0.0   2.4e-09   1.1e-06       5      75 ..     139     201 ..     136     203 .. 0.92
   6 !   10.8   0.0     0.001      0.47       5      76 ..     173     236 ..     169     237 .. 0.72
   7 ?    7.2   0.0     0.014       6.2       8      73 ..     210     267 ..     204     271 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
      TPR_12 10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelle 69
                +   ++ +++++A++l+ek l        pd+p+   + +n   ++ +lg+y eA+e le
  AJA92266.1  8 GIQNFENENFQKAIKLFEKILKSD-----PDNPE---AIINKTSCLAELGKYNEAIEQLE 59
                555666777777777777777777.....77766...899****************9987 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 9.6e-07
      TPR_12  18 rydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 +y eA       +e+  +++ +++p+   +l+n g++++ ++++eeAl+ +  al+i++
  AJA92266.1  50 KYNEA-------IEQL-EIFLKKNPNDFVALYNKGTTLYDMDQHEEALDTFDTALKIDP 100
                 54444.......4444.3444889999****************************9976 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 9.9e-12
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 al+n +++l+ + +++eAl+ +++al i      p++   +++l+n + ++ algr+++A++ +++al+
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTALKID-----PKN---SQALCNKANVLVALGRHDDAIRVYNRALQ 131
                 678**************************.....987...99*************************98 PP

  == domain 4  score: 42.4 bits;  conditional E-value: 1.4e-13
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 +al n a+vl +lgr+d+A++ +++al++      p     +++l+n+g++y  ++++++A++++e al++ +
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQAE-----PR---DVEILNNIGIVYAGQKKHKKAIKFFESALDMQK 168
                 68899*********************9999.....86...599***************************975 PP

  == domain 5  score: 28.8 bits;  conditional E-value: 2.4e-09
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                 +lnn++ v++ ++++ +A++++e al+++    G      + tl+nLg  +++ ++ + A +++++a++++
  AJA92266.1 139 ILNNIGIVYAGQKKHKKAIKFFESALDMQ---KG-----DIDTLCNLGNSLLEIENNKSAYKYFQQAVKLD 201
                 789**************************...33.....599*************************9986 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.001
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 +l nl++ l++ ++   A +++++a+ +      p+      + + L++++  l+ +e Al  +++ l++++
  AJA92266.1 173 TLCNLGNSLLEIENNKSAYKYFQQAVKLD-----PND---FDATFRLAITCNNLKMPERALINFNKLLRRDR 236
                 66788888888888888888888887776.....543...55777777777777777777777777777765 PP

  == domain 7  score: 7.2 bits;  conditional E-value: 0.014
      TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 +la +++ l+  + Al +++k l++       +    + +l+n g  ++++++y  A+  + ++l+
  AJA92266.1 210 RLAITCNNLKMPERALINFNKLLRRD-----RN---NVDVLINKGYSLHLMEKYGRAILCYDKVLK 267
                 56777777777777777777776666.....33...467899999999999999999999999987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0019      0.89       5      30 ..      12      37 ..      10      40 .. 0.92
   2 !   18.8   0.2   2.1e-06   0.00096       5      41 ..      46      82 ..      45      83 .. 0.94
   3 !   26.5   0.0   7.9e-09   3.6e-06       3      42 .]      78     117 ..      76     117 .. 0.94
   4 !   35.7   0.1   1.1e-11     5e-09       2      41 ..     111     150 ..     110     151 .. 0.95
   5 ?    6.9   0.0     0.011       4.9       7      39 ..     150     182 ..     149     185 .. 0.91
   6 !   14.4   0.0     5e-05     0.023       1      35 [.     178     212 ..     178     214 .. 0.88
   7 ?    3.7   0.0      0.11        50      12      39 ..     223     250 ..     222     252 .. 0.88
   8 !   12.2   0.1   0.00025      0.11       1      30 [.     246     275 ..     246     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
      TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaea 30
                +e  ++ +Ai+ ++k lk dPdn+ea
  AJA92266.1 12 FENENFQKAIKLFEKILKSDPDNPEA 37
                6778999*****************98 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.1e-06
      TPR_11  5 yeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41
                 e+Gky+eAie+++  lk +P++  a+yn G ++y +
  AJA92266.1 46 AELGKYNEAIEQLEIFLKKNPNDFVALYNKGTTLYDM 82
                589****************************999976 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 7.9e-09
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                  +y+  + eeA+  + +Alk+dP+n  a++n ++++ ++G
  AJA92266.1  78 TLYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALG 117
                 68999*******************************9988 PP

  == domain 4  score: 35.7 bits;  conditional E-value: 1.1e-11
      TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                 ++++++G+ ++Ai +Y++Al+  P ++e+++n+G +y+ q
  AJA92266.1 111 NVLVALGRHDDAIRVYNRALQAEPRDVEILNNIGIVYAGQ 150
                 89***********************************976 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.011
      TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                 q k ++Ai+ ++ Al+    + + ++nLG+ ++
  AJA92266.1 150 QKKHKKAIKFFESALDMQKGDIDTLCNLGNSLL 182
                 56889************************9876 PP

  == domain 6  score: 14.4 bits;  conditional E-value: 5e-05
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                 G+ + e  +++ A + +++A+kldP++ +a + L+
  AJA92266.1 178 GNSLLEIENNKSAYKYFQQAVKLDPNDFDATFRLA 212
                 7888888899999999*************988886 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.11
      TPR_11  12 eAieaYkkAlkldPdnaeayynLGlayy 39 
                  A+ +++k l+ d +n++++ n G+ ++
  AJA92266.1 223 RALINFNKLLRRDRNNVDVLINKGYSLH 250
                 688899******************9887 PP

  == domain 8  score: 12.2 bits;  conditional E-value: 0.00025
      TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaea 30 
                 G+ ++   ky  Ai +Y k lk dP+  +a
  AJA92266.1 246 GYSLHLMEKYGRAILCYDKVLKQDPQEMNA 275
                 67788889*****************97776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00011      0.05       8      36 ..      12      37 ..       5      38 .. 0.84
   2 !   26.4   0.0   1.8e-08   8.2e-06       8      67 ..      46     102 ..      45     103 .. 0.96
   3 !   40.8   0.0   5.5e-13   2.5e-10       2      64 ..     108     167 ..     107     171 .. 0.94
   4 !   16.2   0.0   2.6e-05     0.012       2      63 ..     176     234 ..     175     239 .. 0.88
   5 ?    4.6   0.0      0.11        52      14      67 ..     222     272 ..     217     272 .. 0.89
   6 ?    3.0   0.0      0.36   1.7e+02      11      40 ..     253     279 ..     252     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
      TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeA 36
                +++ ++++A++++e  lk+d   Pd++eA
  AJA92266.1 12 FENENFQKAIKLFEKILKSD---PDNPEA 37
                7899****************...665554 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.8e-08
      TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                 +++g+y +A+++le++lk++   P +  Al+++g  ++    ++eA++ ++ al+ +p++
  AJA92266.1  46 AELGKYNEAIEQLEIFLKKN---PNDFVALYNKGTTLYDMDQHEEALDTFDTALKIDPKN 102
                 789*****************...99999******************************87 PP

  == domain 3  score: 40.8 bits;  conditional E-value: 5.5e-13
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                 ++a+ ++++g+ ddA++++++al +    P+++e l++ g +++ q+ +++A+ ++++al+  
  AJA92266.1 108 NKANVLVALGRHDDAIRVYNRALQAE---PRDVEILNNIGIVYAGQKKHKKAIKFFESALDMQ 167
                 789***********************...******************************9876 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 2.6e-05
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                 +l++++l+  +   A +++++a+k+d   P + +A + l+  +  ++  ++A+  ++++lr 
  AJA92266.1 176 NLGNSLLEIENNKSAYKYFQQAVKLD---PNDFDATFRLAITCNNLKMPERALINFNKLLRR 234
                 79************************...***********9999998888888777776665 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.11
      TPR_16  14 ddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                 ++A+  ++ +l+rd     +++ l ++g ++     + +A+  y++ l+++p++
  AJA92266.1 222 ERALINFNKLLRRD---RNNVDVLINKGYSLHLMEKYGRAILCYDKVLKQDPQE 272
                 67777899999999...99999*********99999*****9999999999985 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.36
      TPR_16  11 gdyddAaaaleaalkrdpssPdaaeAllll 40 
                  +y +A+  ++ +lk+d   P+   A +++
  AJA92266.1 253 EKYGRAILCYDKVLKQD---PQEMNAVYYK 279
                 58999************...9988888775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.7e-05    0.0076       4      39 ..       4      39 ..       1      44 [. 0.87
   2 !   11.7   0.0    0.0008      0.37      11      41 ..      45      75 ..      41      78 .. 0.90
   3 !   12.7   0.0   0.00039      0.18       8      40 ..      76     108 ..      71     111 .. 0.85
   4 !   24.2   0.1   8.1e-08   3.7e-05       8      38 ..     110     140 ..     109     144 .. 0.93
   5 ?    6.2   0.0     0.048        22       8      38 ..     144     174 ..     142     179 .. 0.83
   6 !   15.0   0.0   7.4e-05     0.034       7      42 ..     177     212 ..     171     214 .. 0.90
   7 ?    5.6   0.0     0.078        36       2      40 ..     206     244 ..     205     248 .. 0.89
   8 ?    3.1   0.0      0.46   2.1e+02      16      39 ..     254     277 ..     246     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.7e-05
      TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawl 39
                ll+ +   ++++++++Ai+l++++l+ +Pd++ea +
  AJA92266.1  4 LLEQGIQNFENENFQKAIKLFEKILKSDPDNPEAII 39
                67778888999*********************9965 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0008
      TPR_14 11 llalGdpdeAiallrralalaPddaeawlll 41
                l++lG++ eAi+ l+  l+++P+d +a++  
  AJA92266.1 45 LAELGKYNEAIEQLEIFLKKNPNDFVALYNK 75
                6899********************9998765 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00039
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                 +  l+  ++++eA++ ++ al+ +P++ +a+  
  AJA92266.1  76 GTTLYDMDQHEEALDTFDTALKIDPKNSQALCN 108
                 56788899*******************999865 PP

  == domain 4  score: 24.2 bits;  conditional E-value: 8.1e-08
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                 a +l alG++d+Ai++++ral++ P d e++
  AJA92266.1 110 ANVLVALGRHDDAIRVYNRALQAEPRDVEIL 140
                 789************************9875 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.048
      TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                 + +++ + ++++Ai+ ++ al+ + +d +++
  AJA92266.1 144 GIVYAGQKKHKKAIKFFESALDMQKGDIDTL 174
                 67899999*************9888877665 PP

  == domain 6  score: 15.0 bits;  conditional E-value: 7.4e-05
      TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                 l+  ll+ ++ + A +++++a++l+P+d +a ++la
  AJA92266.1 177 LGNSLLEIENNKSAYKYFQQAVKLDPNDFDATFRLA 212
                 566778888999***********************9 PP

  == domain 7  score: 5.6 bits;  conditional E-value: 0.078
      TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawll 40 
                 +a+ +la  + +l  p++A+  ++++l+++ ++ ++++ 
  AJA92266.1 206 DATFRLAITCNNLKMPERALINFNKLLRRDRNNVDVLIN 244
                 68899************************9999988775 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.46
      TPR_14  16 dpdeAiallrralalaPddaeawl 39 
                 ++ +Ai +++++l+++P++  a +
  AJA92266.1 254 KYGRAILCYDKVLKQDPQEMNAVY 277
                 67899************9876655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   3.6e-11   1.6e-08       2      58 ..      12      68 ..       4      75 .. 0.92
   2 !   35.9   0.3   1.7e-11     8e-09       1      58 [.      79     136 ..      79     143 .. 0.95
   3 ?    7.6   0.0     0.011       5.3       3      36 ..     149     182 ..     147     188 .. 0.84
   4 !   17.9   0.0   7.3e-06    0.0034       6      57 ..     186     237 ..     181     245 .. 0.90
   5 ?    2.2   0.0      0.57   2.6e+02       4      29 ..     252     277 ..     249     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.6e-11
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                +++++++ A++l+e++l+ dp+n+ea ++   +l +lg ++eA++ L+  ++++p+d
  AJA92266.1 12 FENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFLKKNPND 68
                5778*******************************************9999999995 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.7e-11
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 l+++ +++eAl+ +  al+ dpkn+ a+ + A++l+alg+ d+A+++ +++++++p d
  AJA92266.1  79 LYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAIRVYNRALQAEPRD 136
                 6899**************************************************9986 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.011
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeall 36 
                  ++++  A++++e+al+   ++ + + +L + ll
  AJA92266.1 149 GQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLL 182
                 6899**************9999988877777666 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 7.3e-06
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 +  +A ++++qa + dp++ +a  +LA+ + +l+ ++ A    ++l++ d++
  AJA92266.1 186 NNKSAYKYFQQAVKLDPNDFDATFRLAITCNNLKMPERALINFNKLLRRDRN 237
                 5578************************************999999999998 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.57
      TPR_19   4 egdyaeAlalleqalqedpknaearl 29 
                 +++y +A+  + ++l++dp+  +a +
  AJA92266.1 252 MEKYGRAILCYDKVLKQDPQEMNAVY 277
                 67899999999999999999666655 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   3.4e-14   1.6e-11       1      80 [.      13      93 ..      13      95 .. 0.97
   2 !   26.5   0.0   1.2e-08   5.5e-06      16      81 ..      62     128 ..      58     129 .. 0.89
   3 !   16.1   0.1   2.1e-05    0.0096       2      80 ..     150     229 ..     149     231 .. 0.92
   4 !   15.8   0.4   2.6e-05     0.012       3      52 ..     253     303 ..     251     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.4e-14
                HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
      ANAPC3  1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                +++n+++Ai l+e++l++++++pe++  +  cl ++g+y++A+e l+ + k+n+++  ++y ++ +l++++++eeA+++++
  AJA92266.1 13 ENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFlKKNPNDFVALYNKGTTLYDMDQHEEALDTFD 93
                689***************************************************************************987 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.2e-08
                 H.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3  16 laaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 l++++++  ++y ++ +ly + q+++A++ +++a k+++k+ +++  +A +l++L+++++Ai+++ +
  AJA92266.1  62 LKKNPNDFVALYNKGTTLYDMDQHEEALDTFDTAlKIDPKNSQALCNKANVLVALGRHDDAIRVYNR 128
                 45556666668889*************************************************9875 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 2.1e-05
                 TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
      ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                 q+++k+Ai ++e +l +++ + + +  l+ +l++ ++ k+Ay+++++a kl++++  + + +A ++  Lk  e A+  + 
  AJA92266.1 150 QKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENNKSAYKYFQQAvKLDPNDFDATFRLAITCNNLKMPERALINFN 229
                 789************999999999*****************************************999998888876665 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 2.6e-05
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHH CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.kln 52 
                 ++y  Ai++++++l+++++  +++y+++++  ++++ k+ ++l++k+ k +
  AJA92266.1 253 EKYGRAILCYDKVLKQDPQEMNAVYYKSKSTAKQNDEKQTCNLVSKLlKFD 303
                 67999**************************************99985555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0039       1.8      13      35 ..      15      35 ..      12      36 .. 0.85
   2 ?    4.5   0.0     0.092        42       4      23 ..      40      59 ..      37      68 .. 0.82
   3 ?    4.2   0.0      0.11        52       1      29 [.      71      99 ..      71     103 .. 0.84
   4 !   18.0   0.0   4.6e-06    0.0021       1      32 [.     105     134 ..     105     138 .. 0.84
   5 !   12.5   0.0   0.00025      0.11       2      33 ..     140     169 ..     139     172 .. 0.87
   6 !   12.1   0.0   0.00034      0.16       1      34 [.     173     204 ..     173     208 .. 0.91
   7 ?    5.2   0.0     0.053        25       9      35 ..     249     273 ..     241     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
       TPR_7 13 GdyeeAielyeqsLaltkdpeda 35
                 ++++Ai+l+e+   l +dp+++
  AJA92266.1 15 ENFQKAIKLFEK--ILKSDPDNP 35
                58**********..888888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.092
       TPR_7  4 nLarlysrlGdyeeAielye 23
                n  ++  +lG+y eAie +e
  AJA92266.1 40 NKTSCLAELGKYNEAIEQLE 59
                66678899********9877 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLalt 29
                aL+n + +  ++ ++eeA++ +  +L ++
  AJA92266.1 71 ALYNKGTTLYDMDQHEEALDTFDTALKID 99
                799999*****************955544 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 4.6e-06
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                 aL+n a++ ++lG++++Ai++y ++L    +p
  AJA92266.1 105 ALCNKANVLVALGRHDDAIRVYNRAL--QAEP 134
                 89**********************55..4444 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00025
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33 
                 L+n++ +y  + ++++Ai+++e   al+ + +
  AJA92266.1 140 LNNIGIVYAGQKKHKKAIKFFES--ALDMQKG 169
                 89*********************..6665555 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00034
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34 
                 +L+nL++   +  + + A ++++q  a+  dp+d
  AJA92266.1 173 TLCNLGNSLLEIENNKSAYKYFQQ--AVKLDPND 204
                 79**********************..88887765 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.053
       TPR_7   9 ysrlGdyeeAielyeqsLaltkdpeda 35 
                  + + +y +Ai +y +  +l  dp+++
  AJA92266.1 249 LHLMEKYGRAILCYDK--VLKQDPQEM 273
                 55578999********..*****9987 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00047      0.22       2      33 .]       3      34 ..       2      34 .. 0.86
   2 !   11.4   0.0   0.00088       0.4       9      32 ..      44      67 ..      42      68 .. 0.92
   3 !   13.9   0.0   0.00014     0.065       2      32 ..      71     101 ..      70     102 .. 0.95
   4 ?    7.2   0.0     0.019       8.9       7      31 ..     110     134 ..     104     136 .. 0.78
   5 ?    4.2   0.0      0.17        79       6      27 ..     143     164 ..     142     166 .. 0.88
   6 ?    5.9   0.0     0.052        24       5      32 ..     176     203 ..     173     204 .. 0.88
   7 ?    4.9   0.0       0.1        46       1      29 [.     206     234 ..     206     238 .. 0.90
   8 ?    4.6   0.0      0.13        59       2      32 ..     241     271 ..     240     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00047
                HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPdS 33
                +l+ ++   ++  + +kA++++e+++k+ Pd+
  AJA92266.1  3 SLLEQGIQNFENENFQKAIKLFEKILKSDPDN 34
                5788887778855*****************95 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00088
                HHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  9 syrklgdtdkAlealerlikeYPd 32
                ++ +lg++ +A+e le ++k+ P+
  AJA92266.1 44 CLAELGKYNEAIEQLEIFLKKNPN 67
                778899*****************9 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00014
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                 Aly+ +  ++ ++++++Al++++  +k  P+
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTALKIDPK 101
                 9**************************9997 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.019
                 HHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   7 alsyrklgdtdkAlealerlikeYP 31 
                 a  + +lg++d+A++ ++r ++  P
  AJA92266.1 110 ANVLVALGRHDDAIRVYNRALQAEP 134
                 55556679************99877 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.17
                 HHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   6 lalsyrklgdtdkAlealerli 27 
                 ++  y  ++++ kA++ +e+ +
  AJA92266.1 143 IGIVYAGQKKHKKAIKFFESAL 164
                 789999999**********987 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.052
                 HHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
       TPR_6   5 klalsyrk.lgdtdkAlealerlikeYPd 32 
                 +l+ s+++   +   A +++++ +k  P+
  AJA92266.1 176 NLGNSLLEiE-NNKSAYKYFQQAVKLDPN 203
                 5899999955.8889***********998 PP

  == domain 7  score: 4.9 bits;  conditional E-value: 0.1
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlike 29 
                 dA ++la    +l+ +++Al  +++l+++
  AJA92266.1 206 DATFRLAITCNNLKMPERALINFNKLLRR 234
                 6889***9999999************998 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.13
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                 +l + ++s+  + ++ +A+  +++++k+ P+
  AJA92266.1 241 VLINKGYSLHLMEKYGRAILCYDKVLKQDPQ 271
                 56677889999889**************996 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.1e-09   2.4e-06       7      62 ..      13      68 ..      11      72 .. 0.95
   2 !   10.6   0.0     0.001      0.47      25      65 ..      65     105 ..      62     110 .. 0.93
   3 !   16.3   0.0   1.7e-05    0.0079       8      62 ..     116     170 ..     109     175 .. 0.90
   4 !    9.4   0.0    0.0024       1.1       4      65 ..     146     207 ..     143     213 .. 0.94
   5 ?    3.8   0.0      0.14        66       5      58 ..     181     234 ..     177     245 .. 0.76
   6 ?    0.9   0.0       1.1   5.1e+02      12      63 ..     222     273 ..     216     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.1e-09
       TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62
                ++e++++a++  e +l  +Pd pe +     +la+lG +++A++ Le +l ++p++
  AJA92266.1 13 ENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFLKKNPND 68
                6899*************************************************987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
       TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                 +P+d   ++  G  l+ +++ ++Al+ ++++l ++p++ +a
  AJA92266.1  65 NPNDFVALYNKGTTLYDMDQHEEALDTFDTALKIDPKNSQA 105
                 6999999*****************************99887 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.7e-05
       TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                   +++ a++v++r l+  P+d+e +   G+++a +   ++A++ +e +l+++  +
  AJA92266.1 116 LGRHDDAIRVYNRALQAEPRDVEILNNIGIVYAGQKKHKKAIKFFESALDMQKGD 170
                 57899*******************************************9987655 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0024
       TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                 +++ ++++ +a++  e+ l ++  d++ +   G  l + ++ + A + +++++ l+p++ da
  AJA92266.1 146 VYAGQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENNKSAYKYFQQAVKLDPNDFDA 207
                 79999****************************************************98776 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.14
       TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                 +++ e++  a ++ +  + l+P+d +  +  ++    l  ++ Al  ++  l+ 
  AJA92266.1 181 LLEIENNKSAYKYFQQAVKLDPNDFDATFRLAITCNNLKMPERALINFNKLLRR 234
                 666688899999999999999999999888888877777777777777666655 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 1.1
       TPR_9  12 eralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdap 63 
                 eral   + ll  + + ++ +   G  l+ ++ +  A+ + +  l ++p+  
  AJA92266.1 222 ERALINFNKLLRRDRNNVDVLINKGYSLHLMEKYGRAILCYDKVLKQDPQEM 273
                 6777777777777888888888888888888888888888888888888765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00015     0.069       8      54 ..      21      67 ..      15      76 .. 0.90
   2 !    9.2   0.1    0.0032       1.5       8      44 ..      55      91 ..      55      96 .. 0.93
   3 !   11.4   0.2   0.00066       0.3       3      42 ..      84     123 ..      82     126 .. 0.93
   4 ?    5.8   0.0     0.038        18      12      43 ..     127     158 ..     123     173 .. 0.87
   5 ?    4.1   0.1      0.13        59       1      49 [.     150     198 ..     150     201 .. 0.87
   6 !   16.3   0.0   2.1e-05    0.0095       9      55 ..     192     238 ..     184     247 .. 0.91
   7 ?    3.3   0.2      0.23     1e+02      14      58 ..     265     309 ..     261     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
      TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54
                ++ +e+ l+++pd+ +a ++    l++ g+y eA+eqL  +lk++ +
  AJA92266.1 21 IKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFLKKNPN 67
                566788899******************************99999976 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0032
      TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAleq 44
                +++le  l++np+d  a ++  + l+   ++eeAl+ 
  AJA92266.1 55 IEQLEIFLKKNPNDFVALYNKGTTLYDMDQHEEALDT 91
                57899999***************************97 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00066
      TPR_20   3 adapelaeleaalaanpddldarldlAlallaagryeeAl 42 
                 ++++ l+++++al+ +p++ +a ++ A++l+a gr+++A+
  AJA92266.1  84 QHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAI 123
                 56788999*******************************8 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.038
      TPR_20  12 eaalaanpddldarldlAlallaagryeeAle 43 
                  +al+a+p d+++  +   +++ ++++++A++
  AJA92266.1 127 NRALQAEPRDVEILNNIGIVYAGQKKHKKAIK 158
                 5799**************************97 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.13
      TPR_20   1 qaadapelaeleaalaanpddldarldlAlallaagryeeAleqLleil 49 
                 q+++++ ++ +e+al  ++ d+d+ ++l + ll+ ++++ A + + + +
  AJA92266.1 150 QKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENNKSAYKYFQQAV 198
                 56788899999*****************************998766665 PP

  == domain 6  score: 16.3 bits;  conditional E-value: 2.1e-05
      TPR_20   9 aeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                 + +++a++ +p+d da + lA   +  +  e Al ++ ++l+rdr+ 
  AJA92266.1 192 KYFQQAVKLDPNDFDATFRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 6689*****************************************86 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.23
      TPR_20  14 alaanpddldarldlAlallaagryeeAleqLleilkrdrkwedd 58 
                  l+++p++++a +  ++  ++++++++  ++  ++lk d + + +
  AJA92266.1 265 VLKQDPQEMNAVYYKSKSTAKQNDEKQTCNLVSKLLKFDASHDHE 309
                 5899********************************999887655 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       1.1   4.9e+02      17      37 ..      16      29 ..      11      36 .. 0.58
   2 ?    0.4   0.1       1.4   6.6e+02      12      26 ..      45      59 ..      45      59 .. 0.83
   3 ?    6.6   0.0     0.016       7.1       4      30 ..      71      97 ..      70      98 .. 0.86
   4 !   10.0   0.5    0.0013      0.62       4      30 ..     105     131 ..     104     133 .. 0.92
   5 !   19.2   0.0   1.7e-06   0.00078       4      33 ..     139     168 ..     137     168 .. 0.94
   6 ?    3.0   0.0      0.22     1e+02       3      30 ..     172     199 ..     171     200 .. 0.90
   7 ?   -1.2   0.0       4.5   2.1e+03      26      40 ..     256     270 ..     246     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.1
      TPR_10 17 rydeAealleealairrrllG 37
                ++++A +l+e       ++l 
  AJA92266.1 16 NFQKAIKLFE-------KILK 29
                4555555555.......5555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.4
      TPR_10 12 lrqrgrydeAealle 26
                l ++g+y+eA + le
  AJA92266.1 45 LAELGKYNEAIEQLE 59
                5689******98776 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.016
      TPR_10  4 slnNLanalrqrgrydeAealleeala 30
                +l N + +l+++ +++eA++ ++ al 
  AJA92266.1 71 ALYNKGTTLYDMDQHEEALDTFDTALK 97
                67899*************998888776 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0013
      TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                 +l N an+l ++gr+d+A + + +al+
  AJA92266.1 105 ALCNKANVLVALGRHDDAIRVYNRALQ 131
                 67899*******************998 PP

  == domain 5  score: 19.2 bits;  conditional E-value: 1.7e-06
      TPR_10   4 slnNLanalrqrgrydeAealleealairr 33 
                 +lnN+++++  ++++++A +++e al++++
  AJA92266.1 139 ILNNIGIVYAGQKKHKKAIKFFESALDMQK 168
                 79************************9975 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.22
      TPR_10   3 sslnNLanalrqrgrydeAealleeala 30 
                  +l NL+n l +  + + A +++++a+ 
  AJA92266.1 172 DTLCNLGNSLLEIENNKSAYKYFQQAVK 199
                 5899***************999999986 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 4.5
      TPR_10  26 eealairrrllGpdH 40 
                  +a+ ++ ++l +d+
  AJA92266.1 256 GRAILCYDKVLKQDP 270
                 689999999998886 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.7e-05    0.0077     208     258 ..       8      58 ..       2      81 .. 0.80
   2 !    9.1   0.2    0.0016      0.76     213     256 ..      81     124 ..      64     133 .. 0.84
   3 !   11.9   0.2   0.00023      0.11     198     244 ..     100     146 ..      81     156 .. 0.72
   4 !   16.0   0.1   1.3e-05    0.0061     181     265 ..     117     200 ..     111     209 .. 0.88
   5 ?    4.8   0.1     0.035        16     208     255 ..     212     259 ..     205     297 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                 HHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHH CS
  Coatomer_E 208 AvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsern 258
                  + +   +++++A +l ++ L++d+ ++e++iN + +  +lgk +e++e+ 
  AJA92266.1   8 GIQNFENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQL 58 
                 566677899***********************************8887764 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                 HTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
  Coatomer_E 213 llgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                  ++++eeA     +aL+ d+k+ ++L N   +   lg+ ++++ 
  AJA92266.1  81 DMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAIR 124
                 68899***********************9999999999988765 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00023
                 ---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHH CS
  Coatomer_E 198 kstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvva 244
                 ++++  l  kA v ++lgr+++A  + + aL+ +++d e L N+ ++
  AJA92266.1 100 PKNSQALCNKANVLVALGRHDDAIRVYNRALQAEPRDVEILNNIGIV 146
                 46777888889999999999999999999999999999999987544 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.3e-05
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHH CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsqlkls 265
                 ++  dA  +++   +  ++   +ln   +v   ++++++A +  ++aLd ++ d +tL Nl  + ++++ + ++  ++++q  + 
  AJA92266.1 117 GRHDDAIRVYNRALQAEPRDVEILNNIGIVYAGQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENN-KSAYKYFQQAVKL 200
                 567899999998888889999*****************************************999999998.8888999987665 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.035
                 HHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
  Coatomer_E 208 AvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                 A+ +  l+ +e A    ++ L +d ++ ++LiN   + ++++k   ++
  AJA92266.1 212 AITCNNLKMPERALINFNKLLRRDRNNVDVLINKGYSLHLMEKYGRAI 259
                 77788899999**********************999998888876654 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.015       6.8      14      37 ..      14      37 ..       9      38 .. 0.89
   2 ?    6.6   0.0     0.018       8.4      14      33 ..      48      67 ..      45      69 .. 0.92
   3 !   16.8   0.0   1.2e-05    0.0054       5      38 ..      73     106 ..      70     107 .. 0.86
   4 ?    4.2   0.0       0.1        47      14      34 ..     116     136 ..     114     141 .. 0.90
   5 ?    0.1   0.0       1.8   8.4e+02       7      31 ..     143     167 ..     138     170 .. 0.83
   6 ?   -1.5   0.0       5.8   2.7e+03      18      34 ..     188     204 ..     181     209 .. 0.72
   7 ?   -1.7   0.0       6.9   3.2e+03       4      34 ..     208     238 ..     205     242 .. 0.80
   8 ?    2.3   0.1       0.4   1.8e+02      14      37 ..     252     275 ..     251     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                HT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenrQa 37
                  ++++A ++ + +L+ +P+n  a
  AJA92266.1 14 NENFQKAIKLFEKILKSDPDNPEA 37
                5799*****************876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.018
                HT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPe 33
                lg+Y+eA + ++ +L++ P+
  AJA92266.1 48 LGKYNEAIEQLEIFLKKNPN 67
                89****************98 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C   5 YylAlGhyklgeYseArryvdalLeiEPenrQaq 38 
                 Y      y + +++eA+   d+ L+i+P+n+Qa+
  AJA92266.1  73 YNKGTTLYDMDQHEEALDTFDTALKIDPKNSQAL 106
                 555556688999********************96 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.1
                 HT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  14 lgeYseArryvdalLeiEPen 34 
                 lg++++A r  ++ L+ EP+ 
  AJA92266.1 116 LGRHDDAIRVYNRALQAEPRD 136
                 799****************86 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.8
                 HHHHHHHHT-HHHHHHHHHHHHHHT CS
  Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiE 31 
                 + + ++ ++++++A ++ +  L ++
  AJA92266.1 143 IGIVYAGQKKHKKAIKFFESALDMQ 167
                 667788999**********999876 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 5.8
                 HHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C  18 seArryvdalLeiEPen 34 
                 + A +y ++  +++P+ 
  AJA92266.1 188 KSAYKYFQQAVKLDPND 204
                 55778888888888875 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 6.9
                 HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPen 34 
                  + lA+ +  l+  ++A+   + lL+ + +n
  AJA92266.1 208 TFRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 5678888888888899999999999999888 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.4
                 HT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQa 37 
                 + +Y +A  + d +L+ +P+ ++a
  AJA92266.1 252 MEKYGRAILCYDKVLKQDPQEMNA 275
                 5789***************99887 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00018     0.083     183     292 ..      15     127 ..       6     129 .. 0.88
   2 !   23.1   0.0     7e-08   3.2e-05     184     293 ..     118     230 ..     117     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                 T-HHHHHHHHHHHHTT-GGG.HHHHHHHHHHTT..-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHH CS
       ChAPs 183 krydralellekLkeeepev.villarvlllad..eEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvY 278
                 +++++a++l+ek+ +++p+   +++ +   la+  +  +a++ l+  l+++++d   L  +   l + +++e Al++ + a k+ P +++     ++v 
  AJA92266.1  15 ENFQKAIKLFEKILKSDPDNpEAIINKTSCLAElgKYNEAIEQLEIFLKKNPNDFVALYNKGTTLYDMDQHEEALDTFDTALKIDPKNSQALCNKANVL 113
                 68999********99998652677777766655226679************************************************************ PP

                 HHTT-HHHHHHHHH CS
       ChAPs 279 ikledienALltLN 292
                 ++l+  ++A+   N
  AJA92266.1 114 VALGRHDDAIRVYN 127
                 ****9999987766 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 7e-08
                 -HHHHHHHHHHHHTT-GGGHHHHHH...HHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHHHHHH-TT-HHHHHHHHHHHH CS
       ChAPs 184 rydralellekLkeeepevvillar...vllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakravksaPsefktWalLvkvYi 279
                 r+d a+++ ++  ++ep  v +l     v+  + +  +a+k  +++l+ ++ d + L+   + ll+ ++++ A +  ++avk+ P++f   ++L+ +  
  AJA92266.1 118 RHDDAIRVYNRALQAEPRDVEILNNigiVYAGQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENNKSAYKYFQQAVKLDPNDFDATFRLAITCN 216
                 5677888888877777766666665111566678899************************************************************** PP

                 HTT-HHHHHHHHHT CS
       ChAPs 280 kledienALltLNs 293
                 +l+  e AL+  N 
  AJA92266.1 217 NLKMPERALINFNK 230
                 *********99996 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05    0.0093     161     276 ..      16     131 ..       9     133 .. 0.92
   2 !   19.3   0.1   1.1e-06   0.00051     144     253 ..     101     210 ..      77     225 .. 0.81
   3 !    6.5   0.0    0.0091       4.2     155     247 ..     146     238 ..     132     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
      TPR_15 161 qtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADale 259
                 + ++A++++++ l+ +pd+ e++ +    l +lg+++e+ e l+ + ++  +d +     ++ l  + + ++AL+ +   +k  +k+   l   A +l 
  AJA92266.1  16 NFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFLKKNPNDFVALYNKGTTLYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLV 114
                 5689**********************************9999999999998888877778999999********************************* PP

      TPR_15 260 qagradeAwrlRrqvwr 276
                 + gr d A r+  ++++
  AJA92266.1 115 ALGRHDDAIRVYNRALQ 131
                 **********9888876 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.1e-06
      TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlllLgrpkkALeylrk 239
                 ++++ l   a++  + g++d+A+r+y +Al+++p + e+ +++  ++   g+++  ++++k ++ +    + d +    l+  ll ++++k A +y+++
  AJA92266.1 101 KNSQALCNKANVLVALGRHDDAIRVYNRALQAEPRDVEILNNIGIVYA--GQKKH-KKAIKFFESALdmqKGDIDTLCNLGNSLLEIENNKSAYKYFQQ 196
                 677889999*********************************988888..54443.678887776666557777778899******************* PP

      TPR_15 240 qakenrkdplwlla 253
                   k  ++d+   + 
  AJA92266.1 197 AVKLDPNDFDATFR 210
                 **999999876655 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0091
      TPR_15 155 lyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkd 247
                 +y  + ++++A++ ++ Al+++ ++ +   +l   l++ ++++++ ++ ++  +   +d +    la     L+ p++AL  ++k ++  r++
  AJA92266.1 146 VYAGQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLLEIENNKSAYKYFQQAVKLDPNDFDATFRLAITCNNLKMPERALINFNKLLRRDRNN 238
                 566677777777777777777777777777777777777777766666655555556666666666666777777777777777766555554 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     4e-05     0.018      71     131 ..       3      63 ..       1      66 [. 0.92
   2 !    8.8   0.1    0.0046       2.1      72     123 ..      72     123 ..      68     133 .. 0.88
   3 ?   -0.6   0.0       3.6   1.7e+03      67     105 ..     169     207 ..     152     229 .. 0.70
   4 ?    0.3   0.1         2   9.1e+02      70     103 ..     274     307 ..     244     337 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4e-05
                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
  Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYls 131
                       +le+  +++++++++ a++l ++++ +dp+n ea   k ++l +lg+ +e+    +i+l 
       AJA92266.1   3 SLLEQGIQNFENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQLEIFLK 63 
                      67899999*****************************************999888777775 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0046
                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
  Alkyl_sulf_dimr  72 vlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                      + +k ++ ++ ++ + a+   + ++  dp+n++a   ka++l +lg++  + 
       AJA92266.1  72 LYNKGTTLYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAI 123
                      667888999*************************************987665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.6
                      TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHH CS
  Alkyl_sulf_dimr  67 Ggaekvlekakealkegdyrwaaellnhlvfadpenaea 105
                      G+ +++++  ++ l+ ++ + a +  +++v  dp++ +a
       AJA92266.1 169 GDIDTLCNLGNSLLEIENNKSAYKYFQQAVKLDPNDFDA 207
                      556666666666667777777777777777777766544 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 2
                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H CS
  Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpena 103
                      ++v  k k+ +k++d +  ++l+++l+  d +++
       AJA92266.1 274 NAVYYKSKSTAKQNDEKQTCNLVSKLLKFDASHD 307
                      5677777888888888888888888887654433 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0041       1.9      66     110 ..      10      54 ..       2      63 .. 0.89
   2 ?    4.9   0.1     0.048        22      68     102 ..      46      80 ..      36      98 .. 0.74
   3 !    8.8   0.0    0.0032       1.5      69     115 ..     115     162 ..      95     167 .. 0.75
   4 ?    5.4   0.1     0.033        15      62     117 ..     176     231 ..     163     234 .. 0.86
   5 ?    6.8   2.2     0.013         6      64     122 ..     246     301 ..     232     353 .] 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0041
     DUF4919  66 kelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeea 110
                 ++ ++e+++++i+l e++lk++P +++++ +    + +lgk +ea
  AJA92266.1  10 QNFENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEA 54 
                 57789******************************9999999876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.048
     DUF4919  68 lseeelkeiislaeealkknPfdlkqlnllayayk 102
                  +  +++e+i++ e  lkknP d+ +l++    + 
  AJA92266.1  46 AELGKYNEAIEQLEIFLKKNPNDFVALYNKGTTLY 80 
                 56689*******************99987644433 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0032
     DUF4919  69 seeelkeiislaeealkknPfdlkqlnllayay.kalgkkeeakiysk 115
                      +++i++ ++al+ +P d+++ln++ ++y +++++k+++k +++
  AJA92266.1 115 ALGRHDDAIRVYNRALQAEPRDVEILNNIGIVYaGQKKHKKAIKFFES 162
                 5566789********************998877256666666676665 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.033
     DUF4919  62 kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrl 117
                 +l +  l+ e+ k+++++ ++a+k +P d+ + + la+  ++l++ e+a i+ ++l
  AJA92266.1 176 NLGNSLLEIENNKSAYKYFQQAVKLDPNDFDATFRLAITCNNLKMPERALINFNKL 231
                 556677888999*********************************99999988876 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.013
     DUF4919  64 dkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkllk 122
                     + +e++ ++i    ++lk++P ++++ ++ + +  +++++++     + + kllk
  AJA92266.1 246 GYSLHLMEKYGRAILCYDKVLKQDPQEMNAVYYKSKSTAKQNDEKQ---TCNLVSKLLK 301
                 4566788999*************99766666555555555555555...4444555544 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00079      0.36      10      64 ..       5      56 ..       3      64 .. 0.81
   2 ?    6.0   0.0     0.027        12      11      35 ..      74      98 ..      71     118 .. 0.89
   3 ?    2.0   0.0       0.5   2.3e+02      23      72 ..     120     166 ..     113     173 .. 0.79
   4 ?   -0.5   0.0       3.1   1.4e+03      10      36 ..     243     269 ..     235     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00079
    Rapsyn_N 10 iekGLklyesndtekalrvWrkvLkktsdr.egkfrvLGcLitahsemGkykeale 64
                +e+G++ +e+ + +ka++++ k+Lk   d+ e   +   cL    +e+Gky ea+e
  AJA92266.1  5 LEQGIQNFENENFQKAIKLFEKILKSDPDNpEAIINKTSCL----AELGKYNEAIE 56
                689**********************8877514445555565....69999999997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.027
    Rapsyn_N 11 ekGLklyesndtekalrvWrkvLkk 35
                +kG  ly+ ++ e+al ++  +Lk 
  AJA92266.1 74 NKGTTLYDMDQHEEALDTFDTALKI 98
                69*******************9985 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.5
    Rapsyn_N  23 ekalrvWrkvLkktsdregkfrvLGcLitahsemGkykealefalaqldi 72 
                 + a+rv+ ++L+   +  + ++ +G+++       k+k+a++f    ld+
  AJA92266.1 120 DDAIRVYNRALQAEPRDVEILNNIGIVYAGQ---KKHKKAIKFFESALDM 166
                 6799999999999999999999999988764...4788888887766665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.1
    Rapsyn_N  10 iekGLklyesndtekalrvWrkvLkkt 36 
                 i+kG  l+   +  +a+  + kvLk+ 
  AJA92266.1 243 INKGYSLHLMEKYGRAILCYDKVLKQD 269
                 899999999999999*********975 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.3e-05     0.015      82     181 ..       7     104 ..       1     111 [. 0.85
   2 ?    5.4   0.0     0.028        13     154     179 ..     111     136 ..     108     142 .. 0.87
   3 ?   -0.9   0.1       2.4   1.1e+03      28      66 ..     262     300 ..     247     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
      TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLe...akkeeafaalvaelrGDilvaqgkldeAraaYqaAlaale 177
                 +  +++e++++++A + +e++l++ +d+  +a+++   ++ l++ +ky+eA+++Le   +k+++ f al++  +G  l+ +++ +eA + ++ Al+   
  AJA92266.1   7 QGIQNFENENFQKAIKLFEKILKSDPDN-PEAIINK--TSCLAELGKYNEAIEQLEiflKKNPNDFVALYN--KGTTLYDMDQHEEALDTFDTALKIDP 100
                 556899****************999888.6777765..799**************64448999******97..9*********************9887 PP

      TPR_21 178 ekar 181
                 ++++
  AJA92266.1 101 KNSQ 104
                 7754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
      TPR_21 154 DilvaqgkldeAraaYqaAlaaleek 179
                 ++lva g+ d+A   Y++Al+a   +
  AJA92266.1 111 NVLVALGRHDDAIRVYNRALQAEPRD 136
                 69******************998765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.4
      TPR_21  28 wqdyqeeqaeeAsalYqqlqeaveakdaakakeaaeela 66 
                 + +  ++  +e  a+Y + +++++++d++++ +++++l 
  AJA92266.1 262 YDKVLKQDPQEMNAVYYKSKSTAKQNDEKQTCNLVSKLL 300
                 556666777778888888888888888888777777765 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.33   1.5e+02      72     119 ..      11      58 ..       2      64 .. 0.84
   2 !   16.1   0.0   2.5e-05     0.012      72     123 ..      79     130 ..      64     139 .. 0.89
   3 !    9.9   0.0     0.002      0.92      67     123 ..     108     164 ..      98     174 .. 0.81
   4 ?   -1.9   0.0       8.7     4e+03      67      95 ..     176     204 ..     162     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.33
                 HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHH CS
        BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevY 119
                 +++ +  ++a++  e++++ +P + ++      +la +G+ +eA+e+ 
  AJA92266.1  11 NFENENFQKAIKLFEKILKSDPDNPEAIINKTSCLAELGKYNEAIEQL 58 
                 566677889999999999******9999999*************9975 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.5e-05
                 HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
        BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                 +  + ++eeal++ + +++ +P + ++ +     l ++Gr  +A++vY+r+ 
  AJA92266.1  79 LYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAIRVYNRAL 130
                 567789*******************************************985 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.002
                 HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
        BTAD  67 alaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlr 123
                   a+ +++lGr+++a++ ++++++++P + +    +   +a + +  +A++ +e++ 
  AJA92266.1 108 NKANVLVALGRHDDAIRVYNRALQAEPRDVEILNNIGIVYAGQKKHKKAIKFFESAL 164
                 556778999******************999998888888888888888888888765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 8.7
                 HHHHHHHHTT-HHHHHHHHHHHHHHSTT- CS
        BTAD  67 alaeaelrlGraeealaelealvaehPlr 95 
                  l + +l+++  + a ++ +++v+++P +
  AJA92266.1 176 NLGNSLLEIENNKSAYKYFQQAVKLDPND 204
                 45556677777778888888888888765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.061        28     102     124 ..      37      59 ..       8      64 .. 0.90
   2 ?    2.9   0.0      0.22     1e+02     102     127 ..      71      96 ..      67     104 .. 0.88
   3 !    7.7   0.0    0.0075       3.4     101     127 ..     104     130 ..     100     139 .. 0.90
   4 ?    0.9   0.0      0.97   4.4e+02      80     127 ..     155     198 ..     138     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.061
                 HHHHHHHHHHHTT-HHHHHHHHH CS
     DUF3856 102 avfsravaleelGrkdealkafr 124
                 a+++++ +l+elG+++ea+++++
  AJA92266.1  37 AIINKTSCLAELGKYNEAIEQLE 59 
                 79999999999999999998875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.22
                 HHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 102 avfsravaleelGrkdealkafrmag 127
                 a+++++++l ++ +++eal++f +a 
  AJA92266.1  71 ALYNKGTTLYDMDQHEEALDTFDTAL 96 
                 7899*****************99886 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0075
                 HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 101 aavfsravaleelGrkdealkafrmag 127
                 +a++++a  l  lGr+d+a++ ++ a 
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRAL 130
                 5899*******************9885 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.97
                 HHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856  80 kalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmag 127
                 ka+++f+   +++    k  i ++++ + +l e+ +++ a k+f++a+
  AJA92266.1 155 KAIKFFESALDMQ----KGDIDTLCNLGNSLLEIENNKSAYKYFQQAV 198
                 4555554433322....2337778888888888888888888888876 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1    0.0002      0.09       4      46 ..      12      53 ..      10      75 .. 0.82
   2 ?    0.7   0.0       1.4   6.6e+02       9      43 ..      85     118 ..      76     168 .. 0.69
   3 ?    4.1   0.0      0.12        56       7      53 ..     185     240 ..     179     258 .. 0.82
   4 ?    0.9   0.1       1.2   5.6e+02      11      63 ..     257     282 ..     248     309 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
      RPN6_N  4 laksdpkeaeelykeilskkskedeealreqeqalleLgelyr 46
                 ++++ ++a++l+++il++++++ e a+ ++ ++l eLg+  +
  AJA92266.1 12 FENENFQKAIKLFEKILKSDPDNPE-AIINKTSCLAELGKYNE 53
                56789****************8887.7778899******8644 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
      RPN6_N   9 pkeaeelykeilskkskedeealreqeqalleLge 43 
                  +ea +++ + l+ ++k++ +al ++ + l++Lg+
  AJA92266.1  85 HEEALDTFDTALKIDPKNS-QALCNKANVLVALGR 118
                 5666666667776666443.466666677777764 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
      RPN6_N   7 sdpkeaeelykeilskkskede.........ealreqeqalleLgelyrdqkkaee 53 
                 +++k+a + +++ ++ ++++ +         ++l+  e+al++  +l+r+ +++ +
  AJA92266.1 185 ENNKSAYKYFQQAVKLDPNDFDatfrlaitcNNLKMPERALINFNKLLRRDRNNVD 240
                 478899999999999999666668999999999***************98877654 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.2
      RPN6_N  11 eaeelykeilskkskedeealreqeqalleLgelyrdqkkaeeLaelikesrs 63 
                 +a+  y ++l+++++e +                            +  +s+s
  AJA92266.1 257 RAILCYDKVLKQDPQEMN---------------------------AVYYKSKS 282
                 555566666666664333...........................22222222 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.55   2.5e+02      15      25 ..      15      25 ..      10      31 .. 0.82
   2 ?    1.3   0.0      0.78   3.6e+02      13      22 ..      47      56 ..      45      59 .. 0.84
   3 !   10.7   0.1   0.00088      0.41       8      36 .]      76     102 ..      71     102 .. 0.91
   4 ?    0.5   0.1       1.4   6.5e+02      10      28 ..     146     162 ..     144     170 .. 0.74
   5 ?    4.2   0.0     0.098        45      20      36 .]     190     204 ..     188     204 .. 0.92
   6 ?    3.0   0.0      0.23   1.1e+02       8      25 ..     246     263 ..     245     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.55
                T-HHHHHHH.. CS
       TPR_3 15 kkyqeArelfs 25
                +++q+A+ lf 
  AJA92266.1 15 ENFQKAIKLFE 25
                89*******75 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.78
                HTT-HHHHHH CS
       TPR_3 13 nkkkyqeAre 22
                  +ky+eA+e
  AJA92266.1 47 ELGKYNEAIE 56
                579*****98 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00088
                 HHHHHHTT-HHHHHHH..HHHHHHH-TT- CS
       TPR_3   8 AaefynkkkyqeArelfsYallaildken 36 
                 + ++y++++ +eA+++f+   + ++d++n
  AJA92266.1  76 GTTLYDMDQHEEALDTFD--TALKIDPKN 102
                 5689************99..*******99 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.4
                 HHHHTT-HHHHHHH..HHH CS
       TPR_3  10 efynkkkyqeArelfsYal 28 
                 ++  +kk  +A+ +f  + 
  AJA92266.1 146 VYAGQKKHKKAIKFF--ES 162
                 56779999******5..44 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.098
                 HHHH..HHHHHHH-TT- CS
       TPR_3  20 ArelfsYallaildken 36 
                 A+ +f+  ++ +ld+++
  AJA92266.1 190 AYKYFQ--QAVKLDPND 204
                 99**99..******997 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.23
                 HHHHHHTT-HHHHHHH.. CS
       TPR_3   8 AaefynkkkyqeArelfs 25 
                 ++++++++ky  A+  ++
  AJA92266.1 246 GYSLHLMEKYGRAILCYD 263
                 79********99987665 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0085       3.9      18      97 ..      18      92 ..       6      99 .. 0.78
   2 ?    5.6   0.0      0.04        18       2      30 ..     104     132 ..     103     143 .. 0.83
   3 ?    2.5   0.0      0.36   1.7e+02      39      86 ..     206     253 ..     183     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0085
       TPR_5 18 dkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsdlgrereavsiv 97
                +ka++l+++ L+    +  +  a i  +s L  lG+ +ea++ L+  l+++++++ +  +     +L d+++++ea+ + 
  AJA92266.1 18 QKAIKLFEKILKS---DPDNPEAIINKTSCLAELGKYNEAIEQLEIFLKKNPNDFVALYN--KGTTLYDMDQHEEALDTF 92
                5777788777774...66677899*********************999999988865433..455677777778887665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.04
       TPR_5   2 vaaFeragarDstGhedkavplYrraLae 30 
                 +a+ ++a +    G++d a+ +Y+raL++
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQA 132
                 5677788888899999*********9987 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.36
       TPR_5  39 ratiqLassLRnlGeaeealaLLraeleapsdelddalaaflaLvLsd 86 
                  at  La +  nl  +e+al+  +++l +  +++d  ++   +L L++
  AJA92266.1 206 DATFRLAITCNNLKMPERALINFNKLLRRDRNNVDVLINKGYSLHLME 253
                 68999999999*********9999999999999988888777777765 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.13        59       3      25 ..      71      93 ..      70      94 .. 0.90
   2 !   11.5   0.0   0.00085      0.39       2      23 ..     104     125 ..     103     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.13
       TPR_4  3 allaLArallalGdldeAralle 25
                al++ + +l++  +++eA+++++
  AJA92266.1 71 ALYNKGTTLYDMDQHEEALDTFD 93
                8999***************9875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00085
       TPR_4   2 rallaLArallalGdldeAral 23 
                 +al + A +l alG++d+A ++
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRV 125
                 68999**************776 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.12        54      13      32 ..       5      26 ..       1      31 [. 0.73
   2 ?    3.3   0.0      0.32   1.5e+02      23      36 ..     153     166 ..     141     168 .. 0.81
   3 ?    6.2   0.0     0.038        17      19      36 ..     183     200 ..     174     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
        Sel1 13 ylnGl..gvpkDpekAiewyek 32
                ++ G    +  + +kAi+++ek
  AJA92266.1  5 LEQGIqnFENENFQKAIKLFEK 26
                5666653355699********9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.32
        Sel1  23 pekAiewyekAAeq 36 
                  +kAi+++e A ++
  AJA92266.1 153 HKKAIKFFESALDM 166
                 689********886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.038
        Sel1  19 vpkDpekAiewyekAAeq 36 
                 +  + ++A++++++A ++
  AJA92266.1 183 EIENNKSAYKYFQQAVKL 200
                 5569999********887 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.8   8.3e+02     135     157 ..       8      30 ..       6      34 .. 0.86
   2 ?    4.8   0.0     0.021       9.7      95     156 ..      36      97 ..      25     103 .. 0.86
   3 !    7.8   0.0    0.0025       1.2     101     202 ..     110     212 ..      97     230 .. 0.89
   4 ?   -3.9   0.0       9.3   4.3e+03     145     195 ..     256     273 ..     248     293 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                 HHHHHHHT-HHHHHHHHHHHHHH CS
    PknG_TPR 135 glaeLlegdyeeAaaeFdevlaa 157
                 g+ +  ++++++A++ F+++l+ 
  AJA92266.1   8 GIQNFENENFQKAIKLFEKILKS 30 
                 77888999***********9975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.021
                 HHHHHHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHH CS
    PknG_TPR  95 evpLaevrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevla 156
                 e  + ++    +lG+ +ea e L+ + +++++d+   + +g +   +++ eeA ++Fd+ l+
  AJA92266.1  36 EAIINKTSCLAELGKYNEAIEQLEIFLKKNPNDFVALYNKGTTLYDMDQHEEALDTFDTALK 97 
                 555666667789**********************9999999999999***********9876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0025
                 HHHHHHCT-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHH.HHHT---TT-HHHHHHHH-TT-HHHH CS
    PknG_TPR 101 vrahldlGdveearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAata.ElagetdeekyYrtVwrtdrgvvsAa 198
                 + + + lG +++a ++ ++  ++ ++d  +    g+    +++ ++A++ F++ l++  G+i     L     E+ +++ + ky++   + d +   A+
  AJA92266.1 110 ANVLVALGRHDDAIRVYNRALQAEPRDVEILNNIGIVYAGQKKHKKAIKFFESALDMQKGDIDTLCNLGNSLlEIENNKSAYKYFQQAVKLDPNDFDAT 208
                 5678899*************9***********************************************98752666777788***************** PP

                 HHHH CS
    PknG_TPR 199 FGla 202
                 F la
  AJA92266.1 209 FRLA 212
                 *998 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 9.3
                 HHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT-HHHHHHHH-TT-H CS
    PknG_TPR 145 eeAaaeFdevlaalpGEiaPklaLAataElagetdeekyYrtVwrtdrgvv 195
                  +A+ ++d+vl+  p E                                 +
  AJA92266.1 256 GRAILCYDKVLKQDPQE---------------------------------M 273
                 44444555554444433.................................3 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.074        34      93     113 ..      14      34 ..       8      43 .. 0.90
   2 ?    6.9   0.1      0.01       4.6      21      83 ..      65     117 ..      45     132 .. 0.72
   3 ?   -0.7   0.0       2.2     1e+03      93     110 ..     150     167 ..     119     176 .. 0.66
   4 ?    4.5   0.4     0.055        25      95     113 ..     186     204 ..     146     231 .. 0.81
   5 ?    3.1   0.3      0.15        70      94     128 ..     253     289 ..     249     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.074
                  HHHHHHHHHHHHHHHHH-TT- CS
  TOM20_plant  93 kenfekatqffqqavdedPdn 113
                  +enf+ka ++f++  + dPdn
   AJA92266.1  14 NENFQKAIKLFEKILKSDPDN 34 
                  689*****************9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                  -TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHH CS
  TOM20_plant  21 nPldadnllrWggallelsqfqsvaeakqmiqdaiskleeallidPkkhdalWcignaytsfa 83 
                  nP d   l   g +l ++ q           ++a+  ++ al idPk  +al   +n  ++ +
   AJA92266.1  65 NPNDFVALYNKGTTLYDMDQH----------EEALDTFDTALKIDPKNSQALCNKANVLVALG 117
                  555555555555555555554..........469999**************998888877655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.2
                  HHHHHHHHHHHHHHHHH- CS
  TOM20_plant  93 kenfekatqffqqavded 110
                  +++ +ka +ff+ a d +
   AJA92266.1 150 QKKHKKAIKFFESALDMQ 167
                  345566667777666655 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.055
                  HHHHHHHHHHHHHHH-TT- CS
  TOM20_plant  95 nfekatqffqqavdedPdn 113
                  n + a+++fqqav+ dP++
   AJA92266.1 186 NNKSAYKYFQQAVKLDPND 204
                  55679999****9999985 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.15
                  HHHHHHHHHHHHHHHH-TT..-HHHHHHHHHHHTHHH CS
  TOM20_plant  94 enfekatqffqqavdedPd..ndlyrkslelaakaPe 128
                  e++++a  ++++  ++dP+  n +y ks  +a++  e
   AJA92266.1 253 EKYGRAILCYDKVLKQDPQemNAVYYKSKSTAKQNDE 289
                  678999**********99755789***9888776655 PP

>> SPO22  Meiosis protein SPO22/ZIP4 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.24   1.1e+02     254     273 ..       7      26 ..       2      29 .. 0.84
   2 ?    2.2   0.0      0.23   1.1e+02     251     275 ..      72      96 ..      69     108 .. 0.89
   3 ?    5.2   0.0     0.027        12      37      72 ..     138     173 ..     114     181 .. 0.84
   4 ?    2.3   0.1      0.22        99      38      65 ..     173     200 ..     171     203 .. 0.90
   5 ?   -2.4   0.0       5.8   2.7e+03      11      35 ..     275     299 ..     258     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
       SPO22 254 kgekhykaknydeAaewyel 273
                 +g ++++++n+++A++++e+
  AJA92266.1   7 QGIQNFENENFQKAIKLFEK 26 
                 67799************997 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.23
       SPO22 251 LWnkgekhykaknydeAaewyelsl 275
                 L+nkg+ +y  ++ +eA++ +  +l
  AJA92266.1  72 LYNKGTTLYDMDQHEEALDTFDTAL 96 
                 8999999999999999999998887 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.027
       SPO22  37 rllyniGksllskkkyeeavkWLqraldilekqese 72 
                 ++l niG+    +kk+++a+k+++ ald+ + + ++
  AJA92266.1 138 EILNNIGIVYAGQKKHKKAIKFFESALDMQKGDIDT 173
                 46679999999*****************98866665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.22
       SPO22  38 llyniGksllskkkyeeavkWLqraldi 65 
                 +l n G sll+ +++++a k++q+a ++
  AJA92266.1 173 TLCNLGNSLLEIENNKSAYKYFQQAVKL 200
                 67799********************875 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 5.8
       SPO22  11 AehmlskakceenllrldpeeaeeL 35 
                 A+++ sk+++++n ++++ + + +L
  AJA92266.1 275 AVYYKSKSTAKQNDEKQTCNLVSKL 299
                 6677777776666666655555444 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.56   2.6e+02      52      82 ..       8      38 ..       2      52 .. 0.79
   2 ?    8.2   0.0    0.0041       1.9      23      76 ..      81     134 ..      67     139 .. 0.80
   3 ?   -1.8   0.0       5.1   2.3e+03      45      63 ..     155     173 ..     152     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.56
  HrpB1_HrpK 52 gvlliergrweeAlrlLreveaeasgtpyak 82
                g++  e+++++ A++l++++ ++ +  p a 
  AJA92266.1  8 GIQNFENENFQKAIKLFEKILKSDPDNPEAI 38
                77788999************99998877665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0041
  HrpB1_HrpK  23 asedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeas 76 
                 + +++e+a +  d    + P++ ++    +++l++ gr ++A+r+ +   ++++
  AJA92266.1  81 DMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALGRHDDAIRVYNRALQAEP 134
                 5667777777778788899*************************9988776655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.1
  HrpB1_HrpK  45 aeldllegvlliergrwee 63 
                 ++++++e  l +++g+++ 
  AJA92266.1 155 KAIKFFESALDMQKGDIDT 173
                 6889999999999999875 PP

>> COP23  Circadian oscillating protein COP23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.011       5.3      83     112 ..     104     133 ..      98     233 .. 0.91
   2 ?    2.6   0.0      0.23   1.1e+02      19      53 ..     268     301 ..     261     311 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
       COP23  83 gesCnkenlLftLkpgqdpeqvlqqlfdll 112
                 +  Cnk n+L+ L +++d+ +v ++ +++ 
  AJA92266.1 104 QALCNKANVLVALGRHDDAIRVYNRALQAE 133
                 337*******************99887765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.23
       COP23  19 tesqkvpvirWksesflgggytpqkRCqeVsqrlq 53 
                 +++q+++ + +ks+s + ++ ++++ C+ Vs+ l+
  AJA92266.1 268 QDPQEMNAVYYKSKS-TAKQNDEKQTCNLVSKLLK 301
                 446677778888776.6778899999****98765 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.087        40      13      29 ..      14      30 ..      12      31 .. 0.86
   2 ?    1.5   0.0      0.99   4.6e+02       8      23 ..      43      58 ..      43      65 .. 0.82
   3 ?   -1.1   0.0       6.5     3e+03      15      24 ..      84      93 ..      81      96 .. 0.86
   4 ?    2.7   0.0      0.39   1.8e+02       9      25 ..     112     128 ..     110     132 .. 0.85
   5 ?    0.6   0.0       1.8   8.4e+02      10      25 ..     147     162 ..     141     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.087
         PPR 13 nGkleeAlelfkeMkek 29
                n ++++A++lf++++++
  AJA92266.1 14 NENFQKAIKLFEKILKS 30
                6789*********9876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.99
         PPR  8 sgycknGkleeAlelf 23
                s+++  Gk+ eA+e +
  AJA92266.1 43 SCLAELGKYNEAIEQL 58
                68999*******9855 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6.5
         PPR 15 kleeAlelfk 24
                ++eeAl+ f+
  AJA92266.1 84 QHEEALDTFD 93
                78*****997 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.39
         PPR   9 gycknGkleeAlelfke 25 
                 +++  G++++A++++++
  AJA92266.1 112 VLVALGRHDDAIRVYNR 128
                 67889*********997 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.8
         PPR  10 ycknGkleeAlelfke 25 
                 y+   k+++A+++f+ 
  AJA92266.1 147 YAGQKKHKKAIKFFES 162
                 7778899*******85 PP

>> DUF2796  Protein of unknown function (DUF2796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       8.5   3.9e+03      38      78 ..      77     117 ..      56     125 .. 0.66
   2 ?   10.2  11.3    0.0011      0.52      62     101 ..     287     326 ..     267     345 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.5
     DUF2796  38 etdeqkaklakavakLekaealfalpeaakCkleeaevess 78 
                 +t  + ++ ++a +++++a ++   +++a C+ +++ v + 
  AJA92266.1  77 TTLYDMDQHEEALDTFDTALKIDPKNSQALCNKANVLVALG 117
                 55556667777777777777777777788888777766655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
     DUF2796  62 lpeaakCkleeaevessleeeeedeeeeedehdheheees 101
                  +e++ C+l +  +++++++++e+++e+++ehdheh++ +
  AJA92266.1 287 NDEKQTCNLVSKLLKFDASHDHEHDHEHDHEHDHEHDHMK 326
                 4567788888888888888888777777777777777655 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.8     0.003       1.4     114     171 ..     269     326 ..     246     350 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.003
         Zip 114 asssssesaakksvsndkveeseekedhvaeadtdadskeelrngkqeksesekeqas 171
                   ++ ++ ++k++  +++ +e++ ++ + +  + da++++e+ +++ + +++e+ + +
  AJA92266.1 269 DPQEMNAVYYKSKSTAKQNDEKQTCNLVSKLLKFDASHDHEHDHEHDHEHDHEHDHMK 326
                 3344444445555555566666666666666666666666666666666666655543 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  12.0    0.0048       2.2     165     215 ..     281     333 ..     263     345 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0048
      SelP_N 165 kevtk..aaeekpaeaeektehehahshkqghkhhekhghhHkekeelsesqq 215
                 k+++k  +++++ +  ++  + +++h h++ h+h ++h+h+H + +  ++ q+
  AJA92266.1 281 KSTAKqnDEKQTCNLVSKLLKFDASHDHEHDHEHDHEHDHEHDHMKFIEKIQK 333
                 33333113333344455666666667776666666666666666333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1250  (0.0697194); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2012.06
//
Query:       AJA92267.1  [L=141]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-31  104.7   4.6    7.5e-10   38.2   0.0    4.0  4  TPR_1         Tetratricopeptide repeat
    2.6e-25   86.4   2.9    5.5e-07   29.2   0.0    4.0  4  TPR_2         Tetratricopeptide repeat
    1.7e-20   71.5   6.3    1.8e-05   24.6   0.0    4.1  4  TPR_8         Tetratricopeptide repeat
    5.3e-19   67.6   4.2    7.5e-08   31.9   0.0    3.2  3  TPR_11        TPR repeat
    5.9e-17   60.8   1.1    1.2e-08   34.7   0.0    3.7  3  TPR_17        Tetratricopeptide repeat
      2e-15   56.8   1.3     0.0031   17.7   0.0    3.9  3  TPR_12        Tetratricopeptide repeat
    1.1e-13   51.6   0.0    8.5e-07   29.5   0.1    3.1  3  TPR_16        Tetratricopeptide repeat
    1.3e-12   46.8   0.6     0.0082   16.1   0.0    4.2  4  TPR_7         Tetratricopeptide repeat
    2.1e-12   47.4   0.7    1.3e-07   32.0   0.0    2.8  3  TPR_19        Tetratricopeptide repeat
    8.3e-10   38.7   0.1    9.9e-05   22.9   0.0    3.6  4  TPR_14        Tetratricopeptide repeat
    5.4e-07   29.3   0.5      0.082   12.8   0.0    3.7  4  TPR_10        Tetratricopeptide repeat
    3.2e-06   26.4   1.8    6.9e-05   21.9   0.1    2.0  2  NARP1         NMDA receptor-regulated protein 1
    3.4e-06   27.1   0.0    7.7e-06   26.0   0.0    1.7  2  TPR_9         Tetratricopeptide repeat
    3.5e-06   27.3   0.5        4.7    8.1   0.0    4.1  4  TPR_6         Tetratricopeptide repeat
    1.2e-05   25.3   1.3      0.058   13.4   0.2    2.3  2  SRP_TPR_like  Putative TPR-like repeat
      4e-05   23.8   1.4    7.6e-05   22.9   0.6    1.9  1  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    8.4e-05   22.6   8.5       0.15   12.2   0.6    3.4  3  MIT           MIT (microtubule interacting and transport) dom
     0.0054   16.2   0.4        4.7    6.7   0.1    3.2  3  SHNi-TPR      SHNi-TPR
     0.0061   16.0   0.2      0.012   15.1   0.1    1.4  1  Coatomer_E    Coatomer epsilon subunit
     0.0064   16.6   0.5        1.2    9.2   0.0    3.3  3  DUF3856       Domain of Unknown Function (DUF3856)
  ------ inclusion threshold ------
      0.013   14.8   0.3      0.028   13.6   0.3    1.6  1  TPR_15        Tetratricopeptide repeat
       0.02   15.1   1.7       0.61   10.3   0.0    3.2  4  NRBF2_MIT     MIT domain of nuclear receptor-binding factor 2
      0.023   13.9   0.4      0.096   11.9   0.4    1.8  1  FAT           FAT domain
      0.025   14.7   1.7       0.47   10.6   0.3    2.2  2  DUF357        Protein of unknown function (DUF357)
       0.08   12.4   5.7       0.17   11.3   0.7    2.5  2  SNAP          Soluble NSF attachment protein, SNAP
       0.33   11.9   2.5    1.5e+02    3.9   0.1    3.9  3  NSF           Aromatic-di-Alanine (AdAR) repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.1e-07   0.00015       1      31 [.       8      38 ..       8      41 .. 0.93
   2 !   25.9   0.0   8.2e-09   5.6e-06       2      31 ..      42      71 ..      41      74 .. 0.92
   3 !   38.2   0.0   1.1e-12   7.5e-10       3      34 .]      77     108 ..      75     108 .. 0.94
   4 !   19.0   0.2   1.3e-06   0.00089       1      30 [.     109     138 ..     109     141 .] 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.1e-07
                HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1  1 akalynlGnayfklgkydeAleyyekALeln 31
                akal n G++     +++eA+e+y+kAL++ 
  AJA92267.1  8 AKALVNEGVLSADYDEHKEAIEFYDKALKII 38
                89***************************95 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 8.2e-09
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALeln 31
                +++ n+G  + +l+ky++A+ +y+kA +++
  AJA92267.1 42 ETYLNKGISLVELEKYEDAVTCYDKAATID 71
                79************************9998 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 1.1e-12
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 ++yn+G+a+ +l+k+d+Al  yekA+e+ P +
  AJA92267.1  77 IWYNRGVALTQLEKFDDALSSYEKAIEVSPGY 108
                 7***************************9975 PP

  == domain 4  score: 19.0 bits;  conditional E-value: 1.3e-06
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                 a+a+yn++ ++ ++g+  eA+ ++ k+ el
  AJA92267.1 109 ADAWYNKAELLKHKGQDVEAETCFAKVKEL 138
                 89***********************99888 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.6e-06    0.0032       1      31 [.       8      38 ..       8      41 .. 0.92
   2 !   20.9   0.0   3.6e-07   0.00025       2      34 .]      42      74 ..      41      74 .. 0.92
   3 !   29.2   0.0     8e-10   5.5e-07       3      33 ..      77     107 ..      75     108 .. 0.94
   4 !   17.1   0.3   6.1e-06    0.0042       1      31 [.     109     139 ..     109     141 .] 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
       TPR_2  1 aealynlGlayyklgdyeeAleafekAleld 31
                a+al n G + +  ++++eA+e+++kAl++ 
  AJA92267.1  8 AKALVNEGVLSADYDEHKEAIEFYDKALKII 38
                7899************************985 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.6e-07
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                e + n G ++ +l +ye+A+ +++kA  +d n+
  AJA92267.1 42 ETYLNKGISLVELEKYEDAVTCYDKAATIDTND 74
                7899***********************999775 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 8e-10
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                 ++yn+G a+ +l ++++Al  +ekA+e  P+
  AJA92267.1  77 IWYNRGVALTQLEKFDDALSSYEKAIEVSPG 107
                 8**************************9997 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 6.1e-06
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                 a+a+yn ++++ ++g+  eA+ +f k+ el+
  AJA92267.1 109 ADAWYNKAELLKHKGQDVEAETCFAKVKELE 139
                 79************************98885 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   0.00013     0.091       2      30 ..       9      37 ..       8      40 .. 0.81
   2 !   19.6   0.0     1e-06   0.00071       2      33 ..      42      73 ..      41      74 .. 0.93
   3 !   24.6   0.0   2.6e-08   1.8e-05       3      32 ..      77     106 ..      76     108 .. 0.95
   4 !   15.5   0.1   2.1e-05     0.014       1      31 [.     109     139 ..     109     141 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekalel 30
                +a++n g +  +  +++eA+e+y kal++
  AJA92267.1  9 KALVNEGVLSADYDEHKEAIEFYDKALKI 37
                6777777777777899************9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1e-06
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                e y+n+g  + +l++ye A+ +y ka ++d +
  AJA92267.1 42 ETYLNKGISLVELEKYEDAVTCYDKAATIDTN 73
                78***************************976 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 2.6e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                 ++yn g ++ +l++++ A ++yeka+e +p
  AJA92267.1  77 IWYNRGVALTQLEKFDDALSSYEKAIEVSP 106
                 6***************************99 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 2.1e-05
                 CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                 a+a+yn++ +++ +g+  eA+ ++ k+ el+
  AJA92267.1 109 ADAWYNKAELLKHKGQDVEAETCFAKVKELE 139
                 79************************99986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0033       2.3      10      26 ..      24      40 ..      22      47 .. 0.80
   2 !   31.9   0.0   1.1e-10   7.5e-08       4      39 ..      51      86 ..      48      88 .. 0.92
   3 !   30.5   0.2   3.1e-10   2.2e-07       3      41 ..      84     122 ..      83     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
      TPR_11 10 yeeAieaYkkAlkldPd 26
                 +eAie Y kAlk+ ++
  AJA92267.1 24 HKEAIEFYDKALKIIET 40
                68***********9665 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.1e-10
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                ++e+ kye+A+++Y kA  +d ++  ++yn+G+a+ 
  AJA92267.1 51 LVELEKYEDAVTCYDKAATIDTNDSLIWYNRGVALT 86
                7899*****************************986 PP

  == domain 3  score: 30.5 bits;  conditional E-value: 3.1e-10
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                 a++++ k+++A+ +Y+kA++ +P +a+a+yn ++++  +
  AJA92267.1  84 ALTQLEKFDDALSSYEKAIEVSPGYADAWYNKAELLKHK 122
                 6899***************************99988765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.56   3.8e+02      13      32 ..      41      60 ..      23      62 .. 0.80
   2 !   21.0   0.0   4.2e-07   0.00029       1      33 [.      63      95 ..      63      96 .. 0.96
   3 !   34.7   0.0   1.8e-11   1.2e-08       2      33 ..      98     129 ..      97     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.56
      TPR_17 13 adaynnLAelllknGdlmtA 32
                ++ y n++  l ++ ++++A
  AJA92267.1 41 SETYLNKGISLVELEKYEDA 60
                67888999888888888888 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.2e-07
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +y ka+ +d n++  ++n++++l ++ ++++A+
  AJA92267.1 63 CYDKAATIDTNDSLIWYNRGVALTQLEKFDDAL 95
                8***************************99996 PP

  == domain 3  score: 34.7 bits;  conditional E-value: 1.8e-11
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 y+ka+e  P +ada++n+Aell+++G+  +A+
  AJA92267.1  98 YEKAIEVSPGYADAWYNKAELLKHKGQDVEAE 129
                 9***************************9997 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00033      0.23      44      76 ..       7      39 ..       2      40 .. 0.80
   2 !   17.7   0.0   4.6e-06    0.0031       5      32 ..      77     104 ..      73     108 .. 0.87
   3 !   10.2   0.0     0.001       0.7       3      32 ..     109     138 ..     107     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
      TPR_12 44 tattlrnLgrlyralgryeeAlelleealaiae 76
                 a +l n g l    ++++eA+e++ +al+i e
  AJA92267.1  7 DAKALVNEGVLSADYDEHKEAIEFYDKALKIIE 39
                677888888888888899999999999998865 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 4.6e-06
      TPR_12   5 alnnlaavlrrlgrydeAlellekalei 32 
                 +++n++++l++l+++d+Al+ +eka+e+
  AJA92267.1  77 IWYNRGVALTQLEKFDDALSSYEKAIEV 104
                 6789999999999999999999999987 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.001
      TPR_12   3 atalnnlaavlrrlgrydeAlellekalei 32 
                 a a++n a++l + g+  eA++++ k+ e+
  AJA92267.1 109 ADAWYNKAELLKHKGQDVEAETCFAKVKEL 138
                 78999********************98775 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.02        13      32      62 ..       6      36 ..       2      42 .. 0.86
   2 !   15.9   0.0   2.3e-05     0.016       1      47 [.      45      88 ..      45      90 .. 0.89
   3 !   29.5   0.1   1.2e-09   8.5e-07       1      54 [.      79     129 ..      79     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
      TPR_16 32 daaeAllllgdaalrqgrlaeAaalyraalr 62
                ++a Al + g++ +   +++eA+++y++al+
  AJA92267.1  6 ADAKALVNEGVLSADYDEHKEAIEFYDKALK 36
                57889999999999999************96 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.3e-05
      TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrq 47
                l+++ +++++ +y+dA+  ++ a   d  +++    ++++g+a+ ++
  AJA92267.1 45 LNKGISLVELEKYEDAVTCYDKAATIDTNDSL---IWYNRGVALTQL 88
                67899***************999999977777...********9886 PP

  == domain 3  score: 29.5 bits;  conditional E-value: 1.2e-09
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                 ++++ a+ ++ ++ddA+  +e a++     P  a+A++++++++ ++g   eA+
  AJA92267.1  79 YNRGVALTQLEKFDDALSSYEKAIEVS---PGYADAWYNKAELLKHKGQDVEAE 129
                 6778888899*****************...******************999998 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0096       6.6      14      27 ..      23      36 ..      15      42 .. 0.86
   2 !   14.9   0.0   2.8e-05      0.02       1      31 [.      43      71 ..      43      76 .. 0.83
   3 !   16.1   0.0   1.2e-05    0.0082       2      32 ..      78     106 ..      77     107 .. 0.91
   4 ?    4.3   0.0     0.071        49       1      24 [.     111     134 ..     111     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0096
       TPR_7 14 dyeeAielyeqsLa 27
                +++eAie+y ++L 
  AJA92267.1 23 EHKEAIEFYDKALK 36
                789********764 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.8e-05
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkd 31
                ++ln +   ++l +ye+A+++y +  a t d
  AJA92267.1 43 TYLNKGISLVELEKYEDAVTCYDK--AATID 71
                68999999****************..65544 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.2e-05
       TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                 ++n +++  +l ++++A++ ye+  a++ +p
  AJA92267.1  78 WYNRGVALTQLEKFDDALSSYEK--AIEVSP 106
                 6899*******************..999887 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.071
       TPR_7   1 aLlnLarlysrlGdyeeAielyeq 24 
                 a++n a+l    G+  eA++++ +
  AJA92267.1 111 AWYNKAELLKHKGQDVEAETCFAK 134
                 78999*****************88 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0012       0.8       6      61 ..      23      77 ..      11      82 .. 0.89
   2 !   14.3   0.0   6.3e-05     0.044       2      45 ..      52      95 ..      51      96 .. 0.94
   3 !   32.0   0.0   1.8e-10   1.3e-07       5      54 ..      89     138 ..      85     141 .] 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
      TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61
                 + eA++++ +al+     +e  l+  + l++l  +++A  + d++   d +d+ +
  AJA92267.1 23 EHKEAIEFYDKALKIIE-TSETYLNKGISLVELEKYEDAVTCYDKAATIDTNDSLI 77
                6899********99966.88889999*******************99999998765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.3e-05
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45
                ++ ++y++A+  + +a + d +++ ++++   al +l  +d+A 
  AJA92267.1 52 VELEKYEDAVTCYDKAATIDTNDSLIWYNRGVALTQLEKFDDAL 95
                66789*************************************96 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 1.8e-10
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                 +++++Al+ +e+a++ +p++a+a+++ Ae+l   gq  eAe + +++ e 
  AJA92267.1  89 EKFDDALSSYEKAIEVSPGYADAWYNKAELLKHKGQDVEAETCFAKVKEL 138
                 789****************************************9998775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.057        39      15      30 ..      22      37 ..       8      47 .. 0.82
   2 !    9.6   0.0    0.0026       1.8       7      41 ..      47      81 ..      41      84 .. 0.85
   3 !   22.9   0.0   1.4e-07   9.9e-05       4      44 .]      78     118 ..      76     119 .. 0.95
   4 ?    4.9   0.1     0.084        58       2      26 ..     110     134 ..     109     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.057
      TPR_14 15 GdpdeAiallrralal 30
                ++++eAi+ +++al+ 
  AJA92267.1 22 DEHKEAIEFYDKALKI 37
                6899*********986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
      TPR_14  7 laeallalGdpdeAiallrralalaPddaeawlll 41
                 +  l +l+++++A++++++a   + +d  +w+  
  AJA92267.1 47 KGISLVELEKYEDAVTCYDKAATIDTNDSLIWYNR 81
                5778999************************9876 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.4e-07
      TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                 ++ ++ al +l+++d+A+  +++a++  P+ a+aw+  a+l
  AJA92267.1  78 WYNRGVALTQLEKFDDALSSYEKAIEVSPGYADAWYNKAEL 118
                 888999******************************99986 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.084
      TPR_14   2 eallalaeallalGdpdeAiallrr 26 
                 +a++  ae+l + G+  eA++++ +
  AJA92267.1 110 DAWYNKAELLKHKGQDVEAETCFAK 134
                 79******************99976 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.042        29      17      33 ..      23      39 ..      20      41 .. 0.88
   2 !    7.6   0.0     0.005       3.5       3      30 ..      42      69 ..      40      71 .. 0.90
   3 !   12.8   0.0   0.00012     0.082       7      31 ..      80     104 ..      79     105 .. 0.94
   4 ?   -1.3   0.0       3.2   2.2e+03       9      27 ..     116     134 ..     113     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
      TPR_10 17 rydeAealleealairr 33
                +++eA +++++al i +
  AJA92267.1 23 EHKEAIEFYDKALKIIE 39
                789**********9866 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.005
      TPR_10  3 sslnNLanalrqrgrydeAealleeala 30
                 ++ N ++ l ++ +y++A+  +++a  
  AJA92267.1 42 ETYLNKGISLVELEKYEDAVTCYDKAAT 69
                689999*******************976 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00012
      TPR_10   7 NLanalrqrgrydeAealleealai 31 
                 N ++al+q+ ++d+A+  +e+a+++
  AJA92267.1  80 NRGVALTQLEKFDDALSSYEKAIEV 104
                 779********************96 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.2
      TPR_10   9 analrqrgrydeAeallee 27 
                 a +l + g+  eAe  + +
  AJA92267.1 116 AELLKHKGQDVEAETCFAK 134
                 6778888999999987765 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.016        11     207     260 ..      23      75 ..      15      82 .. 0.70
   2 !   21.9   0.1     1e-07   6.9e-05     188     256 ..      73     139 ..      66     141 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
                 -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
       NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                 + ++A+e+ dka++   t+ e yl+K+  l      ++A+++ ++a  +D++D 
  AJA92267.1  23 EHKEAIEFYDKALKIIETS-ETYLNKGISLVELEKYEDAVTCYDKAATIDTNDS 75 
                 3446777777777777664.7778888777777788888888888888887775 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1e-07
                 SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
       NARP1 188 esallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                 + +l+w +  +A    +l++ + Al+  +kaie +p   + +++Ka++lkh+G+  +A ++  + ++l 
  AJA92267.1  73 NDSLIWYNRGVA--LTQLEKFDDALSSYEKAIEVSPGYADAWYNKAELLKHKGQDVEAETCFAKVKELE 139
                 556666555555..35788999************************************99999998875 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.5   5.9e+03      11      19 ..      31      39 ..      24      41 .. 0.79
   2 !   26.0   0.0   1.1e-08   7.7e-06       6      65 ..      52     111 ..      47     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.5
       TPR_9 11 weralavve 19
                +++al+++e
  AJA92267.1 31 YDKALKIIE 39
                678888887 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.1e-08
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                  + e++e a  +++    ++ +d   ++ RG++l ql+ +  Al   e +++++p  +da
  AJA92267.1  52 VELEKYEDAVTCYDKAATIDTNDSLIWYNRGVALTQLEKFDDALSSYEKAIEVSPGYADA 111
                 567999*************************************************65554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.48   3.3e+02      14      28 ..      22      36 ..       8      37 .. 0.73
   2 ?    5.8   0.0     0.036        25       3      26 ..      44      67 ..      42      70 .. 0.86
   3 !    8.1   0.0    0.0067       4.7       4      31 ..      79     106 ..      77     108 .. 0.89
   4 ?    6.6   0.0      0.02        14       1      27 [.     110     136 ..     110     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.48
                HHHHHHHHHHHHHHH CS
       TPR_6 14 gdtdkAlealerlik 28
                +++ +A+e +++ +k
  AJA92267.1 22 DEHKEAIEFYDKALK 36
                57889*****99886 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.036
                HHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  3 lyklalsyrklgdtdkAlealerl 26
                +++ + s+ +l ++++A++ +++ 
  AJA92267.1 44 YLNKGISLVELEKYEDAVTCYDKA 67
                7889999***88*********986 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0067
                 HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   4 yklalsyrklgdtdkAlealerlikeYP 31 
                 y+++ ++ +l + d+Al  +e+ i+  P
  AJA92267.1  79 YNRGVALTQLEKFDDALSSYEKAIEVSP 106
                 999******88************98666 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.02
                 HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerli 27 
                 dA y+ a++++  g+  +A + + ++ 
  AJA92267.1 110 DAWYNKAELLKHKGQDVEAETCFAKVK 136
                 79*********988999******9986 PP

>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   8.5e-05     0.058       5      44 ..      31      71 ..      21      80 .. 0.73
   2 !   11.4   0.1   0.00035      0.24      20      44 ..      81     105 ..      65     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-05
  SRP_TPR_like  5 yekilrl.egkelkkfkvvaliklekyeeaLkllkkgsals 44
                  y+k l++ e++e    k ++l++lekye+a++  +k+ +++
    AJA92267.1 31 YDKALKIiETSETYLNKGISLVELEKYEDAVTCYDKAATID 71
                  555555313444444599***************99998654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00035
  SRP_TPR_like  20 kvvaliklekyeeaLkllkkgsals 44 
                   + val +lek+++aL+  +k+ ++s
    AJA92267.1  81 RGVALTQLEKFDDALSSYEKAIEVS 105
                   88**************999987555 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.6   1.1e-07   7.6e-05       3      81 ..      22     100 ..      20     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.1e-07
                 T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                   +k+Ai +++++l +  e +e  + ++ +l ++++y+ A + ++ka  ++ ++  ++y  + +l +L+k+++A++ +ek
  AJA92267.1  22 DEHKEAIEFYDKAL-KIIETSETYLNKGISLVELEKYEDAVTCYDKAaTIDTNDSLIWYNRGVALTQLEKFDDALSSYEK 100
                 679***********.888888888889********************99**************************99998 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.6   0.00021      0.15       3      34 ..       7      38 ..       6      43 .. 0.92
   2 ?    6.3   0.2     0.014       9.9      10      31 ..      47      68 ..      38      70 .. 0.80
   3 !    8.1   0.1    0.0039       2.7      11      33 ..      82     104 ..      76     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
         MIT  3 kAlelvkkAveeDnagnyeeAlelYkealelL 34
                 A +lv++ v +    + +eA+e Y +al+++
  AJA92267.1  7 DAKALVNEGVLSADYDEHKEAIEFYDKALKII 38
                5999************************9876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
         MIT 10 kAveeDnagnyeeAlelYkeal 31
                k + + + ++ye+A+ +Y +a 
  AJA92267.1 47 KGISLVELEKYEDAVTCYDKAA 68
                556666779**********996 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0039
         MIT  11 AveeDnagnyeeAlelYkealel 33 
                  v + + +++++Al+ Y++a+e+
  AJA92267.1  82 GVALTQLEKFDDALSSYEKAIEV 104
                 566667899************95 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.37   2.6e+02      18      30 ..      25      37 ..      24      43 .. 0.83
   2 ?    4.5   0.0     0.034        23      13      27 ..      53      67 ..      49      70 .. 0.85
   3 !    6.7   0.1    0.0069       4.7      15      29 ..      89     103 ..      87     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.37
    SHNi-TPR 18 pqAveDlrkaLeL 30
                ++A+e ++kaL++
  AJA92267.1 25 KEAIEFYDKALKI 37
                5899999999998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.034
    SHNi-TPR 13 EnenFpqAveDlrka 27
                E e++++Av+ ++ka
  AJA92267.1 53 ELEKYEDAVTCYDKA 67
                77*******988876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0069
    SHNi-TPR  15 enFpqAveDlrkaLe 29 
                 e+F++A++ ++ka+e
  AJA92267.1  89 EKFDDALSSYEKAIE 103
                 9************87 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.7e-05     0.012     181     256 ..      55     130 ..      48     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                 THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHH CS
  Coatomer_E 181 ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevse 256
                 ek++dA   ++  +    + +l+   + v+  +l+++++A s+ ++a++  + ++++  N   + +h g+d e+ +
  AJA92267.1  55 EKYEDAVTCYDKAATIDTNDSLIWYNRGVALTQLEKFDDALSSYEKAIEVSPGYADAWYNKAELLKHKGQDVEAET 130
                 899*******99998877788899999*******************************************988765 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.64   4.4e+02     115     131 ..      23      39 ..       8      47 .. 0.51
   2 !    9.2   0.0    0.0017       1.2      58     128 ..      78     103 ..      45     109 .. 0.68
   3 ?    0.9   0.0      0.63   4.3e+02     102     129 ..     111     138 ..     107     141 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.64
                 -HHHHHHHHHHHHHHHH CS
     DUF3856 115 rkdealkafrmagemia 131
                  ++ea++ + +a  +i+
  AJA92267.1  23 EHKEAIEFYDKALKIIE 39 
                 33444444444444443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0017
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
     DUF3856  58 haglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmage 128
                 +                                             ++r+val +l + d+al ++++a e
  AJA92267.1  78 W---------------------------------------------YNRGVALTQLEKFDDALSSYEKAIE 103
                 3.............................................5666666666666666666666665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.63
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
     DUF3856 102 avfsravaleelGrkdealkafrmagem 129
                 a +++a  l+  G+  ea   f +++e+
  AJA92267.1 111 AWYNKAELLKHKGQDVEAETCFAKVKEL 138
                 66899999**********9999999886 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     4e-05     0.028     150     245 ..      12     106 ..       3     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
      TPR_15 150 laraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgplaaAlllLgrpkkALeylrkqakenr 245
                 +  + l  + +++++A++ y +Al+   +s++  ++ +  l++l++++    ++  + ++a    +d+ +w   + Al  L++ + AL  ++k  +  +
  AJA92267.1  12 VNEGVLSADYDEHKEAIEFYDKALKIIETSETYLNKGI-SLVELEKYED---AVTCYDKAAtidTNDSLIWYNRGVALTQLEKFDDALSSYEKAIEVSP 106
                 55555666778999999999999999999998888887.8999999995...99999999889899999999999999999999999999998776444 PP

>> NRBF2_MIT  MIT domain of nuclear receptor-binding factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0         1   7.2e+02      29      49 ..      22      42 ..       5      50 .. 0.68
   2 ?   10.3   0.0   0.00089      0.61      19      39 ..      52      72 ..      45      80 .. 0.84
   3 ?    0.7   0.0       0.9   6.2e+02      22      36 ..      89     103 ..      79     107 .. 0.81
   4 ?   -1.0   0.0       3.1   2.2e+03      13      35 ..     114     136 ..     105     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1
   NRBF2_MIT 29 schkkaaaylseamkltkseq 49
                  hk a ++  +a+k+ ++ +
  AJA92267.1 22 DEHKEAIEFYDKALKIIETSE 42
                558888888888888776554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00089
   NRBF2_MIT 19 laaGkyeeaischkkaaayls 39
                +   kye+a++c+ kaa + +
  AJA92267.1 52 VELEKYEDAVTCYDKAATIDT 72
                5567************98755 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.9
   NRBF2_MIT  22 Gkyeeaischkkaaa 36 
                  k+++a+s ++ka +
  AJA92267.1  89 EKFDDALSSYEKAIE 103
                 699999999999976 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.1
   NRBF2_MIT  13 rkadrllaaGkyeeaischkkaa 35 
                  ka+ l   G+  ea +c  k  
  AJA92267.1 114 NKAELLKHKGQDVEAETCFAKVK 136
                 57888888899999999998865 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00014     0.096     250     302 ..      80     125 ..      21     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                 TCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHH CS
         FAT 250 kkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvsk 302
                  +G  +++l+k       ++++l+sy +a e++p+ ++aw++ a +  ++ ++
  AJA92267.1  80 NRGVALTQLEK-------FDDALSSYEKAIEVSPGYADAWYNKAELLKHKGQD 125
                 33444445555.......9*********************9966555544444 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00068      0.47      18      57 ..      25      64 ..      10      67 .. 0.89
   2 ?    3.6   0.1       0.1        71       9      57 ..      84     132 ..      80     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00068
                ..TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
      DUF357 18 deesplgeaaeevlemaesYleDakyflekgdlvnAlasf 57
                +e  + +++a +++e  e Yl+ +   +e +++++A+ ++
  AJA92267.1 25 KEAIEFYDKALKIIETSETYLNKGISLVELEKYEDAVTCY 64
                5677899******************************996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                 HHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
      DUF357   9 alekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasf 57 
                 al +++  +d  s++++a e     a ++++ a+    kg  v+A  +f
  AJA92267.1  84 ALTQLEKFDDALSSYEKAIEVSPGYADAWYNKAELLKHKGQDVEAETCF 132
                 6777777777777888777888889999******9999**999999988 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00025      0.17     135     193 ..      21      79 ..       4      82 .. 0.83
   2 ?    3.3   0.4     0.066        45     128     144 ..      88     104 ..      81     141 .] 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGG CS
        SNAP 135 ieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvakkslennllky 193
                  +  ++A e+y++  +  ++++ +l+      elekye+A++ y+k a+  ++ +l+ y
  AJA92267.1  21 YDEHKEAIEFYDKALKIIETSETYLNKGISLVELEKYEDAVTCYDKAATIDTNDSLIWY 79 
                 556788999999998899999999999999999**************999999888766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.066
                 T--HHHHHHHHHHHHHH CS
        SNAP 128 lgdlekAieaYekAael 144
                 l+++++A+++YekA e+
  AJA92267.1  88 LEKFDDALSSYEKAIEV 104
                 44555555566655552 PP

>> NSF  Aromatic-di-Alanine (AdAR) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.81   5.6e+02       1       8 [.      27      34 ..      27      38 .. 0.85
   2 ?    3.9   0.1      0.22   1.5e+02       1       9 [.      60      68 ..      60      70 .. 0.86
   3 ?    3.2   0.0       0.4   2.7e+02       3      10 ..      96     103 ..      94     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.81
         NSF  1 AakhyekA 8 
                A+++y kA
  AJA92267.1 27 AIEFYDKA 34
                89*****9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.22
         NSF  1 AakhyekAa 9 
                A+ +y kAa
  AJA92267.1 60 AVTCYDKAA 68
                788*****9 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.4
         NSF   3 khyekAae 10 
                 + yekA+e
  AJA92267.1  96 SSYEKAIE 103
                 67****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 910.73
//
Query:       AJA92268.1  [L=108]
Description: succinate dehydrogenase/fumarate reductase transmembrane subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-08   32.6   2.3    9.3e-08   32.1   1.8    1.4  2  Sdh_cyt        Succinate dehydrogenase/Fumarate reductase tra
     0.0047   17.0   1.4     0.0052   16.9   1.4    1.3  1  Ferric_reduct  Ferric reductase like transmembrane component


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   1.8     1e-11   9.3e-08      26     104 ..       4      77 ..       3      95 .. 0.77
   2 ?   -1.0   0.0      0.19   1.7e+03      74      92 ..      86     102 ..      72     107 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-11
     Sdh_cyt  26 hritGvallv.glllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwDlglglelesar 104
                 h  t+++ l+ +++++++  ++ + ++++  +++v+a + s++++ill lll++   H++nG+R++l+ +    ++   +
  AJA92268.1   4 HYGTAIGALFlTVIHIMMR-MTQD-FHESLEYENVIANYESVGYAILLELLLILISVHGFNGLRVILLEM----NQGPTY 77 
                 6668888888677777765.6666.5999************9999999999999999**********976....334444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.19
     Sdh_cyt  74 llllallyHllnGiRhllw 92 
                 l  +a+l  ++ G R +++
  AJA92268.1  86 LGGMAAL--IAYGSRTIIM 102
                 3344444..6888888888 PP

>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.4   5.8e-07    0.0052      36     100 ..       3      61 ..       1      95 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.8e-07
  Ferric_reduct  36 fHkwlgvlafllallHvilyllnflrfsaldeerlldsllkkpynllGvlalllliilaitSlkf 100
                    +H  +++ a++l+++H+++ + ++++      e+l+++++  +y+ +G  +ll l++++i+ ++f
     AJA92268.1   3 IHYGTAIGALFLTVIHIMMRMTQDFH------ESLEYENVIANYESVGYAILLELLLILISVHGF 61 
                    78889********************8......889**************9999999998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 814.66
//
Query:       AJA92269.1  [L=161]
Description: hypothetical protein T478_0970 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.013   15.7   5.9        0.1   12.9   0.9    2.3  2  DUF4134    Domain of unknown function (DUF4134)
        0.7    9.9   8.3       0.12   12.4   1.7    2.1  2  Colicin_V  Colicin V production protein


Domain annotation for each model (and alignments):
>> DUF4134  Domain of unknown function (DUF4134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   1.1e-05       0.1      20      80 ..      38      98 ..      20     105 .. 0.81
   2 ?    5.7   0.3     0.002        18      43      58 ..     110     125 ..      99     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
     DUF4134 20 GaagiseatsevasyfdpvtkliyaiaavvglvgalkvYikwnsgdqdvkksiaawfgaci 80
                G + +++  + +  y+ +  +l+ ++a + g+ +al  Y+  ++ d++vk+ + a+fg+ +
  AJA92269.1 38 GLEHMATEIELLPMYMAASITLTAVVAILAGINIALVAYNIKTQRDKNVKSGAGAIFGGAL 98
                55555666666678888889998888888899999999*******************9987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.002
     DUF4134  43 yaiaavvglvgalkvY 58 
                   + av+g+vg+l ++
  AJA92269.1 110 TSLTAVLGIVGGLAIF 125
                 5689*********998 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   1.3e-05      0.12      26     107 ..      15      99 ..      10     104 .. 0.67
   2 ?    1.3   0.6     0.035   3.1e+02       6      41 ..     116     150 ..     110     155 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
   Colicin_V  26 lsllgwvvafvvasllypslaellae..lilspalaaiiaf.lllfllvllivsllgallsklvsktglglldrllGaifGllkg 107
                 ++++g++ ++ +++l+y    e+  e   ++ + l   +a  ++l  +v +++++  al+   ++ ++ +++ + +GaifG + +
  AJA92269.1  15 FGMIGVISGVSLGTLYYFLTLEMGLEhmATEIELLPMYMAAsITLTAVVAILAGINIALVAYNIKTQRDKNVKSGAGAIFGGALT 99 
                 7889999999888888876555544446333344444555524444445555555555666678*****************8765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.035
   Colicin_V   6 llilllsallGlrrGfvrevlsllgwvvafvvasll 41 
                 l+i++++a++  ++G+ + ++s+ ++ ++++ a + 
  AJA92269.1 116 LGIVGGLAIFP-LQGLELKFISIGALTFSIWWAMRN 150
                 44444444443.589999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1063.87
//
Query:       AJA92270.1  [L=265]
Description: rhodanese-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-38  129.6   0.1    2.4e-19   69.8   0.0    2.1  2  Rhodanese  Rhodanese-like domain
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.29   10.8   0.0    1.5  1  DUF3562    Protein of unknown function (DUF3562)


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   2.7e-23   2.4e-19       3     105 ..      12     111 ..      10     113 .. 0.93
   2 !   58.1   0.0   1.2e-19   1.1e-15       2     106 ..     141     246 ..     140     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 2.7e-23
   Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggr.aaaaaallkklGyknvsvldG 99 
                 k l+e +++++++++DvR ++eY++ghI++Avn+     + ak  ++++ e +++++++ gi+n+++vv+y+d+ g  ++++ ++l++ G+k+v++ld 
  AJA92270.1  12 KILREKIQENSIRIIDVRRDQEYQQGHITNAVNL-----PLAKLLNDDSPESIQKIAQDlGISNETPVVIYDDTFGAlSSRVVWALQYIGHKDVKLLDV 105
                 5688999999999*********************.....89999999999999999999******************99999********766****** PP

   Rhodanese 100 Gfkawk 105
                  f++wk
  AJA92270.1 106 TFSQWK 111
                 *****9 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 1.2e-19
   Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvycdgggr.aaaaaallkklGyknvs 95 
                 a+ l++  e+++v+++D R++  Y ++hIpgA+n+     +r+  ++++ l + e ++ l    gi ++ ++++yc + g  +  a+++lk+ G +nv+
  AJA92270.1 141 AEYLEKVKENKNVVIIDNRERLNYLEQHIPGAINI----PYRTLATDGKILRTKEGMKTLlknrGIPEDAEIITYCGSVGTlSGLAYYALKSIGIPNVK 235
                 67788888999999*********************....4444444444444444444445567****************98888899*********** PP

   Rhodanese  96 vldGGfkawke 106
                 ++  +fk+wk+
  AJA92270.1 236 LYVHSFKEWKS 246
                 *********96 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.2e-05      0.29       2      35 ..      53      86 ..      52      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
     DUF3562  2 ddvdeiiqaiAeetdaPeelVsrlyedavaalae 35
                dd+ e+iq+iA++ ++ +e+    y+d+  al++
  AJA92270.1 53 DDSPESIQKIAQDLGISNETPVVIYDDTFGALSS 86
                68889***********************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1888.04
//
Query:       AJA92271.1  [L=69]
Description: hypothetical protein T478_1477 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 503.21
//
Query:       AJA92272.1  [L=412]
Description: peptidase, M50 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-20   72.0   0.6    1.1e-18   67.4   0.6    2.3  1  Peptidase_M50  Peptidase family M50
    1.2e-12   48.0   0.2      2e-12   47.3   0.2    1.3  1  PDZ_2          PDZ domain
      7e-07   29.0   1.3    1.2e-06   28.2   1.3    1.4  1  PDZ_6          PDZ domain
    2.7e-06   27.6   0.5      6e-06   26.5   0.5    1.6  2  PDZ            PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.6   2.5e-22   1.1e-18       1     246 [.     120     391 ..     120     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.5e-22
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkkspwqrllivlAGpl 96 
                    +f+l + i++v+HE +H++v  l++++++                   +ai +  + G+V+ ++e+            f+k++ ++rl+ + AGp 
     AJA92272.1 120 YFLLSIPIVLVIHEGAHGIVGVLEKINIKT----------------GGFAIFIAMFAGFVEPDEEQ------------FSKAKKISRLRLIGAGPT 187
                    69999***********************66................34678888888*********............****************** PP

                    XXXXXXXXXXXX...........................................-EEECECTTTSCEE-SEEEC-.............XXXXXXX CS
                    xxxxxxxxxxxx...........................................xxxxxxxxxxxxxxxxxxxxx.............xxxxxxx RF
  Peptidase_M50  97 anfilailvfvv...........................................pkkskeseeekrgviGvspkp.............vkkegll 136
                     n+i+a+++ ++                                           +   + + +++  +i++  ++             + ++  +
     AJA92272.1 188 SNVIFAFILGAIlltnplfamglggvpgaeplvdvfyesaaagvlvlsvidgggaQ---QAGIQQNDMIIKIDDVNiasatdlqanpvePGDTVNV 280
                    ********99999***********************99999999999998886431...3366777778888877755555555444433333444 PP

                    XXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXX................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 137 ealkegvektlkvvvltvk.....algklitgklslktlggpisiaqla................seaaeaglssflqllalisvnLgilNLlPip 211
                      l +g e ++ v+++         l +++ +                                 + ++ +++s fl +l +is+ +gi+N+lP+p
     AJA92272.1 281 TVLRDGSEIVFPVTIMASPddperGLIGIMRN----------------DmgqlpepifnfidwnlDTSFGWQFSWFLLWLWMISFFIGIINMLPLP 360
                    44455555555555554445444444444444................33334444444445555999999999********************** PP

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 212 vLDGghllfalleairrkplserkeevanlvglal 246
                    +LDGg+++  ++e+      se++ + ++++ +a+
     AJA92272.1 361 ILDGGKFIHTIIEGRI----SEKTVNGIMMAVYAI 391
                    *************877....444444444444444 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.2   4.4e-16     2e-12      13      81 ..     228     294 ..     214     295 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 4.4e-16
                 ..-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEEEE CS
       PDZ_2  13 tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktvevk 81 
                 + gvlv sV +gg a++ag++++D i+k+d++ + s +dl+ +    +pGdtV++tvlRdg +  + v+
  AJA92272.1 228 AAGVLVLSVIDGGGAQQAGIQQNDMIIKIDDVNIASATDLQAN--PVEPGDTVNVTVLRDGSEIVFPVT 294
                 569*************************************987..579*************98777665 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   1.3   2.7e-10   1.2e-06       2      41 ..     233     270 ..     232     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.7e-10
       PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaal 41 
                 V +V+ g+ A +AG++++D+i++++++++   s +d++a 
  AJA92272.1 233 VLSVIDGGGAQQAGIQQNDMIIKIDDVNI--ASATDLQAN 270
                 789**************************..*****9975 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.4   1.5e+04       8      17 ..      29      38 ..      24      41 .. 0.76
   2 !   26.5   0.5   1.3e-09     6e-06      24      66 ..     227     269 ..     208     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                TTSESSEEEE CS
         PDZ  8 grgglGfslk 17
                + ++ Gfs+k
  AJA92272.1 29 RLERYGFSIK 38
                67899**998 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.3e-09
                 SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHH CS
         PDZ  24 gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheea 66 
                 ++ g+ v +v  gg a+++g++ +D+I+++++v++++ ++++a
  AJA92272.1 227 AAAGVLVLSVIDGGGAQQAGIQQNDMIIKIDDVNIASATDLQA 269
                 45799********7777777******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2916.70
//
Query:       AJA92273.1  [L=514]
Description: ammonium transporter [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.8e-107  357.8  32.0   1.1e-106  357.0  32.0    1.4  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.0  32.0  5.9e-111  1.1e-106       1     399 []      68     511 ..      68     511 .. 0.92

  Alignments for each domain:
  == domain 1  score: 357.0 bits;  conditional E-value: 5.9e-111
                      HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCB.SSSSSCE-........................ CS
  Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgksk.gvsgfign........................ 69 
                      a++l ++ lv+fm++g+a++++gl rskn++n++ ++++ ++++++++vl+Gyslafg    + + f+gn                        
       AJA92273.1  68 AWMLTASSLVLFMTPGVAFFYGGLARSKNAVNTIGMVFVIMGLMSVQWVLWGYSLAFGGIDnDANMFMGNldyvgfnqvshwaplgapspcedt 161
                      7********************************************************997669*******988888888888888888888777 PP

                      ............TTTTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.... CS
  Ammonium_transp  70 ............lglsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvl.... 147
                                   ++  +++  +t++++lf++fq++fa+++ +++ g++++r+kfsa ++f +l+gt+vy p+ hwvwg gg +          
       AJA92273.1 162 wahyyqmqtmkeGDV-CSDTWPGTVPHQLFAMFQATFAIITPALIVGGLVDRMKFSAIVVFVLLWGTFVYDPICHWVWG-GGYIGGGSLDfnpd 253
                      776666555432222.2233334555666**************************************************.88887666557899 PP

                      .......-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHH CS
  Ammonium_transp 148 ......iDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaaga 235
                             DfAg+tvVH+ +g+ +La+al+lg+r g +   +  +++hn+p++vlG+ +LwfgWfgFNaGs   ++++  + a  +T++A+ +++
       AJA92273.1 254 lspsyaLDFAGGTVVHISSGFTALAGALILGRRLGYG---KVPMEPHNVPMVVLGASILWFGWFGFNAGSEVMVDGITVS-AWTVTNTATGMAT 343
                      9999999****************************99...9***************************************.************* PP

                      HHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHH CS
  Ammonium_transp 236 ltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaek 329
                      +t++l+s+ ++gk++++g+a G++AGlVAiT+a ++v p++A+iiG+ Ag +++  v+ +k+  k dD+ldv++vHg+gG+ G++++g +a + 
       AJA92273.1 344 VTWVLMSWAHTGKPSIVGAATGAVAGLVAITPASGWVGPMAAIIIGIAAGTVCYGCVA-FKNARKWDDALDVWGVHGMGGLTGAILTGTLASPH 436
                      *********************************************************7.**********************************9 PP

                      HC.SSHSSTTGGGT-C..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..SB--HHHHHHSHHHHHHSSSSB CS
  Ammonium_transp 330 vv.askisggllsgeg..kqlvvqligilvilayafvvtlilllllklllg..LrvseeeeevglDvaehgetay 399
                         + +  g +++     +q  + ++++ + +ayaf+v+++++++++++    +rv+++eee+glD+++ ge ay
       AJA92273.1 437 IWdTGDGIGAWTGTPEgyEQQAISIVAAGMSIAYAFGVSIVIFKVMDAVWPggIRVTPKEEEIGLDLSQNGERAY 511
                      8788888888887655678899999999999****************986558*******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3793.63
//
Query:       AJA92274.1  [L=161]
Description: ribosomal protein L11, N-terminal domain / ribosomal protein L11, RNA-binding domain multi-domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-23   82.4   0.5    3.3e-23   81.3   0.5    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    2.1e-15   57.0   1.6    3.2e-15   56.4   1.6    1.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.5   3.7e-27   3.3e-23       6      62 ..       5      61 ..       3      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 3.7e-27
  Ribosomal_L11_N  6 kvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqd 62
                     + +  +v++G+A+++PplGpaLGplG+ni+++++++n++T+d+kg+++pV+++v  d
       AJA92274.1  5 QSISAQVTGGEASAGPPLGPALGPLGVNIMEVINKINEKTGDFKGMKVPVTVSVDTD 61
                     56889*************************************************555 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   1.6   3.5e-19   3.2e-15       2      70 .]      71     138 ..      70     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 3.5e-19
                    --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
  Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                     P++s+l++k+a+i kg+g+ g+e v+++ ++ v+++A +K + + a+ ++++++k+i+gt++ +GikV
     AJA92274.1  71 IPSASALILKEANITKGTGTAGTEWVADIGMDAVVKVANVKLETSYAS-EIKSVAKQIIGTCQCLGIKV 138
                    59****************************************766688.*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1195.58
//
Query:       AJA92275.1  [L=90]
Description: hypothetical protein T478_0581 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.3   0.2      0.053   13.2   0.2    1.1  1  DUF2777   Protein of unknown function (DUF2777)


Domain annotation for each model (and alignments):
>> DUF2777  Protein of unknown function (DUF2777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     3e-06     0.053      26      97 ..      11      86 ..       7      90 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-06
     DUF2777 26 wiliddeeeelsLleelleqeieikekkkWkkgelve...dgilksdgevlrlkegekirlek.kllkayeellee 97
                w++ ddee++l L +e l ++iei+e++   k e+ +   +  ++sd   + l ++++ ++e   l+ a+ e+ +e
  AJA92275.1 11 WLYTDDEEKTLYLRHEDLMEMIEILEHGTTAKIEMEDgasSILVNSDSTDFFLAGQKSQKIETvALKIALREFIKE 86
                999***********999999**********9999987322345777888888888877777652455666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 600.68
//
Query:       AJA92276.1  [L=739]
Description: DEAD/DEAH box helicase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-23   82.3   0.2    1.2e-22   80.5   0.0    2.0  2  DEAD             DEAD/DEAH box helicase
    3.1e-13   50.1   0.1    3.1e-13   50.1   0.1    2.7  3  ResIII           Type III restriction enzyme, res subunit
      2e-08   34.5   1.8    7.9e-07   29.4   0.1    3.3  2  Helicase_C       Helicase conserved C-terminal domain
    1.8e-06   28.0   0.1    1.1e-05   25.4   0.1    2.4  2  HHH_2            Helix-hairpin-helix motif
    0.00055   20.5   0.7     0.0015   19.1   0.7    1.8  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.019   14.1   0.0      0.034   13.2   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.18   11.7   2.2        2.2    8.2   0.0    3.2  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   4.7e-26   1.2e-22       3     171 ..      27     193 ..      25     196 .. 0.86
   2 ?   -2.8   0.0       1.8   4.7e+03      90     116 ..     663     688 ..     628     697 .. 0.60

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 4.7e-26
                 HHHHHHHHHH..TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHHHHTTC CS
                 xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   3 iQaeaiplil..gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlskldngv 98 
                  Q+ea+++ l  +++++lv ++T+sGKTl+++++ l+++    +k+++k+++++P+r+L+ + ++++kk+ k+ ++ ++++ ++  + +++++kl +++
  AJA92276.1  27 PQEEAVKAGLfdDKKNILVTIPTASGKTLIAMLATLSHL----SKHKTKVVYLTPLRALTSEKFEEFKKLEKFnLGRKIKVALSTGDSKEKKEKL-EDA 120
                 699999999998889*********************999....688899***********************87776666555555566899999.99* PP

                 SEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.H CS
                 xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
        DEAD  99 divvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.k 171
                 d+++ t + +d  +  ++    + ++ ++V DE++ + d+ ++++++ +l++l++    gk+  ++i lSAT++ +
  AJA92276.1 121 DVIFLTNESMDANMafQQD--WIYDIGLVVSDEIHLIGDDTRGPTLEIVLTRLRSGFI-GKNPPRIIGLSATISnS 193
                 ************7744433..49******************************65554.454557*******9843 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                 HHHHHHTTCSEEEEEHHHHHHHHHCTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  90 qlskldngvdivvgtpgrlddllstgk 116
                 + s+l  ++++v g p++ ++l++ ++
  AJA92276.1 663 DESDL-LRLQVVHGVPEKYLELVKIKQ 688
                 23333.457888888888888775444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   1.2e-16   3.1e-13       3     170 ..      23     191 ..      22     192 .. 0.81
   2 ?   -1.0   0.4      0.58   1.5e+03     141     169 ..     328     357 ..     221     359 .. 0.79
   3 ?   -1.9   0.0       1.1   2.9e+03      87     118 ..     640     665 ..     593     680 .. 0.62

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.2e-16
                 EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--... CS
      ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke..igkkvsgdkkkakek 99 
                 +l e Qeea+++ l  +  +++k++l+ ++T +GKTl+a+ ++ + l+k ++ k++ l p ++l++   eefkk+ + +  +  +    +gd+k++ ++
  AJA92276.1  23 KLFEPQEEAVKAGL--F--DDKKNILVTIPTASGKTLIAMLATLSHLSK-HKTKVVYLTPLRALTSEKFEEFKKLEKFNLGRkiKVALSTGDSKEK-KE 115
                 57889999999987..5..6999****************7777777776.446***********************99977654555588888888.99 PP

                 ....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT-.......--SEEEEEESS-S CS
      ResIII 100 dstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekf.......keavllglTATpe 170
                 + +++++++ t +s+da++     + ++     + +++ DE H +g+++   + + +l  +       ++  ++gl+AT+ 
  AJA92276.1 116 KLEDADVIFLTNESMDANM-----AFQQDWIYDIGLVVSDEIHLIGDDTrgpTLEIVLTRLrsgfigkNPPRIIGLSATIS 191
                 99*****************.....88889999999************8455544444444411123335599*******85 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.58
                 GGGTTS.TTTHHHHHT---SEEEE.EESS- CS
      ResIII 141 aHrlgakkswreilekfkeavllg.lTATp 169
                  H++g ++  r i+e   ++  ++ lTATp
  AJA92276.1 328 FHHAGLDQRCRTIIETEYKNRHIKfLTATP 357
                 477777777777755544444444147777 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                 EEESSS-B--.......-SEEEEEHHHHHHTH CS
      ResIII  87 kkvsgdkkkakekdstnkkilvttiqsldads 118
                 k+++       + ++++ k +v+++q l  +s
  AJA92276.1 640 KFWR------DHAKENEQKKIVSEYQNLIDES 665
                 2222......2234456667777777776555 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.13   3.3e+02       8      58 ..      60     116 ..      53     127 .. 0.62
   2 !   29.4   0.1   3.1e-10   7.9e-07      39     109 ..     319     400 ..     248     402 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                 HHH.HHTTTTSEEEEEESSHH.HHHH...HHHHHHHT....TSTEEEESTTSTHHHHHHH CS
  Helicase_C   8 ell.kleeeggkilifvntid.rlek...vklllekk....gikvavlhgelpqnereei 58 
                 + l +l++++ k++  ++ +  + ek   +k l ek+    +ikva  +g   ++e++e 
  AJA92276.1  60 ATLsHLSKHKTKVVYLTPLRAlTSEKfeeFKKL-EKFnlgrKIKVALSTG--DSKEKKEK 116
                 333578899999999999999755553333444.4446766677777777..34444443 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 3.1e-10
                 T...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS........SSHHHHHHHHTTSSS CS
  Helicase_C  39 k...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp........rnvtsyiqriGRtgR 109
                     +  +a +h+ l q+ r  i +++++ ++++L at  ++ G+++p  ++Vi   +          ++ +y+q+ GR+gR
  AJA92276.1 319 AqmvKNGTAFHHAGLDQRCRTIIETEYKNRHIKFLTATPTLAAGVNLPARRVVIPSVMRytnnglekISILEYKQMCGRAGR 400
                 13456677889999****************************************7777754444433336************ PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.5   6.4e+03      40      52 ..     141     153 ..     140     154 .. 0.90
   2 !   25.4   0.1   4.2e-09   1.1e-05       8      53 ..     686     732 ..     681     738 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.5
       HHH_2  40 vddiGeeiAqsiv 52 
                 + diG +++++i+
  AJA92276.1 141 IYDIGLVVSDEIH 153
                 789*******997 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 4.2e-09
       HHH_2   8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53 
                 I+++G   A++L k+ +k+   Lkka le+L+++d iG + A+si++
  AJA92276.1 686 IKQIGRVRAQILYKNgYKNKTTLKKAPLEKLAAIDKIGMILAKSIKS 732
                 99**********9877*****************************87 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   5.8e-07    0.0015       3      54 ..     682     733 ..     680     736 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.8e-07
                 HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
       HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 
                 eL +++ iG+++A  l+++G++    l++a  e+La+i  iG  +A++i+ +
  AJA92276.1 682 ELVKIKQIGRVRAQILYKNGYKNKTTLKKAPLEKLAAIDKIGMILAKSIKSQ 733
                 899**********************************************987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.034     125     161 ..      36      73 ..      10      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
       T2SSE 125 avrerglilvsGgTgsGKttll.yallkeinksderiv 161
                     +++ilv+ +T sGKt ++  a l+ + k++ ++v
  AJA92276.1  36 LFDDKKNILVTIPTASGKTLIAmLATLSHLSKHKTKVV 73 
                 34569**************8875899999999998887 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.64   1.6e+03      15      27 ..     247     259 ..     244     260 .. 0.93
   2 ?    0.8   0.1      0.18   4.5e+02      24      40 ..     569     585 ..     567     587 .. 0.89
   3 ?    8.2   0.0   0.00086       2.2       3      42 ..     683     723 ..     682     726 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.64
  DNA_pol_lambd_f  15 kkwyakGirtled 27 
                      k+w+  G+ t++d
       AJA92276.1 247 KDWIGLGLDTVDD 259
                      79*********99 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
  DNA_pol_lambd_f  24 tledlrakrakLtreqq 40 
                      +++dl +k++kL  +q+
       AJA92276.1 569 DMDDLINKNEKLYTQQK 585
                      689*************8 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00086
  DNA_pol_lambd_f   3 FtkvyGVGpktAkkwyakGirtledlra.krakLtreqqiG 42 
                      + k+  +G+++A+ +y++G+++   l++   +kL    +iG
       AJA92276.1 683 LVKIKQIGRVRAQILYKNGYKNKTTLKKaPLEKLAAIDKIG 723
                      778999****************9999994337787777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4919.01
//
Query:       AJA92277.1  [L=158]
Description: PUA domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-08   32.6   0.0    8.8e-08   32.0   0.0    1.3  1  PUA       PUA domain
    1.5e-07   31.4   0.0    2.2e-07   30.9   0.0    1.3  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   9.8e-12   8.8e-08       3      73 ..      79     148 ..      77     149 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 9.8e-12
                 EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
         PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                 + vd+ +  ++ +g+s+++  v +++ ++e g  V i+ +  +++avG++ +ss+ +++  +g+++++++ 
  AJA92277.1  79 IEVDADSKPFVEQGKSVFCQHVKRCGSKIEIGSDVPIFFK-KQIIAVGKSILSSNMIKTQSRGMAIRVRDS 148
                 78*************************************9.**************************9975 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   2.4e-11   2.2e-07       8      64 ..      12      67 ..       5      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.4e-11
      TGT_C2  8 dYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrl 64
                d +FG g+ +++ + d+++++s +tgrir v+++g  l+t   +dg   +s++ a++ 
  AJA92277.1 12 DTLFGTGVSKNIPK-DIDFKMSkKTGRIRAVYHNGLLLFTP-RTDGGIAMSIYCAELF 67
                668********986.5************************6.6***999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1134.56
//
Query:       AJA92278.1  [L=61]
Description: hypothetical protein T478_0342 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.022   15.2   0.1    1.4  1  Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain


Domain annotation for each model (and alignments):
>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   1.2e-06     0.022       4      23 ..      27      46 ..      25      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
  Zn-C2H2_12  4 PlCseqFpknvdqdeFeeHV 23
                PlCs+ ++kn++ +   eHV
  AJA92278.1 27 PLCSKCYSKNISEHYPGEHV 46
                ************99877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 428.92
//
Query:       AJA92279.1  [L=306]
Description: homoserine kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-14   52.1   1.4    1.2e-13   51.0   1.4    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain
    3.6e-11   43.3   0.0    9.1e-11   42.0   0.0    1.7  2  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.072   12.7   0.6        1.1    8.9   0.1    2.7  2  DUF2674         Protein of unknown function (DUF2674)


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   1.4   2.1e-17   1.2e-13       2      66 .]      79     145 ..      78     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.1e-17
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDvaasvyGg 66 
                     i+ik+++P g G+GSSAA a+a ++ l++l++l+l ++  ++ a  +e++ + g  + ++vaas++Gg
      AJA92279.1  79 IKIKKNVPAGFGMGSSAASAAACAVGLNKLYNLKLtDTelVEFAGIGEKASA-GTIHYDNVAASALGG 145
                     89********************************863357********9998.999***********8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.6   1.5e+04      67      84 ..      55      72 ..      53      72 .. 0.78
   2 !   42.0   0.0   1.5e-14   9.1e-11       9      84 ..     215     285 ..     203     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.6
  GHMP_kinases_C 67 kdkdeaeqvaralreefe 84
                    ++k+ a  v++a+++ef+
      AJA92279.1 55 PSKNTAGLVVSAMKKEFK 72
                    578888899999988875 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 1.5e-14
  GHMP_kinases_C   9 dlellgellnlsqrs...elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                     + el+g+ +     +   e+   ++ + p ++++++ ++++Ga+g+ +sGa  Gp+v+a++++k +a+++ +a+++ f+
      AJA92279.1 215 NSELIGRSVQ----DvivEP--ARKHMIPGFDKVKKNAMAAGAYGVTISGA--GPSVIAFTDKKHDAKKISNAMKRGFK 285
                     4444444444....688999..9999*************************..*********************99886 PP

>> DUF2674  Protein of unknown function (DUF2674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.066   3.9e+02      31      44 ..     156     169 ..     145     171 .. 0.91
   2 ?    8.9   0.1   0.00018       1.1       8      33 ..     263     288 ..     261     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.066
     DUF2674  31 IvnlvPyedaFlcv 44 
                 +v++ P +d  lcv
  AJA92279.1 156 VVKIQPPNDLVLCV 169
                 799**********8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00018
     DUF2674   8 lvsfderkkDikkIekeleeGWvIvn 33 
                 +++f ++k D kkI++ ++ G    +
  AJA92279.1 263 VIAFTDKKHDAKKISNAMKRGFKAAK 288
                 799*****************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2133.32
//
Query:       AJA92280.1  [L=263]
Description: twin arginine-targeting protein translocase TatC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-49  168.1  16.3    2.7e-49  167.8  16.3    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.8  16.3   1.5e-53   2.7e-49       2     207 .]      10     241 ..       9     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 1.5e-53
                 HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHH....HCCHHHHC.C..................TTS-EE--SSS-HHHHHHHHHHHHHHHHSHHHHHH CS
        TatC   2 hLeeLrkrlirallavaiafiitfvfaeelia....fllepleeae..................eevelivlspleafllklkvslvaglvlasPvily 78 
                 h+eeLrkr+ir+++ ++++++++++f+++ ++     l+ p+ e +                   +v+li ++p +af+ ++ ++ ++g+vl++P+i+ 
  AJA92280.1  10 HIEELRKRVIRSIISILVITVFILTFHATPFDvmgvTLYYPYPE-PlnniaaqftnvmkgelvpDGVQLIQTAPGQAFFSQVYIAALIGIVLSIPIIVR 107
                 *******************9999988777655433333333322.12344445555554444443499******************************* PP

                 HHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTSSTTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HH CS
        TatC  79 qlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seevepllslseylsfvlllllafgiaFelPlvlvllarlglvsae 173
                 ++++f++p+L+++e ++ + + + ++ lf++G+af+y +v+p++l+fl+    s+++ + l++ ++++fvl++llafgi+F+lPl+++ ++  glv+a+
  AJA92280.1 108 EFISFLKPALREREIHVGRSITLPAIGLFITGCAFSYAAVIPFILDFLYrygeSAGLVTFLNIMDFVTFVLQFLLAFGISFQLPLIMYAVSLSGLVDAK 206
                 *************************************************88776666778*************************************** PP

                 HHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
        TatC 174 tlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                 ++r++ ryai++i+v++av+tP  + +++ ++ +P
  AJA92280.1 207 FWRRNLRYAIIAIIVFGAVITPdGSGVTMWFVSLP 241
                 *******************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1886.87
//
Query:       AJA92281.1  [L=328]
Description: biotin synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-19   69.9   0.7    4.8e-18   66.1   0.6    2.2  2  Radical_SAM  Radical SAM superfamily
    8.4e-12   45.1   0.0    2.4e-11   43.6   0.0    1.8  1  BATS         Biotin and Thiamin Synthesis associated domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.6   5.4e-22   4.8e-18       6     166 ..      70     227 ..      67     228 .. 0.89
   2 ?    1.6   0.0     0.035   3.1e+02      28      68 ..     254     295 ..     243     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 5.4e-22
                  EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                  xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                   C+ +CsfC+++       ++++ +s ee+++++  + ++ g   ++++       ++df++   +++++ ++++ i++e++ + ++ e++ +l+elg
   AJA92281.1  70 YCSEDCSFCSQSAFfDTGIDKYQLMSAEEVVRQATDA-KKAGaHSYCLVAAWREPSNKDFEKV-CHIIEEVNEKVGISIECSLGFLTIEQATKLKELG 165
                  6***********99999********************.6888666776666666666889555.55555558************************** PP

                  -SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 102 vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                  v r++++le+  ++ + +++  +ht+++++++l ++r+ag++  +++ +++ Ge+++++eel++ 
   AJA92281.1 166 VIRYNHNLETSESK-FPEIC-TTHTYQDRIDTLNTARKAGLE-LCTGGIIGMGETRKQREELVQA 227
                  **************.*****.9********************.8888888888********9875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.035
                  HHHHHHHHHHHHHHHHHTTSEEEEEE.SSTGGGSTTHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
  Radical_SAM  28 slsveeileevkelkaekgvkevilg.ggepllypdfvelle 68 
                   ls+eeil+ +  l++   +  + ++ g e++l++d  ell+
   AJA92281.1 254 PLSLEEILRVFAVLRFLLPKSIIKISgGREVNLDDDGKELLL 295
                  578999999999999666666555551668888888877765 PP

>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.7e-15   2.4e-11       2      85 ..     238     326 ..     237     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.7e-15
                 --B----TCCCC...........HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH.HHHCCT--EEE-C---TTTGGGSESSTT-TCCCCHHHHHHTT- CS
        BATS   2 iprlrpikdtpl...........lkiiaalRlllPkag.illsgResaefrdq.lllklGansisagsktevggyaflttdgrsleedvkmleelGl 85 
                 ++ l+  ++tpl           l++ a+lR+llPk+   +++gRe + ++d   ll  Gan i+           +lt dg+s+++dvkm++e +l
  AJA92281.1 238 VNLLVAFPGTPLelqtplsleeiLRVFAVLRFLLPKSIiKISGGREVNLDDDGkELLLSGANGIISSG--------YLTLDGNSMQKDVKMIKEIDL 326
                 79999*********************************999*****99999989777***********........*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2286.87
//
Query:       AJA92282.1  [L=125]
Description: hypothetical protein T478_1394 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 781.77
//
Query:       AJA92283.1  [L=454]
Description: FAD binding domain of DNA photolyase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-76  256.5   1.5    2.1e-76  255.9   1.5    1.2  1  FAD_binding_7   FAD binding domain of DNA photolyase
    2.4e-31  108.9   0.1    4.5e-31  108.1   0.0    1.4  2  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> FAD_binding_7  FAD binding domain of DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.9   1.5   2.4e-80   2.1e-76       1     196 [.     261     447 ..     261     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 255.9 bits;  conditional E-value: 2.4e-80
                    HHHHHHHHHHHHHHHHCSTTTTTSSTTGCCTT------HH.HHHHHHTT-SS-HHHHHHHHHHHHHS---HHHHHHHHHHHCTTT-B-HHHHHHHH CS
  FAD_binding_7   1 flreLlwrefyyallaaepelaeralkekfdripweeseeekleaWkeGrTGfPlvDAamrqLretGwmhnrlRmivasFltkdLlidWregeevF 96 
                    f++eL+wr+f+ +l++++p  ++++++ek++ ++w+++++ k+e+W +G TGfP+vDA+mr+L++tG+mhnr+RmivasFltkdL +dWr ge++F
     AJA92283.1 261 FISELYWRDFFSHLMFHFPYSQKKEFQEKYQGLKWSHDKK-KFEKWVNGLTGFPIVDAGMRELKQTGFMHNRCRMIVASFLTKDLQCDWRLGERHF 355
                    899********************************88866.7****************************************************** PP

                    HHH-TT--CCHHHHHHHHHCT-STTS-STT----CCCCHHHCSTT-HHHHHH-GGGTTS-HHHHT-GGGSGCHHHHHHT--TTTSS---SS-HHHH CS
  FAD_binding_7  97 eellvDadlasnagnwqwlagtgadaapafrifnpvkqgkkfDpegeyirrwvpeLkklpakyihepwkapaeeqkkagvvlgkdYpkpivdhkea 192
                    +++l+D+d+++nag+wqw+a+tg+da+p+fr+fnp+ q+kkfDpe+ yi++w+peL +l +k ih+  ++p +         + dYp+p+v hke+
     AJA92283.1 356 AKYLIDYDPCVNAGSWQWSASTGCDAQPYFRVFNPWLQQKKFDPECVYIKKWIPELVNLTTKQIHDIETTPLD--------SSIDYPRPMVIHKEE 443
                    *****************************************************************97766654........578***********9 PP

                    HHHH CS
  FAD_binding_7 193 rkra 196
                    ++r 
     AJA92283.1 444 SARS 447
                    9876 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   5.1e-35   4.5e-31       2     157 ..       7     163 ..       6     171 .. 0.93
   2 ?   -4.3   0.1       1.8   1.6e+04     141     150 ..     384     393 ..     380     398 .. 0.77

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 5.1e-35
                     EEEESS---STT-HHHHHHHCTTSEEEEEEEE-HH..HHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEE CS
  DNA_photolyase   2 lvWfrrDlRlhDNpALaaAaasgepvipvfvldpe..kahklrvgaarvdfllesLadLdeeLrelgirLvvrrgdpadvlpelakelgasavva 94 
                     l+ frrD Rl DN+ L +A++++e+vip+f ++++  ++ +  +g+ r++f++ sL+dL e+ + ++ + ++ + ++ + + + +k+ +++a+++
      AJA92283.1   7 LFVFRRDYRLDDNTSLIQACENSEQVIPCFLFEKNliDKNNPVFGKMRIRFMIDSLKDLFEQAKGKNCEILIKNDSVSSLITSSVKQDEINAIFM 101
                     667********************************87444447**************************************************** PP

                     E---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHCHHHHHC CS
  DNA_photolyase  95 nreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkrwlkelk 157
                     nr+ +p++r rd++ k+a +k++i++es+ d +l ++g+v +++++p+ vFtpf++++ + +k
      AJA92283.1 102 NRDNSPYGRFRDNQFKSASEKNNIAFESYGDLLLRDAGSVLKQNDTPFLVFTPFYRAASQ-FK 163
                     *******************************************9************7766.55 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.8
                     SHSSHHHHHH CS
  DNA_photolyase 141 pykvFtpfrk 150
                     +++vF p+ +
      AJA92283.1 384 YFRVFNPWLQ 393
                     6899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3463.82
//
Query:       AJA92284.1  [L=180]
Description: exosome complex exonuclease RRP4 N-terminal region [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-07   28.8   0.0    1.9e-06   27.5   0.0    1.7  2  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.27   11.0   0.0    1.3  1  DUF5331         Family of unknown function (DUF5331)
        1.2    8.9   6.0        6.1    6.6   5.9    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.2e-10   1.9e-06       3      35 ..       7      39 ..       7      42 .. 0.94
   2 ?   -4.1   0.0       2.6   1.5e+04      24      29 ..     123     128 ..     118     129 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.2e-10
                -TT-EEEETTTSEE-TTEEEETTEEEESSSEEE CS
      ECR1_N  3 tPGevlttdeefmrGhGTYvrggtiyAsvaGtv 35
                +PGe ++  ee+++G++T++++ +i+A+  G +
  AJA92284.1  7 IPGEKIAQIEEYLPGENTFEDNDSIRATTIGEI 39
                7***************************99976 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.6
                 TTEEEE CS
      ECR1_N  24 ggtiyA 29 
                 +gti+A
  AJA92284.1 123 NGTIHA 128
                 456665 PP

>> DUF5331  Family of unknown function (DUF5331)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.5e-05      0.27      46      76 ..      62      95 ..      42     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.5e-05
     DUF5331 46 sslilGvinalePklaqlllpFs...klnsdedk 76
                +++i+Gv++a  P + +++++F+   k+nsd + 
  AJA92284.1 62 GDVIIGVVEANLPSMIAIMIKFVngkKMNSDLEC 95
                689*******************744468888765 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.92   5.5e+03      11      19 ..      24      32 ..      22      34 .. 0.78
   2 ?    6.6   5.9     0.001       6.1       5      24 ..     144     162 ..     141     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.92
                    ---SSS--- CS
  DNA_RNApol_7kD 11 slkkgdpiR 19
                    + + +d+iR
      AJA92284.1 24 TFEDNDSIR 32
                    567899999 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.001
                     SS--B----SSS----SSS- CS
  DNA_RNApol_7kD   5 eCgaevslkkgdpiRCkeCG 24 
                     +C     +k +d+++Ck+CG
      AJA92284.1 144 KCFGT-VVKMRDAVKCKDCG 162
                     55443.46899********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1065.47
//
Query:       AJA92285.1  [L=194]
Description: AAA domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-30  106.8   0.0    1.4e-30  106.4   0.0    1.1  1  AAA_17           AAA domain
    8.3e-07   29.6   0.0    1.6e-06   28.7   0.0    1.5  1  AAA_18           AAA domain
    1.5e-05   25.3   0.0    2.9e-05   24.4   0.0    1.4  1  AAA_28           AAA domain
    2.9e-05   23.8   0.0    4.3e-05   23.2   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
    0.00031   20.7   0.0    0.00033   20.6   0.0    1.4  1  NACHT            NACHT domain
    0.00046   20.5   0.0    0.00066   20.0   0.0    1.6  1  AAA_22           AAA domain
    0.00054   20.2   0.0    0.00096   19.4   0.0    1.5  1  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00087   19.4   0.3     0.0019   18.2   0.3    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0015   18.4   0.0     0.0038   17.1   0.0    1.6  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0016   17.9   0.1     0.0019   17.7   0.1    1.3  1  KTI12            Chromatin associated protein KTI12
     0.0019   18.6   0.1     0.0048   17.3   0.1    1.9  1  AAA              ATPase family associated with various cellul
     0.0025   18.2   0.0     0.0048   17.3   0.0    1.7  1  AAA_16           AAA ATPase domain
     0.0028   17.8   0.0     0.0045   17.1   0.0    1.4  1  AAA_33           AAA domain
     0.0028   17.4   1.0      0.045   13.5   0.1    2.2  2  AAA_24           AAA domain
     0.0029   18.0   0.2     0.0074   16.6   0.2    1.6  1  AAA_19           AAA domain
     0.0035   17.3   0.0      0.006   16.6   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0039   16.6   0.2     0.0087   15.4   0.1    1.6  2  DnaB_C           DnaB-like helicase C terminal domain
     0.0065   16.1   1.2      0.036   13.7   0.2    2.2  2  Ras              Ras family
     0.0068   16.1   0.1      0.013   15.2   0.1    1.6  1  AAA_30           AAA domain
     0.0097   16.4   0.1      0.014   15.9   0.1    1.5  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
       0.01   15.0   0.1      0.016   14.4   0.1    1.3  1  NB-ARC           NB-ARC domain
      0.017   15.0   1.3      0.029   14.3   0.2    1.9  1  NTPase_1         NTPase
      0.024   14.2   0.8      0.037   13.6   0.2    1.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.032   14.0   0.2      0.089   12.6   0.1    1.7  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.034   13.6   0.0      0.054   12.9   0.0    1.4  1  SRPRB            Signal recognition particle receptor beta su
      0.038   13.4   0.0      0.076   12.4   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.05   12.9   0.0      0.068   12.5   0.0    1.3  1  6PF2K            6-phosphofructo-2-kinase
      0.053   13.4   0.2        0.1   12.5   0.2    1.7  1  RsgA_GTPase      RsgA GTPase
      0.063   13.2   0.1       0.13   12.2   0.1    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.066   13.1   0.0       0.15   11.9   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.075   11.9   0.0       0.09   11.7   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.075   12.8   0.2       0.63    9.8   0.0    2.3  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.099   12.4   0.0       0.13   11.9   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.5   0.1       0.24   11.4   0.1    1.7  1  AAA_14           AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.0   2.7e-33   1.4e-30       1     136 []      10     148 ..      10     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 2.7e-33
                 EE-TTSSHHHHHHHHHH.....HHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
      AAA_17   1 lGgPGsGKgtqceklve.....kygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                 +G+PG+GK+ ++ ++ve     k   ++ s+G ++++ea++++  ++rd++r lp +++kelqk+aa+kiae   ++ v vd+h+ i +++gf++glp 
  AJA92285.1  10 VGIPGVGKTSLVTRIVElinaqKHCASVHSYGTVMMDEAANNQV-SDRDNLRHLPVSQQKELQKQAAKKIAEL-TDDVVFVDTHAFISTDEGFYPGLPY 106
                 7**************97333336678899**********99997.8*************************96.7789********************* PP

                 HHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
      AAA_17  95 evleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                 +v++ l+p+++i ++a peei++rr+kd++r+rd  ++e ik
  AJA92285.1 107 HVIQILEPTHLIAISARPEEIYNRRMKDDSRNRDKISIEAIK 148
                 ***************************************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.1e-09   1.6e-06       1     122 [.       7     145 ..       7     153 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.1e-09
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........gvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssaleegknlvidghlaele 87 
                 I++ G+pGvGKt+l  ++ ++ +           g++ +d a++n+ ++ ++     ++++k+     ++++ +++ e  +     +++ +d h     
  AJA92285.1   7 IVIVGIPGVGKTSLVTRIVELINAqkhcasvhsyGTVMMDEAANNQVSDRDNLRhlPVSQQKE----LQKQAAKKIAELTD-----DVVFVDTHAFIST 96 
                 89****************7765445666678999**********9998888777322222222....23333333333332.....5666776654444 PP

      AAA_18  88 seaakdikk..............vvLtaspeell.eRlekRgyeeakik.e 122
                 +e +    +              + + a+pee + +R+++++++ +ki+ e
  AJA92285.1  97 DEGFYP--GlpyhviqilepthlIAISARPEEIYnRRMKDDSRNRDKISiE 145
                 444333..234777999999999*****99777625666666666666543 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.4e-08   2.9e-05       1      83 [.       6      93 ..       6      96 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.4e-08
      AAA_28  1 kivitGgestGKTtlleaLa....ar.gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcDrgll 83
                kivi+G ++ GKT+l+ ++     a+     v+ +++ +++e + ++  + +  + l   +++ l++q+++  a  +++v+f+D+ ++
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVelinAQkHCASVHSYGTVMMDEAANNQVSDRDNLRHLPVSQQKELQKQAAKKIAELTDDVVFVDTHAF 93
                79**************9988454433456677888888888777666655555455556667777777777777789********876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.1e-08   4.3e-05       3     100 ..       6      99 ..       4     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.1e-08
                 EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS..STTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHH CS
       SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf..RaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndk 99 
                  i++vG+ G+GKT+ ++++ +l++++++ + + +  t     aA +Q++   +  + pv ++k      ++ k+a +k  e   dvv+vDT     +d+
  AJA92285.1   6 KIVIVGIPGVGKTSLVTRIVELINAQKHCASVHSYGTVmmDEAANNQVSDRDNLRHLPVSQQK------ELQKQAAKKIAELTDDVVFVDTHAFISTDE 98 
                 699***********************88888887776511579*****999988888866444......566778888888888*******87777666 PP

                 H CS
       SRP54 100 e 100
                  
  AJA92285.1  99 G 99 
                 5 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   6.2e-07   0.00033       3      85 ..       7      87 ..       5     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.2e-07
                EEEEC-TTTCHHHHHHHHHHHHCTS-.SCCCC-SEEEEEETTTTTTS-.......-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEE CS
       NACHT  3 vilqGeaGsGKTtLlqklalawaegk.lpqgafklvFflslrelsrsgna....rsladllfsqlpepaapvsevwavllelperlLl 85
                +++ G +G+GKT L+ ++++++ ++k + ++ +++  ++   +    +n       l+ l +sq++e++++  +    ++el + +++
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQKhCASV-HSYGTVMMDEAA---NNQvsdrDNLRHLPVSQQKELQKQAAK---KIAELTDDVVF 87
                89*******************9766604443.344333322222...222234578999999999999999888...66666666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.2e-06   0.00066       6      59 ..       5      61 ..       2     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-06
      AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsst..sskdllre 59
                + +v++G +G+GKT l+ r++e  +++++ +  ++ ++v ++ ++ +  s +d lr+
  AJA92285.1  5 KKIVIVGIPGVGKTSLVTRIVELINAQKHCASvHSYGTVMMDEAANNqvSDRDNLRH 61
                5589*******************9988887779888888888887775544444444 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.8e-06   0.00096       1      30 [.       6      35 ..       6      65 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.8e-06
                EEEEESSTTSSHHHHHHCHCT-CCC-EEET CS
         Roc  1 KvvlvGdsgvGKtsllkrfvedkfsekeks 30
                K+v+vG  gvGKtsl++r+ve    +k+ +
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINAQKHCA 35
                9******************98655544433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   3.7e-06    0.0019       1      75 [.       6     113 ..       6     175 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-06
                 EEEEEESTTSSHHHHHHHHHT.....STEEESSSTTSSSSEEEEEEE.ETTEE.............................EEEEECGGCSSHHHHHH CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltg.....ekaivsdkpgtTrdinegrvk.lkgke.............................ielvDtpGliegaseek 64 
                 +++ivG p vGK++L+ ++++     +   +s +   T  + e+  + ++  +                             +++vDt  +i+  +e+ 
  AJA92285.1   6 KIVIVGIPGVGKTSLVTRIVElinaqK-HCASVHSYGTVMMDEAANNqVS--DrdnlrhlpvsqqkelqkqaakkiaeltddVVFVDTHAFIS-TDEGF 100
                 699****************97443321.1122222222222222111111..02234444444444455555555555555578888777654.22233 PP

                 ..HHHHHHHHHHC CS
    MMR_HSR1  65 ..glgkaflalee 75 
                   gl  ++ ++ e
  AJA92285.1 101 ypGLPYHVIQILE 113
                 3566666665555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.1e-06    0.0038      81     162 ..      64     149 ..      52     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.1e-06
      CLP1_P  81 lalvkelareveekleenkkakasgliIntpGwvk.glg.a.ellleliealepdvvvvldq..eellnelkrdlp..lskvkvvklpk 162
                 +++ kel +++ +k++e    +++++ ++t+ +++ ++g +  l  ++i++lep+++++++   ee +n   +d     +k++++ ++k
  AJA92285.1  64 VSQQKELQKQAAKKIAE---LTDDVVFVDTHAFIStDEGfYpGLPYHVIQILEPTHLIAISArpEEIYNRRMKDDSrnRDKISIEAIKK 149
                 56667777777766666...599***********84557444666****************9898999888777775667777766666 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.7e-06    0.0019       4      82 ..       7      94 ..       6     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-06
                EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH....TTSSS--GGGHHHHHHHHHHHHHHHHTT.......SEEEE-S---S CS
       KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg...iekdsykdsakekalRsslrsavkrdLsk......ekvVIvDslnyi 82
                +v+ G+P +GK++++ ++ + ++++k    v++  ++     +++++ d  + ++l  s++++ +++  k      ++vV vD  ++i
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQKHCASVHSYGTVMmdeAANNQVSDRDNLRHLPVSQQKELQKQAAKkiaeltDDVVFVDTHAFI 94
                89**********************9999999999999833333344555555555544444444444333111111466666666665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     9e-06    0.0048       2      65 ..       8      89 ..       7     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9e-06
                EEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS.................STTHHHHHHHHHHHHHHHTSTSEEEEEE CS
         AAA  2 llyGppGtGKTllakavakelgve..fleisgsellsk.................yvgesekkirelfkeakekakpsilfiD 65
                +++G pG+GKT+l+  +++ ++++  + ++     + +                  v+++++  ++  k++ e     ++f+D
  AJA92285.1  8 VIVGIPGVGKTSLVTRIVELINAQkhCASVHSYGTVMMdeaannqvsdrdnlrhlPVSQQKELQKQAAKKIAELT-DDVVFVD 89
                789****************98644333333333332113344455666777776666666666666666665554.6788877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.1e-06    0.0048      27      52 ..       7      40 ..       3     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.1e-06
      AAA_16 27 vllsGesGvGKsslvrellralekd........g 52
                ++++G +GvGK+slv+++ + ++++        +
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQkhcasvhsY 40
                689****************999888333333321 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.6e-06    0.0045       2     121 ..       7     138 ..       7     164 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.6e-06
      AAA_33   2 vllvGlpGsGKstlaerl.....lkklgavllssdt.lrrrlfgtdqqsktdytrvl.drlyqilnelarkalsagrnvildatnlsrrer........ 85 
                 +++vG pG+GK+ l++r+     ++k+ a + s  t +++  +++++ +  ++ ++  ++ ++ +++ a+k ++   +v++  t ++ ++         
  AJA92285.1   7 IVIVGIPGVGKTSLVTRIvelinAQKHCASVHSYGTvMMDEAANNQVSDRDNLRHLPvSQQKELQKQAAKKIAELTDDVVFVDTHAFISTDegfypglp 105
                 689**************9555554444433333333244466666665555555554233444555666666677777999888655444411344333 PP

      AAA_33  86 arflklarrlgvpvrivvvet.deetlkeRlakRaan 121
                   ++++++    p +++++++ +ee +++R +  ++n
  AJA92285.1 106 YHVIQILE----PTHLIAISArPEEIYNRRMKDDSRN 138
                 34444443....4555555551344444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   8.5e-05     0.045       3      22 ..       5      24 ..       3      37 .. 0.88
   2 ?    2.7   0.0      0.17        91     148     174 ..      66      92 ..      23     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-05
      AAA_24  3 lkiliyGpsgiGKTtlakel 22
                +ki+i+G +g+GKT+l++++
  AJA92285.1  5 KKIVIVGIPGVGKTSLVTRI 24
                89**************9886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.17
      AAA_24 148 lepklgkktanelkeevDlvlranlkr 174
                  + +l+k++a+++ e  D v++++ + 
  AJA92285.1  66 QQKELQKQAAKKIAELTDDVVFVDTHA 92 
                 456788889999999999999988664 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.4e-05    0.0074       9      60 ..       3      55 ..       1     100 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
      AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkp.eeillvaftgrAakelre 60
                ++k +++++ pG GKT +++ iv+l++++++ +  +++  v + + A +++++
  AJA92285.1  3 ERKKIVIVGIPGVGKTSLVTRIVELINAQKHCASvHSYGTVMMDEAANNQVSD 55
                67899********************9998876442455555555555555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05     0.006       2      34 ..       7      39 ..       6      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                EEEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
       AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltr 34
                +++vG pG+gK++l+ r+ +++n++ +    ++
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQKHCASVHS 39
                689*******************88776655554 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.7e-05    0.0087      22     112 ..       7      94 ..       2      99 .. 0.59
   2 ?   -2.7   0.0       5.5   2.9e+03      18      28 ..     114     124 ..     108     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                 EEEEEXTTSSHHHHHHHHHHHHHHCST.SEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT.TSXHHHHHHHHHHHHHHHHSEEEEEEXSSX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  22 iiiAarpsmGktalalniaenaavkek.lpvavfslemsaeqlvqRllsseaeidskklrtg.klkeedweklteaieelseaklfiddtpal 112
                 i+i + p++Gkt+l++ i+e + ++++ ++v  +   m +e  ++  +s + +++   + +  +l++    + +++i+el++  +f+d ++ +
  AJA92285.1   7 IVIVGIPGVGKTSLVTRIVELINAQKHcASVHSYGTVMMDEA-ANNQVSDRDNLRHLPVSQQkELQK----QAAKKIAELTDDVVFVDTHAFI 94 
                 8999***************99876444144666655555544.333444444444333322213333....3444566677777777766555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.5
                 TTXEEEEEEXT CS
                 xxxxxxxxxxx RF
      DnaB_C  18 kgdliiiAarp 28 
                 + +li i arp
  AJA92285.1 114 PTHLIAISARP 124
                 55566666665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   6.9e-05     0.036       1      23 [.       6      28 ..       6      60 .. 0.81
   2 ?    1.1   0.1       0.5   2.6e+02     116     143 ..      64      92 ..      53      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-05
                EEEEEESTTSSHHHHHHHHHHSS CS
         Ras  1 KlvlvGdsavGKtslllrfvkdk 23
                K+v+vG  +vGKtsl++r v+  
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELI 28
                9****************988755 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.5
                 GGGG-SS-HHHHHHHHHHHT.SEEEEEBT CS
         Ras 116 leekravsteegeelakelg.lkfletSA 143
                 ++++++++++ ++++a+ ++ + f++t A
  AJA92285.1  64 VSQQKELQKQAAKKIAELTDdVVFVDTHA 92 
                 4679999*********9998899999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.5e-05     0.013      20      47 ..       6      38 ..       1      98 [. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
      AAA_30 20 vavltGpAGtGKttalkalreaweaag.....g 47
                  v++G +G GKt +++ ++e+++a++     +
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINAQKhcasvH 38
                4699********************997454431 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.6e-05     0.014      11      73 ..       4      73 ..       1     187 [. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-05
                TSEEEEEESTTSSHHHHHHHHTTSS--........SEEEEEETTCEGGGB-HHHCCHCEEEE-..SS--S-TT CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
    ABC_tran 11 gekvaivGenGaGKStLlkllagllkp........teGeilldgkdlkeqeleslrkeigvlp..qepqlfpe 73
                 +k++ivG  G GK++L+  + +l +           G++ +d++  ++    s r +++ lp  q+++l+++
  AJA92285.1  4 RKKIVIVGIPGVGKTSLVTRIVELINAqkhcasvhSYGTVMMDEAANNQ---VSDRDNLRHLPvsQQKELQKQ 73
                5799*******************99994444444444455444333333...222222222220022233222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1     3e-05     0.016      22      79 ..       6      73 ..       1      88 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE...........EEESXXHHHHHHHXXHHHHHCC CS
      NB-ARC 22 vvalvGmgGvGKttlakqilnksdevegrFdsvawv...........vvsktdkseeiletilkeLsls 79
                 + +vG +GvGKt l++ i++  +  +++  sv+             +vs+ d+ +++  +  keL+++
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINA-QKHCASVHSYgtvmmdeaannQVSDRDNLRHLPVSQQKELQKQ 73
                5889****************99554.4444444443455667777777777777777666666666655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   5.6e-05     0.029       1      25 [.       6      30 ..       6      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.6e-05
                EEEEE--TTSSHHHHHHHHHHHH.. CS
    NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                k++i G pGvGKt lv +++el++ 
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINA 30
                689******************9975 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2     7e-05     0.037       3      33 ..       7      37 ..       5      91 .. 0.79
   2 ?   -2.6   0.0       6.5   3.4e+03      27      39 ..     167     179 ..     131     188 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                EEEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
        cobW  3 tvltGflGsGKTtLlnhllenraglklaviv 33
                +v++G +G GKT+L+++++e  + +k    v
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQKHCASV 37
                79*****************554444444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                 S-EEEEESS-SSC CS
        cobW  27 lklavivNefgev 39 
                   l vi+N+ g++
  AJA92285.1 167 SPLKVILNNEGKI 179
                 3445555555544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017     0.089       1      26 [.       9      34 ..       9      53 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
  ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrs 26
                +vG +G+GKt++v +++e++++++  
  AJA92285.1  9 IVGIPGVGKTSLVTRIVELINAQKHC 34
                79****************99998643 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001     0.054       3      43 ..       4      45 ..       2      95 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                --EEEEE-STTSSHHHHHHHHHHS.S---B---SS-EEETTG CS
       SRPRB  3 kpavllvGlsdsGKTslftrLttd.svkktvtSqessaalkv 43
                ++++++vG+   GKTsl tr+ +  +++k  +S++s  +  +
  AJA92285.1  4 RKKIVIVGIPGVGKTSLVTRIVELiNAQKHCASVHSYGTVMM 45
                6899****************9876555555555555444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.076      24      64 ..       6      44 ..       2      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
  Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                  ++++vG pG GKt l +r+ +l+ + ++  ++   +  +v+
    AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINAQKHCASVH--SYGTVM 44
                  7899******************98766554443..333333 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.068      15      76 ..       6      69 ..       1      99 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS..---GGGGSTT-HHHHHH CS
       6PF2K 15 vivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska..lsdaeffrpdneealkl 76
                 iv+vG+p  gKt + ++++  ++   + + v   g +  + + +   sd +  r+    ++k 
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINAQKHCASVHSYGTVMMDEAANnqVSDRDNLRHLPVSQQKE 69
                69**********************9999999999988765544442344444444333322222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00019       0.1      98     123 ..       3      28 ..       1      90 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                  TTSEEEEECSTTSSHHHHHHHHCTT- CS
  RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                  + k +v+vG  GvGK++L+ ++++  
   AJA92285.1   3 ERKKIVIVGIPGVGKTSLVTRIVELI 28 
                  56889***************998753 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00024      0.13       2      28 ..       7      33 ..       6      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
        MobB  2 lgivgksgsGKTtLleklipelkargl 28
                + ivg  g GKT+L++++++ ++a++ 
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINAQKH 33
                679****************99998875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.15      23      68 ..       7      51 ..       2      94 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
    ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                ++i G  g+GKt+L+ +i+e  +  +k+   + +  ++  +++ + 
  AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELINA-QKHCASVHSYGTVMMDEAANN 51
                7999***************99844.333333333333333333222 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.09      14      49 ..       3      38 ..       1      80 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
  TrwB_AAD_bind 14 etqhilivGttGsGKtqalekllrairargdraivl 49
                   e+++i+ivG  G GKt  ++ +++ i+a+++ a v 
     AJA92285.1  3 ERKKIVIVGIPGVGKTSLVTRIVELINAQKHCASVH 38
                   8999*************************9877665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0012      0.63      35      65 ..       6      36 ..       2      50 .. 0.85
   2 ?   -1.1   0.0       2.6   1.4e+03      24      91 ..      73      89 ..      61     112 .. 0.60
   3 ?   -0.7   0.0         2     1e+03       2      54 ..     123     174 ..     122     187 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
      RuvB_N 35 hvllyGpPGlGkttlakiiakelgvklkits 65
                 ++++G PG+Gkt+l + i + ++++ + +s
  AJA92285.1  6 KIVIVGIPGVGKTSLVTRIVELINAQKHCAS 36
                6899***********9999888888776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.6
      RuvB_N 24 eaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfid 91
                +aakk  e  d                                                   dv+f+d
  AJA92285.1 73 QAAKKIAELTD---------------------------------------------------DVVFVD 89
                44444444444...................................................455555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2
      RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiia 54 
                 rP+++ +   +++ +++ ki iea kk     d +l +    l  + l  i+ 
  AJA92285.1 123 RPEEIYNRRMKDDSRNRDKISIEAIKKELAVQDAML-ASCSVLSGSPLKVILN 174
                 666666666677778888889988887666666544.4444555555555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.13       1      27 [.       7      37 ..       7      89 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
  Viral_helicase1  1 ivvhGvpGcGKStlirkllrts....liltv 27
                     iv+ G+pG GK++l+ ++++      +  +v
       AJA92285.1  7 IVIVGIPGVGKTSLVTRIVELInaqkHCASV 37
                     7999*********999988772222322233 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00046      0.24       2      43 ..       4      50 ..       3      96 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00046
      AAA_14  2 rkilvitGaRrvGKTtllkqlikell......vkkesilyinldderd 43
                rk +vi+G+  vGKT l+ +++ el+      ++  s+  + +d+  +
  AJA92285.1  4 RKKIVIVGIPGVGKTSLVTRIV-ELInaqkhcASVHSYGTVMMDEAAN 50
                57799*************9998.4443444443334444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1275.04
//
Query:       AJA92286.1  [L=151]
Description: hypothetical protein T478_1180 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0065   16.6   0.1     0.0099   16.0   0.1    1.2  1  HTH_34     Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.039   13.9   0.1      0.057   13.4   0.1    1.3  1  HTH_45     Winged helix-turn-helix
      0.057   13.1   0.0      0.076   12.7   0.0    1.2  1  AphA_like  Putative AphA-like transcriptional regulator
       0.12   12.2   0.0       0.22   11.5   0.0    1.4  1  TrmB       Sugar-specific transcriptional regulator TrmB
       0.18   12.2   0.0       0.22   11.9   0.0    1.1  1  Cyclin     Cyclin


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.8e-06    0.0099       7      71 ..      86     150 ..      83     151 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
      HTH_34   7 syLasvdeadfvelkealeatdgnLsvhlkkLekagYie.vdkefkgkkprtllriTpeGreafkk 71 
                   L+ ++  +f+e++++ ++++ nL + l+ Lek+g  + v+k+   + + + lriT++G ++f +
  AJA92286.1  86 LGLLLTNITKFEEIQKKGNLSTNNLDTILQDLEKKGLMQpVEKTGPFG-KSIQLRITEKGAAEFRR 150
                 5566777789**************************998466665555.6899**********976 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.6e-05     0.057      21      64 ..      95     146 ..      82     151 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
      HTH_45  21 kkTkimykanLsykllnkYLdmLvekgli........kkskekYvlTekGle 64 
                 k  +i +k nLs ++l+  L+ L +kgl           ++ + ++TekG  
  AJA92286.1  95 KFEEIQKKGNLSTNNLDTILQDLEKKGLMqpvektgpFGKSIQLRITEKGAA 146
                 5557999*********************877776654447789999*99975 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.076      51      88 ..     112     150 ..      99     151 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
   AphA_like  51 sslellreeGLveavdGeG.mednalLaiteaGrrelqa 88 
                 + l+ l ++GL+++v+  G   ++++L ite+G +e+++
  AJA92286.1 112 TILQDLEKKGLMQPVEKTGpFGKSIQLRITEKGAAEFRR 150
                 456778999*******9996799*************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     6e-05      0.22      17      58 ..      88     129 ..      83     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                 HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB  17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                 Ll     + +ei ++ +++ ++   +L+ Le+kGl + ++++
  AJA92286.1  88 LLLTNITKFEEIQKKGNLSTNNLDTILQDLEKKGLMQPVEKT 129
                 5555666789*************************9988765 PP

>> Cyclin  Cyclin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.2e-05      0.22       6      81 ..      17     101 ..      13     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                 HHHHHHHHHHHHHH--------------T............................T--SS--..SS-HHHHHHHHHHHTT--H CS
      Cyclin   6 qlsllldrlvanndetatasadsksnlensqkqss.......shtkttfaqtpkessFatkavp..aisigsylsrlqkfgesap 81 
                  l++++ rl +++  + + sa  +s+  n  + ss       s+   +f+++p+  +F+tk+ p  +i +g  l+ ++kf e+++
  AJA92286.1  17 PLARIVPRLLRRAGLKENISARPESPRGNFFQESSspdtfreSSSSDNFQESPRREEFSTKNWPkeKIVLGLLLTNITKFEEIQK 101
                 5778888888999999999999999999987777789999999999****************87325888889999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 993.33
//
Query:       AJA92287.1  [L=98]
Description: ATP synthase, subunit F [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-13   49.3   0.0    5.2e-13   49.1   0.0    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.022   14.5   0.0    1.1  1  LUD_dom     LUD domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   5.8e-17   5.2e-13       1      80 [.       3      83 ..       3      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 5.8e-17
                EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEESCSCCGG CS
  ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileIPskegpy 80
                ++ +G++ +vt f+laGv++  v++ +++ e +k+l++++++g++l+++++ e+i++++ +++ e ++P++  +P  +++ 
  AJA92287.1  3 VVTVGSRVFVTSFQLAGVQGKIVDSSDNAFEEIKKLYDDSEVGLVLVSDDLTEQINDKLTKLRAEkSTPLVFALPASGSEK 83
                5689*************************************************************9*********988743 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.4e-06     0.022       4      56 ..      11      63 ..       8      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
     LUD_dom  4 fienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalh 56
                f+++++  g++  ++++ ++a e i++l ++  v+++ +s dl e + +++ +
  AJA92287.1 11 FVTSFQLAGVQGKIVDSSDNAFEEIKKLYDDSEVGLVLVSDDLTEQINDKLTK 63
                88999999***********************************8888744433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 701.58
//
Query:       AJA92288.1  [L=226]
Description: KH domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-07   29.8   0.7      1e-06   28.4   0.2    2.0  2  KH_1      KH domain
     0.0018   18.6   0.0     0.0035   17.7   0.0    1.5  1  KH_6      KH domain
     0.0051   16.6   0.2      0.011   15.6   0.2    1.5  1  KH_2      KH domain
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.25   11.3   0.0    1.8  2  KH_4      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.66   2.9e+03      44      53 ..     127     137 ..     118     142 .. 0.68
   2 !   28.4   0.2   2.3e-10     1e-06       4      65 ..     147     202 ..     144     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.66
                 T.-EEEEEE.S CS
        KH_1  44 derevtisG.s 53 
                  +  +tisG +
  AJA92288.1 127 RDPLITISGrE 137
                 45689999944 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 2.3e-10
                 EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
        KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                 +++  ++v+r+IGk+Gs+I+ I++ t+ ++++   +     +  +++s  + ++  kA+++ie
  AJA92288.1 147 VKISPNKVPRLIGKRGSMIQLIESSTNSQVTIG--Q-----NGLLVVSSeDSNGLLKAIQAIE 202
                 6899999*****************89*****64..3.....4699999999999999999986 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.9e-07    0.0035       3      44 ..     146     190 ..     144     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.9e-07
        KH_6   3 lfeVslslvrRllnhvLeeLgka...gpfeiavGlNGriWvkses 44 
                 l+++s+++v+Rl+ + +++++        ++++G+NG   v+se+
  AJA92288.1 146 LVKISPNKVPRLIGKRGSMIQLIessTNSQVTIGQNGLLVVSSED 190
                 89***********777777753333467*********98777776 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.4e-06     0.011      29      63 ..     147     181 ..     135     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                 EEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHT CS
        KH_2  29 iviresqpgivIGkgGsnikkigkelrkdiekleg 63 
                 + i  ++  ++IGk+Gs+i+ i++  + ++ + ++
  AJA92288.1 147 VKISPNKVPRLIGKRGSMIQLIESSTNSQVTIGQN 181
                 67889999*****************9999976665 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.3     1e+04      32      43 ..     130     141 ..     117     141 .. 0.69
   2 ?   11.3   0.0   5.5e-05      0.25      33      52 ..     147     166 ..     143     174 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.3
        KH_4  32 elnvegedlGrv 43 
                  ++++g +lG++
  AJA92288.1 130 LITISGRELGKI 141
                 477888888876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.5e-05
        KH_4  33 lnvegedlGrvIGkrGrtld 52 
                 ++++++++ r+IGkrG +++
  AJA92288.1 147 VKISPNKVPRLIGKRGSMIQ 166
                 7899**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1609.38
//
Query:       AJA92289.1  [L=170]
Description: adenylyl-sulfate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-49  166.7   0.0    4.2e-49  166.5   0.0    1.0  1  APS_kinase  Adenylylsulphate kinase
    2.2e-06   27.9   0.0    4.4e-06   26.9   0.0    1.4  1  AAA_33      AAA domain
    0.00014   22.3   0.0    0.00019   21.9   0.0    1.3  1  AAA_17      AAA domain
    0.00019   22.0   0.0    0.00031   21.3   0.0    1.5  1  AAA_18      AAA domain
     0.0014   18.2   0.0     0.0021   17.6   0.0    1.4  1  KTI12       Chromatin associated protein KTI12
     0.0015   17.9   0.0     0.0023   17.3   0.0    1.3  1  Zeta_toxin  Zeta toxin
     0.0018   18.5   0.0     0.0032   17.7   0.0    1.4  1  AAA_28      AAA domain
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.14   12.0   0.0    1.5  1  NTPase_1    NTPase


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.0   1.9e-52   4.2e-49       2     156 ..       2     151 ..       1     153 [. 0.94

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 1.9e-52
                 -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHHHHHHHHHHHHCHT CS
  APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyreeReaarelleeal 100
                 ++++w+tGl +sGK+ti ++l+++      +  +LdGd++R+  + +  fs+e R+e+ rrva+++kll ++++ + v++isPy+e+R +are++ + +
  AJA92289.1   2 AFCLWMTGLPCSGKTTIVRKLAET----IPNLAILDGDELREWFSPK-DFSKEARDEHNRRVAHLSKLLLKHNVPMGVSLISPYKENRANAREIIGDDT 95 
                 689*************98777655....567899*******988765.8************************************************** PP

                 EEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETTTS CS
  APS_kinase 101 kfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdtdke 156
                 kf+ev+v+++l++ceerD+kg+Y+kar+Geik+ftGid+pYeaP +++lv+dt+++
  AJA92289.1  96 KFFEVYVNASLAQCEERDVKGMYAKARSGEIKGFTGIDDPYEAPDSADLVLDTENK 151
                 ****************************************************9886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     2e-09   4.4e-06       3     117 ..       6     115 ..       5     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2e-09
      AAA_33   3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvr 100
                 ++ Glp+sGK+t +++l++  +   +l+ d+lr+   ++d       ++++d+ +++++ l +  l+++ ++ +      +++ra+ +++    + ++ 
  AJA92289.1   6 WMTGLPCSGKTTIVRKLAETIPnLAILDGDELREWFSPKDFS-----KEARDEHNRRVAHLSKLLLKHNVPMGVSLISPYKENRANAREIIG-DDTKFF 98 
                 799***************9999999******99999976554.....56788899999888887788888887776667789999*****98.566999 PP

      AAA_33 101 ivvvetdeetlkeRlak 117
                  v+v+++ ++++eR  k
  AJA92289.1  99 EVYVNASLAQCEERDVK 115
                 9************9876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.5e-08   0.00019       1      60 [.       8      64 ..       8     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.5e-08
                EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqke 60
                +G+P sGK+t+++kl+e +    +  Gd lre  +++   +    e r++ +++  +l k+
  AJA92289.1  8 TGLPCSGKTTIVRKLAETIPNLAILDGDELREWFSPKDFsK----EARDEHNRRVAHLSKL 64
                7******************5555555*******99998623....4444444444444444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.4e-07   0.00031       4      44 ..       8      53 ..       6     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.4e-07
      AAA_18  4 tGtpGvGKttlakeLskrl.gf....gvnlrdvakenglllevdpe 44
                tG p++GKtt+ + L++   ++    g++lr+ ++ ++ + e  +e
  AJA92289.1  8 TGLPCSGKTTIVRKLAETIpNLaildGDELREWFSPKDFSKEARDE 53
                9****************98565777877777777777766666666 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   9.2e-07    0.0021       6      39 ..       7      36 ..       1      70 [. 0.68

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.2e-07
                EE--TTSSHHHHHHHHHHHHHHTT--EEEE-THH CS
       KTI12  6 ltGlPssGKstrakeLakaleeekrsvvviddes 39
                +tGlP+sGK+t++++La+++ +      ++d + 
  AJA92289.1  7 MTGLPCSGKTTIVRKLAETIPN----LAILDGDE 36
                8**************9998754....44444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     1e-06    0.0023      20      83 ..       6      61 ..       3      78 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1e-06
  Zeta_toxin 20 llgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdasel 83
                 + G p +GK+++ ++l++ +    n   ld+D+lRe +   ++     +k+a +  ++ +  l
  AJA92289.1  6 WMTGLPCSGKTTIVRKLAETI---PNLAILDGDELREWFSP-KD----FSKEARDEHNRRVAHL 61
                58999***************9...7************9843.22....3334444444444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0032       4      60 ..       7      66 ..       4      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
      AAA_28  4 itGgestGKTtlleaLaar..gypvv.pEaareileeklakgedalpwv.edllafaervl 60
                +tG +++GKTt++++La++  +  ++  +  re ++ k +++e   +++ +++ ++ +++l
  AJA92289.1  7 MTGLPCSGKTTIVRKLAETipNLAILdGDELREWFSPKDFSKEA-RDEHnRRVAHLSKLLL 66
                7999**************98888888888899999888888775.4444466666666665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.4e-05      0.14       3      23 ..       6      26 ..       4      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                EEE--TTSSHHHHHHHHHHHH CS
    NTPase_1  3 fiTGppGvGKtTlvkkvlell 23
                 +TG p +GKtT+v+k++e++
  AJA92289.1  6 WMTGLPCSGKTTIVRKLAETI 26
                68****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1007.40
//
Query:       AJA92290.1  [L=164]
Description: dual specificity phosphatase, catalytic domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-19   68.5   0.0    5.7e-19   68.2   0.0    1.1  1  DSPc             Dual specificity phosphatase, catalytic doma
    1.2e-10   41.3   0.0    1.5e-10   41.0   0.0    1.1  1  Y_phosphatase    Protein-tyrosine phosphatase
    2.5e-06   27.6   0.4    0.00068   19.7   0.0    2.8  2  Y_phosphatase3   Tyrosine phosphatase family
    1.4e-05   25.3   0.0    2.3e-05   24.6   0.0    1.4  1  PTPlike_phytase  Inositol hexakisphosphate
    0.00026   20.6   0.0    0.00037   20.1   0.0    1.2  1  Y_phosphatase2   Tyrosine phosphatase family
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.022   14.4   0.0    1.3  1  CDKN3            Cyclin-dependent kinase inhibitor 3 (CDKN3)
      0.069   13.5   0.6       0.13   12.6   0.6    1.5  1  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
       0.11   12.9   0.1       0.15   12.5   0.1    1.3  1  DSPn             Dual specificity protein phosphatase, N-term


Domain annotation for each model (and alignments):
>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   2.6e-22   5.7e-19      13     120 ..      44     148 ..      35     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.6e-22
                 HHHHHTCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHHHHHHHHHHHHHHTSCHHHHHHHHH CS
        DSPc  13 llsklgitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRSatliiaYlmktknlslneayeflk 111
                  l++ g++ ++ + +e     +   +e ++l++  +d       ++l+++v++++k  q+++ v+VHC aG+ R++t+ ++Yl+k++++s+++a+++++
  AJA92290.1  44 WLQEEGVKTIVTIREEPLD--ENWVNEMNYLHVLSDD-MGVPSFEDLKNSVDYVHKKIQSKEPVMVHCLAGLGRTGTILACYLIKYEKMSAEDAIQHVR 139
                 6677777777765544333..3335788888888777.8999999****************************************************** PP

                 HHSTT-SST CS
        DSPc 112 errpaispn 120
                 e+r    ++
  AJA92290.1 140 EKRHGSIQS 148
                 ***655555 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   6.8e-14   1.5e-10     144     229 ..      77     155 ..      36     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 6.8e-14
                    -SSSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHHHHHHH CS
  Y_phosphatase 144 pdhgvpesaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtleqyifl 229
                     d+gvp s ++l + ++ v+k+  ++++pv+VhC aG gRtgt++a       l + e+++  ++++++r++R+g++q++ q  ++
     AJA92290.1  77 DDMGVP-SFEDLKNSVDYVHKKI-QSKEPVMVHCLAGLGRTGTILACY-----LIKYEKMSAEDAIQHVREKRHGSIQSYVQEEMI 155
                    578888.3445555555555555.5569***************87643.....33335588899***************9885555 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     3e-07   0.00068     104     141 ..      76     122 ..      31     125 .. 0.72
   2 ?    4.8   0.1     0.011        24     194     219 ..     131     157 ..     122     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
  Y_phosphatase3 104 e.........sakkayrkvfealadeepvlfHCtaGKDRTGvlaall 141
                     +         + k+++  v ++++++epv++HC aG  RTG + a  
      AJA92290.1  76 SddmgvpsfeDLKNSVDYVHKKIQSKEPVMVHCLAGLGRTGTILACY 122
                     344444444466678888888999977**************998865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
  Y_phosphatase3 194 leaaldaie.ekygsvegYlreelgls 219
                      e a+++++ +++gs+++Y++ee+ ++
      AJA92290.1 131 AEDAIQHVReKRHGSIQSYVQEEMIFQ 157
                     5667777651689********998776 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     1e-08   2.3e-05      85     153 ..      52     123 ..      27     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-08
                      ...EE-HHHHHHHT..T-EEEEEEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHHHH CS
  PTPlike_phytase  85 tpeevyerelaeel..slrYaRipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtamviat 153
                      t  ++ e++l+e++  +++Y  +   d + p+ ed++  v+++ +  ++k++++++C +G gRT t ++++ 
       AJA92290.1  52 TIVTIREEPLDENWvnEMNYLHVLSDDMGVPSFEDLKNSVDYVHKKiQSKEPVMVHCLAGLGRTGTILACYL 123
                      55555677777776447999999999*******************9899********************986 PP

>> Y_phosphatase2  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.6e-07   0.00037       3     112 ..      18     122 ..      17     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-07
                     --TT-EEEET.TEEEESS--H.HHHHHHHHCT-SEEEE-SSS---HHHHHHHHHCT-EEEE-------GGG----HHHHHHHHHHHH-GGG-SEE CS
  Y_phosphatase2   3 pplnFsaves.elyrssypra.snfsflksLkLktiislspeeesqdelqfleeekiklyhiaiesnkeelveiksdllkkalklllnkenypvl 95 
                     +p+nFs   + +l  s++p + +   +l++  +kti+ +++e+   de      ++++++h+  ++   +  e+ ++++  + k +    + pv+
      AJA92290.1  18 RPDNFSWLIEgKLAGSAIPTSkKEVEWLQEEGVKTIVTIREEPL--DENWV---NEMNYLHVLSDDMGVPSFEDLKNSVDYVHKKIQS--KEPVM 105
                     699***75554********762679***************9955..55444...6789999999998888999999999999999855..56*** PP

                     EE-SSSSSHHHHHHHHH CS
  Y_phosphatase2  96 lhckrGkhrtglvigcl 112
                     +hc  G  rtg++ +c 
      AJA92290.1 106 VHCLAGLGRTGTILACY 122
                     ***************94 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.9e-06     0.022     109     167 ..      77     134 ..      62     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.9e-06
                 -TTS---HHHHHHHHHHHHHHHHTT--EEEE-SSSSSHHHHHHHHHHHHH-SSS-HHHH CS
       CDKN3 109 adggtpdiascleimeelatclknyrktlihcygglgrsclvaaclllylsdsispeqa 167
                  d g p      + ++ +   ++ +   ++hc  glgr+  + ac l+   + +s e+a
  AJA92290.1  77 DDMGVPSFEDLKNSVDYVHKKIQSKEPVMVHCLAGLGRTGTILACYLIKY-EKMSAEDA 134
                 4567888888888888888888999999*****************98864.45566655 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   5.9e-05      0.13      33      85 ..      84     153 ..      57     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
   zf-C2H2_2  33 lvdleglleylrekiee.................kleClyCekefkslealreHmkkkgHckineeeeee 85 
                 + dl++ ++y+++ki++                  l C++ ++e+ s e+  +H+++k+H  i+   +ee
  AJA92290.1  84 FEDLKNSVDYVHKKIQSkepvmvhclaglgrtgtILACYLIKYEKMSAEDAIQHVREKRHGSIQSYVQEE 153
                 5577777888888888888888888888888877789*99999999****************97654433 PP

>> DSPn  Dual specificity protein phosphatase, N-terminal half
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.5e-05      0.15      83     118 ..     115     150 ..      66     164 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
        DSPn  83 aafLigaYavivlklspeealkplasqekppllpFr 118
                 + +++++Y++ ++k+s+e+a+++++++++ +++++ 
  AJA92290.1 115 TGTILACYLIKYEKMSAEDAIQHVREKRHGSIQSYV 150
                 456899*******************98666677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 996.16
//
Query:       AJA92291.1  [L=124]
Description: heme utilization protein ChuX/HutX [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-07   30.3   0.1    3.6e-07   30.0   0.1    1.1  1  ChuX_HutX  Haem utilisation ChuX/HutX
    5.1e-06   26.4   0.1    5.8e-06   26.3   0.1    1.1  1  HemS       Haemin-degrading HemS.ChuX domain


Domain annotation for each model (and alignments):
>> ChuX_HutX  Haem utilisation ChuX/HutX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.1     4e-11   3.6e-07      28     121 ..       2      94 ..       1     109 [. 0.86

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4e-11
                 HHHHHHHHTTS-EEEEEEEESSEEEEEEEE.....--E..EEEE..EESCTSEEEEEEGGGEEEEEEEEEEE.TTEEEEEEEEETTSSEEEEEEEBS CS
   ChuX_HutX  28 feallealeelgevmalvrnegavhEkkGkyenv.lpe..yynlagvlgeseldlhLfldhwahifaveeptkrgesrslqffdadGeavhkvyvrd 121
                 ++++l+++ ++++v ++v+++ga +E   +  ++   +  ++++    ++++ ++h+  + ++ + +v e+  +  s s+ ffd++ e v+  +  +
  AJA92291.1   2 LKEILADIIKVDDVLMVVKSNGATIEMRSNSLSIrQ-KekWITI--GENDGPCHMHVNNEMIKNAEFVIEQKPERTSFSVRFFDEKNERVLGCFF-T 94 
                 579***************************666641.256****..578899****************99987669**************99994.3 PP

>> HemS  Haemin-degrading HemS.ChuX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   6.5e-10   5.8e-06      23     115 ..       2      96 ..       1     114 [. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.5e-10
        HemS  23 lealLealeelgevmalvrNegavqektGpvenlkesghwglvlded..idLrlfldqwaeafavkkptedgvvtSlqfFdaeGeaihkvfgerk 115
                 l+++L+++ +++ v ++v+++ga  e      +++++++w+ + ++d   +++++++ +++a  v +++ + +  S+ fFd++ e ++ +f ++ 
  AJA92291.1   2 LKEILADIIKVDDVLMVVKSNGATIEMRSNSLSIRQKEKWITIGENDgpCHMHVNNEMIKNAEFVIEQKPERTSFSVRFFDEKNERVLGCFFTKM 96 
                 578999999***888888888888888888999**********999889************999999999999***************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 739.20
//
Query:       AJA92292.1  [L=487]
Description: transporter, CPA2 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-36  124.7  52.8    5.1e-36  124.3  52.8    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3  52.8   2.9e-40   5.1e-36       8     373 ..      95     463 ..      87     467 .. 0.84

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 2.9e-40
                     HHHHHH....HHHHTTSXHHHHHHHHHHHHTTTTTS.......HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger   8 allvgl....larrlklpeivgliiaGlllGpsglglieps..eedlevlselglilllFlaGleldlrelrknlksilllallgvlitvvliGl 96 
                     ++++g+    ++++ ++p+i +l+i+G+++Gp++ g+++p    e++ +++ l li+++F+ G++l++ +++k    +++l +lg++++v ++++
      AJA92292.1  95 VIILGVlgeaFFKKTGIPDIAFLMILGVMIGPVI-GIVQPAavIEIVPYFAALALIIIMFDGGYNLKIGQILKTAHFSVILVILGFAAAVGTVSV 188
                     22222246646*********************95.669999999*************************************************** PP

                     HHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHH CS
  Na_H_Exchanger  97 llylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalakeeaggetslllllliflvvavggl 191
                     ++++  +lg+++l+++l+g+i+  ++ ++v  ++ ++ r++e+  ++l  es l+D+++ ++ ++l +++    +g +s++ll+ ++  ++++gl
      AJA92292.1 189 FAHY--GLGWEWLDSILLGTIVGGSSSIIVFGLV-RKLRISEKAKSMLSFESALTDILSTIVAFILFEAV---LTGSFSIDLLGETLGRAIAVGL 277
                     ***8..8999************************.**********************9877777777777...7999999999999999999999 PP

                     HHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHH..HHHHHTTHHHH.........HHHHHHHHHHHHHHH CS
  Na_H_Exchanger 192 llglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvls..eyefsnklsek.........lesfreglfnplfFv 275
                     +lg+ +g    +i+     +++ + +l+l +++l+++la ++g sg+l a++ Gl+l+  +y +++ l+ k         l+s  ++++  +fFv
      AJA92292.1 278 ILGFGVGIPWMFIISK-LSNAQHNYMLTLGVLFLLFFLANSFGESGALTALVFGLMLGnkKYLLKK-LRIKlpehtidnsLHSQVTFIVRAFFFV 370
                     9988888544444444.489**************************************76444444.6666666687777666666********* PP

                     HHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTC.STSXHHH CS
  Na_H_Exchanger 276 lvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyalliv.vvlftvl 369
                     +vGl   +  +    + +i+ +++ vai +gri+ ++++l   g+s  ++ + ++    rg  a++la +  + gl + e y+ +i+ ++l +v+
      AJA92292.1 371 FVGLLASFGQI----EYVIFGIVAAVAIYIGRIIITHTALV-RGFSKLDKKVTSVMIP-RGLAAAVLATIPLTMGLQNGEAYPQIIFfIILSSVI 459
                     *******5555....566666666677779*******9885.4699999999988777.**********************66555505555555 PP

                     HHHH CS
  Na_H_Exchanger 370 vqGl 373
                     + ++
      AJA92292.1 460 ITTI 463
                     5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3062.16
//
Query:       AJA92293.1  [L=337]
Description: putative 3-isopropylmalate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.3e-100  337.0   0.2   1.4e-100  336.8   0.2    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
     0.0032   16.9   0.1     0.0084   15.6   0.0    1.7  2  PdxA      Pyridoxal phosphate biosynthetic protein PdxA
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.019   14.8   0.0    1.3  1  CDC37_M   Cdc37 Hsp90 binding domain
       0.62    9.6   2.9        3.1    7.3   0.2    2.6  2  DUF166    Domain of unknown function


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.8   0.2  3.1e-104  1.4e-100       1     348 []       3     333 ..       3     337 .] 0.93

  Alignments for each domain:
  == domain 1  score: 336.8 bits;  conditional E-value: 3.1e-104
                 EEEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSSSSHHHHHHHHHHHTTEEEEEE CS
      Iso_dh   1 kiallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkekevrpengLlaLrkeldlfanlr 99 
                 +i+l+ gdgiGpe +e++  +l+++++k + ++++++  +G aa+++tg++lp++  e+ik++d+ l+++vg         +  ++aLr++ldl+an+r
  AJA92293.1   3 NISLITGDGIGPELSESVNTILDTISDKFDIKFNVNSLVAGDAALEKTGKALPDDVFESIKSSDACLKAPVGESA------KDVIVALRQKLDLYANIR 95 
                 599********************************************************************9887......6679************** PP

                 EEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHT.TTSEEEEEESTTTTHHHH.HH CS
      Iso_dh 100 pvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeieriaraafelAlkr.gkkkvtlvdKanvlksse.lw 196
                 p+k+++   +   l+    ++vdlvivRe+t+++Y gee + +++      av +  +se++++ria+ afe+A++r ++k+vt+v+K+nv+k ++ l+
  AJA92293.1  96 PAKSYP---NTPALR----DDVDLVIVRENTEDLYTGEEFQVDDT------AVALRIISEKASKRIAKHAFETAMDRsQQKRVTCVHKSNVMKITDgLF 181
                 *****4...233344....58*******************99995......9*************************999****************777 PP

                 HHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHH CS
      Iso_dh 197 rkiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavil 295
                  +++e+v + +ypd+++++++vD++am+l++ p++fdVivt+NlfGDilSDe +++vG+lG++p a+lg +++++fE+vHG+a diagk++aNp++ il
  AJA92293.1 182 ARVCEDVSK-DYPDVTFDQMYVDACAMNLIRAPHEFDVIVTTNLFGDILSDESSQVVGGLGMAPAANLG-DNFGLFEPVHGAAFDIAGKQIANPSSFIL 278
                 777777777.***********************************************************.78*************************** PP

                 HHHHHHHHTTT-HHHH.......HHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
      Iso_dh 296 SaalmLryslgleeaA.......dkiekAvekvleagivTkDlageaakevstsefgdav 348
                 S+ +mL   lg +++        +k+e+ v + +++gi+TkD++ge+    st+ef++++
  AJA92293.1 279 STKMMLDW-LGSKHNDsecisagKKLEDVVLDLIKSGITTKDIGGEK----STHEFTKEI 333
                 ********.99887766888889************************....666666554 PP

>> PdxA  Pyridoxal phosphate biosynthetic protein PdxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.54   2.4e+03      52      76 ..     143     167 ..     102     177 .. 0.61
   2 !   15.6   0.0   1.9e-06    0.0084     256     280 ..     257     281 ..     246     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.54
                 HHHHHHHHHHHHHHHHHHHTTSSSE CS
        PdxA  52 aesGaaalaslekAvelakegevda 76 
                 ++s ++a +++e+A++  ++++v  
  AJA92293.1 143 KASKRIAKHAFETAMDRSQQKRVTC 167
                 3344555666777777766666654 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.9e-06
                 ESS-S-TTCTTTT---THHHHHHHH CS
        PdxA 256 vDhGtafdiagkgkadekSlleAik 280
                 + hG afdiagk++a+++S++ + k
  AJA92293.1 257 PVHGAAFDIAGKQIANPSSFILSTK 281
                 67*****************997766 PP

>> CDC37_M  Cdc37 Hsp90 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.3e-06     0.019      21      64 ..     137     180 ..     118     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-06
     CDC37_M  21 peilseqqkdaLlmeafdaqlegkekkakqvvhqslllqyireL 64 
                  +i+se+++  +  +af+  ++  ++k   +vh+s +++    L
  AJA92293.1 137 LRIISEKASKRIAKHAFETAMDRSQQKRVTCVHKSNVMKITDGL 180
                 479**********************************9977776 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.034   1.5e+02      51      90 ..     107     146 ..      20     172 .. 0.63
   2 ?    7.3   0.2   0.00068       3.1      30      68 ..     189     230 ..     169     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.034
      DUF166  51 lkeaDiviaytlhpDlllelaekakekkvkalivpaeapk 90 
                   ++D+vi  +  +Dl      +++++ v + i++++a k
  AJA92293.1 107 RDDVDLVIVRENTEDLYTGEEFQVDDTAVALRIISEKASK 146
                 3456666666666666666666666666666555555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00068
      DUF166  30 vvevpe.elde.fied.peelLpelkeaDiviaytlhpDlll 68 
                  +++p+ ++d+ +++  + +l+++  e+D++++ +l +D+l 
  AJA92293.1 189 SKDYPDvTFDQmYVDAcAMNLIRAPHEFDVIVTTNLFGDILS 230
                 567777777653677624577888****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2020.90
//
Query:       AJA92294.1  [L=184]
Description: hypothetical protein T478_0902 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      7e-12   46.1   5.7    9.3e-11   42.5   2.5    2.5  2  Hemerythrin  Hemerythrin HHE cation binding domain
     0.0013   18.7   0.9     0.0031   17.5   0.3    1.9  2  RIG-I_C      RIG-I receptor C-terminal domain
  ------ inclusion threshold ------
       0.41   10.5   4.5        2.3    8.1   0.2    2.2  2  DUF2972      Protein of unknown function (DUF2972)


Domain annotation for each model (and alignments):
>> Hemerythrin  Hemerythrin HHE cation binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   2.5   1.6e-14   9.3e-11       4     131 .]       4     136 ..       1     136 [. 0.88
   2 ?    4.1   0.1     0.011        66      12      50 ..     139     178 ..     136     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.6e-14
                  HHHHHHHHHHHHHHHHHHHHHHH.HHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...CCC.HHHHHHHHHHHHHHHHHHHHHH.HHC CS
  Hemerythrin   4 ealdeeHralrallerlralada.aaevhga...lrklaelldelvdeleaHhaaEEellfPlle..drpggravldvlereHdeirelleelr.ell 94 
                  + l+++H+ + + l++l+a     +++ + +   l+  +++ + + d+   Hh +EEe lfP+le  + p   +++  +  +H +  e++e +  +  
   AJA92294.1   4 QSLRKDHKLIEKVLQALDATIKLlKDGKQIPeeiLSPTLDFTQNFTDV--CHHGKEEEALFPALEkaGMPTTMGPIHMMLLDHKRTKEIAEHISlASK 99 
                  6799***********9976666653333333699*************9..*****************9**************************8888 PP

                  HTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
  Hemerythrin  95 kgleepsaaafaelleeladllreHiakEesilfpll 131
                  k le++++a + e le + + + eH+ kE++ lf+++
   AJA92294.1 100 KYLENGDSAYLIETLELYVQHVTEHLWKENNRLFMMA 136
                  8888888888888999999***************996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                  HHHHHHHHHHHHHHHHHHHCCC.HCCHHHHHHHHHHHHHH CS
  Hemerythrin  12 alrallerlraladaaaevhga.lrklaelldelvdelea 50 
                  +l + ++++++ +d+++e+    l k + ++++lvdele+
   AJA92294.1 139 RLNDATNEIDKNMDDIEERKLSeLGKTRSHYESLVDELEK 178
                  56777888888888877777778**************985 PP

>> RIG-I_C  RIG-I receptor C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.34     2e+03      24      44 ..       7      27 ..       4      53 .. 0.69
   2 !   17.5   0.3   5.3e-07    0.0031      53     119 ..      90     161 ..      69     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
     RIG-I_C 24 skiedklkklltrieelsklk 44
                +k++++++k+l++++++ kl 
  AJA92294.1  7 RKDHKLIEKVLQALDATIKLL 27
                567777777777777766663 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.3e-07
     RIG-I_C  53 Yeqwvvklekkaakeeerkkrvca.....ltcaehLrkYndALiinddaRtsdAleyLekflndlkekkfde 119
                   + ++  +kk+ ++ +++  ++        ++ehL k n+ L++ +daR  dA + ++k+++d++e+k +e
  AJA92294.1  90 IAEHISLASKKYLENGDSAYLIETlelyvQHVTEHLWKENNRLFMMADARLNDATNEIDKNMDDIEERKLSE 161
                 555555556666544443333332333334689*******************************99998766 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2   0.00038       2.3     110     161 ..       4      52 ..       1      61 [. 0.77
   2 ?    4.1   1.0    0.0066        39      92     147 ..     106     161 ..      56     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00038
     DUF2972 110 eilkeneklleqvkeyllelieeLkkqkeiekkkklsekdvLeylkkhkkva 161
                 ++l++++kl+e+v + l ++i+ Lk+ k+i ++     +  L++ ++ ++v+
  AJA92294.1   4 QSLRKDHKLIEKVLQALDATIKLLKDGKQIPEEIL---SPTLDFTQNFTDVC 52 
                 689***********************999987642...33455555555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0066
     DUF2972  92 kqkcfyeriiiyikkkdfeilkeneklleqvkeyllelieeLkkqkeiekkkklse 147
                  +    e++ +y+++  +   ken++l+    ++l++  +e+ k+ +  +++klse
  AJA92294.1 106 DSAYLIETLELYVQHVTEHLWKENNRLFMMADARLNDATNEIDKNMDDIEERKLSE 161
                 33445678888888888888888888888888888888888887776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1112.76
//
Query:       AJA92295.1  [L=337]
Description: tryptophan halogenase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-05   22.7   0.0    0.00016   20.7   0.0    1.8  1  Trp_halogenase  Tryptophan halogenase
     0.0018   18.5   0.0     0.0035   17.5   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
     0.0078   16.2   0.1       0.35   10.9   0.0    2.4  2  Toprim_Crpt     C-terminal repeat of topoisomerase
  ------ inclusion threshold ------
      0.043   13.5   0.0      0.082   12.6   0.0    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.062   12.7   0.0       0.12   11.8   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.15   11.3   0.0       0.24   10.6   0.0    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.2e-08   0.00016     197     370 ..     119     287 ..     111     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.2e-08
                     EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT----EEEEEEEE--H.---SSEEEEE-SSEEEEEEEETTEEEE.EEE.E-TTTS-HHHHHHHH CS
  Trp_halogenase 197 eveadlfiDcsGfrgllieqaLktgfedwsdvLltdrAlavqvesee.lvepytrataekaGWtWkiPLqhrlgn.Gyv.yssahadddeAlael 288
                     e e+d+++Dc+Gf++  + +  ++ f   +          v+ e+     + y +     +G +W+ PL +++   G+  y ++h+   +A++e+
      AJA92295.1 119 EKEYDMIVDCTGFNRSYLPKM-EQDFYLPTYEY------KVEYENGVpYDDFYIEPFPGMSGYFWYFPLGENYAHiGAGdYNKNHI---KATDEF 203
                     5689*********99999995.44443222222......2333333223334444556789********99988878754899999...9***** PP

                     HHHCT--TTTS-.EEEE---.EEES-SEETTEEE-CCCTEE--CCCS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHH CS
  Trp_halogenase 289 laeldgkleaep.rkirftt.GrrkqawvknvvalGlasgfvePlestsihliqaalrrLlallpdksdepaaiaefnrevare 370
                     l++ +gk+ a++ r ir+ t  r k +++  vv +G++ g v +l + +i   ++ ++  ++ + d +  + ai++  + +a+ 
      AJA92295.1 204 LKKHGGKVVATKgRPIRLATpDRCKPYYSGKVVGVGESIGTVYALLGEGIIPSMQCVNIFMENMHDFKAYEKAIEKHYSVYAKV 287
                     ********99999****97626778899*****************999998888888777777766655555555555555554 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.2e-06    0.0035       1      55 [.       2      56 ..       2      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.2e-06
                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHH CS
  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvas 55
                   ki+++G+Gv Gs ++ +l++++++v++y+r + +  + + +  ++ e++ +++++
     AJA92295.1  2 KIAVMGMGVAGSYLMARLKNSEHEVVGYERMPTERHDSICAWGTIKEELTNFCKK 56
                   79****************************9988777776666666666666665 PP

>> Toprim_Crpt  C-terminal repeat of topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00012      0.35      23      55 ..      40      80 ..      26      84 .. 0.77
   2 ?    2.7   0.0     0.042   1.3e+02      21      37 ..      87     103 ..      85     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
  Toprim_Crpt 23 Lltkgkt.gllkGFksKkgkkFdAyLvldkdee.......v 55
                 +++ g++ + l++F +K+g++Fd +L+ d +e        v
   AJA92295.1 40 ICAWGTIkEELTNFCKKTGRNFDDFLIHDGKEMhvkmndnV 80
                 5666777789****************988777565555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.042
  Toprim_Crpt  21 keLltkgktgllkGFks 37 
                  k L+t  k gl+k+F++
   AJA92295.1  87 KGLCTYNKLGLIKDFIK 103
                  779************85 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05     0.082       1      31 [.       3      33 ..       3      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
        ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                ia++G+G  Gs+l a+L++  ++v+ + r +
  AJA92295.1  3 IAVMGMGVAGSYLMARLKNSEHEVVGYERMP 33
                89***************99*****9887765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.12      38      73 ..       2      37 ..       1      56 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                  +++++G+G  G+ ++ rlk  + +v++y+r +++++
    AJA92295.1  2 KIAVMGMGVAGSYLMARLKNSEHEVVGYERMPTERH 37
                  789****************************98665 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.9e-05      0.24       2     111 ..       2     133 ..       1     158 [. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.9e-05
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCSHHH...HCHHHHHHHHHHHHH.............HHHHCHHHHCCCCHCCTCEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx...xxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclnggcll...skallgvaedaeias.............evvkklnqgielllgeevvki 78 
                  +++v G G+AG  ++ +l++++++v+ +e     + + +  +g +    ++ + +++++ + ++             +v  k+  g++ l + +++++
   AJA92295.1   2 KIAVMGMGVAGSYLMARLKNSEHEVVGYErmpteRHDSICAWGTIKeelTNFCKKTGRNFDDFLihdgkemhvkmndNV--KFDIGLKGLCTYNKLGL 97 
                  89**************************887777444555555555233444444444444444777765433333211..22222222222333333 PP

                  EESCEEEEETEEEC...............TCEEEEEESEEEE---EEE CS
                  xxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  79 dpgkkkvklekkke...............gdeekiaydklvlAtGssp 111
                  +            +                +e + +yd +v +tG++ 
   AJA92295.1  98 I------------KdfikdcnviygkaprLEELEKEYDMIVDCTGFNR 133
                  2............02222222223333335555667777777777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2126.32
//
Query:       AJA92296.1  [L=47]
Description: hypothetical protein T478_0974 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 308.55
//
Query:       AJA92297.1  [L=164]
Description: winged helix-turn-helix DNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-11   43.7   1.0    1.5e-06   27.6   0.1    2.3  2  HTH_24    Winged helix-turn-helix DNA-binding
    3.5e-06   26.8   0.1      0.095   12.6   0.0    2.4  2  HTH_5     Bacterial regulatory protein, arsR family
    1.3e-05   24.9   0.0     0.0056   16.5   0.0    2.1  2  MarR_2    MarR family
    0.00019   21.3   0.1     0.0066   16.4   0.0    2.3  2  MarR      MarR family
    0.00092   19.3   0.1        1.4    9.1   0.0    2.2  2  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.5   2.5        1.1    9.1   0.2    2.5  3  TrmB      Sugar-specific transcriptional regulator TrmB
       0.05   13.7   0.0        7.4    6.7   0.0    2.2  2  HTH_20    Helix-turn-helix domain
       0.26   11.2   1.6        2.9    7.9   0.1    2.2  2  HTH_11    HTH domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   6.7e-10   1.5e-06       8      44 ..       7      43 ..       1      47 [. 0.93
   2 !   14.9   0.1   6.5e-06     0.015       4      44 ..      77     117 ..      76     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 6.7e-10
      HTH_24  8 ILelLqknprisqreLAerlglSpstvnrrlkrLeee 44
                +Le+++knp+i  +e+ + +++  +t++ ++k+L+ee
  AJA92297.1  7 VLEIIEKNPGIRFNEIMRISNIRNGTLSHYVKKLVEE 43
                69*********************************97 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.5e-06
      HTH_24   4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                  ++kI+  L k+   + +e+ e +  Sps v+  +++L +e
  AJA92297.1  77 SQKKIILFLLKKKTATSQEIREFIEKSPSVVSVNINELFRE 117
                 689*********************************99555 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   4.3e-05     0.095       4      41 ..       3      42 ..       2      43 .. 0.89
   2 !   11.9   0.1   6.8e-05      0.15       1      36 [.      76     111 ..      76     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                HHHHHHHHTT.SS.EEHHHHHHHHTS-HHHHHHHHHHHHH CS
       HTH_5  4 RlkILklLae.ge.lcvcelaeelglsqstvShHLkkLre 41
                R++I+    e ++   + e++++ ++  +t+Sh+ kkL e
  AJA92297.1  3 RREIVLEIIEkNPgIRFNEIMRISNIRNGTLSHYVKKLVE 42
                7888888887788999**********************98 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 6.8e-05
                 SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHH CS
       HTH_5   1 dptRlkILklLaegelcvcelaeelglsqstvShHL 36 
                 d+++  IL+lL ++ +++ e+ e +++s+s vS   
  AJA92297.1  76 DSQKKIILFLLKKKTATSQEIREFIEKSPSVVSVNI 111
                 566778999999999*****************9755 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.5e-06    0.0056      10      58 ..       7      53 ..       5      56 .. 0.94
   2 !    6.3   0.0    0.0039       8.6      11      53 ..      82     122 ..      74     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-06
                HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
      MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                vL  +  +pg  ++ +e+ r  ++  +++s  +k+Lv+   +e +++p+
  AJA92297.1  7 VLEIIEKNPG--IRFNEIMRISNIRNGTLSHYVKKLVEEKSIELERAPR 53
                899999****..********************************99986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0039
                 HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2  11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53 
                 +++L        t +e+ +    s+s vs  +++L +   ve+
  AJA92297.1  82 ILFLLKKKT--ATSQEIREFIEKSPSVVSVNINELFREKIVEK 122
                 444444444..79*********************988888876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06    0.0066       8      44 ..       7      43 ..       6      53 .. 0.91
   2 ?    2.8   0.0     0.049   1.1e+02      13      49 ..      86     122 ..      76     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
        MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekk 44
                +L+i++ +++++  e+ + +++ ++t++  +++L+++
  AJA92297.1  7 VLEIIEKNPGIRFNEIMRISNIRNGTLSHYVKKLVEE 43
                79********************************987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.049
                 HHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR  13 yeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                   +  ++ +e+ ++++ s+s v+  + +L ++  +e+
  AJA92297.1  86 LKKKTATSQEIREFIEKSPSVVSVNINELFREKIVEK 122
                 4556778889999999999999999988887777765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0012       2.8       5      48 ..       7      50 ..       4      56 .. 0.88
   2 !    9.1   0.0   0.00064       1.4       5      44 ..      81     120 ..      79     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
      HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdk 48
                vl +  ++  + f+e+    ++ +g Ls  +kkL + + ie + 
  AJA92297.1  7 VLEIIEKNPGIRFNEIMRISNIRNGTLSHYVKKLVEEKSIELER 50
                67777789999***********************9999998775 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00064
      HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44 
                 ++ +L++++ a+ +e++e +e + +  sv+++ L   + +
  AJA92297.1  81 IILFLLKKKTATSQEIREFIEKSPSVVSVNINELFREKIV 120
                 78899**************************999766555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0046        10      22      58 ..      16      52 ..       7      62 .. 0.81
   2 ?   -1.3   0.0      0.93   2.1e+03       5      17 ..      61      73 ..      57      81 .. 0.77
   3 ?    9.1   0.2   0.00051       1.1      15      68 .]      83     137 ..      75     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0046
                CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                  + +ei +++++   +   ++++L++   +e e+  
  AJA92297.1 16 GIRFNEIMRISNIRNGTLSHYVKKLVEEKSIELERAP 52
                566789********************99998888765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.93
                HHHHHCCCHCHHH CS
        TrmB  5 GLseyEakvYlaL 17
                G++e Eak+ ++L
  AJA92297.1 61 GIQEKEAKICKYL 73
                9999999986666 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00051
                 HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEEE--HH CS
        TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYravdpe 68 
                 l Llk++ at +ei e ++ + s v   +++L +  +Ve++   p  +Y+  +pe
  AJA92297.1  83 LFLLKKKTATSQEIREFIEKSPSVVSVNINELFREKIVEKKYDIPSnKYSLKNPE 137
                 679**************************************99876699998886 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0033       7.4      24      58 ..      16      50 ..       3      53 .. 0.80
   2 ?    5.0   0.0     0.011        25      11      55 ..      77     121 ..      67     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0033
                TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
      HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLvevvr 58
                g  ++e+++   ++  tls+ +++L+e   +e++r
  AJA92297.1 16 GIRFNEIMRISNIRNGTLSHYVKKLVEEKSIELER 50
                555789999999***************88888887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                 HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
      HTH_20  11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55 
                 ++ +i   L  ++ +t  e+ e ++ s++ +s ++++L +  +ve
  AJA92297.1  77 SQKKIILFLLKKKTATSQEIREFIEKSPSVVSVNINELFREKIVE 121
                 4556666668999***********************997777766 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.065   1.4e+02       3      46 ..       4      48 ..       3      54 .. 0.77
   2 ?    7.9   0.1    0.0013       2.9       2      39 ..      78     114 ..      77     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.065
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.eelgvpI 46
                + i+  ++e+++ i  +e+++  n+   t   ++k+L ee+ +++
  AJA92297.1  4 REIVLEIIEKNPGIRFNEIMRISNIRNGTLSHYVKKLvEEKSIEL 48
                4566666577777********999999999999999966665554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0013
      HTH_11   2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39 
                 +++i+ +Ll+++   +++e+ e ++ S ++v   I +L
  AJA92297.1  78 QKKIILFLLKKKT-ATSQEIREFIEKSPSVVSVNINEL 114
                 6899999966665.9*******9999999998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1007.67
//
Query:       AJA92298.1  [L=223]
Description: hypothetical protein T478_0048 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1378.95
//
Query:       AJA92299.1  [L=169]
Description: hypothetical protein T478_0277 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1034.49
//
Query:       AJA92300.1  [L=144]
Description: hypothetical protein T478_1099 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.4   0.0     0.0018   18.0   0.0    1.2  1  Nsp1_C    Nsp1-like C-terminal region
  ------ inclusion threshold ------
      0.082   12.8   0.1       0.15   12.0   0.1    1.4  1  DUF2854   Protein of unknown function (DUF2854)


Domain annotation for each model (and alignments):
>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     2e-07    0.0018      72     102 ..     114     144 .]      95     144 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-07
      Nsp1_C  72 eqnkidqeLeyiesqqdeLeslLdnyEkele 102
                 +++k+d++L++ies+ +eL+ l++++Eke++
  AJA92300.1 114 KSKKLDESLDFIESKYKELHGLVEPLEKEIK 144
                 6799************************985 PP

>> DUF2854  Protein of unknown function (DUF2854)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.7e-05      0.15      67      87 ..     106     126 ..     103     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
     DUF2854  67 DvtryrYgqeahLdealeklg 87 
                  ++ry+Yg++++Lde+l++++
  AJA92300.1 106 ELVRYKYGKSKKLDESLDFIE 126
                 578***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 916.87
//
Query:       AJA92301.1  [L=138]
Description: 6,7-dimethyl-8-ribityllumazine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-33  114.0   0.8    5.2e-33  113.8   0.8    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
     0.0048   16.3   0.1     0.0091   15.3   0.1    1.5  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.8   5.8e-37   5.2e-33       2     133 ..       1     126 [.       1     134 [. 0.90

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 5.8e-37
                    EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHHHC CS
  DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvaeavskglmrvsldt 97 
                    ++iaiVva+fn++it+++++ al+++k+++ +   i++ +VPG f++pl+++kl+++s  +dav++lG+vi+G+t+h+e++a++++++++++s+++
     AJA92301.1   1 MKIAIVVAEFNQKITSRMYDVALETAKKLNLD--VIHTSNVPGIFDMPLVIDKLLQRS-DVDAVVTLGAVIKGQTKHDEVIAHSTARNIAKLSVKH 93 
                    69****************************85..9*********************54.47*********************************** PP

                    TS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHH CS
  DMRL_synthase  98 gvPvifgvltvd.teeqaleraggkagnkGeeaaeaa 133
                    ++Pv  g+  +  +  qa +r+        e+a++a+
     AJA92301.1  94 QKPVSLGISGPGmQVRQAYARIR----PVSENAVNAV 126
                    ***********9999******93....4444444444 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.054   4.9e+02      74     103 ..      15      47 ..       8      49 .. 0.69
   2 !   15.3   0.1     1e-06    0.0091       8      71 ..      33      95 ..      26     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.054
                    HHHHHHHHHHHHHTT-SEEE...EE--TTS--H CS
  Metallophos_3  74 iiklldklfrelgeldvpaf...vvPGkrDaPl 103
                      +++d ++++  +l++ ++    vPG  D Pl
     AJA92301.1  15 TSRMYDVALETAKKLNLDVIhtsNVPGIFDMPL 47 
                    456788888888888766552226999999997 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1e-06
                   EEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT----THHHHHHH CS
  Metallophos_3  8 vlaisdlkgevellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrepdkkeileek 71
                   v+  s++ g +++   + ++++  d+D++v +G ++k+++k de   a+   r+  k  ++++k
     AJA92301.1 33 VIHTSNVPGIFDMPLVIDKLLQRSDVDAVVTLGAVIKGQTKHDEVI-AHSTARNIAKLSVKHQK 95
                   667777888887655556666677********************99.99999998877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1103.52
//
Query:       AJA92302.1  [L=139]
Description: EVE domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-37  128.1   0.1    2.8e-37  128.0   0.1    1.0  1  EVE       EVE domain
  ------ inclusion threshold ------
      0.073   13.0   0.4       0.13   12.1   0.4    1.4  1  SWIB      SWIB/MDM2 domain


Domain annotation for each model (and alignments):
>> EVE  EVE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.1   3.1e-41   2.8e-37       1     145 []       3     136 ..       3     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 3.1e-41
                 -EEEEEEBHHT...SHHHHHCHHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE-GGGG-TTSTT--TTTBTTS--EEEE CS
         EVE   1 ayWllksepde...fsiddlkrkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypdetqfdpkskyydpkskkekpwlrvd 96 
                 +yWl+k ep+    + i dlk++k+++Wdg++n+qa +++r+ kkGD++++Yh+g++ ++ vgi++++s++yp++++ +++             + +vd
  AJA92302.1   3 NYWLAKQEPSGprgYHILDLKKDKTTVWDGIHNNQALKFMRDAKKGDEIIYYHTGTE-RQAVGIMTITSNPYPNPKEDNKR-------------FIVVD 87 
                 7*********7777*******************************************.***************99777555.............99*** PP

                 EEEEEEEEEEEEHHHHTTHGTCTTSHHHHCCT-SEEEE-HHHHHHHHHH CS
         EVE  97 vkpvkklkrplslkelkaepelegmkllrkgrlsvrpvteedwelilel 145
                 vk+ k +k p++l+e+k ++++++++llr  rls +pv++  w++il+l
  AJA92302.1  88 VKFKKLFKTPVTLDEMKLQKSFKNWELLRIMRLSFMPVPPNIWKTILKL 136
                 **********************************************985 PP

>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   1.5e-05      0.13      39      66 ..      78     103 ..      75     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
        SWIB  39 pedkreilcDekLkklfggkdrvkffem 66 
                 +++kr+i+ D k kklf+ +  v++ em
  AJA92302.1  78 EDNKRFIVVDVKFKKLFKTP--VTLDEM 103
                 68***************765..666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 992.15
//
Query:       AJA92303.1  [L=199]
Description: ATP synthase, subunit E [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-22   78.5  10.9    1.1e-21   77.2   9.8    2.1  2  vATP-synt_E     ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
      0.018   15.1   9.3       0.42   10.7   6.4    2.2  2  DivIVA          DivIVA protein
      0.042   14.3   2.1       0.45   11.0   0.1    2.1  2  NBD_C           Nucleotide-binding C-terminal domain
      0.062   13.1   2.5      0.092   12.5   2.5    1.3  1  HD_2            HD containing hydrolase-like enzyme
       0.07   13.6   1.4       0.12   12.8   0.5    1.8  1  KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
       0.13   12.0   8.3      0.073   12.8   6.4    1.5  2  LXG             LXG domain of WXG superfamily
       0.23   11.5   7.2       0.35   10.9   7.2    1.3  1  DHR10           Designed helical repeat protein 10 domain
       0.52    9.6   6.5       0.58    9.4   5.4    1.6  1  DUF3450         Protein of unknown function (DUF3450)


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.89     2e+03     175     195 ..       7      23 ..       3      31 .. 0.51
   2 !   77.2   9.8   4.7e-25   1.1e-21      33     196 ..      45     193 ..      27     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.89
                  ECCCHHHCHHHHHHHHHHCCC CS
  vATP-synt_E 175 vnnTlearLelvleqllpeir 195
                  ++ T++++L++++ +     +
   AJA92303.1   7 LESTIDQVLDRNSAEF----S 23 
                  3445555555544443....3 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 4.7e-25
                  HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCT CS
  vATP-synt_E  33 eekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveea 130
                  ee+ e++ ++ +K+a+   k+++ +a ++ar k L + +e  e+v+e+a++k+a++e+++ eY++l++kL+ +a  +l+  +viv+ + +D++lv++a
   AJA92303.1  45 EEEYEKIIADGKKEADKIEKQIVGSADLEARNKSLLVVQESAEKVLEKAKEKIANMERNS-EYSSLITKLLTEATSALNTSDVIVYTNSKDKDLVQSA 141
                  5677899999**************************************************.************************************5 PP

                  HCCCCCCHHCCSSSS--SEEEEESSEBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCC CS
  vATP-synt_E 131 ldkaaeeykaktkkktvevagdeedfledvlGGvvleaadgkikvnnTlearLelvleqllpeirk 196
                      +  + ++      e++ d     +d++GGv + ++dg ++ +nT++ar+el++  +++ i++
   AJA92303.1 142 ----VSSMSGA------ELSSDL----IDCMGGVKVTSKDGSMSFDNTIDARIELLKPLIRKDIAA 193
                  ....5555552......455566....9****************************9999888876 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9   0.00059       1.3      58     103 ..      19      64 ..       1      71 [. 0.80
   2 ?   10.7   6.4   0.00019      0.42      42      98 ..      53     108 ..      46     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00059
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  58 ykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekive 103
                  +e  ++Lk++l  aq+t  +     ++e e ii++ +k+a+ki +
  AJA92303.1  19 SAEFSQSLKNSLTDAQKTLSDSLPMLEEEYEKIIADGKKEADKIEK 64 
                 4567799999********9999999999999999999999999965 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                 HHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  42 eelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekka 98 
                 ++ k++ ++ e+++   ++le   +k+l+v qe+ae+v ++ak++  ++ +++e+++
  AJA92303.1  53 ADGKKEADKIEKQIVGSADLEAR-NKSLLVVQESAEKVLEKAKEKIANMERNSEYSS 108
                 455778888899999999***99.*************************99999875 PP

>> NBD_C  Nucleotide-binding C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.2    0.0017       3.8      25     105 ..      41     120 ..      28     121 .. 0.65
   2 ?   11.0   0.1    0.0002      0.45      38      83 ..     102     146 ..      93     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                 SEEEEEEHHHHHSCCTCHHHHHHH.HHHHHHCCTCCTSSEEEEEECTGHHHH.HH---HHCCC-HHHH...HHHHHHHHHHHHHH CS
       NBD_C  25 vpvleldvealledeesaeaeier.aleqaeeallaagkdvlvytsrepedvrdaleslqaelglera...geriaaalaeiarr 105
                  p+le + e++++d +++++ ie+ ++  a+ + ++ +k+ lv     ++ +++a e++++   +er+   +++i ++l e +++
  AJA92303.1  41 LPMLEEEYEKIIADGKKEADKIEKqIVGSADLE-AR-NKSLLVVQESAEKVLEKAKEKIAN---MERNseySSLITKLLTEATSA 120
                 677888899999555555555555166665555.44.788888888888878677666666...555555799999999888766 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                 CCTCHHHHHHHHHHHHHCCTCCTSSEEEEEECTGHHHH..HH---HH CS
       NBD_C  38 deesaeaeieraleqaeeallaagkdvlvytsrepedvr.daleslq 83 
                  + + + +i+++l++a++al  +  dv+vyt+ +++d+  +a++s+ 
  AJA92303.1 102 RNSEYSSLITKLLTEATSAL--NTSDVIVYTNSKDKDLVqSAVSSMS 146
                 455678899**********7..589************9755555543 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.5   4.1e-05     0.092      81     166 ..      18     100 ..      11     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
        HD_2  81 anpeireaykevEeeaeekllelLpeelreeyeell.a.deeaeeeekklvkaaDklsalikcleelkagnkeFeeakkeieeklkel 166
                 ++ e+++++k+  + a+++l ++Lp  l+eeye+++   ++ea++ ek++v  aD l+a  k+l  ++   ++   + ++++ek++++
  AJA92303.1  18 NSAEFSQSLKNSLTDAQKTLSDSLPM-LEEEYEKIIaDgKKEADKIEKQIVGSAD-LEARNKSLLVVQESAEK---VLEKAKEKIANM 100
                 567888889999999*********95.9********7358888889********9.89999988888866654...444444444444 PP

>> KAsynt_C_assoc  Ketoacyl-synthetase C-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   5.4e-05      0.12      56     106 ..      65     122 ..      46     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
  KAsynt_C_assoc  56 k.......eeslprLlvlsgrteeaveallekleehlldaellsllneilseeisrlp 106
                     +       e+++++Llv+    e+ +e+  ek++++++++e+ sl+ ++l+e++s l+
      AJA92303.1  65 QivgsadlEARNKSLLVVQESAEKVLEKAKEKIANMERNSEYSSLITKLLTEATSALN 122
                     3445555688999***************************************999887 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.4   3.3e-05     0.073      97     196 ..       4     104 ..       2     109 .. 0.92
   2 ?   -1.5   0.1      0.76   1.7e+03     111     144 ..     106     139 ..      95     146 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
         LXG  97 edfLeqelenglkkakevtee.lkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemts 194
                  ++Le+ +++ l+++++++++ lk+++ ++ ++ sd + + e ++++++++ +k  +k++++i +  d+++ +ks+l  +es  k l++  +++ +m  
  AJA92303.1   4 NSALESTIDQVLDRNSAEFSQsLKNSLTDAQKTLSDSLPMLEEEYEKIIADGKKEADKIEKQIVGSADLEARNKSLLVVQESAEKVLEKAKEKIANMER 102
                 578999*******99988875389*****************************************************************9999999977 PP

         LXG 195 kg 196
                 ++
  AJA92303.1 103 NS 104
                 66 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.76
         LXG 111 akevteelkdeinkilasvsdivslpelddsevk 144
                  ++ ++ l  e+ ++l++ + iv++++ d + v+
  AJA92303.1 106 YSSLITKLLTEATSALNTSDVIVYTNSKDKDLVQ 139
                 4444555555666666666666665555555544 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   7.2   0.00016      0.35      15     102 ..      16     105 ..       6     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
       DHR10  15 Erkarelqaki.dalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                 +r++ e ++++ ++l++++k l+  + +lee  e+ +a  +++ +k++++    +++e++ + l   +e  ++ le+a+ek++ +++++e
  AJA92303.1  16 DRNSAEFSQSLkNSLTDAQKTLSDSLPMLEEeYEKIIADGKKEADKIEKQIVGSADLEARNKSLLVVQESAEKVLEKAKEKIANMERNSE 105
                 66666666666469999999999999999877******************************************************9988 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.4   0.00026      0.58      30     109 ..      18      97 ..       1     104 [. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
     DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrL 109
                 ++a+ sq+ +++l+d +++l++ +  l+ee e++ +  ++ ++ +++q    a+le + +++  ++++ + +lek  +++
  AJA92303.1  18 NSAEFSQSLKNSLTDAQKTLSDSLPMLEEEYEKIIADGKKEADKIEKQIVGSADLEARNKSLLVVQESAEKVLEKAKEKI 97 
                 467789*******************************************************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1849  (0.103129); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1443.52
//
Query:       AJA92304.1  [L=485]
Description: putative glycine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-16   59.9   0.3    6.4e-16   58.3   0.2    1.9  2  HGTP_anticodon  Anticodon binding domain
    3.4e-12   46.7   0.3    5.1e-11   42.9   0.2    2.6  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.012   15.7   0.7        0.1   12.7   0.1    2.6  3  zf-RRPl_C4      Putative ribonucleoprotein zinc-finger pf C4 
      0.094   12.8   0.2         22    5.3   0.1    2.8  2  Zn-ribbon_8     Zinc ribbon domain
       0.11   13.2   0.8       0.38   11.5   0.6    2.0  1  zinc_ribbon_15  zinc-ribbon family
       0.26   11.1   1.7        7.1    6.5   0.3    2.5  2  A2L_zn_ribbon   A2L zinc ribbon domain
       0.29   11.2   2.0       0.46   10.5   0.0    2.3  3  YokU            YokU-like protein, putative antitoxin
        1.4    9.9   4.1    1.3e+02    3.8   0.1    3.5  3  zf-C2H2_4       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.4   7.7e+03      44      64 ..     135     155 ..     131     157 .. 0.82
   2 !   58.3   0.2   2.9e-19   6.4e-16       2      93 ..     392     480 ..     391     481 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.4
                     HHHHHHHTT-SEEEEE-HHHH CS
  HGTP_anticodon  44 kireadllgipfavvvGekel 64 
                      ++ a++ +  f+v +G+++ 
      AJA92304.1 135 EFESAKKFNMMFRVGIGPEDE 155
                     578889999999999999986 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 2.9e-19
                     EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                     v v+ l +k+  l e  +++++ +r + ++  ld  ++ ig+++r+ d++g pfa++v+ ++ e++tvt+r+rd+++qerv ++el+++l +
      AJA92304.1 392 VGVLSLVKKDG-LSEKTDEIYRLIRTK-FDSFLD-HSGAIGRRYRRLDEIGAPFAITVDHQTKEDNTVTIRRRDDMAQERVNISELESILAK 480
                     66777777444.888888888877776.766665.89**************************************************99876 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.2   2.3e-14   5.1e-11       7     178 ..     153     368 ..     146     369 .. 0.73
   2 ?   -2.3   0.0       1.7   3.7e+03     118     147 ..     442     471 ..     397     477 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.3e-14
                   TSEEEEE-SSSHHHHHHHHHHHEE...EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH..HHHHHHHHHHHHHHHHTT.SC CS
                   xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevl...rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld..dslrdlikaisriferlglef 98 
                   +d+e +L+P+ ++ +   +        r k LPl ++q++  +R+E    + LlR+reF q + +vf+ +++l+  d+++++++++ ri  +  +++
    AJA92304.1 153 EDEEAYLRPETCQSIFVDFPRL-FktmRGK-LPLGIAQVGKSFRNEIAPRQSLLRLREFYQAEIEVFCNPGKLNelDKFSEIENTTLRIQISDDIQV 247
                   6899********9976554433.3111555.***************98466******************9988722566777777777766666665 PP

                   EEEEEEGTTSC.......................................BTTSE.EEEEEEEETTTSEEEEEEEEEEEET.HHHHHTTE...EEEC CS
                   xxxxxxxxxxx.......................................xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxx RF
  tRNA-synt_2b  99 raiielmsaks.......................................adykd.kkefeavsesltkgieigtiqklgt.rlserlga...tvld 151
                      +e  +  +                                       a+y+d   +fe+ +      +e++ ++ + +  ls+  +    ++  
    AJA92304.1 248 MTCKEAVE--KgvipnkfvayylglltefykktgidmeksrfrklgekekAFYADvAFDFEVNTT--IGWLELVACNYRSDyDLSSHAKKskeKFEV 340
                   54444444..1457788889999999999999999999999999999999665552568888877..345567777776665666666555555554 PP

                   TTS.SEEEEEEEEEEEEHHHHHHHHHHH CS
                   xxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 152 enn.reksvimicaaigveRllsaileq 178
                   ++n ++  +++   ++g+ R l  ile+
    AJA92304.1 341 MDNdEKVLPHVFEISMGIDRSLYTILEH 368
                   5552666799999999999999999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                   EEEEETTTSEEEEEEEEEEEETHHHHHTTE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 118 feavsesltkgieigtiqklgtrlserlga 147
                   f +++  +tk+ +++ti  +++   er ++
    AJA92304.1 442 FAITVDHQTKEDNTVTIRRRDDMAQERVNI 471
                   334444477777777777776666666655 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         3   6.8e+03      15      27 ..      11      23 ..       7      30 .. 0.81
   2 ?   12.7   0.1   4.5e-05       0.1      18      68 ..      85     142 ..      68     147 .. 0.85
   3 ?   -0.5   0.0      0.59   1.3e+03      54     102 ..     217     267 ..     195     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
  zf-RRPl_C4 15 lnetvyCeaCeiy 27
                l+  +y + Ce+y
  AJA92304.1 11 LERAFYFPSCEVY 23
                56789999***99 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.5e-05
  zf-RRPl_C4  18 tvyCeaCeiyfkvknekqkvelvpike.......lekislrdkLCtkCkeknekekei 68 
                  + C++C   f+ ++   ++++v+i e        ++i ++++ CtkCk + e+ k++
  AJA92304.1  85 IIKCKKCGLTFRADKLISEIANVEIPEsadledfDKMIQEKNIVCTKCKGEFESAKKF 142
                 467*********99999********9889999977889999********998877665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.59
  zf-RRPl_C4  54 LCtkCkeknekeke.ircetfeeylkklklCkeCkervek.vlkndfvknf 102
                  C+  k ++  + + i+ +t++ +++      +Cke vek v+ n+fv ++
  AJA92304.1 217 FCNPGKLNELDKFSeIENTTLRIQISDDIQVMTCKEAVEKgVIPNKFVAYY 267
                 555555444443333666777766666666677888776636777777776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.019        43      26      35 ..      85      94 ..      69     106 .. 0.63
   2 ?    5.3   0.1    0.0096        22      21      36 ..     121     136 ..     113     145 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
  Zn-ribbon_8 26 ltaCPeCgse 35
                  ++C++Cg +
   AJA92304.1 85 IIKCKKCGLT 94
                 4556666652 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0096
  Zn-ribbon_8  21 isdapltaCPeCgsev 36 
                  + ++++++C +C++e 
   AJA92304.1 121 MIQEKNIVCTKCKGEF 136
                  5555555566665532 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00017      0.38      35      81 ..      83     142 ..      80     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
  zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkesse..............kkeCknCgkeveeefky 81 
                     +p+++c+kC+ ++ a+k l +ei + e  e              + +C +C+ e e+  k+
      AJA92304.1  83 DPIIKCKKCGLTFRADK-LISEIANVEIPEsadledfdkmiqekNIVCTKCKGEFESAKKF 142
                     799*************8.7788877777777778888888888888899988887776655 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.033        75      24      31 ..      88      95 ..      83      96 .. 0.72
   2 ?    6.5   0.3    0.0032       7.1       2      12 ..     125     135 ..     124     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.033
  A2L_zn_ribbon 24 CieCgasf 31
                   C++Cg++f
     AJA92304.1 88 CKKCGLTF 95
                   77777776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0032
  A2L_zn_ribbon   2 nlkvCsvCggn 12 
                    +++vC++C+g+
     AJA92304.1 125 KNIVCTKCKGE 135
                    789******98 PP

>> YokU  YokU-like protein, putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00021      0.46      34      56 ..      84     106 ..      80     125 .. 0.93
   2 ?   -1.9   0.1       1.5   3.3e+03      35      42 ..     126     133 ..     108     141 .. 0.70
   3 ?   -3.3   0.1       4.2   9.4e+03      53      65 ..     231     243 ..     222     255 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
        YokU  34 PsieCseCglvyqeeevvkeied 56 
                 P i+C++Cgl+++ +++++ei +
  AJA92304.1  84 PIIKCKKCGLTFRADKLISEIAN 106
                 99******************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
        YokU  35 sieCseCg 42 
                  i+C++C+
  AJA92304.1 126 NIVCTKCK 133
                 57788886 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.2
        YokU  53 eiedqllLvdtkk 65 
                 eie+  l ++ ++
  AJA92304.1 231 EIENTTLRIQISD 243
                 4444444444332 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.068   1.5e+02       2      12 ..      87      96 ..      86     102 .. 0.79
   2 ?    3.8   0.1     0.059   1.3e+02       2      16 ..     128     142 ..     127     144 .. 0.87
   3 ?    1.9   0.1      0.25   5.5e+02       6      22 ..     319     333 ..     317     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.068
   zf-C2H2_4  2 kCpiCgksFss 12
                kC+ Cg +F +
  AJA92304.1 87 KCKKCGLTF-R 96
                8********.4 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.059
   zf-C2H2_4   2 kCpiCgksFsskkaL 16 
                  C+ C++ F s k++
  AJA92304.1 128 VCTKCKGEFESAKKF 142
                 6********998875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.25
   zf-C2H2_4   6 CgksFsskkaLlrHlkt 22 
                 C  +++s ++L++H k+
  AJA92304.1 319 C--NYRSDYDLSSHAKK 333
                 8..99*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3680.95
//
Query:       AJA92305.1  [L=343]
Description: ABC transporter, substrate-binding protein, aliphatic sulfonates family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-29  102.7   0.0    3.6e-29  102.2   0.0    1.1  1  NMT1_2          NMT1-like family
    5.4e-15   55.9   0.0    7.9e-15   55.4   0.0    1.2  1  NMT1            NMT1/THI5 like
    7.8e-08   32.2   0.0    1.1e-07   31.7   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0016   17.9   0.0       0.45    9.9   0.0    2.2  2  SBP_bac_3       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
       0.13   11.6   0.0        0.2   11.0   0.0    1.2  1  NMT1_3          NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0     1e-32   3.6e-29       5     247 ..      31     266 ..      28     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1e-32
      NMT1_2   5 keqlklGfialtdaaplvvakekglfake...GltvelekqaswaelrdkllagelDaahv.ltpapllidlGiggakadmkvlaslnlnGqaitlsnk 99 
                 +++++++f++ + +a  +v  e+++fa+    ++++e++ + s++++ + + ++++D+a+v   p++ +  +     ++d+k+las +  G++ ++++ 
  AJA92305.1  31 QNKIRVAFFPSIIHAVPIVGMENQTFADNlddDMNIEVKIFDSGPQVIESIFSNSVDLAYVgPGPVINGYLKSD---GKDLKILASAANGGASFIIQK- 125
                 67899****987777777777777777777889****************************9999998888887...89*****************75. PP

      NMT1_2 100 lkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldp...eadvklvvvpppqmvanlkagtidgfcvgePwnaqavaegiGvta 195
                          ++l+++ +++   ++ ++a+++ ++t+d+ lr++La++Gl p     dv ++ + +p++   +++g+idg++v+ePw   +v e  Gv +
  AJA92305.1 126 --------NSGLESI-ENY---SGKRVAAPQISNTQDVSLRHYLAQNGLTPaekGGDVFVLNIANPDIYTLFAKGDIDGAWVPEPWATMLVEELDGVRL 212
                 ........4555444.333...5689999**********************99999******************************************* PP

      NMT1_2 196 ltsqelwkdhPekv..lgvredfveknpntaralvkalleAtkwldakkenrae 247
                 ++++e+w+++      l  r+d++eknp+  +  ++a  e  +w++++++  +e
  AJA92305.1 213 FDENEIWPENKFSSvlLIGRSDYIEKNPEIIKNWINANKETVQWINNNPDKSKE 266
                 ********99555457999***************************98887766 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   2.2e-18   7.9e-15      19     215 ..      64     263 ..      61     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2.2e-18
                 TTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHH..HHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHH CS
        NMT1  19 eGldVeivepadpsdatelvasgkadfgvsyqesll..aarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkallak 114
                  +++V+i   ++  +++e + s+ +d++   +  ++    ++ g +++ +a+   +   ++i +k+sg++s++   Gkr++ ++ s+ ++  l++ la+
  AJA92305.1  64 MNIEVKIFDSGP--QVIESIFSNSVDLAYVGPGPVIngYLKSDGKDLKILASAA-NGGASFIIQKNSGLESIENYSGKRVAAPQiSNTQDVSLRHYLAQ 159
                 578888888766..999***********99999999666678999999888877.7888999*********************98899*********** PP

                 TT--GG....G-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EEEE-GGGTT--.---SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHH CS
        NMT1 115 dggdps....dvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelrifaladlgvp.dyyslvlitnekllkenpelvkkFlrAlkkGyey 208
                 +g++p+    dv ++n+ + + ++ +++g +D a+ + e w ++ + +e   +r f   ++ +  ++ s +li   +++++npe++k  + A k+ +++
  AJA92305.1 160 NGLTPAekggDVFVLNIANPDIYTLFAKGDIDGAW-VPEPWATMLV-EELDGVRLFDENEIWPEnKFSSVLLIGRSDYIEKNPEIIKNWINANKETVQW 256
                 ***66533338************************.9999887776.455788899999999888********************************** PP

                 HHHSHHH CS
        NMT1 209 alahPee 215
                 + ++P++
  AJA92305.1 257 INNNPDK 263
                 *****97 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.2e-11   1.1e-07      28     173 ..      63     214 ..      52     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.2e-11
                     SSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-...EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTT CS
  Phosphonate-bd  28 GvevelvvatdyaavvealragqvDiaflgplayvqardqag...veplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsGy 119
                     ++ +e++++++  +v+e++ +++vD+a++gp ++++   +++   ++ la   +        + +i +++s+++s+e+  gk++a ++ s t   
      AJA92305.1  63 DMNIEVKIFDSGPQVIESIFSNSVDLAYVGPGPVINGYLKSDgkdLKILASAAN------GGASFIIQKNSGLESIENYSGKRVAAPQISNTQ-D 150
                     677899999999************************886654111566666654......44557999********************99999.7 PP

                     HHHHHHTCCCCT--HHHHSSEEEE-..-HHHHHHHHHTTSSSEEEEEHHHHHHHH.........H CS
  Phosphonate-bd 120 lvpaalLvkeagldpeddfsevfsg..shdaavlavlsgdadaaavsadaledlv.........a 173
                     +  +++L +++gl+p +  + vf+     +  +   ++gd+d a v++  ++ lv         +
      AJA92305.1 151 VSLRHYL-AQNGLTPAEKGGDVFVLniANPDIYTLFAKGDIDGAWVPEPWATMLVeeldgvrlfD 214
                     777888*.8********99999754357888999999*****99999987777774444444441 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00012      0.45     118     183 ..      53     116 ..      42     127 .. 0.75
   2 !    7.3   0.0   0.00076       2.7      86     176 ..     118     213 ..     112     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                 TSHHHHHHHHHHHCTSEEEEESSHHHHHHHHHTTSSS.EEEEEHHHHHHHHHHCCGCCEEEEECGGC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SBP_bac_3 118 gstaeellkeelkkgaeivefdtleealqaLkngrvd.avvadspvlaylvkknpdkkvvlveepls 183
                 + t ++ l   +  ++e++ fd+ +++++ + +++vd a+v+  pv+++++k ++++ ++l + + +
  AJA92305.1  53 NQTFADNLDDDM--NIEVKIFDSGPQVIESIFSNSVDlAYVGPGPVINGYLKSDGKDLKIL-ASAAN 116
                 344445666533..89999******************7789**************999998.33333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00076
                 EEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHH.HHHHHHC.........TSEE.EEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.........xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SBP_bac_3  86 gqvllvrkkdaskissiksladLkgkkvgvqagstaeel.lkeelkk.........gaei.vefdtleealqaLkngrvdavvadspvlaylvkknpdk 173
                 g +++++k+     s+++s+++ +gk+v++ + s++++  l+++l++         g ++ v    +++ +++ ++g +d + + +p +  lv++ ++ 
  AJA92305.1 118 GASFIIQKN-----SGLESIENYSGKRVAAPQISNTQDVsLRHYLAQngltpaekgG-DVfVLNIANPDIYTLFAKGDIDGAWVPEPWATMLVEELDGV 210
                 667888865.....3677777************999999655544446666777743.332557789999999*******9999999998888877766 PP

                 CEE CS
                 xxx RF
   SBP_bac_3 174 kvv 176
                  ++
  AJA92305.1 211 RLF 213
                 655 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.6e-05       0.2      78     170 ..     104     199 ..      74     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
      NMT1_3  78 plknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekd....lklleelgygesadalkdgqldgaalvaGv 170
                 + k+l+++++  +   +++++k+sg++si++  gkrv+  + ++++++s r  l+  gl+ ++    +  + ++   + ++++++g +dga ++   
  AJA92305.1 104 DGKDLKILASAANGGASFIIQKNSGLESIENYSGKRVAAPQISNTQDVSLRHYLAQNGLTPAEkggdVF-VLNIANPDIYTLFAKGDIDGAWVPEPW 199
                 55788888999999999******************************************9554222122.223556678899999999998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2684.48
//
Query:       AJA92306.1  [L=179]
Description: 2'-5' RNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-24   86.2   0.0      9e-14   51.4   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    1.3e-12   48.0   1.1    3.2e-12   46.8   1.1    1.6  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
    5.3e-10   39.4   0.0    6.6e-10   39.1   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.5e-17     9e-14       5      87 .]      12      87 ..       7      87 .. 0.92
   2 !   33.1   0.0   7.8e-12   4.7e-08       1      87 []      88     170 ..      88     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.5e-17
                HHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
  LigT_PEase  5 eeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                 +i e++ +++++++      ++kp+r ++ H TL+flgevde   ++++++l+ei   + +fe+ ++gvg fp+ ++prvi+
  AJA92306.1 12 TQILENIKKFQENVK-----IDAKPTRTDQIHFTLQFLGEVDEILCEKIKKSLNEI--SFSEFEISLNGVGGFPNLKNPRVIW 87
                567788888899998.....99**********************************..5669*************99*****9 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 7.8e-12
                 EE-CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCCEEE CS
  LigT_PEase   1 lgppeeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrl.rprviy 87 
                 +g++++ ae+l +la+e+e +l +lg+ ++++f+pH+T+ ++++    +v+ + + +++  +ga      v+++ l +s l ++++ y
  AJA92306.1  88 IGIEKNGAEKLISLAKEVEMKLISLGFEQDKKFKPHLTVFRVKKR-IGDVSSIMKDFETTNFGA----EMVSKIKLKKSVLsPKGPEY 170
                 6788999***********************************984.889999999999888886....5699*******999988855 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   1.1   5.4e-16   3.2e-12       4     188 ..       4     160 ..       2     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 5.4e-16
                 EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EEEEEEEEEE.....TTTEEE CS
   AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplslrlkGletfnddpakarVlY 102
                 F++i ++++++ ++++kfqe+v      +d++  +   ++H+Tl  l   ++  +++ k+ L+e++          +++++l+G++ f  + ++ rV++
  AJA92306.1   4 FVAIEISKTQILENIKKFQENVK-----IDAKP-TRTDQIHFTLQFLGEVDEILCEKIKKSLNEIS------F--SEFEISLNGVGGF-PNLKNPRVIW 87 
                 9********************95.....56666.778889*******9888888888888888885......2..789**********.68889***** PP

                 EEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEEEE CS
   AKAP7_NLS 103 akveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihLsq 188
                 +++e+++  ekL  la+ +  ++ + g++++k+   +k+H+T++ ++kr +         d ++i+k+f+ ++fg e +++i+L +
  AJA92306.1  88 IGIEKNG-AEKLISLAKEVEMKLISLGFEQDKK---FKPHLTVFRVKKRIG---------DVSSIMKDFETTNFGAEMVSKIKLKK 160
                 ****888.*******************977655...88*******997766.........456899****************9975 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.1e-13   6.6e-10      18     114 ..      29     127 ..       9     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.1e-13
  2_5_RNA_ligase2  18 dkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsv..sdsealqalraallealpeagdkedsge 106
                       k+++ ++ H tL ++++ de l +++++ l ++   ++ fe++l+g+g F+  k+  v+++ +  ++ e+l  l ++++ +l   g  +d ++
       AJA92306.1  29 AKPTRTDQIHFTLQFLGEVDEILcEKIKKSLNEIS--FSEFEISLNGVGGFPNlKNPrVIWIGIekNGAEKLISLAKEVEMKLISLGFEQD-KK 119
                      45577788*************99999999999995..99***************9999************************999999988.9* PP

  2_5_RNA_ligase2 107 ftPHlTia 114
                      f+PHlT+ 
       AJA92306.1 120 FKPHLTVF 127
                      ******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1420.52
//
Query:       AJA92307.1  [L=172]
Description: cytidine and deoxycytidylate deaminase zinc-binding region [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-27   94.8   0.8    2.9e-27   94.5   0.8    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
      2e-13   50.3   0.1    2.7e-13   49.9   0.1    1.2  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.8   3.3e-31   2.9e-27       2     100 ..       9     134 ..       8     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 3.3e-31
                      HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG...........................TTB-HHHHHHHHHHHHT.S CS
  dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs...........................ktiHAEvnAilkaakng.g 67 
                      ++de+++ +a++a+ ++ +c+  +VGaviv+++++++tgyng+p+g +                            ++HAE nAi+++a  g +
       AJA92307.1   9 SWDEYFMLQAKLASLRS-NCMTRSVGAVIVRDHRQLATGYNGTPPGITncfeggcqrckdrmdgktksgvgldrcLCNHAEANAIMHCAILGiE 101
                      79***************.***********************************************************************99999 PP

                      SCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
  dCMP_cyt_deam_1  68 sklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                        ++ga+ly t+ PC +C+k+ i++gikk+v++
       AJA92307.1 102 AGVKGAVLYSTYVPCLECTKMAITIGIKKFVCL 134
                      9*****************************985 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1     3e-17   2.7e-13       2     117 ..       9     165 ..       8     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 3e-17
  MafB19-deam   2 dkekafrkalaevekatkikedkigavivkdkkviargsn...........................ekelnakataHaEiaalqqAakklkskrldd 72 
                  +++++f+ ++++++ ++++  + +gaviv d++ +a+g+n                              l+    +HaE++a++  a  +++   ++
   AJA92307.1   9 SWDEYFMLQAKLASLRSNCMTRSVGAVIVRDHRQLATGYNgtppgitncfeggcqrckdrmdgktksGVGLDRCLCNHAEANAIMHCAILGIEAGVKG 106
                  689********************************************************99998766556788899********************** PP

  MafB19-deam  73 atlyvtlepCdmCagaivqaglkklvygagnpks..............lnkLkvkekng 117
                  a+ly t  pC  C ++ +  g+kk v   ++p++              + k k++++ +
   AJA92307.1 107 AVLYSTYVPCLECTKMAITIGIKKFVCLDEYPETdynlikeagveieiIDKTKIERWAK 165
                  **************************999999888787777776666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1252.67
//
Query:       AJA92308.1  [L=108]
Description: hypothetical protein T478_0019 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 866.30
//
Query:       AJA92309.1  [L=378]
Description: N2,N2-dimethylguanosine tRNA methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-79  267.4   0.0    2.5e-79  267.2   0.0    1.0  1  TRM             N2,N2-dimethylguanosine tRNA methyltransferas
     0.0047   17.0   0.5     0.0089   16.1   0.5    1.4  1  FYVE            FYVE zinc finger
  ------ inclusion threshold ------
      0.077   13.0   0.7       0.22   11.6   0.7    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.081   13.0   0.7       0.17   11.9   0.7    1.4  1  DZR             Double zinc ribbon
       0.28   11.1   2.9       0.85    9.6   2.9    1.9  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.2   0.0     7e-83   2.5e-79       4     375 ..      14     376 ..      11     377 .. 0.92

  Alignments for each domain:
  == domain 1  score: 267.2 bits;  conditional E-value: 7e-83
                 EEEE----SS..--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT-- CS
         TRM   4 kikvedkevt..vskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve 100
                 k+ v++ ++t  v+ ke+ F+NP+    RDls+++    +++ k  + +   +d+Ls+ G R++R a E+++v++v++ND++++A+++  + +k+n+ e
  AJA92309.1  14 KLFVPKGSMTekVPPKEPAFFNPRASLSRDLSIIA---CSAFWKDYKFPKIFFDGLSGLGARGLRIANEISEVEKVIVNDVNPNALDIALRSAKINNLE 109
                 555666555555999*******************9...56666666666689*********************************************** PP

                 GGEEEE-S-HHHHHC...--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHH CS
         TRM 101 eivvineddAnvlla...ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgavalkselcHEvalRillkavare 196
                 +  +i+e++   +l+   ++++r  ++D+DPfGsp++++d a+++  ++g+L++TaTD+ vL G  +++  r+Y ++++k+e+  E+a+R++l+ v   
  AJA92309.1 110 N-FEISENETCRFLSshsRMNERASIVDIDPFGSPSKYIDCAIRATMHSGMLALTATDLQVLHGLFNKAAKRRYYGTPVKTEFSNEIAIRLILGCVSFV 207
                 9.88888899999997877889999************************************************************************** PP

                 HHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT. CS
         TRM 197 aakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaeke 295
                 a + +   +pl+     +Y+r ++k+ + ++k     ek+g++++C +C +  + +++++ + +c +cg+++++aGPlw+g+l +kef++++ +  ++ 
  AJA92309.1 208 AGRLDISFQPLFVDHDMHYYRTYMKILNTPEKE----EKIGYIIFCRSCKD--RYTEITR-QDKCRKCGHETEIAGPLWIGKLFEKEFIQKMKNVKND- 298
                 **************************9998775....789*********88..5555665.58****************************9876666. PP

                 .-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
         TRM 296 keeelkkrvkklLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                     ++k+  ++++ ++eE+    +yy+l+++as++k+   +l++ ++ l++ g+++s+t ++p +++T+ +++++++++
  AJA92309.1 299 --LIVNKKCDRIIERAEEEAELPATYYTLDEIASMIKSAPLKLNEAIERLRAQGYKASMTSLNPGGFRTDCEIDKITQIF 376
                 ..678**************99999****************************************************9986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   2.5e-06    0.0089      11      33 ..     248     270 ..     241     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                 B-TTT--B--SSS--EE-TTT-- CS
        FYVE  11 kCeiCakkFsllrrrhhCrlCGk 33 
                  C++C+ +++ ++r+  Cr CG+
  AJA92309.1 248 FCRSCKDRYTEITRQDKCRKCGH 270
                 5*********************7 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   6.1e-05      0.22      67      95 ..     243     271 ..     231     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.1e-05
                 E--EEEETTTS-EEECHHHHHS-TTTSSS CS
        HypA  67 vpvkvrCreCgkefeleekalrCpkCgsa 95 
                 +   + Cr+C+ ++++ +++ +C kCg++
  AJA92309.1 243 IGYIIFCRSCKDRYTEITRQDKCRKCGHE 271
                 556789********97666678****985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   4.8e-05      0.17      13      38 ..     247     272 ..     241     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
         DZR  13 rfCseCgtklkavaaedrCpsCgekv 38 
                 +fC  C+ +  + +++d+C +Cg+++
  AJA92309.1 247 IFCRSCKDRYTEITRQDKCRKCGHET 272
                 69*********************975 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.9   0.00024      0.85       1      33 [.     246     274 ..     246     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
                     EEBESTTTSBEEEEECSCCCEEEESSSS-EEES CS
  RNA_POL_M_15KD   1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepa 33 
                     ++FC++C++     + + +    Cr+Cg e ++
      AJA92309.1 246 IIFCRSCKDRYTEITRQDK----CRKCGHETEI 274
                     69*******9888888888....*****99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2852.25
//
Query:       AJA92310.1  [L=81]
Description: hypothetical protein T478_0954 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 580.57
//
Query:       AJA92311.1  [L=205]
Description: translin family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-09   36.2   1.3    2.5e-07   30.9   1.3    2.2  1  Translin  Translin family


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   1.3   1.4e-11   2.5e-07       3     189 ..      24     177 ..      22     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.4e-11
                 HHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.H.HHHHHHHHHHTTSS..........GHHHHGGGTH.HHHHHHHHHHHHHHHHHSS---H CS
    Translin   3 reriikasrditaaskkiifllhrvrsekteaqdkkakik.keakeklkeiakllasvaeelqgsnayrYqrqisgglqeliealsfahYletqtLitl 100
                 re +ik  r++ ++  ++i+++h+ +         +ak+k k+ak+ l+++++++   +      +  rY  +     qel+ea+++ + +e +++ ++
  AJA92311.1  24 REFLIKNNREVIINCSQAIIAIHKND-------LPSAKLKiKKAKSLLAKLKQKA---NG-----DLKRYVLTP---EQELVEAVALLSIIEGKQIPSY 104
                 66677777777777777776666633.......2334444467777777777777...33.....333554333...3777777765555555444444 PP

                 HHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH...HHHHHTTHHH CS
    Translin 101 eevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakdlrkKldvlkq 189
                                + ++++ e Y+lGl+d++gEL R  i ++  g+ + ++ +    ++el+  +  +    ++ k+ r+Kldv + 
  AJA92311.1 105 ---------------KSIKVSGESYILGLLDCIGELKRQVIDQIRIGNSK-NAERYFGIMEELYLILYPFATYDKIVKESRRKLDVNRM 177
                 ...............46788899*************************77.9**************999999977799*******9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1413.09
//
Query:       AJA92312.1  [L=78]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-09   37.5   0.2    1.8e-09   37.4   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0053   16.7   0.1     0.0058   16.6   0.1    1.1  1  GYD             GYD domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2     2e-13   1.8e-09       8      74 ..      13      76 ..       6      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2e-13
                    GGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
  AsnC_trans_reg  8 ghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                    g+    e + e+l++++e++ +y++ G yd++++++++  e++e+ ++ k+++l  v +t t+ v++
      AJA92312.1 13 GA---EEYILEELQQVDEIKNAYVTFGAYDIIAEIHAKTQEEFEKTVSMKVRQLSRVVSTMTLNVIK 76
                    55...677899***************************************************98875 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.5e-07    0.0058      36      82 ..      27      75 ..      14      78 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.5e-07
         GYD 36 kleslyatlGeyDvvvivEapDdetaaa.lslalaasGtvrt.etlraf 82
                ++++ y+t+G yD+++ + a  +e++++ +s+++++   v +  tl ++
  AJA92312.1 27 EIKNAYVTFGAYDIIAEIHAKTQEEFEKtVSMKVRQLSRVVStMTLNVI 75
                57899********************987479999999988765777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 591.74
//
Query:       AJA92313.1  [L=90]
Description: Mut7-C RNAse domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-08   31.9   0.1    1.4e-07   31.2   0.1    1.5  1  DUF5615   Domain of unknown function (DUF5615)
    0.00029   21.0   0.0    0.00029   21.0   0.0    1.0  1  Mut7-C    Mut7-C RNAse domain


Domain annotation for each model (and alignments):
>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.5e-11   1.4e-07       1      57 [.       1      59 [.       1      74 [. 0.90

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.5e-11
     DUF5615  1 mklllDenlsprlvellreaghdvlhvrelgleg...asDeeileyAkeedriivTkDkD 57
                mk+l+De  +    e+l ++g+d+ +v++l  eg    +D  +++yAke+d+i++T+D  
  AJA92313.1  1 MKILVDEM-DDGMDERLIQLGYDAYSVKKLRTEGkklHTDYSVINYAKENDMILITRDTE 59
                99999995.668999999*********99999988999********************64 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.2e-08   0.00029       2      73 ..       2      83 ..       1      90 [] 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-08
      Mut7-C  2 rfllDamlgklakyLRllGydalyasdv........edeellalaakekrillTrdreLlkraklkkg..vlltsrdveeql 73
                ++l+D m   + + L  lGyda   ++         +d ++++ a++++ il+Trd+e  +  +++    +ll+++++ + +
  AJA92313.1  2 KILVDEMDDGMDERLIQLGYDAYSVKKLrtegkklhTDYSVINYAKENDMILITRDTESGQACEENGLpcILLDNNEIFKIV 83
                8899999999************977766688999999********************9887776664465555666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 681.14
//
Query:       AJA92314.1  [L=79]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-11   43.8   0.0    2.2e-11   43.6   0.0    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00067   19.7   0.1    0.00079   19.4   0.1    1.1  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.4e-15   2.2e-11       1      71 [.       6      73 ..       6      76 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.4e-15
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    vl+++e g+    e+++ +l++l+ V+e++ + G yd+l+k+ +  +eal++ +  k+++++ +++t t++
      AJA92314.1  6 VLINCELGS---EEAIISQLKNLEGVIEVHGTFGAYDILAKIESSTVEALRETITWKIRKIEKIRSTLTLM 73
                    789999999...9******************************************************9987 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   8.8e-08   0.00079       6      67 ..       6      69 ..       4      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.8e-08
        NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsa 67
                +++++  ++ +a+  +l++l+gv Evh++ ++  +   iE++++++l +ti+  i++++++ s+
  AJA92314.1  6 VLINCELGSEEAIISQLKNLEGViEVHGTFGAYDILAKIESSTVEALRETITWkIRKIEKIRST 69
                6899******************87***************************9779999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 608.42
//
Query:       AJA92315.1  [L=336]
Description: ketol-acid reductoisomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-67  224.3   0.3    8.6e-67  223.8   0.3    1.2  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    9.5e-55  184.8   1.0    1.5e-54  184.2   1.0    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
      1e-07   31.5   0.0      2e-07   30.6   0.0    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    9.6e-07   29.1   0.2    6.6e-06   26.4   0.1    2.2  3  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0004   20.9   0.1    0.00091   19.8   0.1    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.003   17.7   0.1     0.0063   16.6   0.1    1.5  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.8   0.3   2.9e-70   8.6e-67       2     165 .]      19     182 ..      18     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 223.8 bits;  conditional E-value: 2.9e-70
                 HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHHH CS
        IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkalafahGfnih 100
                 +k+++iaviGyG qG aqa+n++dsgl+v+vglregs +++kAke+g++v++va+a+k+ad+v+il+PD++q++vy+eei pnl+eg+al+f+h+  i 
  AJA92315.1  19 IKDQTIAVIGYGIQGDAQANNMKDSGLKVIVGLREGSPTWNKAKEDGHQVMSVADATKQADIVHILLPDMVQAKVYKEEIGPNLSEGNALSFSHAAAIY 117
                 89************************************************************************************************* PP

                 TTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHHHHHTTHHHH- CS
        IlvN 101 fglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalayakgiGatraG 165
                 ++ i++p++vd ++vAPkgpG+ vre+y +++G+p+++aveqd++g+a++ +l +ak+iG++raG
  AJA92315.1 118 WKWIDAPENVDLIMVAPKGPGSKVRETYLQNFGTPSIVAVEQDKTGNAWDRTLGIAKAIGSARAG 182
                 ****************************************************************9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   1.0   4.9e-58   1.5e-54       1     142 [.     188     330 ..     188     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 4.9e-58
                 HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHS-HHHHHHHHHHHHHH CS
        IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdltagprviteevkeemkeileei 99 
                 FkeE+etD fgEqa LcGg +++v ++FetlveaGy+pe+Ayfe+lhelklivd+i++ Gi++m++++S+ta+yg+lt+gp v+t+++ke+mk++l+ i
  AJA92315.1 188 FKEEVETDWFGEQADLCGGSASMVVNAFETLVEAGYQPEIAYFEVLHELKLIVDMIQRYGINGMWRRVSETARYGGLTRGPMVMTSDTKENMKKVLTMI 286
                 9************************************************************************************************** PP

                 HTTHHHHHHHHHHHT.TSHHHHHHHHHHHTSHHHHHHHHHHHCH CS
        IlvC 100 qsGefakevieenka.grpelkklrkeeaeheiekvgkklralm 142
                 q+G+f ke+i+++++ g++ ++k++k+ + h+ie+vgk++r++m
  AJA92315.1 287 QDGTFNKEWIDNYQNeGKAAFDKYMKDLDGHQIETVGKQMRKMM 330
                 ************9988***************************9 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   6.6e-11     2e-07      20     101 ..       6      87 ..       2      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6.6e-11
                   TTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
  2-Hacid_dh_C  20 egewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpl 101
                   +++w ++++++   ++++t+++iG+G  G a a+ +k  g+kvi+  r  +++  +++e g +++s+ ++ +++Div + lp 
    AJA92315.1   6 AKTW-KDADISLDPIKDQTIAVIGYGIQGDAQANNMKDSGLKVIVGLREGSPTWnKAKEDGHQVMSVADATKQADIVHILLPD 87 
                   5678.9999999***********************************999988778999999*****************9995 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   2.2e-09   6.6e-06       1      85 [.      23     107 ..      23     112 .. 0.94
   2 ?   -2.9   0.0       2.3   6.7e+03      34      64 ..     214     244 ..     209     248 .. 0.76
   3 ?   -0.3   0.0      0.37   1.1e+03      50      73 ..     273     296 ..     242     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.2e-09
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-E CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdi 85 
                    +i++iG G+ G   a+n++++g kv+v  r+ + + + ++e  + + s++++++++d+v +++++  + +   e++ ++l++g+ 
     AJA92315.1  23 TIAVIGYGIQGDAQANNMKDSGLKVIVGLREGSPTWNKAKEDGHQVMSVADATKQADIVHILLPDMVQAKVYKEEIGPNLSEGNA 107
                    59*********************************999999999*********************99999888889999999976 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                    HHHHHHHTTEEE-SSHHHHHHHCSEEEE-SS CS
  NAD_binding_2  34 kveelvaegakaaesieelvasldvvitmvk 64 
                    ++e+lv++g ++     e++++l++++ m++
     AJA92315.1 214 AFETLVEAGYQPEIAYFEVLHELKLIVDMIQ 244
                    5677888888887777888888888887776 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.37
                    HHHHHHCSEEEE-SSSHHHHHHHH CS
  NAD_binding_2  50 eelvasldvvitmvkagkavdevi 73 
                    ++  +++++v+tm+++g+  +e i
     AJA92315.1 273 SDTKENMKKVLTMIQDGTFNKEWI 296
                    455567788888888887666655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     3e-07   0.00091       1      80 [.      23      96 ..      23     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3e-07
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80
                   +i++iG+G +g a a+++  +g    +++v+ +    + ++++e+ g +v++   ++a ++ad+v + ++  + ++v +e
     AJA92315.1 23 TIAVIGYGIQGDAQANNMKDSG---LKVIVGLREGSPTWNKAKED-GHQVMS--VADATKQADIVHILLPDMVQAKVYKE 96
                   59********************...****9976666666666665.555555..***********988887666666665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.1e-06    0.0063      24      82 ..      22      81 ..      12      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                   SEEEEE--SHHHHHHHHHHHHCT-EEEEE..-S-HHHHHHHHCTT-EE--HHHCTTT-SEE CS
  AdoHcyase_NAD 24 kvavvaGyGdvGkGcaaslkglGarvivt..evdPicalqaameGfevvtleevvkkadiv 82
                   +++ v+GyG  G   a+ +k  G +viv   e  P    +a  +G++v+ + +++k+adiv
     AJA92315.1 22 QTIAVIGYGIQGDAQANNMKDSGLKVIVGlrEGSPTW-NKAKEDGHQVMSVADATKQADIV 81
                   67899**********************9722555644.58999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2533.50
//
Query:       AJA92316.1  [L=139]
Description: putative HTH-type transcriptional regulator LysM [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-14   52.1   0.1    8.5e-14   51.1   0.1    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.7e-13   49.7   0.3    4.3e-13   49.0   0.3    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.4e-12   46.9   1.9    1.8e-12   46.6   0.5    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00066   19.5   0.1     0.0016   18.3   0.0    1.6  2  MarR_2          MarR family
    0.00077   19.4   0.2     0.0018   18.2   0.2    1.6  1  HTH_11          HTH domain
     0.0008   18.9   0.0      0.002   17.6   0.0    1.7  1  Sigma70_r4      Sigma-70, region 4
      0.001   19.1   0.4      0.002   18.1   0.4    1.6  1  NapD            NapD protein
     0.0034   18.0   0.5      0.012   16.2   0.1    1.9  2  Mga             Mga helix-turn-helix domain
      0.006   16.4   0.0      0.011   15.5   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.024   14.5   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
      0.011   15.4   0.4      0.025   14.3   0.1    1.7  2  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.016   15.7   0.7       0.28   11.8   0.2    2.2  2  ACT_4           ACT domain
      0.033   14.2   0.0      0.083   12.9   0.0    1.6  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.035   13.5   0.0      0.067   12.6   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.056   13.4   0.0       0.14   12.1   0.0    1.7  2  GYD             GYD domain
      0.057   13.5   0.0       0.13   12.3   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.065   13.1   0.1       0.41   10.6   0.0    2.1  2  HHH             Helix-hairpin-helix motif
      0.069   13.1   1.2      0.098   12.6   0.1    1.8  2  MarR            MarR family
      0.076   11.9   0.1      0.079   11.8   0.1    1.0  1  HECT_2          HECT-like Ubiquitin-conjugating enzyme (E2)-b


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.1   9.1e-17   8.5e-14       2      41 ..       4      43 ..       2      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 9.1e-17
  HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                   D+iD kILe L+ d+R s+ e+++++ lSes+v+rRv+ L
     AJA92316.1  4 DKIDEKILEYLRNDSRESFVEIGKKLKLSESAVRRRVKNL 43
                   9************************************988 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.3   4.5e-16   4.3e-13       1      75 []      66     137 ..      66     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 4.5e-16
                     EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
  AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                     vl+s+++    ++ ++  +l +l  V+ +y +tG yd+ ++++++++ ++++ ++e l+++pgv +t+t i+l+t
      AJA92316.1  66 VLISVDSTT--DTSKVSSRLTKLNAVKTVYEITGQYDISVIIKAPSITEINAAIDE-LRKIPGVIDTNTVIILRT 137
                     789999777..9********************************************.****************86 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.5   1.9e-15   1.8e-12       2      48 .]       4      50 ..       3      50 .. 0.97
   2 ?   -3.3   0.0       7.2   6.8e+03      32      41 ..      77      86 ..      76      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.9e-15
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                d++d kILe+L+ ++r s  e+ ++l lS s+v+rr+k+L+++ +I+
  AJA92316.1  4 DKIDEKILEYLRNDSRESFVEIGKKLKLSESAVRRRVKNLVDSKVIE 50
                99*****************************************9996 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.2
      HTH_24 32 stvnrrlkrL 41
                s v+ rl +L
  AJA92316.1 77 SKVSSRLTKL 86
                6789999887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0016      11      53 ..      11      51 ..       9      53 .. 0.85
   2 ?   -2.5   0.0       5.1   4.8e+03      36      49 ..      77      90 ..      75     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                L +L++   r+ +  e+ ++l+ls sav r++k Lv+   +er
  AJA92316.1 11 LEYLRNDS-RE-SFVEIGKKLKLSESAVRRRVKNLVDSKVIER 51
                56665554.55.999************************9998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                HHHHHHHHHHHHTT CS
      MarR_2 36 savsrilkrLvaaG 49
                s vs +l +L a  
  AJA92316.1 77 SKVSSRLTKLNAVK 90
                56788888876654 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.9e-06    0.0018       3      39 ..       8      43 ..       7      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL 39
                ++ile L ++++  s  e+ ++L++S+++vrr++k L
  AJA92316.1  8 EKILEYL-RNDSRESFVEIGKKLKLSESAVRRRVKNL 43
                68*****.788889*********************99 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.1e-06     0.002      18      43 ..      17      42 ..       7      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.1e-06
                TTT--HHHHHHHHTS-HHHHHHHHHH CS
  Sigma70_r4 18 geglTleEIgerlgiSrerVrqiekr 43
                +   ++ EIg++l +S+++Vr++ k+
  AJA92316.1 17 DSRESFVEIGKKLKLSESAVRRRVKN 42
                666799*****************986 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   2.1e-06     0.002      14      70 ..      75     132 ..      59     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-06
        NapD  14 rlaavkaalaalpgvE.vhasdeegklVvviEaesedeladtieaiealpgVlsaslv 70 
                 ++ +v+ +l++l  v  v+  +++  + v+i a+s  e+ ++i++++++pgV++++ v
  AJA92316.1  75 DTSKVSSRLTKLNAVKtVYEITGQYDISVIIKAPSITEINAAIDELRKIPGVIDTNTV 132
                 55677778888877752666677799****************************9977 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-05     0.012      13      65 ..       2      56 ..       1      66 [. 0.86
   2 ?   -0.3   0.0       1.7   1.6e+03      29      59 ..      88     118 ..      81     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                HHHSHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH..HHHCHCCT-EE CS
         Mga 13 lkeslkyqllkflfeeeevsieelaqelyiSestlkrkikel..nklLkefdlel 65
                lk+ ++ ++l++l ++ + s+ e+ ++l +Ses + r +k+l   k+++ f +e+
  AJA92316.1  2 LKDKIDEKILEYLRNDSRESFVEIGKKLKLSESAVRRRVKNLvdSKVIERFTIEM 56
                56777889*********************************95558999999998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                 SEEEHHHHHHHCT--HHHHHHHHHHHHHHCH CS
         Mga  29 eevsieelaqelyiSestlkrkikelnklLk 59 
                 ++++++e++ ++ iS      +i e+n  + 
  AJA92316.1  88 AVKTVYEITGQYDISVIIKAPSITEINAAID 118
                 5667888888888888888888888888776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05     0.011       8      49 ..      10      50 ..       9      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                iL++l+   +e ++ e+ +++ l+ S+v+R ++ Lv  + +e
  AJA92316.1 10 ILEYLRNDSRE-SFVEIGKKLKLSESAVRRRVKNLVDSKVIE 50
                9*********9.9***********************988877 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.5e-05     0.024       6      42 ..       9      46 ..       8      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHT CS
       HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLrea 42
                kIL +L++ +  ++ e+ ++l+ls+s+v++  k L ++
  AJA92316.1  9 KILEYLRNdSRESFVEIGKKLKLSESAVRRRVKNLVDS 46
                8*******555******************988888776 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.6e-05     0.025       3      46 ..       8      51 ..       7      53 .. 0.96
   2 ?   -2.9   0.0       6.3   5.9e+03      16      27 ..      91     102 ..      88     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
    HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                e+ile+l+++   s  e+   l+ Se  +RR  ++L+ + +++R
  AJA92316.1  8 EKILEYLRNDSRESFVEIGKKLKLSESAVRRRVKNLVDSKVIER 51
                89*************************************99999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
    HTH_DeoR  16 sveelvellgvS 27 
                 +v e++ ++++S
  AJA92316.1  91 TVYEITGQYDIS 102
                 577888899998 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.026        24      46      79 ..      60      93 ..      46      96 .. 0.79
   2 ?   11.8   0.2   0.00029      0.28      28      77 ..      80     128 ..      76     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.026
       ACT_4 46 glaeikitveVkdvehLsrviakLraipgVisVe 79
                + ++  + ++V ++ + s+v  +L +++ V++V+
  AJA92316.1 60 NSTSAIVLISVDSTTDTSKVSSRLTKLNAVKTVY 93
                5666778899999999999999999999999885 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00029
       ACT_4  28 seekanivsvnaktrkkdglaeikitveVkdvehLsrviakLraipgVis 77 
                 s+  +++++v+++ +   g  +i++ ++  ++ +++  i+ Lr+ipgVi+
  AJA92316.1  80 SSRLTKLNAVKTVYEI-TGQYDISVIIKAPSITEINAAIDELRKIPGVID 128
                 5555677788888865.88999**************************97 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.8e-05     0.083       9      55 ..       9      55 ..       3      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-05
     HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsiv 55
                k+le+L   +++ + +e+ k+L lse++++ ++ +L +  ++e ++i+
  AJA92316.1  9 KILEYLRN-DSRESFVEIGKKLKLSESAVRRRVKNLVDSkVIERFTIE 55
                89999998.999999*********************987677766665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.1e-05     0.067      17      52 .]       7      44 ..       5      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
  HTH_Tnp_ISL3 17 eayilellles..rsvkavArqlgvSwtTVwrildryv 52
                  +++ile l+++   s+ ++ + l +S++ V+r+++ +v
    AJA92316.1  7 DEKILEYLRNDsrESFVEIGKKLKLSESAVRRRVKNLV 44
                  57899999999999********************9876 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   1.3e+03      22      39 ..      33      50 ..      18      86 .. 0.61
   2 ?   12.1   0.0   0.00015      0.14      18      64 ..      72     116 ..      60     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
         GYD 22 reeakealveslGgkles 39
                + ++++++++ ++ k+ +
  AJA92316.1 33 ESAVRRRVKNLVDSKVIE 50
                555555554444555433 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
         GYD  18 sperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaal 64 
                 s+++  +++++l  +l   ++++y ++G+yD+ vi+ ap   ++ a+
  AJA92316.1  72 STTDTSKVSSRL-TKLN-AVKTVYEITGQYDISVIIKAPSITEINAA 116
                 566666666666.4544.4899*****************87776665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.13      14      56 ..       9      51 ..       9      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                +il +L+ +   ++ e+ + l ls + ++++++ L++   +e+
  AJA92316.1  9 KILEYLRNDSRESFVEIGKKLKLSESAVRRRVKNLVDSKVIER 51
                599999999999*************************999985 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.4   1.3e+03       2      14 ..      11      23 ..      10      25 .. 0.79
   2 ?   10.6   0.0   0.00043      0.41       5      19 ..     112     126 ..     111     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.4
                HHHHHTSSHHHHH CS
         HHH  2 leglipasreeLl 14
                le l+++sre  +
  AJA92316.1 11 LEYLRNDSRESFV 23
                68899****9765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00043
                 HHTSSHHHHHTSTT- CS
         HHH   5 lipasreeLlalPGV 19 
                 +i+a ++eL ++PGV
  AJA92316.1 112 EINAAIDELRKIPGV 126
                 589***********9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0001     0.098       9      50 ..      11      52 ..       9      55 .. 0.83
   2 ?   -2.4   0.1       5.1   4.9e+03      29      41 ..      74      86 ..      68      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                HHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR  9 LrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                L+ l++    s  e++kkl++s s+v r ++ L++   ieR 
  AJA92316.1 11 LEYLRNDSRESFVEIGKKLKLSESAVRRRVKNLVDSKVIERF 52
                5556666666777***********************999996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                S-HHHHHHHHHHH CS
        MarR 29 vskstvtrvldrL 41
                +++s v+  l++L
  AJA92316.1 74 TDTSKVSSRLTKL 86
                5667777777776 PP

>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   8.4e-05     0.079     257     326 ..      33      98 ..      11     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.4e-05
      HECT_2 257 esivaaqLleliersgsrkflihsedskekkglllwvfnpdlrvsssssssssleaqramKvlYkdeiee 326
                 es v  +  +l++++ +++f+i++++ ++++ + l  +++ ++ s   + ss+l+  +a+K  Y+  + +
  AJA92316.1  33 ESAVRRRVKNLVDSKVIERFTIEMGEMNSTSAIVLISVDSTTDTS---KVSSRLTKLNAVKTVYE-ITGQ 98 
                 667788899******************999999999999999999...8999************9.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 943.85
//
Query:       AJA92317.1  [L=283]
Description: polyprenyl synthetase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-46  157.4   0.0    4.4e-46  157.0   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.0   2.4e-50   4.4e-46       3     200 ..      37     225 ..      35     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 2.4e-50
                      HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllarafe 96 
                      ++ e+l+y +  gGKr+Rp+++llaae ++ +    e++++ a+++ellh+ s +hDDi+D+ + RR +   h ++G ++++++gdf+l+++++
       AJA92317.1  37 EFCEPLKYAL-EGGKRIRPIITLLAAESVG-Q--IDENVYAGACAIELLHTESVIHDDIIDNETQRRHKDPFHIKYGYNTSVLTGDFVLGLILN 126
                      67899*****.*******************.3..34899******************************************************* PP

                      HHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt  97 llaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiq 190
                      + ++l  +++++++ ++++++ + eG++l+ + e+++d++   +e+y +++ yKTa  f+++++l+a+++g s+ee++ l+++g+++G+a+Qi 
       AJA92317.1 127 ISSRL--DKARVTKDLATAAMLMSEGEVLEGKLEESEDVT---FEDYIKVMDYKTATAFEMAAKLGAVIGGGSEEEISGLAEYGKNIGIAYQIK 215
                      *****..999********************9888889999...*****************************99******************** PP

                      HHHHHHHS-H CS
  polyprenyl_synt 191 DDylDlfgdp 200
                      DD++D  +++
       AJA92317.1 216 DDLMDWKNED 225
                      *****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2023.24
//
Query:       AJA92318.1  [L=231]
Description: phosphoglycolate phosphatase, TA0175-type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-32  111.4   2.0    6.6e-20   71.9   0.2    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    4.1e-09   36.3   0.0    0.00012   21.7   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
    1.6e-05   25.3   0.7     0.0024   18.2   0.0    2.6  3  Hydrolase        haloacid dehalogenase-like hydrolase
    0.00017   22.0   0.8     0.0095   16.3   0.0    2.7  2  HAD              haloacid dehalogenase-like hydrolase
     0.0029   16.8   0.0        1.2    8.2   0.0    2.2  2  Trehalose_PPase  Trehalose-phosphatase
  ------ inclusion threshold ------
      0.069   13.3   0.0       0.13   12.4   0.0    1.6  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   1.7e-13     5e-10       1      93 [.       6      98 ..       6     105 .. 0.90
   2 !   71.9   0.2   2.2e-23   6.6e-20     173     253 ..     141     221 ..     102     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.7e-13
                 EEEEIIIII.S-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B-.HHHHHHHHHHHHH CS
  Hydrolase_3  1 ialDlDGTL.lnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstis.kedvkeiikllke 93
                 +a+D+DGT+ ln  +ki+ ++ e +++lk+ g++v++ TGRs  ++  +    gl+l  ++ NG+ i  ++g+i+ ++ i  k+++++ + +lk+
   AJA92318.1  6 LAVDIDGTItLNGFGKIHLQALEKLRNLKNDGHHVIFVTGRSSIEAYFLSIFGGLTLLGVGENGGCI--THGEIMTHKMIGdKNECQNAFSYLKK 98
                 689******99*******************************99998888888999***********..88888877777548899999999887 PP

  == domain 2  score: 71.9 bits;  conditional E-value: 2.2e-23
                  EESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
  Hydrolase_3 173 ssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                    s++ + i+++gv+Kg++l k +++ln +le++ia GD+e D++M+  +++ +A++n+ +e+k++A+ vt++n+ +G+++
   AJA92318.1 141 FDSGYAYHINSRGVDKGSGLIKALEMLNADLEDTIALGDSETDVPMFRTVKNNIAVNNSIPELKEIAKIVTTKNSGEGLLE 221
                  56778999*******************************************************************999876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   2.3e-05     0.069       2      47 ..       3      49 ..       2      55 .. 0.85
   2 !   21.7   0.0   4.1e-08   0.00012     137     242 ..     128     223 ..     119     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                SEEEEE-TBTTTB...S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HH CS
        S6PP  2 klllvsdLDntlv..dgdnealarlnelleaeerkdvllvfaTGRsld 47
                k++l+ d+D+t++     + +l++l++l++  +++ + ++f+TGRs  
  AJA92318.1  3 KKVLAVDIDGTITlnGFGKIHLQALEKLRN-LKNDGHHVIFVTGRSSI 49
                689*********986556789999999999.8889999*******965 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 4.1e-08
                 HHHHHTTTS-EEEEEETTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..EE-SS-TH CS
        S6PP 137 eqlLekreldvkviyssgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriylaeerca 235
                 +++L +++ +v  ++ sg +  +  ++ +kg+ l   ++ l+++le ++  Gds+ D  ++++    + V n+ +e        +ke  +i+  ++++ 
  AJA92318.1 128 QAILDEEGFNVG-LFDSGYAYHINSRGVDKGSGLIKALEMLNADLEDTIALGDSETDVPMFRTVKNNIAVNNSIPE--------LKEIAKIV-TTKNSG 216
                 566666666665.588888889999999************************************************........44444443.466677 PP

                 HHHHHHH CS
        S6PP 236 aGilegl 242
                 +G+legl
  AJA92318.1 217 EGLLEGL 223
                 8888887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.013        37       2      15 ..       4      17 ..       3      35 .. 0.74
   2 ?   -1.3   0.0      0.77   2.3e+03     125     146 ..      28      49 ..      17      58 .. 0.72
   3 !   18.2   0.0     8e-07    0.0024     146     207 ..     125     188 ..     113     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                SEEEEESBTTTBCH CS
                xxxxxxxxxxxxxx RF
   Hydrolase  2 ktvvfDkdGTLttg 15
                k+++ D+dGT+t  
  AJA92318.1  4 KVLAVDIDGTITLN 17
                899*********43 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.77
                 HHHHHHHHTTEEEEEEESSEHH CS
                 xxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 125 eavasLkaagievvlltgdnpe 146
                 e ++ Lk  g  v+ +tg ++ 
  AJA92318.1  28 EKLRNLKNDGHHVIFVTGRSSI 49 
                 4466777788888888877665 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 8e-07
                 HHHHHHHHHTT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                 xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 146 etaeraanqlG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaala 207
                 ++a++++++ G     fd  +a+ i+  +  + +g+ +a++ L+++ e++++ GD+ +D+++++
  AJA92318.1 125 KNAQAILDEEGfnVGLFDSGYAYHINSRGVDKGSGLIKALEMLNADLEDTIALGDSETDVPMFR 188
                 7899999999998889999999999999999*******************************97 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.036   1.1e+02       4     108 ..       9      44 ..       6      63 .. 0.48
   2 !   16.3   0.0   3.2e-06    0.0095     145     188 .]     147     188 ..     111     188 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.036
         HAD   4 DfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfvaevirpklldpgalellaahraaGd 102
                 D+DgT++ +  +   l                                                                     +ale l+  +  G+
  AJA92318.1   9 DIDGTITLNGFGKIHL---------------------------------------------------------------------QALEKLRNLKNDGH 38 
                 6777776663332222.....................................................................33333333333333 PP

         HAD 103 rvvvvS 108
                 +v+ v+
  AJA92318.1  39 HVIFVT 44 
                 333333 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.2e-06
         HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                 +  ++rg +k + l +  a e  ++dle+++a GDs++D+p++r
  AJA92318.1 147 YHINSRGVDKGSGLIK--ALEMLNADLEDTIALGDSETDVPMFR 188
                 3444444444444444..6677999*****************97 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0012       3.5       3      71 ..       9      74 ..       7     114 .. 0.72
   2 !    8.2   0.0    0.0004       1.2     159     209 ..     151     196 ..     147     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                     ETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEE..EEGGGTEEE- CS
  Trehalose_PPase  3 DydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelgl..aaeHGaeirs 71
                     D+dGT++          ++ ++l+ L++L +d +  v++v+Grs  e++ l+   +l l  ++e+G  i+ 
       AJA92318.1  9 DIDGTITLNGF----GKIHLQALEKLRNLKNDGH-HVIFVTGRSSIEAYFLSIFGGLTLlgVGENGGCITH 74
                     66666665555....4556678999*******99.9999*****999665555554444226788866655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0004
                      -S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT...-E CS
  Trehalose_PPase 159 pqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktkesgv 209
                      ++gv KG+ + + le l+ +    +  +++GD  tD  mF++++++    v
       AJA92318.1 151 SRGVDKGSGLIKALEMLNAD---LEDTIALGDSETDVPMFRTVKNNI--AV 196
                      67777888777777777776...555679***************984..33 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.4e-05      0.13       2      43 ..       7      50 ..       6     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                 EEESTTTSEE..TTEE-TTHHHHHHHHHHTT-EEEEEE---SS- CS
  Hydrolase_6  2 lfDidGvLwr..gdkaipgaaealnalraagkpvvllTNnssks 43
                 ++DidG++    ++k+  +a e l+ l++ g +v+++T +ss  
   AJA92318.1  7 AVDIDGTITLngFGKIHLQALEKLRNLKNDGHHVIFVTGRSSIE 50
                 68****998644789999********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1558.19
//
Query:       AJA92319.1  [L=149]
Description: ribosomal protein S15 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-25   88.5   0.2      4e-25   87.6   0.2    1.5  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    2.3e-09   37.3   0.9    3.7e-09   36.7   0.9    1.3  1  Ribosomal_S15    Ribosomal protein S15
     0.0067   16.7   0.1        1.1    9.6   0.1    2.1  2  COMMD1_N         COMMD1 N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.2   6.7e-29     4e-25       1      60 []       1      60 [.       1      60 [. 0.99

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 6.7e-29
                     X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
  Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                     M+r+h++++GkS+S rP+  ++p+W+k+++ee+e li k+ak+G+t+SqIG++LRDq+++
       AJA92319.1  1 MGRLHTHNHGKSHSIRPIDPKKPEWVKQTNEEIEGLITKYAKEGMTSSQIGLKLRDQHAI 60
                     **********************************************************98 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.9   6.1e-13   3.7e-09       9      75 ..      79     143 ..      71     149 .] 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.1e-13
                    SSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHH CS
  Ribosomal_S15   9 qrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkkli 75 
                    +  +    ++++++ +++ +++nl++h+k nk D ++ r+L ++++k ++l  ++k++    +++k+  
     AJA92319.1  79 KLMP----DIPEDLNNIVMKAVNLQKHIKDNKSDSRNVRALELVEAKVHRLSTHYKKTGDidQKWKYKS 143
                    5555....7899999*******************************************66587777654 PP

>> COMMD1_N  COMMD1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0046        27      40      74 ..      23      57 ..      18      60 .. 0.89
   2 !    9.6   0.1   0.00018       1.1      22      69 ..      68     114 ..      64     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0046
    COMMD1_N 40 edefaalvekmksLlksiasadmdlaQLeafLtaq 74
                ++ ++++ e +++L+ + a+  m  +Q+   L++q
  AJA92319.1 23 PEWVKQTNEEIEGLITKYAKEGMTSSQIGLKLRDQ 57
                56789999********************9999887 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00018
    COMMD1_N  22 eeeiteellkeelypdvsedefaalvekmksLlksiasadmdlaQLea 69 
                 ++ it+ l  ++l+pd++e +++++v k+ +L k+i     d   + a
  AJA92319.1  68 NKSITDVLKANKLMPDIPE-DLNNIVMKAVNLQKHIKDNKSDSRNVRA 114
                 6789**9999*******85.6999********9999887777665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1125.85
//
Query:       AJA92320.1  [L=455]
Description: base excision DNA repair protein, HhH-GPD family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-18   67.0   0.0    3.7e-18   66.0   0.0    1.5  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
      4e-07   29.8   0.1    8.4e-07   28.8   0.1    1.5  1  RIO1            RIO1 family
    6.9e-06   25.6   0.5    6.9e-06   25.6   0.5    1.8  2  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.019   15.5   0.9        0.8   10.2   0.1    2.8  2  Pox_H7          Late protein H7
      0.072   12.7   0.0       0.87    9.1   0.0    2.3  2  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0     1e-21   3.7e-18       1     106 [.     293     435 ..     293     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1e-21
                 HHHHHHTTS-HHHHHHHHHHHHHHHS.HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH................................ CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
     HhH-GPD   1 vsailsqqtsderanriierlferfg.fptpedladadeekLrelirelGfyrrKakyikelArilv................................ 66 
                 v ai+ qq+s ++a++i++r+ ++++ fptp ++ + +++kL+++    G++++K++yik l++ ++                                
  AJA92320.1 293 VEAIIYQQLSEASATAITKRFLKLYKkFPTPRQVNNTTDKKLKDI----GLSGTKINYIKGLSKLIIqkkidfkkiaklndqqvieeltkikgignwtt 387
                 679******************************************....************************************************** PP

                 ........S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                 ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  67 ........gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                         +++dv++v D++++++++ l+s+ke +++k +ek  ++++
  AJA92320.1 388 qiylmfclQRKDVFPVGDLGIQKGIRDLFSLKELPDPKTMEKFSARWK 435
                 ********889***********************99999999885554 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   2.3e-10   8.4e-07      54     158 ..      90     194 ..      71     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.3e-10
                 HHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--E.ETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTS..EEEETTEEEE-- CS
        RIO1  54 waekEfrnLkrleeagvpvPkpielkrhvlvmefig.edgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyN..vlvdedkvviID 148
                    +E + L+ +++ ++  Pk i+  ++ lvme+i+ e+ +  +k  ++e +++e ++++++vl+e + l+ +agl H+ LS     v+v ++k +iID
  AJA92320.1  90 NMSNEAKLLQIVNKLDI-GPKFIKNSKNFLVMEYIDgEKIIDWAK--KTEtKSQEVRSVLNNVLRE-CYLLDDAGLDHGELSTIDkhVIVGKNKNTIID 184
                 56678888888888875.5*****************333333333..3332499***********7.77888**********875449*********** PP

                 GTTEEETTST CS
        RIO1 149 vsQaveldhp 158
                 +  + + ++p
  AJA92320.1 185 FESSSTNRKP 194
                 9877766665 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.5   1.9e-09   6.9e-06       3     122 ..      55     164 ..      53     202 .. 0.78
   2 ?   -2.5   0.0      0.74   2.7e+03      25      53 ..     352     380 ..     338     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.9e-09
                 EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHH CS
     Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeak 101
                 k + lG+G +G V+ a+  ++++ivA+K+ + ++ ++++     +E k+l+ ++   i      f ++++ +lv+ey++g+++ d+ + k+  +++e++
  AJA92320.1  55 KCHILGKGYVGMVVLAK--KNNEIVALKIRRIDSPRENM----SNEAKLLQIVNKLDIG---PKFIKNSKNFLVMEYIDGEKIIDWAK-KTETKSQEVR 143
                 6688************9..7*********9998888755....6999999988876664...45566777789************997.78899***** PP

                 HHHHHHHHHHHHHHHTTEE-S CS
     Pkinase 102 kiakqilegleylHskgiiHr 122
                 ++++++l+    l ++g+ H 
  AJA92320.1 144 SVLNNVLRECYLLDDAGLDHG 164
                 ******997776666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.74
                 EEEEEEEEECHCHCHHHHHHHHHHHHHHH CS
     Pkinase  25 kivAvKkikkekakkkkekkvlrEikilk 53 
                 k +  Kki+ +k+ k ++++v++E++ +k
  AJA92320.1 352 KLIIQKKIDFKKIAKLNDQQVIEELTKIK 380
                 56667899999999999999999987665 PP

>> Pox_H7  Late protein H7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.044   1.6e+02     115     142 ..      86     113 ..      71     114 .. 0.84
   2 ?   10.2   0.1   0.00022       0.8     100     142 ..     305     349 ..     290     350 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.044
                 -XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      Pox_H7 115 kkrkkikeakkklkiAlkkgvdydfIkd 142
                   r+++++ +k l+i  k +++ +fIk+
  AJA92320.1  86 SPRENMSNEAKLLQIVNKLDIGPKFIKN 113
                 67899**********************7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                 HH-HHHHHHHHHHT-.-XXXXXXX.XXXXXXXXXXXXXXXXXXXX CS
      Pox_H7 100 keskklkrvikvykt.kkrkkike.akkklkiAlkkgvdydfIkd 142
                 ++++  kr++k+yk+  + +++++ + kklk+   +g   ++Ik+
  AJA92320.1 305 SATAITKRFLKLYKKfPTPRQVNNtTDKKLKDIGLSGTKINYIKG 349
                 456678*******9887777776516799**************96 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00024      0.87      17      57 ..      88     128 ..      73     157 .. 0.87
   2 ?    0.7   0.0     0.095   3.4e+02     164     177 ..     178     191 ..     161     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00024
                     CCHHHHHHHHHHHHHHTTSSS-EEEEETTEEEEE--TCEE- CS
  Choline_kinase  17 lidretElvvfallserglgpklygifenGrieefiesrtl 57 
                      +++ +E++ ++++++ ++gpk++   +n  + e+i+++++
      AJA92320.1  88 RENMSNEAKLLQIVNKLDIGPKFIKNSKNFLVMEYIDGEKI 128
                     5799********************************99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.095
                     TEEEE--GTT-EEE CS
  Choline_kinase 164 kklvlIDFEYagyn 177
                     +k ++IDFE ++ n
      AJA92320.1 178 NKNTIIDFESSSTN 191
                     56689******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3037.11
//
Query:       AJA92321.1  [L=93]
Description: hypothetical protein T478_0613 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   21.8   0.0    0.00016   21.6   0.0    1.1  1  TMEM51           Transmembrane protein 51
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.035   13.8   0.0    1.1  1  Tetraspanin      Tetraspanin family
       0.13   11.7   1.5        2.3    7.7   0.1    2.2  2  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family


Domain annotation for each model (and alignments):
>> TMEM51  Transmembrane protein 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.7e-08   0.00016      17      96 ..       9      88 ..       6      93 .] 0.59

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-08
      TMEM51 17 aLgivmivWsvvPgesea.dkpkasanssskpdkdsgkeek.ksktssvAyVLvGaGvalLlLsicLgirdkkrarqeeeel 96
                a g+ miv  ++ +   a  +p  + +++++ + +   +e+ ++   ++A +LvG+G +l+l+s  +g r k++  ++++e+
  AJA92321.1  9 AGGVSMIVVGMILSGVLAdMTPIGREGMTEEEKYEFMVNEReNEDFKTLAGILVGVGFLLILIS--FGARRKRKGGAKKTEK 88
                445555555555444333234444455555544443333332556779********98777765..7899999988777663 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.9e-06     0.035      15      65 ..      10      73 ..       6      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-06
                 XXXXXXXXXXXXXX..............XXX.....................XXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin 15 igivllavGvwlrl..............khaeaalacllsesaedpailaillivvGvllfllgf 65
                  g+ +++vG+ l +               ++e+     +++++ed+++la +l+ vG+ll+l++f
   AJA92321.1 10 GGVSMIVVGMIL-SgvladmtpigregmTEEEKYEFMVNERENEDFKTLAGILVGVGFLLILISF 73
                 567777776333.135666799999998666666667778999******99************98 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.011        66      15      24 ..      16      25 ..      13      29 .. 0.86
   2 ?    7.7   0.1   0.00038       2.3      20      38 ..      57      76 ..      56      87 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                     HHHHHHHHHH CS
  ATP1G1_PLM_MAT8 15 lgGLifAglL 24
                     ++G+i++g+L
       AJA92321.1 16 VVGMILSGVL 25
                     68*******9 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00038
                     HHHHHHHHHHHHHH.CCHHH CS
  ATP1G1_PLM_MAT8 20 fAglLfivGiliil.Skkck 38
                     +Ag+L  vG+l+il S   +
       AJA92321.1 57 LAGILVGVGFLLILiSFGAR 76
                     8********98765244443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 700.75
//
Query:       AJA92322.1  [L=93]
Description: ribosomal protein L44 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-24   83.9   8.8    7.9e-24   83.9   8.8    1.4  2  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.023   14.9   0.7      0.023   14.9   0.7    2.1  2  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
        0.1   11.9   0.3        1.9    7.9   0.1    2.2  2  zf-TFIIB       Transcription factor zinc-finger


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.6   3.6e+03      53      61 ..       8      16 ..       6      17 .. 0.77
   2 !   83.9   8.8   1.3e-27   7.9e-24       2      75 ..      17      90 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.6
                   EEEETTT-- CS
  Ribosomal_L44 53 rleCteCkk 61
                   r  C +Ck+
     AJA92322.1  8 RSYCPKCKS 16
                   667999997 PP

  == domain 2  score: 83.9 bits;  conditional E-value: 1.3e-27
                   EEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
  Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                   H+++kv+ yk+gk++  a+g+Rr++ +++gygGq+ p++ k aKttKK++l  +Ct+Ckkk +++++R++kfel
     AJA92322.1 17 HQTMKVSIYKAGKRRGSAAGERRHALRKKGYGGQKFPKLAKPAKTTKKVTLIETCTTCKKKMMNKGIRIRKFEL 90
                   *************************************************************************9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   3.8e-06     0.023      20      61 ..       5      46 ..       2      57 .. 0.74
   2 ?    1.4   1.1     0.062   3.7e+02      25      36 ..      70      81 ..      59      86 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
  NOB1_Zn_bind 20 dmtkkFCpkCGnktLkrvavsvdengelklhlkknfqlnlrG 61
                  + t+ +CpkC +++  +v+++   + + +   ++++ l+++G
    AJA92322.1  5 KETRSYCPKCKSHQTMKVSIYKAGKRRGSAAGERRHALRKKG 46
                  789*********999999988776655555555555555554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.062
  NOB1_Zn_bind 25 FCpkCGnktLkr 36
                   C +C +k++++
    AJA92322.1 70 TCTTCKKKMMNK 81
                  466666665554 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1   0.00031       1.9       1      10 [.      10      21 ..      10      32 .. 0.73
   2 ?    2.4   0.0     0.017     1e+02       2       7 ..      71      76 ..      60      90 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00031
    zf-TFIIB  1 kCPkCqd..ele 10
                +CPkC++  +++
  AJA92322.1 10 YCPKCKShqTMK 21
                7****8423676 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.017
    zf-TFIIB  2 CPkCqd 7 
                C +C+ 
  AJA92322.1 71 CTTCKK 76
                666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 676.65
//
Query:       AJA92323.1  [L=140]
Description: putative ribosomal S17 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-17   64.1   6.3    1.2e-17   64.0   6.2    1.2  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.097   12.4   0.0       0.13   12.0   0.0    1.3  1  DUF4525         Domain of unknown function (DUF4525)
       0.23   11.5   1.9       0.24   11.5   1.9    1.2  1  Mit_KHE1        Mitochondrial K+-H+ exchange-related
        2.7    7.9   9.2        1.6    8.7   0.1    2.6  3  Kin17_mid       Domain of Kin17 curved DNA-binding protein


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   6.2   2.6e-21   1.2e-17       9     102 ..       4     101 ..       1     126 [. 0.73

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2.6e-21
                     HHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS--SS...---HHHHHHHHHHH------.----------- CS
  Ribosomal_S17e   9 vKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkgpvrg...islklqeeererrdnyvpev.saldqeaievd 99 
                     +K+ +++++++y +++++dF tnk+ ++e++i++sk l+nkiaGy+t++++r  k + r+   i  + +++er++     pev s+ d + ie+ 
      AJA92323.1   4 IKRISNELMNEYSERFGTDFVTNKQSLNEISIVRSKGLKNKIAGYITKILQRQAKFEERKqmiIDNEKKSQERKQSRSKKPEVeSEEDAASIEIV 98 
                     9**************************************************96665555511144444555555555667776244466667764 PP

                     HHH CS
  Ribosomal_S17e 100 kdt 102
                     + +
      AJA92323.1  99 DGV 101
                     333 PP

>> DUF4525  Domain of unknown function (DUF4525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.9e-05      0.13      74     122 ..      35      83 ..      11      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
     DUF4525  74 lagyadlkrtiavllddilqrlvklenkvdylvvngsaanttnsttgnl 122
                 +     lk  ia  + +ilqr +k+e++ ++++ n+  +     + +++
  AJA92323.1  35 IVRSKGLKNKIAGYITKILQRQAKFEERKQMIIDNEKKSQERKQSRSKK 83 
                 4455579*********************999999987776655444443 PP

>> Mit_KHE1  Mitochondrial K+-H+ exchange-related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.9   5.3e-05      0.24      56     103 ..      38      86 ..       5     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
    Mit_KHE1  56 eegwkkkivelgeklldr.ipyeElaLksipsksakelesekekkkkek 103
                 ++g+k+ki  +++k+l+r  ++eE     i++++++++++++++kk e 
  AJA92323.1  38 SKGLKNKIAGYITKILQRqAKFEERKQMIIDNEKKSQERKQSRSKKPEV 86 
                 467***********9876379**********866664333333333222 PP

>> Kin17_mid  Domain of Kin17 curved DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00035       1.6       3      27 ..       1      25 [.       1      45 [. 0.88
   2 ?    1.7   3.9     0.049   2.2e+02      90     115 ..      66      91 ..      28      99 .. 0.70
   3 ?    1.9   0.7     0.045     2e+02      73     125 ..      80     132 ..      76     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00035
   Kin17_mid  3 leliaentkkvieeyskeFekdFlk 27
                + +i++ +++ ++eys++F +dF++
  AJA92323.1  1 MDRIKRISNELMNEYSERFGTDFVT 25
                667888999**************97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.049
   Kin17_mid  90 yidrspealerkeklekkekaekede 115
                  id++++++erk++++kk + e+e++
  AJA92323.1  66 IIDNEKKSQERKQSRSKKPEVESEED 91 
                 47887777777776666666555554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.045
   Kin17_mid  73 kegkvkveetekgllisyidrspealerkeklekkekaekedeereekllekq 125
                 +++k +ve++e+   i+ +d  ++  + +  ++ +e+ ++e e  eek + ++
  AJA92323.1  80 RSKKPEVESEEDAASIEIVDGVEDPHTDEGVRHVTEEPSSETEVSEEKSIAEE 132
                 6677899999999*******777777777777777777777777777877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1814  (0.101177); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 961.73
//
Query:       AJA92324.1  [L=155]
Description: KH domain protein, NusA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-18   65.5   6.4    2.7e-13   49.5   0.4    2.1  2  KH_2      KH domain
      6e-11   42.1   2.1    0.00021   21.1   0.2    2.2  2  KH_4      KH domain
    1.6e-09   37.7   0.9    1.6e-09   37.7   0.9    2.0  2  KH_5      NusA-like KH domain
    0.00056   19.7   1.5     0.0042   16.9   0.4    2.3  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.4     6e-17   2.7e-13       5      65 ..      18      78 ..      16      84 .. 0.91
   2 !   19.2   1.1   1.7e-07   0.00077       7      58 ..      84     139 ..      78     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6e-17
                HHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
        KH_2  5 slaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk 65
                sl+++++ka++++++ +++++r+i+v+ e+++g++IGkgG+ ik+++ ++ +++e +e+ +
  AJA92324.1 18 SLFQNVTKATARDCIEDEKRDRIIFVVNEGKMGLAIGKGGAHIKSLQNKIDRNVELVEYNE 78
                89************666677***********************************999865 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.7e-07
                 HHHT.ECETEEEEEEEC...CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHH CS
        KH_2   7 avei.kkagvskveIer...tanrviiviresqpgivIGkgGsnikkigkelrkdi 58 
                  ++i  ++ + +++I +      ++++ +  +++g+v+G++G+n +k +  +r+ +
  AJA92324.1  84 LKNIlNEKYITDIKISErldGSFQANVEVDGAKKGVVVGREGRNAEKARILARRYF 139
                 45565777788888877674458999**************************9977 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   6.6e-08    0.0003      21      55 ..      30      64 ..      15      69 .. 0.86
   2 !   21.1   0.2   4.7e-08   0.00021       6      59 ..      82     136 ..      81     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.6e-08
        KH_4 21 teeeeeeeveielnvegedlGrvIGkrGrtldAlq 55
                ++ e+e++++i   v++ ++G+ IGk G  +++lq
  AJA92324.1 30 DCIEDEKRDRIIFVVNEGKMGLAIGKGGAHIKSLQ 64
                5668999***************************9 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.7e-08
        KH_4   6 dilkalvddpeevevtee.eeeeeveielnvegedlGrvIGkrGrtldAlqylvs 59 
                 ++lk++++++   +++++ + + + + +++v+g ++G+v+G++Gr++   + l+ 
  AJA92324.1  82 KLLKNILNEKYITDIKISeRLDGSFQANVEVDGAKKGVVVGREGRNAEKARILAR 136
                 5788888888777777774458899*********************976666665 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.9   3.5e-13   1.6e-09       3      69 .]      38      98 ..      36      98 .. 0.96
   2 ?    0.7   0.1      0.12   5.5e+02      19      31 ..     117     129 ..     107     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.5e-13
        KH_5  3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                +r++++V +++     +G ++gk+G+ ik++ +++ + ++++ve++eD+ ++ +n+l+   ++++ki
  AJA92324.1 38 DRIIFVVNEGK-----MGLAIGKGGAHIKSLQNKI-DRNVELVEYNEDPIKLLKNILNEKYITDIKI 98
                799********.....*******************.*********************9999998875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
        KH_5  19 vGaivgkkGsrik 31 
                  G +vg++G++ +
  AJA92324.1 117 KGVVVGREGRNAE 129
                 6999*****9986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4   9.4e-07    0.0042       4      36 ..      42      74 ..      39     100 .. 0.79
   2 ?    1.6   0.0     0.055   2.5e+02       4      21 ..     110     127 ..     107     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.4e-07
                EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEE CS
        KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvp 36
                + v+  ++g+ IGkgG++Ik+++++   ++ ++
  AJA92324.1 42 FVVNEGKMGLAIGKGGAHIKSLQNKIDRNVELV 74
                5788899****************9535555555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.055
                 EEEGGGHHHHHHTGGGHH CS
        KH_1   4 ilvPsslvgriIGkgGsn 21 
                 ++v+  + g ++G+ G+n
  AJA92324.1 110 VEVDGAKKGVVVGREGRN 127
                 68889999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1118.00
//
Query:       AJA92325.1  [L=383]
Description: CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-09   35.6   1.1    1.8e-08   33.8   1.1    1.8  1  Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glyceroph
     0.0093   15.8   0.0      0.016   15.0   0.0    1.3  1  DUF1944         Domain of unknown function (DUF1944)


Domain annotation for each model (and alignments):
>> Glyphos_transf  CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   1.1     2e-12   1.8e-08      11     291 ..      22     296 ..      14     302 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2e-12
                     -EEEEEEEEBTTTTBS-HHHHHHHHHHHHH-TTSEEEEEESSGGG.....----SS-EEEETTSHH.HHHHHHHEEEEEES....S---TTS--- CS
  Glyphos_transf  11 ldkklvlfesfegkkvsdnpkalfeylrelapkvkivwvvkkdsk.....arlkkgakvvkrnslr.ylllllrakylvsn....snfplyvrkr 95 
                      d+  ++f +  +k+  + ++ l ++l+ +++++ki +v   ++      ++ +  a ++  +++r  ++l+l+ak l+++    ++f+ + +k 
      AJA92325.1  22 SDERSIVFYAE-NKASMNHFRLLISELT-EEKNFKICYVTSVQNDpmlssKSKNIFAFYIGDGTARtKFFLTLKAKILIMDmpdlETFHIKRSKV 114
                     57788999999.4444556888888888.6666777776666666333322222223345666766257899*********88888888899999 PP

                     TTSEEEE--SS--SB--GGG-S---TS-HHHHHHHHHTT-S.EEEESSHHHHHHHH..HHTT--GGGEEES--GGGHHHHHSTT-HHHHHHHHTT CS
  Glyphos_transf  96 knqvylqtwhGtpLkkmGldeeekkaaatkqellrevsswd.ylisaneestsifa..rafnikkeeiletGyPrnDvlvkaesedvkrireelg 187
                      ++ y+ + h +   +       +        ++   +++d  + + +++ ++i +  + +++k ++++ +G+ r D l +++++          
      AJA92325.1 115 YSVHYVYIFHSMFSIH------SYL-------RKGAIDNYDtIFCVGEHHKNEIREteKTYGLKPKKLITYGFGRLDTLLNEKQKF------SQS 190
                     9999999999995555......122.......345789999788999999999976669***********************5555......233 PP

                     --SS-EEEEEE----GGG--GSS----TT-HHHHHHHHTTTEEEEE--SHHHHTT---..TT-TTTEEE-TT-S.....-HHHHHHT-SEEEESS CS
  Glyphos_transf 188 ipkdkkvilyaPTwRddevgesyrfelkldlerlakalgedyvillklHpliqekiki..keksdyvvdvsdee.....dvedlllasDiLiTDY 275
                      ++++k i++aP + +++            ++ l   l+  + +ll++H       k+  k  ++ ++d  +          + ++ s ++i+D+
      AJA92325.1 191 NEDNEKLIIIAPSYGKENLL------EVCGIKLLEILLNSGFRVLLRPHFRTLIDSKKliKAIEEKFIDNPNFTleegiIPPEKFQNSKCMISDW 279
                     455667********999999......45566667789999*********96544444334899999998666663333322356899******** PP

                     -THHHHHGG.GT--EEE CS
  Glyphos_transf 276 SSvmFDyav.ldrPiif 291
                     S + F+ya  ++ P+if
      AJA92325.1 280 SGISFEYAFtFEHPVIF 296
                     *******963799**99 PP

>> DUF1944  Domain of unknown function (DUF1944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-06     0.016      21      59 ..      27      65 ..      24      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
     DUF1944 21 vavyvdkessrkkvqlivselaeesnwkicaDavvlskh 59
                +++y+++++s ++ +l++sel+ee+n+kic  ++v+++ 
  AJA92325.1 27 IVFYAENKASMNHFRLLISELTEEKNFKICYVTSVQNDP 65
                789****************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2970.86
//
Query:       AJA92326.1  [L=88]
Description: ribosomal protein L23 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   54.1   1.7    1.2e-13   51.3   1.7    1.9  1  Ribosomal_L23  Ribosomal protein L23
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.15   11.9   0.0    1.2  1  ALS2CR8        Amyotrophic lateral sclerosis 2 chromosomal re


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.7   1.3e-17   1.2e-13       1      59 [.       8      67 ..       8      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.3e-17
                   SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBE CS
  Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkk 59
                   ++il+P+itEk+++l e+ +k+ F V+k+a+K++i +av+ l++  V kV t++    kk
     AJA92326.1  8 KIILRPYITEKTYALVENeSKICFLVEKEATKPQIAEAVQTLYNEGVLKVDTARTVYGKK 67
                   69***************9669*******************************98655444 PP

>> ALS2CR8  Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.7e-05      0.15     149     187 ..      35      75 ..       7      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
     ALS2CR8 149 reevderivekireltekglkkvsemrr..hlkafvtdelf 187
                 +e ++++i+e++++l ++g+ kv+++r+   +kafv+  + 
  AJA92326.1  35 KEATKPQIAEAVQTLYNEGVLKVDTARTvyGKKAFVKLTST 75 
                 48899**********************98888999965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 677.40
//
Query:       AJA92327.1  [L=103]
Description: hypothetical protein T478_1405 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 843.22
//
Query:       AJA92328.1  [L=147]
Description: hypothetical protein T478_0697 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-15   56.4   1.4    3.2e-15   56.1   1.4    1.1  1  DUF2299   Uncharacterized conserved protein (DUF2299)


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   1.4   1.8e-19   3.2e-15       2     130 ..       8     135 ..       7     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.8e-19
                 HHHHHHHTT-EEEE---TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHHHHHHHHTTTT-EEEEE-TTS-- CS
     DUF2299   2 ikeWLkeeGlkveevpdanaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkeflselkrdLlrlcvdfqlipqdeel 100
                 +++WL++e++ +++ ++++a+f+i+++    +g+  +v++pk++++++vvg++++++ ++  + ++l+e e+++f    k+++ ++c+++++i +  + 
  AJA92328.1   8 VERWLIHENYDFKQGKSEDATFKIIISNSDGLGNDTEVFEPKDQENILVVGIKIDMKTKQLIRFRELNETEQENF----KKKVDDFCYSVKAIGKFLDE 102
                 89*************************************************************************....999999**999999887777 PP

                 ...-EEEEEEEEEG.GG--HHHHHHHHHHHHHH CS
     DUF2299 101 ..pqsiqvskeiyk.dgltknelldavkrvrna 130
                   ++++ v+ ++ k + l++ ++++a++++ ++
  AJA92328.1 103 dgKKKVGVYIVLDKpEQLNQPSFFKALEEIIEM 135
                 779*********975788*********999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1269.08
//
Query:       AJA92329.1  [L=146]
Description: hypothetical protein T478_1347 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-05   22.2  11.5    0.00052   19.7   2.3    2.8  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.015   15.4   3.0      0.015   15.4   3.0    2.3  2  OS-D            Insect pheromone-binding family, A10/OS-D
      0.082   12.6   0.6      0.082   12.6   0.6    2.4  2  Ribosomal_S27e  Ribosomal protein S27
      0.084   13.0   0.4        1.8    8.7   0.0    2.2  2  DUF2614         Zinc-ribbon containing domain
        4.3    7.2  10.4        2.9    7.7   2.6    2.7  2  PADR1           PADR1 (NUC008) domain


Domain annotation for each model (and alignments):
>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   2.3   1.4e-07   0.00052       3      27 ..      65      92 ..      63     105 .. 0.79
   2 !    7.0   2.0    0.0014       4.9       2      19 ..     113     131 ..     112     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                    E-SSS-.-EE.EEEE-SSS.EEEEESST CS
  zf-C4_Topoisom  3 kCPkCg.gdL.vlkrgkkG.kFvGCsnY 27
                    +CP+C  g+L v+k+   + +F+GC+nY
      AJA92329.1 65 ECPECHkGQLsVIKSITTKkRFIGCTNY 92
                    7*****99996667644445******** PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0014
                     EE-SSS-.-EEEEEE-SSS CS
  zf-C4_Topoisom   2 ekCPkCg.gdLvlkrgkkG 19 
                      kCP+C    ++ ++++k 
      AJA92329.1 113 TKCPECQwPTVIFRYSRKQ 131
                     69*****999999999986 PP

>> OS-D  Insect pheromone-binding family, A10/OS-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.74   2.6e+03      60      73 ..      14      27 ..       6      43 .. 0.59
   2 ?   15.4   3.0   4.2e-06     0.015      13      56 ..      76     119 ..      73     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.74
                HHHHHHHHHHHHHT CS
        OS-D 60 keklkkvikalikn 73
                k++++k +k +i+n
  AJA92329.1 14 KRNVTKSTKKIIDN 27
                44445555544444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.2e-06
                 HHT-HHHHHHHHHHHTSSS---HHHHHHHHHHHHHHTTS-TTS- CS
        OS-D  13 iLkndrllkeYvkClldkgpCtpeakelkkvlpealetkCakCt 56 
                 ++k+ +  k+++ C   ++ C+++a  l+k + ++l+tkC +C+
  AJA92329.1  76 VIKSITTKKRFIGCTNYQNGCKASAPLLQKAMLKVLKTKCPECQ 119
                 677788899**********************************6 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.1     0.098   3.5e+02       9      18 ..      65      74 ..      63      91 .. 0.81
   2 ?   12.6   0.6   2.3e-05     0.082       6      26 ..     111     131 ..     108     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.098
                    E-TTTS-EEE CS
  Ribosomal_S27e  9 kCpdCenetv 18
                     Cp+C + + 
      AJA92329.1 65 ECPECHKGQL 74
                    6****99874 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.3e-05
                     EEEE-TTTS-EEEEESS-SS- CS
  Ribosomal_S27e   6 ldvkCpdCenetvvFshaatv 26 
                     l+ kCp+C+  tv+F  + ++
      AJA92329.1 111 LKTKCPECQWPTVIFRYSRKQ 131
                     899************887765 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00051       1.8      44      75 ..      40      71 ..      35      90 .. 0.91
   2 ?    2.5   0.1     0.041   1.5e+02      64      79 ..     109     124 ..     101     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00051
     DUF2614 44 GlllvlastvvyfwiGllstkavqvvcpecek 75
                G++ + a    y ++G+ s k  + +cpec+k
  AJA92329.1 40 GFVSFSAKNKKYTILGTNSPKEGICECPECHK 71
                78888888999*******************98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.041
     DUF2614  64 kavqvvcpeceketkv 79 
                 k ++ +cpec+ +t +
  AJA92329.1 109 KVLKTKCPECQWPTVI 124
                 778899****998866 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.6   0.00081       2.9      15      26 ..      65      76 ..      62      97 .. 0.84
   2 ?    4.0   0.6     0.012        44      15      28 ..     114     127 ..     111     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00081
       PADR1 15 kCpeCkegqlvf 26
                +CpeC++gql +
  AJA92329.1 65 ECPECHKGQLSV 76
                8********976 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
       PADR1  15 kCpeCkegqlvfds 28 
                 kCpeC+  +++f+ 
  AJA92329.1 114 KCPECQWPTVIFRY 127
                 8****987777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1077.36
//
Query:       AJA92330.1  [L=69]
Description: putative ribosomal L37ae protein family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-17   61.1   1.5      9e-17   60.9   1.5    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0014   18.1   1.2     0.0022   17.5   1.2    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0015   17.9   1.9       0.21   11.0   0.1    2.1  2  zf-ribbon_3      zinc-ribbon domain
     0.0036   17.1   1.0      0.005   16.7   1.0    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
     0.0097   15.8   1.0      0.017   15.0   1.0    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.017   14.8   0.2    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.012   15.5   2.0      0.012   15.5   2.0    1.6  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.013   15.5   0.9      0.026   14.6   0.8    1.4  1  DZR              Double zinc ribbon
      0.013   15.5   2.9      0.019   14.9   2.9    1.4  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.018   15.0   2.2       0.33   11.0   0.0    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.023   14.5   0.5        5.4    6.9   0.0    2.3  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.027   14.6   4.8      0.035   14.2   0.4    2.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.043   14.0   1.1      0.067   13.4   1.1    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.079   12.7   0.4      0.081   12.7   0.4    1.2  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.098   12.3   0.4        9.2    6.0   0.0    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        0.1   12.2   5.5       0.99    9.1   0.9    2.4  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.14   12.2   2.3        3.4    7.7   0.2    2.2  2  YhfH             YhfH-like protein
       0.14   12.0   0.6       0.14   12.0   0.6    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.26   11.1   4.4        5.4    6.9   0.6    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.78    9.9   3.4        1.6    8.9   0.4    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        2.5    8.6   8.1        3.7    8.0   1.5    2.2  3  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   1.5   1.1e-19     9e-17      11      68 ..      11      67 ..       2      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.1e-19
                     GTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSS CS
  Ribosomal_L37ae 11 ygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytp 68
                      g+rYG ++rk+  ++   +++k +Cp+cg   v R+avgiw Ckkcg ++aG Ay +
       AJA92330.1 11 LGPRYGIKIRKQFTQVHHLMKQKRKCPECGGP-VIREAVGIWACKKCGLKIAGTAYDV 67
                     69***************************986.78*********************76 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2   2.6e-06    0.0022       2      29 ..      35      60 ..      34      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                  EETTTTCEECHEETSTTCEEESSSSBEE CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                  kCP+Cg++  v  ++ g   C++CGl +
    AJA92330.1 35 KCPECGGP--VIREAVGIWACKKCGLKI 60
                  9******9..999999**********87 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00025      0.21       2      10 ..      33      41 ..      28      48 .. 0.69
   2 !    6.6   0.3    0.0061       5.2      18      26 .]      52      60 ..      51      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
  zf-ribbon_3  2 tvrCPnCGa 10
                 +++CP+CG 
   AJA92330.1 33 KRKCPECGG 41
                 556666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0061
  zf-ribbon_3 18 vCpyCGtkl 26
                 +C++CG k+
   AJA92330.1 52 ACKKCGLKI 60
                 6*****997 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.0   5.9e-06     0.005       4      37 ..      26      59 ..      24      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                EEE--SS--B-TTT-SB--SSSS-EEEETTT--E CS
        C1_1  4 vhrnfkqptfCkhCgeflwgkekqglkCswCkll 37
                vh+ +kq+ +C +Cg ++ +++  +++C+ C+l+
  AJA92330.1 26 VHHLMKQKRKCPECGGPVIREAVGIWACKKCGLK 59
                577789************88***********986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.0     2e-05     0.017      30      55 ..      35      59 ..       2      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                    +C+eCg  + +  +   + C++Cg++
      AJA92330.1 35 KCPECGGPVIR-EAVGIWACKKCGLK 59
                    8**********.9***********97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2     2e-05     0.017       2      29 ..      32      58 ..      31      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
  A2L_zn_ribbon  2 nlkvCsvCggngilnseqgylvCieCga 29
                   + ++C  Cgg++i   + g+  C++Cg+
     AJA92330.1 32 QKRKCPECGGPVIR-EAVGIWACKKCGL 58
                   789***********.***********95 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       8.7   7.4e+03      30      38 ..      15      23 ..      14      24 .. 0.76
   2 ?   15.5   2.0   1.5e-05     0.012      16      44 ..      31      57 ..      27      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.7
  Zn_Tnp_IS1595 30 yriktrglf 38
                   y ik r++f
     AJA92330.1 15 YGIKIRKQF 23
                   778888888 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.5e-05
  Zn_Tnp_IS1595 16 pngfvCPhCgsrkayriktrglfqCkeCr 44
                   ++++ CP Cg+  +++    g + Ck+C+
     AJA92330.1 31 KQKRKCPECGGPVIREA--VGIWACKKCG 57
                   57899*****6555554..57*******7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.8     3e-05     0.026       8      37 ..      29      59 ..      25      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
         DZR  8 lppdarfCseCgtklkavaa.edrCpsCgek 37
                l +++r C+eCg ++ ++a    +C +Cg k
  AJA92330.1 29 LMKQKRKCPECGGPVIREAVgIWACKKCGLK 59
                5677888999999987554468889999855 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.9   2.3e-05     0.019       1      13 [.      35      47 ..      35      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
  DNA_ligase_ZBD  1 hCPvCGsavvRee 13
                    +CP+CG +v+Re 
      AJA92330.1 35 KCPECGGPVIREA 47
                    6**********96 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00038      0.33      17      33 ..      29      45 ..      17      46 .. 0.85
   2 ?    3.7   0.5     0.074        63       2       8 ..      51      57 ..      51      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                --SSTTB-TTT--.-B- CS
     ADK_lid 17 pPkveglCDkCGepLvq 33
                  k++ +C +CG+p ++
  AJA92330.1 29 LMKQKRKCPECGGPVIR 45
                56999*********885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.074
                EE-TTT- CS
     ADK_lid  2 rvCpkCG 8 
                + C+kCG
  AJA92330.1 51 WACKKCG 57
                78****9 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.013        11      12      20 ..      32      40 ..      22      40 .. 0.78
   2 ?    6.9   0.0    0.0063       5.4      12      22 ..      49      59 ..      45      69 .] 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
   zf-C2H2_3 12 gasqCkeCg 20
                ++++C+eCg
  AJA92330.1 32 QKRKCPECG 40
                3456****8 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0063
   zf-C2H2_3 12 gasqCkeCgMv 22
                g  +Ck+Cg++
  AJA92330.1 49 GIWACKKCGLK 59
                5567*****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   4.1e-05     0.035      14      38 ..      22      45 ..      20      48 .. 0.68
   2 ?    2.6   0.4      0.17   1.5e+02      29      33 ..      53      57 ..      46      61 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
  Zn-ribbon_8 14 efevlqsisdaplta.CPeCgsevrr 38
                 +f++++  ++  ++  CPeCg++v r
   AJA92330.1 22 QFTQVHHLMK--QKRkCPECGGPVIR 45
                 6776665552..4444******8865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.17
  Zn-ribbon_8 29 CPeCg 33
                 C++Cg
   AJA92330.1 53 CKKCG 57
                 56665 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.1   7.8e-05     0.067      17      40 .]      35      57 ..      29      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
  Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCvaCd 40
                    Cp+Cg P  r+   g + C  C+
     AJA92330.1 35 KCPECGGPVIREA-VGIWACKKCG 57
                   6**********97.5899**9996 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   9.5e-05     0.081      20      52 ..      35      65 ..      17      69 .] 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                 B--STT---B-EEETTTEEEETTTTEEESS--E CS
  Rep_fac-A_C 20 ACpsedCnkKvveeedgewrCekCdkeveepky 52
                  Cp  +C   v++e+ g w C+kC  +++   y
   AJA92330.1 35 KCP--ECGGPVIREAVGIWACKKCGLKIAGTAY 65
                 699..9******************988776655 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.024        20       4      11 ..      35      42 ..      32      48 .. 0.79
   2 ?    6.0   0.0     0.011       9.2       3      13 ..      51      61 ..      49      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
      zf_UBZ  4 lCerCgke 11
                 C++Cg +
  AJA92330.1 35 KCPECGGP 42
                7****965 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
      zf_UBZ  3 ylCerCgkeip 13
                + C++Cg +i 
  AJA92330.1 51 WACKKCGLKIA 61
                68*****9997 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.9    0.0012      0.99      11      17 ..      34      40 ..      28      42 .. 0.93
   2 ?    5.3   0.3     0.017        15       9      18 ..      49      58 ..      45      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
     zf-tcix 11 rkCpkCG 17
                rkCp+CG
  AJA92330.1 34 RKCPECG 40
                9*****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
     zf-tcix  9 GvrkCpkCGt 18
                G+ +C kCG 
  AJA92330.1 49 GIWACKKCGL 58
                899******5 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2     0.004       3.4      13      22 ..      33      42 ..      29      48 .. 0.77
   2 ?    4.4   0.1     0.043        37      16      23 ..      53      60 ..      51      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
        YhfH 13 kKkCteCGke 22
                k kC+eCG  
  AJA92330.1 33 KRKCPECGGP 42
                569****965 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.043
        YhfH 16 CteCGkei 23
                C +CG +i
  AJA92330.1 53 CKKCGLKI 60
                *****988 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00016      0.14       2      12 ..      34      44 ..      33      46 .. 0.85
   2 ?    0.7   0.2      0.53   4.5e+02       4      10 ..      53      59 ..      51      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                    EE-SSS--EEE CS
  zf-C4_Topoisom  2 ekCPkCggdLv 12
                    +kCP+Cgg+++
      AJA92330.1 34 RKCPECGGPVI 44
                    89******976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.53
                    -SSS--E CS
  zf-C4_Topoisom  4 CPkCggd 10
                    C kCg +
      AJA92330.1 53 CKKCGLK 59
                    99**955 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0063       5.4       1       6 [.      35      40 ..      32      43 .. 0.66
   2 ?    5.9   0.2     0.013        11       2       9 ..      53      60 ..      52      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0063
  zinc_ribbon_2  1 fCpnCG 6 
                   +Cp+CG
     AJA92330.1 35 KCPECG 40
                   455555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.013
  zinc_ribbon_2  2 CpnCGael 9 
                   C++CG ++
     AJA92330.1 53 CKKCGLKI 60
                   99999887 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4    0.0018       1.6      13      26 ..      30      43 ..       4      52 .. 0.86
   2 ?    2.7   0.1      0.16   1.4e+02      18      24 ..      52      58 ..      45      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
    zf-Mss51 13 khvdfeCpdCGipt 26
                 +++ +Cp+CG p+
  AJA92330.1 30 MKQKRKCPECGGPV 43
                567889*****998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
    zf-Mss51 18 eCpdCGi 24
                 C++CG+
  AJA92330.1 52 ACKKCGL 58
                7*****8 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.6      0.02        17      32      46 .]      26      40 ..      24      40 .. 0.72
   2 ?    8.0   1.5    0.0043       3.7       2      10 ..      34      42 ..      33      49 .. 0.73
   3 ?    5.4   0.5     0.029        25      32      46 .]      43      57 ..      42      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
     zf-IS66 32 ViehirpkyaCpcCe 46
                V++    k++Cp+C+
  AJA92330.1 26 VHHLMKQKRKCPECG 40
                556667788888886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0043
     zf-IS66  2 rtCpcCGgl 10
                r+Cp+CGg+
  AJA92330.1 34 RKCPECGGP 42
                78*****96 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.029
     zf-IS66 32 ViehirpkyaCpcCe 46
                Vi+     +aC++C+
  AJA92330.1 43 VIREAVGIWACKKCG 57
                67777889******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 531.77
//
Query:       AJA92331.1  [L=78]
Description: hypothetical protein T478_0868 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 553.47
//
Query:       AJA92332.1  [L=897]
Description: alanine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-83  281.1   0.0    1.6e-83  281.1   0.0    1.6  2  tRNA-synt_2c  tRNA synthetases class II (A)
    1.2e-15   57.3   1.2    1.2e-15   57.3   1.2    2.2  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    1.7e-05   25.2  12.0    0.00039   20.8  12.0    2.6  1  DHHA1         DHHA1 domain
     0.0052   16.1   0.7       0.01   15.1   0.1    1.7  2  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
  ------ inclusion threshold ------
        1.6    7.8   5.3        7.5    5.6   5.2    1.8  1  CAF1          CAF1 family ribonuclease


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.0   4.4e-87   1.6e-83       8     552 .]      81     577 ..      78     577 .. 0.90
   2 ?   -4.4   1.5       1.4   5.1e+03     405     432 ..     730     757 ..     724     783 .. 0.53

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 4.4e-87
                   HHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSS.CGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS--SEEEEEEEEESS...SS-HH CS
  tRNA-synt_2c   8 dfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgke.akpklkravnsQkciRagGkhnDlenVGktarHhTfFeMlGnfsfg...dYfke 100
                   +fF k++Ht +++++vv +++++l+f++A++++f+ ++ +k+  + +++++v  Q c+R++    DlenVG t+rH+  F M+G++s+     Y+k+
    AJA92332.1  81 SFFVKNNHTSINRYPVVCRWRDDLYFTIASIVDFQRVMGSKVvFEFPANPLVVPQTCLRFK----DLENVGVTGRHFSSFCMIGQHSIPndnGYWKD 173
                   6*************************************999966789**************....***********************66668**** PP

                   HHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHE CS
  tRNA-synt_2c 101 eaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrv 195
                   e +++ ++llt+++g+dk+++++ +  +++    ++  e +v++ e    +f    +f+     ++  +  +i+++ g e++++   ++++a+d ++
    AJA92332.1 174 ECVNLDFNLLTQQFGIDKKEITFVEDVWEGggSFGSSLEYFVRGLELGNAVF---TEFQGDLSDYKTLDQRIIDMGAGLERFAWITMGTPTAYDCCF 267
                   *************************999998899999999999999999999...999977777********************************* PP

                   EEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--S CS
  tRNA-synt_2c 196 leiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvp 292
                     i  ++++q++ +++   + L  +         +l+++L +vr+n  ++ +++ ++  + i++          e ++ i DH+r+l fa++dG++p
    AJA92332.1 268 GPITKKLIEQAGIDTN--SSVLT-PYFTEIAKNLELYEDLTQVRKNAIKTTGLTDEQINRIITP---------LEGIYLIIDHIRTLIFAISDGALP 352
                   ************9943..33333.3333334567899********************9999999.........789********************* PP

                   SSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHH CS
  tRNA-synt_2c 293 snegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafk 389
                   sn+g gY lR +lRr v  +++L+lk + l+++++++++ l+++ypel++ +e v+eii+ E+ r++   +r +k++++l k      e + ed+++
    AJA92332.1 353 SNVGGGYNLRIMLRRIVSTMDRLKLKFD-LNEIIDIQIDYLKNTYPELEKTREDVKEIISIETGRYDSSKQRMQKIVSKLNK------EPKVEDLIT 442
                   ****************************.*************************************9876665555555544......45689**** PP

                   HHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTE CS
  tRNA-synt_2c 390 LydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefveeveegeevg 486
                   Ly++ G++++  ke+     +  +i+  ++++    ++skk+k++ +        l+ +++te  l+y+e           + +ef ++v ++ e++
    AJA92332.1 443 LYESDGVTPEYLKEM----KVISEIPSSFYSKLSDLHQSKKQKEQVN------LPLEGIPDTEL-LFYNE-----------DPREFDAKVLKSFENF 517
                   ******999988777....5666789999999999998865555433......56677777766.99999...........899************* PP

                   EEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
  tRNA-synt_2c 487 vvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                   vvLd+T+fYa +GGq+ D+G+i++++    ++d+ k +++v+h++k e    k+gd v+++vd +r
    AJA92332.1 518 VVLDKTAFYARGGGQEPDHGKISGQE----IVDITKHGNIVVHEIKGE--IPKEGDIVSCVVDAKR 577
                   **********************9987....99**************97..99***********876 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 1.4
                   HHCTTXEEXHHHHHHHHHHHHHHHCCHH CS
  tRNA-synt_2c 405 aeekglkvdiegfekameeqrerskkek 432
                   +++++ + + ++ e++++eq+++++ e+
    AJA92332.1 730 VKKREQDSENKEKEEKLKEQEKEKRLEQ 757
                   3444444444444444444444433222 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         2   7.2e+03       5      17 ..     256     269 ..     241     269 .. 0.60
   2 !   57.3   1.2   3.3e-19   1.2e-15       1      44 []     676     719 ..     676     719 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2
                 EETT..EEEEESS- CS
    tRNA_SAD   5 siGd.isvelCgGt 17 
                 ++G+ + ++ C G+
  AJA92332.1 256 TMGTpTAYDCCFGP 269
                 33435677999997 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 3.3e-19
                 EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
    tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                 vr+vsiGd ++e+CgGtHv nT++++ +ki++ ++i++g+ RI+
  AJA92332.1 676 VRIVSIGDLDIEACGGTHVANTSDVEQIKITRTKRIQDGVVRIE 719
                 9******************************************7 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8  12.0   1.1e-07   0.00039      68     138 .]     822     895 ..     727     895 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.1e-07
                 BTTCEEEEEEEECTEEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHHHHHHHHH CS
       DHHA1  68 kkpvivfvakeegdkvkvsarskkd...gvdagelakeaaaklgggGGGH.dlAaGagipaekleealealeeai 138
                 +k+v + ++++++ k++ ++ + ++     +ag+++k ++++lgg GGG  ++A+G+g++++k e+a++ ++++i
  AJA92332.1 822 PKMVYCGLFEQGE-KIRAIVYAGDEiskEKSAGDIVKSISQILGGAGGGSaKFAQGGGTDKSKKEDAIKNAKSMI 895
                 3466666677776.99999999887999*****************************************999876 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.9e-06      0.01      97     179 ..     187     269 ..     176     325 .. 0.72
   2 ?   -2.5   0.0      0.65   2.3e+03     144     214 ..     357     427 ..     355     453 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.9e-06
                   CT--CCCS-EEEEEEEEEEGGGTEEEEEEEEEETTCEEEE..EEEEE.EETTEE.-SS--EEEEEEHHHHHHHHCT-SSGGG-ECCT CS
  tRNA-synt_2e  97 lgidlkehdirfveDdWesptlGawGlGwevwldGmeitq..ftYfq.qvggle.lkpvsveityGleRlamylqevdnvydlewne 179
                   +gid  +++i fveD We    G++G   e ++ G+e+    ft fq +++ ++ l++  +++  GleR a +  ++ + yd  +  
    AJA92332.1 187 FGID--KKEITFVEDVWEG--GGSFGSSLEYFVRGLELGNavFTEFQgDLSDYKtLDQRIIDMGAGLERFAWITMGTPTAYDCCFGP 269
                   5555..568********96..69**************9654499999445555426788899***************9999999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.65
                   TTEE-SS--EEEEEEHHHHHHHHCT-SSGGG-ECCT.TEEHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHH CS
  tRNA-synt_2e 144 gglelkpvsveityGleRlamylqevdnvydlewne.kvtygdvflqneveqsaynfeeadvelllklfeey 214
                   gg++l+ +   i   ++Rl +   + ++++d++ +  k ty ++ +++e  +   ++e+   +   + ++++
    AJA92332.1 357 GGYNLRIMLRRIVSTMDRLKLKF-DLNEIIDIQIDYlKNTYPELEKTREDVKEIISIETGRYDSSKQRMQKI 427
                   56677777777777778877654.677888888766567777777777766666666665555555554444 PP

>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.2    0.0021       7.5     113     207 ..     377     765 ..     369     773 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0021
                 TT--HHHHHTT-B-B--HH..HHHHHHCH-----.....---..................-----TTC.HHHHHH........................ CS
                 xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..................xxxxxxxxxxxxxxx........................ RF
        CAF1 113 ngfdfnkliseGipYlsrk..eeekakerleerkeekekske..................nvkivsdedkefvee........................ 167
                  +fd+n++i+  i Yl++   e ek +e+++e  + ++ +++                  +             e                        
  AJA92332.1 377 LKFDLNEIIDIQIDYLKNTypELEKTREDVKEIISIETGRYDsskqrmqkivsklnkepkV-------------Edlitlyesdgvtpeylkemkvise 462
                 589**************99886666666666652222222222223333333333333440.............1444455555555555555555555 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        CAF1 168 ................................................................................................... 167
                                                                                                                    
  AJA92332.1 463 ipssfysklsdlhqskkqkeqvnlplegipdtellfynedprefdakvlksfenfvvldktafyargggqepdhgkisgqeivditkhgnivvheikge 561
                 666666668888888888888889999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        CAF1 168 ................................................................................................... 167
                                                                                                                    
  AJA92332.1 562 ipkegdivscvvdakrrdgitknhtsthiintsarsvlgswvwqhsafkeedharldithhsaltdedvtkiedaansiiekaipvkienfdrgtaeqk 660
                 9999999999999999999999999999999999999999999999999999999999999999999999999999999999***************** PP

                 ........................................................................-S.HHHHHHHHHHHHHHHHHHHHHHSB CS
                 ........................................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CAF1 168 ........................................................................kskeeeelkeeeklkeeeeekiakqsg 194
                                                                                         +++++e++++eeklke+e+        
  AJA92332.1 661 ygfriyqggvvpvksvrivsigdldieacggthvantsdveqikitrtkriqdgvvriefvsgdgakefvkkREQDSENKEKEEKLKEQEK-------E 752
                 ************************************************************9999877766542222222222222222222.......2 PP

                 THHHHHHHHHC-- CS
                 xxxxxxxxxxxxx RF
        CAF1 195 frlvfealvksrk 207
                  rl  ++++k+r 
  AJA92332.1 753 KRLEQRQIAKERI 765
                 3444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (897 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1525  (0.0850577); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 5631.38
//
Query:       AJA92333.1  [L=294]
Description: prenyltransferase, UbiA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-29  102.5  16.5      3e-29  102.1  16.5    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.76    8.7   8.2      0.029   13.3   2.0    1.7  2  DUF3488   Domain of unknown function (DUF3488)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1  16.5   3.3e-33     3e-29       3     238 ..      19     260 ..      17     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 3.3e-33
        UbiA   3 ipalvg..lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme..rtpnRP......lvsGrispkealifaivllilgllll...alll 88 
                 i++ +g  la+ +g+++d+ +++l+++g++ ++a++ +lNdy+D++ + d++  rt+         l+ G+++pk ++i++i++lilg++++   ++++
  AJA92333.1  19 IAVSLGlsLAWHSGHPIDIIHAFLTFAGVISLHASVDLLNDYWDFKRGIDTKtkRTK--MsggtgvLPEGLLKPKSVYIVGIAFLILGAIIGiyfVIIF 115
                 6666665688888999999*************************9988886633444..3446666**************************9999999 PP

        UbiA  89 npltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrka 187
                 + ++ l++ +a+l +++Y+       +l ++v++ i ++l++++ ++++++s++  ++l+++ v++l+  ++++++++d++ D++ g++tl +++G+ +
  AJA92333.1 116 GITIGLILGFAILSVIFYS-TKIVNWGL-AEVFVTIKGTLIIIGTYFIQSQSIDDFTILAGIVVGVLSSLVLFVTSIPDHDVDKEKGRRTLIIIFGKTN 212
                 9******************.59999999.********************************************************************** PP

        UbiA 188 arillalllavllla.llllllalllllylllalllaalallraarlvrrrd 238
                 a+   ++l++ +l++ +  + ++ +++l+++++l+++++  +  + +++ +d
  AJA92333.1 213 AVK--TFLIFPVLAYgI--IIYGVVSGLFPIYSLIVLLAKPFLILAILHLKD 260
                 ***..777777777743..444444444444444443333333333333333 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.5      0.24   2.2e+03      23      60 ..      14      48 ..       3      58 .. 0.43
   2 ?   13.3   2.0   3.2e-06     0.029      52     175 ..     101     224 ..      79     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.24
     DUF3488 23 wvlllaalllvwrlllarrraplpsrwlllllallava 60
                 ++ ++a+ l+  l la ++   p  ++++ l++++v+
  AJA92333.1 14 LLASVIAVSLG--LSLA-WHSGHPIDIIHAFLTFAGVI 48
                23333333333..2222.22222222455555555554 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.2e-06
     DUF3488  52 lllallavallllsygtllgrdagvalL.vlllalKllElrsrRDalvllllgffllatsflfsqsllfalylllalllllaalvalhasasapslara 149
                 l+l ++  + +++ +g+++g+  g a+L v++++ K+++     +++v +   ++++ t f+ sqs+  + +l  +++++l +lv++ +s + + + + 
  AJA92333.1 101 LILGAIIGIYFVIIFGITIGLILGFAILsVIFYSTKIVNW-GLAEVFVTIKGTLIIIGTYFIQSQSIDDFTILAGIVVGVLSSLVLFVTSIPDHDVDKE 198
                 2333444477788899999*77777766367788888887.567999**************************************************** PP

     DUF3488 150 lrlalkllllalPlalvLFllfPRlq 175
                   + +++++ +   a+  Fl+fP l 
  AJA92333.1 199 KGRRTLIIIFGKTNAVKTFLIFPVLA 224
                 ***********************775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2047.73
//
Query:       AJA92334.1  [L=78]
Description: hypothetical protein T478_0451 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 567.44
//
Query:       AJA92335.1  [L=160]
Description: putative 3-isopropylmalate dehydratase, small subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-23   81.1   0.1    4.6e-22   78.7   0.0    2.1  2  Aconitase_C    Aconitase C-terminal domain
     0.0073   16.0   0.3      0.035   13.7   0.3    2.0  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.0   5.2e-26   4.6e-22      57     130 ..      34     107 ..      11     108 .. 0.85
   2 ?   -2.0   0.1      0.46   4.1e+03      35      43 ..     125     133 ..     109     151 .. 0.50

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 5.2e-26
                  TEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT.-EEEEEST CS
  Aconitase_C  57 gekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennlikng.lLplefke 130
                  +  ++  d +++ k+++ +++v++ knfG+GSSRehA+ al+  Gikavia SF+rIf++n++  + lLp+e+++
   AJA92335.1  34 THAMEGLDPEFPSKVKDGDFIVAG-KNFGCGSSREHAPIALSTCGIKAVIATSFARIFYRNSVDGAfLLPIEVDD 107
                  456677888999999999999998.*************************************9766378999875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.46
                  GTTTCCCCT CS
  Aconitase_C  35 niglgnelv 43 
                  + +++n+  
   AJA92335.1 125 KNEIKNITK 133
                  222222222 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   3.9e-06     0.035      95     165 ..      80     154 ..       7     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-06
                    EEEEEEE-HHHH.HHHHHTT-EEEE--...-TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTS CS
  Aconitase_2_N  95 vvlGgkiaPiFf.ntvedsGalpiead...vskletGdvieikpkegkikkeegevvsefklkpetlldevragg 165
                     v+ ++ a iF+ n v+ +  lpie+d    +k+++ d +ei+  +++ik+ +++   ++k  +e ++  + agg
     AJA92335.1  80 AVIATSFARIFYrNSVDGAFLLPIEVDdetYKKISNSDQLEINIEKNEIKNITKNESYSMKPFSEIIAKIIAAGG 154
                    4788999***986788888899***98333468999***************777777777777889999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1144.57
//
Query:       AJA92336.1  [L=94]
Description: HTH domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-05   23.4   0.1    5.1e-05   23.1   0.1    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00019   21.3   0.0    0.00023   21.0   0.0    1.2  1  HTH_11          HTH domain
     0.0017   18.5   0.0     0.0023   18.1   0.0    1.2  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0053   16.9   0.0     0.0069   16.5   0.0    1.3  1  FUR             Ferric uptake regulator family
     0.0054   16.8   0.0     0.0069   16.4   0.0    1.2  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.022   14.6   0.1    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
      0.017   15.2   0.0      0.032   14.3   0.0    1.5  1  HTH_7           Helix-turn-helix domain of resolvase
      0.017   15.1   0.0      0.018   15.0   0.0    1.1  1  Smg4_UPF3       Smg-4/UPF3 family
      0.018   14.8   0.0      0.034   13.9   0.0    1.5  2  HTH_30          PucR C-terminal helix-turn-helix domain
       0.02   14.8   0.0      0.028   14.3   0.0    1.2  1  MarR_2          MarR family
      0.027   14.3   0.1      0.033   14.1   0.1    1.2  1  TFIIE_alpha     TFIIE alpha subunit
      0.039   13.9   0.0      0.051   13.5   0.0    1.2  1  PadR            Transcriptional regulator PadR-like family
      0.039   13.7   0.0      0.071   12.9   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.053   13.2   0.1       0.14   11.9   0.0    1.7  2  Sigma70_r4_2    Sigma-70, region 4
      0.054   13.7   0.1      0.067   13.4   0.1    1.2  1  HTH_34          Winged helix DNA-binding domain
      0.057   13.7   0.3       0.13   12.5   0.3    1.7  1  UPF0122         Putative helix-turn-helix protein, YlxM / p13
      0.066   13.3   0.1      0.076   13.1   0.1    1.1  1  DUF2250         Uncharacterized protein conserved in archaea 
       0.12   12.0   0.0       0.26   10.9   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
       0.15   11.8   0.0       0.21   11.4   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   5.4e-08   5.1e-05      21      59 ..      19      63 ..      11      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.4e-08
                CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......T CS
        TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr......p 59
                 +++a +iaeel+++ s vY++L +Le+  lVe+ k +       
  AJA92336.1 19 NSKDAPKIAEELNISLSAVYKTLVKLEELTLVEIDKFNfvegkkV 63
                5678999**************************998766665544 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.4e-07   0.00023      18      47 ..      23      53 ..      10      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
      HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelg.vpIe 47
                + ++AeeLn+S ++v++ + +Leel  v+I+
  AJA92336.1 23 APKIAEELNISLSAVYKTLVKLEELTlVEID 53
                668*******************999766665 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.4e-06    0.0023      27      55 ..      25      53 ..      12      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                    HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
  Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyveye 55
                    ++ae+Ln+s s V ++l kLe+  +ve  
      AJA92336.1 25 KIAEELNISLSAVYKTLVKLEELTLVEID 53
                    7*********************9999876 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.4e-06    0.0069      36      67 ..      28      61 ..       7      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.4e-06
                TTTT--HHHHHHHHHHHHHTTSEE..EEEETTSE CS
         FUR 36 edpeislaTVYrtLklleeaglvk..elefedge 67
                e+ +isl+ VY+tL  lee+ lv+  +++f +g+
  AJA92336.1 28 EELNISLSAVYKTLVKLEELTLVEidKFNFVEGK 61
                6789*****************9861145555554 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.3e-06    0.0069      27      57 ..      23      53 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.3e-06
                HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
      HTH_20 27 aselaerldlskntlsyHLrvLeeagLvevv 57
                a+ +ae+l +s + +++ L +Lee  Lve  
  AJA92336.1 23 APKIAEELNISLSAVYKTLVKLEELTLVEID 53
                899*************************965 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.3e-05     0.022       7      46 ..      12      51 ..      10      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                +L++  e+++ +  +aeel++s s+v   L kL+e+ LVe
  AJA92336.1 12 VLFSIIENSKDAPKIAEELNISLSAVYKTLVKLEELTLVE 51
                6899999****************************99986 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.032      26      42 ..      25      41 ..      17      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                TTSSSS---SSSS--SS CS
       HTH_7 26 kIAkevnisRsTvYRyl 42
                kIA+e+nis s vY+ l
  AJA92336.1 25 KIAEELNISLSAVYKTL 41
                9*************976 PP

>> Smg4_UPF3  Smg-4/UPF3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.9e-05     0.018      29      69 ..      48      86 ..      15      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
   Smg4_UPF3 29 lpetvdykyFvpGklskdslkeskysrayinfkdpedlvqf 69
                +  ++d ++Fv+Gk  k +l +s+  ra i+f+++++ +++
  AJA92336.1 48 TLVEIDKFNFVEGK--KVKLYKSRIGRAEITFDNNDATLHL 86
                44589*********..9999***************998876 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.034       7      47 ..      15      55 ..       9      58 .. 0.89
   2 ?   -3.2   0.0       8.4     8e+03      44      53 ..      77      86 ..      74      87 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                HHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTSH CS
      HTH_30  7 aylenggnisatAkaLhvHrnTlryRLrrieellgldlddp 47
                  +en+ ++ + A++L+++   +++ L ++eel+ + +d +
  AJA92336.1 15 SIIENSKDAPKIAEELNISLSAVYKTLVKLEELTLVEIDKF 55
                568999****************************9998876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.4
                TTSHHHHHHH CS
      HTH_30 44 lddpddrlaL 53
                +d+ d+ l L
  AJA92336.1 77 FDNNDATLHL 86
                6677766666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.028       7      52 ..       9      51 ..       4      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
      MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                ++ vL+ +  +      +  +a++l++s sav ++l +L++  Lve
  AJA92336.1  9 HRSVLFSIIENSK---DAPKIAEELNISLSAVYKTLVKLEELTLVE 51
                6789999999997...89************************9998 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.5e-05     0.033      15      70 ..       9      64 ..       3      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-05
                 HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEE CS
  TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswy 70
                 +  vl++++e+++ +   +a+el+i l  + k L +L e  lv++ +    e+k+++
   AJA92336.1  9 HRSVLFSIIENSKDA-PKIAEELNISLSAVYKTLVKLEELTLVEIDKFNFvEGKKVK 64
                 567999***999855.68**************************9886555555555 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-05     0.051      26      64 ..      29      67 ..      20      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                -CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
        PadR 26 llelseGslYpaLkrLekeglveseweesgegpprkyYr 64
                +l++s + +Y++L +Le+  lve  + + +eg++ k+Y+
  AJA92336.1 29 ELNISLSAVYKTLVKLEELTLVEIDKFNFVEGKKVKLYK 67
                4678999******************9999********97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.071      21      40 ..      24      43 ..      21      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
      HTH_23 21 reIAreLgvsrrTvyrwlkr 40
                ++IA+eL++s + vy+ l +
  AJA92336.1 24 PKIAEELNISLSAVYKTLVK 43
                68*************98655 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.14      28      48 ..      22      42 ..      10      47 .. 0.81
   2 ?   -1.7   0.0       2.5   2.3e+03      39      50 ..      62      73 ..      58      74 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                  -HHHHHHHHT--HHHHHHHHH CS
  Sigma70_r4_2 28 sykEIAellgisegtVksrls 48
                  +   IAe+l+is ++V++ l 
    AJA92336.1 22 DAPKIAEELNISLSAVYKTLV 42
                  5567************99885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                  -HHHHHHHHHHH CS
  Sigma70_r4_2 39 segtVksrlsRA 50
                  +++  ksr+ RA
    AJA92336.1 62 KVKLYKSRIGRA 73
                  566678999888 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.1e-05     0.067      12      59 ..      18      66 ..      11      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-05
      HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievdk.efkgkkprtll 59
                +++ d+ ++ e+l+++ ++ ++ l kLe+   +e+dk +f+++k+  l+
  AJA92336.1 18 ENSKDAPKIAEELNISLSAVYKTLVKLEELTLVEIDKfNFVEGKKVKLY 66
                567788899***************************9668888877776 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   0.00014      0.13      38      63 ..      25      50 ..       9      94 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
     UPF0122 38 EiAeefnvsrqavydnikrtekllek 63
                 iAee n+s +avy ++ + e+l + 
  AJA92336.1 25 KIAEELNISLSAVYKTLVKLEELTLV 50
                7***************9999887432 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.1e-05     0.076      25      71 ..      23      69 ..       6      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
     DUF2250 25 aksiakeleipleevrellkkLeelGLlervegktikrteaklKkks 71
                a  ia+el+i+l+ v + l kLeel L+e  + + +  ++ kl k+ 
  AJA92336.1 23 APKIAEELNISLSAVYKTLVKLEELTLVEIDKFNFVEGKKVKLYKSR 69
                55799************************999888888888877665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.26      23      43 ..      26      46 ..      23      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
      HTH_24 23 LAerlglSpstvnrrlkrLee 43
                +Ae+l++S+s+v + l +Lee
  AJA92336.1 26 IAEELNISLSAVYKTLVKLEE 46
                9***********998888876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.21      24      49 ..      26      51 ..      21      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                HHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR 24 lArrtglpkStvhRlLqtLvelGyve 49
                +A+++ ++ S+v+  L  L+el +ve
  AJA92336.1 26 IAEELNISLSAVYKTLVKLEELTLVE 51
                9*********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 735.23
//
Query:       AJA92337.1  [L=171]
Description: NADH-quinone oxidoreductase, B subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-24   86.0   0.1    2.5e-24   85.5   0.1    1.2  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.1   1.4e-28   2.5e-24       3     129 ..      51     159 ..      50     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 1.4e-28
                  HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HH CS
  Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgee 100
                  +cs+++ a++++ +d+     +r+++  +++ +      + +++d++vv+G++trk++++l+l++++++++k+via+G+CA++GG++   ++++ +  
   AJA92337.1  51 CCSVEFGAASSPRYDV-----ERFGI--IEAFG------SLRQCDLVVVQGTITRKMAPRLRLVYDQMPEPKYVIAMGACAITGGLY--FDSYN-V-- 130
                  4999998888889999.....77754..33333......1239********************************************..44233.3.. PP

                  HHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
  Oxidored_q6 101 vgellevvpvdinipGCPphpeailetll 129
                    ++++ +pvd+++pGCPp+pe+++++ +
   AJA92337.1 131 LPGIDGILPVDVYVPGCPPRPETLIQGCM 159
                  458*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1369.23
//
Query:       AJA92338.1  [L=183]
Description: PF03745 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-19   67.9   0.2    8.7e-19   67.0   0.2    1.4  1  DUF309         Domain of unknown function (DUF309)
     0.0087   14.8   0.0      0.011   14.5   0.0    1.2  1  DUF4455        Domain of unknown function (DUF4455)
  ------ inclusion threshold ------
      0.066   13.7   0.1        0.1   13.1   0.1    1.3  1  Calpain_inhib  Calpain inhibitor
      0.098   12.4   0.5       0.44   10.3   0.1    2.0  2  Sh_2           Metapneumovirus Small hydrophobic protein


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.2     2e-22   8.7e-19       2      51 ..      85     134 ..      84     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2e-22
      DUF309   2 eeaielfnegeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrg 51 
                  e+i++fn+++f+e+HE+lE +Wk+ + +e+ l+qglI +A++l+h+++ 
  AJA92338.1  85 SEGIDYFNNERFWECHEILEGVWKNCDGNEKFLVQGLILVAAGLVHYQKD 134
                 69*********************999988******************986 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.4e-06     0.011     219     290 ..      50     121 ..      35     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-06
     DUF4455 219 lqekrlellqkisdllPpaltkskveeWyaslealneqidelhaqflekLreeyeevwqecleeveklkkeL 290
                 +++ + el++k+s++ P ++ k  vee  ++ +a+ e id ++++ + + +e  e vw++c+   + l + L
  AJA92338.1  50 AKSDLDELIDKLSSIGPLDHAKHVVEEIVEKEKAISEGIDYFNNERFWECHEILEGVWKNCDGNEKFLVQGL 121
                 567889*******************************************************97766666665 PP

>> Calpain_inhib  Calpain inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.3e-05       0.1      57     101 ..      41      86 ..       7      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
  Calpain_inhib  57 e..eekesmsddAldaLsdsLgkrepdpeepkkppedkVkeekakee 101
                    +  e + +++++ ld+L+d L++  p     k  +e++V++eka +e
     AJA92338.1  41 KyvELDTTIAKSDLDELIDKLSSIGPLDHA-KHVVEEIVEKEKAISE 86 
                    3456789999****************9999.*************998 PP

>> Sh_2  Metapneumovirus Small hydrophobic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.11     5e+02      95     126 ..      22      53 ..       6     101 .. 0.60
   2 ?   10.3   0.1   9.8e-05      0.44     111     159 ..     113     159 ..     100     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.11
        Sh_2  95 lklttdeerslqpdckqekklceGkivylked 126
                  ++ t+  + +  dc++ kk  e + +  k+d
  AJA92338.1  22 SRIITSGMNLTLRDCRVSKKYVELDTTIAKSD 53 
                 55666666667777777777777666666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.8e-05
        Sh_2 111 qekklceGkivylkedGclgakeGedldcidlvakcvetlcdsnpdyde 159
                 +ek l +G i      G +  ++ edl ci +  + +e+l +sn +y +
  AJA92338.1 113 NEKFLVQGLIL--VAAGLVHYQKDEDLVCISIFNRALEKLENSNGQYYD 159
                 56667777664..4679999999*********************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1299.70
//
Query:       AJA92339.1  [L=266]
Description: ribosomal protein L11 methyltransferase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-34  117.8   0.0    8.4e-34  117.3   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.6e-11   44.2   0.0    2.5e-11   43.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.9e-10   39.8   0.1    5.5e-10   39.3   0.1    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.5e-09   36.8   0.0    5.3e-09   35.8   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.1e-07   32.5   0.0    2.5e-07   31.3   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    1.1e-07   32.8   0.0    2.4e-07   31.7   0.0    1.6  1  Methyltransf_24  Methyltransferase domain
    1.2e-05   25.9   0.0    2.5e-05   24.9   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    0.00013   21.8   0.0    0.00019   21.2   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
    0.00015   22.5   0.0    0.00045   20.9   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
    0.00015   21.5   0.1    0.00042   20.1   0.0    1.8  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    0.00015   21.0   0.1    0.00022   20.5   0.1    1.2  1  Methyltransf_3   O-methyltransferase
    0.00016   21.7   0.0    0.00026   20.9   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
    0.00019   21.0   0.0    0.00024   20.6   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00022   21.2   0.0    0.00041   20.4   0.0    1.6  1  Methyltransf_32  Methyltransferase domain
    0.00034   20.2   0.0      0.001   18.7   0.0    1.7  2  MTS              Methyltransferase small domain
    0.00055   19.6   0.0     0.0011   18.6   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0042   16.2   0.0     0.0068   15.5   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0073   15.4   0.0      0.012   14.8   0.0    1.3  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.043   13.5   0.0    1.5  1  Met_10           Met-10+ like-protein
      0.066   13.3   0.0      0.088   12.9   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.3   0.0   9.4e-37   8.4e-34       1     198 [.      57     251 ..      57     266 .] 0.91

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 9.4e-37
       GCD14   1 gfvyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthr 99 
                 ++vy+l+pt     ++++h tqi+y +D   i  ++ ++ G ++ve GtGsgsl++ +a  v+P+Gh++tf+   + +e a ++ ++ ++s++vt+++ 
  AJA92339.1  57 KYVYLLKPTLHDHVMKMQHSTQIVYPKDFGYIAARMGVQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHEM 155
                 69************************************************************************************************9 PP

       GCD14 100 DvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrtyevrkskleeidlaekrleene 198
                 ++ k+     + +++D   +Dl  Pwe +p++ k+l k++g + +  P ++q+ +   a+ e +ft+ie  e  lr+ e+r  k +++  ++ ++    
  AJA92339.1 156 NLKKSKK-MPL-KDMDLAIIDLGDPWEVLPQVRKML-KSSGSVAAICPTMNQLEKLSVAFVENEFTDIECTEHILRRIEARDGKTRHSYQGIGHTTYLA 251
                 9988754.566.789*99******************.77888999************************************999998877766665554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.8e-14   2.5e-11       3     119 ..      96     206 ..      94     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.8e-14
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.ledekfDlilsnevlnaladpdkil 94 
                      +g +++++G+G+G lt  la+ ++p+++v+ +D +++  e+A++n +k g +  v++++ +  + +k  l+d   Dl +      +l dp ++l
       AJA92339.1  96 SGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSkYVTMHEMNLKKSKKMpLKD--MDLAII-----DLGDPWEVL 182
                      7889**********************************************99899****9999966555665..999666.....7******** PP

  Methyltransf_31  95 eeiervlkpggilliedprllaelp 119
                       ++ + lk+ g +++  p  + +l 
       AJA92339.1 183 PQVRKMLKSSGSVAAICPT-MNQLE 206
                      ***********99877666.55554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   6.2e-13   5.5e-10      42     126 ..      65     149 ..      25     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.2e-13
                 TTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSE CS
        PCMT  42 aYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenv 126
                 + +d +++++  + i  p+  +++   + ++ g++++e+G+GsG lt  la +v+++g+v + +  ++++e a++n+kk ++++ 
  AJA92339.1  65 TLHDHVMKMQHSTQIVYPKDFGYIAARMGVQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSKY 149
                 568999**************************************************************************99853 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   5.9e-12   5.3e-09      38     167 ..      87     213 ..      69     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.9e-12
                      HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S- CS
  Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtD 131
                      ++  +++v++g+k++++ +G+g l+  l++ v+ +g+v   D++++ ++v+ek +k+ g++  ++++   ++L+ +++ + +  +   + ++ D
       AJA92339.1  87 YIAARMGVQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMS--KYVTMHEMNLKKSKK-MPLKDMDLAIIDLGD 177
                      578899*****************************************************98..588888999987664.55667788999999* PP

                      HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHH CS
  Ubie_methyltran 132 klkaLkeayrvlkpGGrlvvlefskvelpllsqaye 167
                        ++L +++++lk  G +  +  +  +l+ ls+a+ 
       AJA92339.1 178 PWEVLPQVRKMLKSSGSVAAICPTMNQLEKLSVAFV 213
                      *******************99999999999999885 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.8e-10   2.5e-07       1      95 [.     100     191 ..     100     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.8e-10
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS.SSTTTEEEEEEESTGGGSSHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp.fedgsfDlvvssgalhhlsdedlekalkeia 90 
                      ++++G+G+G lt  la  + ++++v+ +D+ ++++e a+++++++g+   v+++++++++ +  + + +Dl ++  +       d  ++l +++
       AJA92339.1 100 IVEIGTGSGSLTTFLASIVnPRGHVYTFDVEPKFMEVAEKNIKKAGMskYVTMHEMNLKKSKkMPLKDMDLAIIDLG-------DPWEVLPQVR 186
                      79****************9559**********************99999999*****96643245556888887322.......2334555555 PP

                      HHEEE CS
  Methyltransf_25  91 rvLkp 95 
                      ++Lk 
       AJA92339.1 187 KMLKS 191
                      55554 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   2.7e-10   2.4e-07       1      95 [.     101     189 ..     101     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 2.7e-10
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiDgghaaeavledlea 90 
                      vEiG+ sG  t +l++ ++ +g  +++++d +p   +++++a++    ag++++v++++ ++++  +++  +++Dl++iD g +  +vl+ ++ 
       AJA92339.1 101 VEIGTGSGSLTTFLASIVNPRG--HVYTFDVEP---KFMEVAEKnikkAGMSKYVTMHEMNLKKS-KKMPLKDMDLAIIDLG-DPWEVLPQVRK 187
                      8*****************9999..6********...555555555555**************999.5666699*******99.44444444443 PP

  Methyltransf_24  91 llprl 95 
                         +l
       AJA92339.1 188 ---ML 189
                      ...33 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   2.8e-08   2.5e-05       2      93 ..     102     194 ..     101     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.8e-08
                      EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC...TSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHH CS
  Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaek...lpfednsfDlvvssevlhhvedpekalkeiaRv 87 
                      ++G+G+G+l+  la+ +   ++v+++D+ ++++++a+++++++g+   v++++++++k   +p++d  +Dl ++      + dp ++l +++++
       AJA92339.1 102 EIGTGSGSLTTFLASIVnprGHVYTFDVEPKFMEVAEKNIKKAGMskYVTMHEMNLKKskkMPLKD--MDLAIID-----LGDPWEVLPQVRKM 188
                      89************6666779***********************9998889999999644477877..7776654.....46666666666666 PP

                      EEEEEE CS
  Methyltransf_11  88 LkpgGl 93 
                      Lk  G 
       AJA92339.1 189 LKSSGS 194
                      666665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.1e-07   0.00019      45     125 ..      95     172 ..      60     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.1e-07
  Methyltransf_16  45 lsklsvlELGsGtGlvGlavaell.peakviltDlee.llellkknielnknalkskvkvevLdWgeeleedllekeevDlil 125
                      +s+++++E+G G+G     +a+ + p+ +v+  D+e   +e+ +kni+   + +++ v++++++ ++    ++   + +Dl +
       AJA92339.1  95 QSGQKIVEIGTGSGSLTTFLASIVnPRGHVYTFDVEPkFMEVAEKNIKK--AGMSKYVTMHEMNLKKSK--KM-PLKDMDLAI 172
                      57899******************88**********9879**********..55*****99999986644..55.345567654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-07   0.00045       1      97 [.     101     193 ..     101     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-07
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklL 93 
                      +eiG+G+Gsl+  l+    p+ +++  D+ p+++e a++ ++k +  +   ++  +l  +++ + +  Dl ++      l d+ evl ++rk+L
       AJA92339.1 101 VEIGTGSGSLTTFLASIVnPRGHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHEMNLKKSKKMPLKDMDLAII-----DLGDPWEVLPQVRKML 189
                      69*********99988779***************999999999998776666666666665555588888876.....5788888888888888 PP

  Methyltransf_12  94 kpgG 97 
                      k  G
       AJA92339.1 190 KSSG 193
                      8877 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.7e-07   0.00042       5      49 ..       5      49 ..       3      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.7e-07
     GCD14_N  5 raGdrVqLtDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGs 49
                +aGd V +  +  +k  +   + ++fh+h G+i+H d IG++ Gs
  AJA92339.1  5 KAGDLVLFFYNDSKKWLLKISKKEQFHSHIGVIKHSDAIGKEFGS 49
                67777777777788888889999*****************98775 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.5e-07   0.00022      38     108 ..      87     157 ..      57     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
                     HHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-H CS
  Methyltransf_3  38 fLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegda 108
                     ++   + + + ++++eiG+  G     +a  + + G++ + d++++ +e+a k i+kag+ + + ++e + 
      AJA92339.1  87 YIAARMGVQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHEMNL 157
                     5555566778899*****99998888889999****************************99998876554 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.9e-07   0.00026      12      73 ..      94     156 ..      88     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.9e-07
  Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsd 73 
                      v++g++++ iGt  g l+ +l++  +   +v+  D++++ +e a++ni+kag+++ ++++  +
       AJA92339.1  94 VQSGQKIVEIGTGSGSLTTFLASIvNPRGHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHEMN 156
                      78999****************985266789***********************9988876544 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.7e-07   0.00024     159     256 ..      94     195 ..      87     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
        PrmA 159 vkegeevlDvGtGSGiLa..iaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeeka...dvivaNI.Laevlielaedikklvk 251
                 v++g++++ +GtGSG L+  +a+      +v+  D+++  ++va++N+++ ++++ ++++   +l k++k+   d+ +a I L ++  e ++++ k++k
  AJA92339.1  94 VQSGQKIVEIGTGSGSLTtfLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHE-MNLKKSKKMplkDMDLAIIdLGDP-WEVLPQVRKMLK 190
                 8999*************855677777789************************99886642.222221221112444444423333.455566666666 PP

        PrmA 252 eggll 256
                 ++g++
  AJA92339.1 191 SSGSV 195
                 66655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.6e-07   0.00041      26      94 ..      97     162 ..      86     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.6e-07
  Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeats 94 
                       +++v++G G g L+  la+  ++ + +v+ +d++ + +e aek  +k g  ++k +  +e++ +++++
       AJA92339.1  97 GQKIVEIGTGSGSLTTFLAS-IVNPRGHVYTFDVEPKFMEVAEKNIKKAG--MSKYVTMHEMNLKKSKK 162
                      578*****************.55679***********************9..77777777777776654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06     0.001      29      92 ..      94     160 ..      87     174 .. 0.82
   2 ?   -1.8   0.0       2.2   1.9e+03     125     153 ..     185     217 ..     178     236 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                 CCTCSEEEEET-TTSHHHHHHHH.HTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT CS
         MTS  29 kelsgkvlDlGcGaGvlgaalak.espeaevtlvdvdarAlesakenleankle..vevvasdvlee 92 
                  +  +k++ +G+G G l++ la+  +p+ +v  +dv+ + +e+a++n+++ +++  v++++ ++ + 
  AJA92339.1  94 VQSGQKIVEIGTGSGSLTTFLASiVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSkyVTMHEMNLKKS 160
                 456789**************9983589999**********************998777777776554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                 HHHHEEEEEEEEEEEETTSCHHHH....HHHHH CS
         MTS 125 AkeaLkegGeLliVanrklgyesl....leelf 153
                  +++Lk++G+   +  +  + e+l    +e+ f
  AJA92339.1 185 VRKMLKSSGSVAAICPTMNQLEKLsvafVENEF 217
                 556666666666555444444443333333333 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.3e-06    0.0011       6      86 ..      94     174 ..      89     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                      --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEEEEEE CS
  Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDriLlD 86 
                       q +++i+++ ++ G+ Tt++a +++++g+v+  d++ + ++  ++n+k+ g+   +++ e+ ++k +k+  +  +D +++D
       AJA92339.1  94 VQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFMEVAEKNIKKAGMSkYVTMHEMNLKKSKKMPLK-DMDLAIID 174
                      578899***********************************************93466777888888888875.66766665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.6e-06    0.0068      22      82 ..      88     151 ..      79     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-06
                 HHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTTTCCCEEEE- CS
      RrnaAD  22 IldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkklskdeklkvvh 82 
                 I   + ++  ++++eig+G G lT+ La ++    +v  +   ++++++ +k+++k++ +k v 
  AJA92339.1  88 IAARMGVQSGQKIVEIGTGSGSLTTFLASIVnprGHVYTFDVEPKFMEVAEKNIKKAGMSKYVT 151
                 6666778899*********************995556679999999999999998777666655 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.3e-05     0.012      65     108 ..      91     134 ..      87     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                  --S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH CS
  Fibrillarin  65 elpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl 108
                  ++ +++g+k++ +G++sG+    ++ iv+++g vy+ ++ p+ +
   AJA92339.1  91 RMGVQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKFM 134
                  57799********************************9999877 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.8e-05     0.043      97     163 ..      92     160 ..      87     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                 T.--TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG- CS
      Met_10  97 l.veegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrev 163
                 + v+ g+ +v++  G G ++  +a   +++  v++ d++P+ ++  ++nik   ++k+v+  ++  ++ 
  AJA92339.1  92 MgVQSGQKIVEIGTGSGSLTTFLASIVNPRgHVYTFDVEPKFMEVAEKNIKKAGMSKYVTMHEMNLKKS 160
                 45899***************999998887648***************************9888876655 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.8e-05     0.088      15     110 ..      91     190 ..      70     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                 HHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS...........HHH.TTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS-C CS
        FtsJ  15 kfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm...........apl.pgvttiqgditdpetiekikealserkvdlvvsDgapdvsg 101
                 +++ ++ g+++v++g + G+ + +l+  ++++g+v+ +D+ p            a + + vt+++++ ++ ++++ +      + +dl + D++   + 
  AJA92339.1  91 RMG-VQSGQKIVEIGTGSGSLTTFLASIVNPRGHVYTFDVEPKfmevaeknikkAGMsKYVTMHEMNLKKSKKMP-L------KDMDLAIIDLGDPWEV 181
                 556.67899********************99*********99877777655543333455555566666665555.2......3488888888866666 PP

                 HHHHHHHHH CS
        FtsJ 102 vhdldeylq 110
                   ++ ++l+
  AJA92339.1 182 LPQVRKMLK 190
                 665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2013.02
//
Query:       AJA92340.1  [L=310]
Description: carbohydrate kinase, PfkB family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-24   86.6   0.3    2.9e-24   85.9   0.3    1.2  1  PfkB          pfkB family carbohydrate kinase
     0.0005   19.5   0.2    0.00097   18.6   0.0    1.5  2  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.3   3.2e-28   2.9e-24       4     295 ..      15     286 ..      12     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.2e-28
                 EEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSE...EEEEEEEETT CS
        PfkB   4 vvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtr...tglalivvde 99 
                 + v+G++  d i++ +k         t+++  GGa+   A + a+   +  +i +vG D+  + +  +  k+++d +++ + +++     g++ ++++ 
  AJA92340.1  15 LTVFGSTALDTIRTPKK---------TLKNVLGGAA-TFAAISASFFTKPGLIAVVGSDFPKKYHTVL--KNHLDLKGLTVLNGKTfryDGKYDATMSV 101
                 56788888888888766.........9999999999.9999999***************955554444..67788888888777331114666666665 PP

                 TSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHH CS
        PfkB 100 dgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtfdpnlldplgaqfkeallellaladllkpneeElealt 198
                   + t+ + ++  ad++++    + d+ ++++++y++   ++e + ++ +e  +++ ++   +  + +++      a+ +++  +d++  n+eE++ lt
  AJA92340.1 102 --RETLKTELNVLADFKPT----VPDAYKKSEFVYLAN-NDPEQNAKIIKEFDNVKFSMCDTIEFWIATKR----NAVIKMIKSVDAVVINDEEAKLLT 189
                 ..67888888888888886....89************9.99999999999999999999977777777777....699999****************** PP

                 TSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHT.....THHHHHHHHHHHHHHHHHHTS CS
        PfkB 199 gekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaalle.....gksleealrfanavAalvvqk 292
                 +e+     +++++++k+ + ga+ vv+++G+ Gal++++d  ++   +  + vvD+tGAGDsf+g+++ +l++       ++++++ ++n  ++++v+k
  AJA92340.1 190 KED-----NLIKCAKKMMSWGANYVVIKKGEHGALLFHEDVIFPSVGFSLESVVDPTGAGDSFAGAMIGHLAAknktsFSEIKKSIIYGNVMGSFAVEK 283
                 *99.....789999999999*****************9999999999999*************************9999******************** PP

                 SSS CS
        PfkB 293 kga 295
                 +g 
  AJA92340.1 284 YGL 286
                 996 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1      0.68   6.1e+03     185     210 ..      25      50 ..      15      53 .. 0.70
   2 !   18.6   0.0   1.1e-07   0.00097     112     216 ..     168     260 ..     158     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.68
                   EEEEE----S--BTHHHHHHHHHHHH CS
  Phos_pyr_kin 185 eleaerietknthGtGCtlssaiaae 210
                   ++++++ + kn  G   t+++  a+ 
    AJA92340.1  25 TIRTPKKTLKNVLGGAATFAAISASF 50 
                   55666666678888888888877765 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.1e-07
                   HHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHH CS
  Phos_pyr_kin 112 lkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaia 208
                   +  ++++ ++ ++ N +Ea+ L++     e+++ ++akk+++ ga++V+ik g++ g     +dv++ + ++     e +   +  G+G++++ a+ 
    AJA92340.1 168 VI-KMIKSVDAVVINDEEAKLLTK-----EDNLIKCAKKMMSWGANYVVIKKGEH-GALLFHEDVIFPSVGFS---LESVV--DPTGAGDSFAGAMI 252
                   44.48999999***********98.....99*******************76643.34444468888766643...33333..4689******9999 PP

                   HHHHCTSS CS
  Phos_pyr_kin 209 aelakges 216
                   ++la +++
    AJA92340.1 253 GHLAAKNK 260
                   99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2460.30
//
Query:       AJA92341.1  [L=44]
Description: hypothetical protein T478_1392 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1463  (0.0815996); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 312.80
//
Query:       AJA92342.1  [L=85]
Description: hypothetical protein T478_0518 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 652.84
//
Query:       AJA92343.1  [L=74]
Description: ribosomal protein S28e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-25   87.9   3.9    3.5e-25   87.7   3.9    1.1  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   3.9     2e-29   3.5e-25       4      64 .]      13      73 ..      10      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 2e-29
                    EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
  Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                    ++A +i+++grtG++Gev+qVrv++ egkdkgr+++RnVkG+ r+G +L+L+EterEA++L
      AJA92343.1 13 TPADIIQIVGRTGIAGEVIQVRVKVREGKDKGRVLTRNVKGSPRVGEVLILRETEREAKKL 73
                    79*********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 549.27
//
Query:       AJA92344.1  [L=831]
Description: peptidase family M1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-90  300.2   1.6    8.1e-90  300.2   1.6    2.5  2  Peptidase_M1    Peptidase family M1 domain
    3.6e-60  204.2   3.0    4.6e-59  200.5   2.0    2.3  2  ERAP1_C         ERAP1-like C-terminal domain
    1.7e-49  168.6   3.0    2.5e-49  168.0   1.3    2.1  2  Peptidase_M1_N  Peptidase M1 N-terminal domain
     0.0028   17.1   2.8     0.0038   16.7   0.1    2.2  2  Aminopep        Putative aminopeptidase
  ------ inclusion threshold ------
        3.6    7.7   8.6        0.6   10.1   3.0    2.6  3  Med31           SOH1


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.2   1.6   2.3e-93   8.1e-90       2     218 .]     218     434 ..     217     434 .. 0.99
   2 ?    0.5   0.4       0.1   3.6e+02     141     186 ..     556     605 ..     504     613 .. 0.69

  Alignments for each domain:
  == domain 1  score: 300.2 bits;  conditional E-value: 2.3e-93
                   HHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTTTEEESSGGGGHHHHHH CS
  Peptidase_M1   2 alevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGnlVtmkwWddlwLnEGf 98 
                   +le tkk l  +e+yf+++Yplpkld++a+pdf+agAMEnwg+it+re+ ll+dp++ss+++k+ +aevi HElaHqWfGnlVtmkwW+dlwLnE+f
    AJA92344.1 218 SLELTKKFLGEYEKYFGIKYPLPKLDMLAIPDFAAGAMENWGAITFRETILLYDPKTSSTKTKQFIAEVISHELAHQWFGNLVTMKWWNDLWLNESF 314
                   6899********************************************************************************************* PP

                   HHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE- CS
  Peptidase_M1  99 atyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKGasllrmlekllgeevFqkglksYlkefkyknae 195
                   at+++ +i+dk++pew++++q+l +++++a+s dal++shpi ++v++psei e+Fdsi+Y+KG ++lrmle+++++++Fqkgl++Ylk+++y+nae
    AJA92344.1 315 ATFMATKIVDKFYPEWDLWDQFLEDAMNTAMSLDALKTSHPIDVKVNHPSEIREIFDSISYDKGGCVLRMLENFVTDKNFQKGLQKYLKKYEYSNAE 411
                   ************************************************************************************************* PP

                   HHHHHHHHHHCCCSCHHTHHHHH CS
  Peptidase_M1 196 tedlwdaleealnkdisevmdtw 218
                    +dlw+++ e+++k i+++m+tw
    AJA92344.1 412 GRDLWKSIGEVAKKPIDKIMSTW 434
                   *********************** PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                   SGG-GSHHH.HHHTSSHHHHHHHHHHHHHHHHHCT...HHHHHHHHHHHH CS
  Peptidase_M1 141 tqevekpse.idevFdsiaYeKGasllrmlekllg...eevFqkglksYl 186
                   +++v++  + ++  Fd+ +Y  + +l ++l +l +   +e+F + +k+Y 
    AJA92344.1 556 KKKVQDYLDfTNAYFDEDNYISSLNLAQHLYSLYSlthKEKFSDEIKQYS 605
                   3566666662456799*******999988877643336999999999995 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.033   1.2e+02       3      21 ..      92     111 ..      92     133 .. 0.80
   2 !  200.5   2.0   1.3e-62   4.6e-59       3     314 ..     506     817 ..     505     818 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.033
                 EESGGG-SSSEEEE.-HHHH CS
     ERAP1_C   3 llNdddtGyyrVnY.deesl 21 
                 +lNd  +G+yr +Y d++  
  AJA92344.1  92 ILNDRLLGFYRSKYtDPSGK 111
                 69************777655 PP

  == domain 2  score: 200.5 bits;  conditional E-value: 1.3e-62
                 EESGGG-SSSEEEE-HHHHHHHHHHHH.GGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHHHHHHHHHHHTTSTTHHHHH CS
     ERAP1_C   3 llNdddtGyyrVnYdeeslaalleqll.skklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqalsqlatlksllsadplyaalk 100
                 ++N++ tG+yr+ Yd e l++l+  l+ +k+l  +dR ++ +d ++ +  g+ +++d+ld++ +y  +E++y+    + ++l +l+sl  ++++ +++k
  AJA92344.1 506 IINSGRTGFYRMDYDSETLDNLSL-LIdEKILNYVDRWSIQNDYYSQCVTGKKKVQDYLDFTNAY-FDEDNYISSLNLAQHLYSLYSLTHKEKFSDEIK 602
                 79********************99.666***********************************99.5*****999888888888888874555999*** PP

                 HHHHHHHHHHHHHHHH.T..TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHH CS
     ERAP1_C 101 aflrklleplaeklgw.e.pgeshldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdtsapse 197
                 ++  ++l  ++++lgw + ++e h++a+lrs ++s ++++gd+e ++e +++f+++l++++++++dl  +v+  +a +g+e  +++   +yk++++++e
  AJA92344.1 603 QYSFNFLRTIFDRLGWdAkKNEPHTNALLRSFAISGLGKLGDEEILKESKRRFDKFLKNQNSLSADLQETVFVLVAWSGNETTYKKFTSLYKKAKSQEE 701
                 ****************63366***********************************997668*************8889**************9999** PP

                 HHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HSTTHHHHHHHHHHHCHCCHHHHTSSTS.CHHHHHHHHHTT--SHHHHHHHHHHHC CS
     ERAP1_C 198 keaalralaatpdpellerllnfvlesdevrnqdlrallaglannpegrellwefvkenwdalakrwsgge.ildrivkgllpgftseeelaeieaffa 295
                 k + l+a++ +++++ll ++l+f+l +++vr+q++++++  +a n  g e lw ++k+nw++++k+ + g+ +l+r+v ++ +    +++ +ei++ff+
  AJA92344.1 702 KLRFLAAMCNFQQKNLLLKTLEFTL-GPDVRSQNIQMPIMRIAANLYGKEFLWVWLKKNWKKIVKKAGIGNpLLNRVVASIGQVIE-AKQEKEIRKFFK 798
                 ************************9.99**************999*********************99777799999999999887.9999******** PP

                 HTT--GGGHHHHHHHHHHH CS
     ERAP1_C 296 dkdtpglrrtlkqaletvr 314
                 d++ +g + tl+q++e+vr
  AJA92344.1 799 DNPLRGTEMTLEQTMERVR 817
                 *****************98 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   1.3   7.1e-53   2.5e-49       4     186 .]       7     183 ..       4     183 .. 0.93
   2 ?   -1.5   0.0      0.67   2.4e+03      83     108 ..     493     519 ..     452     525 .. 0.58

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 7.1e-53
                     EEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETTCEEEEEEEEEEE-BS CS
  Peptidase_M1_N   4 hYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqtskytLeieyegelnd 98 
                     +Yd+++++ ++++tfkG    +++ + ++++ vl++ ++kik+  ++  +k++ ++++fk+++k+e  l+i  k+++  ++k++L iey+g lnd
      AJA92344.1   7 NYDIQFEPLFSNFTFKGMEILSFKTT-PSNKFVLNCAEIKIKKCYIL--SKNKTIDVNFKLDAKKES-LSIVSKSKV--SGKIKLCIEYTGILND 95 
                     8**********************999.9*************999999..566667789998888888.777777745..59************** PP

                     SSSEEEEEEEEE.TSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCEEEETTCEEEEEEEEEESBEGGG CS
  Peptidase_M1_N  99 klaGlykstYtd.kgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeeeseklengqkiteFeqtpkmstYL 186
                      l G+y+s+Ytd +g++k++++Tqfea+dAR+afPC+DeP+ KAtf++s+ ++k+++a+Snmp++++++ ++ + i+eFe+tp mstYL
      AJA92344.1  96 RLLGFYRSKYTDpSGKTKYMATTQFEAADARRAFPCWDEPATKATFDVSLLVEKNYMAISNMPVRKKQNFGS-KIIYEFERTPIMSTYL 183
                     *****************************************************************9999985.66*************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.67
                     TCEEEEEEEEEEE-.BSSSSEEEEEEE CS
  Peptidase_M1_N  83 tskytLeieyegel.ndklaGlykstY 108
                     +++++L+ + + ++ n  ++G+y+ +Y
      AJA92344.1 493 SQSIKLKNKERNFIiNSGRTGFYRMDY 519
                     333333333333333555556665555 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.1e-06    0.0038     145     189 ..     278     328 ..     268     352 .. 0.77
   2 ?   -0.5   0.5      0.18   6.3e+02     216     312 ..     580     667 ..     547     673 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
    Aminopep 145 lseeelarlifHElaHq......vlYvkgdtafnEsfAtaVeregverwla 189
                   ++ +a++i HElaHq      ++   +d   nEsfAt+++++ v +++ 
  AJA92344.1 278 KTKQFIAEVISHELAHQwfgnlvTMKWWNDLWLNESFATFMATKIVDKFYP 328
                 456679**********9444332334569******************9985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
    Aminopep 216 atrerLealYasdlsaeekraakaeileelraeyaelkaeelkglagydewvakplnNakllavaaYdelvpafealfeeegrdlerfyaaveeLak 312
                 +++++L +lY+ + +++   + k+  ++ lr+ + +l           d+  ++p  Na l  +a     +   e++++e++r++ +f ++ ++L++
  AJA92344.1 580 NLAQHLYSLYSLTHKEKFSDEIKQYSFNFLRTIFDRLGW---------DAKKNEPHTNALLRSFAISGLGKLGDEEILKESKRRFDKFLKNQNSLSA 667
                 466788888888888888888888888888888887775.........3334567788888888888777778888888888888888888777765 PP

>> Med31  SOH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       3.4   1.2e+04      27      47 ..     387     405 ..     383     409 .. 0.55
   2 ?   -1.2   0.0      0.56     2e+03      57      86 ..     521     551 ..     516     560 .. 0.70
   3 ?   10.1   3.0   0.00017       0.6      29      78 ..     554     605 ..     535     615 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
                 SSSSSTHHHHHH.HGGGGGSTT CS
       Med31  27 kyledeafiaYL.kYLeywkep 47 
                 ++++d++f++ L kYL+     
  AJA92344.1 387 NFVTDKNFQKGLqKYLKK---Y 405
                 466677777665235533...3 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.56
                 H.HHHHHHHHSSTTCCCCTCTCHHHHHHHHH CS
       Med31  57 q.cLkaLellqeeefrkelkkpevvealekq 86 
                 + +L  L+ll +e++ + + + ++ +   +q
  AJA92344.1 521 SeTLDNLSLLIDEKILNYVDRWSIQNDYYSQ 551
                 5589999999999988888777666655555 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00017
                 SSSTHHHHHHHGG.GGGSTTCCCTT--CHHHHHHHHHHSSTT.CCCCTCTCH CS
       Med31  29 ledeafiaYLkYL.eywkepeYakfltyPqcLkaLellqeee.frkelkkpe 78 
                 + +++ + YL++   y+ e++Y++ l+  q L+ L  l+++e f +e+k+ +
  AJA92344.1 554 TGKKKVQDYLDFTnAYFDEDNYISSLNLAQHLYSLYSLTHKEkFSDEIKQYS 605
                 5678999******99********************88876554999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (831 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5655.31
//
Query:       AJA92345.1  [L=182]
Description: zinc-ribbon domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-08   32.2   5.0    8.7e-08   31.6   5.0    1.3  1  zinc_ribbon_2   zinc-ribbon domain
    7.3e-05   22.7   0.9     0.0001   22.2   0.9    1.2  1  DZR             Double zinc ribbon
    0.00015   21.0   4.0    0.00027   20.2   4.0    1.4  1  zf-ribbon_3     zinc-ribbon domain
     0.0077   17.0   0.1      0.011   16.5   0.1    1.3  1  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.089   12.8   1.7       0.27   11.2   1.7    1.8  1  DUF1610         Domain of unknown function (DUF1610)
       0.28   11.1   2.1       0.51   10.3   2.1    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.2    8.3   7.9         15    5.7   1.0    3.0  3  YhfH            YhfH-like protein
        3.5    7.6   5.1         24    4.9   5.1    2.2  1  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
        7.9    6.5   7.5        6.2    6.8   1.8    2.2  2  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   5.0   4.4e-11   8.7e-08       2      22 ..     161     181 ..     160     182 .] 0.96

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.4e-11
  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                    C++CGael ++akFC++CG++
     AJA92345.1 161 CTSCGAELRPGAKFCTKCGSK 181
                    *******************86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.9   5.3e-08    0.0001       1      20 [.     161     180 ..     142     182 .] 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.3e-08
         DZR   1 CpqCgeelppdarfCseCgt 20 
                 C +Cg+el+p+a+fC +Cg+
  AJA92345.1 161 CTSCGAELRPGAKFCTKCGS 180
                 66666666666666666665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.0   1.3e-07   0.00027       5      25 ..     161     181 ..     159     182 .] 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
  zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtk 25 
                  C +CGa + ++++++C++CG+k
   AJA92345.1 161 CTSCGAeL-RPGAKFCTKCGSK 181
                  99****66.***********98 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.6e-06     0.011      65      86 .]     158     179 ..     132     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.6e-06
  zinc_ribbon_15  65 kkeCknCgkeveeefkyCpkCg 86 
                        C +Cg+e+ +  k+C+kCg
      AJA92345.1 158 GGNCTSCGAELRPGAKFCTKCG 179
                     678******************9 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.7   0.00013      0.27       1      11 [.     161     171 ..     161     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
     DUF1610   1 CtSCGaelapr 11 
                 CtSCGael p+
  AJA92345.1 161 CTSCGAELRPG 171
                 ********997 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   0.00026      0.51      14      34 ..     161     181 ..     158     182 .] 0.91

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
     DUF35_N  14 CpdCGtvqfPPravCphCgsd 34 
                 C++CG+   P   +C++Cgs+
  AJA92345.1 161 CTSCGAELRPGAKFCTKCGSK 181
                 *******************96 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.4     8e+02       5      12 ..      45      52 ..      42      54 .. 0.81
   2 ?    5.0   0.4     0.012        24      11      23 ..     152     168 ..     150     171 .. 0.74
   3 ?    5.7   1.0    0.0075        15      13      22 ..     172     181 ..     168     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.4
        YhfH  5 veFfrnLP 12
                 eFf++L+
  AJA92345.1 45 KEFFQKLG 52
                69****97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
        YhfH  11 LPkKk....CteCGkei 23 
                 LP+K+    Ct+CG e+
  AJA92345.1 152 LPPKQsggnCTSCGAEL 168
                 777755555*****886 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0075
        YhfH  13 kKkCteCGke 22 
                 +K Ct+CG++
  AJA92345.1 172 AKFCTKCGSK 181
                 799*****85 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   5.1     0.012        24      19      33 ..     167     181 ..     156     182 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
  zf-dskA_traR  19 ralPgarlCveCqek 33 
                   + +Pga++C  C +k
    AJA92345.1 167 ELRPGAKFCTKCGSK 181
                   679*********887 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4     0.053   1.1e+02       3      10 ..     161     168 ..     160     171 .. 0.78
   2 ?    6.8   1.8    0.0031       6.2       1       9 [.     173     181 ..     173     182 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.053
                 -TTT--B- CS
   Nudix_N_2   3 CsqCGtpv 10 
                 C++CG+++
  AJA92345.1 161 CTSCGAEL 168
                 88888877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
                 -B-TTT--B CS
   Nudix_N_2   1 kFCsqCGtp 9  
                 kFC++CG++
  AJA92345.1 173 KFCTKCGSK 181
                 8******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1270.35
//
Query:       AJA92346.1  [L=493]
Description: cytosol aminopeptidase family, catalytic domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-118  396.1   0.1   1.4e-118  395.7   0.1    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    1.2e-19   70.4   0.2    3.3e-19   69.0   0.2    1.7  1  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do
  ------ inclusion threshold ------
       0.12   11.7   3.2       0.14   11.4   0.7    2.0  2  RE_NgoFVII       NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.7   0.1  2.3e-122  1.4e-118       2     310 ..     176     485 ..     175     486 .. 0.96

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 2.3e-122
                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SSTTSEEEEEEEEEEEEEE-TTSS- CS
  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgakekekklalVGKGitfDtGGlslK 97 
                    ++rd++n p+ne+ p+kl e a+++a++++ ++++v++++e+++k++g++ aVg+gS +++pr++ ley++ k+++k++ lVGK++tfDtGG+slK
     AJA92346.1 176 FTRDVANLPPNECPPAKLGEIAKQIANQNK-MKCTVFSKNEIKSKRLGGVTAVGQGS-KNEPRFIILEYRNGKKEQKPILLVGKAVTFDTGGISLK 269
                    79*********************9988887.9*************************.66************************************ PP

                    -HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEE CS
  Peptidase_M17  98 psasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitamnGktvevlnTDaEGRLvLADalayaeekekpdlivdv 193
                    p+++m+emk D++G+++vlg++ka++elklp+nv+a++p +eNm+sg+a++pgd+++ +nGkt e+lnTDaEGRL+LAD+lay  ++++p+ ++d+
     AJA92346.1 270 PGEKMDEMKFDKCGGCTVLGVMKAISELKLPINVIAIVPSVENMPSGDAFRPGDIVKLFNGKTAEILNTDAEGRLILADGLAYGIKHFQPSSVMDF 365
                    ************************************************************************************9999******** PP

                    E---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE----HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSECGEEEEE-TTTT CS
  Peptidase_M17 194 ATLTgavvvalGkkaaglfsnddelaeelekageeagervwrlpleeeykkqlkskvaDlknvgkkrragaitAalFLkefvketpWaHlDiagta 289
                    ATLTga++valG+++ag++sn+ +la++++++++++ e+vw+lp++++y +++kskvaD++n g +r+ag+itAa+FL++ v+++pW+H+Diagta
     AJA92346.1 366 ATLTGACIVALGTNVAGIVSNNAKLASKVKSSSAKTSEEVWELPINDDYMDMVKSKVADIRNLGMGRAAGTITAAAFLANAVGNVPWVHFDIAGTA 461
                    *****************************************************************9999*************88************ PP

                    E...S.BTTB.S.....EE--TTHHHH CS
  Peptidase_M17 290 l...kekealkke...kgatGvgvrtL 310
                    +   +  +++k +   +gatG+gvr++
     AJA92346.1 462 WiqpS--TKSK-SynsHGATGFGVRLV 485
                    97542..2222.23579********87 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.2   5.5e-23   3.3e-19      15     126 .]      33     143 ..      18     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 5.5e-23
  Peptidase_M17_N  15 ekldealagllsellkegdftGkagevlvlralsgekakrvllVGLGkeeeltaealrkaagaaaralkgakvttiavalp.legknsdekaea 107
                       k++++++ ++s+ l  ++++Gk+g+++ +++   ++++r+l+ GLGk+++lt++ +r + g++ +++ ++++++  +  p   + + d++++a
       AJA92346.1  33 GKFNKKIDQTISQSL--QEIKGKKGKIAIIHSHKEISSERILIAGLGKKNKLTSDVIRDVTGNITKKIHELGIKEFTIITPeKISIKNDQVVSA 124
                      567777777777766..589*************************************************************777777779**** PP

  Peptidase_M17_N 108 aaegallglYrfdrykskk 126
                      ++ega l+lY fd yk++k
       AJA92346.1 125 IVEGANLSLYDFDLYKKEK 143
                      ****************987 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.06   3.6e+02      23      77 ..      12      62 ..       8      69 .. 0.80
   2 ?   11.4   0.7   2.4e-05      0.14      88     148 ..     116     175 ..      71     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.06
                HHHHHHHHXXXXSEEEEEEXSHH.HHXXXHHHHHHHHHHHHHHHHCTSEEEEEXSS CS
  RE_NgoFVII 23 selikllkeqsdikitlivGMyp.leglskrlheallklnkklseegigevkvsys 77
                +++ ++l+  s+ ++++ +G    ++++++   ++l +++ k+     g++ ++ s
  AJA92346.1 12 KKKTSILCAFSIEDTNVAIGLGKfNKKIDQTISQSLQEIKGKK-----GKIAIIHS 62
                5566778888999999999998735689999999999999999.....88888766 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.4e-05
                 EET.TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHHHHHH.HXEEGGGSX CS
  RE_NgoFVII  88 kkdgkplsAliGSANlssnglrtrqrEtlvdldtedafkeldeyiqsllsksiskniaeve 148
                  k+++ +sA++  ANls+  +   ++E + + ++  ++ + d+  q+++++si+   a v+
  AJA92346.1 116 IKNDQVVSAIVEGANLSLYDFDLYKKEKSNKKEPDLTLLTSDKNAQKIIKNSITISDA-VK 175
                 4889***********************************************9765433.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3265.75
//
Query:       AJA92347.1  [L=134]
Description: SnoaL-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-05   23.4   0.0    7.2e-05   23.0   0.0    1.4  1  SnoaL_3    SnoaL-like domain
     0.0008   19.6   0.1     0.0018   18.4   0.1    1.7  1  CaMKII_AD  Calcium/calmodulin dependent protein kinase II ass
  ------ inclusion threshold ------
      0.019   14.6   0.0      0.027   14.1   0.0    1.2  1  AMMECR1    AMMECR1
       0.02   15.3   0.0      0.023   15.1   0.0    1.2  1  DUF4440    Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.6e-08   7.2e-05      47     117 ..      55     130 ..       7     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.6e-08
     SnoaL_3  47 rslkqifakgegisfeltdvrvtesgdvawvtelldvtaa..edgteg......egql..rlTgvlrrtdggWkivhhhlS 117
                 +  +  f  +   ++++ +v+v+  g++a+v+ +l  +    +++  +         +  r+T+vl+r+   Wki h+hlS
  AJA92347.1  55 ALEELRFVSISDYDYKINNVKVSIFGETAVVALELVQKGMlvDNK--AftgehiT--IggRATFVLIRQP-TWKIIHIHLS 130
                 55556666777889******************9986643321222..23455334..355*******987.6********9 PP

>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     4e-07    0.0018       4     126 ..       6     131 ..       3     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4e-07
                 HHHHHHHHHHHHHHTT-HHHHHHHEEEEEEEE-GGGTT-EEESSHHHHG.GGS...SSSS-SEEEEEESEEEEEESTTEEEEEE..EEEEEEE-TT... CS
   CaMKII_AD   4 eiiklletlleaisegdfetytklcdpeltvfepevlgnlveglefhrf.yfekllakrkkavrttilnkrvrllgddsAviay..vrlltlldkn... 96 
                 eiik++et+ e  +++  e  +++  ++ ++f  +      +  ++     +e+l       +  +i+n +v ++g+ +Av+a   v+   l+d++   
  AJA92347.1   6 EIIKIIETFFEIGKSKKLEILKDIQIND-SAFSSFSDVPPYDLKDYATTiALEELRFVSISDYDYKINNVKVSIFGE-TAVVALelVQKGMLVDNKaft 102
                 5666666666666666666666555555.5555555555555555443313455555556678889***********.999996224434466653344 PP

                 S-EEEEEEEEEEEEEEETTEEEEEEEEEE- CS
   CaMKII_AD  97 GkkhtrqseetrVwekrdgkWkivhvHrSa 126
                 G++ t   + t+V  +++  Wki+h+H S 
  AJA92347.1 103 GEHITIGGRATFVLIRQP-TWKIIHIHLSK 131
                 9999**********9876.7*******986 PP

>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-06     0.027      59     116 ..      46     100 ..      43     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                 HHHHHHHHHHHT-TTS----HHHHTTEEEEEEEE---EE--GGG--TTT-EEEEEETT CS
     AMMECR1  59 evaenAlaaAfeDpRFspvtaeElpeleveVsvLtepepivledlevgkhGliiekgs 116
                 +++++A + A+e  RF  ++  +++  +v+Vs+ +e   +    le+ ++G++++++ 
  AJA92347.1  46 DLKDYATTIALEELRFVSISDYDYKINNVKVSIFGETAVV---ALELVQKGMLVDNKA 100
                 6899********************************9998...899999999998653 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.1e-06     0.023      52     107 .]      64     124 ..       7     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.1e-06
                 CEEEEEEEEEEEEEEETTEEEEEEEEEEEECC.T.....TEEEEEEEEEEEEEEEETTEEEE CS
     DUF4440  52 aagrslelteeevrvlgdlAvvtgrytfegrg.d.....gepvegrgrftsvwrkegggWri 107
                 + + ++++++++v++ g++Avv+ +   +g+  d     ge+++  gr t+v+ +++ +W+i
  AJA92347.1  64 ISDYDYKINNVKVSIFGETAVVALELVQKGMLvDnkaftGEHITIGGRATFVLIRQP-TWKI 124
                 2334448899*************999998866555556689999************9.6987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 983.81
//
Query:       AJA92348.1  [L=169]
Description: TIGR00725 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-46  155.9   0.6    6.6e-46  155.8   0.6    1.0  1  LDcluster4       SLOG cluster4 family
    0.00052   20.1   0.0     0.0013   18.8   0.0    1.7  1  Lysine_decarbox  Possible lysine decarboxylase
     0.0041   16.4   0.1      0.012   14.9   0.0    1.7  2  LSDAT_prok       SLOG in TRPM, prokaryote
     0.0042   16.4   0.2       0.12   11.6   0.1    2.1  2  DNA_processg_A   DNA recombination-mediator protein A
  ------ inclusion threshold ------
        0.1   12.2   3.6       0.34   10.5   0.1    2.4  2  DAGK_cat         Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   0.6   1.8e-49   6.6e-46       2     157 .]       5     160 ..       4     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 1.8e-49
  LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilvlssdvv 100
                  +i ++G++++++++e +++a++ G+ +A+++ vl+tGg +Gvm+aas+Gak+ gGlt+Gi+p+ ++ + +n+++di+i++G+gl+ R+++++ls+d v
  AJA92348.1   5 RQILIIGNNDNGCTPELEKTAYDAGKHVAESNSVLITGGLGGVMKAASHGAKDGGGLTIGIIPQ-DDASLANEFCDIVIPSGMGLS-RDFLNALSADGV 101
                 5899******88****************************************************.555667777**********99.************ PP

  LDcluster4 101 iaiggrsGTlsEialaleegkpvivlkgtdellseiiekkekder...kvivaespkelv 157
                 i++gg+sGTlsEi+ a+ ++kp+  +k++     +++++++ d+r   k+i  +spk++v
  AJA92348.1 102 IVVGGGSGTLSEICAAYMYKKPIATIKNSG-GMATKYADQYLDHRenvKIIGFDSPKDAV 160
                 ***************************773.45667777777777678999999999986 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.6e-07    0.0013       1      72 [.      48     117 ..      48     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.6e-07
                      HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHH.HHHHHHHHESEEEE-S-SHHHHHHHHHH CS
  Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmee.RkealveladafvilPGGiGTleEllei 72 
                      m+a+++ga + gg +iGiip+  ++   +ne   ++vi + m   R    +  ad+++++ GG GTl E+  +
       AJA92348.1  48 MKAASHGAKDGGGLTIGIIPQDDAS--LANEFC-DIVIPSGMGLsRDFLNALSADGVIVVGGGSGTLSEICAA 117
                      999***************9988776..334555.57777777651555556679***************9765 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.29     1e+03     143     159 ..      31      47 ..      18      74 .. 0.60
   2 !   14.9   0.0   3.3e-06     0.012     127     167 ..     101     141 ..      91     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
  LSDAT_prok 143 svkagrpilvvaGsgrl 159
                 +v++ + +l+  G g++
  AJA92348.1  31 HVAESNSVLITGGLGGV 47 
                 44444444444444433 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.3e-06
  LSDAT_prok 127 tvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaal 167
                 +++v+Gg+ tl++i ++   ++pi  ++ sg++a + a++ 
  AJA92348.1 101 VIVVGGGSGTLSEICAAYMYKKPIATIKNSGGMATKYADQY 141
                 79********************************9976665 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   3.3e-05      0.12      53     104 ..      17      68 ..       1      76 [. 0.86
   2 ?    3.0   0.0     0.015        52     151     187 ..      95     129 ..      85     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.3e-05
  DNA_processg_A  53 aseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                     ++++ +++a +  k++ae++ + + G+  G+ +aa  +a + gg t++++++
      AJA92348.1  17 CTPELEKTAYDAGKHVAESNSVLITGGLGGVMKAASHGAKDGGGLTIGIIPQ 68 
                     788999999****************************************987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
  DNA_processg_A 151 aglseavlvveaaekSGalitaelAlelgrevfavpg 187
                     a  +++v+vv  +  SG+l  + +A  +++++ ++++
      AJA92348.1  95 ALSADGVIVV--GGGSGTLSEICAAYMYKKPIATIKN 129
                     4445677777..4569999999999999999998765 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6     0.035   1.3e+02      50      89 ..      31      67 ..      16      69 .. 0.73
   2 ?   10.5   0.1   9.6e-05      0.34      46      77 ..      91     120 ..      69     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.035
                HHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE CS
    DAGK_cat 50 eakeegvdlivvaGGDGtvsevlnglleelatkpplgiiP 89
                 ++e+  + +++ GG G v ++++  ++  +  + +giiP
  AJA92348.1 31 HVAES--NSVLITGGLGGVMKAASHGAK-DGGGLTIGIIP 67
                44443..778888887777777777666.7999******9 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.6e-05
                 HHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT CS
    DAGK_cat  46 elakeakeegvdlivvaGGDGtvsevlnglle 77 
                 ++++ ++++   +ivv GG Gt+se++ + + 
  AJA92348.1  91 DFLNALSAD--GVIVVGGGSGTLSEICAAYMY 120
                 555566664..78999999*******999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1186.60
//
Query:       AJA92349.1  [L=206]
Description: superoxide dismutase, Mn [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.9e-39  131.6   0.1    1.6e-38  131.0   0.1    1.3  1  Sod_Fe_C     Iron/manganese superoxide dismutases, C-terminal
    2.5e-29  101.6   1.0    3.9e-29  100.9   1.0    1.3  1  Sod_Fe_N     Iron/manganese superoxide dismutases, alpha-hair
     0.0088   15.5   0.1      0.017   14.6   0.0    1.5  2  DNA_gyraseB  DNA gyrase B


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   0.1   2.7e-42   1.6e-38       1     102 []      99     201 ..      99     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 2.7e-42
                 --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHTT-HHHHHHHHGGGBBHHH CS
    Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyqnkradYieafwnvvnWke 98 
                 p+g++a+ai+++fgs+ +fk+ f+++++ ++gsGw+wLv++++ +k+e   ++nq++p +++ +plL+lDvwehAYyl+yqnkr+dYi+a+wnv+nW+e
  AJA92349.1  99 PTGAIADAINDSFGSFAEFKELFSSKTAPIQGSGWGWLVYNPNsGKVEYKAMPNQTSPRTEGLVPLLGLDVWEHAYYLKYQNKRPDYIAAWWNVINWDE 197
                 899**************************************9867****************************************************** PP

                 HHHH CS
    Sod_Fe_C  99 veer 102
                 v++r
  AJA92349.1 198 VNDR 201
                 *986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   1.0   6.6e-33   3.9e-29       1      82 []       3      92 ..       3      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 6.6e-33
                S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCH..HHHCHCCHHHHHH......HHHHHHHHHHHHHHHHHHHHHTB- CS
    Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekl..eeakkkleelvlk......klekalrnnagghvnHslfwknls 82
                ky+Lpe+pYaydaLePhi+++t+e+Hh+kHh+ Y +++N alekl  e+++k++ee+ ++      + ++a+++n+gg+ nH+lfw++++
  AJA92349.1  3 KYTLPEMPYAYDALEPHIDAQTMEIHHSKHHQKYTDGMNGALEKLspELQDKDIEEILSNinqvpdDVKGAINFNGGGYDNHKLFWNSMK 92
                6********************************************888999999**99999999*99*********************96 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.8e-06     0.017      33      95 ..      68     130 ..      30     132 .. 0.79
   2 ?   -2.9   0.0      0.69   4.1e+03      33      57 ..     170     194 ..     154     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-06
  DNA_gyraseB  33 ievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneyakkkkllkkkeekisg 95 
                    v+ a++++ +  +n+  F N+ +++ GG    ++++a+   + ++a+ k+l+ +k + i+g
   AJA92349.1  68 DDVKGAINFNGGGYDNHKLFWNSMKQNGGGEPTGAIADAINDSFGSFAEFKELFSSKTAPIQG 130
                  35999*****99999***************************************999888776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.69
  DNA_gyraseB  33 ievevalqwtssysenilsFvNnia 57 
                  +e ++ l+++++  + i  + N i+
   AJA92349.1 170 WEHAYYLKYQNKRPDYIAAWWNVIN 194
                  6777788899888888888989887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1482.39
//
Query:       AJA92350.1  [L=155]
Description: 50S ribosomal protein L15e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-43  148.9   4.9    1.6e-43  148.6   4.9    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
       0.09   12.8   0.6        4.6    7.3   0.0    2.3  2  KorB_C          KorB C-terminal beta-barrel domain


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   4.9   1.8e-47   1.6e-43      18     147 ..      19     146 ..       6     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 1.8e-47
                     HHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTS CS
  Ribosomal_L15e  18 lrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgrkpkrqgvnklkpakslqaiaeervgrklpnl 112
                      + +lrer++ +r+e+a +r+erp+rl rArrLGYkakqGivv+r+rv  Gg+++  ++ + gr+pk+ gv+++k+  +++++a++rv +k+pn+
      AJA92350.1  19 NSIVLRERAIVWRKEDAATRIERPSRLLRARRLGYKAKQGIVVIRMRVGTGGMRR--QRPRGGRRPKHLGVTRIKQDDNMKTVANRRVLEKYPNM 111
                     45689**************************************************..9************************************* PP

                     EEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTT CS
  Ribosomal_L15e 113 rvLnSYwvgeDgtykyyEvilvDpshkairndkki 147
                     ++L+SY++ +Dg++ +yEvil Dpsh++i ndk++
      AJA92350.1 112 KLLGSYFLYKDGKHYWYEVILADPSHPSIVNDKEL 146
                     ********************************987 PP

>> KorB_C  KorB C-terminal beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2    0.0064        57       7      27 ..      26      51 ..      23      65 .. 0.86
   2 ?    7.3   0.0   0.00051       4.6      24      40 ..      79      95 ..      56     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0064
      KorB_C  7 kpivqVehD.....rrearlllnrrp 27
                ++iv+ + D     +r+ rll +rr 
  AJA92350.1 26 RAIVWRKEDaatriERPSRLLRARRL 51
                89999999999999**********95 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00051
      KorB_C 24 nrrpsseGlawvkydDd 40
                +rrp+  G+ ++k dD+
  AJA92350.1 79 GRRPKHLGVTRIKQDDN 95
                6*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1100.01
//
Query:       AJA92351.1  [L=158]
Description: PF04034 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-35  120.7   0.0    4.2e-35  120.3   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
      9e-07   28.6   0.1    1.7e-06   27.8   0.1    1.4  1  RLI            Possible Fer4-like domain in RNase L inhibitor
  ------ inclusion threshold ------
      0.046   14.0   0.0        0.1   12.9   0.0    1.7  1  Nif11          Nif11 domain


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0     7e-39   4.2e-35       2     126 ..      33     154 ..      32     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 7e-39
                    EE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHHTT-HHHHHHHHTSSTTHH CS
  Ribo_biogen_C   2 vlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyilglkeeaeellskfkwge 97 
                    +l+p+a+k+l +++++    ++i+ +dcsWa +e+v  k++ +   r+LP L+A+NpvnY+k  kL++vEA+a+a +ilg++e +++ll+kf+wg+
     AJA92351.1  33 LLHPFAQKTLFNHEKSS--FNSITGIDCSWALAEDVFQKNF-VGAARKLPPLLAGNPVNYSKINKLTTVEAIAGAAFILGEEELSQKLLEKFNWGH 125
                    68999****99998766..567**********999997777.889*************************************************** PP

                    HHHHHCHHHHHHH.TT--HHHHHHHHHHH CS
  Ribo_biogen_C  98 eFlelnkelleeYakckdseevvevqkey 126
                    +Fleln++ll++Y+k+k++++v+e+ +ey
     AJA92351.1 126 TFLELNENLLHDYQKVKSEDQVNEIIREY 154
                    ***********************998775 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.8e-10   1.7e-06      10      32 ..       4      24 ..       2      29 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.8e-10
                -------TTHHHHHTTSEEEESS CS
         RLI 10 qCdPKKCtgkkcarfcpvrlvrt 32
                q+dPKKCt+ k+++f++++  ++
  AJA92351.1  4 QDDPKKCTAAKLIKFGLAK--KI 24
                9*****************4..44 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05       0.1      16      43 ..     131     158 .]     107     158 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
       Nif11  16 DpalreqlkacsdheevvalAkeaGyef 43 
                 +++l + ++ +++ ++v ++++e+Gy +
  AJA92351.1 131 NENLLHDYQKVKSEDQVNEIIREYGYAI 158
                 899***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1179.30
//
Query:       AJA92352.1  [L=486]
Description: argininosuccinate lyase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-50  172.1   0.0    3.5e-50  171.2   0.0    1.5  1  Lyase_1    Lyase
    2.2e-13   50.8   0.1    1.3e-12   48.3   0.0    2.3  2  ASL_C2     Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
       0.32   11.4   2.7        3.4    8.1   0.4    3.7  4  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0   5.9e-54   3.5e-50      90     312 .]      81     296 ..      35     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 5.9e-54
                 HHHHHTT..HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHH CS
     Lyase_1  90 vigellg..ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerl 186
                 +i +l+     +e  +k ht++S+nDqv++++rl +++ + + Ll+ l + i++l ++a+e+ +++++ +Thlq+A+   +++ l +ya+ l rd+ r+
  AJA92352.1  81 LIESLVIkkTGIENGGKMHTARSRNDQVALDIRLKIRDDI-NILLQCLIETISTLLKTAQENTKTIMPLYTHLQQAQVGVFSHYLLSYADSLLRDLDRF 178
                 333222222448999*************************.77******************************************************** PP

                 HHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTS CS
     Lyase_1 187 kellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaese 285
                 + l+ r+++++lg+g   gt l +d+      ak l+ +++     +ns++a+s+rD+v+e+++  ++++t+Ls+++eD ++ ss e++++els+  ++
  AJA92352.1 179 MSLYGRVNQSPLGAGPVGGTSLPIDRD---STAKLLG-FAS---LVENSIDATSTRDFVAEYVANSAIMMTNLSRLSEDFIIWSSAEFSFIELSDDFTS 270
                 ***************************...9999999.888...9*****************************************************9 PP

                 SC-TTSTTTEBTHHHHHHHHHHHHHHH CS
     Lyase_1 286 pGSSiMPgKvNPvqlElltgvagrvvG 312
                   SS+MP+K+NP+ lEl++g+ ++v+G
  AJA92352.1 271 -PSSVMPQKKNPDILELTRGKTSQVIG 296
                 .8***********************98 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.5     3e+03      36      65 ..       7      36 ..       3      83 .. 0.63
   2 !   48.3   0.0   2.1e-16   1.3e-12       1      52 [.     359     417 ..     359     463 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.5
                T--GGG--HHHHHHH-TT--GGGGGGSSHH CS
      ASL_C2 36 gkeleeltleelkeisplleedveeaLdpe 65
                gk+l+++tl+ + +i++  + ++++++  e
  AJA92352.1  7 GKDLDDITLSYVSSIKDDSDIAFYDIIGSE 36
                667777777777766544333334433333 PP

  == domain 2  score: 48.3 bits;  conditional E-value: 2.1e-16
                 STTHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-.......T CS
      ASL_C2   1 FstATdlADyLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeis.......p 52 
                 F+ A dlA+ Lv + +pFR AH+ivg++v+la +++k l+el+l+e++++        +
  AJA92352.1 359 FLVALDLAENLVLEKIPFRAAHNIVGNLVQLAHNSKKLLSELELSEIESLRikdikstK 417
                 889*********************************************66443344441 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.66   3.9e+03      15      31 ..      97     113 ..      91     126 .. 0.73
   2 ?   -0.1   0.0      0.21   1.2e+03      23      44 ..     128     149 ..     123     157 .. 0.71
   3 ?   -3.3   0.0       2.2   1.3e+04      36      47 ..     174     185 ..     169     187 .. 0.74
   4 ?    8.1   0.4   0.00057       3.4      17      40 ..     461     484 ..     446     486 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.66
   FlaC_arch  15 eletvkkeneelsksve 31 
                 ++ t+++ n+++  ++ 
  AJA92352.1  97 KMHTARSRNDQVALDIR 113
                 79999999999987774 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
   FlaC_arch  23 neelsksveelkenVkdllsLY 44 
                 +e +s+ +++ +en k ++ LY
  AJA92352.1 128 IETISTLLKTAQENTKTIMPLY 149
                 4666777777777777777777 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.2
   FlaC_arch  36 nVkdllsLYEvV 47 
                 +  + +sLY  V
  AJA92352.1 174 DLDRFMSLYGRV 185
                 5678899**877 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.00057
   FlaC_arch  17 etvkkeneelsksveelkenVkdl 40 
                 ++vk++n++++ks++ l+++Vk l
  AJA92352.1 461 KSVKTQNDNVKKSLTFLEKRVKTL 484
                 789******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3367.54
//
Query:       AJA92353.1  [L=423]
Description: homoaconitate hydratase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-93  312.1   3.5      9e-91  305.2   3.5    2.0  1  Aconitase  Aconitase family (aconitate hydratase)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.2   3.5     5e-95     9e-91       2     461 .]       6     414 ..       5     414 .. 0.89

  Alignments for each domain:
  == domain 1  score: 305.2 bits;  conditional E-value: 5e-95
   Aconitase   2 kiwdahlvee....egiayv.pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaak 95 
                 ki+++  +++    ++i +  +d+v+++dv+g+ +l+ +++ +++      +++++    +v++  dh v          +++++   e++  L++++k
  AJA92353.1   6 KILARASEKNtvspDDIVFAkVDKVMVHDVSGPGVLKVFDKLQKQG----IDTSKLHDPSKVWIAEDHFV--------PSAEKISA--ENIVKLSNFSK 90 
                 6655443322233344666679*****************8877766....78888888889999999999........45566666..99999****** PP

   Aconitase  96 afgi.rvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavig 190
                 +++i + ++ g    GI+H    E+ l+ pg + vg+DSHT++ g+lG++a+G G ++++ vll+ ++++k+p++  +kl+Gkl+++v akD +l+vig
  AJA92353.1  91 KYDIkKHFKYGmgqYGICHTLSHEEALVNPGDVYVGGDSHTNTTGALGAFACGLGHTDVAYVLLNGEIWFKVPETYHFKLNGKLPSHVMAKDFILNVIG 189
                 **77445666666799*********************************************************************************** PP

   Aconitase 191 klrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlep 289
                  ++++g+  + + f G+g++++s+e r+T++NM++E+GA+ g+++ d+kt+eYL+  +r +++         ++  e++ d+daey+k++e ++s+lep
  AJA92353.1 190 DIGNDGGAYNTMQFGGTGIDEMSVESRLTLCNMTTEAGAKNGIIESDQKTVEYLT--QRGATN---------VS--EFHGDSDAEYSKTFEYEASELEP 275
                 *******************************************************..775554.........22..3567999**************** PP

   Aconitase 290 svagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvk 388
                 +v+ p++P++ +   ++                           l+ +++d+ +igSCT +++ed+ aaa++l+     g++vk   +t v P+   + 
  AJA92353.1 276 TVSKPFSPDNITVA-RE---------------------------LSSTELDKSYIGSCTGAKYEDLLAAAKILK-----GRQVKI--RTEVLPAAISIY 339
                 ********985554.22...........................2334589***********************.....*99998..************ PP

   Aconitase 389 ayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRq.gpntrayLaSPelvvaaAlaG 461
                 +++ ++Gl ei+ +aG++v  + C+ C+g   + l+++e +vs++NRNF gR+ + ++++yLaSP++++a+A++G
  AJA92353.1 340 KKAVKDGLIEIFLNAGVTVGPPTCGACCGaHMGVLAKDEICVSTTNRNFPGRMgHVESQTYLASPQVAAASAVTG 414
                 *****************************999*********************5589999*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2949.94
//
Query:       AJA92354.1  [L=378]
Description: fructose-bisphosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-147  492.1   0.1   1.2e-147  491.9   0.1    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.9   0.1  6.4e-152  1.2e-147       1     360 [.       2     358 ..       2     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 491.9 bits;  conditional E-value: 6.4e-152
    FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeatevakelklygaGqDlLkda 99 
                 k+t+svikaDvG+++Ght+++++l+++v++++++++  +llid+y+ ++GDD++++m+ht+gvdne++hkla+daf ++t+vak+ +lygaGqDlLkd+
  AJA92354.1   2 KITVSVIKADVGGIGGHTRPSDNLIQAVRDTVNASS--DLLIDHYIGYCGDDVHIVMSHTHGVDNEKIHKLAYDAFVAGTAVAKNEGLYGAGQDLLKDS 98 
                 89******************************9865..59*********************************************************** PP

    FBPase_3 100 fsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklheGfkfevlDvieekkillsapeelydllallgakery 198
                 fsGnvkG+GPgvaelefeeR++e++ vfaaDktepg fn+p+y++f+d+++++Gl+++++l++G++f+++Dv+e    +ls +++   l a l+ ++ry
  AJA92354.1  99 FSGNVKGMGPGVAELEFEERPNEAFTVFAADKTEPGCFNYPMYRLFVDALSNTGLIVNKSLAKGVDFHIMDVEEATIAKLSLWQDKPVLEAALMYPGRY 197
                 *************************************************************************************************** PP

    FBPase_3 199 vikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfql 297
                 vi+++++k d+e+++ +st+rl++iaG+YvGkDDPv+ivR+q+ +Pa++e+ ++f++ph+vaG++rGshn+plmPv+l++a+ t  ++ p+v +l f++
  AJA92354.1 198 VISSITTK-DGEPIMDASTDRLHNIAGTYVGKDDPVCIVRTQKMFPATEEAGSVFNNPHYVAGNTRGSHNMPLMPVKLNSAA-TINFCIPIVQSLVFSM 294
                 *******9.9***********************************************************************9.9999************ PP

    FBPase_3 298 kegklvgpvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYt.tlpevleklkerf 360
                 ++gk++gp D f++p +d++Re+a+ +a  +R+qG+++p++l ++eleY+ ++++v++ lke++
  AJA92354.1 295 HDGKFTGPFDGFSTPDWDYVREQATIKALAIRSQGFIHPATLVPDELEYAeGYKDVMTGLKEKM 358
                 *************************************************9789********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2506.63
//
Query:       AJA92355.1  [L=185]
Description: ribosomal protein L6 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-13   50.1   6.9    2.3e-07   31.4   0.5    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.5   1.3e-11   2.3e-07       1      76 []      15      87 ..      15      87 .. 0.95
   2 !   22.2   1.1   9.1e-09   0.00016       1      76 []      99     173 ..      99     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.3e-11
                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                  iP+gv+v+ k+   ++v Gp g    ++++  vt+e  v ++kv +  +   dk ++   +t+rsli+n  +GV eg
    AJA92355.1 15 IPEGVTVTYKK-PMITVQGPLGKTWKSFKKIpVTIE--VTDGKVLFKAQGTRDKNRA-IMNTSRSLIRNLCEGVVEG 87
                  8*********5.******************878888..66****************9.****************887 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 9.1e-09
                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                   +P+ v+v +k + ++++ G++ +++ +++ +++v  +    k+++++++g   ++v    A+i+   +++n++ +++ +g
    AJA92355.1  99 FPITVKVDGKTVLIENFQGERAPRKTKVWGDTKVV-P----KGDDVIITGHVLTDVsqtaAEIENGSRVKNKDHRVFLDG 173
                   799*******************************9.6....67777777777777777777************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1340.58
//
Query:       AJA92356.1  [L=175]
Description: flavin reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-25   90.0   0.0    1.5e-25   89.8   0.0    1.1  1  FMN_red         NADPH-dependent FMN reductase
    5.9e-11   42.5   0.0    8.1e-11   42.0   0.0    1.4  1  Flavodoxin_2    Flavodoxin-like fold
  ------ inclusion threshold ------
      0.044   13.7   0.0      0.057   13.3   0.0    1.1  1  PS_pyruv_trans  Polysaccharide pyruvyl transferase
       0.19   12.2   1.2        0.7   10.4   0.2    2.0  2  HTH_44          Helix-turn-helix DNA-binding domain of SPT6


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   3.3e-29   1.5e-25       1     152 [.       1     145 [.       1     148 [. 0.88

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3.3e-29
                 -EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS..--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEEEEEECTTCE-HHHHHHHHCH CS
     FMN_red   1 mkilvisGSlrkgsntrklaewaaealkeagaevelidladl.ilpcalcdkdlesegqtsddvaellekiaaadaliivtPeYngsysgllKnalDrl 98 
                 mk++v+sGS+rk++nt+ ++++++e ++++++ev++i+la+        ++ +  +e + ++++ ++ + i++ad+++++ P+Yn ++s++lKn+++ +
  AJA92356.1   1 MKVVVLSGSPRKNGNTQIMMKHVLEYVNQKDVEVKFINLAEDgF-E--SFK-GAANEVNYNEKTLQAAKDITDADVWLVGIPVYNSMFSAALKNIFEFI 95 
                 9****************************************733.3..344.555667899999999******************************** PP

                 T-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETS CS
     FMN_red  99 srtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgk 152
                 +    +ke +gK ++l+ v+gg      ++    q+++++++i+ p+++++ g+
  AJA92356.1  96 N----YKETEGKTAGLAIVAGGTISFGDVQTLFTQLMSYFRVITNPTVVYSTGE 145
                 8....************999997777666666666666********98887766 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.8e-14   8.1e-11       1     103 [.       1      95 [.       1     164 [. 0.81

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.8e-14
                   -EEEEEE--TTGGCCHHHCHHHHHHHHHCCCTTTEEEEEEHHCC.T-----CCCCHCCHHHHTTCHHHHHHH.HHHHHCSSEEEEEEE-BTTB--HH CS
  Flavodoxin_2   1 mkiLiinahprpeksfssalaqafvealekagphevtvrdLyad.flpvlttrdlaaklayeekpadveseq.iekllaadaivlqfPlwwfgvPai 95 
                   mk++++ ++pr+ + ++  + ++++e +++++  ev+ ++L++d f  +          a++e ++++++ q  +++ +ad+ +++ P+++ +++a+
    AJA92356.1   1 MKVVVLSGSPRK-NGNTQIMMKHVLEYVNQKD-VEVKFINLAEDgFESFKG--------AANEVNYNEKTLQaAKDITDADVWLVGIPVYNSMFSAA 87 
                   9***********.6999***************.9*********96633333........333326999999999*********************** PP

                   HHHHHHHH CS
  Flavodoxin_2  96 lKgwiDrv 103
                   lK+ ++ +
    AJA92356.1  88 LKNIFEFI 95 
                   **988866 PP

>> PS_pyruv_trans  Polysaccharide pyruvyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.057       6     125 ..      18     165 ..      17     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                     HHHHHHHHHHHHTT-EEEEEESSTTT--HHHHHHHHHTS-GGGEE.............................................EEE-- CS
  PS_pyruv_trans   6 lilealvklLrelgpdaeiivltpdpsetkkllkvktpilkklskvllkrlrkkdi.............................ddaddviivG 71 
                     +++++++++++++++++++i+l +d  e++k   +   +++k+++  +++  +  +                             + a ++i+ G
      AJA92356.1  18 IMMKHVLEYVNQKDVEVKFINLAEDGFESFKGAANEVNYNEKTLQAAKDITDADVWlvgipvynsmfsaalknifefinyketegKTAGLAIVAG 112
                     67999*************************99999988888877766666555555*****************************8888888888 PP

                     E....EEEETT-HHH.HHHHHHHHHHS-SSEEEE-SEEE......-S-HHHHHHHHHHH CS
  PS_pyruv_trans  72 gdgtlgndgdlsrlp.dalrllflakkagkpviilgqgi....Gpflnealrkllkkil 125
                     g   + ++gd       +  l+ + + + +p++++++g     G++++++++ +l ++ 
      AJA92356.1 113 G---TISFGDV---QtLFTQLMSYFRVITNPTVVYSTGEaiedGKISDDEVKSRLNEMV 165
                     8...3444444...4457889999999999*******9878888888888888777765 PP

>> HTH_44  Helix-turn-helix DNA-binding domain of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00016       0.7      32      84 ..      13      73 ..       6      77 .. 0.70
   2 ?    0.6   0.1      0.17   7.5e+02      32      52 ..      81     101 ..      59     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                -HHHHHHHHHHHHHHHTS---HHHHHHH-GGGSB-SSTTS-............B--HHHHH CS
      HTH_44 32 eeefkeavkkvleFlvkdelEvPfifqhRkdyllhaekeek........kaeklLneddLw 84
                + +++   k+vle+++++++Ev fi      + + +  +++        +a k ++  d+w
  AJA92356.1 13 NGNTQIMMKHVLEYVNQKDVEVKFINLAEDGFESFKGAANEvnynektlQAAKDITDADVW 73
                556677789****************876555544443333366666666666777777777 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                 -HHHHHHHHHHHHHHHTS--- CS
      HTH_44  32 eeefkeavkkvleFlvkdelE 52 
                 ++ f +a k++ eF++ +e E
  AJA92356.1  81 NSMFSAALKNIFEFINYKETE 101
                 567999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1235.17
//
Query:       AJA92357.1  [L=601]
Description: pentapeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.1e-127  412.0 121.3    8.2e-13   47.7   0.9   14.0 19  Pentapeptide     Pentapeptide repeats (8 copies)
    1.6e-66  220.4  24.3    2.2e-12   47.0   2.7    9.1  9  Pentapeptide_4   Pentapeptide repeats (9 copies)
    3.7e-48  161.4  16.6    4.7e-06   26.6   0.4   12.6 11  Pentapeptide_3   Pentapeptide repeats (9 copies)
    3.1e-05   24.0   9.7       0.86    9.6   0.0    5.4  7  CfAFP            Choristoneura fumiferana antifreeze protein 
  ------ inclusion threshold ------
       0.13   12.9   2.0         29    5.4   0.0    4.5  6  Methyltransf_11  Methyltransferase domain
        1.7    8.7   5.6        2.3    8.3   1.1    3.6  3  Cue1_U7BR        Ubc7p-binding region of Cue1
        5.1    6.5   9.5        6.8    6.1   0.8    3.6  3  Peptidase_A4     Peptidase A4 family


Domain annotation for each model (and alignments):
>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   1.2e-13     3e-10       4      38 ..      70     104 ..      70     106 .. 0.76
   2 !   47.7   0.9   3.2e-16   8.2e-13       1      40 []      92     131 ..      92     131 .. 0.98
   3 !   21.0   0.0   7.5e-08   0.00019       1      40 []     132     171 ..     132     171 .. 0.94
   4 !   21.3   1.3   6.1e-08   0.00016       2      38 ..     163     199 ..     162     199 .. 0.94
   5 !   21.5   0.1   5.3e-08   0.00014       5      38 ..     176     209 ..     175     211 .. 0.91
   6 !   35.0   0.0   3.1e-12   7.8e-09       2      40 .]     193     231 ..     192     231 .. 0.98
   7 !   33.1   0.0   1.2e-11     3e-08       1      40 []     212     251 ..     212     251 .. 0.97
   8 !   33.6   0.2   8.7e-12   2.2e-08       2      40 .]     223     261 ..     222     261 .. 0.95
   9 !   36.5   6.4     1e-12   2.6e-09       1      38 [.     257     294 ..     252     296 .. 0.54
  10 !   10.5   0.1   0.00014      0.36      10      39 ..     317     346 ..     316     346 .. 0.92
  11 !   30.0   0.2   1.1e-10   2.8e-07       2      40 .]     344     382 ..     343     382 .. 0.96
  12 !   39.2   0.1   1.5e-13   3.9e-10       4      40 .]     356     392 ..     354     392 .. 0.96
  13 !   46.0   3.7   1.1e-15   2.8e-12       1      39 [.     373     411 ..     373     412 .. 0.96
  14 !   45.5   1.5   1.6e-15   4.2e-12       2      40 .]     384     422 ..     383     422 .. 0.97
  15 !   31.1   0.0   5.2e-11   1.3e-07       2      40 .]     414     452 ..     413     452 .. 0.96
  16 !   28.4   0.2   3.6e-10   9.3e-07       3      40 .]     450     487 ..     449     487 .. 0.94
  17 !   34.7   6.6   3.7e-12   9.4e-09       2      40 .]     474     512 ..     474     512 .. 0.98
  18 !   31.4   5.9   4.1e-11   1.1e-07       1      40 []     483     522 ..     483     522 .. 0.96
  19 !   30.9   3.4   5.9e-11   1.5e-07       2      39 ..     514     551 ..     514     552 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
                   TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                   s+++L+g  L++++l gA+L+gA+lsgAdL+g+nL
    AJA92357.1  70 SDCDLTGVVLRHVSLAGADLSGADLSGADLTGVNL 104
                   57888888888888888888888888888888876 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 3.2e-16
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   A+LsgA+L+g nL ga+ls+A+L g++l++AdL +anL++
    AJA92357.1  92 ADLSGADLTGVNLVGADLSNAKLFGVDLRQADLYQANLED 131
                   8*************************************86 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 7.5e-08
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   A L g++L+ ++++++nl++A+L +A ++++ L ++ +++
    AJA92357.1 132 AVLDGVDLRDTIMEDVNLNNASLKHAYIYKTILADTEFTN 171
                   6799*****************************9999986 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 6.1e-08
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                   +L ++ +++ + s +n++g +Lt+  +++++LsganL
    AJA92357.1 163 ILADTEFTNVDASYSNFCGQDLTKKIFHNTNLSGANL 199
                   688999******************************8 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 5.3e-08
                   T-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   5 gAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                     n++g +L++  + ++nL+gAnl +++++ + L
    AJA92357.1 176 YSNFCGQDLTKKIFHNTNLSGANLAHTKMQYTYL 209
                   68**************************998877 PP

  == domain 6  score: 35.0 bits;  conditional E-value: 3.1e-12
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   nLsgAnL +++++ + l +A L+++n++ + L g+++sg
    AJA92357.1 193 NLSGANLAHTKMQYTYLGNAILYETNFEESYLVGSDFSG 231
                   9*************************************8 PP

  == domain 7  score: 33.1 bits;  conditional E-value: 1.2e-11
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   A+L+++n+++++L g+++sg +L ++n+ g++L  +nL++
    AJA92357.1 212 AILYETNFEESYLVGSDFSGNSLKKVNFKGSNLYSVNLKN 251
                   89************************************86 PP

  == domain 8  score: 33.6 bits;  conditional E-value: 8.7e-12
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                    L g ++sg +L+++n++g+nL+++nl ++dL++a+L++
    AJA92357.1 223 YLVGSDFSGNSLKKVNFKGSNLYSVNLKNSDLTEADLQN 261
                   589**********************************86 PP

  == domain 9  score: 36.5 bits;  conditional E-value: 1e-12
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                   A+L++A++++a+L++anl++A+  g++++ A+ +gan+
    AJA92357.1 257 ADLQNADFTNADLENANLTDAKIFGVDFTSAKINGANM 294
                   45555555555555555555555555555555555555 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.00014
                   CSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide  10 ganLsganlsgAnLtgAnlsgAdLsganLs 39 
                    +nLs+ ++s+++ ++ ++s +++   ++s
    AJA92357.1 317 YSNLSEKDFSNSKINNMDISESKFHKIDFS 346
                   589*********************999997 PP

  == domain 11  score: 30.0 bits;  conditional E-value: 1.1e-10
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   ++s  + s+ ++ +++++g++L+++nl +A L ganLsg
    AJA92357.1 344 DFSKSDMSNNKMAHVDFEGSDLSYTNLVNAELIGANLSG 382
                   79999********************************98 PP

  == domain 12  score: 39.2 bits;  conditional E-value: 1.5e-13
                   TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   4 sgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                     ++++g++Ls +nl +A L+gAnlsg +L ga+Lsg
    AJA92357.1 356 AHVDFEGSDLSYTNLVNAELIGANLSGINLVGADLSG 392
                   579*********************************8 PP

  == domain 13  score: 46.0 bits;  conditional E-value: 1.1e-15
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   A+L gAnLsg nL ga+lsgAnL+++nlsgA+L++a+L 
    AJA92357.1 373 AELIGANLSGINLVGADLSGANLSNSNLSGANLKDAILD 411
                   89**********************************996 PP

  == domain 14  score: 45.5 bits;  conditional E-value: 1.6e-15
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   nL gA+LsganLs++nlsgAnL +A l +++L g++L+g
    AJA92357.1 384 NLVGADLSGANLSNSNLSGANLKDAILDNSKLYGVDLTG 422
                   99***********************************98 PP

  == domain 15  score: 31.1 bits;  conditional E-value: 5.2e-11
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                    L+g++L+ga+L++++++  + +gA ++gA ++g+ +++
    AJA92357.1 414 KLYGVDLTGAYLENTSFKKVDINGAKFNGAYMMGVSFEN 452
                   79***********************************87 PP

  == domain 16  score: 28.4 bits;  conditional E-value: 3.6e-10
                   -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   +++++L++anL+g ++ g n+ g +l+g ++++a L++
    AJA92357.1 450 FENTDLRNANLQGIHMPGQNFKGLDLTGVNFQNAVLKD 487
                   899*******************************9986 PP

  == domain 17  score: 34.7 bits;  conditional E-value: 3.7e-12
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   +L+g+n+++a L+++n++++nLt+Anl  A L+ an+++
    AJA92357.1 474 DLTGVNFQNAVLKDSNFENSNLTDANLDSAYLNSANFKN 512
                   79***********************************87 PP

  == domain 18  score: 31.4 bits;  conditional E-value: 4.1e-11
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   A L++ n++++nL++anl  A L++An+ + d++++ Ls+
    AJA92357.1 483 AVLKDSNFENSNLTDANLDSAYLNSANFKNVDMTNVSLSN 522
                   6799**********************************97 PP

  == domain 19  score: 30.9 bits;  conditional E-value: 5.9e-11
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   +++++ Ls+++L ga+l++AnL++A ++++ +++a+ +
    AJA92357.1 514 DMTNVSLSNTDLGGADLTNANLNSAKIQNSFFKNAKIE 551
                   689********************************876 PP

>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     2e-07    0.0005      25      76 ..      71     123 ..      64     124 .. 0.88
   2 !   23.9   0.0   1.3e-08   3.4e-05       6      72 ..     117     184 ..     112     188 .. 0.71
   3 !   45.3   0.2   2.7e-15     7e-12       3      76 ..     184     258 ..     182     259 .. 0.95
   4 !   28.6   1.8   4.6e-10   1.2e-06      17      77 .]     243     305 ..     242     305 .. 0.90
   5 !   25.6   0.6   3.9e-09   9.9e-06      16      72 ..     318     375 ..     315     379 .. 0.74
   6 !   31.0   0.0   8.4e-11   2.2e-07       4      68 ..     356     420 ..     354     424 .. 0.87
   7 !   45.4   0.0   2.7e-15   6.9e-12       3      77 .]     415     490 ..     413     490 .. 0.93
   8 !   47.0   2.7   8.6e-16   2.2e-12       8      73 ..     470     536 ..     467     538 .. 0.93
   9 !   11.0   0.2   0.00015      0.37      10      44 ..     527     561 ..     525     565 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2e-07
  Pentapeptide_4  25 dcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                     dc++t++ l +v+++ ++ls +d++++dl+ +++ g +l+n+++ +  l+++d
      AJA92357.1  71 DCDLTGVVLRHVSLAGADLSGADLSGADLTGVNLVGADLSNAKLFGvDLRQAD 123
                     89999999999999999999999999999999999999999999776787776 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.3e-08
  Pentapeptide_4   6 csfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.kl 72 
                     + +++++l ++n++ a l + +++++ + +vn+++++l+++ ++++ l++++F++++ + +nf +  l
      AJA92357.1 117 VDLRQADLYQANLEDAVLDGVDLRDTIMEDVNLNNASLKHAYIYKTILADTEFTNVDASYSNFCGqDL 184
                     44556666666666666666666666669999999999999999999999999999999999955345 PP

  == domain 3  score: 45.3 bits;  conditional E-value: 2.7e-15
  Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdid 76 
                     +t   f+n++ls++n+++++++ + + ++ l ++nF+e+ l  +df++++lk+++F+g+nl +vn+++  l+++d
      AJA92357.1 184 LTKKIFHNTNLSGANLAHTKMQYTYLGNAILYETNFEESYLVGSDFSGNSLKKVNFKGSNLYSVNLKNsDLTEAD 258
                     67889*************************************************************886899987 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 4.6e-10
  Pentapeptide_4  17 nFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd..klkdidF 77 
                     n++ ++l+++++te++l+n+ F++++l+++++++++++ + F+   ++++n ++  k k+++F
      AJA92357.1 243 NLYSVNLKNSDLTEADLQNADFTNADLENANLTDAKIFGVDFTSAKINGANMNNvdKTKTDSF 305
                     7899***********************************************965457777766 PP

  == domain 5  score: 25.6 bits;  conditional E-value: 3.9e-09
  Pentapeptide_4  16 vnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdkl 72 
                      n+se ++ ++ +++ ++s+ +F++ ++s++d ++++++++ F+g++l+ +n+ +++l
      AJA92357.1 318 SNLSEKDFSNSKINNMDISESKFHKIDFSKSDMSNNKMAHVDFEGSDLSYTNLvNAEL 375
                     5666777777777777778888888888888888888888888888888888855565 PP

  == domain 6  score: 31.0 bits;  conditional E-value: 8.4e-11
  Pentapeptide_4   4 trcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                       + f++++ls++n+ +a+l+++n+++++l+ + ++ +nls++++++++lk+a + ++ l +v +
      AJA92357.1 356 AHVDFEGSDLSYTNLVNAELIGANLSGINLVGADLSGANLSNSNLSGANLKDAILDNSKLYGVDL 420
                     5689**************************99999999999999999999999888888877766 PP

  == domain 7  score: 45.4 bits;  conditional E-value: 2.7e-15
  Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.klkdidF 77 
                     +  + + ++ l+n++F++++++++ F+++ ++ v+F++++l++++++++++   +F+g +l++vnf +  lkd +F
      AJA92357.1 415 LYGVDLTGAYLENTSFKKVDINGAKFNGAYMMGVSFENTDLRNANLQGIHMPGQNFKGLDLTGVNFQNaVLKDSNF 490
                     667889999*********************************************************6538999887 PP

  == domain 8  score: 47.0 bits;  conditional E-value: 8.6e-16
  Pentapeptide_4   8 fnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklk 73 
                     f++ +l++vnF +a l+d+nF++++l+++n+d++ l++++f +vd++++s+s+ +l ++ + ++ l+
      AJA92357.1 470 FKGLDLTGVNFQNAVLKDSNFENSNLTDANLDSAYLNSANFKNVDMTNVSLSNTDLGGADLtNANLN 536
                     8999*******************************************************99444776 PP

  == domain 9  score: 11.0 bits;  conditional E-value: 0.00015
  Pentapeptide_4  10 ncklsnvnFsearlrdcnFtecrlsnvnFdecnls 44 
                     +++l+n+n++ a+++++ F+++++ nv+ de++ +
      AJA92357.1 527 GADLTNANLNSAKIQNSFFKNAKIENVTIDEATTD 561
                     67888888888888888888888888888877655 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     1e-05     0.026       2      47 ..      70     112 ..      68     113 .. 0.84
   2 !   17.8   0.0     1e-06    0.0027       2      48 .]     110     153 ..     109     153 .. 0.93
   3 ?    0.6   0.2      0.26   6.6e+02      21      34 ..     167     180 ..     155     185 .. 0.60
   4 !    9.1   0.0   0.00055       1.4      11      47 ..     188     222 ..     183     223 .. 0.92
   5 !   26.6   0.4   1.9e-09   4.7e-06       2      47 ..     225     272 ..     224     273 .. 0.92
   6 !   25.5   0.3   4.2e-09   1.1e-05       4      47 ..     247     287 ..     244     288 .. 0.93
   7 !   11.4   0.1   0.00011      0.28       2      38 ..     336     370 ..     316     378 .. 0.74
   8 !   17.9   0.0     1e-06    0.0026       3      46 ..     377     417 ..     370     423 .. 0.80
   9 !   19.4   0.0   3.3e-07   0.00085       3      47 ..     412     453 ..     410     468 .. 0.59
  10 !   24.1   1.0   1.1e-08   2.9e-05       2      38 ..     486     525 ..     460     534 .. 0.57
  11 !   11.9   0.1   7.4e-05      0.19       3      39 ..     527     561 ..     525     563 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
  Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     s++ ++g   +r++   ga + s+ad+++ad+ g++   ++d+s+a
      AJA92357.1  70 SDCDLTGV-VLRHVSLAGA-DLSGADLSGADLTGVNLV-GADLSNA 112
                     67888888.9999999999.999999999999999998.9999887 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1e-06
  Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48 
                     s+a + g  d+r a  ++a + ++a+++++d+++++++ dv++++a+
      AJA92357.1 110 SNAKLFGV-DLRQADLYQA-NLEDAVLDGVDLRDTIME-DVNLNNAS 153
                     78888899.**********.9*****************.*****985 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.26
  Pentapeptide_3  21 asFsnadFgsadFs 34 
                     + F+n d + ++F+
      AJA92357.1 167 TEFTNVDASYSNFC 180
                     33444444444444 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00055
  Pentapeptide_3  11 dFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                      F++++ sga +  ++ ++   + +a+ + +++F+++
      AJA92357.1 188 IFHNTNLSGA-NLAHTKMQYTYLGNAILY-ETNFEES 222
                     59********.9*****************.****986 PP

  == domain 5  score: 26.6 bits;  conditional E-value: 1.9e-09
  Pentapeptide_3   2 sganFsgaadFrgatFsgaa....sFsnadFgsadFsgarFtgdvdFsga 47 
                     +g+ Fsg+ ++ +++F+g+     + +n+d+++ad+++a Ft ++d+++a
      AJA92357.1 225 VGSDFSGN-SLKKVNFKGSNlysvNLKNSDLTEADLQNADFT-NADLENA 272
                     6899****.**********887767*****************.*****98 PP

  == domain 6  score: 25.5 bits;  conditional E-value: 4.2e-09
  Pentapeptide_3   4 anFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     +n++++ d+++a  ++a +F+nad+++a++ +a +  +vdF+ a
      AJA92357.1 247 VNLKNS-DLTEADLQNA-DFTNADLENANLTDAKIF-GVDFTSA 287
                     7999**.**********.******************.****876 PP

  == domain 7  score: 11.4 bits;  conditional E-value: 0.00011
  Pentapeptide_3   2 sganFsgaadFrgatFsgaasFsnadFgsadFsgarF 38 
                     s++ F++  dF+++  s+   + + dF+++d+s ++ 
      AJA92357.1 336 SESKFHKI-DFSKSDMSNN-KMAHVDFEGSDLSYTNL 370
                     56777777.7777777777.57777777777766654 PP

  == domain 8  score: 17.9 bits;  conditional E-value: 1e-06
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsg 46 
                     gan+sg  ++ ga  sga + sn+++++a++ +a+ + ++ ++g
      AJA92357.1 377 GANLSGI-NLVGADLSGA-NLSNSNLSGANLKDAILD-NSKLYG 417
                     7888888.8888888888.888888888888888887.777766 PP

  == domain 9  score: 19.4 bits;  conditional E-value: 3.3e-07
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsga 47 
                     ++ ++g  d++ga  +++ sF+  d+++a F ga +  +v+F+++
      AJA92357.1 412 NSKLYGV-DLTGAYLENT-SFKKVDINGAKFNGAYMM-GVSFENT 453
                     5555555.6666666666.566666666666666665.5555554 PP

  == domain 10  score: 24.1 bits;  conditional E-value: 1.1e-08
  Pentapeptide_3   2 sganFsgaadFrgatFsgaa....sFsnadFgsadFsgarF 38 
                     +++nF+++ ++++a+ ++a     +F+n d++++++s++  
      AJA92357.1 486 KDSNFENS-NLTDANLDSAYlnsaNFKNVDMTNVSLSNTDL 525
                     33444444.44444444443332245555555555555555 PP

  == domain 11  score: 11.9 bits;  conditional E-value: 7.4e-05
  Pentapeptide_3   3 ganFsgaadFrgatFsgaasFsnadFgsadFsgarFt 39 
                     ga +++a ++  a  +++ +F+na +++++ ++a+ +
      AJA92357.1 527 GADLTNA-NLNSAKIQNS-FFKNAKIENVTIDEATTD 561
                     5666777.7777777777.9**************986 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.88   2.2e+03      30      48 ..      47      64 ..      37     120 .. 0.63
   2 ?   -2.5   0.0       1.8   4.6e+03      58      96 ..     103     141 ..      87     150 .. 0.77
   3 ?   -1.2   0.0      0.72   1.8e+03      59      93 ..     139     173 ..     109     200 .. 0.57
   4 !    5.0   0.1    0.0085        22      41     102 ..     246     302 ..     204     305 .. 0.76
   5 ?    1.9   0.3     0.082   2.1e+02      39      70 ..     325     356 ..     292     399 .. 0.46
   6 !    9.6   0.0   0.00034      0.86      16      96 ..     397     477 ..     389     485 .. 0.90
   7 !    9.0   1.2   0.00052       1.3      22      99 ..     478     560 ..     474     569 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.88
       CfAFP 30 anskcvkstltncyidnse 48
                +nsk  ks  t+  i  s+
  AJA92357.1 47 ENSKTDKSFETYMTIS-SQ 64
                5666666666666553.22 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
       CfAFP  58 qysdayvkksvttdcnidksqlygttctgsrydGvyits 96 
                 +  +a + +++   +++++++ly++   ++  dGv ++ 
  AJA92357.1 103 NLVGADLSNAKLFGVDLRQADLYQANLEDAVLDGVDLRD 141
                 556677777777888899999999999999999998775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.72
       CfAFP  59 ysdayvkksvttdcnidksqlygttctgsrydGvy 93 
                   d+ + +    ++ ++++ +y t  +++++  v 
  AJA92357.1 139 LRDTIMEDVNLNNASLKHAYIYKTILADTEFTNVD 173
                 33333444444444445555555555555544443 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0085
       CfAFP  41 ncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstttgt 102
                   ++ ns+l     t ++ ++a  +++   ++n+ +++++g   t+++ +G  ++    t t
  AJA92357.1 246 SVNLKNSDL-----TEADLQNADFTNADLENANLTDAKIFGVDFTSAKINGANMNNVDKTKT 302
                 344444444.....777888888888888889999999999999999999988877666655 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.082
       CfAFP  39 ltncyidnselessictrsqysdayvkksvtt 70 
                  +n  i+n ++  s   + ++s++ + +++ +
  AJA92357.1 325 FSNSKINNMDISESKFHKIDFSKSDMSNNKMA 356
                 22333333333333333333333333333333 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.00034
       CfAFP  16 ssdGscvntnsqisanskcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyits 96 
                  s+ s  n    i +nsk     lt  y++n+  +   +  +++++ay++     ++++++++l g    g +++G+ +t 
  AJA92357.1 397 NSNLSGANLKDAILDNSKLYGVDLTGAYLENTSFKKVDINGAKFNGAYMMGVSFENTDLRNANLQGIHMPGQNFKGLDLTG 477
                 56667788999999********************99999*************************************98875 PP

  == domain 7  score: 9.0 bits;  conditional E-value: 0.00052
       CfAFP  22 vntnsqisanskcvkstltncyidnselessic.....trsqysdayvkksvttdcnidksqlygttctgsrydGvyitsstt 99 
                 vn    + ++s+ ++s lt  ++d + l+s+       t    s++ +  +  t++n++ +++  +   +++ + v+i  +tt
  AJA92357.1 478 VNFQNAVLKDSNFENSNLTDANLDSAYLNSANFknvdmTNVSLSNTDLGGADLTNANLNSAKIQNSFFKNAKIENVTIDEATT 560
                 55555566666666666666666666665544300001333333444444455555555555555555556666666655554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.011        29       7      70 ..      75     142 ..      72     156 .. 0.74
   2 ?    0.9   0.0      0.29   7.5e+02      19      61 ..     222     263 ..     210     277 .. 0.67
   3 ?    1.6   0.0      0.17   4.5e+02      18      53 ..     275     312 ..     264     352 .. 0.78
   4 ?   -2.1   0.0       2.4   6.1e+03       9      29 ..     403     423 ..     378     441 .. 0.61
   5 ?   -2.5   0.0       3.3   8.5e+03      48      61 ..     486     499 ..     438     524 .. 0.59
   6 ?   -1.3   0.0       1.4   3.5e+03      24      66 ..     528     564 ..     500     572 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
                      TSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-....EEEETTEECCCTSS-TT-EEEEEEES- CS
  Methyltransf_11   7 tGrlaealakrgarvvgvDlskemlklakekaseegl....kvefvvadaeklpfednsfDlvvssev 70 
                      tG +++++  +ga++ g Dls + l+ ++  + +  +     v++++ad+ + ++ed+  D v ++ +
       AJA92357.1  75 TGVVLRHVSLAGADLSGADLSGADLTGVNLVGADLSNaklfGVDLRQADLYQANLEDAVLDGVDLRDT 142
                      577777777777777777777777755555444444455577889*************9998866655 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.29
                      SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT- CS
  Methyltransf_11  19 arvvgvDlskemlklakekaseeglkvefvvadaeklpfedns 61 
                      + +vg D+s + lk ++ k+s+ +  v++  +d+++  ++++ 
       AJA92357.1 222 SYLVGSDFSGNSLKKVNFKGSNLYS-VNLKNSDLTEADLQNAD 263
                      5689999999999999888888775.55555555544443333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                      T.SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECC CS
  Methyltransf_11  18 g.arvvgvDlskemlklakekaseegl.kvefvvadae 53 
                        a+++gvD++ + ++ a+++++++      + ++d e
       AJA92357.1 275 TdAKIFGVDFTSAKINGANMNNVDKTKtDSFYEKSDTE 312
                      248999*********99999999887753334445554 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.4
                      HHHHHHHHTTSEEEEEES-HH CS
  Methyltransf_11   9 rlaealakrgarvvgvDlske 29 
                      +++++     ++++gvDl+ +
       AJA92357.1 403 ANLKDAILDNSKLYGVDLTGA 423
                      333333333355666666555 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 3.3
                      TTEECCCTSS-TT- CS
  Methyltransf_11  48 vvadaeklpfedns 61 
                        +++e+ ++ d+ 
       AJA92357.1 486 KDSNFENSNLTDAN 499
                      23333333344444 PP

  == domain 6  score: -1.3 bits;  conditional E-value: 1.4
                      EES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEE CS
  Methyltransf_11  24 vDlskemlklakekaseeglkvefvvadaeklpfednsfDlvv 66 
                       Dl+++ l     ++ + + +  f  a +e++ + +++ D ++
       AJA92357.1 528 ADLTNANL-----NSAKIQ-NSFFKNAKIENVTIDEATTDSCF 564
                      23333333.....322222.34467888888888888877766 PP

>> Cue1_U7BR  Ubc7p-binding region of Cue1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       2.1   5.5e+03       9      24 ..     254     270 ..     246     271 .. 0.74
   2 ?    8.3   1.1   0.00089       2.3       2      27 ..     314     339 ..     313     353 .. 0.89
   3 ?   -1.0   0.0      0.73   1.9e+03       5      25 ..     416     437 ..     414     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
   Cue1_U7BR   9 lne.dlsdedfkeLdie 24 
                 l+e dl+++df++ d+e
  AJA92357.1 254 LTEaDLQNADFTNADLE 270
                 44458889999888887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00089
   Cue1_U7BR   2 LtKFnVdlnedlsdedfkeLdieeRK 27 
                 L+K++   ++d+s+ +++++di+e K
  AJA92357.1 314 LQKYSNLSEKDFSNSKINNMDISESK 339
                 8999999999**************88 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.73
   Cue1_U7BR   5 FnVdlne.dlsdedfkeLdiee 25 
                 + Vdl+   l++ +fk+ di+ 
  AJA92357.1 416 YGVDLTGaYLENTSFKKVDING 437
                 6788877456799******986 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.0     0.017        42     157     203 ..     217     263 ..     162     319 .. 0.69
   2 ?   -0.8   0.2      0.35   8.9e+02     153     182 ..     334     363 ..     273     380 .. 0.58
   3 ?    6.1   0.8    0.0027       6.8     153     191 ..     504     543 ..     476     563 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.017
  Peptidase_A4 157 anFgtvtFtdasattsdgksvglsgatiidie.qngtvltsvevsgds 203
                   +nF++    ++  + ++ k+v+++g++++ ++ +n + lt++++++++
    AJA92357.1 217 TNFEESYLVGSDFSGNSLKKVNFKGSNLYSVNlKN-SDLTEADLQNAD 263
                   56666666666666666666666666666666333.456666666555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.35
  Peptidase_A4 153 lvplanFgtvtFtdasattsdgksvglsga 182
                    +   +F++++F+++ +++++  +v+++g+
    AJA92357.1 334 DISESKFHKIDFSKSDMSNNKMAHVDFEGS 363
                   333456666666666666666666666655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0027
  Peptidase_A4 153 lvplanFgtvtFtdasattsdgksvglsgatiidie.qng 191
                    ++ anF++v++t++s +++d    +l++a++  ++ qn+
    AJA92357.1 504 YLNSANFKNVDMTNVSLSNTDLGGADLTNANLNSAKiQNS 543
                   56689************98888778888887777775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.41
# Mc/sec: 4378.75
//
Query:       AJA92358.1  [L=263]
Description: hypothetical protein T478_1246 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-06   26.4   6.7    0.00018   21.5   1.9    2.3  2  DZR             Double zinc ribbon
    2.1e-05   25.2   2.7      0.014   16.1   0.4    2.2  2  zinc_ribbon_15  zinc-ribbon family
    8.5e-05   22.1   5.2    0.00021   20.9   5.2    1.7  1  zinc_ribbon_2   zinc-ribbon domain
    0.00032   20.7   1.5     0.0014   18.7   1.4    1.9  1  PRC             PRC-barrel domain
     0.0055   16.1   3.7     0.0055   16.1   3.7    2.4  3  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.015   14.6   3.7      0.015   14.6   3.7    2.3  3  zf-RanBP        Zn-finger in Ran binding protein and others
      0.017   15.1   6.7        1.4    9.0   0.3    2.8  2  zinc-ribbons_6  zinc-ribbons
       0.15   12.1   0.3       0.33   11.0   0.3    1.6  1  DUF2199         Uncharacterized protein conserved in bacteria
       0.15   12.5   3.5        1.7    9.2   0.2    2.3  2  zf-CHY          CHY zinc finger
        1.6    8.8   5.8         32    4.6   0.0    3.2  3  Gin             Inhibitor of sigma-G Gin
        3.8    7.5   7.9        3.4    7.7   0.2    3.1  3  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2     0.003       4.9      13      41 ..      60     108 ..      54     113 .. 0.87
   2 !   21.5   1.9   1.1e-07   0.00018       1      22 [.     241     262 ..     239     263 .] 0.92

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.003
         DZR  13 rfCseCgtklkavaa....................edrCpsCgekvdpe 41 
                  +C++C ++ +  ++                    ++ C  C++ + + 
  AJA92358.1  60 YTCNTCEKEFEGSPKiefenpneevaenlvlaergKYLCNGCDATIAEY 108
                 68*******998888999999999******************9987665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-07
         DZR   1 CpqCgeelppdarfCseCgtkl 22 
                 Cp+C+ +++pd++fC+ Cg kl
  AJA92358.1 241 CPSCNFDNKPDSKFCESCGDKL 262
                 9999999999999999999987 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0013       2.1      38      80 ..      60     110 ..      43     112 .. 0.78
   2 !   16.1   0.4   8.6e-06     0.014      56      86 .]     228     259 ..     213     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
  zinc_ribbon_15  38 lacskCkslleaskelgkeiekkesse........kkeCknCgkeveeefk 80 
                     ++c++C++ +e s + + e  ++e +e        k+ C+ C++++ e  +
      AJA92358.1  60 YTCNTCEKEFEGSPKIEFENPNEEVAEnlvlaergKYLCNGCDATIAEYRE 110
                     58**********99666555555555599******9********9987655 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.6e-06
  zinc_ribbon_15  56 eiekkesse...kkeCknCgkeveeefkyCpkCg 86 
                     +ie++   e     +C++C+   ++++k+C +Cg
      AJA92358.1 228 KIEQTV--EvgnGLRCPSCNFDNKPDSKFCESCG 259
                     333332..244689*******************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   5.2   1.3e-07   0.00021       1      23 []     240     262 ..     240     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                    +Cp+C   +++++kFC+ CG +l
     AJA92358.1 240 RCPSCNFDNKPDSKFCESCGDKL 262
                    6*******************765 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.4   8.3e-07    0.0014       6      67 ..     161     214 ..     157     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.3e-07
                 S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCC CS
         PRC   6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigk 67 
                 ++++ G++V++e+ +k+Gk k v +d  +++++ ++ ++ g      +++ i +  ++ +++
  AJA92358.1 161 FRSIFGMDVFDESAKKIGKAKQVGVDA-NQELVLVISDDEG------NDITISWS-RIGTVG 214
                 589********************9*97.6666666666553......89999998.554444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.48   7.9e+02       2       8 ..      59      65 ..      58      70 .. 0.80
   2 ?   -3.1   0.1       3.8   6.2e+03       5      11 ..      98     105 ..      97     107 .. 0.74
   3 !   16.1   3.7   3.4e-06    0.0055       4      26 .]     240     262 ..     238     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.48
  zf-ribbon_3  2 tvrCPnC 8 
                 +++C+ C
   AJA92358.1 59 KYTCNTC 65
                 7899999 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
  zf-ribbon_3   5 CPnCGa.p 11 
                  C+ C+a +
   AJA92358.1  98 CNGCDAtI 105
                  88898855 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 3.4e-06
  zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtkl 26 
                  rCP+C+  + ++d ++C +CG kl
   AJA92358.1 240 RCPSCNFdN-KPDSKFCESCGDKL 262
                  8********.***********776 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.3       1.1   1.7e+03       6      11 ..      61      66 ..      61      67 .. 0.71
   2 ?   -3.1   0.5       3.2   5.2e+03      21      26 ..      98     103 ..      98     104 .. 0.65
   3 ?   14.6   3.7   9.3e-06     0.015       7      25 ..     241     259 ..     240     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                E-SSS- CS
    zf-RanBP  6 dCskCl 11
                +C++C+
  AJA92358.1 61 TCNTCE 66
                588885 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                 -TTT-- CS
    zf-RanBP  21 CvaCqa 26 
                 C+ C+a
  AJA92358.1  98 CNGCDA 103
                 676766 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 9.3e-06
                 -SSS--EEESSSSB-TTT- CS
    zf-RanBP   7 CskClvqNfawstkCvaCq 25 
                 C++C+++N++ s  C++C+
  AJA92358.1 241 CPSCNFDNKPDSKFCESCG 259
                 ******************7 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.3    0.0021       3.4      15      60 ..      58     106 ..      34     110 .. 0.68
   2 ?    9.0   0.3   0.00084       1.4      12      39 ..     234     262 ..     225     263 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                     SEEE-TTT--EEEEEEE-...SSS-S---EEEETTEEEE--TTTT---- CS
  zinc-ribbons_6  15 eqyhCeaCqedlkkealC...peCeqelevlkaCgavdyfCnkcneLiS 60 
                     ++y+C++C+++++  +     +  e+  e l      +y+Cn c++ i+
      AJA92358.1  58 SKYTCNTCEKEFEGSPKIefeNPNEEVAENLVLAERGKYLCNGCDATIA 106
                     6899999999877544331102333344555555555699999987665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00084
                     E-SSEEE-TTT--EEE.EEEE-SSS-S-- CS
  zinc-ribbons_6  12 krgeqyhCeaCqedlk.kealCpeCeqel 39 
                     + g+ ++C +C+ d k   ++C+ C+++l
      AJA92358.1 234 EVGNGLRCPSCNFDNKpDSKFCESCGDKL 262
                     5567899****9855427899****9987 PP

>> DUF2199  Uncharacterized protein conserved in bacteria (DUF2199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3    0.0002      0.33       1      25 [.      61      83 ..      61     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
     DUF2199  1 kCssCgeeheelpslsfraPdayaa 25
                +C++C++e+e++p + f+ P+   +
  AJA92358.1 61 TCNTCEKEFEGSPKIEFENPNE--E 83
                7*******************86..4 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2    0.0011       1.7      19      67 ..      59     108 ..      54     116 .. 0.80
   2 ?    3.8   0.4     0.049        80      42      62 ..     239     260 ..     222     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
      zf-CHY  19 lyaCreCHeele.dhelerlevkevlcllCeteqekavlCkkCkkefaey 67 
                  y+C++C +e e + ++e  + +e ++ +   +++ + lC+ C+ ++aey
  AJA92358.1  59 KYTCNTCEKEFEgSPKIEFENPNEEVAENLVLAERGKYLCNGCDATIAEY 108
                 59******9976355677667777777777778889999******99999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.049
      zf-CHY  42 vlcllCeteq.ekavlCkkCkk 62 
                 + c  C+  + + ++ C++C+ 
  AJA92358.1 239 LRCPSCNFDNkPDSKFCESCGD 260
                 4577777655366667777764 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.027        43      15      26 ..      57      68 ..      55      71 .. 0.86
   2 ?    4.6   0.0      0.02        32      16      28 ..      94     106 ..      89     110 .. 0.88
   3 ?    0.7   0.1      0.33   5.3e+02      18      28 ..     253     263 .]     251     263 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                SS--EEHHHHHH CS
         Gin 15 lgkfICeeCekk 26
                 +k+ C+ Cek+
  AJA92358.1 57 ISKYTCNTCEKE 68
                68999*****98 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                 S--EEHHHHHHHH CS
         Gin  16 gkfICeeCekkiv 28 
                 gk++C+ C + i 
  AJA92358.1  94 GKYLCNGCDATIA 106
                 89******99986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.33
                 -EEHHHHHHHH CS
         Gin  18 fICeeCekkiv 28 
                 + Ce+C +k+v
  AJA92358.1 253 KFCESCGDKLV 263
                 56****99987 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.5   2.4e+03       5      12 ..      60      68 ..      57      70 .. 0.76
   2 ?    7.7   0.2    0.0021       3.4       5      25 ..      95     117 ..      92     118 .. 0.82
   3 ?    3.5   0.2     0.043        71       5      12 ..     254     261 ..     250     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
  zf-dskA_traR  5 s.CeeCGEp 12
                  + C +C ++
    AJA92358.1 60 YtCNTCEKE 68
                  459999887 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
  zf-dskA_traR   5 s..CeeCGEpIpeaRlralPgar 25 
                   +  C +C  +I+e R  + P+ +
    AJA92358.1  95 KylCNGCDATIAEYREFRKPDET 117
                   447************98888765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.043
  zf-dskA_traR   5 sCeeCGEp 12 
                   +Ce CG++
    AJA92358.1 254 FCESCGDK 261
                   5****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1888.26
//
Query:       AJA92359.1  [L=154]
Description: redoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-32  110.0   0.1      8e-32  109.8   0.1    1.0  1  AhpC-TSA   AhpC/TSA family
    5.9e-21   74.7   0.1    7.1e-21   74.5   0.1    1.0  1  Redoxin    Redoxin
     0.0096   15.8   0.0      0.012   15.5   0.0    1.2  1  SCO1-SenC  SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.1   1.3e-35     8e-32       1     123 [.       5     133 ..       5     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.3e-35
                 TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT CS
    AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakayg 99 
                 vgd+ap+fel ++d +  sl+++kgk+vvl f+ ++++pvC+ el+++++ ++++ e+g++vi++s d p++ k+f+ek+++nfp+l D +++++k+y+
  AJA92359.1   5 VGDQAPKFELVDGDLKFRSLDEFKGKKVVLSFFVAASSPVCEVELCKFRDSLNDISELGAQVIAISNDGPFANKAFAEKNNYNFPVLGDYTSQTIKDYD 103
                 8************************************************************************************************** PP

                 -EETT......TTECSCEEEEE-TTSBEEE CS
    AhpC-TSA 100 vlkee......kglalratfvidkegkiry 123
                 +l ++      +++a r++f++d+e+k+ +
  AJA92359.1 104 ILLKDllhvkdYNAAKRSVFILDEEHKVIW 133
                 **999**********************987 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.1   1.2e-24   7.1e-21       2     145 ..       5     148 ..       4     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.2e-24
                 TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHH.HHHHHHHTT-TSEEEE-TTSHHH CS
     Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndaf.vkefwgkeglkfpvlsDgsaaft 98 
                 +gd+aP+f+l  ++ d +  sl+efkgkkvv+ f+ +a +P+C  e++ + + l++  +e g +v+a++ ++ +f  k+f++k++ +fpvl D +++  
  AJA92359.1   5 VGDQAPKFEL--VDGDLKFRSLDEFKGKKVVLSFFVAASSPVCEVELCkFRDSLNDI-SELGAQVIAIS-NDGPFaNKAFAEKNNYNFPVLGDYTSQTI 99 
                 79*******8..55**********************************666666777.*******7765.4444569999999**************** PP

                 HHTT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHH CS
     Redoxin  99 kalGlrleedaseg....lrtpryavidedgkvvylevepepeteesnaea 145
                 k++++ l+           + ++++++de++kv+++ v ++p + e+++++
  AJA92359.1 100 KDYDILLKDLLH-VkdynAAKRSVFILDEEHKVIWKWVSEDPLK-EPDYNE 148
                 ****87665444.359988999999************9999976.888776 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-06     0.012       3      60 ..      11      68 ..       9     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
   SCO1-SenC  3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqp 60
                +Felvd d + ++ ++++gk +++ f+ +    vC ++l + ++ l+++ e +++v +
  AJA92359.1 11 KFELVDGDLKFRSLDEFKGKKVVLSFFVAASSPVCEVELCKFRDSLNDISELGAQVIA 68
                8***********************************************9999776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1032.36
//
Query:       AJA92360.1  [L=165]
Description: 4Fe-4S binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-12   44.5  10.8    3.2e-09   36.2   2.1    2.3  2  Fer4      4Fe-4S binding domain
    1.2e-08   34.9  16.4    9.9e-05   22.4   0.2    2.1  2  Fer4_10   4Fe-4S dicluster domain
    1.7e-08   34.9   6.5    2.8e-08   34.2   6.5    1.4  1  Fer4_7    4Fe-4S dicluster domain
    1.8e-07   31.2  20.5    5.5e-05   23.2  11.6    2.1  2  Fer4_21   4Fe-4S dicluster domain
    8.7e-07   29.3   1.2     0.0038   17.7   0.1    2.2  2  Fer4_8    4Fe-4S dicluster domain
    9.7e-07   28.9   7.0    2.2e-06   27.7   7.2    1.5  1  Fer4_9    4Fe-4S dicluster domain
    7.8e-06   26.7   2.4     0.0032   18.4   0.0    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
      1e-05   25.3   9.8     0.0016   18.4   1.6    2.3  2  Fer4_2    4Fe-4S binding domain
    1.9e-05   24.5  11.8    4.3e-05   23.4   1.7    2.3  2  Fer4_6    4Fe-4S binding domain
    8.9e-05   22.7   8.0      0.012   16.0   0.9    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0013   19.2   9.8      0.028   15.0   0.8    2.2  3  Fer4_17   4Fe-4S dicluster domain
     0.0014   19.3   4.4       0.16   12.8   0.1    2.3  2  Fer4_15   4Fe-4S single cluster domain
     0.0019   18.7   4.0       0.11   13.0   0.1    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.011   16.6   4.1      0.011   16.6   4.1    2.3  2  Fer4_3    4Fe-4S binding domain
      0.025   15.4   5.3       0.27   12.1   0.1    2.2  2  Fer4_22   4Fe-4S dicluster domain
       0.12   12.6   8.9        0.4   10.9   1.2    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.7     5e-05     0.056       6      18 ..      61      73 ..      58      77 .. 0.89
   2 !   36.2   2.1   2.9e-12   3.2e-09       1      23 [.      98     120 ..      98     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                TTSSS-THHHHHS CS
        Fer4  6 ekCigCGaCvevC 18
                + C+gC +C  +C
  AJA92360.1 61 DHCTGCQLCSIAC 73
                89*********** PP

  == domain 2  score: 36.2 bits;  conditional E-value: 2.9e-12
                 EEEETTTSSS-THHHHHSTTTEE CS
        Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                 ++id+ kC++CG+Cv++CP+ A+
  AJA92360.1  98 PQIDYGKCVFCGLCVDACPFYAL 120
                 68******************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  10.9   9.7e-08   0.00011       7      56 .]      61     116 ..      56     116 .. 0.88
   2 !   22.4   0.2   8.8e-08   9.9e-05       3      24 ..      99     129 ..      97     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.7e-08
     Fer4_10   7 dtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 d C++C+ C  aC            +  ++ g++ ++ + +++++kC +cg Cv+aCP
  AJA92360.1  61 DHCTGCQLCSIAC--EGvaeaigmvKVPDKWGQNAKSIMPQIDYGKCVFCGLCVDACP 116
                 78***********..5569**988777777788888889999***************9 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 8.8e-08
     Fer4_10   3 vidddtCirCgkCvkaCPadl.........t 24 
                 +id  +C+ Cg Cv+aCP+++         +
  AJA92360.1  99 QIDYGKCVFCGLCVDACPFYAlymsndyelS 129
                 789999************9776655444440 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   6.5   2.5e-11   2.8e-08       1      50 [.      62     117 ..      62     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.5e-11
      Fer4_7   1 rCigCgaCvaaCp..vkaieldeeenekgt....ekveidpekClgCgaCvavCPt 50 
                 +C+gC+ C  aC   ++ai + ++ ++ g+      ++id+ kC++Cg Cv++CP+
  AJA92360.1  62 HCTGCQLCSIACEgvAEAIGMVKVPDKWGQnaksIMPQIDYGKCVFCGLCVDACPF 117
                 6***********988899999887666554442233499****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.5   5.5e-07   0.00061      33      59 .]      55      82 ..      42      82 .. 0.72
   2 !   23.2  11.6   4.9e-08   5.5e-05       6      53 ..      61     117 ..      60     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.5e-07
     Fer4_21 33 vlkvvedeCvGCnlCssvCP.vedciem 59
                ++ + +d+C+GC+lCs+ C  v ++i m
  AJA92360.1 55 RHMLFHDHCTGCQLCSIACEgVAEAIGM 82
                456789*************436677655 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.9e-08
     Fer4_21   6 dkCigCgkCliaCedtshqai.........eidaktvl.kvvedeCvGCnlCssvCPv 53 
                 d+C gC++C iaCe +  +ai           +ak+++ ++   +Cv C lC++ CP 
  AJA92360.1  61 DHCTGCQLCSIACE-GVAEAIgmvkvpdkwGQNAKSIMpQIDYGKCVFCGLCVDACPF 117
                 89************.78999988776654322333444245578*************6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00045      0.51       3      16 ..      61      74 ..      48      98 .. 0.73
   2 !   17.7   0.1   3.4e-06    0.0038       4      20 ..     104     120 ..     101     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00045
      Fer4_8  3 ekCieCgaCqsaCp 16
                ++C++C++C  aC 
  AJA92360.1 61 DHCTGCQLCSIACE 74
                46666666666664 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.4e-06
      Fer4_8   4 kCieCgaCqsaCpvlrr 20 
                 kC+ Cg+C +aCp++  
  AJA92360.1 104 KCVFCGLCVDACPFYAL 120
                 8************8865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   7.2     2e-09   2.2e-06       2      48 ..      63     117 ..      62     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2e-09
      Fer4_9   2 CtgCgaCveaC..pagvvvedaaerkarlraase......eaCigCgaCveaCpk 48 
                 CtgC+ C  aC   a+++ + +++ k+ ++a+s        +C++Cg Cv+aCp 
  AJA92360.1  63 CTGCQLCSIACegVAEAIGMVKVPDKWGQNAKSImpqidyGKCVFCGLCVDACPF 117
                 ***********8866777777777777766655578889999***********95 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.6     0.005       5.7      52      64 ..      61      73 ..      51      84 .. 0.79
   2 !   18.4   0.0   2.9e-06    0.0032       1      27 [.     104     130 ..     104     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.005
     Fer4_16 52 eaitgCdiCqdvC 64
                 ++tgC+ C  +C
  AJA92360.1 61 DHCTGCQLCSIAC 73
                5677777777777 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.9e-06
     Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiea 27 
                 +C+ Cg C+++CP  a+ + +++e+ +
  AJA92360.1 104 KCVFCGLCVDACPFYALYMSNDYELSS 130
                 59**************99997776654 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.4   0.00023      0.26       8      20 ..      61      73 ..      56      74 .. 0.93
   2 !   18.4   1.6   1.4e-06    0.0016       3      21 ..      98     116 ..      96     117 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
      Fer4_2  8 drCigCgaCvsaC 20
                d+C+gC  C  aC
  AJA92360.1 61 DHCTGCQLCSIAC 73
                89********999 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.4e-06
      Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                 +++d  +C+ Cg Cv+aCP
  AJA92360.1  98 PQIDYGKCVFCGLCVDACP 116
                 799**************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.8      0.01        12       9      21 ..      63      77 ..      60      80 .. 0.81
   2 !   23.4   1.7   3.9e-08   4.3e-05       2      24 .]      98     120 ..      97     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
      Fer4_6  9 CigCgdCvrvCP..e 21
                C+gC  C ++C   +
  AJA92360.1 63 CTGCQLCSIACEgvA 77
                ***********7554 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 3.9e-08
      Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                 ++id+ kC+ Cg Cv++CP++a+
  AJA92360.1  98 PQIDYGKCVFCGLCVDACPFYAL 120
                 78******************996 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.1   0.00063       0.7       2      15 ..      61      74 ..      60      88 .. 0.90
   2 !   16.0   0.9   1.1e-05     0.012       3      16 ..     104     117 ..     102     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00063
      Fer4_4  2 erCigCgsCvaaCP 15
                + C+gC  C +aC+
  AJA92360.1 61 DHCTGCQLCSIACE 74
                56***********8 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-05
      Fer4_4   3 rCigCgsCvaaCPq 16 
                 +C+ Cg Cv+aCP+
  AJA92360.1 104 KCVFCGLCVDACPF 117
                 8999*********6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   2.9    0.0034       3.8      44      57 ..      61      74 ..      38      78 .. 0.83
   2 !   10.7  11.9   0.00053      0.59       2      57 ..      63     116 ..      62     118 .. 0.78
   3 !   15.0   0.8   2.5e-05     0.028       1      22 [.     104     125 ..     104     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0034
     Fer4_17 44 slCieCgeCerkCP 57
                + C++C++C+ +C 
  AJA92360.1 61 DHCTGCQLCSIACE 74
                78999999999996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00053
     Fer4_17   2 CiqCgyClpeCpsyea...ydnepkkllraaklglleeaekeekaslCieCgeCerkCP 57 
                 C++C+ C  +C   ++   + + p+k+ ++ak+     ++ +   ++C+ Cg+C+ +CP
  AJA92360.1  63 CTGCQLCSIACEGVAEaigMVKVPDKWGQNAKS-----IMPQIDYGKCVFCGLCVDACP 116
                 ***********9877644455567777777665.....3344589*************9 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.5e-05
     Fer4_17   1 rCiqCgyClpeCpsyeaydnep 22 
                 +C  Cg C+++Cp+y+ y ++ 
  AJA92360.1 104 KCVFCGLCVDACPFYALYMSND 125
                 6999**********99976654 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   1.2    0.0057       6.4       5      22 ..      60      77 ..      59      84 .. 0.87
   2 !   12.8   0.1   0.00014      0.16       3      20 ..     100     117 ..      99     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0057
     Fer4_15  5 rdaCigcglCvaeapevf 22
                +d C+gc lC  +++ v 
  AJA92360.1 60 HDHCTGCQLCSIACEGVA 77
                699********9998775 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
     Fer4_15   3 vDrdaCigcglCvaeape 20 
                 +D  +C  cglCv+++p 
  AJA92360.1 100 IDYGKCVFCGLCVDACPF 117
                 8999************94 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.8    0.0089        10       4      17 ..      61      74 ..      60      93 .. 0.89
   2 !   13.0   0.1    0.0001      0.11       1      28 [.     100     129 ..     100     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0089
     Fer4_13  4 dtCiacgaCvelaP 17
                d C++c++C  ++ 
  AJA92360.1 61 DHCTGCQLCSIACE 74
                78********9996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
     Fer4_13   1 VDrdtCiacgaCvelaP..dvFeeddegga 28 
                 +D  +C+ cg+Cv+++P   ++  +d +  
  AJA92360.1 100 IDYGKCVFCGLCVDACPfyALYMSNDYELS 129
                 68889************4445555555444 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   5.6     0.034        38       1      11 [.      63      73 ..      63      74 .. 0.96
   2 ?   16.6   4.1     1e-05     0.011       1      15 []     105     119 ..     105     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
      Fer4_3  1 CtgCgaCvevC 11
                CtgC++C  +C
  AJA92360.1 63 CTGCQLCSIAC 73
                ********999 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ Cg+Cv++CP  A
  AJA92360.1 105 CVFCGLCVDACPFYA 119
                 ************765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.3     0.035        39      80      93 ..      61      74 ..      52      77 .. 0.79
   2 ?   12.1   0.1   0.00024      0.27      65      93 ..      88     116 ..      78     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
     Fer4_22 80 sgCvGCgRCieacp 93
                 +C+GC  C+ ac 
  AJA92360.1 61 DHCTGCQLCSIACE 74
                57888888888886 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00024
     Fer4_22  65 rllhklsefkekfgesgCvGCgRCieacp 93 
                 ++ +  ++++ +++  +Cv Cg C++acp
  AJA92360.1  88 KWGQNAKSIMPQIDYGKCVFCGLCVDACP 116
                 5667778889999***************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.2     0.008         9      84     105 ..      62      83 ..      28      92 .. 0.84
   2 ?   10.9   1.2   0.00036       0.4      58      72 ..     102     116 ..      85     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.008
     Fer4_18  84 eciscllcidacdkvmeklgkp 105
                 +c  c+lc  ac+ v e++g+ 
  AJA92360.1  62 HCTGCQLCSIACEGVAEAIGMV 83 
                 6999*********999999875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00036
     Fer4_18  58 agdcidcescvkvcP 72 
                  g+c+ c+ cv+ cP
  AJA92360.1 102 YGKCVFCGLCVDACP 116
                 556666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1186.05
//
Query:       AJA92361.1  [L=544]
Description: cytochrome B(C-terminal)/b6/PetD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-28   97.5  11.9      8e-28   97.5  11.9    2.3  3  Cytochrome_B     Cytochrome b/b6/petB
    6.3e-25   88.1   7.2    6.3e-25   88.1   7.2    3.1  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    1.4e-09   38.2   2.7    1.4e-09   38.2   2.7    3.5  4  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    0.00022   21.7   2.8    0.00022   21.7   2.8    3.6  4  DUF4405          Domain of unknown function (DUF4405)


Domain annotation for each model (and alignments):
>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5  11.9   1.8e-31     8e-28      13     182 ..      42     210 ..      13     216 .. 0.93
   2 ?   -3.6   0.1       1.9   8.5e+03      98     121 ..     305     330 ..     294     332 .. 0.67
   3 ?   -2.3   0.5      0.75   3.4e+03      68      87 ..     423     442 ..     395     451 .. 0.63

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 1.8e-31
  Cytochrome_B  13 iynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglkktrelvWviGvillllvi 109
                   +  lG l+++ +++  ++G +l fyy p ++ a+ sv++i ++v fG+ ir++h  g+  +++l +lh+   ++ g +k + e  Wv+Gvil  ++i
    AJA92361.1  42 FGFLGMLTFITFIILGVSGALLMFYYEPILDRAWDSVEFINNEVPFGFHIRNIHYHGSNAMVMLALLHMYYQYFSGRYKIRNEILWVTGVILGTVTI 138
                   445788999999999999******************************************************************************* PP

  Cytochrome_B 110 vtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffslh.fllPflllillllhl 182
                    +af+Gy + ++  +  a+ + ++l +aiP+ G t+ +  +gs +  d+ + rf++ h f+lP+++l l+ +h+
    AJA92361.1 139 LEAFTGYDIIFSERAELAISIAASLTNAIPIAGPTIRDAAFGSGFS-DF-VLRFYTQHvFVLPIVMLGLMAVHF 210
                   *****************************************99874.45.569*****9**************8 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.9
  Cytochrome_B  98 Wvi..GvillllvivtafiGyvLpwd 121
                   Wv+  G++ l  ++vt++ G+ +p d
    AJA92361.1 305 WVTafGIVGLAQILVTTYWGFYIPID 330
                   44322777777778888888877765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.75
  Cytochrome_B  68 ngasllflllylhifrglll 87 
                   n  sl+f  l+l +f gl+ 
    AJA92361.1 423 NNMSLFFAGLILIVFAGLFH 442
                   34455555555555555443 PP

>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   7.2   1.4e-28   6.3e-25       1     113 [.     100     210 ..     100     225 .. 0.97
   2 ?   -2.2   0.1      0.83   3.7e+03      16      51 ..     291     330 ..     280     334 .. 0.62
   3 ?    0.2   2.7      0.14   6.5e+02      93     163 ..     346     417 ..     306     443 .. 0.63

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 1.4e-28
  Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfGgelpgeallsrly 94 
                      ++m++l+++Hm  ++f G Yk + e+ W++Gv+l ++t+le+f+Gy +++   +  a++++a++++++P+ g+++  + fG  +   + + r+y
       AJA92361.1 100 NAMVMLALLHMYYQYFSGRYKIRNEILWVTGVILGTVTILEAFTGYDIIFSERAELAISIAASLTNAIPIAGPTIRDAAFGSGFS--DFVLRFY 191
                      58**********************************************************************************7..8899*** PP

  Cytochrom_B_N_2  95 alHilllpalllalivahl 113
                      + H+++lp+++l l+++h+
       AJA92361.1 192 TQHVFVLPIVMLGLMAVHF 210
                      ******************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.83
  Cytochrom_B_N_2  16 ftGaYk..kpRelnWii..GvllllltllegflGysLpdd 51 
                      f   Yk   ++   W++  G++ l  +l++ + G  +p d
       AJA92361.1 291 FLDRYKkfSWKDRPWVTafGIVGLAQILVTTYWGFYIPID 330
                      4455553335556676523667777778888888877776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.14
  Cytochrom_B_N_2  93 lyalHilllpalllalivahlllvekkgqtpsrrkek..nvvgeplvpvnavkmlllflvlvallialalinP 163
                      ly++ ill+p  ++    + ++l+++ +   + +k+k  ++v++  +    ++++++ l+ + +++ la++n+
       AJA92361.1 346 LYVVMILLIPLGIGF-SYMMIYLAKEAERKAKLAKDKgpKKVAQIEFSEKWINWIIIALIAFQVFLNLAAYNA 417
                      667777666644443.333334433333333322222223333333344455555666666666665555554 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.69   3.1e+03      70      84 ..      47      61 ..      12      73 .. 0.70
   2 ?   -2.1   0.1         1   4.7e+03      70      87 ..     194     211 ..     174     226 .. 0.73
   3 !   38.2   2.7     3e-13   1.4e-09       8      87 ..     248     328 ..     244     341 .. 0.85
   4 ?    0.9   0.1      0.13   5.6e+02      53      89 ..     384     420 ..     380     438 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.69
                   HHHHHHHHHHHHHHT CS
  Cytochrom_B_C 70 allvvsfvvLgylGv 84
                   +l +++f++Lg+ G+
     AJA92361.1 47 MLTFITFIILGVSGA 61
                   445667777777665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                    HHHHHHHHHHHHHHTS-S CS
  Cytochrom_B_C  70 allvvsfvvLgylGvqpp 87 
                     ++v+ +v+Lg+++v+ p
     AJA92361.1 194 HVFVLPIVMLGLMAVHFP 211
                    567778888887777655 PP

  == domain 3  score: 38.2 bits;  conditional E-value: 3e-13
                    -TT-.---GGGHHHHHHHHCSSSHH.HHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-S CS
  Cytochrom_B_C   8 PahI.aPeWYflpfYaiLraipakl.lGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqpp 87 
                    P+ I +PeWY++  Ya Lr+  +k+  Gv+  g+ i+ ++l+p+ldr k  s + r p+ +++ ++ +++++v +y G   p
     AJA92361.1 248 PPGItVPEWYLTGLYAFLRTQYDKFvTGVLWPGIFIAAIMLVPFLDRYKKFSWKDR-PWVTAFGIVGLAQILVTTYWGFYIP 328
                    444549**************9887626*****************************.99999999999********998554 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.13
                    -SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSC CS
  Cytochrom_B_C  53 skvksiryrkplakvllallvvsfvvLgylGvqppee 89 
                    +kv +i++ +++ ++++++l++  v+L +++ + + +
     AJA92361.1 384 KKVAQIEFSEKWINWIIIALIAFQVFLNLAAYNAALS 420
                    5788999999999999999999999988877766654 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.8     5e-08   0.00022       2      64 ..      45     112 ..      44     114 .. 0.86
   2 ?   -3.4   0.2       3.4   1.5e+04      13      24 ..     126     137 ..     125     149 .. 0.66
   3 ?   -1.4   1.0      0.81   3.6e+03      52      62 ..     200     210 ..     191     210 .. 0.81
   4 ?   -3.0   1.1       2.5   1.1e+04      52      63 ..     433     444 ..     425     445 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5e-08
     DUF4405   2 idlllllsflvlaiSGillsfavlpsgrgaywa.........flglskhqwrdiHeilgllflilvvlHlgl 64 
                 + +l++++f++l +SG ll f + p    a+           f       +r+iH   + +++ l++lH+++
  AJA92361.1  45 LGMLTFITFIILGVSGALLMFYYEPILDRAWDSvefinnevpF----GFHIRNIHYHGSNAMVMLALLHMYY 112
                 56899*****************99988888888**66666652....557********************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.4
     DUF4405  13 laiSGillsfav 24 
                 l ++G++l  ++
  AJA92361.1 126 LWVTGVILGTVT 137
                 568888886654 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.81
     DUF4405  52 llflilvvlHl 62 
                 +++l+l+++H+
  AJA92361.1 200 IVMLGLMAVHF 210
                 78999999995 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.5
     DUF4405  52 llflilvvlHlg 63 
                 +l +++ ++H++
  AJA92361.1 433 ILIVFAGLFHVY 444
                 233444456665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3501.68
//
Query:       AJA92362.1  [L=133]
Description: hypothetical protein T478_0577 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1012.05
//
Query:       AJA92363.1  [L=119]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   43.9   3.6    3.5e-05   23.4   0.3    3.9  4  TPR_1     Tetratricopeptide repeat
      2e-09   36.9   1.3    0.00018   21.4   0.2    3.2  3  TPR_8     Tetratricopeptide repeat
    9.1e-09   34.8   0.1       0.01   15.9   0.0    3.6  4  TPR_2     Tetratricopeptide repeat
     0.0029   17.8   0.1      0.016   15.4   0.1    2.0  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
  ------ inclusion threshold ------
      0.031   14.8   0.0       0.57   10.7   0.0    2.1  2  TPR_19    Tetratricopeptide repeat
      0.041   14.2   0.0        1.8    8.9   0.0    2.4  2  TPR_12    Tetratricopeptide repeat
      0.083   14.0   0.0       0.12   13.4   0.0    1.3  1  SOXp      SOX transcription factor


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00097       2.5      13      23 ..      17      27 ..      14      27 .. 0.88
   2 ?    0.5   0.0      0.24   6.1e+02      25      33 ..      32      40 ..      31      41 .. 0.89
   3 !    9.8   0.0   0.00028      0.71       7      30 ..      45      68 ..      43      68 .. 0.90
   4 !   23.4   0.3   1.4e-08   3.5e-05       2      34 .]      74     106 ..      73     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00097
                HTT-HHHHHHH CS
       TPR_1 13 klgkydeAley 23
                k++kydeAley
  AJA92363.1 17 KKKKYDEALEY 27
                89********8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                HHHHHHSTT CS
       TPR_1 25 ekALelnPn 33
                ek Le++P+
  AJA92363.1 32 EKGLEHDPD 40
                799*****8 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00028
                HHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_1  7 lGnayfklgkydeAleyyekALel 30
                +G +y+ +g++++ ley +k Le+
  AJA92363.1 45 IGTIYYIKGNPEKTLEYMDKTLEI 68
                79***************8888886 PP

  == domain 4  score: 23.4 bits;  conditional E-value: 1.4e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +al  ++ +y++l++ ++ +e+++k  el+P+n
  AJA92363.1  74 DALAIKASVYLNLKNKEKVIECCNKIKELDPKN 106
                 57778999***********************98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0086        22       9      23 ..      13      27 ..      10      27 .. 0.87
   2 !    7.6   0.0    0.0019       4.9       5      30 ..      43      68 ..      39      68 .. 0.87
   3 !   21.4   0.2   7.2e-08   0.00018       2      34 .]      74     106 ..      73     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0086
                HHHHHTT-HHHHHHH CS
       TPR_8  9 siylklgdyeeAkey 23
                +++ k+++y+eA ey
  AJA92363.1 13 RTLVKKKKYDEALEY 27
                7899********998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                HHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_8  5 ynlgsiylklgdyeeAkeyyekalel 30
                + +g iy  +g+ e+  ey+ k le+
  AJA92363.1 43 FIIGTIYYIKGNPEKTLEYMDKTLEI 68
                789****************9997775 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 7.2e-08
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +a+  ++s+yl+l+++e+ +e+++k  eldp+n
  AJA92363.1  74 DALAIKASVYLNLKNKEKVIECCNKIKELDPKN 106
                 68899**************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1    0.0055        14      11      23 ..      15      27 ..      13      29 .. 0.86
   2 ?   -0.7   0.0      0.82   2.1e+03      25      33 ..      32      40 ..      31      41 .. 0.87
   3 !    8.4   0.0     0.001       2.6       3      30 ..      41      68 ..      39      69 .. 0.88
   4 !   15.9   0.0   3.9e-06      0.01       3      34 .]      75     106 ..      74     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0055
       TPR_2 11 yyklgdyeeAlea 23
                + k+++y+eAle+
  AJA92363.1 15 LVKKKKYDEALEY 27
                66899******98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.82
       TPR_2 25 ekAleldPn 33
                ek le+dP+
  AJA92363.1 32 EKGLEHDPD 40
                899*****8 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.001
       TPR_2  3 alynlGlayyklgdyeeAleafekAlel 30
                + + +G +yy +g++e+ le+++k le+
  AJA92363.1 41 IAFIIGTIYYIKGNPEKTLEYMDKTLEI 68
                56789****************9999986 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 3.9e-06
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 al   + +y++l++ e+ +e+++k  eldP+n
  AJA92363.1  75 ALAIKASVYLNLKNKEKVIECCNKIKELDPKN 106
                 5666799***********************97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.061   1.6e+02      64      77 ..      13      26 ..      12      29 .. 0.81
   2 !   15.4   0.1   6.3e-06     0.016       2      78 ..      18      95 ..      17      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.061
                HHHHHTT-HHHHHH CS
      ANAPC3 64 qcllkLkkyeeAia 77
                ++l+k kky+eA+ 
  AJA92363.1 13 RTLVKKKKYDEALE 26
                56788899999985 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.3e-06
                TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
      ANAPC3  2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78
                +++y++A+ ++  + +   ++p+ a+  +  +y  g+ ++ +e+ +k+ ++   +l ++ ++A ++l Lk+ e+ i +
  AJA92363.1 18 KKKYDEALEYGHGIEKGLEHDPDIAFIIGTIYYIKGNPEKTLEYMDKTlEIGMFDLDALAIKASVYLNLKNKEKVIEC 95
                57788888888888888899****************************9999999*****************999876 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.051   1.3e+02       2      43 ..      16      57 ..      15      68 .. 0.75
   2 ?   10.7   0.0   0.00022      0.57       5      58 ..      53     106 ..      49     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.051
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqlde 43
                ++ ++y+eAl++   + +   ++++++     +++  g++++
  AJA92363.1 16 VKKKKYDEALEYGHGIEKGLEHDPDIAFIIGTIYYIKGNPEK 57
                567899999999988888888888888877777777777766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00022
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 g+++  l+++ + l+    +++a++  A ++l+l++ ++ +++++++ e dp++
  AJA92363.1  53 GNPEKTLEYMDKTLEIGMFDLDALAIKASVYLNLKNKEKVIECCNKIKELDPKN 106
                 677777777788777777788899989*************************95 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.063   1.6e+02      15      25 ..      17      27 ..      13      29 .. 0.59
   2 ?    8.9   0.0   0.00072       1.8       9      32 ..      45      68 ..      40      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.063
      TPR_12 15 rlgrydeAlel 25
                + ++ydeAle+
  AJA92363.1 17 KKKKYDEALEY 27
                45566666665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
      TPR_12  9 laavlrrlgrydeAlellekalei 32
                ++++++  g+ ++ le+ +k lei
  AJA92363.1 45 IGTIYYIKGNPEKTLEYMDKTLEI 68
                6999******************98 PP

>> SOXp  SOX transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05      0.12       3      17 ..       8      22 ..       6      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
        SOXp  3 PRRKtKTLlKkdkys 17
                PRR+++TL+Kk ky 
  AJA92363.1  8 PRRRLRTLVKKKKYD 22
                **************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 881.92
//
Query:       AJA92364.1  [L=67]
Description: ribosomal protein S30 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-11   42.9   3.6    5.5e-11   42.5   3.6    1.3  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   3.6     3e-15   5.5e-11       2      53 ..       3      53 ..       2      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3e-15
                   TBX-STTTTHHHHHS-------------THHHHHHHHHHHTTSSS--SSSSS CS
  Ribosomal_S30  2 vhGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvnvvvggkkkk 53
                    hGsL++AGKVr+qTPKve   k      + + +  + +Rfv +  g ++k+
     AJA92364.1  3 THGSLTKAGKVRGQTPKVEGR-KIVGTNSKLRNKSNFRKRFVLAEIGLGGKM 53
                   6******************99.6666777888889********988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.51
# Mc/sec: 393.39
//
Query:       AJA92365.1  [L=781]
Description: universal stress family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-43  148.5  53.3    3.9e-43  147.9  53.3    1.3  1  AA_permease_2   Amino acid permease
    1.4e-35  122.8  46.4    1.9e-35  122.4  46.4    1.1  1  AA_permease     Amino acid permease
    2.1e-07   30.9   4.4    2.1e-07   30.9   4.4    3.6  5  AA_permease_C   C-terminus of AA_permease
    7.6e-06   26.5   0.0      0.003   18.1   0.0    2.3  2  Usp             Universal stress protein family
  ------ inclusion threshold ------
       0.16   12.2   0.1        0.3   11.3   0.1    1.4  1  DUF2560         Protein of unknown function (DUF2560)
        5.1    5.8  26.9      0.019   13.8   6.9    3.4  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.9  53.3   1.3e-46   3.9e-43       1     399 [.      14     422 ..      14     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 1.3e-46
  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvlas 94 
                    lsl + +++ + s+ig +ifv    ++a +g+al++ +++  +i+ +  +l+yaEl+sa+p  gG y +++++ +++ a+ls+w++wf+  ++ ++
     AJA92365.1  14 LSLKDSIMIGVASMIGGAIFVLVgpGMAQAGAALMIAFLLNGIIT-VFTALTYAELGSAFPATGGGYKWVREGLPRPNAYLSGWMAWFGHTIAGSL 108
                    6889999*********888887667***************99999.6899******999************************************* PP

  AA_permease_2  95 ilsvaasyllnalgp...dlqgntwlt.yliaiaililvalinirgikesakiqnilgilkillpliiliilglitv...dgggfsslstetdtff 183
                    ++++++s+++++l+     ++++ +++ +++a++ +i+++++n+rg + ++k+ n ++ + +  ++ ili++++ +    ++++++    + + f+
     AJA92365.1 109 YAVAFGSFFAHLLKTsgvIGDDTGIPVdKILAVIAIIIFTFVNVRGSSDTGKVGNAITFTQL-AIIGILIVAAIGAMmfaNPNWSD----NYTDFL 199
                    ************9766667777888777999******************************9.58899998888887333446665....3446** PP

  AA_permease_2 184 pngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvlyllvniaflgvvpddei.....anlsnlgsvaalffeavggkvv 272
                    p+g  g +l+++ ++ +f G+e +++  +e  ++kk++p+ai i+l+iv+ +y+l++++f+g+++ + i     + ++++g+++ + ++  + +++
     AJA92365.1 200 PSGVAGLALAMGLTFIAFEGYEIISQAGDEirNPKKNIPRAILISLGIVVSVYILFTFVFIGGLNESVIgmpawEFIGSFGELGIIEAADQFMPFG 295
                    ******************************666669*********************************8888766666666665555555569** PP

  AA_permease_2 273 aiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisylllii 367
                    a iv +++ +s l a+n+ ++++srv +a++++  lP +f+k++ k+ +p++a+i++ i+ lil++ + +   +   + +++s+++l+++  ++++
     AJA92365.1 296 ALIVLAGGLVSTLSALNATTFAASRVSFAMGTQYNLPFVFSKIHpKYRTPFVATIVSGIIMLILAV-S-M---DLTAIAFAASVMFLFLFTQVNLA 386
                    ************************************************************866542.2.2...33345555555555555555565 PP

  AA_permease_2 368 galilr.kkrphl...krpgkilvaiigalfllfll 399
                    +  i r + + ++   k+p ++l+ iig++++  l 
     AJA92365.1 387 SITIRRlYASTVEygfKTPLFPLIPIIGIVTAMGLS 422
                    555555322233334466777766666665544332 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4  46.4   6.4e-39   1.9e-35       2     473 ..      19     454 ..      18     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 6.4e-39
  AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasi 99 
                   ++i ++++iG ++fv  g   +qaG  ++++a+ll g+++++++l+ +e+ +++p +gg y+++++ l +  ++  G++ +f   ++      ++ +
   AJA92365.1  19 SIMIGVASMIGGAIFVLVGPGMAQAGA-ALMIAFLLNGIITVFTALTYAELGSAFPATGGGYKWVREGLPRPNAYLSGWMAWFGHTIA------GSLY 109
                  69*************************.999*************************************************55555555......5555 PP

  AA_permease 100 liqfwelvtdlpkawvt..........gavflvvlliinlvgvkvygeaefi..lalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknn 185
                   + f +++ +l+k+ ++           ++ +++++i+++v+v+++  +  +  ++ +  +aii+ +iv +i+ +  +  +     +++dn++   ++
   AJA92365.1 110 AVAFGSFFAHLLKTSGVigddtgipvdKILAVIAIIIFTFVNVRGSSDTGKVgnAITFTQLAIIGILIVAAIGAMMFA--NP----NWSDNYT---DF 198
                  555555555555555555556689999556666666667777777777666656777788999999999977777777..33....5789999...9* PP

  AA_permease 186 lppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa....aspfvif 279
                  lp+g        +++ + ++   + af G+e++  +++E+++P+k+iP+ail  + +++ +Y+l++++ + +++ +  g  +    +    +++++ +
   AJA92365.1 199 LPSG--------VAGLALAMGLTFIAFEGYEIISQAGDEIRNPKKNIPRAILISLGIVVSVYILFTFVFIGGLNESVIGMPAWEFIGsfgeLGIIEAA 288
                  ****........***********************************************************999999999997777776666666666 PP

  AA_permease 280 ikesgvsvlaplinaviltaalssansslysasRvlyslakdglaPkvl.kkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisalig 376
                   ++  +++ a ++ a+ l+++ls++n+ +++asRv +++  +  +P+v+ k + k++ P +a ++s ii l++ + + l+++          ++ +++
   AJA92365.1 289 DQF--MPFGALIVLAGGLVSTLSALNATTFAASRVSFAMGTQYNLPFVFsKIHPKYRTPFVATIVSGIIMLILAVSMDLTAI--------AFAASVMF 376
                  555..788899***********************************66616679*************************999........33455778 PP

  AA_permease 377 livwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvklhvknk 473
                  l++++ ++l+++ +R+    +   + e gfk++l+pl++i++++  + + + l ++ +                ++ + ++++ i +v++k+++++k
   AJA92365.1 377 LFLFTQVNLASITIRRL---YASTV-EYGFKTPLFPLIPIIGIVTAMGLSIYLLFTHP---------------ESWLIAIIWIAIGFVIYKFYTSKK 454
                  999*********99998...44434.99***********9998777666666666633...............359999999999999999998876 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.83   2.5e+03      21      47 ..      11      37 ..       8      38 .. 0.81
   2 ?   -3.8   0.2       4.8   1.4e+04      36      48 ..     140     152 ..     138     154 .. 0.66
   3 ?   -4.1   0.7         6   1.8e+04      36      42 ..     171     177 ..     165     186 .. 0.45
   4 ?   -3.8   1.0       4.8   1.4e+04      12      22 ..     245     255 ..     241     259 .. 0.61
   5 !   30.9   4.4   7.1e-11   2.1e-07       1      49 [.     402     453 ..     402     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.83
  AA_permease_C 21 mlqLdsltwirfgvwmliglliYflYg 47
                   + +L+ +  i++gv  +ig  i++l+g
     AJA92365.1 11 VRSLSLKDSIMIGVASMIGGAIFVLVG 37
                   567777888999999999999999876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.8
  AA_permease_C  36 mliglliYflYgi 48 
                     +i ++i+ ++ +
     AJA92365.1 140 AVIAIIIFTFVNV 152
                    5677888877665 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 6
  AA_permease_C  36 mliglli 42 
                     +ig+li
     AJA92365.1 171 AIIGILI 177
                    3444443 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 4.8
  AA_permease_C  12 lsIlvNiyLml 22 
                    l+I+v +y+++
     AJA92365.1 245 LGIVVSVYILF 255
                    45666666654 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 7.1e-11
  AA_permease_C   1 FkvPlvPflPalsIlv....NiyLmlqLdsltwirfgvwmliglliYflYgir 49 
                    Fk Pl P++P+++I++     iyL++ ++  +w+ +++w++ig++iY +Y  +
     AJA92365.1 402 FKTPLFPLIPIIGIVTamglSIYLLF-THPESWLIAIIWIAIGFVIYKFYTSK 453
                    9*************972222456655.57789******************765 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     1e-06     0.003       4     108 ..     475     571 ..     474     574 .. 0.91
   2 !    6.0   0.0    0.0053        16       1      44 [.     604     646 ..     604     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                 EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHHT CS
         Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaeee 102
                 r+l ++ +  ++ k  ++A   ak++++e+++l v+  +++++ s       +  ++ ee ++e         +   ++ +v++ +dp e+il++ ee+
  AJA92365.1 475 RVLMVF-DKRSAAKMYKMARSIAKDKDGEITVLDVVNVPRQTPLSLTHGFGDKGLKAIEEFKREI-------TGSLRNRYLVRLAHDPTEAILQTTEEQ 565
                 677788.566677889********************************************99986.......58************************* PP

                 TSSEEE CS
         Usp 103 dadliV 108
                 d++ ++
  AJA92365.1 566 DINTLL 571
                 *99876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0053
                 S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHC CS
         Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidpras 44 
                 m k+I+Va+D+  +s+  le A  + k+ ++++++++ + ++++
  AJA92365.1 604 M-KNIVVAYDKGRHSDLGLEIANSFQKMEESKIRIIRGVIEDPK 646
                 5.9**************************9*9999885444444 PP

>> DUF2560  Protein of unknown function (DUF2560)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.9e-05       0.3      10      69 ..     634     693 ..     627     696 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
     DUF2560  10 kLelykLvlnqnAAAeeAfqFigtDeLkleLFkihyqkggansdivaRtveAvRkakeaL 69 
                 k+ + + v+ +     e ++ i++    leL ki+++k  ++s+i++  ++  +k k+aL
  AJA92365.1 634 KIRIIRGVIEDPKQETEIVNRINEKMFELELPKIQFEKVYSDSNIITELLKNFKKEKNAL 693
                 55677888888888888999999999*****************************99998 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.1    0.0019       5.6       6      62 ..      18      74 ..      13      79 .. 0.88
   2 ?   13.8   6.9   6.2e-06     0.019     128     292 ..     150     321 ..     131     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0019
  Spore_permease  6 qlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe 62
                      +++ v+ ++G +i +l++   +qa++   i+ ll gii ++ +l++ +l + fp 
      AJA92365.1 18 DSIMIGVASMIGGAIFVLVGPGMAQAGAALMIAFLLNGIITVFTALTYAELGSAFPA 74
                    556666899*****************99999*******************9998885 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.2e-06
  Spore_permease 128 lvvkGieslar...eflfiivilliilllillfslklaei...knlrPvlgngikpvlkslkttslsflgveillllvpflkdkk.kvkkaallg 215
                     + v G ++  +    + f  + ++ il++  +  + +a++   +n +  l +g+  +  ++  t ++f g ei+      ++++k ++ +a+l++
      AJA92365.1 150 VNVRGSSDTGKvgnAITFTQLAIIGILIVAAIGAMMFANPnwsDNYTDFLPSGVAGLALAMGLTFIAFEGYEIISQAGDEIRNPKkNIPRAILIS 244
                     4444444444433333333333444444444444444443223799999999999999999***************9999988651688****** PP

  Spore_permease 216 vlistllyllttlivilvlsveqlkkatwptlsllkvievpefierlevllivvwilvifakialylyaavlgisev 292
                     ++i++++y+l t++ i+ l +  +    w ++  +  + + e  +++  ++ ++++ +++ +++  l+a+ +  s+v
      AJA92365.1 245 LGIVVSVYILFTFVFIGGLNESVIGMPAWEFIGSFGELGIIEAADQFMPFGALIVLAGGLVSTLSALNATTFAASRV 321
                     *****************************************9********************999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.55
# Mc/sec: 4312.96
//
Query:       AJA92366.1  [L=433]
Description: ergothioneine biosynthesis protein EgtB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-45  155.2   2.0    3.3e-45  154.7   2.0    1.2  1  FGE-sulfatase  Sulfatase-modifying factor enzyme 1
    6.7e-11   42.8   0.3    2.6e-10   40.9   0.3    2.0  1  DinB_2         DinB superfamily


Domain annotation for each model (and alignments):
>> FGE-sulfatase  Sulfatase-modifying factor enzyme 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.7   2.0   3.7e-49   3.3e-45       3     260 .]     174     431 ..     172     431 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 3.7e-49
                    TTEEEE-SEEEEES-.TSTTGGCCC-S-EEEEES-EEEESS--BHHHHHHHHHHH....H................SSETTEEEEETSCTTBCCTT CS
  FGE-sulfatase   3 pemvlipgGsfemGs.eektandeeapahevtvraFaidkteVTnaqyaafveatgyete................aasqwwaeveganvrhpegr 81 
                    ++ + i+gG +++G+  ++  +d e p h+  ++++ id+   +na+y +f+++ gy++                 +a+  w++ eg ++ +++  
     AJA92366.1 174 KKSIKINGGLYNLGYsGKDYCYDIELPEHKTYLNDYQIDNLLTSNAEYLEFIQDGGYDDYsfwlsdgwdivkknewKAPMYWEK-EGDDWITRDF- 267
                    57899*********999999**************************************88**9999999999987545555555.4555555543. PP

                    C-SSTT-TTSB--S--HHHHHHHHHHHCHHHTS-EE---HHHHHHHHHTT-...SSSSCTTBSTTSCCGB...SSTTTTB--TTCGGS-SS.---T CS
  FGE-sulfatase  82 ksdikkradhPvvhVsweDavaYArwlgkktgegyrLPteaEweyAArggk...kgreypwgdelkpakniwqGslakfekeaaaadsqngrtspv 174
                    + ++k ++d+Pv hVs+++a aY++w++k      rLPteaEwe+AA + +    ++ +pwg+e+              e  a+  +s+ ++ s+v
     AJA92366.1 268 AGKRKINPDEPVCHVSYYEAAAYCKWANK------RLPTEAEWEKAALWNDekeVKTIFPWGNEKP------------TELHANLLESSIWNCSDV 345
                    457899***********************......************9988665567789999955............567778888999999*** PP

                    T-S-B..-TTS-B-TTCSSEEEEEEE--THC.CH-SSCS----SS-SSEEEEC--TTS.TTGGCTSTT-E.EEE-TT--BTTEEE--EE CS
  FGE-sulfatase 175 gsfpp..nalGlyDmaGNvwEWtsdwykkya.lapaeelsqeaekgelrvvkGgswlkaelssllraafrasaetpdtaasdvGfRlvr 260
                    g++++  +++G+y+m+G+vwEWts+++ +y  +++  +  ++++ ++++v++Ggs+ +   s+++r + r ++   d +    GfR+v+
     AJA92366.1 346 GAYEDgkSSYGCYQMIGDVWEWTSSEFMGYPgFKSGFDEYNDKWFTNQKVLRGGSFGTP--SRSIRGSYR-NFFRLDERWLISGFRCVK 431
                    *****99*********************666155577899999**************95..899******.66679999999*****96 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.3   2.9e-14   2.6e-10       2     126 ..      15     144 ..      14     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.9e-14
      DinB_2   2 lerararllalledlteeelnrqpspgkwsiawllaHlgnveelllerlr.....................geeaprpgldpltppsaaealaylaevr 79 
                 ++++r+++l+l+++l  +++  q + +++++ w+++H+ + +e++l +                       g++++ +++     p+++e+l+y++   
  AJA92366.1  15 FNETRNTTLQLVKNLERDDFGVQTAVFMSPPKWHIGHVSWLNEIVLSKTQdnyqffsdelseylnsyynqfGKPHDKSKRGVMSRPTVDEILEYFDVIT 113
                 689***********************************************99999998888888888888887888777777777************** PP

      DinB_2  80 arllallealtdadldrpltaphpglgkltlgdvllfvlqHeqhHle 126
                 +r+++++++    +l+     +         + ++ ++++He +H e
  AJA92366.1 114 NRVREVISR----PLE----KE--------TAYLFTMAIHHECQHQE 144
                 *********....222....22........34689999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3208.63
//
Query:       AJA92367.1  [L=164]
Description: putative nicotinamide-nucleotide adenylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   51.4   0.2    7.6e-12   45.6   0.2    2.1  2  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.047   13.4   0.0       0.22   11.2   0.0    1.9  2  Citrate_ly_lig   Citrate lyase ligase C-terminal domain
       0.05   12.8   0.2        5.6    6.1   0.0    2.2  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
      0.055   13.5   0.1       0.95    9.4   0.0    2.1  2  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.2   1.7e-15   7.6e-12       2      55 ..       5      56 ..       4      68 .. 0.93
   2 !    4.3   0.0    0.0096        43     102     142 ..      75     132 ..      57     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.7e-15
                     EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHH CS
  CTP_transf_like  2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRleml 55
                     + G+F+p+HlGHl+ ++ a++++e  l vg+ s+++++ k +++++a+eR +m+
       AJA92367.1  5 LIGRFQPFHLGHLEAIKFALSKVEH-LHVGIGSSNKSHEK-RNPFTADERKKMI 56
                     68***********************.************88.************8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0096
                      HHHHHHHHHHHEEEEEE.................HTTCEEEEEEECCTTTCSHHHHHH CS
  CTP_transf_like 102 eleeilgnvklvvvsrp.................ekqanvllkaekrtngiSstkire 142
                      ++++  ++ +lv + +p                 ++ + ++  + k +++ S+t ir+
       AJA92367.1  75 DVDDHSKWTHLVDETIPqydvvfsnddfthelygKRGKSIIAVDLKSRSDLSGTNIRN 132
                      777788888888888888888888889999999899999999999***********96 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     5e-05      0.22       8      55 ..       9      61 ..       2      76 .. 0.77
   2 ?    0.0   0.0      0.13   5.8e+02     148     180 ..     120     150 ..      97     152 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5e-05
  Citrate_ly_lig  8 anPftlGhryLvekaakendvvhlfvvkedksl.....fsyeerlklvkkGik 55
                      Pf lGh   ++ a ++ +++h+ + + +ks+     f+++er+k++ + ++
      AJA92367.1  9 FQPFHLGHLEAIKFALSKVEHLHVGIGSSNKSHekrnpFTADERKKMILSSMN 61
                    57************************9887765444449999*****988764 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
  Citrate_ly_lig 148 keeelisaskvrkllkeknleklaelvPkttle 180
                     k+ + +s +++r+l+ + +  + ++++P++t e
      AJA92367.1 120 KSRSDLSGTNIRNLILTDQ--NWKQFLPSGTVE 150
                     4556689999999875442..346788888876 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.003        13       7      27 ..       6      26 ..       2      38 .. 0.80
   2 ?    6.1   0.0    0.0012       5.6     202     237 ..     123     155 ..     109     164 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.003
  HIGH_NTase1  7 IaEYNPfHnGHlyhlekakel 27
                 I  + PfH GHl  ++ a ++
   AJA92367.1  6 IGRFQPFHLGHLEAIKFALSK 26
                 56689*******999877665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
  HIGH_NTase1 202 eiaSAtaiRkalkeekkleelkklvPestleilkee 237
                  +  S t+iR+++ ++   ++ k+++P+ t+e+l++ 
   AJA92367.1 123 SDLSGTNIRNLILTD---QNWKQFLPSGTVEVLTQI 155
                  5679********555...68***********99875 PP

>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.039   1.7e+02     171     194 ..      51      74 ..      39      79 .. 0.79
   2 ?    9.4   0.0   0.00021      0.95      73     114 ..     124     162 ..     117     164 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.039
  HIGH_NTase1_ass 171 hykerilsvLeakiekdviskyie 194
                      + k+ ils ++++iek+v  +yi 
       AJA92367.1  51 ERKKMILSSMNSEIEKNVSLHYIP 74 
                      456779999999999999999985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00021
  HIGH_NTase1_ass  73 GvsGtkireavvegnlekvkdmlPeetievlkeelendnple 114
                       +sGt+ir+ +  +  ++ k+ lP+ t+evl +   +++ le
       AJA92367.1 124 DLSGTNIRNLILTD--QNWKQFLPSGTVEVLTQID-AKKRLE 162
                      58*********876..46789**********9865.444465 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1137.83
//
Query:       AJA92368.1  [L=453]
Description: peptidase dimerization domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-30  107.0   0.0    1.4e-30  106.6   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.2e-18   67.0   0.0    2.3e-18   66.1   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.19   11.2   0.0    1.4  1  Latexin        Latexin
       0.41   11.0   3.7        1.7    9.0   0.2    3.1  3  WG_beta_rep    WG containing repeat


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   3.1e-34   1.4e-30       1     205 [.      83     447 ..      83     449 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.1e-34
                    EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEE CS
                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavf 95 
                    l+++H+Dv+p e+ + w+  pfs+++  +k++GrGa+d+kg +++ ++a++++ ++ ++ + +++++++++EE g++ ++ +l+    ++k ++  
     AJA92368.1  83 LFYNHYDVQPVEPLELWDDpPFSGKIIGNKIFGRGASDDKGELITRIKAVESYLKTYGDVPCNVKFVIEGEEENGSENIGTYLK----KYKKKFSC 174
                    79********999999***********99********************************************65555566666....55555555 PP

                    EEEEESSSBTCHSTETEEEE............................................................................ CS
                    xxxxxxxxxxxxxxxxxxxx............................................................................ RF
  Peptidase_M20  96 elhieepgileagklaigvv............................................................................ 115
                    + +++e g+ + +k  + ++                                                                            
     AJA92368.1 175 DGVVWEFGYVD-QKNRPIIGlgmkgllyveltakesvrdvhssfaviiknpawrliqalntmrdengkilikgwyddikpltkndikliqkepfda 269
                    66789888888.554666668899************************************************************************ PP

                    ....................................................................................EEEEEEEEEESH CS
                    ....................................................................................xxxxxxxxxxxx RF
  Peptidase_M20 116 ....................................................................................kvevelleggap 127
                                                                                                        ++++  l ++a+
     AJA92368.1 270 dgfkkeygvknfvgnknsldakkalvsgvtcniagidsgytgdgaktvlpgsakvkidfrlvpnmdpkklikllekhlrvngfgDITINVLNAEAA 365
                    ***********************************************************************************88999999***** PP

                    EEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEEEEEESS.G.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                    xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20 128 vtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptvmifgpg.s.glaHspnEyvdledlekgikvlarll 205
                    +++n ++++v+++ e+++++fg  v +i  + g+  +  f   + +p++  +g +    ++HspnE+ +++ l+k +k ++ ll
     AJA92368.1 366 ARTNpNEKIVNTVCESTKKIFGDYVLNISNA-GTGPMHAFtniLSVPCI-SVGASyIfCRMHSPNEFAKIDLLHKTTKNICVLL 447
                    *********************9555555444.77777777333555877.4675524789***************998776665 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   5.2e-22   2.3e-18       2     103 ..     195     349 ..     194     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 5.2e-22
                 EB-EEEEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.................................................... CS
   M20_dimer   2 ghkGlaggkit..vkgkagHsgapgagaNAieklarllaeledeegdia...............................................eer 51 
                 g kGl+ +++t     +++Hs++     N+ + l+++l+ ++de+g+i                                                ++ 
  AJA92368.1 195 GMKGLLYVELTakESVRDVHSSFAVIIKNPAWRLIQALNTMRDENGKILikgwyddikpltkndikliqkepfdadgfkkeygvknfvgnknsldaKKA 293
                 789999*****666669******************************99************************************************** PP

                 TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
   M20_dimer  52 slprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeilek 103
                  +++ t+n++gi++G+    ak+v+p++a++kid+Rl+p++dp+++++ +e++l+ 
  AJA92368.1 294 LVSGVTCNIAGIDSGYtgdgAKTVLPGSAKVKIDFRLVPNMDPKKLIKLLEKHLRV 349
                 *****************************************************985 PP

>> Latexin  Latexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.2e-05      0.19      81     149 ..     142     206 ..     127     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.2e-05
                 ---EEEEEESS------HHHHHHHHHHHHH-SS--EEEEES-TTS---GGGHHHHHHHHHHHHHHHHHH CS
     Latexin  81 paievkctvegelkkrqqeedeefykklkklkkpleaqsiPdshGnidpelepiwdLaivassyvmwqk 149
                    +vk+ +eg    ++++  e++ + lkk kk+ +   +  ++G++d++ +pi  L++ +  yv +  
  AJA92368.1 142 VPCNVKFVIEG----EEENGSENIGTYLKKYKKKFSCDGVVWEFGYVDQKNRPIIGLGMKGLLYVELTA 206
                 33444444444....4444455688899************************************97643 PP

>> WG_beta_rep  WG containing repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.5   6.8e+03       3      12 ..       9      18 ..       9      20 .. 0.80
   2 ?    1.8   0.0     0.068   3.1e+02       1      12 [.     181     192 ..     181     194 .. 0.91
   3 ?    9.0   0.2   0.00038       1.7       5      25 ..     237     257 ..     237     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
  WG_beta_rep  3 yiDknGkivi 12
                 +iDkn + ++
   AJA92368.1  9 FIDKNKNSLL 18
                 8***988776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.068
  WG_beta_rep   1 yGyiDknGkivi 12 
                  +Gy+D +++ +i
   AJA92368.1 181 FGYVDQKNRPII 192
                  6********998 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00038
  WG_beta_rep   5 DknGkivippkYddagsFseG 25 
                  D+nGki+i+  Ydd+++++++
   AJA92368.1 237 DENGKILIKGWYDDIKPLTKN 257
                  99***************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3326.11
//
Query:       AJA92369.1  [L=304]
Description: branched-chain-amino-acid transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-52  176.9   0.0    6.2e-52  176.7   0.0    1.1  1  Aminotran_4      Amino-transferase class IV
  ------ inclusion threshold ------
        3.4    8.0   5.0       0.37   11.1   0.3    1.8  2  Lipoprotein_Ltp  Host cell surface-exposed lipoprotein


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.7   0.0   6.9e-56   6.2e-52       2     223 .]      34     265 ..      33     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 6.9e-56
  Aminotran_4   2 lfEtmrvy....ngeiffldeHleRLrksaellglelpfdeeelrkileelleannsengrlrllvsrgggglgaatsepsvavyvsalppgpeseke 95 
                  +fE++r y       if+l+eH++R+ +sa++  +++p++++ ++  + +++ a + +++++r+l   g g +g   ++++v+v++s++++++ + k+
   AJA92369.1  34 IFEGIRCYdtpeGSAIFRLPEHIDRFFNSAKMYSMKMPYSKKKISDGIVSTVNASKLKQCYIRPLAYYGYGTMGLTPTNNKVDVSISCWEWKMGESKA 131
                  7*****999995555677******************************************************************************99 PP

  Aminotran_4  96 .....lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvdedgnvtEgstsNvfivkggelitPplssgiLpGitrrallelaka 187
                        ++ +s++vr+d +s+  +aK+   y + +lar ea ++g+de+++++ +g+v Egs  N+f+vk+g++ tPpl+ +iL+Gitr+++++l+k+
   AJA92369.1 132 gkfsgAKCKISKWVRIDSKSQPMQAKSAAnYSNAALARMEALNAGYDEAIMLNNKGHVAEGSAENIFVVKNGRITTPPLDADILDGITRDSAIKLLKS 229
                  9*************************9877******************************************************************** PP

  Aminotran_4 188 lgleveereitlkdleeadeafltntlrgvlpvrsi 223
                   +++v+e++++++dl +ade+f+t+t+++v  v+++
   AJA92369.1 230 NKIKVIEKNLRINDLLKADEIFMTGTAAEVKSVTRV 265
                  ******************************999975 PP

>> Lipoprotein_Ltp  Host cell surface-exposed lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   4.1e-05      0.37       8      30 ..      61      83 ..      60      88 .. 0.88
   2 ?   -3.3   0.5       1.3   1.2e+04       8      15 ..     157     164 ..     156     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
  Lipoprotein_Ltp  8 kkAksYadtmnmSkqglydqLts 30
                     ++Ak+Y+  m++Sk+++ d  +s
       AJA92369.1 61 NSAKMYSMKMPYSKKKISDGIVS 83
                     79***************987666 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
  Lipoprotein_Ltp   8 kkAksYad 15 
                      k+A +Y++
       AJA92369.1 157 KSAANYSN 164
                      67888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2069.97
//
Query:       AJA92370.1  [L=528]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-12   47.3   0.0    6.8e-12   46.1   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.071   13.1   0.1       0.19   11.8   0.1    1.8  1  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   7.6e-16   6.8e-12       1     165 [.     220     404 ..     220     406 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 7.6e-16
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS...........TTHHHHHHHHHHTC...CCTEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx...xxxxxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly...........pdfvellerlakla...vpgiritvet 84 
                  ++ +rgC ++C fC++++     +  ++ls+e++ +e+k++  + g + v+l+++e lly           + +++l++ l+          +++++ 
   AJA92370.1 220 IEAMRGCGRGCDFCDVNK-----RSKKDLSIERLQREAKIN-LDYGFDSVWLHSDEMLLYgcdnrdfipnrDAITDLWKGLKGMGanfIG--TTHMTF 309
                  5789*************5.....9*****************.8*********************99997775555555555555353333..333333 PP

                  CSSCHGHHHHHHHHHTT.......-SEEEEEEBSSSHHHHHHHHTCTSHH........HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  85 ngtlpdeeklerllelg.......vdrvslgleaaddekvlklmnrghtf........eevlealeklreagikrvvdrivglpGendeeleelle 165
                  +++  d+  ++ +++ +       +   +lg+e++++ +v+k+++  +t+        + v e+ ++l+e+ + +  ++i+g p e+ e+ +++++
   AJA92370.1 310 SAVAADPQLMRNIADVNrqhetgrWLATNLGIETVSPPMVKKHLG-VKTRpfateewgSVVREGAKILNENHWFPAATIIIGWPDETPEDSQATID 404
                  333333666666666666667889********************6.3444469*******************999***************999987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.1e-05      0.19      68     116 ..     135     181 ..      58     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
  B12-binding  68 vkelvellkrirprvkvvvGGahp.sldpeetleaklgiddvvvgegeda 116
                  ++e+++l+k++  ++kv+vGG ++ +l+  + ++   gid vvvge+++ 
   AJA92370.1 135 CAEIIQLKKKY--DFKVAVGGNGAwELAKSDRMKV-HGIDTVVVGEADEL 181
                  36677778887..89******98624445554444.**********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3702.24
//
Query:       AJA92371.1  [L=390]
Description: alanine transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-59  202.1   0.0    1.7e-59  201.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    3.2e-07   30.0   0.0    5.1e-07   29.3   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    7.1e-06   25.2   0.0    1.5e-05   24.2   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    1.1e-05   24.2   0.0    1.6e-05   23.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0044   16.7   0.6       0.84    9.4   0.1    2.7  2  DUF4116          Domain of unknown function (DUF4116)
  ------ inclusion threshold ------
       0.16   11.2   0.0       0.57    9.4   0.0    1.8  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.9   0.0   5.6e-63   1.7e-59       6     351 ..      34     375 ..      30     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 5.6e-63
                    SSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES CS
  Aminotran_1_2   6 LgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp 101
                    L+++++ +  g  ++++v++a+++  + ++++n+y+ ++gl el ea+ak  +  ++l++  e +++v++G +++++++i  + ++ gde+l+p p
     AJA92371.1  34 LNIGDPVQS-GFQPPQNVKQAMID--AINNGNNFYTRSEGLTELTEAIAKKEN-AKGLSIPSE-NILVTNGVSEGLDMVISSI-VEEGDEVLLPGP 123
                    778888776.778***********..*************************99.899999999.*******************.9*********** PP

                    S-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSS CS
  Aminotran_1_2 102 tyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgs 197
                    +y++y  ++rl+gg  +++++ + ++ + d+++++ ++++      kt  i++ sp+NPtG v++++ l++++d+a+++nl++++De+Y   vf+ 
     AJA92371.1 124 YYPPYASYVRLHGGIPIEFSV-DLNSSSPDIDDIKSKITS------KTVAICLISPNNPTGLVFNENALRQIVDVANEHNLYIICDEIYDQIVFD- 211
                    ********************5.58999*************......99**********************************************9. PP

                    SHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.....HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 198 ldavatranveeepnllivgslsKafGlaGeRvGyilgna.....avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrke 287
                    ++++  + +v+ +  ++i++++sK   + G+R+Gyi+ n      ++++ l kl+r  +s   ++q+a++++l  +++   ++ + +++l+ +r++
     AJA92371.1 212 EKFTG-IGKVAGDSPVIILNGFSKVHLMSGWRIGYIAFNNspqldNIRENLPKLARVRIStNLPVQYAALESLTGPQD---YIPKFVSELKVHRDF 303
                    56877.********************************666*******************999**************7...89************* PP

                    HHHHHHHS.TEEEECCSCSSEEEEEETHH...CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS CS
  Aminotran_1_2 288 lrdeLael.glkvlasqsgmflltdlsae...takelskkLleevgvyvtpgtsftv...pgrlRitv.Agl 351
                    + ++L+e  g+++  ++++++ +  +++    ++ke+  +Ll+++gv+ ++g+ f+    +g++Ri + + +
     AJA92371.1 304 VIKRLNEMnGISCSNPKGAFYAFPKIEQNkfnSDKEFVLELLKQKGVLTVHGSGFGEqygSGHFRIVYlPKM 375
                    ******************************************************************994443 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.7e-10   5.1e-07      44     144 ..      97     202 ..      49     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.7e-10
                      ESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB...-GGGB--...-HHHHH CS
  DegT_DnrJ_EryC1  44 vssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpV...hlyGqva...dmdalk 131
                      ++  +++l ++++ + v++gdeV+ p   +   a+ v+  g  p+   vd ++  +d ++i+++it++t aI ++   +  G v+    + ++ 
       AJA92371.1  97 TNGVSEGLDMVISSI-VEEGDEVLLPGPYYPPYASYVRLHGGIPIEFSVDLNSSSPDIDDIKSKITSKTVAICLIspnNPTGLVFnenALRQIV 189
                      333356777776665.667**************************************************9998652225667766433799999 PP

                      HHHHHCT-EEEEE CS
  DegT_DnrJ_EryC1 132 aiaakhglkvieD 144
                      ++a++h+l++i D
       AJA92371.1 190 DVANEHNLYIICD 202
                      9**********88 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     5e-09   1.5e-05      17     175 ..      52     202 ..      45     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5e-09
                  HHHHHHHHCTCCSSSSSSSHHHHHHHHHHHH.HHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHT CS
  Aminotran_5  17 dalqeyytdynanvhrsvhhlgkeatkavee.arekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtg 113
                  +a+ +      +n+ ++ +++++ +t+  e+ a+++ a+ + ++s e+i++t G +e++ +v+ s+   +++gde+++    +       ++l    g
   AJA92371.1  52 QAMIDAI----NNG-NNFYTRSEGLTELTEAiAKKENAKGLSIPS-ENILVTNGVSEGLDMVISSI---VEEGDEVLLPGPYYPPYA-SYVRL--HGG 137
                  4444442....233.567888888888888735677899999**8.********************...*********999888777.55555..59* PP

                  EEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB...--HHHHHHHHHHTT-EEEEE CS
  Aminotran_5 114 akvkvipldeegeldldelekllnektklvaithvsnvtGti...qpveeigklakkkgalvlvD 175
                  + +++    +  + d+d+++++++ kt ++++   +n tG +   + + +i+++a +++ ++++D
   AJA92371.1 138 IPIEFSVDLNSSSPDIDDIKSKITSKTVAICLISPNNPTGLVfneNALRQIVDVANEHNLYIICD 202
                  ***999888999****************************962225688899999999****999 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   5.4e-09   1.6e-05      37     175 ..      56     204 ..      41     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.4e-09
                      CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-......SEEEEESSHHH.HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHH...THHHTTCEEE CS
  Cys_Met_Meta_PP  37 fageekgyeYsRsgnptrsvleeriaaLegg......eaalavssGma.AiaaailallkaGdeivvsddlYggtqrllkk...vlkklgievk 120
                       a ++ +++Y+Rs+  t+  l e+ia+ e++      ++ ++v+ G++  ++++i +++++Gde+++    Y +  ++++    +  +++++ +
       AJA92371.1  56 DAINNGNNFYTRSEGLTE--LTEAIAKKENAkglsipSENILVTNGVSeGLDMVISSIVEEGDEVLLPGPYYPPYASYVRLhggIPIEFSVDLN 147
                      455666799*****9985..8999999999955666645566667766379999****************998766655431114445666666 PP

                      EESTTSHHHHHHHCCTTEEEEEEESS-TTTT----...HHHHHHHHHHTT-EEEEEGT CS
  Cys_Met_Meta_PP 121 fvdtsdleelekaikentklvylEtptnpllkvvD...iekiaklakkagvlvvvDnt 175
                         + d+++++++i+++t ++ l +p np+  v     +++i+++a ++++ ++ D  
       AJA92371.1 148 SSSP-DIDDIKSKITSKTVAICLISPNNPTGLVFNenaLRQIVDVANEHNLYIICDEI 204
                      6555.899*********************96665333399*************99975 PP

>> DUF4116  Domain of unknown function (DUF4116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.1    0.0082        24      14      32 ..     289     306 ..     287     329 .. 0.83
   2 !    9.4   0.1   0.00028      0.84      22      38 ..     333     349 ..     324     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0082
     DUF4116  14 salkylseeLknDkeivlk 32 
                 ++ k++s eLk ++++v+k
  AJA92371.1 289 YIPKFVS-ELKVHRDFVIK 306
                 5678888.9********98 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00028
     DUF4116  22 eLknDkeivlkAvkqng 38 
                 ++ +Dke+vl+ +kq g
  AJA92371.1 333 KFNSDKEFVLELLKQKG 349
                 56689999999999876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00019      0.57     107     167 ..     149     202 ..      44     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                      TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
  Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                         d+++++++i+       k+ +i+l   nn   G v   + lr++ ++a+++++ +++D
       AJA92371.1 149 SSPDIDDIKSKITS------KTVAICLISPNNP-TGLVFNENALRQIVDVANEHNLYIICD 202
                      56788888888888......6899**9999995.9*********************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2871.69
//
Query:       AJA92372.1  [L=61]
Description: hypothetical protein T478_0339 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.015   15.5   0.0    1.1  1  DUF2304   Uncharacterized conserved protein (DUF2304)
       0.02   14.7   0.3       0.03   14.2   0.3    1.3  1  LapA_dom  Lipopolysaccharide assembly protein A domain
      0.021   14.9   0.2      0.031   14.3   0.2    1.3  1  CcmD      Heme exporter protein D (CcmD)


Domain annotation for each model (and alignments):
>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.5e-06     0.015      67      95 ..      25      53 ..      19      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
     DUF2304 67 lfllgivfllvilfslslklskleekike 95
                lf+++i+ l++i+++ s++++k ++++++
  AJA92372.1 25 LFYVSIAGLIIIVLYSSMQTRKEQQRLRR 53
                8************************9986 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   4.9e-06      0.03      26      58 ..      28      57 ..      22      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-06
    LapA_dom 26 afgiGallgwllslwsylrlrrelrrlkkkikk 58
                + ++G+++++l s +   ++r+e +rl+++ +k
  AJA92372.1 28 VSIAGLIIIVLYSSM---QTRKEQQRLRRERRK 57
                557899999999998...777777777776554 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   5.2e-06     0.031      12      43 ..      24      55 ..      24      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-06
        CcmD 12 gitllvlagLilwslrdrrrllrelrrleaRe 43
                g++ +++agLi+ +l    ++++e++rl + +
  AJA92372.1 24 GLFYVSIAGLIIIVLYSSMQTRKEQQRLRRER 55
                67788999999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 410.69
//
Query:       AJA92373.1  [L=239]
Description: urease accessory protein UreD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-40  138.4   0.0    3.6e-40  138.2   0.0    1.0  1  UreD      UreD urease accessory protein


Domain annotation for each model (and alignments):
>> UreD  UreD urease accessory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0     2e-44   3.6e-40       1     210 [.      17     218 ..      17     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 2e-44
                 EEEEE-SS-B-TT-EEEEEEEE-TT-EEEEEE-S-EEE---T.TS-EEEEEEEEE-TT-EEEE----EEE-TT-EEEEEEEEEE-TT-EEEEEEEEE-S CS
        UreD   1 vyllsygGGlvgGDrldldvevgpgarlllttqgatkiyksraekvsrqtlrvrvaagatLellPdpvipfagsryeqtqrfeLapgasllllDwvtsG 99 
                 v++ls++GG+++GDr+++dve++ +a  ++ttqgat+iyk+++ ++++  ++++++++++Le++P+++ip+++sr+ q++++++++++++++++ +++G
  AJA92373.1  17 VFILSPSGGILQGDRYRMDVELRNNAISHITTQGATRIYKMES-NYATHMVTLNLKDNSYLEFIPEQIIPYKNSRFYQKTNLQIDDSSTVVYSETIVPG 114
                 799**************************************75.89***************************************************** PP

                 -CCCT--S-SSEEEEEEEE.EETTEEEEEEEEEE-T-TTST....TTTTT--EEEEEEEES....--HHHHHHTEEE..............EEEE-..S CS
        UreD 100 rtargErwafdryrsrnevwvgdgrlllrDrlllepedesatslaerlagygvvgtlilvgpefeellealreefaalprigaeeaeevlwsasrl..r 196
                 r a+gE ++fd    ++e ++ ++r+ +rD+ ll+p+ +++ +  +++++ +++ ++++++++   ++ ++ + +++l +    +++++  + s l  +
  AJA92373.1 115 RIAMGEMFDFDLCYLKTEGKI-NDRVQFRDSSLLSPKMQKI-QSLAMFDDKTILTSVYILTKK---HVTKVNDMINELFS----HTQNISGGSSILpnD 204
                 *********************.9************866445.445677************944...45555553333333....344445566666633 PP

                 -E.EEEEEESSHHH CS
        UreD 197 glvvvrvlakdaea 210
                 + + +r+l++++e+
  AJA92373.1 205 SGISIRILGNSSED 218
                 4679******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1710.69
//
Query:       AJA92374.1  [L=411]
Description: orc1/cdc6 family replication initiation protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-17   62.0   0.3    8.7e-17   60.9   0.3    1.6  1  Cdc6_C         CDC6, C terminal winged helix domain
    1.6e-12   47.9   0.0    4.2e-12   46.5   0.0    1.7  1  AAA_22         AAA domain
    3.7e-10   40.3   0.9    1.4e-09   38.5   0.1    2.4  2  AAA            ATPase family associated with various cellular
    7.2e-10   39.5   0.0    3.1e-09   37.4   0.0    2.0  1  AAA_16         AAA ATPase domain
    4.9e-06   26.1   0.0    1.3e-05   24.7   0.0    1.7  1  TniB           Bacterial TniB protein
    5.2e-06   26.5   0.1    1.4e-05   25.1   0.0    1.7  1  NACHT          NACHT domain
    2.7e-05   24.2   1.6     0.0001   22.3   0.3    2.2  2  ATPase_2       ATPase domain predominantly from Archaea
    3.6e-05   23.2   0.3       0.17   11.1   0.0    2.3  2  KAP_NTPase     KAP family P-loop domain
    0.00011   21.6   0.0    0.00018   20.9   0.0    1.4  1  DUF2075        Uncharacterized conserved protein (DUF2075)
     0.0003   20.1   0.1     0.0011   18.2   0.0    1.9  3  PIF1           PIF1-like helicase
     0.0004   19.3   0.7       0.15   10.8   0.0    2.2  2  AAA_32         AAA domain
    0.00083   18.9   0.0     0.0017   17.9   0.0    1.5  1  AAA_7          P-loop containing dynein motor region
    0.00098   18.4   0.4     0.0025   17.1   0.1    1.7  2  NB-ARC         NB-ARC domain
    0.00099   19.4   0.5     0.0027   18.0   0.5    1.7  1  AAA_assoc_2    AAA C-terminal domain
      0.001   19.4   1.5     0.0031   17.8   0.2    2.4  2  AAA_19         AAA domain
     0.0012   18.8   1.5     0.0092   16.0   0.4    2.9  2  AAA_5          AAA domain (dynein-related subfamily)
     0.0046   16.8   0.8      0.017   14.9   0.0    2.0  2  AAA_11         AAA domain
     0.0048   16.8   2.6      0.073   13.0   2.7    2.5  2  NTPase_1       NTPase
     0.0052   16.0   0.0       0.01   15.0   0.0    1.5  1  DUF815         Protein of unknown function (DUF815)
     0.0057   16.6   0.3      0.016   15.1   0.0    1.8  1  Rad17          Rad17 P-loop domain
  ------ inclusion threshold ------
       0.01   15.9   0.2       0.03   14.5   0.2    1.9  1  AAA_lid_10     AAA lid domain
      0.016   15.6   0.0      0.048   14.1   0.0    1.9  1  RNA_helicase   RNA helicase
      0.018   14.8   0.6      0.046   13.4   0.6    1.8  1  AAA_24         AAA domain
      0.025   14.0   1.0       0.44    9.9   1.0    2.5  1  ATPase         KaiC
      0.027   14.2   0.0      0.074   12.8   0.0    1.8  1  AAA_30         AAA domain
      0.034   14.0   1.0      0.091   12.6   0.4    2.0  2  Phage-MuB_C    Mu B transposition protein, C terminal
      0.038   12.9   0.1      0.097   11.6   0.0    1.7  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.039   13.6   1.1        6.2    6.5   0.0    2.8  2  DUF359         Protein of unknown function (DUF359)
      0.044   13.7   1.2       0.66    9.9   0.7    2.8  3  T2SSF          Type II secretion system (T2SS), protein F
      0.054   13.5   0.0       0.12   12.3   0.0    1.6  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
      0.063   13.4   0.4       0.17   12.0   0.4    1.8  1  TIP49_C        TIP49 AAA-lid domain
       0.11   11.9   0.0       0.25   10.7   0.0    1.6  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.11   11.3   0.2       0.53    9.1   0.1    2.0  3  AAA_34         P-loop containing NTP hydrolase pore-1


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.3   1.6e-19   8.7e-17      11      82 ..     328     398 ..     321     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.6e-19
                 CSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHHHH CS
      Cdc6_C  11 sgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpddvl 82 
                  ++ e++tgevy +Yk+lC++   + ltqr+v ++lse em gi+  + +++G  +g+t+k++++v+pd v+
  AJA92374.1 328 MKSSEISTGEVYSTYKNLCKDIRQKELTQRRVTQMLSEIEMSGIIAGRIVHQGT-HGNTKKFRITVSPDMVK 398
                 5789*************************************************9.8*************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   7.8e-15   4.2e-12       4     130 ..      60     201 ..      57     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7.8e-15
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..........erlsseellealeqalraravi 92 
                 + + l+v+G +GtGKT++++++l++ +++ +    + ++++ +++++t++  ll  + r+lgl+  +           +ls +e+++++ + l++  v 
  AJA92374.1  60 RPSNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSFPIKLAYTNAKQETTLYGLLVSFGRQLGLGSQKtndekmwlpsTGLSISEVFNRIIHVLDKNEVN 158
                 56789********************976655555999999***********************9999******************************** PP

      AAA_22  93 elliiDEaqhlr...s...eealeeLrsllnlsrkgvqliLvGt 130
                 ++++iDE+++l    +   +++l ++ +++n + +  +l L+G 
  AJA92374.1 159 AVFVIDEIDYLAeliQktgKDVLYQI-TRANERLTTGSLTLIGV 201
                 ***********766624567777777.55554566667777776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   2.5e-12   1.4e-09       1     120 [.      64     216 ..      64     227 .. 0.73
   2 ?   -1.6   0.0       6.1   3.3e+03      39      57 ..     290     308 ..     258     314 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.5e-12
                 EEEESSTTSSHHHHHHHHHHHHTHE......EEEEETTTCSSS............................STTHHHHHHHHHHHHH...HHTS..TS. CS
         AAA   1 vllyGppGtGKTllakavakelgve......fleisgsellsk............................yvgesekkirelfkea...keka..kp. 59 
                 +l+yG pGtGKTl++k v ++++ +       +++  ++   k                            ++  +  +i+e+f+++         +  
  AJA92374.1  64 LLVYGKPGTGKTLVIKKVLSKIQKRveegsfPIKLAYTNA--KqettlygllvsfgrqlglgsqktndekmWLPSTGLSISEVFNRIihvL--DknEVn 158
                 69*******************9644222222233333333..1346678899999999999999999****66666666666666653330..133223 PP

                 EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHH CS
         AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpall 120
                  +++iDEid la+      ++ +++v+ q+ ++ +++++  + +++ig++n+    ++ldp ++
  AJA92374.1 159 AVFVIDEIDYLAELI----QKTGKDVLYQITRANERLTT--GSLTLIGVSNDltfKERLDPRVI 216
                 8**********9999....78899999999999999999..57********9888888888777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.1
                 TTHHHHHHHHHHHHHHHTS CS
         AAA  39 vgesekkirelfkeakeka 57 
                    +e++ir+  ++++e++
  AJA92374.1 290 STVTEEHIRMAAEKIEENK 308
                 4567888888888888776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   5.8e-12   3.1e-09       5     164 ..      41     190 ..      38     199 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.8e-12
      AAA_16   5 ReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellralekd..ggif.lrgkcdqlesaipysalaqalareellrqllde.....aesael 94 
                 R+ e+e++ +s+l  + ++rp+++l++G +G+GK+ +++++l  ++k+  +g f +          ++y    q  +  +ll   +++     +++++ 
  AJA92374.1  41 RDPEQEKItQSLLPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKRveEGSFpI------K---LAYTNAKQETTLYGLLVSFGRQlglgsQKTNDE 130
                 999*****8888889999999***************************54344442......3...333333333333344444444411001122233 PP

      AAA_16  95 eawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwade....aslqllaaLlrlles 164
                   w                +   ++ e+++r++  l ++e   v+v+D+++ + e    +  ++l+++ r+ e+
  AJA92374.1 131 KMWLP--------------STGLSISEVFNRIIHVLDKNEVNAVFVIDEIDYLAEliqkTGKDVLYQITRANER 190
                 33333..............33479999******777777999*********66554444888888887777665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.4e-08   1.3e-05      24     149 ..      50     187 ..      34     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.4e-08
        TniB  24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara...........rvskleqqv 111
                 ++Ll    ++r++nll++G++ +GKt +++k  ++ +++ +e +  +++ + +a ++ +  +l  +  ++lg   ++++           ++s+  +++
  AJA92374.1  50 QSLLPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSFPIKLAYTNAKQETTLYGLLVSFGRQLGLGSQKTNdekmwlpstglSISEVFNRI 148
                 4577777899*********************************************************99*99886666558899999999999****** PP

        TniB 112 lrllrelkvr.vLiiDEihnllagsarkqreflnalksL 149
                 +++l++ +v  v +iDEi+ l +  +++ + +l ++ + 
  AJA92374.1 149 IHVLDKNEVNaVFVIDEIDYLAELIQKTGKDVLYQITRA 187
                 *******996589*****999887777776666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   2.5e-08   1.4e-05       3     114 ..      64     186 ..      62     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.5e-08
                 EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.....................CHHHHCCSC CS
       NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse.....................vwavllelp 80 
                 +++ G++G GKT  ++k+ ++++++  ++     +F ++l+ ++ ++++ +l  ll+s + +++  +++                     ++ vl +++
  AJA92374.1  64 LLVYGKPGTGKTLVIKKVLSKIQKRVEEG-----SFPIKLAYTNAKQET-TLYGLLVSFGRQLGLGSQKtndekmwlpstglsisevfnrIIHVLDKNE 156
                 689***********************777.....567777777776666.8899998888877766666667799999988888888777777777777 PP

                 CCEEEEEE-STT-SS-TCH.........HHHHHC CS
       NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselir 114
                   +++++D +D+l++  ++      +++L ++ r
  AJA92374.1 157 VNAVFVIDEIDYLAELIQK----TGKDVLYQITR 186
                 7888**********97776....44445544443 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   1.8e-07    0.0001       9     153 ..      50     192 ..      44     211 .. 0.85
   2 ?    0.4   0.1      0.92     5e+02     145     200 ..     310     362 ..     264     369 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
    ATPase_2   9 keleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk.eksklvfkai 106
                 ++l+ il +++ + +++YG  g GKt ++k+++++ ++  ++  + i+l   + ++ ++         ++ ++lg   +k++ e++   ++   + + +
  AJA92374.1  50 QSLLPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSFPIKLAYTNAKQETTL---YGLLVSFGRQLGLGSQKTNDEKMWLpSTGLSISEVF 145
                 567888888899999***********************99********998887777776...345556777777777777666666679999999*** PP

    ATPase_2 107 elllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlieslt 153
                 ++++  + k+    + +iDe+ +l +l  +  +++++++ ++ e+lt
  AJA92374.1 146 NRIIHVLDKNEVNAVFVIDEIDYLAELIQKTGKDVLYQITRANERLT 192
                 ***************************99999999999999888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.92
    ATPase_2 145 LlnliesltkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnf 200
                  + l  +++ ek l+++i+ sSe  + e vy  s+ ++ +k i  + l++  + ++
  AJA92374.1 310 VVALRSYPLHEKLLILAIMKSSEISTGE-VY--STYKNLCKDIRQKELTQRRVTQM 362
                 4555667888888888899999888888.55..44555555555555555555555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00031      0.17       4      53 ..      48      94 ..      45     108 .. 0.82
   2 !    9.7   0.1   0.00081      0.44     152     184 ..     136     168 ..     124     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
  KAP_NTPase  4 yasaladilseptlatpivvgLygkWGsGKssllnkledelkefakpvrf 53
                + ++l  il+e+   +p+ + +ygk G+GK+ +++k+ ++++++ ++ +f
  AJA92374.1 48 ITQSLLPILMES---RPSNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSF 94
                566777788876...7999**********************999655555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00081
  KAP_NTPase 152 klqteveelladmektLdalqkrlVvviDdLDr 184
                 + + +++e++++++  Ld+++   V+viD++D 
  AJA92374.1 136 STGLSISEVFNRIIHVLDKNEVNAVFVIDEIDY 168
                 5678999************************95 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   3.4e-07   0.00018       3     122 ..      63     187 ..      61     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.4e-07
     DUF2075   3 vvlVtGvaGtGKtvvllnllael.eddeeert.avylsvNhplvlvlrealakke......ekkkkkeafeklssfinnlsefkkaeekkeepked.vv 92 
                  +lV G++GtGKt+v  ++l ++ ++ ee++   ++++ N ++  +l+  l +        ++k+ +e++  +s+     + f++ ++  ++++++ v 
  AJA92374.1  63 NLLVYGKPGTGKTLVIKKVLSKIqKRVEEGSFpIKLAYTNAKQETTLYGLLVSFGrqlglgSQKTNDEKMWLPSTGLSISEVFNRIIHVLDKNEVNaVF 161
                 689********************5334444441467899999999999988765556677767777777777777766666667777766665554266 PP

     DUF2075  93 ivDEAhrlltksdqaekqseenqlkelmkr 122
                 ++DE   l +      ++++++ l ++ ++
  AJA92374.1 162 VIDEIDYLAE----LIQKTGKDVLYQITRA 187
                 7888766666....3344555555555555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-06    0.0011       4      49 ..      43      88 ..      41     100 .. 0.93
   2 ?   -3.4   0.0       7.4     4e+03      10      27 ..     145     162 ..     130     189 .. 0.59
   3 ?   -2.4   0.0       3.7     2e+03     236     269 ..     327     360 ..     300     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-06
                HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
        PIF1  4 eeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrse 49
                 eQ+k+ ++ +  ++++++ ++ v+G  GtgKt + k++l+k++++
  AJA92374.1 43 PEQEKITQSLLPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKR 88
                59****************************************9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                 HHHH......HCTS-EEE CS
        PIF1  10 fdaiieavlnekgklfFv 27 
                 f++ii+ + +++ + +Fv
  AJA92374.1 145 FNRIIHVLDKNEVNAVFV 162
                 333333333333333333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.7
                 .......HHCHCCS---SS--...........EE CS
        PIF1 236 lkksedkieeivsevygdllqeltdkeyleerai 269
                 ++ks++  +  v ++y++l++++ +ke+ ++r+ 
  AJA92374.1 327 IMKSSEISTGEVYSTYKNLCKDIRQKELTQRRVT 360
                 4555555666666777777777777777666654 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00028      0.15      26      58 ..      57      89 ..      44     108 .. 0.86
   2 !    6.5   0.5    0.0056         3     476     510 ..     269     303 ..     258     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
      AAA_32 26 ikkkgYNifvlGesgtGrttlvkrlleeiakke 58
                ++++  N+ v G++gtG+t ++k++l++i+k+ 
  AJA92374.1 57 MESRPSNLLVYGKPGTGKTLVIKKVLSKIQKRV 89
                777888**********************99875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0056
      AAA_32 476 rfseiadllrEAdywakkegaevveaehVekAlee 510
                   ++  dllr A+ +a+++++++v++eh++ A e+
  AJA92374.1 269 DARRALDLLRVAAEIAERNQESTVTEEHIRMAAEK 303
                 567789**************************986 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.2e-06    0.0017      27      62 ..      55      89 ..      43     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
       AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkeky 62
                 l+ ++  ++l++G+ GtGKt++ik++l+k++k+ +
  AJA92374.1 55 ILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKR-V 89
                344455678999******************9943.3 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.6e-06    0.0025       6     112 ..      50     166 ..      44     197 .. 0.78
   2 ?   -1.9   0.0       2.7   1.5e+03     159     193 ..     250     286 ..     220     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                 HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCC.CCC.CBT.EEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS........HH CS
      NB-ARC   6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnksde.veg.rFd.svawvvvsktdkseeiletilkeLslseddleekeeves........lk 93 
                 + +   L+e+  +    + ++G++G GKt ++k++l+k ++ ve+  F+  +a+    ++ + + +l +  ++L+l +++++  +   +          
  AJA92374.1  50 QSLLPILMESRPS---NLLVYGKPGTGKTLVIKKVLSKIQKrVEEgSFPiKLAYTNAKQETTLYGLLVSFGRQLGLGSQKTNDEKMWLPstglsiseVF 145
                 4455566644444...489******************9765255459**77888888999999999999999999886666665555557888888888 PP

                 HHHHHHCCCT..TEEEEEEEE CS
      NB-ARC  94 rklvrlLltk..rfllvlDDV 112
                 +++ ++L +   + ++v+D +
  AJA92374.1 146 NRIIHVLDKNevNAVFVIDEI 166
                 888888888878899999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                 --HHHHHHHHHHCCTS-GGCHH....CHHHHHHHHHH CS
      NB-ARC 159 Lekdeawellenkvfekkleekes..leevakeivek 193
                 +  d a++l+++++ +++ +  +   l +va ei+e+
  AJA92374.1 250 IVSDAALNLCSAMAGRESGDARRAldLLRVAAEIAER 286
                 4568888899998888887777666677888888776 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5     5e-06    0.0027      13      56 ..     260     302 ..     248     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5e-06
                  XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
  AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeakegkieitledleealq 56 
                  +a+a   +GDaR+aL lL +aae ae+ +++ ++t+e+++ a++
   AJA92374.1 260 SAMAGRESGDARRALDLLRVAAEIAER-NQESTVTEEHIRMAAE 302
                  33444447****************997.9999999999997765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   5.8e-06    0.0031       8      50 ..      59     101 ..      54     203 .. 0.78
   2 ?   -0.7   0.1         3   1.6e+03      32      74 ..     278     320 ..     249     382 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.8e-06
      AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaf 50 
                 ++ ++llv + pGtGKT v+k++++ ++++ ++   +i l+  
  AJA92374.1  59 SRPSNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSFPIKLAYT 101
                 667899******************9999988777666665433 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3
      AAA_19  32 allvelggvkpeeillvaftgrAakelrerlaalgaeatTiHr 74 
                 +++ e+ +++ e+ +     + Aa++++e+ +++ ++ + +H+
  AJA92374.1 278 RVAAEIAERNQESTVTEEHIRMAAEKIEENKEVVALRSYPLHE 320
                 5555555555555555556677888888888777777666663 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   1.7e-05    0.0092       1     111 [.      63     208 ..      63     240 .. 0.68
   2 ?   -1.2   0.0       3.5   1.9e+03      28      48 ..     341     361 ..     331     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------................................... CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar................................... 64 
                 ++l+ G+pGtgK+ +++++++ ++++ve+  ++ ++ +++ k+++ +         + lv  +r                                   
  AJA92374.1  63 NLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSFPIKLAYTNAKQETTL--------YGLLVSFGRqlglgsqktndekmwlpstglsisevfnriihvld 153
                 6899*******************999999998888888888888876........56666666666666666666666666667777777777777777 PP

                 ...G-SEEEEESGGG--HHHHHH....HHHHHHSSEEE..-SSSEEE---..... CS
       AAA_5  65 ...egeilvlDEveraesevlns....Llslleerrllleeggelvkakndd.ll 111
                      +++v+DE++ +   ++++    L ++   +++l+  + +l++++nd  + 
  AJA92374.1 154 kneVNAVFVIDEIDYLAELIQKTgkdvLYQITRANERLTTGSLTLIGVSNDLtFK 208
                 7776777777777776666665411114444444444444444555555554444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                 EEEE--TT--HHHHH--B--. CS
       AAA_5  28 eyvqltrdtteedlkgrreik 48 
                 +y++l +d+++++l++rr ++
  AJA92374.1 341 TYKNLCKDIRQKELTQRRVTQ 361
                 688899999999999999865 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.1e-05     0.017      18      45 ..      62      92 ..      47     135 .. 0.77
   2 ?    0.1   0.1         1   5.7e+02     136     174 ..     293     350 ..     215     380 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
      AAA_11 18 eitliqGPPGtgKTktivellsqllsr...r 45
                +  l+ G+PGtgKT +i ++ls++ +r    
  AJA92374.1 62 SNLLVYGKPGTGKTLVIKKVLSKIQKRveeG 92
                3579*******************95433330 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
      AAA_11 136 lakelrafeeeeek...................eklkkskekskskleqerrklkker 174
                  ++++r  +e++e+                   ++ k s+  + + ++++++ +k+ r
  AJA92374.1 293 TEEHIRMAAEKIEEnkevvalrsyplhekllilAIMKSSEISTGEVYSTYKNLCKDIR 350
                 1111222222222222344445555555555554444444444444444444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.7   0.00013     0.073       2     114 ..      64     176 ..      63     193 .. 0.71
   2 ?    4.6   0.1     0.049        27     116     160 ..     146     189 ..     136     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-.------EEEEEET.T--EEEEEETT.---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-E CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarve.akreprvgkyvvdvesfeelalealrkalseadv 98 
                 +++ G+pG+GKt ++kkvl++++++ v+ g f  +    + ++ +      ++ g++  L +++ + +++ + +  + + ++ + ++++l+k  + + v
  AJA92374.1  64 LLVYGKPGTGKTLVIKKVLSKIQKR-VEEGSFPIKLAYtNAKQETTLYGLLVSFGRQLGLGSQKtNDEKMWLPSTGLSISEVFNRIIHVLDKN-EVNAV 160
                 6788******************765.7777776665542444444444444556888888777757777888899999999888899999974.66679 PP

                 EEE---STTGGG-HHH CS
    NTPase_1  99 iviDEiGkmElkskkf 114
                 +viDEi  +   ++k 
  AJA92374.1 161 FVIDEIDYLAELIQKT 176
                 9999998775444444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.049
                 HHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TTTT CS
    NTPase_1 116 eaveevLk.sekpvlavihrrkdlalveeirerkdvkvfevteenr 160
                 + + +vL+ +e++ ++vi +     l e i++  + +++++t++n 
  AJA92374.1 146 NRIIHVLDkNEVNAVFVIDEI--DYLAELIQKTGKDVLYQITRANE 189
                 334455554566666666666..35666666666666666666664 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.9e-05      0.01      28      80 ..      36      88 ..      17     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
      DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                +d+   d ++e++++     l   + +n+L++G+ GtGK  ++k +l++++++
  AJA92374.1 36 NDILHRDPEQEKITQSLLPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKR 88
                5677789999999***9999999************************999876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     3e-05     0.016      29      95 ..      46     112 ..      38     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
       Rad17  29 eevkewlkadvLesrkkriLLisGPsGCgkstvvk.vLskelgiklrewlnpvslkepdn.qksdfkgl 95 
                 e++ + l    +esr+ + LL+ G +G gk+ v+k vLsk+   +++e + p++l  ++  q++ + gl
  AJA92374.1  46 EKITQSLLPILMESRPSN-LLVYGKPGTGKTLVIKkVLSKIQ-KRVEEGSFPIKLAYTNAkQETTLYGL 112
                 578889999999999776.7899***********73678775.7899*******999988455555555 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   5.5e-05      0.03      45      81 ..     251     287 ..     220     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-05
                 ------HHHHHHHHHHT-TTTTHHHHHHHHHHHHHHH CS
  AAA_lid_10  45 isddaieiasrkvAsvsgdarrAlkiCkrAvEiaekd 81 
                 +sd a+++ s      sgdarrAl + + A+Eiae++
  AJA92374.1 251 VSDAALNLCSAMAGRESGDARRALDLLRVAAEIAERN 287
                 5778888888888899******************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.8e-05     0.048       2      28 ..      65      91 ..      64     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.8e-05
  RNA_helicase  2 wlyGpsgeGKStlakeLakallkklkl 28
                  ++yG++g+GK++++k++ ++++k++++
    AJA92374.1 65 LVYGKPGTGKTLVIKKVLSKIQKRVEE 91
                  79*******************999843 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   8.4e-05     0.046       4      80 ..      63     172 ..      60     189 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-05
      AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...................................swedfldevvelaaeladyk 67 
                 ++l+yG++g+GKT ++k+   + +   +e+G+  ++ +  + ++                                   s+ ++ + +  + ++++   
  AJA92374.1  63 NLLVYGKPGTGKTLVIKKV-LSKIQKRVEEGSFPIKLAYTN-AKqettlygllvsfgrqlglgsqktndekmwlpstglSISEVFNRIIHVLDKNEVNA 159
                 789**************99.666666666666444444432.221333333333333333333333333333333344444444444444455555566 PP

      AAA_24  68 tlviDtideleel 80 
                 + viD id l el
  AJA92374.1 160 VFVIDEIDYLAEL 172
                 6666666666555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   0.00081      0.44      20      52 ..      62      94 ..      59     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00081
      ATPase 20 rvvlitGepGtGKtifalqFlikgaekygepgv 52
                +  l++G+pGtGKt++ ++ l k  ++++e   
  AJA92374.1 62 SNLLVYGKPGTGKTLVIKKVLSKIQKRVEEGSF 94
                5789***********999888776666555444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.074      18      97 ..      61     166 ..      42     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
      AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g...grviglAptgkaAkv.La.......eelgieastiakllkrlk...............grarlepg 89 
                     ++ G +GtGKt ++k++   ++++ +   ++ i lA t++  ++ L        ++lg+ ++ ++    +l                   + ++ 
  AJA92374.1  61 PSNLLVYGKPGTGKTLVIKKVLSKIQKRvEegsFP-IKLAYTNAKQETtLYgllvsfgRQLGLGSQKTNDEKMWLPstglsisevfnriihV-LDKNEV 157
                 4556889************9977777653344344.34555544443325555555554666655555444444444457777777777742.333333 PP

      AAA_30  90 .tllivDEa 97 
                   ++++DE+
  AJA92374.1 158 nAVFVIDEI 166
                 377788876 PP

>> Phage-MuB_C  Mu B transposition protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   0.00017     0.091      26      76 ..     250     302 ..     242     304 .. 0.78
   2 ?   -2.4   0.0       8.4   4.5e+03      33      52 ..     344     363 ..     324     369 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                  SSSSHHHHHHHTTSSS.-S-HHHHHHHHGGGT-TT-TTS.--SSHHHHHHHHT CS
  Phage-MuB_C  26 ltdeelmkllqeiaek.pGaLRaltktLrlAamfAkgeg.eeltadliraAwk 76 
                  +  +++++l++++a +  G  R     Lr+Aa +A+ ++ +++t+++ir A +
   AJA92374.1 250 IVSDAALNLCSAMAGReSGDARRALDLLRVAAEIAERNQeSTVTEEHIRMAAE 302
                  556788999999987624667888899********87650566******9965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.4
                  HHHHTTSSS-S-HHHHHHHH CS
  Phage-MuB_C  33 kllqeiaekpGaLRaltktL 52 
                  +l+ +i +k    R +t+ L
   AJA92374.1 344 NLCKDIRQKELTQRRVTQML 363
                  45566666665556665555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018     0.097       7      43 ..      53      89 ..      47      92 .. 0.89
   2 ?   -2.3   0.0         3   1.6e+03     228     258 ..     142     172 ..     124     193 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
  TrwB_AAD_bind  7 vplpkeretqhilivGttGsGKtqalekllrairarg 43
                   +p+  e+  + +l+ G  G+GKt +++k l +i++r 
     AJA92374.1 53 LPILMESRPSNLLVYGKPGTGKTLVIKKVLSKIQKRV 89
                   79999999999***********************995 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
  TrwB_AAD_bind 228 dlaikallslpesrerrlWfflDElpaLgrl 258
                    +   ++++ + +++e    f++DE++ L +l
     AJA92374.1 142 SEVFNRIIHVLDKNEVNAVFVIDEIDYLAEL 172
                    4445555555566666666778888777665 PP

>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.011       6.2      84     119 ..      53      90 ..      51      92 .. 0.75
   2 ?    4.6   0.5     0.045        24      41      72 ..     280     311 ..     264     367 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
      DUF359  84 lpaillapegsvvvYGqpdeG..vvlvkvteeakeeae 119
                 lp+++  +   ++vYG p++G  +v+ kv +++++++e
  AJA92374.1  53 LPILMESRPSNLLVYGKPGTGktLVIKKVLSKIQKRVE 90 
                 88999999999********9933455566667666665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.045
      DUF359  41 kevievkNpaGtiteelieaikealeseekvl 72 
                 + +i  +N+++t+tee i+   e +e++++v+
  AJA92374.1 280 AAEIAERNQESTVTEEHIRMAAEKIEENKEVV 311
                 5678889******************7777765 PP

>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.3   1.8e+03      31      66 ..      78     112 ..      74     121 .. 0.64
   2 ?   -0.1   0.0       1.5   8.2e+02      45      99 ..     138     191 ..     136     199 .. 0.70
   3 ?    9.9   0.7    0.0012      0.66      22     113 ..     284     374 ..     271     378 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.3
                 HHHHHHHHHHHHHTTSSHHHHHCT-TT.TS-HHHHH CS
       T2SSF  31 laeelkriarrlraGgslsealertpssefpelvvq 66 
                 ++++l++i +r+++G+ ++  l+ t+ ++ + l+  
  AJA92374.1  78 IKKVLSKIQKRVEEGS-FPIKLAYTNAKQETTLYGL 112
                 6889999999999996.5555553333344555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
                 TSSHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHH CS
       T2SSF  45 GgslsealertpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkll 99 
                 G s+se++ r  + ++++  v+ + +++e   Lae +++  +++  +  +++++l
  AJA92374.1 138 GLSISEVFNRIIH-VLDKNEVNAVFVIDEIDYLAELIQKTGKDVLYQITRANERL 191
                 6677777777765.67777777777777777777777777777777766666655 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0012
                 HHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXX CS
       T2SSF  22 laeeaengplaeelkriarrlraGgslsealertpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaallepllllvval 113
                 + +++e+ +  e ++ +a+++++ +    al+++p  e    ++ + ++  ++g +  + ++l +++++++ ++r++  +l e  ++ ++a+
  AJA92374.1 284 AERNQESTVTEEHIRMAAEKIEENKE-VVALRSYPLHEKLLILAIMKSSEISTGEVYSTYKNLCKDIRQKELTQRRVTQMLSEIEMSGIIAG 374
                 44444466666667777777777762.367779998777888999999999*******************************9999999886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.12       9      65 ..      47     106 ..      39     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                 HHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..SS CS
        TsaE   9 algkklakal....gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYelekeg 65 
                 ++ ++l   l     + +l +G+ G+GKT  +++++++++ ++v+  +F +   Y+++k++
  AJA92374.1  47 KITQSLLPILmesrPSNLLVYGKPGTGKTLVIKKVLSKIQ-KRVEEGSFPIKLAYTNAKQE 106
                 4444444444333355699******************984.4999999*999999876654 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00032      0.17       8      61 ..     246     301 ..     237     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
     TIP49_C   8 eEgvkldeeAldlLakigtetS..LRYaiqLltpasilakkrkkkevevedveeve 61 
                 +E+  +++ Al+l + ++ + S   R a+ Ll +a  +a+++++ +v+ e+++ ++
  AJA92374.1 246 FEEGIVSDAALNLCSAMAGRESgdARRALDLLRVAAEIAERNQESTVTEEHIRMAA 301
                 4555689999999999988888557***************************9886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00046      0.25      24      44 ..      63      83 ..      55     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
  Mg_chelatase 24 nlllvGppGsGKtmlakrlps 44
                  nll++G pG+GKt+++k++ s
    AJA92374.1 63 NLLVYGKPGTGKTLVIKKVLS 83
                  89************9988655 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.4   1.3e+03     160     191 ..     144     176 ..     103     211 .. 0.76
   2 ?    9.1   0.1   0.00097      0.53     116     182 ..     307     382 ..     267     395 .. 0.71
   3 ?   -0.4   0.0      0.77   4.2e+02      77     108 ..     372     403 ..     368     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.4
      AAA_34 160 rleqlveWlg.edfdGvivfDEchkaknlakse 191
                  ++++++ l+ ++++ v v DE   +++l+++ 
  AJA92374.1 144 VFNRIIHVLDkNEVNAVFVIDEIDYLAELIQKT 176
                 567888888878889999999988888887643 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00097
      AAA_34 116 eievvalnklkegkkik.....eseelkeGvlFvtYstliseskkkk..ksrleqlveWlg..edfdGvivfDEch 182
                 + evval +++ ++k+      +s+e+++G +++tY+ l ++ ++k+  ++r+ q+++ ++    + G iv+  +h
  AJA92374.1 307 NKEVVALRSYPLHEKLLilaimKSSEISTGEVYSTYKNLCKDIRQKEltQRRVTQMLSEIEmsGIIAGRIVHQGTH 382
                 34455555555554444888878999****************999878899****998776322345566665555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.77
      AAA_34  77 iagiilenllqgrkkavwvsvsedLkeDaerD 108
                 iag i+++ ++g++k+  ++vs d+++ + +D
  AJA92374.1 372 IAGRIVHQGTHGNTKKFRITVSPDMVKTTFKD 403
                 8999*******************998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      698  (0.0389313); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 2848.95
//
Query:       AJA92375.1  [L=189]
Description: respiratory-chain NADH dehydrogenase, 30 Kd subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-32  111.8   0.0    4.1e-32  111.4   0.0    1.2  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.19   11.3   0.0    1.4  1  Rsa3            Ribosome-assembly protein 3


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   4.6e-36   4.1e-32       2     119 ..      58     187 ..      57     189 .] 0.87

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 4.6e-36
                     E--HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--S-.....-EEEEEE............-S-BEE--TTT-STHHHHHHH CS
  Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllslekn....erirvkvevde........eepevpSvtdlfpgadwyERE 83 
                      v++e++++vakf+kd+  + fd+  ++++vD++ ++++ v yhl s+++     + + + +++++        +++++pS+ d+f +++++ERE
      AJA92375.1  58 NVKKEKIIDVAKFIKDN--TPFDHAESVSGVDYPqDKEIGVTYHLGSYTDPeyskQVLALATRAPReetpnpgsDSTKLPSLRDMFYSVEFHERE 150
                     799*************5..88***********9999************544455588999999966555555555999***************** PP

                     HHHHSHHBCTTSSTSS-SSSSTTS.SS-TTSTTS--- CS
  Complex1_30kDa  84 ayDmfGivfeghpdlrrillpedf.eghPLRkdfpls 119
                     +++m+G+ feghpd rr+llped+    PLRkdf  +
      AJA92375.1 151 VFEMLGVYFEGHPDNRRLLLPEDWaDLPPLRKDFMNK 187
                     ************************5555******655 PP

>> Rsa3  Ribosome-assembly protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.1e-05      0.19       1      18 [.      29      46 ..      29      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
        Rsa3  1 FrsfYLqllteeFgdDLD 18
                F++ Y+++++++F+dD++
  AJA92375.1 29 FEKSYVDQIANQFSDDVE 46
                99**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1446.20
//
Query:       AJA92376.1  [L=95]
Description: hypothetical protein T478_0608 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 723.29
//
Query:       AJA92377.1  [L=115]
Description: putative ribosomal protein L18e/L15 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-09   35.3   0.1    7.7e-09   35.2   0.1    1.1  1  Ribosomal_L18    Ribosomal protein 60S L18 and 50S L18e
      2e-06   28.5   3.4    4.4e-06   27.4   3.4    1.6  1  Ribosomal_L27A   Ribosomal proteins 50S-L15, 50S-L18e, 60S-L2
  ------ inclusion threshold ------
       0.14   12.3   0.3       0.34   11.1   0.2    1.7  2  HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   1.3e-12   7.7e-09      38     136 ..      20     112 ..       3     115 .] 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.3e-12
  Ribosomal_L18  38 tdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaGGeiltlDqLalraPtGk 133
                     d+   + v   + +sr+n++ + l+r+ ++++    +++ +v+ g+++    + +  k+sv ++ ++++a ++i+++GGe+l + ++  + PtGk
     AJA92377.1  20 NDAPIWAKVADFVQKSRSNQKIVNLTRINQTTE----DGNAVVITGKILGTGNISH--KVSVSSFSISNAAAKKIIESGGEVLKFSEMIEKFPTGK 109
                    556666677777889*************98887....5689*********999986..9************************************9 PP

  Ribosomal_L18 134 ntv 136
                     + 
     AJA92377.1 110 GVK 112
                    875 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   3.4   7.3e-10   4.4e-06      58     126 ..      29      95 ..       4      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 7.3e-10
                     HHTTTTGTTS------EEEGGGTTTTSSS.......SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
  Ribosomal_L27A  58 delideerleladeaeeidleelaeaglikk...kdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                      +++++ r    ++++ ++l+++ ++   +         K+lg+g++++k++v   ++S++A +kI + GG+v
      AJA92377.1  29 ADFVQKSR----SNQKIVNLTRINQTT--EDgnaVVITgKILGTGNISHKVSVSSFSISNAAAKKIIESGGEV 95 
                     23334443....456789999993333..3355544557********************************99 PP

>> HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   5.7e-05      0.34       4      48 ..       2      45 ..       1      62 [. 0.89
   2 ?   -2.3   0.0      0.87   5.2e+03      36      47 ..     102     113 ..      98     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
  HU-CCDC81_euk_1  4 vteaqprtssalkplltteqllliWdalgeyieeqlekgkgvhip 48
                     vt+a+ +t++ lk + ++e    iW ++++++++  +++k v++ 
       AJA92377.1  2 VTQAKVNTLKILK-KASKENDAPIWAKVADFVQKSRSNQKIVNLT 45
                     7899999999996.89999999*****************999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.87
  HU-CCDC81_euk_1  36 eeqlekgkgvhi 47 
                      +e++ +gkgv+i
       AJA92377.1 102 IEKFPTGKGVKI 113
                      467788999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 888.06
//
Query:       AJA92378.1  [L=179]
Description: hypothetical protein T478_0052 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0027   17.7   3.1     0.0035   17.3   3.1    1.2  1  Trypan_PARP      Procyclic acidic repetitive protein (PARP)
     0.0064   16.8   1.2     0.0096   16.2   1.2    1.2  1  TctB             Tripartite tricarboxylate transporter TctB f
  ------ inclusion threshold ------
      0.037   14.3   6.6      0.098   12.9   6.3    1.7  1  DUF5379          Family of unknown function (DUF5379)
       0.04   14.0   1.7      0.068   13.2   0.1    1.9  2  DUF4366          Domain of unknown function (DUF4366)
       0.32   10.7   5.4       0.43   10.3   0.5    2.5  2  Rer1             Rer1 family
       0.48   10.4   1.6       0.96    9.4   0.2    1.8  2  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.72   10.9  11.3          1   10.4  11.3    1.1  1  Rib_recp_KP_reg  Ribosome receptor lysine/proline rich region
       0.85    9.6   6.1        1.3    9.0   6.1    1.2  1  AIF-MLS          Mitochondria Localisation Sequence


Domain annotation for each model (and alignments):
>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   3.1   1.5e-06    0.0035      48     115 ..      13      77 ..       1     101 [. 0.41

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
  Trypan_PARP  48 kvsdddtngtdpepepepepepepepepepep.......etepeeepepepepepepepepepepepepepgaat 115
                  k ++        e e+++ pe e   + + e        +  pe +  pe+   pe e++p+p  +p  +   at
   AJA92378.1  13 KSNS--------EDENKDLPEIEATEDEKKEIakwtsnsDDAPETTDAPETTDAPETESKPDPTDDPIDKS--AT 77 
                  3333........33333333333222211111223222244555555566555555555555555444433..33 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   4.3e-06    0.0096      55     130 ..      78     166 ..      66     167 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
        TctB  55 eekearedwrkllklvlallaalllyalllep...........lGfilatalflllll..g....reerkwlkalilavvlallvyllFtklL 130
                 ++ ++r +w +l++ +++     ++  +++e            +Gf++  ++++++++  +     +++k++++ i ++v+  l++++F++ L
  AJA92378.1  78 KKLTDRLFWLRLATAIAG----GVIATFAFEDivdveekrwtsIGFMIMLFIATAIVAksWkikiANRKKYVTTGIGSFVFMYLFVWIFSYTL 166
                 333444444445544444....3333333333333355666666*******999777776256776678888888888888888888888765 PP

>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   6.3   4.4e-05     0.098      40      88 ..     117     165 ..      91     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.4e-05
     DUF5379  40 lflfiglvilghlsakvlgeesltqkqwlgsgvlpfflvaivvwilkyn 88 
                 + ++i l i+  + ak +  +  ++k+++ +g+ +f ++++ vwi++y 
  AJA92378.1 117 IGFMIMLFIATAIVAKSWKIKIANRKKYVTTGIGSFVFMYLFVWIFSYT 165
                 44556677777888888999999************************96 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     3e-05     0.068      57     139 ..      21     102 ..      14     108 .. 0.45
   2 ?   -0.1   0.1      0.38   8.6e+02     117     145 ..     115     143 ..     104     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
     DUF4366  57 aDLlalleedeeaakeeeevcactekcaagkvntdcpv..eepepekeaepeepeeepekksn..nglllvvlavaligggaayyfk 139
                 +DL ++   ++e+++ ++ +++ ++  +     td+p     pe+e++ +p++   +++++++    l  + la a+ +gg + +f 
  AJA92378.1  21 KDLPEIEATEDEKKEIAKWTSNSDDAPE----TTDAPEttDAPETESKPDPTDDPIDKSATKKltDRLFWLRLATAI-AGGVIATFA 102
                 5666655444444444333333333323....344444113444444444444444444444452444444455554.555544444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.38
     DUF4366 117 nnglllvvlavaligggaayyfkvlkpkk 145
                  ++  +++l +a + ++  + +k+   kk
  AJA92378.1 115 TSIGFMIMLFIATAIVAKSWKIKIANRKK 143
                 35666777777777778888888887776 PP

>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.011        24      74     124 ..      51     102 ..       3     110 .. 0.72
   2 ?   10.3   0.5   0.00019      0.43      14      47 ..     103     136 ..      96     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
        Rer1  74 eeaaeeeaeegaelptkkdeef.rPfirrlpEfkfWlsatkailialvltff 124
                 ++ ++ +a e ++ p+ +d+   +   ++l +  fWl++ +ai+ ++++tf 
  AJA92378.1  51 DAPETTDAPETESKPDPTDDPIdKSATKKLTDRLFWLRLATAIAGGVIATFA 102
                 33333444444455554444432778899*************9999888864 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
        Rer1  14 ldkltpytleRWiatlvllllfllriillqgfyi 47 
                  + ++    +RW+ + ++++lf++  i+++++ i
  AJA92378.1 103 FEDIVDVEEKRWTSIGFMIMLFIATAIVAKSWKI 136
                 567888899***********************87 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00043      0.96      73     125 ..      87     145 ..      75     149 .. 0.88
   2 ?    4.9   0.5     0.011        24      77     122 ..     123     170 ..     122     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00043
   RseC_MucC  73 lPllllilgallgsall......gssellaalgallglvlgflivrllskrlkkkskfq 125
                 l l++ i+g +++++++       ++ ++++ +++++++++ ++++ ++ ++++++k+ 
  AJA92378.1  87 LRLATAIAGGVIATFAFedivdvEEKRWTSIGFMIMLFIATAIVAKSWKIKIANRKKYV 145
                 5577888888888888899999999999**************************99985 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
   RseC_MucC  77 llilgallgsall..gssellaalgallglvlgflivrllskrlkkks 122
                 l+i++a++++++   +++    + +++  +v+ +l+v+++s +l +  
  AJA92378.1 123 LFIATAIVAKSWKikIANRKKYVTTGIGSFVFMYLFVWIFSYTLVNAG 170
                 678889999999899888888899999999999999999988776655 PP

>> Rib_recp_KP_reg  Ribosome receptor lysine/proline rich region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  11.3   0.00045         1      34     104 ..       5      78 ..       2      84 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
  Rib_recp_KP_reg  34 sekKk.kakkKedkpngkipEsestqepae..ekseseaevvveaepaPvvaaapaavaePvkeeevkakaaka 104
                       +kK   +k   +  n  +pE e t++  +   k  s+++ ++e++ aP ++ ap+++ +P  + +   k+a++
       AJA92378.1   5 KKKKFrAEKSNSEDENKDLPEIEATEDEKKeiAKWTSNSDDAPETTDAPETTDAPETESKPDPTDDPIDKSATK 78 
                      3333323455677788889998888776665667889999999******9999999999998655555555555 PP

>> AIF-MLS  Mitochondria Localisation Sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.1   0.00058       1.3      82     145 ..       6      70 ..       2      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00058
     AIF-MLS  82 kektkaelqplqgekenvaeaekasseapevsvveaevvdaeevpdataav.aeeasacpddaea 145
                 k+k +ae  + + e++++ e e++  e  e++  ++++ da e++da++++ a e ++ pd ++ 
  AJA92378.1   6 KKKFRAEKSNSEDENKDLPEIEATEDEKKEIAKWTSNSDDAPETTDAPETTdAPETESKPDPTDD 70 
                 678899***********************************999999988766677777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1383  (0.0771376); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1358.75
//
Query:       AJA92379.1  [L=231]
Description: triose-phosphate isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-10   40.1   3.2    9.3e-09   35.0   0.9    2.1  2  TIM       Triosephosphate isomerase
     0.0011   18.1   0.1     0.0021   17.3   0.1    1.4  1  IGPS      Indole-3-glycerol phosphate synthase
     0.0024   17.2   0.1     0.0057   16.0   0.1    1.6  1  ThiG      Thiazole biosynthesis protein ThiG
     0.0068   15.5   0.6      0.018   14.1   0.1    1.8  2  FMN_dh    FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.087   11.9   0.1       0.13   11.3   0.1    1.2  1  DUF5081   Domain of unknown function (DUF5081)


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.9   2.6e-12   9.3e-09       2     133 ..      12     137 ..      11     141 .. 0.78
   2 !    8.0   0.1   0.00046       1.7     146     210 ..     130     194 ..     127     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.6e-12
                 EEEEE-TBTS-HHHHHHHHHH.HHHHCHG.CTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHHHHTT-SEEEES-HHHHHHS CS
         TIM   2 liagNwKmnktleeakellkk.lkaklke.ekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaemlkdlgvkyviiGHsErrqlf 98 
                 +++ N K + +++  k +  + +++k+++  kv ++iapp   +     l+++ k+++ aq v+ +k G+ TG +  e +k+ +++  ii HsE r   
  AJA92379.1  12 MFIINCKNYDEIAGDKIIKIAkISEKISKkYKVPIAIAPPHHLIP----LITKFKITVLAQHVDDKKVGSTTGFMVPEIVKKSKINGSIINHSEHRISE 106
                 567777777766544433222355566554889999999987777....466678****************************************9866 PP

                 T--HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT CS
         TIM  99 kEtdelvakKvkaalksglkpilCvGEtleereag 133
                 kE    +   vk+++k +lk++lCv +  e+++  
  AJA92379.1 107 KE----IISLVKRLKKLKLKTVLCVKNVNEAKKYA 137
                 55....4556788999*********9988887765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00046
                 HTTTS-CCCGGCEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEESS- CS
         TIM 146 ilkkldeealknvviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYGGsv 210
                 + +  + ++l+ ++iA eP   iGtg+ +++e+   + +a++ + ++k s++      i+ G  v
  AJA92379.1 130 VNEAKKYAKLNPTFIAIEPPELIGTGRAISTEKPALITNAVKAVSSAKNSTKLLCGAGIVSGQDV 194
                 4555556678999********************99999999988666655554444444444444 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.7e-07    0.0021     145     253 ..     107     223 ..     100     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.7e-07
                 HHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTT..EE-CHHHHHHCHCC-......TTSEEEEESSS-SHHHHHHHCCTT-SEE CS
        IGPS 145 eeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktl..evdlntteeLaklvp......kdvllvaeSGiktredveklkeegvnaf 235
                 +e+ +l++  k+l l+ +  v++ +e ++  kl+  +i +   +L      ++ ++   +++ v+      +++ l +  Gi + +dv+k ke g +++
  AJA92379.1 107 KEIISLVKRLKKLKLKTVLCVKNVNEAKKYAKLNPTFIAIEPPELIGTgrAISTEKPALITNAVKavssakNSTKLLCGAGIVSGQDVSKAKELGSRGI 205
                 55556666666666666666666666666666666666666666633211333333333333333333332679999********************** PP

                 EESHHHHC-TTHHHHHHH CS
        IGPS 236 LvGeslmrqedvekaire 253
                 Lv + ++++++ ek i e
  AJA92379.1 206 LVASGIVKAKNWEKIISE 223
                 ***********9999876 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.6e-06    0.0057     161     219 ..     164     223 ..     148     230 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                 -S-HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHH CS
        ThiG 161 llnkealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvamAra 219
                  l ++a+k + +   +  ++  AGi s +d+ +a elG  ++l+++ + +ak+  ++ + 
  AJA92379.1 164 ALITNAVKAVSSAKnSTKLLCGAGIVSGQDVSKAKELGSRGILVASGIVKAKNWEKIISE 223
                 334445566655444788999*******************************97766555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.15   5.6e+02     197     233 ..      98     133 ..      38     146 .. 0.56
   2 !   14.1   0.1     5e-06     0.018     258     303 ..     166     211 ..     152     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                 CHB-TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHH CS
      FMN_dh 197 kqldpsltwddikwlreqtklplvvKGvltaedakra 233
                 ++++++++ ++i  l +++k +l +K vl+++++++a
  AJA92379.1  98 NHSEHRISEKEIISLVKRLK-KLKLKTVLCVKNVNEA 133
                 23345555555555555554.4556666666666555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5e-06
                 HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
      FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                 i    + v  +++++++l+  Gi +G+Dv kA  lG +++l++  +
  AJA92379.1 166 ITNAVKAVSSAKNSTKLLCGAGIVSGQDVSKAKELGSRGILVASGI 211
                 44445567777889*************************9998665 PP

>> DUF5081  Domain of unknown function (DUF5081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.6e-05      0.13      19      89 ..      75     145 ..      59     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
     DUF5081  19 igvsdvfglPdkkaflLldeevleeakeaLkeKgllteeekltdagfkviellkeYisskkyvRiNnllva 89 
                 +g +  f +P+ +    ++ ++++++++++ eK++++  ++l +   k +  +k+  ++kky ++N  ++a
  AJA92379.1  75 VGSTTGFMVPEIVKKSKINGSIINHSEHRISEKEIISLVKRLKKLKLKTVLCVKNVNEAKKYAKLNPTFIA 145
                 56677799**********************************************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1668.05
//
Query:       AJA92380.1  [L=166]
Description: winged helix-turn-helix DNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-18   64.1   0.0    9.4e-11   41.1   0.1    2.3  2  HTH_24           Winged helix-turn-helix DNA-binding
    3.1e-10   39.8   0.0    3.4e-05   23.6   0.0    2.4  2  HTH_5            Bacterial regulatory protein, arsR family
    3.2e-09   36.6   0.1     0.0009   19.1   0.0    2.2  2  MarR             MarR family
    4.3e-09   36.1   0.3    1.6e-05   24.7   0.1    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.3e-08   34.9   0.5     0.0015   18.7   0.0    2.2  2  HTH_34           Winged helix DNA-binding domain
    5.6e-06   26.1   0.0     0.0037   17.1   0.0    2.3  2  MarR_2           MarR family
    0.00021   21.1   0.1      0.017   14.9   0.1    2.2  2  HxlR             HxlR-like helix-turn-helix
    0.00029   20.8   0.3       0.11   12.5   0.0    2.3  2  HTH_45           Winged helix-turn-helix
    0.00069   19.4   0.0       0.11   12.3   0.0    2.3  2  HTH_IclR         IclR helix-turn-helix domain
     0.0045   17.3   0.0        1.2    9.5   0.0    2.2  2  FaeA             FaeA-like protein
     0.0058   17.0   0.2       0.28   11.5   0.0    2.3  2  Rrf2             Transcriptional regulator
     0.0083   16.6   0.0        0.1   13.1   0.0    2.3  2  HTH_27           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.016   15.3   0.0        0.4   10.8   0.0    2.2  2  HTH_20           Helix-turn-helix domain
       0.02   15.5   0.2        1.2    9.8   0.0    2.4  2  RPA_C            Replication protein A C terminal
      0.021   14.2   1.1       0.12   11.7   0.1    2.1  2  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.026   14.5   0.1        9.2    6.3   0.0    2.6  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.039   14.4   0.0       0.22   12.0   0.0    2.0  2  HTH_40           Helix-turn-helix domain
      0.047   14.1   1.1        1.7    9.0   0.1    2.5  2  Penicillinase_R  Penicillinase repressor
      0.049   13.8   0.3          2    8.7   0.0    2.6  3  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.082   12.6   0.0       0.56    9.8   0.0    2.0  2  RP-C             Replication protein C N-terminal domain
       0.16   11.7   0.0          2    8.2   0.0    2.2  2  HTH_41           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   1.1e-13   9.4e-11       7      48 .]       7      48 ..       1      48 [. 0.94
   2 !   20.9   0.0   2.2e-07   0.00019       5      47 ..      79     121 ..      75     122 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.1e-13
      HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                 I +++++np+i  re+ e+++lS + +++++++Le++G+Ik
  AJA92380.1  7 LIVSEIKRNPGIRFREVMEKINLSNGVLSYYVRKLENNGVIK 48
                6999*************************************8 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.2e-07
      HTH_24   5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                  ++IL  L +n  +  +e+   +g  ++tv+ +l +L+++G +
  AJA92380.1  79 PKAILVSLLENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMV 121
                 578**************************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   4.3e-05     0.037      17      46 ..      19      48 ..       5      49 .. 0.85
   2 !   23.6   0.0     4e-08   3.4e-05       7      45 ..      82     121 ..      80     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5 17 cvcelaeelglsqstvShHLkkLreaGLVe 46
                 + e +e+++ls + +S++ +kL++ G+++
  AJA92380.1 19 RFREVMEKINLSNGVLSYYVRKLENNGVIK 48
                67899**********************997 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4e-08
                 HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
       HTH_5   7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45 
                 IL +L e   + + e++  +g+  +tvS +L+kL + G+V
  AJA92380.1  82 ILVSLLEnDTMEFQEIVSSVGKASATVSFYLSKLVNDGMV 121
                 6666666266*****************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     1e-06    0.0009       7      51 ..       7      51 ..       2      54 .. 0.91
   2 !   15.3   0.0   1.7e-05     0.014       8      53 ..      82     127 ..      80     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
        MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                +i+  ++++++++  e  +k+++s++ ++  +++Le +G i+ ++
  AJA92380.1  7 LIVSEIKRNPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKTQR 51
                57889**********************************998666 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.7e-05
                 HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
        MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53 
                 iL++l e++ +  +e+ + +g  ++tv+  l +L+ +G+++ +ks 
  AJA92380.1  82 ILVSLLENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMVDFKKSN 127
                 9****************************************99985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00096      0.82      24      58 ..      19      53 ..      12      64 .. 0.87
   2 !   24.7   0.1   1.9e-08   1.6e-05      14      66 ..      83     136 ..      80     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00096
                HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                + +e+ e+++++      ++r+Le+ G++++++ +
  AJA92380.1 19 RFREVMEKINLSNGVLSYYVRKLENNGVIKTQRTT 53
                6799**************************99866 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.9e-08
                 CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
        TrmB  14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravd 66 
                  + Ll+++ ++ +ei + +g   ++v  +L++L++ G+V+ +k++ +k+Y +v+
  AJA92380.1  83 LVSLLENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMVDFKKSNlKKRYFVVE 136
                 689******************************************988998876 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0015      11      51 ..      14      54 ..       7      69 .. 0.85
   2 !   14.6   0.2   3.3e-05     0.028       4      53 ..      81     130 ..      80     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
      HTH_34 11 svdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                 +  + f+e+ e++++++g Ls  ++kLe++g i+ + + +
  AJA92380.1 14 RNPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKTQRTTR 54
                577899****************************9987765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-05
      HTH_34   4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53 
                 a+l +L+++d ++f+e+ ++++  ++  s  l+kL + g +  +k+  +k
  AJA92380.1  81 AILVSLLENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMVDFKKSNLKK 130
                 6999****************************************997666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.3e-06    0.0037      10      55 ..       8      51 ..       1      57 [. 0.89
   2 !    6.9   0.0    0.0066       5.7      10      60 ..      82     130 ..      78     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.3e-06
                HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
      MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                +  ++ r+pg  ++ +e+ ++ +ls + +s+ +++L+  G + +++
  AJA92380.1  8 IVSEIKRNPG--IRFREVMEKINLSNGVLSYYVRKLENNGVIKTQR 51
                5679******..******************************9986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0066
                 HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
      MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60 
                 +L  L  ++   +  +e++   g   ++vs  l +Lv  G+v  +++   k
  AJA92380.1  82 ILVSLLENDT--MEFQEIVSSVGKASATVSFYLSKLVNDGMVDFKKSNLKK 130
                 6778888888..9999**************************998875555 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     2e-05     0.017       9      68 ..       7      66 ..       5      78 .. 0.79
   2 ?    4.0   0.0     0.051        43      10      51 ..      82     123 ..      77     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TC CS
        HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltek 68
                li+ e+ +    Rf e+ +++ ++s+ +L+   r+Le++g+i+ +   +v       +te+
  AJA92380.1  7 LIVSEIKRnPGIRFREVMEKI-NLSNGVLSYYVRKLENNGVIKTQRTTRVSRFFINDMTEE 66
                566666663447*********.*********************999888877666666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.051
                 HHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
        HxlR  10 ilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglier 51 
                 ilv+ll+  ++ f+e+   ++k s  + +  L +L +dg+++ 
  AJA92380.1  82 ILVSLLEnDTMEFQEIVSSVGKASA-TVSFYLSKLVNDGMVDF 123
                 5555554499**********98876.56889999999999975 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00013      0.11      24      55 ..      22      53 ..       8      57 .. 0.87
   2 !    6.4   0.1    0.0099       8.5      20      60 ..      92     136 ..      74     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
      HTH_45 24 kimykanLsykllnkYLdmLvekglikkskek 55
                ++m k nLs  +l+ Y+ +L ++g+ik++ ++
  AJA92380.1 22 EVMEKINLSNGVLSYYVRKLENNGVIKTQRTT 53
                7899**********************988765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0099
      HTH_45  20 akkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTe 60 
                  +  +i+ ++     +++ YL++Lv+ g++    ++ k+ Y + e
  AJA92380.1  92 MEFQEIVSSVGKASATVSFYLSKLVNDGMVdfkkSNLKKRYFVVE 136
                 5555667777777778899***********775555556666555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.027        23      16      50 ..      15      49 ..       9      51 .. 0.89
   2 !   12.3   0.0   0.00013      0.11       9      49 ..      83     122 ..      80     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
    HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                +++ +++e+ +++ l+    + +++ L++ G +++
  AJA92380.1 15 NPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKT 49
                56689**************************9986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00013
                 HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
    HTH_IclR   9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                 L  l e +  + ++e+    g + +tv+ +L+ Lv+ G+v 
  AJA92380.1  83 LVSLLENDT-MEFQEIVSSVGKASATVSFYLSKLVNDGMVD 122
                 555555555.89**************************995 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0014       1.2       3      47 ..       6      49 ..       4      56 .. 0.86
   2 ?    5.7   0.0     0.023        19      16      52 ..      92     130 ..      80     132 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
        FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikr 47
                e I++ +++ + + + re+ + + ls     yY  +Le  g ik 
  AJA92380.1  6 ELIVSEIKR-NPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKT 49
                556777777.8889***************************9985 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                 --HHHHHHHHTS-HHHHHHHHHHHHHHSSE..EEE--SS CS
        FaeA  16 ckTreiAdalglsaYQaRyYLeqLekegki..krspvrr 52 
                    +ei   +g +   + +YL +L   g++  k+s++++
  AJA92380.1  92 MEFQEIVSSVGKASATVSFYLSKLVNDGMVdfKKSNLKK 130
                 556788888888888899***********8667999876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00033      0.28      26      59 ..      18      51 ..       7      54 .. 0.86
   2 ?    3.4   0.0      0.11        95      21      56 ..      88     122 ..      69     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
        Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvr 59
                ++ +e+ e+ n+s  +l+  ++kL+++g++k++r
  AJA92380.1 18 IRFREVMEKINLSNGVLSYYVRKLENNGVIKTQR 51
                8899****************************98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                 STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        Rrf2  21 eeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                 e+  +++ +ei ++++     ++  l+kL + g+v 
  AJA92380.1  88 EN-DTMEFQEIVSSVGKASATVSFYLSKLVNDGMVD 122
                 33.44999*************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00012       0.1      21      62 ..      19      55 ..       4      58 .. 0.81
   2 ?    1.0   0.0      0.71   6.1e+02      11      49 ..      86     122 ..      76     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
      HTH_27 21 l.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62
                  ++++++ n++    sy ++kL+++G++      + +r++rv
  AJA92380.1 19 RfREVMEKINLSNGVLSYYVRKLENNGVI------KTQRTTRV 55
                4489*************************......66666666 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.71
      HTH_27  11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                 l++  +++++  +++  +   ++++s  l+kL++ G v 
  AJA92380.1  86 LLE--NDTMEFQEIVSSVGKASATVSFYLSKLVNDGMVD 122
                 444..6777777777777778888998899999999883 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00047       0.4      19      59 ..      12      52 ..       7      54 .. 0.84
   2 ?    2.3   0.0       0.2   1.7e+02      18      54 ..      86     121 ..      72     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00047
                HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                ++r+ g  + e++e + ls   lsy +r+Le  g ++++r+
  AJA92380.1 12 IKRNPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKTQRT 52
                556666667799999***********************996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                 HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
      HTH_20  18 aLaraegltaselaerldlskntlsyHLrvLeeagLv 54 
                 +L +++ + + e+   ++ + +t+s+ L +L+  g v
  AJA92380.1  86 LL-ENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMV 121
                 44.889999999999999999**********999987 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0014       1.2      57      97 ..       7      47 ..       5      51 .. 0.94
   2 ?    3.6   0.0      0.12     1e+02      57      97 ..      81     121 ..      48     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                HHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
       RPA_C 57 likqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                li ++++++ G+ ++e+ +k++ls   +   v++L+n+G+i
  AJA92380.1  7 LIVSEIKRNPGIRFREVMEKINLSNGVLSYYVRKLENNGVI 47
                6778899********************************99 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                 HHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
       RPA_C  57 likqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97 
                 +i  s  +++ ++++ei  +++   ++v   + +L+n+G++
  AJA92380.1  81 AILVSLLENDTMEFQEIVSSVGKASATVSFYLSKLVNDGMV 121
                 33346667888999*******99999*************97 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00014      0.12      84     137 ..       1      52 [.       1      58 [. 0.90
   2 ?    1.6   0.1      0.17   1.4e+02     248     282 ..     108     142 ..      61     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                    SXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEX CS
  RNA_pol_Rpc34  84 lsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvks 137
                    +++ e+l+ s I+   n GI  r++ +k+nL + v+   ++ Le  + ik  + 
     AJA92380.1   1 MESREELIVSEIKR--NPGIRFREVMEKINLSNGVLSYYVRKLENNGVIKTQRT 52 
                    67788888888886..89********************************8775 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.17
                    HHHHHHHHCHSSSCEEETTT.XXXEEEETTHHHHH CS
  RNA_pol_Rpc34 248 iqqlvevLvyDgklekvkvsagyrvqratkqnvlr 282
                    +   ++ Lv Dg ++  k++  +r+  + kq + +
     AJA92380.1 108 VSFYLSKLVNDGMVDFKKSNLKKRYFVVEKQRIAN 142
                    44445667777777777777777777777766655 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.015        13      32      61 ..      28      62 ..      18      65 .. 0.70
   2 ?    6.3   0.0     0.011       9.2      24      54 ..      94     125 ..      68     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                TSSHHHHHHHHHHHHHTTSEE.ET.EE...EEES- CS
   HTH_Crp_2 32 GltretvsrilseLkreglis.rg.rr...irild 61
                +l+   +s   ++L++ g+i+ ++ +r   + i+d
  AJA92380.1 28 NLSNGVLSYYVRKLENNGVIKtQRtTRvsrFFIND 62
                66667788899**********63322222366666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                 HHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
   HTH_Crp_2  24 qeelAsmlGltretvsrilseLkreglis.rg 54 
                  +e+ s +G    tvs  ls+L ++g+++ ++
  AJA92380.1  94 FQEIVSSVGKASATVSFYLSKLVNDGMVDfKK 125
                 5788888999999***************9642 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0         1     9e+02      12      45 ..      17      49 ..      13      83 .. 0.61
   2 ?   12.0   0.0   0.00026      0.22       8      64 ..      86     147 ..      79     166 .] 0.69

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
      HTH_40 12 glsieeIAkerglkesTIegHLaelieegeeidl 45
                g  + e++++ +l+ +    ++ +l ++g  i+ 
  AJA92380.1 17 GIRFREVMEKINLSNGVLSYYVRKLENNGV-IKT 49
                566788889999988888888877777763.333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00026
      HTH_40   8 ll.eeglsieeIAkerglkesTIegHLaelieegeeidl..erl...vseeeekeIeeaiekv 64 
                 ll ++ ++++eI    g + +T+  +L +l+++g  +d+  ++l   +   e+++I++ i+++
  AJA92380.1  86 LLeNDTMEFQEIVSSVGKASATVSFYLSKLVNDGM-VDFkkSNLkkrYFVVEKQRIANLITEY 147
                 6657899**************************96.776332223334445555566665553 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.028        24      41     106 ..      37      97 ..       3      99 .. 0.69
   2 ?    9.0   0.1     0.002       1.7      14      67 ..      88     137 ..      81     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
                      HHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Penicillinase_R  41 llrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfegsvkelvaafveeeklseddl 106
                       +r+L++ g+++++++ r  ++      +++++++ +++ ++l ++  k+++++++e+++++ +++
       AJA92380.1  37 YVRKLENNGVIKTQRTTRVSRFFI----NDMTEEE-SKVASRLRQTTPKAILVSLLENDTMEFQEI 97 
                      577888888888888888776654....3444433.457888888889999999999999887776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                      HHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE---- CS
  Penicillinase_R  14 ekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvs 67 
                      e++ +  +e+v+ + +      +TV   l++Lv+ g+++ +k++ + +Y  + +
       AJA92380.1  88 ENDTMEFQEIVSSVGKA----SATVSFYLSKLVNDGMVDFKKSNLKKRYFVVEK 137
                      55566667777776666....9*********************99999987655 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.18   1.6e+02      28      55 ..      23      50 ..      15      55 .. 0.81
   2 ?   -2.7   0.0       8.5   7.3e+03      19      33 ..      67      75 ..      63      79 .. 0.58
   3 ?    8.7   0.0    0.0023         2      26      56 ..      95     125 ..      80     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                    HHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
  Fe_dep_repress 28 laerLnvspssVsemlkkLekdGyveye 55
                    + e +n s    s  ++kLe++G ++++
      AJA92380.1 23 VMEKINLSNGVLSYYVRKLENNGVIKTQ 50
                    667788888888889********99887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.5
                    HHSSB-HHHHHHHHT CS
  Fe_dep_repress 19 ekkvvktkdlaerLn 33
                    e      +++a+rL 
      AJA92380.1 67 E------SKVASRLR 75
                    3......45555554 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0023
                     HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
  Fe_dep_repress  26 kdlaerLnvspssVsemlkkLekdGyveyek 56 
                     +++ +  + + ++Vs  l+kL +dG v+ +k
      AJA92380.1  95 QEIVSSVGKASATVSFYLSKLVNDGMVDFKK 125
                     566666677889****************998 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.43   3.7e+02      76     113 ..      22      59 ..      19      71 .. 0.82
   2 ?    9.8   0.0   0.00066      0.56      77     114 ..      97     134 ..      73     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.43
        RP-C  76 qLsralglsestlrrhlaaLveaGliirrDspngkRya 113
                 + +++++ls+  l++ +++L + G+i  +      R+ 
  AJA92380.1  22 EVMEKINLSNGVLSYYVRKLENNGVIKTQRTTRVSRFF 59 
                 56789999999*************99888777666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00066
        RP-C  77 LsralglsestlrrhlaaLveaGliirrDspngkRyar 114
                 + +++g +++t++  l++Lv+ G++  + s   kRy  
  AJA92380.1  97 IVSSVGKASATVSFYLSKLVNDGMVDFKKSNLKKRYFV 134
                 55678999****************************76 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0023         2      11      41 ..      22      52 ..      18      58 .. 0.90
   2 ?    0.9   0.0      0.44   3.8e+02      22      38 ..     107     123 ..      96     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
      HTH_41 11 elakeleLSvGlvQkALklLeddkaislerr 41
                e  +++ LS G     + +Le++++i+++r 
  AJA92380.1 22 EVMEKINLSNGVLSYYVRKLENNGVIKTQRT 52
                7889************************995 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.44
      HTH_41  22 lvQkALklLeddkaisl 38 
                 +v + L +L++d+++  
  AJA92380.1 107 TVSFYLSKLVNDGMVDF 123
                 6667799*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1192.90
//
Query:       AJA92381.1  [L=338]
Description: membrane protein, PF03706 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-21   76.7  20.4    3.6e-21   76.0  20.4    1.3  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        0.3   11.6   0.2        0.3   11.6   0.2    2.8  2  DUF1218          Protein of unknown function (DUF1218)
        9.3    6.4  10.5        2.2    8.4   0.3    2.9  2  CcmD             Heme exporter protein D (CcmD)


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0  20.4     6e-25   3.6e-21      34     300 ..      37     319 ..       5     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 6e-25
  LPG_synthase_TM  34 wwlllalllallsvllralrWrlllrsl.garislrrllrayliglfvnnvtPgalgGevvrayllkrkegvslskalasvvverlldllalvl 126
                        l++  ++a l   l +l+ +++ r+  g   s+ rl+++   ++f+  +tP+ +g e++ +y++++ +g+++ska ++ +++ + +++a ++
       AJA92381.1  37 FTLAVVAIMAKLG--LQGLKLAYIARTFlGPFDSIKRLTAMRVGSEFIKFTTPMFVGAEFAVIYYMTK-KGIPTSKASWVALLDIVTEVFAAGV 127
                      3333333333333..7777777777775588889**********************************.************************* PP

  LPG_synthase_TM 127 lgllallllggllaegaavllllalallllavlalllllllrrrlarlarvlkrlarllarfarklasakr..................klvla 202
                      l +la +l   + a+   v+++++l+ ++    ++++l++l  ++++ ++++ ++++ +    +k +++k                     + +
       AJA92381.1 128 LSILAGILAIMYGAY---VVGAVVLGTAVPITGLWIVLFFLSSKRTFTLPRVISFLATA---IGKERGEKYvkqtngwieevcvmsrenLHSSK 215
                      **9999998887665...66666666666555665555555555555555555554432...22223333356689************99999* PP

  LPG_synthase_TM 203 sprrlllafllslliwllealtlylllralgvdvslallllillaltlvgalpplPgGlGvrEaalalllall.......Gvsaaealaaally 289
                      s++++ + f+ s++ w++++  + +++ ++g++v ++ ++ +++ +++++ lp++ gG+G++E++ ++ l++l       +v++ +   a++ +
       AJA92381.1 216 SKKTFTIGFFVSIVSWMCYGISFLVIANGVGYAVEFFDSIMAVMGANAIANLPITVGGSGLAEFGIIAYLNNLdpfnfsaDVDSLQW-NAVIGW 308
                      ************************************************************************976655444444444.79999* PP

  LPG_synthase_TM 290 rlitlylllll 300
                      r++t+y+++++
       AJA92381.1 309 RIATYYIPIAV 319
                      ******99986 PP

>> DUF1218  Protein of unknown function (DUF1218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.5      0.63   3.8e+03      43      57 ..     120     134 ..      88     187 .. 0.68
   2 ?   11.6   0.2     5e-05       0.3      18      57 ..     204     245 ..     193     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.63
     DUF1218  43 wivfaiAvalllvGa 57 
                   vfa++v+ +l+G+
  AJA92381.1 120 TEVFAAGVLSILAGI 134
                 334444445444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5e-05
     DUF1218  18 clccrkekspssakrtlav..vlfvlswivfaiAvalllvGa 57 
                 c+++r++  +s++k+t+++  +++++sw++++i +++++ G+
  AJA92381.1 204 CVMSRENLHSSKSKKTFTIgfFVSIVSWMCYGISFLVIANGV 245
                 66677766666665555550055679*********9999886 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   4.5      0.12   7.1e+02       3      23 ..     139     160 ..     138     166 .. 0.77
   2 ?    8.4   0.3   0.00037       2.2       8      19 ..     231     242 ..     223     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
        CcmD   3 YafYVWlsYgi.tllvlagLil 23 
                 Y++YV +++ + t++ + gL++
  AJA92381.1 139 YGAYVVGAVVLgTAVPITGLWI 160
                 9*******98746666777766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00037
        CcmD   8 WlsYgitllvla 19 
                 W++Ygi++lv+a
  AJA92381.1 231 WMCYGISFLVIA 242
                 **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2510.89
//
Query:       AJA92382.1  [L=304]
Description: oxidoreductase, NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-22   79.3   3.0    3.9e-22   78.8   0.4    2.3  2  CoA_binding     CoA binding domain
    1.6e-09   37.7   0.2    2.9e-09   36.9   0.2    1.4  1  Ligase_CoA      CoA-ligase
    1.6e-06   27.9   0.1    2.6e-06   27.3   0.1    1.4  1  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    4.1e-05   24.1   0.0    6.9e-05   23.3   0.0    1.3  1  CoA_binding_2   CoA binding domain
    0.00043   21.1   0.2     0.0012   19.7   0.1    1.7  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00086   18.9   0.5     0.0016   18.0   0.5    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.061   12.7   0.0       0.11   11.9   0.0    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.083   13.0   0.2       0.35   11.0   0.2    2.0  2  DapB_N          Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.4   1.7e-25   3.9e-22       2      95 ..      19     111 ..      18     112 .. 0.96
   2 ?    0.0   0.1      0.63   1.4e+03      38      67 ..     189     218 ..     160     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.7e-25
                  TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET.TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESS CS
  CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl.glpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviite 95 
                  +++ viv+G++g+   g +h k +l+yg+++v+gv+p+k+g++ +  +pvy++v+e+++ t++++++++vPa++  +a++++++ gik+ v+i e
   AJA92382.1  19 EKKPVIVQGITGK--YGSTHAKLMLEYGTNIVAGVTPGKGGQKFEdKIPVYDTVKEAVDATGAEISIVFVPAKFFLDAAKDALNSGIKLLVAIPE 111
                  5789*********..999***********************999868********************************************9977 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.63
                  TTTTTCEETTEEEESCHHHHHHHCTTTEEE CS
  CoA_binding  38 prkvgtevlglpvyksvdeleektevdvav 67 
                   + +g+ v+g  + ++ d+++++ e +++v
   AJA92382.1 189 IGIGGDPVNGTRMIDAFDMVKDDPELEAMV 218
                  456788999999999999999986544444 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.2   1.3e-12   2.9e-09       1     148 [.     164     281 ..     164     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.3e-12
                 EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHH CS
  Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkai 99 
                 l+++GtL ye  + ++ a              g +q   i++G+d  +         +t++i+a+  +  dpe +++++ +++G g +e++ a+ +  i
  AJA92382.1 164 LSKSGTLLYEISNNLTSA--------------GFGQNITIGIGGDPVN---------GTRMIDAFDMVKDDPELEAMVVVGEIG-GDSEEILAQHIIDI 238
                 678999999999999999..............***************8.........***************************.99999887777777 PP

                 HHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHH CS
  Ligase_CoA 100 keakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalr 148
                    k      p+v ++aG +a++ +++++a+a+  +    a+sk  + +
  AJA92382.1 239 GFKK------PIVGYIAGRQAPKEKRMGHAGAIVMGTYGSAESKISMFA 281
                 6666......************************999999999877655 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   1.2e-09   2.6e-06       2     107 ..     159     266 ..     158     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.2e-09
  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsirdg.rkflsaarraarkkpvvvlksGrseag 95 
                   Gk+a++s+SG+l+ ++ + ++s g+g +  + +G      + + d ++++++dpe ++++++ E  +d  + +++++  +  kkp+v + +Gr++ +
    AJA92382.1 159 GKVAVLSKSGTLLYEISNNLTSAGFGQNITIGIGGdpVNGTRMIDAFDMVKDDPELEAMVVVGEIGGDSeEILAQHIIDIGFKKPIVGYIAGRQAPK 255
                   9**********************999999999998333567889999*****************999961557899****************96555 PP

  Succ_CoA_lig  96 araaashtgala 107
                   +   + h ga++
    AJA92382.1 256 E-KRMGHAGAIV 266
                   4.4567777764 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   3.1e-08   6.9e-05      13     114 ..      30     141 ..      24     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.1e-08
                    TSHHHHHHHHHHHHT--EEE.ESSS-..SEETT.EES----T......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHH CS
  CoA_binding_2  13 gkfgykvlryllehglpvvp.Vnpke..eeilg.ekvyaslae.d.pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaela 98 
                    gk+g   ++ +le g ++v+ V+p +  ++ +   +vy +++e    +  ++  vf+p++  ++ +k+al  g+k ++  p+        e++e+a
     AJA92382.1  30 GKYGSTHAKLMLEYGTNIVAgVTPGKggQKFEDkIPVYDTVKEaVdATGAEISIVFVPAKFFLDAAKDALNSGIKLLVAIPEhvpiRDAMEVIEIA 125
                    677777888888888777655888887655544478999999742567777*********************************977778****** PP

                    HHTT-EEE.ES-HHHH CS
  CoA_binding_2  99 eeagirvvgdrCilve 114
                    ++++  ++g++ ++v+
     AJA92382.1 126 KQKDAIMIGPNTPGVI 141
                    *************997 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   5.3e-07    0.0012       6     116 ..      26     132 ..      22     134 .. 0.87
   2 ?   -2.3   0.0       3.3   7.5e+03      54      70 ..     205     221 ..     197     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.3e-07
                   ETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-SSHHH CS
  GFO_IDH_MocA   6 iGa.GkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlattvee 101
                    G+ Gk+gs h+ +l+ +  ++++va + p++  ++ +  + ++++y+ ++e ++ + +++ iv +p++   + ak+al+ g+++l+  P   ++++
    AJA92382.1  26 QGItGKYGSTHA-KLMLE-YGTNIVAGVTPGKGGQK-F--EDKIPVYDTVKEAVDATGAEISIVFVPAKFFLDAAKDALNSGIKLLVAIPEHVPIRD 117
                   566699999999.55555.57888888888886555.4..799****************************************************** PP

                   HHHHHHHHHHHTS-E CS
  GFO_IDH_MocA 102 akelvelaekkgklv 116
                   a e++e+a++k+ ++
    AJA92382.1 118 AMEVIEIAKQKDAIM 132
                   ***********9876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.3
                   HHHHHTCTTESEEEE-S CS
  GFO_IDH_MocA  54 leelladpeidavivat 70 
                   ++ +++dpe +a +v+ 
    AJA92382.1 205 FDMVKDDPELEAMVVVG 221
                   56667777888888764 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   7.3e-07    0.0016       5     124 ..      21     142 ..      18     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.3e-07
                 S-EEEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT..-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHH. CS
        IlvN   5 kkiaviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkk..advvmiliPDelqkevyeeeiepnlkegkalafahGfni. 99 
                 k + v G  G  G ++a+ + + g ++v g+  g+   +k +++     tv+eav++  a++ ++ +P ++  +      ++ l++g  l  a   ++ 
  AJA92382.1  21 KPVIVQGItGKYGSTHAKLMLEYGTNIVAGVTPGK-GGQKFEDKIPVYDTVKEAVDAtgAEISIVFVPAKFFLDAA----KDALNSGIKLLVAIPEHVp 114
                 556677744999*********************99.555555555555578888764338999999**87766666....5555555555555444432 PP

                 ...HTTSS---TTSEEEEEEESS-SHHH CS
        IlvN 100 ...hfglikppkdvdvvlvAPkgpGhlv 124
                    +++ i++ k+ d +++ P +pG +v
  AJA92382.1 115 irdAMEVIEIAKQKDAIMIGPNTPGVIV 142
                 2227899******************988 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.7e-05      0.11     129     193 ..      44     108 ..      33     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                     SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EE.EEESS--TTTCHHHHHHT--EEEE CS
  Ribul_P_3_epim 129 dlvllmsvePgfgGQkFipevlekikkvrklidekeldlki.evDGGvkldnieqiaeagadvlVa 193
                      + ++  v Pg+gGQkF ++ ++   +v++++d+++ ++ i +v     ld+++ + + g+++lVa
      AJA92382.1  44 GTNIVAGVTPGKGGQKFEDK-IPVYDTVKEAVDATGAEISIvFVPAKFFLDAAKDALNSGIKLLVA 108
                     5567889**********876.578899999999999887642788888888888888888888886 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00016      0.35       2      96 ..      22     107 ..      21     136 .. 0.87
   2 ?   -1.2   0.0      0.96   2.1e+03      93     111 ..     264     282 ..     256     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                 EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S-HHHHHHHHHHHHHTT-EEEE CS
      DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek..advliDFTtpeavlenlklalekgvklVi 96 
                 +v+v G++G+ G++ +k++ e  ++++va+v   +            ++++ +++v+d+++e++++  a++ i F   + +l+ +k al++g+kl +
  AJA92382.1  22 PVIVQGITGKYGSTHAKLMLE-YGTNIVAGVTPGK---G-------GQKFEDKIPVYDTVKEAVDAtgAEISIVFVPAKFFLDAAKDALNSGIKLLV 107
                 599******************.9999999999877...2.......23447899********99999999999999999999999999999999877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.96
                 EEEE--SS--HHHHHHHHH CS
      DapB_N  93 klViGTTGlseeelaelee 111
                 ++V+GT G  e++++  ++
  AJA92382.1 264 AIVMGTYGSAESKISMFAK 282
                 6899999998887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2276.23
//
Query:       AJA92383.1  [L=82]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-09   35.1   0.1    1.1e-08   34.9   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.021   14.9   0.9      0.054   13.6   0.9    1.6  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   1.2e-12   1.1e-08       1      71 [.       6      73 ..       6      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.2e-12
                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    vlv+++  h     e+ +al e++ V+e+  + G yd++ k+  ++  ++e+++ +k++++++v+ t+t+ 
      AJA92383.1  6 VLVQCKIAH---EMEVLKALLEIDLVKEAKGTFGYYDIFTKIQGESSSEIEDIITKKIRNIENVTATTTLS 73
                    678888888...899*****************************************************975 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.9     6e-06     0.054       6      68 ..       6      70 ..       4      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-06
        NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVlsas 68
                ++Vq++ ++  +v++al +++ v E  ++ +   +   i++es+ e+ d+i++ i+++++V +++
  AJA92383.1  6 VLVQCKIAHEMEVLKALLEIDLVkEAKGTFGYYDIFTKIQGESSSEIEDIITKkIRNIENVTATT 70
                69*******************99456666666999999************9877*******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 566.65
//
Query:       AJA92384.1  [L=145]
Description: ribosomal protein S23 (S12) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-47  158.9   0.4    3.7e-47  158.6   0.4    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   0.4   2.1e-51   3.7e-47       1     114 []      30     144 ..      30     144 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 2.1e-51
                      --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--......BTTSTTEEEE CS
  Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk.gkavkDlpGvryk 93 
                      r+el++  ks+++ gapq++G+vlekv+veak+PnsA+Rk+vrv+Likngk+vtaf+p +ga+nf+dEhdev v+G++ + g a++D+pGvr+k
       AJA92384.1  30 RRELGLDRKSNPFAGAPQAKGIVLEKVGVEAKQPNSAVRKCVRVQLIKNGKSVTAFLPRDGAMNFIDEHDEVHVEGMGATqGGAMGDIPGVRFK 123
                      6889999**********************************************************************9878************* PP

                      BETS---TSSSTTTTT----T CS
  Ribosom_S12_S23  94 vvkvagvslkalskykkekpk 114
                      v kv++ sl++l+ +kkekp+
       AJA92384.1 124 VFKVNNTSLRQLVEGKKEKPR 144
                      *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.50
# Mc/sec: 867.70
//
Query:       AJA92385.1  [L=273]
Description: hypothetical protein T478_1069 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0094   15.8   0.0      0.016   15.1   0.0    1.5  2  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.02   14.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.056   12.8   0.1      0.091   12.2   0.1    1.3  1  TehB             Tellurite resistance protein TehB
      0.068   13.9   0.0       0.15   12.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.6e-06     0.016      24      75 ..     116     167 ..     100     230 .. 0.88
   2 ?   -3.1   0.0       1.4   6.1e+03     151     164 ..     236     249 ..     231     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
  Methyltransf_23  24 grvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqe 75 
                      +++LdiG G+G+ + + +  g +v+g+++++++v++  +++k +  +f+ ++
       AJA92385.1 116 KEILDIGSGDGRIAYCGKVLGLNVYGIEIDDMLVDLQNNISKKIMANFNPIC 167
                      69*********99888788899*************99988888888886655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
  Methyltransf_23 151 lkelleeaGlevve 164
                      +k+l  e+Gle+++
       AJA92385.1 236 WKKLIDESGLEIIK 249
                      57899999**9985 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.5e-06      0.02      13      81 ..     106     166 ..      99     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-06
  Methyltransf_32  13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkr 81 
                      + +    +ak  + ++++D+G+G g  +   +     ++l+v+gi++ + lv+  +++ +k+  +fn  
       AJA92385.1 106 ITS----MAKMLNYKEILDIGSGDGRIAYCGKV----LGLNVYGIEIDDMLVDLQNNISKKIMANFNPI 166
                      333....344467899********976665555....799**********************9888655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     2e-05     0.091      23      92 ..     107     180 ..      96     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                 HHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHH..TT-TTEEE..EE--GGG--- CS
        TehB  23 veavkivkpgkvldlgcgqgrnslylsllgydvtawdknensiafleeikek..enlknist..alydineakl 92 
                  + +k+++   +ld+g g+gr +   ++lg +v  ++ +++ +   ++i +k   n++ i +    +d n++ l
  AJA92385.1 107 TSMAKMLNYKEILDIGSGDGRIAYCGKVLGLNVYGIEIDDMLVDLQNNISKKimANFNPICSdaVKFDYNSLGL 180
                 56789999999*************************99999888777776552245555543103445555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05      0.15       1      59 [.     118     174 ..     118     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlp 59 
                      +Ld+G G Gr++       g  +v+g++i++ +++  +++++++ + n++ ++ da +++
       AJA92385.1 118 ILDIGSGDGRIAYCGKVL-G-LNVYGIEIDDMLVDL-QNNISKKIMaNFNPICSDAVKFD 174
                      8*********98777655.6.********9766665.55555443359999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1979.94
//
Query:       AJA92386.1  [L=252]
Description: sulfite exporter TauE/SafE [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-50  169.5  37.0    1.1e-49  169.2  37.0    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
      0.073   13.0   0.5      0.073   13.0   0.5    1.7  2  DUF2678   Protein of unknown function (DUF2678)
       0.12   11.6   0.4       0.27   10.5   0.4    1.6  1  S_4TM     SMODS-associating 4TM effector domain


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2  37.0   1.8e-53   1.1e-49       2     236 .]       8     243 ..       7     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 1.8e-53
        TauE   2 llagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallGallllllpsellkllfgvl 99 
                 + +g++aG++++++G+Ggg+iavP++++ ++ppa+a+  sl+a++ +s+++++++ r+++v++ +++ l+l+ ++G++lGa+++  + +  +++lf+++
  AJA92386.1   8 IPLGFAAGVLGSIVGLGGGIIAVPAMTFaGFPPALAASNSLFAAFSNSVASTVSYARQKRVEFGIGIKLGLMCIPGTILGAFVSDMMTPVTFQILFAFV 106
                 789*************************66*********************************************************999********* PP

        TauE 100 llllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwplllll 198
                 l+++a+++++++ + +++ ++++   i+++ + +++G++s+l+GiGgG++ vpl+++  g+p+++a+ t+ l+ ++ sl+g+l++ ++g+ d+  +++l
  AJA92386.1 107 LIASAVYIFIKRAIDEKPYNKTALMMIFSAGASFFAGIISSLFGIGGGIIFVPLMVIGIGIPMRRAAPTAQLILMFASLSGLLVHSALGHPDYLQAFFL 205
                 **********9988777777778888878888899**************************************************999*********** PP

        TauE 199 lpgallGallGarlarrlsertlrrlfallllvlgvkl 236
                 ++ga+ G+llGarl+  ++er+l++l+ ++ll+++vkl
  AJA92386.1 206 AVGAFGGGLLGARLSLEIKERKLKILVTIVLLAAAVKL 243
                 ***********************************986 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.2e-05     0.073      23      89 ..      61     124 ..      45     141 .. 0.75
   2 ?   -3.2   0.1       1.3   7.5e+03      99     106 ..     231     238 ..     221     246 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
     DUF2678  23 tsardriinlvvgg.ltsllvlvtvvssfvfpslppkplniffavcillisssvivlifwyrqgdlep 89 
                 ++ar++ +++ +g  l  + +  t++ +fv   + p +++i+fa++++  +s   v if  r  d +p
  AJA92386.1  61 SYARQKRVEFGIGIkLGLMCIPGTILGAFVSDMMTPVTFQILFAFVLI--AS--AVYIFIKRAIDEKP 124
                 5799999*****96145555668********************98654..33..35556666666555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
     DUF2678  99 lasivllc 106
                 l++ivll 
  AJA92386.1 231 LVTIVLLA 238
                 23333333 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.4   4.5e-05      0.27      17      83 ..      56     127 ..      50     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.5e-05
       S_4TM  17 aAqrqlYsrakrlqalrvilsvvlaivlsvlavlvps.....lktylallgllwllldvlvldrlqkkekek 83 
                  A +++Y+r kr+++ + i   ++ i +++l+++v++       ++l++++l+ +++++++ + + +k  +k
  AJA92386.1  56 VASTVSYARQKRVEFGIGIKLGLMCIPGTILGAFVSDmmtpvTFQILFAFVLIASAVYIFIKRAIDEKPYNK 127
                 5999*********************************87777667777777777888877777766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1848.70
//
Query:       AJA92387.1  [L=348]
Description: glycosyltransferase-like protein, family 2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-25   90.5   0.0    1.7e-25   89.8   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    2.4e-17   63.6   0.0    3.6e-17   63.0   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00012   22.1   0.0    0.00018   21.5   0.0    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    0.00032   20.4   0.6     0.0023   17.6   0.6    2.4  1  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
       0.15   12.6   0.0       0.28   11.7   0.0    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   4.7e-29   1.7e-25       1     169 [.      11     181 ..      11     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 4.7e-29
                      EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-T CS
  Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdp 94 
                      s++i  yN  k+l+e+++s+    +y+++eii+vD++StD+++  ++e    +p + +i +++n G+  + n g+r+++g+++++l+ D+++dp
       AJA92387.1  11 SIIILNYNAGKLLEECVDSIYHS-NYKNYEIIIVDNNSTDSSHIECKEK---FPLIDLIENKKNYGYCEGNNIGIRKSKGKFVIILNPDTIVDP 100
                      8**********************.*************************...69**************************************** PP

                      THHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.......EEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHHC CS
  Glycos_transf_2  95 dwleklvealekdgadvvlgqrprifgetdeiernkrv.......generlyfkerkrslkgnlsfeigsaallrrealeel 169
                      +w  +l+   +k g+ ++++  + + +++  i+ + ++       + ++++ + e++++   ++ + +g++   +++++e+l
       AJA92387.1 101 NWMNELLLGHQKFGD-GIYQPKFLTIDNESIIQSTGNMiqlfgfgYSRNKGDKDEQQFNNMETVNYASGTCLFTSKKIFEKL 181
                      ************666.66666666667777777777778****************************************986 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0     1e-20   3.6e-17       4     229 ..      10     242 ..       8     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1e-20
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdD 97 
                      +++++ ++n+ + l+e+++s+  + y ++e+++v+++s+++   +++e   ++p +  +++ n++n   +g+ ++ n ++r  k+++v++++ D
       AJA92387.1  10 ISIIILNYNAGKLLEECVDSIYHSNYKNYEIIIVDNNSTDSSHIECKE---KFPLI--DLIENKKN---YGYCEGNNIGIRKSKGKFVIILNPD 95 
                      79*********************9****************98777877...****6..89988886...6788899****************** PP

  Glyco_tranf_2_3  98 tvvePdtlkrllqffltpkvgavgtpvfl..lnrs......tlvsal..galefaerhl..rflaarralgvltlnGsgslirrevlkelegld 179
                      t+v+P+    ll    ++  + +++p+fl  +n+s      ++++    g   + +++   ++ ++ ++ +v + +G++++   ++++ le +d
       AJA92387.1  96 TIVDPNWMNELLLG-HQKFGDGIYQPKFLtiDNESiiqstgNMIQLFgfG---YSRNKGdkDEQQFNNMETVNYASGTCLFTSKKIFEKLEFFD 185
                      ******97665544.46655677777766232333444222444444333...33333333889999*****999******************* PP

  Glyco_tranf_2_3 180 p.lflltdDyelglrlrragfrtayvpgaavrev......fpsslkayikqrnRwvy 229
                        lf   dD++l+ r+ ++g++++yvp ++v +       ++s++k +  +rnR ++
       AJA92387.1 186 SfLFAYHDDLDLCWRASMQGIQSYYVPTSIVFHPsegfsfKWSNFKFFLLERNRLYC 242
                      *999999***********************999977777778************986 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     5e-08   0.00018       2     129 ..      89     224 ..      88     286 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5e-08
  Glyco_trans_2_3   2 illlDaDtvlppdclreiaa.elaspevaivqgpvl.vmnva..nwleelaalf...f.aedhgkdilvrealgrvvpsv.Gsgaflrrsalqe 86 
                      +++l  Dt ++p+  +e++  + + +  +i+q + l ++n +    + +++ lf   +  +   kd  +++++ ++v  + G + f++ + +++
       AJA92387.1  89 VIILNPDTIVDPNWMNELLLgHQKFG-DGIYQPKFLtIDNESiiQSTGNMIQLFgfgYsRNKGDKDEQQFNNM-ETVNYAsGTCLFTSKKIFEK 180
                      67777788888877777755233343.3788877441454331133344444445444355566666665555.5555555************* PP

  Glyco_trans_2_3  87 vggwdgdessvsEDfdmglrlqrkGyrvrfvpes.lvkeksplt 129
                      + ++d+  ++  +D+d++ r+ ++G + ++vp s +++ +  ++
       AJA92387.1 181 LEFFDSFLFAYHDDLDLCWRASMQGIQSYYVPTSiVFHPSEGFS 224
                      *****999************************996444333333 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   6.4e-07    0.0023      30     176 ..      62     207 ..      12     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.4e-07
  Glyco_tranf_2_5  30 veiiairnaksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmiGvvGakslpesg.vwweskkkvgkvietskeeake 122
                      +++i+ +++  ++e+ n ++++s+ k+++ l+ D+ i+ ++++++ll      +k G  G+   k l+ +   +++s  +++++     +++k 
       AJA92387.1  62 IDLIENKKNYGYCEGNNIGIRKSKGKFVIILNPDT-IVDPNWMNELLLGH---QKFGD-GIYQPKFLTIDNeSIIQSTGNMIQLFGFGYSRNKG 150
                      56777777799***********************8.89********9655...77774.99999999887745668888888888888888888 PP

  Glyco_tranf_2_5 123 lraeeeeseyeeVeaidGllmatqydv....pwredlftgfhfYdvsqslefekagyk 176
                       ++e++ +++e+V+   G  ++t + +    ++ +  f   +  d++ + + + +g +
       AJA92387.1 151 DKDEQQFNNMETVNYASGTCLFTSKKIfeklEFFDS-FLFAYHDDLDLCWRASMQGIQ 207
                      778889999999999999999999999555544444.333344588888887777765 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.7e-05      0.28       1      52 [.      17      71 ..      17     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
  Glyco_tranf_2_4  1 rneadiLpefla..hhlalgfdrilvydndstDgtrailkel.pevkllhvdksy 52
                     +n+ ++L+e+++  +h ++   +i+++dn+stD +   +ke  p ++l++++k+y
       AJA92387.1 17 YNAGKLLEECVDsiYHSNYKNYEIIIVDNNSTDSSHIECKEKfPLIDLIENKKNY 71
                     589999*****966777777778**********9988887755888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2315.88
//
Query:       AJA92388.1  [L=151]
Description: putative HTH-type transcriptional regulator LrpA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-11   44.1   0.0    2.7e-11   43.3   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.2e-11   42.6   1.9    7.5e-11   41.4   1.9    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    6.9e-10   38.6   0.0    1.3e-09   37.7   0.0    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    3.7e-06   26.8   0.2    5.5e-06   26.2   0.2    1.3  1  MarR            MarR family
    0.00013   21.8   0.5    0.00029   20.7   0.5    1.6  1  HTH_11          HTH domain
     0.0029   17.8   0.4      0.006   16.8   0.4    1.5  1  Ribosomal_S25   S25 ribosomal protein
     0.0047   17.1   0.3     0.0089   16.2   0.3    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.023   14.5   0.9      0.059   13.3   0.2    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.026   14.6   0.0      0.042   13.9   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.037   14.6   0.4      0.082   13.5   0.4    1.5  1  Mga             Mga helix-turn-helix domain
      0.043   14.0   0.2        0.1   12.9   0.2    1.7  1  Rio2_N          Rio2, N-terminal
      0.082   13.1   0.2       0.15   12.3   0.2    1.4  1  HTH_34          Winged helix DNA-binding domain
       0.12   12.3   0.0       0.18   11.7   0.0    1.3  1  MarR_2          MarR family
       0.12   12.7   0.3       0.37   11.2   0.2    1.8  2  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   2.1e-14   2.7e-11       2      74 ..      71     140 ..      70     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.1e-14
                     EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
  AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                     ++++++++    +++++ l e++ V+e+  vtG +d+++ +++++l++++++++ek+++++g+  +e++i ++
      AJA92388.1  71 GINMDSKR---RDAIIDNLFEIDGVREISEVTGRFDIMVTMYAKSLNDMHKVVSEKIGKIEGILGSESFIEMK 140
                     57888788...9*********************************************************9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   1.9   5.9e-14   7.5e-11       2      47 ..       5      50 ..       4      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.9e-14
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                de+d+kIL++L  +++is   L+e++++ +s v  r+krL ++ lI
  AJA92388.1  5 DELDLKILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLI 50
                99****************************************9998 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0     1e-12   1.3e-09       1      41 [.       4      44 ..       4      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1e-12
  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                   +De+D+kIL++L  da+is+ +L+e++++  s v  R++rL
     AJA92388.1  4 IDELDLKILSELSNDASISVPKLSEKININSSVVYSRIKRL 44
                   6***************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   4.3e-09   5.5e-06       6      56 ..       9      59 ..       4      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.3e-09
                HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
        MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56
                ++iL  l++  ++sv +L +k+++++s v   ++rL k+ li+R+    + 
  AJA92388.1  9 LKILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQRYTIDVND 59
                78******************************************9876555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.5   2.3e-07   0.00029       3      48 ..       9      57 ..       8      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.eelg...vpIes 48
                l+il  L +++  is  +L+e++n+  ++v+ +Ik+L + ++   + I+ 
  AJA92388.1  9 LKILSEL-SNDASISVPKLSEKININSSVVYSRIKRLlKQKLiqrYTIDV 57
                589999*.66666************************6666567766665 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   4.7e-06     0.006      46      89 ..      10      53 ..       4      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.7e-06
  Ribosomal_S25 46 kllkevpkyklitpsvvserlkingslArraLreleekgliklv 89
                   k+l+e  +   i++  +se+++in s+  + ++ l++++li+++
     AJA92388.1 10 KILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQRY 53
                   8999*************************************986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3     7e-06    0.0089      23      60 ..      25      61 ..      21      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
  B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvkqsiidsatkk 60
                     L+  +++ ++ +++r+k L k++LI + +i d+++k 
      AJA92388.1 25 KLSEKININSSVVYSRIKRLLKQKLIQRYTI-DVNDKE 61
                    6888899************************.888775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.6e-05     0.059       7      54 ..       5      52 ..       3      65 .. 0.91
   2 ?   -1.1   0.0       1.4   1.8e+03      25      49 ..      92     116 ..      90     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                HHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
        TrmB  7 seyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                 e + k+   L +  + ++ +++e++++  s vY+ +++L++  l++r
  AJA92388.1  5 DELDLKILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQR 52
                6788899999999999999***********************999987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                 HCHHCCCTTSSCHCHHHHHHHHHHC CS
        TrmB  25 adeiaeelgvprskvYevLrsLedk 49 
                 ++ei+e +g+    v  + +sL d+
  AJA92388.1  92 VREISEVTGRFDIMVTMYAKSLNDM 116
                 6888888887665555555555555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.042      13      56 ..       9      52 ..       4      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
      HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                ++il++L+ ++  +++ l e + +  + ++ +++ L +  L+ +
  AJA92388.1  9 LKILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQR 52
                89************************************999965 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   6.4e-05     0.082      17      65 ..       7      57 ..       4      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH..HHHCHCCT-EE CS
         Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikel..nklLkefdlel 65
                l++++l  l +++++s+ +l+++  i +s ++  ik+l  +kl++ + + +
  AJA92388.1  7 LDLKILSELSNDASISVPKLSEKININSSVVYSRIKRLlkQKLIQRYTIDV 57
                7899********************************986567788999887 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   7.8e-05       0.1       8      61 ..       8      57 ..       1      70 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
      Rio2_N  8 dfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktaky 61
                d+++L+       n   +++ +++e  +++++ v +r++rllk+kli+r t+  
  AJA92388.1  8 DLKILSE----LSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQRYTIDV 57
                5555543....3566778899999999**********************76654 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00012      0.15       3      45 ..       9      51 ..       7      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
      HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                l++ls L+ + +++  +l+e+++++++  ++ +k L k++ i+
  AJA92388.1  9 LKILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQ 51
                89**********************************9998876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00014      0.18      10      54 ..      11      53 ..       7      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                +L +L +     ++v  l ++ ++  s v  ++krL ++ L++r 
  AJA92388.1 11 ILSELSNDAS--ISVPKLSEKININSSVVYSRIKRLLKQKLIQRY 53
                7889999998..9*****************************986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00029      0.37      16      56 ..      11      51 ..       7      54 .. 0.87
   2 ?   -1.9   0.0       3.4   4.3e+03      37      49 ..     104     116 ..      91     138 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                +L++ +++ ++s+ +++e+ ni+ s++   +++L k++l++
  AJA92388.1 11 ILSELSNDASISVPKLSEKININSSVVYSRIKRLLKQKLIQ 51
                4666677778***************************9997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                 S-HHHHHHHHHHH CS
        Rrf2  37 ispsylekilakL 49 
                 i  ++ +k l+ +
  AJA92388.1 104 IMVTMYAKSLNDM 116
                 4333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1078.02
//
Query:       AJA92389.1  [L=453]
Description: ABC transporter, permease protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-27   95.3   9.5    3.5e-27   95.3   9.5    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.17   11.9   0.0    2.6  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.24   2.2e+03      59      68 ..      28      37 ..      13      53 .. 0.49
   2 !   95.3   9.5   3.9e-31   3.5e-27       1     184 [.     267     452 ..     267     453 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.24
  BPD_transp_1 59 llllsaapyv 68
                   l+l +++++
    AJA92389.1 28 GLILVSIITI 37
                  2222222222 PP

  == domain 2  score: 95.3 bits;  conditional E-value: 3.9e-31
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                   g++ G++++ +r+kk+d++++++ +v+++lP + ++i+l +     +i  + +l++ +l+++s+++++ + r++ l++  ++++eaa+++G ++ +i
    AJA92389.1 267 GLVYGVYSG-YRGKKTDEVMMRFNDVIYALPALPFLIILAV-----TISNSIFLMIGFLMIFSWVGIAKVSRSMSLQIKTRQYIEAAKIMGQKDSKI 357
                   7899*****.****************************995.....999999********************************************* PP

  BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.............nggvlalviavlllnlvadilqrlldp 181
                   +++++lP++lp+++++++++++++++  + l+flg    lg++ + +++g+ ++ ++             + + + ++i  l+++++ ++l ++++p
    AJA92389.1 358 IFRHILPQLLPYAFASIAISVPAAITTEAGLSFLG----LGDPSF-PTWGQILHDANtygaaaqgfwwwiVPPGILIAITGLAFVFIGNALDAIVNP 449
                   ***********************************....998766.67888887777789999********************************** PP

  BPD_transp_1 182 rvr 184
                   +++
    AJA92389.1 450 KLK 452
                   *97 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17       9      42 ..      12      46 ..       6      56 .. 0.81
   2 ?   -4.0   1.5       1.7   1.5e+04      32      32 ..     313     313 ..     300     329 .. 0.55
   3 ?   -2.5   0.7      0.59   5.3e+03      16      34 ..     430     449 ..     427     451 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
      OppC_N  9 rFkrNklAvvglvilllllliaifaPliaPydp.q 42
                 F++ kl + g +il  l+l++i+   ++P +  q
  AJA92389.1 12 EFLKSKLGLTGIFILSGLILVSIITISVIPASTfQ 46
                69**********************87777755454 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.7
      OppC_N  32 f 32 
                 f
  AJA92389.1 313 F 313
                 1 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.59
      OppC_N  16 Avvglvilll.llliaifaP 34 
                 A+ gl+++ +  +l ai++P
  AJA92389.1 430 AITGLAFVFIgNALDAIVNP 449
                 34444443333444466665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3358.93
//
Query:       AJA92390.1  [L=340]
Description: flap structure-specific endonuclease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.8e-23   80.5   0.0    2.6e-22   79.0   0.0    1.8  2  XPG_I       XPG I-region
    2.1e-21   76.3   0.0    5.2e-21   75.0   0.0    1.6  2  XPG_N       XPG N-terminal domain
      0.001   19.6   0.0     0.0026   18.3   0.0    1.9  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.023   15.0   0.4      0.023   15.0   0.4    2.1  2  DUF4878     Domain of unknown function (DUF4878)


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   5.7e-26   2.6e-22       1      94 []     140     236 ..     140     236 .. 0.92
   2 ?   -3.4   0.1       2.9   1.3e+04      57      76 ..     314     331 ..     301     339 .. 0.43

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 5.7e-26
                 HHHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT.......EEECEEEEEEHHHHHHHHT--HHHHHHHHHHHCET CS
       XPG_I   1 klmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkk.....kekekkkvevidlekvlkelgltreqlidlaillgcD 94 
                 +l+gip ++Ap+E+EA +a L+ +g++ a +s+D D++lFGa++++rn++++ +  +     +++ ++ +e+i+ +k l+ +gltr++l+d  il+g+D
  AJA92390.1 140 DLFGIPHIQAPSEGEATAASLTITGQAFASASQDFDSILFGAKRLVRNFTNSGR--RklpnrNSYIEVLPEMIEFQKNLDSMGLTRQELVDTGILIGTD 236
                 589**********************************************93333..234788999999*****************************99 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                 T..EEECEEEEEEHHHHHHH CS
       XPG_I  57 kkekekkkvevidlekvlke 76 
                 +  k++++ ++ +l+k l++
  AJA92390.1 314 S--KDRVETSMNRLKKSLEK 331
                 3..33333344444444443 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   1.2e-24   5.2e-21      17     101 .]      12     101 ..       4     101 .. 0.94
   2 ?   -3.8   0.0         4   1.8e+04      51      70 ..     121     140 ..     114     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.2e-24
                 EEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S--GGGHHHHHHHHHHHHHH CS
       XPG_N  17 rsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkapdlkkeelekrserrqea 101
                 ++ ++e++ +k++aiDa+  +y+fl  +r ++g +l+      tsh++gl+ r + +l++gikP++VFdgk+p+lk+ e+ekr+++++ea
  AJA92390.1  12 EKTQLESFTNKVVAIDAYNAIYQFLAIIRGPEGLHLTDsqgrvTSHITGLLFRNINFLTMGIKPVYVFDGKPPSLKSAEIEKRKQIKKEA 101
                 4689*****************************99999999*********************************************9985 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4
                 E-BS-HHHHHHHHHHHHHHH CS
       XPG_N  51 alentshlmglfsrllrlld 70 
                 a ++ts   g++++ ++lld
  AJA92390.1 121 AQQTTSMRDGMVEDSKKLLD 140
                 34557788888888888776 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.8e-07    0.0026      19      53 ..     238     272 ..     221     335 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.8e-07
  5_3_exonuc  19 nipGvpgiGektAakLlkeygsleeilenldelke 53 
                 n  G + +G+ktA+k++k+++ le+i +  ++l++
  AJA92390.1 238 NPDGFERVGPKTAIKMIKQHKRLEDIPQIQEQLEQ 272
                 567999*******************9994444433 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4     5e-06     0.023      10      45 ..      99     134 ..      93     140 .. 0.89
   2 ?   -1.0   0.1      0.48   2.1e+03      22      60 ..     297     332 ..     290     337 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5e-06
     DUF4878  10 eeavknFleavkeGdvedaikyltestreedalaek 45 
                 +ea+  + +a++ Gd+eda+ky+ + t   d++ e+
  AJA92390.1  99 KEATVKYEKAISAGDMEDARKYAQQTTSMRDGMVED 134
                 78999**********************999999887 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.48
     DUF4878  22 eGdvedaikyltestreedalaeklkgkfkelkakaekk 60 
                 e d+e  +kyl e+     + ++ +++  + lk + ekk
  AJA92390.1 297 ETDYEGIVKYLSEERD---FSKDRVETSMNRLKKSLEKK 332
                 6788888888877543...34444444444444454444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2273.97
//
Query:       AJA92391.1  [L=167]
Description: hypothetical protein T478_1487 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1272.62
//
Query:       AJA92392.1  [L=549]
Description: methionine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.7e-137  457.2   0.6   4.7e-137  456.9   0.6    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
    3.3e-20   71.9   1.0    4.2e-06   25.3   0.0    4.1  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    5.7e-13   48.9   0.4    3.1e-05   23.5   0.0    2.4  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    3.3e-08   33.6   0.3    9.5e-08   32.1   0.0    1.8  2  Anticodon_1     Anticodon-binding domain of tRNA
    6.4e-06   25.3   0.1       0.01   14.8   0.0    3.2  3  tRNA-synt_1f    tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.018   12.9   1.1      0.025   12.5   1.1    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
      0.041   14.3   0.0       0.38   11.2   0.0    2.1  2  FhuF            Ferric iron reductase FhuF-like transporter
      0.078   12.7   0.1       0.16   11.7   0.1    1.5  1  DUF3804         Protein of unknown function (DUF3804)
      0.085   13.2   0.1       0.23   11.8   0.1    1.8  1  DUF3010         Protein of unknown function (DUF3010)
       0.12   12.5   0.2       0.33   11.2   0.2    1.7  1  XhlA            Haemolysin XhlA
       0.14   11.8   0.0       0.25   11.0   0.0    1.3  1  Gene66          Gene 66 (IR5) protein
       0.84    9.6   8.1        1.4    8.8   0.4    2.3  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
          1    9.9   6.9        3.2    8.3   6.7    1.9  1  zf-CHY          CHY zinc finger
        1.1    9.3   9.1        2.7    8.1   1.5    2.4  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
        1.2    9.5   7.1       0.91    9.9   5.4    1.7  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        1.2    9.1   7.2        4.1    7.5   7.0    1.8  1  zinc-ribbons_6  zinc-ribbons
        2.8    8.0  10.6          4    7.5   6.6    2.2  2  DZR             Double zinc ribbon
        5.9    6.9   7.5        8.1    6.5   0.4    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.9   0.6  4.7e-140  4.7e-137       2     390 ..       6     392 ..       5     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 456.9 bits;  conditional E-value: 4.7e-140
                   EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHH CS
  tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehk 97 
                   ++t+alpY+ng++HlGh++ ++++aD+ +R+ +++g e +++c++D +Gtpi ++ ek + tp+e+v++ +++  e+f+ ++i fd +++t+see+ 
    AJA92392.1   6 IITSALPYSNGEIHLGHVAsTYLPADVTTRFLKQNGVEAYYICASDDYGTPILIQSEKLKQTPQEYVAHWNKRDYEDFTAFDIGFDFFYKTSSEENI 102
                   79*****************9***************************************************************************** PP

                   HHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E................EEE.EEEEEE-GGGGHHH CS
  tRNA-synt_1g  98 elvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkkleptelinpksaisgskpevketehlffklskfekk 194
                   ++vq++fkk++++g+iyekei q++c+++++flpdr+v+gtCP c++e++++d ce+cg+   p+e++np+++i+g++p+ k+t+h+ffkl++f++ 
    AJA92392.1 103 SFVQDVFKKIEKNGHIYEKEIIQAFCTSCDKFLPDRFVKGTCPFCNAEDQYSDLCEKCGRI--PEEIENPHCSICGETPVQKSTNHYFFKLKNFSEP 197
                   ************************************************************8..55******************************** PP

                   HHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEE CS
  tRNA-synt_1g 195 lkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfig 289
                   l e++ e+ + l++ vkk+v++w+kegL d++i+rd++wG+p+P  g ++kv+Y W+d  + Yis+t ++   ++++ + k++W +  +++++hfig
    AJA92392.1 198 LLEYL-ENAPYLQKDVKKYVENWIKEGLVDWDITRDIPWGVPIPidGLKDKVFYGWFDNHLAYISSTLKFL--NDKNIDGKSFW-N--DADIYHFIG 288
                   *****.99999**********************************99**********************99..4456799****.4..899****** PP

                   GGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-.TTS-EEE-HHHHHHHHHHHCCCHH CS
  tRNA-synt_1g 290 kdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeap.ekkDldfswedfvervNseLadkl 383
                   kdi+++H +f+Pa+ lg  +e+klp+ + + ++lt+egkK+SkSr++ +  k++le+++ad+lR+yl++ +p  ++Dl+f we+f  ++NseL+++l
    AJA92392.1 289 KDIVYHHYLFLPAMRLGieKEFKLPDYIPTRGHLTLEGKKISKSRNWYIGLKDFLEKFPADYLRFYLISINPySQDDLNFDWEQFSTKINSELIGNL 385
                   *****************9999************************************************66516789******************** PP

                   HHHHHHH CS
  tRNA-synt_1g 384 gnlvnRv 390
                   gnlvnR+
    AJA92392.1 386 GNLVNRA 392
                   ******8 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   9.1e-09   9.1e-06      25     173 ..       5     135 ..       1     141 [. 0.83
   2 !   25.3   0.0   4.2e-09   4.2e-06     360     433 ..     167     241 ..     160     248 .. 0.92
   3 !   15.3   0.0   4.6e-06    0.0046     559     598 ..     324     364 ..     244     369 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.1e-09
  tRNA-synt_1  25 filvdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkr 121
                   i++   Py +G++H+Gh+  + l  d+ +r+ +++G e+ y    D  G +i  + ek                  ++  +e++a+  ++  ++++ 
   AJA92392.1   5 AIITSALPYSNGEIHLGHVASTYLpADVTTRFLKQNGVEAYYICASDDYGTPILIQSEKL-----------------KQTPQEYVAHWNKRDYEDFTA 85 
                  5777888**************999669*************************97765543.................233345566666666777777 PP

  tRNA-synt_1 122 lGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktal 173
                  + + +Df   y+T ++e    v+ vf+++ ++g+iy+ + +  ++t++   l
   AJA92392.1  86 FDIGFDF--FYKTSSEENISFVQDVFKKIEKNGHIYEKEIIQAFCTSCDKFL 135
                  7776666..699*****************************9***9998665 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.2e-09
  tRNA-synt_1 360 hsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhripl 433
                   + p+c+  ++  + ++t+ +f ++k++ + +l+ +e++ +  k  +k  ++w+++   dW i R+  WG++ip+
   AJA92392.1 167 IENPHCSICGETPVQKSTNHYFFKLKNFSEPLLEYLENAPYLQKDVKKYVENWIKEgLVDWDITRDIPWGVPIPI 241
                  5679999999988999**************************************87479***************7 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 4.6e-06
  tRNA-synt_1 559 eeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrd 598
                   eG+K+SKs   +i  +d ++k  ad lR++li  +++++d
   AJA92392.1 324 LEGKKISKSRNWYIGLKDFLEKFPADYLRFYLIsINPYSQD 364
                  58*******************************87888775 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   3.2e-08   3.1e-05      21     125 ..      16     122 ..       3     135 .. 0.90
   2 !   23.2   0.0   3.7e-08   3.7e-05     211     292 ..     285     369 ..     272     378 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.2e-08
                   S--BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----S.B--BGGGGHHHHHHHHHHH CS
  tRNA-synt_1e  21 dashlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkpt.leprvsekvdeiielvekl 115
                    ++hlGh a +++  D+  r+l++ g +  ++    D    i+ ++++ +++ +e ++++ +  ++d++a ++     +++   e+++ + ++ +k+
    AJA92392.1  16 GEIHLGHvASTYLPADVTTRFLKQNGVEAYYICASDDYGTPILIQSEKLKQTPQEYVAHWNKRDYEDFTAFDIGFDFfYKTSSEENISFVQDVFKKI 112
                   578****4567999***********************************************************8765156777889*********** PP

                   HHTTSEEE-T CS
  tRNA-synt_1e 116 iekgyaYavs 125
                    ++g+ Y+ +
    AJA92392.1 113 EKNGHIYEKE 122
                   *******976 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 3.7e-08
                   EEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-..EEE- CS
  tRNA-synt_1e 211 hsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsq..ldfk 292
                   h  G+D+++ h+    a+        +l  y    ghl++eg+k+sks + +i +kd+l+kf +  lR++l+s + +sq  l+f+
    AJA92392.1 285 HFIGKDIVYHHYLFLPAMRLGIEKeFKLPDYIPTRGHLTLEGKKISKSRNWYIGLKDFLEKFPADYLRFYLISINPYSQddLNFD 369
                   67788888877777777777665546778899999************************************99764443126665 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.7   2.6e+03      22     135 ..      80     114 ..      61     131 .. 0.55
   2 !   32.1   0.0   9.5e-11   9.5e-08       6     118 ..     419     523 ..     414     545 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
  Anticodon_1  22 yrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelwqreeeelgkkesimlaewpekaeelekele 119
                  y+  +a++  ++ff+++ +   + +v++ +                                                                    
   AJA92392.1  80 YEDFTAFDIGFDFFYKTSSEENISFVQDVF-------------------------------------------------------------------- 109
                  333344445555555555555555554444.................................................................... PP

  Anticodon_1 120 eeevellkeivkairk 135
                             k i+k
   AJA92392.1 110 -----------KKIEK 114
                  ...........44443 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 9.5e-11
  Anticodon_1   6 selnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPfmPfitEelwqreeeelgkkesi 102
                  +++ +l++++ + +ee  +++a+++l+ef +  + + y++  +p+ ++      ++ + ++   +++++ ++l+ f+P  ++++w     +lg +  +
   AJA92392.1 419 QKIKSLAEDIGKLMEENHLDRALKQLMEF-SAHF-NQYFQHKEPWKKGPG----TNaCIYLSVNAVRSIAICLQSFLPKSSQKIW----SQLGLDGNV 506
                  68999***********************7.7778.**********85533....34499**************************....899999999 PP

  Anticodon_1 103 mlaewpe.kaeelekel 118
                  +  +w e ++ el+  +
   AJA92392.1 507 SDVNWNEmSNLELKSGH 523
                  99999985554444433 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.019        19      34      71 ..      15      53 ..       2      56 .. 0.80
   2 ?    2.3   0.1     0.065        65     104     183 ..      68     163 ..      63     170 .. 0.73
   3 !   14.8   0.0     1e-05      0.01     277     322 ..     325     369 ..     320     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.019
  tRNA-synt_1f 34 SGliHiGnlrev.ltadlvaralrkrgeevrlilisDdm 71
                   G iH+G +  + l ad+  r l++ g e+  i+ sDd+
    AJA92392.1 15 NGEIHLGHVASTyLPADVTTRFLKQNGVEAYYICASDDY 53
                  49******996516677778888999************8 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.065
  tRNA-synt_1f 104 hesyaehfnaelvesLdelgievefisatelYksglydeaikealenreki..keilekyrgee...reet.............yspylpvcekcgr 182
                    ++y+ h+n++  e   +++i ++f  +t+  ++  + + + + +e++ +i  kei++ + ++    +                   y+ +cekcgr
    AJA92392.1  68 PQEYVAHWNKRDYEDFTAFDIGFDFFYKTSSEENISFVQDVFKKIEKNGHIyeKEIIQAFCTSCdkfL--PdrfvkgtcpfcnaEDQYSDLCEKCGR 162
                   57899*****999999**********999999999999999999999888855567777765543222..023455555555544556666666666 PP

  tRNA-synt_1f 183 v 183
                   +
    AJA92392.1 163 I 163
                   5 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 1e-05
  tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                   + g+k+s+S+  ++ l+d le  + + lrf++++ +P ++ +l++d
    AJA92392.1 325 E-GKKISKSRNWYIGLKDFLEKFPADYLRFYLISINPYSQDDLNFD 369
                   4.55***************************************998 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   2.5e-05     0.025     601     672 ..     107     186 ..      96     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
    PolC_DP2 601 svkeaakkkgei.eveiarrkCkkCgk....etlearCeeCgekteeklvCkkcee...eveeekcekcekeakavkkkk 672
                 +v + ++k+g+i e ei +  C++C+k    + ++ +C+ C+++ + +  C+kc++   e+e+ +c+ c+++  ++++++
  AJA92392.1 107 DVFKKIEKNGHIyEKEIIQAFCTSCDKflpdRFVKGTCPFCNAEDQYSDLCEKCGRipeEIENPHCSICGETPVQKSTNH 186
                 44455555778879************83332457889*****************99654555777999998876655544 PP

>> FhuF  Ferric iron reductase FhuF-like transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038      0.38      80     115 ..     243     280 ..     231     283 .. 0.88
   2 ?    0.3   0.0      0.81     8e+02      56     116 ..     437     500 ..     421     501 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                 GGSHHHHIIIIIIIHHHHHHHH..HHTTSS-HHHHHHH CS
        FhuF  80 elreevfyglfvnhlaplieal..aaagglsekllWsn 115
                  l+++vfyg f+nhla+++ +l    + +++ k +W+ 
  AJA92392.1 243 GLKDKVFYGWFDNHLAYISSTLkfLNDKNIDGKSFWND 280
                 56789****************98889999*******86 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.81
                 T-EES-TT----TTSGGGB----GGGS...HHHHIIIIIIIHHHHHHHHHHTTSS-HHHHHHHH CS
        FhuF  56 kaellpelpalpeevkrlltddpeelr...eevfyglfvnhlapliealaaagglsekllWsnv 116
                  +++l +l +++++ ++++ +++++++      + +l vn ++ ++ +l++  + s + +Ws++
  AJA92392.1 437 LDRALKQLMEFSAHFNQYFQHKEPWKKgpgTNACIYLSVNAVRSIAICLQSFLPKSSQKIWSQL 500
                 4566666667777777788888888888888888999999999999999988888888888877 PP

>> DUF3804  Protein of unknown function (DUF3804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00016      0.16      76     109 ..      82     115 ..      39     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                 EEEEEEEEEEEEETTEEEEEB-EEEEEEEEETTE CS
     DUF3804  76 aitvftlkekfsykgdlnddlsivslifkkidek 109
                  +t+f ++  f yk + ++++s v  +fkki++ 
  AJA92392.1  82 DFTAFDIGFDFFYKTSSEENISFVQDVFKKIEKN 115
                 699****************************976 PP

>> DUF3010  Protein of unknown function (DUF3010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00023      0.23      17      64 ..     392     439 ..     380     457 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
     DUF3010  17 llslekelfelpdvrtkklslkdnesteeireFqktfaklmedykvdk 64 
                 +l +++ +f+ +  + +k+  kd+es+++i++ ++++ klme++++d+
  AJA92392.1 392 ALGFTNKTFDGVVPEPEKFDEKDSESEQKIKSLAEDIGKLMEENHLDR 439
                 57889999*************************************997 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00033      0.33      22      47 ..     409     434 ..     404     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
        XhlA  22 kleekaaeaeekiknleedlkklesn 47 
                 k +ek +e e+kik+l ed+ kl + 
  AJA92392.1 409 KFDEKDSESEQKIKSLAEDIGKLMEE 434
                 6789******************9765 PP

>> Gene66  Gene 66 (IR5) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.25     135     183 ..     117     165 ..     115     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
      Gene66 135 HaatCsvsqlYEkallrlleealgigetPladaerywkalleavaaege 183
                 H     + q++   + ++l  +++ g+ P+++ae  +  l+e  +  +e
  AJA92392.1 117 HIYEKEIIQAFCTSCDKFLPDRFVKGTCPFCNAEDQYSDLCEKCGRIPE 165
                 55555666777799****************************9988776 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0014       1.4      24      46 ..     126     150 ..     123     154 .. 0.90
   2 ?    4.2   2.0     0.041        41      25      45 ..     156     177 ..     152     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                 EE-HHHHHHHHH..TT-B-TTT--B CS
  zf-C3HC4_3  24 vlCeeCaekllk..rkkkCpiCrrp 46 
                 ++C +C + l +   k +Cp+C+++
  AJA92392.1 126 AFCTSCDKFLPDrfVKGTCPFCNAE 150
                 69********98999*******976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.041
                 E-HHHHHHHHH.TT-B-TTT-- CS
  zf-C3HC4_3  25 lCeeCaekllk.rkkkCpiCrr 45 
                 lCe+C +  ++ ++++C iC +
  AJA92392.1 156 LCEKCGRIPEEiENPHCSICGE 177
                 7****9999889********76 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.7    0.0033       3.2      40      73 ..     140     176 ..     126     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
      zf-CHY  40 kevlcllCeteqekavlCkkCkk...efaeyfCpiCk 73 
                  + +c +C++e++ + lC+kC++   e+++ +C+iC 
  AJA92392.1 140 VKGTCPFCNAEDQYSDLCEKCGRipeEIENPHCSICG 176
                 4457*****************9977777777999996 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.022        22      19      42 ..     127     149 ..     121     151 .. 0.84
   2 ?    8.1   1.5    0.0027       2.7      16      45 ..     153     181 ..     151     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
    zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgs 42 
                  C++C k +  +    ++C+fC++
  AJA92392.1 127 FCTSCDKFLPDRFVK-GTCPFCNA 149
                 799999999888777.******97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
    zf-C2HC5  16 aapnClnCGkiiCakeglskpCsfCg.spll 45 
                 +  +C +CG i  + e++  +Cs Cg +p+ 
  AJA92392.1 153 YSDLCEKCGRIPEEIENP--HCSICGeTPVQ 181
                 5668**************..9****955544 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.4   0.00091      0.91       4      42 ..     143     180 ..     140     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00091
     zf-Di19   4 tCPyCgkeltvkeLveHvedeHrveskevvCPvCaekvt 42 
                 tCP+C+ e + + L+e +    ++e ++  C++C e+  
  AJA92392.1 143 TCPFCNAEDQYSDLCEKCGR-IPEEIENPHCSICGETPV 180
                 8*****************98.689999999****86633 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.0    0.0041       4.1       3      37 ..     128     162 ..     126     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                     -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S CS
  zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeq 37 
                     C +C++ l  r  + +C  C+++ +   lC++C+ 
      AJA92392.1 128 CTSCDKFLPDRFVKGTCPFCNAEDQYSDLCEKCGR 162
                     *********************************96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  10.3     0.045        45       1      49 []     128     176 ..     119     176 .. 0.54
   2 ?    7.5   6.6     0.004         4       1      42 [.     144     184 ..     144     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.045
         DZR   1 CpqCgeelppdar..fCseCgtklkavaaedrCpsCgek.vdpearfCpeCG 49 
                 C +C + lp++    +C+ C+++ +    +d C +Cg+   + e   C  CG
  AJA92392.1 128 CTSCDKFLPDRFVkgTCPFCNAEDQY---SDLCEKCGRIpEEIENPHCSICG 176
                 44455555554444455555554331...56666666664555555566665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.004
         DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgek.vdpea 42 
                 Cp C++e ++ +  C++Cg  ++ + ++ +C+ Cge  v++ +
  AJA92392.1 144 CPFCNAE-DQYSDLCEKCGRIPE-EIENPHCSICGETpVQKST 184
                 9****99.9999*******9986.666889*****98677665 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0081       8.1      64      96 ..     119     151 ..      90     156 .. 0.76
   2 ?    3.7   1.7     0.059        59      72      99 ..     156     182 ..     149     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0081
                 EEEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
        HypA  64 ieevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                 +e++ +++ C++C+k    +   + +Cp C+++d
  AJA92392.1 119 YEKEIIQAFCTSCDKFLPDR-FvKGTCPFCNAED 151
                 6788899*******766644.34789****9986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.059
                 EETTTS-EEECHHHHHS-TTTSSS-EEE CS
        HypA  72 rCreCgkefeleekalrCpkCgsadvei 99 
                  C++Cg+  e+  ++ +C  Cg++ v+ 
  AJA92392.1 156 LCEKCGRIPEEI-ENPHCSICGETPVQK 182
                 6*****777744.3479*****998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 3692.74
//
Query:       AJA92393.1  [L=68]
Description: hypothetical protein T478_0559 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 516.66
//
Query:       AJA92394.1  [L=98]
Description: PF04242 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-20   72.2   0.1    3.6e-20   72.0   0.1    1.0  1  DUF424    Protein of unknown function (DUF424)


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1     2e-24   3.6e-20       5      92 .]      12      98 .]       8      98 .] 0.97

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2e-24
                TE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEEEEEEEE- CS
      DUF424  5 dllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvphaqigkl 92
                ++  ++++cd el++kt+++g++++++++ +y ++ ++e+ea   L ++  +N+vge++v+la+  G+  ++s+ +i+gvp+ +++k+
  AJA92394.1 12 GN-LMLNICDPELVDKTLHDGDTKIKINPNYYAERNVDEHEAKTLLTQCNSINMVGEKTVSLAIGLGIGSEKSIRRIEGVPFLIVFKM 98
                55.79********************************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 739.17
//
Query:       AJA92395.1  [L=287]
Description: DNA adenine methylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-65  219.3   2.6      8e-65  219.1   2.6    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.039   14.0   0.1      0.096   12.7   0.1    1.6  1  DUF2089          Protein of unknown function (DUF2089)
       0.12   11.8   0.3       0.18   11.2   0.0    1.4  2  ZnuA             Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.1   2.6   1.3e-68     8e-65       1     260 []      19     269 ..      19     269 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.1 bits;  conditional E-value: 1.3e-68
                      STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TCTTGGC.TSHHHHHHH CS
  MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelekllekeelenereyfyel 92 
                      ++GgKr+l++e+++++pk +  t++epF GggaV+f++++   +  + ++D+n+dli  y  +i+++  +li+ le++ ++   ++++ey+ye+
       AJA92395.1  19 WVGGKRQLMQELENNFPK-QFGTYHEPFLGGGAVMFNLLSkePKLSCNVSDFNSDLILAYI-TIRDKLGKLIESLENHSKN-YHDDSTEYYYEV 109
                      9*****************.888****************996666778889***********.**************96655.6679******** PP

                      HHHHH...HHH-HHHH.HHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHHHHHHHHH..CCEEEC-CHHHHTT--TTE.EEEE CS
  MethyltransfD12  93 reefnkkidaireaee.aidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelklrseklkn..akiecgdfdavllkakieddivYl 183
                      r+++       + ++e ++++++lnr++f+gl+rvnkkg+fnvp g+y++p++v++++l+++s+ l++   ki+c  f+avl +  +++d++Y+
       AJA92395.1 110 RKQEP------KLQIEkVSRLIFLNRTCFNGLYRVNKKGQFNVPLGRYTNPNIVNKENLTSVSKILQSekIKISCRGFEAVLDDT-KKGDLIYF 196
                      *7777......444444888****************************************************************9.5555**** PP

                      --S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEESEESHHHHHHCTT...SEEEEECCCCHH CS
  MethyltransfD12 184 DPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsfkdtklfrelyksYnnesileveelrai 260
                      DPPY+p+++tan+t+y++++f+++d  rla+++++l +++g  vllsns  ++k +++++++ ++ +i +++++rai
       AJA92395.1 197 DPPYQPISSTANFTSYTHRDFTEDDLERLATLANQL-NSKGCHVLLSNS--NSKVVKDIFSE-KHWKISSINANRAI 269
                      ************************************.799999******..***********.99999999988876 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.6e-05     0.096      50      86 ..      64     100 ..      60     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
     DUF2089  50 GnlkevekelgisYpTvrnrldeileaLgyeeeeeee 86 
                  n+++ ++ l ++Y T+r +l +++e+L+ ++++ ++
  AJA92395.1  64 CNVSDFNSDLILAYITIRDKLGKLIESLENHSKNYHD 100
                 58899999*********************99886633 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1      0.94   5.6e+03     113     135 ..      87     109 ..      79     119 .. 0.58
   2 ?   11.2   0.0   3.1e-05      0.18     144     233 ..     183     269 ..     160     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.94
                 HHHHTGGGHHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxx RF
        ZnuA 113 LveadpanadtyeanaaayiekL 135
                 L+e  + + ++y++   +y +++
  AJA92395.1  87 LIESLENHSKNYHDDSTEYYYEV 109
                 33445566666666666666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.1e-05
                 HHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS.HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-STSSS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ZnuA 144 eelaeipeekrklvtthdafgylarayglevagiagiste.aaqiaalieeikeagvkaifveplaspklaetlaeeagvkvatlysldsl 233
                 ++l++ ++    l+ + ++++    + +++ ++   ++++  +++a l+++++++g +++++  ++++k+++++ +e + k+  ++   ++
  AJA92395.1 183 AVLDDTKKG--DLIYFDPPYQPISSTANFTSYTHRDFTEDdLERLATLANQLNSKGCHVLLS--NSNSKVVKDIFSEKHWKISSINANRAI 269
                 555645544..59999999999**********999999999********************9..789************999988875555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2022.28
//
Query:       AJA92396.1  [L=449]
Description: arylsulfatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-24   85.2   0.0    4.7e-23   82.1   0.0    2.4  1  Sulfatase      Sulfatase
    7.1e-11   42.3   0.1    5.9e-05   22.8   0.0    2.2  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
      9e-05   22.7   0.7    0.00028   21.1   0.7    1.8  1  DUF4976        Domain of unknown function (DUF4976)
     0.0019   17.6   0.0     0.0049   16.3   0.0    1.6  1  Metalloenzyme  Metalloenzyme superfamily
     0.0037   17.2   2.7     0.0053   16.6   0.5    2.5  3  DUF4994        Domain of unknown function


Domain annotation for each model (and alignments):
>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   1.3e-26   4.7e-23       1     308 [.       4     348 ..       4     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.3e-26
                 EEEEEEEESSE-TTGSGGGTTTSCSSHHHHHHHHTSEEESSEE-SSSSHHHHHHHHHHSS-HHHHTHSSCCSTTTHHCTTTS-HHHHHHHHTT-EEEEE CS
   Sulfatase   1 pnvvliladdlgagdlglyggktattpnldrlaeeglrftnfysaaplcspsraalltgryphnsgvasntevgggglpqteatLpellkeaGYntaai 99 
                 pn++++++d++++ d  +   kt  tpn+d+l ++g+ f++++s+a+++ p+ ++lltg yp  s    ++e  ++++ ++  ++++ lk++ Y+ + +
  AJA92396.1   4 PNILFLIIDSFRS-DKFFHKEKTSVTPNIDKLIQRGVYFSQTISSASSSLPAISSLLTGNYPFDSF--KQNE-KKSEIVESSMFFLKELKKRNYEMYGF 98 
                 9**********77.66788888888************************************88855..2332.239999999999***********888 PP

                 EES-SCCSGGGSHHCCTTTSEEEETSSSCHHTCCCCCCCCCECTCCCTTTTCSHHHHHHHHHHHHHHCCC.TSSEEEEEEE-TTSSSTCTCGGHTCCGS CS
   Sulfatase 100 gkwhlgwssrqsvyknrgfdrflgfptgsaalkdpekseyngevlrvppeggysddrlldealefllarn.dkpfflylatlapHappeapdeyakkya 197
                  +  l+  s ++         ++g     + +++ ++s+ +              d + de++  +++++ + ++f y++++  H+p    ++++ +  
  AJA92396.1  99 IPKILTNLSLEK---------IFG----DNLDSYDDNSTLY--------------DGIGDELIAKMKEKKeKSKWFWYIHLNDIHGPAIFHKDFQHE-- 168
                 888888776666.........888....3334443444444..............44555555555555559**************98888888777.. PP

                 TTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCG......................................... CS
   Sulfatase 198 tffddgseaarqlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhgaslee......................................... 255
                 +f+d          ++y ++v+ +D+ +g++++++      ++tlvv+ +Dhg  ++                                          
  AJA92396.1 169 DFEDVN-----LGKNQYERMVSLMDKWLGKIFEEI----DFEKTLVVISADHGSDVGVfdkemdrlnlqirnkkkipkgkafdvshkiisrspgflkpm 258
                 333322.....7889********************....*****************88***************************************** PP

                 ........................................HHTTSSSCTTCSSSHHHHBEEEEEEETTTSHCEEECSEEEGGGHHHHHHHHTT CS
   Sulfatase 256 ........................................sngplrggkganayeggtrvPllvwwpgekaprvseelvshiDlfptildlag 308
                                                            +  +gk+ +  ++ + +Pll  + g +++++ ++ v ++D+fpt+++l+g
  AJA92396.1 259 rkilsksytkrreniienslepdlkkleslqlspykkrimE--NIILGKS-QVFDERFVIPLLFTGYGVNENKIIDKQVRSVDIFPTVFSLVG 348
                 **********************************9998643..3445666.78*************************************998 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.6e-08   5.9e-05       2      58 ..       7      64 ..       6      66 .. 0.88
   2 !   17.5   0.0     7e-07    0.0025     196     253 ..     179     233 ..     149     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-08
                  EEEEETT-BTTHHHHHGS..TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-H CS
  Phosphodiest  2 lvislDGlradlldrlae..llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyP 58
                  l++++D++r d +++  +   +pn+++L+++gv++   + +  + + p+ +sl+TG yP
    AJA92396.1  7 LFLIIDSFRSDKFFHKEKtsVTPNIDKLIQRGVYFS-QTISSASSSLPAISSLLTGNYP 64
                  6899*********9855469****************.55556689*************9 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 7e-07
                   HHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEH.TTSEEEGGGTSTGGH CS
  Phosphodiest 196 evedalrrvDkaigdLlealderglsaetniilvSDHGmadvs.ddkvielndlleekg 253
                   + e  ++  Dk++g+++e++d +    +t +++++DHG      d+++++ln  +++k+
    AJA92396.1 179 QYERMVSLMDKWLGKIFEEIDFE----KTLVVISADHGSDVGVfDKEMDRLNLQIRNKK 233
                   47889999*************88....9**********999887788888998888886 PP

>> DUF4976  Domain of unknown function (DUF4976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.7   7.8e-08   0.00028      32      90 ..     381     438 ..     352     448 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.8e-08
     DUF4976  32 eyPaehavkrhygvrteryklihfykd.idewelyDlkkDpkelknlyddpeyeevvkel 90 
                 ++  e++ ++ +g+rt +yk  +  +d +++  lyDl+ Dp e +n+ ++++ +  v+e+
  AJA92396.1 381 NFSDEKTDTKVIGIRTSDYKYFRDRDDcMKNVHLYDLHSDPLEEENISENNKNK--VNEM 438
                 445566678899********9988776357899**************9877654..3334 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0049     154     194 ..     180     220 ..     171     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                    HHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS. CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Metalloenzyme 154 tiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkr 194
                    + +++  +D+ +++i+++i+ +++++v+ ADHg +  + ++
     AJA92396.1 180 YERMVSLMDKWLGKIFEEIDFEKTLVVISADHGSDVGVFDK 220
                    56778899*************************99877764 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.4   8.6e+03      77      90 ..     169     182 ..     162     190 .. 0.46
   2 ?   -2.8   0.0       1.7     6e+03      21      33 ..     267     279 ..     258     283 .. 0.72
   3 !   16.6   0.5   1.5e-06    0.0053      67      98 .]     411     442 ..     385     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
     DUF4994  77 egekenvaekhpek 90 
                  +e  n+ +++ e+
  AJA92396.1 169 DFEDVNLGKNQYER 182
                 34444443333333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
     DUF4994  21 kkdReyvieqaan 33 
                 +k Re++ie++ +
  AJA92396.1 267 TKRRENIIENSLE 279
                 5678999999865 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.5e-06
     DUF4994  67 epqLydlkkdegekenvaekhpekvkelkelL 98 
                 +  Lydl++d+ e+en+ e++ +kv+e+++lL
  AJA92396.1 411 NVHLYDLHSDPLEEENISENNKNKVNEMERLL 442
                 568*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3316.16
//
Query:       AJA92397.1  [L=134]
Description: NUDIX domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   40.6   0.0    2.7e-10   40.4   0.0    1.0  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.5e-14   2.7e-10       5     129 ..       6     131 ..       2     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.5e-14
                 EEEEEEEETTSEEEEEEES..SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEECSGCSST CS
       NUDIX   5 avgvvllnekgevLlvrrs..kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfl.eevegelepn 99 
                  v  +l+n+  ++Ll++rs   k+ ++ W+ + G +e +E+p + A+ E++EE+G ++ +++l+ + +    +   y++  + +y fl   ++ e+++n
  AJA92397.1   6 IVTTFLTNSG-KILLLKRSqkVKTMKNlWAGISGIIENDEKPLNRAIIEIFEEVGMKKSEVKLVKEGDVIMIESPQYENHQWEVYPFLfSCNHKEIKLN 103
                 5777888888.5*******874444557***************************99999999987777777777777778888777767777777777 PP

                 STTTEEEEEEEEHHHHHHHHTHCTHHHHHH CS
       NUDIX 100 denevsevrwvpleellkeklaaesrkllp 129
                    e s+++w+++e++++ + +++ +k+l 
  AJA92397.1 104 --WENSDAQWIDVEAINDFTTVPSLEKVLT 131
                 ..78899*********88887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 985.78
//
Query:       AJA92398.1  [L=269]
Description: hydrolase, carbon-nitrogen family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-54  185.6   0.0    1.2e-54  185.4   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.0   6.6e-59   1.2e-54       1     261 []       3     251 ..       3     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 6.6e-59
                   EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBS...SSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTEEEE CS
  CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgy...keeahfleaAeaglgetlallaalarkngiavvigliereltngklqa 94 
                   ++A+vQ +  ++++e+nl k+l +i++Aa+++ad++ +PE+  +     +  +++ + Ae+++ge++ ++a+ a++n i +v+++ e+ ++++++  
    AJA92398.1   3 KIALVQFKA-STEKEKNLPKILGYIKQAAKNNADMVTFPEYMMFYTpstQTAKQVAQEAETINGEFVSAVAQSAKDNSIGIVGTMYEKSRKKDRV-- 96 
                   69*******.79*****************************9985588877778888888****************************99*****.. PP

                   EEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHH CS
  CN_hydrolase  95 yntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigfpellralalkgaeilvnlserapvpksmgppq 190
                   y t ++++++g+++gkyrK+hL    ++  ++ e+  +++g++   + +t+vgk+G++iCy+ +fpe +r+la+ g+eilv    +a+v + m +++
    AJA92398.1  97 YDTSFIVNKKGEVTGKYRKIHL----YDALGFKESNKMSSGTEiPLPTKTSVGKMGMLICYDLRFPEMSRTLASSGTEILVV--PSAWVNGPMKEEH 187
                   *********************8....789**************75566**********************************..77*********** PP

                   HHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHHHHH CS
  CN_hydrolase 191 wellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglgeeeegvliaeidladvratrr 261
                   w++l ++ra+engc+via  + g       ++ g S ++dp Gril +  + + g+ ++ i l++v ++r+
    AJA92398.1 188 WLTLNKSRAIENGCYVIAPDHLGH------VYSGRSLAVDPYGRILLDMKKRQ-GIGYVNISLDKVHEIRK 251
                   ************************......****************9999999.9**********999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1948.65
//
Query:       AJA92399.1  [L=139]
Description: glyoxalase-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-09   37.5   0.0    2.4e-09   37.1   0.0    1.1  1  Glyoxalase_2  Glyoxalase-like domain
    1.2e-08   35.2   0.0    2.1e-08   34.4   0.0    1.4  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
     0.0015   19.3   0.0     0.0018   19.0   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.015   15.6   0.0        4.3    7.6   0.0    2.1  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
       0.15   12.2   0.0       0.18   11.9   0.0    1.2  1  CppA_N        CppA N-terminal


Domain annotation for each model (and alignments):
>> Glyoxalase_2  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   6.7e-13   2.4e-09       3     113 ..       8     117 ..       6     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.7e-13
                   ----EES-HHHHHHHHHHTT---EEEE-SSEEEETTS-.EEEEHHHHHH-------S--SS-EEEEEES-HHHHHHHH..GGGS-EEEEEEE-TTS- CS
  Glyoxalase_2   3 lillvvkdieeskkFYedvlelkikldfGenvsfetgf.alkedlkelinldesiaeqsnnfeLyFevedvdaflqklkeaeniellhelkekpWgq 98 
                   +i+l vkd+e+s kFY+++l ++ik +  ++v   +    + +   + i ++++   + n + ++  v d+++++++l  a+ ie+  +++e++ g+
    AJA92399.1   8 NIILEVKDLENSIKFYHEILGMPIKNERRNWVDLGQQSgGILSLHPASITTSHTGPSKENGILIGLTVGDLHSAMEELSAAK-IEIFRDIQERQAGK 103
                   799*****************************99766546666666777778888999********************7666.***********999 PP

                   EEEEEE-TT--EEEE CS
  Glyoxalase_2  99 rvirfyDpDkhiiEi 113
                     i + DpD+ +i +
    AJA92399.1 104 NAI-ILDPDGYLISL 117
                   876.88****99976 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   5.9e-12   2.1e-08       2     127 ..       6     116 ..       5     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5.9e-12
                 EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.TSEEEEEEEEEHCHHHHHHHHHHHTTG CS
  Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee.tvhhvafialdvedvgkaldrlkeagv 99 
                 i+ + l v+dle s++FY+++LG+ +  +             +++ g+++ ++++ +++s   +h     + + +   +i l+v d+  a ++l++a++
  AJA92399.1   6 IGNIILEVKDLENSIKFYHEILGMPIKNERR----------NWVDLGQQSGGILSLHPASITTSHT----GpSKENGILIGLTVGDLHSAMEELSAAKI 90 
                 6777888************************..........4445555555555555555555554....223456789******************** PP

                 EEEEEEECHHCTEEEEEEEEETTSEEEE CS
  Glyoxalase 100 kvvaepgrhyfgalysfyfrDpdGille 127
                 ++ + ++ +  g+  +  + DpdG+l+ 
  AJA92399.1  91 EIFRDIQERQAGKNAI--ILDPDGYLIS 116
                 *999998888887775..9******985 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     5e-07    0.0018       2     103 ..       9     114 ..       8     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5e-07
  Glyoxalase_6   2 vvldaadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.......paknrvHldlavedldaevarlvalGArvlreprdgt 91 
                   + l ++d +  ++F+ ++lg++ + e+      ++v + ++++  l+++++         +++n + + l+v dl+ ++++l a+  +  r+ ++++
    AJA92399.1   9 IILEVKDLENSIKFYHEILGMPIKNER-----RNWVDLGQQSGGILSLHPASIttshtgpSKENGILIGLTVGDLHSAMEELSAAKIEIFRDIQERQ 100
                   678999*********************.....556666666777777777766778888767889**********9999877777777777777777 PP

  Glyoxalase_6  92 hgr..vlaDPeGne 103
                   +g+  ++ DP+G  
    AJA92399.1 101 AGKnaIILDPDGYL 114
                   6669*******976 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0033        12       6      26 ..      12      32 ..       8      64 .. 0.78
   2 ?    7.6   0.0    0.0012       4.3       3      55 ..      71     120 ..      70     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0033
                  E-S-HHHHHHHHHH.TT-EES CS
  Glyoxalase_4  6 vVeDleaavarfsallGvgpw 26
                   V+Dle  ++++ ++lG+   
    AJA92399.1 12 EVKDLENSIKFYHEILGMPIK 32
                  69***************8433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                   EEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEE CS
  Glyoxalase_4   3 igivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLiep 55 
                   ig+ V Dl+ a++++sa   ++ +++++++ q  ++a+ l  +g   i L ep
    AJA92399.1  71 IGLTVGDLHSAMEELSA-AKIEIFRDIQER-QAGKNAIILDPDG-YLISLFEP 120
                   78999999999999997.888877777654.4455566666665.45666665 PP

>> CppA_N  CppA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     5e-05      0.18       5      70 ..      10      71 ..       7     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
      CppA_N  5 vlrvnnrdlniafyqetlGlkllseenalavfsdwaeaeelfvieespslrtraveGtkklakiii 70
                +l v + +  i+fy e lG+ +  e    + +++++ +    ++   p+  t +  G+ k + i+i
  AJA92399.1 10 ILEVKDLENSIKFYHEILGMPIKNERRNWVDLGQQSGG----ILSLHPASITTSHTGPSKENGILI 71
                79999*********************999999988443....555667777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1050.12
//
Query:       AJA92400.1  [L=263]
Description: methylthioadenosine phosphorylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-46  157.4   0.0    3.9e-46  157.2   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.014   15.7   0.2      0.029   14.7   0.2    1.5  1  DUF4368    Domain of unknown function (DUF4368)
       0.17   12.3   0.0       0.27   11.6   0.0    1.3  1  DUF1064    Protein of unknown function (DUF1064)


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   6.4e-50   3.9e-46       2     234 .]       7     244 ..       6     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 6.4e-50
                 EEEEESSH.HHHHHHHHH..EEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SEEEEEEEEEESSTTT-TT-EE CS
   PNP_UDP_1   2 iaiivgsp.gevellaes..pleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvkaiiriGtaGglnpdlkvGDvv 92 
                 i+i +g++ ++  ll+e   ++ +tp+g++  + ++++G+ +g+++ ++ ++G    i +++++++a+i++ ke+gvk+ii+ +++G+l++++++ D++
  AJA92400.1   7 IGIFGGTGiYDSGLLKEPkeIAIDTPYGKP--SDTITIGEFNGRKIaFLPRHGkkhtIPPHMINYRANIWAFKELGVKRIIAPSAVGSLKEEFAPRDFA 103
                 899999999666666666668*********..*********6666659*************************************************** PP

                 EEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT-- CS
   PNP_UDP_1  93 ipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.GvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgip 190
                 +p+++++f+  ++  + +++ + ++ ++d+ ++pel +++  ++ +++ k+h   ++++ +g++++t+ae++++++ ga +++M+ ++++qlAre++i+
  AJA92400.1 104 LPTQFLDFTKSRKGSFSEDGRVIHISVADP-FCPELQKAILDVTDKQELKIHKeATYVCIEGPRFSTKAESKFYKSTGAEIIGMTLVPECQLAREAQIC 201
                 *************99999998999999999.*********************99********************************************* PP

                 EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHHHH CS
   PNP_UDP_1 191 faairvvsdlaaggadaeatheeveefaqeaaknaaalllalla 234
                 +a+i++v+d ++ +a+++ t +ev e++ ++++ +++ll++l++
  AJA92400.1 202 YASISTVTD-YDVWAEKPVTAKEVIETLSKNVELTKKLLTELID 244
                 *********.899****************************985 PP

>> DUF4368  Domain of unknown function (DUF4368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   4.8e-06     0.029      25      46 ..     231     252 ..     222     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-06
     DUF4368  25 ieeLtpeilnelIekIeVheae 46 
                   eLt+++l elI+kI V++++
  AJA92400.1 231 NVELTKKLLTELIDKIPVSKSC 252
                 569***************9865 PP

>> DUF1064  Protein of unknown function (DUF1064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.5e-05      0.27       6     114 ..     157     256 ..     153     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
     DUF1064   6 akkvvidgikFDskaeakyYqeLkllkaagkilkleLqpkfeLqekfkknGkkyrkikYvaDFliykedgkveviDvkGmatkdakikkklFeakyrev 104
                 a  v i+g +F  kae+k+Y+      + ++i+ + L p+ +L+ + +     y +i+ v+D+ ++ e + v   +v     k++++ kkl ++   ++
  AJA92400.1 157 ATYVCIEGPRFSTKAESKFYK-----STGAEIIGMTLVPECQLAREAQIC---YASISTVTDYDVWAE-KPVTAKEVIETLSKNVELTKKLLTELIDKI 246
                 667999**************9.....7899*************9887765...***********9975.677778888889999999999998887777 PP

     DUF1064 105 kltlivkslk 114
                 +++ ++ + k
  AJA92400.1 247 PVSKSCSCEK 256
                 7777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1989.61
//
Query:       AJA92401.1  [L=258]
Description: daunorubicin resistance ABC transporter membrane protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-32  111.8  20.7    2.9e-32  111.8  20.7    1.6  2  ABC2_membrane    ABC-2 type transporter
    1.3e-13   50.8  31.8    1.3e-13   50.8  31.8    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.7e-06   27.6  28.1    5.1e-05   22.7  28.1    2.2  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8  20.7   4.9e-36   2.9e-32       3     208 ..       6     218 ..       4     220 .. 0.90
   2 ?   -1.5   0.2      0.23   1.4e+03     114     125 ..     234     245 ..     221     255 .. 0.45

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 4.9e-36
  ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnr...........pgllffsvlflafsaltsvapvferergvlere 85 
                    ++a+++re++++ +++ +g++ rliqp ++++v+g +f +++   ++                pg+l+ +++f++  ++ +v ++++r+ g++++ 
     AJA92401.1   6 TYAIFWREMKRYRKSK-SGVIIRLIQPAIWIVVMGNIFAGTQplIQS----VgfdgeyiefmaPGVLILTAIFTS--IFGGVNTLWDRRYGFMNKA 94 
                    5799*****9887777.777*******************86644222....133456788899************..9999999************ PP

  ABC2_membrane  86 lvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rf.flflllllltalaasslgllisalapsfedasqlaslvllpllllsGf 178
                    l+sp+ s+s+++l+k+l+  +++++q+ ++l +++ l g+ +      + ++ +++l+++ +s+++++++a a+s+e++  +++++ +pl+lls++
     AJA92401.1  95 LTSPI-SRSSIALGKMLAISMIAAFQSSLILGMALAL-GVSMPhlWMiAPIMGIVILFSIGFSGISVMVAAAAKSQETFWGIINFLGMPLFLLSPA 188
                    *****.******************************9.**99854225888899****************************************** PP

  ABC2_membrane 179 fipidsmpkwlqwiaylnPltyavealrsn 208
                    ++p++ mp wl  +a +nP++y+v ++r  
     AJA92401.1 189 LFPLELMPDWLASVAAFNPVSYTVILVREM 218
                    ********9***************999976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.23
  ABC2_membrane 114 ifllivyflvgl 125
                    ++ +++++++gl
     AJA92401.1 234 VLGIFSILMIGL 245
                    222222222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8  31.8   2.1e-17   1.3e-13     158     344 ..      57     247 ..      48     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.1e-17
  ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgipfgnlgl...llllfl 246
                       +  f+++ +li+ +++t++f  v+ + +++ + +   l+s++s++++ l+k+l++ +++++q+ lil++  a+g  +++ +l+    ++  ++
       AJA92401.1  57 EYIEFMAPGVLILTAIFTSIFGGVNTLWDRRYGFMNKALTSPISRSSIALGKMLAISMIAAFQSSLILGMalALG--VSMPHLWMiapIMGIVI 148
                      5788999*9999*****************************************************9999723566..8888664412377**** PP

  ABC2_membrane_3 247 lfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd.plweillsliilalfavvy 339
                      lf++ ++ ++ ++ ++ k++et  ++i ++ ++l++++ +lfple +p++l+ ++ ++P ++   +   +++g+    + ++s+++l +f++++
       AJA92401.1 149 LFSIGFSGISVMVAAAAKSQETFWGIINFLGMPLFLLSPALFPLELMPDWLASVAAFNPVSYTVILVREMMSGYvDSLSAMTSIAVLGIFSILM 242
                      ********************************9999999********************************999888899************** PP

  ABC2_membrane_3 340 lllal 344
                      + la 
       AJA92401.1 243 IGLAS 247
                      99986 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7  28.1   8.5e-09   5.1e-05     106     285 ..      91     252 ..       7     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.5e-09
  ABC2_membrane_2 106 lkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalal 199
                      +   L++P+sR++i lgK+++ ++i      a+  +++l++a+  alg++++  +++  ++ +v+l+ ++ f ++++++++ a+s+++   +  
       AJA92401.1  91 MNKALTSPISRSSIALGKMLAISMI-----AAFQSSLILGMAL--ALGVSMPHLWMIAPIMGIVILFSIG-FSGISVMVAAAAKSQETFWGIIN 176
                      6778*****************9999.....5556665555555..5555555666666777777778877.7************8887777777 PP

  ABC2_membrane_2 200 glfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                      +l + l +l + +l+++  ++        +   +  ++p s+  +l++e+ +g    +++s++t++++l +  + +++l+ ++F r
       AJA92401.1 177 FLGMPL-FLLSPALFPLELMPD-------WLASVAAFNPVSYTVILVREMMSGYV--DSLSAMTSIAVLGIFSILMIGLASYVFTR 252
                      777666.666677767444444.......455689******************95..56*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1546.88
//
Query:       AJA92402.1  [L=105]
Description: hypothetical protein T478_1177 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 771.61
//
Query:       AJA92403.1  [L=92]
Description: acylphosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-25   89.8   0.8    1.2e-25   89.7   0.8    1.0  1  Acylphosphatase  Acylphosphatase
     0.0068   16.2   0.6       0.01   15.6   0.6    1.4  1  SH3_13           ATP-dependent RecD-like DNA helicase SH3 dom
  ------ inclusion threshold ------
       0.17   12.1   0.1       0.22   11.8   0.1    1.2  1  DUF2871          Protein of unknown function (DUF2871)


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.8   2.1e-29   1.2e-25       2      85 .]       7      90 ..       6      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.1e-29
  Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdFei 85
                     +++vtGrVQgv+FR+ ++  A + ++kG+vrNl+dg+Veiv ege +++e + +++k+gp ++rvde+e +e++ ++ef++Fe+
       AJA92403.1  7 HIFVTGRVQGVFFRQSTKVMAIKNNVKGWVRNLDDGRVEIVGEGEIQDIENLTQWCKTGPANSRVDEFELSEENVTDEFENFEV 90
                     799*******************************************************************************85 PP

>> SH3_13  ATP-dependent RecD-like DNA helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.6   1.7e-06      0.01      21      54 ..      14      47 ..       4      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
      SH3_13 21 vggrvfrvgDkVmqlkNnydkgvfNGDiGiikei 54
                v+g +fr   kVm +kNn +  v N D G ++ +
  AJA92403.1 14 VQGVFFRQSTKVMAIKNNVKGWVRNLDDGRVEIV 47
                57888********************999999866 PP

>> DUF2871  Protein of unknown function (DUF2871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.7e-05      0.22       8      33 ..       5      30 ..       1      34 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
     DUF2871  8 alvylilgllsGvfyReftklneftg 33
                 + +++ g ++Gvf+R+ tk++++++
  AJA92403.1  5 RIHIFVTGRVQGVFFRQSTKVMAIKN 30
                5678899**************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 659.73
//
Query:       AJA92404.1  [L=163]
Description: hypothetical protein T478_0075 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   15.1   0.5      0.037   14.3   0.5    1.4  1  Big_3     Bacterial Ig-like domain (group 3)
      0.065   13.9   0.2        4.4    8.0   0.1    2.4  2  MBG_2     MBG domain (YGX type)


Domain annotation for each model (and alignments):
>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   4.1e-06     0.037      15      66 ..      64     118 ..      62     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-06
       Big_3  15 daedlfvsatykdGdae...vpfddvevsgsvdstkaGeytvtvtykg.vsatftV 66 
                 d e++f++ +++d ++    +++++ ++   +d++++G+yt+++t     + +++V
  AJA92404.1  64 DGEGVFYRIVDDDYNTVdkgIAETKMSIRY-FDVKETGVYTIILTSLAqENMNYEV 118
                 568888888888888755667777777777.*************988867777777 PP

>> MBG_2  MBG domain (YGX type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.011     1e+02      21      52 ..      17      50 ..      14      64 .. 0.87
   2 ?    8.0   0.1   0.00049       4.4      45      66 ..      97     120 ..      71     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.011
       MBG_2 21 ytvsGlvngDtlsslt.gtlsrtagenvGtY.ai 52
                ++ +G+v ++++ s +  +l+ t++  +G Y +i
  AJA92404.1 17 ASGTGIVFSEAERSFQiMSLKQTESDEIGMYfEI 50
                56799********999*************99766 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00049
       MBG_2  45 envGtYaitasglsss..NYtity 66 
                 + +G Y+i +++l+++  NY+++ 
  AJA92404.1  97 KETGVYTIILTSLAQEnmNYEVEL 120
                 567**********99989***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.89
# Mc/sec: 553.88
//
Query:       AJA92405.1  [L=248]
Description: calcineurin-like phosphoesterase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-17   64.7   0.6    2.4e-17   64.1   0.6    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    1.5e-15   57.8   0.1    2.3e-15   57.2   0.1    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    3.4e-05   23.3   0.3    0.00013   21.4   0.2    2.0  3  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
      0.001   19.0   0.0     0.0024   17.8   0.0    1.5  1  DUF2124        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
      0.078   11.6   0.0       0.13   10.8   0.0    1.3  1  MutL           MutL protein


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.6   6.8e-21   2.4e-17       1     204 []       1     182 [.       1     182 [. 0.69

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 6.8e-21
                  EEEEEEESBTBTTCCTHHHHHHHHHHHHHHH...TTESEEEEESTSSSSS...HHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.HHHHHHHHHHHH CS
  Metallophos   1 lrilvigDlHlalgggqlddllkllddllre...ekpdlvllaGDlvdrg...dlekellellaalvkypipvylllGNHegfee.ellnkygylgif 91 
                  ++i++++D+H      + +  +++++++++e     pd+v+++GDl+++g   ++e  + el+++     ++v+++ GNH+ +++ ++l++       
   AJA92405.1   1 MKIVQLSDVH-----FGTQFRDDIFNQVIDEvneLSPDAVIITGDLTNEGlkeEYEG-CKELISKINV--KKVIAVSGNHD-YRNtGYLHF------- 82 
                  89********.....66666666666663333336***************9855555.8888888888..799********.666666666....... PP

                  HHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHH CS
  Metallophos  92 sepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnleleapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdeale 185
                         +++f +  +++l ++   v++  G   p              ++++ e g    +wl++++k+ +++++i+  H+ l  g+ ++ +d+ + 
   AJA92405.1  83 -------KKYFPFQTINELDDD--VVVVTLGTaRP--------------DRDEGEVGyrqTLWLERTMKKFENKVTILAMHHHLI-GIPDTGSDRLTI 156
                  .......777888888887777..55555554222..............223333335657788885555555555555555555.466666666666 PP

                  .......HHHHHTTESEEEEESSSSE CS
  Metallophos 186 .......dllkkygvdlvisGHtHvy 204
                         +   + +v lv++GH H++
   AJA92405.1 157 idagdvlRATLDAKVNLVLCGHKHRP 182
                  88887766688888**********85 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.1   6.5e-19   2.3e-15       1     164 [.       1     218 [.       1     219 [. 0.74

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 6.5e-19
  Metallophos_2   1 MklaiiSDlH....snldaleavlealkevgvdaiihaGDl.eeeepevleellela......pvlaVrGNnD......................e 63 
                    Mk++ +SD+H     + d+ ++v+++++e ++da+i +GDl +e+  e  e ++el       +v+aV GN+D                      +
     AJA92405.1   1 MKIVQLSDVHfgtqFRDDIFNQVIDEVNELSPDAVIITGDLtNEGLKEEYEGCKELIskinvkKVIAVSGNHDyrntgylhfkkyfpfqtineldD 96 
                    9*********998766788999******************98777676666666666666899****************99999999999999973 PP

  Metallophos_2  64 ev.veedvlreaaelgtdlpeeaelel........agekvlliHgdpl............gvkdalaellkeaeegsdvvvcGHtHvpevekeggv 138
                    +v v+    +++ + ++++  +++l l        +++++l +H++               ++ ++ +++   ++++++v+cGH H+p + +  ++
     AJA92405.1  97 DVvVVTLGTARPDRDEGEVGYRQTLWLertmkkfeNKVTILAMHHHLIgipdtgsdrltiIDAGDVLRAT--LDAKVNLVLCGHKHRPWMWDFSNL 190
                    3345555555555566655333333332233222355559999999559***999998553333333333..447888**********999999** PP

  Metallophos_2 139 lvvnPGsvgeprdgdpe..tyaildtde 164
                    l+ n+G  + +r +     +y i+++++
     AJA92405.1 191 LIANAGTTSSKRVRGFFenSYNIITVEN 218
                    ******9988866554455777777765 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   3.5e-08   0.00013      17      75 ..      16      74 ..       1     104 [. 0.72
   2 ?    0.1   0.0      0.11   4.1e+02       4      44 ..      61     107 ..      58     158 .. 0.62
   3 ?   -1.9   0.0      0.46   1.7e+03     213     253 ..     173     222 ..     163     225 .. 0.53

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3.5e-08
                   -GGGHHHHHHHHHHH--SEEEEES-----HHHHHHHHHHHHTT---.-THHHHHHHHHHH CS
  Metallophos_3 17 evellerlveviedkdpDllvlvGdlvkaeakadeyesaqeerrep.dkkeileekneii 75
                   + + ++++++ +++ +pD+++++Gdl  +e+ ++eye ++e   +   kk+i    n+++
     AJA92405.1 16 RDDIFNQVIDEVNELSPDAVIITGDL-TNEGLKEEYEGCKELISKInVKKVIAVSGNHDY 74
                   45899*********************.99********88876655525677765555444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                    ---EEEEEE--TT..-GGGHHHHH....HHHHHH--SEEEEES---- CS
  Metallophos_3   4 lvrkvlaisdlkg..evellerlv....eviedkdpDllvlvGdlvk 44 
                     v+kv+a+s+ ++  ++ +l+  +    ++i++ d D++v++   ++
     AJA92405.1  61 NVKKVIAVSGNHDyrNTGYLHFKKyfpfQTINELDDDVVVVTLGTAR 107
                    56777777766652233344322211226788888888887644444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.46
                    EEEE-SS--EE.EEETTEEEEE--B........GGGTEEEEEETTTTEEE CS
  Metallophos_3 213 vvvvghavkeh.eelgktlvvnPGa........leeGdfavvdleekkve 253
                    +v++gh ++       + l+ n G         + e  + ++ +e+kk++
     AJA92405.1 173 LVLCGHKHRPWmWDFSNLLIANAGTtsskrvrgFFENSYNIITVENKKIQ 222
                    56666665554333444555555541111111133556777777777776 PP

>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.6e-07    0.0024      68     126 ..      21      79 ..      12      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.6e-07
                 EEEEEE-.-S-EEEEEEEGGGGSTTTS--HHHHHHHHHHHEEEEEEEEEETTHHHHTTH CS
     DUF2124  68 mqleeeaeeekadvvvllGGlampkikveaedvkeliekiekkkviGvcfmsifekagW 126
                  q+ +e++e ++d+v++ G l+ + +k e e  keli+ki+ kkvi v+  + ++++g+
  AJA92405.1  21 NQVIDEVNELSPDAVIITGDLTNEGLKEEYEGCKELISKINVKKVIAVSGNHDYRNTGY 79 
                 5889999*****************************************98887777776 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.7e-05      0.13     112     164 ..      23      76 ..       7      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.7e-05
        MutL 112 dleelrelrpdiiLLaGG.tDgGnkevllenAellaeaklklpviyAGNkaare 164
                  ++e++el+pd ++++G  t++G ke      el++++++k  + + GN + r+
  AJA92405.1  23 VIDEVNELSPDAVIITGDlTNEGLKEEYEGCKELISKINVKKVIAVSGNHDYRN 76 
                 6899*************9789****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1882.12
//
Query:       AJA92406.1  [L=451]
Description: hypothetical protein T478_1399 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3546.03
//
Query:       AJA92407.1  [L=96]
Description: hypothetical protein T478_0762 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.076   13.1   0.2      0.097   12.7   0.2    1.1  1  PBS_linker_poly  Phycobilisome Linker polypeptide


Domain annotation for each model (and alignments):
>> PBS_linker_poly  Phycobilisome Linker polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.4e-06     0.097       5      71 ..      19      83 ..      15      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-06
                     HHHHHHHHHHHHHCSSSHHHCCCSTHHHHHHHHT.TSS-HHHHHHHHHCSHHHHHHHTTTS-HHHHHH CS
  PBS_linker_poly  5 eleeviraaYrqvferdkvleserlselesklkn.geisvrefvralakSelYrkrfyeklsnyrvie 71
                     e e++i+++++ + e+    e     e+es ++n g+ +v++   ++++ + Y ++ +e++++ r+++
       AJA92407.1 19 ENESLIKQIFKEINEKG---ERYDVDEIESWFENeGSWNVKDVKTRIVNISHYAQSRFEQTNKFRIVD 83
                     66778888888887777...555568999999864899***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1299  (0.0724525); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 728.70
//
Query:       AJA92408.1  [L=99]
Description: putative DNA-binding protein Alba [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-07   28.7   0.1    1.1e-06   28.3   0.1    1.2  1  Alba      Alba
  ------ inclusion threshold ------
      0.024   14.3   0.2      0.037   13.6   0.2    1.4  1  YycI      YycH protein
      0.062   12.8   0.1      0.083   12.4   0.1    1.2  1  MTS       Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.9e-10   1.1e-06       5      64 ..      20      76 ..      16      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.9e-10
                E-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
        Alba  5 VsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                V++  ++m+ ++ +l+ +  ++ +  vl a G+ I +Av +a+i+ ++++kg  ++++++
  AJA92408.1 20 VKD-ESVMTGALDVLTAM--DSSKRAVLLAKGNLIPNAVAIANIVTENMLKGNSKIENIK 76
                666.899999********..677777788****************************997 PP

>> YycI  YycH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   6.2e-06     0.037     159     190 ..      46      77 ..      32      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-06
                 EEEEB--HHHHHHHHHHTT-S-TTEEEEEEEE CS
        YycI 159 ekkelisareAvetLyennelkenskvteikL 190
                  k +li+++ A+ + +++n lk nsk+++ikL
  AJA92408.1  46 AKGNLIPNAVAIANIVTENMLKGNSKIENIKL 77 
                 5789**************************98 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.4e-05     0.083      58     103 ..      33      82 ..      24      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                 EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT...TSTTS-EEEEEE CS
         MTS  58 vtlvdvdarAlesakenleankle.vevvasdvle...eveekkfdlivs 103
                 +t++d ++rA+ +ak nl  n+++ +++v++++l+   ++e+ k+d ++s
  AJA92408.1  33 LTAMDSSKRAVLLAKGNLIPNAVAiANIVTENMLKgnsKIENIKLDSVIS 82 
                 799*********************99999999986111455667777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 792.88
//
Query:       AJA92409.1  [L=282]
Description: SPFH domain/Band 7 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-24   86.3   5.9    3.8e-24   85.7   5.8    1.4  1  Band_7    SPFH domain / Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   5.8   2.1e-28   3.8e-24       2     176 ..      31     206 ..      30     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 2.1e-28
      Band_7   2 iieegevgvv..vrfGklsr.vlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrv.pddapklvaaveresanldnlirrv 96 
                 i+++g +gv+   +  +l++ +le Glhfi+Pf +sv+   vr+ +++ s   t  ++D + v +++tv+y+  p+ ++ l+++v  + ++ +++i+++
  AJA92409.1  31 IVDAGFRGVLlhWNAVDLVDpPLEEGLHFIVPFQDSVIPLEVRTLKYTKST--TSASQDLQTVSTEITVNYHPePTRVNYLYKEV--GLDYENRIIQPT 125
                 789999999944555555557*****************9999999999999..********************99**********..************ PP

      Band_7  97 lesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaeaea.qaeiaraea 176
                 +e+++++v++++++eel+ +r  +++++++e++++l+ ++++ + v+itd++++  +aqa+++k +ae++a qae+   + 
  AJA92409.1 126 VEEVVKQVTANYNAEELITKRPLVKQDIQDEITARLADFNITTEIVSITDFQFSVLFAQAIESKVEAEQRAlQAENDLKRI 206
                 ***********************************************************************9777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2055.69
//
Query:       AJA92410.1  [L=343]
Description: oxidoreductase, NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-20   72.7   0.0    7.6e-20   71.9   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00089   19.3   0.0     0.0015   18.5   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   8.5e-24   7.6e-20       1     120 []       7     126 ..       7     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 8.5e-24
                   EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-S CS
  GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlat 97 
                   l++++iG+ +i+++ + p   +++++e+  + + +  + +++a++f+++ + ++e++++d+ idav++ tp gth+el  +a++agkhv +EK  + 
    AJA92410.1   7 LKFGVIGCSRIAKRSVIPAILKSEFTELEIIGSASDGKVKEFAKEFKCKKFGSYEDVFSDDSIDAVYISTPIGTHAELSNRATAAGKHVYVEKSATY 103
                   589********888877877777************************************************************************** PP

                   SHHHHHHHHHHHHHHTS-EEEE- CS
  GFO_IDH_MocA  98 tveeakelvelaekkgklvsvgy 120
                   +++ a+e+ve a++++++++ g+
    AJA92410.1 104 SLTNAREMVESAKQNNVRLMEGF 126
                   ******************99875 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-07    0.0015       1     115 [.     138     246 ..     138     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-07
                     HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEEEEEEEEEE CS
  GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrk..kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaavmsvlnlek 93 
                     KelI ++k+G+ v+++      ++g +a++ +  r+   k+gG+l d g++ i   + +f ++p++v  + r +q+++  +++++    vl +e 
      AJA92410.1 138 KELISENKIGQLVAFN-----GSFGFPAFPEGDIRYndLKGGGFLNDSGCYPICASRMIFDEEPISVGCTLRYNQADNPVDVKGTS---VLIYEN 224
                     9**************7.....555555555555555559****************************9886656666666666666...9***** PP

                     TTEEEEEEEECCTSSSEEEEEE CS
  GFO_IDH_MocA_C  94 gsgevitlesgvskglsiryvi 115
                     ++ ++i++++g + ++++++++
      AJA92410.1 225 NKNASISFGNGNYYQAKYEVWG 246
                     *************999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2474.36
//
Query:       AJA92411.1  [L=91]
Description: peptidyl-prolyl cis-trans isomerase C [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-24   86.5   0.1    2.4e-24   86.1   0.1    1.2  1  Rotamase_3  PPIC-type PPIASE domain
      2e-24   86.4   0.1    2.4e-24   86.1   0.1    1.1  1  Rotamase    PPIC-type PPIASE domain
    2.8e-07   31.4   0.0    3.2e-07   31.2   0.0    1.1  1  Rotamase_2  PPIC-type PPIASE domain
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.15   11.8   0.0    1.2  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.1   5.4e-28   2.4e-24      15     111 ..       4      88 ..       1      91 [] 0.91

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 5.4e-28
  Rotamase_3  15 svkvshIlistkgkesrseeeakakadsllaalkegadFaalAkeySdDpaskenGGelgwftkgqmvkeFedavfslkkgeiskvvktdfGyHiik 111
                 ++k shIl++            +++a ++l+++k+g++F a+Ake S  p+ +++ G+lg+ftkg+mvkeFed++f+l++ge+s++vkt+fGyHiik
  AJA92411.1   4 KIKCSHILVE-----------KQSQALQILEEIKNGKKFGAAAKEISSCPS-SKKEGDLGYFTKGMMVKEFEDVAFNLEIGEVSAPVKTQFGYHIIK 88 
                 6777888885...........478999*********************998.66679***************************************9 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.1   5.2e-28   2.4e-24      19      95 ..      15      89 ..       5      91 .] 0.96

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 5.2e-28
                HHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEETTEEEEEEE CS
    Rotamase 19 kakaeeileqlksgedtFeelArkySddknsakngGdlgwvekgqlppefekaafslkkGeisepvetkfGfhiikl 95
                + +a +ile++k+g++ F ++A++ S  ++s k++Gdlg+++kg +++efe++af+l+ Ge+s+pv+t+fG+hiik+
  AJA92411.1 15 QSQALQILEEIKNGKK-FGAAAKEIS-SCPSSKKEGDLGYFTKGMMVKEFEDVAFNLEIGEVSAPVKTQFGYHIIKR 89
                67999**********9.*********.************************************************96 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     7e-11   3.2e-07      32     104 ..      14      88 ..       4      91 .] 0.67

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7e-11
  Rotamase_2  32 dqvaaeaalalakagaekdfaalakgnskk.....aadlgifesasnlpeelakaafalkpgevsgpvetdngyyivk 104
                  q +a ++l++ k g  k+f a+ak+ s +     ++dlg+f++   + +e+++ af+l+ gevs pv+t++gy+i+k
  AJA92411.1  14 KQSQALQILEEIKNG--KKFGAAAKEISSCpsskkEGDLGYFTKG-MMVKEFEDVAFNLEIGEVSAPVKTQFGYHIIK 88 
                 344444444444444..5666666665555222225555577665.4667**************************98 PP

>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.15     106     145 ..      20      58 ..      15      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                 HHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS CS
  NTPase_I-T 106 evveevkegeelgevmdelfgtenikqkeGaigllTkglv 145
                 +++ee+k+g+++g + +e+++   + +keG  g++Tkg++
  AJA92411.1  20 QILEEIKNGKKFGAAAKEISSCP-SSKKEGDLGYFTKGMM 58 
                 6899**************76665.77899********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 715.46
//
Query:       AJA92412.1  [L=59]
Description: hypothetical protein T478_1499 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.093   12.9   0.6        2.4    8.3   0.0    2.0  2  UBA_2     Ubiquitin associated domain (UBA)


Domain annotation for each model (and alignments):
>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00013       2.4       3      18 ..      19      34 ..      18      38 .. 0.88
   2 ?    3.1   0.1    0.0057     1e+02      17      30 ..      42      55 ..      40      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00013
       UBA_2  3 edvvsaLsktMGYdkd 18
                 dv+s+Ls++M   kd
  AJA92412.1 19 IDVISQLSERMSVIKD 34
                59*********99888 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0057
       UBA_2 17 kdeIieaLekaeks 30
                 +eIi ++e+  k+
  AJA92412.1 42 EQEIISVIERVVKQ 55
                58*******98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 447.44
//
Query:       AJA92413.1  [L=178]
Description: tRNA ribose 2'-O-methyltransferase aTrm56 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-47  160.2   0.6    2.4e-47  159.8   0.6    1.2  1  Trm56           tRNA ribose 2'-O-methyltransferase, aTrm56
    1.4e-05   25.2   0.1      2e-05   24.8   0.1    1.2  1  SpoU_methylase  SpoU rRNA Methylase family
     0.0067   15.8   0.1     0.0081   15.5   0.1    1.3  1  SPOUT_MTase_2   AF2226-like SPOUT RNA Methylase fused to THUM
  ------ inclusion threshold ------
      0.022   14.0   0.0      0.027   13.7   0.0    1.2  1  LSDAT_prok      SLOG in TRPM, prokaryote
       0.09   12.9   0.0       0.16   12.1   0.0    1.4  1  DUF531          Protein of unknown function (DUF531)
       0.18   12.0   0.0       0.56   10.5   0.0    1.8  1  WXG100          Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.8   0.6     8e-51   2.4e-47       1     119 []      60     176 ..      60     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.8 bits;  conditional E-value: 8e-51
                 H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS---HHHHHHHHHHHHC.--TTT CS
       Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhsevaalaifldrllegkele 99 
                 wGgef+ve+ +++kk++k+   e+ ++vhltmyGe+i++v +ei+k++ ++l+vvGaekvpr++ye++dynvsv+nqPhse++alai+ldrl +gk+++
  AJA92413.1  60 WGGEFEVEFFEDWKKVLKSKI-EEYKIVHLTMYGEKIDDVAKEIRKNQ-NILIVVGAEKVPRTIYEKSDYNVSVSNQPHSEISALAIVLDRLHKGKQFD 156
                 *****************9966.799*******************9975.5************************************************* PP

                 ---TT-SSEEE--SSS-EEE CS
       Trm56 100 kefedaklkviPsergkkvv 119
                 ++f++++ ++iP+++gkkvv
  AJA92413.1 157 MKFDNSDRTIIPTKKGKKVV 176
                 ******************95 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   6.7e-09     2e-05      18     126 ..      28     135 ..      17     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.7e-09
                     HHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC....CSHHHTTEEEEEEBTTTBS CS
  SpoU_methylase  18 iaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls....eidlkekvalvfGnEdkGl 108
                     +a +a+afgas++++ +      +++++kr+       +e++ +++++++lk   ee +++v ++ +g++++    ei+ ++++++v+G E+  +
      AJA92413.1  28 VALVARAFGASKIYMNE--VDPEIENTIKRMNKTWGGEFEVEFFEDWKKVLKSKIEE-YKIVHLTMYGEKIDdvakEIRKNQNILIVVGAEK--V 117
                     566899*********55..33348888999998888999999***********7777.***********999444444666**********7..7 PP

                     -HHHHCTSSEEEE----T CS
  SpoU_methylase 109 snelleladrlvkIpmsg 126
                     ++ + e+ d+ v++  ++
      AJA92413.1 118 PRTIYEKSDYNVSVSNQP 135
                     888888888888876655 PP

>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.7e-06    0.0081      83     149 ..      71     132 ..      13     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
  SPOUT_MTase_2  83 dlyqlvrkrrkkellivtdPeGeeisevkeelaealrkakevvvlvGsReGiPkGlfrfadfvvDla 149
                    d  ++++++ ++  ++ +   Ge+i++v+    +++rk++++ ++vG+   +P+ +++ +d+ v ++
     AJA92413.1  71 DWKKVLKSKIEEYKIVHLTMYGEKIDDVA----KEIRKNQNILIVVGAE-KVPRTIYEKSDYNVSVS 132
                    44455667777777888888888887766....5678999*******95.5***********98875 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.9e-06     0.027     103     181 ..      58     138 ..      28     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.9e-06
  LSDAT_prok 103 erWGdE..spwlarlatala...ekkpsvtvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaalrgdseearlkalve 181
                 ++WG E  +++  +  ++l    e+++ v + + G++  ++d++++++++++il+v G +++  +i ++ +++ + +  +++ e
  AJA92413.1  58 KTWGGEfeVEFFEDWKKVLKskiEEYKIVHLTMYGEK--IDDVAKEIRKNQNILIVVGAEKVPRTIYEKSDYNVSVS-NQPHSE 138
                 6788752256677777777766445556669999999..8**************************99998877773.333333 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05      0.16     109     153 ..      95     137 ..      78     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
      DUF531 109 peevaeeilrkksvllliGlGrkGlPkellklakyhlditekgvs 153
                  ++va+ei +++ +l+++G     +P+ ++++++y++ ++++  s
  AJA92413.1  95 IDDVAKEIRKNQNILIVVG--AEKVPRTIYEKSDYNVSVSNQPHS 137
                 57999**999998887775..677***************988776 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00019      0.56      24      58 ..      42      78 ..      26     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                HHHHH.HHHHHHHHCGCGCTHHHCHHHHHHHH.HHHH CS
      WXG100 24 edelq.rlkaevdalqsgWsGaaadafqaefe.ewkq 58
                ++e++ +++++++ ++ +W G+  ++f++ ++  +k 
  AJA92413.1 42 MNEVDpEIENTIKRMNKTWGGEFEVEFFEDWKkVLKS 78
                444444899**********************944444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1258.84
//
Query:       AJA92414.1  [L=266]
Description: tryptophan synthase, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-81  272.6   1.1    2.3e-81  272.5   1.1    1.0  1  Trp_syntA       Tryptophan synthase alpha chain
    1.6e-07   31.0   0.7    2.1e-06   27.4   0.2    2.3  2  His_biosynth    Histidine biosynthesis protein
    4.6e-06   25.9   0.3    4.1e-05   22.8   0.1    2.2  2  FMN_dh          FMN-dependent dehydrogenase
    3.4e-05   23.2   4.2    5.7e-05   22.5   4.2    1.5  1  DHO_dh          Dihydroorotate dehydrogenase
    4.5e-05   22.9   0.3    6.3e-05   22.4   0.3    1.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    0.00047   19.4   0.1     0.0028   16.9   0.1    2.0  1  IGPS            Indole-3-glycerol phosphate synthase
     0.0017   17.4   0.6     0.0053   15.8   0.5    1.8  2  IMPDH           IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.011   15.0   0.6      0.024   14.0   0.6    1.6  1  TMP-TENI        Thiamine monophosphate synthase
      0.029   13.6   0.4       0.34   10.1   0.1    2.2  2  DUF871          Bacterial protein of unknown function (DUF871
      0.073   13.4   0.1        4.7    7.5   0.0    2.7  3  PucR            Purine catabolism regulatory protein-like fam
       0.13   11.7   3.1       0.47    9.9   0.9    2.7  3  PcrB            PcrB family


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.5   1.1   1.4e-84   2.3e-81       1     251 [.       8     258 ..       8     266 .] 0.94

  Alignments for each domain:
  == domain 1  score: 272.5 bits;  conditional E-value: 1.4e-84
                 HHHHHCTTB-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EEEEE-CHHH CS
   Trp_syntA   1 faklkaenraafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPivlltylnlv 99 
                 f++lk+++++a++ y++ag+p+   +l+++++l ++g+d+iElG+pfsdP+adGP+Iq a++ +L++g+++++++ +v+++r ke+++P+vl+ty n++
  AJA92414.1   8 FKELKSRKESALISYIMAGYPSERATLSAVRGLIQGGTDIIELGFPFSDPIADGPTIQMASTESLNNGTKIDNFFAIVKKIR-KESDIPLVLMTYTNIL 105
                 7899******************************************************************************.9*************** PP

                 CCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCT. CS
   Trp_syntA 100 lsygeerflaelkeagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelverlkklt. 197
                 ++  +++f+ ++k+ag+dgli+pD+  ee++e+v+aakk g++++flv+p+t+++rlk+++++++gf Y+v++ G+Tg+++++++ + +++++ k++  
  AJA92414.1 106 YNQTYQKFISRAKQAGIDGLILPDMAIEESKEYVKAAKKIGMDTIFLVSPNTEKDRLKQIIKSTSGFLYMVAVFGTTGVQTKIHKYTIDALKNTKNAAk 204
                 *********************************************************************************************999886 PP

                 .SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHCTTTSHHHHHHHHHHHH CS
   Trp_syntA 198 .avPvavGFGistkeqvkqva.kvadGvivGSalvkkieeeaeekeqalekleela 251
                  + Pv vGFGist+++v++ + ++ad+vivGSa +k+ie++ ++k q   ++++++
  AJA92414.1 205 gKIPVGVGFGISTEKDVQKYVsSGADAVIVGSANIKIIENTPASKIQS--RIATFT 258
                 789****************999*****************765554432..333333 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.086   1.4e+02      88     125 ..     114     151 ..      76     183 .. 0.82
   2 !   27.4   0.2   1.3e-09   2.1e-06      63     107 ..     194     240 ..     178     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.086
                   HHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEE CS
  His_biosynth  88 veelleagadkviigtaavknpelikelaekfgsqkiv 125
                   + ++ +ag+d +i+  +a+++++   ++a+k+g + i+
    AJA92414.1 114 ISRAKQAGIDGLILPDMAIEESKEYVKAAKKIGMDTIF 151
                   45556788888888888888888888888888887765 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.3e-09
                   HHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
  His_biosynth  63 dlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavk 107
                   d+++++ ++ +  ipv vG GI++ +dv++++++gad vi+g+a +k
    AJA92414.1 194 DALKNTKNAAKgkIPVGVGFGISTEKDVQKYVSSGADAVIVGSANIK 240
                   5555544443333*******************************887 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.19     3e+02     121     142 ..     106     127 ..      70     150 .. 0.72
   2 !   22.8   0.1   2.5e-08   4.1e-05     250     302 ..     185     237 ..     173     263 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
                 SHHHHHHHHHHHHHCTESEEEE CS
      FMN_dh 121 drelteellkraeaagykalvl 142
                  +++ ++++ ra++ag++ l+l
  AJA92414.1 106 YNQTYQKFISRAKQAGIDGLIL 127
                 4566778888888888888776 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.5e-08
                 SSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
      FMN_dh 250 qldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRp 302
                 q      tid+L +  +a++g+i+v v  Gi++ +Dv k +  GAdav++G +
  AJA92414.1 185 QTKIHKYTIDALKNTKNAAKGKIPVGVGFGISTEKDVQKYVSSGADAVIVGSA 237
                 66667789*******************************************76 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   4.2   3.5e-08   5.7e-05     169     278 ..     126     240 ..      62     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.5e-08
                 E-SSSSHHHHHHHHHHHHHHTECEE..EE...BSEE--CTTCCGCCCCTT..SSEEEEE..GGGHHHHHHHHHHHHHHTTT.S-EEEES.S--SHHHHH CS
      DHO_dh 169 laPdltdeekkdiadvllelkldgi..ivtNttvqrlaidlkseknvkan..ktGGlsG..kalkdialkvirelykrlkkeipiIgvG.GiesgeDal 260
                 + Pd++ ee k+ ++ +++ ++d i  ++ Nt   rl+  +ks++        +G   G   ++ +  +  + + ++  k++ip+ gvG Gi++ +D+ 
  AJA92414.1 126 ILPDMAIEESKEYVKAAKKIGMDTIflVSPNTEKDRLKQIIKSTSGFLYMvaVFG-TTGvqTKIHKYTIDALKNTKNAAKGKIPV-GVGfGISTEKDVQ 222
                 77*********************98335679999999999999999887675344.555225799*******************7.7777********* PP

                 HHHHHTECEEEESHHHHH CS
      DHO_dh 261 ekieaGAslvqvytalvf 278
                  ++  GA +v v++a+++
  AJA92414.1 223 KYVSSGADAVIVGSANIK 240
                 ***************986 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3   3.9e-08   6.3e-05      68     196 ..     109     237 ..      76     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.9e-08
                     SHHHCHHHHHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS.----CC.HHHHHHHHHHHH CS
  Ribul_P_3_epim  68 evdrivpefaeagasiisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgG.QkFipe.vlekikkvrkli 160
                       ++++ +  +ag + + +   a+e+ k+ ++  k++G+ ++  + p+t  + l++++++    l m    g  G Q  i++ +++ +k+ ++++
      AJA92414.1 109 TYQKFISRAKQAGIDGLILPDMAIEESKEYVKAAKKIGMDTIFLVSPNTEKDRLKQIIKSTSGFLYMVAVFGTTGvQTKIHKyTIDALKNTKNAA 203
                     45666677777777777777779999************************************999998888887757666661455566666555 PP

                     HHHT---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
  Ribul_P_3_epim 161 dekeldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                     +    ++ + v  G+++ + +++ ++ gad++++gsa
      AJA92414.1 204 K---GKIPVGVGFGISTeKDVQKYVSSGADAVIVGSA 237
                     5...59999***9**762689**************98 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.7e-06    0.0028     124     240 ..     114     237 ..      82     249 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                 HHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHH...HHHHHHTT-......SEEEEE..SEETTTTEE-CHHHHHHCHCC-TTSE CS
        IGPS 124 ieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeee...leralklga......kiiGvN..nRnLktlevdlntteeLaklvpkdvl 211
                 i +a+++g d   Li+  +  ee +e+++aak++g++ +  v+ ++e   l++++k+++       ++G    +  ++++++d    ++ ++ ++ ++ 
  AJA92414.1 114 ISRAKQAGIDG--LILPDMAIEESKEYVKAAKKIGMDTIFLVSPNTEkdrLKQIIKSTSgflymvAVFGTTgvQTKIHKYTIDAL--KNTKNAAKGKIP 208
                 55555555555..666666667778************987776554422377778777622222234444411234555655532..222333334456 PP

                 EEEESSS-SHHHHHHHCCTT-SEEEESHH CS
        IGPS 212 lvaeSGiktredveklkeegvnafLvGes 240
                 +    Gi+t++dv+k+ ++g++a++vG++
  AJA92414.1 209 VGVGFGISTEKDVQKYVSSGADAVIVGSA 237
                 66678**********************98 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.96   1.6e+03     154     173 ..      32      51 ..       4      52 .. 0.74
   2 !   15.8   0.5   3.3e-06    0.0053      55     126 ..     117     238 ..      93     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.96
                 -SHHHHHHHHHTT-SEEEE- CS
                 xxxxxxxxxxxxxxxxxxxx RF
       IMPDH 154 ataegakaLieagadavkvG 173
                 at ++++ Li+ g d++  G
  AJA92414.1  32 ATLSAVRGLIQGGTDIIELG 51 
                 78889999999999999887 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.3e-06
                 HHTTSE.EEE-SSS-HHHHHHHHHHHHTS...................................................TTSXBXTTSXB-EEEEE-S CS
                 xxxxxx.xxxxxxxxxxxxxxxxxxxxxx...................................................xxxxxxxxxxxxxxxxxxx RF
       IMPDH  55 areGgi.gvihknlsieeqaeevkkvkrs...................................................pnaakdekgrllvgaavgv 101
                 a++ gi g+i  ++ iee  e vk+ k+                                                    +n+++ +kg++ vg + g+
  AJA92414.1 117 AKQAGIdGLILPDMAIEESKEYVKAAKKIgmdtiflvspntekdrlkqiikstsgflymvavfgttgvqtkihkytidalKNTKNAAKGKIPVGVGFGI 215
                 555555589999999999999999999989999999999999999999999999999999999999999999999999877777778899999888888 PP

                 STTHHHHHHHHHHTT-SEEEEE-ST CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 102 kedalervkalveagvdvlvvdsah 126
                 +  +++ v++ v++g+d+++v sa+
  AJA92414.1 216 S--TEKDVQKYVSSGADAVIVGSAN 238
                 7..5788999999999999999887 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   1.5e-05     0.024      72     180 ..     120     237 ..      85     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
    TMP-TENI  72 vgadgvHlgqddlpvaearellgpdliiG......lSvhslee.aeeaealgadYigvGpifpTdtKkda.eplgleglkelaeale..iPvvaiGGi. 159
                 +g+dg+ l   d++++e +e +++ + iG      +S +++++ ++++ ++   ++ + ++f T+  + + +   ++ lk++++a++  iPv +  Gi 
  AJA92414.1 120 AGIDGLILP--DMAIEESKEYVKAAKKIGmdtiflVSPNTEKDrLKQIIKSTSGFLYMVAVFGTTGVQTKiHKYTIDALKNTKNAAKgkIPVGVGFGIs 216
                 555555554..666666666666666666333333798999888**********************99999*************999999*97766662 PP

    TMP-TENI 160 tlenvaevleagadgvavvsa 180
                 t+++v++ + +gad v v sa
  AJA92414.1 217 TEKDVQKYVSSGADAVIVGSA 237
                 6678************99876 PP

>> DUF871  Bacterial protein of unknown function (DUF871)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00021      0.34      12      51 ..     131     171 ..     124     204 .. 0.76
   2 ?    1.7   0.0     0.074   1.2e+02     205     252 ..     219     264 ..     214     266 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                 --HHHHHHHHHHHHTT--EEEEE.E---------HHHHHHH CS
      DUF871  12 sleenkaylekaaklgfkriFts.lhipeedkeevlkelke 51 
                  +ee+k+y++ a+k+g++ iF+   + +++  ++++k  + 
  AJA92414.1 131 AIEESKEYVKAAKKIGMDTIFLVsPNTEKDRLKQIIKSTSG 171
                 689******************97566666666666665554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.074
                 HHHHHHHHSTT--EEEE-SS---HHHHHHHHHHHHHSEEEEEE--... CS
      DUF871 205 lqakeLlatgliDdvliGdayaseeelkalskllnkealelkveleee 252
                   +++++++g  D v++G a ++  e    sk +++++ +++ +l+++
  AJA92414.1 219 KDVQKYVSSG-ADAVIVGSANIKIIENTPASK-IQSRIATFTKKLKNK 264
                 5678899999.************999999999.699999998888665 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.1   3.5e+03      60      83 ..       5      28 ..       2      40 .. 0.70
   2 ?    7.5   0.0    0.0029       4.7      44      95 ..      96     147 ..      84     167 .. 0.85
   3 ?    2.9   0.0      0.08   1.3e+02      13      73 ..     177     235 ..     164     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
        PucR 60 aelvrelaeagvaaLviklgreip 83
                +e  +el++++ +aL+ ++ +  p
  AJA92414.1  5 KEKFKELKSRKESALISYIMAGYP 28
                666789999999999988754444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
        PucR  44 LllttglalkddpealaelvrelaeagvaaLviklgr.eipeelieaadelgl 95 
                 L+l t  ++    +++++++ + ++ag+ +L++   + e ++e ++aa++ g+
  AJA92414.1  96 LVLMTYTNIL-YNQTYQKFISRAKQAGIDGLILPDMAiEESKEYVKAAKKIGM 147
                 8999999996.466899****************99645778999999999876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.08
        PucR  13 vvaGkagldrpVrwvhvlevpdiaellrggeLllttglalkddpealaelvrelaeagvaa 73 
                  v G  g+++++++ ++  +   ++   +g + +  g++++ ++++++++v + a+a +++
  AJA92414.1 177 AVFGTTGVQTKIHKYTIDALK-NTKNAAKGKIPVGVGFGIS-TEKDVQKYVSSGADAVIVG 235
                 456888999999887665555.5566779999999999998.8999999999999887776 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.8   1.3e+03      43      64 ..      77      99 ..      69     115 .. 0.68
   2 ?    1.9   0.1     0.077   1.3e+02      17      89 ..     133     202 ..     124     205 .. 0.77
   3 ?    9.9   0.9   0.00029      0.47     168     215 ..     193     246 ..     156     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.8
                HHHHHHHHHHHHCT.SSS-EEEE CS
        PcrB 43 tldntvrllkkvsr.iklPivle 64
                + dn   ++kk+++  ++P+vl 
  AJA92414.1 77 KIDNFFAIVKKIRKeSDIPLVLM 99
                44555555555543278999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.077
                 S-CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETTBSST CS
        PcrB  17 enpdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDalFvmsllnsana 89 
                 e+  E v+++ + g D++ +  s + + d+  +++k  s +    ++ +  ++gv  ++  + + +l n +na
  AJA92414.1 133 EESKEYVKAAKKIGMDTIFLV-SPNTEKDRLKQIIKSTSGFLY--MVAVFGTTGVQTKIHKYTIDALKNTKNA 202
                 566789999999999999986.678999999999999965554..4445567888888888888888888886 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00029
                 HHHHHHHHHHHS.SSEEEEESS--SHHHHHHHHCC.SSEEEE-C....HHHHHH CS
        PcrB 168 veevialkkkle.karlivGGGirsaEkAkevvea.ADvivvGn....vveekd 215
                 +++++++k+  + k+ + vG Gi  + + +++v   AD+++vG     ++e+ +
  AJA92414.1 193 IDALKNTKNAAKgKIPVGVGFGISTEKDVQKYVSSgADAVIVGSanikIIENTP 246
                 4555555555541344668899*9999999999999******962222355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1634.77
//
Query:       AJA92415.1  [L=277]
Description: NeuB family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-68  229.2   0.2    5.7e-68  229.0   0.2    1.0  1  NeuB      NeuB family


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.0   0.2   3.2e-72   5.7e-68       1     241 []      22     259 ..      22     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.0 bits;  conditional E-value: 3.2e-72
                 HHHHHHHHT-SEEEEEE--HHHH--GGGGG--......TT-S-HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGG CS
        NeuB   1 lieaAaeagadavKfQtfkaeelvskeakkaeyqkkekekeesqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSge 99 
                 li++A++ag+davKfQ+++ e+++sk+  ++   +++++++ +q +  + le+s +++k + +yc++++i +  + +d +s + ++++++++ K+aS+ 
  AJA92415.1  22 LIDVAVSAGCDAVKFQKRSVEKVYSKKLLDSP--RDSPWGK-TQRAQKNGLEFSISQYKIIDRYCKSRKIPWYVSCWDIDSQTSMRKFKTKYNKVASAM 117
                 79************************876666..5666665.899999*************************************************** PP

                 TT-HHHHHHHHTT-S-EEEE-TT--HHHHHHHHHHH.HHHT--EEEEE----SS--GGG--THHHHHHHHH-TSEEEEE--SS.SSHHHHHHHHHT--E CS
        NeuB 100 ltnlpllekiaktgkpvilStGmatleeieeavevlreagaeklvllhCtseYPapledvnLkaietlkeafgvpvGySDHtl.giavaiaAvalGAkv 197
                 l +++lle iak +k  ++StGm++++eie+av+++ ++ +  + l+h  s+YP+p++++nLk i+tlk++f+++vGyS+H++  + v++ Av lGA+ 
  AJA92415.1 118 LIHTKLLETIAKEKKYTFISTGMSSMKEIETAVKIF-KKFKCPFELMHSHSAYPMPVSEANLKIIQTLKKQFKCNVGYSGHESsSYIVSLSAVLLGATS 215
                 ************************************.677889**************************************99678899********** PP

                 EEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS--TT CS
        NeuB 198 iEkHftldrnlegpDhkaSlepeelkelveairnvekalgegek 241
                 iE+H+tldr++ g+D++aSlep+ l++lv++ir v ++lg+g+k
  AJA92415.1 216 IERHITLDRSMYGSDQAASLEPDGLHRLVRDIRIVDQMLGNGKK 259
                 *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1881.71
//
Query:       AJA92416.1  [L=884]
Description: ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-180  600.0   0.0   5.7e-180  599.3   0.0    1.3  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    1.2e-27   95.7   0.0    3.1e-27   94.4   0.0    1.8  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    1.1e-21   77.2   0.0      3e-21   75.8   0.0    1.9  1  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
       0.16   12.0   0.7       0.92    9.5   0.0    2.4  3  SecA_SW          SecA Wing and Scaffold domain
       0.31   11.2   1.5          5    7.3   0.0    3.4  4  HEPN_RES_NTD1    HEPN/RES N-terminal domain 1


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.3   0.0  1.6e-183  5.7e-180       1     524 []     281     782 ..     281     782 .. 0.97

  Alignments for each domain:
  == domain 1  score: 599.3 bits;  conditional E-value: 1.6e-183
                      EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAamvylevwHpDiekf 94 
                      s+Cfvl + d++ +I++t+++aal++k+ggGvG+n s+lR++g++v++t+g asGpvsfm++i++v+dv+kqgGkRrGA+m++++v+HpDiekf
       AJA92416.1 281 SACFVLGMPDDMGKIMKTTSDAALIFKSGGGVGINYSELREEGDIVASTSGVASGPVSFMNIINTVTDVIKQGGKRRGANMGIMDVSHPDIEKF 374
                      79******************************************************************************************** PP

                      XXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXX.........................XXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC  95 idaKekntgeeenrlsnlnisvgvpdlFmeavke..dkdwtLfsPrtvvkleklygeefeeeyeeleekakikkkevkakeLfeeiaesawetg 186
                      i+ K     +e  +l+n+n+svgv+ +F++a+ +  d+ +tL s r+                        +  +e++a +L++ ia+saw+++
       AJA92416.1 375 ITNK-----TEPGVLENFNVSVGVWGDFWNALVDseDGAYTLRSTRD-----------------------GSPVREINAHHLIDLIATSAWKSA 440
                      ****.....4688*******************986688999999993.......................234569****************** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 187 ePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpe 280
                      ePg++f+D iN+ nv+ ka gg+ ratN+CgE+ l++yes   CnL+sinLa++ k++++g+ efdw+++++ +++++r+Ldnvidvn+yp+pe
       AJA92416.1 441 EPGLIFFDLINKYNVFAKARGGPLRATNPCGEQSLYPYES---CNLGSINLANLTKRTADGQYEFDWQKYEEIVRKTTRFLDNVIDVNHYPVPE 531
                      ****************************************...*************************************************** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X......XX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxx RF
  Ribonuc_red_lgC 281 iekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef....eekekedwe 370
                      i+ ++k++RriGlGvmg+ad+l kl+ipy+s+e+ +f+ k+ e+l+yy++++Sv lA+ rg+fpl +k++y +g+ p++++    ++++  dw+
       AJA92416.1 532 INVASKESRRIGLGVMGVADLLYKLRIPYNSKEGYEFMGKLSEALSYYSMEESVALAQSRGAFPLCSKTEYPEGKIPIAGYyekpKQRHYYDWD 625
                      *********************************************************************************8775445599*** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 371 eLreeikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki...lesvqgleeipeei 461
                       L ++i+k+G+r+  +t++aPTg+ S++a++s+g+eP falv++k+vtvg+f+++n+ fee L+++gl+seell+k+   ++sv+g++eipe i
       AJA92416.1 626 ALIAKIQKHGVRHVLTTTVAPTGTLSMLADCSNGMEPTFALVFEKRVTVGRFFYTNKIFEEVLRENGLYSEELLAKVadnYGSVKGIDEIPEWI 719
                      *****************************************************************************888888*********** PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 462 krvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                      +++f+ta+di+++dh+ aqa++q wi ++i ktin+pn++++edvk++yllA++lGlKg+t+Y
       AJA92416.1 720 QNIFVTAMDIHWTDHLMAQAVWQDWIGNAIAKTINMPNDVSAEDVKAAYLLAHELGLKGITVY 782
                      **************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   8.8e-31   3.1e-27       1      83 []     123     278 ..     123     278 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 8.8e-31
  Ribonuc_red_lgN   1 kkltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd............................................... 47 
                      k++++n+l+vl++rYl++++++ei E+p q+f+Rv++++ i ++l+d                                               
       AJA92416.1 123 KEFDLNCLRVLASRYLFRNKKNEITETPTQLFERVSILIGIGDLLHDssvfnaagttpqnieeakeyltkldqfdykfkideyylnqyhfrglv 216
                      689******************************************************************************************* PP

  Ribonuc_red_lgN  48 ..........................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                +++++ ++++e+ydlm++q flp+sPt+mnaG +lg
       AJA92416.1 217 ngyidlaqkgqakisfkelltkiaakEFTDYGARITEYYDLMVNQVFLPNSPTMMNAGGRLG 278
                      **********************************************************9986 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   8.5e-25     3e-21       3      85 ..      14     103 ..      12     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 8.5e-25
                 EE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT...-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHH CS
    ATP-cone   3 ViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg...isteeIqdlvektliehpdyavaaayilyrnlrk 85 
                 ++KR+G +  fd++kI++ai kA+ +    +++ ++ +++ v +++ +++  +   +s+e+Iqd+ve tlie+++ ++a++yilyr++r+
  AJA92416.1  14 IRKRNGDTTKFDQDKITNAIYKALLAtsegDRDLAQSLTNGVLNKLSSQGFGTenpPSVEDIQDMVESTLIEQGHSEIAKSYILYRHERR 103
                 99*********************999777777779999999999998885544579*******************************997 PP

>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.63   2.3e+03      63      70 ..      76      83 ..       6     201 .. 0.59
   2 ?    9.5   0.0   0.00026      0.92     104     150 ..     645     737 ..     609     751 .. 0.64
   3 ?   -1.8   0.0      0.76   2.7e+03      49     110 ..     790     856 ..     782     864 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.63
                HHHHHHHH CS
     SecA_SW 63 ldliedvv 70
                +d++e+++
  AJA92416.1 76 QDMVESTL 83
                22222222 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00026
                 T...............................................HHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
     SecA_SW 104 e...............................................elaeellekaekayekkeeeiellrelervvlLevlDkaWkehLda 150
                                                                   +eell+k+ ++y    + i+++ e  ++++++++D +W++hL a
  AJA92416.1 645 AptgtlsmladcsngmeptfalvfekrvtvgrffytnkifeevlrengLYSEELLAKVADNYG-SVKGIDEIPEWIQNIFVTAMDIHWTDHLMA 737
                 144555555555555555555555566666666666655555555665567778888888888.455578899999****************86 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.76
                 HHHCTHHCHHHHHHHHHHHHHHHHHCHHHHS.SS.CSHHHHHHHHHCCCSSSTSST.........HHHHHH CS
     SecA_SW  49 evLegesedlrerildliedvveeiveesvpeeekeewdleglleelkeefsvele.........elaeel 110
                 +vL+ + e+ +++++ + +d++++++++++++       l++++e+lk +++ el+         e++e+l
  AJA92416.1 790 QVLHMTGENSQKTFEVTATDYLHDYITNNIKN----PYILKQINEALKVVVPQELPrqdhvaaepEIEEKL 856
                 56655555555555555666666666444432....34467777777777776666666665555555555 PP

>> HEPN_RES_NTD1  HEPN/RES N-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0014         5      97     121 ..     494     518 ..     488     525 .. 0.84
   2 ?    0.1   0.0      0.25   8.8e+02      95     119 ..     612     637 ..     608     644 .. 0.77
   3 ?   -3.4   0.0       2.9     1e+04      67      84 ..     688     706 ..     673     739 .. 0.52
   4 ?   -2.2   0.0       1.3   4.6e+03      57      84 ..     805     832 ..     787     835 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
  HEPN_RES_NTD1  97 lsedealkysWeaFkelvkhksRyv 121
                     + d +++++W+++ e+v++ +R++
     AJA92416.1 494 RTADGQYEFDWQKYEEIVRKTTRFL 518
                    566788999***************7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.25
  HEPN_RES_NTD1  95 yglsedealkysWeaFkelv.khksR 119
                    y+++++++ +y+W+a    + kh  R
     AJA92416.1 612 YYEKPKQRHYYDWDALIAKIqKHGVR 637
                    88999*********998877245555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.9
  HEPN_RES_NTD1  67 i.eleaendeLiediadal 84 
                    + e+   ++eL+ ++ad+ 
     AJA92416.1 688 LrENGLYSEELLAKVADNY 706
                    4444455555555555443 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.3
  HEPN_RES_NTD1  57 ydtedlleevieleaendeLiediadal 84 
                    +++ d l+++i ++++n  ++++i +al
     AJA92416.1 805 VTATDYLHDYITNNIKNPYILKQINEAL 832
                    3678889999999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (884 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 5782.60
//
Query:       AJA92417.1  [L=64]
Description: hypothetical protein T478_0894 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 495.62
//
Query:       AJA92418.1  [L=200]
Description: DNA-directed RNA polymerase, alpha subunit, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-22   79.6   0.0    4.6e-22   78.5   0.0    1.6  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    3.1e-13   48.9   0.0      4e-13   48.6   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   5.1e-26   4.6e-22       1     112 []      44     146 ..      44     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 5.1e-26
                    EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBESSSSCEESSTTSEEEEEETT-E CS
  RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkledadveivnpdilIakLrkgqe 93 
                    V + en+svl+DE vaHr glipl+++ +              +  +e++++ l+L+   ++e   + +gdlk++d++v + ++di+I++L++gq+
     AJA92418.1  44 VDMLENSSVLADEGVAHRVGLIPLKTDLESS------------KADNENDKIMLTLDSGISDEtrtILSGDLKSQDSNVVPTSDDIPIVTLAPGQS 127
                    67789********************776666............2445556689***9988888888****************************** PP

                    EEEEEEEEEESSEECTTT- CS
  RNA_pol_A_bac  94 leleakvkkGiGkehakfs 112
                    +++ea+++ G G ehak++
     AJA92418.1 128 IKFEAHARLGKGTEHAKWN 146
                    ******************7 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   4.5e-17     4e-13       3      69 .]      16     189 ..      14     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 4.5e-17
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................................................... RF
   RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea....................................................................... 30 
                  ++gv + ++NaLRri+l+ vp +a+e+                                                                       
  AJA92418.1  16 KIKGVPLQYANALRRICLNGVPIYAVESvdmlenssvladegvahrvgliplktdlesskadnendkimltldsgisdetrtilsgdlksqdsnvvpts 114
                 689***********************************************9999999999999999999999999999999999999999999888888 PP

                 ..............................xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   RNA_pol_L  31 ..............................pvvkvn..........tdkdklilevetdgslkPeealkeAlkiLkekl 69 
                                                    n          +++d+ il+ve++g+l+P+ +++++++ L +kl
  AJA92418.1 115 ddipivtlapgqsikfeaharlgkgtehakW----NsanivtltesDKDDERILTVESTGALNPKHIILSSVEQLASKL 189
                 8885555555554444444444444444430....14444445588999**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1377.93
//
Query:       AJA92419.1  [L=387]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-05   22.9  19.3    4.2e-05   22.9  19.3    2.3  2  Zip       ZIP Zinc transporter
     0.0051   16.6   0.6     0.0051   16.6   0.6    5.1  7  LapA_dom  Lipopolysaccharide assembly protein A domain


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   7.2     0.025   2.2e+02       8      92 ..     140     226 ..     136     236 .. 0.63
   2 !   22.9  19.3   4.7e-09   4.2e-05     177     330 ..     237     381 ..     226     384 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.025
         Zip   8 iiaililsllgllgpllvpkiskl...lsklllslllafavGvllgtaflhLlPealealeesqleee.hthplagllvllGflllllv 92 
                 +++ +i +l+g+++ ++  +++     l k++++++laf +G l+  ++  ++ ea+e ++e +l++  ++++l   +v+l+fl+l+ +
  AJA92419.1 140 VFLGMIGFLIGVVPIMIGLLWYPFikkLGKSTFNFFLAFTMGLLVFLGIDAVI-EATE-ISENHLSSIfNGELLIATVVILSFLALYGI 226
                 444455555555555555555544566799************99977766666.3444.333333444344477777888888877766 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4.7e-09
         Zip 177 eklaslkvraiilllglilHsfidGLAlG.vssssstgislfiAvll..HelpeelglgaiLlkaglsrkkavllnllfaltaplGiliGilvrsises 272
                 +kl++  ++++++ +g+++H++ +GLA+G + +  + ++s+f+ + +  H+  e+l++ a+L k++++  k + l l+ ++ a+ G+ iG +       
  AJA92419.1 237 SKLSQGLAMSLMIAIGIGFHNLGEGLAVGaAIALGEVALSTFLIIGFatHNTTEGLAIAAPLTKSKAKIFKMIGLGLIAGVPAIFGCWIGGF------- 328
                 567778889********************96666677777666554444*****************************************99....... PP

         Zip 273 sgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalml 330
                 s + + + i+la+ aG    v l  +     ++ek  s++  + + ++g+ +G ++m 
  AJA92419.1 329 SFSPLFTLIFLAIGAGAIFQVVLSIFQY---MKEK--SDILSNTSLFAGVSVGLIVMY 381
                 9***************988666544433...4444..466666666666666666665 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.5      0.78     7e+03      21      30 ..      19      28 ..      14      33 .. 0.69
   2 ?   -2.3   1.8      0.45   4.1e+03      25      35 ..     145     155 ..     138     166 .. 0.58
   3 ?   -3.2   0.8      0.85   7.6e+03       9      20 ..     173     183 ..     171     188 .. 0.43
   4 ?   -2.0   0.1      0.35   3.2e+03      20      28 ..     213     221 ..     205     244 .. 0.62
   5 ?   -0.8   0.3      0.15   1.4e+03      18      30 ..     242     254 ..     233     256 .. 0.55
   6 !   16.6   0.6   5.6e-07    0.0051      17      49 ..     331     363 ..     317     368 .. 0.91
   7 ?   -1.0   0.1      0.18   1.6e+03      28      40 ..     370     382 ..     366     386 .. 0.51

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.78
    LapA_dom 21 llllvafgiG 30
                l + ++f++G
  AJA92419.1 19 LAIMIVFLLG 28
                4566666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.45
    LapA_dom  25 vafgiGallgw 35 
                 + f+iG++ ++
  AJA92419.1 145 IGFLIGVVPIM 155
                 44555554444 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.85
    LapA_dom   9 nflfaqvelpLs 20 
                 nf++a  ++ L 
  AJA92419.1 173 NFFLAF-TMGLL 183
                 555442.33333 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.35
    LapA_dom  20 sllllvafg 28 
                 +++++++f+
  AJA92419.1 213 ATVVILSFL 221
                 445555544 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.15
    LapA_dom  18 pLsllllvafgiG 30 
                  L++ l +a+giG
  AJA92419.1 242 GLAMSLMIAIGIG 254
                 3455555566665 PP

  == domain 6  score: 16.6 bits;  conditional E-value: 5.6e-07
    LapA_dom  17 lpLsllllvafgiGallgwllslwsylrlrrel 49 
                  pL +l+++a+g+Ga++ ++ls+++y++ ++ +
  AJA92419.1 331 SPLFTLIFLAIGAGAIFQVVLSIFQYMKEKSDI 363
                 59**************************99876 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 0.18
    LapA_dom  28 giGallgwllslw 40 
                 ++G+ +g++++++
  AJA92419.1 370 FAGVSVGLIVMYL 382
                 4555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2521.61
//
Query:       AJA92420.1  [L=407]
Description: TIGR00300 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-32  112.5   0.3    4.5e-32  110.4   0.3    2.1  2  Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
     0.0019   17.9   1.5      0.096   12.4   0.1    2.4  2  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
      0.003   17.1   0.2     0.0098   15.4   0.1    1.8  2  Citrate_bind    ATP citrate lyase citrate-binding
     0.0085   15.4   2.5      0.048   12.9   0.5    2.6  3  DS              Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> Saccharop_dh_N  LOR/SDH bifunctional enzyme conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.3     1e-35   4.5e-32       2      99 ..       6     103 ..       5     104 .. 0.98
   2 ?   -2.2   0.0       1.2   5.6e+03       6      31 ..     308     333 ..     306     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 1e-35
                     EEEEEEEXXTTSSHHHHHHHHHHHTTXEEEEEEEEXXSSTTSXEEEEEEEEESSHHHHHHHHHHHHHHHHHSCCCCEEEECESSCTTB--TTB-- CS
  Saccharop_dh_N   2 reveleGhliDsgilnkvldlileaggsfevlefevGkkkkdtSyaelevsaedeevLeeileeltelgaelveeedvklekaekdgvlpedFYs 96 
                     + +e++GhliDs++l+k++d++++++g+fev +++vGk k+d+Sya+l+v ++++++L+ei+++l++ ga++++++++k+++a k++v+p++FYs
      AJA92420.1   6 KIIEVKGHLIDSLVLTKIFDRVMDLDGKFEVMKISVGKLKTDESYAKLRVIGKNKTHLSEIMTALHREGATTKTQKNCKTKSALKNMVFPDNFYS 100
                     689******************************************************************************************** PP

                     --S CS
  Saccharop_dh_N  97 ttn 99 
                     ttn
      AJA92420.1 101 TTN 103
                     **9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                     EEEXXTTSSHHHHHHHHHHHTTXEEE CS
  Saccharop_dh_N   6 leGhliDsgilnkvldlileaggsfe 31 
                     l G l D g l+ v+  i ea+ +++
      AJA92420.1 308 LAGSLRDDGPLPDVITDIAEAQREYK 333
                     78999999999999999999988875 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.2    0.0067        30       9      66 ..     195     255 ..     187     273 .. 0.72
   2 !   12.4   0.1   2.1e-05     0.096      69     134 ..     330     396 ..     314     399 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0067
                   HH-S...SEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGG CS
  TPP_enzyme_M   9 kaak...rpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglh 66 
                   +++k   ++v++ G  +   ga++++++++++ +i  v   ++  v + +      +lg+ 
    AJA92420.1 195 NTKKkrgKIVLVGGPAIVHTGAADAVAKMIKTGHINAVLAGNALAVHDVEYATLGTSLGMK 255
                   44443336788888888888************99999988888877776665444466665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                   HHHHHHHHH-SEEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC....--SEEEECTHHHHH CS
  TPP_enzyme_M  69 kaanealeeaDlvlalGarfddirttgsepefapea.kiihididpaeigkny....qvdlaivgdvketl 134
                   ++ +++l++a  v+++ + ++ i t++      p + k+i idi++ ++ k      + +l+iv+dv+++l
    AJA92420.1 330 REYKKVLKDASMVIMVSTMLHSIATGNML----PANvKVIVIDINQPTVTKLMdrgtWQALGIVSDVGAFL 396
                   5667899***************8776543....44559********99888875444688********998 PP

>> Citrate_bind  ATP citrate lyase citrate-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.2e-06    0.0098      65     117 ..     174     226 ..     167     242 .. 0.93
   2 ?   -2.3   0.0       0.6   2.7e+03     112     136 ..     323     347 ..     317     365 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
  Citrate_bind  65 sGapseeqtyeyaktildlmtrekrpdgkvliiGggianftnvaatfkgiira 117
                   sG+ se+ t + a+++ + + ++k+++gk++++Gg  +  t  a++++ +i++
    AJA92420.1 174 SGSSSERPTQHIARKVAEDIINTKKKRGKIVLVGGPAIVHTGAADAVAKMIKT 226
                   899*****************************************999998875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.6
  Citrate_bind 112 kgiiraleelksklkehkvkiyvrr 136
                   + i +a +e+k+ lk++ + i v +
    AJA92420.1 323 TDIAEAQREYKKVLKDASMVIMVST 347
                   5678889999999999988888865 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   1.1e-05     0.048      20      96 ..     191     263 ..     164     274 .. 0.80
   2 ?   -0.3   0.0      0.11     5e+02     148     164 ..     291     307 ..     268     317 .. 0.77
   3 ?   -0.3   0.0      0.11     5e+02      14      53 ..     323     368 ..     321     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
          DS  20 idilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLre 96 
                  di+n   k+++ +i+l    +++ +G  + +a+++k ++++++ +  +   +D+  a+   t lg ++++d +L  
  AJA92420.1 191 EDIINT--KKKRGKIVLVGGPAIVHTGAADAVAKMIKTGHINAVLAGNALAVHDVEYATLG-TSLG-MKVKDGTLAV 263
                 344443..5677889999999*********************************9998877.7887.5577766655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.11
          DS 148 deeSilywAykndipvf 164
                  +++i+y + k++ip  
  AJA92420.1 291 LRRGIMYECVKKNIPFV 307
                 4589**********954 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.11
          DS  14 tslgeaidilnkmrkdekctiflgl......tsnlissGlreiiad 53 
                 t+++ea ++++k+ kd ++ i+++       t+n+ ++ ++ i+ d
  AJA92420.1 323 TDIAEAQREYKKVLKDASMVIMVSTmlhsiaTGNMLPANVKVIVID 368
                 5788999999999999888888874333333788888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3065.33
//
Query:       AJA92421.1  [L=62]
Description: hypothetical protein T478_0664 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 498.29
//
Query:       AJA92422.1  [L=87]
Description: putative H/ACA RNA-protein complex component Gar1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-08   32.3   0.0    7.9e-08   32.2   0.0    1.2  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
       0.17   11.2   0.0       0.18   11.1   0.0    1.0  1  DUF1668   Protein of unknown function (DUF1668)


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   8.8e-12   7.9e-08      21      78 ..       2      55 ..       1      83 [. 0.79

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.8e-12
                EEEEEEEEEETT.EEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEE CS
        Gar1 21 leiGtvssiven.evviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysV 78
                +e+G+v++  ++  v+++ + s   +v+ +++il+++n ++i kV+E +Gpv++p+ s 
  AJA92422.1  2 QEVGEVMHLANSgRVIVRLN-S---EVP-EGQILCDSNSQKIAKVTELIGPVSSPFASA 55
                79******998846666666.4...566.7*************************9764 PP

>> DUF1668  Protein of unknown function (DUF1668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     2e-05      0.18      70     134 ..       6      84 ..       2      87 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2e-05
     DUF1668  70 efaal..agdkivavdqs..grtllYdtktravvtlPslkspkllpvsvav..........gdklYvldrspkdekagr 134
                 e+++l  +g+ iv    +  +  +l+d ++++++++ +l  p  +p++ a+          g+k+++ld+ p+++k +r
  AJA92422.1   6 EVMHLanSGRVIVRLNSEvpEGQILCDSNSQKIAKVTELIGPVSSPFASAIpltnnlrkinGKKVFALDQAPAKKKSRR 84 
                 56666667888888866677559***********************9999999*******8888********9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 699.29
//
Query:       AJA92423.1  [L=442]
Description: phosphomethylpyrimidine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     8e-170  565.1   0.4   9.2e-170  564.9   0.4    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family
  ------ inclusion threshold ------
      0.052   13.8   3.1      0.063   13.5   1.2    2.0  2  Spore_GerAC   Spore germination B3/ GerAC like, C-terminal


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.9   0.4    1e-173  9.2e-170       1     414 [.       3     423 ..       3     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 564.9 bits;  conditional E-value: 1e-173
  ThiC_Rad_SAM   1 tqleaarkgiiteemeevaekenvepefvreevaeGrivipanknhkek..pvaiGkglrtkvnaniGtsadasdieeEveKlkvalkagadtvmdL 95 
                   tq+++ar+g+ t+em+++a++e+v+ + +  ++a+G+i+ip+n+ +kek   vaiGkg++tkvn+niGts+  ++i+eE+eK+kva+k+ adt+mdL
    AJA92423.1   3 TQMTSARRGVATDEMKQIAKDEDVTLDWLIPKIASGSIIIPSNNVRKEKihNVAIGKGTKTKVNVNIGTSTLNVNIDEEIEKAKVAVKYHADTIMDL 99 
                   8******************************************999655569********************************************* PP

  ThiC_Rad_SAM  96 stggdideirekileespvpvgtvpiYqalee...kekkveelteeellevieeqaedGvdfltiHagvtlellellkkekRltgivSrgGsllaaw 189
                   s ggd+  +r+k+le++p+++gtvpiY+a++    k+k+  ++te+++l++ e++++dGvd+ tiH+g+t+e+++++ k +R++g+vS+gG+++aaw
    AJA92423.1 100 SDGGDVGIVRRKLLEAAPITFGTVPIYEAYNFgveKHKNPLDITEDDFLKAFENNIKDGVDYTTIHSGITKEIAKRILKVERYAGVVSKGGTITAAW 196
                   *****************************98787799************************************************************ PP

  ThiC_Rad_SAM 190 mlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPf 286
                   ml+ +kenp+ +++d+++e++++ydvt+Slgd+lRpGsi D++de q++e+i++++l+kra+e++vqvm+eGPGHvpl+e++anv+l k+l  ++P+
    AJA92423.1 197 MLKYDKENPYITHYDYMMELAQKYDVTFSLGDALRPGSILDSHDELQVQEMINISRLAKRANEKDVQVMIEGPGHVPLNEVAANVRLAKSLIGDVPY 293
                   ************************************************************************************************* PP

  ThiC_Rad_SAM 287 yvlGplvtDiapgYDhitsaiGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                   yvlGplvtDia g+Dhi+saiGaa++a+ G+dllCy+tp+EHl+lP++e+vk+G+ia++iaaha+dl+k ++k  ++d ++++aR++ldwekq++l+
    AJA92423.1 294 YVLGPLVTDIASGHDHIASAIGAAVSASEGVDLLCYLTPSEHLALPNAEEVKAGLIAYRIAAHAGDLVKLREKSIKWDMKMTEARRTLDWEKQLALS 390
                   ************************************************************************************************* PP

  ThiC_Rad_SAM 384 ldpekareireeklpe..eeeaCsmCgekCavk 414
                   +dpe+a +i+ ++ ++  ++  C+mCg  C + 
    AJA92423.1 391 IDPENAAKIHGRTGQHpgNNVPCTMCGGACVYL 423
                   **********999887779999********875 PP

>> Spore_GerAC  Spore germination B3/ GerAC like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.2   7.1e-06     0.063      15      77 ..      20      82 ..      13     100 .. 0.80
   2 ?   -1.0   0.0       0.2   1.8e+03      18      49 ..     143     174 ..     131     265 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-06
                 E-HHHHHHHHHHTT-----EEEEE.ETTEEEE.EEEEEEE.EEEEEEE-SSSEEEEEEEEEEE CS
  Spore_GerAC 15 Ldeeetrgllllrgkvksgvitiplpkgkdekvsveissskskikvkiengkpsfdikikleg 77
                 + ++e   l +l  k+ sg+i ip ++  +ek+  +   + +k+kv+++ g+ + +++i+ e 
   AJA92423.1 20 IAKDEDVTLDWLIPKIASGSIIIPSNNVRKEKIHNVAIGKGTKTKVNVNIGTSTLNVNIDEEI 82
                 56789999*****************99999997777777778899999888888877776653 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.2
                  HHHHHHHHHTT-----EEEEE.ETTEEEE.EE CS
  Spore_GerAC  18 eetrgllllrgkvksgvitiplpkgkdekvsv 49 
                   e   l+ + +++k gv + ++++g +++++ 
   AJA92423.1 143 TEDDFLKAFENNIKDGVDYTTIHSGITKEIAK 174
                  55555566666666666555555555554222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3480.43
//
Query:       AJA92424.1  [L=261]
Description: precorrin-3B C(17)-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-38  130.6   0.0    9.2e-38  130.3   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   5.1e-42   9.2e-38       1     212 [.       4     215 ..       4     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 5.1e-42
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea...yeeiaealaealragkdVvllvsGDPlvyg 94 
                   kly+VGvGpG+ +++T rA ++++++d ++g++  +  +++dl++            ke +  a     e a + ++++++gk V l++sGDP +yg
    AJA92424.1   4 KLYIVGVGPGHHDHMTFRAKQVIEESDTIVGYT-TYVNLVEDLIQG-----------KEIHSYAmtqEVERAHQCIDLAKEGKVVSLVSSGDPGIYG 88 
                   79*******************************.*******99964...........444444421134445555********999999******** PP

  TP_methylase  95 tgselvealrareagie......veviPGvsslqaaaarlgiplteggevlsvl..lpglakeeereleallangdtlvllkapr.k.....laela 177
                   +++ ++e l++   g +      ve iPGvs+l+++a+ +g pl  ++ v s +    +++     ++ +++a+gd+++++++p+ k     l++++
    AJA92424.1  89 MAGLIFEVLAE--SGWDpksglhVELIPGVSALNSCASIIGSPLMTDFAVCSMSdlMVPWE--IIVKRVEAAAQGDFVLVIYNPKsKkrvhqLQDTR 181
                   *******9998..4444444444***************************99998555555..666666667779**********7478999***** PP

  TP_methylase 178 elLkealyddttpvavveragtedervvrgtleel 212
                   ++L+++ +++ttpva++++a ++ e+v+ + le++
    AJA92424.1 182 KILLKH-RKPTTPVAIIKEAYRDSETVIITDLEHM 215
                   ******.77799********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1812.14
//
Query:       AJA92425.1  [L=204]
Description: putative membrane-bound metal-dependent hydrolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.1   7.2    0.00018   20.9   6.3    1.7  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   6.3     1e-08   0.00018       5     132 ..      55     167 ..      49     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-08
        YdjM   5 tHallGaalglalaallgaakeavllavavlgAllPDiDhpsstlgrklgllskklaklvgHRgftHSllflallalvlllllrlfgrsalrlglllll 103
                  H+l Ga++gl+ ++         +++++ + A++ D Dh   +l  +l +  +          ++HS++f++++++v+ ++lr  + +      ++++
  AJA92425.1  55 GHILWGAVIGLGTLSIR------YIILGGSF-AIFLDSDHLLQFLDIELVS--R----------MSHSIPFAVIVSIVFFVILRGKDIR----ICAVAF 130
                 34444444444444443......23333333.7999999999999888855..4..........89*****************999988....556777 PP

        YdjM 104 g.vlsHlllDlltk.......yGvpllwPfskkkvrl 132
                 g vlsH++ D++           +pl+ Pf+ + +++
  AJA92425.1 131 GaVLSHIAFDIFLAdvalnsdTEFPLFSPFTFETISF 167
                 76*********99988888788889999997444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1508.14
//
Query:       AJA92426.1  [L=39]
Description: hypothetical protein T478_0099 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.8   0.0     0.0023   17.7   0.0    1.1  1  FAM165    FAM165 family
  ------ inclusion threshold ------
        0.1   12.5   0.1       0.11   12.4   0.1    1.0  1  TMEM154   TMEM154 protein family


Domain annotation for each model (and alignments):
>> FAM165  FAM165 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.6e-07    0.0023      17      41 ..      13      37 ..       8      39 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-07
      FAM165 17 tliLCLaFAGvKiyQrKklEaklkk 41
                 ++L L+ AGv iy r ++ ++ ++
  AJA92426.1 13 VILLALGIAGVMIYERTRIRQEKQQ 37
                5899**************9766554 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05      0.11      68      95 ..      11      38 ..       7      39 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
     TMEM154 68 llillllvviiliqkkkrkrsKddekse 95
                ++++ll ++i  +++++r+r++++++++
  AJA92426.1 11 ITVILLALGIAGVMIYERTRIRQEKQQD 38
                67888888888888**********8766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 316.01
//
Query:       AJA92427.1  [L=188]
Description: CDP-alcohol phosphatidyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-10   41.4   0.8    1.9e-10   41.4   0.8    2.4  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
       0.19   11.6   2.1       0.35   10.7   2.1    1.4  1  ECSCR            Endothelial cell-specific chemotaxis regulat


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.8   2.1e-14   1.9e-10       2      66 .]      26      92 ..      25      92 .. 0.88
   2 ?    0.4   1.3      0.13   1.1e+03      30      34 ..     154     158 ..      96     184 .. 0.52

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.1e-14
                     -HHHHHHHHHHHHHHHHHGGGS-H........HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
  CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp......lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                      Pn++T ++l+l++++ + + +  +      l+l+ + ll+++++D++DG++AR  n+ s+ G +lDs+ D
       AJA92427.1 26 SPNVFTGIGLALAFVSSI-I-Y--GigfefsLILGGIALLASGFFDIVDGQVARYANKMSKSGGFLDSIFD 92
                     6***********999995.4.2..2347899889999999*****************************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
                      HHHHH CS
  CDP-OH_P_transf  30 ailll 34 
                      ai+ +
       AJA92427.1 154 AIIGM 158
                      22222 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.1   3.9e-05      0.35      16      44 ..     147     175 ..     137     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.9e-05
       ECSCR  16 setvltvaafgvisfivilvvvviilvsv 44 
                 +e +l +a +g+i f+ i v++vii+  +
  AJA92427.1 147 AERLLVIAIIGMIGFMEIAVIIVIIIAGI 175
                 6889******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1553.14
//
Query:       AJA92428.1  [L=486]
Description: glutamine synthetase, type I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.9e-115  385.5   0.0   2.3e-115  385.3   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
      1e-27   95.7   0.1    2.4e-27   94.5   0.1    1.7  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
        0.3   11.0   2.9          3    7.7   0.0    2.9  3  DUF2527     Protein of unknown function (DUF2627)


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.3   0.0  3.8e-119  2.3e-115       2     345 .]     119     483 ..     118     483 .. 0.96

  Alignments for each domain:
  == domain 1  score: 385.3 bits;  conditional E-value: 3.8e-119
                 T-HHHHHHHHHHHHHHTTC.EEEEEEEEEEEEESEECCCE...SSEEEEEEE.T........B...B.TSS-TTBHCCCCCTCCHHHHHHHHH.HHTT- CS
  Gln-synt_C   2 rdPRsvlkralarlaeeGl.tvvvgpElEFflfdkeedke...asksllevdse........ekgrpaekggyfsvapvdeaedlrreiveal.ealgi 87 
                  dPR + ++a+a ++ +G+   + gpE+EFf+fdk++++     ++++++++s         +++    ++gy++ +p d+ +++r+e v++l +++gi
  AJA92428.1 119 SDPRGICQKAEAFVKTQGFdFSNWGPEVEFFVFDKVHWDVltpYKGQSYSIESSespwsqegTGYPMGLQEGYYPSTPSDTLAPFRNECVDVLnDNFGI 217
                 79*****************66799**************987666677777777799****99899999*************************6789** PP

                 -EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEESSB-TTSGGGB-HHHHHHHHHH CS
  Gln-synt_C  88 eveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgknlfadeddeyalselarhfigGl 185
                   +++hhEvat+ Q+Ei++k++ + ++aD ++ +K+vv++vA++ g+ at mpKp++ d+GsgmH+++Slw k+++n f+d+d+  +ls+++r+f gG+
  AJA92428.1 218 LCDNHHHEVATAgQCEIDIKYDLMTNSADGAQSYKYVVRNVAQQFGKVATMMPKPISMDAGSGMHTNVSLW-KKDENTFYDKDEVLELSQTGRYFCGGV 315
                 ***********99**********************************************************.99**********9************** PP

                 HHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-.....TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-S CS
  Gln-synt_C 186 lkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa.....skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdl 279
                 ++hak lta+t+pt+nSY+RlvpgyeaPv++aw+ +NRsa +Rip      + +  kr+E+R+pd+++NPYL+++a+laAgldGi++k+epg+pv++d+
  AJA92428.1 316 MEHAKGLTAITNPTTNSYHRLVPGYEAPVYIAWSSSNRSATIRIPGhfkgeKYAYMKRMEYRVPDPASNPYLVFSAVLAAGLDGIKKKMEPGDPVKEDI 414
                 **********************************************99765556689****************************************** PP

                 SSS-TTTH..TSS-B--SSHHHHHHHHHCS.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
  Gln-synt_C 280 yelspeer..kgieelPasleeAlealeed.ellkevlgeevieaylalkraEleeleeevsdwelery 345
                 y+++++er  +gi++lPa+l  Al++le+d ++l+ ++++ev+++ ++l r + +e+  ++++ e+  y
  AJA92428.1 415 YKMTKSERkkHGIDTLPANLGRALDELESDrKYLNPIFSNEVLDKIIDLERRDHREIAIRPHPHEFYLY 483
                 *******9999******************************************************9876 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.1     4e-31   2.4e-27       2      82 ..      29     110 ..      28     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 4e-31
                 --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E.EEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE- CS
  Gln-synt_N   2 vkfvdlqFtDikgklkhvtipadelsedaleegv.sFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicdvyd 82 
                 +kf+dlqFt ++g+++h ti+ad ++ d +e+g+ ++DGSsi gf++i +SD++LkPd+st++i+P+  ekktar++cdvy+
  AJA92428.1  29 IKFIDLQFTGLTGRFHHTTISADTFTPDQMEDGLpKLDGSSIVGFTDIADSDLILKPDPSTFAIIPWLTEKKTARLLCDVYW 110
                 89******************************************************************9999*********7 PP

>> DUF2527  Protein of unknown function (DUF2627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.03   1.8e+02      23      34 ..     343     354 ..     340     356 .. 0.83
   2 ?   -3.2   0.1       1.4   8.1e+03      17      27 ..     375     388 ..     374     391 .. 0.55
   3 ?    7.7   0.0   0.00051         3       4      19 ..     451     466 ..     449     468 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
     DUF2527  23 ePYlsASsSNvS 34 
                   Y++ SsSN S
  AJA92428.1 343 PVYIAWSSSNRS 354
                 56********99 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
     DUF2527  17 EYRF...SAePYls 27 
                 EYR      +PYl 
  AJA92428.1 375 EYRVpdpASNPYLV 388
                 66652224578875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00051
     DUF2527   4 IFSKEVLSKdVdVEYR 19 
                 IFS EVL K +d E R
  AJA92428.1 451 IFSNEVLDKIIDLERR 466
                 9***********9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3440.63
//
Query:       AJA92429.1  [L=65]
Description: ribosomal protein S27 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-16   60.4   0.9    1.1e-16   60.2   0.9    1.0  1  Ribosomal_S27e  Ribosomal protein S27
    1.3e-06   27.8   0.8    1.7e-06   27.4   0.8    1.2  1  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00046   20.2   0.7    0.00047   20.1   0.7    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
     0.0024   17.9   0.4     0.0027   17.8   0.4    1.1  1  DUF2318         Predicted membrane protein (DUF2318)
     0.0056   16.7   0.9     0.0056   16.7   0.9    1.1  1  zf-RING_9       Putative zinc-RING and/or ribbon
  ------ inclusion threshold ------
      0.017   14.9   3.5        2.1    8.2   0.5    2.1  2  ZZ              Zinc finger, ZZ type
      0.027   14.4   0.4        7.4    6.5   0.0    2.1  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.061   13.4   0.6      0.073   13.2   0.6    1.1  1  zf-C2H2_7       Zinc-finger
       0.12   12.1   5.6       0.24   11.2   5.6    1.4  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.14   12.2   4.4       0.53   10.4   4.5    1.7  2  zinc_ribbon_6   Zinc-ribbon
       0.16   12.3   3.9       0.25   11.6   3.9    1.3  1  zinc_ribbon_9   zinc-ribbon
       0.16   12.0   0.7       0.16   12.0   0.7    2.1  2  zf-BED          BED zinc finger
          2    8.3   5.8        2.2    8.2   1.4    2.2  2  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.9   8.1e-20   1.1e-16       1      53 [.      11      63 ..      11      65 .] 0.95

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 8.1e-20
                    -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEE CS
  Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqiler 53
                    p skF +vkC +Ce e++v+sh++t+v C sCg+vL + tG  a+++ ++le 
      AJA92429.1 11 PSSKFNKVKCHECESEQIVYSHSSTQVICNSCGNVLSKATGSIAQINGKVLEA 63
                    689*******************************************9999885 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.8   1.3e-09   1.7e-06       2      30 ..      19      47 ..      18      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-09
                  EETTTTCEECHEETSTTCEEESSSSBEEE CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVle 30
                  kC +C s+++v+ ++++ ++C +CG+Vl 
    AJA92429.1 19 KCHECESEQIVYSHSSTQVICNSCGNVLS 47
                  9**************************96 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   3.4e-07   0.00047      37      70 ..      15      49 ..       9      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.4e-07
  Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqkkatee 70
                 f++++C+eC++e+ivy     +  C+sC++  ++ 
   AJA92429.1 15 FNKVKCHECESEQIVYSHSSTQViCNSCGNVLSKA 49
                 7899******99999976666666*****987665 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.4     2e-06    0.0027      36      64 ..      19      49 ..       4      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
     DUF2318 36 aCevC..ekkgYvqegeelvCknCgvrfald 64
                 C+ C  e+  Y ++  +++C++Cg++++++
  AJA92429.1 19 KCHECesEQIVYSHSSTQVICNSCGNVLSKA 49
                599**76667899*************99865 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   4.1e-06    0.0056     154     185 ..      16      46 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
   zf-RING_9 154 kgfiCelCkseellfpfqlktverCekCkavf 185
                 +++ C+ C+se++++++ +++v  C++C++v+
  AJA92429.1  16 NKVKCHECESEQIVYSHSSTQVI-CNSCGNVL 46 
                 5789************9988887.*****987 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0015       2.1       3      15 ..      16      28 ..      14      32 .. 0.80
   2 ?    7.8   0.1     0.002       2.8       3      12 ..      35      44 ..      33      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                S-EE-TTT-S..E CS
          ZZ  3 kkytCdgCseapl 15
                +k++C++C +  +
  AJA92429.1 16 NKVKCHECESEQI 28
                799*****99544 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.002
                S-EE-TTT-S CS
          ZZ  3 kkytCdgCse 12
                 +++C+ C++
  AJA92429.1 35 TQVICNSCGN 44
                799*****98 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0066       9.1       9      31 ..       4      27 ..       3      27 .. 0.76
   2 ?    6.5   0.0    0.0054       7.4       4      15 ..      39      50 ..      38      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                    SBEEEEECSCCCE.EEESSSS-EE CS
  RNA_POL_M_15KD  9 NlLlpkedkegkn.feCrqCgYee 31
                    ++ l++e  ++ n + C  C +e+
      AJA92429.1  4 DHVLVPEPSSKFNkVKCHECESEQ 27
                    5666777777777899****9986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0054
                    ESTTTSBEEEEE CS
  RNA_POL_M_15KD  4 CpkCgNlLlpke 15
                    C +CgN L  ++
      AJA92429.1 39 CNSCGNVLSKAT 50
                    9*****997655 PP

>> zf-C2H2_7  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   5.3e-05     0.073       6      50 ..       2      47 ..       1      50 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.3e-05
   zf-C2H2_7  6 kkPh.yiPrPpGkPykykcfqcPftcnikshlynhmkyslcknsls 50
                kk h  +P P  k  k kc  c     + sh    +  + c n ls
  AJA92429.1  2 KKDHvLVPEPSSKFNKVKCHECESEQIVYSHSSTQVICNSCGNVLS 47
                7777348*************************99999999999998 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.6   0.00017      0.24       3      30 ..      17      45 ..      16      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
  A2L_zn_ribbon  3 lkvCsvCggngilnseqgy.lvCieCgas 30
                    ++C+ C ++ i++s ++   +C+ Cg++
     AJA92429.1 17 KVKCHECESEQIVYSHSSTqVICNSCGNV 45
                   689***********77775167*****96 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.5   0.00038      0.53      21      54 ..       9      43 ..       2      44 .. 0.81
   2 ?    5.2   0.4     0.015        21      23      37 ..      30      44 ..      29      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
  zinc_ribbon_6 21 eeyknkkvkilCnDCekksevkfhvl.glkCkeCg 54
                   +e ++k  k+ C+ Ce+++ v+ h    + C++Cg
     AJA92429.1  9 PEPSSKFNKVKCHECESEQIVYSHSStQVICNSCG 43
                   56678999*************99975156899996 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
  zinc_ribbon_6 23 yknkkvkilCnDCek 37
                   y+++ ++++Cn C++
     AJA92429.1 30 YSHSSTQVICNSCGN 44
                   6778899******86 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.9   0.00018      0.25       5      29 ..      20      44 ..      19      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
  zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCgg 29
                   Ch+C  +  v ++++ +v+C++Cg+
     AJA92429.1 20 CHECESEQIVYSHSSTQVICNSCGN 44
                   *****99999999999999****96 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9     0.048        66      12      33 ..      13      35 ..       3      36 .. 0.71
   2 ?   12.0   0.7   0.00011      0.16      14      29 ..      34      49 ..      27      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.048
                GGSS--EETTTT.EE----SSTH CS
      zf-BED 12 lkeqkavCryCg.kilsrgggtt 33
                 k +k++C  C+ +++ +++++t
  AJA92429.1 13 SKFNKVKCHECEsEQIVYSHSST 35
                57799******735677775554 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                SS--EETTTTEE---- CS
      zf-BED 14 eqkavCryCgkilsrg 29
                ++ ++C+ Cg++ls  
  AJA92429.1 34 STQVICNSCGNVLSKA 49
                799**********986 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.4    0.0016       2.2       9      20 ..      13      24 ..      11      36 .. 0.71
   2 ?    3.0   0.5     0.067        93      14      20 ..      35      43 ..      30      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
   zf-C2H2_3  9 ksfgasqCkeCg 20
                ++f++++C+eC+
  AJA92429.1 13 SKFNKVKCHECE 24
                89*********6 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.067
   zf-C2H2_3 14 sq..CkeCg 20
                +q  C+ Cg
  AJA92429.1 35 TQviCNSCG 43
                3456****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 515.08
//
Query:       AJA92430.1  [L=394]
Description: amidohydrolase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-38  130.7   0.2    9.4e-38  130.4   0.2    1.1  1  Amidohydro_1  Amidohydrolase family
    1.3e-11   44.7   0.0    7.6e-06   25.7   0.0    2.3  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.2     1e-41   9.4e-38       2     344 .]      50     390 ..      49     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 1e-41
                   EEE-EEEEEEECETTECSSS....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEE CS
  Amidohydro_1   2 vlPGlIDaHvHleqsllrga....tledwl.............vppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilg 81 
                   ++PG++++H+H+ +s +++     ++++ +             +p++ ++ ++++ +k ++k G+tt++d+++   +g+ +l+ a++++p+   ilg
    AJA92430.1  50 LIPGFVNSHTHIADSIGKDLsinaDVNSKIhpmfglkqkllkeTPKSSLSKYIKKSAKSMIKKGITTFIDFREGGLDGVLLLKSALDNIPIRCVILG 146
                   89*************99888888844444466668888889************************************************99999999 PP

                   ESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTT CS
  Amidohydro_1  82 gkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthle 177
                           ++ + k+++++ ++ + e  k+    + +  +++ ++  ++  + lk  +    k ++  aiHa+et+  v  +++  g     +t + 
    AJA92430.1 147 R------IDYYNTKNEIKQNLSFPNENTKKLTQLLKNcDGIGISGTNENASSNLKSYS----KTKKIRAIHAAETQDSVNTSKKITG-----KTEVQ 228
                   9......777888888888888886667666666666788888888888877877666....799**************66666666.....45667 PP

                   STCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT CS
  Amidohydro_1 178 vaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye 274
                   +a+    l++    l h+++ t ++++l +++    g++ cp++ns l++g++++  + + G + ++gtD + ++ns+++++e+ ++ k+++g  + 
    AJA92430.1 229 RAML---LNP--SFLIHMTFATNNDLKLAAKN--TRGIVVCPRANSALSEGIPNISLMQKFGCNLTIGTD-NVMINSPDIFREMDYLWKVTMGISQ- 316
                   7554...666..567788888888****9999..9999999**************999777*********.*****************99998777. PP

                   TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEEE CS
  Amidohydro_1 275 deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGklv 344
                      + + +ke+l+maT n+ k l+   k+G i++ + AD +++d    d+       a++v  ++ +++k v+++G++v
    AJA92430.1 317 ---ARFNPKEILKMATVNAGKMLNQ--KIGCIKENYLADCIFIDKnslDLepmnnvHASIVHRASEKSIKAVMIGGEIV 390
                   ...55*******************9..******************76622678889********************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.3e-07    0.0038       3      23 ..      43      63 ..      41      80 .. 0.90
   2 !   25.7   0.0   8.5e-10   7.6e-06     310     472 ..     237     390 ..     202     391 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.3e-07
  Amidohydro_3  3 iDakGrlvlPGFvDsHtHlag 23
                  iD++++l++PGFv sHtH+a 
    AJA92430.1 43 IDCSNLLLIPGFVNSHTHIAD 63
                  9*****************875 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 8.5e-10
  Amidohydro_3 310 rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwpri.gaavmrktrrggevlrpd 405
                    l+h ++ t+++++ +a+    + v+p+ n            +  +g++++ ++ + g +++ g+D   +++ + p i + ++ ++++++g      
    AJA92430.1 237 FLIHMTFATNNDLKLAAKNTRGIVVCPRANS-----------ALSEGIPNISLMQKFGCNLTIGTD---NVMINSPDIfREMDYLWKVTMG---ISQ 316
                   6666666677777777777777777755555...........556678******************...5555555542567788888775...667 PP

  Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.........vrltvvdGrvv 472
                    ++   e+l++ T ++ k+l++    G +++ + AD + +d++ ld++p+++++a          +++++++G++v
    AJA92430.1 317 ARFNPKEILKMATVNAGKMLNQKI--GCIKENYLADCIFIDKNSLDLEPMNNVHASivhraseksIKAVMIGGEIV 390
                   78*******************998..******************************9999*999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2967.04
//
Query:       AJA92431.1  [L=259]
Description: RIO1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.4e-47  159.8   0.0    8.4e-47  159.2   0.0    1.3  1  RIO1       RIO1 family
  ------ inclusion threshold ------
        0.8   10.0   6.0        4.1    7.7   3.4    2.2  2  RSB_motif  RNSP1-SAP18 binding (RSB) motif


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.2   0.0   9.4e-51   8.4e-47       2     181 ..      72     246 ..      71     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 9.4e-51
                 EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHH CS
        RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkd 100
                 V++a + +++++a+Kiy ++t++Fkkr++y +g++rf++   k+ ++++v lwa+kEf+n+++ ++ g+pv kp ++ +++l+m+f g+dg +  +l +
  AJA92431.1  72 VFWAKDPEENDIALKIYLVTTSNFKKRSQYLTGDPRFTSV--KKGTKNIVYLWARKEFQNISKCYDCGIPVVKPRHVSKNILIMDFEGKDGKPENTLLE 168
                 9************************************976..99*****************************************************99 PP

                 CG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHHHHHHHTTC-- CS
        RIO1 101 veeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveniikfFrrkgve 181
                  e    +e+ y++ +e +  l+k+a+lvH+D+SeyN++ +++++ ++D++ av+ +hpn  +fL+rD++ni +fF ++g +
  AJA92431.1 169 SE---IDENDYHQSIELISDLFKKAKLVHGDFSEYNIFKTKNGLKLFDLGSAVDRTHPNTMNFLKRDINNITNFFVKRGLT 246
                 99...77888999*****************************************************************987 PP

>> RSB_motif  RNSP1-SAP18 binding (RSB) motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.4   0.00045       4.1      44      74 ..       6      34 ..       1      38 [. 0.67
   2 ?    2.6   0.0     0.018   1.6e+02      59      74 ..     176     191 ..     156     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00045
   RSB_motif 44 ekrreskaskekkkeeeppakllDdlFrkTk 74
                ek+ e k   ++k e+++++k+lDd F+k k
  AJA92431.1  6 EKKIELK--IKSKLEQKKKKKTLDDGFKKNK 34
                3333333..4556667777**********88 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.018
   RSB_motif  59 eeppakllDdlFrkTk 74 
                   + + l++dlF+k k
  AJA92431.1 176 YHQSIELISDLFKKAK 191
                 3335999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1891.91
//
Query:       AJA92432.1  [L=89]
Description: lipoprotein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.6      0.025   14.6   0.6    1.1  1  MerT      MerT mercuric transport protein


Domain annotation for each model (and alignments):
>> MerT  MerT mercuric transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   1.4e-06     0.025       9      71 ..      16      83 ..       9      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-06
        MerT  9 gallagglaailaslcclgpl...vllllgvsgawign.ltvle.pyrpifiaaalvalffawrriyr 71
                g+ + g++    a++c  gp+   ++ ++g +g+     ltv e p r   i++ ++++f + + + r
  AJA92432.1 16 GSSIIGTIIGASAGACSCGPIafsIITTFGTAGSIASSfLTVYEvPIRLTSIGILVIVIFVTTKSLSR 83
                445667777889********855567789****98764389998789999999988888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 638.24
//
Query:       AJA92433.1  [L=167]
Description: D,D-heptose 1,7-bisphosphate phosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-11   44.2   0.1    9.9e-10   38.8   0.1    2.2  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.2e-10   41.3   0.2    1.4e-10   41.2   0.2    1.1  1  PNK3P           Polynucleotide kinase 3 phosphatase
    1.6e-10   40.9   0.0    2.5e-10   40.3   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
    7.3e-06   26.4   0.0      1e-05   25.9   0.0    1.2  1  Hydrolase       haloacid dehalogenase-like hydrolase
    0.00012   22.5   0.0    0.00015   22.2   0.0    1.1  1  HAD             haloacid dehalogenase-like hydrolase
     0.0031   17.6   0.1     0.0051   16.9   0.1    1.5  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   15.3   3.6       0.09   12.5   0.2    2.1  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
      0.058   13.7   0.0      0.075   13.3   0.0    1.3  1  HAD_SAK_2       HAD domain in Swiss Army Knife RNA repair pro


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.1   4.4e-13   9.9e-10      61     177 ..      13     145 ..       2     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 4.4e-13
       HAD_2  61 kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsk...s........reaveekleql..giesyFdvivtsedvekk.....KPdpevi 141
                  i++ +++y+++  +  +++++ v ++++ Lk++++ + ++T++   +         +a+ +kl+++  + ++ +d i+   +   +     KP+p +i
  AJA92433.1  13 VINQKRDDYVKNISE--LEIFEYVPNAINLLKKNNFLIILITNQsiiNrkivtldtLNAIHKKLQNFlnEHNTSIDAIYFCPHKPDEncdcrKPQPGLI 109
                 677777777777777..777777777777777777777777776332211111111122233333321122356777777654444444555******* PP

       HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagikvia 177
                 +ka ++++++ ee +++GDs+tDieaa  a+++++ 
  AJA92433.1 110 LKATKEFDINLEESWFIGDSQTDIEAANLANCNSFL 145
                 *******************************99876 PP

>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.2     6e-14   1.4e-10      17     129 ..      18     131 ..       4     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 6e-14
       PNK3P  17 gkefakdaddwkllsesvlekLkklkeegykivifsNqggvvek.ktkkslekfkekieallkeldvpl.lvyaatkk.d...kyRKPetGmweelkkd 109
                      k+ ++ ++++  v++ ++ lk++++ i++++Nq+ + +k  t ++l+ + +k++++l+e ++++  +y  ++k d     RKP++G++ + +k+
  AJA92433.1  18 RDDYVKNISELEIFEY-VPNAINLLKKNNFLIILITNQSIINRKiVTLDTLNAIHKKLQNFLNEHNTSIdAIYFCPHKpDencDCRKPQPGLILKATKE 115
                 3344455666666664.9*************************988999****************98863456665543445679*******9988776 PP

       PNK3P 110 leekleidkeksfyvGDaag 129
                 +    +i+ e+s ++GD   
  AJA92433.1 116 F----DINLEESWFIGDSQT 131
                 6....569*********865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.1e-13   2.5e-10       2      49 ..     101     147 ..     100     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.1e-13
                     .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEES CS
  Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVl 49 
                     ++KP+p+++  a ++++++ ee+++iGD+  tDi++An a ++s LV 
      AJA92433.1 101 CRKPQPGLILKATKEFDINLEESWFIGDS-QTDIEAANLANCNSFLVN 147
                     89***************************.****************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.6e-09     1e-05     100     209 ..      12     139 ..       3     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.6e-09
                 HHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHHTT.....GGGESEEEEHHCES.............STTTSHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.....xxxxxxxxxxxxxx.............xxxxxxxxx RF
   Hydrolase 100 vallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.raanqlG.....ddyfdaviasdiet.............vakpspegk 179
                  +++q+r + v  i++  ++++ +  a++ Lk++++ ++l+t+++  + +  +++ l+      + f ++++++i++             + kp p   
  AJA92433.1  12 GVINQKRDDYVKNISEL-EIFEYVPNAINLLKKNNFLIILITNQSIINRKiVTLDTLNaihkkLQNFLNEHNTSIDAiyfcphkpdencdCRKPQPGLI 109
                 45567788888888855.89999*******************9999666655555566665553344444444444456777778889999******** PP

                 HHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 180 vaaireLqgkpeevamVGDgvnDaaalaaA 209
                 ++a +e+ ++ ee  ++GD+ +D++a+  A
  AJA92433.1 110 LKATKEFDINLEESWFIGDSQTDIEAANLA 139
                 **************************9877 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   6.7e-08   0.00015      74     187 ..      29     136 ..       2     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.7e-08
         HAD  74 erfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepll.aelg.....adevlatelevdd..rltgelglegkpvrg.egkvaalrewla 163
                 e f         + p a  ll+   ++++ ++++++   ++ +++  + l+      +++l+++  + d  ++  +   ++ ++   +  +  + +  a
  AJA92433.1  29 EIFE--------YVPNAINLLK---KNNFLIILITNQSIINRKIVTlDTLNaihkkLQNFLNEHNTSIDaiYFCPH--KPDENCDCrKPQPGLILK--A 112
                 2222........7799999999...********************999***8544444445554333346666666..333333331344444444..7 PP

         HAD 164 aegegidleevvayGDspsDlpll 187
                  ++ +i lee++++GDs +D++++
  AJA92433.1 113 TKEFDINLEESWFIGDSQTDIEAA 136
                 999******************997 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.3e-06    0.0051       1      45 [.       6      60 ..       6      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.3e-06
                 EEEESTTTSE..........ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HH CS
  Hydrolase_6  1 flfDidGvLw..........rgdkaipgaaealnalraagkpvvllTNnssksee 45
                 +++D dGv+            + ++++ +++a+n l++++  ++l+TN+s  +++
   AJA92433.1  6 IFLDRDGVINqkrddyvkniSELEIFEYVPNAINLLKKNNFLIILITNQSIINRK 60
                 5789999999666555555559999************************988865 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.015        33      82     120 ..      32      73 ..       5     100 .. 0.58
   2 ?   12.5   0.2     4e-05      0.09     195     248 ..     112     165 ..     108     167 .] 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                  HHHHHHHHHHHHTTCEEEEEESSEEEESTT..........THHHHHHH CS
  Hydrolase_3  82 edvkeiikllkennveillytedkvyvlnk.........eksekkkke 120
                  e v + i+llk+nn  i+l t+++++  +          +      k+
   AJA92433.1  32 EYVPNAINLLKKNNFLIILITNQSIINRKIvtldtlnaiH------KK 73 
                  5566778888888888888888887777774443222211......11 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4e-05
                  HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGG CS
  Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnne 248
                    ke++i+lee   +GD++ Die  + a+    + n s+++  aA+ ++k +n+
   AJA92433.1 112 ATKEFDINLEESWFIGDSQTDIEAANLANCNSFLVNDSHNLMYAAQEIIKLKNS 165
                  57899*************************99999************9998875 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.075       2      80 ..       6      95 ..       5     149 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
   HAD_SAK_2  2 iFLDiDGVLnpekskkrregeedea..ldpeaverlkriveatgakiVlsstWrrred............eelkallkaag.rpriigvtpdlp 80
                iFLD DGV+n+++    ++  e e   + p+a++ lk    + +  i+l ++     +            ++l+++l +++ +   i   p+ p
  AJA92433.1  6 IFLDRDGVINQKRDDYVKNISELEIfeYVPNAINLLK----KNNFLIILITNQSIINRkivtldtlnaihKKLQNFLNEHNtSIDAIYFCPHKP 95
                9***********9999888766555443334444444....45555555555544444444454443333356666666664333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1232.12
//
Query:       AJA92434.1  [L=73]
Description: hypothetical protein T478_0698 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.012   15.2   0.1      0.012   15.1   0.1    1.0  1  5TM-5TMR_LYT  5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   6.9e-07     0.012      87     135 ..      13      61 ..       6      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.9e-07
  5TM-5TMR_LYT  87 istilagllaGlihrklkrrrkkltvlvalligllveilqmllilllak 135
                   ++ i++gl++G+i ++  rr +  +  + l++g+ + +++++l l+++ 
    AJA92434.1  13 LAPIFIGLIGGIIAYFAIRRDDPQKAKRCLMVGIGLTAVNVILNLAILS 61 
                   66799*************9999999999999999999988888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.50
# Mc/sec: 441.31
//
Query:       AJA92435.1  [L=177]
Description: cob(I)yrinic acid a,c-diamide adenosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-65  219.0   0.2    5.2e-65  218.9   0.2    1.0  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
     0.0049   16.9   0.5     0.0066   16.5   0.5    1.4  1  AAA_14          AAA domain


Domain annotation for each model (and alignments):
>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.9   0.2   5.9e-69   5.2e-65       1     172 []       3     177 .]       3     177 .] 0.98

  Alignments for each domain:
  == domain 1  score: 218.9 bits;  conditional E-value: 5.9e-69
  CobA_CobO_BtuR   1 ekglihvytGdGKGKttAAlGlalRalgaglkvlvvqFlKgekesgElaalkkl..eielerlgkegfv..kmeeeekeedaaaakealekakea 91 
                     ekgl++vytG+GKGKttAAlG+alRa+g ++kv+++qF+Kg++++gE ++ kkl  ++el+ +g +gfv    +++ +ee++++a+ea++ ++e+
      AJA92435.1   3 EKGLVIVYTGNGKGKTTAALGMALRAIGYDHKVCMLQFIKGSWHYGEMDSSKKLepNFELIAVG-KGFVgiLDDNSPREEHEKYAAEAVRICREK 96 
                     58****************************************************877*******.9***987778899***************** PP

  CobA_CobO_BtuR  92 laseeydlvvlDEinyalklglldeeevlellkkkpeklelvlTGrnapeelleaADlvtemkkvkHpydkgikarkGiey 172
                     + se+yd+++lDE+nya++lgl+d++e+++++k+kp++l+lvlTGr+ +ee++e+ADlvtemk++kHp+++gika+kGi++
      AJA92435.1  97 IFSEKYDVIILDEVNYAITLGLIDVQEIIKIIKEKPSDLDLVLTGRDVKEEIVELADLVTEMKEIKHPFKSGIKAKKGIDF 177
                     *******************************************************************************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   7.4e-07    0.0066      44     103 ..      83     145 ..      14     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.4e-07
      AAA_14  44 kkladpe.kllelileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnsk 103
                 +k+   + +  ++++ek+ +ek  +++lDE+ ++      ++++++k + ++ ++ld+++tG   k
  AJA92435.1  83 EKY---AaEAVRICREKIFSEKYDVIILDEVNYAitlglIDVQEIIKIIKEKPSDLDLVLTGRDVK 145
                 222...2357899999965559999********989999999********************6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1277.67
//
Query:       AJA92436.1  [L=104]
Description: hypothetical protein T478_0035 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.036   13.5   2.0       0.72    9.3   0.0    2.0  2  DUF2938        Protein of unknown function (DUF2938)
      0.082   13.2   4.3       0.63   10.4   4.1    1.9  1  DUF3021        Protein of unknown function (DUF3021)
       0.14   11.4   1.5       0.16   11.1   1.5    1.0  1  Peptidase_M56  BlaR1 peptidase M56
       0.18   11.5   4.0        2.5    7.8   0.4    2.2  2  FeoB_C         Ferrous iron transport protein B C terminus


Domain annotation for each model (and alignments):
>> DUF2938  Protein of unknown function (DUF2938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5    0.0062        28      71      97 ..      22      48 ..       8      54 .. 0.87
   2 ?    9.3   0.0   0.00016      0.72      48      78 ..      62      92 ..      49      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0062
     DUF2938 71 ilfaallvllvgaeWlaePtllpalvv 97
                i fa++++++v  +W  +P + +++v+
  AJA92436.1 22 IEFAIVIAVAVVISWQVNPFFEDSVVM 48
                78*****************99998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00016
     DUF2938 48 aiakaepvkgeralGwlahYliGilfaallv 78
                  ++ ep  + +al w++  ++Gi+faa ++
  AJA92436.1 62 CTMSDEPEMQQTALNWIFWGIVGIVFAAWYL 92
                445566777889***************9765 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.1   0.00014      0.63       8      53 ..      24      89 ..      17      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00014
     DUF3021  8 iliGiligliislvislfsgettll....................estavlkqvllsaliGvlfal 53
                + i i+++++is  ++ f+++++++                    e+++++ ++++++++G++fa 
  AJA92436.1 24 FAIVIAVAVVISWQVNPFFEDSVVMygweceqtsqitdctmsdepEMQQTALNWIFWGIVGIVFAA 89
                44445555566777777888877779*************************************985 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   3.6e-05      0.16      27     113 ..       9      94 ..       4     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
  Peptidase_M56  27 llsaiaaYalWlivllallipfipesavslpvkfetskinsaaskaplasaaskvlddkasalatdvkkvewktilkillliWivga 113
                    + s+ + +  W+++ +a++i+++     ++ + fe s  + + +  ++++ +   ++d+ + ++t+++ + w  +  i+ ++W +ga
     AJA92436.1   9 VPSESWPFFSWFVIEFAIVIAVAVVISWQVNPFFEDSVVMYGWECEQTSQITDCTMSDEPEMQQTALNWIFWGIV-GIVFAAWYLGA 94 
                    567889999*************88444448888999999999999999999999999999999999999999765.99999999887 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4   0.00056       2.5       2      21 ..      17      36 ..      16      48 .. 0.83
   2 ?    5.2   0.2    0.0036        16       4      20 ..      77      93 ..      74     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00056
      FeoB_C  2 fslYllgilvallvalllkk 21
                fs++++ ++++++va ++++
  AJA92436.1 17 FSWFVIEFAIVIAVAVVISW 36
                99**************9988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0036
      FeoB_C  4 lYllgilvallvalllk 20
                +++ gi+ ++++a+ l 
  AJA92436.1 77 WIFWGIVGIVFAAWYLG 93
                7899**********994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 762.00
//
Query:       AJA92437.1  [L=275]
Description: hypothetical protein T478_1428 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-10   38.4   8.2    1.6e-05   24.4   2.7    2.9  3  HTH_24         Winged helix-turn-helix DNA-binding
    6.4e-08   32.3   1.3    7.1e-05   22.6   0.4    2.7  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      6e-05   22.8   0.8      0.011   15.5   0.0    2.7  3  HTH_5          Bacterial regulatory protein, arsR family
    6.9e-05   22.7   0.0       0.53   10.2   0.0    2.3  2  MarR_2         MarR family
    0.00014   21.5   0.3      0.012   15.3   0.0    2.7  2  HTH_41         Helix-turn-helix domain
     0.0037   17.2   1.0        1.1    9.2   0.4    2.5  2  MarR           MarR family
     0.0042   16.7   2.6     0.0057   16.3   0.8    1.9  2  DUF1280        Protein of unknown function (DUF1280)
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.058   13.3   0.0    2.0  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.021   14.8   0.9       0.54   10.2   0.2    2.7  3  HTH_11         HTH domain
      0.033   14.8   0.3      0.093   13.3   0.3    1.9  1  Mga            Mga helix-turn-helix domain
       0.12   12.3   0.6        1.6    8.7   0.1    2.3  2  HTH_36         Helix-turn-helix domain
       0.15   12.4   0.0        4.3    7.7   0.0    2.4  2  CbiX           CbiX
       0.43   10.7   3.8        1.2    9.2   3.8    1.7  1  GvpK           Gas vesicle protein K
        2.3    8.0   4.8       0.52   10.1   0.3    2.3  3  HTH_DeoR       DeoR-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     4e-06    0.0051      26      48 .]       2      24 ..       2      24 .. 0.96
   2 ?   -2.2   0.0       2.5   3.1e+03      19      30 ..      48      59 ..      46      62 .. 0.77
   3 !   24.4   2.7   1.2e-08   1.6e-05       1      44 [.     114     157 ..     114     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4e-06
      HTH_24 26 rlglSpstvnrrlkrLeeeGlIk 48
                +lg+S ++v  r++++e+ G+I+
  AJA92437.1  2 ELGISGGAVGSRINKMEKLGIIE 24
                69********************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
      HTH_24 19 sqreLAerlglS 30
                +q+e+ + + l 
  AJA92437.1 48 NQKEIIKNVKLA 59
                689999888875 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.2e-08
      HTH_24   1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeee 44 
                 l +td++IL++L ++pr  + +L++ + lS  t+nr l++L+++
  AJA92437.1 114 LTRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQNN 157
                 579*********************************99999886 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0023       2.9      26      42 .]       2      18 ..       1      18 [. 0.95
   2 ?   -2.2   0.0       3.1     4e+03       7      17 ..      88      98 ..      87      99 .. 0.80
   3 !   22.6   0.4   5.6e-08   7.1e-05       1      41 [.     114     154 ..     114     155 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
  HTH_AsnC-type 26 rvGlSestvlrRvrrLe 42
                   ++G+S  +v  R++++e
     AJA92437.1  2 ELGISGGAVGSRINKME 18
                   69**************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.1
  HTH_AsnC-type  7 kILeaLqedaR 17
                    +L+ L+ed R
     AJA92437.1 88 ELLQKLMEDVR 98
                   58899999988 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 5.6e-08
  HTH_AsnC-type   1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                    L ++D+ IL++L +d+R   ++L++ + lS+ t+ r +++L
     AJA92437.1 114 LTRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKL 154
                    678*******************************9988887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.016        21      24      47 .]       2      25 ..       1      25 [. 0.94
   2 ?   -3.1   0.1       5.9   7.5e+03       4      14 ..      86      96 ..      84     102 .. 0.68
   3 !   15.5   0.0   8.8e-06     0.011       5      41 ..     119     156 ..     116     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                HHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5 24 elglsqstvShHLkkLreaGLVek 47
                elg+s ++v    +k++++G++ek
  AJA92437.1  2 ELGISGGAVGSRINKMEKLGIIEK 25
                799*******************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.9
                HHHHHHHHTTS CS
       HTH_5  4 RlkILklLaeg 14
                ++++L+ L+e 
  AJA92437.1 86 KIELLQKLMED 96
                67888888884 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 8.8e-06
                 HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHH CS
       HTH_5   5 lkILklLaege.lcvcelaeelglsqstvShHLkkLre 41 
                 l+IL+ L + + + + +l+++++ls  t+ + L kL +
  AJA92437.1 119 LEILNELIQDPrKRIEQLSKDTELSTKTINRGLEKLQN 156
                 89*********99******************9999976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00042      0.54      30      53 ..       2      25 ..       1      26 [. 0.95
   2 !   10.2   0.0   0.00041      0.53       2      48 ..     113     157 ..     112     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                HHTSSHHHHHHHHHHHHHTTSEEE CS
      MarR_2 30 rlglsksavsrilkrLvaaGLver 53
                +lg+s +av  +++++++ G +e+
  AJA92437.1  2 ELGISGGAVGSRINKMEKLGIIEK 25
                79********************96 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00041
                 T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
      MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaa 48 
                  lt++++ +L++L   p++  ++ +l + + ls  +++r l++L+  
  AJA92437.1 113 NLTRTDLEILNELIQDPRK--RIEQLSKDTELSTKTINRGLEKLQNN 157
                 69**************973..9**********************975 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.052        66      15      36 ..       2      23 ..       1      25 [. 0.92
   2 !   15.3   0.0   9.1e-06     0.012       7      37 ..     131     161 ..     129     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.052
      HTH_41 15 eleLSvGlvQkALklLeddkai 36
                el++S G v + ++++e+ ++i
  AJA92437.1  2 ELGISGGAVGSRINKMEKLGII 23
                799**************99988 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 9.1e-06
      HTH_41   7 ktIeelakeleLSvGlvQkALklLeddkais 37 
                 k+Ie+l+k+ eLS  ++  +L++L+++  i+
  AJA92437.1 131 KRIEQLSKDTELSTKTINRGLEKLQNNESIQ 161
                 79***********************999887 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0098        13      26      49 ..       2      25 ..       1      26 [. 0.91
   2 !    9.2   0.4   0.00088       1.1       1      48 [.     114     161 ..     114     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0098
                HHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR 26 klgvskstvtrvldrLekkGlieR 49
                 lg+s ++v   + ++ek G ie+
  AJA92437.1  2 ELGISGGAVGSRINKMEKLGIIEK 25
                589999****************97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00088
                 --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR   1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                 lt+t ++iL  l + +  ++ +L k  ++s+ t+ r l +L  ++ i+
  AJA92437.1 114 LTRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQNNESIQ 161
                 89***************************************9998776 PP

>> DUF1280  Protein of unknown function (DUF1280)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       0.3   3.8e+02     116     151 ..     107     145 ..      80     151 .. 0.54
   2 !   16.3   0.8   4.5e-06    0.0057      33     151 ..     151     272 ..     127     275 .] 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.3
     DUF1280 116 grevkkkvvvvqlkdvekll...srRleeLaasgkLvfd 151
                 +++++++ ++  l+ +++l+   ++R+e+L+++ +L  +
  AJA92437.1 107 NTKITHNLTRTDLEILNELIqdpRKRIEQLSKDTELSTK 145
                 333444444444444444442226799999999888765 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4.5e-06
     DUF1280  33 vkflakseefkfk..lkLspeetfvlkvklkLsdsqlkelKkflkeklgfd.vfpsrkkikelekkvsskelYeisvekvekktksgrevkkkvvvvql 128
                 +++l+++e+ +f+  ++ s+ e+f+++  + ++++ + ++ k +++  g d ++ +  + +++   + s++ +++++ +      +g+ +++  +  ++
  AJA92437.1 151 LEKLQNNESIQFTliYDPSKIEGFLCYAVVAMTQEDIPKMLKKFEDEFGEDyLMTPFLAKNQVVLFLYSESIFKMDEMTERVAKVEGTITTELFIPKKI 249
                 566666666666511556899***************97665555555555515678888899999999*******998888877899888888888999 PP

     DUF1280 129 kdvekllsrRleeLaasgkLvfd 151
                    ek l++Rle+L +s+ L++ 
  AJA92437.1 250 DMPEKWLEKRLETLTKSQTLHLS 272
                 999****************9875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6     2e+03      32      54 ..       3      25 ..       2      28 .. 0.81
   2 ?   13.3   0.0   4.6e-05     0.058       4      52 ..     112     160 ..     109     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                TTSSCHCHHHHHHHHHHCTSEEE CS
        TrmB 32 lgvprskvYevLrsLedkGlVer 54
                lg++   v + ++++e+ G++e+
  AJA92437.1  3 LGISGGAVGSRINKMEKLGIIEK 25
                67777777788999*****9997 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.6e-05
                 CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE CS
        TrmB   4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlV 52 
                 ++L+ ++ ++   L++  ++++++++++++++  ++++ L++L +   +
  AJA92437.1 112 HNLTRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQNNESI 160
                 789****************************************997765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.14   1.8e+02      24      46 ..       2      23 ..       1      30 [. 0.90
   2 ?   -3.1   0.0       6.1   7.8e+03      35      43 ..      86      94 ..      84     101 .. 0.58
   3 ?   10.2   0.2   0.00042      0.54       5      41 ..     121     156 ..     117     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
      HTH_11 24 eLnvSrrtvrrdIkaLeelgvpI 46
                eL++S  +v  +I ++e+lg  I
  AJA92437.1  2 ELGISGGAVGSRINKMEKLG-II 23
                79*****************9.44 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.1
      HTH_11 35 dIkaLeelg 43
                 I+ L++l+
  AJA92437.1 86 KIELLQKLM 94
                566666665 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00042
      HTH_11   5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41 
                 il  L++      +e+L++ +++S++t+ r +++L+ 
  AJA92437.1 121 ILNELIQDPR-KRIEQLSKDTELSTKTINRGLEKLQN 156
                 7777744444.5899********************86 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   7.2e-05     0.093      15      56 ..      96     156 ..      82     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                 H...................SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH CS
         Mga  15 e...................slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk 56 
                 +                   ++++++l  l+++ ++ ie+l++   +S  t++r +++l++
  AJA92437.1  96 DvrvmsvfeadntkithnltRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQN 156
                 44444555555555555666899**********************************9975 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.27   3.4e+02      36      55 .]       4      23 ..       2      23 .. 0.84
   2 ?    8.7   0.1    0.0013       1.6      28      50 ..     133     155 ..     129     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.27
      HTH_36 36 glsknTvsraikeLeqlGyi 55
                g+s   v + i++ e+lG+i
  AJA92437.1  4 GISGGAVGSRINKMEKLGII 23
                6666779999********98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
      HTH_36  28 qetlakrlglsknTvsraikeLe 50 
                  e l+k+++ls +T+ r + +L 
  AJA92437.1 133 IEQLSKDTELSTKTINRGLEKLQ 155
                 5789*****************97 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.18   2.3e+02      65      89 ..      76      99 ..      41     110 .. 0.84
   2 ?    7.7   0.0    0.0033       4.3      66      97 ..     181     210 ..     173     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                SHHHHTHHHHHCT--SSSS-TTEEE CS
        CbiX 65 GvhvkeDIpeeleeaeeahpkdvei 89
                Gv vkeD+++ +e++++  + dv++
  AJA92437.1 76 GVIVKEDMQQKIELLQKLME-DVRV 99
                999**********9999999.7766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                 HHHHTHHHHHCT--SSSS-TTEEEEE---CCC CS
        CbiX  66 vhvkeDIpeeleeaeeahpkdveieytepLGt 97 
                  +++eDIp++l+++e++++   ++ +t+ L +
  AJA92437.1 181 AMTQEDIPKMLKKFEDEFG--EDYLMTPFLAK 210
                 4799**************9..44555555544 PP

>> GvpK  Gas vesicle protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.8   0.00092       1.2      21      82 ..      87     155 ..      85     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00092
        GvpK  21 veLlrqllE...rqaiRRmeag......dlsdeeierlgetLmkleeeleelkesfgleeedLnldLgplg 82 
                 +eLl++l+E      +  +ea+      +l+ +++e l e ++  ++++e+l ++ +l+++ +n  L++l+
  AJA92437.1  87 IELLQKLMEdvrV--MSVFEADntkithNLTRTDLEILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQ 155
                 7999999996441..333443311222279999********************************999986 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       5.4   6.9e+03      35      46 ..      14      25 ..      13      26 .. 0.78
   2 ?   10.1   0.3    0.0004      0.52       4      42 ..     120     158 ..     117     162 .. 0.91
   3 ?   -3.0   0.1         5   6.4e+03       6      19 ..     260     273 ..     257     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5.4
    HTH_DeoR 35 LneLeeqglltR 46
                +n++e+ g++++
  AJA92437.1 14 INKMEKLGIIEK 25
                688888888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
    HTH_DeoR   4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqg 42 
                 +il  l q+   ++e+l+   + S++Ti R L++L++  
  AJA92437.1 120 EILNELIQDPRKRIEQLSKDTELSTKTINRGLEKLQNNE 158
                 688899999999************************986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5
    HTH_DeoR   6 lellkqqgklsvee 19 
                 le l ++++l++ +
  AJA92437.1 260 LETLTKSQTLHLSQ 273
                 67888999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2026.16
//
Query:       AJA92438.1  [L=349]
Description: ATP synthase, subunit C [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-52  179.1   7.7    2.2e-52  178.7   7.7    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7   7.7   1.2e-56   2.2e-52       7     332 ..      17     338 ..      12     341 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 1.2e-56
                     HHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HHHHHHHHHHHHHHHHHHHHHHH CS
  vATP-synt_AC39   7 amrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsrefldyllyrydidNvklllrg 101
                      +r++lL++ d++ L+++++l+++++ +k+t Y ++  ++ s+p++ +++e al+  la++  k+ + +  +  ++ld+++ ++ i N+kl+l+g
      AJA92438.1  17 SKRGQLLKRPDLQTLAESRDLDELVTRIKNTKYIDA-VNSVSKPYTAEKLEMALKTYLANQQYKIAKASGNA--KILDAFFQKFIISNLKLILKG 108
                     5799*******************************9.666677************************99999..********************* PP

                     HHH.T--GGGS-..--.S..S.SS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHHHHHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH.. CS
  vATP-synt_AC39 102 klsgdldleeleeklhpl..g.elsaldldklieaksveelyeallgtpyakyleealdeleetgdleiienaLdkayledllkfckklggetae 193
                     k+ + ++++e+  +++      +   +++ k++ +k++ee +++l+ +p+ + +++a++ ++et++++++++  dk+y++++ k+ ++ ++++  
      AJA92438.1 109 KILE-KSQDEISTYFNMEaeElTKQRDTVVKALVSKDLEEAVSSLASSPFNSEIQKAVELYNETKNIQAFDIYFDKMYYQNVSKSLRSENDQD-- 200
                     ***6.777*******87787557778888********************************************************99999999.. PP

                     .HHHHHHHHHHHHHHHHHHHTTTSS......T...--SS-.S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHH CS
  vATP-synt_AC39 194 ilreilgfeiDlrniniilrskkygelskedrkkllipgg.slypeglealaeaedveellaalkyteygelleealeeagslksledaldealv 287
                      +++ +g+eiD+ ni++++r k++g l  e +++l +    +++ + ++++ +ae+v+++l+ l  t+y++l+ e++++ +++ ++e+a++   +
      AJA92438.1 201 -ISHVFGMEIDFFNIMTVVRGKFWG-LDDERIQDLSCAATlNIPNQVMDRMRAAESVKDALDELASTKYKDLVPETEDDVEAIAEFEHAFEMGYY 293
                     .**********************99.455559999****************************************9999666************* PP

                     HHHHTTTSSSTSTHHHHHHHHHHHHHHHHHHHHHHHHHHT--SHH CS
  vATP-synt_AC39 288 kllkkafrqqfsvgvfyaYlklkeqEirnlrwIaegiaqglpkek 332
                     k +  af + f+++++++  kl  +E+rn+  Ia g++q++p e+
      AJA92438.1 294 KAINGAFSKMFNFATVIGISKLIGYEVRNIGSIAFGVEQKIPVET 338
                     ***99************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.20s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2624.88
//
Query:       AJA92439.1  [L=102]
Description: putative 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-20   70.3   0.1    1.3e-19   69.9   0.1    1.1  1  Rieske    Rieske [2Fe-2S] domain
      7e-08   32.4   0.0    8.2e-08   32.1   0.0    1.0  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1   1.4e-23   1.3e-19       5      88 ..       6      89 ..       3      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.4e-23
                EEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTHHH.EEEE CS
      Rieske  5 vakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPaprp.laty 88
                ++k+s+++ g++++v+v  ++++v +  +g+++A +d+CtH+ga+lseg++ e+++++C +H ++++ ++Gk+ k Pa+ + l++y
  AJA92439.1  6 ACKSSELEAGKMKKVSVDSKEILVANV-NGNYFACDDTCTHAGASLSEGSL-ENSTVTCGWHAAQFScETGKMEKFPAKINdLKSY 89
                79************************7.***********************.777**********************986546655 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   9.1e-12   8.2e-08       5     103 ..       6     100 ..       4     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.1e-12
                 EEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS-TT..SB-BEE-EEESTSEE CS
    Rieske_2   5 vckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecledee..vslkvypvrvedgkv 101
                  ck ++l +++ + + vd k+++++ + +++ +A d++++ +  + ls+G +++     +v++  +  +f+ +tG++ ++++    lk y v ve + v
  AJA92439.1   6 ACKSSELEAGKMKKVSVDSKEILVANV-NGNYFACDDTCTHA-GASLSEGSLENS----TVTCGWHAAQFSCETGKMEKFPAkiNDLKSYTVVVESEDV 98 
                 599************************.9************5.778*****9988....******************997664589***********99 PP

                 EE CS
    Rieske_2 102 ev 103
                  +
  AJA92439.1  99 FI 100
                 87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 756.39
//
Query:       AJA92440.1  [L=300]
Description: putative transcription initiation factor IIB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-37  127.5   2.6    3.3e-18   65.5   0.2    2.2  2  TFIIB           Transcription factor TFIIB repeat
    9.8e-12   44.2   0.4    1.6e-11   43.5   0.4    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    3.7e-05   23.5   0.1     0.0029   17.4   0.1    2.3  2  Cyclin_N        Cyclin, N-terminal domain
     0.0025   17.5   0.5     0.0052   16.5   0.5    1.4  1  Ribosomal_S27e  Ribosomal protein S27
     0.0027   17.0   2.6       0.02   14.3   2.6    2.2  1  zf-ribbon_3     zinc-ribbon domain
     0.0083   16.1   0.8       0.14   12.2   0.0    2.3  2  HTH_Mga         M protein trans-acting positive regulator (MG
  ------ inclusion threshold ------
       0.01   15.9   1.2      0.023   14.7   0.5    1.9  2  TFIIB_C_1       Transcription factor IIB C-terminal module 1
      0.015   15.3   0.1      0.026   14.6   0.1    1.3  1  RB_B            Retinoblastoma-associated protein B domain
      0.022   15.3   0.2      0.044   14.4   0.2    1.7  1  RPA_interact_C  Replication protein A interacting C-terminal
      0.036   14.0   0.3       0.19   11.7   0.0    2.2  3  HTH_11          HTH domain
      0.055   13.0   0.0       0.32   10.6   0.0    2.1  2  Sigma70_r4      Sigma-70, region 4
      0.074   12.7   0.1       0.11   12.0   0.1    1.3  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
      0.079   13.1   1.3       0.15   12.2   1.3    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        0.1   12.4   0.0       0.15   11.8   0.0    1.2  1  MCPVI           Minor capsid protein VI
       0.11   12.6   0.0        1.6    8.8   0.0    2.2  2  Cyclin_C        Cyclin, C-terminal domain
       0.15   11.8   0.5       0.77    9.5   0.1    2.3  3  Sigma70_r4_2    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.2   2.9e-20   3.2e-17       3      70 ..     125     192 ..     123     193 .. 0.94
   2 !   65.5   0.2   2.9e-21   3.3e-18       1      71 []     217     287 ..     217     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.9e-20
                 HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHH CS
       TFIIB   3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekt 70 
                 ++ d+l L + V ++A +++++a e+k++kGrs +g++AAc+y Acr  e+ rt+ ++++ ++++ k 
  AJA92440.1 125 KLKDKLSLTDAVIEKAAYIYRKAIEKKLVKGRSIQGLVAACVYAACRDTETPRTLDNVADGINIRRKD 192
                 6779********************************************************99998875 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 2.9e-21
                 HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
       TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                 i+r+a+ ++L ek +++A+e++++a++ +v++G+ p+g+aAA+ly+Ac  e+ ++tqkeis+ + V+e+ti
  AJA92440.1 217 IPRIASVAGLGEKTKRKAVEILRKAKKIGVVAGKDPTGLAAAALYLACITEGGNKTQKEISEASGVTEVTI 287
                 899******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.4   1.5e-14   1.6e-11       2      43 .]       8      49 ..       7      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.5e-14
                  EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                  +CP C+ t l++D ++ge+vC++CGlVl + s   gpewr f
    AJA92440.1  8 RCPSCNKTALITDDNSGEIVCKSCGLVLSEGSEAAGPEWRSF 49
                  7******99*******************************87 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.6e-06    0.0029      24     123 ..     110     205 ..      90     208 .. 0.80
   2 ?    3.7   0.0     0.044        49      44      88 ..     223     267 ..     214     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.6e-06
                 SSS-HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTT.SS-HHHHHHHHHHHHHH CS
    Cyclin_N  24 pelnpemRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitde.afteeeilemErliLet 121
                 ++++++ R+ +++ + ++  k++lt  ++  a+ ++ + ++kk v+ + +q ++a+c++ A++  e+ p +l++++   d+  ++++++ +  rl++++
  AJA92440.1 110 SSVDKNLRQ-ALSEMDKLKDKLSLTDAVIEKAAYIYRKAIEKKLVKGRSIQGLVAACVYAACRDTET-PRTLDNVA---DGiNIRRKDVARCYRLVFRE 203
                 445556666.4455789999*******************************************9999.66666554...45568888888888888888 PP

                 TT CS
    Cyclin_N 122 Ln 123
                 L+
  AJA92440.1 204 LD 205
                 76 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.044
                 HTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHH CS
    Cyclin_N  44 kfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKve 88 
                 +  l ++t   av++l +  +   v  ++   ++a++L+lA+ +e
  AJA92440.1 223 VAGLGEKTKRKAVEILRKAKKIGVVAGKDPTGLAAAALYLACITE 267
                 55666777777899999999999999999999**********775 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.5   4.6e-06    0.0052       9      38 ..       8      37 ..       6      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                    E-TTTS-EEEEESS-SS-EEESSSTCEEEE CS
  Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvLve 38
                    +Cp C+++  + +  +  + C sCg vL e
      AJA92440.1  8 RCPSCNKTALITDDNSGEIVCKSCGLVLSE 37
                    7**************************986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.6   1.7e-05      0.02       2      26 .]       6      35 ..       5      35 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
  zf-ribbon_3  2 tvrCPnCGa.p.lssd...dnvCpyCGtkl 26
                 ++rCP+C++   +++d    +vC++CG +l
   AJA92440.1  6 EQRCPSCNKtAlITDDnsgEIVCKSCGLVL 35
                 78*******964765422258******987 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2       0.2   2.2e+02       3      30 ..     125     152 ..     123     153 .. 0.91
   2 !   12.2   0.0   0.00013      0.14      22      48 ..     272     298 ..     262     300 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.2
     HTH_Mga   3 dikrklkLlelLteneksltldelakeL 30 
                 + k+kl L ++++e + +++ + + k+L
  AJA92440.1 125 KLKDKLSLTDAVIEKAAYIYRKAIEKKL 152
                 6689********************9998 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00013
     HTH_Mga  22 tldelakeLglseltlqsdiseLnelF 48 
                 t +e++++ g +e+t+++++  L++++
  AJA92440.1 272 TQKEISEASGVTEVTIRNRCAGLKTFL 298
                 668*********************887 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   2.1e-05     0.023       6      94 ..     120     199 ..     116     203 .. 0.89
   2 ?   -1.7   0.0       2.7   3.1e+03      19      32 ..     227     240 ..     217     265 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
   TFIIB_C_1   6 rnalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvldpslkdvelrrkevvrevkl 94 
                 ++ ++ l ++    +av+e+a  + ++ + k+  +g+ +   +  +aac+  a+  +++P      r+ld     ++ rrk+v r  +l
  AJA92440.1 120 LSEMDKLKDKLSLTDAVIEKAAYIYRKAIEKKLVKGRSI---QGLVAACVYAACRDTETP------RTLDNVADGINIRRKDVARCYRL 199
                 568999***********************9999888876...5789************99......999**9***********987665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.7
   TFIIB_C_1  19 deavleealelakr 32 
                 +e+ +++a+e++++
  AJA92440.1 227 GEKTKRKAVEILRK 240
                 67777777777764 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.3e-05     0.026       8      94 ..     114     198 ..     109     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
        RB_B   8 kvyklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvyr 94 
                 k ++ a + + +L ++L+l++ + ek+  + ++++  e++l+k R +  ++ ++vY+ ++ t++ +++ ++ +  + + +  ++ yr
  AJA92440.1 114 KNLRQALSEMDKLKDKLSLTDAVIEKAAYIYRKAI--EKKLVKGRSIQGLVAACVYAACRDTETPRTLDNVADGINIRRKDVARCYR 198
                 55678899999**********99999888888887..568**********************9999999887766655555555555 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.9e-05     0.044       2      30 ..       9      40 ..       8     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
  RPA_interact_C  2 CPvCkkrklkets..evifCe.Cglrletsee 30
                    CP C+k+ l  ++    i+C+ Cgl l+  +e
      AJA92440.1  9 CPSCNKTALITDDnsGEIVCKsCGLVLSEGSE 40
                    *********99773356***99****998433 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.2   2.5e+03      19      34 ..     124     139 ..     122     140 .. 0.83
   2 ?   -3.3   0.1       8.2   9.2e+03       3      13 ..     232     242 ..     231     244 .. 0.69
   3 ?   11.7   0.0   0.00017      0.19      15      42 ..     270     297 ..     260     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.2
      HTH_11  19 eeLAeeLnvSrrtvrr 34 
                 ++L+++L+++ +++ +
  AJA92440.1 124 DKLKDKLSLTDAVIEK 139
                 57999***99998865 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
      HTH_11   3 lqilelLlear 13 
                 ++ +e+L++a+
  AJA92440.1 232 RKAVEILRKAK 242
                 56678888777 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00017
      HTH_11  15 pisgeeLAeeLnvSrrtvrrdIkaLeel 42 
                 + + +e++e  +v++ t+r++++ L++ 
  AJA92440.1 270 NKTQKEISEASGVTEVTIRNRCAGLKTF 297
                 56899******************99975 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.3   1.4e+03      18      35 ..     174     191 ..     166     204 .. 0.77
   2 ?   10.6   0.0   0.00028      0.32      18      40 ..     268     290 ..     258     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                 TTT--HHHHHHHHTS-HH CS
  Sigma70_r4  18 geglTleEIgerlgiSre 35 
                 + ++Tl  +++  +i r 
  AJA92440.1 174 ETPRTLDNVADGINIRRK 191
                 7899**999998888665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00028
                 TTT--HHHHHHHHTS-HHHHHHH CS
  Sigma70_r4  18 geglTleEIgerlgiSrerVrqi 40 
                 g + T++EI+e  g+++ ++r +
  AJA92440.1 268 GGNKTQKEISEASGVTEVTIRNR 290
                 6789*****************86 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.11      78     144 ..      87     153 ..      67     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                     SSHHHHHHHHHHHHHHHHHH.S-HHHHHHH-GGGGGGTT--GGGGGT-HHHHHHHHHHHHHHHHHHT CS
  HMG_CoA_synt_C  78 PfcklvqkslarllynDflanassdkeeevkekleekddlkldesltdkdlekallkiakelfkkkv 144
                     P +  +++s+ r+   D++++a+s+ ++++++ l+e+d+lk + sltd  +eka     k + kk v
      AJA92440.1  87 PLSSAMKQSFDRIRTWDSRSQAHSSVDKNLRQALSEMDKLKDKLSLTDAVIEKAAYIYRKAIEKKLV 153
                     77778899****************************************9999987654444444433 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3   0.00013      0.15      16      40 .]       7      32 ..       6      32 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
  Auto_anti-p27 16 etCpvC.gvPLmrdrkggkvyCvaCd 40
                   + Cp C ++ L  d ++g+++C +C+
     AJA92440.1  7 QRCPSCnKTALITDDNSGEIVCKSCG 32
                   67************999********6 PP

>> MCPVI  Minor capsid protein VI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.15      10     102 ..      62     154 ..      57     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                 XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       MCPVI  10 srplrghdiGtsdlrGGafsWgsLgssitsglkniGsfikntgsk.ivnsstfqqlkqglkesnvlenvadlagetlsalvDigrlkvqkdlek 102
                 ++++  hd+G s + G  ++  + g+ + s++k+    i+   s+   +ss  + l+q l e + l++   l    ++    i r++++k+l k
  AJA92440.1  62 GTSITMHDMGLSTVIGA-VNKDATGKPLSSAMKQSFDRIRTWDSRsQAHSSVDKNLRQALSEMDKLKDKLSLTDAVIEKAAYIYRKAIEKKLVK 154
                 466778******99875.***************98888888877725799999*************************************9944 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.37   4.1e+02      49      86 ..     163     200 ..     160     207 .. 0.84
   2 ?    8.8   0.0    0.0014       1.6      45      86 ..     253     294 ..     248     300 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.37
                 HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHH CS
    Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcveli 86 
                 aa++++a++  ++p   +++   + +  +d+  c++l 
  AJA92440.1 163 AACVYAACRDTETPRTLDNVADGINIRRKDVARCYRLV 200
                 89999999998888888888888888999999999875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                 HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHH CS
    Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcveli 86 
                   +Aaaal+la+ t + ++ ++++ + +g+++  +++ +  +
  AJA92440.1 253 TGLAAAALYLACITEGGNKTQKEISEASGVTEVTIRNRCAGL 294
                 569***********9999999*********999988766555 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.1   4.6e+03      42      53 ..     111     122 ..     110     123 .. 0.71
   2 ?   -1.5   0.0       1.9   2.1e+03      14      29 ..     143     158 ..     141     159 .. 0.84
   3 ?    9.5   0.1   0.00069      0.77      26      46 ..     270     290 ..     267     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.1
                   HHHHHHHHHHHH CS
  Sigma70_r4_2  42 tVksrlsRArkk 53 
                   +V+++l++A+  
    AJA92440.1 111 SVDKNLRQALSE 122
                   788888888765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                   HHHHHHHHHHTS---H CS
  Sigma70_r4_2  14 rqreifllryleglsy 29 
                   ++r++++ + ++g s+
    AJA92440.1 143 IYRKAIEKKLVKGRSI 158
                   6899999999999887 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00069
                   ---HHHHHHHHT--HHHHHHH CS
  Sigma70_r4_2  26 glsykEIAellgisegtVksr 46 
                   ++++kEI+e  g++e+t+++r
    AJA92440.1 270 NKTQKEISEASGVTEVTIRNR 290
                   5799***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2212.81
//
Query:       AJA92441.1  [L=210]
Description: pyridoxamine 5'-phosphate oxidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-20   73.7   0.0    1.9e-20   73.3   0.0    1.2  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    7.5e-10   38.9   0.0    1.7e-09   37.7   0.0    1.6  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.26   11.7   0.0    1.5  1  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   3.1e-24   1.9e-20       3     140 ..      13     159 ..      11     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 3.1e-24
                   HHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCC.T--ECEEEEE....EEEEEE-SE.GG.EEE.EEEEEEEEEEEE CS
  Pyridox_ox_2   3 eeilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalr.gapvcvvvte....vdglvlars.fn.sln.yrSVvvrGraee 90 
                     i ++L+e+ +gr++  d +g p i+P+n+v+ +ds+y+h++  +++++ ++ +++v ++v +    + ++  + + ++ + + y SVv++G+a +
    AJA92441.1  13 TKIIKFLNEENTGRISSIDeQGFPQIIPMNFVFLNDSVYMHSHIRGEKIENIKrNSKVGFEVDRnlefLPSYFSDPEdASlADTlYISVVIKGEALL 109
                   57899**************5555*********************99999999974446666655556699999999999998899************ PP

                   E--HHHHHHHCCCHHHHHSTTT.GGCSB---CCCCCTEEEEEEEEEEEEEE CS
  Pyridox_ox_2  91 vtdeeekaealellvekivpgr.wenlrpptrkelkatsvlrlkieevsgr 140
                   v++ eek  al++l++k++p+  +++   ++ + l at+v+++ ++e+ g+
    AJA92441.1 110 VENNEEKVLALNGLMKKYQPEGrYKPMD-KDMDVLDATAVIKIIPKEMNGK 159
                   *******************988677554.77888899***********998 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.9e-13   1.7e-09       4      80 ..      14     106 ..      11     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.9e-13
                     HHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT..................GSEEEEEEEE CS
  Putative_PNPOx   4 elreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde..................lgrgvrieGt 80 
                     ++ +fl+e+++++++++de+G P++ p++++++++    +++++ + +k +n+++n++v++ ++ +                   l+++v i+G+
      AJA92441.1  14 KIIKFLNEENTGRISSIDEQGFPQIIPMNFVFLNDS--VYMHSHIRGEKIENIKRNSKVGFEVDRNLeflpsyfsdpedasladtLYISVVIKGE 106
                     6678*****************************999..**********************98876655555555555555555555555555555 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.26      30      70 ..     100     140 ..      80     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-EESS--HHH CS
  ParD_antitoxin  30 seviraaLrLLeeretklkaLreaLeegeqsGeaepfDlda 70 
                     s vi+    L+e++e k+ aL  ++++ +  G  +p D d 
      AJA92441.1 100 SVVIKGEALLVENNEEKVLALNGLMKKYQPEGRYKPMDKDM 140
                     669999999***************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1570.55
//
Query:       AJA92442.1  [L=505]
Description: matrixin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-12   46.5   2.6    1.1e-05   25.0   0.1    2.9  3  TPR_1            Tetratricopeptide repeat
    2.2e-11   43.0   0.4    0.00023   21.0   0.0    2.7  2  TPR_2            Tetratricopeptide repeat
    5.1e-10   39.4   0.7    3.8e-09   36.6   0.7    2.1  1  Peptidase_M10    Matrixin
      4e-08   32.8   2.4      0.021   15.0   0.0    3.6  3  TPR_8            Tetratricopeptide repeat
    4.2e-07   30.3   0.0    8.5e-07   29.3   0.0    1.5  1  Reprolysin_5     Metallo-peptidase family M12
    4.4e-07   30.1   0.1     0.0084   16.4   0.0    2.4  2  TPR_12           Tetratricopeptide repeat
    8.5e-07   28.8   0.1    1.7e-06   27.8   0.1    1.5  1  Peptidase_M57    Dual-action HEIGH metallo-peptidase
      5e-06   26.1   0.5      0.011   15.4   0.0    3.4  3  TPR_11           TPR repeat
    8.6e-06   26.2   0.0        0.6   11.1   0.0    3.3  3  TPR_14           Tetratricopeptide repeat
    1.7e-05   24.5   0.1      0.093   12.8   0.0    2.6  2  TPR_7            Tetratricopeptide repeat
    5.5e-05   23.2   0.4       0.26   11.4   0.0    2.8  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00016   22.1   0.3       0.72   10.4   0.0    2.9  2  TPR_19           Tetratricopeptide repeat
    0.00075   20.1   0.0       0.11   13.1   0.0    2.2  2  TPR_16           Tetratricopeptide repeat
     0.0064   16.5   0.1      0.015   15.3   0.1    1.6  1  Peptidase_M54    Peptidase family M54
  ------ inclusion threshold ------
      0.014   16.0   0.5      0.036   14.6   0.5    1.7  1  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik
      0.021   15.3   0.0      0.053   14.0   0.0    1.6  1  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.024   15.0   0.7        2.6    8.6   0.0    3.9  4  TPR_17           Tetratricopeptide repeat
      0.024   15.2   0.0        8.8    7.2   0.0    2.6  2  TPR_6            Tetratricopeptide repeat
      0.035   14.3   1.8        2.7    8.3   0.0    2.6  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
      0.093   12.6   0.2         14    5.7   0.0    2.5  2  TPR_10           Tetratricopeptide repeat
       0.13   12.2   0.0       0.22   11.4   0.0    1.4  1  Reprolysin_2     Metallo-peptidase family M12B Reprolysin-lik
       0.17   11.9   6.4        0.5   10.4   0.2    2.9  2  TPR_3            Tetratricopeptide repeat
       0.18   10.8   1.8       0.31   10.0   1.8    1.3  1  Peptidase_M66    Peptidase M66


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.4e-08   1.1e-05       4      34 .]      43      73 ..      43      73 .. 0.97
   2 ?   -2.3   0.0       6.1   4.7e+03       7      22 ..      80      95 ..      75     107 .. 0.73
   3 !   20.7   0.1   3.4e-07   0.00026       3      34 .]     110     141 ..     108     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
                HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                ly ++n +f  g+y eA+e y+k Le+ P+n
  AJA92442.1 43 LYEKANEHFMIGEYHEAIELYDKILEISPSN 73
                799**************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.1
                HHHHHHHTT-HHHHHH CS
       TPR_1  7 lGnayfklgkydeAle 22
                +G a+ +l++++  + 
  AJA92442.1 80 KGIALDNLERHKASIL 95
                7889999999887765 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 3.4e-07
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                 al +lG+ + + g+y++Al y+e+A el P+n
  AJA92442.1 110 ALIGLGVGFGNYGEYKQALTYFEQAYELAPEN 141
                 8899**************************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.9e-07   0.00023       4      34 .]      43      73 ..      41      73 .. 0.96
   2 !   19.5   0.1   9.4e-07   0.00073       3      34 .]     110     141 ..     108     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.9e-07
       TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                ly+ ++ ++  g+y eA+e+++k le+ P n
  AJA92442.1 43 LYEKANEHFMIGEYHEAIELYDKILEISPSN 73
                799**************************87 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.4e-07
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                 al  lG    + g+y++Al +fe+A el+P+n
  AJA92442.1 110 ALIGLGVGFGNYGEYKQALTYFEQAYELAPEN 141
                 677888888899******************97 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.7   4.9e-12   3.8e-09       7     141 ..     350     483 ..     345     495 .. 0.63

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.9e-12
                    EEEEESSSX..TTSXHHHHHHHHHHHHHHHHTTSSSEEEEESSSCESEEEEEESSSSSSSS.......SXBSSSSESEEEBSSSSTT..TTEEEEE CS
                    xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxx..xxxxxxx RF
  Peptidase_M10   7 ltyrilnet..pdleeeevrkairrAfkvwsevtplkFtevkkgeadikieFgrgehgdgy.......pfdgkggvlahafapgegl..ggdihfd 91 
                    l y+i+ ++  p+l+ ++  +++++ fk+w+++   +F+  +     +ki+F + + + +          d  +gvl+ha    +g+   +   + 
     AJA92442.1 350 LEYKIFVNDqpPALPLDH-VSTLTNSFKMWEDM---EFNAND--GKKVKINFVTTNTKTNAnlwvtwvVRDLGEGVLGHANLG-KGIveVALGGYG 438
                    667776555213355544.45678899999998...677644..445666666544444331111121457788999999994.433002333455 PP

                    TTS-EESSTS-.SSSEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCTXTT CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M10  92 ddeqWtlgeekveqgvslflVaaHEiGHalGLeHssdkdalmyplykeek 141
                     d +++l      +   ++++ +HE+GH +GL+Hs+d++++myp +k+++
     AJA92442.1 439 CDGNFQLF-----HVNTVEYIMTHELGHGIGLRHSEDPNSIMYPSMKNTQ 483
                    55566554.....567899**************************99544 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.021       4      34 .]      43      73 ..      40      73 .. 0.90
   2 ?    3.9   0.0       0.1        78       5      34 .]      78     107 ..      74     107 .. 0.87
   3 !   12.0   0.1   0.00026       0.2      15      34 .]     122     141 ..     119     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldpdn 34
                +y +++ ++  g+y+eA+e y k le++p+n
  AJA92442.1 43 LYEKANEHFMIGEYHEAIELYDKILEISPSN 73
                78899999999******************86 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.1
                 HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +++g ++++l+++++++  + k+ + dp+n
  AJA92442.1  78 LMKGIALDNLERHKASILEFYKVNQQDPKN 107
                 78999**************99999999986 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00026
                 T-HHHHHHHHHHHHHHHHH. CS
       TPR_8  15 gdyeeAkeyyekaleldpdn 34 
                 g+y++A  y+e+a el+p+n
  AJA92442.1 122 GEYKQALTYFEQAYELAPEN 141
                 89****************86 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.1e-09   8.5e-07      70     171 ..     365     489 ..     291     501 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.1e-09
  Reprolysin_5  70 tgdaselLnefq....sassalrgqqnddlailflmtnfsggvGlAwlgqlcnsgsagsvstrveks...........nsvvvstatevqvvaHElG 151
                    + +s+l n+f+     +++a++g++  ++++++++t+++ ++++ w+    ++g+ g  +     +           n+++    t  ++++HElG
    AJA92442.1 365 LDHVSTLTNSFKmwedMEFNANDGKKV-KINFVTTNTKTNANLWVTWVVRDLGEGVLGHANLGKGIVevalggygcdgNFQLFHVNTVEYIMTHELG 460
                   456777888888888667888888666.5*******************88777777666665544446678889999999999999999******** PP

  Reprolysin_5 152 HnfGavHDcdsss.........esqsCsl 171
                   H +G +H  d +s         ++++C l
    AJA92442.1 461 HGIGLRHSEDPNSimypsmkntQYAYCML 489
                   *******5554444577777766666765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00029      0.23      10      51 ..      47      87 ..      39      94 .. 0.74
   2 !   16.4   0.0   1.1e-05    0.0084      39      76 ..     102     139 ..      83     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
      TPR_12 10 aavlrrlgrydeAlellekaleia.rrllGpdhpltattlrnL 51
                a+ ++  g+y+eA+el++k lei  +++  ++++   ++l nL
  AJA92442.1 47 ANEHFMIGEYHEAIELYDKILEISpSNA--KTSLMKGIALDNL 87
                555677899************9995555..6666666666665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-05
      TPR_12  39 pdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                  + p  +t+l++Lg  +   g+y++Al ++e+a+++a+
  AJA92442.1 102 QQDPKNITALIGLGVGFGNYGEYKQALTYFEQAYELAP 139
                 6778899****************************986 PP

>> Peptidase_M57  Dual-action HEIGH metallo-peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.1e-09   1.7e-06     125     151 ..     443     469 ..     371     474 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.1e-09
  Peptidase_M57 125 lesysvdvnehvithelGhtvGlRhsD 151
                    ++   v+++e+++thelGh +GlRhs+
     AJA92442.1 443 FQLFHVNTVEYIMTHELGHGIGLRHSE 469
                    345689*******************96 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.011       2      29 ..      48      75 ..      47      84 .. 0.86
   2 ?    1.2   0.0      0.39     3e+02      18      35 ..      98     115 ..      87     118 .. 0.78
   3 ?    5.2   0.3     0.022        17       8      27 ..     122     141 ..     121     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
      TPR_11  2 dayyeqGkyeeAieaYkkAlkldPdnae 29
                ++ +  G+y eAie Y k l+++P+na 
  AJA92442.1 48 NEHFMIGEYHEAIELYDKILEISPSNAK 75
                667778********************97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.39
      TPR_11  18 kkAlkldPdnaeayynLG 35 
                  k  + dP+n +a+ +LG
  AJA92442.1  98 YKVNQQDPKNITALIGLG 115
                 566689********9999 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.022
      TPR_11   8 GkyeeAieaYkkAlkldPdn 27 
                 G+y++A++ +++A +l P+n
  AJA92442.1 122 GEYKQALTYFEQAYELAPEN 141
                 9***************9998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00077       0.6      10      40 ..      49      79 ..      42      83 .. 0.81
   2 ?    3.2   0.0      0.26     2e+02       5      42 ..      78     115 ..      74     116 .. 0.90
   3 !    8.7   0.0    0.0043       3.4      15      36 ..     122     143 ..     118     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00077
      TPR_14 10 allalGdpdeAiallrralalaPddaeawll 40
                 ++  G++ eAi+l++++l+  P++a + l+
  AJA92442.1 49 EHFMIGEYHEAIELYDKILEISPSNAKTSLM 79
                556669******************9976555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.26
      TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawllla 42 
                 l+ + al +l++++++i  + ++ +++P++ +a++ l+
  AJA92442.1  78 LMKGIALDNLERHKASILEFYKVNQQDPKNITALIGLG 115
                 566889999************************99886 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0043
      TPR_14  15 GdpdeAiallrralalaPddae 36 
                 G++++A++++++a +laP++ +
  AJA92442.1 122 GEYKQALTYFEQAYELAPENHV 143
                 99****************9976 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0018       1.4      13      29 ..      54      70 ..      43      76 .. 0.84
   2 !   12.8   0.0   0.00012     0.093       5      31 ..     114     140 ..     110     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
       TPR_7 13 GdyeeAielyeqsLalt 29
                G+y eAiely + L++ 
  AJA92442.1 54 GEYHEAIELYDKILEIS 70
                9***********77765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
       TPR_7   5 LarlysrlGdyeeAielyeqsLaltkd 31 
                 L++ + + G+y++A++++eq+ +l+ +
  AJA92442.1 114 LGVGFGNYGEYKQALTYFEQAYELAPE 140
                 555566669***********7777765 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00034      0.26      11      36 ..      50      75 ..      43      89 .. 0.86
   2 !    8.9   0.0     0.002       1.6       9      35 ..     116     142 ..     114     146 .. 0.86
   3 ?   -2.7   0.0       8.7   6.8e+03      37      48 ..     199     210 ..     194     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                HHHHT-HHHHHHHHHHHHHHTTS-HH CS
  Fis1_TPR_C 11 hyklgeYseArryvdalLeiEPenrQ 36
                h+ +geY eA ++ d +Lei P+n  
  AJA92442.1 50 HFMIGEYHEAIELYDKILEISPSNAK 75
                6679*******************975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.002
                 HHHHHHT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenr 35 
                 +G    geY++A+ y ++  e+ Pen+
  AJA92442.1 116 VGFGNYGEYKQALTYFEQAYELAPENH 142
                 6666779*******************8 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.7
                 HHHHHHHHHHHH CS
  Fis1_TPR_C  37 aqsLkeliedki 48 
                 ++sL+ lie++i
  AJA92442.1 199 VKSLQFLIENEI 210
                 7899999*9998 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00092      0.72       5      41 ..      54      90 ..      51     111 .. 0.84
   2 !    8.5   0.1    0.0036       2.8       5      24 ..     122     141 ..     121     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00092
      TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgql 41
                g y eA++l+ ++l+ +p na   l   +al +l + 
  AJA92442.1 54 GEYHEAIELYDKILEISPSNAKTSLMKGIALDNLERH 90
                889******************9999888888777665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
      TPR_19   5 gdyaeAlalleqalqedpkn 24 
                 g y +Al ++eqa++ +p+n
  AJA92442.1 122 GEYKQALTYFEQAYELAPEN 141
                 89****************98 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00014      0.11       1      58 [.      44      99 ..      44     107 .. 0.91
   2 ?    4.6   0.0     0.067        52      11      32 ..     122     140 ..     119     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
      TPR_16  1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyr 58
                +++a++++  g+y +A+++++  l+     P +a  +l +g a+  + r+++ + ++y+
  AJA92442.1 44 YEKANEHFMIGEYHEAIELYDKILEIS---PSNAKTSLMKGIALDNLERHKASIlEFYK 99
                6788899999*****************...************************88885 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.067
      TPR_16  11 gdyddAaaaleaalkrdpssPd 32 
                 g+y +A+ ++e+a +++   P+
  AJA92442.1 122 GEYKQALTYFEQAYELA---PE 140
                 67888888888888888...55 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.9e-05     0.015     126     172 ..     430     479 ..     370     497 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                    EE-T--......SHHHH.HHHHHHHHHHHHHHHTT----S-.TSTTS--S CS
  Peptidase_M54 126 lalsikefyte.dkeLf.lervvkevlhelGhlyGLshCke.dCvmnfsn 172
                    + +++  +  + + +Lf ++ v   ++helGh  GL h ++ + +m +s 
     AJA92442.1 430 VEVALGGYGCDgNFQLFhVNTVEYIMTHELGHGIGLRHSEDpNSIMYPSM 479
                    555555443334667773566666789*******************9985 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   4.6e-05     0.036      59     124 .]     401     468 ..     366     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
  Reprolysin_3  59 rgqagyDlvhlftardesgvgGlAyv.gsvcnsskkagvnsgssvlgkvga.....dtvaHEiGHnfganHt 124
                     +a+  +  ++++  e gv+G A + +++ +++ +     g+ ++ ++ +     + ++HE+GH +g++H+
    AJA92442.1 401 KTNANLWVTWVVRDLGE-GVLGHANLgKGIVEVALGGY---GCDGNFQLFHvntveYIMTHELGHGIGLRHS 468
                   23566666666666665.89999998533333333322...22222332223445699*************6 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.8e-05     0.053      59     122 ..      30      93 ..      17      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-05
                      HHHHHHHTTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
  Alkyl_sulf_dimr  59 akrlvelmGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                      +  + e + ++ ++ eka+e++  g+y+ a+el +++++  p+na++  +k  al++l +++ s
       AJA92442.1  30 GDTYGEGIRDVPNLYEKANEHFMIGEYHEAIELYDKILEISPSNAKTSLMKGIALDNLERHKAS 93 
                      5566666778999********************************9999999999998887765 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.3   2.6e+03      12      33 ..      39      60 ..      38      61 .. 0.76
   2 ?    8.6   0.0    0.0033       2.6       1      30 [.      62      91 ..      62      94 .. 0.90
   3 ?    0.7   0.0       1.1   8.9e+02       4      32 ..      99     127 ..      96     128 .. 0.74
   4 ?   -0.6   0.2       2.9   2.2e+03       1      20 [.     130     151 ..     130     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.3
      TPR_17 12 nadaynnLAelllknGdlmtAr 33
                +++ ++++A+ + ++G++ +A+
  AJA92442.1 39 DVPNLYEKANEHFMIGEYHEAI 60
                5677888888888888888887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0033
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlm 30
                ly k le+ P+na+   +++ +l ++ +++
  AJA92442.1 62 LYDKILEISPSNAKTSLMKGIALDNLERHK 91
                7********************999988765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.1
      TPR_17   4 kaleldPnnadaynnLAelllknGdlmtA 32 
                 k+ ++dP+n  a+  L++ + + G++++A
  AJA92442.1  99 KVNQQDPKNITALIGLGVGFGNYGEYKQA 127
                 56679******999999766666666665 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.9
      TPR_17   1 lylkaleldPnn..adaynnLA 20 
                 ++++a el P n  ++ y++ A
  AJA92442.1 130 YFEQAYELAPENhvVENYYEFA 151
                 589999******8888888776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       8.8       4      32 ..      44      72 ..      42      73 .. 0.77
   2 ?    5.3   0.0     0.046        36       6      31 ..     114     139 ..     109     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  4 yklalsyrklgdtdkAlealerlikeYPd 32
                y  a  +++ g++ +A+e+++++++  P 
  AJA92442.1 44 YEKANEHFMIGEYHEAIELYDKILEISPS 72
                44455566658*************98885 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.046
                 HHHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                 l+  + + g++ +Al+++e+  +  P
  AJA92442.1 114 LGVGFGNYGEYKQALTYFEQAYELAP 139
                 55555565799999999999877766 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0034       2.7      25      65 ..      42      83 ..      37      96 .. 0.80
   2 ?    4.3   0.6     0.059        46      36      75 ..     121     163 ..      92     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0034
                HHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHH CS
      ANAPC3 25 dayllAlclylngqykrAyellrka.klnskslgcrylfAqc 65
                ++y +A  ++  g+y++A+el++k  ++ +++ +  + ++ +
  AJA92442.1 42 NLYEKANEHFMIGEYHEAIELYDKIlEISPSNAKTSLMKGIA 83
                78999999***************9988888887776666555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.059
                 TT-HHHHHHHHHCT.SHHHC-H..HHHHHHHHHHHHTT-HHHH CS
      ANAPC3  36 ngqykrAyellrka.klnsksl..gcrylfAqcllkLkkyeeA 75 
                  g+yk+A++++++a +l+++++  +  y fA   +k   y+eA
  AJA92442.1 121 YGEYKQALTYFEQAyELAPENHvvENYYEFALNTVKKYPYNEA 163
                 4677777777777777776666566666666655555555555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.041        32      12      31 ..      50      69 ..      45      70 .. 0.84
   2 ?    5.7   0.0     0.019        14       8      31 ..     114     137 ..     108     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.041
      TPR_10 12 lrqrgrydeAealleealai 31
                ++  g+y+eA +l+++ l+i
  AJA92442.1 50 HFMIGEYHEAIELYDKILEI 69
                55669***********9997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
      TPR_10   8 LanalrqrgrydeAealleealai 31 
                 L++   + g+y++A+ ++e+a+++
  AJA92442.1 114 LGVGFGNYGEYKQALTYFEQAYEL 137
                 555555569************986 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.22      56     146 ..     387     472 ..     344     495 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
  Reprolysin_2  56 evrr.lnllsqlegekdydlahlvllgtfsggvlGLayvg.qicqkeassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdndgs 146
                    +++ +  +   + + +  l + +++++ ++gvlG a +g +i +  ++      g     n + +  +++   ++ HE+GH  G  H  d +
    AJA92442.1 387 DGKKvKINFVTTNTKTNANLWVTWVVRDLGEGVLGHANLGkGIVEVALGG----YGCD--GNFQLFH-VNTVEYIMTHELGHGIGLRHSEDPN 472
                   33333455666667778888888889**************8676554444....3333..3444444.34445569************88755 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.059        46      12      25 ..      51      64 ..      44      67 .. 0.86
   2 ?   10.4   0.2   0.00064       0.5      15      36 .]     122     141 ..     114     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
                HHTT-HHHHHHH.. CS
       TPR_3 12 ynkkkyqeArelfs 25
                ++ ++y eA+el++
  AJA92442.1 51 FMIGEYHEAIELYD 64
                56799*******87 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00064
                 T-HHHHHHH..HHHHHHH-TT- CS
       TPR_3  15 kkyqeArelfsYallaildken 36 
                 ++y +A+ +  +++++ l++en
  AJA92442.1 122 GEYKQALTY--FEQAYELAPEN 141
                 89*******..77*******99 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.8    0.0004      0.31     168     210 ..     427     469 ..     418     487 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0004
  Peptidase_M66 168 nGkyanghGGlgggssGivtgdatltgefiHEqGHalGLpHyl 210
                    +G+ +   GG g  ++      +t++ ++ HE+GH +GL H+ 
     AJA92442.1 427 KGIVEVALGGYGCDGNFQLFHVNTVEYIMTHELGHGIGLRHSE 469
                    566666678877775554555577888999***********43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2893.95
//
Query:       AJA92443.1  [L=336]
Description: eukaryotic-type DNA primase, large subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   80.4   0.3    2.8e-22   79.4   0.3    1.6  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.3   1.6e-26   2.8e-22      17     194 ..     160     313 ..     140     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.6e-26
                      G....GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--.............TTSSTTGGSHHHHT CS
  DNA_primase_lrg  17 r....rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesyvaedvqeeedskisaknidklake 106
                      +    ++ + kG++ l+ +e ++l++++  ++++++++s +  ++ +     e++ +kl++l ++++                    ++++  +
       AJA92443.1 160 EwkliNRKVTKGKVHLTPHETVRLVRKELDRHIYTKINSSSTPQMII---GFETYVDKLKQLAKKFE--------------------VKTVESK 230
                      25555677999999999999999999999999999999988888776...45667777889999998....................89999** PP

                      T--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS CS
  DNA_primase_lrg 107 sfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltk 194
                       fPpC+++++e l+k+++l+h+gr+ l++Fl + g ++++i +l+k+a     ++++   + y+ +   G   + t+y+++sCek+++k
       AJA92443.1 231 EFPPCIKHAIEVLEKGENLPHSGRFMLATFLLNKGQTVEQIAPLFKNA-----PDYNPkVTIYQLNQLSG-TSGTTEYKCPSCEKVKSK 313
                      ***********************************************9.....****95666********.8899***********765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1932.80
//
Query:       AJA92444.1  [L=246]
Description: KR domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-65  220.5   1.6    1.6e-65  220.2   1.6    1.1  1  adh_short       short chain dehydrogenase
    1.9e-46  158.5   0.9    2.3e-46  158.3   0.9    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    6.9e-17   61.9   0.2    8.8e-17   61.6   0.2    1.2  1  KR              KR domain
    6.5e-05   22.5   0.9    0.00033   20.2   0.3    2.3  2  Epimerase       NAD dependent epimerase/dehydratase family
    0.00046   20.1   1.1      0.001   19.0   0.5    1.7  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.033   14.3   0.2       0.55   10.3   0.1    2.3  2  ClpB_D2-small   C-terminal, D2-small domain, of ClpB protein
      0.096   12.2   1.1        0.3   10.6   0.3    1.9  2  NmrA            NmrA-like family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.2   1.6   6.3e-69   1.6e-65       1     193 [.       5     198 ..       5     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.2 bits;  conditional E-value: 6.3e-69
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kvv++tGassGIG+ +ak+lak+Gak+v+ +r+ ++le+++ke+ ++g +++++++Dvt+++++++lv++a +k+g++dvLvnNAG+   + +++l+ +
  AJA92444.1   5 KVVVITGASSGIGHSTAKALAKKGAKIVAGARRLDRLETLKKEITDDGGEITICETDVTKKADCDNLVKQALDKYGTVDVLVNNAGLMPLSFVKSLKVD 103
                 89************************************************************************************************* PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGT.EEEEEEEESSBSSHHHHHHCTH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptg.irvnavaPGlvdTdmakelrek 193
                 ew+r+i+vN++gv+ +t+av+p+m +++sG+I+n+sSvag+  ++ +++Y+A+K+av+++++ l++el+ ++ irv+++ PG+v+T+++++++e+
  AJA92444.1 104 EWDRMIDVNIKGVLYCTAAVVPTMTEKKSGHIINISSVAGRIVFPAGSVYCATKHAVTAFSEGLRQELSVRKnIRVTSIEPGVVQTELTNTITED 198
                 ********************************************************************98877****************999876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.9   8.9e-50   2.3e-46       1     213 [.      11     224 ..      11     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 8.9e-50
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   Ga sgIG+ +Akala++Ga++v+  ++ ++ +   +e+++++g+  ++e+DVt+++++++lv+++ +k+g++D+lvnnag +p   + + +++ +e+
    AJA92444.1  11 GASSGIGHSTAKALAKKGAKIVAGARRLDRlETLKKEITDDGGEItICETDVTKKADCDNLVKQALDKYGTVDVLVNNAGLMPL--SFVKSLKVDEW 105
                   899*****************999999988856666667777666556*************************************..777779***** PP

                   HHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGG.GTEEEEEEEE--BHCTGGGGSTTHHHHH CS
  adh_short_C2  96 draldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgp.kgiRvNavspgpikTlaasgikgfdell 189
                   dr++dvn++++++++ a++p m+e+  g i+n+ssv++++v+p  ++y+a+K+a+ a++  l  el   k+iRv ++ pg+++T++++ i+ +d+l+
    AJA92444.1 106 DRMIDVNIKGVLYCTAAVVPTMTEKksGHIINISSVAGRIVFPAGSVYCATKHAVTAFSEGLRQELSVrKNIRVTSIEPGVVQTELTNTIT-EDSLQ 201
                   ********************8887779***************************************8659********************8.67777 PP

                   HHHHHHSTTSS-B-HHHHHHHHHH CS
  adh_short_C2 190 eelearaplgrlgtpeevaeaalf 213
                     +e+   ++   +++++ +a++f
    AJA92444.1 202 GFIEKGKQMEA-LQADDISNAIIF 224
                   77777777666.9********998 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.2   3.4e-20   8.8e-17       3     166 ..       7     170 ..       5     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.4e-20
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 ++itG+  g+G ++a+ la+kga+ +v  +R+    ++ ++l +e+++ g e+++++ Dv++k++  +l++++ ++ +++   ++ Ag++  + +++++
  AJA92444.1   7 VVITGASSGIGHSTAKALAKKGAK-IVAGARR---LDRLETLKKEITDDGGEITICETDVTKKADCDNLVKQALDKYGTVDVLVNNAGLMPLSFVKSLK 101
                 79********************97.7777777...344555889******************************************************* PP

                 HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalaeyrrsq 166
                  +++++++   +kG+     ++ +    ++  +++ +SS+ag +  +  + Y a+ + + a+ e  r++
  AJA92444.1 102 VDEWDRMIDVNIKGVLYCTAAVVPtmteKKSGHIINISSVAGRIVFPAGSVYCATKHAVTAFSEGLRQE 170
                 **************998887766555559999******************************9876654 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   1.3e-07   0.00033       1      63 [.       7      75 ..       7     174 .. 0.83
   2 ?    0.1   0.0      0.17   4.5e+02     209     234 ..     209     234 ..     174     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHH CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkee 63
                +++tGa+  iG  ++kal++kg ++++ +r+ ++ +t ++e +      +++e d+t+++++++l+k+ 
  AJA92444.1  7 VVITGASSGIGHSTAKALAKKGAKIVAGARRLDRLETLKKEITddggeiTICETDVTKKADCDNLVKQA 75
                68**********************6666666444444443333899**************988888863 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                 EEEEEEHHHHHHHHHHHHHHHTT-ST CS
   Epimerase 209 lRdflyveDvaeaillvlehvdagdk 234
                 +++ l ++D+ +ai++++++++  + 
  AJA92444.1 209 QMEALQADDISNAIIFAIDAPNHMNV 234
                 46778899**********99665544 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5     4e-07     0.001       1      98 [.      11     140 ..      11     152 .. 0.67
   2 ?    1.2   0.0      0.11   2.9e+02      53      73 ..     112     132 ..      69     225 .. 0.42

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4e-07
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHT.......T-SEEEES-.........--TCCH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele.....aeeglevvegdvtdvedlaealk.......gadaVvsal.........ggggkd 74 
                     GA+ ++G+  +k l+++ g +++a +R+ ++l+ l+     +  +++++e dvt+++d  + +k        +d+ v ++         +     
      AJA92444.1  11 GASSGIGHSTAKALAKK-GAKIVAGARRLDRLETLKkeitdDGGEITICETDVTKKADCDNLVKqaldkygTVDVLVNNAglmplsfvkS----- 99 
                     9**********999999.5*************9776444444479************999988844444433455444443333322220..... PP

                     HHH...................HHHHHHHHHHCT--EEEEEEE CS
  NAD_binding_10  75 eeg...................aknivdaakeagvkRfvlvsa 98 
                                           ++++v  + e++  +++ +s+
      AJA92444.1 100 --LkvdewdrmidvnikgvlycTAAVVPTMTEKKSGHIINISS 140
                     ..01222233344455666666666666776666666666666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                     HHHHHHTT-SEEEES---TCC CS
  NAD_binding_10  53 dlaealkgadaVvsalggggk 73 
                      ++ +l  + aVv ++  +++
      AJA92444.1 112 NIKGVLYCTAAVVPTMTEKKS 132
                     444444444444444433333 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00021      0.55      34      55 ..      20      41 ..      12      55 .. 0.81
   2 ?    1.4   0.0      0.14   3.5e+02      55      79 ..     186     210 ..     185     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                   HHHHHHHHTSBTTTBTCCHHHH CS
  ClpB_D2-small 34 aldalaekgydpeyGARpLrri 55
                     +ala+kg + + GAR L+r+
     AJA92444.1 20 TAKALAKKGAKIVAGARRLDRL 41
                   6789****************96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
                    HHHHHTHHHHHHHHHTTSSSTTSEE CS
  ClpB_D2-small  55 iiqreiedplaeeilsgelkegdtv 79 
                    ++q e+++++ e  l+g +++g+++
     AJA92444.1 186 VVQTELTNTITEDSLQGFIEKGKQM 210
                    6899**************9999886 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00012       0.3       1      65 [.       7      75 ..       7      84 .. 0.87
   2 ?   -0.2   0.0      0.23   5.9e+02     177     205 ..     210     237 ..     169     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT- CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvealkgv 65
                ++++Ga+  +G s ++al+k+g k+ a  R +   + l k++ + G e+   + d+  k+  ++++k++
  AJA92444.1  7 VVITGASSGIGHSTAKALAKKGAKIVAGARRLdrLETLKKEITDDGGEITicETDVTKKADCDNLVKQA 75
                6899**************************986567778899999887644789999999999999997 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                 S-EE-HHHHHHHHHHHHHHHHHHHTTEEE CS
        NmrA 177 avlldaeeDiGafvikilkdprklkgkri 205
                 +  l + +Di +++i +++ p+ ++++ i
  AJA92444.1 210 MEAL-QADDISNAIIFAIDAPNHMNVNEI 237
                 3334.889999999999999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1447.09
//
Query:       AJA92445.1  [L=636]
Description: 2-oxoacid:acceptor oxidoreductase, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-54  185.0   0.0    2.4e-54  184.5   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.6e-32  111.5   0.2    8.2e-32  110.7   0.2    1.4  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    2.5e-14   53.4   0.0    6.1e-14   52.2   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    1.6e-07   31.3   0.0    3.4e-07   30.2   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
     0.0014   18.3   0.0     0.0026   17.4   0.0    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
       0.13   11.5   0.5       0.22   10.7   0.5    1.3  1  PUL              PUL domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   0.0   8.1e-58   2.4e-54       2     229 ..     252     494 ..     251     496 .. 0.84

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 8.1e-58
                 HHHHCTEEEEEE--BTTTCC..HHHHHCHC..CCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHHHHHTT--EEEEEEEE CS
       POR_N   2 aaiaagvdviaaYPITPsse..iaeelael..lakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlglaageelPvvivvvaR 96 
                 ++i ag++++++YPITP+++   + e +e   +++ ++g + v+q+e+Ei+ai+++iG++++G+r+aT TSg+G++Lmie l +a+ +e+Pvvi+ ++R
  AJA92445.1 252 GKIIAGCRFQSYYPITPATDesNFLETNEIleINEDRPGSTLVIQTEDEISAIGMAIGSSLTGVRSATCTSGPGFVLMIECLSWAGINEVPVVITFYQR 350
                 67889***************663333333311344444899********************************************************** PP

                 E-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HEEEEEEC-SGG.....GS----.-SBXXXX CS
       POR_N  97 alpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshevekvelpdee....delklik.ekleeye 185
                 ++pstgl++r  q Dl+ a+     +++ iv as+nv + f ++++ fn+A  ++vP+i+++D+f++  +v + +  de     d  kl + +++++y+
  AJA92445.1 351 SGPSTGLPTRHGQDDLLCAInsgvgEFPRIVYASGNVSDSFYDTANVFNYADVFQVPIIHMMDKFIA-SSVTTCQRFDETkvniDRGKLLDePPSNAYK 448
                 *******************************************************************.5666666665552103333333313344555 PP

                 XXXX...SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
       POR_N 186 rkey...aldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                 r++    +l+p++ i  +   +++tg+e + +g+++ed   ++ve++
  AJA92445.1 449 RFDHtadGLSPRSKIGLENGIFWNTGDESDVEGHISED-PVNRVEMM 494
                 5544999*******************************.77777766 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.2   2.7e-35   8.2e-32       2     176 ..      14     217 ..      11     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 2.7e-35
                 TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEEEEECTCGTT-CCHHHCTS CS
         POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggiiiynseelkpdelkkakee 100
                 G Gv+ta++i+++++++ Gy+++++rey s+i+G hsy+ vr+sd++i++si+  + ++l+a+daet+++h++++ ++giiiy+s+  + ++ +     
  AJA92445.1  14 GSGVETAANIFSQVFSKMGYQIFGKREYYSNIKGEHSYFAVRVSDKQIRSSIK--GTNMLIAFDAETIFRHANDVLENGIIIYDSTLENIKVSDVITF- 109
                 99********************************************6666666..******************************8766666666555. PP

                 -HHHHHHH.......................T-EEEEE-HHHHHHHCCC..........CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHH CS
         POR 101 erelkerl.......................gvrvygvdatkiakeiggn.........eraaNtvmlGalaallglplealeeaikkrfpkkkeviek 167
                 +++ ker                        g+ +  v+++ ++ e++ +          r+ N++++  +++ll +p e+l e i+  f kkk+++++
  AJA92445.1 110 DNDFKERMegflksnnkentikgilelaserGASIHSVSFRSLLFELSEKienpriktmIRMFNVLGVSLSLGLLMIPTEKLTESINSIFSKKKAIADM 208
                 5566666689******************************9999877777777888899**************************************** PP

                 HHHHHHHHH CS
         POR 168 Nlkafragy 176
                 N+ a++ +y
  AJA92445.1 209 NVSAANFAY 217
                 ******999 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0     2e-17   6.1e-14       2      99 ..     521     611 ..     520     614 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2e-17
                 SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGTSEEEEEE--GGG----H CS
     PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkkskvkvvnfvaglgGrditv 99 
                 e+ +v  Gs+ g + +a+d+l++egi++G++ +++l PFP+e lk+  ++ k +++++ n++    Gql++ +k+ l+k    +  ++ +  Gr +t 
  AJA92445.1 521 EFCVVSWGSTQGPILDAIDMLKNEGINIGFVEIKLLHPFPKELLKKSFSNSKTIIDVEANYT----GQLGSIIKQNLEKD---PDYYILKYTGRPMTC 611
                 7899*********************************************************5....*********99877...555666677777666 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.1e-10   3.4e-07       7     101 ..     517     606 ..     512     627 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                      ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSSEEEEEE CS
  Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdgldapvkrvg 100
                      ++  + ++v++Gs+    l+A+++L++egi++  v +  + p+ ke++++s  + + ++ ve +++ g +gs + + l +    + d ++++ +
       AJA92445.1 517 HSDGEFCVVSWGSTQGPILDAIDMLKNEGINIGFVEIKLLHPFPKELLKKSFSNSKTIIDVEANYT-GQLGSIIKQNLEK----DPDYYILKYT 605
                      5567889******************************************************99887.8898888888877....5555555555 PP

                      E CS
  Transketolase_C 101 g 101
                      g
       AJA92445.1 606 G 606
                      5 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.7e-07    0.0026      41     109 ..     293     359 ..     277     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.7e-07
                   EEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHHS.. CS
  TPP_enzyme_N  41 rvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrgqgv 109
                    v+++ +E +a+++A g +   g +  + +tsgpG++ ++  l  A  + +P+++   +r+  ++g ++
    AJA92445.1 293 LVIQTEDEISAIGMAIGSSLT-G-VRSATCTSGPGFVLMIECLSWAGINEVPVVITFYQRSGPSTGLPT 359
                   579999***********9665.4.7778889************************99999888887333 PP

>> PUL  PUL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   7.5e-05      0.22      92     190 ..     116     222 ..     113     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
         PUL  92 rvsayfaeeeggktissllslllssals.ssap..........kalennrmlalRllaNlFssplgrelllskaeslletleslltssllssnknlria 179
                 r  +++ ++++++ti+ +l+l+++ + s  s            k+++    +++R+++ l  s ++  l++   e+l e++ s++++  ++      ++
  AJA92445.1 116 RMEGFLKSNNKENTIKGILELASERGASiHSVSfrsllfelseKIENPRIKTMIRMFNVLGVSLSLGLLMI-PTEKLTESINSIFSK--KKAIADMNVS 211
                 6667777778889********999999864444899**999986665569999***988888888888888.559*********996..5779999*** PP

         PUL 180 latlllNlavl 190
                 +a +++N+a++
  AJA92445.1 212 AANFAYNYAAA 222
                 *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.61
# Mc/sec: 3154.46
//
Query:       AJA92446.1  [L=234]
Description: hypothetical protein T478_0847 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1453.03
//
Query:       AJA92447.1  [L=570]
Description: succinate dehydrogenase or fumarate reductase, flavoprotein subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-99  331.9   0.2    7.8e-99  331.6   0.2    1.1  1  FAD_binding_2   FAD binding domain
    2.1e-34  118.3   0.4    3.3e-34  117.6   0.4    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    8.5e-07   28.5   0.0    1.6e-05   24.3   0.0    2.5  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0011   18.1   0.1        0.1   11.7   0.3    2.2  2  GIDA            Glucose inhibited division protein A
     0.0022   16.8   1.1       0.86    8.2   0.6    2.5  3  HI0933_like     HI0933-like protein
     0.0049   16.2   0.7      0.025   13.8   0.2    2.2  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.015   14.7   0.2       0.21   10.9   0.3    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
      0.074   12.1   0.1       0.11   11.5   0.1    1.2  1  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.6   0.2  3.5e-102   7.8e-99       1     416 [.       8     389 ..       8     390 .. 0.97

  Alignments for each domain:
  == domain 1  score: 331.6 bits;  conditional E-value: 3.5e-102
                    SEEEE--SHHHHHHHHHHHHTTT..-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHHHHHHHHTHHHHHH CS
  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGl..kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqplveafveaapeavd 94 
                    D+i+ GsGlAGL+AA+eaa++++  k+ v+ k+q+++++++ ++Gg +av ++      ++d++e+h++dt+k++d ladq+ +e +++ +p ++ 
     AJA92447.1   8 DLIIAGSGLAGLRAAIEAAKKNQkiKIGVIAKTQVMRSHSVSAEGGTAAVIQED-----KGDTIESHIYDTVKGSDFLADQDTAEKLCHMMPNEIF 98 
                    89******************76657999***********************333.....479********************************** PP

                    HHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEE CS
  FAD_binding_2  95 eLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevr 189
                    +Le++g+p+sr+e+g++d+r +Gg s + r  + a d+       g+  + +l+++++k + ++f+++++++++i+++++  G+++ + +sg+  +
     AJA92447.1  99 QLEHWGMPWSRQENGKIDQRNFGGYSFP-RATY-AIDK------VGFFEMQTLYDTCQKFDnIEFLNEWYITSIIHDGKQFCGITAIETSSGSFYT 186
                    ****************************.****.9**9......99999**********99***************999********99999999* PP

                    EEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBT CS
  FAD_binding_2 190 irakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrF 285
                    i+ ka+++atgG+gr           + ++t a   t dgl++a+rag+al+d  me+vqfhPt+++    +sgiLite++rgeGg+l++kdG rF
     AJA92447.1 187 IKGKALIIATGGAGR----------IFSYSTYALSSTPDGLDMAYRAGMALKD--MEFVQFHPTGIL----PSGILITEGARGEGGYLLNKDGDRF 266
                    ***************..........****************************..************....************************* PP

                    H.......GGGS-HHHHHHHHH.HHHHTTTS......CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEE CS
  FAD_binding_2 286 m.......nelasrdvvsrailekeiaeggs......eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpa 368
                    m       +ela+rd+vsr+i+ +ei+eg++      e+++ ld++h l+ e+++a+l +i+e+ +++ +      idpad+pi        ++p 
     AJA92447.1 267 MknyaagkMELAPRDIVSRSIM-TEINEGRGfkhetgEDCMKLDLRH-LGDEKIKAKLGGIREISIKFSG------IDPADEPID-------IRPV 347
                    **********************.************************.*******************999......******999.......**** PP

                    EEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
  FAD_binding_2 369 qhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                    +hy+mgG++t+ +g +       ++G +AaGe+a+ +vhganrlg+ns
     AJA92447.1 348 CHYMMGGIHTNIDGAA------ELQGVWAAGEAACNSVHGANRLGANS 389
                    ****************......************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.4   1.5e-37   3.3e-34       2     128 .]     447     570 .]     446     570 .] 0.97

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1.5e-37
                     HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH.HTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTBEBTTS-SEETTT-S CS
  Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrer.lknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaHaredfperdDenwl 95 
                     +e  +i+++k+ v+R++++L+e+lk+++el+++ +k  +v+d+ k++N+++ +++el++++++Ae+++ +A +RkESrGaH r+dfp+rdD+n+l
      AJA92447.1 447 QEVAEILNAKAYVYRNHNDLAEGLKKVRELKQKtWK--HVDDSAKEYNTNFQNVMELDSMFRVAEIVLLGAINRKESRGAHSRTDFPTRDDANFL 539
                     78899****************************999..899****************************************************** PP

                     EEEEE...TT-SS-EEEEEE--GGG--S---SS CS
  Succ_DH_flav_C  96 khtlasldaakeeveleyepveletlkpkeRsY 128
                     +htla++d++  e+ ++ +pv++++ kp eR+Y
      AJA92447.1 540 HHTLAYYDPS--EPIMKKHPVTITKYKPVERKY 570
                     *****99866..9*******************9 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     7e-09   1.6e-05       2     114 ..       8     203 ..       7     229 .. 0.81
   2 ?    0.7   0.0      0.11   2.4e+02     255     278 ..     352     375 ..     333     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7e-09
                  SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........................................ CS
                  xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias........................................ 57 
                  d+++ G+G AGl+aa+++a+  +++k+ ++ ++++++  + +      + ++ a +++                                        
   AJA92447.1   8 DLIIAGSGLAGLRAAIEAAKknQKIKIGVI-AKTQVMRSHSVS-----AEGGTAAVIQedkgdtieshiydtvkgsdfladqdtaeklchmmpneifq 99 
                  899*****************4335666666.333333333333.....222222222223344566899***************************** PP

                  .............................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC...TCEEEEEESEEEE-- CS
                  .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
  Pyr_redox_2  58 .............................................evvkklnqgielllgeevvkidpgkkkvklekkke...gdeekiaydklvlAt 107
                                                               + ++k+  +ie+l++  +++i+++ k++   +  e   g+  +i+ ++l++At
   AJA92447.1 100 lehwgmpwsrqengkidqrnfggysfpratyaidkvgffemqtlyDTCQKFD-NIEFLNEWYITSIIHDGKQFCGITAIEtssGSFYTIKGKALIIAT 196
                  ******************************************9995555555.689999999********99998777767779999*********** PP

                  -EEE-BC CS
                  xxxxxxx RF
  Pyr_redox_2 108 Gssprdl 114
                  G+  r++
   AJA92447.1 197 GGAGRIF 203
                  *988877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                  TTEEE--TTSBESSTTEEE-GGGC CS
                  xxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 255 rggivvdeflrtnvpgiyaiGDva 278
                   ggi ++  ++ + +g++a+G  a
   AJA92447.1 352 MGGIHTNIDGAAELQGVWAAGEAA 375
                  58999999999**********999 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.3   4.5e-05       0.1       1      37 [.       8      44 ..       8      75 .. 0.78
   2 !    4.1   0.0    0.0091        20      99     156 ..     141     202 ..     122     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                d+i+ G G+AG+ AA++aa+++ k+++ +    ++++
  AJA92447.1  8 DLIIAGSGLAGLRAAIEAAKKNQKIKIGVIAKTQVMR 44
                67999*****************999887665555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0091
                 HHHHHHHHTSTTEEEEES.-EEEEEECTTEEEE...EEETTS-..EEEECEEEE--TT-BT-EE CS
        GIDA  99 kevteklenepnleiiee.eveeliveekkvkg...vvtedge..tikakavviatGtflkgki 156
                 +++ ++ ++ +n+e ++e  ++++i + k+ +g   + t++g+  tik ka +iatG   +g+i
  AJA92447.1 141 QTLYDTCQKFDNIEFLNEwYITSIIHDGKQFCGitaIETSSGSfyTIKGKALIIATGG--AGRI 202
                 45567788888998777625678877777766622266888872245667*******9..4444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.6   0.00038      0.86       2      28 ..       8      34 ..       7      55 .. 0.86
   2 !    6.3   0.0    0.0015       3.3     115     189 ..     143     229 ..     138     236 .. 0.73
   3 ?   -3.3   0.0       1.2   2.6e+03     292     350 ..     444     501 ..     431     508 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00038
                 SEEEE--SHHHHHHHHHHHHTT--EEE CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVll 28
                 d+i+ G G AGl aAi+aak+++++ +
   AJA92447.1  8 DLIIAGSGLAGLRAAIEAAKKNQKIKI 34
                 89****************999998764 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
                  HHHHHHH.HT-EEE-S--EEEEECETTE.EEEEE...TTE...EEEESEEEE----S......S-GGGT--SHHHHHHHHTT--EEE CS
  HI0933_like 115 llkelke.agvklrletevksvekeedgkfrvkt.k.see...eleadklvlAtGGl......SiPklGstgkgyklaeqfghtivp 189
                  l  ++++  ++++  e  ++s+ ++ +++  +++ + s++   +++ ++l++AtGG+      S   l st++g ++a  +g+ + +
   AJA92447.1 143 LYDTCQKfDNIEFLNEWYITSIIHDGKQFCGITAiEtSSGsfyTIKGKALIIATGGAgrifsySTYALSSTPDGLDMAYRAGMALKD 229
                  55666664678888888899999988888777665322222448999*********7555644667899999999999999887665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.2
                  BHHHHHTTTS-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE--SEE--T CS
  HI0933_like 292 slknalaellpkrlvevlleealieeedkklaqlskkelkklaealkaltvkvngtegl 350
                  ++k+ +ae+l+ +   +  ++ +++e  kk+++l++k+ k++ ++ k+++ + ++ ++l
   AJA92447.1 444 EVKQEVAEILNAKAYVYRNHN-DLAEGLKKVRELKQKTWKHVDDSAKEYNTNFQNVMEL 501
                  677788888888877777666.4447778888888888888888877777777666665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   1.1e-05     0.025      13      49 ..       2      39 ..       1      68 [. 0.84
   2 ?   -0.2   0.0      0.22   4.9e+02     212     233 ..     365     387 ..     354     388 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                HHHTEEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEES CS
        Thi4 13 lkyaesDvvivGaGssGLtaayylakk.pdlkvailer 49
                 + +e D++i G+G +GL aa   akk  ++k+ ++ +
  AJA92447.1  2 TDSIEFDLIIAGSGLAGLRAAIEAAKKnQKIKIGVIAK 39
                567899********************988999988865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                 ETTEEE-TH.HHHHHHT-EB--S CS
        Thi4 212 vpnlyvaGm.evaevdganRmGp 233
                 ++++++aG  + + v+ganR+G+
  AJA92447.1 365 LQGVWAAGEaACNSVHGANRLGA 387
                 56788888615689*******97 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   9.2e-05      0.21       1      24 [.       8      31 ..       8      36 .. 0.93
   2 ?    1.0   0.0     0.094   2.1e+02      92     144 ..     143     197 ..     117     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGak 24
                  D+++ G+g+aG+ AAi Aa++ +k
    AJA92447.1  8 DLIIAGSGLAGLRAAIEAAKKNQK 31
                  99******************9887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.094
  FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg 144
                   +++   + ++++ l +  +++++ +gk+  ++t+ + + g  +ti++k  i ATg
    AJA92447.1 143 LYDTCQKFDNIEFLNEWYITSIIHDGKQFCGITAIETSsGsFYTIKGKALIIATG 197
                   444444558999999999999****9896666655555477**********9998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.9e-05      0.11       1      38 [.       8      44 ..       8      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllf 38
                   D+++ G+G+Agl+ A + +++++++k+++i a  ++++
     AJA92447.1  8 DLIIAGSGLAGLRAAIEAAKKNQKIKIGVI-AKTQVMR 44
                   9*****************************.6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3437.25
//
Query:       AJA92448.1  [L=119]
Description: hypothetical protein T478_0736 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  DUF5557   Family of unknown function (DUF5557)


Domain annotation for each model (and alignments):
>> DUF5557  Family of unknown function (DUF5557)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.3e-05      0.22      22      77 ..      59     114 ..      42     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
     DUF5557  22 sltnmegsigikgcefkswlfkfyqarsqvllcgevknlylltsnkttvkeqnacl 77 
                 s    eg + i  +e k    + y +  + +   e+kn y++ s +tt+  + a+l
  AJA92448.1  59 SQKVEEGELDIEAVEQKLIEDRHYTSTNRWVPTKEIKNGYVINSRHTTLVSDAAAL 114
                 555679999***************************************98888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 764.97
//
Query:       AJA92449.1  [L=242]
Description: putative cytochrome C-type biogenesis protein CcdA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-48  164.9  19.7    2.6e-48  164.7  19.7    1.0  1  DsbD      Cytochrome C biogenesis protein transmembrane regio


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.7  19.7   1.5e-52   2.6e-48       1     212 [.       9     222 ..       9     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 1.5e-52
        DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvktekkkv.....kvllkallFvlGlslvfvslglsaafl.gqllkdvkevirrvaglivillGlhf 93 
                 aflaG+ sf++PCilp++Pa+l+yisg+++++vkt+++ +     +v+l++++FvlG+s+vf++lg+++  +  + ++++ +  ++++g+i+i +G  +
  AJA92449.1   9 AFLAGIGSFFAPCILPMVPAFLAYISGTTLSEVKTKNNVIsinksNVFLNSIFFVLGFSVVFSTLGVAINSIfYENANQIVSEFNQIGGIIIIGFGAYM 107
                 69*********************************86655888889********************9986551677889*******************9 PP

        DsbD  94 lgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlalaaskeslakgallllvyvlGlaipfllvglllellkkklkslkky 192
                 +   ki +l+ +k++    k+a + +  ++l+G++Fa+gw+PC+gP+l+++++laa++     +  lll+y++G++ipf+++g l+++  + + ++ k+
  AJA92449.1 108 ILSHKIRILNIEKKIF--PKSAGARFPVSFLFGMAFAAGWTPCVGPILGTIITLAATSP--GIAFNLLLAYSIGMGIPFMIMGALISKSSRIISKIGKH 202
                 99999*********95..5667777789*******************************..9999********************************** PP

        DsbD 193 skaveiaggvllvllGvlll 212
                  k+ +++ g+++++lG+l++
  AJA92449.1 203 LKYYTVLFGMVIIVLGILVF 222
                 ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1438.49
//
Query:       AJA92450.1  [L=311]
Description: quinolinate synthetase complex, A subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.5e-113  378.2   5.0   2.9e-113  378.0   5.0    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.0   5.0  1.6e-117  2.9e-113       2     299 .]       5     309 ..       4     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 378.0 bits;  conditional E-value: 1.6e-117
                 HHHHHHHHHTEEEEEETTS-HHHHHH-SEEE-HHHHHHHCCC-SSSEEEEES-HHHHHHHHHHSTTSEEE-SSTT---HHHCT--HHHHHHHHHHSTTS CS
        NadA   2 eikelkkeknavilaHnYqedeiqeiadfvGDSleLarkaaeteaevivfcGVhFMaetakiLspekkvllpdleagCsladmitaeeveelkeelpda 100
                 +i+elkkek++vilaHnY+ +e+q+iadfvGDSl Lar+aa+t +++i+fcGVhFMaeta+i+spekkvl+pd++agCsl+d+i+ e+++++k+e+p+a
  AJA92450.1   5 KIEELKKEKDVVILAHNYEIPEVQDIADFVGDSLGLARQAAKTPHKTILFCGVHFMAETAAIISPEKKVLIPDTNAGCSLSDSINLEQLKKWKSEHPNA 103
                 89************************************************************************************************* PP

                 -EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS.-SEEEEES-HHHHHHHHHHH.SEEEEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS.... CS
        NadA 101 avvtYvNssaevKalsdivcTSsnavkvvealk.ekkilflPDqnLgryvakklgekkiilwkgaCsvHeefkaeeveelkeehpdakvlvHPEc.... 194
                 + v YvN++ae+K++ d++cTSsnav+vv+a++ +k+ilflPD +Lg+yvak +g+k++++w+g+C+vH+ +++++v+e  ++  +a++l+HPEc    
  AJA92450.1 104 IAVGYVNTTAEIKSELDYCCTSSNAVNVVKAIPdDKEILFLPDMFLGSYVAKMTGRKNMLIWAGECHVHAGITPDHVKEKLNSLANAEFLIHPECsctt 202
                 ********************************659**************************************************************** PP

                 .......-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSEEE.....ECSSSSSTTGGG--HHHHHHHHHHT-S.B----HHH CS
        NadA 195 .......keevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapekefialsaeaaeeavCetMkkitleklleaLeeleeeeikvdeev 286
                        + +  +++  + ST++++++vk+s+++ef+++Te+g+++r+kk++p+k+fi +    +e+a Ce+Mk+itlek++++L ++++  ++v++e+
  AJA92450.1 203 pmmydvaNGSYSSNQVQILSTEGMMNHVKNSKSNEFVVATETGILYRMKKQNPDKKFIPA----SEKAECEYMKMITLEKVYNSLLNETN-VVTVPKET 296
                 **999998899999999*****************************************33....33789****************99988.9******* PP

                 HHHHHHHHHHHHH CS
        NadA 287 aekAkkalermle 299
                 a+kA+ a+erml+
  AJA92450.1 297 ADKARLAIERMLA 309
                 ***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2124.71
//
Query:       AJA92451.1  [L=352]
Description: DegT/DnrJ/EryC1/StrS aminotransferase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-103  346.6   0.0   2.2e-103  346.4   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0015   17.9   0.2      0.011   15.0   0.2    2.0  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.039   12.5   0.0      0.063   11.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.14   11.5   0.0        0.2   11.1   0.0    1.2  1  PALP             Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.4   0.0  4.8e-107  2.2e-103       5     360 ..      13     347 ..       9     348 .. 0.93

  Alignments for each domain:
  == domain 1  score: 346.4 bits;  conditional E-value: 4.8e-107
                      HHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSS CS
  DegT_DnrJ_EryC1   5 eeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyn 98 
                      e  ea+ ++l+++ +  g+ v++FE++fa+y+g+k+a +vssG  Al+++L+alg+g+  +VI+p+++F+a+an+++ ++akp++ D+d d+  
       AJA92451.1  13 EMEEAAIHALRNESFVGGESVSKFEEEFAKYTGTKYAASVSSGNGALQISLMALGIGESHKVITPTNSFIASANCIRMTNAKPILTDIDMDDGG 106
                      566788899************************************************************************************* PP

                      B-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS.-SSS-EEEEESTHHHH CS
  DegT_DnrJ_EryC1  99 idpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnl.ttGeGGavvtndeela 191
                      id ++ e+ ++    aI+pVh+yG+++d+d++k  a+++++++ieDa++A+Ga+ykgkkvG+lgd+++fSFyptKn+   G+GG+ +t+dee+ 
       AJA92451.1 107 IDLSNNENNVN----AIIPVHIYGNPCDFDSVKSFAEEQKIPIIEDACQAHGAEYKGKKVGSLGDIGCFSFYPTKNMtVGGDGGMTTTDDEEIV 196
                      *******9996....9*************************************************************5568************* PP

                      HHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCC CS
  DegT_DnrJ_EryC1 192 ekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveee 285
                       k++ +r  G+k   +k+ + +  lG+ +rl+ ++AAig++qL++lde +arRrei+++y+++L +      l+++k+ k +++h++++  e  
       AJA92451.1 197 LKIKSIRDNGRK---TKNEFDK--LGFTMRLNTVNAAIGRVQLKHLDEKTARRREIVSIYRKNLVQDC---ILPENKDGK-SVYHQIVIKHE-- 279
                      **********98...3455555..5*************************************997733...356666665.89999999888.. PP

                      HHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
  DegT_DnrJ_EryC1 286 aevkrdelvealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                         krde+ ++l +++ig+ ++y++p+h+q +y+e   +   +lpn+e++++++lsLp+yp+lt++++ +++e +
       AJA92451.1 280 ---KRDEIRKELADNQIGSAIYYETPIHKQLIYQEFG-Y---ELPNSEKFSKKILSLPSYPQLTDDQALEICEHV 347
                      ...89*****************************996.4...49***************************9987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   2.5e-06     0.011      10     112 ..      10     110 ..       7     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-06
                      --HHHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE- CS
  Beta_elim_lyase  10 gteamsdaqaaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlk 102
                       t +m +a + a    es+ + ++v ++e+++a+++g+++a  v +G +A +i+l++l     ++vi   ++ i    +  +   + + l+d++
       AJA92451.1  10 FTVEMEEAAIHALR-NESFVGGESVSKFEEEFAKYTGTKYAASVSSGNGALQISLMALGiGESHKVITPTNSFIASANCIRMTNAKPI-LTDID 101
                      57788888877765.567777789*********************************9956666666666655555544444333333.55555 PP

                      EBTTTBE-HH CS
  Beta_elim_lyase 103 nkeaGkmdle 112
                       ++ G +dl 
       AJA92451.1 102 MDD-GGIDLS 110
                      555.656555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05     0.063      54     180 ..      33     155 ..      26     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                      HHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHH.HHHHHCCTTEEEEEEES CS
  Cys_Met_Meta_PP  54 rsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdle.elekaikentklvylEt 145
                      +s +ee+ a+  g++ a  vssG +A++ +++al + +  ++++ ++ +  + + ++ +  k  +  + +d++d   +l +  ++   ++ +  
       AJA92451.1  33 VSKFEEEFAKYTGTKYAASVSSGNGALQISLMALgIGESHKVITPTNSFIASANCIRMTNAKPIL--TDIDMDDGGiDLSNNENNVNAIIPVHI 124
                      6789***********************999999855667789999*******9999988877533..334444433144444444444555666 PP

                      S-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTT CS
  Cys_Met_Meta_PP 146 ptnpllkvvDiekiaklakkagvlvvvDntfaspl 180
                       +np    +D+ ++ ++a +++++++ D++ a ++
       AJA92451.1 125 YGNP----CDFDSVKSFAEEQKIPIIEDACQAHGA 155
                      6666....699999999999999999888877665 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05       0.2      52     149 ..      39     140 ..      17     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                 T....TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTH CS
        PALP  52 g....tgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygti 146
                 +    tg+k  +  ssGN ++ ++++a  +G    +  p ++  + +  +r+ +a+ ++++ d d+      + +++ + ++ v+ ++np  ++  ++ 
  AJA92451.1  39 EfakyTGTKYAASVSSGNGALQISLMALGIGESHKVITPTNSFIASANCIRMTNAKPILTDIDMDDGGIDLSNNENNVNAIIPVHIYGNPCDFDSVKSF 137
                 3455568899999***********************************************999999888888888888889999999988777777666 PP

                 HHH CS
        PALP 147 glE 149
                 + E
  AJA92451.1 138 AEE 140
                 665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2479.86
//
Query:       AJA92452.1  [L=99]
Description: 4a-hydroxytetrahydrobiopterin dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-28   96.7   0.1    7.6e-28   96.5   0.1    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
  ------ inclusion threshold ------
      0.073   13.2   0.0        0.1   12.7   0.0    1.3  1  IF-2       Translation-initiation factor 2


Domain annotation for each model (and alignments):
>> Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   8.4e-32   7.6e-28       2      91 .]       5      93 ..       4      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 8.4e-32
   Pterin_4a  2 klseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenDfklAakidel 91
                kls++eiq+ l+el+gW+  ++ +l++e++f+df  a++f++      +++nHhp+++++ynk+ + l+Thd+gg+++nD++lA+ +d++
  AJA92452.1  5 KLSDNEIQEGLRELNGWSV-QNGKLHKEIEFSDFDVAWNFMTIAVVEIQKMNHHPEWFNVYNKLVIDLMTHDVGGISQNDINLAKYLDKI 93
                89*********999****9.777****************************************************************986 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.2e-05       0.1      41      66 ..      66      91 ..      50      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                STEEEECEEEESSB-HHHHHHHHHST CS
        IF-2 41 evkvkvihsgvGaitesDvelasasn 66
                +  ++ + ++vG i+++D++la+  +
  AJA92452.1 66 KLVIDLMTHDVGGISQNDINLAKYLD 91
                56789999**************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 604.54
//
Query:       AJA92453.1  [L=460]
Description: ATP synthase alpha/beta chain, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-68  230.3   0.0    2.6e-68  229.9   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      8e-12   45.5   3.7    2.8e-11   43.8   3.1    2.2  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
    0.00094   19.3   0.8     0.0031   17.6   0.8    1.9  1  HAS-barrel     HAS barrel domain
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.32   11.5   0.0    1.4  1  DUF2779        Domain of unknown function(DUF2779)


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.9   0.0   5.8e-72   2.6e-68       1     213 []     135     353 ..     135     353 .. 0.97

  Alignments for each domain:
  == domain 1  score: 229.9 bits;  conditional E-value: 5.8e-72
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlvantsnepvaareasiytg 93 
                  G++v+D ++++v+Gq++ i++++g+ ++ +++++++q+       + a+++++iG + +e++ + ++++e++++kr+vl++n +++p+++r+++++++
   AJA92453.1 135 GVSVIDGMLTLVRGQKLPIFSGSGMSHNILAAQIARQAAIIgtddSfAVVFAAIGVQYSEAEYFKRSLEESGALKRSVLFLNLADDPAIERIITPRVA 232
                  899**********************************8543776558*************************************************** PP

                  HHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEE CS
                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  94 itlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgf 190
                  +t+AEy+++  g++vl+i+++++++aeAlreis++ +e+p+++gyp+yl+++l+++yERag+++ ++Gsvt+v++++++++D+++p+++ t +it+g+
   AJA92453.1 233 LTVAEYLAYdLGMHVLVILTDMTNYAEALREISAAREEVPGRKGYPGYLYTDLSTIYERAGRLRGKKGSVTQVPILTMPSDDITHPIPDLTGYITEGQ 330
                  *******9889*************************************************************************************** PP

                  EEB-HHHHHTTBSSSBCTTTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 191 ivLdkklaqrkhfPainvlvSvS 213
                  +vL ++l++++++P+in+l+S+S
   AJA92453.1 331 LVLGRDLFRQGVYPPINILMSLS 353
                  *********************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   3.1   6.2e-15   2.8e-11       1      69 []      12      78 ..      12      78 .. 0.87
   2 ?   -1.6   0.0      0.89     4e+03      33      48 ..     423     438 ..     413     439 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.2e-15
                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                   i ++ Gp+v+v+++     + ++++e+e +e g+ +lg +l++g++k++v+v+++t+Gls+ Gt  k+ G
     AJA92453.1 12 IAEIKGPLVIVDGVDN--AAFDELVEIETTE-GERRLGKVLEVGNGKAVVQVFEGTTGLSVaGTNAKFVG 78
                   6789*******77778..6666666666669.********************************999976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.89
                    STEEEEEEEEEETTEE CS
  ATP-synt_ab_N  33 gtlllgvalnlgedkV 48 
                    ++ ++++ l+l+ ++V
     AJA92453.1 423 ENRTIEETLGLQWNCV 438
                    6899999999998887 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8     7e-07    0.0031      11      88 ..      16      78 ..       9      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7e-07
  HAS-barrel 11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt........gvkvlG 88
                 ++++ v+g+ +  + e+Veie+++ge++lG+v+ + +                       + +v++++e+t        ++k +G
  AJA92453.1 16 KGPLVIVDGVDNAAFDELVEIETTEGERRLGKVLEVGN-----------------------GKAVVQVFEGTtglsvagtNAKFVG 78
                688999***99***************************.......................7888888887776555555555555 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.32      39      88 ..     361     437 ..     339     458 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
     DUF2779  39 v......ehkeflaespntdpreelieeLikiieke......gsvvvynksfEksrlkela...............q 88 
                        +h+e+ +++ +   r + +++L+ i++k         ++ + ++fEk+ l + +                
  AJA92453.1 361 GegstraDHQEISNQNYDAYSRAQEVRALAGIVGKAgltpvdLNYMNFGDEFEKKFLTQAIdenrtieetlglqwnC 437
                 24455669*************************99999999999*************99986666666666666652 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3262.55
//
Query:       AJA92454.1  [L=529]
Description: lysine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-106  356.6   0.0   1.8e-106  356.1   0.0    1.1  1  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.011   14.5   1.1      0.083   11.6   0.0    2.4  3  tRNA-synt_1g     tRNA synthetases class I (M)
      0.042   13.9   0.8        6.4    6.9   0.1    2.8  2  THUMP            THUMP domain
      0.056   11.7   0.0       0.11   10.7   0.0    1.5  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
       0.08   12.7   0.5       0.24   11.2   0.1    2.0  2  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym
       0.15   11.4   0.0       0.29   10.4   0.0    1.5  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.1   0.0  5.9e-110  1.8e-106       2     349 ..      11     367 ..      10     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 356.1 bits;  conditional E-value: 5.9e-110
  tRNA-synt_1f   2 aWadklaeklieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpekllekylgkpltsi 97 
                   +W+dkla +li er+k+   ++  + vesG+++SG +HiG+l++ ++a+ v  al+++g + +li++sDd+DglRk+p+ +p++ le+++gkp++ i
    AJA92454.1  11 TWIDKLASELI-EREKQLGrDTSLIRVESGLGASGIPHIGSLGDAVRAYGVKLALENMGYKSELIAYSDDLDGLRKIPAGFPDS-LEEHIGKPVSLI 105
                   6**********.55555555999*************************************************************.************ PP

  tRNA-synt_1f  98 PdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyrgeereetyspylpvcekcgrvdttevvevdae 194
                   Pd  g+hesy++ ++++l++ L++lgie++f++a+++Yk+gl++e+i+++l ++e+i + +e   g+e+ ++++py pvc +c+r+  +e++e+  +
    AJA92454.1 106 PDHTGEHESYGMNMSSRLLDGLEKLGIEYTFKRARDTYKEGLLQEQIHTILTQSERIGAKIEDLVGQEKYQKFLPYFPVCAQCSRLYVAEATEYLPD 202
                   ************************************************************************************************* PP

  tRNA-synt_1f 195 eeeieYkc..........eecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkgge 280
                   e++++Ykc          + cG+e+e+di++  gKL Wkv++a+rW+a++++fE++GkD+++   Sv+v++++a ++l++++P+++ Ye++l+kgg+
    AJA92454.1 203 ERKVRYKCcdaeiggkkiKGCGYEGEADIKKDLGKLAWKVEFAARWSAFDIRFEAYGKDIMD---SVKVNDWVAdDVLNFPHPHHIKYEMFLDKGGK 296
                   **************************************************************...******************************** PP

  tRNA-synt_1f 281 kmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf....aeqeeeeek 349
                   k+s+S Gnv+t + wl++++pe++ +l+++ +++ a +l ++ +i++l+deY++le+++f     ++e++  k
    AJA92454.1 297 KISKSLGNVVTSQTWLKFGTPESILLLLYK-RITGARELGFE-DIPSLMDEYNELEKIFFgkikLDNEAKLVK 367
                   ******************************.***********.*****************6654333344444 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.21   6.1e+02      73     145 ..     122     194 ..     111     214 .. 0.61
   2 ?    0.4   0.3     0.072   2.1e+02     118     159 ..     188     227 ..     182     243 .. 0.79
   3 ?   11.6   0.0   2.8e-05     0.083     308     353 ..     278     323 ..     243     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.21
                   HHHHHHHHTT---SEEEETTSHHHHHHHH.HHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........ CS
  tRNA-synt_1g  73 eikelfkklnisfdkygrttseehkelvq.eifkklkekgliyekeieqlycpkderflpdryvegtCPkckse 145
                   +  + ++kl+i+++ ++r+ ++ ++ l q +i + l++ + i  k    +  +k ++flp   v  +C     +
    AJA92454.1 122 RLLDGLEKLGIEYT-FKRARDTYKEGLLQeQIHTILTQSERIGAKIEDLVGQEKYQKFLPYFPVCAQCSRLYVA 194
                   55566677777774.66666666665554146666666677777777777777777777776666666544433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.072
                   EEEEEETTTTEEE-G.GG-EE........-TTS-EE-TTSSB- CS
  tRNA-synt_1g 118 ieqlycpkderflpd.ryvegtCPkckseeargdqceecgkkl 159
                    + ly  ++ ++lpd r v+ +C  c  +e  g++++ cg + 
    AJA92454.1 188 CSRLYVAEATEYLPDeRKVRYKC--CD-AEIGGKKIKGCGYEG 227
                   678999********946699999..66.457788888888665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2.8e-05
                   T----S-EEEE--EEE--------------HHHHHHHH-HHHHHHH CS
  tRNA-synt_1g 308 elklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYy 353
                   ++  p+++  + +l   gkK+SkS g+vv+ +++l+  +++ +   
    AJA92454.1 278 NFPHPHHIKYEMFLDKGGKKISKSLGNVVTSQTWLKFGTPESILLL 323
                   678999****************************998766665555 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0099        30      61     110 ..     225     274 ..     196     278 .. 0.91
   2 ?    6.9   0.1    0.0021       6.4      49     113 ..     456     529 .]     389     529 .] 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0099
                 ESSHHHHHHHHHHHHHHHHHHCT-.EEEEEEEESSSTSSSHHHHHHHHHHH CS
       THUMP  61 eadledileaakeivkkkfeeeke.tFaVrvkrrgkhfeftsreinrevGk 110
                 +++  di++   ++ +k  ++     F +r+++ gk+  ++s+++n+ v++
  AJA92454.1 225 YEGEADIKKDLGKLAWKVEFAARWsAFDIRFEAYGKD-IMDSVKVNDWVAD 274
                 667889**************98779************.********99887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0021
                 TECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS..........SSHHHHHHHHHHHHHH CS
       THUMP  49 giqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhf..........eftsreinrevGkaiv 113
                  ++++i+v  ++  ++ed+ + +++i k   +e+k  F+V      ++           ++++++++ ++Gk+++
  AJA92454.1 456 ALSKLIIV-LEKDGEIEDLQNEIYQIAKGDDIEPKDFFKVLYQIILSTTrgpkigpfilDIGKKNVAEKIGKYVK 529
                 45566666.999****************************99999999999999******************985 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0      0.83   2.5e+03     107     145 ..     115     153 ..     111     158 .. 0.77
   2 ?   10.7   0.0   3.8e-05      0.11     547     579 ..     281     313 ..     248     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.83
  tRNA-synt_1 107 wkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavke 145
                  + ++++++  + +++lG+ + f+r + T +++l + +++
   AJA92454.1 115 YGMNMSSRLLDGLEKLGIEYTFKRARDTYKEGLLQEQIH 153
                  556667777778899***********9999998665554 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.8e-05
  tRNA-synt_1 547 fkevlvhglvrdeeGrKmSKslgNvidpldvik 579
                  + + +   + +d+ G+K+SKslgNv+ +++ +k
   AJA92454.1 281 HPHHIKYEMFLDKGGKKISKSLGNVVTSQTWLK 313
                  55556667889***************9987665 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.2   3.7e+03      28      37 ..     346     355 ..     346     356 .. 0.84
   2 ?   11.2   0.1   7.9e-05      0.24      26      62 ..     391     427 ..     388     429 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
  PolyA_pol_RNAbd  28 feEllKlLls 37 
                      ++El+K++ +
       AJA92454.1 346 YNELEKIFFG 355
                      68*****986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.9e-05
  PolyA_pol_RNAbd  26 RifeEllKlLlsghpeaglelLretgLlkylfPelaa 62 
                      R+  El K++ +++ ++  ++L+++ ++k   Pe+++
       AJA92454.1 391 RLLLELSKIFKEDRISRINKKLVDYRAIKETSPEIDR 427
                      9999**************************99*9975 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   9.6e-05      0.29     246     282 ..     290     326 ..     244     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.6e-05
                   -EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
  tRNA-synt_1e 246 hlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                   +l   g+k+sksL+n++t +  lk  +p+ + lll++
    AJA92454.1 290 FLDKGGKKISKSLGNVVTSQTWLKFGTPESILLLLYK 326
                   5666799*****************9999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3779.04
//
Query:       AJA92455.1  [L=139]
Description: secondary thiamine-phosphate synthase enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-37  127.7   0.0    2.6e-37  127.5   0.0    1.0  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   0.0   1.4e-41   2.6e-37       1     115 []      20     136 ..      20     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 1.4e-41
                 E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT...T-GGGTTS..THHHHHHHHHH-SEEEEEEETTEE---TTE CS
     UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee...eYrhnaegpdnadaHlkssllgssltipvedgklalGtwq 96 
                 +it++ve++v +sg+keGl+lv ++h tas++in+n ++++++D+e++le+l+p+e   +Yrhn+ g+dnadaHlk+ ++g+++++ +++g+l++G w+
  AJA92455.1  20 NITPDVEKLVVKSGIKEGLCLVNAMHITASVFINDN-ESGLHHDYEKWLEELAPHEpidHYRHNDTGEDNADAHLKRQVMGREVVVAITNGQLDFGPWE 117
                 69**********************************.******************9999*****99********************************* PP

                 EEEEEESS-SSEEEEEEEE CS
     UPF0047  97 siylveldgpreRkvvvqv 115
                  i++ e+dg+r+++v+v++
  AJA92455.1 118 TIFYGEFDGRRNKRVLVKI 136
                 ***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1101.48
//
Query:       AJA92456.1  [L=281]
Description: lysine biosynthesis enzyme LysX [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-32  112.2   0.0    3.4e-32  111.6   0.0    1.3  1  RimK            RimK-like ATP-grasp domain
    2.7e-06   26.9   0.0    3.5e-06   26.5   0.0    1.2  1  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    4.1e-06   26.9   0.0    6.4e-06   26.3   0.0    1.3  1  ATP-grasp_3     ATP-grasp domain
    8.6e-05   22.1   0.0    0.00019   21.0   0.0    1.6  1  CPSase_L_D2     Carbamoyl-phosphate synthase L chain, ATP bin
     0.0024   17.2   0.1       0.14   11.4   0.0    2.8  3  ATPgrasp_ST     Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.026   14.1   0.0    1.5  1  ATP-grasp       ATP-grasp domain
      0.018   14.6   0.0      0.027   14.0   0.0    1.3  1  Synapsin_C      Synapsin, ATP binding domain
      0.021   14.1   0.0       0.52    9.5   0.0    2.4  3  ATPgrasp_YheCD  YheC/D like ATP-grasp
      0.096   12.1   0.0       0.19   11.1   0.0    1.4  1  ATP-grasp_5     ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.6   0.0   1.7e-35   3.4e-32       1     187 [.      86     276 ..      86     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 1.7e-35
                 HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.....GGG--....EEEEE--SS-SEEE CS
        RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.....lkeai....lvqeyieeaenedi 90 
                 a +Kl ++ lL ka++++p +++a +++ a + +ek   +fP ++K   gs G  v   ++ ++++ ++e+         i    ++ e+++    +di
  AJA92456.1  86 AGNKLFTHMLLQKAGVPTPDATVAFSKDSALEALEKH--GFPKIIKPTVGSWGRMVSKLNDMDAAEGIIEGreamyP---IhhihFLEEFVQR-PPRDI 178
                 569999******************************9..6*******************************553331...2222455566653.349** PP

                 EEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEET.TEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
        RimK  91 RvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrak.rgllvlEvnsspglekiektlgidiakkliea 187
                 Rv+v++d+v a++ r s +G++++n h+Gg ae  ++++e++++ ika +a+  +++G+Dl++++ +gl+v E+n   + +++ + +g+di k ++e 
  AJA92456.1 179 RVIVIGDNVAAGIYRNSGDGNWKTNTHLGGSAETCEITKELEDICIKAKDAVFGDIVGIDLMESNeKGLVVHEINNTTEFRNVVRVTGVDIPKLMLEH 276
                 ************************************************************999763789999*******************9999875 PP

>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.8e-09   3.5e-06      12     154 ..     103     242 ..      88     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.8e-09
                 S--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTT..TS-EEEEE--GGGGG-EEEEEEETTEE-SEEEEEE--SS CS
   GSH-S_ATP  12 ipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksilellteeg..kepviaqrylpeikeGDkRillvdGepigyalaRvpaeg 107
                 +p++ v+ +k++  + le++g   i+KP  g+ G+ v ++++ d+  + i+e   ++   ++   + ++++   + D R++++ G+ + + + R + +g
  AJA92456.1 103 TPDATVAFSKDSALEALEKHGFpKIIKPTVGSWGRMVSKLNDMDAA-EGIIEGREAMYpiHHIHFLEEFVQRPPR-DIRVIVI-GDNVAAGIYRNSGDG 198
                 567777776666666666666559****************998765.5666655444311334456677776665.9**9998.566666********* PP

                 -S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
   GSH-S_ATP 108 evRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                 + ++n + gg+ae+ e+t++ + i+ + ++++  +   +vG+D++++
  AJA92456.1 199 NWKTNTHLGGSAETCEITKELEDICIKAKDAVFGD---IVGIDLMES 242
                 *************************9998887765...688888764 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.2e-09   6.4e-06       1     155 [.      86     253 ..      86     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.2e-09
                  HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE. CS
  ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvsllsd 82 
                  a +Kl+t   L++agv++P       +    e le+   + ++Kp  G+ g  v++ ++ ++ae +ie  e          + ef++  p  + +++ 
   AJA92456.1  86 AGNKLFTHMLLQKAGVPTPdatvafsKDSALEALEKHGFPKIIKPTVGSWGRMVSKLNDMDAAEGIIEGREamypihhihFLEEFVQRPPRDIRVIVI 183
                  579****************9988776555666667778999***********************9999888999*9999999******9999999996 PP

                  SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEE CS
  ATP-grasp_3  83 gekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd.eepyviEvN 155
                  g +++   + r+  + ++k +   G++++   e ++e+++++ ++  ++     +vG+Dl+ ++ ++++v E+N
   AJA92456.1 184 G-DNVAAGIYRNSGDGNWKTNTHLGGSAETC-EITKELEDICIKAKDAV--FGDIVGIDLMESNeKGLVVHEIN 253
                  5.788889999999999999******99987.78999999999999999..6679******7765899999**9 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   9.3e-08   0.00019       7     109 ..      94     192 ..      88     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.3e-08
                  HHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SS.SEEEEEEEEEET CS
  CPSase_L_D2   7 ealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkg.pkeiEvevlrDa 103
                   +l+k++vp+ +++ a   + + al++ +++g+P iik+++g  G+     ++ +  + +++   a+ +    ++  ++e+++++ p++i v v+ D+
   AJA92456.1  94 MLLQKAGVPTPDATVA--FSKDSALEALEKHGFPKIIKPTVGSWGRMVSKLNDMDAAEGIIEGREAMYP---IHHIHFLEEFVQRpPRDIRVIVIGDN 186
                  57899*****999999..999*******************99988866666666655555554333332...355569*****98459*********9 PP

                  TS-EEE CS
  CPSase_L_D2 104 kgnvit 109
                      i+
   AJA92456.1 187 VAAGIY 192
                  876665 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   7.1e-05      0.14      20      84 ..      87     147 ..      78     162 .. 0.86
   2 ?   -0.5   0.0      0.29   5.9e+02     128     181 ..     162     208 ..     157     218 .. 0.71
   3 ?    1.9   0.1     0.055   1.1e+02     229     266 ..     220     256 ..     213     267 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.1e-05
  ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitered 84 
                   +Kl +  l+++ag+++p+  + +++ + +++le+  +++++  +iKp+ gs+G+ ++++++++ 
   AJA92456.1  87 GNKLFTHMLLQKAGVPTPDATVAFSKDSALEALEK--HGFPK--IIKPTVGSWGRMVSKLNDMDA 147
                  69*****************9999999988888887..46655..9************99988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
  ATPgrasp_ST 128 kqdpeleklspesvntiRvitflkdkkvevmlamlRlgtkaskvDgkaNlhqGg 181
                  +  + le++      +iRvi++    + +v   + R + +++    k N h Gg
   AJA92456.1 162 HHIHFLEEFVQRPPRDIRVIVI----GDNVAAGIYRNSGDGN---WKTNTHLGG 208
                  5555666666666679*****9....5555556777777777...456887776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.055
  ATPgrasp_ST 229 lelaakaaeklpglgylGwDivldeekgplllElNarp 266
                   +++ ka +  +   ++G+D+   +ekg+++ E+N++ 
   AJA92456.1 220 EDICIKAKD-AVFGDIVGIDLMESNEKGLVVHEINNTT 256
                  567777777.5556799*****************9875 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.026       1      72 [.      96     171 ..      96     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                 HHTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.....GTTCEEEEE-- CS
   ATP-grasp   1 leklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.....keekvivEefv 72 
                 l+k+g+p+p+ +++ sk+++ ea+e+ g+p ++K +++g+ G+  s +++ + +e ++e        ++   +Eefv
  AJA92456.1  96 LQKAGVPTPDATVAFSKDSALEALEKHGFPKIIK-PTVGSWGRMVSKLNDMDAAEGIIEGReamypIHHIHFLEEFV 171
                 5899******************************.********9999999988888887664444444444455555 PP

>> Synapsin_C  Synapsin, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-05     0.027      99     129 ..     176     210 ..     158     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
  Synapsin_C  99 ydirvqkigsnyka.ymrtsisgnwkant...gsa 129
                  dirv  ig+n  a   r s  gnwk+nt   gsa
  AJA92456.1 176 RDIRVIVIGDNVAAgIYRNSGDGNWKTNThlgGSA 210
                 69*********99834699*********9443444 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00026      0.52      11      72 ..      88     147 ..      77     182 .. 0.70
   2 ?    1.9   0.0     0.055   1.1e+02     140     167 ..     187     214 ..     171     229 .. 0.79
   3 ?   -1.4   0.0      0.57   1.1e+03     206     226 ..     234     254 ..     204     266 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00026
  ATPgrasp_YheCD  11 nKwevyelLskdpelrpyLPetellesledleemlekyks.vylKpanGskGkgilriekeek 72 
                     nK  ++ lL+k     p   +t+ + s+++  e lek+++  ++Kp+ Gs G+ + +++ +++
      AJA92456.1  88 NKLFTHMLLQKAG--VPTPDATVAF-SKDSALEALEKHGFpKIIKPTVGSWGRMVSKLNDMDA 147
                     4555555555544..4444467777.99999999*****988***************998333 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.055
  ATPgrasp_YheCD 140 vtgiaaRiagkgsittnlsrGGtalple 167
                     v++ + R +g+g+  tn + GG+a + e
      AJA92456.1 187 VAAGIYRNSGDGNWKTNTHLGGSAETCE 214
                     66778899***************98765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.57
  ATPgrasp_YheCD 206 ElGlDlgidkegkvWllEvNs 226
                      +G+Dl+  +e+ + + E+N 
      AJA92456.1 234 IVGIDLMESNEKGLVVHEINN 254
                     369999988888898888885 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.6e-05      0.19      16      52 ..      93     129 ..      88     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
  ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlK 52 
                  + ll+  g+p+++  +a s+++a+ea e+ g+p  +K
   AJA92456.1  93 HMLLQKAGVPTPDATVAFSKDSALEALEKHGFPKIIK 129
                  5699*****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2064.08
//
Query:       AJA92457.1  [L=207]
Description: methionine biosynthesis protein MetW-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-16   59.8   0.0    9.3e-16   58.3   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    1.3e-15   57.6   0.0    1.7e-15   57.2   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.4e-15   57.4   0.0    1.6e-15   57.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.2e-14   53.4   0.0    5.3e-14   52.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    5.7e-12   46.2   0.0    8.6e-12   45.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-08   34.2   0.1    2.8e-08   33.1   0.0    1.5  2  Methyltransf_9   Protein of unknown function (DUF1698)
    2.7e-08   33.7   0.0    3.5e-08   33.3   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    2.9e-08   33.4   0.0      9e-06   25.3   0.0    2.2  2  Methyltransf_4   Putative methyltransferase
    8.3e-08   31.8   0.0      1e-07   31.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    4.3e-06   26.4   0.1    5.2e-05   22.9   0.1    2.0  2  DOT1             Histone methylation protein DOT1
    1.8e-05   24.4   0.0    3.1e-05   23.6   0.0    1.3  1  MTS              Methyltransferase small domain
      5e-05   22.7   0.2    0.00024   20.5   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.2e-05   22.8   0.0    8.1e-05   22.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0001   22.0   0.0    0.00019   21.1   0.0    1.4  2  MetW             Methionine biosynthesis protein MetW
     0.0016   18.4   0.0     0.0025   17.8   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0018   17.5   0.1     0.0074   15.4   0.1    1.9  1  Pox_MCEL         mRNA capping enzyme
     0.0029   17.0   0.0     0.0046   16.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0031   17.5   0.0     0.0051   16.8   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0039   16.3   0.0     0.0056   15.8   0.0    1.2  1  DREV             DREV methyltransferase
     0.0078   15.7   0.0        1.2    8.6   0.0    2.5  2  CheR             CheR methyltransferase, SAM binding domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.032   13.7   0.0    1.6  2  Methyltransf_5   MraW methylase family
      0.022   13.8   0.0      0.025   13.7   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.023   15.0   0.0      0.064   13.6   0.0    1.8  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
      0.028   13.7   0.0       0.49    9.6   0.0    2.1  2  Methyltransf_2   O-methyltransferase domain
      0.079   12.4   0.0       0.11   11.9   0.0    1.2  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.3e-18   9.3e-16       2      97 .]      44     134 ..      43     134 .. 0.90
   2 ?   -2.0   0.0       8.4     6e+03      75      89 ..     161     175 ..     155     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.3e-18
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG.SSHHHHHHHHHHHHHHEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh.lsdedlekalkeiarvLk 94 
                      Ld+GcG+G ++++++++ +  k +g+D s+ m+++a++++++   + +f + d+e+++ ++ +fD+++s+ +l + ++   +e al++++++Lk
       AJA92457.1  44 LDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISS--TRESFFVTDLESWNTKE-KFDVIFSMESLYYsVP---MEPALEKVFKLLK 131
                      9****************669********************64..599**********9775.*******877877344...689********** PP

                      EEE CS
  Methyltransf_25  95 pgG 97 
                      +gG
       AJA92457.1 132 KGG 134
                      **9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.4
                      GGSSHHHHHHHHHHH CS
  Methyltransf_25  75 hhlsdedlekalkei 89 
                       + s+++++k+++ei
       AJA92457.1 161 DLRSEKEWKKMFREI 175
                      566789999999998 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.4e-18   1.7e-15      11     162 ..      30     179 ..      15     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.4e-18
  Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeq..eaaepqgkfdlIvlrevlehvpdppe 100
                      ++l++l+  l+++ r LdiGcG G + + +++++   + +g+D s ++++ a++++ +  ++f+    e ++ ++kfd+I ++e+l+   +++ 
       AJA92457.1  30 QFLDKLS--LKEKFRFLDIGCGNGWVVRKMSQKPScvKAIGIDKSKMMIKNAKSKISSTRESFFVTdlESWNTKEKFDVIFSMESLYYSVPMEP 121
                      5566666..78888****************9985448****************9999999999888445566888******************* PP

  Methyltransf_23 101 llrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGlev 162
                      +l ++++llk gG +++ +     ++d+ l   +   +++  + + s++++k++++e G++ 
       AJA92457.1 122 ALEKVFKLLKKGGTFYCGTDF---YSDNTLTTRWV-KDMNIPMDLRSEKEWKKMFREIGFTT 179
                      *****************9984...55555443222.3333557999**************86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.3e-18   1.6e-15       3     111 ..      39     140 ..      37     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.3e-18
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkilee 96 
                      ++ r+lD+GCG+G  + ++  +  +  + +GiD s+ +i+ A+++ +   +++ +F + d e+ +++   ekfD+i+s e l++   ++ +le+
       AJA92457.1  39 EKFRFLDIGCGNGWVVRKMS-QKPSCVKAIGIDKSKMMIKNAKSKIS---STRESFFVTDLESWNTK---EKFDVIFSMESLYYSVPMEPALEK 125
                      56789***************.6678899****************655...88999********8854...9*********************** PP

  Methyltransf_31  97 iervlkpggillied 111
                      ++++lk+gg + + +
       AJA92457.1 126 VFKLLKKGGTFYCGT 140
                      **********99743 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   7.4e-17   5.3e-14       1      96 []      44     138 ..      44     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 7.4e-17
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                      Ld+GcG+G +++++ ++    + +g+D sk m+k ak+k+s  +   +f v d+e+ + ++ +fD+++s e+l +   +e al+++ ++Lk+gG
       AJA92457.1  44 LDIGCGNGWVVRKMSQKPscVKAIGIDKSKMMIKNAKSKISSTR--ESFFVTDLESWNTKE-KFDVIFSMESLYYSVPMEPALEKVFKLLKKGG 134
                      8**************66667**********************99..579******987666.**************99**************** PP

                      EEEE CS
  Methyltransf_11  93 llvi 96 
                      ++++
       AJA92457.1 135 TFYC 138
                      *986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   1.2e-14   8.6e-12       1      99 []      44     136 ..      44     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.2e-14
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L+iGcG+G ++r + +k + ++ +g+D s+ +i++ak k+++ + +++ + +le  +       ++fD++++ + l +  +++ +l+++ klLk
       AJA92457.1  44 LDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISSTR-ESFFVTDLESWNTK-----EKFDVIFSMESLYYSVPMEPALEKVFKLLK 131
                      8********************************99999999888.57777888888754.....49**************************** PP

  Methyltransf_12  95 pgGrl 99 
                      +gG +
       AJA92457.1 132 KGGTF 136
                      ***75 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   3.8e-11   2.8e-08     114     215 ..      37     136 ..      25     149 .. 0.75
   2 ?   -2.3   0.1       2.2   1.6e+03      92     111 ..     156     175 ..     152     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.8e-11
                     -TT-.EEEEET-TTSHHHHHHHHCT.-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG-S-HHH.HHHHH CS
  Methyltransf_9 114 lkgr.tildvGcgnGyhlwrmvgeg.aklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyhrrsPld.hllql 205
                     lk++ + ld+GcgnG+ + +m  +     ++Gid s++ +   +a  k++ ++++++     +e  ++ e fd++fsm  ly+   P++  l ++
      AJA92457.1  37 LKEKfRFLDIGCGNGWVVRKMSQKPsCVKAIGIDKSKMMIK--NAKSKIS-STRESFF-VTDLESWNTKEKFDVIFSMESLYYS-VPMEpALEKV 126
                     5555368********99888876641456899999987654..5656666.4444444.4799*******************85.6776378899 PP

                     HCTEEEEEEE CS
  Methyltransf_9 206 kdqlvkgGel 215
                      + l+kgG++
      AJA92457.1 127 FKLLKKGGTF 136
                     9999999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                     EEE--SEEHHHHHHHHGGGS CS
  Methyltransf_9  92 vdidteWrsdwkWdrvlphl 111
                     ++i  + rs+  W+++ + +
      AJA92457.1 156 MNIPMDLRSEKEWKKMFREI 175
                     67888999999999987776 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   4.9e-11   3.5e-08      46     146 ..      42     140 ..      17     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 4.9e-11
        NodS  46 dalevGcaaGalterla..pyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdgql 142
                   l++Gc  G +  +++  p c +   +d  +  i+ a+ ++   +  s+ v+d++  +t+ekfd+i   e lyy    + +  a++ + +ll+ +g++
  AJA92457.1  42 RFLDIGCGNGWVVRKMSqkPSCVKAIGIDKSKMMIKNAKSKISS-TRESFFVTDLESWNTKEKFDVIFSMESLYY---SVPMEPALEKVFKLLKKGGTF 136
                 579***********998446788889999999**********99.677999************************...57899***************9 PP

        NodS 143 vfGs 146
                   G+
  AJA92457.1 137 YCGT 140
                 8886 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.3e-08     9e-06       4      48 ..      42      86 ..      39     101 .. 0.92
   2 !    6.3   0.0    0.0084         6      98     131 ..     121     157 ..     117     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-08
                    EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHC CS
  Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieal 48
                     +l+iGcG+G+++ ++++k   ++ +Gi++++ +++++ +ki   
      AJA92457.1 42 RFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISST 86
                    699************************************999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0084
                     HHHHHHHHHEEEEEEEEEEES...HHHHHHHHHHHHH CS
  Methyltransf_4  98 ellkelarvLkkgGvlelaTD...veeyaeemlkvle 131
                       l+++ + LkkgG ++  TD   ++ ++ + +k ++
      AJA92457.1 121 PALEKVFKLLKKGGTFYCGTDfysDNTLTTRWVKDMN 157
                     5689999**************6555556666666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.4e-10     1e-07      42     176 ..      19     150 ..      11     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.4e-10
                 -HHHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH-.-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGG CS
        CMAS  42 tLeeAqlaKldlileklelkpGmtlLdiGcGWGslvrraveryd.vkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafeh 139
                 ++e+   + ++  l+kl+lk+  + LdiGcG G +vr++ ++   vk +g+  Sk   k ak ++ ++   ++  v+ l+  + +ek+d + s++ +  
  AJA92457.1  19 EMEKGHGTTVNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPScVKAIGIDKSKMMIKNAKSKISSTR--ESFFVTDLESWNTKEKFDVIFSMESLYY 115
                 5666667778999**************************998433888888888888888888887655..666666555557899*******998754 PP

                 TSGGGHHHHHHHHHHHS-TT-EEEEEEEEE--HHHHH CS
        CMAS 140 vgkenydtffkklkkllkedGllllhtitslhkkela 176
                       +   +k++kllk++G++   t +  +++ ++
  AJA92457.1 116 S--VPMEPALEKVFKLLKKGGTFYCGTDFYSDNTLTT 150
                 3..3345567888889999998887776665555444 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   7.3e-08   5.2e-05      30      87 ..      27      84 ..      22     103 .. 0.84
   2 ?    3.3   0.0     0.073        52     102     169 ..      82     150 ..      78     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.3e-08
                HHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHH CS
        DOT1 30 flsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqke 87
                 ++++ldk+ lk++  F+D+G G G vv +++ +  c +++G+++++   + a+++ +
  AJA92457.1 27 TVNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKIS 84
                6889****************************************99887776666544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.073
                 -EEEESS-S.TT-HHHHHHGGG-SEEE.E--TT--HHHHHHHHHHHTT--TT-EEEESS-SS-TT----S CS
        DOT1 102 kiefirksF.venekveeiieeadvil.vNNfaFdaelnkqlkellqdlkegtkiislkslvpskykins 169
                 ki+ +r+sF v++ +  +  e+ dvi+ +    +   ++ +l+++++ lk+g+      ++ +++   ++
  AJA92457.1  82 KISSTRESFfVTDLESWNTKEKFDVIFsMESLYYSVPMEPALEKVFKLLKKGGTFYCGTDFYSDNTL-TT 150
                 56666666614455566788899***94466778999***************988888887776654.44 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.4e-08   3.1e-05      23     102 ..      31     108 ..      21     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.4e-08
                 HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
         MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                 +l++l+ +++ + lD+GcG+G +  ++ ++ + ++   +d++++ ++ ak  +++++   +++ +d+ +  +++kfd+i 
  AJA92457.1  31 FLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISSTR--ESFFVTDLESWNTKEKFDVIF 108
                 677788888888***************************************999888..58999999999999*****96 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   3.3e-07   0.00024      44     151 ..      36     138 ..      22     143 .. 0.82
   2 ?   -0.4   0.0      0.85   6.1e+02      27     214 ..     160     178 ..     146     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.3e-07
                      -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHH CS
  Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLk 137
                      + k+  ++lD+ +G g +  k+s++  +  k +++D +++m+k ++ k+  +      f +++ e  + +++ fDv+     l     ++ aL+
       AJA92457.1  36 SLKEKFRFLDIGCGNGWVVRKMSQK-PSCVKAIGIDKSKMMIKNAKSKISSTR---ESFFVTDLESWN-TKEKFDVIFSMESLYYSVPMEPALE 124
                      4567779*********888777765.5678999**************997654...457777776665.567899998888898889999**** PP

                      HHHHHEEEEEEEEE CS
  Ubie_methyltran 138 eayrvlkpGGrlvv 151
                      ++++ lk GG++++
       AJA92457.1 125 KVFKLLKKGGTFYC 138
                      ************99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.85
                      HHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
  Ubie_methyltran  27 lslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                      + l+  + Wkk                                                                                   
       AJA92457.1 160 MDLRSEKEWKK----------------------------------------------------------------------------------- 170
                      55555555555................................................................................... PP

                      EEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEE CS
  Ubie_methyltran 121 tvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllakdldsyryLvesirafPdqetlkeliedaGfk 214
                                                                                                            ++++ Gf+
       AJA92457.1 171 --------------------------------------------------------------------------------------MFREIGFT 178
                      ......................................................................................55555554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-07   8.1e-05      61     123 ..      27      88 ..      18     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                 HHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTC.EEEEEESBHHHHHHHHHHHHHCTT CS
        PCMT  61 mvalalellelkkgarvLevGsGsGyltavlarlvgekg.rvvsierikelveeakrnlkkldl 123
                 +v  +l+ l+lk++ r L++G+G G+    +++   +++ ++++i+++k ++++ak ++     
  AJA92457.1  27 TVNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQK--PSCvKAIGIDKSKMMIKNAKSKISSTRE 88 
                 5667889999***************977766664..444479***************9987654 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.6e-07   0.00019      12      81 ..      38     109 ..      30     132 .. 0.83
   2 ?   -3.1   0.0       6.8   4.9e+03     133     174 ..     148     191 ..     144     200 .. 0.54

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-07
        MetW  12 kpgsrvldlGcGdGellellkee.kqvdgrGleldeegvaecvakGlsviqgdldkdlenfedk.sfdyvvl 81 
                 k++ r ld+GcG+G +++ + ++   v++ G+++++  ++++ +k  s  +    +dle ++ k +fd++  
  AJA92457.1  38 KEKFRFLDIGCGNGWVVRKMSQKpSCVKAIGIDKSKMMIKNAKSKISSTRESFFVTDLESWNTKeKFDVIFS 109
                 67889*********999877554167*******************999999999*****9986527998754 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.8
        MetW 133 lPyeWydtpni..hlltikdfvelceelnlkvedrvaldekgrk 174
                 l  +W +  ni   l + k++ ++ +e++++  ++ + d k+++
  AJA92457.1 148 LTTRWVKDMNIpmDLRSEKEWKKMFREIGFTTRSKHVTDPKNKS 191
                 55556666665222345555666666666666555555555544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.5e-06    0.0025      14      61 ..      39      86 ..      30     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
  Methyltransf_18 14 kgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakenieka 61
                     ++ r++DiG+  g +  ++ ++  + k+i +D ++  +++ak++i+++
       AJA92457.1 39 EKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISST 86
                     55689***************************************9875 PP

>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     1e-05    0.0074      52     111 ..      29      87 ..      26     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
    Pox_MCEL  52 seyasktkldesnklkvLdldcgkGgDLeKy.ekgeIsklvatDiaeesieeckeRYnklr 111
                 ++++ k +l  ++k+++Ld++cg+G   +K  +k    k +++D ++  i+++k +  ++r
  AJA92457.1  29 NQFLDKLSL--KEKFRFLDIGCGNGWVVRKMsQKPSCVKAIGIDKSKMMIKNAKSKISSTR 87 
                 667777777..899****************83577999***************98873332 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.4e-06    0.0046     145     232 ..      24     109 ..      23     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
        PrmA 145 HpTTklclealeklvkege.evlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadviva 232
                 H+TT    ++l+kl  +++ ++lD+G+G G +    ++k    k++++D  ++ +k ak+ ++  ++++++ v+  e+  ++ek+dvi++
  AJA92457.1  24 HGTTVN--QFLDKLSLKEKfRFLDIGCGNGwVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKIS--STRESFFVTDLESWNTKEKFDVIFS 109
                 777765..8999997777669*********77778899999999************9998776..566777676666666679****986 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.2e-06    0.0051      13      75 ..      28      87 ..      22     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-06
  Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklg 75
                     v+++l++  + +++++ +D+G+G+g+  + +++   +   +k +gid ++ ++++a+   +  +
       AJA92457.1 28 VNQFLDK-LSLKEKFRFLDIGCGNGWVVRKMSQ---KpSCVKAIGIDKSKMMIKNAKSKISSTR 87
                     6666777.4667899******************...5489*************99986555444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.8e-06    0.0056      92     161 ..      37     113 ..      27     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
        DREV  92 dqedkklldlGaGdGeitkrvaptfeevyat..elsetmrdrlkkk.....kynvlsalelqetdvkldlilclnll 161
                  +e+ + ld+G G+G + +++++  + v a   + s+ m+++ k k     +   ++ le  +t+ k+d+i +++ l
  AJA92457.1  37 LKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIgiDKSKMMIKNAKSKisstrESFFVTDLESWNTKEKFDVIFSMESL 113
                 467889****************999988876226688888776554222223335677775559*******988765 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.023        17      24      84 ..      32      83 ..      16      90 .. 0.73
   2 !    8.6   0.0    0.0017       1.2     125     175 ..      93     140 ..      82     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                HHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHHTE CS
        CheR 24 lakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAkagv 84
                l+k + ++++r++ +gc++G        +++++ +k     vk +++D +++++++Ak+ +
  AJA92457.1 32 LDKLSLKEKFRFLDIGCGNG-------WVVRKMSQKPS--CVKAIGIDKSKMMIKNAKSKI 83
                55666667888888888888.......46666333333..5999999*******9999876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0017
                 --TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE-T CS
        CheR 125 lnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLllGh 175
                  +l + ++ ++k+Dvif+ + l Y  + + e  le++ + lk+gg  + G 
  AJA92457.1  93 TDLES-WNTKEKFDVIFSMESLYYSVP-M-EPALEKVFKLLKKGGTFYCGT 140
                 55555.9*************9977544.3.567899999******999995 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-05     0.032       9      72 ..      28      91 ..      22     110 .. 0.85
   2 ?   -1.7   0.0       2.2   1.6e+03     220     238 ..     120     138 ..     118     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                    THHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EE CS
  Methyltransf_5  9 lqevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrlt 72
                    +++ ++ l+ ke+  ++D   G+g   +++ ++ s  ++igid+ k ++++ak+++++  + + 
      AJA92457.1 28 VNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKMMIKNAKSKISSTRESFF 91
                    5788999*****************9999988888888*****************9999887743 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                     HHHHHHHHHHEEEEEEEEE CS
  Methyltransf_5 220 eelleaalellakggrlav 238
                     e +le++++ll+kgg +  
      AJA92457.1 120 EPALEKVFKLLKKGGTFYC 138
                     5678889999999988754 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.5e-05     0.025      17      95 ..      26     105 ..      24     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-05
                 HHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HH..HHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHC CS
      RrnaAD  17 kvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElder..LakllqkklskdeklkvvhqDflkfetpeevt 95 
                 +++n+ ldkl l+ek   l+ig G G   +++ +    v ++ +d++  ++k  + k+s +++     +D   ++t+e+  
  AJA92457.1  26 TTVNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSkmMIKNAKSKIS-STRESFFVTDLESWNTKEKFD 105
                 5799****************************777766666666654116666666666.777777888999999988665 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     9e-05     0.064      55      90 ..      36      73 ..      27      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-05
  AdoMet_MTase 55 seeketsfvdvgcgngllvyvlaae..gykgygidlrk 90
                  s ++++ f d+gcgng +v  ++++    k  gid  k
    AJA92457.1 36 SLKEKFRFLDIGCGNGWVVRKMSQKpsCVKAIGIDKSK 73
                  4567899***********98877651145556665544 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00069      0.49      42     109 ..      19      87 ..       9     101 .. 0.84
   2 ?    2.0   0.0      0.15   1.1e+02     194     209 ..     162     177 ..     121     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00069
                     HHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS---- CS
  Methyltransf_2  42 glqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsage 109
                      +++    ++++ l +  l++  +++D+G G G ++++++++   +k+i  D ++  +++Ak+++s++ 
      AJA92457.1  19 EMEKGHGTTVNQFLDKLSLKEKFRFLDIGCGNGWVVRKMSQKPSCVKAIGIDKSKmMIKNAKSKISSTR 87 
                     566677778899999999999999*****************999999**9**98735889999975544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                     ---HHHHHHHHHHCT- CS
  Methyltransf_2 194 eRteaeyeellseaGf 209
                      R+e+e+++++ e Gf
      AJA92457.1 162 LRSEKEWKKMFREIGF 177
                     69*************9 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.11      30     105 ..      39     113 ..      17     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                 -S-EEEEES-TTSHHHHHHHHTT-EEEEE..ES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSG CS
        TehB  30 kpgkvldlgcgqgrnslylsllgydvtaw..dknensiafleeikekenlknistalydineaklderydfilstvvl 105
                 +  + ld+gcg+g     +s +   v+a+  dk ++ i++ ++ ++    +  s  + d+++ + +e++d i+s   l
  AJA92457.1  39 EKFRFLDIGCGNGWVVRKMSQKPSCVKAIgiDKSKMMIKNAKSKISS---TRESFFVTDLESWNTKEKFDVIFSMESL 113
                 55678*********999999999888875227777777776655544...444577999*************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1451.94
//
Query:       AJA92458.1  [L=206]
Description: phosphoribosylglycinamide formyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-52  175.6   0.1    9.3e-52  175.4   0.1    1.0  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   0.1   5.2e-56   9.3e-52       3     181 .]       4     187 ..       2     187 .. 0.96

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 5.2e-56
                     EEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCC.CCCCHHHHHHHHCTT-....SEEEEES--S-- CS
  Formyl_trans_N   3 ivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekklepr.sqfeeelaeelkelka....dlivlagymkll 92 
                     + +lisg gsn++ +l+a kk+++  + ++v+snk++a+gl  a++ +i t+v+e +k++ +  q+++e+++ lk++k+     l++lag+m+++
      AJA92458.1   4 LGILISGRGSNMESILKAIKKKKIPINPAVVISNKPNAKGLAIAKKMGIQTEVIESSKYKGKrLQYDKEIISTLKKYKVtpsnGLVCLAGFMRII 98 
                     5689******************************************************9977489************99444459********** PP

                     -HHHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  93 pkelvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalveal 181
                     ++ +++++++kilniHp+LLP+f+G++a+++a+e G k +G+t+hfvde++DtG i++q+ v+i ++dt+++l++++  +eh+++++a+
      AJA92458.1  99 SPYFIKEYKNKILNIHPALLPAFPGLDAQKQAIEFGSKFSGCTVHFVDEGVDTGSIIIQEIVKINNNDTEKSLSKKILVKEHEIYPKAV 187
                     **************************************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1465.79
//
Query:       AJA92459.1  [L=132]
Description: hypothetical protein T478_0123 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 946.20
//
Query:       AJA92460.1  [L=47]
Description: hypothetical protein T478_0280 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 351.65
//
Query:       AJA92461.1  [L=100]
Description: hypothetical protein T478_0897 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0073   15.9   0.6      0.012   15.3   0.6    1.3  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.6   6.6e-07     0.012       5      32 ..      41      67 ..      33      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-07
        SWIM  5 lddervrlnkatCsCpefqk....ngipCkHa 32
                +d++      ++CsC+ + +    n+ pC H+
  AJA92461.1 41 IDPD-----SKFCSCSGYYFgmikNKSPCYHL 67
                5555.....89*******99***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 783.61
//
Query:       AJA92462.1  [L=128]
Description: hypothetical protein T478_0544 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.5   0.1      0.028   14.3   0.1    1.2  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   1.6e-06     0.028      96     134 ..       6      53 ..       2      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-06
  tRNA-synt_1c_C  96 sleearkkkg.iihWvsa...eeaveaevrlYdrLfkeee.de....d 134
                     ++++++ + +  ++W+ +   ++++++e+rlYd+ +k+e+  +    +
      AJA92462.1   6 TFGSEEGSGEeLVQWLNEeakKKKMKFEARLYDYVIKTENfGTfemfS 53 
                     555554445559****99887788999********9998876654331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 958.14
//
Query:       AJA92463.1  [L=271]
Description: NAD(P)H-binding protein, PF13460 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-13   50.8   0.0    1.9e-11   43.9   0.0    2.9  1  Epimerase       NAD dependent epimerase/dehydratase family
    5.2e-09   35.5   2.4    8.7e-06   24.9   0.1    3.4  3  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    6.7e-09   35.9   0.0    2.3e-07   30.9   0.0    2.1  2  NAD_binding_10  NAD(P)H-binding
    1.5e-08   34.2   0.5     0.0012   18.0   0.0    2.9  3  NAD_binding_4   Male sterility protein
    3.5e-06   26.3   0.0    0.00022   20.5   0.0    2.5  1  RmlD_sub_bind   RmlD substrate binding domain
    0.00048   19.8   0.0     0.0074   15.9   0.0    2.0  2  NmrA            NmrA-like family
  ------ inclusion threshold ------
      0.034   14.4   2.2      0.045   14.0   0.3    2.2  2  MSV199          MSV199 domain
      0.069   13.1   0.0       0.12   12.4   0.0    1.3  1  PAC2            PAC2 family
      0.092   12.1   0.1       0.39   10.1   0.0    1.9  2  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.0   9.3e-15   1.9e-11       1     228 [.       9     184 ..       9     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 9.3e-15
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 +++ Ga+Gf+G++l k l++++++ i ++r+                 ++++     ++ + +++ + ihlA   gv+ +s d+  f++ n+++t +++
  AJA92463.1   9 VVISGARGFVGKNLKKFLAKNNIHTIPISRQ-----------------NFKN----SKFPSLKKASHFIHLA---GVGSESVDQDSFVKVNVELTKTVI 83 
                 6899***************************.................2222....34566568899****5...56677778899************* PP

                 HHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSS CS
   Epimerase 100 eaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkq 198
                 + ++k+++k++ ++s     G +              +++s Y ++K  +e+l+++     gl+++i+r++ + G           +++ i+k  ++k 
  AJA92463.1  84 SLCKKNNIKNIFYFSG---LGVS-------------KNSRSSYFISKFNAEQLIKKS----GLRYTIFRPSYILGSD-------DYLTKNISKQILKK- 154
                 ********99999998...4422.............25799*************965....9999***********9.......45555555555566. PP

                 SEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
   Epimerase 199 evtllgdgtalRdflyveDvaeaillvleh 228
                 ++++ g+g+ l + + ++Dv+++i   l  
  AJA92463.1 155 QILIPGSGKFLLQPISIDDVCKCITVGLHS 184
                 8*********************99877666 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0044       8.8       1      27 [.      10      35 ..      10      53 .. 0.67
   2 !   24.9   0.1   4.4e-09   8.7e-06      64     128 ..      49     110 ..      38     180 .. 0.86
   3 ?   -3.5   0.1         2     4e+03     193     235 ..     210     252 ..     201     262 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0044
   3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevr 27
                v+ G++GF+G++l k  +  ++++++ 
  AJA92463.1 10 VISGARGFVGKNLKKF-LAKNNIHTIP 35
                789*********9655.5555455554 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 4.4e-09
   3Beta_HSD  64 legvdvvihlaslvdvagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgee 128
                 l++++  ihla++      + +d++ kvnv+ T++v++ c+k++++ + Y S ++v  + s++  
  AJA92463.1  49 LKKASHFIHLAGVGSE--SVDQDSFVKVNVELTKTVISLCKKNNIKNIFYFSGLGVSKN-SRSSY 110
                 5677888999888754..468999*****************************998665.55444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2
   3Beta_HSD 193 lkqlaklglalfkigdeevlsdrvYvgNvawahilAaralqdp 235
                 +   +k +++ ++++ +++l+d  ++  v +  il   ++ + 
  AJA92463.1 210 VSSKIKIKKINLESAYKSALNDISFAYGVEDLNILVGNYVGNH 252
                 4455555556666666666666666666666666655555554 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.044        87       1      35 [.      13      46 ..      13      56 .. 0.75
   2 !   30.9   0.0   1.1e-10   2.3e-07      74     148 ..      67     138 ..      54     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHH CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklael 35
                    GA G vG+ l k l++++ +++  + R+  k +++
      AJA92463.1 13 GARGFVGKNLKKFLAKNN-IHTIPISRQNFKNSKF 46
                    9***********999995.7777788875444433 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 1.1e-10
                     HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHHHHHHHHHHHHSSSEEEEEEE-CEE- CS
  NAD_binding_10  74 deeg........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaakraaeellrasgldwTivrpggLtd 148
                     d+++        +k+++  +k++++k + + s++gv ++             ++y++ k  ae+l+++sgl +Ti rp+++  
      AJA92463.1  67 DQDSfvkvnvelTKTVISLCKKNNIKNIFYFSGLGVSKN-----------SRSSYFISKFNAEQLIKKSGLRYTIFRPSYILG 138
                     444455556666************************952...........23579***********************99743 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.16   3.2e+02       1      20 [.      11      30 ..      11      37 .. 0.76
   2 !   13.5   0.1   1.5e-05     0.029      86     141 ..      50     105 ..      37     109 .. 0.83
   3 !   18.0   0.0   6.2e-07    0.0012     171     209 ..     105     139 ..      99     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.16
                   EE-TTSHHHHHHHHHHHHHS CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrtt 20
                   + Ga GF+Gk L + L +++
     AJA92463.1 11 ISGARGFVGKNLKKFLAKNN 30
                   67********9976666554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.5e-05
                    HH--EEEE--SS-S.STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE.GGGTT CS
  NAD_binding_4  86 eevdviihsaAtvnfdepykellrvNveGtrevlelakklkklkvllhvST.ayvng 141
                    ++ ++ ih a+  +   + + +++vNve t+ v++l+kk + +  + ++S  +++++
     AJA92463.1  50 KKASHFIHLAGVGSESVDQDSFVKVNVELTKTVISLCKKNNIK-NIFYFSGlGVSKN 105
                    678899********999*********************99888.8888887555554 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 6.2e-07
                    TCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-- CS
  NAD_binding_4 171 glpntYeqsKalaEklvrearrrsglpvvivRpsiitge 209
                    +    Y  sK+ aE+l+++ +    l+ +i+Rps+i+g+
     AJA92463.1 105 NSRSSYFISKFNAEQLIKKSG----LRYTIFRPSYILGS 139
                    55679************9876....889********994 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.1e-07   0.00022       3     166 ..       9     154 ..       7     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                    EEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHS.HHHHHHHHTHHHHHHHHHHHHCT-EEE CS
  RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEse.eeaayavnaeavealAeaaaavgalLi 97 
                    +++ Ga+G +G++L+k la++++++++++r+++  ++  +++++ +       +++A        Es  +++  +vn+e ++++  ++++ +++ i
     AJA92463.1   9 VVISGARGFVGKNLKKFLAKNNIHTIPISRQNFKNSKFPSLKKASH------FIHLAGV----GSESVdQDSFVKVNVELTKTVISLCKKNNIKNI 94 
                    899*************************999998888877776654......4788764....55665488999*******************999 PP

                    EEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESS...SSS-HHHHHHHH CS
  RmlD_sub_bind  98 hvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvyge...kgknfvktmlrl 166
                    ++     F G   +       ++ ++ Y  +K + Eq ++++g +++i+R s+++g+     kn  k++l++
     AJA92463.1  95 FY-----FSGLGVS-------KNSRSSYFISKFNAEQLIKKSGLRYTIFRPSYILGSddyLTKNISKQILKK 154
                    87.....9998655.......667899****************************98666678888888776 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.07   1.4e+02       1      42 [.       9      51 ..       9      70 .. 0.79
   2 !   15.9   0.0   3.7e-06    0.0074      76     207 ..      73     194 ..      65     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.07
                EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHHH CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdt.kselakslke 42
                +++ Ga G  Gk + ++l+k++ ++  + R+  k+ +  slk+
  AJA92463.1  9 VVISGARGFVGKNLKKFLAKNNIHTIPISRQNfKNSKFPSLKK 51
                6788*****************9999988887665555555554 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.7e-06
                 S-HHHHHHHHHHHHHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS- CS
        NmrA  76 skeiedgkklvdAakeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenflsllaqlkvgdtappedkvtllgpgn 174
                 + ++e  k++++  k+  +k+++y s    +++s       + f sK++ e+ ++++g++yt++++    +    l      ++ +++  k ++l pg+
  AJA92463.1  73 KVNVELTKTVISLCKKNNIKNIFYFSGLGVSKNS-----RSSYFISKFNAEQLIKKSGLRYTIFRPSYILGSDDYLT-----KNISKQILKKQILIPGS 161
                 567788899999999999**98875544445466.....5789**********************975444333222.....23333333445666666 PP

                 TTS-EE.-HHHHHHHHHHHHHHHHHHHTTEEEEE CS
        NmrA 175 pkavll.daeeDiGafvikilkdprklkgkrikl 207
                  k  l  ++ +D+ + +  +  + +k+++k+i+l
  AJA92463.1 162 GKFLLQpISIDDVCKCIT-VGLHSSKFSNKIIDL 194
                 444444668888888764.444556666666665 PP

>> MSV199  MSV199 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.3e-05     0.045      45     119 ..      13      92 ..       1      99 [. 0.75
   2 ?   -1.6   0.0       1.5     3e+03      52      71 ..     189     208 ..     173     231 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
      MSV199  45 GeykkqkkkfkklLkrnnieykelkykdeeielypslkeeikllk.....knaiaqkkWlilevkdfKkailrlntknse 119
                 G      k++kk+L +nni+ + ++ ++ + +++pslk+  ++++      + + q  ++ ++v+  K++i   + +n +
  AJA92463.1  13 GARGFVGKNLKKFLAKNNIHTIPISRQNFKNSKFPSLKKASHFIHlagvgSESVDQDSFVKVNVELTKTVISLCKKNNIK 92 
                 555556799******************************99888622222456677778888877777766555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
      MSV199  52 kkfkklLkrnnieykelkyk 71 
                 +k+++l+  ++i +++l  k
  AJA92463.1 189 NKIIDLVGPRKITFQKLVTK 208
                 55666666666666666533 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.1e-05      0.12      82     134 ..      75     123 ..      40     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                 H.HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHH CS
        PAC2  82 e.efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeellee 134
                 + e++k+++++++++++k +++++gl+  +      +r + ++  ++ e+l+++
  AJA92463.1  75 NvELTKTVISLCKKNNIKNIFYFSGLGVSKN-----SRSSYFISKFNAEQLIKK 123
                 2679***********************6654.....466555777777777754 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0002      0.39       2      82 ..      11      97 ..      10     106 .. 0.67
   2 ?   -0.2   0.0      0.26   5.3e+02     149     179 ..     106     136 ..     102     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEE.......SS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE- CS
  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrs.......ssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynL 82
                   i G  Gf+G +l ++L +++ + + i r++       s+ ++++  hla   +e   ++ +++k++++ ++ +++l ++ ++++++ +
     AJA92463.1 11 ISGARGFVGKNLKKFLAKNNIHTIPISRQNfknskfpSLKKASHFIHLAGVGSE-SVDQDSFVKVNVELTKTVISLCKKNNIKNIFYF 97
                   89*****************99988887743211111122233344455554433.345667888888888888888888888888766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                    --SHHHHHHHHHHHHHHHHHHHH---EEEEE CS
  GDP_Man_Dehyd 149 PrsPYaaaKlyadwivvnyreayglfavngi 179
                     rs Y ++K  a++++++    y +f  + i
     AJA92463.1 106 SRSSYFISKFNAEQLIKKSGLRYTIFRPSYI 136
                    6888889999888888887777777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1923.88
//
Query:       AJA92464.1  [L=279]
Description: nucleotidyl transferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-25   89.6   0.1    3.6e-25   89.0   0.1    1.3  1  NTP_transferase  Nucleotidyl transferase
    0.00027   21.3   0.0    0.00035   21.0   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.17   11.9   0.1       0.44   10.5   0.1    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.1     6e-29   3.6e-25       2     241 ..       4     271 ..       3     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 6e-29
                      EEEE--S--GGGTTCCTTSSGGGSEETTE.....T...ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT............... CS
  NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgk.....e...rliqatlsrlansgieeiivvltqehsflveeqlkegskfg............... 72 
                       vI a G+GtRL P t++++k +vpv  k     +   +l+q+ ++++ + ++++  +v+ +e++ ++e++++  + +                
       AJA92464.1   4 VVITAAGKGTRLLPFTKEMPKEMVPVFSKvsvnkKvvmPLLQYIYEQMYSMNFRDYCFVVGREKR-SIEDHFTPHDAYLkeisgdyrkymnsfy 96 
                      6999*********************965433332457899***************7777776555.66777765554445788*********** PP

                      .....SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSST...TSEEEEEEESS-CTTSEEEEEC...T CS
  NTP_transferase  73 .....vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaak...gtvtfgivpveeateyGviead...e 155
                            ++  + ++++ g  dAv+  +++++ e+    ++v +gD+ i  +++  +k+ ie a+k    +++++ ++  ++++yGv +++   +
       AJA92464.1  97 kklenSHLVWINQNKPLGFGDAVKRTERYVGTED----FIVHAGDVAILSKVKHPIKRLIEVAKKnpeAKAILLCKEIIDPKRYGVPTIEkisN 186
                      **998888899999999***************99....8*******99885555555544433332215999999***********99998852 PP

                      TS..BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
  NTP_transferase 156 eg..rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                       +   v++ +EKP+++k s++    +Y+f s+++  l +++++ k +e ++td+++ +++e+k+ la+  +++e   DvG+++s+ + 
       AJA92464.1 187 -NlfSVKEVIEKPEKPK-SNFGILALYYFRSDIFSSL-RKIKPGKGKEFQLTDAIQNLIKEKKQVLAIPLNKNEDEIDVGNVESYKNS 271
                      .346*************.*******************.66******************************9999999*******9765 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.8e-08   0.00035       1     118 [.       4     162 ..       4     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.8e-08
                   EEEEEESS-TTT....TT.THHHHCCCCC.........CHHHHHHHHHCTT.-CEEEEECSH..CHHHH.........................HHT CS
  NTP_transf_3   1 aviLAGGrSsRm....gg.dKallplggk.........pllervldalraagvdevvvvggd..eevla.........................ala 56 
                   +vi A+G+++R+    ++ +K ++p+  k         pll+++++++ ++++++ + v+g+  +++++                          l+
    AJA92464.1   4 VVITAAGKGTRLlpftKEmPKEMVPVFSKvsvnkkvvmPLLQYIYEQMYSMNFRDYCFVVGRekRSIEDhftphdaylkeisgdyrkymnsfykKLE 100
                   5899********7766347*******777799999******************88888877734456666666777777777766666666543333 PP

                   TCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--H..HHHHHHHHCHHHHTSSE CS
  NTP_transf_3  57 rlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltp..elverllaaaaasgadv 118
                        v+ ++++  g + +++   r + +++ ++v a+D++ l++  + ++rl++ a++++++ 
    AJA92464.1 101 -NSHLVWINQNKPLGFGDAVKRTERYV-GTEDFIVHAGDVAILSKvkHPIKRLIEVAKKNPEAK 162
                   .35666666677899999999999999.9**********9999852255888888887766544 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   7.4e-05      0.44      13      48 ..       3      38 ..       1      41 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.4e-05
                    EEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETT CS
  Prot_ATP_ID_OB 13 raiVktssdeevvvslagavpremLrpgDlVavdkd 48
                    +++++  ++ +++++ ++  p+em+ +   V+v+k+
      AJA92464.1  3 KVVITAAGKGTRLLPFTKEMPKEMVPVFSKVSVNKK 38
                    68999999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1952.54
//
Query:       AJA92465.1  [L=251]
Description: ribosomal protein S5 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-22   78.1   0.3    6.3e-22   77.3   0.3    1.4  1  Ribosomal_S5     Ribosomal protein S5, N-terminal domain
    1.1e-14   53.6   0.1    1.8e-14   52.9   0.1    1.3  1  Ribosomal_S5_C   Ribosomal protein S5, C-terminal domain
  ------ inclusion threshold ------
       0.19   11.9   0.1       0.38   11.0   0.1    1.4  1  DOMON            DOMON domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.3   1.1e-25   6.3e-22       1      65 []     100     164 ..     100     164 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 1.1e-25
                   XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
  Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                   lk++v+++  +qk+t  G+ t+f+alv++G++nG++G+G+gk+k+++ Ai+kA ++A +n+vpv+
    AJA92465.1 100 LKTEVIDVGLIQKMTPNGQSTRFKALVAAGNQNGWLGIGLGKSKQMRIAIEKANNAAFLNVVPVN 164
                   799************************************************************96 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.1   3.1e-18   1.8e-14       2      62 ..     186     247 ..     185     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 3.1e-18
                     EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHT CS
  Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkkl 62 
                     gk g+v++ + p p+G G++agg +r +l+laG+kD ++ + g + +   + kA + +Lk++
      AJA92465.1 186 GKSGSVTIEILPGPKGLGLVAGGKIRNLLKLAGVKDAWTHTSGsTATMASTSKALLACLKQT 247
                     9******************************************9999999**********98 PP

>> DOMON  DOMON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.4e-05      0.38      15      43 ..     117     146 ..     110     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
       DOMON  15 gdeiefelsgkvn.tngyvaiGfsddgkMs 43 
                 g++ +f++   +  +ng+++iG++++++M 
  AJA92465.1 117 GQSTRFKALVAAGnQNGWLGIGLGKSKQMR 146
                 666666665555537**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1839.84
//
Query:       AJA92466.1  [L=378]
Description: hypothetical protein T478_0106 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.65    9.9   0.0    2.1  2  TDP43_N   Transactive response DNA-binding protein N-terminal


Domain annotation for each model (and alignments):
>> TDP43_N  Transactive response DNA-binding protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.15   2.7e+03      22      42 ..      61      81 ..      54      95 .. 0.74
   2 ?    9.9   0.0   3.6e-05      0.65      14      52 ..     228     266 ..     216     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.15
     TDP43_N 22 tLllsTLqaqfpgAtGLkYrn 42
                 L ++++ a++ +A+ L +  
  AJA92466.1 61 LLAMTSIDAAISKAQVLVFAP 81
                467999999999999888765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 3.6e-05
     TDP43_N  14 Eipled..DgtLllsTLqaqfpgAtGLkYrnpetgakRgvr 52 
                 E+ l+d  Dg   l +L++ f gA+ L Y    +g+++g+ 
  AJA92466.1 228 ELYLDDfiDGLFDLRSLSSSFEGASSLMYLI--NGSMKGLD 266
                 7777777799999*****************9..99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2646.32
//
Query:       AJA92467.1  [L=92]
Description: PF04248 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-32  109.9   1.5    4.6e-32  109.8   1.5    1.0  1  NTP_transf_9  Domain of unknown function (DUF427)


Domain annotation for each model (and alignments):
>> NTP_transf_9  Domain of unknown function (DUF427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   1.5   2.6e-36   4.6e-32       1      92 [.       1      87 [.       1      88 [. 0.98

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 2.6e-36
                  EEEE-SS-EEEEES--EEEEETTS--EEEB-GGGB-GGGEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEEESS--TT-GGGTT-BEE-T CS
  NTP_transf_9  1 vrvklngtvvaetddavvveetglppryYfppedvklellkpsdtttvCpwKGeasyyslavdgkevkdaaWsYpeptpeaaeikgyvaFya 92
                  +++++n++v+ae+dd+vvve+     ++Yfp +++k e++++++t+t CpwKG asyys++v+gk+++d aW+Yp p++ea++ik++vaF++
    AJA92467.1  1 MKAVWNDAVIAESDDTVVVEG-----NHYFPSNSIKNEYFHKTETSTSCPWKGVASYYSVTVNGKTNTDCAWYYPVPSKEAEKIKDRVAFWN 87
                  6899*****************.....*****************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 691.82
//
Query:       AJA92468.1  [L=228]
Description: ERCC4 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-24   85.4   0.0    8.2e-24   84.6   0.0    1.4  1  ERCC4       ERCC4 domain
    4.7e-08   33.5   0.1    1.8e-07   31.7   0.1    2.0  1  HHH_5       Helix-hairpin-helix domain
     0.0042   17.2   0.0      0.011   15.9   0.0    1.8  1  HHH_2       Helix-hairpin-helix motif
     0.0048   16.7   0.9          4    7.5   0.2    3.0  3  HHH         Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.13   12.6   0.0    2.4  2  HHH_3       Helix-hairpin-helix motif
      0.022   15.4   0.2      0.074   13.7   0.1    1.9  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
      0.072   13.5   0.1       0.22   11.9   0.0    1.9  2  HHH_8       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   3.2e-27   8.2e-24       1     156 []      10     131 ..      10     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 3.2e-27
                 EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHHHHHHH.H-SEEEEEEES-G CS
       ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqvsrlkrngykkpillvegld 99 
                 +D+re ksgi++  l+  gv+++i+tl igdy ++    ++                +verk++ dl +si dgrl++q+srl + +y++pillveg+ 
  AJA92468.1  10 VDEREKKSGIPKL-LAAIGVKTEIKTLVIGDY-IV---APE---------------TVVERKTIADLLSSIFDGRLFDQCSRLTE-HYQHPILLVEGNV 87 
                 8****99******.******************.77...788...............*****************************.***********55 PP

                 GGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHHHH CS
       ERCC4 100 qykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewlanl 156
                    + +               n+   ++aL++++l f+++++ t sa +ta++l +l
  AJA92468.1  88 DEIEELT-------------DNPLIFYGALSTVALEFKIPVIPTPSATHTAKLLVSL 131
                 5555421.............45557****************************9875 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   6.8e-11   1.8e-07       4      55 ..     160     210 ..     157     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.8e-11
                 HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
       HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                 L s++G+ +k A++ll++ ++++ d++ a v eLak pG+G+ +A++i+  l
  AJA92468.1 160 LCSLPGVAEKSAIRLLEK-FGTPLDVLCAPVTELAKTPGLGEAKAKKIKKML 210
                 679***************.*****************************8655 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.1e-06     0.011       7      59 ..     162     214 ..     152     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
       HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFenek 59 
                 +++ V ek A  L ++F++      a + eL++ ++ Ge  A++i++ ++n++
  AJA92468.1 162 SLPGVAEKSAIRLLEKFGTPLDVLCAPVTELAKTPGLGEAKAKKIKKMLQNKN 214
                 678999************9888889************************9986 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.8   1.7e+04      10      13 ..      90      93 ..      85      94 .. 0.53
   2 !    6.5   0.0    0.0032       8.2      13      29 ..     160     176 ..     150     177 .. 0.90
   3 !    7.5   0.2    0.0016         4      11      28 ..     190     207 ..     188     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.8
                HHHH CS
         HHH 10 reeL 13
                +eeL
  AJA92468.1 90 IEEL 93
                4555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0032
                 HHTSTT-SHHHHHHHHH CS
         HHH  13 LlalPGVGpktAeaIls 29 
                 L++lPGV +k A + l+
  AJA92468.1 160 LCSLPGVAEKSAIRLLE 176
                 99**********99886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0016
                 HHHHTSTT-SHHHHHHHH CS
         HHH  11 eeLlalPGVGpktAeaIl 28 
                  eL++ PG G+++A +I 
  AJA92468.1 190 TELAKTPGLGEAKAKKIK 207
                 599999**********96 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.64   1.6e+03      13      31 ..     157     175 ..     149     177 .. 0.76
   2 ?   12.6   0.0     5e-05      0.13      11      35 ..     187     211 ..     179     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.64
       HHH_3  13 aeeLqklpGlgpklAknIv 31 
                 ++ L  lpG+ +k A +++
  AJA92468.1 157 LSVLCSLPGVAEKSAIRLL 175
                 56788999*9999997766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5e-05
       HHH_3  11 AsaeeLqklpGlgpklAknIvayRe 35 
                 A ++eL+k pGlg+++Ak+I ++ +
  AJA92468.1 187 APVTELAKTPGLGEAKAKKIKKMLQ 211
                 7789****************87644 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   5.7e+03      26      47 ..     119     140 ..     112     162 .. 0.51
   2 ?   13.7   0.1   2.9e-05     0.074      23      68 ..     163     218 ..     159     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
  5_3_exonuc  26 iGektAakLlkeygsleeilen 47 
                  ++   akLl    + +e+ + 
  AJA92468.1 119 PSATHTAKLLVSLSTRKELTKG 140
                 5555556666666666665552 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.9e-05
  5_3_exonuc  23 vpgiGektAakLlkeygs.leeilenldelke.........kklkekLeenkeear 68 
                  pg+ ek A++Ll+++g+ l+ + + + el++         kk+k+ L++++++ +
  AJA92468.1 163 LPGVAEKSAIRLLEKFGTpLDVLCAPVTELAKtpglgeakaKKIKKMLQNKNKNFK 218
                 69***************956666665544333344444444888888888877765 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         7   1.8e+04       3      11 ..      52      60 ..      51      62 .. 0.68
   2 ?   11.9   0.0   8.6e-05      0.22      30      68 .]     170     211 ..     169     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7
                HHHHHHHHH CS
       HHH_8  3 eiadaLeel 11
                 iad+L+ +
  AJA92468.1 52 TIADLLSSI 60
                578888877 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.6e-05
                 HHHCCCCC-SS-HHHH.TT..HCTTSTT--HHHHHHHHHHHH CS
       HHH_8  30 rAaraiealpeeitsl.ee..eltklpgiGkkiaakieeile 68 
                  A+r +e+ +++++ l +   el k pg+G++ a+ki+ +l+
  AJA92468.1 170 SAIRLLEKFGTPLDVLcAPvtELAKTPGLGEAKAKKIKKMLQ 211
                 7999***********9844567***************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1698.92
//
Query:       AJA92469.1  [L=506]
Description: gamma-aminobutyrate metabolism dehydratase/isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-94  316.8   0.0    2.3e-94  316.1   0.0    1.3  1  HpaB_N        4-hydroxyphenylacetate 3-hydroxylase N terminal
    3.5e-73  245.0   0.7      5e-73  244.5   0.7    1.2  1  HpaB          4-hydroxyphenylacetate 3-hydroxylase C terminal
  ------ inclusion threshold ------
       0.15   11.7   0.1       0.33   10.6   0.1    1.5  1  zf-Tim10_DDP  Tim10/DDP family zinc finger


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.1   0.0   3.8e-98   2.3e-94       1     272 []      10     277 ..      10     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: 316.1 bits;  conditional E-value: 3.8e-98
                 -HHHHHHHHHHS---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHHHHHHHHHHHHHHHTTT--S- CS
      HpaB_N   1 TgeeYlesLrdkgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDllkkrkairelarktggclgR 99 
                 TgeeY+esL+ ++ +vY+ Ge V++ ++hp++rp++++va++Ydla ++e  +l+  +s+ +ge+vnrf+hi++s+eDl+ ++k++r+l + tg+c++R
  AJA92469.1  10 TGEEYIESLKGRDLKVYLFGELVKEPVSHPMIRPSINAVAKTYDLAVEEE--ELAFPKSSISGERVNRFLHIAESAEDLVLQNKMQRKLGQLTGTCFQR 106
                 8**********7777********************************998..8999999999************************************* PP

                 -THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS-TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEE CS
      HpaB_N 100 cpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkgdRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladei 197
                 c+++da+n l  ++ + d  ek+gtk y++++ +++++vq+++lv+ +a+td+kgdRs++pseqedpd+++++v+++d+G++V+Gak+++Tg+++++++
  AJA92469.1 107 CVGMDAMNSLHSTTFEiD--EKHGTK-YHQRLLEFIKMVQHENLVIGGAMTDVKGDRSLAPSEQEDPDLFLHIVDRDDKGVYVTGAKAHQTGTINSHWM 202
                 ****************99..999*99.************************************************************************ PP

                 EE---SS-..TTSGGG-EEEEEETT-TTEEEEE------.-.S..-TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
      HpaB_N 198 lvlptramlkeedkdyavafavpvdapGlklicresfed.k.leesefdyplssrfdendalvvfDdVfVPwerVfl 272
                 +v+pt+++  e+dkdya++ a+pvdapG+++i++++++d + +e+ ++d+++s +f++++++v+fD+Vf+P+e +f+
  AJA92469.1 203 IVMPTMRL-LENDKDYAIVGALPVDAPGITYIYGRQSCDtRsMEPGDIDVGNS-EFGGQETMVIFDRVFIPNEMIFM 277
                 *****877.89****************************855899********.**********************8 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.5   0.7   8.3e-77     5e-73       1     201 [.     284     481 ..     284     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 244.5 bits;  conditional E-value: 8.3e-77
                 HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-TTS-EE--HHHHHHHHHHHHHHH CS
        HpaB   1 agklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdpsGvylPdlllanaarvlvtrly 99 
                 a++lve+f+++hr sy +  +k + +d+liG+aa++ae+nG+ k sh+++k++e+++l+e +ya++iaa+++++k +sGv+l d +lan+++++vtrl+
  AJA92469.1 284 ASMLVERFTCYHRRSY-V--CKTGLGDVLIGAAAAIAEYNGVPKVSHIKDKIIEMTHLNESIYAAGIAASYQGHKMKSGVFLNDDMLANVCKHNVTRLP 379
                 5789************.6..9****************************************************************************** PP

                 HHHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHHHHHHTSHHHHHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHH CS
        HpaB 100 priveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllklawdltgsefggrhelyerhgaGspeaqriaiyrqydleekkelvk 198
                 +++++++qd+aGG+l+tlPsea+f++ e+gpllekyl+g++g+++e+R+++l+l++++t++  +++++++++hgaGsp+aqri+i rq++l  kk+l+k
  AJA92469.1 380 YELARLAQDVAGGILVTLPSEAEFRSAETGPLLEKYLKGKSGIEVENRMRILRLIENMTMGRNAVGYLTESMHGAGSPQAQRIQIARQMQLGYKKQLAK 478
                 *************************************************************************************************** PP

                 HHC CS
        HpaB 199 kll 201
                 +l+
  AJA92469.1 479 NLA 481
                 *98 PP

>> zf-Tim10_DDP  Tim10/DDP family zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.6e-05      0.33      10      38 ..      90     118 ..      85     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
  zf-Tim10_DDP  10 anaqelvnkltekCfkkCigkypgssLds 38 
                    ++q  + +lt +Cf++C+g    +sL s
    AJA92469.1  90 NKMQRKLGQLTGTCFQRCVGMDAMNSLHS 118
                   57999999***********6656666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3400.56
//
Query:       AJA92470.1  [L=428]
Description: aspartate--tRNA(Asn) ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-87  291.5   0.0    8.2e-87  291.2   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.6e-12   47.2   0.2      3e-12   46.3   0.2    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
    0.00048   19.7   0.6      0.098   12.1   0.0    2.8  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.16   12.2   0.8        0.3   11.3   0.3    1.6  2  Dysbindin        Dysbindin (Dystrobrevin binding protein 1)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.2   0.0   1.8e-90   8.2e-87       3     313 ..     115     422 ..     113     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 291.2 bits;  conditional E-value: 1.8e-90
                  CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-SHHHHHHHHHCTHSEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqspqlylellivagidrvfq 96 
                  + rl+ r ld+r++k+ ++++lrs+v++++r+ l +++fiei+tP ++ s++e+ga lF +       ++f    +L+qspqly+e + ++ ++rvf+
   AJA92470.1 115 DNRLNSRALDMRNQKTASIFKLRSQVLASIRETLIKRKFIEINTPKIIGSASEGGADLFSL-------DYFgkqaYLAQSPQLYKEQMTIG-LERVFE 204
                  689**********************************************************.......66666667***************.****** PP

                  EEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS-- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx RF
  tRNA-synt_2  97 iaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrltykeaieklnei......gkdld 188
                  i+  +RaE+s+t rhl+EFt++++e + +++ d+m+vle ++ +++k++ e+s k  +++i ++ k + +pf+r++y++a+e+l +       g+dl+
   AJA92470.1 205 ISSFYRAEKSHTGRHLSEFTSVDIEAAMMDYTDVMDVLESIVVDVFKNTAENS-KTEQQDIGHEIKIPDSPFERVSYTQALEELGNLdiklefGEDLQ 301
                  *************************************************8888.66667777777888999************8877999999***** PP

                  HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 189 kaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgG 286
                    ++r l + ++  ++f+td+P +lkpFy  +++dd++l++s+Dl +  +El +G  R++dpe+l+ +lk+++ld   +++f++ l+ + +G+pph+G
   AJA92470.1 302 DSHLRSLGD-KHPGFFFLTDWPMKLKPFYIHEKDDDPTLSRSFDLQYGYLELSSGGRRLHDPEQLKSRLKEQNLD---PASFEEHLKTFGWGMPPHSG 395
                  *********.999**********************************777*************************...******************** PP

                  EEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 287 lglGldRlvmlllgsesIrdviaFPkl 313
                  +g+GldRl+++l+g +++r+v+++P+ 
   AJA92470.1 396 WGMGLDRLMTVLIGIDNVREVTLYPRD 422
                  *************************95 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.2   6.7e-16     3e-12       2      75 ..      22      94 ..      21      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.7e-16
                     EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEEEEEE CS
  tRNA_anti-codon  2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg..elelkveeiel 75
                      + G+v++   r+ gk++f+++rD tg+ qv++   +a++l+e l + +vvr+ G+v++++ +  ++e+++ e+++
       AJA92470.1 22 LFGGWVVDL--RKLGKMAFLTVRDVTGMCQVIVKG-DAMSLLEGLNRQSVVRILGKVQASKAKdfDFEVSAIELQV 94
                     578******..************************.************************8887767777666655 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.31   1.4e+03      17      43 ..     135     161 ..     122     164 .. 0.80
   2 !    4.6   0.1    0.0044        20     103     154 ..     201     255 ..     188     264 .. 0.74
   3 !   12.1   0.0   2.2e-05     0.098     212     234 ..     394     416 ..     377     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.31
                   SHHHHHHHHHHHHHHCTTCEESSTTSE CS
  tRNA-synt_2d  17 hpltkvleeikeiflelgfeevegpev 43 
                   +  ++vl  i+e++++ +f e++ p++
    AJA92470.1 135 KLRSQVLASIRETLIKRKFIEINTPKI 161
                   455789999**********99999886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0044
                   EEEEEEEEEBSST.-SSSB-SEEEEE..EEEEEETT--HHHHHHHHHHHHHHHCT CS
  tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqv..eglvvdenvsladlkgvleellkklfg 154
                   +++ i   +R ++    +hl eF++v  e  ++d    ++ l  ++ +++k+  +
    AJA92470.1 201 RVFEISSFYRAEKsHTGRHLSEFTSVdiEAAMMDYTDVMDVLESIVVDVFKNTAE 255
                   7899999*****977889*****98722556666666666666666666666544 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.2e-05
                   EEEEEEHHHHHHHHHT-SSGHHH CS
  tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                    ++G+G++Rl  + +gi+++Re+
    AJA92470.1 394 SGWGMGLDRLMTVLIGIDNVREV 416
                   58*******************86 PP

>> Dysbindin  Dysbindin (Dystrobrevin binding protein 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.7   7.7e+03      35      81 ..      85     134 ..      76     138 .. 0.54
   2 ?   11.3   0.3   6.7e-05       0.3      51      93 ..     220     262 ..     213     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
   Dysbindin  35 qylstgyLqiterRe...PlgSvSSlEVnvDlLeqmeLtDisDqEaldVF 81 
                   +s+  Lq+  + e   P+  +  lE ++D       +D+  q  + +F
  AJA92470.1  85 FEVSAIELQVLAKAEyplPIDPIGRLESDIDNRLNSRALDMRNQKTASIF 134
                 55555555554333332356666666666665444444566666665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.7e-05
   Dysbindin  51 lgSvSSlEVnvDlLeqmeLtDisDqEaldVFldsdgeenaleS 93 
                 l+   S++++  +++ ++ +D+ +  ++dVF ++ ++ ++ + 
  AJA92470.1 220 LSEFTSVDIEAAMMDYTDVMDVLESIVVDVFKNTAENSKTEQQ 262
                 67788999***********************999877665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2927.02
//
Query:       AJA92471.1  [L=162]
Description: hypothetical protein T478_0319 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   14.0   0.3       0.12   13.3   0.1    1.5  2  PdaC      Deacetylase PdaC
        0.1   12.7   0.0       0.76    9.9   0.0    1.9  2  DUF5343   Family of unknown function (DUF5343)


Domain annotation for each model (and alignments):
>> PdaC  Deacetylase PdaC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   9.5e+03      33      37 ..      17      21 ..       3      55 .. 0.60
   2 ?   13.3   0.1   1.4e-05      0.12      34      87 ..     112     162 .]      69     162 .] 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                HHHHH CS
        PdaC 33 iekda 37
                +e ++
  AJA92471.1 17 YEIQC 21
                23333 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.4e-05
                 HHHHHHHHHHHHHHHH.HHHHTT---S-EEEEEEEEEEEE-SSEEEEEEEEEEE CS
        PdaC  34 ekdadkflkeyekeakeeakkndfpkrpyelevdyevkynsekilSlslssyey 87 
                 +k+ +++++++ + +  +   nd+p+   ++  +ye++ n++k+lS+++s+  +
  AJA92471.1 112 QKKHKRYIEDVHDLQT-QHLFNDLPF--IQYDENYEITENKPKFLSMDISKIDF 162
                 5666667777765555.556678888..56678***************998766 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.054   4.8e+02      74     110 ..       3      39 ..       1      58 [. 0.66
   2 ?    9.9   0.0   8.5e-05      0.76      70     124 ..      74     129 ..      64     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.054
     DUF5343  74 kalaeaikeaYsdlFeln.edaqnldkeelknlfrtvt 110
                 k ++++ike +s  +e++ +++ + ++  l +++ ++t
  AJA92471.1   3 KFFQKWIKENFSISYEIQcDEMITEPRSIL-QKLDSHT 39 
                 678999999999999999555555555544.4455555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.5e-05
     DUF5343  70 dtskkalaeaikeaYsdlFelnedaqnldkeelknlfrtvtgks.dervvkrvant 124
                 ++++ al +  k++Y +lF ++++ ++   e l +++r+ + k   e+v + +++ 
  AJA92471.1  74 ENFGMALWQKPKNGYDELFLAEKNCTTVCHEILHEMLRQKKHKRyIEDVHDLQTQH 129
                 667777888889****************************9999888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1180.75
//
Query:       AJA92472.1  [L=373]
Description: hypothetical protein T478_1179 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.25   11.2   1.3        7.6    6.4   0.1    2.8  3  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain


Domain annotation for each model (and alignments):
>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2    0.0077   1.4e+02      24      47 ..      46      69 ..      41      93 .. 0.76
   2 ?   -2.0   0.0      0.16   2.9e+03      14      41 ..     110     139 ..      95     146 .. 0.75
   3 ?    6.4   0.1   0.00042       7.6      40      92 ..     299     352 ..     293     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0077
  Glutaredoxin2_C 24 aplpEFatqsAreyftkkkeksig 47
                      ++pEFa++ A++ f +  + +  
       AJA92472.1 46 NTFPEFAKRFAKNLFDQINSDESP 69
                     689************876655544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.16
  Glutaredoxin2_C  14 krLllPRfvkaplpEFat..qsAreyftkk 41 
                       r+l   fvk+++p F+   +++ +yf++ 
       AJA92472.1 110 LRILNSNFVKMTFPVFNGlfDASTDYFKDD 139
                      466677789999999987778888888765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.00042
  Glutaredoxin2_C  40 kkkeksigdfeellaktpeliaelnalLeelepliksseavng.elSvdDillf 92 
                       k++     fee ++++++++++ +a Le+l   + +++ ++   l+v+  +lf
       AJA92472.1 299 LKMNDVKDGFEETMNHSKSYLNDAQAALEKLPDSFSHRKFLEFlFLTVEHYNLF 352
                      455566669**********************99887777766666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2298.06
//
Query:       AJA92473.1  [L=95]
Description: winged helix-turn-helix [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-11   43.4   0.1      3e-11   43.1   0.1    1.1  1  HTH_45    Winged helix-turn-helix
    5.8e-06   26.1   0.0    7.4e-06   25.8   0.0    1.1  1  MarR_2    MarR family
    0.00026   21.4   0.0    0.00034   21.0   0.0    1.1  1  HTH_27    Winged helix DNA-binding domain
     0.0084   15.9   0.0     0.0093   15.7   0.0    1.1  1  DUF4364   Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.026   14.6   0.0    1.2  1  HTH_20    Helix-turn-helix domain
      0.048   13.5   0.0      0.086   12.7   0.0    1.4  2  TrmB      Sugar-specific transcriptional regulator TrmB
      0.071   13.3   0.0       0.23   11.6   0.0    1.8  2  Mrr_N     Mrr N-terminal domain
      0.073   13.4   0.0      0.098   13.0   0.0    1.2  1  Rrf2      Transcriptional regulator
       0.09   12.6   0.0       0.18   11.7   0.0    1.5  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.1   1.5e-14     3e-11       1      76 [.       6      88 ..       6      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.5e-14
      HTH_45  1 rRskleIiadILeaisegeak...kTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleela 76
                +Rs++ I+ dIL+++ +g+++    ++i  +anLs   +    ++L++ gl+    ++++ k+++TekGl++ +++k++++l 
  AJA92473.1  6 YRSEMGIMGDILDVTMNGGQQgviVSAISRRANLSHYAVLDKCEKLINAGLVetrrDDRNRKFMITEKGLKFFDEFKNFQNLL 88
                6**************98887633379*********99999999*********998777999******************9975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.7e-09   7.4e-06      11      60 ..      17      64 ..      14      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.7e-09
                HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
      MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                L +  +++ + + v+++ rr +ls+ av   +++L  aGLve+r++  D+
  AJA92473.1 17 LDVTMNGGQQGVIVSAISRRANLSHYAVLDKCEKLINAGLVETRRD--DR 64
                5555555555689*******************************99..44 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-07   0.00034      14      68 .]      23      74 ..      16      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
      HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                + + +++ +++++r n++  ++    +kL+++GLve+    +d+r++ + +T+kG
  AJA92473.1 23 GGQQGVIVSAISRRANLSHYAVLDKCEKLINAGLVETR---RDDRNRKFMITEKG 74
                566677789**************999*********777...66799999999999 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.6e-06    0.0093      29      75 ..      37      83 ..      17      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.6e-06
     DUF4364 29 eytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfen 75
                  ++   + +  ++L+++gl+e+++++ +  + iTekG +  ++f+n
  AJA92473.1 37 ANLSHYAVLDKCEKLINAGLVETRRDDRNRKFMITEKGLKFFDEFKN 83
                44444455555689*****************************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.026      21      59 ..      24      62 ..      12      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
      HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                + +g+ +s++ +r  ls   + +  ++L  agLve++r 
  AJA92473.1 24 GQQGVIVSAISRRANLSHYAVLDKCEKLINAGLVETRRD 62
                5678999******************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.086      25      58 ..      30      63 ..      25      73 .. 0.86
   2 ?   -3.3   0.0       4.5     9e+03      10      20 ..      80      90 ..      79      93 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 25 adeiaeelgvprskvYevLrsLedkGlVerekgr 58
                ++ i++++++++  v +  ++L+++GlVe+++  
  AJA92473.1 30 VSAISRRANLSHYAVLDKCEKLINAGLVETRRDD 63
                789**************************99865 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                CCCHCHHHHHH CS
        TrmB 10 EakvYlaLlkl 20
                E+k ++ Ll++
  AJA92473.1 80 EFKNFQNLLES 90
                67777777765 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.59   1.2e+03       5      37 ..      13      43 ..      10      47 .. 0.68
   2 ?   11.6   0.0   0.00012      0.23      58      85 ..      48      78 ..      34      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.59
       Mrr_N  5 mlplLealadgsehrlkeirervaerfglseee 37
                m  +L +  +g  +    i++++++r++ls ++
  AJA92473.1 13 MGDILDVTMNGGQQG--VIVSAISRRANLSHYA 43
                666677766644443..5888888888888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
       Mrr_N 58 rtyLkkagllespk...rgvwkiTekGrevl 85
                + +L +agl+e+ +   + ++ iTekG ++ 
  AJA92473.1 48 CEKLINAGLVETRRddrNRKFMITEKGLKFF 78
                57899******998887889*******9976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.9e-05     0.098      16      59 ..      18      61 ..       6      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
        Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                + +++ +++ v +++i++r n+s+  +    +kL +aglv+++r
  AJA92473.1 18 DVTMNGGQQGVIVSAISRRANLSHYAVLDKCEKLINAGLVETRR 61
                56778888889*******************************98 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.9e-05      0.18      56      88 ..      48      79 ..      40      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
     DUF1495 56 essLielGLveeeeeseglklYklteeGieive 88
                 + Li+ GLve+   ++  + + +te+G ++ +
  AJA92473.1 48 CEKLINAGLVET-RRDDRNRKFMITEKGLKFFD 79
                567*******75.5566667899*****99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 728.70
//
Query:       AJA92474.1  [L=375]
Description: sulfate adenylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-84  282.9   0.2    2.5e-84  282.0   0.2    1.4  2  ATP-sulfurylase  ATP-sulfurylase
      9e-44  148.9   0.0    1.7e-43  148.0   0.0    1.5  1  PUA_2            PUA-like domain
  ------ inclusion threshold ------
      0.091   12.5   0.1        0.2   11.4   0.0    1.6  2  DUF1415          Protein of unknown function (DUF1415)


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.67     4e+03     135     166 ..      87     118 ..      84     139 .. 0.71
   2 !  282.0   0.2   4.1e-88   2.5e-84       2     211 ..     160     368 ..     159     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.67
                      HHHHHHHHCHHHCTSEEEE---EEEETTTTEE CS
  ATP-sulfurylase 135 daqellakvagelgiepvkfeeavYckkegev 166
                      da ++l k ++ +gi ++ +e ++ ++k+ ++
       AJA92474.1  87 DAGDVLLKNPDGTGIAVLHVEDVYSYDKQATM 118
                      67778888888899999999887655555444 PP

  == domain 2  score: 282.0 bits;  conditional E-value: 4.1e-88
                      CCB.-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHHTSEEEEEEEB-SB-STTSTTHHHHHHHHHHHHHHHS-GGGEEE-BB-SB- CS
  ATP-sulfurylase   2 eyrltPaevreefkekgwdkVvAfqtrnplHraHeellkraleeeadglllhplvgptkpgdvpaevrvrayealieeylpkdrvvlallplam 95 
                      + r+tP+++re f++ gw+++vAfqtrnp+H aHe+l+k+a++ ++dg++++pl+g++kpgd+++e++v+aye++ie+y+p++++ la+l+++m
       AJA92474.1 160 KHRMTPTQTRELFEKVGWKTIVAFQTRNPPHVAHEMLQKTAIT-TRDGVFVNPLIGKKKPGDFKDEIIVKAYEVMIEKYYPENKCQLATLHTEM 252
                      679****************************************.6999********************************************** PP

                      --SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHHCTSEEEE---EEEETTTTEEEECCCC.GCCGGEEE--HHHHHC CS
  ATP-sulfurylase  96 ryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvagelgiepvkfeeavYckkegevasektc.hkkeevesisgtelrk 188
                       yaGprEa+ hai+r+nyGcth+i+Grdhagvg+fY+p++a++++++++ el+iep++f  ++Yc+k+ ++++ + c    e++e+isgt++r+
       AJA92474.1 253 KYAGPREAIHHAIMRQNYGCTHIIIGRDHAGVGKFYDPFAAHKIFDDYP-ELEIEPIFFPAFFYCNKCLTFTNPNVCpCAPEHREQISGTKMRE 345
                      ***********************************************99.6**************************98889************ PP

                      CHHTT----TTTS-HHHHHHHHH CS
  ATP-sulfurylase 189 llregeeipewfsrpevlkvLre 211
                      ++++ge + + + rpev++v+ +
       AJA92474.1 346 MINNGESPSKFILRPEVAEVIIN 368
                      ********************976 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   0.0   2.9e-47   1.7e-43      26     158 ..      19     151 ..       2     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 2.9e-47
                 HTS-EEE--HHHHHHHHHHHTTTTTT-SCC--HHHHHHHHHHSEETTS-E-SS---EEEECCHCHHHTT-SEEEEEETTTEEEEEEEEEEEEE-HHHHH CS
       PUA_2  26 kelpsielskrelqdlellaeGgfsPLegFmreedyesvleemrLadgllwsiPivLdvseedakklkegdrvaLkdkegellAileveeiyeldkeee 124
                 + l s+++s+  ++d+e +a G+fsPLegF++++d+esv+++ rLa+g+ w++P vLdv+ee+ kk+k++ +v+Lk+++g+ +A+l+ve++y++dk+  
  AJA92474.1  19 SGLISVDISADLANDVENIADGIFSPLEGFLNQQDFESVISKGRLANGTAWTMPTVLDVDEETGKKMKDAGDVLLKNPDGTGIAVLHVEDVYSYDKQAT 117
                 357789********************************************************************************************* PP

                 HHHHHS---TTSHHHHHHCTS-SEEEEEEEEE-S CS
       PUA_2 125 aekvfgttdeaHPgvkkvleqgevlvgGkvevle 158
                 ++ v+gt+d +HPgv+k+ +++++lvgGk++ ++
  AJA92474.1 118 MNGVYGTNDDSHPGVAKTNSMKDFLVGGKIDYIQ 151
                 *******************************998 PP

>> DUF1415  Protein of unknown function (DUF1415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.3e-05       0.2      83     135 ..     225     276 ..     186     296 .. 0.85
   2 ?   -3.5   0.0       1.3   7.7e+03      18      29 ..     326     337 ..     323     354 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
     DUF1415  83 dlldlaealleelelegvlqvasfHpdyqFegeeaddaenytnRspypilhll 135
                  ++++ e ++e+   e++ q+a++H + +++g + +++++   R  y + h++
  AJA92474.1 225 IIVKAYEVMIEKYYPENKCQLATLHTEMKYAGPR-EAIHHAIMRQNYGCTHII 276
                 367888999999999*****************98.89**************98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.3
     DUF1415  18 nlCPFAkkvvek 29 
                 n+CP A + +e+
  AJA92474.1 326 NVCPCAPEHREQ 337
                 899999776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2278.47
//
Query:       AJA92475.1  [L=393]
Description: hypothetical protein T478_0279 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.3   0.2      0.049   12.9   0.2    1.1  1  EpsG      EpsG family
      0.063   13.5   0.0       0.15   12.3   0.0    1.5  1  ASH       Abnormal spindle-like microcephaly-assoc'd, ASPM-SP


Domain annotation for each model (and alignments):
>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   5.4e-06     0.049       3      66 ..       5      71 ..       3      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-06
        EpsG  3 lvlilililvllagfrygvGtDyf.tYveifesisnlsys..fd.snfEpgyvllnllvkslgfdyqf 66
                ++lil+l+ ++ ++f  ++  Dy+  Y++if +  ++s++  ++ + + p ++  ++l+ s+g+d+++
  AJA92475.1  5 IFLILFLVPIAQFAFAEEI-PDYDkPYAPIFFNKPVYSWTekVEiTIIAPSWNTGMNLIDSIGGDPNY 71
                6899999999999999999.*******************94422455556999999999999999886 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.15      18      82 ..     300     366 ..     297     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                 ----EEEEEEE-EEESS-SS--EEEEEEEE--XXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekg..fsveetelevqpgesvtltvtwtPteegav 82 
                 +  +G++   + +++N+ ++++e ++   ++ e++  +s+++ + +v p +++ ++v+wt +e+g+ 
  AJA92475.1 300 ELDIGKTGMIFSKIRNTLDYTQEFTYIVQIKNENNnvISLSWVTGQVIPSQELGMSVSWTVQETGKY 366
                 66789999999999*****9976665444444333126888888****************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2614.93
//
Query:       AJA92476.1  [L=206]
Description: ribonuclease HII [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.5e-42  143.6   0.6    7.5e-42  143.4   0.6    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.6   4.2e-46   7.5e-42       1     197 [.       4     198 ..       4     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 4.2e-46
                 EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH...HHTTTS-HHHHHHHHHHHHHHHHHHTCE CS
   RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeiky..aseneinlneikaaltlaviklleklgv 97 
                 +G+D aGrG+++Gp+v+a++ +ek+++++l+klgv DSKkLs++kre L k+i k +   ++++   +   + + e nln+++a+ +++vi  l+++  
  AJA92476.1   4 CGVDDAGRGSMIGPMVIAGISIEKKNIPKLRKLGVRDSKKLSPKKRELLYKEIVKLVDDYHVIRIPPRTidKYVFEHNLNHLEAKKMAEVISNLNPDLS 102
                 7*****************************************************888877777766665446678899999999999999999999999 PP

                 ECCECCCE--SSHHHHHHHHHHHHC.CEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-T CS
   RNase_HII  98 kvdeilvdgvttpeslkkkleqiik.ikvtvekkadekyllvaaASiiAkverdeelellkrkpgtldkgsGyasdektrallkkgats..klpdivrl 193
                 +vd+ +v+    ++++ +++ +  k  kv   + ad+++++v+aASiiAkv+rd  + +l++ +   + gsGy+sd+k+ + +kk + s   lp+  r 
  AJA92476.1 103 YVDSCDVN----AARFGREISDLSKkSKVKSYHYADSRFVVVSAASIIAKVSRDRSIMRLNKTA---NLGSGYPSDKKSVNYVKKVVSSkkSLPTSIRK 194
                 99999998....778889999988889999************************9888888876...7*****************99998899****** PP

                 TSHH CS
   RNase_HII 194 sfkt 197
                 s+k 
  AJA92476.1 195 SWKP 198
                 **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1554.36
//
Query:       AJA92477.1  [L=322]
Description: hypothetical protein T478_0607 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.21   11.5   0.1       0.71    9.8   0.1    1.8  2  Dioxygenase_N  Catechol dioxygenase N terminus


Domain annotation for each model (and alignments):
>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.29   5.2e+03      24      40 ..      42      58 ..      38      61 .. 0.76
   2 ?    9.8   0.1     4e-05      0.71      23      41 ..      90     108 ..      77     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.29
                   --HHHHHHHHHHHHHHH CS
  Dioxygenase_N 24 lteeEwwaavdfLtrvG 40
                   +    +  +v+++++ G
     AJA92477.1 42 IDDTAFVSGVQYMIENG 58
                   55666889999999877 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4e-05
                    T--HHHHHHHHHHHHHHHH CS
  Dioxygenase_N  23 dlteeEwwaavdfLtrvGq 41 
                     lte+E+ +a+++L+++G 
     AJA92477.1  90 TLTENEFVNALQYLIKMGI 108
                    79***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1948.94
//
Query:       AJA92478.1  [L=203]
Description: metallo-beta-lactamase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-19   68.8   1.7    7.6e-18   65.2   1.7    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.052   13.1   0.1      0.076   12.5   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   1.7   8.4e-22   7.6e-18       2     197 .]       9     169 ..       8     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 8.4e-22
                  CCCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH CS
  Lactamase_B   2 gpdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll 97 
                  gp + +sy++e     ++i+iD+ ++ ++         ++ + ++++++++TH+H DH+ g+++l++   v+++ +++ +    m  +          
   AJA92478.1   9 GPMQNFSYIVEdeSTHEAIVIDPSWDLDKIISI-----IDEQNLQPKYIVNTHWHDDHTRGNEELAKMLSVKIVQHEASTLQNDMTVK---------- 91 
                  78899******8888****************98.....9***************************9988887766666666666666.......... PP

                  TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE CS
  Lactamase_B  98 lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp 195
                                 +d++ +g+ +l+v+++pgh+ +++++  +  + +f+GD+l++g+ gridl+++ a  +++s+ + + +       +++ v++p
   AJA92478.1  92 --------------NGDSIKFGCSELVVYHTPGHSKDSICLVGD--GKIFSGDTLFVGNCGRIDLPGGSASELYHSLFDVLHS------LDDNLVMYP 167
                  ..............99******************9999888655..559****************888888888887766662......344444555 PP

                  SS CS
  Lactamase_B 196 gH 197
                  gH
   AJA92478.1 168 GH 169
                  87 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.5e-06     0.076       3      63 ..      27      79 ..      25     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-06
                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE CS
  Lactamase_B_2  3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap 63
                   i+iD+++dl +   +        ++  + + ++ th H DH+ g   l+++    ++++ +
     AJA92478.1 27 IVIDPSWDLDKI-ISII-----DEQNLQPKYIVNTHWHDDHTRGNEELAKMLS--VKIVQH 79
                   89******6544.3333.....233346789***************9999543..555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1536.98
//
Query:       AJA92479.1  [L=256]
Description: peptidase, S54 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-32  110.8  21.8    5.6e-32  110.8  21.8    1.5  2  Rhomboid  Rhomboid family
  ------ inclusion threshold ------
      0.031   14.8   1.2       0.14   12.7   0.1    2.3  2  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.67     6e+03     112     115 ..      29      32 ..      13      63 .. 0.59
   2 !  110.8  21.8   6.3e-36   5.6e-32       9     147 ..      85     237 ..      83     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.67
                 CCCC CS
    Rhomboid 112 llnl 115
                 ++ +
  AJA92479.1  29 VFGI 32 
                 2222 PP

  == domain 2  score: 110.8 bits;  conditional E-value: 6.3e-36
                 HHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC.... CS
    Rhomboid   9 rlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaesesplvGaSGaifgllgallvlvprnrkllrkliia.... 103
                 +l+ts+f+H+g++Hl++Nml+l++fG ++e ++G+++++ +yl+ g++++l++++ +a s+ p+vGaSGai+g+lga+lv++pr++ + ++++++    
  AJA92479.1  85 TLITSTFMHGGIMHLGGNMLFLWIFGDNIEAKFGRVKYIGIYLMWGVGAGLIHIYGDAGSGIPAVGASGAIAGILGAYLVMFPRAKVMTFVMLGFfwrm 183
                 69*****************************************************************************************99999998 PP

                 ........CCCCCCCCCCHHHCTSS.....STTTHHHHHHHHHHHHHHHHHHCC CS
    Rhomboid 104 .....llllllfillnlvlgllpra.....ggvsnlAHlgGllaGlllgllllr 147
                        +l ++++++ +l ++ +      ggv++lAH+gG+  Gl +g++  +
  AJA92479.1 184 mhipaKFFLPFWLIFQNLLPFFIGGfgvagGGVAFLAHIGGFFLGLGVGYFYKK 237
                 88877666666666655554444446899*****************99998765 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.15   1.3e+03      21      39 ..      24      42 ..      18      65 .. 0.66
   2 ?   12.7   0.1   1.6e-05      0.14       9      62 ..      84     137 ..      81     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
     DUF1751 21 vwkvlvslltlllggkylE 39
                +++v+v  + +++ g+++E
  AJA92479.1 24 IMNVIVFGIEVAITGQFIE 42
                5566666777777777777 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-05
     DUF1751   9 wtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllv 62 
                  tl+t++f+   ++++  ++l l+++g  +E   g+  ++   l+ +v+++l+ 
  AJA92479.1  84 LTLITSTFMHGGIMHLGGNMLFLWIFGDNIEAKFGRVKYIGIYLMWGVGAGLIH 137
                 59***********************************99999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1875.24
//
Query:       AJA92480.1  [L=100]
Description: 4Fe-4S binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-10   40.3  11.1    2.9e-05   23.7   0.5    2.2  2  Fer4      4Fe-4S binding domain
    4.9e-09   36.6   3.2    6.9e-09   36.2   3.2    1.2  1  Fer4_7    4Fe-4S dicluster domain
    1.7e-08   34.4   1.5    2.5e-08   33.9   1.5    1.2  1  Fer4_21   4Fe-4S dicluster domain
    2.4e-07   30.5   9.9    0.00026   20.9   3.6    2.2  2  Fer4_6    4Fe-4S binding domain
    5.9e-06   26.1   9.0     0.0023   17.9   2.1    2.3  2  Fer4_2    4Fe-4S binding domain
    6.8e-06   26.5   4.5     0.0038   17.7   0.7    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.2e-05   25.3   4.7    7.2e-05   22.9   5.1    1.8  2  Fer4_9    4Fe-4S dicluster domain
    1.4e-05   25.1   8.4    0.00018   21.6   9.0    2.0  2  Fer4_10   4Fe-4S dicluster domain
    6.6e-05   23.1   7.1      0.019   15.4   2.0    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00071   20.5   5.5       0.27   12.2   0.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
     0.0018   19.1   2.7       0.44   11.4   0.5    2.1  2  Fer4_22   4Fe-4S dicluster domain
      0.002   18.5   6.6      0.015   15.8   6.6    1.9  1  Fer4_8    4Fe-4S dicluster domain
     0.0025   18.6  10.6      0.087   13.8   3.4    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0038   17.9  10.4     0.0061   17.3   2.2    2.3  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.015   15.9   7.2       0.42   11.2   7.1    2.1  1  Fer4_17   4Fe-4S dicluster domain
       0.93    9.7  10.3        1.8    8.8   2.7    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   4.4     2e-07   0.00022       2      18 ..       8      24 ..       7      25 .. 0.94
   2 !   23.7   0.5   2.6e-08   2.9e-05       2      23 ..      47      68 ..      46      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                EEETTTSSS-THHHHHS CS
        Fer4  2 videekCigCGaCvevC 18
                 ide +CigC +Cve+C
  AJA92480.1  8 DIDEQRCIGCALCVEIC 24
                69*************** PP

  == domain 2  score: 23.7 bits;  conditional E-value: 2.6e-08
                EEETTTSSS-THHHHHSTTTEE CS
        Fer4  2 videekCigCGaCvevCPvgAI 23
                v+ +e+Ci  GaC+ vCP+  I
  AJA92480.1 47 VFYPERCITDGACIGVCPTKSI 68
                688****************877 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   3.2   6.2e-12   6.9e-09       1      51 [.      13      66 ..      13      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.2e-12
      Fer4_7  1 rCigCgaCvaaCp...vkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                rCigC  Cv+ C     ++++++++e  k+ +  ++ pe+C++ gaC+ vCPt+
  AJA92480.1 13 RCIGCALCVEICTslgPDVLRVKPVEGWKRGKAFVFYPERCITDGACIGVCPTK 66
                8***********777789*******999999999******************96 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   1.5   2.2e-11   2.5e-08       3      55 ..       9      67 ..       7      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.2e-11
     Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvl......kvvedeCvGCnlCssvCPved 55
                ide++CigC +C+  C   + + +++++ + +          ++C+    C+ vCP++ 
  AJA92480.1  9 IDEQRCIGCALCVEICTSLGPDVLRVKPVEGWkrgkafVFYPERCITDGACIGVCPTKS 67
                9***********************888776443333225569**************854 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   3.6   2.3e-07   0.00026       1      19 [.       6      24 ..       6      26 .. 0.93
   2 !   13.4   0.4   5.6e-05     0.063       6      23 ..      50      67 ..      45      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
      Fer4_6  1 vveidpdkCigCgdCvrvC 19
                ++ id+++CigC  Cv +C
  AJA92480.1  6 IPDIDEQRCIGCALCVEIC 24
                5789*************** PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.6e-05
      Fer4_6  6 pdkCigCgdCvrvCPega 23
                p++Ci  g+C+ vCP++ 
  AJA92480.1 50 PERCITDGACIGVCPTKS 67
                89*************975 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.1     2e-06    0.0023       4      21 ..       8      25 ..       5      26 .. 0.89
   2 !   12.1   0.6   0.00015      0.17       3      22 .]      46      65 ..      44      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
      Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                 +d++rCigC  Cv  C 
  AJA92480.1  8 DIDEQRCIGCALCVEICT 25
                58***************5 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
      Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                +v+ ++rCi  gaC+ +CP+
  AJA92480.1 46 FVFYPERCITDGACIGVCPT 65
                7889999*744********7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.7   3.4e-06    0.0038       1      17 [.       9      25 ..       9      39 .. 0.89
   2 !   10.5   0.2   0.00064      0.71       4      18 ..      51      65 ..      50      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
     Fer4_13  1 VDrdtCiacgaCvelaP 17
                +D+++Ci+c++Cve++ 
  AJA92480.1  9 IDEQRCIGCALCVEICT 25
                89*************94 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00064
     Fer4_13  4 dtCiacgaCvelaPd 18
                ++Ci +gaC  ++P 
  AJA92480.1 51 ERCITDGACIGVCPT 65
                79************5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.4   5.6e-05     0.063      33      47 ..      11      25 ..       2      28 .. 0.77
   2 !   22.9   5.1   6.4e-08   7.2e-05       1      50 [.      13      67 ..      13      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
      Fer4_9 33 eeaCigCgaCveaCp 47
                e++CigC  Cve+C 
  AJA92480.1 11 EQRCIGCALCVEICT 25
                4589*******9997 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 6.4e-08
      Fer4_9  1 kCtgCgaCveaC...pagvvvedaaerkarlraase..eaCigCgaCveaCpkga 50
                +C+gC  Cve C     +v + + +e+  r +a+    e+Ci+ gaC+ +Cp++ 
  AJA92480.1 13 RCIGCALCVEICtslGPDVLRVKPVEGWKRGKAFVFypERCITDGACIGVCPTKS 67
                6***********6665566777777777777665558999************985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   9.0   1.6e-07   0.00018       4      56 .]       9      64 ..       6      64 .. 0.83
   2 !   13.5   0.5   5.2e-05     0.058       5      22 ..      49      66 ..      45      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
     Fer4_10  4 idddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                id+++Ci+C+ Cv+ C ++l     +v+  +  ++++a    +e+C++ gaC+ +CP
  AJA92480.1  9 IDEQRCIGCALCVEIC-TSLgpdvLRVKPVEGWKRGKAFVFYPERCITDGACIGVCP 64
                89**************.5559997666666666666666779**************9 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.2e-05
     Fer4_10  5 dddtCirCgkCvkaCPad 22
                 +++Ci  g+C  +CP++
  AJA92480.1 49 YPERCITDGACIGVCPTK 66
                57999999*******994 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.0   1.7e-05     0.019       2      14 ..      12      24 ..      11      30 .. 0.92
   2 !   10.6   0.2   0.00062      0.69       1      16 [.      50      65 ..      50      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
      Fer4_4  2 erCigCgsCvaaC 14
                +rCigC  Cv +C
  AJA92480.1 12 QRCIGCALCVEIC 24
                79*********** PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
      Fer4_4  1 qerCigCgsCvaaCPq 16
                +erCi  g+C+ +CP+
  AJA92480.1 50 PERCITDGACIGVCPT 65
                69*************7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   1.7     0.001       1.1      52      64 ..      12      24 ..       4      26 .. 0.77
   2 !   12.2   0.1   0.00024      0.27       1      17 [.      52      68 ..      52      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
     Fer4_16 52 eaitgCdiCqdvC 64
                ++++gC+ C+++C
  AJA92480.1 12 QRCIGCALCVEIC 24
                5788888888888 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00024
     Fer4_16  1 rCgtCgkCaevCPtnai 17
                rC+t g+C+ vCPt+ i
  AJA92480.1 52 RCITDGACIGVCPTKSI 68
                69999*********998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.5   0.00039      0.44      76      93 ..       8      25 ..       3      27 .. 0.85
   2 !    8.1   0.1    0.0043       4.9       1      21 [.      52      72 ..      52      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
     Fer4_22 76 kfgesgCvGCgRCieacp 93
                 ++e+ C+GC  C+e c+
  AJA92480.1  8 DIDEQRCIGCALCVEICT 25
                578999***********7 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0043
     Fer4_22  1 rClsCgaCtlvCptCsCfdve 21
                rC++ gaC  vCpt s f ++
  AJA92480.1 52 RCITDGACIGVCPTKSIFWMR 72
                7*************8877665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   6.6   1.3e-05     0.015       3      64 ..      12      66 ..      10      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
      Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                ++Ci+C +C + C +l     + +  +g + + +    +       ++C t gaC  vCp++
  AJA92480.1 12 QRCIGCALCVEICTSLGPDVLRVKPVEGWKRG-KAFVFY------PERCITDGACIGVCPTK 66
                58***********8777777666677776666.333334......89*************86 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.4   7.8e-05     0.087       1      12 [.      14      25 ..      14      28 .. 0.92
   2 !    9.3   0.7    0.0021       2.4       1      14 [.      53      66 ..      53      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.8e-05
      Fer4_3  1 CtgCgaCvevCP 12
                C+gC +Cve C 
  AJA92480.1 14 CIGCALCVEICT 25
                ***********6 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0021
      Fer4_3  1 CtgCgaCvevCPvg 14
                C+  gaC  vCP++
  AJA92480.1 53 CITDGACIGVCPTK 66
                77779*******87 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.2   5.5e-06    0.0061       3      20 ..       9      26 ..       8      49 .. 0.81
   2 ?    5.7   1.3     0.022        24       6      20 ..      51      65 ..      46      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.5e-06
     Fer4_15  3 vDrdaCigcglCvaeape 20
                +D+++Cigc+lCv+ ++ 
  AJA92480.1  9 IDEQRCIGCALCVEICTS 26
                8**************943 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
     Fer4_15  6 daCigcglCvaeape 20
                ++Ci +g+C+ ++p+
  AJA92480.1 51 ERCITDGACIGVCPT 65
                79*********9985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.1   0.00038      0.42       1      58 [.      13      65 ..      13      68 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
     Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                rCi+C+ C++ C s+      + k+++      +++     + ++Ci+ g C  +CP 
  AJA92480.1 13 RCIGCALCVEICTSLGPDVL-RVKPVEG----WKRGKAFVFYPERCITDGACIGVCPT 65
                7*********9988765444.3344444....34444456899*************96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.7    0.0016       1.8      84      98 ..      13      27 ..       3      42 .. 0.78
   2 ?    6.0   0.9     0.012        13      60      74 ..      52      66 ..      41      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
     Fer4_18 84 eciscllcidacdkv 98
                 ci c+lc++ c+++
  AJA92480.1 13 RCIGCALCVEICTSL 27
                588888888888765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
     Fer4_18 60 dcidcescvkvcPtg 74
                 ci+ ++c+ vcPt+
  AJA92480.1 52 RCITDGACIGVCPTK 66
                6999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 606.61
//
Query:       AJA92481.1  [L=210]
Description: hypothetical protein T478_0318 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0049   17.2   0.1      0.012   16.0   0.0    1.7  1  Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
      0.006   16.5   0.2      0.014   15.3   0.2    1.5  1  CAT_RBD   CAT RNA binding domain


Domain annotation for each model (and alignments):
>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-06     0.012      32      68 ..     110     146 ..      86     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-06
                 HHHHHHHHHHHHHHHHHHHHHTCSSCCCHHHHHHHHH CS
    Cas_Cmr5  32 kklPalIltnGLgqalAfllskgkkkkedahkklleh 68 
                 +k+P+ I++nG+  a+Af ++ g++ +++  +k+++ 
  AJA92481.1 110 HKVPIAIKSNGMYMAIAFNKATGNAINKKDVEKFYQI 146
                 799********************55555555554443 PP

>> CAT_RBD  CAT RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.6e-06     0.014      29      53 ..     125     149 ..     123     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                 TTTT--TTSEEETTTSSEEEEE-SH CS
     CAT_RBD  29 IGFgkkkgdeideekieKvFvlkde 53 
                 I+F+k +g+ i+++++eK + + d+
  AJA92481.1 125 IAFNKATGNAINKKDVEKFYQIADD 149
                 9********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1662.04
//
Query:       AJA92482.1  [L=50]
Description: hypothetical protein T478_0520 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.49   10.1   5.1       0.41   10.4   0.7    2.1  2  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn


Domain annotation for each model (and alignments):
>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   2.3e-05      0.41      23      29 ..       2       8 ..       1      11 [. 0.83
   2 ?    2.3   0.3    0.0076   1.4e+02       3      18 ..      24      46 ..      22      47 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.3e-05
     zf-RRN7 23 yCrrCht 29
                +CrrCh+
  AJA92482.1  2 ICRRCHH 8 
                9*****9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0076
     zf-RRN7  3 kgppCgv..Cgc....rsftl.d 18
                ++ +C +  C c    + f + d
  AJA92482.1 24 RRGACQIpdCTCnqflDAFEEiD 46
                77888888866644777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 309.78
//
Query:       AJA92483.1  [L=304]
Description: hypothetical protein T478_0440 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0029   17.8   0.0     0.0064   16.7   0.0    1.6  1  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.035   14.0   0.0    1.6  1  Y_Y_Y            Y_Y_Y domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.2e-07    0.0064       4      55 ..      53     109 ..      51     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.2e-07
  CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGaf....rlrglppgtysvtv...s 55 
                      G+V+d+  +p+++  V +t    g+++  +td +G+f     ++ l+p tys+ v    
       AJA92483.1  53 GTVVDHAYRPLSNIDVKLT--IAGESHMLKTDGNGEFgkqiDVSELKPRTYSILVfatD 109
                      9******************..79**************5544467788888888775542 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     4e-06     0.035      29      63 ..      86     123 ..      65     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-06
                 ....EEEEES--SEEEEEEEEEEETTS-B-SS-EEEEE CS
       Y_Y_Y  29 q...easytnlppGdYtlkVkakdndgqwnyditslsf 63 
                     ++  ++l+p +Y ++V+a+d++g++ +  t+l++
  AJA92483.1  86 EfgkQIDVSELKPRTYSILVFATDENGKKGMARTTLEV 123
                 345599*************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1898.15
//
Query:       AJA92484.1  [L=123]
Description: hypothetical protein T478_0666 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 781.93
//
Query:       AJA92485.1  [L=382]
Description: toprim domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-08   34.3   0.7      6e-08   33.0   0.3    2.0  2  Toprim_4  Toprim domain
    7.6e-06   26.3   0.2    2.6e-05   24.5   0.0    2.0  2  Toprim_2  Toprim-like
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.05   13.8   0.1    2.0  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   9.8e+03      65      76 ..     135     146 ..     108     155 .. 0.69
   2 !   33.0   0.3     1e-11     6e-08       3      75 ..     172     232 ..     170     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
    Toprim_4  65 aeGeataerlae 76 
                  eG+++ e++ e
  AJA92485.1 135 SEGQEMLEEVHE 146
                 477777777666 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 1e-11
    Toprim_4   3 iiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerla 75 
                 +i+VEg+aD ++l +ag+ n+ a+ gg++   + i+ e  ++          ++v+ ++dgD +G    ++l+
  AJA92485.1 172 VILVEGRADIINLLRAGYDNALAFEGGRI--DESIK-ELCEQ---------KEKVVAFTDGDRAGGFILKELK 232
                 79***************************..66666.66666.........399***********76666655 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.3   7.6e+03      24      47 ..     129     152 ..     118     154 .. 0.69
   2 !   24.5   0.0   4.4e-09   2.6e-05       1      68 [.     173     235 ..     173     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
    Toprim_2  24 valgGtalteaalkllerypekkv 47 
                  ++++++  +++l+++++++++k+
  AJA92485.1 129 WSTNSVSEGQEMLEEVHENNSEKI 152
                 577778777788888777766655 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 4.4e-09
    Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaell 68 
                 +++Eg  D + l+++g +   n++a  G    ++ +k+l ++ ++kvv  +D D+aG    k+l++++
  AJA92485.1 173 ILVEGRADIINLLRAGYD---NALAFEGG-RIDESIKELCEQ-KEKVVAFTDGDRAGGFILKELKSVV 235
                 69***************8...********.888888888888.688***********99999999877 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   8.4e-06      0.05       2      88 ..     172     236 ..     171     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-06
                 EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT CS
      Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawellevlk 88 
                 +++vEg +d +++ +a   g+ +++a  G  +d                     +kel ++ ++++  tD+Dr+G  i +el +v+ 
  AJA92485.1 172 VILVEGRADIINLLRA---GYDNALAFEGGRIDES-------------------IKELCEQKEKVVAFTDGDRAGGFILKELKSVVH 236
                 6889999999999999...8999999999998877...................7*********************99999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2933.08
//
Query:       AJA92486.1  [L=221]
Description: hypothetical protein T478_1024 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1447.33
//
Query:       AJA92487.1  [L=228]
Description: MIP family channel protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-38  132.5  18.5    2.2e-38  132.2  18.5    1.0  1  MIP       Major intrinsic protein


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2  18.5   1.2e-42   2.2e-38       7     227 .]       5     214 ..       2     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 1.2e-42
                 HHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHH CS
         MIP   7 flravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllGaiv 105
                 +l+ +  E ++t++lv++++gs + +++++ +     ++++   a+a  +al ++vy ++++S aH+NPavT++ +++++is+++ ++Y++a ++Gai+
  AJA92487.1   5 NLQIFTVELVGTFILVIFATGSIV-LDAEMFNG----ELGIPFHAVAPFVALLIGVYSFGKVSLAHFNPAVTIGYYITGHISKIQILYYVAAEIIGAIL 98 
                 6777889**************777.88887663....35677777778999************************************************ PP

                 HHHHHHHHCHHHHHHTTTTSSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHT CS
         MIP 106 aaallklltkglesraglfanslkpglsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpavvln 204
                 +++++ +++     +a+l+an+++   s++  + vE++  ++L+ v+f ++    k+ +g ++++aig +v l il+ + ++Ga+mNpAr+l+pa+++ 
  AJA92487.1  99 GSLFVLTIIGD---KADLGANVPNFDFSMLLIFPVEVLASAMLMGVIFYVVYT--KGLRG-FSGVAIGGIVGLDILFLAFISGASMNPARALAPALLSG 191
                 ****9999888...699*******************************87754..33335.599*********************************** PP

                 HSTTTTHHHHHHHHHHHHHHHHH CS
         MIP 205 kfedhwvylvGPliGailgalvY 227
                   e+ w y+ +P++G i++a+++
  AJA92487.1 192 VVENLWLYWTAPFVGTIIAAFAF 214
                 ********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1355.18
//
Query:       AJA92488.1  [L=331]
Description: putative rRNA pseudouridine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-25   89.4   0.3    2.1e-14   54.1   0.0    3.4  2  TruB_N    TruB family pseudouridylate synthase (N terminal do
    8.8e-20   70.6   0.0    2.7e-19   69.0   0.0    1.9  2  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    1.1e-13   50.9   0.1      2e-13   50.1   0.1    1.4  1  PUA       PUA domain
    1.8e-12   47.1   0.0    5.4e-12   45.6   0.1    1.8  2  DKCLD     DKCLD (NUC011) domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.0   4.8e-18   2.1e-14       1      51 [.      57     107 ..      57     112 .. 0.96
   2 !   29.1   0.1   2.4e-10   1.1e-06      73     149 .]     111     170 ..     107     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 4.8e-18
                 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEET CS
      TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlg 51 
                 kr+l++ k+Gh+GtLDp+++GvL++++ge+Tk+l +ll  +KeY+a  rl+
  AJA92488.1  57 KRILEIPKAGHSGTLDPQVSGVLPLGLGEGTKALGVLLMGPKEYHALGRLH 107
                 899*******************************************99997 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 2.4e-10
                 -HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
      TruB_N  73 teekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                 ++ekle++l+ f+Gei q pp+ SAv                  r++r+ tiyelelle +e+ v l++ c++GtYi
  AJA92488.1 111 SKEKLEQILELFRGEIFQKPPQRSAVV-----------------RQTRSRTIYELELLEQKERLVLLRILCEAGTYI 170
                 789***********************9.................99******************************9 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.99   4.4e+03      34      46 ..       1      13 [.       1      34 [. 0.72
   2 !   69.0   0.0   6.1e-23   2.7e-19       1      63 [.     171     236 ..     171     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.99
                B-HHHHHHHHHHH CS
    TruB_C_2 34 vtledLedavlly 46
                +tl++Le++v++ 
  AJA92488.1  1 MTLKQLENLVKID 13
                6899999977643 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 6.1e-23
                 HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
    TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                 R+L  D+Ge+Lg g+ ++eLRR rv +f+e+++vt+++L+da++++ke  d++ L ++++P+e+ l
  AJA92488.1 171 RKLYYDMGELLGPGGSMIELRRSRVHQFNENNLVTMHQLADAYATWKEnkDDSkLLKIIRPVEETL 236
                 9***********************************************874447*********987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.1   4.5e-17     2e-13       2      73 ..     241     312 ..     240     313 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 4.5e-17
                 EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
         PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                  vv+ d+A++  ++ga+L +pGv+++   +e+gd V i++++ge+va++ +++s +e+++ ++g + +++r+
  AJA92488.1 241 SVVIRDSAIDSMCHGAQLAIPGVLQISQYLEKGDLVGIYSQKGEIVALAESLLSENEIKEQTKGYAFQTKRI 312
                 79**************************************************************99999887 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.1   1.2e-15   5.4e-12       7      58 .]       2      53 ..       1      53 [. 0.96
   2 ?   -2.5   0.0       1.3   5.6e+03       9      42 ..     237     273 ..     233     273 .. 0.59

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.2e-15
                ...XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
       DKCLD  7 lLknydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                 Lk+ ++l+   +  t+ ++G+   kR+ie++++yG+i +DKP +P+SHEVV
  AJA92488.1  2 TLKQLENLVKIDDDMTNPENGTYYNKRTIEQLLEYGLILIDKPPGPTSHEVV 53
                5899999999999**************************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.3
                 .XXX-EEESS-----TTSS--...GGG--HHHHHHTE CS
       DKCLD   9 knydkllvrtehytplpaGss...PlkRpieeyikyG 42 
                  +++++++r ++   + +G +   P   +i++y++ G
  AJA92488.1 237 SEIKSVVIRDSAIDSMCHGAQlaiPGVLQISQYLEKG 273
                 5666667777766666666533335555677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2502.36
//
Query:       AJA92489.1  [L=405]
Description: transporter, CPA2 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-59  202.1  49.7    1.5e-59  201.8  49.7    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8  49.7   8.1e-64   1.5e-59       3     376 ..      16     394 ..      10     396 .. 0.89

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 8.1e-64
                     HHHHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS...............HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHH CS
  Na_H_Exchanger   3 llillallvgl...larrlklpeivgliiaGlllGpsglg..lieps........eedlevlselglilllFlaGleldlrelrknlksilllal 84 
                     +l+++a    l   l++r+klp ++g+++aG+++Gp+ lg  l++p            l +l e+g i++lF aGle+ ++e+++ +k+++ +++
      AJA92489.1  16 ILLAAAK---LmgeLFSRIKLPIVLGELLAGMIIGPFALGafLLHPEtgesilkiGPELRTLGEIGAIVILFMAGLEMTPKEFLRGGKASFTVGT 107
                     2222233...34659*************************8745555777778778*************************************** PP

                     HHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTXXXXXTSSSTSXH CS
  Na_H_Exchanger  85 lgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalakeeaggetsllll 179
                     lgv++++++ Gll+     +g++ l+a+ ++++l+at++++ +++lke +++++  ++l+++++v++D++a+ +l+v+ +l + ea ++++ll +
      AJA92489.1 108 LGVIVPFFA-GLLVFQ--AFGYDALQAMMIATALTATSIAISIQVLKEFNKIKSPEARLIIAAAVVDDILAIAVLSVVTSLGSAEAIDNIDLLDV 199
                     *********.**9997..89*************************************************************99888888888888 PP

                     HHHHHHHHHHHHHHHH.HHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger 180 lliflvvavgglllgl.vigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplf 273
                       ++l v++++ ++ + +i  l+++it +++++  +   ++ +  ++aa++a  lg+s i+gaf++G++ls +++ +k++  ++ ++  +f+plf
      AJA92489.1 200 TFTILKVLGFFAAILIaAIFILPKVITPRIWKSTGSVEGIATASFFGAAAIAGTLGLSPIVGAFAVGMALSATKVFEKIENFISRIG-LIFAPLF 293
                     888887777766655404555667777777999999999999*****************************8888888888899999.******* PP

                     HHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHH CS
  Na_H_Exchanger 274 FvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftv 368
                     F+++G+++d+  +n  l+vl+l ++++++ + +++l+  l + l+ ++    + +g+g+++rg+v l++a +g ++g+l+ ++y++++++v +t+
      AJA92489.1 294 FAIIGAQVDFRTVN--LDVLMLSAVVIAIAISTKLLGCGLPSILFLKNKTAGMRVGIGMISRGEVGLIVAGVGLSSGVLTGDVYTTIVLMVAVTT 386
                     *********99997..9999999999999999****99999999988888889999*************************************** PP

                     HHHHHHHH CS
  Na_H_Exchanger 369 lvqGlslk 376
                     ++ +++lk
      AJA92489.1 387 IITPIWLK 394
                     *9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2541.52
//
Query:       AJA92490.1  [L=49]
Description: hypothetical protein T478_0431 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0013   18.8  13.8     0.0013   18.8  13.8    2.0  2  Metallothio  Metallothionein


Domain annotation for each model (and alignments):
>> Metallothio  Metallothionein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3     0.014   2.6e+02      46      54 ..       4      12 ..       2      17 .. 0.57
   2 !   18.8  13.8   7.1e-08    0.0013       3      28 ..      15      42 ..      13      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.014
  Metallothio 46 qgCvCkgaa 54
                 q C+C+ a+
   AJA92490.1  4 QACGCEAAT 12
                 456665543 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 7.1e-08
  Metallothio  3 p..eCnCaeggsCvCsdsCkctgCkCts 28
                 p  eC+Ca  g+C C+++Ckct   C+ 
   AJA92490.1 15 PdyECDCAMQGTCLCANDCKCTVDVCKE 42
                 5559******************988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 381.75
//
Query:       AJA92491.1  [L=152]
Description: SCO1/SenC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-35  120.4   0.2    4.8e-35  120.2   0.2    1.0  1  AhpC-TSA       AhpC/TSA family
    3.6e-25   88.4   0.1    4.4e-25   88.1   0.1    1.0  1  Redoxin        Redoxin
    3.5e-07   30.3   0.0    4.6e-07   30.0   0.0    1.3  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
    0.00065   20.0   0.0    0.00082   19.7   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
    0.00093   18.8   0.0     0.0011   18.5   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)
     0.0015   18.4   0.0     0.0028   17.6   0.0    1.5  1  SCO1-SenC      SCO1/SenC
  ------ inclusion threshold ------
      0.014   15.6   0.9        1.6    9.0   0.0    2.5  3  CUTL           CUT1-like DNA-binding domain of SATB
      0.066   14.2   0.1       0.11   13.4   0.1    1.4  1  DUF3986        Protein of unknown function (DUF3986)
       0.14   13.0   0.0        0.7   10.7   0.0    1.8  2  FtsQ           Cell division protein FtsQ


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.2   2.4e-38   4.8e-35       2     121 ..       5     130 ..       4     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 2.4e-38
                 TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT- CS
    AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygv 100
                 g+++p+f+l++adg+ v+ s++kg++ v++fyp+d++p+Ctte+ +++k y++fk++g+e++g+s d++ sh+kf++k ++++ ll+D e +v+k++gv
  AJA92491.1   5 GKAVPKFQLEDADGNLVKSSQLKGQKYVVYFYPRDFTPGCTTEADEFSKDYKKFKKAGIEIVGISKDDVTSHRKFCDKMNIPYILLADVETEVCKKFGV 103
                 789************************************************************************************************ PP

                 EETT......TTECSCEEEEE-TTSBE CS
    AhpC-TSA 101 lkee......kglalratfvidkegki 121
                 +  +       ++  r+tf+++++gki
  AJA92491.1 104 WGLKkfmgreFMGINRSTFLVNEKGKI 130
                 *8889*****9***************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.1   2.2e-28   4.4e-25       2     139 ..       4     143 ..       3     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 2.2e-28
                 TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHH CS
     Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftka 100
                 +g+++P+f+l++   dgn v+ s++kg+k vv+f+p+ f+P C++e+ ++ k ++++k+ g+++v+++ d+ +  ++f++k ++++++l+D + ++ k+
  AJA92491.1   4 EGKAVPKFQLED--ADGNLVKSSQLKGQKYVVYFYPRDFTPGCTTEADEFSKDYKKFKKAGIEIVGISKDDVTSHRKFCDKMNIPYILLADVETEVCKK 100
                 7999******88..**********************************999999999****************************************** PP

                 TT-TTEEE.GGG....EEE-EEEEEEETTEEEEEEESSSCHT.S CS
     Redoxin 101 lGlrleedaseg....lrtpryavidedgkvvylevepepet.e 139
                 +G  +  ++ +g       +++++++e+gk+ +++  + p++  
  AJA92491.1 101 FG-VWGLKKFMGrefmGINRSTFLVNEKGKIFKVFPKVKPKGhA 143
                 **.5566666668994445679***************9995532 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.3e-10   4.6e-07       2      55 ..      51     108 ..      50     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
  AhpC-TSA_2   2 Lsrdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglk...r 55 
                 +s+d +++++ag+++v+i+++d+ s +kF++  ++p+ l++D + ++ +++g++   +
  AJA92491.1  51 FSKDYKKFKKAGIEIVGISKDDVtSHRKFCDKMNIPYILLADVETEVCKKFGVWglkK 108
                 57899******************99***************************984441 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   4.1e-07   0.00082       2      79 ..      30     102 ..      28     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.1e-07
                    SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S- CS
  Thioredoxin_8   2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkyn 79 
                    k+v+ ++  ++ p c++   + ++ y+k+k k ++eiv +s d    + +k++ k++ p +     d    +++kk++
     AJA92491.1  30 KYVVYFYPRDFTPGCTTEADEFSKDYKKFK-KAGIEIVGISKDDV-TSHRKFCDKMNIPYIL--LADV-ETEVCKKFG 102
                    8999999999*********99999999999.7***********95.8999999999444333..3322.345555555 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.7e-07    0.0011      86     176 ..      42     135 ..      29     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.7e-07
      DUF899  86 pgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl..svflrdd.grvfhtYs 176
                 pgC++ ad++ ++ ++++++++ ++ +s+  +++  ++ ++m     + +++e+++ ++f+v   ++ + +e  g+  s+fl ++ g++f+ + 
  AJA92491.1  42 PGCTTEADEFSKDYKKFKKAGIEIVGISKDDVTSHRKFCDKMNIPYILLADVETEVCKKFGVWGLKKFMGREFMGInrSTFLVNEkGKIFKVFP 135
                 89*************************************************************99999999999997789999999****9985 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0028       2     132 ..       9     128 ..       8     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
   SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriigltGskeeiakaa 100
                  +F+l d dg+ v++++l+g+ ++v+f     +  C+t+  + ++ ++++++++ ++  ++      +D++   ++++++++  +i l + ++e+   +
  AJA92491.1   9 PKFQLEDADGNLVKSSQLKGQKYVVYFYPRDFTPGCTTEADEFSKDYKKFKKAGIEIVGIS------KDDVTSHRKFCDKMNIPYILLADVETEV---C 98 
                 58*************************99999999*******9999999999966654443......6677777777777776666666655543...4 PP

   SCO1-SenC 101 kefrvyvekvedeesdytvdHsssvyLvdpdg 132
                 k+f+v   k+   ++   +    s++Lv+++g
  AJA92491.1  99 KKFGVWGLKKFMGRE--FMGINRSTFLVNEKG 128
                 555555444444444..555666666666655 PP

>> CUTL  CUT1-like DNA-binding domain of SATB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.016        32      56      70 ..      46      60 ..      41      62 .. 0.86
   2 ?    9.0   0.0   0.00081       1.6      50      68 ..      90     109 ..      82     111 .. 0.80
   3 ?   -3.2   0.0       4.9   9.8e+03      59      72 .]     125     138 ..     119     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.016
        CUTL 56 aKCqEFGrWYKkykk 70
                +   EF + YKk+kk
  AJA92491.1 46 TEADEFSKDYKKFKK 60
                5678**********9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00081
        CUTL  50 yanVSaaKCqEFGrW.YKky 68 
                  a+V ++ C+ FG+W  Kk+
  AJA92491.1  90 LADVETEVCKKFGVWgLKKF 109
                 599************44555 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
        CUTL  59 qEFGrWYKkykkiK 72 
                 +E G+ +K + k+K
  AJA92491.1 125 NEKGKIFKVFPKVK 138
                 57788899998887 PP

>> DUF3986  Protein of unknown function (DUF3986)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.7e-05      0.11      26      77 ..      24      75 ..      10      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
     DUF3986 26 KrknedvWvvyfdfedygvekdelslskf.dkyalfdkyGykvysikakdlde 77
                 + +++++vvyf   d++    +++ ++f ++y+ f+k G+++  i+ +d++ 
  AJA92491.1 24 SQLKGQKYVVYFYPRDFTPGC-TTEADEFsKDYKKFKKAGIEIVGISKDDVTS 75
                5678899**********6555.59999**99***************8888875 PP

>> FtsQ  Cell division protein FtsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.8   1.6e+03      10      56 ..      12      57 ..       7      77 .. 0.47
   2 ?   10.7   0.0   0.00035       0.7       9      49 ..     121     152 .]     115     152 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.8
                EEEETT--B-C......CCBS.S-EEE......S-HHHHHCCS-HHHHH CS
        FtsQ 10 alidaeGevfeade.eaedek.lPlltGpegsekevlevlaelpeelkp 56
                +l da+G++++ ++ +    + +++   p +  +    + +e++++ k+
  AJA92491.1 12 QLEDADGNLVKSSQlKG---QkYVVYFYPRDFTPGCTTEADEFSKDYKK 57
                55588888887622222...22333332433333333333333333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00035
                 EEEEETT--B-C.....CCBSS-EEE......S-HHHHHCC CS
        FtsQ   9 dalidaeGevfeadeeaedeklPlltGpegsekevlevlae 49 
                  +l++++G++f++        +P +  p+g++kevle++++
  AJA92491.1 121 TFLVNEKGKIFKV--------FPKVK-PKGHAKEVLEAFQK 152
                 59*********87........9****.*********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1118.66
//
Query:       AJA92492.1  [L=120]
Description: zinc-ribbon domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-07   30.9   5.0    2.9e-07   30.0   5.0    1.5  1  zinc_ribbon_2   zinc-ribbon domain
    6.8e-07   28.5   2.4      1e-06   27.9   2.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
    2.8e-06   27.2   1.4    4.1e-06   26.7   1.4    1.3  1  DZR             Double zinc ribbon
     0.0017   19.1   1.3     0.0023   18.6   1.3    1.2  1  zinc_ribbon_15  zinc-ribbon family
     0.0041   17.4   1.7       0.33   11.3   0.1    2.3  2  GFA             Glutathione-dependent formaldehyde-activating
     0.0058   16.5   4.5        1.1    9.3   0.3    2.4  2  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.014   15.5   0.7      0.021   14.9   0.7    1.3  1  DHHC            DHHC palmitoyltransferase
        0.2   11.3   4.5       0.44   10.2   4.5    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.28   11.1   5.6        6.1    6.8   0.3    2.5  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        0.4   10.8   5.9        5.3    7.2   0.6    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.79    9.3   3.8        2.9    7.5   3.8    1.8  1  DUF2321         Uncharacterized protein conserved in bacteria
        1.2    9.4   7.0        3.4    7.9   0.7    2.5  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   5.0   1.9e-10   2.9e-07       1      23 []      97     119 ..      97     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.9e-10
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                    fC++CG ++++ akFC +CG++l
     AJA92492.1  97 FCSECGSKNSPQAKFCRECGANL 119
                    9*******************987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   2.4   6.8e-10     1e-06       1      26 []      94     119 ..      94     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.8e-10
  zf-ribbon_3   1 stvrCPnCGa.plssddnvCpyCGtkl 26 
                  ++++C++CG+ + s+++++C  CG+ l
   AJA92492.1  94 EEQFCSECGSkN-SPQAKFCRECGANL 119
                  5899******99.***********976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   1.4   2.8e-09   4.1e-06       1      22 [.      98     119 ..      81     120 .] 0.83

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.8e-09
         DZR   1 CpqCgeelppdarfCseCgtkl 22 
                 C++Cg++++p+a+fC eCg++l
  AJA92492.1  98 CSECGSKNSPQAKFCRECGANL 119
                 8888888888888888888877 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.3   1.6e-06    0.0023      57      86 .]      87     116 ..      68     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-06
  zinc_ribbon_15  57 iekkessekkeCknCgkeveeefkyCpkCg 86 
                      ++++s+e++ C++Cg++ +++ k+C +Cg
      AJA92492.1  87 ANDGSSEEEQFCSECGSKNSPQAKFCRECG 116
                     456677779********************9 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00022      0.33      17      58 ..      62     104 ..      59     108 .. 0.73
   2 !    6.1   0.3    0.0095        14      46      59 ..     106     119 ..     103     120 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
         GFA  17 tanavvkaealelleg...elkeykktadsgnkvtrsfCpeCgsp 58 
                 + + ++ ++++e ++g   + + y  +a+ g+  +++fC+eCgs+
  AJA92492.1  62 APVQIIDDDKFE-ATGalfKSNLYG-SANDGSSEEEQFCSECGSK 104
                 667788999999.555455445555.4778888888*******96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0095
         GFA  46 kvtrsfCpeCgspl 59 
                   + +fC+eCg++l
  AJA92492.1 106 SPQAKFCRECGANL 119
                 55679******986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.4   0.00095       1.4       2      10 ..      97     105 ..      96     109 .. 0.82
   2 !    9.3   0.3   0.00071       1.1       1      10 [.     110     119 ..     110     120 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00095
                 B-TTT--B- CS
   Nudix_N_2   2 FCsqCGtpv 10 
                 FCs+CG++ 
  AJA92492.1  97 FCSECGSKN 105
                 ******986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00071
                 -B-TTT--B- CS
   Nudix_N_2   1 kFCsqCGtpv 10 
                 kFC++CG+ +
  AJA92492.1 110 KFCRECGANL 119
                 9******987 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   1.4e-05     0.021       3      26 ..      93     116 ..      91     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
        DHHC   3 kelkfCstcniykpprskHcrvCn 26 
                 +e++fCs+c     p++k+cr+C+
  AJA92492.1  93 EEEQFCSECGSKNSPQAKFCRECG 116
                 799********************7 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.5   0.00029      0.44       4      26 ..      96     117 ..      94     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
  zf-NADH-PPase   4 rFCgrCGaptepaeggwarvCpa 26 
                    +FC+ CG+++ p++  ++r C a
     AJA92492.1  96 QFCSECGSKNSPQAK-FCRECGA 117
                    8***********998.8887765 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9    0.0062       9.3       2       9 ..      96     103 ..      96     104 .. 0.90
   2 ?    6.8   0.3    0.0041       6.1       2       8 ..     110     116 ..     109     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0062
                     EBESTTTS CS
  RNA_POL_M_15KD   2 kFCpkCgN 9  
                     +FC++Cg+
      AJA92492.1  96 QFCSECGS 103
                     7*****96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0041
                     EBESTTT CS
  RNA_POL_M_15KD   2 kFCpkCg 8  
                     kFC++Cg
      AJA92492.1 110 KFCRECG 116
                     7*****9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5    0.0081        12      15      21 ..      96     102 ..      93     103 .. 0.94
   2 ?    7.2   0.6    0.0035       5.3      14      21 ..     109     116 ..     106     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0081
     UPF0547  15 qfCphCG 21 
                 qfC++CG
  AJA92492.1  96 QFCSECG 102
                 8*****9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0035
     UPF0547  14 aqfCphCG 21 
                 a+fC++CG
  AJA92492.1 109 AKFCRECG 116
                 89*****9 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.8    0.0019       2.9      17      44 ..      86     113 ..      79     120 .] 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
     DUF2321  17 svnkkeelveeyCekcGektitkcpkCs 44 
                 s+n+ + + e++C++cG+k   + + C+
  AJA92492.1  86 SANDGSSEEEQFCSECGSKNSPQAKFCR 113
                 6777788889*******99766544443 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0023       3.4      21      32 ..      93     104 ..      86     107 .. 0.85
   2 ?    4.4   1.1     0.027        41      22      32 ..     108     118 ..     104     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
  NOB1_Zn_bind  21 mtkkFCpkCGnk 32 
                    + +FC++CG+k
    AJA92492.1  93 EEEQFCSECGSK 104
                   6789******97 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
  NOB1_Zn_bind  22 tkkFCpkCGnk 32 
                   + kFC +CG +
    AJA92492.1 108 QAKFCRECGAN 118
                   679******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.48
# Mc/sec: 750.40
//
Query:       AJA92493.1  [L=76]
Description: LSM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-24   83.2   0.2    8.5e-24   83.0   0.2    1.0  1  LSM       LSM domain
     0.0037   17.4   0.1     0.0045   17.1   0.1    1.2  1  SM-ATX    Ataxin 2 SM domain
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.057   13.1   0.0    1.2  1  Hfq       Hfq protein
       0.07   13.5   0.0      0.079   13.4   0.0    1.2  1  RTBV_P12  Rice tungro bacilliform virus P12 protein
      0.081   12.8   0.0       0.16   11.9   0.0    1.5  2  BPL_C     Biotin protein ligase C terminal domain
       0.13   12.4   0.0       0.19   11.9   0.0    1.2  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.2   2.9e-27   8.5e-24       2      67 .]       9      73 ..       8      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 2.9e-27
                HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
         LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                 l+++inkkv+++lk+g+++ G L+gfDq+mNl L++ ee+  ++  +++lg +++RG+n+v+is+
  AJA92493.1  9 VLDESINKKVLIKLKGGKTITGMLQGFDQHMNLLLDQSEEIPSEG-DSKSLGSIVVRGDNVVMISP 73
                699******************************************.******************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.5e-06    0.0045       7      56 ..       9      56 ..       4      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                HHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS..... CS
      SM-ATX  7 lltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansks 56
                +l  ++ k+v +++k G++++G +++++    +++ L+   +++++++++
  AJA92493.1  9 VLDESINKKVLIKLKGGKTITGMLQGFDQ--HMNLLLDQSEEIPSEGDSK 56
                566677799********************..**************33322 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.057      14      43 ..      16      45 ..       8      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                -EEEEEETTS-EEEEEEEEE-SSEEEEEET CS
         Hfq 14 ipvtifLvnGiklkGviksfDnftvlLesd 43
                 +v i L  G  + G++++fD+++ lL ++
  AJA92493.1 16 KKVLIKLKGGKTITGMLQGFDQHMNLLLDQ 45
                57999******************9777443 PP

>> RTBV_P12  Rice tungro bacilliform virus P12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-05     0.079      55      92 ..      31      68 ..       5      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-05
    RTBV_P12 55 alqeidkkinnlttqvsklpttsgsssagaivpagsnt 92
                 lq  d+++n l  q   +p+   s s g+iv  g n 
  AJA92493.1 31 MLQGFDQHMNLLLDQSEEIPSEGDSKSLGSIVVRGDNV 68
                699******************************99986 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05      0.16       2      38 ..      14      50 ..      13      55 .. 0.86
   2 ?   -3.0   0.0       2.3     7e+03      29      34 ..      62      67 ..      57      72 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                TTSEEEEEE.TSCEEEEEEEEE-TTSEEEEEETTE.EE CS
       BPL_C  2 sGqeVtled.edgkveGiavGIdddGaLllktddglqp 38
                +++ V +++ ++++++G+ +G d + +Lll++ ++ +p
  AJA92493.1 14 INKKVLIKLkGGKTITGMLQGFDQHMNLLLDQSEE-IP 50
                7999*****777777******99999999988887.55 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                EEEETT CS
       BPL_C 29 llktdd 34
                +++ d+
  AJA92493.1 62 VVRGDN 67
                444444 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.2e-05      0.19      10      42 ..      13      41 ..      10      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
    DUF150_C 10 flGelVkvklklpvegrkkftGkivevdeetit 42
                +++++V +klk    g+k +tG ++ +d+ +  
  AJA92493.1 13 SINKKVLIKLK----GGKTITGMLQGFDQHMNL 41
                78999999*99....*************87733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 503.91
//
Query:       AJA92494.1  [L=156]
Description: winged helix-turn-helix DNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-10   38.6   3.7    2.9e-05   23.5   1.9    2.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-09   36.8   0.1     0.0026   17.6   0.0    2.4  2  HTH_5           Bacterial regulatory protein, arsR family
    2.5e-05   24.1   0.0      0.087   12.7   0.0    2.1  2  MarR_2          MarR family
      3e-05   23.8   0.7      0.034   14.0   0.0    2.2  2  TrmB            Sugar-specific transcriptional regulator TrmB
    8.9e-05   22.0   6.4    0.00011   21.6   6.1    1.4  1  RepL            Firmicute plasmid replication protein (RepL)
    0.00091   19.1   0.4      0.043   13.8   0.2    2.2  2  MarR            MarR family
     0.0018   18.4   0.7        1.3    9.3   0.3    2.3  2  HTH_34          Winged helix DNA-binding domain
     0.0048   17.2   0.7          2    8.8   0.1    2.4  2  Rrf2            Transcriptional regulator
     0.0082   16.6   0.3      0.034   14.6   0.2    2.0  2  HTH_40          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.022   14.7   0.1    1.7  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.013   15.2   0.0        0.5   10.2   0.0    2.2  2  HTH_IclR        IclR helix-turn-helix domain
      0.022   14.7   0.1       0.04   13.8   0.1    1.6  1  PAX             'Paired box' domain
      0.033   14.5   0.1       0.31   11.4   0.0    2.1  2  FaeA            FaeA-like protein
      0.036   13.8   0.5       0.12   12.1   0.1    2.2  2  HTH_38          Helix-turn-helix domain
      0.089   13.0   3.0       0.15   12.3   2.8    1.4  1  Ribosomal_S25   S25 ribosomal protein
      0.094   12.5   0.1        1.2    8.9   0.0    2.2  2  LexA_DNA_bind   LexA DNA binding domain
      0.098   12.5   1.3       0.76    9.7   0.2    2.4  3  HxlR            HxlR-like helix-turn-helix
       0.17   12.1   0.6       0.76   10.0   0.0    2.3  3  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   3.2e-05     0.032       9      45 ..       7      43 ..       3      46 .. 0.93
   2 !   23.5   1.9   2.9e-08   2.9e-05      18      48 .]      93     123 ..      62     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
      HTH_24  9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                + l++k p+ s++e+ +++ lS + ++ +l +L+e+G
  AJA92494.1  7 IDLIEKMPGVSYNEIVRETRLSNGVISHYLIKLMESG 43
                5789999**************************9998 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.9e-08
      HTH_24  18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                  +q+e+++r++ S st++  lk L+++ +I+
  AJA92494.1  93 STQNEISKRVNKSASTISVSLKDLQRNNIIE 123
                 79***************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.8e-06    0.0038      19      46 ..      19      46 ..       3      47 .. 0.90
   2 !   17.6   0.0   2.6e-06    0.0026      19      46 ..      96     123 ..      78     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.8e-06
                HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5 19 celaeelglsqstvShHLkkLreaGLVe 46
                 e+++e++ls + +Sh+L kL+e+G Ve
  AJA92494.1 19 NEIVRETRLSNGVISHYLIKLMESGEVE 46
                69**********************9776 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.6e-06
                 HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
       HTH_5  19 celaeelglsqstvShHLkkLreaGLVe 46 
                  e+++ +++s st+S  Lk L   +++e
  AJA92494.1  96 NEISKRVNKSASTISVSLKDLQRNNIIE 123
                 69*********************99997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00094      0.94      11      54 ..       7      48 ..       5      53 .. 0.90
   2 !   12.7   0.0   8.7e-05     0.087      23      54 ..      94     125 ..      70     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00094
                HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                +  +   pg  ++ +e++r+++ls + +s  l +L + G ve++
  AJA92494.1  7 IDLIEKMPG--VSYNEIVRETRLSNGVISHYLIKLMESGEVEKE 48
                566888999..9***************************99987 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.7e-05
                 EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2  23 tvgelarrlglsksavsrilkrLvaaGLverr 54 
                 t++e+ +r + s s++s  lk+L++   +er+
  AJA92494.1  94 TQNEISKRVNKSASTISVSLKDLQRNNIIERV 125
                 99****************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0021       2.1      23      63 ..      16      56 ..       6      62 .. 0.84
   2 !   14.0   0.0   3.5e-05     0.034      23      55 ..      93     125 ..      78     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
        TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                 + +ei +e+ ++   +  +L +L++ G Ve+e  ++ +Y 
  AJA92494.1 16 VSYNEIVRETRLSNGVISHYLIKLMESGEVEKEGIKRGKYF 56
                567899***************************98877775 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-05
                 CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
        TrmB  23 atadeiaeelgvprskvYevLrsLedkGlVere 55 
                 +t +ei+++++ + s++  +L+ L +  ++er+
  AJA92494.1  93 STQNEISKRVNKSASTISVSLKDLQRNNIIERV 125
                 7899***************************97 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   6.1   1.1e-07   0.00011      34     108 ..      52     125 ..      34     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
        RepL  34 rdfnFvkvwienliatldliGnk.ktrlvyylidnlnsnntliatnRelaeetgislktvsetlkileeanilkkk 108
                 r+  F k   ++  +++ l+ n+    + + li+n n  n+ i t+ e++++ + s  t+s+ lk l+  ni+ + 
  AJA92494.1  52 RGKYFLKNIPKKDRKMITLLRNNtNNDIFKLLIKNFN--NNTISTQNEISKRVNKSASTISVSLKDLQRNNIIERV 125
                 5556777777777788888866515678999999986..6679******************************984 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.076        76      10      49 ..       8      47 ..       6      51 .. 0.89
   2 !   13.8   0.2   4.3e-05     0.043      14      49 ..      88     124 ..      79     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.076
                HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                 +++ +++ s  e+ +   +s++ ++  l +L + G +e+
  AJA92494.1  8 DLIEKMPGVSYNEIVRETRLSNGVISHYLIKLMESGEVEK 47
                6799999**********************99999997776 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-05
                 HSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        MarR  14 eqgplsvs.eLakklgvskstvtrvldrLekkGlieR 49 
                 +++ +s + e+ k+++ s st++  l+ L +++ ieR
  AJA92494.1  88 NNNTISTQnEISKRVNKSASTISVSLKDLQRNNIIER 124
                 445555557***************************9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0043       4.3      12      47 ..      13      48 ..       1      63 [. 0.81
   2 !    9.3   0.3    0.0013       1.3      15      49 ..      93     127 ..      79     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0043
      HTH_34 12 vdeadfvelkealeatdgnLsvhlkkLekagYievd 47
                   ++++e+  ++++++g +s  l kL + g +e +
  AJA92494.1 13 MPGVSYNEIVRETRLSNGVISHYLIKLMESGEVEKE 48
                678999**********************99988755 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0013
      HTH_34  15 adfvelkealeatdgnLsvhlkkLekagYievdke 49 
                  + +e+++ ++ +++ +sv lk L+ ++ ie+ + 
  AJA92494.1  93 STQNEISKRVNKSASTISVSLKDLQRNNIIERVIM 127
                 56789**********************99987655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0098       9.8      25      71 ..      15      61 ..       4      72 .. 0.81
   2 !    8.8   0.1     0.002         2      18      56 ..      85     123 ..      80     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0098
                -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHC CS
        Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakpp 71
                 vs +ei +++ +s  ++++ l kL ++g v+ +  k+G y L+  p
  AJA92494.1 15 GVSYNEIVRETRLSNGVISHYLIKLMESGEVEKEGIKRGKYFLKNIP 61
                2899***************************9887777888887655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.002
                 HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        Rrf2  18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                 ++ ++++  + +ei++r+n s+s ++  l+ L+++++++
  AJA92494.1  85 KNFNNNTISTQNEISKRVNKSASTISVSLKDLQRNNIIE 123
                 556667778999*************************98 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   3.4e-05     0.034      12      65 ..      15      76 ..       3     117 .. 0.71
   2 ?    0.2   0.0       1.1   1.1e+03      16      36 ..      96     116 ..      90     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-05
      HTH_40 12 glsieeIAkerglkesTIegHLaelieegeeidlerl.........vseeeekeIeeaiekvg 65
                g s  eI +e +l+ + I  +L++l+e+ge ++ e +         ++++++k I+   ++ +
  AJA92494.1 15 GVSYNEIVRETRLSNGVISHYLIKLMESGE-VEKEGIkrgkyflknIPKKDRKMITLLRNNTN 76
                78999***********************96.44433333333444455555555554444333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
      HTH_40  16 eeIAkerglkesTIegHLael 36 
                  eI+k+ + + sTI   L +l
  AJA92494.1  96 NEISKRVNKSASTISVSLKDL 116
                 577777777777776555554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       7.3   7.3e+03       5       8 ..      34      37 ..      20      51 .. 0.62
   2 ?   14.7   0.1   2.3e-05     0.022      23      53 ..      94     124 ..      67     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.3
                HHHH CS
   HTH_Crp_2  5 rfLl 8 
                ++L+
  AJA92494.1 34 HYLI 37
                3444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.3e-05
                 HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
   HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglisr 53 
                 tq e++ +++ + +t+s  l++L+r ++i+r
  AJA92494.1  94 TQNEISKRVNKSASTISVSLKDLQRNNIIER 124
                 9****************************94 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005       0.5       9      51 ..       7      48 ..       6      49 .. 0.86
   2 ?    2.8   0.0       0.1     1e+02      21      50 ..      95     124 ..      88     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                +d++++ p+ ++  e+ r+t l+    +++L  L+e G ve++
  AJA92494.1  7 IDLIEKMPG-VSYNEIVRETRLSNGVISHYLIKLMESGEVEKE 48
                566666666.89**************************99986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                 HHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
    HTH_IclR  21 lselArrtglpkStvhRlLqtLvelGyveq 50 
                   e+++r   + St +  L+ L++  ++e+
  AJA92494.1  95 QNEISKRVNKSASTISVSLKDLQRNNIIER 124
                 579*************99999999888876 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     4e-05      0.04      32     101 ..      14      86 ..       1     114 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4e-05
         PAX  32 sgvrpcvisrqlrvshgcvskilgryqetgsirpgviggskpk.vatpevvkkieeykren..psifaweird 101
                  gv   +i r  r+s+g++s+ l +  e+g +    i   k      p+   k+  + r+n    if   i++
  AJA92494.1  14 PGVSYNEIVRETRLSNGVISHYLIKLMESGEVEKEGIKRGKYFlKNIPKKDRKMITLLRNNtnNDIFKLLIKN 86 
                 4889999*************************98888777665256788888877766655114566665554 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.31       2      54 ..       3      54 ..       1      60 [. 0.83
   2 ?    0.9   0.0       0.6     6e+02      16      50 ..      93     127 ..      76     132 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSS CS
        FaeA  2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGv 54
                ke +++ + +   ++  +ei   + ls   + +YL +L   g +++  ++rG 
  AJA92494.1  3 KEIVIDLIEK-MPGVSYNEIVRETRLSNGVISHYLIKLMESGEVEKEGIKRGK 54
                3444444444.6778899*********************************95 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.6
                 --HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
        FaeA  16 ckTreiAdalglsaYQaRyYLeqLekegkikrspv 50 
                  + +ei + +  sa  +   L+ L++   i+r+ +
  AJA92494.1  93 STQNEISKRVNKSASTISVSLKDLQRNNIIERVIM 127
                 44457777777777777778999999999999865 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.6   6.6e+03       9      18 ..      64      73 ..      63      74 .. 0.77
   2 ?   12.1   0.1   0.00012      0.12      22      38 ..      94     110 ..      77     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.6
      HTH_38  9 eReeIerlla 18
                +R +I  l++
  AJA92494.1 64 DRKMITLLRN 73
                8999988876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
      HTH_38  22 slreIArrLgrspsTIs 38 
                 ++ eI +r+++s sTIs
  AJA92494.1  94 TQNEISKRVNKSASTIS 110
                 577*************8 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.8   0.00015      0.15      40      97 ..      76     133 ..      47     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
  Ribosomal_S25  40 dketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvskhraqvi 97 
                    ++++++ l+k+  +  + t+  +s+r++ ++s     L++l+++++i++v+ +++++i
     AJA92494.1  76 NNDIFKLLIKNFNNNTISTQNEISKRVNKSASTISVSLKDLQRNNIIERVIMNKSSKI 133
                    5677888999****************************************99998877 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.3     3e+02      27      58 ..      17      47 ..       5      52 .. 0.81
   2 ?    8.9   0.0    0.0012       1.2      11      58 ..      79     124 ..      70     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.3
                   -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
  LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                   s  ei r+ +l+    + + L +L   G +e 
     AJA92494.1 17 SYNEIVRETRLS-NGVISHYLIKLMESGEVEK 47
                   678999999997.6667778999999998875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                    HHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
  LexA_DNA_bind  11 vldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58 
                    +++l+ ++ +++    +  ei+++++ kS+s++   Lk L+r  +ier
     AJA92494.1  79 IFKLLIKNFNNNTIS-TQNEISKRVN-KSASTISVSLKDLQRNNIIER 124
                    555555555555443.789******9.89*************999998 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.6   1.6e+03      21      51 ..      18      47 ..       5      53 .. 0.63
   2 ?    1.2   0.1      0.34   3.4e+02      16      41 ..      48      72 ..      36      86 .. 0.82
   3 ?    9.7   0.2   0.00077      0.76      22      56 ..      96     129 ..      80     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
        HxlR 21 fselkralpkisqkmLaqrLreLeqdglier 51
                ++e+ r+   +s+ ++++ L +L ++g +e+
  AJA92494.1 18 YNEIVRET-RLSNGVISHYLIKLMESGEVEK 47
                55565555.6666677777777766666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.34
                TS-EEHHHHHHHSTTS-HHHHHHHHH CS
        HxlR 16 kgkkRfselkralpkisqkmLaqrLr 41
                +g kR + + +++pk  +km++  Lr
  AJA92494.1 48 EGIKRGKYFLKNIPKKDRKMITL-LR 72
                58899999999****99999875.45 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00077
                 HHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESS CS
        HxlR  22 selkralpkisqkmLaqrLreLeqdglierevype 56 
                 +e+++++ + s ++++ +L+ L+++++ier+++++
  AJA92494.1  96 NEISKRV-NKSASTISVSLKDLQRNNIIERVIMNK 129
                 6777777.6688999***************99886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.7   2.7e+03      38      53 ..      31      46 ..       6      51 .. 0.65
   2 ?   10.0   0.0   0.00076      0.76      23      49 ..      93     119 ..      83     125 .. 0.86
   3 ?   -2.1   0.0       4.7   4.6e+03      45      54 ..     145     154 ..     144     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                    HHHHHHHHHHHTTSEE CS
  Fe_dep_repress 38 sVsemlkkLekdGyve 53
                     +s  l kL + G ve
      AJA92494.1 31 VISHYLIKLMESGEVE 46
                    4566677777777665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00076
                     B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
  Fe_dep_repress  23 vktkdlaerLnvspssVsemlkkLekd 49 
                      ++ ++++r n s+s++s +lk L+++
      AJA92494.1  93 STQNEISKRVNKSASTISVSLKDLQRN 119
                     46789*******************997 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.7
                     HHHHTTSEEE CS
  Fe_dep_repress  45 kLekdGyvey 54 
                     kL+ + +v+y
      AJA92494.1 145 KLSTNNLVKY 154
                     99999***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1069.61
//
Query:       AJA92495.1  [L=465]
Description: phenylalanine--tRNA ligase, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-86  289.5   0.1    4.2e-86  288.4   0.0    1.5  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.9e-08   33.4   0.0    1.3e-06   28.1   0.0    2.8  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00014   21.3   0.2     0.0015   18.1   0.1    2.6  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00031   21.0   2.0    0.00064   20.0   0.3    2.5  3  PheRS_DBD3       PheRS DNA binding domain 3
      0.003   17.5   0.3      0.015   15.3   0.1    2.0  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
     0.0062   15.7   0.0      0.022   13.8   0.0    1.9  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.054   13.6   0.0    1.6  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
      0.041   13.0   0.2      0.098   11.7   0.1    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
       0.18   12.1   0.8       0.44   10.9   0.2    1.9  2  CBM_2            Cellulose binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.5e+03      21      41 ..      89     109 ..      79     145 .. 0.68
   2 !  288.4   0.0   2.1e-89   4.2e-86       2     244 ..     200     464 ..     199     465 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                   HHHHHHHHHHHCTTCEESSTT CS
  tRNA-synt_2d  21 kvleeikeiflelgfeevegp 41 
                   k+ e+i++++   gf+++  +
    AJA92495.1  89 KTFEQIRSVLSGAGFNVAIAN 109
                   577889999999999876433 PP

  == domain 2  score: 288.4 bits;  conditional E-value: 2.1e-89
                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-...................... CS
  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka...................... 76 
                   idv+++ ++i a+++hpl+++++ei+eif++lgf+e+ g+  +s+f+nfdaL++pqdhpaR++qdtFyl++ e++                      
    AJA92495.1 200 IDVEADVPSIFAARTHPLQDTIDEIREIFVNLGFSEILGNMTQSSFWNFDALFTPQDHPARELQDTFYLENLESKnpasssqiknvssshkknwkyd 296
                   89*******************************************************************87777799******************** PP

                   ....ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETT CS
  tRNA-synt_2d  77 ....veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpf 168
                       +++k++LRthtt+v+i++l e+k   ++i+s+grvfR+++v ++hl+eF+q+eg+v+++n +l+dl+g+ +e++kkl g + k++f p++fp+
    AJA92495.1 297 wklsESQKMVLRTHTTCVTIKHLaEQKPENARIFSVGRVFRNEKVSYKHLVEFNQIEGIVIGNNTTLRDLMGIQKEFYKKL-GLT-KIKFWPTFFPY 391
                   ****999****************55555789**************************************************.**9.*********** PP

                   EEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
  tRNA-synt_2d 169 tePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                   tePs+++ vy  ek +kw+El+g+G++rpev++++gi  +++++a+G G+eR+amlky+++D+Re+++n+l +lr+
    AJA92495.1 392 TEPSLQTMVYN-EKLGKWIELFGMGIFRPEVTKPLGI--DKPVLAWGGGIERIAMLKYELDDVREFYNNNLSWLRS 464
                   ***********.*************************..9*********************************986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.17   3.3e+02       5      35 ..      75     104 ..      72     119 .. 0.85
   2 !   28.1   0.0   6.4e-10   1.3e-06      14     209 ..     213     433 ..     204     434 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
  tRNA_synthFbeta   5 lPkapttegelnkeqklrrklrdllagaGln 35 
                      lP+ ++    l++e k+ +++r++l+gaG+n
       AJA92495.1  75 LPERKLINM-LKEEPKTFEQIRSVLSGAGFN 104
                      677777777.778899999***********8 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 6.4e-10
  tRNA_synthFbeta  14 elnkeqklrrklrdllagaGlnEvitysfvsekeldkll...eddderk..............................avelanPlsedqs.v 73 
                      + ++ q++ +++r++ +++G++E++     s+ ++ ++l   +d++ r+                                +    lse q+ v
       AJA92495.1 213 RTHPLQDTIDEIREIFVNLGFSEILGNMTQSSFWNFDALftpQDHPARElqdtfylenlesknpasssqiknvssshkkNWKYDWKLSESQKmV 306
                      46899*******************988877777777777765666777799****************************999999999988725 PP

  tRNA_synthFbeta  74 lRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefep 166
                      lRt  +   ++ la+   ++ e+ r+F +g+vf+++  + +   e +++ +++ g++               dl gi +++ ++lg++k++f p
       AJA92495.1 307 LRTHTTCVTIKHLAE---QKPENARIFSVGRVFRNEkVSYKHLVEFNQIEGIVIGNN-----------TTLRDLMGIQKEFYKKLGLTKIKFWP 386
                      788777766666665...6677789***********888899***************...........************************** PP

  tRNA_synthFbeta 167 aehpalhpgrsAeikvdgk....evGvlGelhpevleafdlkqrvyv 209
                      +  p+ +p  +  ++ ++     e+  +G + pev + ++++++v +
       AJA92495.1 387 TFFPYTEPSLQTMVYNEKLgkwiELFGMGIFRPEVTKPLGIDKPVLA 433
                      ********87777764433667877779**************99875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   7.5e-07    0.0015       3      31 ..       7      35 ..       5      45 .. 0.91
   2 ?   -2.2   0.0       1.6   3.2e+03       6      17 ..      78      89 ..      77      90 .. 0.85
   3 ?   -0.6   0.0      0.49   9.8e+02      29      48 .]      98     117 ..      98     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.5e-07
      HTH_24  3 etdrkILelLqknprisqreLAerlglSp 31
                ++++kILe+Lqk p+ s  +L++ + lS+
  AJA92495.1  7 DIEKKILETLQKTPNQSPEQLSKNTELSI 35
                799************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
      HTH_24  6 rkILelLqknpr 17
                rk+++ L+++p+
  AJA92495.1 78 RKLINMLKEEPK 89
                899*****9996 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.49
      HTH_24  29 lSpstvnrrlkrLeeeGlIk 48 
                 lS +  n  + + +++G+Ik
  AJA92495.1  98 LSGAGFNVAIANAKKNGWIK 117
                 678889999**********7 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   3.2e-07   0.00064      16      53 ..      89     127 ..      76     132 .. 0.66
   2 ?   -2.0   0.0       2.3   4.5e+03       2      23 ..     137     157 ..     136     162 .. 0.72
   3 ?   -2.7   0.0       3.9   7.9e+03      14      34 ..     359     379 ..     349     381 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.2e-07
  PheRS_DBD3  16 isqkelkklggdpvakiGfskAmknkWikkdkgdg.kvv 53 
                  + +++  +++ + +++++++A kn+Wik++k+++  +v
  AJA92495.1  89 KTFEQIRSVLSGAGFNVAIANAKKNGWIKIEKNNSdSLV 127
                 5555664444445699****************7765555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
  PheRS_DBD3   2 hEarvfaavppeggisqkelkk 23 
                 +E ++ + +  e++isq+e+++
  AJA92495.1 137 PEEKLLSFI-GEKTISQEEITN 157
                 677777888.5455***99954 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.9
  PheRS_DBD3  14 ggisqkelkklggdpvakiGf 34 
                 + +++ +l+ + ++ + k+G+
  AJA92495.1 359 NNTTLRDLMGIQKEFYKKLGL 379
                 348899998886766666665 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.36   7.2e+02      80     110 ..     217     265 ..     208     325 .. 0.68
   2 !   15.3   0.1   7.5e-06     0.015      31     131 ..     323     411 ..     295     428 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.36
                   HHHHHHHHHHHHHHTT.SCEEEEEEGTTSC....................B CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................x RF
  tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaks....................a 110
                   l+d i +i +if +lg++   i++ m + s                     
    AJA92495.1 217 LQDTIDEIREIFVNLGFS--EILGNMTQSSfwnfdalftpqdhparelqdT 265
                   689999999******966..6777777555555555555555555555551 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 7.5e-06
                   EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  31 rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefraiielmsaksadykdkkefeavsesltk 127
                   +++    +++ +++++R+Ek + +    + eF+q +g v++ +      lrdl+   ++++++lgl + +       + +  +++++ +++ e+l+k
    AJA92495.1 323 KPE--NARIFSVGRVFRNEKVSYKH---LVEFNQIEGIVIGNNT----TLRDLMGIQKEFYKKLGLTKIKFWPT---FFPYTEPSLQTMVYNEKLGK 407
                   233..4799***********95667...66***********988....899**************996644443...33678999999999999999 PP

                   EEEE CS
                   xxxx RF
  tRNA-synt_2b 128 giei 131
                    ie+
    AJA92495.1 408 WIEL 411
                   9886 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   2.7e+03      28      45 ..     220     237 ..     215     267 .. 0.84
   2 !   13.8   0.0   1.1e-05     0.022      93     119 ..     328     353 ..     324     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                  HHHHHHHHHHHTT-EE-- CS
                  xxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2  28 vtkavrkyleengfieie 45 
                   ++ +r+++ + gf ei 
   AJA92495.1 220 TIDEIREIFVNLGFSEIL 237
                  577899999999999996 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.1e-05
                  EEEEEEEEE--S--BTTB-S-CEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                  r+f+++r+FR+E+++ + hl EF qie
   AJA92495.1 328 RIFSVGRVFRNEKVSYK-HLVEFNQIE 353
                  89************965.555*****9 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-05     0.054       9      47 ..       3      41 ..       1      45 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                HCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHH CS
       HTH_9  9 ehFGevvakVvetLlrkgrltlrelvkktkLsldqVkks 47
                + F ++ +k+ etL ++  ++  +l+k+t+Ls dq++++
  AJA92495.1  3 QVFHDIEKKILETLQKTPNQSPEQLSKNTELSIDQIRRG 41
                56778889****************************987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.9e-05     0.098      42      95 ..      74     155 ..      41     249 .. 0.72
   2 ?   -2.0   0.0      0.75   1.5e+03      69      95 ..     342     390 ..     323     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
  ABC2_membrane_3  42 sslsqqlvealeasps.velvyevdseeeakkalkngdidgilvipkgfskdll...........................k 95 
                          ++l+++l+++p+ +e++ +v s + ++ a+ n + +g + i+k++s++l+                            
       AJA92495.1  74 GLPERKLINMLKEEPKtFEQIRSVLSGAGFNVAIANAKKNGWIKIEKNNSDSLVsikekpietpeekllsfigektisqeeI 155
                      44568899*****985499********************************9996666655555555555544444444441 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.75
  ABC2_membrane_3  69 eakkalkngdidgilvipkgfskdll......................k 95 
                      + k++++ ++i+gi++ ++  ++dl+                      +
       AJA92495.1 342 SYKHLVEFNQIEGIVIGNNTTLRDLMgiqkefykklgltkikfwptffP 390
                      5677778889999999999999999877777766555555555555554 PP

>> CBM_2  Cellulose binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   4.9e+03      52      72 ..      98     118 ..      90     133 .. 0.74
   2 ?   10.9   0.2   0.00022      0.44      18      45 ..     279     306 ..     269     329 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                 EEEETTEEEEEE-STT-EE-T CS
       CBM_2  52 vsqsGnsvtatnvswNgtiap 72 
                 +s++G +v++ n++ Ng i++
  AJA92495.1  98 LSGAGFNVAIANAKKNGWIKI 118
                 567777788888888877765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00022
                 EEEEEE-SSS-EES-EEEEE--TTEEEE CS
       CBM_2  18 svtvkNsgssaingWtvewtlpagqrvt 45 
                 s ++kN +ss  ++W+ +w+l+++q+++
  AJA92495.1 279 SSQIKNVSSSHKKNWKYDWKLSESQKMV 306
                 568*******************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3148.62
//
Query:       AJA92496.1  [L=259]
Description: hypothetical protein T478_1020 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.9   0.2      0.028   14.9   0.2    2.7  3  DUF1410   Protein of unknown function (DUF1410)
      0.041   13.9   0.0        0.4   10.7   0.0    2.2  2  CE2_N     Carbohydrate esterase 2 N-terminal
        2.6    8.1   6.5        1.4    9.0   0.2    3.1  3  DUF5640   Family of unknown function (DUF5640)


Domain annotation for each model (and alignments):
>> DUF1410  Protein of unknown function (DUF1410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   4.7e-06     0.028      19      46 ..      39      76 ..      14      92 .. 0.87
   2 ?   -1.4   0.1      0.57   3.4e+03      29      35 ..     153     159 ..     122     182 .. 0.60
   3 ?   -1.4   0.1       0.6   3.6e+03      27      27 ..     214     214 ..     194     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-06
     DUF1410 19 nnkefkie........dakidknkktli.d.lnnLann 46
                +++ f++e        ++ +dk+kk+++ + l++L+nn
  AJA92496.1 39 DGHSFVVEvtgnldvtNLDFDKDKKSITlFvLSSLENN 76
                5666777788999999************989******9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.57
     DUF1410  29 kidknkk 35 
                 +id+n+ 
  AJA92496.1 153 NIDENQS 159
                 2344444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.6
     DUF1410  27 d 27 
                  
  AJA92496.1 214 S 214
                 3 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.7e-05       0.4      29      84 ..      76     129 ..      69     135 .. 0.87
   2 ?    0.1   0.0      0.13     8e+02      40      64 ..     187     210 ..     173     225 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                 EEEEEEEEE..SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE CS
       CE2_N  29 tslsvrlkdkedkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvk 84 
                 +sl++++++  +     + ++iDg++++   + g+++t+ +++ +  g+h+++++ 
  AJA92496.1  76 NSLEISFRN--QLIGGDYSIFIDGDKFMPDLKAGSNTTFLTMDFSGMGKHKIEIFG 129
                 567777777..77788999*******999988999999****************85 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                 SSS-EEEEEEETTS--EEEEE-SS- CS
       CE2_N  40 dkgknrlaviiDgkrvkdlkldgee 64 
                   ++ ++ v+iDg + +d+++++++
  AJA92496.1 187 PFDDGSFIVMIDGVE-SDYTIEDNT 210
                 566778899999998.555554443 PP

>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.15   8.7e+02      48      75 ..      56      84 ..      24      94 .. 0.57
   2 ?    0.4   0.2      0.12   6.9e+02      17      43 ..     114     140 ..     104     166 .. 0.81
   3 ?    9.0   0.2   0.00023       1.4      35      55 ..     200     220 ..     189     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.15
                EEEESS----EEE.-EEESSSEEEE-SST CS
     DUF5640 48 idfeaekkedcey.efsvngntLtLtggs 75
                +df+++kk    +   s+++n+L++   +
  AJA92496.1 56 LDFDKDKKSITLFvLSSLENNSLEISFRN 84
                35555333332220345566666655554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                 EEEE-SSS-EEEEEEETTEEEEEE-SS CS
     DUF5640  17 tYkFdedGtgelelskaaykftYtiee 43 
                 t  F + G+ ++e+  ++y  t++i +
  AJA92496.1 114 TMDFSGMGKHKIEIFGTTYLDTFNIRD 140
                 557999999999999999887777654 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00023
                 EEEEEE-SSSSEEEEEESS-- CS
     DUF5640  35 ykftYtieedqLkidfeaekk 55 
                 ++ +Ytie+++++i f+++++
  AJA92496.1 200 VESDYTIEDNTMNISFNSDNE 220
                 5569**********9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1944.80
//
Query:       AJA92497.1  [L=48]
Description: hypothetical protein T478_0800 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 348.62
//
Query:       AJA92498.1  [L=334]
Description: diphthamide biosynthesis enzyme Dph2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-62  212.3   0.0    1.2e-62  212.0   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.0   6.9e-67   1.2e-62       2     297 ..      26     322 ..      25     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 6.9e-67
  Diphthamide_syn   2 Pegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd...rlpvlYvfveieldvehlvetlkknfkekk 91 
                      P+g+lp+ +e a ++ ++f++  ++l+Dtt+G C+++   a+ lga++l  +Gh+   ++    + +v+ + +  ++ +++++ ++ + + ++k
       AJA92498.1  26 PDGMLPQVQETAVNItKKFDIPAFVLADTTWGTCDLNSNGAKVLGAEILFNIGHTNKLETFpgeQDNVIMIDAFDNVPFDAVIPKALEIL-NGK 118
                      ******************************************************9888655666*******999999999**********.799 PP

  Diphthamide_syn  92 kivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdailyigdgrfhllslmlsnpklpvyrydpyskklt 185
                      +i+l+++ q+ h++e+vk++le+ g+ v k+++ + +l++g+v+gc++  + e++eevda l++g+ +fh+ ++++s+ k+++y +dpy ++++
       AJA92498.1 119 TISLITDSQHLHQVESVKKQLEDGGVFV-KIGKGKGQLNDGQVFGCEFYPAMETKEEVDANLFLGQSNFHAAGVAIST-KVKTYILDPYFNEVR 210
                      9*********************666544.4889999**********99999999************************.78************* PP

  Diphthamide_syn 186 eesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeF 279
                      + +  a+kl ++   +i ka++ak++G+ivg +++q    ++ + kk+l+e+gk++ l++++ ++ ++L+nf+ idaf++vaCpr+s+d+  eF
       AJA92498.1 211 DVTNFAEKLEKKATLKIYKAMEAKVFGVIVGLKEGQFAKVTALKFKKELEERGKEVQLLALTDITSDRLKNFTGIDAFIQVACPRISTDN--EF 302
                      *****************************************************************************************6..8* PP

  Diphthamide_syn 280 ekPvltpyElevalg..ere 297
                      +kP+l+   ++ +l+  ++e
       AJA92498.1 303 DKPMLSTPQANALLKmlNNE 322
                      **********9999965444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2300.70
//
Query:       AJA92499.1  [L=138]
Description: archease protein family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-30  105.1   1.6    3.7e-30  105.0   1.6    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   1.6   2.1e-34   3.7e-30       1     137 [.       3     137 ..       3     138 .] 0.94

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 2.1e-34
                 EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EEEE.E-SSSEEEEEEEE- CS
    Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkvdeeeeeeeleleaearg 99 
                 y++l+h  D iie+++++l+eaf+ a+++++e++ d  kv++ +++++ v+++dl+ lL+++L+e+++l  t+ f+ k++++d   ++e++e++ae+ g
  AJA92499.1   3 YRTLEHATDAIIEVTADNLKEAFQIAGISVIETILDSTKVDEIDSRKLVVKGKDLKYLLYNWLEEIIILTITDGFAGKRIEIDI-LRNENYEIHAEVFG 100
                 99******************************************************************************8865.66789********* PP

                 ---.-TT--------B--S---EEEEETTEEEEEEEEE CS
    Archease 100 ekfdkekhevqtevKAvTyhelrieeeddgweayvvvD 137
                 e ++ +khe++ e+K  T+he++i+e+d ++ ++ ++D
  AJA92499.1 101 EAINLKKHEFKVEIKSPTFHEMEIKEDD-KIVMKYLLD 137
                 *************************976.666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1015.61
//
Query:       AJA92500.1  [L=41]
Description: hypothetical protein T478_0530 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 306.21
//
Query:       AJA92501.1  [L=276]
Description: menaquinone biosynthesis protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-77  258.5   0.0      8e-77  258.3   0.0    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.34   11.2   0.0    1.8  2  Imm26           Immunity protein 26


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.3   0.0   8.9e-81     8e-77       1     266 []       3     261 ..       3     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 258.3 bits;  conditional E-value: 8.9e-81
                     EEEEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-S CS
  VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleele 95 
                     +++Gh+p+++d+f+fya+++ kv+s+ + v++v+ed+e+ln+++ + elDv+++S++a+a+i + y++L+  s++++G  yg+++ +++p++  e
      AJA92501.1   3 ISVGHTPDSDDAFMFYAMFTDKVKSDDFSVTHVIEDIENLNKKAKNPELDVTAVSVHACAYIPN-YVMLR--SGGSFGINYGPIVTATKPMTIEE 94 
                     68***********************************************************765.*****..***************88776655 PP

                     SS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCHHHTGGGGTTEEEEEHHHHHHHHH.SS-EEEEEEEE CS
  VitK2_biosynth  96 gelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIgesaltyaeeglkkvlDLgelWeelt.glPlvlglwvv 188
                      + ++++a+pge+t+++lLl+l++ ++     ++ve++f++i++av +g+ d+gL+I+e +l + eeg +k+lD ge+W e + glP++lg++v+
      AJA92501.1  95 IK-KSKIAIPGEMTSAYLLLQLMIGKF-----DYVEMNFSDIPEAVRSGKvDVGLVIHETQLSFGEEGIQKILDVGEWWHEKSgGLPVPLGVNVM 183
                     44.78*********************9.....9**************************************************77********** PP

                     ECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHHC CS
  VitK2_biosynth 189 rrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevlekhlelYvnelsydlgeegragleeflelaae 266
                     +++l++e + ++++ l+eS+++a++++ ++++ya+++++ +++e +ek++ +Yvne+++d+ge+g+++++ ++e+a+e
      AJA92501.1 184 SEKLGEELIYKFDKYLQESIKFARDNIPDALDYAMKYSRGKSRELIEKFVLMYVNEVTVDMGEAGEKAVRLMFEMAKE 261
                     ***************************************************************************986 PP

>> Imm26  Immunity protein 26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.34      11      61 ..      26     106 ..      19     124 .. 0.82
   2 ?   -1.9   0.0      0.44     4e+03      25      42 ..     170     202 ..     134     211 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
       Imm26  11 dngkyafGrvisder..............................lmggglvieiydivseneeidleeitnssllfepii 61 
                 +++ + + +vi+d++                                gg + i +++iv+ ++ +++eei++s+++++  +
  AJA92501.1  26 KSDDFSVTHVIEDIEnlnkkaknpeldvtavsvhacayipnyvmlRSGGSFGINYGPIVTATKPMTIEEIKKSKIAIPGEM 106
                 55667777888887788888888888888888888888888887777999*************************998655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.44
       Imm26  25 r...............lmggglvieiydivsen 42 
                 +               ++g  l++++ ++ +e+
  AJA92501.1 170 KsgglpvplgvnvmseKLGEELIYKFDKYLQES 202
                 044444444444444456666777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1733.55
//
Query:       AJA92502.1  [L=127]
Description: prefoldin, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-19   70.0  24.0    1.7e-19   69.7  24.0    1.0  1  Prefoldin_2  Prefoldin subunit
  ------ inclusion threshold ------
        1.7    8.8  13.1       0.58   10.3   1.5    2.7  3  KIP1         KIP1-like protein
        2.1    7.8   9.3       0.34   10.4   4.4    1.8  2  DUF1221      Protein of unknown function (DUF1221)
        2.3    8.4   9.4        2.2    8.5   2.5    2.0  2  DUF4809      Domain of unknown function (DUF4809)
        2.3    8.7  17.0        3.2    8.2  17.0    1.2  1  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7  24.0   4.7e-23   1.7e-19       1     104 [.      12     115 ..      12     116 .. 0.99

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.7e-23
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkee 98 
                  qe+i k+qq+qq lq + +q++q+e++  e++ +leel+++ + ++v+k  G +l+k dk+++++eLee+ke  +++++ l kq+e+l++ l+e++++
   AJA92502.1  12 QEQIGKMQQSQQNLQSILMQKQQVEMENAESDRALEELKKASDGDQVFKYAGSILIKSDKKSLIDELEEKKELSKTKSTVLAKQEERLKTSLQEQEQK 109
                  89************************************************************************************************ PP

                  HHCCTS CS
  Prefoldin_2  99 lqkklq 104
                  +q++l+
   AJA92502.1 110 IQEMLK 115
                  ****97 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.9    0.0068        24      13      47 ..       8      42 ..       3      52 .. 0.85
   2 ?   -0.7   0.8      0.43   1.6e+03      48      61 ..      67      80 ..      31      87 .. 0.52
   3 ?   10.3   1.5   0.00016      0.58       9      32 ..      92     115 ..      86     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0068
        KIP1 13 skwLqetlseldekvkemlklieedadsfakraem 47
                 +wLqe++  + +  +++ +++ + ++ +++ ae 
  AJA92502.1  8 PPWLQEQIGKMQQSQQNLQSILMQKQQVEMENAES 42
                58*******************98888888877775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.43
        KIP1 48 yykkrpeLielvee 61
                  + ++ Li+ +ee
  AJA92502.1 67 IKSDKKSLIDELEE 80
                33344444444444 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00016
        KIP1   9 sskqskwLqetlseldekvkemlk 32 
                   kq++ L++ l+e ++k++emlk
  AJA92502.1  92 LAKQEERLKTSLQEQEQKIQEMLK 115
                 5799******************97 PP

>> DUF1221  Protein of unknown function (DUF1221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.12   4.4e+02     181     200 ..      18      36 ..      10      69 .. 0.57
   2 ?   10.4   4.4   9.5e-05      0.34     161     204 ..      67     115 ..      61     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.12
     DUF1221 181 ltksekrladlLlkkleese 200
                 +++s++ l+ +L++k++ +e
  AJA92502.1  18 MQQSQQNLQSILMQKQQ-VE 36 
                 44455555555555443.22 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.5e-05
     DUF1221 161 wkeDrwlllellkekkksas.....ltksekrladlLlkkleeseklng 204
                 +k D++ l+++l+ekk+ ++     l+k+e+rl+  L+++ ++ +++ +
  AJA92502.1  67 IKSDKKSLIDELEEKKELSKtkstvLAKQEERLKTSLQEQEQKIQEMLK 115
                 799*************665556678*********999998887666554 PP

>> DUF4809  Domain of unknown function (DUF4809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.7      0.01        36      64     117 ..      13      66 ..       6      69 .. 0.87
   2 ?    8.5   2.5   0.00062       2.2      59     102 ..      71     115 ..      67     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
     DUF4809  64 emleEvlifkkeekevkfkeesanvtfkskdqkiqvkkkledlqelfeevnqiL 117
                 e+++ +++ +++ +++ +++++ ++   + d  +   kk++d  ++f+ +  iL
  AJA92502.1  13 EQIGKMQQSQQNLQSILMQKQQVEMENAESDRALEELKKASDGDQVFKYAGSIL 66 
                 55666788889999999999999999999*******************999998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00062
     DUF4809  59 qelllemleEvlifkkeekevkfkeesa.nvtfkskdqkiqvkkk 102
                 ++ l+++leE   ++k + +v  k+e++ +++ ++++qkiq   k
  AJA92502.1  71 KKSLIDELEEKKELSKTKSTVLAKQEERlKTSLQEQEQKIQEMLK 115
                 57899****************998766527789999999997665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  17.0    0.0009       3.2     124     200 .]      17     111 ..       8     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0009
      AAA_23 124 llgskkiilnlilflgqer..........feefelkdkkerleelekeleeledekkllekleqekekek........eleeleeeleeilkele 200
                 ++++++++l+ il+++q+            ee++++++ +++ ++  ++  ++d+k+l+++le++ke  k        + e l+  l+e++++++
  AJA92502.1  17 KMQQSQQNLQSILMQKQQVemenaesdraLEELKKASDGDQVFKYAGSILIKSDKKSLIDELEEKKELSKtkstvlakQEERLKTSLQEQEQKIQ 111
                 35667778888888888886655555544333444555558888888888888888888888766666666677666644444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3436  (0.191645); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 871.43
//
Query:       AJA92503.1  [L=157]
Description: hypothetical protein T478_1088 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.073   12.9   0.0       0.21   11.4   0.0    1.8  1  DIX           DIX domain
       0.09   12.9   0.2         15    5.8   0.0    2.2  2  GBS_Bsp-like  GBS Bsp-like repeat


Domain annotation for each model (and alignments):
>> DIX  DIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.21      22      58 ..      49      86 ..      45     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
         DIX 22 krpdqiTLkdfKellpkkGnyryffKtldedfe.gvVk 58
                +++++iTL  f + + +++n  +  K  ++df+ g   
  AJA92503.1 49 SSKSEITLTGFSNEIVQNSNIEFSIKLSNPDFNcGDLY 86
                55679***************************766655 PP

>> GBS_Bsp-like  GBS Bsp-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0017        15      51      89 ..      65     103 ..      50     105 .. 0.89
   2 ?    5.3   0.1    0.0024        22      50      80 ..     112     142 ..     109     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0017
  GBS_Bsp-like  51 sdgtykvtvniknhkneaGkYnvhvYvtdkngkqkglgs 89 
                   ++ +++ +++++n +++ G   + +Y t++++kq++++s
    AJA92503.1  65 QNSNIEFSIKLSNPDFNCGDLYITIYDTSSSEKQVLTQS 103
                   56778999************************9998876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0024
  GBS_Bsp-like  50 qsdgtykvtvniknhkneaGkYnvhvYvtdk 80 
                   q+++t  v+ n ++  +++G+Y++hv + ++
    AJA92503.1 112 QNNNTLPVDENYSELITKSGTYEIHVEIFNE 142
                   5677778888888888999999999966555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1106.16
//
Query:       AJA92504.1  [L=331]
Description: archaeal ribosomal protein L3 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-73  247.6   5.1    6.2e-73  245.9   5.1    1.7  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.9   5.1   3.4e-77   6.2e-73       1     357 [.       1     326 [.       1     331 [] 0.91

  Alignments for each domain:
  == domain 1  score: 245.9 bits;  conditional E-value: 3.4e-77
                   XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--EEEEEEEEE.EEET CS
  Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppmvivgvvgy.vetp 96 
                   m hrk ++pr+gsl ++pr Ra++  ++v+++Pk   ++p  l a +GyKaG  +iV  +d+  ++ ++k++v   tv+ tpp++ivg++gy ++t+
    AJA92504.1   1 MGHRKRSQPRRGSLAYSPRIRAKSMEARVRAWPKVAGDEP-RLLAHAGYKAGCVQIVSIDDREHTPSHGKQLVTLGTVIATPPITIVGIRGYsIDTN 96 
                   89********************************999965.7889***********************************************77999 PP

                   TEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHH CS
  Ribosomal_L3  97 rGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvvrviahtvirktkslaqKkahllEiqvngGtiae 193
                   +   +  + +a++l ++v+  l     k           k e     +  e+ l++ik+    +  i+ t   +++ l+ Kk+ + E++v+gG i +
    AJA92504.1  97 HTRNAEFDSFAKDLPKNVQNNL-----K----------IKTE-GTPLDEAEKHLKKIKE----IFAIVTTTPVDVN-LEMKKPYIFEVKVEGGDIPK 172
                   9888888999999999988888.....1..........2222.2233344556778877....6666677777888.9******************* PP

                   HHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEET CS
  Ribosomal_L3 194 kldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigk 290
                   ++ f+++ l ktv+v++vF++g ++D +++tkGkG++Gv+ RWg k+++ k  ++ R ++++g+  p  V++tv+raGq+G+h+R+e++k+i+ + +
    AJA92504.1 173 QFAFTKDLLGKTVKVDQVFESGTYVDTAAITKGKGWQGVIYRWGAKRKQHKSRKTVREIGSLGPISPQSVMYTVPRAGQTGFHQRVEYDKRIMIMSN 269
                   ********************************************************************************************99888 PP

                   TTSSTTTSSTTT.SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-E CS
  Ribosomal_L3 291 gedaknastefdltekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeev 357
                              ++ e +i+P+GGf h+G v++dfi+vkGsvpG+ +rl+klrk ++ + ++  +++v
    AJA92504.1 270 ----------TEKEEYKINPDGGFKHFGNVTGDFIIVKGSVPGTYRRLIKLRKQIRNEPKKVVKPNV 326
                   ..........3455779**************************************999888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2322.39
//
Query:       AJA92505.1  [L=121]
Description: PF01796 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-13   48.7   0.4    8.2e-13   48.1   0.4    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    6.2e-05   22.8   0.1    9.7e-05   22.2   0.1    1.3  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0074   16.0   1.5      0.012   15.3   1.5    1.4  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
       0.02   14.9   0.4       0.03   14.4   0.4    1.2  1  DZR             Double zinc ribbon
      0.027   15.2   0.3      0.036   14.8   0.3    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.048   13.3   0.1       0.06   13.0   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.062   13.5   0.2       0.08   13.2   0.2    1.2  1  PHF5            PHF5-like protein
      0.095   12.5   0.7          1    9.1   0.2    2.6  3  zinc_ribbon_5   zinc-ribbon domain
       0.14   12.6   0.7        5.3    7.5   0.0    2.3  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.16   11.4   3.8        7.4    6.1   0.4    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.19   11.8   4.0       0.32   11.1   0.1    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.4   5.1e-16   8.2e-13       4      63 ..      48     109 ..      46     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 5.1e-16
                    E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEE.EES..TT-B-EEE CS
  OB_aCoA_assoc   4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvd.pdevriGmrVrav 63 
                    l+g G+v+++t++  +p gf++ aPy+++v eLd+ g+r+ + l  +  p+++ iG++V+++
     AJA92505.1  48 LKGAGKVVTYTIMTVPPAGFEDLAPYAWVVMELDDsGIRVSGFLAKIStPEDLPIGTPVKVT 109
                    789************************************999999999677799******85 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   5.9e-08   9.7e-05       2      36 ..       9      43 ..       9      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.9e-08
     DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsddl 36
                daa+ g +++++C++CG        +C  Cgs+++
  AJA92505.1  9 DAAKSGNILARKCAKCGEILLATVYYCKSCGSKEF 43
                79*****************87666********987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.5   7.6e-06     0.012       1      22 [.      20      41 ..      20      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.6e-06
  zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                   +C +CG+ l  ++ +C  CG++
     AJA92505.1 20 KCAKCGEILLATVYYCKSCGSK 41
                   8*******************85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   1.8e-05      0.03      29      49 .]      19      39 ..       4      42 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
         DZR 29 drCpsCgekvdpearfCpeCG 49
                ++C +Cge + ++  +C++CG
  AJA92505.1 19 RKCAKCGEILLATVYYCKSCG 39
                667777777777777777776 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   2.2e-05     0.036      61      86 .]      14      39 ..       2      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
  zinc_ribbon_15 61 essekkeCknCgkeveeefkyCpkCg 86
                     ++ +++C++Cg+ + + + yC +Cg
      AJA92505.1 14 GNILARKCAKCGEILLATVYYCKSCG 39
                    334489*******************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.7e-05      0.06      74      98 ..      19      43 ..       5      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
     TackOD1 74 rlCpsCksghlnvrevCpkCkSidi 98
                r C +C    l   ++C++C+S ++
  AJA92505.1 19 RKCAKCGEILLATVYYCKSCGSKEF 43
                78********************987 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   4.9e-05      0.08      54      79 ..      17      42 ..       4      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
        PHF5 54 leekciicgskgvsdayyclecvrle 79
                l++kc  cg+    + yyc++c   e
  AJA92505.1 17 LARKCAKCGEILLATVYYCKSCGSKE 42
                4789******************8776 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00064         1      27      35 ..      20      28 ..      17      30 .. 0.88
   2 ?    0.1   0.0      0.43   7.1e+02       5      11 ..      35      41 ..      33      55 .. 0.84
   3 ?   -1.4   0.0       1.2     2e+03      14      23 ..      80      89 ..      78      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00064
  zinc_ribbon_5 27 rCakCaevF 35
                   +CakC+e+ 
     AJA92505.1 20 KCAKCGEIL 28
                   8******95 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
  zinc_ribbon_5  5 CpdCdtk 11
                   C  C++k
     AJA92505.1 35 CKSCGSK 41
                   8999986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
  zinc_ribbon_5 14 lvdsklKksg 23
                   l+ds +++sg
     AJA92505.1 80 LDDSGIRVSG 89
                   8999999998 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.073   1.2e+02       2      11 ..      19      29 ..      18      33 .. 0.78
   2 ?    7.5   0.0    0.0033       5.3       4      30 ..      35      67 ..      33      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.073
     zf-IS66  2 rtCpcCGg.ll 11
                r+C++CG  ll
  AJA92505.1 19 RKCAKCGEiLL 29
                68999998775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0033
     zf-IS66  4 CpcCGg.l.....lkpigedrvreeldipPakf 30
                C+ CG+ +     lk +g++ +  +  +pPa f
  AJA92505.1 35 CKSCGSkEfgdtiLKGAGKVVTYTIMTVPPAGF 67
                ******77************8889999999987 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0045       7.4      16      24 ..      18      26 ..      16      28 .. 0.81
   2 ?    6.0   0.3     0.005       8.1       3      17 ..      33      46 ..      31      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0045
  zf-ribbon_3 16 dnvCpyCGt 24
                 +++C++CG+
   AJA92505.1 18 ARKCAKCGE 26
                 688999995 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.005
  zf-ribbon_3  3 vrCPnCGaplssddn 17
                 ++C +CG++ + +d+
   AJA92505.1 33 YYCKSCGSK-EFGDT 46
                 578888888.88877 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.32       3      13 ..      20      30 ..      19      32 .. 0.88
   2 ?    1.5   0.7       0.2   3.2e+02       4       9 ..      35      40 ..      34      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
      zf-ACC  3 KCpsCgemlyk 13
                KC +Cge+l++
  AJA92505.1 20 KCAKCGEILLA 30
                9*******985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
      zf-ACC  4 CpsCge 9 
                C sCg+
  AJA92505.1 35 CKSCGS 40
                ****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 874.97
//
Query:       AJA92506.1  [L=190]
Description: PF08819 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-44  152.0   0.3    1.6e-44  151.8   0.3    1.1  1  DUF1802   Domain of unknown function (DUF1802)


Domain annotation for each model (and alignments):
>> DUF1802  Domain of unknown function (DUF1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   0.3   8.8e-49   1.6e-44       2     155 ..       4     159 ..       3     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 8.8e-49
     DUF1802   2 LkewavaveaLeeGrqivllrKggireergkFeveeeeflLYPtvehqkaellkpeyaallepvasestpe.kveikawAeveeavevsdeealealsk 99 
                 Lkewa++v+aLe+G+q+v+lrKggi e+  +F++e+++f+L+Pt+ehq+++++kpe+++ l++v +++ ++   +i+++Ae+     ++++e +++ls+
  AJA92506.1   4 LKEWATVVKALEQGKQTVILRKGGILETASGFNIESKKFFLFPTWEHQETKHVKPEFHDFLNEVLDKKPKAgFNKISSYAEILFEKDIESNEIINQLSS 102
                 9***************************************************************98887778889************************ PP

     DUF1802 100 lhiwteeavedrlkykpkqpltvlllRvyrleepvelpetpeyagckswvdlpes..e 155
                 +hiw+++++++r ++kp++p+++++l++++++e + lp ++e++gcksw++l+++  +
  AJA92506.1 103 FHIWSDSYIQERRNWKPEKPMKAVFLKIMKVPE-FDLPLKSEFSGCKSWIELNSNfqD 159
                 *******************************87.588899************998643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1348.67
//
Query:       AJA92507.1  [L=161]
Description: PIN domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-15   55.0   0.2    1.6e-14   54.1   0.2    1.3  1  PIN_6           PIN domain of ribonuclease
    6.4e-05   23.5   0.2    9.8e-05   22.9   0.2    1.3  1  PIN             PIN domain
    0.00091   18.7   0.2     0.0019   17.7   0.2    1.5  1  RecR            RecR protein
    0.00093   18.7   0.7       0.02   14.3   0.1    2.1  2  PIN_5           PINc domain ribonuclease
     0.0012   18.8   0.1     0.0023   17.9   0.1    1.4  1  zinc-ribbons_6  zinc-ribbons
     0.0024   17.9   0.9      0.022   14.7   0.7    2.0  2  zinc_ribbon_11  Probable zinc-ribbon
     0.0094   16.2   1.1      0.016   15.4   1.1    1.5  1  PIN_2           PIN domain
     0.0095   15.9   0.9      0.016   15.2   0.9    1.4  1  DUF4411         Domain of unknown function (DUF4411)
  ------ inclusion threshold ------
      0.018   14.9   0.9      0.029   14.2   0.9    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.041   14.2   0.1      0.069   13.5   0.1    1.5  1  DUF3134         Protein of unknown function (DUF3134)
      0.056   13.5   0.6      0.097   12.7   0.6    1.3  1  DZR             Double zinc ribbon
      0.096   12.9   1.9       0.18   12.0   1.9    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.097   12.5   2.4       0.21   11.4   2.4    1.6  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
        0.1   12.7   2.1        0.3   11.2   2.1    1.8  1  Zn-ribbon_8     Zinc ribbon domain
       0.11   12.5   3.1       0.26   11.3   3.1    1.9  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.13   11.8   5.4        1.7    8.1   5.4    2.3  1  zf-ribbon_3     zinc-ribbon domain
       0.15   12.0   2.9       0.77    9.7   2.9    1.9  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.23   12.4   3.6        3.2    8.8   0.3    2.6  2  zf-C2H2_4       C2H2-type zinc finger
       0.25   11.3   2.5       0.48   10.4   2.5    1.4  1  zf-RING_5       zinc-RING finger domain
       0.56   10.3   4.7        1.4    9.0   1.1    2.2  2  zf-C2H2_6       C2H2-type zinc finger
       0.78    9.8   3.5         72    3.5   3.5    2.4  1  zf-BED          BED zinc finger
          1   10.0   3.4          5    7.8   0.3    2.5  2  zf-C2H2         Zinc finger, C2H2 type
        1.2    9.6   6.0        2.5    8.7   1.0    2.3  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
        1.5    8.7   5.2         39    4.1   5.1    2.3  1  zinc_ribbon_2   zinc-ribbon domain
        2.1    8.7   4.5        1.1    9.6   1.9    1.9  1  zf-C2H2_jaz     Zinc-finger double-stranded RNA-binding


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.2   2.3e-17   1.6e-14       2      88 ..       5      91 ..       5      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.3e-17
       PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkare.rlellp..lelevrePspesvkkvtefakktGDlsvLSktDievlALtye 88
                +lDa+a+ +    ++  ++++++tt+ V +Ei+  ka++  le+l+   +l++r+Ps++++++v++++ ktGD ++ Sk+D++++AL++e
  AJA92507.1  5 ILDATAFYAG--IPF-VSNDSFMTTSIVYEEIQHIKAKQgALEMLQqtNRLQIRDPSEKNIAIVKDASIKTGDSTTISKQDMSIIALALE 91
                7899999988..554.46799************9888887899998545**************************************986 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   1.4e-07   9.8e-05      30     121 ..      22     108 ..       4     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.4e-07
                 EEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
         PIN  30 elvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrvak 121
                   +t+++v++E+ ++ a+        +  +e l++ ++l+i + +++  +++++ + k g    ++  D+ i+A+A+e++++li t D    +vak
  AJA92507.1  22 SFMTTSIVYEEIQHIKAK--------QGALEMLQQTNRLQIRDPSEKNIAIVKDASIKTGdsttISKQDMSIIALALENDCELI-TDDFAVTNVAK 108
                 556777777777777777........888888888*************************************************.**987777765 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.7e-06    0.0019       9      36 ..     122     150 ..     118     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.7e-06
                 HHHHHHH-EE-TTT--.EESSSS-CCCCS CS
        RecR   9 LqeakekvrhCsrCgn.lteedlCaICsd 36 
                 ++++ + +++Cs+Cg  ++ e  C+IC +
  AJA92507.1 122 IKTVGKWISYCSICGKeFSKEKECPICGN 150
                 67777889******973699999****87 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.085        61      45      88 ..      22      64 ..      13      71 .. 0.70
   2 !   14.3   0.1   2.8e-05      0.02     156     191 ..      79     114 ..      71     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.085
       PIN_5 45 cyip.psvykElkeflkreeveeeviakldtwlvkkspdryevki 88
                 +++ + vy+E++++  +++  e    +    l +++p++ ++ i
  AJA92507.1 22 SFMTtSIVYEEIQHIKAKQGALEM--LQQTNRLQIRDPSEKNIAI 64
                456647789999998887776544..3445567777887777766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.8e-05
       PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrl 191
                 s++D+ ++ LA E d +++++D  ++++a++l +++
  AJA92507.1  79 SKQDMSIIALALENDCELITDDFAVTNVAKQLKIKT 114
                 89******************************9985 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.2e-06    0.0023      17      40 ..     130     153 ..     116     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
                     EE-TTT--EEEEEEE-SSS-S--- CS
  zinc-ribbons_6  17 yhCeaCqedlkkealCpeCeqele 40 
                       C+ C ++++ke+ Cp C+++l+
      AJA92507.1 130 SYCSICGKEFSKEKECPICGNKLN 153
                     57*******************997 PP

>> zinc_ribbon_11  Probable zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.54   3.9e+02      65      95 ..      51      81 ..      42      95 .. 0.79
   2 !   14.7   0.7   3.1e-05     0.022      89     120 ..     119     152 ..      93     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.54
  zinc_ribbon_11 65 acayldpeekeeerlkklrekivadyalpkv 95
                    +   +dp+ek+   +k    k+  + +++k 
      AJA92507.1 51 RLQIRDPSEKNIAIVKDASIKTGDSTTISKQ 81
                    56789*****999999988888888888665 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.1e-05
  zinc_ribbon_11  89 dyalpkvrkw..ycvlcdedyegkklcpackdgv 120
                        +  v kw  yc +c ++++ +k cp c++ +
      AJA92507.1 119 TKGIKTVGKWisYCSICGKEFSKEKECPICGNKL 152
                     3446677888889*****************9876 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.1   2.3e-05     0.016      25     113 ..      19     101 ..       3     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
       PIN_2  25 kaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslyeskikeAkeriarvDpdDtpfvAlaLlleapiWTeDk 113
                 ++ +++++  ++eei++ k++    + l++ +  ++ +  e++i iv+ ++++      +  + +  ++D+ ++AlaL  ++ + T+D 
  AJA92507.1  19 SNDSFMTTSIVYEEIQHIKAKQGALEMLQQTNRLQIRDPSEKNIAIVKDASIKTG----DSTTIS--KQDMSIIALALENDCELITDDF 101
                 556788999999999999999999999999999999999*******999887644....444444..58*****************995 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   2.2e-05     0.016      88     137 ..      64     112 ..      16     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
     DUF4411  88 vesekyskaakkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknkvkI 137
                 + +++  k+ +++  s+ D  +iA+Al++++ ++T + + +n  k + kI
  AJA92507.1  64 IVKDASIKTGDSTTISKQDMSIIALALENDCELITDDFAVTNVAK-QLKI 112
                 2233333334566679**********************9888877.7777 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   4.1e-05     0.029      24      47 ..     130     152 ..     125     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-05
                 EE-HHHHHHHHHTT-B-TTT--B- CS
  zf-C3HC4_3  24 vlCeeCaekllkrkkkCpiCrrpi 47 
                  +C+ C +++ +++k+CpiC  + 
  AJA92507.1 130 SYCSICGKEF-SKEKECPICGNKL 152
                 68********.89*******9876 PP

>> DUF3134  Protein of unknown function (DUF3134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.6e-05     0.069      20      52 ..      38      70 ..      32     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.6e-05
     DUF3134 20 qesslLdWLessGRLiardeeeeeeleeeeeei 52
                 ++  L+ L++++RL  rd++e++  + +++ i
  AJA92507.1 38 AKQGALEMLQQTNRLQIRDPSEKNIAIVKDASI 70
                55666999***************9988666655 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   0.00014     0.097      14      39 ..     131     153 ..     126     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
         DZR  14 fCseCgtklkavaaedrCpsCgekvd 39 
                 +Cs Cg++ ++   e+ Cp Cg k++
  AJA92507.1 131 YCSICGKEFSK---EKECPICGNKLN 153
                 9999**99985...999**9999865 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.9   0.00025      0.18       1      32 [.     122     151 ..     122     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
  NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                   ik+v +w+  C  C k +++ +   Cp CGnk
    AJA92507.1 122 IKTVGKWISYCSICGKEFSKEKE--CPICGNK 151
                   89999***********9987665..*****97 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.4    0.0003      0.21      21      40 .]     130     148 ..     128     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
  zf-C3HC4_2  21 vfCqkCilrsLeekneCPlC 40 
                 ++C+ C ++  ++++eCP+C
  AJA92507.1 130 SYCSICGKE-FSKEKECPIC 148
                 68******9.69******** PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   0.00042       0.3       8      39 ..     132     155 ..     131     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
  Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsevrrv 39 
                  C  Cg+ef +        +++CP Cg ++ r 
   AJA92507.1 132 CSICGKEFSK--------EKECPICGNKLNRK 155
                  9999999992........556******87774 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.1   0.00037      0.26      68      95 ..     127     151 ..      28     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                 --EEEETTTS-EEECHHHHHS-TTTSSS CS
        HypA  68 pvkvrCreCgkefeleekalrCpkCgsa 95 
                 +   +C+ Cgkef++e k  +Cp Cg++
  AJA92507.1 127 KWISYCSICGKEFSKE-K--ECPICGNK 151
                 45678*********77.3..6****986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.4    0.0024       1.7       4      26 .]     131     152 ..     130     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
  zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtkl 26 
                  +C+ CG+    s  + Cp CG kl
   AJA92507.1 131 YCSICGKeF--SKEKECPICGNKL 152
                  799999988..7778899999987 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.9    0.0011      0.77       6      28 ..     131     150 ..     128     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
  Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgt 28 
                   C++Cgke+++e+    Cp Cg 
   AJA92507.1 131 YCSICGKEFSKEKE---CPICGN 150
                  5**********965...899885 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0044       3.2       2      12 ..     131     141 ..     130     144 .. 0.81
   2 ?    4.3   0.2      0.12        89       2      10 ..     144     152 ..     143     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0044
   zf-C2H2_4   2 kCpiCgksFss 12 
                 +C+iCgk Fs 
  AJA92507.1 131 YCSICGKEFSK 141
                 6********64 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
   zf-C2H2_4   2 kCpiCgksF 10 
                 +CpiCg   
  AJA92507.1 144 ECPICGNKL 152
                 7****8765 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.5   0.00067      0.48      24      43 ..     131     149 ..     130     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00067
   zf-RING_5  24 fCekClkkllekeavCpiCr 43 
                 +C+ C k+ + ke++CpiC+
  AJA92507.1 131 YCSICGKEFS-KEKECPICG 149
                 8999999999.99******7 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.1     0.002       1.4       4      13 ..     132     141 ..     131     143 .. 0.89
   2 ?    2.6   0.1       0.2   1.5e+02       3       9 ..     144     150 ..     144     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
   zf-C2H2_6   4 CsvCsksFps 13 
                 Cs+C+k+F++
  AJA92507.1 132 CSICGKEFSK 141
                 ********97 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
   zf-C2H2_6   3 eCsvCsk 9  
                 eC++C++
  AJA92507.1 144 ECPICGN 150
                 8****97 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.5       0.1        72      18      28 ..     144     154 ..     126     160 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                 EETTTTEE--- CS
      zf-BED  18 vCryCgkilsr 28 
                 +C +Cg++l+r
  AJA92507.1 144 ECPICGNKLNR 154
                 45566666655 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3     0.007         5       2      12 ..     131     141 ..     130     144 .. 0.86
   2 ?    2.7   0.2      0.28     2e+02       2      11 ..     144     153 ..     143     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.007
                 EETTTTEEESS CS
     zf-C2H2   2 kCpdCgksFkr 12 
                 +C++Cgk F+ 
  AJA92507.1 131 YCSICGKEFSK 141
                 5********86 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                 EETTTTEEES CS
     zf-C2H2   2 kCpdCgksFk 11 
                 +Cp+Cg + +
  AJA92507.1 144 ECPICGNKLN 153
                 6****96655 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.15   1.1e+02       3      13 ..     132     142 ..     131     142 .. 0.87
   2 ?    8.7   1.0    0.0034       2.5       1       8 [.     143     150 ..     143     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.15
  Zn-C2H2_12   3 CPlCseqFpkn 13 
                 C +C++ F+k+
  AJA92507.1 132 CSICGKEFSKE 142
                 779******95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0034
  Zn-C2H2_12   1 KeCPlCse 8  
                 KeCP+C++
  AJA92507.1 143 KECPICGN 150
                 9*****97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   5.1     0.055        39       1      23 []     131     152 ..     131     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.055
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                    +C+ CG+e   ++k Cp CG +l
     AJA92507.1 131 YCSICGKE-FSKEKECPICGNKL 152
                    68888887.56788899999876 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.9    0.0015       1.1       3      15 ..     131     143 ..     129     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                  BBTTTTBBBSSHH CS
  zf-C2H2_jaz   3 YCvlCdKyFksen 15 
                  YC +C K F++e+
   AJA92507.1 131 YCSICGKEFSKEK 143
                  **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1110.98
//
Query:       AJA92508.1  [L=198]
Description: hypothetical protein T478_0682 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1423.22
//
Query:       AJA92509.1  [L=372]
Description: putative dehypoxanthine futalosine cyclase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-17   64.4   0.0    4.8e-17   62.8   0.0    1.8  2  Radical_SAM      Radical SAM superfamily
  ------ inclusion threshold ------
      0.092   12.0   0.0       0.52    9.6   0.0    2.1  2  MATalpha_HMGbox  Mating-type protein MAT alpha 1 HMG-box


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.41   3.6e+03      84     113 ..      21      49 ..      15      61 .. 0.74
   2 !   62.8   0.0   5.4e-21   4.8e-17       3     166 ..      69     241 ..      67     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.41
                  ECSSCHGHHHHHHHHHTT-SEEEEEEBSSS CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaad 113
                   ng++p +e   rll+   d++ +gl a++
   AJA92509.1  21 LNGIRPKKEDYLRLLKSD-DVYLMGLVAGN 49 
                  699999988888888867.88888887766 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 5.4e-21
                  EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG........ CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
  Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlaklavpgiritvetngtlpd........ 90 
                   t+ C  +C+fCa+++   +++ +++l+++ei++ vk + +++     ++i+gg +p l  +++e+ +++++ + p++ ++  +    ++        
   AJA92509.1  69 YTNVCITDCKFCAFYRP-PNHEEAYTLTLDEIEARVKTG-WDMFkiRQVLIQGGHNPKLGIEYYEDSFKMIRSKFPNVGVHGLSTSEIDMiatvekss 164
                  6899************6.9********************.999996678889999*******************888888888877776688888888 PP

                  .HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                  .xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 .eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeeleellel 166
                   +e+l rl+++g   +   g+e+++d  v++++  ++ + +++++ ++   e+g++  + +++ ++ e+d +++e+++ 
   AJA92509.1 165 tKEILSRLKDAGlQSVPGAGAEILTDS-VKEIISpKKIDSDDWIRIMKESFELGLP-ASATMMYGHVETDNDIVEHYDK 241
                  8**************************.****************************.9*****************9986 PP

>> MATalpha_HMGbox  Mating-type protein MAT alpha 1 HMG-box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   5.8e-05      0.52      19      67 ..     220     269 ..     200     274 .. 0.75
   2 ?   -0.8   0.0     0.087   7.8e+02     160     187 ..     338     365 ..     328     371 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 5.8e-05
  MATalpha_HMGbox  19 allammkeaveivake.sreakakkakkklNgFmgfRsYylkLfsdlqqk 67 
                      a+ +mm  +ve+ + + ++ +k  k +k lNgFm+f  +  +  + l qk
       AJA92509.1 220 ASATMMYGHVETDNDIvEHYDKIAKLQKDLNGFMAFIPWSFEPNNTLMQK 269
                      55566666666666666667899999**********87766555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.087
  MATalpha_HMGbox 160 nkeqplteldlltkileaGyivdneeal 187
                        +  lt   ++++i + Gy  ++ +  
       AJA92509.1 338 ARSTELTDKRIIESIKQIGYSAEERDNF 365
                      4556789999**********98887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2373.82
//
Query:       AJA92510.1  [L=186]
Description: 5-formyltetrahydrofolate cyclo-ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-39  134.8   0.0    3.5e-39  134.6   0.0    1.0  1  5-FTHF_cyc-lig   5-formyltetrahydrofolate cyclo-ligase family
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.17   11.8   0.0    1.1  1  Sulfotransfer_2  Sulfotransferase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   3.9e-43   3.5e-39       1     187 []       7     179 ..       7     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 3.9e-43
                     HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-SEEEE----TTS---HHHHHHHHHTTEEEEEEEECSSCTEECEEEEEECCCCCCC CS
  5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqeakrvalyvsvkgeidtkelikklleegkevllPrvrlesgslkvvrlttlkeedsl 95 
                     K++lRk ll+++++ s + ++  s+++++++ + k  +eak + +y+s++ e++t eli  llee+k v lPr+++       +++ + ++ ++l
      AJA92510.1   7 KAALRKHLLEKRDSTSFDLIEIHSQKIISKLMKTKVISEAKSIGCYYSIGSEVQTVELITHLLEEKKIVSLPRISNGM-----MSFRKIEDLTKL 96 
                     789************************************************************************999.....99999******* PP

                     CCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTST-SS--EEEEE--GGGEES-----ST----SEEE-S CS
  5-FTHF_cyc-lig  96 esgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkggagdkpltvglaldeqlverlPleehDvpvdevvte 187
                     e+g++ ++eP+++++ e+   k d+vlvP+v+ d+eG+R+G+G+G+yD++l++ +       +++gl +++q+v+++P+++ Dv++d ++te
      AJA92510.1  97 EKGEFDIPEPKDNAQVEE---KHDVVLVPCVGLDNEGNRIGYGAGFYDKYLEKKNL------IKIGLSYSKQIVKTIPISDGDVKMDWIITE 179
                     ***************988...79****************************99888......****************************97 PP

>> Sulfotransfer_2  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17     138     225 ..      10      98 ..       1     116 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
  Sulfotransfer_2 138 Fleclsnlapersr..nnrhwap.acd.lctpcladydlvgkyetleedrnailrllallnlknvavfgltefprktqtanttrrsnstras 225
                      + ++l+++ ++ s+  ++ h ++ +++ ++t+++ + + +g+y ++ ++++ +++++ l  l+++++ +l ++++ ++ ++++++  +++++
       AJA92510.1  10 LRKHLLEKRDSTSFdlIEIHSQKiISKlMKTKVISEAKSIGCYYSIGSEVQTVELITHL--LEEKKIVSLPRISNGMM-SFRKIEDLTKLEK 98 
                      55667777766666667889777888999******************************..77777778888888554.5555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1158.51
//
Query:       AJA92511.1  [L=211]
Description: TENA/THI-4 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-16   58.7   0.0    7.1e-16   58.5   0.0    1.1  1  Haem_oxygenas_2  Iron-containing redox enzyme
    1.7e-15   57.4   0.1      2e-15   57.2   0.1    1.1  1  TENA_THI-4       TENA/THI-4/PQQC family
  ------ inclusion threshold ------
       0.14   12.7   0.1        0.4   11.2   0.0    1.8  2  Gly_radical      Glycine radical


Domain annotation for each model (and alignments):
>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   1.2e-19   7.1e-16       3     159 ..      39     185 ..      37     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.2e-19
  Haem_oxygenas_2   3 flrqrapyklvfgdwlalvhsrltdrevkrallenlsEElGdgdlernHvelyrrllkalGldeeplealpelpetlalinlfeavalsrrllg 96 
                      + ++++ ++++ ++ +  ++      ++k++l++n+ EE        +H  l+++++ ++G++e++l+  + l +t ++++ +  ++ s ++  
       AJA92511.1  39 YSKEYYQLVKQVPQFMEPMVNDAS-SDMKDELVQNMKEES-------EHIPLWEKFAGSMGISESELQGYEGLEKTNRAVSNLGSLMDSFDNG- 123
                      667888888999999988888888.9*************9.......6*************************66666666655555555555. PP

  Haem_oxygenas_2  97 allGallalEllvsletlklaeelre.lgldeea.peyfdlHvtiDnaHaamaleaviellatee 159
                        ++a++a+E   +++ +  +e+l+e +g+d ++ +eyf +H t+D  Haa +  ++i+++  ++
       AJA92511.1 124 --ACAMYAFEKEIPKVSQTKLEGLKEfYGIDTKDaTEYFEEHMTADIRHAASWQ-KIINNTSIDD 185
                      ..99***************************9999******************6.9998876554 PP

>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.1   3.4e-19     2e-15       9     171 ..      15     176 ..       5     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.4e-19
                 HHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT-HHHHHCTTT--HHHHHHHH CS
  TENA_THI-4   9 keyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrlaealGlsreelsktkpspatkayvr 107
                 k++ +HpF++++++G+l+ +++++y +++y  +k+ ++++  ++  +s+   + el  + ++ ++e+i l++++a + G+s++el+ ++ +++t  +v+
  AJA92511.1  15 KSLLKHPFYEMWSDGKLELDSLKGYSKEYYQLVKQVPQFMEPMVNDASSDMKD-ELV-QNMKEESEHIPLWEKFAGSMGISESELQGYEGLEKTNRAVS 111
                 33455***********************************9777766666555.444.457888899*************************9999998 PP

                 HHHHHHCHS-HHHHHHHHHHHHHHHHHHH.HHHCCHHH...S-TSCHHHHHHHHHCSHHHHHHHHHHH CS
  TENA_THI-4 108 ylldlarrgslaeavaallpclfvyqeia.erlkeklr...alegpeyyewvkeyaseefraaveeak 171
                  l +    +s+   ++a+++++  +  ++ ++l   l+     + ++  e+++e+ +++ r+a +++k
  AJA92511.1 112 NLGS--LMDSFDNGACAMYAFEKEIPKVSqTKLE-GLKefyGIDTKDATEYFEEHMTADIRHAASWQK 176
                 7765..579**************99999945555.555366566666777788888888888777744 PP

>> Gly_radical  Glycine radical
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.2   6.9e+03      49      67 ..     105     123 ..      98     129 .. 0.72
   2 ?   11.2   0.0   6.7e-05       0.4       3      66 ..     143     208 ..     141     211 .] 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                  HCC-CCCCCCHHCCCCCCT CS
  Gly_radical  49 eeeerienlatlldgyfeg 67 
                  +++  + nl +l+d++ +g
   AJA92511.1 105 KTNRAVSNLGSLMDSFDNG 123
                  4566788888999887654 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.7e-05
                  STTSHHCCHHHCHCHHCCCC..CCTSECGCETTEETTECCCCHHHHHHHCC-CCCCCCHHCCCCCC CS
  Gly_radical   3 pganpmegrdkegplaslnS..vakldyevaldgislnlkavpdalgkeeeerienlatlldgyfe 66 
                  +g ++++g+d++ +++ ++   +a + ++   ++i +n ++  +++  ++e+ ++  + lld+++e
   AJA92511.1 143 EGLKEFYGIDTKDATEYFEEhmTADIRHAASWQKIINNTSIDDSVMLTTAEKSVAAQNLLLDSCYE 208
                  688999************9988999*********************99***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1471.97
//
Query:       AJA92512.1  [L=133]
Description: nucleoside pyrophosphate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-53  178.9   0.0    4.9e-53  178.8   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.0   2.7e-57   4.9e-53       1     131 [.       3     133 .]       3     133 .] 0.99

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 2.7e-57
                 EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHHHHHHH--SSTTTSSTTS CS
         NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiekvreliGatnpaeaapgt 99 
                 e+tl ++KPd+v+r+ligeiisr+e+kg++i++lkm+++t+e+a e+Y+ hk+kpff el+e+mtsgpvv+ v+eg++a+++ r+++Gat++ ea+pg+
  AJA92512.1   3 EQTLFIVKPDGVQRKLIGEIISRFEKKGFTILKLKMFTFTKELATEFYSVHKDKPFFGELLEYMTSGPVVVTVVEGNNAVATTRQMVGATKSFEAEPGS 101
                 89************************************************************************************************* PP

                 HHHHH-SSSTT-SEEE-SSHHHHHHHHHHHST CS
         NDK 100 iRadfgvslgeNlvHgSdseesaereiklfFk 131
                 iR+dfg+  +eN++H+Sds+es ++e++++Fk
  AJA92512.1 102 IRGDFGLGFTENIIHASDSTESFDKEVSVVFK 133
                 ******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 952.79
//
Query:       AJA92513.1  [L=144]
Description: GtrA-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.1e-25   87.2  13.0      1e-24   87.0  13.0    1.0  1  GtrA        GtrA-like protein
  ------ inclusion threshold ------
       0.01   15.5   8.0       0.44   10.1   1.2    2.1  2  DUF2715     Domain of unknown function (DUF2715)
      0.026   14.9   0.0      0.041   14.2   0.0    1.3  1  MqsR_toxin  Motility quorum-sensing regulator, toxin of MqsA


Domain annotation for each model (and alignments):
>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0  13.0   1.8e-28     1e-24       1     117 []      21     138 ..      21     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.8e-28
        GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl.lkqflkFvlvsllglllnllilwllveklgleallakl 98 
                 +F ivG++g+lv+l++l++l+ ++g+ y+++++ia+ v+i++nF++nr+wtF ++ + k+    ++kF+++s++g++++l+i++ lve     ++  + 
  AJA92513.1  21 QFYIVGASGVLVNLGILYILTDIAGFWYVASQIIAISVSITTNFFFNRYWTFGSHVEDKKnSVMYIKFLIISAIGMAIQLGITVTLVESSAFYHMYGAG 119
                 59****************************************************9999888999*********************************** PP

        GtrA  99 vgiivalvlnyvlsklfvF 117
                 +gi+va  +nyvl+++++F
  AJA92513.1 120 IGIAVASGINYVLNRRVTF 138
                 ******************9 PP

>> DUF2715  Domain of unknown function (DUF2715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2   7.4e-05      0.44     106     140 ..      22      61 ..       8      87 .. 0.74
   2 ?    9.4   4.8   0.00012      0.73      47     127 ..      45     140 ..      45     144 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.4e-05
     DUF2715 106 s.....fgvpiqldvqyyftksvGisisvtgtvgiglsit 140
                        gv ++l++ y++t+  G+   +++ + i++sit
  AJA92513.1  22 FyivgaSGVLVNLGILYILTDIAGFWYVASQIIAISVSIT 61 
                 2344447999********************9999999953 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00012
     DUF2715  47 GftfminadaAiggkiltalvlsaqlLiGYtfrvgek......fyltpaiGiglsasilakssfas.........fgvpiqldvqyyftksvGisi 127
                 Gf ++ +  +Ai+++i t+++++    +G  ++ +++      f ++ aiG+ + ++i+++  + s         +g+++  +++y ++++v + i
  AJA92513.1  45 GFWYVASQIIAISVSITTNFFFNRYWTFGSHVEDKKNsvmyikFLIISAIGMAIQLGITVTLVESSafyhmygagIGIAVASGINYVLNRRVTFGI 140
                 677778888888888888888888888888887665323333266788999999998888888777888899988999999999999999875544 PP

>> MqsR_toxin  Motility quorum-sensing regulator, toxin of MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.8e-06     0.041      58      93 ..      64      99 ..      57     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-06
                STTTT--EEEE--EETTE.E--EEEEEETTEE.EEE CS
  MqsR_toxin 58 yadhrvWqDvYhveteegkelYiKlklrenvlvvis 93
                +  +r+W +  hve +++ ++YiK+ + + + ++i+
  AJA92513.1 64 FFFNRYWTFGSHVEDKKNSVMYIKFLIISAIGMAIQ 99
                66789********************99988876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1071.98
//
Query:       AJA92514.1  [L=640]
Description: acetate--CoA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-94  316.1   0.0    3.4e-94  315.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    8.3e-25   87.6   0.0    1.8e-24   86.5   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
      4e-15   55.5   4.4    1.1e-14   54.1   4.4    1.7  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
      0.067   12.7   0.0       0.16   11.5   0.0    1.7  1  DUF3201        Protein of unknown function (DUF3201)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.9   0.0   7.5e-98   3.4e-94       6     422 ..      73     506 ..      68     507 .. 0.86

  Alignments for each domain:
  == domain 1  score: 315.9 bits;  conditional E-value: 7.5e-98
                  HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE. CS
  AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvli. 99 
                  + + +k+a+ +   +g+++++TY+e+  +v++lA++L+slGvkkgdrV i+lp+ pe+ +++la++++Ga++ ++ ++++++ l+  +eds++k++i 
   AJA92514.1  73 DSKSEKPAILWegeDGTDRKITYKEMFVEVKKLANVLKSLGVKKGDRVTIYLPMIPELPISMLACARIGAIHTVVFSGFSSKSLSDRVEDSQSKIIIt 170
                  567799***99999999********************************************************************************9 PP

                  ........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHH CS
  AMP-binding 100 ........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshr 182
                          +    ++  e +++ a++++ vk viv+++ + + +   +++  +    e      +++++e l++ d +yi+YTSGTTGkPKGV +  +
   AJA92514.1 171 adggyrkgK---IINlKEIVDDSASSVQFVKNVIVYQRTGQKIQ-LNEKDLLWH---EvmqnssEECDAEILDSTDSLYILYTSGTTGKPKGVLHGIG 261
                  887764331...33434455556666666777776665553322.222222222...12334556889999**************************6 PP

                  HHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHH CS
  AMP-binding 183 nlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvlealle.sgalkaak 277
                   +++ ++s + +   f++k++dv+++++++ +++g+++ ++++ll+Gat v++++ ++ +d+ ++++ i+k++vt+++++P++l++l++  +++    
   AJA92514.1 262 GYLTHLYSTY-K-WaFDIKDTDVYFCTADIGWVTGHSYVVYGPLLHGATQVMYEGAPDhPDSSRMWDIIQKYGVTIFYTTPTALRMLMKfGDDIP--- 354
                  6666666642.2.3477889**************************************99999999***********************887777... PP

                  HHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEE CS
  AMP-binding 278 kakdlsslrlvllggeplspellrffralfge...evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGell 368
                  ++ +ls lrl+ ++gep++pe+++++ ++ g+   ++++++++TEt+g+++     +  e+   k+gs+  p+pg ++++vDe  g++v+ +++G l 
   AJA92514.1 355 NSFNLSTLRLLGTVGEPINPEVWKWYFNVIGKkkcPIIDTWWQTETGGMLISplpgI--ETIPLKPGSATLPIPGLDIEVVDET-GNEVESETKGSLI 449
                  3448999**********************9999*****************7676442..33334699***************85.************* PP

                  EEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
  AMP-binding 369 vrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                  ++ p  g+  g +k+ e+ +++++s+ + ++  GD +  d dGyl+++gR++d++k+
   AJA92514.1 450 IKTPwpGMLLGLWKDAEKYKDVYWSKfESLYYPGDYAIKDSDGYLWLLGRSDDVLKV 506
                  ***9778*****************86778**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   4.1e-28   1.8e-24       1      76 []     515     594 ..     515     594 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 4.1e-28
                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---..HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sea..leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                    e+Es +vsh +Vae aV G+pdevkGe ++afV lk++   s +  l+ eL++ +r+++gp+a+p++++fv++lpktrsGK
     AJA92514.1 515 ELESSIVSHNDVAESAVCGIPDEVKGESIIAFVMLKENvstS-EeqLRSELRETIRTQIGPIATPSQFYFVNKLPKTRSGK 594
                    89*********************************9886532.246**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   4.4   2.4e-18   1.1e-14       8      54 ..      21      66 ..      15      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.4e-18
                HHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHH CS
      ACAS_N  8 SiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyN 54
                + +d+ +FW++ ak l+W++p++++l++ ++pf++WF+GGk+N++yN
  AJA92514.1 21 AKNDYVSFWNNCAKSLSWFEPWTETLQW-NPPFARWFVGGKINASYN 66
                56899***********************.9****************9 PP

>> DUF3201  Protein of unknown function (DUF3201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.16      58     126 ..     569     636 ..     554     640 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                 ETTEEEEEETTEEEEEEEEEGGG--HHHHHHHHHH-SEEEEESS-TTT-EEEE..TTS---HHHHHHHH CS
     DUF3201  58 kpqievgatpesyyfvvavpkeklskefledvleafeklfiygaedfledvynclresplseevidriv 126
                 + qi   atp  +yfv  +pk + s +++  +l+a+ k    g    led   +   +   +e+ + i 
  AJA92514.1 569 RTQIGPIATPSQFYFVNKLPKTR-SGKIMRRLLKAIAKNETIGDVSTLEDGAAVNEIQSAFQELQKNIE 636
                 56667779*************87.77899**********999999999997663333333366666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4491.59
//
Query:       AJA92515.1  [L=128]
Description: cyclophilin-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-10   39.2   0.0    6.1e-10   39.0   0.0    1.1  1  Cyclophil_like   Cyclophilin-like
    1.3e-06   28.3   0.0      2e-06   27.7   0.0    1.2  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   6.9e-14   6.1e-10       5     118 ..      13     123 ..       9     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.9e-14
                     EEET.TEEEEEEEETT...HHHHHHHHC-SEEEEEEECT.TEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS--TT-TTSB--SSSE CS
  Cyclophil_like   5 idie.sseveveLddt...etaraikealPiesrvntWg.eEiYfstpvklekeenakevveagdiaywppGkalclffGktPisddeirpaspv 94 
                     ++i+ +++++ eL+ +   + +  i  +lP++++++  g   +Y +  ++ +  e ++++ ++gdia+   G+a+c f   t       +     
      AJA92515.1  13 LEIKgKIKIKCELKRHlspSLVGTIIRSLPVTGTIHILGtSGVYVESHIESG-GERTRNEFKKGDIAFLSVGHAFCFFHKDT-------KVGKDL 99 
                     5565688999999998888999*************9887257*********9.999999***********************.......778889 PP

                     EEEEEEEC-GGGGGG--TTEEEEE CS
  Cyclophil_like  95 nviGrivedlellkkvkdgekvrv 118
                       iG+i+e+ + l++ ++g++v +
      AJA92515.1 100 TPIGKILEGVDELLNASSGDEVSI 123
                     99*******************987 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   2.2e-10     2e-06      21     110 ..      37     119 ..      32     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.2e-10
  Cyclophil_like2  21 lleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGrieedaeelaealkelsgd 110
                      +++ lP+t t+  +++   +   ++++++ ++ ++++ k+Gd+a+ + ++ +++f+kd++    ++lt++G+i e   ++ e+l+  sgd
       AJA92515.1  37 IIRSLPVTGTIHILGTSGVYV--ESHIESGGERTRNEFKKGDIAFLSVGHAFCFFHKDTK--VGKDLTPIGKILE---GVDELLNASSGD 119
                      566677777777777555544..48899999999*************************5..599********44...444446555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 959.33
//
Query:       AJA92516.1  [L=229]
Description: methyltransferase, UbiE/COQ5 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-21   76.6   0.0    2.1e-21   76.3   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      4e-12   46.6   0.0    5.8e-12   46.1   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.2e-11   45.2   0.0    1.7e-11   44.7   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.4e-06   27.4   0.1      6e-06   26.1   0.1    1.6  1  Methyltransf_31  Methyltransferase domain
    0.00016   21.6   0.0    0.00018   21.4   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    0.00057   20.6   0.0     0.0009   19.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.029   14.2   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
      0.043   13.1   0.0       0.07   12.4   0.0    1.5  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   9.4e-25   2.1e-21       9     226 ..      10     223 ..       4     229 .] 0.89

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 9.4e-25
                      XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE CS
  Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief 102
                      v +v  ++   yD++n+ +slg     ++  +k   vk+g k+lD  +G g+++ + ++ v++  k+++ D    mLk + +        +i+ 
       AJA92516.1  10 VIDVLREIIPVYDKVNSFISLGKDVEHRNRAIKG-RVKKGDKILDAGSGFGNMSKTAAKIVDNDLKIILYDPLVPMLKNTDRLFD----RKIDS 98 
                      789999******************9999987775.5799**************************************98765544....47999 PP

                      EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS-HH.HHHHHHHHH CS
  Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllakdld.syryLvesi 195
                       ++  e++pf+d+ fD v  ++ lr+    ++a+ e++rvlk  G+ v++++ k+  p +++  + y   +lPv+  +    l  ++  L  + 
       AJA92516.1  99 ACGVFEHVPFQDKEFDAVLSGYSLRDAISLKTAISEMHRVLKEDGKWVIVDLGKPDEPFFRFGVTFYLRMILPVIALIAGGRLGlKFGTLYGTY 192
                      **************************************************************************9755555443367779**** PP

                      HHS--HHHHHHHHHHTTEEEEEEEE.EGGGTE CS
  Ubie_methyltran 196 rafPdqetlkeliedaGfksveyes.ltgGvv 226
                      + +P++++l++++ +  f+ ve+e+ l gG++
       AJA92516.1 193 KLWPQNKKLESMLLE-KFSRVEFEKdLMGGAI 223
                      ************987.4999999872445544 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   2.6e-15   5.8e-12       1      95 [.      52     146 ..      52     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 2.6e-15
                      EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      Ld+G+G G +++  ak +    +++  D+   mlk   +   ++   ++  ++ +e++pf+d+ fD+v+s  +l     ++ a++e++RvLk +
       AJA92516.1  52 LDAGSGFGNMSKTAAKIVdndLKIILYDPLVPMLKNTDRLFDRK---IDSACGVFEHVPFQDKEFDAVLSGYSLRDAISLKTAISEMHRVLKED 142
                      8**************7777779************7775555554...889******************************************** PP

                      EEEE CS
  Methyltransf_11  92 Gllv 95 
                      G+ v
       AJA92516.1 143 GKWV 146
                      *977 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   7.6e-15   1.7e-11       1      97 []      51     143 ..      51     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 7.6e-15
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      +Ld+G G G++++ +ak + ++ k++  D+   ml+++ + ++    +++  +g +e++pf+d++fD+v+s ++  + +   l++a++e++rvL
       AJA92516.1  51 ILDAGSGFGNMSKTAAKIVdNDLKIILYDPLVPMLKNTDRLFD---RKIDSACGVFEHVPFQDKEFDAVLSGYS--LRDAISLKTAISEMHRVL 139
                      8*****************9779********************4...48***********************655..45566799********** PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      k++G
       AJA92516.1 140 KEDG 143
                      **99 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   2.7e-09     6e-06       2     111 ..      46     149 ..      45     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.7e-09
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkile 95 
                      +kg ++lD+G+G G+ ++ +a+ +  + ++++ D    +++      +  ++d      g +e+ +  ++d+ fD +ls   l +  +++ ++ 
       AJA92516.1  46 KKGDKILDAGSGFGNMSKTAAKIVDNDLKIILYDPLVPMLKNTDRLFD-RKID---SACGVFEHVP--FQDKEFDAVLSGYSLRDAISLKTAIS 133
                      6899*****************877779*************99988755.4444...4445555599..99999**********99999****** PP

  Methyltransf_31  96 eiervlkpggillied 111
                      e++rvlk++g  +i d
       AJA92516.1 134 EMHRVLKEDGKWVIVD 149
                      **********999876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.2e-08   0.00018      20     124 ..      45     154 ..      29     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.2e-08
  Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqi 105
                       ++g ++Ld G G G++++ +++ +    +++++D+      +++      ++k  + +   +  +++++ fd + + ++l    ++  +++ +
       AJA92516.1  45 VKKGDKILDAGSGFGNMSKTAAKIVDndlKIILYDPLVP---MLKntdrlFDRKIDSACGVFEHVPFQDKEFDAVLSGYSLRDAISLKTAISEM 135
                      477889*************9988764445*******654...44333356444444444444577789************************** PP

  Methyltransf_23 106 atllkpgGylllseplasl 124
                      ++ lk++G  ++ + ++++
       AJA92516.1 136 HRVLKEDGKWVIVDLGKPD 154
                      ************9998876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     4e-07    0.0009       1      98 [.      52     144 ..      52     145 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4e-07
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklL 93 
                      L+ G+G G++++  ++    d++++ +D+   +++++ + + ++++  + ++e    ++        fD+v++   l     ++ ++++++++L
       AJA92516.1  52 LDAGSGFGNMSKTAAKIVdNDLKIILYDPLVPMLKNTDRLFDRKIDSACGVFEHVPFQDK------EFDAVLSGYSLRDAISLKTAISEMHRVL 139
                      89**********99888899**************99999999999988888888888865......9*************************** PP

  Methyltransf_12  94 kpgGr 98 
                      k +G+
       AJA92516.1 140 KEDGK 144
                      ***96 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.029     109     158 ..      98     149 ..      32     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                     EES-T.TS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEEEEEE CS
  Methyltransf_8 109 vacdl.akvPledesvdvavfclslm.gtnladflkeanrvlkvGGllkvae 158
                      ac +  +vP +d+  d ++   sl  +  l++ + e++rvlk  G + + +
      AJA92516.1  98 SACGVfEHVPFQDKEFDAVLSGYSLRdAISLKTAISEMHRVLKEDGKWVIVD 149
                     47988799*****************835699*****************9976 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.1e-05      0.07      57      84 ..      42      69 ..      32     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                TTT--TT-EEEEES-TTSHHHHHHHHHH CS
        CMAS 57 klelkpGmtlLdiGcGWGslvrravery 84
                k ++k+G+++Ld G G+G++ ++a++  
  AJA92516.1 42 KGRVKKGDKILDAGSGFGNMSKTAAKIV 69
                6689******************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1765.57
//
Query:       AJA92517.1  [L=238]
Description: ribosomal family S4e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-15   57.3   1.6    3.1e-15   55.8   0.5    2.2  2  Ribosomal_S4e  Ribosomal family S4e
    9.6e-08   32.0   0.6    1.8e-07   31.1   0.6    1.5  1  RS4NT          RS4NT (NUC023) domain
     0.0019   17.9   0.1     0.0039   16.9   0.1    1.6  1  S4             S4 domain
  ------ inclusion threshold ------
      0.074   13.2   0.2        6.9    6.9   0.0    3.0  3  CDC48_N        Cell division protein 48 (CDC48), N-terminal d


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.34   1.5e+03      42      69 ..      54      80 ..      46      84 .. 0.75
   2 !   55.8   0.5   6.9e-19   3.1e-15       2      75 .]      97     169 ..      96     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.34
                   EEEEEETTS-EEEESSTT-STTEEEEEE CS
  Ribosomal_S4e 42 ipqlvthdGrtirypdpdikvnDtvkid 69
                   ++ + +  ++ ++y+ + ikv  ++  +
     AJA92517.1 54 KTVTSLREAKSVIYAGK-IKVDGVIRKS 80
                   56677888899999998.9998887655 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 6.9e-19
                    TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
  Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                    ++ yrl+++    +++++I+++e++ K   +k+ktt+k+g++q+ +hdG+t++ + p ++v+Dt+++++++ kI
     AJA92517.1  97 NKTYRLVPQDGTLLKPIEIEDSEKTKKFALVKSKTTIKNGKTQIGFHDGKTLIDETP-VSVGDTCVLQIPDIKI 169
                    899******************************************************.************9988 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.6     4e-11   1.8e-07       3      33 ..       6      36 ..       5      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4e-11
                ----EETTTS-TTS---SSSSSEE----SSS CS
       RS4NT  3 pkkHLKrlaAPkhWpldkkegvfavkPspGP 33
                ++k+LKr++AP +W + +k+++f+++ +pG+
  AJA92517.1  6 GSKKLKRQMAPLFWGITRKNKRFVLTVKPGA 36
                68****************************7 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   8.8e-07    0.0039      14      48 .]      57      91 ..      44      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.8e-07
                SSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
          S4 14 ssrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                 s reA+  I +G+++V+G ++k+  +  + +Dv+
  AJA92517.1 57 TSLREAKSVIYAGKIKVDGVIRKSLHHGAGLMDVV 91
                588********************999988888886 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0015       6.9      41      73 ..      50      84 ..      39      87 .. 0.81
   2 ?    3.0   0.0     0.026   1.2e+02      32      47 ..      88     103 ..      83     116 .. 0.85
   3 ?   -2.0   0.0      0.96   4.3e+03      35      58 ..     113     136 ..     109     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0015
                CCEEEEEEEBSTTST..TTTEEEE-HHHHHHHT-- CS
     CDC48_N 41 rkTvaivwpaepede..gkgiIrmdgvtRknagvs 73
                r T+  v ++++ ++    g+I++dgv+Rk ++ +
  AJA92517.1 50 RDTIKTVTSLREAKSviYAGKIKVDGVIRKSLHHG 84
                4577778888777766789***********98765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.026
                 TSEEEEECCCCEEEEE CS
     CDC48_N  32 gdvveiegkrkTvaiv 47 
                 +dvve+eg++kT+ +v
  AJA92517.1  88 MDVVELEGSNKTYRLV 103
                 69********999877 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.96
                 EEEECCCCEEEEEEEBSTTSTTTT CS
     CDC48_N  35 veiegkrkTvaivwpaepedegkg 58 
                 +eie ++kT  +++   + + ++g
  AJA92517.1 113 IEIEDSEKTKKFALVKSKTTIKNG 136
                 788887778777766666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1752.18
//
Query:       AJA92518.1  [L=53]
Description: hypothetical protein T478_0071 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.3   0.4      0.085   12.9   0.4    1.3  1  zf-BED    BED zinc finger


Domain annotation for each model (and alignments):
>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   4.7e-06     0.085      18      43 ..       5      33 ..       2      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-06
                EETTTTEE----...SSTHHHHHHHHHS- CS
      zf-BED 18 vCryCgkilsrg...ggttnLkrHLrrkH 43
                vC+ C+++ls +    ++++ +  ++ +H
  AJA92518.1  5 VCNLCERKLSEHtyeESIKCAMELIKQGH 33
                8*************99***9987555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 395.77
//
Query:       AJA92519.1  [L=137]
Description: hypothetical protein T478_0331 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-06   26.2   0.1    9.3e-06   25.9   0.1    1.1  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.041   14.3   2.6      0.079   13.4   2.6    1.5  1  EF-1_beta_acid  Eukaryotic elongation factor 1 beta central a


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1     1e-09   9.3e-06       1     109 [.      11     116 ..      11     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1e-09
                 XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS- CS
  dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvae 99 
                 ++++rlae+q++ +++ + ++  + +++ ++   +   ++ + + L ++  e L++ +   p++++ + ++L +l+++G +++ ++  +L  L+++v  
  AJA92519.1  11 LKAKRLAEMQKNFSEQDQLND--NTNNEPEK--PKPTLRDYVVNSLGHRGMEVLQNAEYQFPNESKIIIEKLGELISTGDINETLDGGKLLVLFRSVGI 105
                 689********9987665332..33333333..678889999999****************************************************98 PP

                 .--XXXXX..X CS
  dsDNA_bind 100 .kkketkivis 109
                   + e+ki+++
  AJA92519.1 106 sIRMENKINVE 116
                 76777888876 PP

>> EF-1_beta_acid  Eukaryotic elongation factor 1 beta central acidic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.6   8.8e-06     0.079       7      24 ..       3      19 ..       2      21 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-06
  EF-1_beta_acid  7 EEEDeEaerlreeRLaaY 24
                    EE D+E e l+++RLa+ 
      AJA92519.1  3 EE-DKELEMLKAKRLAEM 19
                    66.*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1032.23
//
Query:       AJA92520.1  [L=292]
Description: dihydropteroate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-47  162.9   0.0    2.1e-47  161.9   0.0    1.5  1  Pterin_bind  Pterin binding enzyme
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.21   11.7   0.0    1.6  1  Med28        Mediator complex subunit 28


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   2.3e-51   2.1e-47       1     244 []      18     269 ..      18     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 2.3e-51
                  EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT-.-CCHHHHHHHHHHHHHHHHHHHCTSEEEEE-S-HHHHHHHHHTTSEEE CS
  Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPga.ervdeeeelervvpvlealrdeadvpisiDttkaevaeaAlkagadiv 97 
                  mgilN++p+sf++++++   +++ +   +m e+GA+i+Digg st P   + v+e+ e er+ + ++ +++ +++pis+Dt +a+va++Al+ g d++
   AJA92520.1  18 MGILNISPESFYKKSIKSTKSEISKYLCDMEENGANIIDIGGMSTAPYLkTIVSEKIESERITKTIKIIQNLSNIPISVDTCRASVAKDALELGIDVI 115
                  9**********************************************98799***************999999************************* PP

                  EETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTTTS...STTHHHHHHHHHTHHHH CS
  Pterin_bind  98 NdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGvaperillDpgigf...gkteehnlellrrldel 192
                  Nd+sg++ d++m+++v +++  +++            +++ + + +   ++ l+++++ a++a + +++i++Dp igf   + + ++nl   +  ++ 
   AJA92520.1 116 NDISGLKYDKNMPKIVEKYNPSLILCSYS--------KKLVKGNPISVTKQLLNQSIKIAKKAQISKDKIVVDPAIGFfrrSSDVKNNLPYTKITSDW 205
                  ***************************99........336788889999999**************************99755566665433222222 PP

                  HHTTS.............SEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SEEEES CS
  Pterin_bind 193 reale.............vpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadivrVh 244
                    +++             +p+ll++S+ksflg+ll  ++++eR++gta + +l++ +Ga+i+r+h
   AJA92520.1 206 -AQRDieiikklkllkstFPILLSISNKSFLGKLLGKEDPSERNTGTAIAEMLSIINGASIIRTH 269
                  .22222333334468889***************996667*************************9 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.3e-05      0.21      51     118 ..      21      86 ..       6      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
       Med28  51 ykvapeellmkHlqktseqlatqlkalrekgqnvfgdgtkidstidyleklkqvlsdaedvykvrdev 118
                  +++pe++ +k +++t  +++  l  + e+g n++  g    st  yl+++     + e + k+++ +
  AJA92520.1  21 LNISPESFYKKSIKSTKSEISKYLCDMEENGANIIDIGG--MSTAPYLKTIVSEKIESERITKTIKII 86 
                 579*******************************98776..489999998877777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2036.88
//
Query:       AJA92521.1  [L=277]
Description: DnaJ domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-21   74.6   6.9    6.2e-21   74.3   5.6    1.9  2  DnaJ      DnaJ domain
  ------ inclusion threshold ------
       0.44   11.0   2.8       0.23   12.0   0.4    1.7  2  FtsX      FtsX-like permease family
        3.4    8.5   6.6        8.3    7.3   0.2    2.7  3  YMF19     Plant ATP synthase F0


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.7e+03      35      44 ..      68      77 ..      58      81 .. 0.65
   2 !   74.3   5.6     1e-24   6.2e-21       1      63 []     211     271 ..     211     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                CHHHHHHHHH CS
        DnaJ 35 kdpeaeekFk 44
                 +p+ e+kF 
  AJA92521.1 68 LNPDDEKKFS 77
                4567778886 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 1e-24
                 HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
        DnaJ   1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63 
                 +yY iL++++d+se+eIk++Yrkla++yHPD+n  + ++eek  +in+AyevLsd++ +++YD
  AJA92521.1 211 NYYLILELTNDSSESEIKSQYRKLAKQYHPDRN--KDSSEEKMAQINKAYEVLSDKKLKAEYD 271
                 79*******************************..45689**********************9 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.1   6.4e+03      72      86 ..       9      15 ..       4      25 .. 0.47
   2 ?   12.0   0.4   3.8e-05      0.23      36      93 ..      86     157 ..      76     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
        FtsX 72 iivlllllallagll 86
                ++++l+        +
  AJA92521.1  9 LFLILI--------F 15
                222222........2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.8e-05
        FtsX  36 G...lglgllaaqllsdvllssvf..........sselkisidlitvliiivlllllallagllsiski.lk 93 
                 G    g+ l++a+ + + l++ +f          s   +++i++++++++++++++++  + ++ +++i l+
  AJA92521.1  86 GwqkSGNYLVVAESSDSSLSAKFFydsgaqvnppSAVSDYYISPEDLYLTFAIAIIIIAGVFVYLARHIiLR 157
                 34446666777777777777777755554444444999******************9999988888877444 PP

>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   1.5e+04      18      27 ..      10      19 ..       6      49 .. 0.51
   2 ?    7.3   0.2    0.0014       8.3      19      70 ..     136     182 ..     132     200 .. 0.63
   3 ?    4.4   0.5     0.011        64      26      73 ..     204     249 ..     198     265 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
       YMF19 18 fFitlYivll 27
                f i+++ + +
  AJA92521.1 10 FLILIFPISN 19
                4444444333 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0014
       YMF19  19 FitlYivllknilpkiarilklrkkllsslssevsklkkeqknlivskdsal 70 
                 F ++  +++  +  ++ar + lrkk +  + +  sk ++++    ++++s+ 
  AJA92521.1 136 FAIAI-IIIAGVFVYLARHIILRKKTSYDYAKLDSKKNRDY----EKYHSEW 182
                 44443.4556777789**********999885444444433....3333333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.011
       YMF19  26 llknilpkiarilklrkkllsslssevsklkkeqknlivskdsalanv 73 
                 +++n lp+ + il l +  ++s ++  s+ +k  k++    +++ +++
  AJA92521.1 204 YNENSLPNYYLILELTNDSSESEIK--SQYRKLAKQYHPDRNKDSSEE 249
                 56899*************9999987..444444444443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1190  (0.0663729); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1964.14
//
Query:       AJA92522.1  [L=149]
Description: TIGR04272 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0071   16.3  17.6        1.7    8.7   0.5    4.0  4  zinc_ribbon_6   Zinc-ribbon
  ------ inclusion threshold ------
      0.016   15.2   8.1       0.11   12.5   1.3    2.3  2  Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
       0.06   13.3   5.2        1.2    9.2   0.3    2.5  2  SCIFF           Six-cysteine peptide SCIFF
        9.8    6.5  15.4         10    6.5   3.4    2.4  2  LIM             LIM domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.5   0.00038       1.7      27      44 ..      10      27 ..       4      32 .. 0.83
   2 !    5.2   0.7    0.0048        22      29      37 ..      33      41 ..      27      46 .. 0.77
   3 !    6.9   4.6    0.0014       6.5      26      54 ..     103     131 ..      97     133 .. 0.81
   4 !    5.8   0.4     0.003        14      29      39 ..     127     137 ..     123     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00038
  zinc_ribbon_6 27 kvkilCnDCekksevkfh 44
                   + + +C DC+k ++v+f 
     AJA92522.1 10 MHDATCGDCGKDCQVPFE 27
                   56679***********95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0048
  zinc_ribbon_6 29 kilCnDCek 37
                    ++CnDC +
     AJA92522.1 33 PVYCNDCFQ 41
                   699****76 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0014
  zinc_ribbon_6  26 kkvkilCnDCekksevkfhvlglkCkeCg 54 
                    ++ + +C  C+++++v+f+  g k   C+
     AJA92522.1 103 EMHTTTCAECGTECQVPFKPNGEKPVYCN 131
                    456779****************9966664 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.003
  zinc_ribbon_6  29 kilCnDCekks 39 
                     ++CnDC ++ 
     AJA92522.1 127 PVYCNDCFQEK 137
                    599****8765 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.7    0.0018       8.2       5      28 ..      12      35 ..       9      49 .. 0.87
   2 ?   12.5   1.3   2.5e-05      0.11       5      28 ..     106     129 ..     103     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                    EEE-SSBTT--EEEEEEETTEEEE CS
  Molybdop_Fe4S4  5 ktaCpyCgvgCglevhvkdgkivk 28
                    + +C  Cg  C++  +++++k v+
      AJA92522.1 12 DATCGDCGKDCQVPFEPRQDKPVY 35
                    679**************9998876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.5e-05
                     EEE-SSBTT--EEEEEEETTEEEE CS
  Molybdop_Fe4S4   5 ktaCpyCgvgCglevhvkdgkivk 28 
                      t+C+ Cg+ C++  +++++k v+
      AJA92522.1 106 TTTCAECGTECQVPFKPNGEKPVY 129
                     79*************999999876 PP

>> SCIFF  Six-cysteine peptide SCIFF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7    0.0037        17      15      28 ..      10      23 ..       7      24 .. 0.86
   2 ?    9.2   0.3   0.00026       1.2      14      28 ..     103     117 ..     100     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0037
       SCIFF 15 lkkggCgeCqtSCq 28
                +++  Cg+C   Cq
  AJA92522.1 10 MHDATCGDCGKDCQ 23
                67789********9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00026
       SCIFF  14 tlkkggCgeCqtSCq 28 
                 +++++ C eC t Cq
  AJA92522.1 103 EMHTTTCAECGTECQ 117
                 578899********9 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   4.2    0.0044        20      30      57 ..      20      43 ..      11      44 .. 0.72
   2 ?    6.5   3.4    0.0022        10      28      57 ..     108     137 ..     104     138 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0044
                TTT-SB-CTT.CEEETTEEEEHHHHHHH CS
         LIM 30 sdCqkeLkegsfyekdgklyCkkdylkk 57
                 dCq +++++    +d+ +yC++++++ 
  AJA92522.1 20 KDCQVPFEPR----QDKPVYCNDCFQDH 43
                4677777777....5999*******875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0022
                 B-TTT-SB-CTT.CEEETTEEEEHHHHHHH CS
         LIM  28 tCsdCqkeLkegsfyekdgklyCkkdylkk 57 
                 tC++C++e +     + ++ +yC++++++k
  AJA92522.1 108 TCAECGTECQVPFKPNGEKPVYCNDCFQEK 137
                 45555555544422234778*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1117.43
//
Query:       AJA92523.1  [L=142]
Description: hypothetical protein T478_0863 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1113.79
//
Query:       AJA92524.1  [L=78]
Description: hypothetical protein T478_1452 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0021   17.8   0.0     0.0048   16.7   0.0    1.8  1  HTH_23    Homeodomain-like domain
  ------ inclusion threshold ------
      0.018   14.9   0.1       0.64   10.0   0.0    2.2  2  TrmB      Sugar-specific transcriptional regulator TrmB
      0.048   13.3   0.1       0.14   11.8   0.1    1.9  1  GntR      Bacterial regulatory proteins, gntR family
      0.083   12.7   0.0       0.15   11.9   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0048      13      41 ..      17      50 ..       5      57 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
      HTH_23 13 llae.....GlsvreIAreLgvsrrTvyrwlkry 41
                ll++      + ++++ +eLgv+r Tv+r+ +  
  AJA92524.1 17 LLDKgvtdkQDIYTKVVDELGVPRPTVRRVARDL 50
                555444455788999**************98765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.014        64      39      56 ..      10      27 ..       5      32 .. 0.79
   2 ?   10.0   0.0   0.00014      0.64      27      48 ..      31      52 ..      29      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                HHHHHHHHHHCTSEEEES CS
        TrmB 39 vYevLrsLedkGlVerek 56
                +  +++sL+dkG+ ++++
  AJA92524.1 10 IKAAINSLLDKGVTDKQD 27
                56789*******988775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                HHCCCTTSSCHCHHHHHHHHHH CS
        TrmB 27 eiaeelgvprskvYevLrsLed 48
                ++  elgvpr++v +v r L +
  AJA92524.1 31 KVVDELGVPRPTVRRVARDLRN 52
                6889************999976 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.1e-05      0.14      28      51 ..      30      53 ..       6      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                HHHHHHHTS-HHHHHHHHHHHHHT CS
        GntR 28 reLaaefgVsrttvReALrrLeae 51
                 ++++e+gV r+tvR++ r L  e
  AJA92524.1 30 TKVVDELGVPRPTVRRVARDLRNE 53
                57899*************999876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.3e-05      0.15      23      44 ..      31      52 ..      29      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                HHHHHHTS-HHHHHHHHHHHHH CS
    HTH_IclR 23 elArrtglpkStvhRlLqtLve 44
                 + +++g+p++tv+R  + L +
  AJA92524.1 31 KVVDELGVPRPTVRRVARDLRN 52
                57899**********9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 545.14
//
Query:       AJA92525.1  [L=563]
Description: acetolactate synthase, large subunit, biosynthetic type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-59  198.8   0.1    4.2e-58  195.8   0.0    2.1  2  TPP_enzyme_N    Thiamine pyrophosphate enzyme, N-terminal TPP
    1.4e-48  164.1   0.0    3.1e-48  163.0   0.0    1.5  1  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain
    2.9e-44  150.5   0.6    6.3e-44  149.4   0.0    1.9  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.28   10.9   0.0    1.5  1  TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.0   9.3e-62   4.2e-58       3     168 ..       7     170 ..       5     173 .. 0.98
   2 ?    0.6   0.0     0.084   3.8e+02      64      97 ..     433     468 ..     418     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 9.3e-62
                   HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE CS
  TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgd 99 
                   +a+al +aL+++gv++vfg+pG+ +lp++d+l ++ +ir++l+rhEq+aa++Adg+ r+++kpgv+++tsgpGatn+lt++a+A+ d+ P+++++g+
    AJA92525.1   7 GATALMKALEKEGVKEVFGLPGGANLPMYDELGKS-NIRHILVRHEQSAAHMADGFGRVSRKPGVCFATSGPGATNLLTGIATAQADSAPMVAVTGQ 102
                   899********************************.6************************************************************ PP

                   --CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-EE CS
  TPP_enzyme_N 100 rptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvlleev 168
                   +p++++g++++q e d+ ++++p  ky++++++pee+p ++++ + +a +grpgPv+l++pkdv++ e 
    AJA92525.1 103 VPVAMIGKDAFQ-ESDIIGMANPALKYSYQPRTPEEIPTMVKQGFYIAETGRPGPVLLDIPKDVQQNEG 170
                   ************.****************************************************9875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.084
                   S-EEEEE-C.HHHHHHCH.HHHHHHHHHT--EEEEE CS
  TPP_enzyme_N  64 kpgvvlvts.gpGatnal.talaeAkvdriPllvls 97 
                   +p v +v   g G  n++  +la+A ++ +P++v+ 
    AJA92525.1 433 RPDVPVVDIaGDGSFNMTeHSLATAVLEDLPVIVFL 468
                   555555555466788887358999999999999975 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.0   6.9e-52   3.1e-48       3     135 ..     196     327 ..     194     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 6.9e-52
                   HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEEES-SSSTCCCTTTTTT CS
  TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeeaDlvlalGarfddirttgsepe 99 
                   +a+ell +ak+p+il+Gggv+ s a +el++ ae l iPvvtt++gkg++pe+hpl+lg +g+hg+++an+++ eaD+vla+G+rf+d r++g+++e
    AJA92525.1 196 RAVELLLSAKKPIILAGGGVIISSAFAELQSIAELLMIPVVTTFKGKGAFPENHPLSLGPIGMHGHAEANKLMTEADCVLAIGTRFSD-RSVGTFEE 291
                   79**************************************************************************************.999***** PP

                   TTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHH CS
  TPP_enzyme_M 100 fapeakiihididpaeigknyqvdlaivgdvketle 135
                   f ++ kiih d+dpaeigkn ++++a+vgdv+++l+
    AJA92525.1 292 FEKNLKIIHMDVDPAEIGKNQTTSVAVVGDVRTSLR 327
                   *9988***************************9996 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.8   7.9e+03      38      59 ..      84     106 ..      77     111 .. 0.69
   2 !  149.4   0.0   1.4e-47   6.3e-44       2     153 .]     391     538 ..     390     538 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                   HHHHHHST.TSEEEEEEEHHHHH CS
  TPP_enzyme_C  38 iGaklakp.drevvaivGDGgfl 59 
                   +G++ a+  ++++va++G    +
    AJA92525.1  84 TGIATAQAdSAPMVAVTGQVPVA 106
                   67777755257999999865555 PP

  == domain 2  score: 149.4 bits;  conditional E-value: 1.4e-47
                   SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCC CS
  TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfggk 98 
                   +G++++wa+ ++++  p+++++s+glgtmG+g+paAiGak a+pd +vv i+GDG+f m+ + latav ++lp++v+++nN ++gm+ ++q+ f+++
    AJA92525.1 391 VGQHQMWASLFFDAIHPGTFFSSTGLGTMGWGFPAAIGAKTARPDVPVVDIAGDGSFNMTEHSLATAVLEDLPVIVFLINNYSLGMVAQWQRTFYDR 487
                   9************************************************************************************************ PP

                   TTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
  TPP_enzyme_C  99 rksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                   r +g++   +k +d++klae++Ga+g+r ++   +ele+a+k+ l+++  ++i++
    AJA92525.1 488 RMVGVD--LKKCPDYVKLAESYGAQGIRAQSM--DELEKAIKDGLNSDVATVIDI 538
                   ****99..58889***************6566..*******************97 PP

>> TPP_enzyme_M_2  Middle domain of thiamine pyrophosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.2e-05      0.28      88     204 ..     261     385 ..     202     387 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.2e-05
                     SHHHHHHHTT-SEEEEESB---SHHHHHHHHH---SEEEEEESS-SB--TT--SEEEEES-HHHHHH.........HS---------SHHHHHHH CS
  TPP_enzyme_M_2  88 npkvkeeLaqadiviqfGsrlvsKrllqflaelkpeeyWlvdesqgrldpahhrkrrfvakveewlr.........ahpaesqkpWalellalse 173
                     ++++++ +++ad v+ +G+r+  + +  f +  k+ +  ++d  +  +  ++ ++  +v +v++ lr         a  a++ +pW+++++++++
      AJA92525.1 261 HAEANKLMTEADCVLAIGTRFSDRSVGTFEEFEKNLKIIHMDVDPAEIGKNQTTSVAVVGDVRTSLRifgkllmdkAVRASDDNPWLKHVKETKQ 355
                     78999***********************999999988888888888888888888888888877665222121111223334477********99 PP

                     HHHHHHHTT.TTSSSHHHHHHTGGGGS-TT- CS
  TPP_enzyme_M_2 174 klaelveqqldeefgEaqlahqlaellpeqg 204
                        e ++ +  +e+g a++ ++l+ellp+++
      AJA92525.1 356 YWRENLKIH-PGEMGAAKILRKLRELLPKES 385
                     999999976.789***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3926.08
//
Query:       AJA92526.1  [L=135]
Description: F420-dependent enzyme, PPOX class [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-15   56.1   0.0    4.3e-15   55.7   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.013   15.5   0.0    1.3  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   4.8e-19   4.3e-15       1      83 [.       1      82 [.       1      86 [. 0.92

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 4.8e-19
                    HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEEEEEEE CS
  Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrieGtael 83
                    +d +++ +l++ ++v+lAT  +dG P+v+pv++ + d +  i++ t++ + k++n+ ++prva++++d +      +i+G+++ 
      AJA92526.1  1 MDSKAELLLNGKNLVFLATTMPDGAPQVTPVWGNFEDSH--ILINTAEGRLKHKNILRDPRVAVSVVDSKnPLDMTSIRGKVTE 82
                    57788999**************************88888..***************************9988888888888875 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.4e-06     0.013       5      64 ..       5      66 ..       2     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-06
                  HHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEE CS
  Pyridox_ox_2  5 ilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvte 64
                  ++ lL+ + +  la+++ dg+p ++Pv   +++ ++++ +a+g  +++ +   p v+v+v +
    AJA92526.1  5 AELLLNGKNLVFLATTMpDGAPQVTPVWGNFEDSHILINTAEGRLKHKNILRDPrVAVSVVD 66
                  566888899999999997888*********************99888777744457777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1021.27
//
Query:       AJA92527.1  [L=124]
Description: putative holo-[acyl-carrier-protein] synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   59.5   1.5    3.8e-16   59.2   1.5    1.1  1  ACPS      4'-phosphopantetheinyl transferase superfamily
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.46   10.6   0.0    1.9  2  4PPT_N    4'-phosphopantetheinyl transferase N-terminal domai


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   1.5   4.2e-20   3.8e-16       2     114 .]      10     114 ..       9     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4.2e-20
                 EEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTTS-SSSS--GGG-EEEE-TTS-EEEE-S-SSEEEEEEE CS
        ACPS   2 vGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKalgpglrklldfksievledstgrptlellseakkkawkl 100
                 +GiDi++++r+rk+   +++++ k+ift+ E++++++ +++ +  +fa+ +a+KEA+ K++ ++      f++ie  +  ++rp ++ +++++kk+  +
  AJA92527.1  10 IGIDIVEIERFRKKKFIENESFYKKIFTDLEIQYCRKFSDPYP--HFAGKFALKEAVQKSIAHNT----LFNKIETFH-TNSRPKIK-IKNQEKKYDFI 100
                 9*************999999***********************..****************6666....578888777.66789999.77777888888 PP

                 E-....SSEEEEEE CS
        ACPS 101 eslkidkdyviavv 114
                 +s +++k+y+ia++
  AJA92527.1 101 TSISHEKKYAIAIA 114
                 888889*****996 PP

>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.2   1.8e+03      20      58 ..      56      70 ..      52      86 .. 0.66
   2 ?   10.6   0.0   5.2e-05      0.46      51      67 ..      98     114 ..      94     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
      4PPT_N 20 GRicAraalarlgleavpllsgerraPlwpaglvgSIsH 58
                G ++ ++a ++                        SI+H
  AJA92527.1 56 GKFALKEAVQK------------------------SIAH 70
                55555555554........................4444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.2e-05
      4PPT_N  51 glvgSIsHtdglaaAav 67 
                 +++ SIsH++++a+A++
  AJA92527.1  98 DFITSISHEKKYAIAIA 114
                 6889***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 917.35
//
Query:       AJA92528.1  [L=244]
Description: methylenetetrahydrofolate reductase (NAD(P)H) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-08   32.6   0.0    4.1e-07   29.6   0.0    2.0  1  MTHFR     Methylenetetrahydrofolate reductase
  ------ inclusion threshold ------
       0.34   10.7   1.4         24    4.8   0.1    2.7  3  RFX5_N    RFX5 N-terminal domain


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   4.6e-11   4.1e-07      12     130 ..       2     122 ..       1     202 [. 0.77

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.6e-11
                 EEEEEE---SSHHH...HHHHHHHHHHHGGGG-SEEEE---CCCTTHHHHHHHHHHHHHHH.-S-EEEEEESTTS-HHHHHHHHHHHHHCT--EEEEE- CS
       MTHFR  12 lisfEffpPkteeg...ernLleridrleevkplfvdvTwgaggstaeltssiakviqqel.gleailhlTctdaskeeldkalekakelGirnilALr 106
                 +i +E  pPk +++    + L eri+++++   +++ vT+   g ++ + + i + i+q++ +l++ + l  +d++ +e+++++++a ++ i  il L 
  AJA92528.1   2 TIRYEINPPKVSDPpsrIELLDERIEQISKFC-DGIHVTDSVLGIERISPLLIGAEIKQKHpKLNVTISLRVIDKTISEITDIVDSAINANIDGILILM 99 
                 6789*******987332567889999999776.9**********9998889898888876549************************************ PP

                 -S--TT-GGC---S----SHHHHH CS
       MTHFR 107 GDppkdedkweekeeefkyaldLv 130
                 GDp +++d +++ +  +  ++ L+
  AJA92528.1 100 GDPSPEND-YKSGVIPSFAVKHLI 122
                 ***99988.555554444344444 PP

>> RFX5_N  RFX5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.2   1.1e+04      14      23 ..      87      96 ..      80      96 .. 0.74
   2 ?    4.3   0.1    0.0038        34      32      45 ..     127     140 ..     123     144 .. 0.90
   3 ?    4.8   0.1    0.0026        24      10      39 ..     144     174 ..     142     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.2
      RFX5_N 14 avqsKvdgiL 23
                a+   +dgiL
  AJA92528.1 87 AINANIDGIL 96
                6777899997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0038
      RFX5_N  32 leKLYLYLqLPsGp 45 
                 +eK+ L+L LPs p
  AJA92528.1 127 NEKINLFLSLPSKP 140
                 79**********77 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0026
      RFX5_N  10 sicKavqsKvdgiL.qdveKFtDleKLYLYL 39 
                  i+K v sK +g + q v+  + + +L  YL
  AJA92528.1 144 KISKKVESKPNGFVtQVVHDISQVKRLHDYL 174
                 59*********96537789999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1714.72
//
Query:       AJA92529.1  [L=437]
Description: putative glutamate-1-semialdehyde-2,1-aminomutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-54  184.7   0.1    3.1e-54  184.2   0.1    1.3  1  Aminotran_3  Aminotransferase class-III


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.1   1.7e-58   3.1e-54      10     359 ..      41     374 ..      10     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 1.7e-58
                  CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHHH CS
  Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKla 107
                  ++v + aeG +l dvd ++y+D   + ++++lGha+ +v k ++ q++k ++   + ++ne+a++l+ek+ k++p   +k+ +a +G+eA++ +++la
   AJA92529.1  41 PFVTKSAEGKFLRDVDSNKYVDYWMGHWSLILGHAQKQVQKKAAGQLKKGWM---HGTSNENAIALSEKISKAVPV-AEKIRYASTGTEATMYSVRLA 134
                  4778899*******************************************65...559******************.9******************** PP

                  HHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB.-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETT CS
  Aminotran_3 108 rkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpf.lpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqge 204
                  r+       t k+ i +++g++HG t   l + +    +++  g +   ++v+l+++              l+e l+ l k  k+++a+v++Ep+ g 
   AJA92529.1 135 RA------VTGKKIIAKIDGGWHGYTTDLLKTVNWPFDVSESQGLTdEEHIVSLPLNN-------------LEESLRIL-KSVKKDLAGVLIEPVLGG 212
                  **......9*******************998877745555555555567777777774.............22334333.467799************ PP

                  TTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT.TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS.........B--TTT CS
  Aminotran_3 205 gGvvvaspeflaklrelckkhdvllivDEvqtGf.GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs.........hgsTfg 292
                  gG ++a++e+l++++e++k+++ l++ DE+ tGf  r G l+  +   + pD++tl+K ++gG+p+ ++++++e+mq  +++           g+Tf+
   AJA92529.1 213 GGAIPATQEYLQGIQEMAKRNNSLFMLDEIVTGFrFRYGCLYPKM--KLDPDIVTLGKIVGGGFPIGVICGKDEIMQHANTSInskknrtyiGGGTFS 308
                  **********************************88***999877..999***************************9987768899****99***** PP

                  T-HHHHHHHHHHHHHHHH..TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETT CS
  Aminotran_3 293 Gnplacavalavleiiee..ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevk 359
                  +npl +++   +l i+++  ++l ++ + lg++ ++ L+++ +++ vi  v gkG ++   ++ +  ++
   AJA92529.1 309 ANPLSMMAGETTLGILKNkeNTLYKKLDGLGNQTTKMLRKIFSDE-VI--VTGKGSLFMTHFPRNGMTE 374
                  ****************986688*******************9776.66..7799999988888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3209.71
//
Query:       AJA92530.1  [L=288]
Description: ribosomal protein L10 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-18   66.9   0.0    2.8e-18   65.7   0.0    1.7  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    1.7e-18   66.6   2.2    2.7e-18   65.9   0.9    2.0  3  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   3.1e-22   2.8e-18       1      71 []     111     181 ..     111     181 .. 0.99

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 3.1e-22
  RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                   Ar G++A+ dv+ip+++++ aPg++ + +++ g+ tk+++G+i++ ++++ +k+Ge+++ + a lL++L+i
    AJA92530.1 111 ARGGDTASMDVVIPPKNTGIAPGPMLTDFKENGIATKIDQGTIWIMKETVPVKQGEVISEKLAGLLSKLDI 181
                   9********************************************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.9     3e-22   2.7e-18       3      98 ..       9     105 ..       7     107 .. 0.94
   2 ?    0.1   0.0       0.1   8.9e+02      51      67 ..     101     117 ..      99     164 .. 0.81
   3 ?   -3.1   0.0         1     9e+03      50      59 ..     260     269 ..     230     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 3e-22
                    CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S...SCGCCSSSEEEEEESS-TCHHHHCC CS
  Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek...lkellkgpvalvftnedpvalakvl 95 
                    ++kK++++++l+el kkyk++++v++e+++ +ql  lRk l+++ +e++ +K +++++A++++g+      l+e ++g+++++ftn++p++l  +l
     AJA92530.1   9 PKKKAQMYQQLQELPKKYKVLALVRMEKVRGSQLLPLRKTLQGE-VEIVSIKDKVAKLAFAQAGIT-GidkLSEKITGQCVFMFTNMSPFKLNVLL 102
                    78*****************************************9.*****************9997.3357*********************9988 PP

                    CCC CS
  Ribosomal_L10  96 eef 98 
                     ++
     AJA92530.1 103 GKN 105
                    776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                    EEESCCCCCCCCHCCTS CS
  Ribosomal_L10  51 kvvKntlmrrAleetge 67 
                      +Kn++m  A ++  +
     AJA92530.1 101 LLGKNKVMLFARGGDTA 117
                    6799**99999877655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1
                    EEEESCCCCC CS
  Ribosomal_L10  50 lkvvKntlmr 59 
                        K ++++
     AJA92530.1 260 TEDTKEQVLQ 269
                    3333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2080.60
//
Query:       AJA92531.1  [L=70]
Description: putative cobalt transporter subunit CbtB (proposed) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-13   50.3   2.1    2.6e-13   49.9   2.1    1.3  1  CbtB      Probable cobalt transporter subunit (CbtB)
  ------ inclusion threshold ------
      0.014   15.3   1.9       0.02   14.8   1.9    1.3  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> CbtB  Probable cobalt transporter subunit (CbtB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   2.1   2.9e-17   2.6e-13       9      51 .]      15      70 .]       4      70 .] 0.76

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.9e-17
        CbtB  9 rllqlvaAllLGlllvylvgfsqaaa..............lHnaaHDtRHaagfPCH 51
                 ++++++Al++  + +++vgf+q+ +              +H+++HD+RHaagfPCH
  AJA92531.1 15 KIAVAALALVFV-FGLFVVGFDQGHIfslvmgeqafdemfIHELTHDMRHAAGFPCH 70
                223333333332.225889************************************** PP

>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.9   2.3e-06      0.02      21      47 ..      12      38 ..       4      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.3e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        SecE 21 EllkttvvVlvfvvimglflflvDlvf 47
                 + k++v+ l+ v+++glf+ ++D+++
  AJA92531.1 12 GTSKIAVAALALVFVFGLFVVGFDQGH 38
                57899********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 494.14
//
Query:       AJA92532.1  [L=42]
Description: hypothetical protein T478_1390 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1162  (0.0648112); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 307.04
//
Query:       AJA92533.1  [L=87]
Description: hypothetical protein T478_1353 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 676.31
//
Query:       AJA92534.1  [L=280]
Description: methyltransferase, UbiE/COQ5 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-22   79.0   0.2      5e-22   78.3   0.1    1.5  2  Methyltransf_31  Methyltransferase domain
    1.1e-20   74.1   0.0    1.8e-20   73.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.9e-20   73.2   0.8    1.9e-19   70.0   0.8    2.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.7e-19   68.3   0.0    1.2e-18   67.6   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.2e-13   51.3   0.0    1.8e-13   50.6   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    1.7e-12   47.9   0.0    3.3e-12   47.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.7e-07   31.0   0.1    3.7e-07   29.8   0.1    1.6  1  MTS              Methyltransferase small domain
    3.2e-06   26.9   0.0    4.9e-06   26.3   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      1e-05   24.8   0.0    1.6e-05   24.2   0.0    1.2  1  Fibrillarin      Fibrillarin
    1.3e-05   24.8   0.7     0.0061   16.1   0.1    2.6  2  CheR             CheR methyltransferase, SAM binding domain
    1.8e-05   24.6   0.0    2.9e-05   23.9   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    6.5e-05   22.1   0.0    0.00012   21.3   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00024   20.5   0.1    0.00031   20.1   0.1    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00078   19.6   0.0     0.0014   18.8   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase
     0.0008   18.6   0.0     0.0011   18.2   0.0    1.2  1  DREV             DREV methyltransferase
     0.0027   17.5   2.5       0.34   10.6   1.2    2.3  2  N6_N4_Mtase      DNA methylase
     0.0043   16.7   0.1      0.017   14.8   0.0    1.9  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0045   17.0   0.3     0.0074   16.3   0.0    1.5  1  Methyltransf_32  Methyltransferase domain
     0.0068   15.7   0.1      0.019   14.3   0.1    1.8  1  GidB             rRNA small subunit methyltransferase G
     0.0099   15.2   0.0      0.027   13.7   0.0    1.6  2  Rsm22            Mitochondrial small ribosomal subunit Rsm22
  ------ inclusion threshold ------
      0.015   14.5   0.1      0.027   13.6   0.1    1.4  1  Methyltransf_3   O-methyltransferase
      0.019   14.6   0.0      0.029   14.0   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.019   14.4   0.0       0.03   13.7   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.022   14.2   0.3      0.077   12.5   0.1    2.0  2  SieB             Super-infection exclusion protein B
      0.055   13.1   0.0      0.089   12.5   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.056   12.7   0.0      0.096   12.0   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
       0.11   12.1   0.1        6.1    6.5   0.1    2.8  2  UPF0020          Putative RNA methylase family UPF0020
       0.15   12.1   0.0       0.31   11.0   0.0    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1   7.8e-25     5e-22       2     112 ..      50     155 ..      49     206 .. 0.91
   2 ?   -3.1   0.0       9.3     6e+03      73      84 ..     236     247 ..     220     267 .. 0.57

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 7.8e-25
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkile 95 
                      +k  +vlDl+CGtG  t++l +++g+k++++ iD se a++ A++       +n++F ++d+e+ +  +e  kfD i+++ +l  +++ +k+l+
       AJA92534.1  50 KKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKW--TGDAKNLHFIRADAEKVQ--FE-TKFDAITCQYALFFFPNEQKVLK 138
                      78899****************************************6..56899*************..99.9********************** PP

  Methyltransf_31  96 eiervlkpggilliedp 112
                      +++++lk++g + ++ +
       AJA92534.1 139 NMKKLLKKDGTITLAVH 155
                      ***********998765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.3
  Methyltransf_31  73 ekfDlilsnevl 84 
                      ekfD ++ ++  
       AJA92534.1 236 EKFDSLTKFQKA 247
                      566665555443 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   2.9e-23   1.8e-20       1      97 []      55     148 ..      55     148 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 2.9e-23
                      EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      vLdl+cGtG +t++l +++g k++++++D se++l++a++   +++ n++f+++dae+++fe  +fD++++++al ++++e+  k+lk+++++L
       AJA92534.1  55 VLDLACGTGLVTKKLIRKVGsKGQIYAIDSSESALKIAKKWTGDAK-NLHFIRADAEKVQFET-KFDAITCQYALFFFPNEQ--KVLKNMKKLL 144
                      9******************779********************8765.**************98.********9999999766..9********* PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      k++G
       AJA92534.1 145 KKDG 148
                      **99 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.8   2.9e-22   1.9e-19      38     221 ..      42     210 ..       8     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.9e-22
                      HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S- CS
  Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtD 131
                      ++ +l+  k++ +vlD+a+Gtg ++ kl ++vg+kg++  +D +e+ Lk+++k   +   +n++f+ a+ae+++fe   fD +t  + l  +++
       AJA92534.1  42 KLLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKWTGD--AKNLHFIRADAEKVQFET-KFDAITCQYALFFFPN 132
                      566788889999***************************************987644..579*************86.7*************** PP

                      HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEE CS
  Ubie_methyltran 132 klkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllakdldsyryLvesirafPdqetlkeliedaGfksveyesl 221
                       +k+Lk++ + lk  G+++     k ++p ++         +l  + k++ + l +y      + +f  +et+++ i++aGfk++  +++
       AJA92534.1 133 EQKVLKNMKKLLKKDGTITLAVHGKYNVPYFDC--------ILESVKKFIPDYLPKYP----EMDRFGTKETFADAIKKAGFKKIVVKKF 210
                      *****************9988777777765554........55566666666666664....57899***************99877766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   1.8e-21   1.2e-18       1      94 [.      56     150 ..      56     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.8e-21
                      EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      Ld++cGtG+++++l +++   ++++++D s+ +lk+ak+ + ++++ + f++adaek++fe  +fD+++++ +l+++++ +k+lk+++++Lk++
       AJA92534.1  56 LDLACGTGLVTKKLIRKVgskGQIYAIDSSESALKIAKKWTGDAKN-LHFIRADAEKVQFET-KFDAITCQYALFFFPNEQKVLKNMKKLLKKD 147
                      8**************666699***********************96.99***********99.******************************* PP

                      EEE CS
  Methyltransf_11  92 Gll 94 
                      G++
       AJA92534.1 148 GTI 150
                      *87 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   2.8e-16   1.8e-13      11     161 ..      41     203 ..      26     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.8e-16
  Methyltransf_23  11 dklerllpklraggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpd 97 
                      +kl++l++  +++  vLd++cGtG +++ l r+ g   +++++D s+ a +ia+     ak+ ++  +d++   + + kfd I++ + l  +p+
       AJA92534.1  41 KKLLELSK-IKKSDTVLDLACGTGLVTKKLiRKVGSkgQIYAIDSSESALKIAKkwtgDAKNLHFIRADAE-KVQFETKFDAITCQYALFFFPN 132
                      78888985.99*************87777769999999**************9976662333333333111.222356**************** PP

  Methyltransf_23  98 ppellrqiatllkpgGylllseplasl........kedrllldwlylvpagrhisffsarslkelleeaGle 161
                        ++l+++++llk +G + l +++++         ++ +++    ++    +  +f + ++++++ ++aG++
       AJA92534.1 133 EQKVLKNMKKLLKKDGTITLAVHGKYNvpyfdcilESVKKFIPDYLPKYP-EMDRFGTKETFADAIKKAGFK 203
                      **********************9987677676665555555555555555.666777777777777777776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   5.2e-15   3.3e-12       1      98 [.      56     149 ..      56     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 5.2e-15
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklL 93 
                      L++ cGtG +++ l +k  +  +++++D s+sa++ ak+ + + +     n+++   d+++ + + +fD++++  +l  +++ ++vl+n++klL
       AJA92534.1  56 LDLACGTGLVTKKLIRKVgSKGQIYAIDSSESALKIAKKWTGDAK-----NLHFIRADAEKVQFETKFDAITCQYALFFFPNEQKVLKNMKKLL 144
                      89****************9***************55555555555.....5666666666666667**************************** PP

  Methyltransf_12  94 kpgGr 98 
                      k++G 
       AJA92534.1 145 KKDGT 149
                      ***97 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   5.8e-10   3.7e-07      23     103 ..      43     123 ..      38     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.8e-10
                 HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
         MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                 Lle  + ++s++vlDl+cG+G+++ +l ++  +   + ++d +  Al++ak+   + k +++++  d+ +   e kfd+i +
  AJA92534.1  43 LLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSKGqIYAIDSSESALKIAKKWTGDAK-NLHFIRADAEKVQFETKFDAITC 123
                 444444457889*************99888765544**************98666555.699*****9999999******87 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   7.7e-09   4.9e-06      33     143 ..      42     151 ..      38     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.7e-09
        NodS  33 qilrlslaqgsiadalevGcaaGalterlapyck...rltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraa 128
                 ++l+ls+ ++s   +l++ c +G +t++l        ++  +d  e+a++ a++ + ++ ++ +i +d ++++ + kfd i +   l++  + +++   
  AJA92534.1  42 KLLELSKIKKS-DTVLDLACGTGLVTKKLIRKVGskgQIYAIDSSESALKIAKKWTGDAKNLHFIRADAEKVQFETKFDAITCQYALFFFPNEQKV--- 136
                 67788776654.679**************8765311257899***********************************************9998765... PP

        NodS 129 vrnlvsllapdgqlv 143
                 ++n+ +ll+ dg++ 
  AJA92534.1 137 LKNMKKLLKKDGTIT 151
                 899999999999875 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.4e-08   1.6e-05      61     177 ..      42     156 ..       5     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                  TT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHH CS
  Fibrillarin  61 kglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarila 158
                  k l+  +ikk + vL l  ++G     +   vg++g +ya++ s+ +l+   + + + kn+  i +DA+k  ++++  +++ + +a    p++ ++  
   AJA92534.1  42 KLLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKWTGDAKNLHFIRADAEK-VQFETKFDAITCQYALFFFPNEQKV-L 137
                  4456678*************************************************************98.5799999*************99886.5 PP

                  HHHHHHEEEEEEEEEEEEH CS
  Fibrillarin 159 knaklflkeggyllisika 177
                  kn+k  lk++g++ ++++ 
   AJA92534.1 138 KNMKKLLKKDGTITLAVHG 156
                  8*************99985 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0047         3      34      90 ..      54     102 ..      36     111 .. 0.68
   2 !   16.1   0.1   9.6e-06    0.0061     121     173 ..     103     152 ..      99     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0047
                 EEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHHTEEECCHH CS
        CheR  34 riwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAkagvykeeel 90 
                 +++  +c++G       ++ k+ l ++++ k +i+A+D+++++l+ Ak+ + ++++l
  AJA92534.1  54 TVLDLACGTG-------LVTKK-LIRKVGSKGQIYAIDSSESALKIAKKWTGDAKNL 102
                 5556666665.......34444.444444599***************9977666666 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.6e-06
                 EEEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
        CheR 121 kFeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                 +F + ++ +  ++++k+D i+c+  l +f +e  +kvl+++ + lk++g + l
  AJA92534.1 103 HFIRADAEK-VQFETKFDAITCQYALFFFPNE--QKVLKNMKKLLKKDGTITL 152
                 566666666.8999***************766..57*************9875 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.5e-08   2.9e-05      64     148 ..      42     123 ..      34     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.5e-08
                 HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEE CS
        PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihv 148
                 ++lel ++kk + vL++ +G+G  t  l r vg+kg++ +i+ +++  + ak+   + d++n++++ +D +k ++ ++ +dai  
  AJA92534.1  42 KLLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKW--TGDAKNLHFIRADAEK-VQFETKFDAITC 123
                 5688888*******************************************9996..67899*******9876.666677888866 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.9e-07   0.00012      18      93 ..      39     117 ..      24     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.9e-07
                 HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHH CS
      RrnaAD  18 vineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkklskdeklkvvhqDflkfetpee 93 
                 v ++ l+ +++++++tvl+++ G+G+ T++L   +    q  ++ + e+ +k+ +k   ++++l  + +D+ k ++  +
  AJA92534.1  39 VTKKLLELSKIKKSDTVLDLACGTGLVTKKLIRKVgskGQIYAIDSSESALKIAKKWTGDAKNLHFIRADAEKVQFETK 117
                 56788889999********************88887878999************99777************99999874 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   4.8e-07   0.00031      53     240 ..      42     233 ..      25     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-07
                 HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E..EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHH CS
        CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvk..vvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtff 149
                  +le  ++k+ +t+Ld+ cG G ++++ +++ + k  + ++  S+   k akk   ++ + +  + +     +++ k+d++    a+  + + n ++  
  AJA92534.1  42 KLLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSKgqIYAIDSSESALKIAKKWTGDAKNLHFIRADAE-KVQFETKFDAITCQYAL--FFFPNEQKVL 137
                 56778899***********************98753389999999999999999988887777777655.4789*******998776..555666899* PP

                 HHHHHHS-TT-EEEEEEEEE--HHHHHCTTCCC.HHHHHHT..STT.S---BHHHHHHHHHHTT-EEEEEEE-HHHHHH.HHHHHHHHHHHTHHHH CS
        CMAS 150 kklkkllkedGllllhtitslhkkelaerglkl.kfidkei..FPg.GelpsieeieeeiseagftvvdveslrahYak.TLkaWaealqenkdea 240
                 k++kkllk+dG+++l    +++         ++ kfi  ++  +P+  +  + e+ ++ i++agf+ + v+++  +Y   T +++ +++++++++ 
  AJA92534.1 138 KNMKKLLKKDGTITLAVHGKYNVPYFDCILESVkKFIPDYLpkYPEmDRFGTKETFADAIKKAGFKKIVVKKFVFKYSPgTFSDYWNNYKKHLSKP 233
                 ************99887777776655432222239**9998778873467778888999**************99998548888888888887765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.2e-06    0.0014      11      96 ..      45     126 ..      40     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.2e-06
                 HHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S CS
        FtsJ  11 eidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgditdpetiekikealserkvdlvvsDga 96 
                 e+    k +k+ +tv+Dl++++G  ++ l +++g kg+++a+D  +             +++++i++d  + + +          k+d +++  a
  AJA92534.1  45 EL---SK-IKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESalkiakkwtGDAKNLHFIRADAEKVQFET---------KFDAITCQYA 126
                 43...34.56789*******************************99855554333223366666666666665555.........4555555544 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0011      93     188 ..      50     154 ..      39     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
        DREV  93 qedkklldlGaGdGeitkrvaptfee...vyatelsetmrdrlkk.....kkynvlsa.lelqetdvkldlilclnlldrcfdplklledirsalepng 182
                 +++ ++ldl  G G +tk++   +     +ya + se   +  kk     k+ + + a  e  + + k+d i+c   l    +  k+l+++++ l+ +g
  AJA92534.1  50 KKSDTVLDLACGTGLVTKKLIRKVGSkgqIYAIDSSESALKIAKKwtgdaKNLHFIRAdAEKVQFETKFDAITCQYALFFFPNEQKVLKNMKKLLKKDG 148
                 46789**************9999876678***99998654333221222277777754156666999*******************************9 PP

        DREV 183 rvival 188
                  + +a+
  AJA92534.1 149 TITLAV 154
                 999886 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.013       8.4     176     230 ..      35      93 ..       2      94 .. 0.67
   2 !   10.6   1.2   0.00053      0.34      36      69 ..     134     196 ..     128     270 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                  --HHHHHHHHHHH.S-TT-EEEETT-TTTH.HHHHHHHTT-E..EEEEESSHHHHHHHH CS
  N6_N4_Mtase 176 kPvallerlIkls.tkkgdivlDpFaGSGt.Tavaakelgrk..fiGieieeeyvelae 230
                   P    ++l++ls  kk d+vlD  +G+G  T +  ++ g k   + i+ +e+++++a+
   AJA92534.1  35 GPFGVTKKLLELSkIKKSDTVLDLACGTGLvTKKLIRKVGSKgqIYAIDSSESALKIAK 93 
                  57777889997772466**********99513344444444465677777777777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00053
                  HHHHHHHHHHEEEEEEEEEEE-CCCHHT.............................HHHHHH CS
  N6_N4_Mtase  36 ekvlkevrrvLkddgsifiniddseikk.............................elkala 69 
                  +kvlk+++++Lk+dg+i + +  ++  +                             e +a a
   AJA92534.1 134 QKVLKNMKKLLKKDGTITLAVHGKYNVPyfdcilesvkkfipdylpkypemdrfgtkETFADA 196
                  589**********************99844444444444444444444444444444444444 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.6e-05     0.017       6      71 ..      49     112 ..      44     124 .. 0.78
   2 ?   -1.2   0.0         2   1.3e+03     117     135 ..     133     151 ..     129     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                      --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
  Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                       ++ +t+lDl+++ G  T  +   + +kg+++A+d +++ lk  ++  ++   +n+  ++aDa k+
       AJA92534.1  49 IKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKW-TG-DAKNLHFIRADAEKV 112
                      57899**************999999************9998755544.33.456678888888777 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                      HHHHHHHHCCCEEEEEEEE CS
  Methyltr_RsmB-F 117 qkellsaaidllkkgGvlv 135
                      ++++l+ + +llkk+G++ 
       AJA92534.1 133 EQKVLKNMKKLLKKDGTIT 151
                      6789999999999999985 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0074      19      91 ..      46     111 ..      37     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
  Methyltransf_32  19 elakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                        +k +++ tv+D+++G g  +  l   ++  k ++++id++e+  +    +a+k   ++ k+l+f+ ++ e+
       AJA92534.1  46 L-SKIKKSDTVLDLACGTGLVTKKLIR-KVGSKGQIYAIDSSESALK----IAKKWTGDA-KNLHFIRADAEK 111
                      3.567889******************9.7789********9876555....555555444.555555555444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     3e-05     0.019      96     151 ..      98     158 ..      12     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                 T-SSEEEEES-CCCTTTTT-EEEEEEC.-...SSSHHHHHHHHCCCEEEEEEE.EEEESS- CS
        GidB  96 klenveivearaeekqeeekydvvtsR.A...laslnelteillkllkeggli.lalKGks 151
                 + +n+++++a+ae+ q e k+d++t+  A   + + +++ + ++kllk+ g+i la+ Gk+
  AJA92534.1  98 DAKNLHFIRADAEKVQFETKFDAITCQyAlffFPNEQKVLKNMKKLLKKDGTItLAVHGKY 158
                 5689*********************985533356788999999999999887636777775 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   4.3e-05     0.027      37     128 ..      54     140 ..      48     157 .. 0.79
   2 ?   -2.0   0.0       2.7   1.7e+03      15      36 ..     157     180 ..     150     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
       Rsm22  37 slldvgegpgtalwaaselweeleevlvidaseelleiskelaadapelkeaalrrsvirealeleea.dLviisyvLleledesreklvknl 128
                 ++ld++ g+g ++        +  +++ id se++l+i+k+ + da++l+ ++       e++++e++ d +++ y L+ + +e++  ++kn+
  AJA92534.1  54 TVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKWTGDAKNLHFIRADA----EKVQFETKfDAITCQYALFFFPNEQK--VLKNM 140
                 578888888877777777777899************************99994333....467999888*********99888653..44444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
       Rsm22  15 tyav..lrrvLdelaervpdflPk 36 
                 +y+v     +L+++++ +pd+lPk
  AJA92534.1 157 KYNVpyFDCILESVKKFIPDYLPK 180
                 55552234799***********97 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.3e-05     0.027      42     135 ..      46     136 ..      24     154 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                     HHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S-GGG CS
  Methyltransf_3  42 LvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDaDkss 135
                     L k+  +  vl++   tG     +  ++   G+i aid  + a +ia+k+    g a+ +++i++da kv  e + d  + ++ + f   +++ 
      AJA92534.1  46 LSKIKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKWT---GDAKNLHFIRADAEKVQFETKFDAITCQYALFFFPNEQKV 136
                     55677777899999999*999999************************985...7779999********9999888888888888887665554 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-05     0.029      10     104 ..      48     146 ..      41     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
        MetW  10 likpgsrvldlGcGdGellellkeekqvdg..rGleldeegvaecv.....akGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkevldellri 101
                  ik+  +vldl cG G + + l  + + +g  + ++ +e++++ +      ak l+ i+ d++k   +fe  +fd +  + +l    n ++vl+++ ++
  AJA92534.1  48 KIKKSDTVLDLACGTGLVTKKLIRKVGSKGqiYAIDSSESALKIAKkwtgdAKNLHFIRADAEK--VQFE-TKFDAITCQYALFFFPNEQKVLKNMKKL 143
                 588999**********999888766666552245676666654332122337889999888876..5665.67**********************9887 PP

        MetW 102 grr 104
                  ++
  AJA92534.1 144 LKK 146
                 554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-05      0.03     159     232 ..      49     123 ..      39     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
        PrmA 159 vkegeevlDvGtGSGiLaia.aakLgak.kvvavDiDevAvkvakeNaelNkveaklevalseellk.eekadviva 232
                 +k+ ++vlD+ +G+G+ +     k+g k +++a+D  e A+k+ak+     k  + ++  + +e ++ e+k+d i +
  AJA92534.1  49 IKKSDTVLDLACGTGLVTKKlIRKVGSKgQIYAIDSSESALKIAKKWTGDAKNLHFIR--ADAEKVQfETKFDAITC 123
                 68899**********998652568887658**************98765444433333..33333333577887776 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.8   1.8e+03     108     137 ..      63      93 ..      40      98 .. 0.67
   2 ?   12.5   0.1   0.00012     0.077      59      98 ..     220     259 ..     205     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.8
        SieB 108 eLlekgiltkasnvsniaikettak.ykiqp 137
                 +L+ k+ + k+++  +i+  ++ ++ +ki++
  AJA92534.1  63 GLVTKKLIRKVGSKGQIYAIDSSESaLKIAK 93 
                 6788888888888766644333333366655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
        SieB  59 kekik..kkreqkkvekklknLteeekavLreflnqgksvlt 98 
                 +++++  kk+  k  ++k+++Lt+ +ka Lre++++  ++l+
  AJA92534.1 220 SDYWNnyKKHLSKPLREKFDSLTKFQKANLREMIKD--KTLE 259
                 4445566899*************************9..3444 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.089      37     140 ..      48     149 ..      40     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
       GCD14  37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsg..kvDavfLDlPaPweaiphaak 133
                 ++k+   v++   G+g ++++++r v+ +G++++++  e+  + a++   + +  +++        k  f+++ +      a+f+ +P+  + +++++k
  AJA92534.1  48 KIKKSDTVLDLACGTGLVTKKLIRKVGSKGQIYAIDSSESALKIAKKWTGDAKNLHFIRADA---EKVQFETKFDAitCQYALFF-FPNEQKVLKNMKK 142
                 5777888999999**************************99999998766666555555555...55555444433003345554.7888888888888 PP

       GCD14 134 alkkegg 140
                  lkk+g+
  AJA92534.1 143 LLKKDGT 149
                 8877776 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015     0.096      50     164 ..      39     152 ..      35     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                     HHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT.-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---.--SEEEEESSGGGS- CS
  Methyltransf_2  50 vakkvleafdleglkslvDvGGGtGalakaivsayPt.ikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP.eaDaillkrvlhDws 141
                     v+kk+le +++++  +++D+  GtG + k+  ++  +  ++   D +e   + Ak+   +g +++++f+  d  k +   + Dai  +  l+ + 
      AJA92534.1  39 VTKKLLELSKIKKSDTVLDLACGTGLVTKKLIRKVGSkGQIYAIDSSEsALKIAKKW--TGDAKNLHFIRADAEKVQFEtKFDAITCQYALFFFP 131
                     5799***********************999998875314555566665246778888..99*************99998799************9 PP

                     HHHHHHHHHHHHHH--TT-EEEE CS
  Methyltransf_2 142 dekcvklLkrvkkalpagGkviv 164
                     +e+  k+Lk++kk l+++G + +
      AJA92534.1 132 NEQ--KVLKNMKKLLKKDGTITL 152
                     985..99************9976 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0095       6.1      67     127 ..      67     123 ..      39     126 .. 0.65
   2 ?   -1.3   0.0       2.3   1.5e+03     147     171 ..     135     159 ..     133     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0095
                 HHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
     UPF0020  67 aeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                 +++ ++   + ++y++D+ +++++ a++    a+     +f  ada k++  e ++d+i +
  AJA92534.1  67 KKLIRKVGSKGQIYAIDSSESALKIAKKWTGDAKN---LHFIRADAEKVQ-FETKFDAITC 123
                 34444444667789999999999999887766654...455556666666.4457888877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                 HHHHHHHHH-TT..-EEEEEESSHH CS
     UPF0020 147 eflrelkrvlrgggrlvlltsenka 171
                 ++l+ +k+ l+++g + l+++++ +
  AJA92534.1 135 KVLKNMKKLLKKDGTITLAVHGKYN 159
                 78999*******9999999988765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.31       2      87 ..      62     152 ..      61     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                 HHHHHHHHHHHTT-..EEEEEESSHHHHHHHHH.TT.ES..EEEET.TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEE CS
  ADH_zinc_N   2 vGlaavqlAkalGa..eviavdsseeklelakk.lG.ad..eviny.kea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvv 87 
                  Gl + +l +  G   +++a+dsse+ l++akk  G a+  ++i +  e+ +++ +  ++t      + f +++ +++l++  kllk++G++++
  AJA92534.1  62 TGLVTKKLIRKVGSkgQIYAIDSSESALKIAKKwTGdAKnlHFIRAdAEKvQFETKFDAIT---CQYALFFFPNEQKVLKNMKKLLKKDGTITL 152
                 67777778888888889****************7787653355555644457999999999...334466677779999999999**9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1723.04
//
Query:       AJA92535.1  [L=97]
Description: rhodanese-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-12   46.0   0.1    9.1e-12   45.4   0.1    1.2  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1   5.1e-16   9.1e-12       3     105 ..       8      96 ..       6      97 .] 0.80

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 5.1e-16
   Rhodanese   3 kelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGyknvsvldGGf 101
                 ++lk+ +++   +++DvR+p+e + g I+++ n+               +++  ++ +l   ++k++ vyc++g r + aa  l k+G     +l+GG+
  AJA92535.1   8 DQLKQEQDQF--VIIDVREPDEVANGAIENSQNM--------PLGLVIRNAKKGQIDDL---KDKKICVYCASGYRGNIAADELAKAG-FSAINLEGGY 92 
                 6677777554..4*********999*********........45555555555555665...89************8888777777**.79******** PP

   Rhodanese 102 kawk 105
                 +aw 
  AJA92535.1  93 MAWT 96 
                 ***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 722.31
//
Query:       AJA92536.1  [L=427]
Description: MOFRL family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-62  210.1   0.0    4.9e-62  209.5   0.0    1.3  1  DUF4147   Domain of unknown function (DUF4147)
    7.9e-30  103.3   0.0    1.9e-29  102.0   0.0    1.7  1  MOFRL     MOFRL family
  ------ inclusion threshold ------
       0.19   11.1   0.0        0.3   10.5   0.0    1.2  1  DUF3530   Protein of unknown function (DUF3530)


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.5   0.0   8.2e-66   4.9e-62       3     228 ..      18     249 ..      16     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 209.5 bits;  conditional E-value: 8.2e-66
                 HHHHHHHHHTTSHHHHHHTTHHH.H--............-SEEEEEESTTHHHHHHHHH.HHHG..EEEEEEETT---..--TT-EEEEE-SSS--HHH CS
     DUF4147   3 raifeaaveavdpeklvkralsl.kee.....eldlskkkrvvvvgaGKAaaamaaaleeealk..sgvvvvkkghae..ekerievleaahplPdees 91 
                  +i+++++ a +p++++k+ +s+ k       ++dl+k+++++++++GK a +m + +++ ++k  +g+vvv+k+ +   +k+ +e+++a+hplP+++s
  AJA92536.1  18 LKILNEGIIASSPSQHLKKYISKnK-IqfstsKIDLKKFNNIFLIAVGKSAGTMTEYVSQ-KIKfnHGIVVVPKEVTPklNKKIFEIINAGHPLPNRNS 114
                 6899*****************8851.24555699**********************9995.44455******8665554455569************** PP

                 HHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TT CS
     DUF4147  92 veaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddld 190
                 ++a ++++e+++k++++d+vl+liSGGgSAl ++P   i+l dk  ++++L++sGa+I+e+ +VRkhls ikGGrL + ++  + +s+++SDV+gdd++
  AJA92536.1 115 LKAGKNLVEFLNKTQKNDFVLFLISGGGSALSVYPN-LISLRDKILVNEELIRSGANINEITCVRKHLSLIKGGRLIQNMNC-KGISFVVSDVIGDDIT 211
                 ***********************************8.9*****************************************998.99************** PP

                 TGGG-TTS-----HHHHHHHHHHTT---..-HHHHHHH CS
     DUF4147 191 vIASGPtvpdsstfadalailekykleeklpesvrelL 228
                  I+SG t +d+stf+dal+il+k++l+++lp+s  ++L
  AJA92536.1 212 SISSGMTSYDKSTFTDALKILKKFSLQHTLPNSTLSVL 249
                 ********************************999888 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   3.2e-33   1.9e-29       2     109 .]     320     418 ..     319     418 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.2e-33
                 EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HHHHHHTT-HHHHHHHTT-EE-- CS
       MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldakeaLanndsyeffeklgallkt 100
                 ++++gGE+tv+v g+GkGGrnqel+l+l  +lk+   +++++++s+gtDGiDG+t+ aG i++++          d +++L+nnds +ff+k+g l+kt
  AJA92536.1 320 CIIFGGEPTVNVIGNGKGGRNQELVLRLYEKLKHK--KPDFTFASIGTDGIDGNTKFAGSIFSTKYN-------YDGRSYLKNNDSSSFFKKFGGLIKT 409
                 89****************************99876..79***********************88765.......56789******************** PP

                 ---S----E CS
       MOFRL 101 gpTgtNVnD 109
                 g T++NVnD
  AJA92536.1 410 GITQNNVND 418
                 ********9 PP

>> DUF3530  Protein of unknown function (DUF3530)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     5e-05       0.3     189     242 ..      48      99 ..      29     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5e-05
     DUF3530 189 aflnqrgaenivllghgtgAywaarylaekksakvdaLvlvdarepaeaaekqL 242
                 + ++ ++ +ni l++ g++A+  ++y+++  + k ++ ++v ++e  ++ +k++
  AJA92536.1  48 SKIDLKKFNNIFLIAVGKSAGTMTEYVSQ--KIKFNHGIVVVPKEVTPKLNKKI 99 
                 556667778********************..45555555555555555556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2922.59
//
Query:       AJA92537.1  [L=1409]
Description: peptidase, S8/S53 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-39  134.2   0.0    1.2e-38  133.1   0.0    1.5  1  Peptidase_S8  Subtilase family
    3.7e-06   26.7   3.0      0.046   13.4   0.2    3.6  4  Big_3_3       Bacterial Ig-like domain (group 3)
    0.00014   21.9   0.3       0.07   13.2   0.1    3.2  3  DUF916        Bacterial protein of unknown function (DUF916)
    0.00024   21.8   2.6    0.00053   20.7   0.1    2.8  3  fn3_5         Fn3-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0   2.7e-42   1.2e-38       1     298 []     147     695 ..     147     695 .. 0.82

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 2.7e-42
                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE--.-TTSG......................................................... CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx........................................................ RF
  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvi.deegag........................................................ 40 
                   g+++++a++DtGvd s+pd+++ +  +++ + +  d +g+g                                                        
    AJA92537.1 147 GNDITIAIIDTGVDFSNPDMQHALARDSENFPIMlDPDGQGliltnatfaanidqygtiknftksslynttsdvyvkprgggvflnieqngdgtsll 243
                   789******************88777666554431444445***************99999999999999999999999999999999999999999 PP

                   ..................................................................................GGEETT-SS-TT-SC CS
                   ..................................................................................xxxxxxxxxxxxxxx RF
  Peptidase_S8  41 ..................................................................................fngadsettstnwar 55 
                                                                                                     f              
    AJA92537.1 244 vynsmfpmfgsspllngtlnddmrigtdkhdyiesksgiyhlgvmyqgspsqpqvvpvlvvdskesgyydtiipdmstswqdF-------------- 326
                   99999999999999888888888888888888888888888888888888888888888877777775555554444444440.............. PP

                   -S...........................................................................................SS.. CS
                   xx...........................................................................................xxxx RF
  Peptidase_S8  56 dd...........................................................................................ngns 61 
                                                                                                                +g  
    AJA92537.1 327 -TknstdkkiefdfdftddvhhvigdgnefliydydndgefdysvgtlgaqvldiygvieneseiddtfgaingtllppinrngeffgvmtdvQG-- 420
                   .2555555666666666677777777777777777777888888888888888888888888888888888888888888886666666554444.. PP

                   ..HHHHHHHHHH-B...........SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHH......HHHHHH..CT-SEEEE-EESCETTCHHCHH CS
                   xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  62 ieHGthvAGiaaan.........apeegekngvapgakilsvkvldtsggsmetgtelira......ieeaae..dkvdvinmslgestslpktgrs 141
                     HGt  AG+++ +         + ++ ++ gvap+aki+ vk+l   +  +   ++l++a      ie+ +    ++d+i++s+g  +  p+++  
    AJA92537.1 421 --HGTGSAGTIISKglveydiynDTKKFNIRGVAPDAKIIPVKAL---WFGDILYAWLWSAgfdnddIEWNFSgnTRADIISNSWG-VSTFPNFEYA 511
                   ..*******************5555555678**************...6666556999999999999888887547889*******.5555555555 PP

                   HHHH..........HHHHHH.CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES.....................TTSSB-TT--B- CS
                   xxxx..........xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxx RF
  Peptidase_S8 142 ieal..........ainravnkk.gvlvviSaGNngktgsslqagspvgtpstsknvitvgayt.....................tegkiapfSsrG 206
                   +             + n + +++ gvl+v+SaGN+g      +   ++g p  s   i+vga+t                       +++ +fSsrG
    AJA92537.1 512 PGFDllslvmttlsLPNSFSEDYpGVLMVSSAGNSG------HGYGTIGLPNASPTGISVGATTnnvfvgygpfkdeprfgnstkYSDHVVDFSSRG 602
                   543359999999998899999999************......8999**************************************99999******** PP

                   TT.......-EEEE-S-CCCCCCCCCHHHTTTHH.EEEE-SHHHCHHHHHHHHHHHHHHHTT....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 207 pssdgklkpdivapGgnivstwsrqsnnsaglss.yqsmsGTSmAsPnaagaaAlllsalpk....ltpetvraallntAqdlgkadniesfaqGaG 298
                   p+  g  kpd++  G+ ++  +s  + +++++++ + ++ GTSm++P ++g aAl++++l++    ++p++v+ +l+ tA+d+    +  +f qG G
    AJA92537.1 603 PTLIGDPKPDLMSIGAYSFTPASVTKPSQDYDQDpFGMFGGTSMSAPIVSGTAALVMQELKDnsksFSPADVKNILMSTANDM----HNDVFTQGSG 695
                   *****************777777777667777668***********************88888*****************665....7889999987 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   4.8e+03      95     119 ..     229     253 ..     227     256 .. 0.85
   2 ?   -1.8   0.0      0.48   2.1e+03      31      64 ..    1174    1208 ..    1152    1224 .. 0.68
   3 !   13.4   0.2     1e-05     0.046       4      76 ..    1230    1296 ..    1227    1311 .. 0.85
   4 !   11.4   0.0   4.1e-05      0.18       2      51 ..    1316    1366 ..    1315    1393 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
     Big_3_3  95 VelswveegkdvysleYPrlFPsle 119
                 V l  +++g+++  l Y  +FP + 
  AJA92537.1 229 VFLNIEQNGDGTSLLVYNSMFPMFG 253
                 567788999*************875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
     Big_3_3   31 vtksllstilvdntpPtvsi.segkkisdgavvkg 64  
                  + +   st+++dn pP + +  ++   sd  ++ +
  AJA92537.1 1174 TLVAKFSTLTSDNIPPQIILeLDDFVKSDHIIIPE 1208
                  34445569999*****9999666666666666655 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1e-05
     Big_3_3    4 tvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladal 76  
                  t  f+ ++l +Gk++l+++a d+f+  + +++   +++d   P +++    + ++++vv +  ++++++ d+ 
  AJA92537.1 1230 TTGFNSNNLDDGKHSLTINAIDKFGLATSETFD--FTLDSELPNLEL----QSQNNTVVSKRLDIQVSISDQN 1296
                  5679*********************99988887..9999********....8889999998889999999864 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 4.1e-05
     Big_3_3    2 nytvtfdlkelpeGkynlvlaakdtfnnqvtksllstilvdnt.pPtvsis 51  
                  ++ + fd+++l eG+y +++ a+d  +n v  ++ ++i + +  pP  sis
  AJA92537.1 1316 QKSYSFDVSDLDEGEYFIEVSAQDMAKNSVLSKIIFEIDHSVVdPPKTSIS 1366
                  5789*******************************9998876427777774 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.8   1.3e+04      35      49 ..     327     341 ..     307     343 .. 0.70
   2 !    5.1   0.0    0.0049        22      15      48 ..     754     787 ..     744     792 .. 0.85
   3 !   13.2   0.1   1.6e-05      0.07      60     119 ..     949    1005 ..     941    1006 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
      DUF916  35 ikNssdkeitveitv 49 
                  kNs+dk+i+++ ++
  AJA92537.1 327 TKNSTDKKIEFDFDF 341
                 479999999988765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0049
      DUF916  15 kksYFdLkvkpgqeqelevkikNssdkeitveit 48 
                 ++s+F  +++pg++++ + ki+N +++++t++i 
  AJA92537.1 754 QTSWFGGRLNPGATTSASFKIENPTNSTLTIKIL 787
                 45889999***********************985 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 1.6e-05
      DUF916   60 idYskskekkdkslkvslselvkipkeitlpakesktvklkikmPkeefdGvilGGiyve 119 
                   dYs s++      k s+ +++  ++ i++p+k+s +v++ki++ k++++G++ G i++e
  AJA92537.1  949 FDYSLSASYF---KKDSWADIILDKEIISIPPKQSMDVSVKIETQKDQTTGIYDGFIKFE 1005
                  5666666653...357999****9****************************99988875 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.67     3e+03       8      31 ..     766     789 ..     763     848 .. 0.76
   2 !   20.7   0.1   1.2e-07   0.00053      56     114 ..     961    1015 ..     941    1016 .. 0.81
   3 ?   -3.2   0.0       3.1   1.4e+04      41      70 ..    1234    1249 ..    1215    1283 .. 0.49

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
       fn3_5   8 dkfsftltlkNtsnkaltykvsan 31 
                  ++s  ++++N +n +lt+k+  +
  AJA92537.1 766 ATTSASFKIENPTNSTLTIKILPE 789
                 567888899999999999988655 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.2e-07
       fn3_5   56 e..aaltfetskvtvpAnssktvtvtldlpsdakkkngyfveGfvtlkdsedknpelsvPY 114 
                  +  a + ++++ + +p+++s +v+v++  ++   +++  ++ Gf++++++  +   ++vP+
  AJA92537.1  961 DswADIILDKEIISIPPKQSMDVSVKIETQK---DQTTGIYDGFIKFEGEHHS---VNVPV 1015
                  356888999999*****************44...44789**********9888...88886 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.1
       fn3_5   41 eegklilkaaspeikeaaltfetskvtvpA 70  
                  ++ +l++ ++s++              ++A
  AJA92537.1 1234 NSNNLDDGKHSLT--------------INA 1249
                  3333333333333..............333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.48
# Mc/sec: 8891.56
//
Query:       AJA92538.1  [L=86]
Description: phosphoribosylformylglycinamidine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-15   56.6   0.2    2.4e-15   56.5   0.2    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   1.3e-19   2.4e-15       1      75 [.       5      81 ..       5      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.3e-19
                EEEEEEEE-TTS--HHHHHHHHHHHHT.THTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHT.TS-TTTEEEEE CS
        PurS  1 kakveVtlKkgvlDpqGkavkkalksl.gyeevedvrvgkyieleleaedeeeaeeeveemcekl.LaNpviedyei 75
                ++ v ++ K+g+ Dp+G ++ ++l    + ++++++r g ++++++++++e++a++ + ++c++l ++Np + +++ 
  AJA92538.1  5 QVSVVIENKPGISDPEGDTILNDLVLKdKNTNITQIRSGTILKFSITESNEQNAKDSIIKICDELrIYNPLVSKVTA 81
                589*********************99966667***************************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 640.08
//
Query:       AJA92539.1  [L=397]
Description: translation-associated GTPase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-30  106.6   0.5    2.3e-30  105.4   0.5    1.6  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    5.5e-20   71.6   0.0    5.9e-19   68.2   0.0    2.5  3  MMR_HSR1       50S ribosome-binding GTPase
      4e-13   49.2   0.1    9.8e-13   47.9   0.1    1.7  1  TGS            TGS domain
    2.7e-06   27.0   0.3    1.2e-05   24.9   0.1    2.2  3  FeoB_N         Ferrous iron transport protein B
     0.0072   16.3   0.8      0.057   13.3   0.1    2.2  2  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.014   15.5   0.2      0.052   13.8   0.2    1.9  1  YchF-GTPase_C  Protein of unknown function (DUF933)


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.5   7.8e-34   2.3e-30       1     112 []     221     325 ..     221     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 7.8e-34
  MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlvlkrygsTGVqealnaavf 99 
                 a+NKaDl ++ + iek+ ++++    v+p sA++El Lrka k++li+Y pgde+f+ k++   +l+e+q++aL+  ++ v++++++TGVq++ln+++f
  AJA92539.1 221 AANKADLCDDLKIIEKISTNFK----VIPSSAETELLLRKATKAELINYVPGDESFSGKDN--VQLSEQQNNALHLAKN-VMTKIQTTGVQQILNSIIF 312
                 89******************99....9*******************************999..66**********9999.******************* PP

  MMR_HSR1_C 100 elldlivVYPVed 112
                 ++ld+ivVYPVed
  AJA92539.1 313 DVLDMIVVYPVED 325
                 ***********97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0     2e-22   5.9e-19       1      87 [.       2     116 ..       2     154 .. 0.78
   2 ?   -0.6   0.0      0.46   1.4e+03      75     114 .]     181     224 ..     145     224 .. 0.56
   3 ?   -0.8   0.0      0.54   1.6e+03      68      98 ..     352     383 ..     281     393 .. 0.68

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2e-22
                 EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.......................EEEEECGGCSSHHHHHHHHHHHHHHHHC. CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.......................ielvDtpGliegaseekglgkaflalee. 75 
                 +++++G+ NvGKSt+++a t++ ++ +++p+tT+++n g   lk  +                       ++l+D++Gl+ ga+e+kglg++fl     
  AJA92539.1   2 QIGLLGKANVGKSTFFSAATETLVQSGNFPFTTIEPNVGVCYLKI-NcectnlenrcendlchdgirfvpVKLIDVAGLVPGAHEGKGLGNQFLTDAMk 99 
                 589************************************988441.123334444555566666666666********999*************85545 PP

                 TSEEEEEEETT.....T CS
    MMR_HSR1  76 adlillvvdas.....e 87 
                 ad++++vvd+s     +
  AJA92539.1 100 ADALIHVVDVSgstdiQ 116
                 9********88644441 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                 CTSEEEEEEETT....TTCSHHHHHHHHHHHHH...TTSEEEEEEES CS
    MMR_HSR1  75 eadlillvvdas....eeklkpldeeleellee...akkplilvlnk 114
                 ++d +l+ ++++    + ++   d ++  +l++     kpl++++nk
  AJA92539.1 181 QVDQVLISMSLKtkkaQ-DW--SDDDIMGFLKSlrkIAKPLLIAANK 224
                 35666666665543321.23..3334433333233377889988887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.54
                 HHHHHHHCT.SEEEEEEETTTTCSHHHHHHHH CS
    MMR_HSR1  68 kaflaleea.dlillvvdaseeklkpldeele 98 
                  af  +++  + +l+ +da++++    d+el+
  AJA92539.1 352 LAFTIHQDIgNGFLHAIDAKTKQRIGADHELK 383
                 34444555447788888877443333444444 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   3.3e-16   9.8e-13       4      59 ..     336     391 ..     329     392 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.3e-16
                 EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
         TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                 ++Pd+++  l++g+t++++A  Ih+++++ f++A+  +  qr g dh+L+++d+++Iv
  AJA92539.1 336 VLPDARL--LKKGSTAKELAFTIHQDIGNGFLHAIDAKtkQRIGADHELKNNDIIKIV 391
                 4566666..************************************************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1     4e-09   1.2e-05       2      43 ..       2      43 ..       1      53 [. 0.91
   2 ?   -3.0   0.0       1.5   4.5e+03      72      88 ..      92     109 ..      84     112 .. 0.72
   3 ?   -3.2   0.0       1.8   5.4e+03     101     122 ..     211     232 ..     207     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4e-09
                EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                ++ l+G+ nvGk+t+f a t++  + gN+p +t+e + g + 
  AJA92539.1  2 QIGLLGKANVGKSTFFSAATETLVQSGNFPFTTIEPNVGVCY 43
                6899*******************************9998875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                 HHHH.CTSSSEEEEEEEG CS
      FeoB_N  72 dfll.eeepdvvvnvvda 88 
                 +fl+   ++d++++vvd 
  AJA92539.1  92 QFLTdAMKADALIHVVDV 109
                 555523578999999996 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                 HHHTTSSEEEEEETHHHHHHTT CS
      FeoB_N 101 llelgvpvvlalnmideaekkg 122
                 l  + +p+++a n+ d  ++ +
  AJA92539.1 211 LRKIAKPLLIAANKADLCDDLK 232
                 5667788888888888776554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.12   3.7e+02     104     119 ..       5      20 ..       2      29 .. 0.80
   2 !   13.3   0.1   1.9e-05     0.057      14      73 ..     180     242 ..     160     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                  EECSTTSSHHHHHHHH CS
  RsgA_GTPase 104 lvGqSGvGKStLinal 119
                  l+G+  vGKSt+  a 
   AJA92539.1   5 LLGKANVGKSTFFSAA 20 
                  79*********98765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.9e-05
                  ES--EEEEEEESTTTT...--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHH CS
  RsgA_GTPase  14 aNvdqllivvslkepe...lslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeele 73 
                  + vdq+li +slk+++    s + +  fL  + +   +++i+ nK+Dl+++ + +e+++++++
   AJA92539.1 180 SQVDQVLISMSLKTKKaqdWSDDDIMGFLKSLRKIAKPLLIAANKADLCDDLKIIEKISTNFK 242
                  679*********976511156778888899998889999************996666665554 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.7e-05     0.052      17      49 ..     343     375 ..     339     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
  YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevikyedl 49 
                    +kkg+ta++ A +iH+D+ +gF++a   k ++ 
     AJA92539.1 343 LKKGSTAKELAFTIHQDIGNGFLHAIDAKTKQR 375
                    689********************9976666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2694.93
//
Query:       AJA92540.1  [L=314]
Description: alcohol dehydrogenase, iron-dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-48  163.6   0.0    1.1e-47  162.7   0.0    1.4  2  Fe-ADH        Iron-containing alcohol dehydrogenase
    2.6e-17   63.4   0.0    3.6e-17   62.9   0.0    1.3  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    3.3e-06   26.5   0.0     0.0037   16.5   0.0    2.2  2  DHQ_synthase  3-dehydroquinate synthase
     0.0015   17.9   0.0     0.0024   17.2   0.0    1.3  1  PFK           Phosphofructokinase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.0   2.3e-51   1.1e-47       4     307 ..      10     278 ..       7     286 .. 0.88
   2 !    2.8   0.0    0.0094        42     317     364 .]     259     302 ..     248     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 2.3e-51
                 EEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-E.EEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHHHHH CS
      Fe-ADH   4 ivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagie.vtvfdgvepnptleeveeaaalareegadvviavGGGsviDtAKaia 101
                 i fg++al++ +     +  k+al+vt+       +l dk l ++   gi+ + ++d+v+p+p++e+v+e+++ ++++++ + i++GGGs++D+ K++a
  AJA92540.1  10 IQFGEDALSQAE-----YP-KNALVVTTVPP----ELSDKWLGKM---GIQdYILYDKVQPEPSIEMVKEVIDEYKSKNISAMIGLGGGSSMDVVKYAA 95 
                 556666665433.....33.68999997773....5889999999...665166********************************************* PP

                 HHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT CS
      Fe-ADH 102 lllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskk 200
                   ++                  ++ i iPTt GtG+e+t ++v+    +g+k+ ++++++l+d a++D  ++ ++P +v+ +++ Da a+a E y sk 
  AJA92540.1  96 SEMG------------------VEKILIPTTFGTGAEMTTYCVLK--FDGKKKLLREDRFLADRAVIDSYFMNGTPEQVIKSSVCDACAQATEGYDSKL 174
                 ****..................999********************..4447999999****************************************** PP

                 ---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT CS
      Fe-ADH 201 anplsdalaleairliaknleravadgedleareqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlara 299
                  n+l+++l+++a+  +++++ +  +++      e+  ++s+l+g++f+n+++++ Hal++ ++   g+phg++++ +   + + n++  ++r++++ ++
  AJA92540.1 175 GNDLTKTLCKQAFDVLYDAIMN--DKP------ENYPYGSMLSGMGFGNCSTTLGHALSYVFSN-EGVPHGYSLSSCTTVAHKHNKSIFYDRFKEIIEK 264
                 ****************999976..445......8889***************************.9********************7779********* PP

                 .............T CS
      Fe-ADH 300 lgge......sdee 307
                 +g +      + ++
  AJA92540.1 265 MGFDkldlkaDVNQ 278
                 *9888755433333 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0094
                 HHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T.SGGGGSSS---HHHH CS
      Fe-ADH 317 rellkelglptsLselgvdeedldklaeaalkd.rslannpreltaedv 364
                 +e+++++g+     +l++++ d+ + a+ +++d ++l  np ++++edv
  AJA92540.1 259 KEIIEKMGFD----KLDLKA-DVNQAADVVMTDkGHLDPNPIPISKEDV 302
                 4455554444....556666.89************************97 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.0   8.1e-21   3.6e-17      51     192 ..      51     193 ..      26     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 8.1e-21
    Fe-ADH_2  51 vveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtv.akaaaPlaviaDldvlae 148
                 ++++v++e+++e v++++++ ++k++ +++++GgG+ +D++ky++++ +v+ + +pT+        +++ l+ dgkk+ +  +  ++   ++D  +++ 
  AJA92540.1  51 LYDKVQPEPSIEMVKEVIDEYKSKNISAMIGLGGGSSMDVVKYAASEMGVEKILIPTTFGTGAEMTTYCVLKFDGKKKLLrEDRFLADRAVIDSYFMNG 149
                 678899*********************************************************************9999977777888899******** PP

    Fe-ADH_2 149 APrrllasGvGDllgkytaladwklanevseplaklsaamvqea 192
                  P++ + s v D+ ++ t  +d+kl+n++++ l+k++++ + +a
  AJA92540.1 150 TPEQVIKSSVCDACAQATEGYDSKLGNDLTKTLCKQAFDVLYDA 193
                 *************************************9987544 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.2e-07    0.0037      18      66 ..      63     109 ..      54     112 .. 0.83
   2 !    7.9   0.0   0.00033       1.5     180     259 ..     215     287 ..     139     289 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-07
                   HHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SH CS
  DHQ_synthase  18 kildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttl 66 
                    + +++ e k +  s++i lGGG  +D++ ++A+ +  Gv+ + +Ptt 
    AJA92540.1  63 MVKEVIDEYKSKNISAMIGLGGGSSMDVVKYAASEM--GVEKILIPTTF 109
                   4555566666777799*****************975..*********95 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00033
                   GTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT.-HHHHHHHHTTCT CS
  DHQ_synthase 180 nlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkelleveellealkkDk 259
                   n   t+gHa+  +++ e + HG + +   ++a+++ +++  +    ++r +++++k+g++  l+ + +v+++++++++Dk
    AJA92540.1 215 NCSTTLGHALSYVFSNEGVPHGYSLSSCTTVAHKHNKSI--F----YDRFKEIIEKMGFDK-LDLKADVNQAADVVMTDK 287
                   33359*********************9999999888555..3....468888889988875.444447888888888887 PP

>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.4e-07    0.0024      76     132 ..      60     111 ..      37     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.4e-07
                 SHHHHHHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT- CS
         PFK  76 eregrkkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTidN 132
                 + e +k++++++k ++i+a++ +GG  s+++++  ++e+ g    ++ ++iP T   
  AJA92540.1  60 SIEMVKEVIDEYKSKNISAMIGLGGGSSMDVVKYAASEM-G----VEKILIPTTFGT 111
                 446699******************************998.9....999****99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2347.55
//
Query:       AJA92541.1  [L=270]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.16   12.5  14.6       0.82   10.2   1.0    3.7  3  DUF202           Domain of unknown function (DUF202)
        8.5    6.4  12.5        1.2    9.2   2.5    2.5  3  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00023       2.1      41      64 ..      14      37 ..       3      39 .. 0.81
   2 ?   10.2   1.0   9.2e-05      0.82      16      57 ..      57     114 ..      52     122 .. 0.74
   3 ?   -3.6   6.0       1.8   1.7e+04      18      52 ..     183     215 ..     177     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
      DUF202 41 kilglilivlgiltllvglvrylr 64
                k++ l+++ +gil+l+++++ y++
  AJA92541.1 14 KLIILGFVSIGILFLIYARFEYQE 37
                556678****************85 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.2e-05
      DUF202  16 tslalialglallrffl....tgepsalgkilg............lilivlgiltllv 57 
                 ++++++++g++l +f++    tg+ +al++i++            +++iv gi++  +
  AJA92541.1  57 FAISIGMIGVGLRKFQKrvaaTGNTTALSMICSntlgskakktfvITFIVYGIFFSMT 114
                 79************98888886666665555545555555555559999999998776 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.8
      DUF202  18 lalialglallrffltgepsalgkilglilivlgi 52 
                 +al++ ++ +++   tg+  ++g++ gl+++  ++
  AJA92541.1 183 TALAVNAISITKK--TGGLGSIGAATGLFIACPTC 215
                 6777777777774..66666666666655444333 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.005        45      47      93 ..      19      77 ..      14      87 .. 0.49
   2 ?   -3.6   0.1       1.2   1.1e+04      40      45 ..     104     109 ..      93     119 .. 0.48
   3 ?    9.2   2.5   0.00013       1.2      11      81 ..     175     253 ..     171     269 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.005
  Phage_holin_3_6 47 allalllllvala..........lalaa.....lwlaalivaavllvlagvlalvglkklkk 93
                     +++++++l++  a          +   +     l  a+ i++a+ + + gv ++   k++++
       AJA92541.1 19 GFVSIGILFLIYArfeyqeitpdA---VqsiqrLGTAFYILFAISIGMIGVGLRKFQKRVAA 77
                     222222222222344444433331...12224566677777666666666666666666554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.2
  Phage_holin_3_6  40 lgaagv 45 
                      +++ g+
       AJA92541.1 104 FIVYGI 109
                      222222 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00013
  Phage_holin_3_6  11 lssLvrteleLakaElkeeakragsgagllgaagvlallalllllvala........lala.a.lwlaalivaavllvlag 81 
                      +s Lv t  +La   ++  +k  g g + ++ ++++a+ + +  ++ l+        +  + a   l +l +a+ + +l +
       AJA92541.1 175 VSYLVATNTALAVNAISITKKTGGLGSIGAATGLFIACPTCVGSFLSLFigatsavvF--TiAiTELQTLFIAITVPILVL 253
                      6889*********************************988776666664122333222..212444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1966.04
//
Query:       AJA92542.1  [L=93]
Description: hypothetical protein T478_1401 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.17   12.0  10.0      0.044   13.9   2.4    2.1  2  DUF1272          Protein of unknown function (DUF1272)
       0.23   11.5  11.2        1.9    8.6  11.2    2.1  1  DZR              Double zinc ribbon
        1.6    8.9   8.4        3.9    7.6   8.4    1.6  2  DUF2318          Predicted membrane protein (DUF2318)
        1.8    8.4   6.9       0.44   10.4   1.5    2.4  3  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
        2.5    8.1   6.8        3.2    7.8   2.2    2.6  2  ADK_lid          Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.8     0.024        84       8      21 ..       3      16 ..       1      22 [. 0.82
   2 ?   13.9   2.4   1.2e-05     0.044       7      38 ..      22      52 ..      18      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.024
     DUF1272  8 CecCdkdlppdsee 21
                Ce+C+++l++ s++
  AJA92542.1  3 CENCKCTLSKPSKT 16
                99999999988764 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.2e-05
     DUF1272  7 nCecCdkdlppdseearicsyEctFCaeCaee 38
                 C++C  +l++++e++ i   E  FC++C + 
  AJA92542.1 22 VCNQCRVQLKTENEDSEIVK-EEQFCESCRQD 52
                5*****************87.779*****864 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  11.2   0.00052       1.9       1      37 [.       3      52 ..       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00052
         DZR  1 CpqCgee......lppdarfCseCgtklkavaa.......edrCpsCgek 37
                C +C+        ++ +  +C++C+ +lk +++       e++C sC ++
  AJA92542.1  3 CENCKCTlskpskTSLQTGVCNQCRVQLKTENEdseivkeEQFCESCRQD 52
                77887774434334445559********987779*************986 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.4    0.0011       3.9      52      90 ..       1      42 [.       1      51 [. 0.71
   2 ?    1.1   0.2      0.12   4.3e+02      26      43 ..      35      52 ..      29      60 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
     DUF2318 52 lvCknCgvrfaldsige.kkGGCnpipl..eytvkgdkivis 90
                ++C+nC+ +++++s  + ++G Cn++ +  + + ++ +iv +
  AJA92542.1  1 MICENCKCTLSKPSKTSlQTGVCNQCRVqlKTENEDSEIVKE 42
                89********9877666599*****99932344444444433 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.12
     DUF2318 26 sdgklrvaldaCevCekk 43
                +d++++   + Ce C+++
  AJA92542.1 35 EDSEIVKEEQFCESCRQD 52
                566666666788888654 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.21   7.4e+02      10      21 ..       2      13 ..       2      18 .. 0.77
   2 ?   10.4   1.5   0.00012      0.44       8      24 ..      20      36 ..      20      50 .. 0.77
   3 ?   -1.7   0.1      0.74   2.7e+03      11      18 ..      46      53 ..      45      61 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.21
                     SS-TTEEEETTC CS
  DHODB_Fe-S_bind 10 aClgCvvktkgg 21
                     +C  C ++ ++ 
       AJA92542.1  2 ICENCKCTLSKP 13
                     699999998765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                     SSSS-TTEEEETTCTT. CS
  DHODB_Fe-S_bind  8 vGaClgCvvktkggdgg 24
                     +G+C +C+v+ k+++++
       AJA92542.1 20 TGVCNQCRVQLKTENED 36
                     6**********998776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.74
                     S-TTEEEE CS
  DHODB_Fe-S_bind 11 ClgCvvkt 18
                     C +C+ + 
       AJA92542.1 46 CESCRQDD 53
                     88898654 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.2   0.00089       3.2       3      31 ..       2      30 ..       1      32 [. 0.80
   2 ?    1.9   0.2     0.061   2.2e+02      19      28 ..      41      50 ..      36      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00089
                E-TTT--EEETTT.B--SSTTB-TTT--.- CS
     ADK_lid  3 vCpkCGrsYhvvf.npPkveglCDkCGepL 31
                +C++C+ + + +  +   + g+C  C ++L
  AJA92542.1  2 ICENCKCTLS-KPsKTSLQTGVCNQCRVQL 30
                9*********.5434456********9887 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.061
                SSTTB-TTT- CS
     ADK_lid 19 kveglCDkCG 28
                k+e +C  C 
  AJA92542.1 41 KEEQFCESCR 50
                8999**9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 676.35
//
Query:       AJA92543.1  [L=85]
Description: PF01868 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   50.8   0.3    1.7e-13   50.3   0.3    1.3  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.3   9.3e-18   1.7e-13       6      83 ..       9      82 ..       4      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 9.3e-18
                SXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHHC CS
     UPF0086  6 adlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRae 83
                 dl+G ev + +skn+++vgikG + +Etkn+++i t +++ k +pK+ + ++ +      +e d ++l+ rp +R e
  AJA92543.1  9 FDLIGQEVVISDSKNKEIVGIKGKITMETKNMFVINT-ENGKKNIPKNICQLSNND---GIIETDSTKLNKRPYERLE 82
                69***********************************.9*********99877554...3578888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 584.87
//
Query:       AJA92544.1  [L=188]
Description: DNA-3-methyladenine glycosylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-57  193.6   0.0    2.1e-57  193.4   0.0    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
     0.0046   17.2   1.2      0.012   15.9   0.4    2.1  3  PheRS_DBD3     PheRS DNA binding domain 3
  ------ inclusion threshold ------
      0.049   12.8   0.1      0.062   12.5   0.1    1.2  1  Phage_cap_E    Phage major capsid protein E


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   3.4e-61   2.1e-57       1     172 [.       6     183 ..       6     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 3.4e-61
  Pur_DNA_glyco   1 effdrdalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgrternavmFgppgtlYvYliygihhclnvvte.eegeasaVLiRa 95 
                    +f++r++++vAkeL+Gk+l+r+ + +k++g+i+EtEAY g++D Asha+ ++t+rn+vmFgp g++YvY++yg++++lnvv++ ++++a+aVLiR+
     AJA92544.1   6 KFYERETVTVAKELIGKTLTRKFKGKKLSGIITETEAYRGKDDLASHAATKMTDRNKVMFGPVGMSYVYFTYGMYFMLNVVAKsKRQNAGAVLIRG 101
                    59**********************99*******************************************************96156789******* PP

  Pur_DNA_glyco  96 levveglelmrarrg......lanGPgkLcqaLgidkelngadlleseelvlekeeaeeeeivagpRiGiskaaelpwRfyik 172
                    + + eg+++m ++rg      ++nGP+k++ a++i+++ n+ d+++++ ++++ +  + ++i+++pRiGiska e++w f i+
     AJA92544.1 102 IFPQEGIKTMIRNRGisdlskITNGPAKITMAMDISMKENNIDVTKNSIIYIS-DGIPIKKIKKSPRIGISKAMEKKWNFSIN 183
                    ******************9999***********************99999**9.79************************986 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2   1.2e+04      17      35 ..      56      71 ..      53      72 .. 0.65
   2 ?   -1.8   0.0      0.68   4.1e+03      30      33 ..     128     131 ..     116     152 .. 0.55
   3 !   15.9   0.4     2e-06     0.012      12      42 ..     154     178 ..     145     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
  PheRS_DBD3 17 sqkelkklggdpvakiGfs 35
                ++++ +k+    ++ +G+s
  AJA92544.1 56 KMTDRNKV---MFGPVGMS 71
                56666666...56778886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.68
  PheRS_DBD3  30 akiG 33 
                 aki 
  AJA92544.1 128 AKIT 131
                 4443 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2e-06
  PheRS_DBD3  12 peggisqkelkklggdpvakiGfskAmknkW 42 
                 + +gi++k++kk+   p   iG+skAm +kW
  AJA92544.1 154 S-DGIPIKKIKKS---P--RIGISKAMEKKW 178
                 4.56******766...4..8*********** PP

>> Phage_cap_E  Phage major capsid protein E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     1e-05     0.062     227     282 ..      27      81 ..       4     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
  Phage_cap_E 227 endlrdgftfgG..itfeeydgtyvdgdgtskpfipddevllfptgvadgfttygapa 282
                  +   ++g ++ G   + e y+g+++ ++ + +++ + ++v++ p+g++ ++ tyg  +
   AJA92544.1  27 K---FKGKKLSGiiTETEAYRGKDDLASHAATKMTDRNKVMFGPVGMSYVYFTYGMYF 81 
                  3...344444447778899*******99****************99666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1374.15
//
Query:       AJA92545.1  [L=41]
Description: hypothetical protein T478_0856 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.056   13.7   0.0      0.067   13.4   0.0    1.0  1  SWIRM-assoc_3  SWIRM-associated domain at the C-terminal


Domain annotation for each model (and alignments):
>> SWIRM-assoc_3  SWIRM-associated domain at the C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.8e-06     0.067      23      54 ..       5      36 ..       2      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-06
  SWIRM-assoc_3 23 evPaalveaHvknveaaaektgkvdpavgLek 54
                     P  ++++  k++e+ a+k+g ++++ gLek
     AJA92545.1  5 SMPVCFTNEQYKKIEEIAKKKGMLNSSQGLEK 36
                   6799999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 303.45
//
Query:       AJA92546.1  [L=182]
Description: CBS domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-14   52.9   0.2      4e-09   36.8   0.0    2.3  2  CBS             CBS domain
      2e-13   50.2   0.2    3.3e-13   49.5   0.2    1.4  1  HTH_3           Helix-turn-helix
    1.7e-07   31.2   0.4    3.5e-07   30.1   0.2    1.7  2  HTH_19          Helix-turn-helix domain
    1.8e-06   28.2   0.0    2.7e-06   27.6   0.0    1.2  1  HTH_31          Helix-turn-helix domain
     0.0035   17.3   0.0     0.0084   16.1   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.018   14.9   0.0    1.4  1  HTH_25          Helix-turn-helix domain
       0.02   15.0   0.0      0.034   14.2   0.0    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.045   13.3   0.0      0.084   12.4   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
       0.11   12.3   0.1       0.43   10.4   0.0    2.0  2  LacI            Bacterial regulatory proteins, lacI family
       0.14   12.1   0.1          1    9.4   0.0    2.2  2  Pou             Pou domain - N-terminal to homeobox domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.3e-12     4e-09       1      55 [.      67     120 ..      67     122 .. 0.91
   2 !   14.2   0.1   2.5e-05     0.045       1      53 [.     130     179 ..     130     182 .] 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.3e-12
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 +g++++ ++v ++p+ tl+ea+ +m ++++s++P+ d+++  vG++t++ ++  +
  AJA92546.1  67 AGELCSQKIVKLKPTNTLGEAMVKMDKEKISQIPIFDGND-AVGVITDSGIIGHM 120
                 689**********************5555*******9999.********999766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.5e-05
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHH CS
         CBS   1 Vgdimtrdvvtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllr 53 
                 ++dim + ++ v  +t+ + ++ l+ +  +s ++  V +  k++Gi+t  D+l+
  AJA92546.1 130 IEDIMEPAPPIVENETPASTLAPLI-K--YSkCI-LVRKGTKIIGIITGADVLK 179
                 579******9***************.7..66266.7866669*******99997 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.2   1.9e-16   3.3e-13       1      49 [.       8      56 ..       8      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.9e-16
                HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
       HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                +k+ R++ +++q++LA ++Gvs s i++iE+G+++Ps  t+k++ ++L 
  AJA92546.1  8 IKQQRLKINMTQKDLANLVGVSTSMINQIESGRSAPSYNTAKRIFEVLA 56
                8********************************************9996 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.2     2e-10   3.5e-07       3      52 ..       7      55 ..       5      59 .. 0.93
   2 ?   -3.0   0.0       4.3   7.7e+03      21      32 ..      88      99 ..      85      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2e-10
      HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                 +k+ R + ++tq++la+ +g+s s+i++iE+g++  ps+++ ++i e l
  AJA92546.1  7 SIKQQRLKINMTQKDLANLVGVSTSMINQIESGRS-APSYNTAKRIFEVL 55
                58888999**************************9.*********98865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
      HTH_19 21 rlgisrskisai 32
                ++++++ kis+i
  AJA92546.1 88 MVKMDKEKISQI 99
                567788888876 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.5e-09   2.7e-06      10      59 ..      12      60 ..       8      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.5e-09
      HTH_31 10 ReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldpa 59
                R + +++q+++A ++gvs s ++++E+Gr   ps  +  ++ ++l   ++
  AJA92546.1 12 RLKINMTQKDLANLVGVSTSMINQIESGRS-APSYNTAKRIFEVLASKES 60
                556689************************.5*********999976555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.7e-06    0.0084      17      41 ..      12      36 ..       3      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                EEEEEHHHHHHHHHTTSSHHHHHHH CS
   HTH_Crp_2 17 eielpltqeelAsmlGltretvsri 41
                ++++++tq++lA+++G++ + +++i
  AJA92546.1 12 RLKINMTQKDLANLVGVSTSMINQI 36
                689***************9999976 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     1e-05     0.018       3      35 ..       9      41 ..       7      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                HHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
      HTH_25  3 raaRearglsleevaketkIrkdylealEeddf 35
                +++R++ +++ +++a+   ++++++ ++E++++
  AJA92546.1  9 KQQRLKINMTQKDLANLVGVSTSMINQIESGRS 41
                899***************************987 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.034      72     115 ..       6      49 ..       2      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
  MqsA_antitoxin  72 afiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvk 115
                     + i++ r k++++q+++a++ G+ +   ++ e+G++ p+  + k
      AJA92546.1   6 ESIKQQRLKINMTQKDLANLVGVSTSMINQIESGRSAPSYNTAK 49 
                     579999*******************************9987765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.7e-05     0.084      20      42 ..      16      38 ..      10      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                T--HHHHHHHHTS-HHHHHHHHH CS
  Sigma70_r4 20 glTleEIgerlgiSrerVrqiek 42
                ++T++++++  g+S + + qie+
  AJA92546.1 16 NMTQKDLANLVGVSTSMINQIES 38
                69*******************96 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00024      0.43       3      39 ..      20      56 ..      18      59 .. 0.89
   2 ?   -1.5   0.0       1.3   2.3e+03      24      38 ..     122     134 ..     108     135 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                HHHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHHHH CS
        LacI  3 kDVArlAGVSkaTVSrvLnnkerVseetrerVeaame 39
                kD+A l GVS++ + ++ ++++  s +t++r++++++
  AJA92546.1 20 KDLANLVGVSTSMINQIESGRSAPSYNTAKRIFEVLA 56
                9***********9999999999999999999998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                 SSSTHHHHHHHHHHH CS
        LacI  24 erVseetrerVeaam 38 
                 + Vs+++  r+e +m
  AJA92546.1 122 DGVSKKI--RIEDIM 134
                 4455554..455555 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00056         1      12      31 ..       7      26 ..       5      38 .. 0.81
   2 ?   -0.0   0.0       0.5   8.9e+02      26      44 ..      83     101 ..      69     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00056
         Pou 12 efkqkRiklgltQadvglaL 31
                  kq+R+k+++tQ+d+++  
  AJA92546.1  7 SIKQQRLKINMTQKDLANLV 26
                689************98754 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.5
         Pou  26 dvglaLgklygkefSqttI 44 
                 ++g+a+ k+  +++Sq  I
  AJA92546.1  83 TLGEAMVKMDKEKISQIPI 101
                 5788999999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1319.96
//
Query:       AJA92547.1  [L=65]
Description: hypothetical protein T478_1011 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   12.8   1.6       0.49    9.3   0.0    2.0  2  TMEM171   Transmembrane protein family 171
       0.12   12.9   1.9       0.84   10.1   3.0    1.7  2  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   5.5e-05      0.49      11      33 ..       4      26 ..       1      32 [. 0.88
   2 ?    2.9   0.4    0.0049        44     115     131 ..      39      55 ..      37      60 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.5e-05
     TMEM171 11 eerdrqvsklifflfvfGavllc 33
                +e++rq +   ffl++fGa+ll+
  AJA92547.1  4 NEHNRQKKGGGFFLIIFGALLLF 26
                6889999999***********96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0049
     TMEM171 115 GfLfLtsGmLisilgiw 131
                 G ++L+sG+L+  +g++
  AJA92547.1  39 GVVCLISGILVGSVGFY 55 
                 67777777777777665 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0041        36      36      58 ..       6      28 ..       2      35 .. 0.76
   2 ?   10.1   3.0   9.4e-05      0.84      20      63 ..      17      58 ..      14      61 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0041
      DUF202 36 psalgkilglilivlgiltllvg 58
                +++  k  g++li++g+l+l+++
  AJA92547.1  6 HNRQKKGGGFFLIIFGALLLFLA 28
                444456779999****9999886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.4e-05
      DUF202 20 lialglallrffltgepsalgkilglilivlgiltllvglvryl 63
                li++g++ll f  ++  ++ +  lg+++++ gil+ +vg+++ +
  AJA92547.1 17 LIIFGALLL-FLAPNLYTD-NPELGVVCLISGILVGSVGFYTRF 58
                556666666.223444444.7889****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 515.18
//
Query:       AJA92548.1  [L=269]
Description: acetyltransferase (GNAT) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-11   42.7   0.0    1.2e-10   41.6   0.0    1.5  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00044   19.9   2.0    0.00064   19.4   0.1    2.0  2  GNAT_acetyltran  GNAT acetyltransferase
    0.00058   19.8   0.0      0.001   19.0   0.0    1.3  1  FR47             FR47-like protein
    0.00071   19.7   0.7     0.0019   18.3   0.1    2.0  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0012   18.8   0.0     0.0024   17.8   0.0    1.5  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0047   17.3   0.0     0.0082   16.5   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0048   17.0   0.0      0.042   13.9   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.031   14.9   0.0      0.063   14.0   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   5.3e-14   1.2e-10      14     117 .]      24     123 ..      14     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5.3e-14
                     HHHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EEEEETTEH CS
  Acetyltransf_1  14 ppnedaseeefeesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki.vlaveednd 106
                     + ++d  +e++ ++   ++e  l+v+e ++ +i +  +  +pd  ++ ++ie++ V +++r++G++++++ +lee a+++ ++   +l + + n+
      AJA92548.1  24 FSWGDYIHEVWDNW---IDEgNLIVIENNQVPISMTHAAFYPD--EKMIWIEGIRVEKNFRKNGVAQKMISYLEETAKSKKCEISrML-IASENK 112
                     67899999998888...77747777999999************..8**********************************77555466.7788** PP

                     HHHHHHHHTTE CS
  Acetyltransf_1 107 aairlYeklGF 117
                     ++  l +klG+
      AJA92548.1 113 PSLSLAKKLGY 123
                     ******88**8 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.9e-07   0.00064     153     242 ..      37     131 ..      11     132 .. 0.78
   2 ?   -0.1   0.3      0.24   5.5e+02      60      95 ..     190     227 ..     154     268 .. 0.54

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
  GNAT_acetyltran 153 fkkkGlGvvilkngeivsgasSysv.yekgieie.idTkedyrrkgLAtivaaalileclkrg..lyPsWDaa.neaSvaLaekLGYefekeYk 241
                      +  +G  +vi +n+  +s+  + ++  ek+i ie i  ++++r++g A+++ + l +++  ++  +     a  n++S++La+kLGY+  ++++
       AJA92548.1  37 WIDEGNLIVIENNQVPISMTHAAFYpDEKMIWIEgIRVEKNFRKNGVAQKMISYLEETAKSKKceISRMLIASeNKPSLSLAKKLGYTIISKWN 130
                      55566667888889999999988862567888977****************99987777655411445566668**************999987 PP

  GNAT_acetyltran 242 v 242
                       
       AJA92548.1 131 Y 131
                      5 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
  GNAT_acetyltran  60 ekekkeekrfilvpqseeweelieeil..geklkkitr 95 
                      +k++++ +++ ++ +se++e++i   l  g + +k+ +
       AJA92548.1 190 QKDNEKTNTLGIITESESFENTIILELisGTNSEKMIK 227
                      33334444555555666666554322200222222222 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.5e-07     0.001      24      81 ..      69     127 ..      60     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.5e-07
                 EEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEE CS
        FR47  24 lgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekie 81 
                 + ++ v++++r+ G ++++++ l +     + +++ ++++ +N+ps +l +klG++ i 
  AJA92548.1  69 IEGIRVEKNFRKNGVAQKMISYLEETAKSkKCEISRMLIASENKPSLSLAKKLGYTIIS 127
                 66799*******************9998867888999******************9984 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   8.6e-07    0.0019      86     138 ..      75     127 ..      44     136 .. 0.85
   2 ?   -1.9   0.1       1.4   3.2e+03      98     117 ..     225     244 ..     215     266 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.6e-07
  Acetyltransf_4  86 erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvg 138
                     e+  +k+g+++++i +le+ +k    e     ias+n++s  ++k+lG+++  
      AJA92548.1  75 EKNFRKNGVAQKMISYLEETAKSKKCEISRMLIASENKPSLSLAKKLGYTIIS 127
                     5678999**************99999999999*****************9976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
  Acetyltransf_4  98 lidaleqvlkeqnienllae 117
                     +i++  + + + n+ ++ + 
      AJA92548.1 225 MIKFTQNLAHQKNYSKIRIL 244
                     66666666666665555443 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.1e-06    0.0024      14     109 ..      27     126 ..       7     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
  Acetyltransf_10  14 kefispealrerieegealllvaeeggkivGvi..el.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpf 100
                       ++i+ e ++++i+eg+  l+v e+++ ++ +   +   d++   i+ + V++++r++G++++++ ++ee a+ ++ ++ ++ + + +    ++
       AJA92548.1  27 GDYIH-EVWDNWIDEGN--LIVIENNQVPISMThaAFyPDEKmiWIEGIRVEKNFRKNGVAQKMISYLEETAKSKKCEIsRMLIASENkPSLSL 117
                      55655.88889994444..578888888886664467667778999*************************99999999988888888799999 PP

  Acetyltransf_10 101 YeklGFkav 109
                       +klG++ +
       AJA92548.1 118 AKKLGYTII 126
                      999998765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.7e-06    0.0082       3      75 ..      41     124 ..      31     125 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.7e-06
                     EEEEEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEEEEEEEE...THHHHHHHHHHTTEE CS
  Acetyltransf_7   3 gevfVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea.ae....kgiileqlel...naekaikfYeklGFe 75 
                     g+++V+e+++ ++ +  ++ +      +i+++ V +++r++G++++++ + +e    k+++++   l   ++++++++ +klG++
      AJA92548.1  41 GNLIVIENNQVPISMTHAAFYPdekmIWIEGIRVEKNFRKNGVAQKMISYlEEtaksKKCEIS-RMLiasENKPSLSLAKKLGYT 124
                     5567888888888766666655667667777*****************975223444446533.122332223677788888876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.9e-05     0.042       3     127 ..       6     125 ..       5     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                     EEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHH CS
  Acetyltransf_9   3 relteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlar 97 
                     r ++++d + vl++ +  F + +  +    e +++ ++e++ +++e+n   +++ ++  +         k+ ++ g+ v  + r++gv++k++ +
      AJA92548.1   6 RLAQDSDKKVVLNFCQNTFSWGDYIH----EVWDNWIDEGNLIVIENNQVPISMTHAAFYP------DEKMIWIEGIRVEKNFRKNGVAQKMISY 90 
                     67889999999999999999988864....6789999999999999999999998876553......4489************************ PP

                     HHHHHHHTT--EE.EE--SSH....HHHHTTT-EE CS
  Acetyltransf_9  98 aleemreegqpls.llfPssi....piYrrfGyei 127
                     + e +++++ ++s +l++s+     ++ +++Gy i
      AJA92548.1  91 LEETAKSKKCEISrMLIASENkpslSLAKKLGYTI 125
                     ********999985677754333447777777765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.8e-05     0.063      56     138 .]      43     124 ..       4     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
  Acetyltransf_3  56 waivlkdtgv.iGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                     ++++++++ v i +     +++e   +  g+++ + f+ +G+a+ + + l e a +  + e  +  i+ eN+ S  +++klG++
      AJA92548.1  43 LIVIENNQ-VpISMTHAAFYPDEKMIWIEGIRVEKNFRKNGVAQKMISYLEETA-KSKKCEISRMLIASENKPSLSLAKKLGYT 124
                     44444555.55666655555555555777999999*******************.566699999******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1915.48
//
Query:       AJA92549.1  [L=344]
Description: glycosyltransferase family 28 C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-14   53.5   0.0    6.9e-14   52.2   0.0    1.6  2  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    3.7e-07   29.7   0.0     0.0079   15.5   0.0    2.2  2  Glyco_trans_1_3  Glycosyl transferase family 1
  ------ inclusion threshold ------
      0.096   13.0   0.2        0.2   12.0   0.2    1.5  1  CCDC117          Coiled-coil domain-containing protein 117
       0.11   12.9   0.0       0.25   11.8   0.0    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   5.7e+03      65      82 ..     144     162 ..     136     163 .. 0.70
   2 !   52.2   0.0   1.5e-17   6.9e-14       2     149 ..     196     330 ..     195     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                      SHHHHHHHH-.EEEECS-C CS
  Glyco_tran_28_C  65 kmaeaikaad.LvIsRAGa 82 
                       m+e +++a+ ++I  +G+
       AJA92549.1 144 TMQEMLQKANrVIIPESGT 162
                      5788888887777766665 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 1.5e-17
                      EEEEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--E CS
  Glyco_tran_28_C   2 ilVtGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkpl 95 
                      +l  GG+   + L++    + k+ e     + +++ tG++ +ee  ++  +l+       f++++ e+i aadLvIs AG +ti E++++g p 
       AJA92549.1 196 VLCAGGTEAGKFLIKKTINAIKKVEAD---IDLVLVTGPEIKEEFGNEIRNLG-------FVENLHEVIFAADLVISLAGKSTIDESVVYGTPG 279
                      667788888888888777777777776...89*************99999995.......********************************** PP

                      EEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS---S- CS
  Glyco_tran_28_C  96 IlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaaeklrla 149
                      I++p + +   +q+ Nak++  ++ ++  +++ + +e++ +   e ++++ +la
       AJA92549.1 280 IFIPIKNHF--EQEDNAKDMGFNFEDIFNLENLI-EERINKDRNEQRQNGVDLA 330
                      *******99..*********99999999999998.8888887777777666555 PP

>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06    0.0079       2     122 ..       3     122 ..       2     159 .. 0.82
   2 !   12.2   0.0   1.8e-05      0.08     246     292 ..     245     295 ..     237     309 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
  Glyco_trans_1_3   2 rilYgvsGeGaGhasRsrvvlehLarghevkvvvsgraldvLeke.fdvneivglsivyeenrvrklktllknlqvaaklaknvkalvelv.ed 93 
                      +il+  s  G Gha+R +++++++      kv +   a+++ +++ ++ n++++      +n   kl+  lk l    k  kn k++ + + ++
       AJA92549.1   3 KILFFSSPIGLGHATRDLAIINQMEL-ESCKVFSGSSAIQFFQRNdIEANDVYSPPKFEVQNG--KLEKSLKWLWSYYKYYKNCKEISNDIiRK 93 
                      788888889*************9854.5799**********9776369****99877666664..33444566777777888888877665588 PP

  Glyco_trans_1_3  94 frpdlvvtDFealtallakrhkLPvisvd 122
                       +p+l+++D +  ++ +a+++++P i + 
       AJA92549.1  94 EEPELIISDEDFASIAVAQEQGIPNIVIT 122
                      99**********************99875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.8e-05
  Glyco_trans_1_3 246 gFleDLa....taraviagagftLmtealyLkkPlLavPvarqFeqvlnal 292
                      gF+e+L     +a  vi+ ag + + e++  + P + +P+++ Feq  na 
       AJA92549.1 245 GFVENLHevifAADLVISLAGKSTIDESVVYGTPGIFIPIKNHFEQEDNAK 295
                      777777522225788*******************************99985 PP

>> CCDC117  Coiled-coil domain-containing protein 117
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.4e-05       0.2      15      62 ..      97     146 ..      85     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
     CCDC117  15 RiilEDee..dleadsvsrrPvLvlsDslkeglkrgiddiltkkviesvs 62 
                  +i+ De+   + + + +  P +v+ D+l + +  g++ i+ kk+ + ++
  AJA92549.1  97 ELIISDEDfaSIAVAQEQGIPNIVITDILETKFTSGFGAIVEKKMNKTMQ 146
                 4566666666999999999*************************999886 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.5e-05      0.25      18      80 ..     206     264 ..     193     297 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                      HHHHHHH.HHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---THHHHHHHH-SEEEE-- CS
  Glyco_trans_1_4  18 dllleav.pllrkk..dvrlvivGdgprpeeleelaagleerveftGfvedlaellaaadvfvaPs 80 
                      ++l+++   +++k   d+ lv+v  gp   e++e+  g  ++++ +Gfve+l e++ aad+++   
       AJA92549.1 206 KFLIKKTiNAIKKVeaDIDLVLVT-GP---EIKEEF-G--NEIRNLGFVENLHEVIFAADLVISLA 264
                      455555545555332259*****9.73...677666.3..89*******************99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2649.55
//
Query:       AJA92550.1  [L=537]
Description: peptidyl-prolyl cis-trans isomerase, cyclophilin-type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-46  157.0   0.1    7.4e-46  156.3   0.1    1.3  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3   0.1   4.1e-50   7.4e-46       2     150 ..      30     179 ..      29     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 4.1e-50
  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgkts.ageqekkggesiraipdEitsklkhkrGalamart 96 
                    v +et+  Gr++ie f++ aP++venF+ l ++gfY gt+FhR+i+gfm+qgGdp++ +s   ++e+ +g   + i++E+ +++ hkrG+++mar+
     AJA92550.1  30 VVLETD-SGRLIIEFFPQFAPNHVENFVTLSEDGFYTGTIFHRIIEGFMIQGGDPKSADSsVSMSEWGTGDPGYSIDAEF-NSIEHKRGIVSMARS 123
                    7899*6.**************************************************999633334444446789*****.899************ PP

  Pro_isomerase  97 gkepnsagsqFfItlkeaphldgkytvFGkVv..eGmdvvekiekvetde.erpkkn 150
                     ++pns+gsqFfI+ k+ ++ldg+ytvFG+++  e+++++++i++++t   ++p ++
     AJA92550.1 124 -SDPNSGGSQFFIVHKDSNFLDGQYTVFGRILtnESFETLDRIATMNTAPnDQPMDA 179
                    .79*****************************99***********999888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3810.59
//
Query:       AJA92551.1  [L=219]
Description: hypothetical protein T478_0026 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.7   3.3      0.079   12.6   3.3    1.8  1  Snf7      Snf7


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.3   4.4e-06     0.079       3     171 ..      38     204 ..      36     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-06
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
        Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkkv 101
                  ++L+ ++ kld   ++l+++ +k+ +++   ++  +    ++l +++++ +k  + + n +  le + l + + ++  ++++++  +   m+  ++ +
  AJA92551.1  38 VKRLQAQIGKLDGMCQKLQERDQKIFQKIVAAQQAHDTYSSKVLSNELVEVRKVNKIMTNAKMGLERIELRLTTFHDLGDTVTTLMPTIGLMNGLKSSL 136
                 57899*****************************************************************************************98887 PP

                 CCHHHHHHHHHHHHHH.HHHTCHHHHHHHHHTT-..GGTTHHHHHHHHHHHHHHHHHCSH.HHHHHHHTXXXS CS
        Snf7 102 didkidklmdeiedqm.ekaeeisEalsrsldda..deedEeeleaeLdaLeqelgdeelldesvklpevPse 171
                       k m    +++  + e++   + +++ +   +   Ee ++ae d +++e ++  +++++++ p+vP++
  AJA92551.1 137 V-----KFMPGADQEIgRMTEMLGGLMTETFSSSgsSFGVEESTNAESDSILAEAAAVAESQSGEQFPSVPTT 204
                 6.....566555555413345556666666666664667899999*********99999999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1542.67
//
Query:       AJA92552.1  [L=138]
Description: DoxX family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-13   49.9   7.6    3.5e-13   49.9   7.6    1.6  2  DoxX      DoxX
    4.8e-07   29.8   0.9    4.8e-07   29.8   0.9    1.5  2  DoxD      TQO small subunit DoxD
     0.0038   17.3   5.5     0.0054   16.8   5.5    1.3  1  DoxX_2    DoxX-like family


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   7.6   5.9e-17   3.5e-13       5      84 ..      18      92 ..      14      93 .. 0.95
   2 !    9.2   1.1    0.0003       1.8       7      46 ..      83     117 ..      77     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.9e-17
        DoxX  5 lRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtllvatltvh 84
                 R  +gv+fi+hG++k+ +   +g+ +++ ++g+  p+ + + +al+E+v g+lll+G+ltR++ ++l +++l+a+++v 
  AJA92552.1 18 MRATIGVIFIVHGFGKFGN---PGFGGWISSMGI--PAEMQIPIALAEFVPGILLLIGVLTRISGALLSIVMLGAIFLVK 92
                6999*************96...699*********..9999999**********************************996 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0003
        DoxX   7 lllgvlfiahGlqkltgfglegtaaslaalglpppellay 46 
                 ++lg++f+++G+++ltg      +++ ++l l+++ l ++
  AJA92552.1  83 VMLGAIFLVKGATSLTG-----DKGYEFDLILLAASLVVI 117
                 89**************5.....555555555555555555 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.56   3.3e+03       5      17 ..      18      30 ..      15      37 .. 0.70
   2 !   29.8   0.9   8.1e-11   4.8e-07      71     146 ..      56     132 ..      46     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.56
        DoxD  5 lRlalgliflsag 17
                +R ++g+if+  g
  AJA92552.1 18 MRATIGVIFIVHG 30
                7777888877655 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 8.1e-11
        DoxD  71 ftlvEiivGlllliGlltRlsslvafalalg.ialsayWlgstcedEyqiglllvaaelvliltgsgklslDylllk 146
                 ++l E + G+llliG+ltR+s+  +  + lg i+l  + +  t    y+  l+l aa+lv+i++g g++s+  l++k
  AJA92552.1  56 IALAEFVPGILLLIGVLTRISGALLSIVMLGaIFLVKGATSLTGDKGYEFDLILLAASLVVIVSGPGRISISHLIKK 132
                 6778999*************9876655555427889999999999**************************998865 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.5     9e-07    0.0054       5      80 ..      21      90 ..      17     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9e-07
      DoxX_2  5 llalffllsGvakllraeevvakfaqlgfpssfvrllGvvellgalgLllplvtaprltplAavglallmvgAiat 80
                 + ++f++ G+ k+   + +   + ++g+p+ +   ++++e++ +++Ll++     +lt +  ++l ++m+gAi+ 
  AJA92552.1 21 TIGVIFIVHGFGKF-GNPGFGGWISSMGIPAEMQIPIALAEFVPGILLLIG-----VLTRISGALLSIVMLGAIFL 90
                67789999999999.77888888999*************************.....69****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 971.16
//
Query:       AJA92553.1  [L=202]
Description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-24   84.3   0.0    9.9e-24   84.2   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.5e-06   26.9   0.0    5.6e-05   23.0   0.0    2.3  1  Peptidase_C26  Peptidase C26
    4.3e-05   23.5   0.0    0.00023   21.1   0.0    1.9  1  SNO            SNO glutamine amidotransferase family
      0.005   16.5   0.0     0.0053   16.4   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   2.2e-27   9.9e-24       2     186 ..       6     196 ..       5     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 2.2e-27
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT.... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaiefgr.... 90 
                 + D++++++ +l+ +l ++g++v+++      +++    k++dg+l++ G+g+        ++ +    + + ++kiP+LGICLGm + ++++ +    
  AJA92553.1   6 IFDYGAGNIFSLKTSLEKNGASVDIITSF---DQS----KKYDGLLLP-GVGNFDpairsiRDYSALGFHDFVKEKIPVLGICLGMEMFFKQSQEgkek 96 
                 6899*********************9843...444....479999875.67777776888877777777788888******************998999 PP

                 .......EEE....EEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTT CS
      GATase  91 .......kvv....kekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpe 178
                        +vv     +k  +h+g+++    +++++l+g +n   +++ H+y ++p    +++++v+ ++  + ++ +++e++  f+g+QFHPE++ + +
  AJA92553.1  97 gldvmngEVVllpnDMK-IPHMGWNSLEITKDSKILEGVENNSWVYFVHSYRAKP---DNSDIIVANAD-YGIKVPAVVEDNL-FFGTQFHPEKSGKIG 189
                 99777665559997777.********9999999**********************...78887775555.7779******999.*********998776 PP

                 HHHHHHHH CS
      GATase 179 gpellfnf 186
                  + +++nf
  AJA92553.1 190 -SLMIQNF 196
                 .6666666 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.3e-08   5.6e-05      98     216 .]      66     183 ..      31     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
  Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe........q..saashavkvekgsllaellgseeievnslHhqaikelae 183
                    ++  +++++P+lgiC+G++++         q+ e +++  d ++ e        +       +++++k+s + e ++ ++  v  +H+   k  ++
     AJA92553.1  66 FHDFVKEKIPVLGICLGMEMF-------FKQSQEGKEKGLDVMNGEvvllpndmKipHMGWNSLEITKDSKILEGVE-NNSWVYFVHSYRAKPDNS 153
                    456799*************99.......44554445555555555544444333255677889*********99999.99********99876555 PP

  Peptidase_C26 184 elrveAvaeDgv.iEaieseeakafvlgvQwHPE 216
                    ++ ++A a+ g+ + a+   +    ++g Q+HPE
     AJA92553.1 154 DI-IVANADYGIkVPAVVEDN---LFFGTQFHPE 183
                    55.556666664255554444...99*******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.1e-08   0.00023      12     174 ..      18     187 ..      11     202 .] 0.66

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.1e-08
                 HHHHHHTTSEEEEE-SGGGGCC-SEEEE-S.S-.HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCEEE.......E CS
         SNO  12 veaikkclaenktvkrkedlaevdaliiPG.Ge.stamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkvkv.......k 101
                    ++k +a    + + ++ ++ d+l++PG G+   a++ + +       +++fvk+   +vlG C G+ ++ k+ ++ + k l++++ +v       k
  AJA92553.1  18 KTSLEKNGASVDIITSFDQSKKYDGLLLPGvGNfDPAIRSIRDYSA--LGFHDFVKEK-IPVLGICLGMEMFFKQSQEGKEKGLDVMNGEVvllpndmK 113
                 567888888889999999***********95442457777776655..4689999998.9***************999999999999855422211113 PP

                 TTTT-SCCGEEEEEEEETT.TCSEEEEEESS--EEEEE-.TTTCEEEEECT.T.EEEEEE.ETTEEEESS-GGGSTT CS
         SNO 102 rnafGrqvdsfekeldfkn.liekftavfiraPvieeilddeavkvlyeld.g.eivvak.qkkilatsfhPelaed 174
                     G      +k+ ++ + ++++    f+ +    ++  d++  ++ + d g ++ ++   + +++t fhPe + +
  AJA92553.1 114 IPHMGWNSLEITKDSKILEgVENNSWVYFVHS---YRAKPDNSDIIVANADyGiKVPAVVeDNLFFGTQFHPEKSGK 187
                 34456555555555554330335555555544...455544555555555657677666636688999999998754 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-06    0.0053      15     117 ..      13     107 ..       3     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
    GATase_3  15 dldpLeaepevrvrfvplkdeslg..edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglL 111
                 ++  L+   e+++  v++ + s++  +++d ++lpG  +   ++ + r+   +   ++++++++pvlgiC G+ m+ ++  +  g+       +gl+++
  AJA92553.1  13 NIFSLKTSLEKNGASVDIIT-SFDqsKKYDGLLLPGVGNFDPAIRSIRD-YSALGFHDFVKEKIPVLGICLGMEMFFKQSQE--GK------EKGLDVM 101
                 55555555555544444222.2222356************999999999.567789*******************9998543..43......4566666 PP

    GATase_3 112 dietef 117
                 + e+++
  AJA92553.1 102 NGEVVL 107
                 666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1509.93
//
Query:       AJA92554.1  [L=361]
Description: ParA/MinD ATPase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-99  331.8   0.2    3.1e-99  331.4   0.2    1.1  1  ParA            NUBPL iron-transfer P-loop NTPase
    8.4e-18   64.3   0.7    3.6e-17   62.3   0.1    2.4  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.3e-13   51.1   0.0    8.9e-13   48.4   0.0    2.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
    4.5e-09   36.5   2.4    1.4e-07   31.6   2.4    2.2  1  AAA_31          AAA domain
    2.8e-07   30.1   0.0    4.2e-07   29.5   0.0    1.3  1  MipZ            ATPase MipZ
    7.6e-07   29.1   0.8     0.0077   16.1   0.0    2.3  2  AAA_26          AAA domain
      5e-06   26.2   0.1    0.00079   19.0   0.1    2.4  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    1.4e-05   24.5   1.7    3.4e-05   23.2   0.8    2.0  2  ArsA_ATPase     Anion-transporting ATPase
     0.0033   16.8   0.4      0.008   15.5   0.2    1.7  1  VirC1           VirC1 protein
     0.0036   15.6   0.0     0.0051   15.1   0.0    1.1  1  FTHFS           Formate--tetrahydrofolate ligase
     0.0045   16.5   0.2      0.016   14.7   0.2    1.8  1  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
  ------ inclusion threshold ------
      0.013   14.5   0.2      0.021   13.8   0.2    1.3  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
      0.015   15.1   0.0      0.028   14.2   0.0    1.5  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
      0.017   14.7   0.7      0.037   13.6   0.7    1.5  1  AAA_25          AAA domain
       0.13   12.1   0.1       0.28   11.1   0.1    1.5  1  APS_kinase      Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.4   0.2  2.6e-102   3.1e-99       2     245 ..      96     339 ..      95     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 331.4 bits;  conditional E-value: 2.6e-102
        ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfllesedeavvwrGpmkskai 100
                 vk+vi v+SgKGGVGKStv+ nlAlaL+++g+kvgllDaDiyGpsip +lg+++  +e++++kl+P + +++kv+S+gf+ e+e++a ++rGp++s+++
  AJA92554.1  96 VKNVIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKDGAMEVEDNKLQPATFNDLKVVSFGFFAEQEHQAAIYRGPIISGIL 194
                 9***********************************************************99************************************* PP

        ParA 101 kqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklae 199
                 kq+l d++w +lDyLi+DlPPGtgD+ lt+aq++p++g+++Vttpq+va +++ kai mf+k++v++lGvveNms+f+cp+c++k++ifg+gg++k++e
  AJA92554.1 195 KQFLVDTNWTDLDYLIVDLPPGTGDIPLTLAQTIPITGILVVTTPQDVASNVAVKAIGMFDKLNVPILGVVENMSYFACPDCTKKHYIFGNGGAKKISE 293
                 *************************************************************************************************** PP

        ParA 200 elgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                 ++++p+lgeipl++ i+e sd gkp++++++es+ a+a++  a++v
  AJA92554.1 294 KHEIPFLGEIPLNSGIMEGSDLGKPVMMTNTESPSADAFRIAAKNV 339
                 ***************************************9988887 PP

>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.1     3e-20   3.6e-17       2      67 ..       5      70 ..       4      78 .. 0.96
   2 ?   -2.5   0.1         5     6e+03      16      32 ..     238     254 ..     235     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3e-20
                    HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT- CS
  FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgv 67
                    ++vl+ L+tV+DP l +d+vs+g++++++++ g+ +++++lt+pac++ e+i++d+++a+  + g+
      AJA92554.1  5 DQVLEKLATVVDPDLKKDIVSMGMIKDLELNSGDLKFTLELTTPACPFNEEIEEDVRKAIDEIDGI 70
                    79***********************************************************99995 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                     TSSBCCCCT---EEEE- CS
  FeS_assembly_P  16 lgvdlvslglvreidie 32 
                     +++d+ s+ +v++i + 
      AJA92554.1 238 TPQDVASNVAVKAIGMF 254
                     67888888888888655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   7.4e-16   8.9e-13       2     127 ..     101     318 ..     100     319 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 7.4e-16
                 EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH....HTTEB-HHHH.......................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxx.......................................... RF
        CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai....leglendiep.......................................... 54 
                  +as+kGGvGK+t+++nLa al++ g +V l+DaD  +++  +     +g      +                                          
  AJA92554.1 101 GVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLmlgmKDGAM----Evednklqpatfndlkvvsfgffaeqehqaaiyrgpiisgilk 195
                 59**************************************998555433333....344558999********************************** PP

                 ..................................................CCHCCCHHHHHHCHCHHHH..EEEEEEEE..ESS...-TTCHH....HH CS
                 ..................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx....xx RF
        CbiA  55 ..................................................dlkrllellealgkkkalllkiagvvlnr..vdgeneetllke....al 97 
                                                                    + + ++++ +l       + i+gvv n+  +  ++ +++++     + 
  AJA92554.1 196 qflvdtnwtdldylivdlppgtgdipltlaqtipitgilvvttpqdvasnVAVKAIGMFDKLN------VPILGVVENMsyFACPDCTKKHYIfgngGA 288
                 *******************************99999999999988776664444466666666......558888888733344444444444111155 PP

                 HHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  98 eelkqrygvpvlgviprdeavaeapargep 127
                 +++ +++++p+lg+ip +++++e    g+p
  AJA92554.1 289 KKISEKHEIPFLGEIPLNSGIMEGSDLGKP 318
                 566666699999999999999887776666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   2.4   1.2e-10   1.4e-07       2      40 ..      98     136 ..      97     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.2e-10
      AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                  vI +a  KGGvGK+T s+nla al+++g kv l D+D 
  AJA92554.1  98 NVIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADI 136
                 5999*********************************96 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   3.5e-10   4.2e-07       2      71 ..      99     168 ..      98     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.5e-10
                 EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SS CS
        MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealals 71 
                 vi ++  kGG Gkst+++ +a aL+++Ga+v+ +d d+   ++   l+ +   +e ++ +L+ +++  l+
  AJA92554.1  99 VIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMKDGAMEVEDNKLQPATFNDLK 168
                 788999*******************************988888777777776666666666655555544 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.6   0.00023      0.27       5      33 ..     102     130 ..      98     132 .. 0.89
   2 !   16.1   0.0   6.5e-06    0.0077     121     195 ..     222     310 ..     212     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
      AAA_26   5 vtgtdtgvGKTvvslgLvralkrkgvkvg 33 
                 v++   gvGK++vsl L+ al+++g+kvg
  AJA92554.1 102 VASGKGGVGKSTVSLNLALALSQTGAKVG 130
                 7777889********************98 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6.5e-06
      AAA_26 121 adiaknlgapvilVargglg.tinqllltiealrqknvrvlGvilNk..vrnpe...........nvetlekksgipvlGvvPylpdle 195
                   +a+++ +  ilV+++ ++ + n ++ +i ++ + nv++lGv+ N   ++ p+             +++++k++ip lG++P ++ ++
  AJA92554.1 222 LTLAQTIPITGILVVTTPQDvASNVAVKAIGMFDKLNVPILGVVENMsyFACPDctkkhyifgngGAKKISEKHEIPFLGEIPLNSGIM 310
                 56788888887888877666266888899*****************85523332445667777779*****************998765 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.6e-07   0.00079       7      50 ..     105     148 ..      99     174 .. 0.84
   2 ?    4.9   0.0     0.012        15     193     254 ..     288     348 ..     241     359 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.6e-07
   Fer4_NifH   7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggk 50 
                 GkGG+Gkst s nl+ al+++g kv ++  D    s  l+lg k
  AJA92554.1 105 GKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPSIPLMLGMK 148
                 9************************9999998888887777765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
   Fer4_NifH 193 iekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilenkklviPk 254
                 ++k+ e+ +++ l  +P++  + + +   k v+  ++es+ a+ +r  a++++ +   v   
  AJA92554.1 288 AKKISEKHEIPFLGEIPLNSGIMEGSDLGKPVMMTNTESPSADAFRIAAKNVAAQCSIV-AA 348
                 678899999***********9999999999999999999************99887544.33 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.8   2.8e-08   3.4e-05       6      38 ..     103     135 ..      98     139 .. 0.90
   2 ?   -1.0   0.0      0.67     8e+02     117     137 ..     198     219 ..     150     274 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.8e-08
                  EEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
  ArsA_ATPase   6 vgGKGGVGKttvsaatavklsekgkkvllistD 38 
                   +GKGGVGK+tvs  +a+ ls++g kv l+  D
   AJA92554.1 103 ASGKGGVGKSTVSLNLALALSQTGAKVGLLDAD 135
                  58************************9887665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                  HHHHHCSSSSEEEEESBS.CCH CS
  ArsA_ATPase 117 lkyvkeeeydvvvlDtaP.TGh 137
                  l  ++ ++ d++++D +P TG+
   AJA92554.1 198 LVDTNWTDLDYLIVDLPPgTGD 219
                  4455566789999999985554 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   6.7e-06     0.008       2      40 ..      98     136 ..      97     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
       VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                 ++i ++s kGG Gk+t  + l  al + g +v+l++ad 
  AJA92554.1  98 NVIGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDADI 136
                 67899********************************95 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.3e-06    0.0051      34     108 ..      72     151 ..      53     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-06
                 TTEEEE-CHHCCTCT..TTS-.-EEEEEEESS--TT--SHHHHHHHHHHHHHHTT--EE...EEE----SHHHHCST--S CS
       FTHFS  34 kykakvslkvlerll..kekkkgklilvtaitPtplGeGKttttigLaqalnklgkkav...aalRepslGPvfgiKGgA 108
                 +   kv+ kv+e ++  +++  + +  v +++  + G GK+t+++ La al+++g k+    a +  ps+  ++g+K gA
  AJA92554.1  72 NFDMKVTAKVMEGRSldADEAMATVKNVIGVASGKGGVGKSTVSLNLALALSQTGAKVGlldADIYGPSIPLMLGMKDGA 151
                 555677777776443003445566778999**************************986222468889998899999998 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.4e-05     0.016       4     153 ..     100     246 ..      97     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
    CBP_BcsQ   4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieqregwaraeldgapwrqaaleyapgldllPfGelnveekenlqqlaek. 101
                 + +   +GGvG+++++  La al + g +v ++D+   ++   +  + +  ++g ++  +++++++ a++   ++l+++ fG  +++e+++     +  
  AJA92554.1 100 IGVASGKGGVGKSTVSLNLALALSQTGAKVGLLDA---DIYGPSIPLMLGMKDGAME--VEDNKLQPATF---NDLKVVSFGFFAEQEHQAAIYRGPIi 190
                 5566668**************************96...7788888888888888765..45556776654...7999*****99999988654444433 PP

    CBP_BcsQ 102 aeallaalkelk.eqyrwillDlpagasaltrellaladlv..llvvep.danchv 153
                 ++ l+++l   + ++ +++++Dlp g+ ++  +l ++  ++  l v++p d+++ v
  AJA92554.1 191 SGILKQFLVDTNwTDLDYLIVDLPPGTGDIPLTLAQTIPITgiLVVTTPqDVASNV 246
                 7778888888888999********99988766666554332214444443555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   1.8e-05     0.021      29      66 ..      97     135 ..      79     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                 SEEEEE.EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
        MeaB  29 aqvvGl.tGvPGaGkstlvealglelrrrGkrvavlavD 66 
                  +v+G+  G  G+Gkst+  +l+l l + G +v++l  D
  AJA92554.1  97 KNVIGVaSGKGGVGKSTVSLNLALALSQTGAKVGLLDAD 135
                 57899845999***********************99877 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.4e-05     0.028       1      42 [.     105     144 ..     105     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
      CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgt 42 
                 G+  +GKST++ +L+  + + g k+ ++D+D+  ++  +P +
  AJA92554.1 105 GKGGVGKSTVSLNLALALSQTGAKVGLLDADIYGPS--IPLM 144
                 66789***************************9887..4444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   3.1e-05     0.037      33      61 ..      98     127 ..      94     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
      AAA_25  33 gelallaGapgtGKttlaldlalava.tGk 61 
                 + +++  G +g+GK+t+ l+lala++ tG 
  AJA92554.1  98 NVIGVASGKGGVGKSTVSLNLALALSqTGA 127
                 6678999*****************997775 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00023      0.28       8      39 ..     104     135 ..      97     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                 ESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
  APS_kinase   8 tGlsgsGKstianalekkLvekgisvylLdGd 39 
                 +G  g GKst++ +l+ +L ++g +v lLd d
  AJA92554.1 104 SGKGGVGKSTVSLNLALALSQTGAKVGLLDAD 135
                 7999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2527.10
//
Query:       AJA92555.1  [L=86]
Description: PF09630 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-36  122.5   1.7    5.2e-36  122.4   1.7    1.0  1  DUF2024   Domain of unknown function (DUF2024)


Domain annotation for each model (and alignments):
>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.4   1.7   2.9e-40   5.2e-36       1      81 []       3      83 ..       3      83 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 2.9e-40
                -EEEEEEEEE--SSS--EEEEEEES---HHHHHHHHHHHHHHHT---S---TTTEEEEEEEE--HHHHHHHHHHSEEEE-- CS
     DUF2024  1 mkvavfDtyvkkkdGkvlHFDvlvdekdeekaleyakeyLkskgeeeakvtskeCkfCHseeaeeeveeaikkqGyyiiel 81
                m+++v+Dtyvk+kdG+++HFDv++d++d+++a+ +ake+L+++gee+a+vt +eC+fCH++ a+e ve++ik++Gy+i+++
  AJA92555.1  3 MDIHVYDTYVKAKDGHTMHFDVITDKQDHDQAIAFAKEWLATVGEEGATVTGEECQFCHTQGAPEPVENEIKEKGYFIQKM 83
                99*****************************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.54
# Mc/sec: 482.53
//
Query:       AJA92556.1  [L=466]
Description: putative aspartate kinase, monofunctional class [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-48  165.1   0.3    2.9e-48  164.6   0.3    1.2  1  AA_kinase  Amino acid kinase family
    8.4e-14   51.1   1.9    1.3e-07   31.3   0.1    3.2  4  ACT_7      ACT domain
    9.4e-10   38.1   1.2    3.5e-05   23.5   0.1    3.1  3  ACT        ACT domain
  ------ inclusion threshold ------
      0.042   13.8   0.5          4    7.5   0.2    3.2  3  DUF771     Domain of unknown function (DUF771)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6   0.3   6.4e-52   2.9e-48       1     241 []       1     289 [.       1     289 [. 0.88

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 6.4e-52
                 TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH....TCCCCCHHHC....E..HHHHHHHHH............... CS
   AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal....ksglssgelaaglrstleeagevatr............... 79 
                 +++VvK+GG+sl++ ++  ++++++ + ++  ++nk vvV+++  ++td+l+++    ++g +++ ++ +l   ++++ + a +               
  AJA92556.1   1 MKLVVKFGGTSLATVKD--IKNVVKTVDKI-AKKNKTVVVCSAvDGTTDELIQIsllvEKGNKKDANR-MLAKISQKHKQFADHlitnpkiskslsskl 95 
                 689************99..***********.999999******9**********77766666666665.444444444444444666777777777799 PP

                 .........................HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..........HHHTTTCEEECCHHHHHHHTT-EEEEES CS
   AA_kinase  80 .........................dalaslgerlvaallaaglpavglsaaaldateagr........degsdgnvesvdaeaieelleagvvpvltg 145
                                          d+l s+ge+l+  l++  l++ + ++ +l   eag+        + +  ++ + + +++i+e l+++ +pv++g
  AJA92556.1  96 nsdlseleelvnglillgevtprsyDYLISFGEKLSIDLVSFSLQELKNKSMPLSGKEAGIvtdsnfgdSRPLMDTTKIRLSKTINEHLNKNLIPVVAG 194
                 9999999999999*******************************7777777777777777776665776666666666677****************** PP

                 EEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 146 figldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                 f+g+d++ +   +grg+sD++a+++A +++Ad++++++dV+G ++adpk +++a+ll+++s++ea e    +a++G+k +hp++++++ +++ip++I++
  AJA92556.1 195 FAGADQHDHtttFGRGGSDYTATIIASCIDADEIWLMSDVEGMMTADPKLIKNAKLLKQVSYSEAIE----MARFGAKQIHPRTFEPLLSKKIPMRIRS 289
                 *******************************************************************....**************************85 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.9   8.5e+03      47      63 ..      51      67 ..      50      69 .. 0.83
   2 ?   -3.8   0.0       2.6   1.2e+04      20      32 ..      84      96 ..      79      98 .. 0.80
   3 !   31.3   0.1   2.9e-11   1.3e-07      18      64 ..     331     380 ..     316     380 .. 0.92
   4 !   17.7   0.3   5.2e-07    0.0023       3      65 .]     394     458 ..     392     458 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                EEEEEEGGGHHHHHHHH CS
       ACT_7 47 dyiLVpeedlekAveaL 63
                +++LV++ +++ A ++L
  AJA92556.1 51 ISLLVEKGNKKDANRML 67
                78999999999998887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.6
                S--HHHHHHHHHH CS
       ACT_7 20 vtGivaklaspLa 32
                +++i ++l+s+L+
  AJA92556.1 84 NPKISKSLSSKLN 96
                7899999999997 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 2.9e-11
                 -SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
       ACT_7  18 fdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                 f  +G +ak++s+L++++I+  ++S   ++ ++ i+V++edl +A ++L+
  AJA92556.1 331 FAGPGAAAKIFSVLSKNDINAMMVSsnpSESSITIVVKKEDLHRAENVLE 380
                 5569******************************************9996 PP

  == domain 4  score: 17.7 bits;  conditional E-value: 5.2e-07
                 EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
       ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                  ++++ + v+gsg+++  +Gi+++++ +  + + ++ +i+   ++    ++V+++d +++v  Lh+
  AJA92556.1 394 IPNVAIIAVIGSGMRG-KVGIASRVFLAAQKSNSNVMMIAqgsSELNLAFVVKDNDCKAVVTSLHN 458
                 578999**********.**********************9999*********************97 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.76   3.4e+03      37      63 ..      47      71 ..      39      73 .. 0.75
   2 !   23.5   0.1   7.7e-09   3.5e-05      11      60 ..     334     380 ..     333     381 .. 0.96
   3 !   12.0   0.1     3e-05      0.13       6      51 ..     406     448 ..     401     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.76
                STTECEEEEEEEEEEHHHHHHHHHHHH CS
         ACT 37 edkvagivfvvivvdeedleevlealk 63
                e     i+ +v++++ +d+  +l+++ 
  AJA92556.1 47 EL--IQISLLVEKGNKKDANRMLAKIS 71
                33..67889999999999999998875 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 7.7e-09
                 TTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
         ACT  11 PGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                 PG++a++f++l++++iN  ++++ +se    +i++vv ++d  ++e+vle
  AJA92556.1 334 PGAAAKIFSVLSKNDINAMMVSSNPSES---SITIVVKKEDLHRAENVLE 380
                 9**************************9...8***************998 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 3e-05
                 EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEE CS
         ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvd 51 
                 g+++++G+++rvf a  + + N+ +i q+sse    +++fvv   d
  AJA92556.1 406 GMRGKVGIASRVFLAAQKSNSNVMMIAQGSSEL---NLAFVVKDND 448
                 899*****************************9...8999988777 PP

>> DUF771  Domain of unknown function (DUF771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00088         4      25      56 ..      62      93 ..      45      99 .. 0.83
   2 ?    2.3   0.0     0.037   1.7e+02      23      56 ..     228     262 ..     224     275 .. 0.83
   3 ?   -1.1   0.0      0.43   1.9e+03      49      70 ..     286     308 ..     282     311 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00088
      DUF771 25 tlkdlekklskssewikeniLenprfrkeldi 56
                + + +  k+s++++ + ++++ np+++k l++
  AJA92556.1 62 DANRMLAKISQKHKQFADHLITNPKISKSLSS 93
                55667789999******************998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.037
      DUF771  23 ywtlkdlekklskssewike.niLenprfrkeldi 56 
                 +w ++d+e  +    + ik+ ++L++  +++ +++
  AJA92556.1 228 IWLMSDVEGMMTADPKLIKNaKLLKQVSYSEAIEM 262
                 69****************98579999999999987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.43
      DUF771  49 rfrkeldi.ekggfvlypkgkgk 70 
                 r+r+  d+ ++g+ v  p++k k
  AJA92556.1 286 RIRSSFDVnNQGTLVTLPHSKSK 308
                 78889999667778888988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3364.27
//
Query:       AJA92557.1  [L=406]
Description: translation-associated GTPase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-31  108.1   0.6    7.5e-31  107.0   0.1    1.8  2  MMR_HSR1_C     GTPase of unknown function C-terminal
    5.1e-21   74.9   0.1    1.6e-19   70.0   0.0    2.7  2  MMR_HSR1       50S ribosome-binding GTPase
    3.6e-07   29.9   0.5      0.011   15.3   0.1    2.7  2  GTP_EFTU       Elongation factor Tu GTP binding domain
    1.4e-06   28.3   0.0    2.6e-06   27.4   0.0    1.4  1  TGS            TGS domain
    1.6e-05   24.5   0.1     0.0003   20.4   0.2    2.5  2  FeoB_N         Ferrous iron transport protein B
    6.2e-05   23.1   1.3       0.15   12.1   0.0    3.3  3  Dynamin_N      Dynamin family
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.064   13.5   0.0    1.7  1  YchF-GTPase_C  Protein of unknown function (DUF933)
      0.094   12.5   0.7         28    4.4   0.1    3.9  4  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
        1.5    9.3   4.5        5.3    7.5   4.5    2.0  1  AAA_23         AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.2   6.3e+03      62      92 ..     153     182 ..     133     191 .. 0.71
   2 !  107.0   0.1   3.8e-34   7.5e-31       1     112 []     224     332 ..     224     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.2
  MMR_HSR1_C  62 klkeldekqkkaLekirdlvlkrygsTGVqe 92 
                 + ++l+++ ++  +++   + + y++ GV++
  AJA92557.1 153 NRDKLSKNIRDGTDQVDA-LTELYQGIGVKK 182
                 455678888888888877.667777777764 PP

  == domain 2  score: 107.0 bits;  conditional E-value: 3.8e-34
  MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlvlkrygsTGVqealnaavf 99 
                 ++NK+D+p ad+n+++l+e+y++   +vp+sA++El Lr+a++q likY pg+e+f++ +   +el++kq +aL+ i++ ++ +y  TGVq a+n  vf
  AJA92557.1 224 VANKIDVPGADKNFNRLRERYNEV-ITVPASADSELTLRRAEQQDLIKYSPGSEQFDVVKP--EELNDKQTNALNFIKQDIMGEYMRTGVQFAINVTVF 319
                 79********************55.5********************************999..56********************************** PP

  MMR_HSR1_C 100 elldlivVYPVed 112
                 +ll++ +++PV d
  AJA92557.1 320 KLLKMNAIFPVAD 332
                 ***********86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   8.1e-23   1.6e-19       1      87 [.       4     120 ..       4     160 .. 0.76
   2 ?    1.5   0.0      0.16   3.1e+02      93     114 .]     206     227 ..     181     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 8.1e-23
                 EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE..............ETTEE.............EEEEECGGCSSHHHHHHHHHHHHHH CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk..............lkgke.............ielvDtpGliegaseekglgkafla 72 
                 +++i+G++N+GK+t++n+ t +  ++s++p+tT++++ g+ +              +   +             iel+D+pGli++a ++kglg++fl+
  AJA92557.1   4 KIGIIGKTNTGKTTFFNSATLASTEISSYPFTTKKPQNGTAQaitlcvhmefkvqcE---PnhskcadgwryipIELIDLPGLIKDAWKGKGLGNQFLS 99 
                 69*************************************998655555544444430...03444444444444***********999*********** PP

                 HHC.TSEEEEEEETT.....T CS
    MMR_HSR1  73 lee.adlillvvdas.....e 87 
                 +   +d++l+vvd+s     +
  AJA92557.1 100 IAAqSDALLHVVDCSgsidaS 120
                 88769********99555551 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                 HHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  93 ldeeleelleeakkplilvlnk 114
                 + +el+++l++  kp+++v+nk
  AJA92557.1 206 QTKELAKILRKISKPTLIVANK 227
                 458999999999********98 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0     5e-05     0.099       3      81 ..       2      84 ..       1     125 [. 0.66
   2 !   15.3   0.1   5.4e-06     0.011     108     154 ..     204     265 ..     197     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
                EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...........TTCSSEEEEEEEESSSG CS
    GTP_EFTU  3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...........ketkkylinliDtPGHv 81
                +++igiig +++GKtT+  + + ++ +is+         ++ + ++  ++ iT  + +++++           + ++   i liD PG +
  AJA92557.1  2 VIKIGIIGKTNTGKTTFFNSATLASTEISSYPF------TTKKPQNGTAQAITLCV-HMEFKvqcepnhskcaDGWRYIPIELIDLPGLI 84
                5789****************9999999998433......34444555555555543.333334455666655457888888888888865 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.4e-06
                 THHHHHHHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHHHHH.............H CS
    GTP_EFTU 108 epqteevlrlalkegvpiivfiNKmDrl..kaelkeiveevkqklsrk.............e 154
                 + qt+e++++++k   p+ ++ NK+D +  +++++++ e +++ ++               +
  AJA92557.1 204 MGQTKELAKILRKISKPTLIVANKIDVPgaDKNFNRLRERYNEVITVPasadseltlrraeQ 265
                 78**************************9989999999988877733355544333333331 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.3e-09   2.6e-06       7      59 ..     340     398 ..     334     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.3e-09
                 TSSEEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
         TGS   7 dGkvpd....lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                 +G+v      l+ gatv+ +A+ Ih++l k +++A+      r + +++L+d dv+++v
  AJA92557.1 340 KGRVLPdlflLKDGATVKNLANEIHTDLSKGLLHAKDLRynLRLPTHYQLRDRDVISLV 398
                 66665458889****************************989**************998 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   1.5e-07    0.0003       2      43 ..       4      45 ..       3      54 .. 0.89
   2 ?    0.8   0.0      0.16   3.2e+02      49      88 ..      75     113 ..      63     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
      FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                ++ ++G+ n+Gktt+fn+ t a+++++ +p +t + ++g+ +
  AJA92557.1  4 KIGIIGKTNTGKTTFFNSATLASTEISSYPFTTKKPQNGTAQ 45
                7899**************************999888887765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                 EEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEG CS
      FeoB_N  49 veivDlPGiYslsayseeekvardfll.eeepdvvvnvvda 88 
                 +e++DlPG   +++  + + + ++fl    + d++++vvd 
  AJA92557.1  75 IELIDLPGL--IKDAWKGKGLGNQFLSiAAQSDALLHVVDC 113
                 789*****7..667777888888888547778888888886 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0067        13       1      20 [.       5      24 ..       5      72 .. 0.66
   2 !   12.1   0.0   7.3e-05      0.15     102     143 ..      74     118 ..      63     125 .. 0.88
   3 ?    2.4   0.2     0.072   1.4e+02      66     125 ..     162     247 ..     120     269 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0067
                EEEEEBTTTTHHHHHHHHHT CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlg 20
                i ++G+++ GK+++ n+ + 
  AJA92557.1  5 IGIIGKTNTGKTTFFNSATL 24
                789*************8333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.3e-05
                 SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-CC CS
   Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdls 143
                  ++l+DlPGl++ + + +   +   +++ ++d++l+v++++ ++ 
  AJA92557.1  74 PIELIDLPGLIKDAWKGKglgNQFLSIAAQSDALLHVVDCSGSID 118
                 589*********9999998999999999***********998776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.072
                 HHHHHHHHHHHHHHHTSSSS--SS............................................-EEEEEEETTS-SEEEEE---B-SSSGTTSH CS
   Dynamin_N  66 sevreeieketekiagankgiskk............................................villkilsllvkgltlvDlPGldsvnkrdqe 120
                  + ++                  +                                             il ki +++    + +D+PG+d++ +r  e
  AJA92557.1 162 RDGTD------------------QvdaltelyqgigvkkshviqalkttgledtpfdefemgqtkelaKILRKISKPTLIVANKIDVPGADKNFNRLRE 242
                 33333..................0333333333333333333666666666677777777777777776666666666666666999999998777764 PP

                 HHHHH CS
   Dynamin_N 121 lvkey 125
                   +e 
  AJA92557.1 243 RYNEV 247
                 44444 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.064      17      46 ..     350     379 ..     347     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
  YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraeviky 46 
                    +k+g+t+++ A +iH+D++kg ++a+ ++y
     AJA92557.1 350 LKDGATVKNLANEIHTDLSKGLLHAKDLRY 379
                    6899********************998877 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.014        28       3      19 ..       4      20 ..       2      35 .. 0.82
   2 ?    0.4   0.0      0.25     5e+02     105     136 ..     165     196 ..     158     198 .. 0.85
   3 ?   -0.0   0.0      0.33   6.6e+02      38      74 ..     225     264 ..     211     280 .. 0.61
   4 ?    1.5   0.0      0.11   2.2e+02      21      60 ..     281     317 ..     276     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.014
   PduV-EutP  3 killiGkvgsGKttLtq 19
                ki +iGk+++GKtt  +
  AJA92557.1  4 KIGIIGKTNTGKTTFFN 20
                6779**********865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
   PduV-EutP 105 eenieaveelLksaGaekifevsavekegiee 136
                 +++++a  el +  G++k   ++a++ +g+e+
  AJA92557.1 165 TDQVDALTELYQGIGVKKSHVIQALKTTGLED 196
                 67788888889999**************9985 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.33
   PduV-EutP  38 deviDtPG...eylenrklysalivtsaeadvialvqdat 74 
                  + iD PG   ++   r+ y+ +i++ a+ad    +  a+
  AJA92557.1 225 ANKIDVPGadkNFNRLRERYNEVITVPASADSELTLRRAE 264
                 4567777744446666667777777777766555554444 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.11
   PduV-EutP  21 lkgeelkYkktqaiefsdeviDtPGeylenrklysalivt 60 
                 +k eel+ k+t a++f ++  D  Gey+    +  a++vt
  AJA92557.1 281 VKPEELNDKQTNALNFIKQ--DIMGEYMRTG-VQFAINVT 317
                 56799999********998..668***9875.45555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.5    0.0027       5.3      24     153 ..       7     209 ..       5     303 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
      AAA_23  24 ItGpNGaGKTTildAiklaLygetprlsrks.........grgfeksdveiese......................gkvkayveltfenkdgry..... 86 
                 I+G++ +GKTT+++  +la ++ ++   +++          + +++ +++++ e                                             
  AJA92557.1   7 IIGKTNTGKTTFFNSATLASTEISSYPFTTKkpqngtaqaITLCVHMEFKVQCEpnhskcadgwryipielidlpgL----------------Ikdawk 89 
                 99******************996644333333344444443344444444444455555522222222222222220................022223 PP

      AAA_23  87 ..................................................trsiererelskkkgkttkkaklellei.deleqfisellgskki.iln 133
                                                                    + + + ++  +++ ++ +k+++++++  d+l+++  + +g+kk+  ++
  AJA92557.1  90 gkglgnqflsiaaqsdallhvvdcsgsidasgkitepgsgdpvsdfadieEELVMWYQKILEGNRDKLSKNIRDGTDQvDALTELY-QGIGVKKShVIQ 187
                 33344444444444444455555555555555555555555555555555566777777777777777777777776634443333.345544442446 PP

      AAA_23 134 lilflgqer..feefelkdkke 153
                  +   g e+  f+efe  ++ke
  AJA92557.1 188 ALKTTGLEDtpFDEFEMGQTKE 209
                 6666666666655555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2820.08
//
Query:       AJA92558.1  [L=132]
Description: prokaryotic JAB domain-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-09   37.3   0.0    2.5e-09   36.9   0.0    1.2  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.033   14.2   0.0    1.5  2  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.8e-13   2.5e-09      13     115 ..      27     120 ..      16     123 .. 0.62

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.8e-13
    Prok-JAB  13 rrahpeEtcGlllgke...seseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpggsarPSetDrrdaaalarvkalliivgd. 107
                 +  hp+E   +l g++   +   e  vvp  +        ++++  +  ++      + +++g++HSHp+g a+PS++D++++++l     + +iv + 
  AJA92558.1  27 KINHPDEMILILKGHSkkgKMFVEGLVVPPFQ--------EAAPTFAGFPA-NQLPFDSDYIGMVHSHPAGTAEPSSEDLHNFFGL-----VSVIVKAp 111
                 55678888888888773332222222333222........23333333344.7788899*************************84.....34444443 PP

    Prok-JAB 108 .kaeelraw 115
                  + e++ aw
  AJA92558.1 112 yEDEDIFAW 120
                 444444555 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.6   5.4e+03      21      40 ..       9      28 ..       3      33 .. 0.63
   2 ?   14.2   0.0   3.6e-06     0.033      66      85 ..      78      97 ..      70     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                -EEEEEEE-TTSBEEEEEEE CS
        RadC 21 EefvvllLdsknrliadeel 40
                E+ +v+l d++  ++++ ++
  AJA92558.1  9 ERSLVFLNDTRDGIVSYCKI 28
                66777777777666666555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.6e-06
                EEEEEEE-TTS--S--HHHH CS
        RadC 66 avilaHnhPsgdlepSeeDi 85
                 + ++H hP g++epS+eD+
  AJA92558.1 78 YIGMVHSHPAGTAEPSSEDL 97
                5668***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 965.74
//
Query:       AJA92559.1  [L=207]
Description: ribosomal protein S4 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-12   45.1   0.4    1.2e-11   44.1   0.0    1.8  2  S4        S4 domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       0.4   7.1e+03       8      20 ..      55      66 ..      54      67 .. 0.77
   2 !   44.1   0.0   6.9e-16   1.2e-11       1      46 [.     103     148 ..     103     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.4
                HHTTSSSSHHHHH CS
          S4  8 arlglassrreAr 20
                ar++la  r e+r
  AJA92559.1 55 ARSLLAV-RQEVR 66
                5788888.88888 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 6.9e-16
                 EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
          S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                 rR +++++++ + ++  +Arq+I+hG+Vl+  +v++ psy Vk  +
  AJA92559.1 103 RRFQTIVFKKFFFKTPYQARQAISHGHVLIGDRVINRPSYVVKIDE 148
                 799****************************************655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1554.08
//
Query:       AJA92560.1  [L=131]
Description: hypothetical protein T478_0744 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 999.59
//
Query:       AJA92561.1  [L=276]
Description: oxidoreductase NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-12   48.4   0.0    2.5e-12   47.4   0.0    1.5  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    2.4e-08   34.2   0.0    3.5e-08   33.7   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
  ------ inclusion threshold ------
      0.092   12.9   0.1       0.36   11.0   0.1    1.8  2  NAD_binding_6    Ferric reductase NAD binding domain
      0.095   11.9   0.0       0.13   11.5   0.0    1.2  1  Methyltransf_34  Putative SAM-dependent methyltransferase


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   5.6e-16   2.5e-12       2     103 ..     122     243 ..     121     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 5.6e-16
                    EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT......EEEEEEEESSCT....TTSSSEESSHHHHHHHHHHH CS
  NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg......rlkvvavvsree....agweggkgrvqdalleells 87 
                    i+gGtG+aP++s+ +++ +   dk+++v+++G+ + ++l yre+l  l+ +  +      ++k+ a+ sr++    ++w+g+ grv++ l+     
     AJA92561.1 122 IGGGTGLAPFVSFAQHLHDI-GDKRELVVLHGASYVDELSYRERLTDLELESVDrgtdkwNFKYRAAISRPQewlnRSWTGQIGRVEQFLRARPGR 216
                    89**************9997.99**********************999877665567778889988866655222279*********999775555 PP

                    ...........HSSTTEEEEEECSHHH CS
  NAD_binding_1  88 ...........lkkeethvyvCGppgM 103
                               ++k++t++y+CG +g 
     AJA92561.1 217 vspleelvgekITKDNTMFYICGWQGT 243
                    778999999**9***********8765 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   7.8e-12   3.5e-08       3      96 ..       5     102 ..       3     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 7.8e-12
                    EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEEC...ETTCCEEEEEE.BSSTTECCEEEEEEE--...TT-HHHHHHHCS-TT-EEEEEE CS
  FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlk...ikgeaviRsYtpissenekGelellvkvy...pgGkmsqaLdelkigdtleikG 92 
                    +++ ++ + ed++ifr+  + +    ++ +Gq++ l l+    +++ + R+Y+++s++++k ++e++++ +     G+++ a+ +lk gd ++ + 
     AJA92561.1   5 TVSYVQLLREDLAIFRVVPEGPFP--EYKAGQFLTLGLPvksENNRVINRAYSIASHPENKKYFEFVIRWVrkpYPGRLTTAMFNLKEGDPIQWRK 98 
                    677788889999999999998888..9**********995433355578**********************88878**************999887 PP

                    EE-S CS
  FAD_binding_6  93 PlGk 96 
                      G+
     AJA92561.1  99 ANGT 102
                    7776 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.9e-05      0.36       4      26 ..     119     141 ..     117     151 .. 0.85
   2 ?   -1.2   0.0      0.42   1.9e+03     113     145 ..     208     241 ..     156     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                    xxxxxxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6   4 vllvagGiGitpfisilkdllkk 26 
                    ++ ++gG+G++pf+s++++l   
     AJA92561.1 119 IVCIGGGTGLAPFVSFAQHLHDI 141
                    799****************9765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.42
                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
  NAD_binding_6 113 kihfgRPnlkevlkdi.askhknssvgvfvCGpp 145
                    ++  +RP   + l+++  +k  ++++ +++CG +
     AJA92561.1 208 QFLRARPGRVSPLEELvGEKITKDNTMFYICGWQ 241
                    5556666666666666445567788889999976 PP

>> Methyltransf_34  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.13      83     130 ..     110     174 ..      38     190 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
  Methyltransf_34  83 eekeekklkvlciGGGag.aElvalaallre................keeekessssslsltlvD 130
                       + e ++ +++ciGGG g a +v++a  l++                +e + +++ ++l+l+ vD
       AJA92561.1 110 PNGEPDERRIVCIGGGTGlAPFVSFAQHLHDigdkrelvvlhgasyvDELSYRERLTDLELESVD 174
                      23333788********9878999999999843333344444444454445555555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2070.41
//
Query:       AJA92562.1  [L=223]
Description: NADPH-dependent F420 reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-17   62.4   0.0    7.7e-17   61.7   0.0    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00057   20.3   0.0     0.0011   19.4   0.0    1.4  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.004   17.2   0.2     0.0065   16.5   0.2    1.5  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.024   14.8   0.2      0.078   13.1   0.1    1.9  2  DapB_N          Dihydrodipicolinate reductase, N-terminus
      0.026   14.2   0.0      0.046   13.4   0.0    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.027   13.5   0.2      0.047   12.7   0.2    1.6  1  PDH             Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.6e-20   7.7e-17       1      96 [.       2     104 ..       2     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.6e-20
                    EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHH CS
  F420_oxidored   1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvlavkpedveevlselakd 84 
                    k+gii G+G mg+++a ++ +     h+++++ sr+ e+a++ a+e++            ++t++dn ++a+e+d++vl++++e++++++sel ++
     AJA92562.1   2 KVGIIgGTGGMGKGFAVRWCKD----HNVLIG-SRDAERANASAQEYSelvkeaygsinGNITGTDNTTVAKESDILVLSIPYENIDAICSELLPQ 92 
                    79******************99....9***88.**************************9************************************ PP

                    HHTTSEEEEESS CS
  F420_oxidored  85 alkgklvisvla 96 
                       + +v+s  +
     AJA92562.1  93 INDNCVVVSPIV 104
                    *********876 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.7e-07    0.0011       1      92 [.       2      98 ..       2     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.7e-07
                    EEEEETTTSHHHHHH.HHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHHHHH...HHTTSE CS
  Semialdhyde_dh  1 kvaivGatGyvGqel.lrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvskelapkl...aeagvk 92
                    kv+i+G+tG +G+ + +r  ++h  +  ++ + +++   ++++e+vk+ ++  + +++ +d+  + ke di++l+ p +   ++  +l   ++ +++
      AJA92562.1  2 KVGIIGGTGGMGKGFaVRWCKDHNVLIGSRDAERANASAQEYSELVKEAYGSINGNITGTDNTTVaKESDILVLSIPYENIDAICSELlpqINDNCV 98
                    7**************77888889999999999999999*********************8888878***********99888887777333344555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.2e-06    0.0065      53     102 ..      54     106 ..       2     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                     --TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE....- CS
  NAD_Gly3P_dh_N  53 lpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvs....l 102
                     ++ n++  td ++++k++di+vl +P + +  ++ +l + ++++ ++vs    +
      AJA92562.1  54 INGNITG-TDNTTVAKESDILVLSIPYENIDAICSELLPQINDNCVVVSpivpM 106
                     4555544.6778999******************************999955553 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.6e-05     0.078       1      72 [.       1      74 [.       1      83 [. 0.80
   2 ?   -1.0   0.0      0.62   1.9e+03      21      44 ..     108     129 ..     101     179 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS..--S-BEB.SSHHHHHHH-SEEE CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg..klgvavt.ddleevlekadvli 72
                +kv+++G +G mGk  +    ++ ++ l +  d+++ ++++++ +el++    +++ ++t +d ++v++++d+l+
  AJA92562.1  1 MKVGIIGGTGGMGKGFAVRWCKDHNV-LIGSRDAERANASAQEYSELVKEAygSINGNITgTDNTTVAKESDILV 74
                89**************9999996555.555557777799999999999876669999999455555555599987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.62
                 HHSTTEEEEEEEETTC..STTTTTBH CS
      DapB_N  21 eeaedlelvaavdrke..selegkda 44 
                 ++++++e va  ++k+  +    + +
  AJA92562.1 108 KTDTGFECVAIKENKPfsH----QTV 129
                 5555666666555555222....222 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.5e-05     0.046       3     100 ..       6     101 ..       4     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                 EES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEE CS
        ApbA   3 ilGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsaeekselepidlvivtvKayqteealeeikplldpntvvl 99 
                 i G+G++G  +a++  k  ++v +  r++ r++a  ++ ++l +e  g+ +   + + +++    +++ d+++++++    ++ ++e+ p +++n+vv+
  AJA92562.1   6 IGGTGGMGKGFAVRWCK-DHNVLIGSRDAeRANASAQEYSELVKEAyGSINGNITGTDNTT---VAKESDILVLSIPYENIDAICSELLPQINDNCVVV 100
                 679************87.999*999****9****999999999999666666666666666...999*****************************998 PP

                 E CS
        ApbA 100 l 100
                 +
  AJA92562.1 101 S 101
                 6 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.6e-05     0.047      36      76 ..      60     100 ..      22     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                 EES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEE CS
         PDH  36 atddieavkeadivvlavPvevilevlkelaphlkedalit 76 
                  td+   +ke di vl++P e i  +  el p+++ +++++
  AJA92562.1  60 GTDNTTVAKESDILVLSIPYENIDAICSELLPQINDNCVVV 100
                 45557889***************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1593.78
//
Query:       AJA92563.1  [L=234]
Description: ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-33  116.5   0.2      2e-33  115.8   0.2    1.3  1  ABC_tran        ABC transporter
    5.6e-07   29.2   1.3      2e-06   27.4   1.3    1.8  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.3e-05   24.8   0.2    2.9e-05   23.7   0.2    1.5  1  AAA_29          P-loop containing region of AAA domain
    4.4e-05   23.9   0.1    5.9e-05   23.5   0.1    1.4  1  AAA_16          AAA ATPase domain
    0.00012   22.0   0.8    0.00022   21.2   0.2    1.7  2  RsgA_GTPase     RsgA GTPase
    0.00034   20.4   0.1     0.0035   17.1   0.0    2.0  2  AAA_15          AAA ATPase domain
     0.0018   17.9   0.1      0.081   12.5   0.0    2.2  2  AAA_25          AAA domain
     0.0028   18.2   0.1     0.0069   16.9   0.0    1.6  2  AAA_23          AAA domain
     0.0033   16.8   0.1       0.12   11.7   0.0    2.2  2  ATPase          KaiC
     0.0034   16.6   0.0     0.0034   16.6   0.0    1.2  1  G-alpha         G-protein alpha subunit
      0.005   16.6   0.4        0.2   11.3   0.0    2.3  2  AAA_30          AAA domain
     0.0064   16.6   1.4      0.012   15.7   1.4    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
      0.007   15.5   0.0      0.013   14.6   0.0    1.5  1  T2SSE           Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   16.0   0.3      0.017   15.4   0.3    1.7  1  AAA_22          AAA domain
      0.014   14.8   0.1      0.024   14.0   0.1    1.4  1  FtsK_SpoIIIE    FtsK/SpoIIIE family
      0.014   14.6   0.2      0.045   13.0   0.0    1.8  2  Zeta_toxin      Zeta toxin
      0.018   14.9   1.5       0.15   11.8   1.3    2.0  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      0.029   13.2   0.5       0.11   11.2   0.0    2.1  3  ABC_ATPase      Predicted ATPase of the ABC class
      0.049   13.2   2.1      0.098   12.2   0.4    2.1  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.052   13.5   0.0      0.091   12.7   0.0    1.3  1  Thioredox_DsbH  Protein of unknown function, DUF255
      0.053   13.4   0.0      0.085   12.7   0.0    1.4  1  APS_kinase      Adenylylsulphate kinase
      0.074   13.2   0.8       0.14   12.3   0.8    1.8  1  AAA_33          AAA domain
      0.086   12.7   0.5       0.21   11.5   0.2    1.8  2  NACHT           NACHT domain
       0.32   11.0   4.3        1.7    8.7   4.3    2.1  1  Dynamin_N       Dynamin family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.2   2.6e-36     2e-33       1     136 [.      25     172 ..      25     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 2.6e-36
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH............HHHT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren............esde 83 
                 l++vsl++++ge v ivG++G+GKStLl+++  l kpt+G++ ldgk++++    q  +  ++++g+++q ++l p+ltv en            + ++
  AJA92563.1  25 LDDVSLSIRRGEFVLIVGSSGSGKSTLLNMIGLLDKPTSGKVILDGKETTTlndgQVSQYRNEKLGFVFQFANLLPDLTVLENvmlpqqiqrsseDVRQ 123
                 79**********************************************999999999999999************************999865433333 PP

                 CHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  84 eiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +++++l k+gl++  +++     +++SgGq qr a+ar l+++p+++l+DEpt
  AJA92563.1 124 NATDLLIKVGLEDQIHKRS----NKISGGQAQRAAIARGLVNRPTIVLADEPT 172
                 3777777777777555555....*****************************9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   1.3   2.7e-09     2e-06      24     213 ..      35     219 ..      20     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                 SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-H.H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
       SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtk.k 121
                  +f  ivG+ GSGKs ll+ i    G      l + +  ++i   ke   ++ ++v+  ++ne+  ++ +  ++    +v ++     +i++++    +
  AJA92563.1  35 GEFVLIVGSSGSGKSTLLNMI----GL-----LDKPTSGKVILDGKETTTLNDGQVSQ-YRNEKLGFVFQFANLLPDLTVLENVMLPQQIQRSSEDVrQ 123
                 36999**************99....63.....55667788888889***********9.6888888888888877777777777766666665555445 PP

                 HHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                 xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 122 evsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                 + ++ll ++g++ +       +SgG+ + +a+a       v++  ++l De   +LD     kv++l k+  k+    fi+++++++++ ++d+++ ++
  AJA92563.1 124 NATDLLIKVGLEDQihkrsnKISGGQAQRAAIAR----GLVNRPTIVLADEPTGNLDSVTAGKVVKLAKTMAKElnQTFIIVTHDKHQFPDVDRIITIK 218
                 667778777777666666669*****99999875....457888999********************9987776525699***************9987 PP

                 E CS
                 x RF
       SMC_N 213 k 213
                  
  AJA92563.1 219 D 219
                 5 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   3.9e-08   2.9e-05      13      40 ..      26      53 ..      23      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.9e-08
      AAA_29 13 dghtieidlkgatlltGpsGsGKSTllD 40
                d+ +++i++ +++l++G sGsGKSTll 
  AJA92563.1 26 DDVSLSIRRGEFVLIVGSSGSGKSTLLN 53
                66788898777***************94 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   7.8e-08   5.9e-05       6      51 ..      19      61 ..      17     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.8e-08
      AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                ++++++L ++  ++r+g  e vl++G sG+GKs+l++++   l k 
  AJA92563.1 19 DAQVKALDDVSLSIRRG--EFVLIVGSSGSGKSTLLNMIG-LLDKP 61
                68899998887778877..79***************9987.56666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   2.9e-07   0.00022      88     142 ..      23      75 ..       7      83 .. 0.77
   2 ?   -2.5   0.0       5.7   4.2e+03       9      30 ..     187     208 ..     176     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.9e-07
                  TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-------------- CS
  RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTt 142
                  ++l++++  ++  +++++vG+SG GKStL+n++   ++   g+v      Gk TTt
   AJA92563.1  23 KALDDVSLSIRRgEFVLIVGSSGSGKSTLLNMIGLLDKPTSGKVIL---DGKETTT 75 
                  5667777777766999***************997766665565544...4777776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                  TTTTEES--EEEEEEESTTTT- CS
  RsgA_GTPase   9 vrpkvaNvdqllivvslkepel 30 
                   ++ +  ++q +i+v+ +++++
   AJA92563.1 187 AKTMAKELNQTFIIVTHDKHQF 208
                  4555666777788877776655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0035      12      67 ..      23      83 ..      23     146 .. 0.72
   2 ?    1.3   0.0      0.29   2.2e+02     324     367 ..     163     206 ..     150     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
      AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.....kkvikiekedlei 67
                ++l+dv++++    + +++G  +sGKS++l+++ l+ + + + +     k+++++++ ++++
  AJA92563.1 23 KALDDVSLSIRRGeFVLIVGSSGSGKSTLLNMIGLLDKPT-SGKvildgKETTTLNDGQVSQ 83
                67888888888878*******************8888766.222466663333333333333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
      AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                 + i+l +EP  +L       ++kl k +a++ ++  ii TH  h
  AJA92563.1 163 PTIVLADEPTGNLDSVTAGKVVKLAKTMAKELNQTFIIVTHDKH 206
                 55666677777777777778899999999999977899***987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00011     0.081      30      50 ..      32      52 ..      13      59 .. 0.90
   2 ?    3.1   0.0     0.084        63     164     189 ..     179     204 ..     165     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
      AAA_25 30 lpagelallaGapgtGKttla 50
                +++ge++l++G +g+GK+tl+
  AJA92563.1 32 IRRGEFVLIVGSSGSGKSTLL 52
                689****************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.084
      AAA_25 164 dvgalvealeriarrtgaavllvhHv 189
                  +g++v+ ++ +a++++ ++++v H 
  AJA92563.1 179 TAGKVVKLAKTMAKELNQTFIIVTHD 204
                 3599*********************5 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.2e-06    0.0069      20      40 ..      36      56 ..       7      59 .. 0.84
   2 ?   -2.2   0.0       6.6   4.9e+03     102     102 ..     120     120 ..      62     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-06
      AAA_23 20 gltlItGpNGaGKTTildAik 40
                 ++lI+G  G+GK+T+l+ i 
  AJA92563.1 36 EFVLIVGSSGSGKSTLLNMIG 56
                578**************9986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.6
      AAA_23 102 k 102
                 +
  AJA92563.1 120 D 120
                 1 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00016      0.12       5      35 ..      22      51 ..      19      54 .. 0.87
   2 ?    2.8   0.0     0.082        62     143     164 ..     182     204 ..     172     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
      ATPase  5 IeglDeilkgGipegrvvlitGepGtGKtif 35
                ++ lD++    i +g+ vli+G++G+GK+++
  AJA92563.1 22 VKALDDVS-LSIRRGEFVLIVGSSGSGKSTL 51
                67788886.789****************987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.082
      ATPase 143 ilrqlvrvl.kklgvTailvsek 164
                  + +l++++ k+l++T i+v+  
  AJA92563.1 182 KVVKLAKTMaKELNQTFIIVTHD 204
                 5778899999*********9974 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.6e-06    0.0034      26      51 ..      38      76 ..      19     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.6e-06
                EEEEESTTSSHHHHHHHHHHHCS--.............- CS
     G-alpha 26 llllGqseSGKsTilkqlkllykkg.............f 51
                +l++G+s+SGKsT+l+ + ll k++              
  AJA92563.1 38 VLIVGSSGSGKSTLLNMIGLLDKPTsgkvildgketttL 76
                79*******************999866666555555443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00027       0.2      17      49 ..      34      66 ..      18      76 .. 0.72
   2 ?    3.5   0.1      0.07        52      85     132 ..     159     212 ..     111     232 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
      AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                +  +++++G  G+GK+t+l+ +  + +   g+v
  AJA92563.1 34 RGEFVLIVGSSGSGKSTLLNMIGLLDKPTSGKV 66
                335899*************99876666555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.07
      AAA_30  85 rlepgtllivDE.agmvdtkqlaallkaaeka.....gakvilvGDerQlasVe 132
                  +++ t+++ DE +g +d+ ++ +++k a++      ++ +i+  D++Q + V+
  AJA92563.1 159 LVNRPTIVLADEpTGNLDSVTAGKVVKLAKTMakelnQTFIIVTHDKHQFPDVD 212
                 344557777777556777777777777776633445456677777777777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.4   1.6e-05     0.012       2      42 ..      38      82 ..      37     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                EEEEESTTSSHHHHHHHH..HTS..TEEESSSTTSSSSEEEEEEE CS
    MMR_HSR1  2 vaivGrpNvGKStLinal..tge..kaivsdkpgtTrdinegrvk 42
                v+ivG + +GKStL+n +  +++    +v      T++ n g+v+
  AJA92563.1 38 VLIVGSSGSGKSTLLNMIglLDKptSGKVILDGKETTTLNDGQVS 82
                89**************98544444323444444444445555554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.8e-05     0.013     114     149 ..      20      55 ..       5      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
       T2SSE 114 lkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                  + k  + ++ ++r+   +l+ G  gsGK+tll+++
  AJA92563.1  20 AQVKALDDVSLSIRRGEFVLIVGSSGSGKSTLLNMI 55 
                 555555667788999999***************975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.3   2.3e-05     0.017       4      29 ..      34      59 ..      32     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-05
      AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                +  +++++G sG+GK+tll+++   +
  AJA92563.1 34 RGEFVLIVGSSGSGKSTLLNMIGLLD 59
                56799**************9987765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.2e-05     0.024      41      58 ..      37      54 ..      15      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                  SEEEE--TTSSHHHHHHH CS
  FtsK_SpoIIIE 41 hllvaGatgsGKStalnt 58
                   +l++G++gsGKSt ln 
    AJA92563.1 37 FVLIVGSSGSGKSTLLNM 54
                  69**************95 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-05     0.045      16      38 ..      35      57 ..      23      77 .. 0.76
   2 ?   -1.3   0.0       1.5   1.1e+03      27      66 ..     180     216 ..     177     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
  Zeta_toxin 16 PklillgGqpGAGKselaellkd 38
                   +l++G++G+GKs+l++++  
  AJA92563.1 35 GEFVLIVGSSGSGKSTLLNMIGL 57
                5679***************9865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
  Zeta_toxin  27 AGKs.elaellkdelerqgnvvrldpDdlRelhPeyeeilk 66 
                 AGK  +la+ +++el  ++ ++ +  D  + ++P+++ i+ 
  AJA92563.1 180 AGKVvKLAKTMAKEL--NQTFIIVTHD--KHQFPDVDRIIT 216
                 555325667777777..6777777777..567788777776 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3    0.0002      0.15       1      22 [.      37      58 ..      37      95 .. 0.79
   2 ?    1.3   0.0      0.33   2.4e+02     237     298 ..     145     204 ..     100     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
      AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                + +++G  gsGKS+LL  + ll
  AJA92563.1 37 FVLIVGSSGSGKSTLLNMIGLL 58
                679**************99888 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
      AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                 +S G+ + +a++  l  ++   +++l DEp  +L+     ++++l k  ++++ Q  i++TH+
  AJA92563.1 145 ISGGQAQRAAIARGLVNRP---TIVLADEPTGNLDSVTAGKVVKLAKTMAKELNQTfIIVTHD 204
                 5555555533333444444...89999999999999777777777744444444444999997 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.11     240     264 ..      30      55 ..      26      87 .. 0.81
   2 ?   -1.6   0.0       1.2   8.7e+02     322     348 ..     144     170 ..     110     175 .. 0.73
   3 ?   -1.7   0.0       1.3   9.5e+02     377     418 ..     184     224 ..     176     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                 EEE-SS.EEEEEE-TTSSHHHHHHHH CS
  ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                 + i++G  +lIvG+   GKsTLL+ +
  AJA92563.1  30 LSIRRGeFVLIVGSSGSGKSTLLNMI 55 
                 689999999**************976 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                 S--HHHHHHHHHHHHHHTT-SEEEEEG CS
  ABC_ATPase 322 dASGStsqAanimealeagakllLiDE 348
                 + SG   q a+i++ l ++ +++L DE
  AJA92563.1 144 KISGGQAQRAAIARGLVNRPTIVLADE 170
                 457777777777777777777777777 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                 HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE CS
  ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkd 418
                 v++++ + k+l+ + i+v+    ++ +  d++i +++ k+  
  AJA92563.1 184 VKLAKTMAKELNQTFIIVTHDKHQF-PDVDRIITIKDGKAFS 224
                 6777888888887777776665554.5568999888766554 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00013     0.098       3      33 ..      38      68 ..      36      98 .. 0.74
   2 ?    0.1   0.0      0.72   5.4e+02     104     126 ..     203     225 ..     154     233 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                EEEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
        cobW  3 tvltGflGsGKTtLlnhllenraglklaviv 33
                ++++G+ GsGK+tLln +    +  +  vi+
  AJA92563.1 38 VLIVGSSGSGKSTLLNMIGLLDKPTSGKVIL 68
                689*************987555555555665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.72
                 HHHHHCCCECEEEEEEETTTH.C CS
        cobW 104 eelksdltldavvavvDaknlea 126
                 ++ ++   +d ++++ D+k++++
  AJA92563.1 203 HDKHQFPDVDRIITIKDGKAFSE 225
                 33344455666777777766643 PP

>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.091      64      90 ..     189     215 ..     185     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
  Thioredox_DsbH  64 evaallnesfvsvkvDreerPdldkiy 90 
                     ++a+ ln++f+ v  D+ + Pd+d+i 
      AJA92563.1 189 TMAKELNQTFIIVTHDKHQFPDVDRII 215
                     6899********************985 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.085       2      89 ..      35     116 ..      34     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                 -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE----SHHHH CS
  APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlvafisPyreeR 89 
                 g  v++ G sgsGKst+ n++   L +     ++LdG +  + Ln   g+ ++ R+e++  v + a+ll d ++  l  ++ P + +R
  AJA92563.1  35 GEFVLIVGSSGSGKSTLLNMIG-LLDKPTSGKVILDGKET-TTLND--GQVSQYRNEKLGFVFQFANLLPDLTV--LENVMLPQQIQR 116
                 66799************99997.67777788899999875.44554..77788888888888888888887654..344444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   0.00019      0.14       2      18 ..      38      54 ..      37     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
      AAA_33  2 vllvGlpGsGKstlaer 18
                vl+vG +GsGKstl+  
  AJA92563.1 38 VLIVGSSGSGKSTLLNM 54
                799**********9864 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00028      0.21       3      20 ..      38      55 ..      36      66 .. 0.89
   2 ?   -1.6   0.0       2.9   2.2e+03      58      58 ..     109     109 ..      60     157 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                EEEEC-TTTCHHHHHHHH CS
       NACHT  3 vilqGeaGsGKTtLlqkl 20
                v++ G +GsGK+tLl  +
  AJA92563.1 38 VLIVGSSGSGKSTLLNMI 55
                89*************876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.9
                 H CS
       NACHT  58 l 58 
                 +
  AJA92563.1 109 M 109
                 2 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.3    0.0023       1.7       1      18 [.      38      55 ..      38     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                EEEEEBTTTTHHHHHHHH CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                +++vGs  sGKS++ln +
  AJA92563.1 38 VLIVGSSGSGKSTLLNMI 55
                689*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1630.08
//
Query:       AJA92564.1  [L=425]
Description: peptide chain release factor 1, archaeal and eukaryotic forms [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-30  105.2   0.0    6.2e-29  101.0   0.0    2.4  2  eRF1_2          eRF1 domain 2
    1.6e-17   64.0   3.7    3.7e-17   62.8   1.1    2.5  2  eRF1_3          eRF1 domain 3
    5.5e-11   42.6   0.1    1.9e-10   40.9   0.0    1.9  2  eRF1_1          eRF1 domain 1
    5.1e-08   33.3   0.0    1.2e-07   32.1   0.0    1.6  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    5.6e-07   29.9   0.0    1.2e-06   28.8   0.0    1.5  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
     0.0053   16.5   0.1      0.014   15.1   0.1    1.7  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
       0.06   13.2   1.3        6.6    6.6   0.1    2.5  2  Phage_integr_3  Archaeal phage integrase
        1.4    9.5   5.7         51    4.4   3.8    3.0  2  zf-3CxxC        Zinc-binding domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   2.8e-32   6.2e-29       2     132 ..     150     278 ..     149     279 .. 0.97
   2 ?    1.5   0.0      0.16   3.5e+02     100     129 ..     286     316 ..     280     321 .. 0.72

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 2.8e-32
                 EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHHHHHHHHH CS
      eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiilagpgfvkeefldkdllda 100
                 +gl+ +d + A  gll+g + evlk+  + v +Kh++Ggqsa+rf++lre +l+ ++++va    ++f+  d+ k+kg+i+ gpg++ke+f+++++l++
  AJA92564.1 150 IGLLAIDAKDAGWGLLHGDKLEVLKETGSGVAGKHRQGGQSAKRFQKLREMELQYYFNRVAHITREYFI--DIYKVKGLIVSGPGPTKEDFIKNEYLEY 246
                 688999*************************************************************99..89************************** PP

                 HHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHC CS
      eRF1_2 101 elkkkviklvdvsyggesglnevlekaaevlk 132
                 +l++++i ++d+sy g +g++e+  k ++ l+
  AJA92564.1 247 RLQNNIIATIDASYSGSEGIREAFAKCSDILS 278
                 **************************999987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                 HHHHTCCEEEEE-S-T.SCHHHHHHHHCCHH CS
      eRF1_2 100 aelkkkviklvdvsyg.gesglnevlekaae 129
                 ++  +k ++ +++++g g +gl+ev+e   +
  AJA92564.1 286 KKIIEKLFQEINTNSGlGSYGLKEVIEMLRN 316
                 44556888888888875899******98655 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.32   7.2e+02      70      99 ..      17      46 ..       4      52 .. 0.74
   2 !   62.8   1.1   1.6e-20   3.7e-17       2     112 ..     283     421 ..     282     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.32
                HHHHHHHHHHHTT-EEEEE-TTSHHHHHHH CS
      eRF1_3 70 lieelvenveesgakveiisseseeGeqlv 99
                + + l e  ++sg   e+i+   ++G+ql 
  AJA92564.1 17 IRKTLEELTQQSGRGTELITVYIPKGQQLH 46
                5566677788999999**********9995 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 1.6e-20
                 HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS..........................-HHH-HHHHHH..... CS
      eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv..........................ketgeelelve..... 69 
                 ++ekk++e++++e+++++g+  YG +ev ++l+ +    +++s+++++sr + k+k                           +    e e+++     
  AJA92564.1 283 VEEKKIIEKLFQEINTNSGLGSYGLKEVIEMLRNNIAAMVVISDNINMSRIEKKCKRcshveeelieqgkriarktemksqkcS----ECEAMDfemtd 377
                 89************************************************88666667*******************9975553....33333333445 PP

                 ..HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
      eRF1_3  70 ..lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                   li+ ++  ++++g+kve++s ++e+G +l  ++g iaaiLRy+
  AJA92564.1 378 qdLIDFIALIASQTGTKVEVVSGKTEHGVML-GSLGNIAAILRYN 421
                 88*****************************.************7 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   8.3e-14   1.9e-10       2     128 ..      19     143 ..      18     144 .. 0.88
   2 ?   -1.8   0.0       1.3   2.8e+03      32      51 ..     347     366 ..     338     403 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 8.3e-14
                 EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSEEEEEEEEEEGGGG-- CS
      eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agvlrisGkvieenehvk 95 
                 k l++  + +++g++++t+++++ ++l +++  ++++++++ ++++  +r         ++v   L   +++++++k+   +g+++++G    e +  +
  AJA92564.1  19 KTLEEltQQSGRGTELITVYIPKGQQLHEVMTQLREEQGTADNIKSDLTR---------THVVDSLSKVQQRLKLYKKtpeKGLVVFCGALPREGGG-P 107
                 556665566799************************************99.........89999999999999999998888*************97.4 PP

                 TTS..EEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
      eRF1_1  96 lga..fhtldlelkrpftiikee.wdsfalerLkea 128
                  g+     +++e+++++t++ ++ +d+f++++Lk++
  AJA92564.1 108 PGSevVKIYEIEPPKDLTTSLYRcDDHFHTDILKDM 143
                 444115679************999**********98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                 HCHTTHEEEEEEEECHHH.. CS
      eRF1_1  32 liapgdsvrastvrkvqres 51 
                 li++g +++ +t  k q+ s
  AJA92564.1 347 LIEQGKRIARKTEMKSQKCS 366
                 66666666666666665533 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   5.3e-11   1.2e-07       7      91 ..     155     240 ..     150     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.3e-11
     acVLRF1   7 lvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarll..aeesaevvlgGdrslvaevle 91 
                 ++ +++   g+++g++l+  k+  + v g++++GG+S +Rf++ re + +  +++va+  ++ +    +++ +++ G+  + +++ +
  AJA92564.1 155 IDAKDA-GWGLLHGDKLEVLKETGSGVAGKHRQGGQSAKRFQKLREMELQYYFNRVAHITREYFidIYKVKGLIVSGPGPTKEDFIK 240
                 455555.7899*************************************************999933344444888888777666655 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   5.4e-10   1.2e-06       7     121 ..     141     257 ..     136     271 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.4e-10
  baeRF_family10   7 lealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklleerg.verlvlgGdeee 100
                      + l+++  +g++ +d+++a +   ++++le  +e  + v g++++gg+ s +rfq+ +e+  + ++++vA+++++++ +   v+ l+++G+   
      AJA92564.1 141 KDMLQDDNIIGLLAIDAKDAGWGLLHGDKLEVLKETGSGVAGKHRQGGQ-SAKRFQKLREMELQYYFNRVAHITREYFIDIYkVKGLIVSGPGPT 234
                     5678888889***************************************.*************************98866544*********666 PP

  baeRF_family10 101 taal..ldrlpkalrarvvgtlp 121
                     ++ +   + l  +l+  +++t++
      AJA92564.1 235 KEDFikNEYLEYRLQNNIIATID 257
                     66662244588888888888765 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   6.3e-06     0.014      18      48 ..     305     335 ..     290     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.3e-06
                     ESHHHHHHHHHTTTESEEEEETTSSSGGHHH CS
  Ribosomal_L7Ae  18 lGlkevtkalergeaklvilAedvepeekkk 48 
                     +Glkev+  l+++ a +v+++++++  +++k
      AJA92564.1 305 YGLKEVIEMLRNNIAAMVVISDNINMSRIEK 335
                     7***********************9999887 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0029       6.6       6      63 ..      14      71 ..      10      89 .. 0.86
   2 ?    5.2   0.1    0.0082        18       5      64 ..     272     334 ..     268     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0029
                    HHHHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTEEEEEE CS
  Phage_integr_3  6 deevrealeelkekseevelvykllvfsGiRLkevlklLreyDpekliveddiarYpi 63
                      ++r++leel+++s +   +  + +  G  L+ev++ Lre   + + +++d++r ++
      AJA92564.1 14 MYKIRKTLEELTQQSGRGTELITVYIPKGQQLHEVMTQLREEQGTADNIKSDLTRTHV 71
                    568***********9999999********************99999999999888776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0082
                     -HHHHHHHHHHHHHH-HHHHHHHH.HHHHH--...-HHHHHHHHHS..GGG-EEETTEEEEEEE CS
  Phage_integr_3   5 tdeevrealeelkekseevelvyk.llvfsGi...RLkevlklLreyDpekliveddiarYpia 64 
                     + +++   ++ ++ek + +e +++ +   sG+    Lkev+++Lr+  ++  +++d+i    i+
      AJA92564.1 272 KCSDILSNFRMVEEK-KIIEKLFQeINTNSGLgsyGLKEVIEMLRNNIAAMVVISDNINMSRIE 334
                     668899999999997.77777776377899984446**********777777888888766555 PP

>> zf-3CxxC  Zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7     0.088     2e+02      35      49 ..     326     340 ..     268     342 .. 0.75
   2 ?    4.4   3.8     0.023        51      36      64 ..     327     353 ..     307     399 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.088
    zf-3CxxC  35 gevkvrlfgQrCkkC 49 
                  ++++  ++++Ck+C
  AJA92564.1 326 DNINMSRIEKKCKRC 340
                 567888888888888 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.023
    zf-3CxxC  36 evkvrlfgQrCkkCkkleepkldeeevek 64 
                 ++++  ++++Ck+C+++ee  +++ +  +
  AJA92564.1 327 NINMSRIEKKCKRCSHVEEELIEQGK--R 353
                 56666777777777555444444322..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1370  (0.0764125); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2989.99
//
Query:       AJA92565.1  [L=740]
Description: PF10102 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-09   36.4   0.3      2e-08   34.7   0.3    2.0  1  DUF2341   Domain of unknown function (DUF2341)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   1.1e-12     2e-08       1      51 [.      71     122 ..      71     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.1e-12
     DUF2341   1 dgsdiRfvdsdgtt.LpywieswdantekaliWvkvpsipangnktikiyyg 51 
                 dg+di f+ +dgtt L++ ie ++++t++ ++Wvk+p++ a++ ++i+iyy 
  AJA92565.1  71 DGTDIIFTANDGTTrLAHEIERYNTSTGEVIAWVKIPTLSASTGTDIYIYYK 122
                 799************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 5184.19
//
Query:       AJA92566.1  [L=81]
Description: hypothetical protein T478_0590 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 610.44
//
Query:       AJA92567.1  [L=247]
Description: ribosomal protein L2, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-34  117.3   2.2    8.3e-34  116.5   2.2    1.4  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
      4e-06   26.7   0.0    1.3e-05   25.0   0.0    2.0  1  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain
  ------ inclusion threshold ------
       0.15   11.9   0.1       0.33   10.8   0.1    1.5  1  NIL             NIL domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   2.2   1.4e-37   8.3e-34       3     120 ..      92     220 ..      91     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 1.4e-37
                     SS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT----STTHHHHT.....TB CS
  Ribosomal_L2_C   3 GnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklgkAgrkrwl.....gr 92 
                     Gnv+ ++nip Gtiv+n+e++ g+gg+++++aG+ a+v+++ ++ v++kl Sg+ +k++ ++rA+iG++++g+ +++++++Ag k+++     ++
      AJA92567.1  92 GNVISIQNIPDGTIVCNVEKQFGDGGSFIKTAGADATVFSHADDGVILKLASGKFKKLNPKNRAMIGTLAGGGVEDRPFMRAGVKMMRfkskgQK 186
                     9****************************************99******************************************99999**99* PP

                     S----SSSS-TTTSSS--SS....SS..--SSSS CS
  Ribosomal_L2_C  93 rpkvrGvamnpvdHphGGGe....Gk..tksrka 120
                     +p vrGva  ++ HphGGG+    G+  t+sr+a
      AJA92567.1 187 YPIVRGVAQAAYVHPHGGGRhqhvGQssTVSRDA 220
                     ********************66665433444555 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   2.3e-09   1.3e-05       1      75 [.      11      81 ..      11      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.3e-09
                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE CS
  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtv 75
                  Gr+   +r+++ ++     +ky+ ++     e+ kg ++++ + +gR  p+  v +edg  ++i ap g kvG+ +
    AJA92567.1 11 GRGGMqFRAAATQKLK--PAKYPSFSL---DEERKGEIIDLVHESGRDVPLSKVRFEDGAISFIPAPLGTKVGQRI 81
                  7888779999888888..889999998...4567899*************************************98 PP

>> NIL  NIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.5e-05      0.33      24      51 ..      83     110 ..      80     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.5e-05
                 HT-EEEEEEEEEEEETTEEEEEEEEEEE CS
         NIL  24 lglevnIlqGsveriqgtpfGqlviels 51 
                 +gl+ +I+ G+v  iq+ p G++v +++
  AJA92567.1  83 FGLNSEIIDGNVISIQNIPDGTIVCNVE 110
                 8999********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1889.88
//
Query:       AJA92568.1  [L=335]
Description: thioredoxin-disulfide reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-55  185.9   1.9    1.1e-54  185.7   1.9    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-24   87.0   6.6    2.1e-21   76.5   1.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      1e-19   70.8   1.3    2.2e-18   66.6   0.1    2.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-05   24.6   2.5    0.00028   20.1   0.1    3.1  4  FAD_binding_2   FAD binding domain
      3e-05   23.4   0.1       0.01   15.1   0.1    2.7  2  Thi4            Thi4 family
    5.4e-05   22.5   0.3       0.17   11.0   0.0    3.2  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00036   19.7   7.8      0.012   14.7   0.0    4.2  5  GIDA            Glucose inhibited division protein A
    0.00043   19.8   2.2     0.0073   15.7   0.2    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
    0.00064   19.1   0.3       0.12   11.6   0.1    2.9  3  FAD_binding_3   FAD binding domain
     0.0015   18.2   7.8       0.11   12.0   0.0    3.7  4  DAO             FAD dependent oxidoreductase
     0.0017   18.4   1.9       0.58   10.1   0.0    3.3  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0019   17.0   2.9      0.016   13.9   0.1    3.2  4  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.019   15.2   0.1       0.07   13.4   0.0    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.027   14.9   0.3       0.13   12.7   0.0    2.1  2  NAD_binding_7   Putative NAD(P)-binding
       0.04   13.6   0.0         11    5.6   0.0    2.6  3  MAF_flag10      Protein of unknown function DUF115
      0.082   11.7   0.4       0.65    8.8   0.1    2.4  3  Trp_halogenase  Tryptophan halogenase
       0.26   10.3   1.0        4.6    6.2   0.1    2.6  3  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.7   1.9     1e-57   1.1e-54       1     291 [.      33     317 ..      33     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 185.7 bits;  conditional E-value: 1e-57
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCCCHCCTCEEEEESCEEEEETE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgielllgeevvkidpgkkkvklek 89 
                  +dv++iG+GpAG++a ++ ++a ++++++   g +++g+ + ++ +++++++ e +          ++ +++n+ i    +  vv++d+ +k +k+ +
   AJA92568.1  33 YDVIIIGAGPAGYTAGIYCSRARHDTLII--SGLLPGGQLMNTTDVENYPGFDEGIMgpdlmltmrKQAERMNTTI---IDDVVVNVDFRAKPFKVLT 125
                  69***********************9999..999*******************99999*99988776666666553...35469************53 PP

                  EECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  90 kkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsa 187
                     g  e++++++++++tG++pr++gi+G+++  gk+v++++++++    +++  i+vvGgG + +E A +l+k++++v+++++rd +       +s+
   AJA92568.1 126 ---G-SEEYEAKAVIVCTGATPRKIGIEGEQTFSGKGVSYCATCDGAFFRNQD--IAVVGGGDTCMEEATFLTKFASKVHIIHRRDAFR------ASK 211
                  ...3.469*****************************************9998..*********************************7......888 PP

                  HHHHH.HHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCT CS
                  xxxxx.xxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 188 aleea.lekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvag 279
                  +++++ l +e++ev++++++++i+g+++     l+ +++++++++++  v+va+G +p+tel+  k +le+de+g+i  +++ +t+v+g++ +GDv  
   AJA92568.1 212 IMQDRaLSNENIEVHWNSVIEDIKGDQKvqqiILKdTKTGENKTLEMGGVFVAIGHEPNTELF--KNQLEMDENGYIIQKQNTETSVKGVFTAGDVH- 306
                  8887615666*****************96655333577777777******************6..89******************************. PP

                  ECCSS--HHHHH CS
                  xxxxxxxxxxxx RF
  Pyr_redox_2 280 gkggpelaqaAv 291
                   ++++++a++A 
   AJA92568.1 307 -DHRYRQAVTAA 317
                  .99999999996 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   2.6e-05     0.028       1      27 [.      36      61 ..      36      73 .. 0.90
   2 !   76.5   1.0     2e-24   2.1e-21     102     305 .]     109     303 ..      86     303 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                 iIiGaGPaG +a+i + +a   d li+
   AJA92568.1 36 IIIGAGPAGYTAGIYCSRARH-DTLII 61
                 8******************99.56777 PP

  == domain 2  score: 76.5 bits;  conditional E-value: 2e-24
  Pyr_redox_3 102 eeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrg 196
                    V +v+  ++ f+v t +e+yeAk vi+ tG    P+k +i+Ge+    + + y    + + +++q+++V+Gg+++ ++ A+ l +  ++V++++r+
   AJA92568.1 109 DVVVNVDFRAKPFKVLTGSEEYEAKAVIVCTGA--TPRKIGIEGEQTfsgKGVSYCATCDGAFFRNQDIAVVGGGDTCMEEATFLTKFASKVHIIHRR 204
                  45889999************************9..**********97644566666667888899********************************* PP

  Pyr_redox_3 197 seiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvk...tedgkkvev.kddvvlatGykpdlsflkkslfeldedgrpvlt 290
                  +  ++++         ++++r    +++e+i+v+ n+ +++ik +++  ++    t++g++ +     v++a+G +p+++++k +++e de+g++ ++
   AJA92568.1 205 DAFRASK---------IMQDRA---LSNENIEVHWNSVIEDIKGDQKVQQIIlkdTKTGENKTLeMGGVFVAIGHEPNTELFK-NQLEMDENGYIIQK 289
                  9766653.........344443...23456888888888888866555555422344444444424567778**********9.888999***99877 PP

  Pyr_redox_3 291 eeteetnvpglflaG 305
                  ++t et v+g+f aG
   AJA92568.1 290 QNT-ETSVKGVFTAG 303
                  665.788******99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.33   3.5e+02       2      28 ..      35      61 ..      34      64 .. 0.83
   2 !   66.6   0.1   2.1e-21   2.2e-18       2      80 ..     175     247 ..     174     250 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.33
                EEEECSSHHHHHHHHHHHHTTSEEEEE CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                v+++G+G  g  ++ + ++ ++++ ++
  AJA92568.1 35 VIIIGAGPAGYTAGIYCSRARHDTLII 61
                89********99999988888777665 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 2.1e-21
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHH.HHTTEEEECSEEEEEEEEETTSEEEEEEET CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqekl.ekngievllntkveeiegsedgvesvklkd 80 
                 ++vvGgG++ +E+A++l+++++kV++++r+d ++      aski+q++  ++++iev++n+++e i+g+++ v+++ lkd
  AJA92568.1 175 IAVVGGGDTCMEEATFLTKFASKVHIIHRRDAFR------ASKIMQDRAlSNENIEVHWNSVIEDIKGDQK-VQQIILKD 247
                 89********************************......******9984555*****************9.9***9986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   2.7e-07   0.00028       1      31 [.      34      64 ..      34      74 .. 0.91
   2 ?    1.7   0.1       0.1   1.1e+02     185     205 ..     125     145 ..      79     191 .. 0.60
   3 ?   -1.8   0.0       1.2   1.2e+03       1      35 [.     174     208 ..     174     211 .. 0.86
   4 ?    0.6   0.0      0.22   2.3e+02     173     401 ..     239     305 ..     190     320 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.7e-07
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                   Dvi+iG+G AG++A++ +++a +++++++  
     AJA92568.1 34 DVIIIGAGPAGYTAGIYCSRARHDTLIISGL 64
                   9**************************9975 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                    TCEEEEEESEEEE-----GG. CS
  FAD_binding_2 185 grevrirakavvlatgGfgra 205
                     + ++++akav++ tg+ +r+
     AJA92568.1 125 TGSEEYEAKAVIVCTGATPRK 145
                    445578999******999983 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                    D+ V+G+G   +  A+ +++   kv ++   ++f+
     AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFASKVHIIHRRDAFR 208
                    899*****999999999999999999998877766 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.22
                    EEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--T CS
  FAD_binding_2 173 rvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLite 268
                    +v  +++++ ++g++ +++  +v +                                                                       
     AJA92568.1 239 KVQQIILKDTKTGENKTLEMGGVFV----------------------------------------------------------------------- 263
                    4444444433333333333333333....................................................................... PP

                    HHHHTT-EEE-TTSSBTHGGGS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE....... CS
  FAD_binding_2 269 alrgeGgilvdkdGrrFmnelasrdvvsrailekeiaeggseanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavk 364
                                                                                                                 a+ 
     AJA92568.1 264 ---------------------------------------------------------------------------------------------AIG 266
                    .............................................................................................333 PP

                    EEEEEEEES-EEEBETTSBE..STTEEESSBTEEE-STC CS
  FAD_binding_2 365 vvpaqhytmgGvetdengrv..ldadgqpipGLYAaGev 401
                      p +  +   +e deng    ++++++ ++G + aG v
     AJA92568.1 267 HEPNTELFKNQLEMDENGYIiqKQNTETSVKGVFTAGDV 305
                    333333333334455555554445555566666666665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   9.9e-06      0.01      17      47 ..      32      61 ..      27      73 .. 0.78
   2 !    5.3   0.0    0.0096        10      15      52 ..     170     206 ..     163     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.9e-06
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEE CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvail 47
                  Dv+i+GaG++G ta+ y +++    ++i+
  AJA92568.1 32 SYDVIIIGAGPAGYTAGIYCSRA-RHDTLII 61
                57*****************9998.4455554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0096
                 HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS CS
        Thi4  15 yaesDvvivGaGssGLtaayylakkpdlkvailersvs 52 
                 + ++D+++vG+G + +  a  l+k    kv i+ r+ +
  AJA92568.1 170 FRNQDIAVVGGGDTCMEEATFLTKF-ASKVHIIHRRDA 206
                 5679*******************99.899999998755 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   1.4e+02       2      13 ..      32      43 ..      31      58 .. 0.85
   2 !   11.0   0.0   0.00016      0.17     121     231 ..     113     210 ..      95     221 .. 0.67
   3 !    6.6   0.0    0.0035       3.7     286     341 ..     214     268 ..     210     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
  K_oxygenase  2 ilDligiGiGps 13
                  +D+i+iG+Gp+
   AJA92568.1 32 SYDVIIIGAGPA 43
                 69*********7 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
  K_oxygenase 121 evepdeeeeeelltveskdaegeeeelearnlvlgvGtepk.iPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkv 217
                  +v+++++     ++v +    g +ee+ea+++++ +G +p  i    e++ + + v   ++      +  ++++iaVvG+G +  e +  l++ ++  
   AJA92568.1 113 NVDFRAK----PFKVLT----G-SEEYEAKAVIVCTGATPRkIGIEGEQTFSGKGVSYCATCDG---AFFRNQDIAVVGGGDTCMEEATFLTKFAS-- 196
                  4444443....366665....3.68999*********776414333333332233333333333...358999*************9988877655.. PP

  K_oxygenase 218 elklvtrsealepl 231
                  +++++ r++a++++
   AJA92568.1 197 KVHIIHRRDAFRAS 210
                  9999***9999865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0035
  K_oxygenase 286 eqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATGYr 341
                  +++  ++e++++  n+ +e+++ ++k   ++ l+++++ge++tle+  v++A G +
   AJA92568.1 214 QDRALSNENIEVHWNSVIEDIKGDQK-VQQIILKDTKTGENKTLEMGGVFVAIGHE 268
                  55666778899999999999999996.899999****************9999975 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.1e-05     0.012       1      28 [.      34      61 ..      34      81 .. 0.83
   2 ?    3.8   0.0     0.024        26     109     167 ..     102     157 ..      92     166 .. 0.70
   3 ?    0.5   0.1      0.23   2.4e+02       1      32 [.     174     204 ..     174     212 .. 0.86
   4 ?    1.3   0.1      0.14   1.5e+02      96     142 ..     208     254 ..     202     267 .. 0.78
   5 ?   -0.5   0.0      0.47   4.9e+02     349     390 ..     291     333 ..     279     335 .] 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                dvi+iG+G AG+ A + ++r+ +++l+i
  AJA92568.1 34 DVIIIGAGPAGYTAGIYCSRARHDTLII 61
                8************************998 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                 TTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSC CS
        GIDA 109 pnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGr 167
                  n +ii + v +++ + k  k  v++  e+++akav++ tG+    ki i  +++ +G+
  AJA92568.1 102 MNTTIIDDVVVNVDFRAKPFK--VLTGSEEYEAKAVIVCTGA-TPRKIGIEGEQTFSGK 157
                 567788888888877444444..34566899**********9.7777777666666555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.23
                 CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
        GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                 d+ V+GgG   +e A  + +   kv +i h+ 
  AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFASKVHII-HRR 204
                 799*****************99999998.444 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.14
                 HHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEEC CS
        GIDA  96 lyskevteklenepnleiieeeveeliveekkvkgvvtedgetikak 142
                 + sk ++++  +++n+e+  ++v e i  ++kv+ ++++d +t ++k
  AJA92568.1 208 RASKIMQDRALSNENIEVHWNSVIEDIKGDQKVQQIILKDTKTGENK 254
                 4578899999999*****877765544779******99998876665 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.47
                 TSBBSSSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHHCT CS
        GIDA 349 tLetkkvkgLflAGqinGteGY...eEaaaqGllAGinaarkakg 390
                 + et+ vkg+f+AG++     Y   + aa+ G++++i + +++ +
  AJA92568.1 291 NTETS-VKGVFTAGDVHDHR-YrqaVTAAGFGCMSAIDVDKYLSE 333
                 55665.9999****999887.611134555888888888777765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   6.9e-06    0.0073       1      36 [.      34      68 ..      34      76 .. 0.86
   2 ?   -2.1   0.0       1.8   1.9e+03     105     144 ..     102     140 ..      81     141 .. 0.67
   3 ?    2.8   0.0     0.058        61      89     133 ..     209     255 ..     174     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.9e-06
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGG 36
                  Dv+++G+gpaG++A i + ra   +l+++     GG
    AJA92568.1 34 DVIIIGAGPAGYTAGIYCSRARHDTLIIS-GLLPGG 68
                  9************************9996.345555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
  FAD_oxidored 105 llntrlveveke.gkriesvtveskegrktirAkvfiDATg 144
                   +  t +++v+++ + r +  +v +  g ++++Ak +i +Tg
    AJA92568.1 102 MNTTIIDDVVVNvDFRAKPFKVLT--GSEEYEAKAVIVCTG 140
                   444555566665445556666654..789999999999997 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.058
  FAD_oxidored  89 akavlee.mlaeagvtvllntrlvevekegkriesvtveske.g.rkt 133
                   a +++++  l++++++v  n+++++++ ++ +++++++++ + g +kt
    AJA92568.1 209 ASKIMQDrALSNENIEVHWNSVIEDIKGDQ-KVQQIILKDTKtGeNKT 255
                   4455554156889**************985.9******9988765555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00011      0.12       2      23 ..      33      54 ..      32      63 .. 0.80
   2 ?    3.7   0.0     0.028        30       3      35 ..     174     206 ..     172     225 .. 0.86
   3 ?    0.4   0.0      0.29   3.1e+02     108     154 ..     210     257 ..     206     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                   EEEEEE--SHHHHHHHHHHHHT CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea 23
                   +dV+I+GaGpaG +++   s+a
     AJA92568.1 33 YDVIIIGAGPAGYTAGIYCSRA 54
                   69*************9887776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.028
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                    d+++VG+G + +  a++L++   +v+++ +r+ 
     AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFASKVHIIHRRDA 206
                    789******************999****99875 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.29
                    HHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
  FAD_binding_3 108 eriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvr 154
                     +i+ ++a +   ++v+++  +e ++ d++  +  ++d +tge++t++
     AJA92568.1 210 SKIMQDRALSNEnIEVHWNSVIEDIKGDQKVQQIILKDTKTGENKTLE 257
                    6899999988888**********99999999999999*******9985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.5    0.0031       3.3       1      26 [.      34      61 ..      34      76 .. 0.81
   2 !   12.0   0.0   0.00011      0.11     147     207 ..      90     146 ..      81     168 .. 0.75
   3 ?   -0.4   0.2      0.65   6.9e+02       1      29 [.     174     204 ..     174     215 .. 0.73
   4 ?    0.2   0.0      0.41   4.4e+02     154     206 ..     215     272 ..     202     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0031
                EEEEECTSHHHHHHHHHHHHTT..EEEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtll 26
                dv+iiG+G +G ++  + +r+   ++++
  AJA92568.1 34 DVIIIGAGPAGYTAGIYCSRARhdTLII 61
                9*****************9765556665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll 207
                  l+  ++++ae+   +i+    v++++ +  k  +v   t  +e  +a+av++++Ga  +++
  AJA92568.1  90 DLMLTMRKQAERMNTTIIDD-VVVNVDFR-AKPFKV--LTGsEE-YEAKAVIVCTGATPRKI 146
                 58999***************.99999554.356777..553233.46799******976644 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.65
                 EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
         DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29 
                 d++++GGG + +  A +L++    V ++ ++
  AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFAskVHIIHRR 204
                 8*******88777777776642367777777 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.41
                 HHH.HHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE..EEE--GGGHH.H CS
         DAO 154 raa.ealGveilegtevtgleeedgkvwgve.rttp.gendaada..vVnaaGawsd.l 206
                 ++a  +  +e++ ++ ++++ + d kv+++  ++t+ gen++ +   v +a G+  + +
  AJA92568.1 215 DRAlSNENIEVHWNSVIEDI-KGDQKVQQIIlKDTKtGENKTLEMggVFVAIGHEPNtE 272
                 55414556999999999999.44678888889777779884323355999999876553 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1       0.2   2.1e+02       2      12 ..      37      47 ..      36      60 .. 0.84
   2 !   10.1   0.0   0.00055      0.58     109     155 ..      97     141 ..      90     142 .. 0.85
   3 ?    4.1   0.0      0.04        42     110     155 ..     216     267 ..     206     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
  NAD_binding_9  2 ivGaGprGlav 12
                   i+GaGp+G ++
     AJA92568.1 37 IIGAGPAGYTA 47
                   9*******876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00055
  NAD_binding_9 109 arlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                    +++ e+++ +++ + vv+++ ra+ ++v l++ ++++a+aV++++G 
     AJA92568.1  97 KQA-ERMNTTIIDDVVVNVDFRAKPFKV-LTGSEEYEAKAVIVCTGA 141
                    444.5689999**************998.889999**********96 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.04
  NAD_binding_9 110 rlpegvtvevh.raevvdleeradgqavlladg.....aslaadaVvLAlGh 155
                    r+ ++ ++evh ++ ++d++ +++ q+++l+d      ++l++  V++A+Gh
     AJA92568.1 216 RALSNENIEVHwNSVIEDIKGDQKVQQIILKDTktgenKTLEMGGVFVAIGH 267
                    55556688888466667899999998888854412222469**********9 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   1.6e-05     0.016       1      29 [.      33      61 ..      33      67 .. 0.93
   2 ?    0.7   0.0      0.16   1.7e+02     132     164 ..     111     141 ..      90     151 .. 0.71
   3 ?   -0.3   0.0      0.31   3.3e+02       2      35 ..     174     207 ..     173     214 .. 0.85
   4 ?   -1.6   0.0      0.77   8.1e+02     117     151 ..     216     249 ..     205     268 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlll 29
                 +dvi+iG+G+AG  a i ++++ +++l++
   AJA92568.1 33 YDVIIIGAGPAGYTAGIYCSRARHDTLII 61
                 59*******************99999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.16
                  EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
  HI0933_like 132 vksvekeedgkfrvktkseeeleadklvlAtGG 164
                  v +v+ +++  f+v t ++ee+ea+++++ tG 
   AJA92568.1 111 VVNVDFRAKP-FKVLT-GSEEYEAKAVIVCTGA 141
                  4455444444.88888.9************996 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.31
                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
  HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                  d++v+GgG   +  A  + k  ++V ++ + +++
   AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFASKVHIIHRRDAF 207
                  89**********9999999999999999887655 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.77
                  HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTE CS
  HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktksee 151
                  ++l++++++++ ++ +++++ +++   ++ +k+++
   AJA92568.1 216 RALSNENIEVHWNSVIEDIKGDQKV-QQIILKDTK 249
                  5678889999999999999554433.444443222 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.7e-05      0.07       1      27 [.      37      62 ..      37      98 .. 0.84
   2 ?   -1.5   0.0       2.9     3e+03       1      29 [.     177     205 ..     177     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-05
                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                   I+GaG +G +a  ++++a++d l++ +
     AJA92568.1 37 IIGAGPAGYTAGIYCSRARHDTLII-S 62
                   9********************9998.4 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                    +vG+G + +  A +L+k   +v+++ +rd
     AJA92568.1 177 VVGGGDTCMEEATFLTKFASKVHIIHRRD 205
                    89999888888888888777787776665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.3   1.4e+03       9      22 ..      34      47 ..      31     139 .. 0.79
   2 ?   12.7   0.0   0.00012      0.13       5      60 ..     170     235 ..     169     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
  NAD_binding_7  9 kvlvvGgGevAark 22
                    v+++G+G+ +++ 
     AJA92568.1 34 DVIIIGAGPAGYTA 47
                   58899999988765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev...keele..........elvklaeeelekdle 60 
                    ++++ + vvGgG+  ++ +  l ++  kv+++  +    +   +          e+++++ + + +d++
     AJA92568.1 170 FRNQDIAVVGGGDTCMEEATFLTKFASKVHIIHRRDafrA---SkimqdralsnENIEVHWNSVIEDIK 235
                    578999**************************99953330...23443444444444444333333333 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.016        17      10      35 ..      17      42 ..      10      62 .. 0.85
   2 ?    5.6   0.0     0.011        11      67     150 ..     105     191 ..     102     201 .. 0.78
   3 ?    0.9   0.0       0.3   3.2e+02      23      61 ..     171     208 ..     166     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
  MAF_flag10 10 nlkpslkellnkfkgnkpaiivgaGP 35
                n +p++ ++ +k k + ++ii+gaGP
  AJA92568.1 17 NDEPKTPDFPKKTKTSYDVIIIGAGP 42
                5567778888877778********** PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
  MAF_flag10  67 gIkPDivvslDpqeasyevfkeaekkgdiplvfasgvnpellkkykgpkiflvtgstqa....lelleeekne.ilfgGgsvantaldl 150
                  I+ D+vv++D     ++v+ + e+ +   ++ ++g+ p+++  ++g++ f+ +g+ ++     +++++++ + +++gG ++ + a +l
  AJA92568.1 105 TIIDDVVVNVDFRAKPFKVLTGSEEYEAKAVIVCTGATPRKI-GIEGEQTFSGKGVSYCatcdGAFFRNQD-IaVVGGGDTCMEEATFL 191
                 6888**************999999998888999999999999.7899999999998888887544553333.34778888877776665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.3
  MAF_flag10  23 kgnkpaiivgaGPSLeknlellkelrdkaviiaadtalk 61 
                 ++ +++ +vg+G +  ++  +l + ++k+ ii    a++
  AJA92568.1 171 RN-QDIAVVGGGDTCMEEATFLTKFASKVHIIHRRDAFR 208
                 34.899999999999999999999999999986655554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00062      0.65       1      25 [.      34      58 ..      34      64 .. 0.86
   2 ?   -1.1   0.0       0.6   6.3e+02     160     210 ..      95     142 ..      92     154 .. 0.77
   3 ?   -1.2   0.0      0.66     7e+02       1      29 [.     174     199 ..     174     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00062
                    EEEEE--SHHHHHHHHHHHHHTTTS CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgk 25
                    +++i+G+G+aG++a +++++a +++
      AJA92568.1 34 DVIIIGAGPAGYTAGIYCSRARHDT 58
                    699****************998654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                     HHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
  Trp_halogenase 160 LrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                     +r+ ae+ + t++++ vv+v+ +++ + + l  +  +e+ea  +i c+G  
      AJA92568.1  95 MRKQAERMNTTIIDDVVVNVDFRAKPF-KVL--TGSEEYEAKAVIVCTGAT 142
                     789999999999999999999988655.333..345668888899999875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.66
                     EEEEE--SHHHHHHHHHHHHHTTTSSEEE CS
  Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevt 29 
                     +i +vGGG      A+ l k  ++   v 
      AJA92568.1 174 DIAVVGGGDTCMEEATFLTKFASK---VH 199
                     699******999999999998833...33 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0043       4.6       1      13 [.      34      46 ..      34      74 .. 0.82
   2 ?    1.6   0.0      0.11   1.1e+02     112     160 ..     111     159 ..      91     165 .. 0.75
   3 ?   -1.2   0.0      0.74   7.8e+02       1      30 [.     174     201 ..     174     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0043
  Lycopene_cycl  1 DvvviGaGpAgls 13
                   Dv++iGaGpAg  
     AJA92568.1 34 DVIIIGAGPAGYT 46
                   9**********76 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
  Lycopene_cycl 112 veeeea.geslvvleggrkirarlvvdarglaslkkarrlglQtfyGvev 160
                    v+++++ ++   vl g ++ +a++v++ +g a ++k    g Qtf G  v
     AJA92568.1 111 VVNVDFrAKPFKVLTGSEEYEAKAVIVCTG-ATPRKIGIEGEQTFSGKGV 159
                    4444445677789999**************.7777777788999998766 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.74
  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                    D++v+G+G   +  A  l   k + kv +i
     AJA92568.1 174 DIAVVGGGDTCMEEATFL--TKFASKVHII 201
                    899999999999888888..6666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2185.83
//
Query:       AJA92569.1  [L=109]
Description: nitrogen regulatory protein P-II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-12   45.9   0.4      8e-12   45.7   0.4    1.1  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.4   4.4e-16     8e-12       2     102 .]       5     102 ..       4     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 4.4e-16
                 EEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCE.EEECTTEEEEEE.EEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEEEE CS
        P-II   2 eaiirpekleevkeaLekagvkgltvtevkGrGkqkgh.telyrgaeyeve.llpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveevir 98 
                 e+i+  +++ ++ e  +++++ glt+t+v+GrG++    + +++g+e+ v  + +k ++++v+++++ ek+v++i ++ +      GkiF++++ ++i 
  AJA92569.1   5 EIILSENDVMSISEGFKQIDIGGLTITKVRGRGEKTAPeILVHKGSEVFVPhFGDKYRIMVVIPESKEEKAVNIIKNNSRG-----GKIFISQLLRAID 98 
                 68999999*************************98754256678888877669*******************988776665.....67*********** PP

                 TTTT CS
        P-II  99 irtg 102
                 i+tg
  AJA92569.1  99 IKTG 102
                 ***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 921.89
//
Query:       AJA92570.1  [L=161]
Description: ribosomal L18p/L5e family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-15   57.5   2.4    5.1e-13   49.3   0.6    2.5  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    0.00069   20.0   0.4      0.001   19.4   0.4    1.2  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.6   5.7e-17   5.1e-13       7     105 ..       7      98 ..       2     107 .. 0.88
   2 !    8.3   0.1   0.00023       2.1     143     162 ..     107     126 ..      93     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 5.7e-17
  Ribosomal_L5e   7 frrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnyaaaYatglllarrllkklgl 102
                    ++r r  kt+Y++rk +++  +         + V vtn+++ +qi++ +i+gdkvla+a+s+ l k g k + +n  a+Y+tg++ ++++l++  +
     AJA92570.1   7 LQRIRSEKTNYRKRKIMLMGKR-------DFITVNVTNENTQVQIVKPEIKGDKVLASAHSRFLLKDGWKGSRKNIPASYLTGYMAGKKALSNGVT 95 
                    5788999*******99988543.......3578**********************************************************98877 PP

  Ribosomal_L5e 103 dki 105
                    d i
     AJA92570.1  96 DAI 98 
                    766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00023
  Ribosomal_L5e 143 gakvfgalkgavdgglsiph 162
                    + ++ +alkg++d+g+++p 
     AJA92570.1 107 TDRMAAALKGVIDAGVKVPA 126
                    46889*************95 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.4   1.1e-07     0.001      15     115 ..      19     123 ..       5     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                     TTT--TTSSS-EEEEEE-SS-EEEEEE-TT..T--EEEEECS-SCCCT...S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTSSS-CHHHH CS
  Ribosomal_L18p  15 rkklsgtaerprlvvfrsnrhiyaQviddv..kgktlasastlekelk...lkstknkeaakkvgeliAerakekgiekvvfDrggykYhGrvaa 104
                     ++k++ + +r  ++v  +n++  +Q++      +k+lasa +     k   + s+kn+ a+   g +  ++a+ +g+++++   g  +Y  r+aa
      AJA92570.1  19 KRKIMLMGKRDFITVNVTNENTQVQIVKPEikGDKVLASAHSRFLL-KdgwKGSRKNIPASYLTGYMAGKKALSNGVTDAILYSGTRRYTDRMAA 112
                     566777778999***************8742257899999884332.2244699999*************************************9 PP

                     HHHHHHCTSSB CS
  Ribosomal_L18p 105 lAdaaReaGlk 115
                       +++ +aG+k
      AJA92570.1 113 ALKGVIDAGVK 123
                     88888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1203.94
//
Query:       AJA92571.1  [L=153]
Description: hypothetical protein T478_0354 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.4   1.2        5.8    6.7   0.6    2.1  2  TK        Thymidine kinase


Domain annotation for each model (and alignments):
>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0013        24      90     128 ..      27      64 ..      23      79 .. 0.72
   2 ?    6.7   0.6   0.00032       5.8      84     118 ..      95     130 ..      70     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0013
          TK  90 eqdivelseklanegkivivagLdtdFerklFenilkll 128
                 ++ ++e+ +k ++e+  +iv +L++     +F n +kl+
  AJA92571.1  27 KKRMTEFFSKNDEEKAEIIVNALNAGP-TIPFPNFSKLF 64 
                 567889999***************863.34555555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00032
          TK  84 DEaqFfe.qdivelseklanegkivivagLdtdFer 118
                 D    f+ + i e+  +++n++k+v++a++++ F r
  AJA92571.1  95 DKIILFNlDAIFEIFLQVDNQKKQVLIASIKAVFDR 130
                 666678878999*******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1158.08
//
Query:       AJA92572.1  [L=425]
Description: hypothetical protein T478_1425 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00088   19.5   0.1        2.1    8.6   0.0    4.1  3  NPCBM_assoc    NPCBM-associated, NEW3 domain of alpha-galacto
     0.0015   18.7   1.0       0.16   12.2   0.3    3.4  4  FixG_C         IG-like fold at C-terminal of FixG, putative o
     0.0058   15.4   0.0     0.0092   14.7   0.0    1.2  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
     0.0067   16.7   2.7        2.9    8.2   0.9    2.5  2  DUF11          Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.034   14.4   8.0        4.2    7.7   4.6    3.8  3  CARDB          CARDB
      0.046   14.4   0.1       0.14   12.9   0.1    1.8  1  Sec23_BS       Sec23/Sec24 beta-sandwich domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00071       2.1       5      77 ..      52     129 ..      47     131 .. 0.79
   2 ?    4.1   0.2     0.018        54       7      29 ..     170     192 ..     168     253 .. 0.84
   3 ?    0.3   0.0      0.28   8.2e+02      41      78 ..     325     362 ..     321     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00071
  NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWt.....vvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                  + v +t+ ++n gt+ +t+++ +lslP+  +      v++  ++ ++  +G t+  t+ V ++++a   dy  t+ ++
   AJA92572.1  52 KNVPFTVIMSNVGTQDITGIKGKLSLPAAYQspsgrGVAMMADNDQKASAGNTFALTFFVDVSDKAPIKDYSGTIDLT 129
                  56789**********************999864444455555555589999999999999999999998887666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
  NPCBM_assoc   7 vtltltvtndgtaaatnvslsls 29 
                  + + ++++n g+a++ nv + l+
   AJA92572.1 170 NDVVIEISNAGSAPLNNVDIVLQ 192
                  56788999999999999998776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.28
  NPCBM_assoc  41 pasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                  ++ +++++p+  v +++ +       +G++++t+++r+
   AJA92572.1 325 TQYIDEIEPDSPVPFNIPIDFEGVSLTGEHDITIEVRY 362
                  566778899999999999999999999*********97 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1     3e+03      64      87 ..      40      62 ..      25      72 .. 0.69
   2 ?    1.2   0.0      0.13     4e+02      67     102 ..      95     131 ..      79     148 .. 0.63
   3 !   12.2   0.3   5.2e-05      0.16      33     117 ..     185     271 ..     164     273 .. 0.86
   4 ?    0.7   0.0      0.19   5.7e+02      70     107 ..     330     369 ..     297     378 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                .S--EEEE-TT-EEEEEEEEEE-G CS
      FixG_C 64 raekeitvapgekrkvpvfvrvpa 87
                 + ++i+vapg  ++vp++v +  
  AJA92572.1 40 TEGNKIEVAPGD-KNVPFTVIMSN 62
                456889999985.57888887765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                 -EEEE-TT-EEEEEEEEEE-GGG.-SSSEE.EEEEEEE CS
      FixG_C  67 keitvapgekrkvpvfvrvpaea.lkkkst.pitfkvt 102
                 +  +  +g++  +++fv v  +a +k + + +i ++ +
  AJA92572.1  95 NDQKASAGNTFALTFFVDVSDKApIK-DYSgTIDLTFS 131
                 5566789999*********8888533.22224444443 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 5.2e-05
                 EEEEEEEEE-SSS-EEEEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEEEEEG.GGTEEEEEEEEEE CS
      FixG_C  33 NsYtlkilNktekprrytlsveglpglelagraekeitvapgekrkvpvfvrvpaealkkkst.pitfkvtdd.deketverksrFv 117
                 N   + ++N +++ ++   sv++l+++ +++ + +  t++p++++++ + v vp+  ++++ + p+t+  +d   e etv+r + F+
  AJA92572.1 185 NNVDIVLQNDQTSVASTSSSVTNLENVIFDQTHWDVGTIPPQSSVTFSLKVFVPETVKNEPLHlPMTISYYDAhGELETVTRVTDFY 271
                 6667778999999999999999999999977778999********************9999999******96547778899999996 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.19
                 EE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE..EG.GGT CS
      FixG_C  70 tvapgekrkvpvfvrvpaealkkkstpitfkvt..dd.dek 107
                 +++p++ + + + +  +  +   ++++it++v+  d+  e+
  AJA92572.1 330 EIEPDSPVPFNIPIDFEGVS-LTGEHDITIEVRykDSmREE 369
                 56666666666666666665.45688999999853332333 PP

>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-06    0.0092     107     173 ..     145     212 ..     132     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-06
                    SEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET..SS-BEEEEETSSTTHHHHHHHH CS
  EPSP_synthase 107 gevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg..lklkgveikaevsSqqvtslll 173
                    + + LtGd  ++ RPi+  l++++++++ ie+++  ++apl+     l+  +++++++ sS++  ++++
     AJA92572.1 145 FTFKLTGDSIVNLRPISGALTSITNNDVVIEISNA-GSAPLNNVDivLQNDQTSVASTSSSVTNLENVI 212
                    6789***************************8888.9***98555788889999999999998766665 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0017         5       9      44 ..      46      82 ..      37     120 .. 0.73
   2 !    8.2   0.9   0.00098       2.9      17      84 ..     171     243 ..     161     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
       DUF11  9 evrpGd.tvtytltvtNtgpasangvvvtDtlPagla 44
                ev+pGd +v +t++++N g+++ +g++ +  lPa+ +
  AJA92572.1 46 EVAPGDkNVPFTVIMSNVGTQDITGIKGKLSLPAAYQ 82
                899***89**************999887777776655 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00098
       DUF11  17 tytltvtNtgpasangvvv..tDtlPaglayvsvsas....qgtasaltsv..gsLeagesatlsftvrvtrtaas 84 
                 ++++  +N g a++n+v +  +     +++  s s+s    ++++  +t    g++++ +s t+s++v v+ t ++
  AJA92572.1 171 DVVIEISNAGSAPLNNVDIvlQN---DQTSVASTSSSvtnlENVIFDQTHWdvGTIPPQSSVTFSLKVFVPETVKN 243
                 5789999*******888551132...455555555555566444433333355****************9999876 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.16   4.9e+02      19      44 ..      52      77 ..      40     158 .. 0.76
   2 ?    7.7   4.6    0.0014       4.2      14      58 ..     163     209 ..     152     252 .. 0.76
   3 ?    4.1   0.0     0.018        55      22      92 ..     293     368 ..     268     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.16
                SEEEEEEEEEE-SSS-EEEEEEEEEE CS
       CARDB 19 eentitvtvkNqGtaasgatkvalyl 44
                +++ +tv  +N Gt++ + +k +l l
  AJA92572.1 52 KNVPFTVIMSNVGTQDITGIKGKLSL 77
                66777777888888877777766654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0014
                 EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE..EEEEESEE- CS
       CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelv..gtvtvpsLa 58 
                 +++  ++n + ++++N G+a   ++ + l  d+++v  ++++v++L+
  AJA92572.1 163 ALTSITNNDVVIEISNAGSAPLNNVDIVLQNDQTSVasTSSSVTNLE 209
                 667789******************************87666775554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.018
                 EEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT-SS-- CS
       CARDB  22 titvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..ategevtltvvvDpdnevaE 92 
                 t+  ++ N+G+ +     v+l + g+++   +t+++ ++++++ +  ++ +  e    +ge+++t+ v  +++  E
  AJA92572.1 293 TVIGEILNEGNSDGLFGFVTLKARGDSNikeSTQYIDEIEPDSPVPFNIPIDFEgvSLTGEHDITIEVRYKDSMRE 368
                 5555789999999888888899988888889***********9988888877778888899999988877777666 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.6e-05      0.14      29      91 ..     205     270 ..     190     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
                 BESSEESECSESEEEEEEEETT--EEEEEEE..SSBTCTTSEEEEEEEEEEEETTSE..EEEEEEEE CS
    Sec23_BS  29 vsekeiGeggtsewklcsldpdstlavyfdi..deklksgkqayiQfatlYthssge..rrlRVttv 91 
                 v++ e  + + ++w+++++ p+s++++ +++    +  +++ +++ + ++Y +++ge  + +RVt +
  AJA92572.1 205 VTNLENVIFDQTHWDVGTIPPQSSVTFSLKVfvP-ETVKNEPLHLPMTISYYDAHGEleTVTRVTDF 270
                 3333444566778******************864.34557999999999999999862256788866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3212.36
//
Query:       AJA92573.1  [L=137]
Description: translation elongation factor IF5A [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-06   27.0   2.3    5.1e-06   26.5   2.3    1.2  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
  ------ inclusion threshold ------
      0.016   15.2   0.3        0.3   11.1   0.0    2.7  3  EFP_N     Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   2.3   5.6e-10   5.1e-06       2      69 .]      75     135 ..      74     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.6e-10
                 -EEEEEEEEEE-SS.EEEEEETT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
      eIF-5a   2 VkrkeyqLidIqdDgflsLmdddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                 ++++  q+i+ ++   ++ m  dget+e ++++   +++++ +k+e+g+d  ++++++mG+ ki+++K
  AJA92573.1  75 IDKRVGQIISMTGS-EIQVM--DGETFETVDIQ--MVDEEVDGKLEQGQD--IEYWNVMGRTKIMRIK 135
                 77888899999877.77777..59999999999..99*************..**************98 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.4e-05       0.3      15      33 ..      26      44 ..      24      48 .. 0.94
   2 ?    0.5   0.0     0.071   6.4e+02       7      22 ..      79      94 ..      76     107 .. 0.59
   3 ?   -1.1   0.0      0.22     2e+03      12      38 ..     109     135 ..     109     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.4e-05
                TEEEEEEEEEEEEETTS-- CS
       EFP_N 15 gklyvVlefehvkpGkGqa 33
                g+++++ e++ +kpGk +a
  AJA92573.1 26 GEPCRISEYDTSKPGKHGA 44
                9***************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.071
                TT-EEEETTEEEEEEE CS
       EFP_N  7 kGlvieidgklyvVle 22
                 G++i + g  ++V++
  AJA92573.1 79 VGQIISMTGSEIQVMD 94
                5666666666555554 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.22
                 EETTEEEEEEEEEEEEETTS--EEEEE CS
       EFP_N  12 eidgklyvVlefehvkpGkGqafvrvk 38 
                 e+dgkl + +++e+    + ++++r+k
  AJA92573.1 109 EVDGKLEQGQDIEYWNVMGRTKIMRIK 135
                 577887777788888877888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 939.15
//
Query:       AJA92574.1  [L=360]
Description: glycosyltransferase, group 1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-24   85.4   0.0    8.1e-24   84.1   0.0    1.7  2  Glycos_transf_1  Glycosyl transferases group 1
    3.5e-22   79.3   0.0    5.9e-22   78.5   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.7e-06   27.2   0.0    9.5e-06   25.9   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.044   13.8   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
       0.09   12.9   0.1       0.16   12.0   0.1    1.4  1  Pox_A22          Poxvirus A22 protein


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.92   3.3e+03      59      96 ..      61      96 ..      56     100 .. 0.54
   2 !   84.1   0.0   2.3e-27   8.1e-24      42     171 ..     209     335 ..     196     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.92
                     HHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEE CS
  Glycos_transf_1 59 ekelkklaeelelsdnviflgevsredleellknadif 96
                     +k++ +l+  +    +v f+ ++s+  le+++kn  +f
       AJA92574.1 61 KKKFNDLINDYDP--DVVFVDRQSHFGLETIKKNIPLF 96
                     4444444444444..55555566666666666555555 PP

  == domain 2  score: 84.1 bits;  conditional E-value: 2.3e-27
                      CCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTT CS
  Glycos_transf_1  42 kqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdg 134
                      k+  p+v++  +G+g+++k++ ++ e++++    ++lg++s +e++ e+l+  d+++lp  ++  ++++ EAma  +p+iasn+gg++e++ ++
       AJA92574.1 209 KK-LPDVHFYWVGDGQYKKQILDKLEKYKN---FHYLGFLSyPEKIREYLTEIDVYALPTGMDTTPLSCREAMAMEKPIIASNVGGIPEMIYHE 298
                      33.6999******99998888777777765...99****99999************************************************** PP

                      TSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
  Glycos_transf_1 135 etGllvkpnnaealaeairklledeelrerlgenark 171
                      +tGllv ++++e++++ i+ l+e+++ + +lg+++r+
       AJA92574.1 299 KTGLLVNEGDHETWINSIKYLIENKDVATKLGKQSRE 335
                      ********************************99986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.7e-25   5.9e-22      22     134 .]     206     322 ..     187     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.7e-25
                      HHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---...THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT-- CS
  Glyco_trans_1_4  22 eavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv...edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv 109
                      e v++l   dv+++ vGdg+ ++ ++ ++++++ ++++++Gf+   e+++e+l + dv+ +P+   +++l+  Eama+++p++a++vggi+e++
       AJA92574.1 206 EVVKKLP--DVHFYWVGDGQyKK-QILDKLEKY-KNFHYLGFLsypEKIREYLTEIDVYALPTgmDTTPLSCREAMAMEKPIIASNVGGIPEMI 295
                      3335555..69********9766.554466555.79*******99778***************9889*************************** PP

                      ..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4 110 ..gengllvppgdpealaeailrLled 134
                        +++gllv++gd e +++ i  L+e+
       AJA92574.1 296 yhEKTGLLVNEGDHETWINSIKYLIEN 322
                      *99*********************986 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.6e-09   9.5e-06      17      91 ..     275     351 ..     264     352 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.6e-09
  Glyco_trans_1_2  17 EaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhraeqll 91 
                      Ea+a+  +++++   g++e++  +k+++l+   d+e ++  i+yl++n + + +++++ re   +++++d  a++++
       AJA92574.1 275 EAMAMEKPIIASNVGGIPEMIYHEKTGLLVNegDHETWINSIKYLIENKDVATKLGKQSRELLSEKFNWDIVARKFI 351
                      9*****************************99**************************************9999986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.044      40     159 ..      40     161 ..      17     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
  Glyco_transf_4  40 vvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye.......krllkarlkplsrllrale 127
                     +vr + +   ++ r+l ++ + +++  l+  ++pDvv +     +  + l   + ++ipl +++ g++        k            +++ l+
      AJA92574.1  40 LVREVDYAKGFPSRNLGDWFSKKKFNDLINDYDPDVVFVDRQSHF--G-LETIK-KNIPLFVYLRGHFWmeqewakK-----------TIYKGLL 119
                     34444444467778889999*****************87775554..3.34444.8*******97777444665542...........2222222 PP

  Glyco_transf_4 128 rrl............lrradrviavSeatadelrerygvppeki 159
                      r+            +r ++ ++ + +++ d ++e  ++p++k 
      AJA92574.1 120 MRTvlnlrqknaekvFRECQGIFMTADYLEDVIKE--HIPNAKT 161
                     22223333333444489999999999999999999..7777766 PP

>> Pox_A22  Poxvirus A22 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.6e-05      0.16      42     124 ..      60     150 ..      40     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
     Pox_A22  42 errvardils.ynvdvvllEkqgr.....rsknvkfiyfikgllyskk..tkvlvvkPvlkggsYrdRKkrsvevFlnlislfgikdilse 124
                  +++ +d+++ y++dvv +++q +      +kn+ +  +++g ++ ++  +k ++ k  l     + R+k++ +vF++   +f + d l++
  AJA92574.1  60 SKKKFNDLINdYDPDVVFVDRQSHfgletIKKNIPLFVYLRGHFWMEQewAKKTIYKGLLMRTVLNLRQKNAEKVFRECQGIFMTADYLED 150
                 56778898877***********853322258999999******998551256667778888899999999999999999999988887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2719.66
//
Query:       AJA92575.1  [L=489]
Description: NAD(P)H-binding protein, PF13460 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-14   53.8   0.1    3.8e-14   53.0   0.1    1.4  1  NAD_binding_10   NAD(P)H-binding
    3.3e-13   49.7   0.1      5e-13   49.1   0.1    1.3  1  NmrA             NmrA-like family
    8.2e-13   48.4   0.1    2.4e-12   46.9   0.1    1.7  2  Epimerase        NAD dependent epimerase/dehydratase family
    7.6e-07   28.4   0.0    1.7e-06   27.3   0.0    1.6  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      4e-05   23.2   0.3    7.1e-05   22.4   0.0    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    0.00086   18.5   0.0     0.0015   17.7   0.0    1.4  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0015   18.1   0.0     0.0035   16.8   0.0    1.7  1  adh_short        short chain dehydrogenase
     0.0071   15.5   0.1      0.016   14.4   0.1    1.6  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
      0.018   14.4   0.0      0.044   13.1   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.045   13.9   0.1       0.17   12.1   0.0    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.056   13.4   0.0      0.095   12.7   0.0    1.4  1  PAC2             PAC2 family
      0.073   13.0   0.0       0.16   11.9   0.0    1.5  1  KR               KR domain
      0.076   11.8   0.1       0.13   11.1   0.1    1.2  1  NRDD             Anaerobic ribonucleoside-triphosphate reduct
      0.084   12.0   0.2       0.27   10.3   0.2    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1     3e-17   3.8e-14       1      99 [.      31     134 ..      31     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3e-17
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-....--TCC.......HHHH..HHHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal....ggggk.......deeg..akniv 82 
                     GAtG +G++l+++l +  g++vta+ R+ ++ +     ++++ v +d+++ ++l +a+kg+++ +  l    g++++       +     a+n +
      AJA92575.1  31 GATGFIGKKLTERLSKT-GYKVTAMSRTLHQNS-----DNVKFVAADALELDTLSNAFKGVETAFYLLhsmeGSKKEweqfadrE--KvqAQNFL 117
                     9****************.5**********9988.....59**********************98888866543333366666433..267***** PP

                     HHHHHCT--EEEEEEET CS
  NAD_binding_10  83 daakeagvkRfvlvsai 99 
                     +aa++agvkR+++++++
      AJA92575.1 118 KAAENAGVKRIIYLGGL 134
                     ************99876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   3.9e-16     5e-13       1     228 [.      27     251 ..      27     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 3.9e-16
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG...........S-HHHHHHHHHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy...........skeiedgkklvdA 88 
                 Ilv+GaTG +Gk +++ l k g+kv a+ R ++++      +  v++v++d+ + + l++a+kgv+++f  + ++           + e  + ++  +A
  AJA92575.1  27 ILVTGATGFIGKKLTERLSKTGYKVTAMSRTLHQN------SDNVKFVAADALELDTLSNAFKGVETAFYLLHSMegskkeweqfaDREKVQAQNFLKA 119
                 9*****************************98764......46699************************999889999999999866666777899** PP

                 HHHHS-SEEEEEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHH CS
        NmrA  89 akeaGvkhfiySslgddndrsnaeepavphfdsKaeieeyvralgipytfvyagffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiG 187
                 a +aGvk++iy +   ++          +h  s +e+ + + + +ip t ++a +  +   +++a l+   ++ p   ++ ++  ++   ++ a+e++ 
  AJA92575.1 120 AENAGVKRIIYLGGLVNESLE-----LSKHMRSRHEVGKILASGTIPVTELRASVIVGAEGGSYAMLRYLVERLPL--MVCPRWVKSTTQPI-AVENVV 210
                 ***********7665555333.....57899*****************************9999998888888887..77777777777888.****** PP

                 HHHHHHHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHHTS- CS
        NmrA 188 afvikilkdprkl.kgkriklagntlsgneivelfekkigkt 228
                  + + ++k+p+++ k+  i  +   ++++++++l++  i+++
  AJA92575.1 211 DYLVGAMKNPSTAgKIFEIGGPD-KMTYEQMMRLYSSIINRN 251
                 ************98999998885.679*********999987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   1.9e-15   2.4e-12       1     114 [.      27     132 ..      27     134 .. 0.92
   2 ?   -2.7   0.0       2.5   3.2e+03     214     241 .]     205     230 ..     200     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.9e-15
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtlnll 99 
                 ilVtGatGfiG+ l+++l + gy+v++++r      +++ +++++v +d ++ + l ++fk  ++++ + l    + + s ++ ++f+++  + ++n l
  AJA92575.1  27 ILVTGATGFIGKKLTERLSKTGYKVTAMSRT----LHQNSDNVKFVAADALELDTLSNAFK--GVETAFYL--LHSMEGSKKEWEQFADREKVQAQNFL 117
                 8******************************....55666777******************..99999999..77788888888889999********* PP

                 HHHHHHTCTEEEEEE CS
   Epimerase 100 eaarkagvkrllfls 114
                 +aa  agvkr+++l+
  AJA92575.1 118 KAAENAGVKRIIYLG 132
                 *************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                 EHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 214 yveDvaeaillvlehvdagdkgeiyniG 241
                  ve v++ ++ +++++++  +g+i+ iG
  AJA92575.1 205 AVENVVDYLVGAMKNPST--AGKIFEIG 230
                 58999**********877..47799998 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.3e-09   1.7e-06       1     114 [.      28     131 ..      28     147 .. 0.79
   2 ?   -4.2   0.0       5.2   6.7e+03     212     230 ..     200     218 ..     190     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-09
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnv 99 
                 +vtG++GF+G++l ++L +++   +v        +++    +++++ k++ +D ++ d+l++a +gv+  ++l   ++  +k  e+  ++  v+  +n 
  AJA92575.1  28 LVTGATGFIGKKLTERLSKTGY--KVT-----AMSRT--LHQNSDNVKFVAADALELDTLSNAFKGVETAFYLLHSMEGSKKEWEQFADREKVQ-AQNF 116
                 69*****************995..333.....23333..34455566699**********************9444444444455555555555.8*** PP

   3Beta_HSD 100 leacvkagvrvlvYt 114
                 l+a+ +agv++++Y 
  AJA92575.1 117 LKAAENAGVKRIIYL 131
                 **************6 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 5.2
   3Beta_HSD 212 lsdrvYvgNvawahilAar 230
                 +++++ v+Nv++  + A++
  AJA92575.1 200 TTQPIAVENVVDYLVGAMK 218
                 5678899999999998877 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.6e-08   7.1e-05       1      43 [.      28      69 ..      28     127 .. 0.84
   2 ?   -2.9   0.1       2.6   3.4e+03     253     285 ..     296     328 ..     286     341 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.6e-08
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCT CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehla 43
                   L+TG +GfiG  l+e+L + gy+v+ + r   + n ++++ +a
     AJA92575.1 28 LVTGATGFIGKKLTERLSKTGYKVTAMSRT-LHQNSDNVKFVA 69
                   9***********************997654.444556655444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                    EECHHCHHCCHHCCCHHHHHH............ CS
  GDP_Man_Dehyd 253 hsvrefvelaflelgktiewegkgeeevgrake 285
                     sv+efv ++++++ + i+   +++   + +++
     AJA92575.1 296 KSVEEFVPVNLKHMTEAIKEAREEQVAFKPIEK 328
                    578888888888888777665444444443333 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.2e-06    0.0015       3      42 ..      27      77 ..      25     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHH CS
  RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaea 42
                   ilvtGa+G +G++L+++l++ g++v+a++r+           ++d  + ++
     AJA92575.1 27 ILVTGATGFIGKKLTERLSKTGYKVTAMSRTlhqnsdnvkfvAADALELDT 77
                   9***************************99976666655555444444444 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.7e-06    0.0035       3      38 ..      27      62 ..      25      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHH CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekle 38
                +lvtGa++ IG+++ ++l k G+kv++++r+  +  
  AJA92575.1 27 ILVTGATGFIGKKLTERLSKTGYKVTAMSRTLHQNS 62
                89*************************999855443 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.2e-05     0.016       1      36 [.      29      62 ..      29      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksges 36
                   +TGaTGF+Gk L e+L +t    k++++ R+  ++s
     AJA92575.1 29 VTGATGFIGKKLTERLSKTGY--KVTAMSRTLHQNS 62
                   7***************99987..8888888655544 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.5e-05     0.044      33      88 ..      21      78 ..       2      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                  -GTTSEEEEES.-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHH CS
  2-Hacid_dh_C 33 elsgktvGiiG.lGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleel 88
                  ++++  + + G +G IG+++ +rl++ g kv+a++r+ ++++ +++ + ++  +l++l
    AJA92575.1 21 KINDYSILVTGaTGFIGKKLTERLSKTGYKVTAMSRTLHQNSdNVKFVAADALELDTL 78
                  566666777774799**********************998875555555566666665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.17       7      71 ..      33     100 ..      27     122 .. 0.82
   2 ?   -2.2   0.0       3.2   4.1e+03       4      40 ..     438     473 ..     437     483 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                    -SHHHHHHHHHHHHTT-EEEEE-SS...HHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHH CS
  NAD_binding_2   7 lGvMGsnmalnllkagykvavynrt...kekveelvaegakaaesieelvasldvvitmvkagkavde 71 
                    +G +G+++ ++l k gykv+++ rt   ++   ++va+ a  +++++++++++++ + ++++ +  ++
     AJA92575.1  33 TGFIGKKLTERLSKTGYKVTAMSRTlhqNSDNVKFVAADALELDTLSNAFKGVETAFYLLHSMEGSKK 100
                    5889*******************99433355567888889999**********999999987766555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHH CS
  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelva 40 
                    fiG G+ G  + +   +  +kv vy+ + e+v+e + 
     AJA92575.1 438 FIGAGIAGLAIFSS-HNVFHKVRVYQARGESVKESAG 473
                    78888888777654.4667888888888888877665 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.4e-05     0.095      67     148 ..      87     175 ..      40     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                 SEEEEEEE.......E-HSCHHH.HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT........-CEEEEHHHH CS
        PAC2  67 rdllvlqg.......repilqye.efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.ees........eyggivgitg 148
                 + +++l++       +e+ +  e   a++ l+ ae  gvk++++Lggl ++          ++++ ++ +++ + ++   s        ++++ivg+ g
  AJA92575.1  87 TAFYLLHSmegskkeWEQFADREkVQAQNFLKAAENAGVKRIIYLGGLVNES---------LELSKHMRSRHEVGKIlA-SgtipvtelRASVIVGAEG 175
                 566666666666655555555554557789*******************544.........456666666666655522.1233444457778887766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.16       3      45 ..      27      68 ..      26      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHH CS
          KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskali 45
                 l+tG++G +G++l++ l + g  ++  +sR+ ++++d+ +++
  AJA92575.1 27 ILVTGATGFIGKKLTERLSKTGY-KVTAMSRTLHQNSDNVKFV 68
                69****************99996.58999**977777766555 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.8e-05      0.13     370     420 ..     290     340 ..     283     344 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.8e-05
                 EEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE---TTHHHHHHH CS
        NRDD 370 kkigeseeakefalkvlkhmrekadelkeetglnfsleatPaEslsgrfak 420
                  ++ +++  +ef+   lkhm e+++e++ee+     +e+tP E++s++  +
  AJA92575.1 290 DSYVKDKSVEEFVPVNLKHMTEAIKEAREEQVAFKPIEKTPEEKTSYKVNQ 340
                 55668899999*******************777778***********9876 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00021      0.27       1      26 [.      27      52 ..      27     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                     EEEETTTSHHHHHHHHHHHHHB-SEE CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkki 26
                     +lvtGa+G iG++l++++ k+  k  
       AJA92575.1 27 ILVTGATGFIGKKLTERLSKTGYKVT 52
                     89***************998865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 3620.54
//
Query:       AJA92576.1  [L=258]
Description: kinase-binding protein CGI-121 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-08   35.3   0.2      5e-08   33.5   0.0    2.1  3  ThiS         ThiS family
    8.5e-07   29.2   4.6    1.4e-06   28.5   4.6    1.4  1  CGI-121      Kinase binding protein CGI-121
  ------ inclusion threshold ------
      0.017   15.5   0.2      0.077   13.4   0.2    2.3  1  Urm1         Urm1 (Ubiquitin related modifier)
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  TGS          TGS domain
       0.24   11.8   5.6      0.056   13.8   1.9    1.8  2  Endotoxin_C  delta endotoxin
       0.97    9.7   4.9        2.8    8.3   4.9    1.9  1  SIN1_PH      SAPK-interacting protein 1 (Sin1), Pleckstrin-ho


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.7e-11     5e-08       8      77 .]      11      85 ..       4      85 .. 0.88
   2 ?   -2.1   0.0       2.1   6.3e+03      21      40 ..     109     129 ..     102     144 .. 0.63
   3 ?   -3.5   0.0       5.6   1.7e+04      19      35 ..     172     188 ..     163     198 .. 0.60

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.7e-11
                HHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG...TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS  8 relag.eeelelaegstvaelleaLgerypela...lerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                r+  + ++ +  ++ + ++ell +L  + pe +     +++ +avNg + +   + dt+lk +D+v i+p++ GG
  AJA92576.1 11 RKSFQtDSLEITQSIDDISELLSHLISKKPENTpdfDGKNLLIAVNGVDSSAlAGIDTKLKQNDVVNIIPIIHGG 85
                55555567777888999*************999***99**************77********************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                 TSBHHHHHHHHHHHTCHHG.T CS
        ThiS  21 gstvaelleaLgerypela.l 40 
                   + +e l +L +++p+l+  
  AJA92576.1 109 SNSNKEYLLSLRKKFPKLQlQ 129
                 555567777888888877752 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.6
                 SSTSBHHHHHHHHHHHT CS
        ThiS  19 aegstvaelleaLgery 35 
                 ++ + + e+++++g   
  AJA92576.1 172 GNTTQINEAIKNVGLSP 188
                 45566666666666555 PP

>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   4.6   4.8e-10   1.4e-06      15     138 ..     120     233 ..      98     254 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 4.8e-10
                 C..CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS--HHHHHHHHHHHS-S CS
     CGI-121  15 lskraeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvssseadeeevlkslkevveg 113
                  +k ++l+   + ++ il+keh    ++ ++++++++ l + ++++++l+++  +++I+ea+k+ g+s++++  +++ ++++    ++++k ++++ + 
  AJA92576.1 120 RKKFPKLQLQAISSKFILDKEHAKKIITISIIQKSNNHLLSDKIETDLLLRFGNTTQINEAIKNVGLSPNQN-FILIALGNK----SHQIKLFESIRDD 213
                 3334566679999*********************************************************99.777777776....3333333333333 PP

                 EEE--SHHHHHH--HHHHHHHTT-- CS
     CGI-121 114 elvpleeeleeltdwkkikkiYkln 138
                   + +++      + + +kk+++++
  AJA92576.1 214 LDIIFKK-----NNQNFLKKHFQIS 233
                 3344444.....3445555555555 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.6e-05     0.077      62      96 .]      51      85 ..       1      85 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                EEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
        Urm1 62 ilvLindaDwellgekdyelkdkDkivFistlhGG 96
                +l+ +n +D + l   d++lk++D++  i  +hGG
  AJA92576.1 51 LLIAVNGVDSSALAGIDTKLKQNDVVNIIPIIHGG 85
                6899******************************9 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.8e-05      0.26      39      59 ..      55      79 ..      48      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.8e-05
                ECS....EEEETTSBB-SSEEEEEE CS
         TGS 39 VnG....qrvgldhvLedgdvveIv 59
                VnG     + g+d++L+++dvv I+
  AJA92576.1 55 VNGvdssALAGIDTKLKQNDVVNII 79
                788888899***************8 PP

>> Endotoxin_C  delta endotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.9   1.9e-05     0.056      62     138 ..      86     164 ..      82     165 .. 0.87
   2 ?   -1.9   0.1       1.3     4e+03      30      30 ..     217     217 ..     173     242 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                  ESS-EEEEEEEEETTCCCEEEE---TT-GGG...CC-SCCCEEEEEEEE-EEE.ECC-CEEEEEEECC-STTC.EEEEEEE CS
  Endotoxin_C  62 snsdtklsvsignssinaqvnlpstmsggen...ltlkyesFkyvefsttftf.seseeetltlsitnessnqelyiDkIE 138
                  s+++t++s++i+n+si   +++++++s++e+   l++k+ + ++  +s++f + +e  ++ +t+si ++s+ ++l+ DkIE
   AJA92576.1  86 STAKTNVSLTIKNNSIR-LFEINKSNSNKEYllsLRKKFPKLQLQAISSKFILdKEHAKKIITISIIQKSN-NHLLSDKIE 164
                  8999************9.**********99998888899999***********666666777777777666.79******9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                  E CS
  Endotoxin_C  30 v 30 
                  +
   AJA92576.1 217 I 217
                  1 PP

>> SIN1_PH  SAPK-interacting protein 1 (Sin1), Pleckstrin-homology
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.9   0.00093       2.8      11      91 ..      82     165 ..      77     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00093
     SIN1_PH  11 kqkm.laksevtLaIdgekieidpvknkkka.tkfwaksqKtvsyhidsvvhckiserksskalfrivvkk.sssefKrydfea 91 
                 ++   +ak++v L+I ++ i +  +++++++ + +++ ++K  +++++ + +  i++++++k+ + i + + s+++  +  +e+
  AJA92576.1  82 IHGGsTAKTNVSLTIKNNSIRLFEINKSNSNkEYLLSLRKKFPKLQLQAISSKFILDKEHAKKIITISIIQkSNNHLLSDKIET 165
                 5555589*************99999887777555667779*********************99999977663344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1753.63
//
Query:       AJA92577.1  [L=438]
Description: hypothetical protein T478_0655 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.8   1.5      0.055   13.2   0.3    1.8  2  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase


Domain annotation for each model (and alignments):
>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   3.1e-06     0.055       1      45 [.      51      95 ..      51      97 .. 0.96
   2 ?   -1.8   0.0      0.12   2.1e+03     153     179 ..     131     159 ..     102     185 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-06
                SSSHHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT CS
    PDEase_I  1 YHNfrHAadVlqalfyllkkeklkeeltpleilalliaalcHDvd 45
                YHN  H ++V+ ++ +  k++  ++++++ +   l+ +al HD+d
  AJA92577.1 51 YHNVDHELEVTYVTLVAGKHSLEENYISKTDLNYLFASALLHDFD 95
                ******************99999999*****************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.12
                 HHHHHTGCCCS-H..HHHHHHHHHHHHHH CS
    PDEase_I 153 ikaaDisnptkpw..eiskkwaelvleEf 179
                 + +a is ++ pw  +i  +  +l+++ f
  AJA92577.1 131 LICAIISRTVYPWagDIITNTEKLIQNYF 159
                 34777777777772223333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3263.20
//
Query:       AJA92578.1  [L=347]
Description: putative Xaa-Pro dipeptidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-58  197.8   0.0    2.4e-58  197.3   0.0    1.2  1  Peptidase_M24  Metallopeptidase family M24
    1.8e-09   38.4   0.0    3.6e-09   37.4   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   0.0   2.7e-62   2.4e-58       3     208 ..     125     330 ..     123     331 .. 0.94

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 2.7e-62
                    HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESS.....SSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEEEE CS
  Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglaf.....ppivasgenaavlhytpndrvlkegdlvlidagaeydgyasDit 93 
                    ++ka++i ++++  + ++ik g +e el+a++  +   +++  + ++     p i+a g+n+a++h++ ++r++k+++l+++d++ +y+gy+sD t
     AJA92578.1 125 LKKASKIIDEMFGICQKKIKAGQKESELQAILMSY-AVENEMFDTGYrstlnPLIIAGGPNGALPHAQVTNRKFKKNELIVVDLTLRYKGYVSDAT 219
                    799************999***************88.5566655555555566***************999************************** PP

                    EEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEE CS
  Peptidase_M24  94 rTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpg 189
                    rT+++Gk ++e++++ye+v+e q+a++kavkp ++++++d+a+re++ + g++k+f h++GHg+Gl+vh+  p++   +++++kle++m +t+Epg
     AJA92578.1 220 RTFAIGKISNEEKNVYEIVKESQKAGLKAVKPKIDCKKVDNACREIIDESGYGKYFIHSTGHGIGLDVHEL-PTIG--PRSSTKLEKNMAITVEPG 312
                    *********************************************************************98.**98..789*************** PP

                    EEEETTTEEEEEBEEEEEE CS
  Peptidase_M24 190 iyfapgeggvriedtvlvt 208
                    iy +p ++gvried ++vt
     AJA92578.1 313 IY-IPKKFGVRIEDSLVVT 330
                    **.99999**********9 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0     4e-13   3.6e-09      12     130 ..       8     114 ..       6     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4e-13
                   TT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHHHHHHHHHHT-EEEE-TTSSBHHHH CS
  Creatinase_N  12 kgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveyddpvealadllkellesekrvgveldaltvafy 107
                   +g+d+++  +penl+Y+tGf    g++  +l  +++g+ +++ ++l++++a+ee  ++ ev++ d+   +    lk+ l+  ++v  + ++  +  +
    AJA92578.1   8 TGCDMIVALEPENLFYMTGF---WGEAIGIL--EKNGKtTIIAPELEVGRAKEEG-VDCEVIQSDR-GMSSLLTLKKFLK--GKVCTDCQN--YPVM 93 
                   689*****************...********..888888****************.******9998.4444444555555..899999997..6667 PP

                   HHHHHHCTTSEEEETHHHHHHHH CS
  Creatinase_N 108 ealkealpdaelvdaselieelR 130
                   ++lk+ +p  +++++ e +++ R
    AJA92578.1  94 QSLKKSFP--KIKSSIEPFNKSR 114
                   79999999..6666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2500.24
//
Query:       AJA92579.1  [L=228]
Description: DnaJ domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.2   4.4    5.9e-18   64.8   4.4    1.8  1  DnaJ      DnaJ domain
    2.2e-09   37.7   1.9    2.2e-09   37.7   1.9    1.9  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    1.2e-07   32.3   2.8    4.4e-07   30.6   2.8    1.9  1  Fer4_15   4Fe-4S single cluster domain
     0.0079   16.3   2.1       0.02   15.0   2.1    1.7  1  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.074   12.9   9.3       0.24   11.3   4.8    2.3  2  Fer4      4Fe-4S binding domain
        3.6    8.5   8.5       0.34   11.8   0.8    2.6  2  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   4.4     2e-21   5.9e-18       2      59 ..       6      62 ..       5      65 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2e-21
                HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHH CS
        DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekR 59
                 Y+ L+++++++ +e+k aYrklal++HPDkn k++e+e+kFk i+eAy +L++++k 
  AJA92579.1  6 AYKTLEINSNSDFEEVKYAYRKLALQHHPDKN-KNSESEKKFKIITEAYHFLKNQNKH 62
                6*******************************.999******************9986 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.1   6.3e+03      23      41 ..      56      74 ..      46      79 .. 0.51
   2 !   37.7   1.9   7.4e-13   2.2e-09       1      57 [.     158     215 ..     158     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.1
     Fer4_13 23 ddeggasvvaeqptseeek 41
                 ++++++   ++p++ +e+
  AJA92579.1 56 LKNQNKHSSRQKPEKATEE 74
                3344444444555554444 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 7.4e-13
     Fer4_13   1 VDrdtCiacgaCvelaPdvFeeddeggasvvae..qptseeekadaeeAadaCPvesIg 57 
                 VD++ Ci+c +C ++aP vF +d++  +s  +    +++ ++ +++ +Aa++CP+++I 
  AJA92579.1 158 VDQSLCIGCCSCEMIAPGVFTIDKN-TKSNPKSrvYNKKGAKNQKIINAAETCPTKAII 215
                 9**********************98.556655523355567789*************96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   2.8   1.5e-10   4.4e-07       1      66 []     156     216 ..     156     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.5e-10
     Fer4_15   1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66 
                 V vD+++Cigc  C   ap vf++d++ ++  +  +        +  + +++  Aa++CP++AI+v
  AJA92579.1 156 VDVDQSLCIGCCSCEMIAPGVFTIDKNTKSNPKS-R----VYNKKGAKNQKIINAAETCPTKAIIV 216
                 679***********************99997773.2....3366788999**************97 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.1   6.7e-06      0.02       5      58 ..     153     213 ..     150     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.7e-06
     Fer4_19   5 eitiednrelCihsgnCvkglpevFdpkrkpwi.......kpdeasteeiievverCPSGA 58 
                 e+++  +++lCi+  +C   +p+vF  +++          ++ +a+ ++ii+++e+CP  A
  AJA92579.1 153 ELKVDVDQSLCIGCCSCEMIAPGVFTIDKNTKSnpksrvyNKKGAKNQKIINAAETCPTKA 213
                 6789999******************8777644445556678889999***********755 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.8   8.2e-05      0.24       2      16 ..     157     171 ..     156     172 .. 0.89
   2 ?    4.0   0.1     0.016        47      15      23 ..     206     214 ..     206     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.2e-05
                 EEETTTSSS-THHHH CS
        Fer4   2 videekCigCGaCve 16 
                  +d+++CigC  C++
  AJA92579.1 157 DVDQSLCIGCCSCEM 171
                 69***********96 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                 HHHSTTTEE CS
        Fer4  15 vevCPvgAI 23 
                 +e CP+ AI
  AJA92579.1 206 AETCPTKAI 214
                 578*****9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9      0.35     1e+03      42      62 ..      52      72 ..      21      98 .. 0.51
   2 ?   11.8   0.8   0.00011      0.34      30      93 ..     113     174 ..      97     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
     Fer4_22 42 leeftkvaggenvrkekkerl 62
                  +f k +++++ r++ ++ +
  AJA92579.1 52 AYHFLKNQNKHSSRQKPEKAT 72
                223333334444444333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
     Fer4_22  30 egervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacp 93 
                 + e +++++s + ++++k+ ++ ++ k+ ++r   +  +k  e+k  +++s C+GC  C++  p
  AJA92579.1 113 NEEWWKRYESEFWDKYEKTVNE-QTDKQPEDRGFPK-KRKEFELKVDVDQSLCIGCCSCEMIAP 174
                 4555666667777777776666.3334444443222.334445666779**********98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1708  (0.0952647); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1629.59
//
Query:       AJA92580.1  [L=58]
Description: hypothetical protein T478_1416 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 446.15
//
Query:       AJA92581.1  [L=632]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit E [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-62  209.7   0.0    7.5e-62  209.2   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    1.3e-18   67.3   9.5    1.3e-18   67.3   9.5    2.5  3  GatB_Yqey  GatB domain
    4.1e-07   30.1   0.8    2.1e-06   27.9   0.5    2.4  2  GAD        GAD domain
     0.0012   18.9   4.1     0.0012   18.9   4.1    2.2  2  YqeY       Yqey-like protein
  ------ inclusion threshold ------
      0.022   14.9   2.5        6.4    6.9   0.0    2.6  2  SurA_N     SurA N-terminal domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.2   0.0   2.1e-65   7.5e-62       2     271 ..      12     445 ..      11     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 2.1e-65
                 EEEEEEEEEB--SB-SSSSSBSSSSCE..........STTSS--TTTTTS...........................TT..--.EEHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxx...........................xxxxxx.xxxxxxxxxxxxxxx RF
      GatB_N   2 viGlEiHaqlktksKlFssasteeege..........epnsevsevdlal...........................PGtlPv.lnkeavelaikaala 62 
                 ++GlEiH+ql+tk+KlF++++  ee+e          +++se++++d a+                           P   P+ l+ +a ++a+ ++ a
  AJA92581.1  12 KVGLEIHQQLDTKKKLFCDCTPIEEEEfsrkfsrklrAAKSELGKIDPAAlfestksktivyyanprssclvcedeeP---PHsLDISAKKIALLISSA 107
                 89******************987544455677788856999999999999************************9998...999*************** PP

                 TTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SE.EEEEEEE.TEEEEEEEEEEEE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N  63 lnceiaeeskfdRKnyfypdlpkgyQitqkeepla.keGslel.ekkvrierihlEeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearav 159
                 l+++i +e++++RK+++++++++g+Q+t+    l+ ++G++e+  +kv++++i+lEeDa+k v++e ++ +++l+R+GvpL+Ei+ +p   +p+ ++++
  AJA92581.1 108 LESKIFSEIHVMRKTVIDGSNTTGFQRTM----LVsQGGHIEVnGEKVGVQSICLEEDAGKLVKDEGNHRFFSLDRLGVPLVEIALDPVEGDPKFVKDI 202
                 *****************************....555999***97789**************************************************** PP

                 HHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH............................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
      GatB_N 160 veklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqiell............................. 229
                 + +l++llr+++++ +++  G++R+DvN+Sv+ +         +E+K++++l+++ek+ie+e++rq  l                              
  AJA92581.1 203 ALTLGRLLRVTKKVMRGI--GTIRQDVNISVEGG-------GVIEVKGVQQLDQLEKIIEFEAKRQHGLKlisdkinqigfteisrkedvfditdimqe 292
                 ******************..************44.......78***********************999889*************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
      GatB_N 230 ................................................................................................... 229
                                                                                                                    
  AJA92581.1 293 cnskiikksikkqekifgikikklkgifgfepysdirlgkeigqlvrffgiggvfhsdelpnygieetdikrviekldvqnddafliiagekisvgfai 391
                 *************************************************************************************************** PP

                 ...............-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHH CS
                 ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 230 ...............qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseel 271
                                 eTr+++++ g t+ lR+++ a   r++pe+d+p++++se+ 
  AJA92581.1 392 dsiinrielakegppAETRAATQN-GDTIFLRPRPGA--SRMYPETDIPTVKVSEKE 445
                 **********************99.**********88..6*************9986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.6      0.84     3e+03      77     119 ..     266     308 ..     239     312 .. 0.65
   2 ?   -2.4   0.2       1.1   3.9e+03      33      66 ..     446     479 ..     438     481 .. 0.57
   3 !   67.3   9.5   3.7e-22   1.3e-18       2     148 .]     486     627 ..     485     627 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.84
                 HHHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTS CS
   GatB_Yqey  77 eeiieekgLkqisdeeeleklveeviaenpkavedyksgkeka 119
                 ++ i++ g++ is +e + ++ + + + n+k +++  +++ek 
  AJA92581.1 266 SDKINQIGFTEISRKEDVFDITDIMQECNSKIIKKSIKKQEKI 308
                 4445566666666666666666666666666666666666655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                 XXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHH CS
   GatB_Yqey  33 leieelkltpeqlaellkliaegkIskkiakevl 66 
                 l+ + ++++++  a + +l ++ +I+++ a++++
  AJA92581.1 446 LSEAVSNIPKSWEASIKELESKYEINNQLAEQIF 479
                 3333355556666666666666677777777776 PP

  == domain 3  score: 67.3 bits;  conditional E-value: 3.7e-22
                 HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHHHH CS
   GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeeiieekgLkqisdeeeleklve 99 
                  fe+++++ ++++  +  +l  ++++l++ gl+ +   l++eq+ + ++l+ e+kI+k++++ ++e+++ +   ++ +++e+  ++q++d eel k+++
  AJA92581.1 486 IFEQICSKKQSSPNFVVSILCSTITNLERSGLDSSL--LNDEQIMKTFELLGEEKINKESIEIIFEQIMSKkADNVLQALEKASITQLTD-EELDKILD 581
                 69******9887777777777788999999988777..9******************************8868899**************.******** PP

                 HHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
   GatB_Yqey 100 eviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                 ++i++n   ++++k+ + +al  l+G  Mk+++Gka +k++ne lk k+
  AJA92581.1 582 DIIQKN---MNKVKEEQSRALSGLMGIAMKEVRGKASGKIINEKLKAKI 627
                 ******...9************************************986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.5   5.9e-10   2.1e-06       1      90 [.     298     386 ..     298     390 .. 0.92
   2 ?   -3.4   0.0       3.4   1.2e+04      73      83 ..     411     421 ..     409     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.9e-10
                 HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEEEEEEEEHHH CS
         GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDillfvAdkkkt 90 
                 +++ +k+ +++ ++++++  +++ + e     +++ke g   +++ +++g +++++++ + + e+ +k+++e+++++++D++l++A++k +
  AJA92581.1 298 IKKSIKKQEKIFGIKIKK-LKGIFGFEPYSDIRLGKEIGQLVRFF-GIGGVFHSDELPNYgIEETDIKRVIEKLDVQNDDAFLIIAGEKIS 386
                 5788999999*******9.7999999888888*******999998.*****************************************9865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.4
                 CT--TTEEEEE CS
         GAD  73 vgaeegDillf 83 
                 + +++gD++++
  AJA92581.1 411 AATQNGDTIFL 421
                 67899***997 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.69   2.5e+03      38      58 ..     280     306 ..     249     309 .. 0.62
   2 !   18.9   4.1   3.5e-07    0.0012      22     142 ..     501     626 ..     485     627 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.69
                 TS......S--HHHHHHHHHHHHHHHH CS
        YqeY  38 rk......elsdeevlkvlakevkqRr 58 
                 ++      ++ +e   k+++k +k+++
  AJA92581.1 280 KEdvfditDIMQECNSKIIKKSIKKQE 306
                 333333335666777888999888865 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.5e-07
                 HHHHHHHHHHHHHHHTTS..S--HHHHHHHHH..HHHHHHHHHHHH.HHHHT-HHHHHHHHHHHHHHGGGS-----HHHHHHHHHHHHH....HTT--B CS
        YqeY  22 tlrllkaaikqeevderk..elsdeevlkvla..kevkqRresiee.fekagRedlaekekaEievleeYlPeqlseeeiealvkeaia....evgaes 111
                 ++++l ++i++ e +      l+de+++k  +   e k  +esie+ fe+     + +k+++ ++ le+   +ql++ee++++++++i+    +v++e+
  AJA92581.1 501 VVSILCSTITNLERSGLDssLLNDEQIMKTFEllGEEKINKESIEIiFEQI----MSKKADNVLQALEKASITQLTDEELDKILDDIIQknmnKVKEEQ 595
                 667777777777777665434888888887552257788888888624443....34455556677788888999999999887777761111568889 PP

                 GGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
        YqeY 112 mkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                 ++++  +m++++++v+Gka gk +++ +k+k
  AJA92581.1 596 SRALSGLMGIAMKEVRGKASGKIINEKLKAK 626
                 9*************************99987 PP

>> SurA_N  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0018       6.4      64      95 ..     438     469 ..     432     480 .. 0.89
   2 ?    6.3   1.3    0.0026       9.4      57     106 ..     560     612 ..     535     624 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0018
      SurA_N  64 girvddeelnqaiaeiAkeNkltldqlraala 95 
                  ++v+++el +a+++i k+ + ++++l+++ +
  AJA92581.1 438 TVKVSEKELSEAVSNIPKSWEASIKELESKYE 469
                 699************************99865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0026
      SurA_N  57 lqeaektgi.rvddeelnqaiaeiAkeNkltldqlraalae..dGlsydefre 106
                 lq  ek++i +++deel++ +++i ++N  ++++ +++  +   G++ +e+r 
  AJA92581.1 560 LQALEKASItQLTDEELDKILDDIIQKNMNKVKEEQSRALSglMGIAMKEVRG 612
                 444455555379****************9998876554322124666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 4691.03
//
Query:       AJA92582.1  [L=102]
Description: hypothetical protein T478_1479 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.047   14.1   0.4      0.066   13.7   0.4    1.2  1  DUF5301      Domain of unknown function (DUF5300)
       0.15   12.5   0.8       0.35   11.3   0.4    1.7  2  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> DUF5301  Domain of unknown function (DUF5300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   7.3e-06     0.066      23      65 ..      20      62 ..      11      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-06
     DUF5301 23 ketevkvtdkeeIkeilsilkkakktkkeSvndqPnvdeyikv 65
                 + +  +++ +++k++l++lk+++++ ++S+  +P++d+++k+
  AJA92582.1 20 AQAKQALKNGKDLKQVLTALKENRDQIEKSTGRRPDIDDTTKL 62
                3333357999****************************99987 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   3.9e-05      0.35      14      36 ..      18      40 ..      16      49 .. 0.82
   2 ?   -1.2   0.0      0.32   2.8e+03      37      49 ..      77      89 ..      65      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
                 HHHHHHHHHHHT--HHHHHHHTT CS
  FumaraseC_C 14 AakIAkeAlkegktlreavlelg 36
                 A + Ak+Alk+gk l+++  +l+
   AJA92582.1 18 AEAQAKQALKNGKDLKQVLTALK 40
                 6677**************88765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.32
                 -.-HHHHHHHT-H CS
  FumaraseC_C 37 llteeeldelldp 49
                  +++e++ e++d 
   AJA92582.1 77 DIDDEKFWEAVDY 89
                 3788999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1789  (0.0997825); expected 358.6 (0.02)
Passed bias filter:                      952  (0.0530983); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 788.70
//
Query:       AJA92583.1  [L=175]
Description: putative membrane protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-09   36.8  11.8    4.6e-09   36.5  11.8    1.0  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
      0.031   14.5   5.1      0.082   13.2   4.7    1.9  1  EI24      Etoposide-induced protein 2.4 (EI24)
      0.061   13.4   0.4        3.6    7.7   0.1    2.5  2  YpmT      Uncharacterized YmpT-like


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5  11.8   7.8e-13   4.6e-09       2     153 ..       8     166 ..       7     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 7.8e-13
      SpoIIM   2 lllflvgillgallaa....snfa.eqis...seskensalslflaifanNlrvalllfllGllllgiptilvl.linGfvlGavaalvaefgglllfl 91 
                 +l+f++ +++++++      s+++ e+i+   s  +e   +   + if++N+++al +f+ G+   g++  l+    +Gf   a+aa+ ae  +l  ++
  AJA92583.1   8 ILFFIFTAIFAVVYGGsavtSEPTeEEIEeimSFFEEIVDTIDGIGIFVHNTTIALPMFIPGF---GVVWGLFSaYSTGFAYSAIAATNAEVAQLNPLA 103
                 67777777777777777766333354444455666666667789******************5...888888887999*******999999988***** PP

      SpoIIM  92 llilPhgilelpaiiiagaaglrlgkal.rsrrkalkeakrellklllllvp.llliAaliEaf 153
                 +l+ P g++e+ a+ ia++ +  l+k++ r+++++ k+  + l+ + ++ v+ llli++++E +
  AJA92583.1 104 VLLTPFGLMEVGAYSIAMSRSTLLAKDViRKNWNQIKND-KLLISIEIGAVVaLLLIGGIVEMW 166
                 ****************************65445555544.4455555555556*********86 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.7   1.4e-05     0.082      62     141 ..      10      93 ..       1     163 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                 HHHHHHHH......HHHHHHHHHH.HH....CCTTSHHHHHHHHHHHHHHHHHHHHHHHTTHHH....HHHHHHHHHHHHHHHHHHHHHH CS
        EI24  62 alllaapf......ygllaekvekrhl....glvkslaeslkslllllllllvllplliPvvglilsplllswltayfycfeyldlaagr 141
                  +++ a+f        + +e +e+ +     ++++++ +++  + +++  + ++lp++iP++g     +++++++ay  +f y ++aa +
  AJA92583.1  10 FFIFTAIFavvyggSAVTSEPTEE-EIeeimSFFEEIVDTIDGIGIFVHNTTIALPMFIPGFG-----VVWGLFSAYSTGFAYSAIAATN 93 
                 222222222221222222222222.1123337899999*******************99**99.....89*************9999955 PP

>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.013        79       3      26 ..       6      28 ..       4      39 .. 0.72
   2 ?    7.7   0.1    0.0006       3.6       8      38 ..      70     100 ..      66     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
        YpmT  3 riyvyFsllsllfslyFGglayqh 26
                ri  +F + + +f++++Gg a  +
  AJA92583.1  6 RI-ILFFIFTAIFAVVYGGSAVTS 28
                44.46668888999****999866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0006
        YpmT   8 FsllsllfslyFGglayqhlvaenmDkvYLn 38 
                 F+++  lfs y  g+ay  ++a n +   Ln
  AJA92583.1  70 FGVVWGLFSAYSTGFAYSAIAATNAEVAQLN 100
                 899999****************998766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1292.77
//
Query:       AJA92584.1  [L=234]
Description: hypothetical protein T478_1095 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.032   14.1   0.0    1.4  1  SprT-like  SprT-like family


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-06     0.032      30      82 ..      63     119 ..      25     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-06
   SprT-like  30 nttaGranlkr....atvrhhasIeLseklldsrsedrllntLaHElcHlalfvisg 82 
                 +  +G  + ++    ++++ h  I++s++l+    +  ++ +LaHE+ H++ ++++ 
  AJA92584.1  63 SLDIGILYARTiplvVKNSIHVVIQISAPLVAFGLKGTIHAILAHEFLHYLELMTRL 119
                 55556555555666677888999****************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1720.13
//
Query:       AJA92585.1  [L=411]
Description: snoRNA-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-63  214.9   0.1    1.5e-63  214.4   0.1    1.2  1  Nop       snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
      0.053   13.5   1.8        1.4    8.9   0.2    2.4  2  DUF2481   Protein of unknown function (DUF2481)


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.4   0.1   1.7e-67   1.5e-63       2     218 ..     139     351 ..     138     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 1.7e-67
                 HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT..HHHHHHHHHHHHCHHHH-SSS-S-HHHHHHHHHHHHHHHHHH CS
         Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee.deelakevimaakvtastsmgaelseedlknikelcdrvlele 99 
                 ld+ dk in +++r+rewY+ hFpEL++++++   Ya++v + +  re+++++   +   +++++++++   ++s g +++e++l+ +++l++++lel 
  AJA92585.1 139 LDDTDKIINGMSSRLREWYGLHFPELDNIIDSINGYAQIVVAGK--RENITDDVFvNAGFPDSKVQMLSLVKEKSRGGDITEKNLEIVQNLAKNILELF 235
                 7899************************************8877..6888665223445999999999998999************************* PP

                 HHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHH CS
         Nop 100 elrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRlla 197
                 +lr+el++ ++++m+++APNlsa++G++v+ar++++aG+L+++a mPastiq+lGaekalfralk ++n pk+G+++++ +v+ a+p+++++kiaR++a
  AJA92585.1 236 DLRNELEKQVDEQMNEVAPNLSAVLGTTVGARILAKAGSLQKMATMPASTIQVLGAEKALFRALKtGSNPPKHGILFQHAVVH-AAPRWQRGKIARAIA 333
                 *****************************************************************888***************.66************* PP

                 HHHHHHHHHHHTT----SHHH CS
         Nop 198 aKvalaaRiDafsekdgslGk 218
                 aK+a+a+R+D  ++    l k
  AJA92585.1 334 AKAAIASRVDVHGS---GLNK 351
                 **********5432...2222 PP

>> DUF2481  Protein of unknown function (DUF2481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00016       1.4      20      48 ..      57      85 ..      35     122 .. 0.80
   2 ?    3.7   0.1    0.0065        58      11      49 ..     219     258 ..     207     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00016
     DUF2481 20 anndveldellklqkelnqlmnentiekq 48
                  ndv l++llk +    qlmne  +e  
  AJA92585.1 57 LVNDVGLQDLLKKKSIESQLMNEVKLEDI 85
                469**********9999******999864 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0065
     DUF2481  11 rqreiisyianndveldell.klqkelnqlmnentiekqk 49 
                 ++ ei+  +a+n +el +l   l+k++++ mne + +   
  AJA92585.1 219 KNLEIVQNLAKNILELFDLRnELEKQVDEQMNEVAPNLSA 258
                 5679999********9887526999999999997765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1270  (0.070835); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2748.77
//
Query:       AJA92586.1  [L=251]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0045   17.2   0.5      0.011   15.9   0.0    1.9  2  DUF4079          Protein of unknown function (DUF4079)
  ------ inclusion threshold ------
        1.1   10.0   5.6        2.4    8.9   0.7    3.0  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.2       1.7   1.5e+04      65      72 ..      46      53 ..      40      61 .. 0.49
   2 !   15.9   0.0   1.2e-06     0.011       3      82 ..      67     138 ..      65     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.7
     DUF4079 65 aigglvll 72
                a++g++ll
  AJA92586.1 46 AAAGIALL 53
                44443332 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-06
     DUF4079   3 llHPvlmvllvfpllgavaylGwqtrqrrlqskaerkekipkkvrdeHvklgslllllvvlgaigglvllylrrgklfps 82 
                 l HP lm +l++p +g++   G+++ +r lq +        ++      k+ +l l+++v+g + + v+  l+ g ++p 
  AJA92586.1  67 LEHPYLMNILFAPAFGIGFLYGLKISERALQPS--------ETRSAFKRKIMKLFLFFLVIGGLFSSVNFALHGGAMIPD 138
                 56**************************87777........233344568999999999999999999999998887765 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.027   2.4e+02      31      67 ..      81     123 ..      21     133 .. 0.69
   2 ?   -0.2   0.3      0.19   1.7e+03      33      69 ..     162     199 ..     148     205 .. 0.48
   3 ?    8.9   0.7   0.00027       2.4      30      72 ..     193     236 ..     185     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.027
  NADH-u_ox-rdase  31 itaafplallalekls.Psvagka.....mtlagligflggfl 67 
                      + ++f ++l + e++  Ps  ++a     m+l  +  ++gg++
       AJA92586.1  81 FGIGFLYGLKISERALqPSETRSAfkrkiMKLFLFFLVIGGLF 123
                      2224455555554432466655557777766666666666654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
  NADH-u_ox-rdase  33 aafplallaleklsPsvagka.mtlagligflggflla 69 
                      + +  ++++++ ++++ +g +   l  +i+f g+f+++
       AJA92586.1 162 FLIVSSITIMAAATRRIVGLNgGMLGKIITFAGTFVFF 199
                      33333344444333333222244466666666666554 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00027
  NADH-u_ox-rdase  30 aita.afplallaleklsPsvagkamtlagligflggfllayqn 72 
                      a t+ +f +  + l + +P++++  + + +  g++gg+++++++
       AJA92586.1 193 AGTFvFFSMISMSLTQSDPTNSQIYLYTCYHAGIIGGAMYQMNR 236
                      2333356666666667779998877****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1792.84
//
Query:       AJA92587.1  [L=143]
Description: universal stress family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-25   90.5   0.0    1.5e-25   90.4   0.0    1.0  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   8.3e-30   1.5e-25       3     141 .]       6     143 .]       4     143 .] 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 8.3e-30
                 SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH.. CS
         Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva.. 99 
                  +IlV++D+s++s + l  A+ lak+ +a++i+lh++ ++++g  +++ +  + + ++l  +   a+    ++e++gv+ + +++ g+p+ ei+++a  
  AJA92587.1   6 NKILVPLDNSKNSFRGLSSAIYLAKNCDAKIIALHAVYAPPKGDFDTSGKFNKNHKKQLDSMMDIAE---NQCEKAGVAFDQKIVYGNPGYEIAKFAnt 101
                 69***********************************************************999987...6*************************955 PP

                 HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 100 eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                  ++++d++V+Gsrgrs+ ++l++GS+s+ vl++++ +Vl+++
  AJA92587.1 102 SRNKIDMVVIGSRGRSSAKELFFGSTSQFVLHKSKPSVLIIK 143
                 699*************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1079.18
//
Query:       AJA92588.1  [L=266]
Description: acetylglutamate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-38  133.3   3.6    1.1e-38  133.2   3.6    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   3.6   6.3e-43   1.1e-38       5     241 .]       4     245 ..       1     245 [. 0.94

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 6.3e-43
                 EEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHG CS
   AA_kinase   5 vKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeagevatrdalaslgerlvaallaaglp 99 
                 +K+GGs++++       + +++i++   +++ +++VhGgg+ + +  ++  g ++++  +    + r+t++e+ e+ t+++ + +++ +v++l+++g++
  AJA92588.1   4 IKIGGSVVDNLHP----STIADIKKV-AQKEGVILVHGGGKEVTKVTEQ-LGKEPKFVVSpsgiKSRYTDKETSEIFTMVMSGRINKTIVQMLQKNGIN 96 
                 9********9988....999999999.99999*****************.899999988889999********************************** PP

                 EEEE-GGGTCEECCCE..................HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESS CS
   AA_kinase 100 avglsaaaldateagr................degsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdV 182
                 avgls+ +  ++ea+r                d g++g++++v++e i++++e+g+ pv+++++ ++ee e++++++D++aa +A  ++ dk++++t+V
  AJA92588.1  97 AVGLSGMDGKTIEANRkkklmimnekgrkqmiDGGYTGKISNVNSELIKTIMEKGYTPVISPIA-ISEESEFLNVDGDRAAANVAGHVNSDKVLFITNV 194
                 **************************************************************76.99999*99************************** PP

                 SSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 183 dGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                 dG++  d       +l++++s ++a+e     + +Gm+ k++aa +a++ g+ ++ I+n
  AJA92588.1 195 DGLLMED-------KLVEKLSLEKAKE-IMPKIGFGMEKKILAATEALEMGVSEALIAN 245
                 ******9.......6666666666666.555999******************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1885.85
//
Query:       AJA92589.1  [L=125]
Description: hypothetical protein T478_0880 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 968.59
//
Query:       AJA92590.1  [L=305]
Description: LAO/AO transport system ATPase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-70  235.1   4.8    8.2e-70  234.8   4.8    1.0  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
    2.2e-06   27.4   0.1    6.2e-06   25.9   0.1    1.8  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
    4.8e-06   26.5   0.2     0.0024   17.7   0.0    2.3  2  ATP_bind_1    Conserved hypothetical ATP binding protein
    5.4e-06   25.9   1.2    1.4e-05   24.5   1.1    1.8  1  KAP_NTPase    KAP family P-loop domain
    1.8e-05   24.7   2.9     0.0015   18.5   0.1    2.7  2  RsgA_GTPase   RsgA GTPase
    0.00031   21.0   0.5     0.0046   17.2   0.0    2.6  3  AAA_22        AAA domain
     0.0013   19.0   2.8     0.0064   16.7   3.7    1.3  1  MnmE_helical  MnmE helical domain
     0.0015   17.7   5.8       0.03   13.4   0.1    2.4  2  IIGP          Interferon-inducible GTPase (IIGP)
     0.0021   17.8   0.4     0.0044   16.8   0.1    1.7  2  PRK           Phosphoribulokinase / Uridine kinase family
     0.0029   18.0   0.4      0.013   15.9   0.4    2.2  1  AAA_16        AAA ATPase domain
     0.0048   17.0   3.6      0.026   14.6   3.6    2.4  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0049   17.4   0.7      0.016   15.8   0.1    2.1  2  AAA_18        AAA domain
     0.0063   17.0   0.2     0.0063   17.0   0.2    2.2  2  ABC_tran      ABC transporter
  ------ inclusion threshold ------
      0.013   15.5   0.8       0.05   13.5   0.1    2.0  2  NACHT         NACHT domain
      0.015   15.0   0.3      0.034   13.9   0.3    1.6  1  AAA_30        AAA domain
      0.021   14.7   0.1      0.077   12.9   0.0    2.0  2  APS_kinase    Adenylylsulphate kinase
      0.022   13.0   2.1      0.059   11.6   0.1    1.9  2  Virul_Fac     Putative bacterial virulence factor
      0.023   15.2  13.4       0.58   10.6   0.0    2.7  2  AAA_23        AAA domain
      0.025   14.7   3.2        2.3    8.3   0.1    2.4  2  DUF87         Helicase HerA, central domain
      0.026   14.4   0.6      0.085   12.8   0.0    2.1  2  NTPase_1      NTPase
      0.028   13.9   0.5        5.9    6.4   0.0    2.5  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.031   13.1   2.0      0.076   11.8   0.1    2.0  2  AAA_35        AAA-like domain
      0.043   14.2   0.4       0.24   11.8   0.0    2.4  2  RNA_helicase  RNA helicase
      0.057   12.9   0.1       0.24   10.9   0.0    2.0  2  AAA_7         P-loop containing dynein motor region
      0.061   13.1   0.2       0.14   11.9   0.2    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.063   12.5   2.3       0.07   12.3   0.1    1.9  2  NB-ARC        NB-ARC domain
      0.064   13.0   2.3       0.14   11.9   0.0    2.4  2  AAA_24        AAA domain
      0.084   13.2   0.2       0.17   12.3   0.2    1.7  1  AAA_19        AAA domain
      0.097   12.8   4.3        9.7    6.3   1.6    2.9  3  Flagellin_N   Bacterial flagellin N-terminal helical region
       0.31   11.1   1.6         13    5.9   0.0    3.2  3  PPR_3         Pentatricopeptide repeat domain
       0.43   11.2   3.6       0.74   10.4   3.6    1.3  1  DUF1053       Domain of Unknown Function (DUF1053)


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.8   4.8   1.4e-72   8.2e-70       1     262 [.      15     268 ..      15     273 .. 0.93

  Alignments for each domain:
  == domain 1  score: 234.8 bits;  conditional E-value: 1.4e-72
                 HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-- CS
        MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslps 99 
                 +a+ai ++e++  ea++l++++ + +G++ v+G+tG  GaGks l+++l +el++   + avlavDP+s +tGG+ilGD++R++e ++d g +iRs++s
  AJA92590.1  15 IAKAISIMENDPKEARKLIKKIYKLSGKSVVIGITGPAGAGKSSLINRLSMELKKLKLKPAVLAVDPTSHVTGGAILGDRVRMTE-STDTGTYIRSIAS 112
                 59*********************************************************************************98.689********** PP

                 ---HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCST CS
        MeaB 100 rGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaDkkeaekaarelraaleleee 198
                 rGa G +a+  r+ +++le aGf+ ++ie vG+Gq evd+ +++d++vv   p++GD +q+ik+Gi ei+Di+ vnk+D+ +a++  + l+  +  +ee
  AJA92590.1 113 RGATGAIAHSVRNSLRVLEYAGFNPIIIESVGAGQTEVDISKIADITVVTFNPHTGDSIQTIKAGITEIGDIYLVNKSDLDGATQLFQALQDFIGTDEE 211
                 ***********************************************************************************9999999988877665 PP

                 TBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        MeaB 199 kekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrrerakeelrelvedellkrv 262
                      ++ +lktsa++++Gi+el+++++e ++  +k    +  ++ r ++el  ++ +++ +++
  AJA92590.1 212 -----EAVILKTSAKKNKGIKELASKLKELMKQKSKDK--KTSEKTRLESELEDIILNNVRQEI 268
                 .....579********************9988777764..444555677777888888887766 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   1.1e-08   6.2e-06       2     166 ..      45     206 ..      44     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
                 EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCC......HCCCT............EEEETTTTECCHCTT-HHHHHHHHHHHHT CS
        cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaell......retgve...........ivelenGciCctlredllkelealeeree 81 
                 v+++tG+ G+GK++L+n+l    ++ +lk av+  +  +    +++l      +    e           +   ++G i +++r+    +l+ le    
  AJA92590.1  45 VIGITGPAGAGKSSLINRLSmeLKKLKLKPAVLAVDPTSHVTGGAILgdrvrmT----EstdtgtyirsiASRGATGAIAHSVRN----SLRVLEYA-- 133
                 789****************988888999********997777777774444331....133456665555555566777777444....44444444.. PP

                 T-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHH CS
        cobW  82 rldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerl 166
                  ++ i+iE++G  +  +v         d+   a ++vv  +   + +++i++      +  d+ ++nK Dl  +++l ++l++ +
  AJA92590.1 134 GFNPIIIESVGAGQT-EV---------DISKIADITVVTFNP--HTGDSIQTIKAGITEIGDIYLVNKSDLDGATQLFQALQDFI 206
                 4999*******8775.45.........566667777777733..46667777666677899*********999888877776655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.2e-06    0.0024       1      36 [.      48      83 ..      48      87 .. 0.94
   2 !    6.7   0.0    0.0093       5.4     181     240 ..     179     238 ..     158     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-06
  ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAa 36
                ++GpaG+GK++++++ls  l++ + ++av+  DP +
  AJA92590.1 48 ITGPAGAGKSSLINRLSMELKKLKLKPAVLAVDPTS 83
                68********************************86 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0093
  ATP_bind_1 181 edvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslidealq 240
                 +++ ++ l+++++ +   +l++a+ +++ + ++  ++l  s++k+++i++l s+++e+++
  AJA92590.1 179 TEIGDIYLVNKSDLDGATQLFQALQDFIGTDEEEAVILKTSAKKNKGIKELASKLKELMK 238
                 5666667777777778899***************9******************9998875 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   1.1   2.4e-08   1.4e-05       5     163 ..      29     258 ..      26     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-08
  KAP_NTPase   5 asaladilseptlatpivvgLygkWGsGKssllnkledelkefa....................................................... 48 
                 a +l++ + + + ++++v+g++g+ G+GKssl+n+l  elk+ +                                                       
  AJA92590.1  29 ARKLIKKIYKLS-GKSVVIGITGPAGAGKSSLINRLSMELKKLKlkpavlavdptshvtggailgdrvrmtestdtgtyirsiasrgatgaiahsvrns 126
                 678999999887.9****************************998899999999999999999999999888888888888888888888888888888 PP

  KAP_NTPase  49 ...........................kpvrflfaefnawsfkggddavaellaaLadaleeeygqlatkllrakklkalkikgkiklrkacaiplvli 120
                                            k  ++++++fn+   ++  + +++ ++++ d     ++ l+  + +    +al+   +++    +a++l+ +
  AJA92590.1 127 lrvleyagfnpiiiesvgagqtevdisKIADITVVTFNPHTGDS-IQTIKAGITEIGDIYLVNKSDLDGATQLF---QALQDFIGTD--EEEAVILKTS 219
                 88888888888888888888888888866666777777766654.55555555555555444444443333333...2233333333..3333333322 PP

  KAP_NTPase 121 levalflliegasllavlsraaklkeeaplkklqteveellad 163
                  ++       +++l ++l+++ k k++++ ++++t  e++l+d
  AJA92590.1 220 AKKNK----GIKELASKLKELMKQKSKDKKTSEKTRLESELED 258
                 22211....2234444455555555555555555555555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.6e-06    0.0015      90     123 ..      33      67 ..       8      87 .. 0.69
   2 ?    6.1   0.2     0.016       9.2      46      99 ..     180     235 ..     149     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.6e-06
                  HHHHHHHCTTSEEE..EECSTTSSHHHHHHHHCTT- CS
  RsgA_GTPase  90 leelkellkdktsv..lvGqSGvGKStLinallpel 123
                  ++++ + l++k +v  + G+ G+GKS+Lin+l  el
   AJA92590.1  33 IKKIYK-LSGKSVVigITGPAGAGKSSLINRLSMEL 67 
                  333333.44444332379**************9875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                  T-EEEEEEE-GGG--HHHHHHHHHHH..HHHTTSEEEE--TTTHTTHHHHHHHCTT CS
  RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkee..lealgyevllvsaktkegleelkellkd 99 
                  +i  + ++nK Dl   ++ +++l++   + + +  +l++sak+++g++el+++lk+
   AJA92590.1 180 EIGDIYLVNKSDLDGATQLFQALQDFigTDEEEAVILKTSAKKNKGIKELASKLKE 235
                  56667789*****99999444444431144556778999*************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.9e-06    0.0046       9      60 ..      47      94 ..      40     128 .. 0.79
   2 ?    1.1   0.0      0.75   4.3e+02      54      89 ..     196     240 ..     156     268 .. 0.59
   3 ?   -2.1   0.0       7.6   4.4e+03      16      32 ..     272     288 ..     270     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.9e-06
      AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60
                 +tG++G+GK+ l++rl ++l++ +     +p v+ v+++s  +   +l + 
  AJA92590.1 47 GITGPAGAGKSSLINRLSMELKKLK----LKPAVLAVDPTSHVTGGAILGDR 94
                59******************96443....48888888888887766666555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.75
      AAA_22  54 kdllrellralglelka.........erlsseellealeqalrar 89 
                 ++l+++l  ++g + ++         +++  +el ++l + ++++
  AJA92590.1 196 TQLFQALQDFIGTDEEEavilktsakKNKGIKELASKLKELMKQK 240
                 444444444444444444444444443333333333333333332 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 7.6
      AAA_22  16 tGKTtllrrlleqldee 32 
                 +GK+ +   +l++ +e 
  AJA92590.1 272 IGKSKSFSSYLKKVQEK 288
                 69****99999997543 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.7   1.1e-05    0.0064      87     155 ..     170     260 ..     147     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                   xxxxxxxxxx...........xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
  MnmE_helical  87 rgellreGik...........Dllkeke...........ekeeeevlkiSaktgegieeLeeaike.leleeieeeplltnaRhkealekal 155
                   + + ++ Gi+           Dl  +++           ++ee+ +lk+Sak+++gi+eL +++ke +++ ++++++   ++R  + le+ +
    AJA92590.1 170 SIQTIKAGITeigdiylvnksDLDGATQlfqalqdfigtDEEEAVILKTSAKKNKGIKELASKLKElMKQ-KSKDKKTSEKTRLESELEDII 260
                   55667777777777777777744444445556667777667778888*******************5554.333444555555544444432 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   5.2e-05      0.03      14      55 ..      23      63 ..      13      66 .. 0.79
   2 !    6.9   0.7    0.0048       2.8     253     361 ..     174     293 ..     164     305 .] 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                HT-HHHHHHHHHHHHHHHHT--EEEEEEESTTSSHHHHHHHH CS
        IIGP 14 egnlqkvvsiikeaikeiesaklkiavtGdsGnGkssFinaL 55
                e++ +++ + ik+ i +++ + + i +tG +G+Gkss in L
  AJA92590.1 23 ENDPKEARKLIKK-IYKLSGKSVVIGITGPAGAGKSSLINRL 63
                5555666666665.6778999999****************88 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0048
                 HHT--BSS-CCCSS--HHHHHHHHHHHHHHHHHTT-SHHH...HHHHHHHTTS-HHHHHCTSSGGGTSSTBSSSHH.HHHHHHHHHHHHHHHT...... CS
        IIGP 253 lkaalvsiiplltllkesdlenleeslklyrkvFGlDdes...lqevArdlgaevkdlkaelkslelfkltkddsi.lerltravkaflrvkg...... 341
                 +ka + + i  + l+++sdl+ +++ +++ + + G D+e    l+  A + +  +k+l  +lk l  +k +++ +  + rl +  + ++  +       
  AJA92590.1 174 IKAGI-TEIGDIYLVNKSDLDGATQLFQALQDFIGTDEEEaviLKTSA-KKNKGIKELASKLKELMKQKSKDKKTSeKTRLESELEDIILNNVrqeist 270
                 56664.56788889999********************97522233333.33455666666655555554443333202233333433332222122222 PP

                 ...TSSSTT-B--HHHHHHHHHH CS
        IIGP 342 ...yleavvtllrklyykrklfl 361
                      ++  ++l+k+  k+ + +
  AJA92590.1 271 migKSKSFSSYLKKVQEKKIDPF 293
                 22266666666666666665555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   7.7e-06    0.0044       1      36 [.      45      80 ..      45     110 .. 0.84
   2 ?   -2.4   0.0       5.8   3.4e+03      72      89 ..     227     244 ..     194     269 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
         PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegd 36
                vIg++g+ GaGk+++ ++l   +++ k+k+a+   d
  AJA92590.1 45 VIGITGPAGAGKSSLINRLSMELKKLKLKPAVLAVD 80
                8***************************99987554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.8
         PRK  72 dllyevlkelkegkkvdk 89 
                 ++l ++lkel + k+ dk
  AJA92590.1 227 KELASKLKELMKQKSKDK 244
                 344444444444443333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   2.2e-05     0.013      21      52 ..      40      73 ..      27     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
      AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd..g 52
                sg + ++ ++G++G GKssl+++l  +l+k   +
  AJA92590.1 40 SGKSVVIGITGPAGAGKSSLINRLSMELKKLklK 73
                566678889*************999877765552 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   3.6   4.6e-05     0.026       2      26 ..      46      70 ..      45     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                EEEEESTTSSHHHHHHHHHTSTEEE CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltgekaiv 26
                ++i G   +GKS+Lin+l+ e  + 
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELKKL 70
                89****************9642222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.8e-05     0.016       1      25 [.      46      79 ..      46     164 .. 0.79
   2 ?   -0.3   0.1       2.6   1.5e+03      44      67 ..     242     267 ..     200     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-05
      AAA_18  1 IlltGtpGvGKttlakeLskrl.gf........g 25
                I++tG++G+GK++l ++Ls +l ++        +
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELkKLklkpavlaV 79
                89****************8887444555555550 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.6
      AAA_18  44 e..aldeskrldedkldklldaleen 67 
                 +  +++e+ rl+ +  d +l+++++ 
  AJA92590.1 242 KdkKTSEKTRLESELEDIILNNVRQE 267
                 12345556666666666666665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.1e-05    0.0063      12      36 ..      44      68 ..      34     118 .. 0.90
   2 ?    0.1   0.5       1.8   1.1e+03      26      80 ..     197     263 ..     192     301 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
                SEEEEEESTTSSHHHHHHHHTTSS- CS
                xxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 12 ekvaivGenGaGKStLlkllagllk 36
                 +++i+G+ GaGKS+L++ l+ +lk
  AJA92590.1 44 VVIGITGPAGAGKSSLINRLSMELK 68
                5799**************9998876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.8
                 HHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH............H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx............x RF
    ABC_tran  26 tLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren............e 80 
                  L+++l      +e+e  + +++ k+ + +++l ++++ l ++++ ++++  +++            +
  AJA92590.1 197 QLFQALQDFIGTDEEEAVILKTSAKKnKGIKELASKLKELMKQKSKDKKT-SEKTrleselediilnN 263
                 55556666555555555555555555444444444444333332222222.12221222333333330 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.6e-05      0.05       3      30 ..      46      73 ..      44      79 .. 0.88
   2 ?   -0.2   0.1       1.4   8.4e+02      97     150 ..     233     293 ..     224     299 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-05
                EEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
       NACHT  3 vilqGeaGsGKTtLlqklalawaegklp 30
                + ++G+aG GK+ L+ +l +++++ kl+
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELKKLKLK 73
                5699******************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                 TCH....................HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE..EEEE-- CS
       NACHT  97 lgq...........kekqpvrtlLselirkkllpeasllltvrpralrdleeqleeaivlevegf 150
                 l++           +ek++++  L+++i  ++ +e s    +  ++++   ++l++ +  ++ +f
  AJA92590.1 233 LKElmkqkskdkktSEKTRLESELEDIILNNVRQEIS----TMIGKSKSFSSYLKKVQEKKIDPF 293
                 4444444555444445555555555555554444444....444444444444444444445555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   5.9e-05     0.034      15      54 ..      40      81 ..      30     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.9e-05
      AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaag..grviglAp 54
                +++  v  +tGpAG+GK+ +++ l   +++ +    v+++ p
  AJA92590.1 40 SGKSVVIGITGPAGAGKSSLINRLSMELKKLKlkPAVLAVDP 81
                455568889*************99766666541244444445 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.8   3.3e+03      78      98 ..      15      35 ..       9      39 .. 0.82
   2 ?   12.9   0.0   0.00013     0.077       2      37 ..      43      78 ..      42      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                EEE----SHHHHHHHHHHHHC CS
  APS_kinase 78 lvafisPyreeReaarellee 98
                ++ +is ++++ ++ar+l+++
  AJA92590.1 15 IAKAISIMENDPKEARKLIKK 35
                778899999999999999986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
  APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLd 37
                +vv+ +tG +g+GKs++ n+l+ +L++ + +  +L 
  AJA92590.1 43 SVVIGITGPAGAGKSSLINRLSMELKKLKLKPAVLA 78
                78999*********************9998877775 PP

>> Virul_Fac  Putative bacterial virulence factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001     0.059      22      64 ..      22      64 ..       9      73 .. 0.87
   2 ?    1.0   0.3      0.16        91     544     581 ..     225     264 ..     201     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
   Virul_Fac 22 lieklrrsrnaarrlgkaaerpmsvgvFGlSQAGKSyLiSaLA 64
                ++++ + +r+  +++ k + +++ +g+ G+  AGKS Li  L+
  AJA92590.1 22 MENDPKEARKLIKKIYKLSGKSVVIGITGPAGAGKSSLINRLS 64
                66777899*******************************9887 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
   Virul_Fac 544 GvsrlaekLekvakpelKleriee..qldeiaeelvearL 581
                 G++ la+kL++++k+++K ++ +e  +l++++e+++ ++ 
  AJA92590.1 225 GIKELASKLKELMKQKSKDKKTSEktRLESELEDIILNNV 264
                 8999999999999999999888762256777777776655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     0.001      0.58      21      37 ..      45      61 ..      25      67 .. 0.90
   2 ?    4.4  10.7      0.08        46      73     152 ..     213     299 ..     139     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
      AAA_23 21 ltlItGpNGaGKTTild 37
                +  ItGp GaGK+++++
  AJA92590.1 45 VIGITGPAGAGKSSLIN 61
                567************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.08
      AAA_23  73 ay.veltfenkdgry......trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkk 152
                 a+ ++ + ++++g++      ++ ++++ + +k+++kt+ +++le +  ++ +q+is+ +g++k+ ++++   ++++ ++fe +dk+
  AJA92590.1 213 AViLKTSAKKNKGIKelasklKELMKQKSKDKKTSEKTRLESELEDIILNNVRQEISTMIGKSKSFSSYLKKVQEKKIDPFEAADKL 299
                 223555555555555776666666666666666777777777777888899999999999999999999999999998888877664 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0039       2.3      26      60 ..      46      81 ..      16      84 .. 0.90
   2 ?    6.9   0.6      0.01         6     156     201 ..     217     264 ..     154     295 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
       DUF87 26 lAilgsTGsGKSntvavLleelle.kkgatililDp 60
                ++i g +G+GKS ++  L  el + k +  +l +Dp
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELKKlKLKPAVLAVDP 81
                689999*****************7666668888887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
       DUF87 156 elrklknqaiarlldkledllrkggsf..snsstdliallleklekeg 201
                 + + +kn+ i++l +kl++l+++++++  ++++t+l+++l++++ ++ 
  AJA92590.1 217 KTSAKKNKGIKELASKLKELMKQKSKDkkTSEKTRLESELEDIILNNV 264
                 344444445555555555555544444444444444444444444333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.085       2      27 ..      46      71 ..      45      76 .. 0.89
   2 ?   -2.0   0.1       5.1     3e+03      70      93 ..     246     268 ..     220     288 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                EEEE--TTSSHHHHHHHHHHHH...G CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                + iTGp G GK+ l+++++ +lk+  
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELKKLK 71
                78*******************98765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                 EETTEEE-HHHHHHHHHHHHHHHH CS
    NTPase_1  70 rvgkyvvdvesfeelalealrkal 93 
                   +k  ++  ++e+++l+++r+++
  AJA92590.1 246 TSEKTRLE-SELEDIILNNVRQEI 268
                 33333333.455666666665544 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.01       5.9       4      30 ..      44      70 ..      42      84 .. 0.87
   2 ?    5.2   0.1     0.024        14     155     192 ..     200     237 ..     153     239 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                EEEEEEESTTSSHHHHHHHHHHHTTSS CS
    GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgai 30
                + igi g   +GK++L+ rL +++++ 
  AJA92590.1 44 VVIGITGPAGAGKSSLINRLSMELKKL 70
                5799****************9988775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.024
                 HHHHHH.HHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 155 ekleky.gekgekevpvvfgSalkgegvktllealvell 192
                 ++l+++ g+++ +e  ++ +Sa+k++g+k+l + l el+
  AJA92590.1 200 QALQDFiGTDE-EEAVILKTSAKKNKGIKELASKLKELM 237
                 23333325565.58899************9998887765 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00013     0.076      27      67 ..      39      79 ..      22      86 .. 0.81
   2 ?    0.6   0.4      0.35     2e+02      28      96 ..     179     247 ..     170     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
      AAA_35 27 iekpGalirikapkkmGKtSLlarilakakqqgyktvsldl 67
                ++ + ++i i +p   GK+SL++r+  + k+ + k ++l +
  AJA92590.1 39 LSGKSVVIGITGPAGAGKSSLINRLSMELKKLKLKPAVLAV 79
                4445679*******************999999988888766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
      AAA_35  28 ekpGalirikapkkmGKtSLlarilakakqqgyktvsldlqladkeilsdldkflrwfcanvsrqLkle 96 
                 ++ G +  ++ +   G t L + + ++  + + ++v l+ +  +++ +++l + l+ + ++ s+  k +
  AJA92590.1 179 TEIGDIYLVNKSDLDGATQLFQALQDFIGTDEEEAVILKTSAKKNKGIKELASKLKELMKQKSKDKKTS 247
                 555555556666666777777777777777777777777777777777777777776666554443333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00041      0.24       3      34 ..      48      76 ..      46      92 .. 0.77
   2 ?   -1.1   0.1       4.3   2.5e+03      17      17 ..     263     263 ..     222     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsv 34
                  ++Gp+g GKS+l+++L+ +l    klk k+ v
    AJA92590.1 48 ITGPAGAGKSSLINRLSMELK---KLKLKPAV 76
                  89***************9998...44444555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
  RNA_helicase  17 e 17 
                   +
    AJA92590.1 263 N 263
                   2 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00041      0.24      36      67 ..      46      77 ..      16      86 .. 0.80
   2 ?   -1.4   0.0       2.5   1.5e+03      44      63 ..     272     291 ..     246     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
       AAA_7 36 vllvGptGtGKtviikdllkkldkekylslti 67
                + ++Gp+G GK+++i++l  +l+k k++++++
  AJA92590.1 46 IGITGPAGAGKSSLINRLSMELKKLKLKPAVL 77
                4579******************9998888766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
       AAA_7  44 tGKtviikdllkkldkekyl 63 
                  GK+   +++lkk++++k+ 
  AJA92590.1 272 IGKSKSFSSYLKKVQEKKID 291
                 68999999999999987765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00025      0.14      24      39 ..      45      60 ..      34      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
      AAA_29 24 atlltGpsGsGKSTll 39
                ++ +tGp G+GKS+l+
  AJA92590.1 45 VIGITGPAGAGKSSLI 60
                5569***********9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.07       5      45 ..      29      68 ..      26      73 .. 0.80
   2 ?   -0.7   0.2       1.1   6.5e+02      73      96 ..     233     256 ..     193     268 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                HHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
      NB-ARC  5 vekviekLlekdelqslvvalvGmgGvGKttlakqilnksd 45
                 +k+i+k   k + +s+v+++ G +G GK+ l++    +++
  AJA92590.1 29 ARKLIKKIY-KLSGKSVVIGITGPAGAGKSSLINRLSMELK 68
                578999999.5666679***************988766655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.1
                 HHHHHCCCTTSSSS-STTSHHHHH CS
      NB-ARC  73 lkeLslseddleekeeveslkrkl 96 
                 lkeL ++++++++ +e+  l+ +l
  AJA92590.1 233 LKELMKQKSKDKKTSEKTRLESEL 256
                 344444444444444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.14       2      35 ..      43      83 ..      42     145 .. 0.80
   2 ?    0.2   0.7      0.89   5.1e+02     133     161 ..     238     265 ..     192     291 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
      AAA_24  2 klkiliyGpsgiGKTtlakel.......gpkplfidtekGl 35
                ++ i i+Gp+g+GK++l+++l       + kp+++ ++  +
  AJA92590.1 43 SVVIGITGPAGAGKSSLINRLsmelkklKLKPAVLAVDPTS 83
                57899***************988888886677776666555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.89
      AAA_24 133 trkdedpegeakytrlepklgkktanelk 161
                 ++k +d++++ ++trle++l++   n+++
  AJA92590.1 238 KQKSKDKKTS-EKTRLESELEDIILNNVR 265
                 3333333333.556666666666655555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00029      0.17       9      55 ..      42      86 ..      34     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00029
      AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAa 55
                k+ v+ +t+++G GK+ +++    +l++l+      +l+v +t++ +
  AJA92590.1 42 KSVVIGITGPAGAGKSSLINRLSMELKKLKLK--PAVLAVDPTSHVT 86
                5567889********************99955..5788888887754 PP

>> Flagellin_N  Bacterial flagellin N-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.8   1.6e+03      30      60 ..      40      70 ..      18      74 .. 0.76
   2 ?    5.4   0.1     0.031        18      24      58 ..      97     131 ..      91     149 .. 0.90
   3 ?    6.3   1.6     0.017       9.7      70     122 ..     215     264 ..     190     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.8
                 TSBTTSSTTS-HHHHHHHHHHHHHHHHHHHH CS
  Flagellin_N 30 tGlridsalddaaglaisvslrsqiaglsql 60
                 +G+ +  + + +ag++ s  +++ + +l++l
   AJA92590.1 40 SGKSVVIGITGPAGAGKSSLINRLSMELKKL 70
                 7999999999999999998877777666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                  HHHHHTTSBTTSSTTS-HHHHHHHHHHHHHHHHHH CS
  Flagellin_N  24 aqeelstGlridsalddaaglaisvslrsqiagls 58 
                   +e   tG++i s ++ +a+ ai+ s r  ++ l+
   AJA92590.1  97 MTESTDTGTYIRSIASRGATGAIAHSVRNSLRVLE 131
                  577889**********************9998887 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.017
                  HHHHHHHHHHHHHHHHHHHHHHHHHHT-TTTS-SHHHHHHHHHHHHHHHHHHH CS
  Flagellin_N  70 rlqtaqgalselsdilqrlkelavaasndsnsdedrqslqaelqqLtdelnri 122
                  +l+t+ +  + +++ + +lkel+ ++s+d++++e ++ l++el++ +  ln++
   AJA92590.1 215 ILKTSAKKNKGIKELASKLKELMKQKSKDKKTSE-KTRLESELEDII--LNNV 264
                  6888999999999************999999777.999999999886..5555 PP

>> PPR_3  Pentatricopeptide repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.022        13      26      51 ..      52      77 ..      48      78 .. 0.88
   2 ?    0.4   0.4       1.2   7.2e+02      24      44 ..     220     240 ..     216     241 .. 0.86
   3 ?    1.2   0.0       0.7     4e+02      28      48 ..     272     292 ..     267     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
       PPR_3 26 anagnkklalevlermkkkgikPtvv 51
                a ag+  l+++  +++kk ++kP v+
  AJA92590.1 52 AGAGKSSLINRLSMELKKLKLKPAVL 77
                6789*******************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
       PPR_3  24 ayanagnkklalevlermkkk 44 
                 a +n g k+la++  e mk+k
  AJA92590.1 220 AKKNKGIKELASKLKELMKQK 240
                 567888899**********97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.7
       PPR_3  28 agnkklalevlermkkkgikP 48 
                  g+ k  +  l+++++k+i P
  AJA92590.1 272 IGKSKSFSSYLKKVQEKKIDP 292
                 67888889999********99 PP

>> DUF1053  Domain of Unknown Function (DUF1053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.6    0.0013      0.74      31      91 ..     231     290 ..     209     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0013
     DUF1053  31 iplkksklqdkkersasekarleeelderleqaIdglsskklwkrsedlkkftliFkeksl 91 
                  +lk+   q++k+++ sek rle el++ + +++ +  s+ + ++s+ +  ++ + +ek++
  AJA92590.1 231 SKLKELMKQKSKDKKTSEKTRLESELEDIILNNVRQEISTMI-GKSKSFSSYLKKVQEKKI 290
                 455666678899************************999999.9*****999988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2234  (0.124603); expected 358.6 (0.02)
Passed bias filter:                      889  (0.0495845); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 2024.75
//
Query:       AJA92591.1  [L=65]
Description: hypothetical protein T478_0265 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.19   11.1   4.3       0.19   11.0   4.3    1.0  1  DUF4191          Domain of unknown function (DUF4191)
       0.33    9.7   8.2       0.35    9.6   8.2    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
       0.34   11.4   1.3       0.46   10.9   1.3    1.4  1  PhoR             Phosphate regulon sensor protein PhoR
       0.52   10.1   1.8       0.61    9.8   1.8    1.2  1  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
       0.55    9.5   3.7        0.6    9.4   3.7    1.1  1  SLATT_5          SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.3   5.3e-05      0.19      22      70 ..       4      54 ..       1      63 [. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.3e-05
     DUF4191 22 dkkllwlllaaflvvvvvfvvlgll..lgslilllilgillgllvalivlt 70
                dk+ l ++++ f+   ++fv+  ++  +++++l+ i+gi++++l+ li + 
  AJA92591.1  4 DKANLLVIIISFIFGSALFVITIIAgfIMGHYLFGIVGIIISILCILIGFI 54
                67766677777776666666554442124799**********999998775 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.2   9.7e-05      0.35     384     436 ..       9      61 ..       2      65 .] 0.54

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 9.7e-05
     DUF2207 384 salglgliilglilillallllvlllvfllilllillliaiivlllfsrllgr 436
                  ++++ +i+ + ++++ ++++++++ ++++i+++i+ +++i++ ++  + + +
  AJA92591.1   9 LVIIISFIFGSALFVITIIAGFIMGHYLFGIVGIIISILCILIGFIKLGKFNK 61 
                 22222233333333333333333338888888888888888888886555544 PP

>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.3   0.00013      0.46      10      52 ..      20      63 ..       6      65 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
        PhoR 10 allllaallvgllvgalaalll..lalllllawhlyqllrLsrWL 52
                al+++ + ++g+++g++ + ++  ++++l+++  + +l ++++ +
  AJA92591.1 20 ALFVITI-IAGFIMGHYLFGIVgiIISILCILIGFIKLGKFNKKI 63
                4555555.99********999998888888888888888887766 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.8   0.00017      0.61      25      50 ..      27      52 ..      17      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
  Phage_holin_2_4 25 faGflasselialvGlavAliGlLvn 50
                     +aGf+    l ++vG+++ ++ +L+ 
       AJA92591.1 27 IAGFIMGHYLFGIVGIIISILCILIG 52
                     79********************9996 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.7   0.00017       0.6      28      84 ..       5      57 ..       2      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00017
     SLATT_5 28 rknklstfslsllSvylivlsllsnkssestinenlldflsiilSilvlvislless 84
                + n l++++ ++++ +l+v+ ++      + + + l+ +++ii+Sil ++i+++  +
  AJA92591.1  5 KANLLVIIISFIFGSALFVITIIA----GFIMGHYLFGIVGIIISILCILIGFIKLG 57
                566778888889999999999999....99*********************998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 443.38
//
Query:       AJA92592.1  [L=377]
Description: hypothetical protein T478_0635 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.71   10.3   3.9        9.8    6.6   0.2    3.2  2  Mg-por_mtran_C  Magnesium-protoporphyrin IX methyltransferase


Domain annotation for each model (and alignments):
>> Mg-por_mtran_C  Magnesium-protoporphyrin IX methyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4    0.0074   1.3e+02      49      72 ..     145     168 ..     142     193 .. 0.77
   2 ?    6.6   0.2   0.00055       9.8      59      92 ..     300     333 ..     288     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0074
                     S-----------B-HHHHHHHHHH CS
  Mg-por_mtran_C  49 fprsdrstaiylvaeeklrealaa 72 
                     f r+ r+ +i++v+e+++++  ++
      AJA92592.1 145 FVRKRRTQRIEQVEEKEVQKNDET 168
                     8899**************987555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00055
                     --B-HHHHHHHHHHTTEEEEEEEEEE-SS-EEEE CS
  Mg-por_mtran_C  59 ylvaeeklrealaaaglkvkrterissgfYisql 92 
                      l +e+++++ +a+ + k++++e++ss+f  s+l
      AJA92592.1 300 KLKTEKEIESKIAKLEKKLEKEEKVSSNFVKSTL 333
                     456899***********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      5019  (0.279938); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                       372  (0.0207485); expected 17.9 (0.001)
Passed Fwd filter:                        95  (0.00529868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 1.76u 0.33s 00:00:02.09 Elapsed: 00:00:00.57
# Mc/sec: 1976.45
//
Query:       AJA92593.1  [L=267]
Description: adenylate/guanylate cyclase catalytic domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-13   48.4   0.0    1.1e-12   48.0   0.0    1.1  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   5.9e-17   1.1e-12       5     164 ..      75     243 ..      72     260 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 5.9e-17
  Guanylate_cyc   5 sydevtilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglpeekaahaaklaelaLdmleal....eev.ave 95 
                    +++++ +++ d+vg+t++      ++v  ++ +  +++   ++++++   k++Gda + ++  + ++  +a +++  a  m++ +    + + ++ 
     AJA92593.1  75 EKQSMVVMYVDLVGSTDITLTLPEEKVAIIISSFAQEMAYAVKHHGGFVLKFVGDAVIGYFVHQ-SSLIAADNAIGAAKSMIKIIeegiNPIlNQY 169
                    678899**************99455555666777789*******************87776555.4445555555555555555520033331333 PP

  Guanylate_cyc  96 skeglkvrvGihtGpvvagviG..akkprydvwGntvnlAsrmestgkagkiqvseetyellk...eeqfelte 164
                    + ++l v++Gi+ G+ ++   G  a+k + d+ G + n+A++++  +k+++i + e++y   +   +++f+ +e
     AJA92593.1 170 DYPDLFVKIGIDFGTNMIVRYGsdAEKSHVDLLGPAMNIAAKIQGKAKPQEILIGEDVYTRIHpslQKEFSKKE 243
                    48*************98888887799*********************************998876666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1950.71
//
Query:       AJA92594.1  [L=442]
Description: decarboxylase, UbiD family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-91  304.9   0.0    9.2e-91  304.7   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.7   0.0   5.2e-95   9.2e-91       1     406 []       9     393 ..       9     393 .. 0.94

  Alignments for each domain:
  == domain 1  score: 304.7 bits;  conditional E-value: 5.2e-95
                 HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..----EE--GCG- CS
        UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkppippkvveseka 99 
                 +++l+k +e++ ik++v++++Eia i+ ++   g  allFen+k++  +f +++nl+gtr+r+ala + s+ ++i e + + +++    +pk     k+
  AJA92594.1   9 ISKLKKSKEIKIIKKKVSTKFEIAGITAKAD--GTSALLFENIKQN--NFNLVSNLVGTRKRFALAVN-SKENKIHESIYSSIKK--AKKPKITP--KG 98 
                 689**************************98..899*******755..7******************9.6678999999988886..35888885..46 PP

                 GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHH CS
        UbiD 100 pcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPal 198
                 ++ e++       +Ls+LP++t+++++ Gp+it+++v++++ e +++n  ++R++ +dk+++ +++++++++++++ +ak+ g e+l+va+++Gv+Pa+
  AJA92594.1  99 KFFENT-----SKNLSELPIVTHFEKESGPFITSAIVYSQNHEFKTQNSAFHRLMPVDKTHFSIRMVEGRHSHRNFMNAKEHG-EDLKVAITVGVHPAI 191
                 677555.....469*********************************************************************.9************** PP

                 HHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCC CS
        UbiD 199 tlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkp 297
                  +a++ ++  g +El++a  l g ++ l+kc+ ++++vp+  Eiv+eG i  ++t +E  +++++ +y+++rd +p+f+++++++R++pi++ ++ g  
  AJA92594.1 192 SIAGAYQADWGKDELHIANSLLGNKLTLTKCPYTGMHVPSGTEIVMEGKILQDKTDKEW-MVEMLRTYDHPRD-QPLFELEKMYYRNNPIFHDILSGYG 288
                 ****************************************************9866665.9**********99.5*****************9999999 PP

                 SHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CC CS
        UbiD 298 peedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpd 396
                  e+++l+g+++e+ +  ++kk+ p+ ++v l   g  +l+av++i+k+   + kk+++ ++a ++  sl K+v +vD+d+++ + ++v++a+atr+++d
  AJA92594.1 289 -EHHLLMGMPIESKLNGIIKKKYPSTNQVVLSNGGSHWLHAVAQISKKPSTNVKKIINEIFASHR--SL-KMVTIVDDDIEPSNSEQVEYAMATRFQAD 383
                 .***********************999999998888777******88878999**********99..99.***************************** PP

                 CCEEEECCCE CS
        UbiD 397 rDlviiegtr 406
                 +D+v+i+++r
  AJA92594.1 384 KDMVLIKNVR 393
                 ******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3138.13
//
Query:       AJA92595.1  [L=344]
Description: 3-beta hydroxysteroid dehydrogenase/isomerase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-45  154.7   0.0    3.6e-45  154.3   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
      2e-29  103.1   0.0    4.9e-29  101.8   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.6e-19   70.0   0.2    2.2e-19   69.6   0.2    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.6e-06   27.4   0.0    7.1e-06   26.0   0.0    1.6  2  NAD_binding_10   NAD(P)H-binding
    0.00056   19.1   0.1     0.0023   17.1   0.0    1.8  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00087   18.5   0.0       0.04   13.1   0.0    2.1  2  NAD_binding_4    Male sterility protein
     0.0016   18.0   0.0     0.0028   17.1   0.0    1.3  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.084   13.1   0.0       0.27   11.5   0.0    1.8  2  VF530            DNA-binding protein VF530


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.0   1.6e-48   3.6e-45       1     240 [.       8     255 ..       8     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 1.6e-48
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT..-HHHHHHHHHHHT-SEEEE--S.---HHHHHHSHHHHHHHHTH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldlt..drsalerlfkeeqpdavihlAa.vggvaassedpadfieknlq 93 
                 +lVtG++ fi s+lv++l ++g +v+++d ls+++++++ +     ++v+ dl    ++++++lf+  + ++v+h+Aa  gg +   ++pad+  +n++
  AJA92595.1   8 VLVTGGASFISSHLVDNLVNQGATVTVVDDLSNGKKENLSKSWdsiKFVQQDLEyvSKNEMKKLFD--GNEIVFHFAAdHGGRGYIDTHPADVC-SNFA 103
                 79*****************************9999988887779998888777622666*******..89********9999999999999976.7*** PP

                 HHHHHHHHHHHHTCTEEEEEEEGGGGT...........SCSSSSBSTCSTTS--....--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS CS
   Epimerase  94 gtlnlleaarkagvkrllflsSsevYG...........kdaeqpkeettltgpl....kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprn 177
                 +  ++++a++ + v++++f sS++vY+           k     kee+++ ++l         Y+ aKl++e +++++++qygl+ + +r  + yGpr 
  AJA92595.1 104 IDHHVFDACNNSSVEKIIFSSSACVYPtelqneigsdyKL----KEEDSDCDKLngflSADVEYGWAKLMSEVQMKSFNKQYGLKGCPVRFVTAYGPR- 197
                 ***************************6655555544433....55555444444456999*************************************. PP

                 -TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEE CS
   Epimerase 178 gegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyni 240
                   ++v++ i ali k+ e+ ++  ++g+g++ Rdf yveD++++++l++e+ ++      +n+
  AJA92595.1 198 --EDVTHAIIALIYKAVEKMDPYQIWGNGQQERDFTYVEDIVTGSILAAEKISDM---TPINL 255
                 ..88**************99******************************95553...34555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   2.2e-32   4.9e-29       1     332 []       9     320 ..       9     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 2.2e-32
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-..HHHHHHHHHHHT-SEEEE--S---HHHHTTS CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltD..ssslerllaevqpdevynLAAqshVdvsfek 94 
                    L+TG+a fi s+l++ L+++g +v++++++s+     + e+l k       +++k+++ Dl+   ++++++l++    + v+++AA    +  +++
     AJA92595.1   9 LVTGGASFISSHLVDNLVNQGATVTVVDDLSNG----KKENLSK-----SWDSIKFVQQDLEYvsKNEMKKLFDGN--EIVFHFAADHGGRGYIDT 93 
                    9***********************998766554....4566654.....246799*****97533899*******9..579******999999987 PP

                    HHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB......-TT........S-----SHHHHHHHHHHHHHHHHHHHH---EE CS
  GDP_Man_Dehyd  95 PeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpq......tEt........tpfyPrsPYaaaKlyadwivvnyreayglfav 176
                      + +  n+   +++++a+ +  +e   +++++S++ vY +  +  +      +E+          +++   Y+ aKl+++  +++++++ygl  +
     AJA92595.1  94 HPADVCSNFAIDHHVFDACNNSSVE---KIIFSSSACVYPTELQNEIgsdyklKEEdsdcdklnGFLSADVEYGWAKLMSEVQMKSFNKQYGLKGC 186
                    6667777788899******999886...8999*******987432221112224543444444345667999************************ PP

                    EEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHH CS
  GDP_Man_Dehyd 177 ngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiew 272
                      ++   ++pr     vt+ i+  + ++ ++  +  + Gn+++ Rd+++v+D+v++  l+ ++       i++ +  ++++ v+ ++++++k i+ 
     AJA92595.1 187 PVRFVTAYGPRE---DVTHAIIALIYKAVEKMDPYQIWGNGQQERDFTYVEDIVTGSILAAEK-------ISDMTPINLGTGVRYKMIDVVKMICE 272
                    ***********3...599*********99999888889******************9886664.......44555666666666777777666664 PP

                    H............TTGGCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
  GDP_Man_Dehyd 273 egkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                                  g +  e+d+ + +p+ +  +  d+s+ak+ LgW+pk+s++++++++
     AJA92595.1 273 VL------------GWEPKEFDFDTSKPTGALSRSLDNSRAKQLLGWEPKFSLKQGLEKT 320
                    32............2334579999********************************9986 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.2   9.6e-23   2.2e-19       1     236 [.       9     251 ..       9     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 9.6e-23
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvt..dkdkleealegvdvvihlaslvdvag...kltedeimkvnvk 94 
                 +vtGga F+ ++lv +Lv+ +   +v v+D   + ++ + +++ + +k+++ D+   +k+++++  +g ++v+h a+    +g   +   d +   n  
  AJA92595.1   9 LVTGGASFISSHLVDNLVNQG--ATVTVVDDLSNGKKENLSKSWDSIKFVQQDLEyvSKNEMKKLFDGNEIVFHFAADHGGRGyidTHPADVC--SNFA 103
                 69*******************..5999999888888878899999999*****9544899***************998888883212223333..3666 PP

   3Beta_HSD  95 GTrnvleacvkagvrvlvYtSsaevv...gpnslgeeilngdEeleyesl.....hqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGeg 185
                   + v +ac +++v+++++ Ssa v     +n  g +    +E+   ++l         y   K ++E  +++ N    + g  l  c +R ++ yG++
  AJA92595.1 104 IDHHVFDACNNSSVEKIIFSSSACVYpteLQNEIGSDYKLKEEDSDCDKLngflsADVEYGWAKLMSEVQMKSFNK---QYG--LKGCPVRFVTAYGPR 197
                 679*****************99976511123444444444555555555455432445699999999999999999...555..99************* PP

   3Beta_HSD 186 dkllvpllkqlaklglal...fkigdeevlsdrvYvgNvawahilAaralqdpk 236
                 ++++ + +  ++k  +++      g+ ++  d++Yv+ ++   ilAa ++ d  
  AJA92595.1 198 EDVTHAIIALIYKAVEKMdpyQIWGNGQQERDFTYVEDIVTGSILAAEKISDMT 251
                 ***999998888877666442456999999*******************99874 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.2e-09   7.1e-06       1     103 [.      12     130 ..      12     158 .. 0.75
   2 ?   -1.8   0.0       1.1   2.4e+03     162     181 ..     189     208 ..     168     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.2e-09
                     TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCT.TTCEEEE--TT..-CCHHHHHHTT-SEEEES---TCC.....HHHH........ CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleae.eglevvegdvt..dvedlaealkgadaVvsalggggk.....deeg........ 77 
                     G+   + ++lv+ l+++g  +vt++  +    k ++l+++ + ++ v+ d++  +++++++ ++g ++V+  ++ +g+     + +         
      AJA92595.1  12 GGASFISSHLVDNLVNQG-ATVTVV-DDlsNGKKENLSKSwDSIKFVQQDLEyvSKNEMKKLFDGNEIVFHFAADHGGrgyidT-HPadvcsnfa 103
                     66677999*********6.888765.4422223344554448999999999855789************988866666466641.2256677777 PP

                     .HHHHHHHHHHCT--EEEEEEETTTTS CS
  NAD_binding_10  78 .aknivdaakeagvkRfvlvsaigvgd 103
                        ++ da++++ v+++++ s+++v+ 
      AJA92595.1 104 iDHHVFDACNNSSVEKIIFSSSACVYP 130
                     78889********************94 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                     S----EEEHHHHHHHHHHHC CS
  NAD_binding_10 162 pfkggsisradVAdvlvavl 181
                     +f ++  +r+dV ++++a++
      AJA92595.1 189 RFVTAYGPREDVTHAIIALI 208
                     56677889999999999986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-06    0.0023       1     136 [.       8     132 ..       8     139 .. 0.80
   2 ?   -0.6   0.0      0.25   5.7e+02     138     168 ..     163     190 ..     160     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-06
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------.HHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKh.VPlv 93 
                      vlvtG++  i s+lv++++++ ++  ++ + +  k  +++k+ +      ++k+   + +  v  k++++k+++  + ++vfh AA       +
       AJA92595.1   8 VLVTGGASFISSHLVDNLVNQGATVTVVDDLSNGKKENLSKSWD------SIKFV-QQDLEYV-SKNEMKKLFD--GNEIVFHFAADHGgRGYI 91 
                      89*********************999999999999999999862......23333.3334444.6789******..*******99966515677 PP

                      HHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--S CS
  Polysacc_synt_2  94 eenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtn 136
                      +++p+++   N    ++v +a+ ++ v+k+++ S+   v+Pt 
       AJA92595.1  92 DTHPADV-CSNFAIDHHVFDACNNSSVEKIIFSSS-ACVYPTE 132
                      7777775.567777899************998665.5677775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                      HHHHHHHHHHHHHHGGG--SSS--EEEEEEE CS
  Polysacc_synt_2 138 mGatKrlaekllqalakeseekktkfvvvRf 168
                      +G +K+++e  + +++k+ +    k + vRf
       AJA92595.1 163 YGWAKLMSEVQMKSFNKQYG---LKGCPVRF 190
                      78888888888888888874...34444444 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.016        37       1      25 [.      10      34 ..      10      48 .. 0.78
   2 !   13.1   0.0   1.8e-05      0.04      76     203 ..      63     190 ..      42     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                   EE-TTSHHHHHHHHHHHHHS-.TEE CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                   +TG+  F+ ++L+ +L+++ + v++
     AJA92595.1 10 VTGGASFISSHLVDNLVNQGATVTV 34
                   6999999999999999988876544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.8e-05
                    --HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.......HHH--EEE CS
  NAD_binding_4  76 LseedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeege.keekldedera 167
                    +s++++++l +  ++++h aA+    + +++    +  N    ++v++ +++ +    +++ S+a+v++++ ++    + +  + kee  d d+++
     AJA92595.1  63 VSKNEMKKLFDGNEIVFHFAADHGGRGYIDThpaDVCSNFAIDHHVFDACNNSSVE-KIIFSSSACVYPTELQNE---IGSDYKlKEEDSDCDKLN 154
                    57899999*************988777555532245567778899******88777.999****99998887542...222222144444444445 PP

                    ETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE CS
  NAD_binding_4 168 klkglpntYeqsKalaEklvrearrrsglpvvivRp 203
                       +   +Y + K ++E  +++ +++ gl+ + vR 
     AJA92595.1 155 GFLSADVEYGWAKLMSEVQMKSFNKQYGLKGCPVRF 190
                    55555569*****************99999887775 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0028       3      68 ..       8      72 ..       7      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT..SHHHHHHHH CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt..dreevealv 68
                vlvtG++s I   ++++l+++Ga+v+vvd  ++  +e +++     +++ ++q D++  +++e+++l+
  AJA92595.1  8 VLVTGGASFISSHLVDNLVNQGATVTVVDDLSNGKKENLSKSW---DSIKFVQQDLEyvSKNEMKKLF 72
                89*************************9988877755555544...4699999999977777888776 PP

>> VF530  DNA-binding protein VF530
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.27      20      44 ..     162     186 ..     153     192 .. 0.89
   2 ?   -2.9   0.0       3.7   8.2e+03      10      24 ..     263     277 ..     259     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                 HT-HHHHHHHTTSSSTTSS--HHHH CS
       VF530  20 eygweeLaerinircFksnpsikSs 44 
                 eygw++L +++++++F+++  +k +
  AJA92595.1 162 EYGWAKLMSEVQMKSFNKQYGLKGC 186
                 7*****************9888876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                 HHHHHHHHHHHT-HH CS
       VF530  10 lekileeLveeygwe 24 
                 + ++++ + e  gwe
  AJA92595.1 263 MIDVVKMICEVLGWE 277
                 557899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2342.85
//
Query:       AJA92596.1  [L=216]
Description: hypothetical protein T478_1363 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1554.17
//
Query:       AJA92597.1  [L=232]
Description: precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-32  111.0   0.0    8.4e-32  110.8   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   4.7e-36   8.4e-32       1     212 [.       3     207 ..       3     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 4.7e-36
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aealragkdVvllvsGDPlvy..g 94 
                   k++ VGvGpG+p+++T  + +++ ++dvv+g++ ++ + +++++++           k+ le ++++++ea+   a ++ +++++ ++GD +++   
    AJA92597.1   3 KVFAVGVGPGSPKYVTDIVKDVISQCDVVIGYG-YTIKTIEEYVKD-----------KKILEVTMQNQEEAYqEIAKEDNHTILVPFTGDVNFSesE 87 
                   6899*****************************.******999954...........778888877788888655555556799999*******666 PP

  TP_methylase  95 tgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeereleallangdtlvllkapr.k.......laelaelLkea 183
                   ++++l+e+  +      ve+iPG+ss q aa+r+++p ++++++++++ +++++++ ++ +al++ g +++l+ +p+ k        +e+a+ Lk+ 
    AJA92597.1  88 VVDRLIEIYDE------VEIIPGISSTQVAASRAKVPTDKSKVITMHISTSIEEKKLELQKALID-GLSVILVPRPWpKvpekhfmQSEIAKYLKQN 177
                   66777766666......*******************************77777666666666666.9999***999987888999999********* PP

  TP_methylase 184 .lyddttpvavveragtedervvrgtleel 212
                    ++    +v+v+e ++te+e+ ++gt+e+l
    AJA92597.1 178 gFDTSKMKVHVYESITTENETSFEGTVEQL 207
                   ***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1633.62
//
Query:       AJA92598.1  [L=274]
Description: transglutaminase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-41  142.1   0.0    1.7e-41  141.4   0.0    1.3  1  Transglut_core2  Transglutaminase-like superfamily
    9.6e-11   41.7   0.0    1.6e-10   41.0   0.0    1.4  1  TPR_9            Tetratricopeptide repeat
    0.00037   20.2   0.5      0.002   17.8   0.4    2.2  2  TPR_1            Tetratricopeptide repeat
    0.00086   19.3   3.1     0.0024   17.9   0.3    2.6  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
     0.0017   18.5   1.7     0.0055   16.8   0.2    2.5  2  TPR_8            Tetratricopeptide repeat
     0.0045   17.0   0.2      0.014   15.4   0.2    1.9  1  TPR_2            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.6   0.1      0.038   14.5   0.1    1.5  1  TPR_19           Tetratricopeptide repeat
        0.2   11.9   0.3       0.95    9.6   0.0    2.0  2  LAM_C            Lysine-2,3-aminomutase


Domain annotation for each model (and alignments):
>> Transglut_core2  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   7.6e-45   1.7e-41       4     155 .]      45     192 ..      42     192 .. 0.96

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 7.6e-45
  Transglut_core2   4 laeLdalaaevraelsseraaaekleaLnellyeelgFagneddyydprnslldqVLerrrGiPislsvvylevArrlglplegvgfPghflvr 97 
                      l++++++  ++r+++++ +++   +  Lne+l++   F+g+ ddyy+p+n +l+ VLer  GiPi+l+++y e+A+ ++l+l+ vgfP h++v+
       AJA92598.1  45 LERIKEIGINFRNRITESKNPTYLISLLNEFLFDVEEFQGDLDDYYNPKNNFLNYVLERSSGIPITLCILYTEIAKYADLDLKIVGFPSHVIVK 138
                      56788888999***9999999999********************************************************************** PP

  Transglut_core2  98 vgespegevliDPfnaGrllskedleellraalgaeaeltreflapasnrdvltRllr 155
                      ++    +e+++DPfn+Grll+ edl+e+l +++g+++e+++e+l+++s++++l R+lr
       AJA92598.1 139 YE----EEMILDPFNRGRLLELEDLQEILYQNYGDSVEFQAEYLNQISDEKILIRMLR 192
                      99....67************************************************97 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   7.1e-14   1.6e-10       1      72 [.     194     265 ..     194     266 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.1e-14
       TPR_9   1 lkaiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                 lk+ +  +  +e a  +  ++l + P++++e+rd G+l+++l ++  Al+ L+ yl+++p+a+d++ + +++
  AJA92598.1 194 LKNSYTDSFAYEMASMCNRMILEILPESADEIRDMGILEEKLKNYDNALEFLNKYLEMEPNAEDVDFVLELI 265
                 7999999999999999**************************************************999987 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   2.7e+03      16      33 ..     203     220 ..     196     221 .. 0.77
   2 !   17.8   0.4   9.1e-07     0.002       7      33 ..     228     254 ..     226     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                 -HHHHHHHHHHHHHHSTT CS
       TPR_1  16 kydeAleyyekALelnPn 33 
                  y+ A  + +  Le+ P+
  AJA92598.1 203 AYEMASMCNRMILEILPE 220
                 589999999999999886 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.1e-07
                 HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                 +G +  kl++yd Ale+ +k Le +Pn
  AJA92598.1 228 MGILEEKLKNYDNALEFLNKYLEMEPN 254
                 688999********************8 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       4.7   1.1e+04      36      48 ..     174     186 ..     174     186 .. 0.86
   2 ?    0.9   0.0      0.21   4.7e+02      17      33 ..     204     220 ..     201     223 .. 0.90
   3 !   17.9   0.3   1.1e-06    0.0024      13      44 ..     234     265 ..     232     274 .] 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.7
                 HHHHHHHHHHHHH CS
  Fis1_TPR_C  36 QaqsLkeliedki 48 
                 Qa+ L+++ ++ki
  AJA92598.1 174 QAEYLNQISDEKI 186
                 8999999999887 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                 HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  17 YseArryvdalLeiEPe 33 
                 Y++A  +++++Lei Pe
  AJA92598.1 204 YEMASMCNRMILEILPE 220
                 9************9887 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.1e-06
                 HHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHH CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQaqsLkeli 44 
                 kl++Y++A+++++  Le+EP+ + +    eli
  AJA92598.1 234 KLKNYDNALEFLNKYLEMEPNAEDVDFVLELI 265
                 9*******************998875544444 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.99   2.2e+03      24      31 ..      24      31 ..      22      33 .. 0.83
   2 !   16.8   0.2   2.4e-06    0.0055      11      33 ..     232     254 ..     227     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.99
                HHHHHHHH CS
       TPR_8 24 yekaleld 31
                +ek+l+l+
  AJA92598.1 24 IEKCLKLA 31
                69***997 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
                 HHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  11 ylklgdyeeAkeyyekaleldpd 33 
                  +kl++y++A e+++k+le++p+
  AJA92598.1 232 EEKLKNYDNALEFLNKYLEMEPN 254
                 589******************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   6.4e-06     0.014       6      33 ..     227     254 ..     222     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.4e-06
       TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                  +G + +kl++y+ Ale+++k le +Pn
  AJA92598.1 227 DMGILEEKLKNYDNALEFLNKYLEMEPN 254
                 6799999********************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.7e-05     0.038      17      58 ..     214     255 ..     207     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
      TPR_19  17 alqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 +l+  p++a+   ++ ++  +l+++d A + L++++e++p+ 
  AJA92598.1 214 ILEILPESADEIRDMGILEEKLKNYDNALEFLNKYLEMEPNA 255
                 489999**********************************94 PP

>> LAM_C  Lysine-2,3-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.6   1.3e+03      30      60 ..      64      95 ..      58     119 .. 0.79
   2 ?    9.6   0.0   0.00043      0.95      24      87 ..     168     232 ..     165     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.6
       LAM_C 30 qPnyllsqsedkvv.lrnfeGvitsypePeny 60
                +P yl+s  ++    + +f+G +  y +P+n 
  AJA92598.1 64 NPTYLISLLNEFLFdVEEFQGDLDDYYNPKNN 95
                58899998777654367899999999999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
       LAM_C  24 GGkialqPnyllsqsedkvvlrnfeGvitsypePeny.vkgkaddyfkevypdtekkkeevGisa 87 
                 G  +  q +yl   s++k+++r       sy++   y +++ ++ +  e+ p+ +++  ++Gi +
  AJA92598.1 168 GDSVEFQAEYLNQISDEKILIRMLRNLKNSYTDSFAYeMASMCNRMILEILPESADEIRDMGILE 232
                 56688999**************************99977889999****************9953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.53
# Mc/sec: 1570.08
//
Query:       AJA92599.1  [L=133]
Description: hypothetical protein T478_1501 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00082   19.7   0.0     0.0011   19.4   0.0    1.2  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.9e-08    0.0011       6      65 ..      60     121 ..      55     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.9e-08
                      SHHHHHHHHHS-EEHHHHHHT--GG..G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
  Penicillinase_R   6 aevmeilwekgeatvkevveeleee..kelaysTVktllrrLvkKgllsrekegrafiYspl 65 
                      +++ +  +  g+ t++++ e+ e+e     + s + t l r + K+ ++r k+gr+ +Y+ l
       AJA92599.1  60 WHIVDKYYPTGKFTSSDILEKYEDEfnEPIKLSVISTYLARFTSKNKVERAKKGREWAYHTL 121
                      5566666778999***********974445999**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 955.04
//
Query:       AJA92600.1  [L=524]
Description: carboxyl transferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     2e-182  607.3   0.2   2.3e-182  607.1   0.2    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    2.2e-06   27.4   0.1    5.5e-06   26.1   0.0    1.7  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.1   0.2  2.5e-186  2.3e-182       2     494 .]      37     522 ..      36     522 .. 0.99

  Alignments for each domain:
  == domain 1  score: 607.1 bits;  conditional E-value: 2.5e-186
                     SCTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHHHHTEE CS
  Carboxyl_trans   2 ehprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeaikagep 95 
                     +h++Gkltareridll d+gsF+e+++ + h   e+ + kkk+ +dgvv g+G+v+Gr+v+v+a d+tvlgg+l+++ ++k++k ++ a+++g+p
      AJA92600.1  37 QHDKGKLTARERIDLLCDDGSFVEIDAMVTHHYHEYDMqKKKFFTDGVVGGYGNVNGRQVYVFAYDFTVLGGTLSQMGAKKITKLMDHAVRNGCP 131
                     8*************************************999****************************************************** PP

                     EEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHH CS
  Carboxyl_trans  96 ligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveetskifltGpdvikkvlgreevtseelgG 190
                     +igi dsgGa  riqeg+ sl+g+++if+ n +asg++pqi+  +g++aGg++Y+pa++d+vimve+ +++++tGp+v+k+vlg ee++ e+lgG
      AJA92600.1 132 IIGIADSGGA--RIQEGILSLDGFADIFYHNELASGVVPQITASIGPSAGGAVYSPAMTDFVIMVEKAGTMYVTGPEVVKTVLG-EEISFEDLGG 223
                     **********..************************************************************************.********** PP

                     SHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSST CS
  Carboxyl_trans 191 atqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAk 282
                     a++h tksGvah++a+++ ++++ i++llsy+P   +nn e++P ++t+d+p+r    li+ivP+++ kpyD++e+i  + d+++F+Ei+e +A+
      AJA92600.1 224 AMTHGTKSGVAHFVAQNEYQCMDYIKSLLSYIP---QNNSEAPPSIKTSDDPNRLdnnLINIVPEDSLKPYDMKEIIYSILDDNKFFEIHELFAQ 315
                     *********************************...77788*************888888*********************************** PP

                     TEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-T CS
  Carboxyl_trans 283 tvVvGfArlgGipvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilr 377
                     +vVvGf+r++G++vG+vAn++   aG  l+ids+ Kaarfir+cd+  +P+++l+d++G+++G++qe++gi++hG+kl++a+ ea+vPkit++++
      AJA92600.1 316 NVVVGFGRMNGKTVGIVANQPMFLAG-ALDIDSSNKAARFIRFCDCYGIPIITLVDTPGYMPGSNQEHNGIIRHGSKLLYAYCEATVPKITIVIG 409
                     **************************.******************************************************************** PP

                     EEEHHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTT CS
  Carboxyl_trans 378 kayGGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetrakl 472
                     kayGGay++m+sk+++ d+++awpta+iaVlg egav+i+ rk++a+a+    ++++ +kk  +e+ e+++npyvaa+ g +D vidp+etr  l
      AJA92600.1 410 KAYGGAYIAMGSKNLRTDVNYAWPTAQIAVLGSEGAVKIMNRKDLANAD----NPEELLKKLKDEFTEKFANPYVAASNGTVDTVIDPAETRPML 500
                     ***********************************************99....999*************************************** PP

                     SSSEEEHGGGHHHHHHHHHHHH CS
  Carboxyl_trans 473 vialelewkkarklparkrrni 494
                     ++ale++ +k+ k  +rk++ni
      AJA92600.1 501 IKALEMLSNKRDKQLPRKHGNI 522
                     ********************97 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.41   3.7e+03      65      75 ..     130     140 ..     108     188 .. 0.59
   2 !   26.1   0.0   6.1e-10   5.5e-06      66     153 ..     364     451 ..     309     465 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.41
                 -EEEEEEEE-- CS
        MdcE  65 rpilvlvDvas 75 
                  pi+ ++D+ +
  AJA92600.1 130 CPIIGIADSGG 140
                 34444444444 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 6.1e-10
                 EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEESS-HHHHHHHHT- CS
        MdcE  66 pilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvavmdkasaArvTkr 153
                 pi+ lvD+++   g  +E  Gi    + l  a+  A +   p i++++Gka  Ga++a+g   l +++  a p +q+av++   a ++ +r
  AJA92600.1 364 PIITLVDTPGYMPGSNQEHNGIIRHGSKLLYAYCEATV---PKITIVIGKAYGGAYIAMGsknLRTDVNYAWPTAQIAVLGSEGAVKIMNR 451
                 9*********************************9986...9****************98666789999**************99999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3597.70
//
Query:       AJA92601.1  [L=634]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      9e-12   45.7   0.1    2.5e-11   44.3   0.1    1.8  1  Radical_SAM  Radical SAM superfamily
    3.8e-07   30.2   0.0    1.4e-06   28.4   0.0    1.9  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.035   14.2   0.0    1.8  1  DUF3791      Protein of unknown function (DUF3791)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   4.1e-15   2.5e-11       4     161 ..     168     329 ..     165     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.1e-15
                  ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...........CCTEEEEEEECSSCHG CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxx RF
  Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...........vpgiritvetngtlpd 90 
                   rgC+++C+fC+ +    +  r r    e++ +e+++++ ++  k   ++g + ++    +++l+ ++kl+                   +t  +   
   AJA92601.1 168 NRGCPYQCTFCDWGMA--TFSRTRKYLEERLFKEIEWFA-DN--KMRYIHGCDANFGIFRERDLRIARKLKevclekhyptkFFVAWAKNTTDQI--- 257
                  69************95..********************5.64..455556666666666666666666666668876665542222222233333... PP

                  HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                  xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeele 161
                    ++++l++ g +  v+l ++++d+e +lk+++  +  f+++ +++ ++re+ i+  + +i+glpGe+ + ++
   AJA92601.1 258 LPIARELRDGGvLGGVTLAVQSLDPE-TLKIIKrANIKFSKFSDLTSTFRENEIPTYTEIIIGLPGETLDSFK 329
                  5589*****99***************.******999*******************9999*********99886 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.3e-10   1.4e-06      41     120 ..      26     105 ..      12     106 .. 0.85
   2 ?   -1.9   0.0      0.53   3.2e+03      90     120 ..     378     404 ..     377     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.3e-10
  B12-binding  41 edivaairae.kpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                  +++ ++i++  + d+++ S+ + ++ e +++l++++k+++p+  +v+GG+ +    + + e+ + +d+ v gege  l +l
   AJA92601.1  26 DKVNQNIEECdESDILLCSC-YVWNWEITTHLAKEVKKRNPKCLIVFGGPQVPDFTDGFFEKYPFVDILVHGEGEIILKNL 105
                  6777888888889*******.****************************98766666666544************988876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.53
  B12-binding  90 hpsldpeetleaklgiddvvvgegedaleal 120
                  h s++ +e+le+ ++i+   vg   +++e+l
   AJA92601.1 378 HSSIHKDEILEN-EEIV---VGASSYTFEDL 404
                  779999999997.7745...59999999987 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.8e-06     0.035      21      60 .]     413     452 ..     412     452 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
     DUF3791  21 vykllkksgvldylidcYevlHtqSkeyivedideylknk 60 
                 v+  +++ gv++ ++++Ye  H +S+   +e i ey++++
  AJA92601.1 413 VFTTFQNLGVFQEIKNYYEQTHGLSIVSFFETILEYCRTR 452
                 67889********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4204.82
//
Query:       AJA92602.1  [L=250]
Description: sirohydrochlorin cobaltochelatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-32  112.5   0.0      2e-15   57.0   0.0    2.1  2  CbiX            CbiX
    6.1e-06   25.7   0.8    8.4e-06   25.3   0.8    1.2  1  CbiK            Cobalt chelatase (CbiK)
    1.3e-05   24.5   0.0     0.0026   16.9   0.0    2.0  2  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   3.3e-19     2e-15       1     106 [.      10     112 ..      10     113 .. 0.92
   2 !   53.8   0.0   3.4e-18   2.1e-14       1     106 [.     138     240 ..     138     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 3.3e-19
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 +GSr++e+ ee+e ++e+++ekg+++  e +fle++ p +e++++++ ++ v+++++vP+fl +G  vk       ++++ +++ ++++ +t+p+  h+
  AJA92602.1  10 RGSREREAGEELEMICEKVKEKGNYDFTEFCFLEVVPPFIEDGMDTCLKKDVEQMTIVPYFLYPGRKVKI---AVADAMKYQKDTKIKFLVTKPMTMHK 105
                 7*********************************************************************...44455555555567************ PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                 +++e+++
  AJA92602.1 106 KLVELVD 112
                 ****986 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 3.4e-18
                 -STSSCCHHHHHHHHHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSSSHHHHTHHHHHCT--SSSS-TTEEEEE---CCCSC CS
        CbiX   1 HGSrdpesneeveklaeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfaGvhvkeDIpeeleeaeeahpkdveieytepLGthp 99 
                 HGS+dp+s   +  +++el+ +  ++ v  ++le+e p++ee+++++ +++ +  ++v +fl +G hvk D+ + l  a ++     ++++t++LGt++
  AJA92602.1 138 HGSKDPNSGISIDYVVDELKPS--YRNVSRCYLEIEGPTIEEGIQACKKNNPEVLIIVFYFLHEGAHVKIDVNNDLLPALDNAN-LNKVFVTKHLGTDE 233
                 *********************5..55**********************************************996654444444.469*********** PP

                 CHHHHHH CS
        CbiX 100 lvaevlk 106
                 ++++++ 
  AJA92602.1 234 KMIDLIL 240
                 ****986 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.8   1.4e-09   8.4e-06      44     259 ..      23     245 ..      18     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-09
                 HHHHHHHHHH-........----..-HHHHHHHHHHCT--EEEEEE--SCSSHHHHHHHHHHHHHGGGSS.EEEEE--SCS......SHHHHHHHHHHH CS
        CbiK  44 iiikklkerde........ievd..tpeealeklkeegykevivqplhiipGeeyeklkreVkkfkkkfe.kiklgrPlldykGvedsteDykevveal 131
                 +i +k+ke+ +        +ev   + e+ ++   ++  +++ + p +++pG++    ++   k++k+ + k  +++P+   k + +  ++  +v  +l
  AJA92602.1  23 MICEKVKEKGNydftefcfLEVVppFIEDGMDTCLKKDVEQMTIVPYFLYPGRKVKIAVADAMKYQKDTKiKFLVTKPMTMHKKLVELVDN--RVTTTL 119
                 67777777777666666664443113467777778889999**************99999999999887646689***9888766655543..344455 PP

                 H.TTS----TTEEEEEEE---SCHHHHHHHHHHHHHHH..CT-S.EEEEETTSS.S-HHHHHHHHHHHT--EEEEEE-SSS--HHHHCCCCSSSTTSHH CS
        CbiK 132 k.deierarkdealvfvgHGtehesnavyaeldkvlke..kdfkqvvvgtvegy.PeveevieelkkkgikevkliPlmlvAGdHaknDmasdeedswk 226
                 k ++i++ +++  ++ +gHG++ + +++   +d+v++e   ++++v  + +e   P++ee i+  kk++ +   ++ ++l  G H+k D+    +++  
  AJA92602.1 120 KeNSIDTPKENVDVLIIGHGSKDPNSGI--SIDYVVDElkPSYRNVSRCYLEIEgPTIEEGIQACKKNNPEVLIIVFYFLHEGAHVKIDV----NNDLL 212
                 50556656688889999*****999886..799999986567999*999999644*************9998888889999*********....55678 PP

                 HHHHHTT--EEE----GGGSHHHHHHHHHHHHH CS
        CbiK 227 ealeaaGikveiilkgLGeieeirsifikhike 259
                  al++a ++   + k LG +e++ ++ +++ +e
  AJA92602.1 213 PALDNANLNKVFVTKHLGTDEKMIDLILERARE 245
                 888988888888889999999988888887666 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.3e-07    0.0026      76     192 ..      22     139 ..       9     157 .. 0.86
   2 !    5.6   0.1    0.0012       6.9     241     314 ..     172     244 ..     171     247 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.3e-07
                     HHHHHHHHHH-.--EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT-SSEEEEE---TT-HHHHHHHHH CS
  Ferrochelatase  76 ealekelaerg.idvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkreapevrvirqfydhpgyiealae 169
                     e ++++++e+g  d+  ++  + ++P+ied ++   +++ve+++++p + + +   ++ ++ ++++  k    ++++ v +    h++++e + +
      AJA92602.1  22 EMICEKVKEKGnYDFTEFCFLEVVPPFIEDGMDTCLKKDVEQMTIVPYFLYPG-RKVKIAVADAMKYQKD--TKIKFLVTKPMTMHKKLVELVDN 113
                     567788888778999999999************************99776555.4567777777777655..6899******************* PP

                     HHHHHHTTS-...HC.C-EEEEEEE- CS
  Ferrochelatase 170 sikealeelp...eekkakllfsaHg 192
                     +++ +l+e++   +++++++l+  Hg
      AJA92602.1 114 RVTTTLKENSidtPKENVDVLIIGHG 139
                     ********998875557999999999 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0012
                     SSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHHHHH CS
  Ferrochelatase 241 ePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealadlve 314
                     +P +++ ++++++++  +++++   F  +   ++ +++  +  ++++a+++k+ + + l++++++i+++ + ++
      AJA92602.1 172 GPTIEEGIQACKKNN-PEVLIIVFYFLHEGAHVKIDVNNDLLPALDNANLNKVFVTKHLGTDEKMIDLILERAR 244
                     599999999999998.99*************************************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1777.42
//
Query:       AJA92603.1  [L=593]
Description: translation initiation factor aIF-2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-31  110.0   0.0    5.8e-31  107.5   0.0    2.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.6e-23   82.8   0.9    1.2e-21   76.8   0.3    2.6  2  IF-2         Translation-initiation factor 2
    2.6e-21   75.3   0.1    9.1e-21   73.6   0.1    2.0  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    5.7e-08   32.8   0.1    3.1e-07   30.5   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
    6.2e-06   26.5   0.1    0.00028   21.2   0.0    2.8  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00031   20.9   0.0     0.0031   17.7   0.0    2.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0006   19.9   0.2      0.057   13.5   0.1    3.0  2  Dynamin_N    Dynamin family
    0.00065   19.6   0.0     0.0028   17.5   0.0    2.1  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0099   15.8   2.8       0.31   10.9   0.1    3.4  3  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.097   12.3   0.0    2.3  1  Ras          Ras family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   3.2e-34   5.8e-31       5     192 ..       7     217 ..       4     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 3.2e-34
                 EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEET CS
    GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvda 103
                  ++++ghvD+GKt+L+d++   tg   +++   +++    +l+++  + +  +      ++e k   i +iDtPGH+ F++   rg +++D+a+lvvd+
  AJA92603.1   7 IVAVLGHVDSGKTSLLDKIR-GTGVQGREAGGITQHIGASFLPDDIIQKLCGSLYEKLGNAENKVPGILVIDTPGHEVFTNLRARGGSAADIAILVVDI 104
                 689****************9.5555444333334566788888887665544333322223699*********************************** PP

                 TTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHHH..........................HHHHHHHHHTTT CS
    GTP_EFTU 104 veGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsrk..........................eeklekygekge 165
                 ++G +pqt+e l+++ +++vp++v++NK+D++                       q ++++                          e+  +++ +k  
  AJA92603.1 105 NRGFQPQTNESLKILESRKVPFVVALNKVDMIsgwqqtddayiS-----------QAIKKQspsiqtnideqiynvvgalsilgyqsEAFYRVQDFK-- 190
                 ********************************777655533332...........333333333344455557777777777666544444444444.. PP

                 TTEEEEEEBTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 166 kevpvvfgSalkgegvktllealvell 192
                 ke+++v++Sa +g g+ +ll +lv l+
  AJA92603.1 191 KEISIVPVSARSGVGIPELLAVLVGLT 217
                 68******************9998765 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.3   6.8e-25   1.2e-21       2     104 ..     341     444 ..     340     445 .. 0.91
   2 ?    3.8   0.0     0.035        62      26      60 ..     513     549 ..     509     569 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 6.8e-25
                 CCHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH.ST.....EEEEEESSSCTHHHHHCCCCCTSEEEEE CS
        IF-2   2 eelfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa.sn.....aiiigFnvkvskkakklaekegvkirly 94 
                 e+++e++  ++++ ++i+k+D+ GsleA++e+L++      ++++ ++++G++t++Dv+ a+a ++     ++i++Fnvkv  +ak++++++++++++ 
  AJA92603.1 341 ESEMESVFIDTETTGLILKCDTIGSLEAITEMLRRQ-----QIPIAKADIGPVTRRDVMQAKAiKDkdrhlGVILAFNVKVFDDAKTECDESHIRVFED 434
                 6677778878899**********************8.....6*********************62256789**************************** PP

                 SSHHHHHHHH CS
        IF-2  95 nvIYkliddv 104
                 +vIY lid +
  AJA92603.1 435 KVIYSLIDTY 444
                 *******976 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.035
                 HHHHHHHHHHCTT..SSTEEEECEEEESS.B-HHHHH CS
        IF-2  26 sleAlkeaLekles.eevkvkvihsgvGa.itesDve 60 
                 sleA  + ++++++ eev ++v ++ +G  i+e+Dv 
  AJA92603.1 513 SLEADGKTVQEVKTgEEVACSVQNVTIGRqINEEDVF 549
                 788888999999889*************65*****96 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.1   5.1e-24   9.1e-21       4      86 .]     468     550 ..     465     550 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 5.1e-24
                  EEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-EEE CS
  GTP_EFTU_D4   4 kikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdily 86 
                  k++ l+g+ fr+ +pa+ G++v  G+++ ++   +++G+++G+i +++  gk+++e+k+G+eva s+++ ++Grqi+e+d++y
   AJA92603.1 468 KFTFLKGYTFRNNNPAVFGIRVDIGTLRQKIAFTNKNGKKIGNIHSLEADGKTVQEVKTGEEVACSVQNVTIGRQINEEDVFY 550
                  7899****************************************************************************988 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.7e-10   3.1e-07       2     114 .]       8     132 ..       7     132 .. 0.78
   2 ?   -1.6   0.0       1.5   2.8e+03      65      86 ..     331     352 ..     312     413 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.7e-10
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EE...................EEEEECGGCSSHHHHHHHHHHHHHH.HHCTSEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.ke...................ielvDtpGliegaseekglgkafla.leeadli 79 
                 va++G+  +GK++L+ ++ g+ ++  +  g T++i    +  ++  +                   i ++DtpG  e       +++  ++    ad++
  AJA92603.1   8 VAVLGHVDSGKTSLLDKIRGTGVQGREAGGITQHIGASFLP-DDiIQklcgslyeklgnaenkvpgILVIDTPG-HE------VFTNLRARgGSAADIA 98 
                 89*******************99999*********877665.222224555556666666667777********.44......2333233213348*** PP

                 EEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  80 llvvdaseeklkpldeeleelleeakkplilvlnk 114
                 +lvvd++ ++++p+ +e  ++le++k p++++lnk
  AJA92603.1  99 ILVVDIN-RGFQPQTNESLKILESRKVPFVVALNK 132
                 *****99.77************99*********98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                 HHHHHHHHHHCTSEEEEEEETT CS
    MMR_HSR1  65 glgkaflaleeadlillvvdas 86 
                 +++++f++  e+++  + +d +
  AJA92603.1 331 EIAEEFKKTLESEMESVFIDTE 352
                 4455555544444444444422 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00028       4      74 .]     249     325 ..     246     325 .. 0.91
   2 ?    2.1   0.2      0.14   2.6e+02      18      62 ..     497     538 ..     484     544 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                  EEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSGSSTTCEEE CS
  GTP_EFTU_D2   4 algrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgledaiivGdtlt 74 
                  a +++++G l+k+d++++ +     + i+t+ ++l+ + +++de+           ++ a+aG+++a ++l+  ++ G t++
   AJA92603.1 249 ANMILIDGHLQKDDNIVLAKR---DSVIITKPKALLLP-KPLDEMrdprdkfkpidEVQAAAGIKIASPDLDG-VLPGTTVY 325
                  567899************553...458***********.88********************************.9****986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                  EEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
  GTP_EFTU_D2  18 evrilgndtskkeivtrissletfhededeavaganaGvivaikg 62 
                  ++ +    +++k  ++ i sle+  + ++e+  g+ +   v  + 
   AJA92603.1 497 KIAF--TNKNGK-KIGNIHSLEADGKTVQEVKTGEEVACSVQNVT 538
                  5555..333233.599***************99999988877665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0031       2     120 .]       8     135 ..       7     135 .. 0.70
   2 ?   -0.3   0.0      0.64   1.2e+03      15      36 ..     216     237 ..     215     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                 EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGG.SG.....GCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEE.G CS
         Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtk.ik.....gvendkkvkkvklniWDtaGqerfrslhplylreaalailvyd.s 89 
                 v ++G   +GKtsll+++    ++ +e    ++ ig++fl  ++ + +      ++ n  + k   + + Dt G+e f +l+    ++a++ailv+d +
  AJA92603.1   8 VAVLGHVDSGKTSLLDKIRGTGVQGREaggiTQHIGASFLPDDIIQkLCgslyeKLGNA-ENKVPGILVIDTPGHEVFTNLRARGGSAADIAILVVDiN 105
                 5789*************98766665442222799*****99877542212221133333.345567899****************************44 PP

                 HHHH.CHHHHHHHHHHHCSSS-EEEEEE-TTT CS
         Roc  90 rsse.nlkeWlkelkkvagkspvilvgnkiDl 120
                 r ++ + +e lk l++  +k p+++  nk+D+
  AJA92603.1 106 RGFQpQTNESLKILES--RKVPFVVALNKVDM 135
                 4454244445555543..46788888999995 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                 HHHCHCT-CCC-EEETTTTEEE CS
         Roc  15 llkrfvedkfsekekstigvdf 36 
                 l ++f+++k +++ek+t g+ +
  AJA92603.1 216 LTQQFLSKKLEQEEKQTRGIVL 237
                 7899*************99865 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   3.2e-05     0.057       1      34 [.       8      41 ..       8      43 .. 0.94
   2 ?    2.8   0.0     0.059   1.1e+02      94     148 ..      64     114 ..      52     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                +av+G++ sGK+S+l+++ g  +  r+++ +T+ 
  AJA92603.1  8 VAVLGHVDSGKTSLLDKIRGTGVQGREAGGITQH 41
                79*************************9999975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.059
                 EEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHH CS
   Dynamin_N  94 kilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnseal 148
                  + + +v+g+ ++D+PG     +    l  +    adi ++v++ n  +  + ++
  AJA92603.1  64 GNAENKVPGILVIDTPGHEVFTN----LRARGGSAADIAILVVDINRGFQPQTNE 114
                 56677899999******776333....3344446677777777777666555444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   1.9e+03       1      15 [.      10      24 ..      10      27 .. 0.87
   2 !   17.5   0.0   1.6e-06    0.0028      81     233 ..      58     211 ..      43     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
  ATP_bind_1  1 vvGpaGsGKttfvga 15
                v+G++ sGKt++  +
  AJA92603.1 10 VLGHVDSGKTSLLDK 24
                89********99876 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
  ATP_bind_1  81 wldeeleke.ed..dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek.lek 175
                  l e+l++  ++    l++DtPG   + ++++ +         + a +++ +vD +r  +p +       +l+++ + ++P+vv+lnk+D+++   +  
  AJA92603.1  58 SLYEKLGNAeNKvpGILVIDTPGHEVFTNLRARGG--------SAADIAILVVDINRGFQPQTNE-----SLKILESRKVPFVVALNKVDMISGWqQ-T 142
                 55666766634445689******888888888888........8999*********998877644.....569999***************994432.2 PP

  ATP_bind_1 176 eleffedvealslllekee..................ekykklaeaiaelleefalvlrflplssekeesiedlls 233
                 +  ++      s++++k++                  +   ++ ea    +++f+  ++++p+s++++ +i +ll+
  AJA92603.1 143 DDAYI------SQAIKKQSpsiqtnideqiynvvgalSILGYQSEAFY-RVQDFKKEISIVPVSARSGVGIPELLA 211
                 22222......2222222222222334455666665433333333333.345555555666777777766666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.059   1.1e+02      98     122 ..       4      28 ..       1      44 [. 0.79
   2 ?    0.1   0.0      0.36   6.4e+02     152     163 ..      72      83 ..      67      88 .. 0.80
   3 !   10.9   0.1   0.00018      0.31      15      64 ..      94     154 ..      81     234 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.059
                  TTSEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                  ++ +++++G+   GK++L+++++++
   AJA92603.1   4 RQPIVAVLGHVDSGKTSLLDKIRGT 28 
                  66789999**************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                  TEEEESS-SSSS CS
  RsgA_GTPase 152 gglliDtPGfre 163
                  g l+iDtPG + 
   AJA92603.1  72 GILVIDTPGHEV 83 
                  789******765 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00018
                  S--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH.............H CS
  RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee.............e 64 
                    d +++vv ++   +++++ +  L ++e+++++ v++lnK+D+++  +             +
   AJA92603.1  94 AADIAILVVDIN-RGFQPQT-NESLKILESRKVPFVVALNKVDMISGWQqtddayisqaikkQ 154
                  567788888888.7777765.77899*******************987755555555443331 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.4e-05     0.097      44     119 ..      67     144 ..       8     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                 TTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG......G CS
         Ras  44 dgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee......k 119
                 ++k   + + DT G e f++lr    + a+ ++lv di++   f+  ++   +i +    +vp+v+  nKvD+ +      +
  AJA92603.1  67 ENKVPGILVIDTPGHEVFTNLRARGGSAADIAILVVDINR--GFQPQTNESLKILESR--KVPFVVALNKVDMISgwqqtdD 144
                 4666677899*************************99975..6877666555555555..4999999999999775555541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4118.53
//
Query:       AJA92604.1  [L=347]
Description: PhoU domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-26   91.0  12.8    2.4e-19   69.6   1.0    2.3  2  PhoU            PhoU domain
    8.3e-08   32.0   0.1    1.3e-06   28.2   0.0    2.8  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.35   10.9   0.0    1.7  1  DUF1905         Domain of unknown function (DUF1905)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   1.0   3.9e-23   2.4e-19       2      88 ..     149     239 ..     148     240 .. 0.93
   2 !   26.4   4.8   1.2e-09   7.2e-06       1      89 []     255     335 ..     255     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 3.9e-23
                 HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriardlERigDhavniaer 88 
                 +rm +++++m  dal +l+e+++ela+evi+ dd++dr+ + i+r+l  a+ ++  l+e    + r+ l+++ i++++ERigDhav +a+ 
  AJA92604.1 149 KRMLSMAKSMQTDALLSLKEGNDELAQEVINSDDDVDRFGFYIIRQLTIAIENQHMLEEmgfkNSRDCLGYRVIVKNIERIGDHAVTLAQD 239
                 79********************************************8888876666666899************************99985 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 1.2e-09
                 HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaerv 89 
                 +++m + +++++d+++ al+++d   a+  i++ + i ++e+++ ++    l ++++ ae    ++ ++ria ++ Ri+ +a +i e+v
  AJA92604.1 255 IEKMNDFALTAIDNTCLALFKNDYLEAENAIKESNNIKKYEDDVLKA----LEQSKNSAE----IFRVRRIAENIRRIAEYASDIGEIV 335
                 679*************************************9999666....544444444....677999****************986 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.2e-10   1.3e-06       1      34 [.      12      45 ..      12      58 .. 0.83
   2 ?   -0.1   0.0      0.15   9.2e+02      24      41 ..      63      81 ..      57      85 .. 0.73
   3 ?   -2.1   0.0      0.66   3.9e+03      26      44 ..     139     158 ..     138     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.2e-10
                    EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTT CS
  MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgd 34
                    f++ +s++v++Pk++ ++ g+++Gd v++ ++g 
      AJA92604.1 12 FTGKSSYIVSLPKDWIKDQGLKQGDQVTVGRNGS 45
                    8999***********************9977665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.15
                    TCEEEEEECTT.CCCCCCC CS
  MazE_antitoxin 24 Gdevelevdgd.kiilrpl 41
                     + ++++++++ + i+r+l
      AJA92604.1 63 SSNLIISPEDEkSTIVRKL 81
                    5568999999977777766 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.66
                     EEEEEECTT.CCCCCCCHHS CS
  MazE_antitoxin  26 evelevdgd.kiilrplksl 44 
                      vel+vdg  k +l+  ks+
      AJA92604.1 139 LVELSVDGAfKRMLSMAKSM 158
                     599***99888888777766 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.9e-05      0.35      53      80 ..      13      40 ..       8      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                SSTT-EEEEE-HHHHHHHT--TTSEEEE CS
     DUF1905 53 mgkggyiLpvkaavrkaigkeaGdtvtv 80
                 gk +yi+ + ++  k +g++ Gd+vtv
  AJA92604.1 13 TGKSSYIVSLPKDWIKDQGLKQGDQVTV 40
                6889***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2530.34
//
Query:       AJA92605.1  [L=175]
Description: HD domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-16   58.6   0.1    8.9e-16   58.0   0.1    1.3  1  HD_4           HD domain
     0.0008   19.6   0.1      0.002   18.3   0.1    1.6  1  HD             HD domain
  ------ inclusion threshold ------
      0.013   15.6   1.5      0.017   15.2   1.5    1.2  1  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   1.5e-19   8.9e-16       1     127 [.       7     124 ..       7     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.5e-19
        HD_4   1 Alelaaelha.gqrkltgepllahalevAailaelg.ldaetviAalLhdvvedalsl.eeirerfGeevarLvegvsklkrlqkvaaadeaeekaeqv 96 
                 A+ +a+++ha + rk  ++ +++h+  v++ l++++ ++ + ++A+ Lhd++ed++++ ++i++rfG++va++v  v+k +rl k++         +++
  AJA92605.1   7 ARSFAKRKHAgQLRKNGKTTTFSHLKDVVKNLKKMKvTNVDIICAGWLHDTIEDTDTDfDAIKDRFGKNVAEIVVSVTKDNRLPKKQ---------REI 96 
                 899*******77788888999**************978899**************7777***************************4.........333 PP

        HD_4  97 enlRkmLlAmveDirvvliklAdrlqtlrsl 127
                 +  ++ L +     ++ l+k+Ad l +   +
  AJA92605.1  97 KYAKD-LKSS--NSKAKLVKIADILANVNDA 124
                 33332.2222..2356666666666665555 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.4e-07     0.002       2     121 ..      28     120 ..      27     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHTTCCHHHHHHHH CS
          HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld..ledvaklirehheswegkkrp 98 
                 + H   V k ++++        +++ + +a+ lHD+++++  d+   k           k  aei+  v k+++l+       + i++  + +      
  AJA92605.1  28 FSHLKDVVKNLKKMKVT-----NVD-IICAGWLHDTIEDTDTDFDAIKD-------RFGKNVAEIVVSVTKDNRLPkkQ----REIKYAKDLK------ 103
                 67888888888888874.....444.56************998555543.......35666666666666666554221....2222222222...... PP

                 HHHHCCTSCHHHHHHHHHHHHHH CS
          HD  99 rglaerqlslearivklaDrlaa 121
                          + a++vk+aD la+
  AJA92605.1 104 ------SSNSKAKLVKIADILAN 120
                 ......34567899999998876 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.5   2.9e-06     0.017      12     101 ..      23     143 ..      22     175 .] 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-06
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
  NAD_binding_6  12 GitpfisilkdllkkskkealktkkikliwvvressslewfkdvLneleeeksegnieihiYlTseyeaedasdqlissiegenseslk....... 100
                    G t++ s+lkd++k++k  ++k++++ +i++   ++ +e  +   + ++++  ++  ei + +T+++  ++++ ++  +++ + s+s++       
     AJA92605.1  23 GKTTTFSHLKDVVKNLK--KMKVTNVDIICAGWLHDTIEDTDTDFDAIKDRFGKNVAEIVVSVTKDNRLPKKQREIKYAKDLKSSNSKAklvkiad 116
                    7899************9..***********************99********99999************999998888876666665557787666 PP

                    ..........................x RF
  NAD_binding_6 101 ..........................q 101
                                              +
     AJA92605.1 117 ilanvndapnagknarwekqqfvkksK 143
                    666665555555555555554444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1164.95
//
Query:       AJA92606.1  [L=559]
Description: dihydroxy-acid dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.8e-209  696.7   4.5     2e-209  696.5   4.5    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.5   4.5  1.1e-213    2e-209       1     517 []      33     552 ..      33     552 .. 0.98

  Alignments for each domain:
  == domain 1  score: 696.5 bits;  conditional E-value: 1.1e-213
    ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqllDalvlisgCDKivPgllma 99 
                 k ++g++++ +e +pc+ hl +la+++k+gv+e g++p ef+ti+vsDgiamg+egm++sL+sRe+iads+e m++a+++Dalv i+gCDK++Pg++m+
  AJA92606.1  33 KSFVGVCHTGNEATPCNIHLPNLAQQAKQGVTEGGATPREFSTIAVSDGIAMGHEGMKSSLISREVIADSIELMVRAHQYDALVGIAGCDKSLPGTMMG 131
                 789************************************************************************************************ PP

    ILVD_EDD 100 aarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkela 196
                 ++rlniP++fv+gG++++g  +  +l++++v+eavg++ agkis eele++e+ acp aGsC+gm+TAntma++ ea+Glslpgsas pa++++r++++
  AJA92606.1 132 MIRLNIPSVFVYGGTIMPGMLDgrELTVVDVYEAVGSYDAGKISAEELENIENVACPNAGSCGGMFTANTMASISEAIGLSLPGSASPPAEDDRRNKMV 230
                 ******************88555699************************************************************************* PP

    ILVD_EDD 197 eeagkrivelvekdlkprdiltkeafeNAivvllalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeL 295
                  e+gk+ ++l++  +kp di+t eafeN i++l a+GGStN +lHllA+A+eag++lt+ddf+++ +k+p+la++kP g+y m++l+++GG+p v+k+L
  AJA92606.1 231 LETGKACAKLLQLGIKPLDIVTFEAFENSITMLNAVGGSTNGILHLLAMANEAGINLTYDDFERIRKKTPHLADMKPGGNYVMNSLDKIGGIPLVMKKL 329
                 *************************************************************************************************** PP

    ILVD_EDD 296 lkagllhgdvltvtgktlaenlee...aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkika 391
                 l+++l+hgd ltvtgkt++enlee    ev +q++i+p+e+p+++ g+  +LkG LapeG v+Kt++ve  +++f+g+A+vfd+ee a+ea+ kg+i++
  AJA92606.1 330 LDKNLIHGDSLTVTGKTIKENLEElaiVEVPDQQIIKPVEQPIHEVGTAVILKGTLAPEGGVIKTAGVE--MTEFTGTAKVFDREEYAFEAVSKGEIDE 426
                 **********************99866566**************************************9..**************************** PP

    ILVD_EDD 392 gdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlelevseeelaaRraa 490
                 gdvvviryeGPkGgpGm+Eml++t+al+g+glgkkva++tDGRfSG+++g++ighv+PEA +gGpialv+dGD i+i +e+++l+l+vseeel++R+++
  AJA92606.1 427 GDVVVIRYEGPKGGPGMREMLSTTAALVGQGLGKKVAMVTDGRFSGGTRGFMIGHVAPEAFVGGPIALVKDGDKISIKLEDNSLNLHVSEEELSKRKEQ 525
                 *************************************************************************************************** PP

    ILVD_EDD 491 wkp.ekkvktrgllakyaklvssaseGA 517
                 w++ ++  +++g+lak+a+lv sa++GA
  AJA92606.1 526 WRRpAP-NYSTGALAKFASLVGSAANGA 552
                 *98333.345*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 4215.75
//
Query:       AJA92607.1  [L=173]
Description: putative 50S ribosomal protein L5P [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-22   77.5   0.0    1.2e-21   76.6   0.0    1.5  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.8e-13   50.6   0.2    3.4e-13   49.7   0.2    1.5  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.6   0.0   1.4e-25   1.2e-21       1      84 [.      64     146 ..      64     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1.4e-25
  Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak.....tdeear 84 
                     piG+ vt+rg+++ e+l++lle++ +r++      ++sfd+ GnvsfGi e+i++p+i+yd+++gi G+++t+ + ++     t+ +++
      AJA92607.1  64 PIGAAVTVRGNDAQELLKRLLEAKGNRIK------SRSFDNMGNVSFGILEHIDIPGIKYDPKIGILGLNVTVRLARPgfsvaTRSKHK 146
                     8****************************......******************************************988765333333 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.2   3.8e-17   3.4e-13       1      57 []       7      60 ..       7      60 .. 0.99

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.8e-17
                  SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
  Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                  NvM+++rl+K+v+nmg+G++g+    +e a k L eI+  k   + akk+i++++iR
    AJA92607.1  7 NVMKEIRLDKVVLNMGLGKSGDA---VEIAKKALGEISNKKVNDRPAKKAIRDWGIR 60
                  9**********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1308.39
//
Query:       AJA92608.1  [L=368]
Description: DNA repair and recombination protein RadA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-90  302.4   0.1    2.7e-90  302.1   0.1    1.1  1  Rad51            Rad51
    1.4e-10   41.1   0.2      2e-10   40.6   0.2    1.1  1  RecA             recA bacterial DNA recombination protein
    4.9e-09   35.9   0.3    9.7e-09   34.9   0.3    1.5  1  ATPase           KaiC
    3.9e-05   23.3   0.0    6.1e-05   22.7   0.0    1.3  1  AAA_25           AAA domain
    0.00013   22.5   0.1    0.00045   20.8   0.1    2.0  1  HHH_5            Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.04   13.6   0.0    1.7  1  AAA_24           AAA domain
      0.029   14.9   0.0       0.06   13.9   0.0    1.5  1  ABC_tran         ABC transporter
       0.05   13.6   0.0       0.11   12.5   0.0    1.5  1  RNA_pol_RpbG     DNA-directed RNA polymerase, subunit G
      0.055   13.8   0.1       0.11   12.7   0.1    1.6  1  AAA_22           AAA domain
       0.07   13.0   0.0       0.16   11.8   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      0.085   13.3   0.0       0.19   12.1   0.0    1.5  1  RNA_helicase     RNA helicase
       0.13   12.2   0.0       0.22   11.4   0.0    1.4  1  NACHT            NACHT domain
       0.13   12.1   0.0       0.74    9.7   0.0    2.2  1  ATPase_2         ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.1   0.1     2e-93   2.7e-90       2     254 ..      65     312 ..      64     313 .. 0.98

  Alignments for each domain:
  == domain 1  score: 302.1 bits;  conditional E-value: 2e-93
                 S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HH CS
       Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldke 100
                 +fvsa+el++kr+++ ++tt +++lD+l  GGiet+++te++Gef++Gktq+cht+cv vq  ++ gG eg ++yid+e tfrper+v+ia+  ++d+e
  AJA92608.1  65 DFVSANELYKKRQTIGKITTATEALDTLFAGGIETQALTEVYGEFGCGKTQFCHTMCVQVQKSKQEGGLEGGVLYIDSENTFRPERIVSIAQANGMDPE 163
                 69************************************************************************************************* PP

                 HHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------ CS
       Rad51 101 evlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsa 199
                 +vl+n+ +aRay++ hq  +l++a++l++e++++l++ Ds++ l+R+++ grg la+Rqqkl+k+++ L +la+ ++va + tnqv++++d+    + +
  AJA92608.1 164 KVLDNIIVARAYNSSHQILILEEASTLIKEHNIQLIVADSAVGLFRSEYLGRGTLATRQQKLNKFVHLLVRLAETYNVAAIATNQVMSSPDQ----MFG 258
                 *******************************************************************************************9....559 PP

                 ------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
       Rad51 200 dpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                 dp+kP+gG+v+ah+st R++l+k  g++Ri+++vdsP+ pe++++fa+ge G++d
  AJA92608.1 259 DPTKPVGGNVVAHTSTYRVYLKK-SGKKRIARMVDSPHHPEMDVIFALGEAGVID 312
                 ********************976.69***************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   1.4e-13     2e-10      27     224 ..      75     284 ..      61     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.4e-13
                 .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT...T...--EEEEESS----HH....HHHHTT--....GGG-EEE CS
        RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkk...g...gvaafidaehaldpk....yakklGvd....idellvs 111
                 +++++  i++ + ald+ +  GG+    ++e+yG    Gkt ++  + +++qk+   g   g + +id+e ++ p+     a++ G+d    +d+++v+
  AJA92608.1  75 KRQTIGKITTATEALDTLF-AGGIETQALTEVYGEFGCGKTQFCHTMCVQVQKSkqeGgleGGVLYIDSENTFRPErivsIAQANGMDpekvLDNIIVA 172
                 45789999********866.5*********************99999999998533332224578********996333368999**966656789999 PP

                 --SSHHHH...HHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE-----------------HH CS
        RecA 112 qpdtGeqa...leiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGr 207
                 +  +  +    le a +l++   i+liv ds   l  ++e  G     +++ + + + + +  l    +  n+++i  nq+      mfg+p    GG+
  AJA92608.1 173 RAYNSSHQiliLEEASTLIKEHNIQLIVADSAVGLF-RSEYLG---RGTLATRQQKLNKFVHLLVRLAETYNVAAIATNQVMSSPDQMFGDPTKPVGGN 267
                 98776554122566779**************99997.555544...4455555555678888888889999**************************** PP

                 HHHHH-SEEEEEEEES- CS
        RecA 208 alkfyasvrldvrriee 224
                  +   ++ r+ ++++++
  AJA92608.1 268 VVAHTSTYRVYLKKSGK 284
                 *********99998875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.3     7e-12   9.7e-09       2     167 ..      83     260 ..      82     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 7e-12
      ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepg.....vfvtveepa..edlrenakslGwdlekleeegklaiidasesae 93 
                  t +e lD+++ gGi  ++ + ++Ge G+GKt f+ +  ++  ++++e g     +++  e +   e +   a++ G+d ek+ ++  +++  a++s++
  AJA92608.1  83 TTATEALDTLFAGGIETQALTEVYGEFGCGKTQFCHTMCVQVQKSKQEGGleggvLYIDSENTFrpERIVSIAQANGMDPEKVLDN--IIVARAYNSSH 179
                 68999*********************************9998887777642223379999987566********************..66666666654 PP

      ATPase  94 esaeekdkedleelieelaeaikeikakrvviDsitgl..aye.......ekeavaReilrqlvrvlkklgvTailvsekss........s 167
                 +            ++ee  + ike +++ +v Ds  gl  +++       ++++++ + ++ lvr  + ++v ai ++++ s         
  AJA92608.1 180 Q----------ILILEEASTLIKEHNIQLIVADSAVGLfrSEYlgrgtlaTRQQKLNKFVHLLVRLAETYNVAAIATNQVMSspdqmfgdP 260
                 4..........23566677788888888888888877743211122211156677777888888888999999999999888555544443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.4e-08   6.1e-05      10     185 ..      77     245 ..      68     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.4e-08
      AAA_25  10 vsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal..rddarllvl 106
                 ++++++ ++ + ++ l+ g +  ++l+ ++G  g+GKt ++  +++ v + k+  g      g Vly++ E++    ++R+  + +a+  ++   + vl
  AJA92608.1  77 QTIGKITTATEALDTLFAGGIETQALTEVYGEFGCGKTQFCHTMCVQVQKSKQEGG----LEGGVLYIDSENTF--RPERIVSIAQANgmDP---EKVL 166
                 567778999999*************************************9998866....68***********9..5677777776663222...2233 PP

      AAA_25 107 dlagveslpLfak.drggtl.ltadvdaleaaieevegvrlvviDplsralgg.......densnsdvgalvealeriarrtgaavll 185
                 d     ++ ++ +  + +++ +   +++    i+e ++++l+v D+   +++          +++ + +++v  l r+a+ +++a ++
  AJA92608.1 167 D-----NIIVARAyNSSHQIlI---LEEASTLIKE-HNIQLIVADSAVGLFRSeylgrgtLATRQQKLNKFVHLLVRLAETYNVAAIA 245
                 3.....2222222123333323...3456888999.88*****999887776633333222233333577777777777777776665 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   3.3e-07   0.00045       6      57 .]       3      54 ..       1      54 [. 0.95

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-07
                TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
       HHH_5  6 svsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                s+ G+Gp+t ++l +aGi  + dl+   + e+a+++ +  +tA ++++ +++
  AJA92608.1  3 SLAGVGPVTTRKLNDAGIHNIMDLVVRGPVEIAELTSMDIDTAGKLVEKARE 54
                789*********************************************9996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-05      0.04       7     130 ..     105     246 ..     102     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
      AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvelaaeladyktlviDtideleelclaevir 87 
                 +yG+ g GKT ++ ++             +  +l+id e+      + ++++i        e++ld +   +a ++  ++l++  ++ l +    ++i 
  AJA92608.1 105 VYGEFGCGKTQFCHTMcvqvqkskqegglEGGVLYIDSEN---TFRPERIVSIAqangmDPEKVLDNIIVARAYNSSHQILILEEASTLIKEHNIQLIV 200
                 8*******************88888888878888888888...44666666666777887788888888888888888888888888888888777777 PP

      AAA_24  88 qnekaeskedkgdgkG.ygelaeefrrllkklqelrk..nvifiah 130
                 ++++     +   g+G  +  ++++++++  l  l +  nv +ia 
  AJA92608.1 201 ADSAVGLFRSEYLGRGtLATRQQKLNKFVHLLVRLAEtyNVAAIAT 246
                 7777776677777777777777788888877777777666666664 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.4e-05      0.06       8      80 ..      97     188 ..      93     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-05
                 EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH...................H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...................x RF
    ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren...................e 80 
                 ++   ++ + Ge G+GK+ ++ +++ ++++ + e  l+g  l    e ++  ++i  + q + ++pe+ v +n                    
  AJA92608.1  97 IETQALTEVYGEFGCGKTQFCHTMCVQVQKSKQEGGLEGGVLYIdSENTFRPERIVSIAQANGMDPEK-VLDNiivaraynsshqilileeaS 188
                 6677788999******************99555554575554444678888999*************9.999977777664333333333330 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.2e-05      0.11      15      85 ..     165     232 ..     151     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
  RNA_pol_RpbG  15 klkdlkivkikcqneeielDiiselnifkeedkveviisrekPeyldgkdFcghGylvtekeeenkiitli 85 
                    l ++ ++++ + +++i   i++e +++ +e ++++i+  +        ++ g+G+l+t++++ nk++ l+
    AJA92608.1 165 VLDNIIVARAYNSSHQI--LILEEASTLIKEHNIQLIVADSAVGLFR-SEYLGRGTLATRQQKLNKFVHLL 232
                   46666777776666666..58999**************999888877.8****************999875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.2e-05      0.11       4     102 ..      99     206 ..      97     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-05
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...............erpevvfvtlpsstsskdllrellralglelkaerlsseell.ealeqal 86 
                 t+ ++ v+Ge G+GKT  + ++  q +  +k+e                ++ ++v++  +++++++++l ++  a       ++ s + l+ e     +
  AJA92608.1  99 TQALTEVYGEFGCGKTQFCHTMCVQVQ-KSKQEGgleggvlyidsentfRPERIVSIAQANGMDPEKVLDNIIVARA-----YNSSHQILIlEEASTLI 191
                 678889******************975.5555557777777777777765555566666666666666666554444.....34566777777777777 PP

      AAA_22  87 raravielliiDEaqh 102
                 +++   +l++ D a  
  AJA92608.1 192 KEHNI-QLIVADSAVG 206
                 77777.8888887655 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.16       8      30 ..       6      28 ..       2      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
  DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledlra 30
                     GVGp+t +k+ ++Gi ++ dl+ 
       AJA92608.1  6 GVGPVTTRKLNDAGIHNIMDLVV 28
                     9*******************986 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.19       3      26 ..     105     128 ..     104     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
  RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                   +yG+ g+GK++++++++ +++k+ 
    AJA92608.1 105 VYGEFGCGKTQFCHTMCVQVQKSK 128
                   79*****************99765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00016      0.22       5      51 ..     105     151 ..     102     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                 EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.. CS
       NACHT   5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna 51 
                 + Ge G+GKT + + ++++ +++k+++g    v+++ +  + r++++
  AJA92608.1 105 VYGEFGCGKTQFCHTMCVQVQKSKQEGGLEGGVLYIDSENTFRPERI 151
                 78***********************9987777777776666666555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00053      0.74      19      68 ..      99     154 ..      96     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
    ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldef 68 
                 ++    +YG  g+GKt++   +  + +++++       v+y+++ ++ + +++ + 
  AJA92608.1  99 TQALTEVYGEFGCGKTQFCHTMCVQVQKSKQegglegGVLYIDSENTFRPERIVSI 154
                 5566679***********99987777554444778866666666555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2540.45
//
Query:       AJA92609.1  [L=253]
Description: ABC-2 family transporter protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-21   76.1  23.3    2.4e-21   76.1  23.3    1.7  2  ABC2_membrane    ABC-2 type transporter
    1.9e-14   53.6  39.2    3.9e-14   52.5  28.0    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.21   11.8   0.0       0.21   11.8   0.0    2.2  2  DUF3493          Low psii accumulation1 / Rep27
       0.56   10.1  17.7       0.04   13.9  10.3    2.1  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1  23.3   5.5e-25   2.4e-21      17     210 .]      17     219 ..       4     219 .. 0.81
   2 ?   -1.2   0.7      0.26   1.1e+03     105     116 ..     231     242 ..     221     252 .. 0.41

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 5.5e-25
  ABC2_membrane  17 dpslgllwrliqplllalvfgtvfgnlgnsedglnr...............pgllffsvlflafsaltsvapvferergvlerelvsplyslsayv 97 
                    +p  + +w++++pl++++v g+++ +l       ++                g+++f +++ +  +++++ +++  +r  + ++  s+ y++s+y+
     AJA92609.1  17 NPGFI-IWQILFPLIYIFVAGFAYTSLI------ENvpfgnkdlsypaflaSGMIGFNIMNST--LISGI-IIWNDRRHGMFEQIMSGPYTRSDYI 102
                    66566.9******************733......22233444566677677777777777777..78888.5555555555555666666****** PP

  ABC2_membrane  98 lakvlvelpvsllqalifllivyflv..gldls..rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwl 189
                    l+++++  +++l+ a +++++ y+++  ++d s   + l++++ ++ a+++ s++ +is+ ++s e ++++++ v+l++ + s +f+p +  p+ l
     AJA92609.1 103 LSNIVTIGIIGLVSAGLITAVGYPVFfeSVDFSivTIPLLIFASVVGAILFGSIASIISTRLRSSEGFNVIINTVFLFFAFASTAFYPAQGAPQPL 198
                    ************************98554444444447779999999999999***************************************9899 PP

  ABC2_membrane 190 qwiaylnPltyavealrsnlf 210
                        y+nPl+y+v+++r+++f
     AJA92609.1 199 ATAFYINPLSYLVDIVRAGIF 219
                    9999*************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.26
  ABC2_membrane 105 lpvsllqalifl 116
                    + +++l++++f+
     AJA92609.1 231 IFLIVLASVLFV 242
                    112222222222 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.6   0.00017      0.75       2      31 ..      19      45 ..      18      54 .. 0.79
   2 !   52.5  28.0   8.7e-18   3.9e-14     150     344 ..      46     245 ..      43     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00017
  ABC2_membrane_3  2 sfliitlllPiilvlllglifsnsvedden 31
                     +f+i+++l+P+i+++++g+++ +     en
       AJA92609.1 19 GFIIWQILFPLIYIFVAGFAYTSLI---EN 45
                     69*****************965444...44 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 8.7e-18
  ABC2_membrane_3 150 tqleeelsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgipfg..n 237
                       +  ++  ++  fl++ +i + ++  t++     i +++++++ e++++ + +++ y+ls+i+++++++l+++ li+++   +f  +++f+   
       AJA92609.1  46 VPFGNKDLSYPAFLASgMIGFNIMNSTLI-SGIIIWNDRRHGMFEQIMSGPYTRSDYILSNIVTIGIIGLVSAGLITAVgypVFFESVDFSivT 138
                      55667788888899995666665555555.555799*****************************************97446444445555559 PP

  ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgdplwe.illsli 330
                      + ll++ ++++++++ +++  +s+  ++se  +++i  v+l++ +++++++p +  p +l+++f+i+P++++ +     i+g+ + + +++ +i
       AJA92609.1 139 IPLLIFASVVGAILFGSIASIISTRLRSSEGFNVIINTVFLFFAFASTAFYPAQGAPQPLATAFYINPLSYLVDIVRAGIFGQ-ITDfVIMEMI 231
                      99999***********************************************************************8889*99.656577**** PP

  ABC2_membrane_3 331 ilalfavvylllal 344
                      +l+++a v++++a 
       AJA92609.1 232 FLIVLASVLFVIAT 245
                      ***********996 PP

>> DUF3493  Low psii accumulation1 / Rep27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.7e-05      0.21      22      45 ..      54      77 ..      47      84 .. 0.89
   2 ?   -4.2   1.6         4   1.8e+04      21      31 ..     178     188 ..     176     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
     DUF3493 22 lYlafaaSaliGalifllrllaar 45
                 Y af aS++iG+ i+ + l+++ 
  AJA92609.1 54 SYPAFLASGMIGFNIMNSTLISGI 77
                69*****************99986 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4
     DUF3493  21 flYlafaaSal 31 
                 fl++afa  a+
  AJA92609.1 178 FLFFAFASTAF 188
                 88999988775 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  10.3   8.8e-06      0.04      15     178 ..      22     181 ..      19     182 .. 0.72
   2 ?    0.7   0.8       0.1   4.5e+02      54      67 ..     230     243 ..     201     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-06
  ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefysls.vfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsv 107
                      +w +++ ++ + + +++y  l+++  + + +  s+   +  +++ +  +  ++i++++i + +  +++ +++  P +r  ++l+ ++++ ++ +
       AJA92609.1  22 IWQILFPLIYIFVAGFAYTSLIENVPFGN-KDLSYPaFLASGMIGFNIMNSTLISGIIIWNDRRHGMFEQIMSGPYTRSDYILSNIVTIGIIGL 114
                      56655544444444566666666555443.33333303445567778888999************************************99876 PP

  ABC2_membrane_4 108 llmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpliltlvytia 178
                      +   +      +++  + f +++++ v++ l ++  ++  ++f +++ i+ + l +s  + +i++ v+ ++
       AJA92609.1 115 VSAGL----ITAVGYPVFFESVDFSIVTIPLLIFASVVGAILFGSIASIISTRLRSSEGFNVIINTVFLFF 181
                      66644....44455555666666667777777777777777888888888899***********9998885 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.1
  ABC2_membrane_4  54 ftlllllplilgii 67 
                      + +l++l  +l +i
       AJA92609.1 230 MIFLIVLASVLFVI 243
                      22222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1775.74
//
Query:       AJA92610.1  [L=674]
Description: PF03190 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-74  249.7   0.1    2.4e-74  248.7   0.1    1.6  1  Thioredox_DsbH   Protein of unknown function, DUF255
    3.9e-10   39.8   0.0    7.5e-10   38.9   0.0    1.5  1  Thioredoxin_7    Thioredoxin-like
    2.3e-07   30.5   6.5    0.00025   20.6   0.4    3.9  4  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
    8.6e-07   27.8   1.1    4.9e-05   22.0   0.3    2.8  3  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
    0.00049   19.3   1.5       0.33   10.0   0.0    2.9  2  Glyco_hydro_88   Glycosyl Hydrolase Family 88
     0.0051   16.4   2.0      0.016   14.8   0.5    2.2  2  Glyco_hydro_76   Glycosyl hydrolase family 76
     0.0064   16.9   0.0      0.023   15.1   0.0    2.0  1  Thioredoxin_2    Thioredoxin-like domain
  ------ inclusion threshold ------
      0.028   13.7   0.2       0.25   10.6   0.1    2.3  3  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim
       0.03   13.7   1.8       0.95    8.7   0.6    2.3  2  Pec_lyase        Pectic acid lyase


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.7   0.1   1.2e-77   2.4e-74       2     162 ..       3     163 ..       2     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.7 bits;  conditional E-value: 1.2e-77
  Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDreerPdldkiymeavqa 96 
                     n+l++e+spYllqh++npv+W++w++e+l+kak+e+kpi+ls+Gys+chWChvm++esfe+++va+++ne+fv++kvDreerPdld+iy++++q+
      AJA92610.1   3 NNLSQETSPYLLQHKDNPVEWFAWNDESLKKAKDENKPIFLSVGYSSCHWCHVMAHESFENDDVAKIMNENFVNIKVDREERPDLDDIYQKICQM 97 
                     99********************************************************************************************* PP

  Thioredox_DsbH  97 ltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaeelleal 162
                      tg+ggWPl+vfltpd+kpf+ gtYfp  +++grpgf ++++++a++w+e+ +++ ++ae+++++l
      AJA92610.1  98 STGQGGWPLSVFLTPDQKPFYVGTYFPVLDSYGRPGFGSLCRQLAQAWKEKPKDVGTSAEQFMANL 163
                     *************************************************************99887 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.8e-13   7.5e-10       1      83 []      22     112 ..      22     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.8e-13
                    ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG........-TT-..--SSEEEEE-T CS
  Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani.......lelde..qgvPvvafldp 83 
                    ew ++ de l ka+ ++kp+++ +g s c+ C++++ +  ++++v+++++e+fv  +vd +er + +        ++ +   g P  +fl+p
     AJA92610.1  22 EWFAWNDESLKKAKDENKPIFLSVGYSSCHWCHVMAHESFENDDVAKIMNENFVNIKVDREERPD-LddiyqkiCQMSTgqGGWPLSVFLTP 112
                    69999******************************9998888899999************99887.33444554332224244888888776 PP

>> C5-epim_C  D-glucuronyl C5-epimerase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00049      0.98      35      64 ..     274     303 ..     268     317 .. 0.85
   2 !   20.6   0.4   1.3e-07   0.00025      33      82 ..     417     471 ..     410     481 .. 0.79
   3 ?    0.7   0.1      0.16   3.1e+02      36      61 ..     478     503 ..     473     509 .. 0.84
   4 ?    0.2   0.0      0.23   4.5e+02      34      64 ..     544     574 ..     540     591 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
   C5-epim_C  35 isvllrAYeltgdekYlkaakkalksfkip 64 
                   v+++AY+ t+d  Yl++  k l++++ +
  AJA92610.1 274 PPVYAEAYQITKDPFYLDVVTKTLDYVLRE 303
                 5699******************99988765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.3e-07
   C5-epim_C  33 qaisvllrAYeltgdekYlkaakkalksfkipvekGGvlktledk.....kiwye 82 
                  +is++++ Y+ +g+ekYl+a+ +a k+f  + +k+G+ + ++++     + +++
  AJA92610.1 417 MMISAFAKGYRISGNEKYLNASVNAAKYFSEQFSKHGFIHRTFKNdtpklNGYLD 471
                 689**********************************987665543444333444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.16
   C5-epim_C  36 svllrAYeltgdekYlkaakkalksf 61 
                   l+  +e t d+ +l++a+k  +++
  AJA92610.1 478 NSLIDVFEITADSYFLDMAQKIAHYM 503
                 5688889*************987765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.23
   C5-epim_C  34 aisvllrAYeltgdekYlkaakkalksfkip 64 
                 a+ +ll+  +l +de +l+++k+ l++  ++
  AJA92610.1 544 AANALLKLHHLVNDETFLQISKQILELNGTS 574
                 56678888999************99986665 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.035        69     135     157 ..     278     300 ..     251     328 .. 0.69
   2 !   22.0   0.3   2.5e-08   4.9e-05     129     267 ..     417     556 ..     402     561 .. 0.77
   3 ?    2.1   0.0     0.027        54     178     208 ..     542     572 ..     534     579 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.035
                      HHHHHHH--HHHHHHHHHHHHHH CS
  Glyco_hydro_127 135 vayyqatgkeklldvatrladyl 157
                       ++yq t++   ldv+t+  dy+
       AJA92610.1 278 AEAYQITKDPFYLDVVTKTLDYV 300
                      34566666666666666666666 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.5e-08
                      HHHHHHHHHHHHH--HHHHHHHHHHHHHHHH.......HHCCS-CCHHHHHTTT.HHCTHHHHHHHHHHHHT-CHHHHHHHHCCHHCCHCCT-H CS
  Glyco_hydro_127 129 kliegavayyqatgkeklldvatrladylee.......vleklgdeqlqkalvp.ehggieealvklyelTgdkrYldlAkrfidergldpekl 214
                      ++i++  + y+ +g+ek l++ +++a+y++e       + +++++++ + +++  + + +  +l++++e+T d+ +ld+A+++ +  + +    
       AJA92610.1 417 MMISAFAKGYRISGNEKYLNASVNAAKYFSEqfskhgfIHRTFKNDTPKLNGYLdDYSYLVNSLIDVFEITADSYFLDMAQKIAHYMIEH---F 507
                      69999999*********************661222222245677777777777625555669***********************99944...6 PP

                      CTTT-SSTCGCHHCHHCCHHHHHHHHHHHHHHHHHCTTHCCHHHHHHHHHHHH CS
  Glyco_hydro_127 215 aykqdelpvrhqntaigkavRatylysgladvyeetgddkllkaaerlwdnvv 267
                      ++++ +   + ++t+   +vR       + d+   +g++  ++a+ +l++ v+
       AJA92610.1 508 WNENEKSFYFTADTHESLIVR----PKNYYDLSVPSGNSVAANALLKLHHLVN 556
                      999999999999********9....3455555555666666666666666665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.027
                      CTHHHHHHHHHHHHT-CHHHHHHHHCCHHCC CS
  Glyco_hydro_127 178 ggieealvklyelTgdkrYldlAkrfiderg 208
                      + +  al+kl+ l++d+ +l+++k++ + +g
       AJA92610.1 542 SVAANALLKLHHLVNDETFLQISKQILELNG 572
                      456689******************9987666 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00017      0.33     126     179 ..     267     317 ..     206     329 .. 0.67
   2 !    6.8   0.4    0.0015         3      33     109 ..     417     508 ..     389     526 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                     EETHHHHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHHHBETTTSEB-SEEET CS
  Glyco_hydro_88 126 lWlDgLfMaipllaklskvtgepkyldeaikqflltarhlfdpetGlyyhgwde 179
                     l+  +L+  +p++a+++++t++p yld ++k ++++ r +   + Gl+y ++d 
      AJA92610.1 267 LYDNALL--PPVYAEAYQITKDPFYLDVVTKTLDYVLREMT-STLGLFYSAQDA 317
                     2244454..77888888888888888888888777777765.355666666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                     HHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-...............CTTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS- CS
  Glyco_hydro_88  33 vflsglleayeatgdkeyldyakawadslideggk...............telelDdidigllllllyeltkderykeaaeeladyvlakpp 109
                     +++s++++ y ++g+++yl++  + a+ + ++  k               + +  D+  ++  l++ +e+t d+ +   a+++a y++++  
      AJA92610.1 417 MMISAFAKGYRISGNEKYLNASVNAAKYFSEQFSKhgfihrtfkndtpklNGYLDDYSYLVNSLIDVFEITADSYFLDMAQKIAHYMIEHFW 508
                     46677777777777777777777766666666666666777777766663333334444566667777777777777777777776665433 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.24   4.8e+02     167     206 ..     281     318 ..     268     330 .. 0.54
   2 !   14.8   0.5     8e-06     0.016      20     131 ..     398     511 ..     379     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.24
                     HHHH--CHHHHHHHHHHHHHHHHSCSBTTTS-B-SEEETT CS
  Glyco_hydro_76 167 arytgnetYlewAekvwdWvedvgliddedwlvyDgasve 206
                     +++t++  Yl++ +k+ d+v + ++  ++ +l+y   + +
      AJA92610.1 281 YQITKDPFYLDVVTKTLDYVLR-EMT-STLGLFYSAQDAD 318
                     5666666666666666666655.342.3333333332344 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8e-06
                     TECCTCTCBSCES-GHHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHHCCCT..CEE-SSSTTCTC.....SSEHHHHHHHHHHHHHHHHH..... CS
  Glyco_hydro_76  20 nesggtpgnlpdpyywWeagalfgalidywrltgdstyndlitqallaqag..enydympanqsr.....tegnDDqafwglaamtaaernfpep 107
                      ++ ++pg+ ++ +  W+  ++++a+ + +r++g+++y +   +a ++ ++  +++ ++ ++ ++     + + DD  + + + ++  e+     
      AJA92610.1 398 RSKRDQPGTDDKVITSWNS-MMISAFAKGYRISGNEKYLNASVNAAKYFSEqfSKHGFIHRTFKNdtpklNGYLDDYSYLVNSLIDVFEI----- 486
                     4556788888888888985.**************99887777776666444232233666655554443366779**************9..... PP

                     H--HHHHHHHHHHHHHHHHC.B-SC CS
  Glyco_hydro_76 108 tdepswLalAqavfntqasr.wdee 131
                     t +  +L++Aq++ ++++++ w+e+
      AJA92610.1 487 TADSYFLDMAQKIAHYMIEHfWNEN 511
                     88999***************99987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.023       1      65 [.      34      89 ..      34     123 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
  Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkd 65
                   ak ++kp+++ +  ++C  C+ +  e +e+ddv ++     ++++    +v+i+ ++e+  +++d
     AJA92610.1 34 AKDENKPIFLSVGYSSCHWCHVMAHESFENDDVAKI-----MNEN----FVNIKVDREERPDLDD 89
                   6789********************************.....7777....5555555555444444 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.63   1.3e+03      79     119 ..     266     307 ..     210     325 .. 0.48
   2 ?    1.8   0.0     0.057   1.1e+02     265     314 ..     402     452 ..     387     456 .. 0.78
   3 ?   10.6   0.1   0.00012      0.25      95     181 ..     428     513 ..     416     530 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                    EHHHHHHHHHHHHHHHT.TT-TTHHHHHHHHHHHHHHHTEET CS
  GlcNAc_2-epim  79 daYdhaFvllalasala.ageeeakdlldetlavlekhlwee 119
                     +Yd a     +a+a++ + ++ + d++++tl+ + +++ + 
     AJA92610.1 266 MLYDNALLPPVYAEAYQiTKDPFYLDVVTKTLDYVLREMTST 307
                    445555555555554441233344555555555555544443 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.057
                    S-BSS--EE..HHHHHHHHHHHHHHHHHH--CHHHHHHHHHHHHHHHHTB-T CS
  GlcNAc_2-epim 265 gkpvddakl..lWpqtEalkaaaalaeltgearylewyarvaeylerhlidp 314
                    ++p  d+k+  +W  +  + a a++++ +g+++yl+   ++a+y+ + +  +
     AJA92610.1 402 DQPGTDDKVitSWNSMM-ISAFAKGYRISGNEKYLNASVNAAKYFSEQFSKH 452
                    55555666555677775.889999************9999999999887765 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00012
                    TTT-TTHHHHHHHHHHHHHHHTEETTTTEE--EE-TTSS-BEEH.HHHHHHHHHHHHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGTT CS
  GlcNAc_2-epim  95 aageeeakdlldetlavlekhlweekaglvkeesdkefsklrgs.npnMhlleAmLalaeatgdkeyleraeeiaelvisefadaesg 181
                     +g+e++ ++  ++ +   +++  +k+g+++ +++++  kl g       l++ ++ ++e+t d+ +l+ a++ia+ +i++f ++++ 
     AJA92610.1 428 ISGNEKYLNASVNAAKYFSEQF--SKHGFIHRTFKNDTPKLNGYlDDYSYLVNSLIDVFEITADSYFLDMAQKIAHYMIEHFWNENEK 513
                    5677777666666677776665..4679999999998888855414447899******************************998864 PP

>> Pec_lyase  Pectic acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.017        34      48      74 ..     277     303 ..     274     315 .. 0.88
   2 ?    8.7   0.6   0.00048      0.95      16     109 ..     385     487 ..     374     513 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
   Pec_lyase  48 laevykatkdekykdavrkglefllka 74 
                  ae+y+ tkd  y d v k+l+++l+ 
  AJA92610.1 277 YAEAYQITKDPFYLDVVTKTLDYVLRE 303
                 599*********************975 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
   Pec_lyase  16 eltekeakkvlk..ekkkeegtiDndatv...tellflaevykatkdekykdavrkglefllkaqYsnGgw.pqfy....PlkkgYsehitfnDdamvr 104
                 e+ ++ +kk+l+  +k+++ gt D   t      +  +a+ y+ +++eky +a  ++ +++ + q+s+ g+    +    P+ +gY +   +  ++++ 
  AJA92610.1 385 EILNRSSKKLLDvrSKRDQPGTDDKVITSwnsMMISAFAKGYRISGNEKYLNASVNAAKYFSE-QFSKHGFiHRTFkndtPKLNGYLDDYSYLVNSLID 482
                 4444444444440044444677777666522134678899********************866.66555542334333338888899999998888888 PP

   Pec_lyase 105 vlnll 109
                 v+++ 
  AJA92610.1 483 VFEIT 487
                 88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (674 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4554.48
//
Query:       AJA92611.1  [L=432]
Description: FAD dependent oxidoreductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-37  127.7   0.0    9.6e-37  127.4   0.0    1.1  1  DAO             FAD dependent oxidoreductase
    2.8e-07   29.5   0.1      0.012   14.2   0.0    2.4  2  Mqo             Malate:quinone oxidoreductase (Mqo)
    0.00044   19.6   0.0       0.15   11.3   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0013   18.0   0.0     0.0062   15.8   0.0    1.9  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.061   13.1   0.0    1.7  1  Sda             Sporulation inhibitor A
      0.022   13.9   1.1       0.47    9.6   0.2    2.1  2  DUF5107         Domain of unknown function (DUF5107)
      0.037   12.7   0.0       0.18   10.4   0.0    1.9  2  HI0933_like     HI0933-like protein
      0.049   13.7   0.2       0.14   12.2   0.2    1.7  1  DUF1398         Protein of unknown function (DUF1398)
       0.11   11.4   0.6       0.49    9.2   0.6    1.9  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.4   0.0   4.8e-40   9.6e-37       1     349 [.       5     402 ..       5     405 .. 0.79

  Alignments for each domain:
  == domain 1  score: 127.4 bits;  conditional E-value: 4.8e-40
                 EEEEECTSHHHHHHHHHHHHT.T..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHH.HHHHHHHHHHHHHHHHHSSTTSEEEEEEEEEESSHHH CS
         DAO   1 dvviiGGGiiGlstAyeLarr.g..VtllekgdiagsgaSgrnsgllhsglrylpeasela.rlslealeelreleeelgididyrrtGllslaadeee 95 
                 d++i GGGi G ++ y+ +      V+++ek++ +++++Sgrn+g++h  ++  pe+ +++ + ++ ++e+++ l+e++    ++ + G++ +a +e++
  AJA92611.1   5 DIAILGGGILGTTISYWISNLyDssVCVIEKESNVAQHTSGRNTGVVHTPFYLNPEKKKIFaKSAQSSHELWKTLAENTM--SPWNEIGTIEVALNETQ 101
                 8*****************8654469**************************87777666664777788********9864..78***********9998 PP

                 HHHHHHHHHHH.HHTTT..TEE.EEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEEEECT.E CS
         DAO  96 lealdkllall.leagl..dae.lldaeevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtgl.eeedgkvwgverttp.g 188
                    l ++++++  e+g+  ++  lld++e++++e ++++   +l+++++   d+ klt+ + +   ++  e+l++  v+++ +++d  + +v + t+  
  AJA92611.1 102 HKTL-EKYQKWgIENGVleENLvLLDSNEIKQKEKNVEC-FSGLLCKSDVSTDYSKLTQEIKKISVQNSTEFLFQKSVKSFiKNDD--AIQV-NFTDnS 195
                 8889.6666666778987444337***99*****97655.567999999*******************************724443..4556.333323 PP

                 EEEEEEEEEE--GGGHH.HHHTTCTT....TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSE......EETTC CS
         DAO 189 endaadavVnaaGawsd.llgllkel....dlpispvrgqvlvlkplseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtad......eesgd 275
                 ++ ++ +++n+ G  s  ++   k++          +rg+++   +     v + +i+ v   +  ++ +++ + r++g++ +G++a+      + +g+
  AJA92611.1 196 SI-ECSYLINCSGGNSLdIA---KQFdlfeSYSDLHFRGEYWIAHNSYADIV-KTNIYSVARhPEFPFLDPHWIKRANGTTEIGPNAVpvptpeTYDGF 289
                 32.4688********97444...3332233234488********55444454.447887777899**********************988765533333 PP

                 SSTSCSHH.................................HHHHHHHHHHHHSGGGCG...EEEEEEEEEE..E.TTSSEEEEEEE.TEEEEEEEEEC CS
         DAO 276 ddpevdee.................................didellealrklfPqlgd...vlrkwaGlrp..l.pdglpligetp.gvkglylatGh 334
                  + ++++                                    d++ +++ +++P+l++    ++  aG+r+    pdg+++ +  + +  + ++  ++
  AJA92611.1 290 VT-DIPSTisklgeiltggakklflnpdfislishefrssiSKDAMVQRVMNFIPSLKPdyfTKKGTAGIRTpvIsPDGNFISDVMErEGHNSFHIVNY 387
                 33.333337788889999999999999999999999999989999***********855573446899****86259**888877444455******** PP

                 TTTHHHHHHHHHHHH CS
         DAO 335 sghGltlapatGkll 349
                 +++G t apa   l+
  AJA92611.1 388 NSPGATGAPAYSALI 402
                 *********966555 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.5e-05     0.029       2      54 ..       3      52 ..       2      63 .. 0.87
   2 !   14.2   0.0   6.1e-06     0.012     175     434 ..     149     396 ..     123     422 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
         Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGH 54
                k d+ ++G+Gi+ +t++ ++++l  + s+ v+e+ ++va+  s    n+G  H
  AJA92611.1  3 KFDIAILGGGILGTTISYWISNLY-DSSVCVIEKESNVAQHTSG--RNTGVVH 52
                78*********************7.56899**********9986..4666666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 6.1e-06
         Mqo 175 tdvnfgaltrqllkalekkkgvelklkhevkdlkreedgkWkvkvkdlktgekkkvkakfvfiGaGGgalklLqksgipeakgyggfPvsGqflvcknp 273
                    ++ +lt+++ k ++ ++++e+ ++++vk++ +++d   +v+++     ++++++ +++   +GG++l++ ++ ++ e  +y+ +   G++ +++n+
  AJA92611.1 149 VSTDYSKLTQEIKK-ISVQNSTEFLFQKSVKSFIKNDD-AIQVNFT-----DNSSIECSYLINCSGGNSLDIAKQFDLFE--SYSDLHFRGEYWIAHNS 238
                 4569*****99765.557799**************999.3444444.....5678999**************99988866..69999999**9998875 PP

         Mqo 274 evveqheakvYgkaavgaPPmsvpHlDtRvidgkksllfGPfagfstk.flkegslldllksvklsnllpllavglknldLvkYlie....qvlk..sk 365
                   ++  ++ +Y+ a+    P   pH   R  +g ++   GP a   +     +g ++d++++++   l  +l+ g+k+l L    i+    + +   sk
  AJA92611.1 239 -YADIVKTNIYSVARHPEFPFLDPHWIKRA-NGTTE--IGPNAVPVPTpETYDGFVTDIPSTIS--KLGEILTGGAKKLFLNPDFISlishEFRSsiSK 331
                 .56778899******999999999987775.56655..49999865541567899999999885..577888888887766554433111133322257 PP

         Mqo 366 edrlealreflpeakkedWelv.vaGqRvqvikkdeekggvlefGtevvasa.dgslaalLGasPGAstav 434
                 ++ ++++ +f+p+ k + ++ + +aG R  vi  d +      f  +v++ +  +s+  +   sPGA  a 
  AJA92611.1 332 DAMVQRVMNFIPSLKPDYFTKKgTAGIRTPVISPDGN------FISDVMEREgHNSFHIVNYNSPGATGAP 396
                 7788999999999998887654389999999988543......4445554431344555555666666555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0031       6.2     144     178 ..       5      40 ..       2      58 .. 0.81
   2 !   11.3   0.0   7.3e-05      0.15     183     236 ..     154     207 ..     143     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0031
                  EEEEES-SHHHHHHHHHHHHH.T-EEEEEESSSSSS CS
                  xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
  Pyr_redox_2 144 rivvvGgGyiGvElAaalakl.gkevtlveardrll 178
                  +i++ GgG  G+ ++  +++l  + v ++e  +++ 
   AJA92611.1   5 DIAILGGGILGTTISYWISNLyDSSVCVIEKESNVA 40 
                  589999999999999999998455599999988886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.3e-05
                  HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavG 236
                  ++l++++++   ++  e+ +++svk +++n++ ++v  +d+++i++++++ + G
   AJA92611.1 154 SKLTQEIKKISVQNSTEFLFQKSVKSFIKNDDAIQVNFTDNSSIECSYLINCSG 207
                  5688999999999*******************999**************99987 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.35   6.9e+02       2      40 ..       4      43 ..       3      52 .. 0.78
   2 !   15.8   0.0   3.1e-06    0.0062      45     167 ..     100     211 ..      96     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.35
                   EEEEEE--SHHHHHHHHHHHH.TTHHEEEEESSSSSCCSS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLse.aGvrvvlvekrsttvvlp 40
                    d++I G+G  G + +   s+ +  +v+++ek s+ ++++
     AJA92611.1  4 FDIAILGGGILGTTISYWISNlYDSSVCVIEKESNVAQHT 43
                   5889*********999988862444699999999888776 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.1e-06
                    EEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHH.CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCC CS
  FAD_binding_3  45 lnqrtmellrqlGledrilaegapnelmgealynelsdtpkaradle.lesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvt 139
                    ++ +t+e +++ G+e+ +l+e  +   ++e+ ++e     k  +  + l+++    t+y+  +l++ + +  ++  +++ f++ v+s+ ++++ ++
     AJA92611.1 100 TQHKTLEKYQKWGIENGVLEENLVLLDSNEIKQKE-----KNVECFSgLLCKSDVSTDYS--KLTQEIKKISVQNSTEFLFQKSVKSFIKNDDAIQ 188
                    57789999999999999999987766666666666.....44444445667777777775..56666777777889******************** PP

                    CEEEECCTTEEEEEEEEEEEE--GTT-H CS
  FAD_binding_3 140 aevrdketgeeetvrakYlvGaDGgrSt 167
                     +++d++      +++ Yl+ + Gg+S 
     AJA92611.1 189 VNFTDNS-----SIECSYLINCSGGNSL 211
                    ****995.....8*************94 PP

>> Sda  Sporulation inhibitor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.1e-05     0.061      16      32 ..     308     324 ..     307     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
         Sda  16 AlelnLdpDFIeLieeE 32 
                 A++l L+pDFI+Li  E
  AJA92611.1 308 AKKLFLNPDFISLISHE 324
                 99************998 PP

>> DUF5107  Domain of unknown function (DUF5107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00024      0.47     192     283 ..      15     108 ..       9     115 .. 0.86
   2 ?    3.0   0.0     0.025        49     160     246 ..     163     252 ..     147     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
                 E...EEESS-SS..........SEEEEE-TTTS-EEEEE--TTT--EEEEEE--SSG.GGGGG.SSSSSS--EEEEEEES-S-TTS-EEE.-TT CS
     DUF5107 192 Gldlsfyknkdvsksyfvag..nafgaYtpskgiGllhiadesdapGkklWlygvaeedkiWedlLtdddgqYveiqaGlildqsaklellePg 283
                 G  +s++ ++  + s  v      ++ +t  +++G++h   + +   kk+++ + +  ++ W+ l  +  +++ ei +  +  ++++ ++le +
  AJA92611.1  15 GTTISYWISNLYDSSVCVIEkeSNVAQHTSGRNTGVVHTPFYLNPEKKKIFAKSAQSSHELWKTLAENTMSPWNEIGTIEVALNETQHKTLEKY 108
                 67899999999988888875578999*************************************8889999999999887777777777776665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.025
                 EE--TT-EEE--SSEHHHS-.-BGGG--S..-EE...EEESS-SS..........SEEEEE-TTTS-EEEEE--TTT--EEEEEE--SSG CS
     DUF5107 160 vkvadDtefvfPgkekvkas.kkekdikewpetGldlsfyknkdvsksyfvag..nafgaYtpskgiGllhiadesdapGkklWlygvae 246
                 + v++ tef f +  k   +  +  +++   ++ ++ s+  n    +s  +a+  + f +Y   +  G + ia++s a   k  +y+va+
  AJA92611.1 163 ISVQNSTEFLFQKSVKSFIKnDDAIQVNFTDNSSIECSYLINCSGGNSLDIAKqfDLFESYSDLHFRGEYWIAHNSYADIVKTNIYSVAR 252
                 677888999998877543330333444443488999999999999999999977899999*99999999999999999999999999988 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.17   3.3e+02       2      37 ..       5      41 ..       4      85 .. 0.85
   2 ?   10.4   0.0   9.2e-05      0.18     115     167 ..     156     211 ..     119     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.17
                 SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS-H CS
  HI0933_like  2 dviviGgGaAGlmaAisa.akrgkrVlllekakklgr 37
                 d++++GgG  G   +  + +  +++V ++ek++++++
   AJA92611.1  5 DIAILGGGILGTTISYWIsNLYDSSVCVIEKESNVAQ 41
                 899*****99999998885678999*****9998876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9.2e-05
                  HHHHHHHHT-....EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
  HI0933_like 115 llkelkeagv....klrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                  l++e+k+  v    ++  +++vks+ k++d  ++v+ ++++++e+++l+  +GG+S+
   AJA92611.1 156 LTQEIKKISVqnstEFLFQKSVKSFIKNDDA-IQVNFTDNSSIECSYLINCSGGNSL 211
                  55666655541111567799*****998888.9***99****************996 PP

>> DUF1398  Protein of unknown function (DUF1398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   7.2e-05      0.14      11      53 ..     151     193 ..     144     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                 ---HHHHHHHHHH-SSEEEEETTTSEEEEE-SSS-EEEEE-ST CS
     DUF1398  11 adfpafiqelkrlgvskYeyfvadgnvkyvgendevvevkakr 53 
                  d++++ qe+k++ v++ + f+ +  vk + +nd  ++v+ + 
  AJA92611.1 151 TDYSKLTQEIKKISVQNSTEFLFQKSVKSFIKNDDAIQVNFTD 193
                 79************************************98765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6   0.00025      0.49     146     225 ..     146     223 ..       5     251 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00025
                     --EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE- CS
  Trp_halogenase 146 syAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedw 225
                     +   + d +++ + +++++ ++  + +  k+v+  +++d++++ ++ +d  ++e    i csG ++l i++ ++  fe++
      AJA92611.1 146 KSDVSTDYSKLTQEIKKISVQNSTEFLFQKSVKSFIKNDDAIQ-VNFTDNSSIECSYLINCSGGNSLDIAKQFD-LFESY 223
                     44456788889999999999999999999****99**999996.8999*******************9999754.34555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2798.55
//
Query:       AJA92612.1  [L=125]
Description: hypothetical protein T478_0483 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 950.42
//
Query:       AJA92613.1  [L=252]
Description: alpha/beta hydrolase, PF05990 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-14   53.0   0.1    4.8e-14   52.4   0.1    1.1  1  DUF900         Alpha/beta hydrolase of unknown function (DUF9
    5.1e-10   38.8   0.0    7.3e-10   38.3   0.0    1.1  1  DUF726         Protein of unknown function (DUF726)
    2.5e-06   27.6   0.0    3.7e-06   27.0   0.0    1.3  1  Cutinase       Cutinase
      4e-06   26.8   0.1    6.4e-06   26.1   0.1    1.4  1  Lipase_3       Lipase (class 3)
    1.6e-05   24.6   3.0      3e-05   23.6   3.0    1.5  1  DUF676         Putative serine esterase (DUF676)
    6.5e-05   22.6   0.1    8.8e-05   22.2   0.1    1.4  1  LIDHydrolase   Lipid-droplet associated hydrolase
    0.00039   20.1   0.0    0.00069   19.3   0.0    1.4  1  Abhydrolase_8  Alpha/beta hydrolase
     0.0025   17.1   0.0     0.0032   16.8   0.0    1.4  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0051   16.2   0.4     0.0069   15.7   0.1    1.4  2  Lipase         Lipase
  ------ inclusion threshold ------
      0.015   14.4   0.1      0.026   13.6   0.1    1.5  1  DUF1749        Protein of unknown function (DUF1749)
      0.038   13.9   0.0      0.086   12.7   0.0    1.5  1  VirJ           Bacterial virulence protein (VirJ)
      0.044   13.0   0.0      0.063   12.4   0.0    1.3  1  LCAT           Lecithin:cholesterol acyltransferase
       0.19   11.8   0.0        0.3   11.2   0.0    1.4  1  Thioesterase   Thioesterase domain
       0.58   10.0   3.7       0.75    9.7   0.5    2.7  3  DUF4295        Domain of unknown function (DUF4295)


Domain annotation for each model (and alignments):
>> DUF900  Alpha/beta hydrolase of unknown function (DUF900)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.1   3.8e-17   4.8e-14      14     171 ..      38     206 ..      31     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.8e-17
      DUF900  14 kksaakeilvfvhGynnsFedavlraaqiaddlk...nqgaivvfsWPsagklldynyDre........saeasrdalekllrylatkksakkihllaH 101
                 k s++ ei++ +hG +n+ ++a+ +  +  + lk   ++  +v++s  s+   + y++            a+   ++l k+++ l+ k++  ki l+ H
  AJA92613.1  38 KISQKSEIVIMIHGLRNNKSGALAKYVIAEKRLKtlnYKHDVVGYSYDSNTAGVQYKSTALsalkvgvtIAKKNGKNLSKFIKDLKSKNPSIKIRLMGH 136
                 678999*****************99776655444222888************9998877651122222145677899********************** PP

      DUF900 102 SmGtwlvlealrqlaieadepaveakikeviLaAPDidvdvfkkqle.slgkes...keltvyvsrdDraLklS 171
                 S G +++l+++++la++ ++   + +i+ v L+ + i ++  + +++ +   ++   k++  y+s++D +Lk+ 
  AJA92613.1 137 SLGAQVILSTIESLAKNSEN---NGIIESVHLFGASIPANSLSPKIHgN-KFQKivnKKIMNYYSPYDDVLKAA 206
                 ***************99975...67**************9999999952.43334569*************985 PP

>> DUF726  Protein of unknown function (DUF726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   5.7e-13   7.3e-10     194     289 ..     102     204 ..      92     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 5.7e-13
      DUF726 194 nvsleraakaGklLAdallsraq..GeRpvtLiGfslGARviyvCLlelakk.kalglvenvillGaPvtte...ak.vwlkvrsvvsgRlvnvysenD 285
                 +v+++ a+k Gk L + + + +    +  + L+G+slGA vi++ +  lak+ ++ g++e v l+Ga ++++   +k +  k++ +v  +++n ys  D
  AJA92613.1 102 KVGVTIAKKNGKNLSKFIKDLKSknPSIKIRLMGHSLGAQVILSTIESLAKNsENNGIIESVHLFGASIPANslsPKiHGNKFQKIVNKKIMNYYSPYD 200
                 788999**********997644412566799********************988999*********9777652223325689**************999 PP

      DUF726 286 ylLg 289
                  +L+
  AJA92613.1 201 DVLK 204
                 8886 PP

>> Cutinase  Cutinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.9e-09   3.7e-06      40     149 ..      87     202 ..      61     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.9e-09
                 EEEE------CGG...STTSS-HHHHHHHHHHHHHHHHH-TT-EEEEEEETHHHHHHHHHHTT.....S-HHHHHHEEEEEEES-TTCCCCTT...... CS
    Cutinase  40 avqgvnYpAdleq...lyegseeagakeaaalvqslaskCPdtkivlgGYSqGaqvidnaieggatatlpaavadkvaavvlfGdpsnvaglp...... 129
                 +  gv+Y+ +  +   +  + +++  k++++ +++l+sk P  ki l+G S Gaqvi  +ie     + +++ +  + +v lfG    +++l+      
  AJA92613.1  87 NTAGVQYKSTALSalkVGVTIAKKNGKNLSKFIKDLKSKNPSIKIRLMGHSLGAQVILSTIES---LAKNSENNGIIESVHLFGASIPANSLSpkihgn 182
                 55678888887775443445567777899**********************************...44455556679********99988888888999 PP

                 S-TTS-GGGEEEE--TT-GG CS
    Cutinase 130 evsklyaskikslCdagDpi 149
                 +++k+ + ki ++  + D +
  AJA92613.1 183 KFQKIVNKKIMNYYSPYDDV 202
                 99999999999987777755 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1     5e-09   6.4e-06      33     122 ..      91     186 ..      55     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5e-09
                 -EEEHHHHHHHH......S-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHH.HHHTT-SS---EEEEEES----B-HHHHHHHHT-TTE CS
    Lipase_3  33 gkvhsgfleaye......eslreqvlkelkrllekypeysivvtGHSLGgalAlLaald.lvengenekkkvtvvtfGqPrvgnkefaklvdsqlnk 122
                 ++ +s  l+a++      ++  +++ k +k+l++k+p+++i + GHSLG+ + +L++++ l++n en+    +v  fG+    n+   k + ++++k
  AJA92613.1  91 VQYKSTALSALKvgvtiaKKNGKNLSKFIKDLKSKNPSIKIRLMGHSLGAQV-ILSTIEsLAKNSENNGIIESVHLFGASIPANSLSPKIHGNKFQK 186
                 4444555555555555555778899999********************9876.66666527788888899999999999888888888888877776 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   3.0   2.3e-08     3e-05       3     115 ..      41     164 ..      39     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
      DUF676   3 kkdhLvVlvHGlqgn...........saDlelikeqlekikeklpeekieflmsennesktfkgidvlgerlaeevlevvkkkkdk..nkkiSfvghSl 88 
                 +k+ +v+++HGl  n           ++ l+ ++ +   +   ++ +   +  ++ + s    g++ ++++ ++ + +++k+ k+k   +ki ++ghSl
  AJA92613.1  41 QKSEIVIMIHGLRNNksgalakyviaEKRLKTLNYKHDVVGYSYDSNTAGVQYKSTALSALKVGVT-IAKKNGKNLSKFIKDLKSKnpSIKIRLMGHSL 138
                 7889***********875433333333333333333333333344444444444444444444554.34455677778888888778878********* PP

      DUF676  89 Ggliaraaiaklkekemtlkeaikgle 115
                 G  ++ + i  l ++ +  +++i+ ++
  AJA92613.1 139 GAQVILSTIESLAKNSE-NNGIIESVH 164
                 *********99886664.456666665 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   6.9e-08   8.8e-05      69     120 ..     112     168 ..      63     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.9e-08
  LIDHydrolase  69 edflkellek.aksekdvklilvGHSvGaYialevlkrlsers....ikkvvlLfPt 120
                    + l +++++ ++++  +k+ l+GHS Ga ++l ++++l ++s    i++ v Lf+ 
    AJA92613.1 112 GKNLSKFIKDlKSKNPSIKIRLMGHSLGAQVILSTIESLAKNSenngIIESVHLFGA 168
                   3568889988888999*********************99988888998888888864 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.4e-07   0.00069      21     124 ..      45     144 ..      34     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.4e-07
  Abhydrolase_8  21 VsVtvpGvdttlrrtlatmvaearglraeaaaaeeaagkpesvAviAWlgYeaPagaskevatddrAaagAaeLnallrdlratsvpgqhlallgH 116
                    + +++ G+  + +++la+ v +++ l+   ++  + +g +      A + Y++ a  + +v     A++   +L+++++dl++++ p+ ++ l+gH
     AJA92613.1  45 IVIMIHGLRNNKSGALAKYVIAEKRLKTLNYKH-DVVGYSYDSN-TAGVQYKSTALSALKV-GVTIAKKNGKNLSKFIKDLKSKN-PSIKIRLMGH 136
                    556677777777777777777666665544443.4666666443.4678999986655554.566899999*************9.********** PP

  Abhydrolase_8 117 SYGSlvas 124
                    S G+ v  
     AJA92613.1 137 SLGAQVIL 144
                    ***86644 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0032      60     114 ..     113     169 ..      40     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
  Hydrolase_4  60 dDlaafvekvkeehpelplfllGhSmGGliallyl..lrypdkvaglilsaPalkik 114
                  + l++f++ +k+++p  ++ l+GhS+G+ + l+ +  l + ++ +g+i s  +++  
   AJA92613.1 113 KNLSKFIKDLKSKNPSIKIRLMGHSLGAQVILSTIesLAKNSENNGIIESVHLFGAS 169
                  67999***************************9998744444456777665555544 PP

>> Lipase  Lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.4e-06    0.0069      68     160 ..      41     142 ..      15     152 .. 0.79
   2 ?   -4.0   0.0       5.4     7e+03     147     158 ..     161     172 ..     154     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.4e-06
                 TTSEEEEEE--TT-TT.........TTTHHHHHHHHHHTT...--EEEEEEE-HHHHSS-HHHHHHHHHHHHHHHHHHHHHHHHHH---GGGEEEEEET CS
      Lipase  68 tskktrliihgftvkg........leeswlsklvkalekv...ekvnvivvdwksgsealyaqavenirvvgaevakllseLeeelnyseenvhliGss 155
                 ++++++++ihg + +         + e+ l+ l  +   v    ++n   v++ks++ +  ++ v+  ++ g++ +k+++ L+   + +  +++l+G+s
  AJA92613.1  41 QKSEIVIMIHGLRNNKsgalakyvIAEKRLKTLNYKHDVVgysYDSNTAGVQYKSTALSALKVGVTIAKKNGKNLSKFIKDLK--SKNPSIKIRLMGHS 137
                 4556777788877665567766665555555444443333446899************************************9..577999******** PP

                 CHHHH CS
      Lipase 156 lgaHv 160
                 lga v
  AJA92613.1 138 LGAQV 142
                 ***87 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.4
                 GGEEEEEETCHH CS
      Lipase 147 envhliGsslga 158
                 e+vhl G s+ a
  AJA92613.1 161 ESVHLFGASIPA 172
                 789999988765 PP

>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-05     0.026      80     130 ..     108     154 ..      30     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
     DUF1749  80 LkrDaeeieklveYlkktksGeekkekvvlmGHstGsqdvlyYltssnerd 130
                  k++ ++++k ++ lk +    +   k+ lmGHs G+q +l  + s  +++
  AJA92613.1 108 AKKNGKNLSKFIKDLKSK----NPSIKIRLMGHSLGAQVILSTIESLAKNS 154
                 566667777777777777....4678***************9988765544 PP

>> VirJ  Bacterial virulence protein (VirJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.7e-05     0.086      49     103 ..     110     166 ..     106     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
        VirJ  49 evaaDldrlikkyakrwkkkkvvliGysfGaDvlPaaynkLkaatrdk..vklvsll 103
                 + +++l++ ik+ +++    k+ l+G+s Ga v+  +++ L +++ ++  ++ v l+
  AJA92613.1 110 KNGKNLSKFIKDLKSKNPSIKIRLMGHSLGAQVILSTIESLAKNSENNgiIESVHLF 166
                 66899************************************9887664225566665 PP

>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.9e-05     0.063     107     160 ..     114     168 ..      66     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
        LCAT 107 kLkelieealk.lsgkkvvliaHSmGnllvlyflkwveaeaWvdqhikafislga 160
                 +L ++i      +   k+ l++HS+G++++l +++++ ++   +  i++    ga
  AJA92613.1 114 NLSKFIKDLKSkNPSIKIRLMGHSLGAQVILSTIESLAKNSENNGIIESVHLFGA 168
                 56666655555477889*******************9998866777776655555 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023       0.3      54     107 ..     117     173 ..     111     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                   HHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHC...T-SEEEEEEESCCCCCC CS
  Thioesterase  54 eyaealrqiqpegPyalfGhSlGgllAfevArqLesq...Glavkslflidssapse 107
                    +++ l++ +p    +l+GhSlG+++   + + L ++      + s+ l+++s p  
    AJA92613.1 117 KFIKDLKSKNPSIKIRLMGHSLGAQVILSTIESLAKNsenNGIIESVHLFGASIPAN 173
                   678899999****************98888888877755555677888888887755 PP

>> DUF4295  Domain of unknown function (DUF4295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.99   1.3e+03      23      31 ..      51      59 ..      37      76 .. 0.62
   2 ?    9.7   0.5   0.00058      0.75       4      28 ..     103     126 ..     100     127 .. 0.80
   3 ?   -2.0   0.0       2.5   3.2e+03      16      23 ..     243     250 ..     237     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.99
     DUF4295 23 mvKspKTGa 31
                  +++K+Ga
  AJA92613.1 51 GLRNNKSGA 59
                455555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00058
     DUF4295   4 vVAtlkkgasgkkytKvIkmvKspK 28 
                 v  t++k+ +gk+++K+Ik  Ks +
  AJA92613.1 103 VGVTIAKK-NGKNLSKFIKDLKSKN 126
                 54567777.8************975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.5
     DUF4295  16 kytKvIkm 23 
                 +y+K Ik+
  AJA92613.1 243 SYAKTIKS 250
                 79999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1705.50
//
Query:       AJA92614.1  [L=369]
Description: hypothetical protein T478_1270 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.5   0.6      0.011   15.5   0.6    2.6  2  PKD       PKD domain
      0.019   15.1   0.0      0.066   13.4   0.0    1.8  2  ASH       Abnormal spindle-like microcephaly-assoc'd, ASPM-SP
      0.068   11.8   0.1      0.083   11.5   0.1    1.1  1  NPAT_C    NPAT C terminus
      0.074   12.9   0.0       0.12   12.2   0.0    1.2  1  Carot_N   Orange carotenoid protein, N-terminal


Domain annotation for each model (and alignments):
>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.3   1.4e+03      28      43 ..     131     143 ..     103     147 .. 0.55
   2 ?   15.5   0.6   2.5e-06     0.011      19      67 ..     304     353 ..     281     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                 EEEE--SS--EEEEET CS
         PKD  28 ysWdfgdgsvvqvlse 43 
                  +W++g    vq l++
  AJA92614.1 131 IRWNVGE---VQWLES 143
                 2377777...666655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.5e-06
                 ES.-SS-SEEE..EE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
         PKD  19 avpdganvtys..WdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                 +v+dg+ vt s  W +g+  +++++ +p  + ++++ G+Ye+tv ++ +v 
  AJA92614.1 304 QVQDGNGVTVSlaWITGQ-LAAGQSFSPALSWIPTASGSYEATVFVWESVD 353
                 457877777777799999.*************************9998775 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   6.2e+03      69      93 ..     184     208 ..     181     211 .. 0.80
   2 ?   13.4   0.0   1.5e-05     0.066      18      87 ..     276     347 ..     271     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                 XXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  69 tltvtwtPteegavrevLqflvndv 93 
                 +l++t t+ ++g    ++ f+ +d 
  AJA92614.1 184 SLMITETNEATGIFEGTVSFTADDE 208
                 6778888888999999999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.5e-05
                 ----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
         ASH  18 dvkvGssaerlLtveNpseepaevkvskvpaaekgfsveete..levqpgesvtltvtwtPteegavrevLq 87 
                 +v v +  + + +++N+++ +++ ++   +++ +g++v+ ++   ++++g+s++  ++w Pt++g+  +++ 
  AJA92614.1 276 EVSVDQQVQIEADLVNGQDRDQSFAYLVQVQDGNGVTVSLAWitGQLAAGQSFSPALSWIPTASGSYEATVF 347
                 6888888899999********9999999999********999999********************9998875 PP

>> NPAT_C  NPAT C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.9e-05     0.083       6     130 ..     243     369 .]     241     369 .] 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
      NPAT_C   6 isgenlptiilSspaKspeknaelskclsseetagaevkdsalveQkllvlkpkd.saasslniqneectvfsla.gtsnvskdggf...iqLlpatst 99 
                 i+g  +   i+ + +++p++na+++++   + + +  v +  ++e  l+  + +d s+a  +++q +++++ sla +t +++    f   +  +p++s 
  AJA92614.1 243 ITGTAIVGTIVPPLERAPAANARVVDSFGNSLS-EVSVDQQVQIEADLVNGQDRDqSFAYLVQVQDGNGVTVSLAwITGQLAAGQSFspaLSWIPTASG 340
                 8999999999************99997665544.33488889999999987755428899999999998877776489999987665322556999999 PP

      NPAT_C 100 afgnsnniliatCvtdpaalgttvtqsnvvv 130
                 +++ +  ++    v +p+al+ tv+ s  vv
  AJA92614.1 341 SYEATVFVW--ESVDNPTALSDTVSVSIRVV 369
                 999875555..78***********9997665 PP

>> Carot_N  Orange carotenoid protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05      0.12      45      85 ..     261     301 ..     250     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                 HHHHCCCHHHHHHHHCS-HHHHHHHHHHHHCT--SHHHHHH CS
     Carot_N  45 aaelelaekllnqikqlseeeQlqvmrdlvnkkdteisraY 85 
                 aa+ ++++++ n ++++s ++Q+q+  dlvn +d + s aY
  AJA92614.1 261 AANARVVDSFGNSLSEVSVDQQVQIEADLVNGQDRDQSFAY 301
                 688899999999***********************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2402.02
//
Query:       AJA92615.1  [L=315]
Description: mevalonate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-16   59.5   1.5    5.6e-16   58.5   1.0    1.8  2  GHMP_kinases_N  GHMP kinases N terminal domain
    6.1e-12   45.7   0.0    1.8e-11   44.3   0.0    1.7  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.028   14.6   2.1      0.028   14.6   2.1    1.9  2  DUF3091         Protein of unknown function (DUF3091)
       0.15   12.3   5.3      0.063   13.5   2.3    1.9  2  DUF2666         Protein of unknown function (DUF2666)


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   1.0   1.3e-19   5.6e-16       2      66 .]      92     157 ..      91     157 .. 0.92
   2 ?   -3.5   0.0       2.8   1.3e+04      40      54 ..     209     223 ..     202     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.3e-19
                     EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee..aklaleaerlaqggngsggDvaasvyGg 66 
                     i+i+s+iP+gaGLGSS+A++va++a + +l+++  e+  ++l+++ae+ +   n+sg D ++sv+Gg
      AJA92615.1  92 IKIESDIPIGAGLGSSSACCVAAAASVSNLFNNTNEKevLELSIQAEKTIF-PNSSGADCTVSVHGG 157
                     89*****************************75543357*********998.**************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                     HHHHHHHHHHHHHHH CS
  GHMP_kinases_N  40 klaleaerlaqggng 54 
                     +l+ e erl+ ++  
      AJA92615.1 209 ELCSEEERLVTKALE 223
                     678888888876555 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0     4e-15   1.8e-11       1      72 [.     221     289 ..     220     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4e-15
  GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdea 72 
                     +le ++ +dle++g+++ ++q    ++++g+++++l ++ +++++ + +gak++GaGgG++++al+++ ++ 
      AJA92615.1 221 ALESMKSNDLETMGKCMAQNQIY--LEQIGVSNDILLSITKEIEQIT-FGAKITGAGGGGCIIALTQKNNDL 289
                     5788899***************6..889*******************.******************877764 PP

>> DUF3091  Protein of unknown function (DUF3091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.1   6.2e-06     0.028      17      93 ..     190     263 ..     181     265 .. 0.90
   2 ?   -3.2   0.1       2.2   9.9e+03      24      44 ..     283     303 ..     281     307 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.2e-06
     DUF3091  17 revleeikrlkeklkqlfdelqSkkenmtCnkPenidekdlenLenlikkkqstkvalnvfklkkkyllkvkenlen 93 
                  +v+e++k++k + + +f el S++e++  +  e ++ +dle + + ++++q   ++l+ + + +++ll + +++e+
  AJA92615.1 190 DKVVEQVKKFKDENSDIFSELCSEEERLVTKALESMKSNDLETMGKCMAQNQ---IYLEQIGVSNDILLSITKEIEQ 263
                 689******************************************9998765...7888899999999999999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
     DUF3091  24 krlkeklkqlfdelqSkkenm 44 
                  +++++l++++++++ + +n+
  AJA92615.1 283 TQKNNDLSEFMNTTKYQTHNV 303
                 556667777777666555554 PP

>> DUF2666  Protein of unknown function (DUF2666)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.2   5.3e+03      72      84 ..      59      71 ..      29      93 .. 0.64
   2 ?   13.5   2.3   1.4e-05     0.063      47     124 ..     177     254 ..     168     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                .HHHHHHHHHHHH CS
     DUF2666 72 keedisevleklk 84
                k+e++s++ +k++
  AJA92615.1 59 KDENVSNIEKKFR 71
                3444444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.4e-05
                 HHTT--HHHHHHHTTT--S--S....HHHHHHHHHHHHT-.............---HHHHHHH.HHHHHHTTT--SS-- CS
     DUF2666  47 dylpfDlekleeiadeikkkkkgrvkeedisevleklkspattkklnkitdskegkeilkvil.arivLerlGiktkve 124
                 ++l +D e+++++ + + ++kk + +++di   l   ++   tk l++++++ + + + k ++ ++i Le++G+  ++ 
  AJA92615.1 177 NFLIIDSEQVHATDKVVEQVKKFKDENSDIFSELCSEEERLVTKALESMKSN-DLETMGKCMAqNQIYLEQIGVSNDIL 254
                 7999******************99999***9999999999999999988655.556666666516788******99984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2204.13
//
Query:       AJA92616.1  [L=174]
Description: HD domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-36  125.5   0.3    2.1e-36  125.3   0.3    1.0  1  HD_3      HD domain
      1e-15   58.0   0.3    1.3e-15   57.6   0.3    1.2  1  HD_2      HD containing hydrolase-like enzyme
    0.00023   21.4   0.0    0.00054   20.2   0.0    1.6  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.3   3.5e-40   2.1e-36       2     139 ..      10     145 ..       9     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 3.5e-40
        HD_3   2 ekLKfqkRqgwl.qtgrvreesvaeHmwrvalmalllseelkekvdiarvikmfLiHDlvEiltgDiispdelakeekeeeekeaaerilkllpeelae 99 
                  +LK+ +R+gw  + g ++ esvaeH++++++m+++ls++ +  +d ++v+km+++HD +E+  gD ++ ++++  +k+e e+ a+++il+ lp+++++
  AJA92616.1  10 AELKKLPRSGWKiKVGLENSESVAEHSYMMSVMSMVLSDMKS--LDSEKVLKMAILHDWAESKIGDFMP-EQIGYDKKSELENYAMSEILESLPQKIQN 105
                 68*********7255789**********************99..**********************976.66*************************** PP

        HD_3 100 ellalweEFeeretkeakfakdlDklepllqalekegdsl 139
                 +++++w+EF  ret+e+k++++lDkle+ lqa ++e+d  
  AJA92616.1 106 DYQNIWDEFLSRETPESKLVYELDKLEMALQAKIYEKDVD 145
                 ************************************9864 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.3   2.2e-19   1.3e-15       1     141 [.       4     137 ..       4     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.2e-19
        HD_2   1 eFfallsrlkyieRwalmrn...treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGD.lptpvKyanpeireaykevEee 95 
                 eFf  +++lk + R + + +    ++e+vaeHs+ +++++++l  +++      ld e+++++a++HD +E  +GD +p ++ y ++      +e+E+ 
  AJA92616.1   4 EFFFQIAELKKLPRSGWKIKvglENSESVAEHSYMMSVMSMVLSDMKS------LDSEKVLKMAILHDWAESKIGDfMPEQIGYDKK------SELENY 90 
                 5999999999999977665533468999**********9999987765......9*********************88999999765......699999 PP

        HD_2  96 aeekllelLpeelreeyeell.adeeaeeeekklvkaaDklsalikc 141
                 a +++le+Lp++++++y++++ +  + e+ e klv   Dkl+  +++
  AJA92616.1  91 AMSEILESLPQKIQNDYQNIWdEFLSRETPESKLVYELDKLEMALQA 137
                 *********************4355556679**********988776 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     9e-08   0.00054       2      50 ..      33      83 ..      32     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9e-08
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH....H CS
          HD  2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk....e 50
                +eHs+++  ++  l +      d+e++l++a+lHD ++ ++gd++ +     +
  AJA92616.1 33 AEHSYMMSVMSMVLSDMKS--LDSEKVLKMAILHDWAESKIGDFMPEQigydK 83
                7999999999999999888..**********************8887644321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1300.85
//
Query:       AJA92617.1  [L=218]
Description: hypothetical protein T478_1382 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   19.0   0.3     0.0015   18.7   0.3    1.3  1  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   8.1e-08    0.0015      95     161 ..     125     194 ..      32     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.1e-08
    Cas_Cas4  95 kkgveikeGvleypkekkreevelte.elreelekaikei...eeiissekppkvkkkkiCkkCayaelCl 161
                 + + ++  Gv+ y++ k  e ++++  ++++  e++i+++   +++++++k+p  +++  C+ C y+e C+
  AJA92617.1 125 MYAYDKVDGVIIYINGKGDE-ISFSVtKHKKMFEETIRRVrvlNDLLKEKKTPILETSVECTDCQYFERCY 194
                 34555556999998876544.444330334445666666511168999**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1738.55
//
Query:       AJA92618.1  [L=182]
Description: hypothetical protein T478_1473 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1419.70
//
Query:       AJA92619.1  [L=86]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-07   28.9   0.4    1.1e-06   28.5   0.4    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.4   6.1e-11   1.1e-06      27      75 .]      34      82 ..      11      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 6.1e-11
                    EEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
  AsnC_trans_reg 27 vecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75
                    +e+  v G yd+++k  + + e l+ ++ + ++++++v++t t++v+e+
      AJA92619.1 34 LEIQGVYGVYDIIVKLSSDNSEKLRSIVTDDIRKIENVQSTLTMLVIEQ 82
                    5888899***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 593.13
//
Query:       AJA92620.1  [L=398]
Description: hypothetical protein T478_1455 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00048   20.2   0.1    0.00074   19.6   0.1    1.3  1  PepSY_TM_like_2  Putative PepSY_TM-like


Domain annotation for each model (and alignments):
>> PepSY_TM_like_2  Putative PepSY_TM-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.1e-08   0.00074      69     142 ..     296     368 ..     255     398 .] 0.75

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.1e-08
  PepSY_TM_like_2  69 lpeelaqwlkkqlalsaakreaewsddevylslprpggdasllidretgeveleetsrgwiallnDLHkGrntG 142
                       pee ++ l++  +++a++ ++e++++e  l+lp pg++a  +++ ++g+++ ee     +++ +DL kG+   
       AJA92620.1 296 TPEEHQKKLDQIENIKAREVKNEVEEKEKGLALPIPGTKAASELAEKSGQMNEEEMV-NKLSFADDLKKGQVEN 368
                      6778888899999999***********************************977765.579*********8554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2649.18
//
Query:       AJA92621.1  [L=108]
Description: hypothetical protein T478_0641 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 754.52
//
Query:       AJA92622.1  [L=229]
Description: universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-57  193.6   0.0    3.7e-57  193.4   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.042   13.3   0.0    1.8  2  QueC             Queuosine biosynthesis protein QueC
      0.078   13.0   0.0       0.16   12.0   0.0    1.6  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   6.1e-61   3.7e-57       1     217 [.       1     223 [.       1     225 [. 0.95

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 6.1e-61
  Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGip.likletaGeeekevedLkgtlkkld....vea 88 
                      mk a+l+sGGkDs++a++ a k  + v+ L ++ ++ +es+  h +n++++ l++es+Gip li++  + e+e e ++L++ +   +    +e+
       AJA92622.1   1 MKLAALFSGGKDSTYAIHLAKKLsHSVDVLLTLYPHSDESHLLHHPNIKFTTLQSESMGIPqLIEEIPSVENETEFKKLEKLITLAKekysIEG 94 
                      89******************99779***********************************868888889999*******998854334455*** PP

  Diphthami_syn_2  89 vviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrridkklidelkklsekygidkagegGea 182
                      +v G+i s+yqk  +  +C++  l  + PLW+k+pe +++e +ee+fe i+ +v+  gld+s+LG++id + +  l++l++k+g +  +egGea
       AJA92622.1  95 IVHGGILSKYQKDNFSLICQQNDLEIISPLWNKNPESYMKELLEENFEYIISSVSCDGLDDSWLGQKIDENRLKTLENLQNKFGFNLNFEGGEA 188
                      ********************************************************************************************** PP

  Diphthami_syn_2 183 etlvlDaPlfkkrlevkelekkwderrgyldiera 217
                      et+v + Plfkk l +++ +++wd+ rg ++i  a
       AJA92622.1 189 ETFVTNCPLFKKPLFIQDSRTEWDGYRGRFEILEA 223
                      ****************************9998665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.1e-06     0.042       4      38 ..       5      39 ..       2      92 .. 0.87
   2 ?   -1.3   0.0      0.21   1.3e+03     147     183 ..     113     150 ..     102     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-06
                EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTS CS
        QueC  4 vllSGGlDSttvlalakkegkevealtfdYgqrhk 38
                 l+SGG DSt ++ lakk  + v +l   Y +  +
  AJA92622.1  5 ALFSGGKDSTYAIHLAKKLSHSVDVLLTLYPHSDE 39
                69**********************99999977644 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.21
                 HHTS--EEE-TTTT--HHHHHHHHHHTTHHH.HH-B-S CS
        QueC 147 gedkkieieaPlidlsKaeivklgkelgvpl.eetlsC 183
                  +++++ei  Pl + + +  +k   e ++++   ++sC
  AJA92622.1 113 CQQNDLEIISPLWNKNPESYMKELLEENFEYiISSVSC 150
                 478999999***99999999988888885541456666 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.7e-05      0.16       2      53 ..       3      92 ..       2     111 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                 EEEE--SSCTCHHHHHHHHHHCTTH......................................EEEEEE-STB-HHHHHHHHHHHHHTT- CS
  PAPS_reduct  2 lvvsvsgGkdslVllhLalkafkpv......................................pvvfvdtghefpetiefvdeleerygl 53
                 l+ ++sgGkds+  +hLa k  + v                                      ++  v+ + ef+++ +++   +e+y +
   AJA92622.1  3 LAALFSGGKDSTYAIHLAKKLSHSVdvlltlyphsdeshllhhpnikfttlqsesmgipqlieEIPSVENETEFKKLEKLITLAKEKYSI 92
                 5789*****************999856666666666665555555555555555555555554455555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1587.55
//
Query:       AJA92623.1  [L=267]
Description: hypothetical protein T478_0962 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00037   21.2   1.9     0.0017   19.1   1.9    2.0  1  zinc_ribbon_15  zinc-ribbon family
    0.00066   19.7   1.3    0.00087   19.3   0.4    1.7  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.031   14.3   0.1      0.054   13.5   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.16   11.7   2.6       0.23   11.2   0.9    2.1  2  zinc_ribbon_2   zinc-ribbon domain
        1.8    8.1   4.9        5.3    6.6   4.9    1.9  1  zf-ribbon_3     zinc-ribbon domain
        2.4    7.9   5.7        7.3    6.3   0.2    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.9   5.7e-07    0.0017      64      86 .]     225     261 ..     139     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.7e-07
  zinc_ribbon_15  64 e..............kkeCknCgkeveeefkyCpkCg 86 
                                    kk C  Cg +  ee+++Cp+Cg
      AJA92623.1 225 LeplqsnlkqesqgtKKMCGACGDSWPEEVSFCPSCG 261
                     044444444445555*********************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7   8.1e+03      17      22 ..     174     179 ..     173     188 .. 0.61
   2 !   19.3   0.4   2.9e-07   0.00087      22      49 .]     232     261 ..     207     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
         DZR  17 eCgtkl 22 
                 +Cg+k 
  AJA92623.1 174 TCGQKY 179
                 455443 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.9e-07
         DZR  22 lkavaa..edrCpsCgekvdpearfCpeCG 49 
                 lk++++  +++C +Cg + ++e +fCp+CG
  AJA92623.1 232 LKQESQgtKKMCGACGDSWPEEVSFCPSCG 261
                 4444447799*******************9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.8e-05     0.054      59      95 ..     229     263 ..     199     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                 T-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS CS
        HypA  59 gaeLeieevpvkvrCreCgkefeleekalrCpkCgsa 95 
                 +++L+ e++  k +C  Cg ++ +e +   Cp+Cg +
  AJA92623.1 229 QSNLKQESQGTKKMCGACGDSWPEEVS--FCPSCGWE 263
                 48999******************8854..6****965 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.88   2.6e+03       5      12 ..     175     182 ..     174     183 .. 0.79
   2 ?   11.2   0.9   7.8e-05      0.23       2      20 ..     243     261 ..     242     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
  zinc_ribbon_2   5 CGaelqdn 12 
                    CG +  d+
     AJA92623.1 175 CGQKYRDK 182
                    99998876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.8e-05
  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCG 20 
                    C  CG   ++++ FCp CG
     AJA92623.1 243 CGACGDSWPEEVSFCPSCG 261
                    88899999**********9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.9    0.0018       5.3       5      23 ..     243     261 ..     239     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
  zf-ribbon_3   5 CPnCGaplssddnvCpyCG 23 
                  C +CG    +++++Cp+CG
   AJA92623.1 243 CGACGDSWPEEVSFCPSCG 261
                  78899966999*******9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0024       7.3      14      28 ..     233     247 ..     230     248 .. 0.87
   2 ?    3.0   1.3     0.028        83       5      10 ..     256     261 ..     255     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
  zf-NADH-PPase  14 epaeggwarvCpaCg 28 
                    ++++ g+++ C aCg
     AJA92623.1 233 KQESQGTKKMCGACG 247
                    67889*********8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.028
  zf-NADH-PPase   5 FCgrCG 10 
                    FC+ CG
     AJA92623.1 256 FCPSCG 261
                    999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1832.78
//
Query:       AJA92624.1  [L=65]
Description: hypothetical protein T478_0600 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 459.61
//
Query:       AJA92625.1  [L=120]
Description: hypothetical protein T478_0373 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   17.6   0.0     0.0048   16.7   0.0    1.6  2  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.037   14.0   0.1       0.06   13.4   0.1    1.4  1  DUF4947   Domain of unknown function (DUF4947)


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.4e-07    0.0048       4      49 ..      14      59 ..      10      82 .. 0.86
   2 ?   -2.8   0.0      0.69   6.2e+03      21      36 ..      96     111 ..      95     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.4e-07
                CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHC CS
        TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedk 49
                + L+e  ak++l ++ +g++++++i+++l+++   + +  ++L++ 
  AJA92625.1 14 IKLTEVQAKIFLHVVINGKMNTSKISNDLKISLDDATQNSKKLVEL 59
                679****************************977776666666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.69
                 CCCHHCHHCCCTTSSC CS
        TrmB  21 gpatadeiaeelgvpr 36 
                 +++++d i  +l+v++
  AJA92625.1  96 KNLNVDNIGVALEVSY 111
                 5778888888888876 PP

>> DUF4947  Domain of unknown function (DUF4947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.7e-06      0.06      97     133 ..       5      41 ..       2      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.7e-06
     DUF4947  97 enikalfekGklteeqakafllaavDLaq.avkisssr 133
                 + ik l+ + klte qak fl + ++ ++ ++ki s++
  AJA92625.1   5 QIIKTLVSEIKLTEVQAKIFLHVVINGKMnTSKI-SND 41 
                 789*******************999877526677.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 886.77
//
Query:       AJA92626.1  [L=249]
Description: putative glutamate racemase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-11   44.0   0.0    3.1e-11   43.6   0.0    1.2  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
  ------ inclusion threshold ------
      0.013   15.1   0.6      0.048   13.3   0.2    1.9  2  ToxS          Trans-membrane regulatory protein ToxS
      0.022   14.7   1.3       0.21   11.5   1.1    2.2  1  Lipase_GDSL   GDSL-like Lipase/Acylhydrolase
       0.12   13.0   0.5        1.8    9.1   0.1    2.8  3  Pyr_redox     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   6.9e-15   3.1e-11       3     220 ..       7     205 ..       5     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 6.9e-15
                   EC.SCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CC.S-TCHHHHHCH.T..THHHHHHHHHHHHC.TTESEEEE--CHHHHHHHHHHHH-SSEEE CS
  Asp_Glu_race   3 gm.gpeatlsvlrklveatpaesdqehlplivlndsa.ipdrteaieeesgddpvlklleaakkLek.agadaiviaCnTahavadelqkkikiPvl 96 
                   ++ ++ ++ls++++++++t+a         i+l+d++ +p + ++++++     ++ + + ++k ++  ++d+iv+a nT++ ++   ++k++  v+
    AJA92626.1   7 VFdSGLGSLSIIKAIQKRTKADI-------IYLADKKnFP-YGKKTKSQ----LYKIITDTIQKISEkFNPDVIVLASNTPSLLF---REKLPDNVI 88 
                   7789999********99999988.......9999999788.66666444....3447777777765449************6555...567899999 PP

                   ECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCCHC..HHHH.TT-TTSHHHHHHHHHHH....HHHTTT-SE CS
  Asp_Glu_race  97 giveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqaiy..eelk.aGevteearrailklle....rlaergada 186
                     v + +e+++  ++++v++L+T++  ks+  ++ +++ +++       e++ ++n  ++  +el+  G++ + ++++++++ +    + +e++++ 
    AJA92626.1  89 T-VLPPLEKIQ--KASNVAILTTEIVAKSKELENYISEFNNL-------EDVLKIN--CSelVELVeTGKFLTNEKNCVKTISKvlkdEFKENNIKI 173
                   9.444566665..59***********************6567.......6666666..5556677789**6666455555555533344479***** PP

                   EEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHH CS
  Asp_Glu_race 187 viLGCTelplllekaealekeksvpvidptdila 220
                     L  T+lp+l + ++++ +  +++++dp+d +a
    AJA92626.1 174 ATLSSTHLPFLSPFLKKIFR--GIEFLDPADDVA 205
                   ***************99998..69*****99877 PP

>> ToxS  Trans-membrane regulatory protein ToxS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.23     1e+03      40      76 ..      24      61 ..       7      68 .. 0.68
   2 ?   13.3   0.2   1.1e-05     0.048      32     113 ..      90     174 ..      71     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.23
        ToxS 40 eqtsnvvylPnkt...Ysrvsvvklyseeeekelvinise 76
                 ++++++yl +k+   Y ++++ +ly   ++  ++ +ise
  AJA92626.1 24 RTKADIIYLADKKnfpYGKKTKSQLYKIITD--TIQKISE 61
                4567888998775445888888888876665..4445555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
        ToxS  32 dlgplrkveqtsnvvylPnktYsrvsvvkly.seeee..kelvinisesGeWdisgnYLlveptefkdvtsgqskdfseeqlkli 113
                  l pl+k++++snv  l  +   ++  ++ y se ++  + l in se  e   +g++L  e + +k ++   +++f+e+++k+ 
  AJA92626.1  90 VLPPLEKIQKASNVAILTTEIVAKSKELENYiSEFNNleDVLKINCSELVELVETGKFLTNEKNCVKTISKVLKDEFKENNIKIA 174
                 56799*********************9998844333322567788899999999***************************9985 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.1   4.7e-05      0.21      93     131 ..      42      91 ..      28     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                  CEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCH...........C CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
  Lipase_GDSL  93 kkeaeeyiknlreaikelkeegapkaivvlvsppglgp...........q 131
                  kk++++++k ++++i+ ++e+++p  iv+ ++ p+l              
   AJA92626.1  42 KKTKSQLYKIITDTIQKISEKFNPDVIVLASNTPSLLFreklpdnvitvL 91 
                  7899*******************************999444444444440 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.56   2.5e+03      48      67 ..      95     115 ..      69     123 .. 0.72
   2 ?    9.1   0.1   0.00041       1.8      25      59 ..     139     175 ..     129     180 .. 0.84
   3 ?    0.3   0.0      0.24   1.1e+03      51      70 ..     217     236 ..     191     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.56
                 HHHHHT.TEEEECSEEEEEEE CS
   Pyr_redox  48 eklekn.gievllntkveeie 67 
                 ek++k  ++ +l+ + v++ +
  AJA92626.1  95 EKIQKAsNVAILTTEIVAKSK 115
                 444444489999988888876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00041
                 EEEEESSSSSS..TTSSHHHHHHHHHHHHHTTEEEEC CS
   Pyr_redox  25 Vtvversdkll..rllDeeaskilqeklekngievll 59 
                 V +ve ++ l   +++ +++sk+l++++++n+i++ +
  AJA92626.1 139 VELVETGKFLTneKNCVKTISKVLKDEFKENNIKIAT 175
                 667777777777788889****************987 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.24
                 HHTTEEEECSEEEEEEEEET CS
   Pyr_redox  51 ekngievllntkveeiegse 70 
                 ++n  ++++ +++++++ + 
  AJA92626.1 217 KNNSLTIYTTKSPKALQRNL 236
                 44466666666666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1317  (0.0734564); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1774.87
//
Query:       AJA92627.1  [L=744]
Description: FTR1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-18   66.7  19.2    2.5e-17   63.0  18.6    2.4  1  FTR1      Iron permease FTR1 family
  ------ inclusion threshold ------
       0.18   11.7   3.0       0.54   10.1   2.8    2.0  1  Atthog    Attenuator of Hedgehog
       0.31   11.2   3.6        0.6   10.2   0.6    2.9  3  DUF4363   Domain of unknown function (DUF4363)
        1.8    9.1   6.2         89    3.6   1.8    3.7  3  DUF1211   Protein of unknown function (DUF1211)


Domain annotation for each model (and alignments):
>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0  18.6   5.6e-21   2.5e-17     135     299 ..     461     629 ..     416     638 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 5.6e-21
        FTR1 135 lfilsFlivlREGlEavLfvaaivaytvk...rvsalilgvvlGali.avvlglliyrglvklslqsffilegflLllvaagLfsvgtlellekaeacn 229
                 +fi+sF i++REGlEavL+++ai +y+     ++   ++   +G++i a++++++i  + + +s++ ++++e +  l ++a+Lf+v+ +++l k e + 
  AJA92627.1 461 AFISSFSIIFREGLEAVLILGAIITYLEAsrnHKFKKYVHYGIGLAIgATAVTWVIASYIIEISGANRELIEAIAALSATAVLFYVS-FWILNKIEHKR 558
                 599*************************99998888999999998773699************************************.*********** PP

        FTR1 230 gkdyiefkkskslskisllslllvaflavereg...leivlaliGwantgplglivyaavwlvvlillgllli 299
                 + +    k+ ++++ +  + +++ +f+ v+reg   ++++ a+++ a +  +   v+ +++l+++ llg++  
  AJA92627.1 559 WMEFVKAKVFQASAAGGTSVFIMLSFFTVYREGfetVLFYQAMFSFAKY--MEFYVGLGFILGIVSLLGIYFG 629
                 *********************************7777777778888877..5599999999999999998865 PP

>> Atthog  Attenuator of Hedgehog
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.8   0.00012      0.54      48      88 ..     531     571 ..     514     625 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
      Atthog  48 ivGiicitatvillvlshwerevvkyarwlgfsamvlfcla 88 
                 i  i++++at +l+ +s+w  + +++ rw+ f+   +f  +
  AJA92627.1 531 IEAIAALSATAVLFYVSFWILNKIEHKRWMEFVKAKVFQAS 571
                 667999**************************987777554 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.6   0.00013       0.6      10     103 ..      35     128 ..      28     131 .. 0.89
   2 ?   -2.4   0.0       1.2   5.2e+03      16      35 ..     236     255 ..     229     261 .. 0.77
   3 ?   -0.6   0.0      0.31   1.4e+03      58      88 ..     358     388 ..     356     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
     DUF4363  10 stdelsekleeleeaienedweeakekleelekeWekkkkklsifiehdeldeietslaklka.yietedkeealaelaelkfllehikekekls 103
                 +++ ++++l+ +  ++en+d e++k+ +e  + + +k+ +kl   ++ +  de+ +sl +l++  ++ e+ +  ++e+ ++++++e i+e e+ +
  AJA92627.1  35 VIEVTETSLNLALTSLENQDFESTKNFIEFGSTHFSKNLEKLRN-VDASLTDEVHISLLDLQTrQLNPENLSTVSSEITRIVEIFEAIPEDEEYN 128
                 556678889999999**************9999*****999986.689999********998636999***********************9877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
     DUF4363  16 ekleeleeaienedweeake 35 
                 e   el+ +++n+d+++a++
  AJA92627.1 236 ELYAELMIELDNGDYKKAEQ 255
                 44567778889999999987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.31
     DUF4363  58 deldeietslaklkayietedkeealaelae 88 
                 de+d i ++l +++ + e +d++ a+a+ ++
  AJA92627.1 358 DEIDFIREQLMATEIFYELGDTQAAYASART 388
                 89999*****************999998876 PP

>> DUF1211  Protein of unknown function (DUF1211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.026   1.2e+02       8      21 ..       8      21 ..       2      67 .. 0.76
   2 ?    1.6   0.0     0.084   3.7e+02      12      50 ..     432     470 ..     429     472 .. 0.82
   3 ?    3.6   1.8      0.02        89      11      64 ..     509     564 ..     505     587 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.026
                HHHHHHHHHHHHHS CS
     DUF1211  8 avfAIaiTLlvlei 21
                a+fAIa+ L v+  
  AJA92627.1  8 AIFAIAMLLFVIPS 21
                9**********944 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.084
                 HHHHHHHHHS---HHHHHHHHHHTHHHHHHHHHHHHHHH CS
     DUF1211  12 IaiTLlvleikvpeeellaallellpsllayllsFlvva 50 
                 I  T++ le ++ e+e l + + ++  ++a++ sF +++
  AJA92627.1 432 ISTTIISLERSLDESERLVSGTGTIAPMIAFISSFSIIF 470
                 566888887777777777888888999*********996 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.02
                 HHHHHHHHHHS---....HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
     DUF1211  11 AIaiTLlvleikvp....eeellaallellpsllayllsFlvvasfWlnhhrlfrrik 64 
                 A a+T ++ +  +     ++el++a+++l+ + + + +sF ++    ++h+r+++++k
  AJA92627.1 509 ATAVTWVIASYIIEisgaNRELIEAIAALSATAVLFYVSFWILNK--IEHKRWMEFVK 564
                 555555554332223355899********************9976..46666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 5364.70
//
Query:       AJA92628.1  [L=178]
Description: class I glutamine amidotransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-22   77.9   0.0      9e-22   77.8   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    3.6e-10   40.0   0.1    0.00035   20.4   0.1    2.2  2  Peptidase_C26  Peptidase C26
     0.0057   16.5   0.0      0.077   12.8   0.0    2.0  2  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   1.5e-25     9e-22       2     186 ..       4     175 ..       3     178 .] 0.83

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.5e-25
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekek 98 
                 l+Dn++ +t+ +++ l + g+k + +  d+ ++      +++d  ++sg  ++ +    +  ++i +a ++k+ +LGIC+G  +la+++g+++ k +  
  AJA92628.1   4 LVDNGSVFTKDIANTLSNSGIKFDQKSSDQINLDD---ISDYDSFILSGRRNNDSqmNAKNSKIILHAVNEKKKLLGICYGAEILALALGGTIRKSS-- 97 
                 89******************999999999766666...58*********9999999866666777777777999*******************9988.. PP

                 EEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
      GATase  99 ehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnf 186
                     g++++ ++++ l +g+    ++  +H+ye+ +   + + l+v+a+se+ ++++ + +k+  ++g+QFHPE+t    g++++++f
  AJA92628.1  98 -VIRGEQEIISNDNTLCEGK---NTVFESHSYEISK---LGSSLDVIAESEN-CKNEIVKHKELLIYGTQFHPEMTK--DGQSMIEKF 175
                 .5666667777677888887...457889*******...***********76.567777777778*********875..455777766 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   5.8e-08   0.00035      91     128 ..      58      95 ..      40     110 .. 0.85
   2 !   17.8   0.0   3.5e-07    0.0021     165     216 .]     114     163 ..     103     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.8e-08
  Peptidase_C26  91 dalelaLiraalergvPilgiCrGlqllnvalGGtlyq 128
                    +a + ++i +a+++++ +lgiC G ++l+ alGGt+ +
     AJA92628.1  58 NAKNSKIILHAVNEKKKLLGICYGAEILALALGGTIRK 95 
                    5566788999*************************976 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.5e-07
  Peptidase_C26 165 seeievnslHhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                    + +  v   H+  i++l+++l v+A +e    E ++++e    ++g Q+HPE
     AJA92628.1 114 EGKNTVFESHSYEISKLGSSLDVIAESENCKNEIVKHKE--LLIYGTQFHPE 163
                    466778889***************************999..78********9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.03   1.8e+02      29      86 ..      37      90 ..      20     100 .. 0.68
   2 !   12.8   0.0   1.3e-05     0.077     147     184 ..     138     177 ..     111     178 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.03
                GGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEET CS
         SNO 29 edlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskele 86
                +d+ + d++i+ G      +  +++ +    +   + n +k +lG C G  +l+  l+
  AJA92628.1 37 DDISDYDSFILSGRRNNDSQMNAKNSK----IILHAVNEKKKLLGICYGAEILALALG 90
                566666777776655544333333333....3444556679999***99888877665 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.3e-05
                 EEECT..TEEEEEEETTEEEESS-GGGSTTHCHHHHHHHH CS
         SNO 147 lyeld..geivvakqkkilatsfhPelaeddirvhdyfve 184
                 +   +   eiv  k   i +t fhPe+++d++ + + fv+
  AJA92628.1 138 AESENckNEIVKHKELLIYGTQFHPEMTKDGQSMIEKFVK 177
                 2223332488888888999*************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1416.29
//
Query:       AJA92629.1  [L=275]
Description: PF11959 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-33  114.6   0.0    4.7e-33  114.0   0.0    1.3  1  DUF3473          Domain of unknown function (DUF3473)
      8e-12   45.1   0.0    9.4e-11   41.7   0.0    2.1  2  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> DUF3473  Domain of unknown function (DUF3473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0   5.2e-37   4.7e-33       1     128 [.     140     273 ..     140     275 .] 0.94

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 5.2e-37
     DUF3473   1 SSvfPvrhdlyGipdaprkpfrikkekgk......llElPvstlklggrnlplaGGgyfRlfPyalikallrrlnregrpavlYfHpwEldpd.qprvk 92 
                 SS++P++++lyG+pda+ kp++i++++ +      ++E+P+ ++k++g+++p++GG+y+R +P+++i  +++++++++ p  +Y+H wEl p+  p++ 
  AJA92629.1 140 SSIVPAKTSLYGMPDAEIKPYTITSNSLEknsngkITEFPILVTKFLGKTIPAGGGFYLRTLPMKIITNAIKNYEKKNIPSTFYIHSWELTPEfMPKI- 237
                 9*********************9998655778888*********************************************************945799. PP

     DUF3473  93 gaslksrfrhylnlkrteerlrrllsdfeFttveel 128
                 ++s k  f +y+nl ++++++++ll++feFt++e++
  AJA92629.1 238 KMSKKDDFITYHNLGKAFDKMDSLLDEFEFTSFENF 273
                 5*******************************9976 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0     1e-14   9.4e-11      20     123 ..      35     138 ..      16     139 .. 0.85
   2 ?    1.2   0.0     0.037   3.3e+02      21      42 ..     206     227 ..     200     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1e-14
                      CHHHHHHHHHHCT--EEEEE-HHHHCH-HHHHHHHHHTTEEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHH. CS
  Polysacc_deac_1  20 ntteilpvLkkykvkatffvigglvedypdevremaasGveignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatv. 112
                      + ++il++L+k++ +atffv+g+l e  p++   + ++G+ei+ Ht++h+++ +l    +++ +e+  + + + ++ ++r fr+P  s ++++ 
       AJA92629.1  35 GIEKILELLRKKESNATFFVVGELLEFKPELFDIILENGHEIAFHTMKHDRIDSLN---FQNIFETEIRKFHSLTNGKSRGFRAPSFSLNQKSs 125
                      5689**********************************************988876...45557777788899999999999999999766654 PP

                      ..HHHHHHTT.EE CS
  Polysacc_deac_1 113 ..levarelgfay 123
                        ++v+++ +++y
       AJA92629.1 126 wlIDVLENNNYTY 138
                      4466666666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.037
                      HHHHHHHHHHCT--EEEEE-HH CS
  Polysacc_deac_1  21 tteilpvLkkykvkatffvigg 42 
                       t++++  +k++++ tf++ ++
       AJA92629.1 206 ITNAIKNYEKKNIPSTFYIHSW 227
                      577888889*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2061.51
//
Query:       AJA92630.1  [L=349]
Description: putative glyceraldehyde-3-phosphate dehydrogenase, type II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-07   31.4   0.0    4.6e-07   30.0   0.0    1.7  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
     0.0028   17.2   0.2      0.034   13.8   0.1    2.6  2  Gp_dh_C         Glyceraldehyde 3-phosphate dehydrogenase, C-t
     0.0044   17.3   0.1      0.036   14.4   0.0    2.5  2  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
     0.0055   17.3   0.0      0.011   16.4   0.0    1.5  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
     0.0092   16.4   0.0      0.019   15.4   0.0    1.5  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.3e-10   4.6e-07       2      83 ..       3      91 ..       2     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH........HHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHH CS
      DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag........ellglgklgvavtddleevlekadvliDFTtpeavlen 83
                kv v+G+ G +G+++++ +++++++elv++ + ++ + +   +         e  +   +++++t ++e++l+++d +iD +   +  +n
  AJA92630.1  3 KVFVNGY-GSIGSRIIQFIKDDPEIELVGVGKYSPDSKVTDAINrgfkvyvpEKNQNAFSDFTITGNIEAALDESDLVIDASPGGVGFKN 91
                89*****.**********************999995555444446799999877788899*********************944444444 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   9.4e-06     0.034      52     112 ..     190     251 ..     147     297 .. 0.75
   2 ?    0.6   0.2       0.1   3.7e+02      11      36 ..     270     294 ..     265     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                 EEE-THHHHHHHHSGGGTTTEEEEEEEESSSSEEEEEEEEEESST.S-HHHHHHHHHHHHH.T CS
     Gp_dh_C  52 ptstgaakavglVlpelkgkldglAvrVPtpnvsvvdlvveleke.vtveevnaalkeaae.g 112
                 + s +++ +v++ + + +  l   A++VPt +++++ + ++++++  +v+e+  ++k++    
  AJA92630.1 190 TQSPHHGDDVKSYFGK-ESPLFVRAIKVPTRQMHLHIMDIRFKETaPSVDEIHGIFKNEYGvA 251
                 5677999999999986.8889999*****************9998689*********986553 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                 HHEEEEEEEEEEEECTTTSBSSSS-- CS
     Gp_dh_C  11 kfgikkglmttvhaytndQkllDgps 36 
                 +fg k   m  +ha +  Qk+ D+ +
  AJA92630.1 270 NFGFKDTNMIHIHANMT-QKIDDTIQ 294
                 7999*********9985.68888765 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     1e-05     0.036       2      35 ..       3      36 ..       2      56 .. 0.87
   2 ?   -0.9   0.0      0.58   2.1e+03       6      41 ..     145     181 ..     142     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS- CS
     Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaindltd 35
                kv +nG+G IG  +++ + +++e+e+v + +   
  AJA92630.1  3 KVFVNGYGSIGSRIIQFIKDDPEIELVGVGKYSP 36
                899**************************99544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                 ESTSHHHHHHHHHHH.HHTTCEEEEEE-TS-HHHHHH CS
     Gp_dh_N   6 nGfGRIGrlvlrall.eekelevvaindltdletlay 41 
                  G+GRI   + +    + k+++v  +++ +d+e+   
  AJA92630.1 145 TGMGRILEPLRKNFGnSIKRFDVTLVRRWADIEQTDE 181
                 6777775544444443334777777777777766554 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.1e-06     0.011       1      66 [.       8      82 ..       8      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.1e-06
                   --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT.............HHHHHT--CB---HHHHHHHHS-EEEEE- CS
  NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd.............rkallasealtldlddliahldpdvvVEc 66
                   G+G iGs++++ +k++++   +elv+v + + + +  d             +++ + + ++t ++++ ++  + d+v+++
     AJA92630.1  8 GYGSIGSRIIQFIKDDPE---IELVGVGKYSpDSKVTDainrgfkvyvpekNQNAFSDFTITGNIEAALD--ESDLVIDA 82
                   99***************5...9999999988533333379**********9999****************..******98 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.4e-06     0.019       8      81 ..       9      90 ..       3      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.4e-06
                    TSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG..........GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHH CS
  Semialdhyde_dh  8 tGyvGqellrlLeehpevelvvllsssrsaGkklaeavk..........aleegkdlkvedvdeeelkevdivflalpagvske 81
                     G +G+++++ ++++pe+elv +   s    +k+++a +          +++  +d++++   e++l+e d+v+ a p+gv  +
      AJA92630.1  9 YGSIGSRIIQFIKDDPEIELVGVGKYSP--DSKVTDAINrgfkvyvpekNQNAFSDFTITGNIEAALDESDLVIDASPGGVGFK 90
                    699*******************998888..666666666688899999999999999**99999999************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2647.15
//
Query:       AJA92631.1  [L=69]
Description: hypothetical protein T478_1376 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0027   16.6   7.5     0.0031   16.5   7.5    1.0  1  Spc7           Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.065   13.4   5.9      0.071   13.2   5.9    1.0  1  DUF848         Gammaherpesvirus protein of unknown function (
      0.098   12.4   8.2       0.17   11.6   0.1    2.0  2  DASH_Spc34     DASH complex subunit Spc34
       0.12   13.0   4.1       0.19   12.3   4.1    1.4  1  BST2           Bone marrow stromal antigen 2
       0.23   11.6   5.5        2.1    8.5   5.5    1.9  1  Fib_alpha      Fibrinogen alpha/beta chain family
       0.24   11.9   6.8       0.48   10.9   6.8    1.5  1  DUF16          Protein of unknown function DUF16
       0.28   10.2   5.0       0.32   10.1   5.0    1.1  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
       0.34   11.6   3.7       0.65   10.7   3.3    1.6  1  SlyX           SlyX
       0.34   10.7   7.3          3    7.7   2.0    2.1  2  DivIC          Septum formation initiator
       0.36   10.6   3.1       0.39   10.5   3.1    1.1  1  Iron_permease  Low affinity iron permease
       0.41   10.6  12.4        2.2    8.3   5.4    2.0  2  Prefoldin_2    Prefoldin subunit
       0.57   10.3   2.0          2    8.5   0.4    2.0  2  GPHR_N         The Golgi pH Regulator (GPHR) Family N-termina
        0.7    9.7   4.9       0.74    9.6   4.9    1.0  1  Spc29          Spindle Pole Component 29
       0.83    8.2   9.2       0.86    8.1   9.2    1.0  1  FapA           Flagellar Assembly Protein A
        1.8    8.1   7.3       0.59    9.7   2.2    1.9  2  TPD52          Tumour protein D52 family


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   7.5   2.6e-06    0.0031     198     262 ..       3      67 ..       1      68 [. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.6e-06
        Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                 ++++e++++e++++++ i +k+ke++elq+ l    +ki+ l e+++el++ei+e  + l+e+k+
  AJA92631.1   3 ENDIEKTKQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKERKQ 67 
                 5789***************************************************9998888875 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.9   5.9e-05     0.071      56     116 ..       7      67 ..       2      69 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-05
      DUF848  56 keikalveavdteieakkkelslLkklnrkkvarveeLtdkvlelkeevsleldsleeaqe 116
                 ++ k+ ++++d+ i +k+ke++ L+k+ + +  +++ L ++ +el++e++   d+l+e ++
  AJA92631.1   7 EKTKQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKERKQ 67 
                 67899*********************99999999999************999899988765 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.6     0.026        30     222     252 ..       4      34 ..       1      37 [. 0.79
   2 ?   11.6   0.1   0.00014      0.17     176     208 ..      37      69 .]      33      69 .] 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.026
  DASH_Spc34 222 ddsesetskskdvdelirkEeeeIeeLerkl 252
                 +d e+ +++ + +deli k ++e +eL++ l
  AJA92631.1   4 NDIEKTKQEIVKIDELIVKKQKEMNELQKVL 34 
                 445566666899***************9865 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
  DASH_Spc34 176 akekieelreeYeelseeieeleaeiaeQkkqL 208
                 +  ki+ l e+Yeel++ei+el ++ +e+k+++
  AJA92631.1  37 EPSKIDILGENYEELRNEIKELGDKLKERKQRI 69 
                 556888999*********************985 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.1   0.00016      0.19      26      87 ..       6      67 ..       2      69 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2 26 LtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                + ++++++ + +  +   ++ + +L++ L  e ++     ++ +el++eik+L +kL++ ++
  AJA92631.1  6 IEKTKQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKERKQ 67
                567778888888888888889999************999*******************9876 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.5    0.0018       2.1      87     129 ..      10      52 ..       2      68 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                 HHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  87 eeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                 ++ei++++e i+++ +++++Lq+vl    +ki  L ++ ++++
  AJA92631.1  10 KQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELR 52 
                 4567777777777777777777777777666666655544443 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.8    0.0004      0.48      31      85 ..       8      62 ..       1      69 [] 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HH CS
       DUF16 31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetl 85
                 +kq++ ki++ + k+++++n+l++       ki+ l ++ +  ++e++++++ l
  AJA92631.1  8 KTKQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKL 62
                5899999999999999999999998888888888878777777777777555544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.0   0.00026      0.32      44      97 ..      15      69 .]       3      69 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
       Atg14 44 kiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97
                ki++++ +k+ e ++l++ ++ +  k++ l    ++lr++++el dkl+++k++i
  AJA92631.1 15 KIDELIVKKQkEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKERKQRI 69
                5556666655589999999999999999999999999999999999999999987 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.3   0.00054      0.65       2      56 ..      10      64 ..       9      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
        SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                ++ ++++ + +   ++ ++eL++v++    +id l +  ++l++++kel ++ ++
  AJA92631.1 10 KQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKE 64
                57899999999999**********************************9988764 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.0    0.0025         3      17      45 ..       4      32 ..       1      37 [. 0.80
   2 ?    6.6   0.3    0.0053       6.3      18      39 ..      47      68 ..      39      69 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0025
                XHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       DivIC 17 laykqlkqeiaalqaelaklkaeneeLea 45
                +++ ++kqei+++ + ++k+++e +eL++
  AJA92631.1  4 NDIEKTKQEIVKIDELIVKKQKEMNELQK 32
                56778889999999999999988888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0053
                HHHHHHHHHHHHHHHHHHHHHH CS
       DivIC 18 aykqlkqeiaalqaelaklkae 39
                +y +l++ei++l ++l++ k++
  AJA92631.1 47 NYEELRNEIKELGDKLKERKQR 68
                5777788888888777777776 PP

>> Iron_permease  Low affinity iron permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.1   0.00033      0.39      72     118 ..      13      59 ..       2      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
  Iron_permease  72 qlkLdeLirasksaknrlidleelteeeleelakeyerlaeaakeee 118
                     +k+deLi  +++  n+l ++  ++ ++++ l ++ye+l+++ ke  
     AJA92631.1  13 IVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELG 59 
                    48************************************998877654 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.4    0.0018       2.2      68     101 ..       3      36 ..       1      40 [. 0.85
   2 ?    7.3   0.8    0.0036       4.3      80     102 ..      43      65 ..      37      69 .] 0.49

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Prefoldin_2  68 eerketlekeiktlekqleklekeleelkeelqk 101
                  e+++e+ ++ei ++ + + k++ke++el+++l++
   AJA92631.1   3 ENDIEKTKQEIVKIDELIVKKQKEMNELQKVLMI 36 
                  6678999999999999999999999999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0036
                  HHHHHHHHHHHHHHHHHHHHHCC CS
  Prefoldin_2  80 tlekqleklekeleelkeelqkk 102
                   l +++e+l++e++el ++l+++
   AJA92631.1  43 ILGENYEELRNEIKELGDKLKER 65 
                  34444455555555554444444 PP

>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0017         2      43      68 .]       2      27 ..       1      27 [. 0.94
   2 ?    1.6   0.0      0.24   2.9e+02      49      68 .]      50      69 .]      36      69 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
      GPHR_N 43 teadinslearlehtrellaekrkel 68
                +e+di ++++ + +++el+++k+ke+
  AJA92631.1  2 SENDIEKTKQEIVKIDELIVKKQKEM 27
                79*********************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.24
      GPHR_N 49 slearlehtrellaekrkel 68
                 l++ ++   ++l e+++++
  AJA92631.1 50 ELRNEIKELGDKLKERKQRI 69
                56777888889999999985 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.9   0.00062      0.74     111     164 ..       5      58 ..       1      67 [. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
       Spc29 111 siyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                  i +  ++iv+++  + +++ e++eL++ l  +   ++ L e ++el +e+k+l
  AJA92631.1   5 DIEKTKQEIVKIDELIVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKEL 58 
                 578888999******************************************887 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   9.2   0.00072      0.86     343     407 ..       3      68 ..       1      69 [] 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00072
        FapA 343 eeeleeleeeleklkkk.ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkee 407
                 e+++e++++e+ k+++  +kk +++++ +++ +   ++++ l e++e+l++e++el ++lke k++
  AJA92631.1   3 ENDIEKTKQEIVKIDELiVKKQKEMNELQKVLMIEPSKIDILGENYEELRNEIKELGDKLKERKQR 68 
                 466777777777777773333333444666777777888888888888888888888888877765 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.2   0.00049      0.59      34      67 ..       4      37 ..       2      42 .. 0.89
   2 ?    2.4   0.2     0.091   1.1e+02      20      44 ..      39      63 ..      35      69 .] 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00049
       TPD52 34 seLakleeeivtLrqvLaakekhlaelkrklGlt 67
                +++ k+++eiv + ++++ k+k++ el++ l + 
  AJA92631.1  4 NDIEKTKQEIVKIDELIVKKQKEMNELQKVLMIE 37
                5789************************988665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.091
       TPD52 20 septlteeereeLkseLakleeeiv 44
                s++++  e+ eeL++e+ +l ++++
  AJA92631.1 39 SKIDILGENYEELRNEIKELGDKLK 63
                5567778889999999988877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1799  (0.10034); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 508.48
//
Query:       AJA92632.1  [L=60]
Description: hypothetical protein T478_1129 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-05   22.3   0.4    9.2e-05   22.3   0.4    1.0  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.4   5.2e-09   9.2e-05       2      50 ..       5      53 ..       4      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.2e-09
                HCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        SecE  2 kFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfskl 50
                 +fk+ ++ +k   + +++ + +    Vl +++ +gl++f++ ++f+++
  AJA92632.1  5 LYFKNIVNTIKLTKKSDKEVYKQHLRLVLFGFATVGLLGFGIQFIFATI 53
                69********************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 419.20
//
Query:       AJA92633.1  [L=400]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2398.49
//
Query:       AJA92634.1  [L=276]
Description: ribosomal protein L11 methyltransferase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-56  190.6   0.0    3.1e-56  190.3   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.9e-05   24.2   0.1    2.9e-05   23.6   0.1    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      9e-05   22.2   0.0    0.00019   21.1   0.0    1.5  2  Cons_hypoth95    Conserved hypothetical protein 95
    0.00027   20.7   0.1    0.00056   19.7   0.1    1.5  1  Methyltransf_31  Methyltransferase domain
    0.00063   19.4   0.1     0.0013   18.4   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0013   18.0   0.1     0.0017   17.6   0.1    1.3  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
     0.0038   16.8   0.2      0.011   15.3   0.2    1.8  1  MTS              Methyltransferase small domain
     0.0044   17.0   0.0      0.011   15.7   0.0    1.7  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0082   16.8   0.0      0.015   16.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.025   15.2   0.0      0.055   14.1   0.0    1.7  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.3   0.0   1.7e-59   3.1e-56       2     199 .]      21     221 ..      20     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 190.3 bits;  conditional E-value: 1.7e-59
                 EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHHHHHTT-- CS
      Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfsskleaErerlaklve 99 
                  f++iGd++i++++++l   k++ig+++l++    ++++ + s veg +Rt++lev+aG+d+t+t+ kEngcrf +Dv k +fs++l++Erer+a lv+
  AJA92634.1  21 AFDQIGDIIIVRIPDSLVSKKQIIGKTLLEQVsTANSIFYQSSPVEGDYRTRKLEVIAGEDKTQTEYKENGCRFIVDVEKAFFSPRLSTERERIAGLVK 119
                 599***************************9989***************************************************************** PP

                 TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEE CS
      Met_10 100 egevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir...eqladrvvmnlpksaieFldkvlaalkdgg 195
                 +gev +++f G+G f++ +ak     +v+ idlnP + ++ ken + Nk++  v ++++D+ +vi+   + +adr++m lp+++ eFld++l+ lk++g
  AJA92634.1 120 DGEVMINMFGGVGMFSLLAAK-NTSCTVYNIDLNPVAAQLCKENAQINKLKGEVISLNGDATKVINeqlTGKADRILMLLPERSDEFLDSALNGLKNNG 217
                 ********************9.77788**************************************96667789************************** PP

                 EEEE CS
      Met_10 196 vihy 199
                 vihy
  AJA92634.1 218 VIHY 221
                 ***9 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   1.6e-08   2.9e-05     158     257 ..     117     220 ..     111     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
        PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk......eekadvivaNILaevlielaedikklv 250
                 lvk ge ++ +  G G+ ++ aak    +v+ +D+++vA +  keNa++Nk++ ++ + l+++++k      ++kad i+   L e   e+++++ + +
  AJA92634.1 117 LVKDGEVMINMFGGVGMFSLLAAKNTSCTVYNIDLNPVAAQLCKENAQINKLKGEV-ISLNGDATKvineqlTGKADRILM-LLPERSDEFLDSALNGL 213
                 6889999999999****************************************988.666666664444456688888875.67777788888888888 PP

        PrmA 251 kegglli 257
                 k++g++ 
  AJA92634.1 214 KNNGVIH 220
                 8777764 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   3.7e+03       6      19 ..      67      80 ..      65      86 .. 0.82
   2 !   21.1   0.0   1.1e-07   0.00019      41     159 ..     120     236 ..      97     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                   CCCTTXEEEXTTXX CS
  Cons_hypoth95  6 GkakgrkLkvlegk 19
                   G ++ rkL+v  g+
     AJA92634.1 67 GDYRTRKLEVIAGE 80
                   89999999998875 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.1e-07
                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HHHHHHH CS
  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPyakellieevlell 136
                    +g+ ++++f+G G  +l A+      ++ ++ ++ a++++ken +  kl++e+  l+ da++ ++++   +++ d + +  P ++++++  +l+ l
     AJA92634.1 120 DGEVMINMFGGVGMFSLLAAKNTSCTVYNIDLNPVAAQLCKENAQINKLKGEVISLNGDATKVINEQ--LTGKADRILMLLPERSDEFLDSALNGL 213
                    466789**********************************************************998..45677999999999999999******* PP

                    HHTT-EEEEEEEEEEEECCSSS- CS
  Cons_hypoth95 137 eekkllkenalvvvetekekelp 159
                    +++++++  + +  +++++   +
     AJA92634.1 214 KNNGVIHYYSHMHADKKQDAPKL 236
                    *****999888888776664433 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.1e-07   0.00056       6     113 ..     123     225 ..     119     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnevlnaladpdkileei 97 
                      +++    G G +++ +a   ++ ++v++iD ++ a +l++enaq ++l+ +v    gd+++ ++++l+  k D il      +   +d++l ++
       AJA92634.1 123 VMINMFGGVGMFSLLAA--KNTSCTVYNIDLNPVAAQLCKENAQINKLKgEVISLNGDATKvINEQLT-GKADRILM----LLPERSDEFLDSA 209
                      56666678899999999..5789**************************8888888*****8887677.79999887....3567788888888 PP

  Methyltransf_31  98 ervlkpggilliedpr 113
                       + lk++g++   ++ 
       AJA92634.1 210 LNGLKNNGVIHYYSHM 225
                      8889999988766555 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   7.1e-07    0.0013       2      80 ..     122     199 ..     121     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.1e-07
  Methyltransf_15   2 rvilDlfsGaGGnvi.qfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                      +v++ +f+G G  +  + +++ ++v+ i+ n+   +++++Na++   + ++    gd ++++++  + k+  d +++  P
       AJA92634.1 122 EVMINMFGGVGMFSLlAAKNTSCTVYNIDLNPVAAQLCKENAQINKLKGEVISLNGDATKVINEQLTGKA--DRILMLLP 199
                      57899*****9876515556699*************************************9999888887..66666555 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   9.2e-07    0.0017      50     149 ..      90     219 ..       4     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.2e-07
                 -...............................EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--.GGEEEE-S-HHHHHC. CS
         TRM  50 k...............................ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve.eivvineddAnvlla. 115
                 +                                 +++ + + G+ ++  a+ +++  +v+  D+++ A +l keN+++n+ + e v + ++dA+ +++ 
  AJA92634.1  90 NgcrfivdvekaffsprlstereriaglvkdgEVMINMFGGVGMFSLLAAKNTSC--TVYNIDLNPVAAQLCKENAQINKLKgE-VISLNGDATKVINe 185
                 3455666666666666666666666666666544567788899999999998554..67878********************55.555555**999996 PP

                 --SS-EEEEE.E--SS--GGGHHHHHHHEEEEEEE CS
         TRM 116 ekkkrfdviD.lDPfGspapfldsavqsvkekglL 149
                 + + + d i  l P   + +fldsa++ +k++g++
  AJA92634.1 186 QLTGKADRILmLLP-ERSDEFLDSALNGLKNNGVI 219
                 56666776651555.566899****9999999986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   5.9e-06     0.011      36      92 ..     125     180 ..     114     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.9e-06
                 EEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTT CS
         MTS  36 lDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvlee 92 
                 + +  G+G+ ++ +ak + + +v  +d +  A +++ken++ nkl++ev+  ++ ++
  AJA92634.1 125 INMFGGVGMFSLLAAK-NTSCTVYNIDLNPVAAQLCKENAQINKLKGEVISLNGDAT 180
                 5566799**9998887.66669************************88887665443 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.3e-06     0.011       1      95 [.     130     229 ..     130     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.3e-06
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT.......TESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC..SHHHHHHHHHCEEEEEEEEECSC CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakkl.......GadevinykeadlverikeltggegvdvvfecvG..sgatleaalkllkpgGrlvvvGg 90 
                 gvG++ + +Ak   ++v+ +d ++  ++l+k++       G  evi  +  d  + i e   g ++d ++  +   s + l++al+ lk +G + ++  
  AJA92634.1 130 GVGMFSLLAAKNTSCTVYNIDLNPVAAQLCKENaqinklkG--EVISLNG-DATKVINEQLTG-KADRILMLLPerSDEFLDSALNGLKNNGVIHYYSH 224
                 8*******************************977777663..3333333.667777666633.77777777776677788888888888888887776 PP

                 TSSEE CS
  ADH_zinc_N  91 gkgee 95 
                 ++ ++
  AJA92634.1 225 MHADK 229
                 55444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.6e-06     0.015       7      97 .]     130     217 ..     125     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.6e-06
                      TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGB..SSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEE CS
  Methyltransf_25   7 GtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedl..pfedgsfDlvvssgalhhlsdedlekalkeiarvLkpg 96 
                      G G ++l +ak+  +++v+ +D+++ + + ++e+a+ ++l  +v  ++gda+++  ++  g+ D +++      l+ e+ +++l+ + + Lk++
       AJA92634.1 130 GVGMFSLLAAKNT-SCTVYNIDLNPVAAQLCKENAQINKLkgEVISLNGDATKVinEQLTGKADRILML-----LP-ERSDEFLDSALNGLKNN 216
                      8899999999996.7********************9999966666688898885224677888988883.....22.33456666666666666 PP

                      E CS
  Methyltransf_25  97 G 97 
                      G
       AJA92634.1 217 G 217
                      5 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.1e-05     0.055       6      54 ..     130     181 ..     128     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                      TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC CS
  Methyltransf_11   6 GtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaek 54 
                      G G ++   ak+  ++v+++Dl++ + +l+ke+a+ ++l  +v  + +da+k
       AJA92634.1 130 GVGMFSLLAAKNTsCTVYNIDLNPVAAQLCKENAQINKLkgEVISLNGDATK 181
                      67888888887777*********************99987755557777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1970.90
//
Query:       AJA92635.1  [L=278]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.3        4.4    7.4   0.1    2.7  3  DUF4717   Domain of unknown function (DUF4717)


Domain annotation for each model (and alignments):
>> DUF4717  Domain of unknown function (DUF4717)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.32   5.8e+03      27      42 ..      67      82 ..      66     101 .. 0.50
   2 ?    7.4   0.1   0.00025       4.4      39      62 ..     136     159 ..     112     167 .. 0.79
   3 ?    2.0   0.0     0.012   2.1e+02      24      35 ..     214     225 ..     209     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.32
     DUF4717 27 aSSvGElwqvvdmaqq 42
                +S vG +  v +++ +
  AJA92635.1 67 VSPVGNMVNVDQITVD 82
                5666666555443333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00025
     DUF4717  39 maqqEedetseaaavrdHlfdLaf 62 
                  a +E++++s+++ + dH +d  +
  AJA92635.1 136 FAMEENEKMSQTIMIEDHSLDYEL 159
                 5668899************99754 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.012
     DUF4717  24 hFvaSSvGElwq 35 
                 +  aSSvG+ w 
  AJA92635.1 214 NHKASSVGDFWT 225
                 5679*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1946.52
//
Query:       AJA92636.1  [L=345]
Description: putative alcohol dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-30  104.9   0.6    3.8e-30  104.0   0.6    1.5  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    6.3e-17   61.8   0.5      1e-16   61.1   0.5    1.3  1  ADH_zinc_N       Zinc-binding dehydrogenase
    0.00035   19.9   0.6    0.00076   18.8   0.6    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0015   17.9   0.7     0.0032   16.9   0.6    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0033   17.2   0.1     0.0068   16.2   0.1    1.6  1  Methyltransf_31  Methyltransferase domain
     0.0049   17.9   0.1     0.0083   17.2   0.1    1.4  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
     0.0064   16.2   0.9      0.017   14.9   0.3    1.8  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
  ------ inclusion threshold ------
       0.01   16.1   0.1       0.02   15.1   0.1    1.5  1  TrkA_N           TrkA-N domain
      0.011   16.5   0.3       0.15   12.9   0.1    2.4  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.033   13.9   0.0      0.052   13.2   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.039   13.9   0.8        0.3   11.0   0.1    2.7  3  S1-like          S1-like
      0.061   14.0   5.0       0.12   13.1   2.2    2.8  2  CoA_binding      CoA binding domain
      0.066   12.7   2.5       0.37   10.3   2.5    1.9  1  DOT1             Histone methylation protein DOT1
       0.12   12.9   0.1       0.25   11.8   0.1    1.5  1  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.6     3e-33   3.8e-30       1     109 []      34     146 ..      34     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3e-33
                 TTEEEEEEEEEEE-HHHHHHHTTS...TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE.-SSSHHHHTT-GGG-TTBEETTTSS-SSS CS
       ADH_N   1 pgevlikvkaagiCgsDlhilkgg...kelevklplilGHEivGeveevgpevkklkvGdrVvveplis.cgeCaaCkegeenlCeeakllgvsldGgf 95 
                 p+evlik++a+g+C+s lh ++g+     ++ ++p ++GHE+vG++ e+g++v+k+k+GdrV + pl + c +C +C eg+e lCe+ +++g +l+Gg+
  AJA92636.1  34 PDEVLIKIEACGVCHSQLHGIEGDwqeIGIPPSFPTVPGHEVVGKIIEIGEKVTKFKIGDRVGITPLLKsCMNCTYCDEGKEYLCENSEITGETLRGGY 132
                 68*********************864444677889******************************99988***************************** PP

                 BSEEEECGGGEEEE CS
       ADH_N  96 aeyvvvpekklvkl 109
                 +e + ++e++l k+
  AJA92636.1 133 TEFINASENFLTKV 146
                 *******9999875 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.5     8e-20     1e-16       1     128 [.     187     308 ..     187     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 8e-20
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET.TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEE CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny.kea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeeef 97 
                 gvG++a+q+Ak  G+ev+++++++e l  a+klGa+ ++   ++  ++  ++k+  g   +d+++ ++ s  + ++a+k++k+gG++ +  +gk ++  
  AJA92636.1 187 GVGHMAIQFAKVEGCEVTGISRKKEHLNVAEKLGAEKTFQFtESQeEFLTKVKDDYG--YFDAAVVFAPSDMVTDTAIKSVKKGGTVIIATVGKIPN-- 281
                 9***************************************96444589999999994..899999999999***************99888654443.. PP

                 EHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
  ADH_zinc_N  98 dlrnlllkeksilGsllgslreefkealdll 128
                     l+++ek+++G+l gs  ++++++++++
  AJA92636.1 282 ---FLAFEEKTVRGTLIGS-MKDMEKVIEIA 308
                 ...5779************.79999998875 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.6   5.9e-07   0.00076      28     125 ..     177     272 ..     162     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.9e-07
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEE CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsViv 125
                  + k+ + G G +G  Ai+ ak  g +Vt +  +++ l+  e+lga+     ++++e++  +vk+      ++ + +     +vt++ +ks k+g  ++
   AJA92636.1 177 NKKIAIYGIGGVGHMAIQFAKVEGCEVTGISRKKEHLNVAEKLGAEKTFQFTESQEEFLTKVKDDYGYFDAAVVFA--PSDMVTDTAIKSVKKGGTVI 272
                  56899*************************************9988655566666666677777777777777764..45699999999999986554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   2.5e-06    0.0032      35      82 ..     176     223 ..     165     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                   TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEE CS
  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvel 82 
                   ++k+++i G+G +G+ +++ +k  g++v++++r+k++ + +e+lg+e+
    AJA92636.1 176 KNKKIAIYGIGGVGHMAIQFAKVEGCEVTGISRKKEHLNVAEKLGAEK 223
                   689*******************************98766555555533 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.3e-06    0.0068      13     127 ..     187     303 ..     166     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
  Methyltransf_31  13 GtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsnevlnaladpdkileeiervlkpgg 105
                      G G+ ++++a+   +++ev+Gi +++e +++A++  +++ ++ ++ +q+++ ++ k+ +    fD  +       +a +d +   +++ +k+gg
       AJA92636.1 187 GVGHMAIQFAK--VEGCEVTGISRKKEHLNVAEKLGAEKTFQ-FTESQEEFLTKVKDdYG--YFDAAVV------FAPSDMVTDTAIKSVKKGG 269
                      7899******4..46899****************99999997.55566666664434344..5888666......6778888889999999999 PP

  Methyltransf_31 106 illiedpr............llaelpakveeesk 127
                       ++i+++             +   l++++++++k
       AJA92636.1 270 TVIIATVGkipnflafeektVRGTLIGSMKDMEK 303
                      9999998866666666555533333344444444 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   6.5e-06    0.0083       2     124 ..     220     334 ..     219     343 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.5e-06
                   T-SEEE..ETTSTTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHH CS
  ADH_zinc_N_2   2 GAdevi..dyrtedfe...aatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyeflfsmkasaqadilee 92 
                   GA++ +     +e+f    ++   + +D+++  + ++   + ++k +++gG+++  + g    +  + +a++  +++v+ +++     s  +d +e+
    AJA92636.1 220 GAEKTFqfTESQEEFLtkvKDD-YGYFDAAVVFAPSDMVTDTAIKSVKKGGTVIIATvG----KIPNFLAFE--EKTVRGTLIG----S-MKD-MEK 303
                   5555554333355555543222.356999999999999988888999887998654434....233444442..3444444444....5.789.*** PP

                   HHHHHHHHH----EEEEEEGGGHHHHHHHHHS CS
  ADH_zinc_N_2  93 laalieeGklrpvvdrvfpleeaaeAhryles 124
                   + +  +++++++v + +fple+a+e +++l++
    AJA92636.1 304 VIEIAQKNNFKVVTE-SFPLEQANEVLERLKN 334
                   ***********9998.8*********999986 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   1.3e-05     0.017      22      95 ..     169     241 ..     162     265 .. 0.78
   2 ?   -0.8   0.0      0.79     1e+03     189     228 ..     282     320 ..     262     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                    HHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSS.STTHSHH CS
  ELFV_dehydrog  22 lkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerks.vkeykks 95 
                    +k ++    ++k++ai G G vg++a+++++  g +v+++s ++  +   e l  e+  ++ e++++ ++++k++
     AJA92636.1 169 IKAAE--PEKNKKIAIYGIGGVGHMAIQFAKVEGCEVTGISRKKEHLNVAEKLGAEKTFQFTESQEEfLTKVKDD 241
                    44433..348899******************************99999999999999999988887767777743 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.79
                    T----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHH CS
  ELFV_dehydrog 189 rlswteeevdeklkkimkeifkavveeaeeykqelvkgan 228
                     l ++e++v+  l   mk++ ++v+e a++++ ++v+++ 
     AJA92636.1 282 FLAFEEKTVRGTLIGSMKDM-EKVIEIAQKNNFKVVTESF 320
                    56688888999999888885.7888999988888777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   1.6e-05      0.02       1      95 [.     180     275 ..     180     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                 EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE.EEES-TTSHHHHHHT..TGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEE CS
      TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle.vvvgdatdeevLeea..giekadaviaatgddeanilavllakelnpkkkiiar 95 
                 i+i G G vG   ++  +  g++ v++i +++e+++ +++ g+e +++   ++ee+L +   +   +da ++ +++d ++  a++++k+   +  iia 
  AJA92636.1 180 IAIYGIGGVGHMAIQFAKVeGCE-VTGISRKKEHLNVAEKLGAEkTFQFTESQEEFLTKVkdDYGYFDAAVVFAPSDMVTDTAIKSVKKG--GTVIIAT 275
                 7899**********999997775.******************888**************9777889**************9999999972..2336665 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012      0.15       2      91 ..     179     273 ..     178     274 .. 0.78
   2 ?    1.0   0.0      0.57   7.3e+02      36      69 ..     310     343 ..     289     345 .] 0.55

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESS.....HHHHHTCT.TESEEEE-S-GGGHHHHHHHHHHTT-EE CS
  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysd.....leelladp.eidavivatpngtheelakaaleagkhv 89 
                   ++ai G+G +g + + ++ +  ++ ev+++  ++  ++ +vae++g+e    +++     l ++++d    da++v  p++   + a++ +++g  v
    AJA92636.1 179 KIAIYGIGGVGHMAI-QFAKV-EGCEVTGISRKK--EHLNVAEKLGAEktfQFTEsqeefLTKVKDDYgYFDAAVVFAPSDMVTDTAIKSVKKGGTV 271
                   89************9.55555.799****97654..5888999999998874444444444444444456**********************99988 PP

                   EE CS
  GFO_IDH_MocA  90 ll 91 
                   ++
    AJA92636.1 272 II 273
                   86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.57
                   HHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE- CS
  GFO_IDH_MocA  36 aeraeavaesfgveaysdleelladpeidaviva 69 
                   +++ + v esf +e  +++ e l++++i+a  v 
    AJA92636.1 310 KNNFKVVTESFPLEQANEVLERLKNSDIEARAVL 343
                   2335555777777766665544444545544444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     4e-05     0.052       1      45 [.     180     225 ..     180     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                 EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEE CS
        ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrlts 45 
                 iai G+G++G + a + ak  g++vt i r++ +l+  +k G + t+
  AJA92636.1 180 IAIYGIGGVGHM-AIQFAKvEGCEVTGISRKKeHLNVAEKLGAEKTF 225
                 89********86.7899999************999877777765554 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.4e+03      29      41 ..      75      87 ..      72     103 .. 0.84
   2 ?   11.0   0.1   0.00024       0.3       8      28 ..     235     255 ..     232     274 .. 0.85
   3 ?   -1.7   0.0       2.2   2.8e+03      16      33 ..     277     294 ..     269     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
     S1-like 29 vkGrlpkvgdrVl 41
                v+G++ ++g++V 
  AJA92636.1 75 VVGKIIEIGEKVT 87
                7888889999885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
     S1-like   8 VTklqdtfGfvDeevfFqrsv 28 
                  Tk++d++G+ D  v+F  s 
  AJA92636.1 235 LTKVKDDYGYFDAAVVFAPSD 255
                 7****************8765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.2
     S1-like  16 GfvDeevfFqrsvvkGrl 33 
                 G + +   F+ ++v+G+l
  AJA92636.1 277 GKIPNFLAFEEKTVRGTL 294
                 667777789999999986 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.2   9.3e-05      0.12       2      91 ..     176     273 ..     175     276 .. 0.68
   2 ?   -1.9   0.0       4.5   5.8e+03      54      83 ..     298     333 ..     287     342 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                  TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TT.TTTCEET...TEEEESCHHHHHHHC.T....TTEEEEES-HHHHHHHHHHHHHTT-SEE CS
  CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnpr.kvgtevl...glpvyksvdeleekt.e....vdvavitvPaesaqeavdelveagikgi 90 
                  k++k++++G+gg g+ ++ +f++  +++++ +   +++  v+++ +   + +  +s +e  +k+ +     d+av+++P++ + +++++ v++g  +i
   AJA92636.1 176 KNKKIAIYGIGGVGH-MAIQFAKVEGCEVTGISRKKEHlNVAEKLGaekTFQFTESQEEFLTKVkDdygyFDAAVVFAPSDMVTDTAIKSVKKGGTVI 272
                  789999999999954.446666666665555555444433333333555444445555555555524569***********************99888 PP

                  E CS
  CoA_binding  91 v 91 
                  +
   AJA92636.1 273 I 273
                  6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                  HHHHHHHC....TTTEEEEES..-HHHHHHHHHHHH CS
  CoA_binding  54 vdeleekt....evdvavitv..Paesaqeavdelv 83 
                  ++++e+ +    + + +v+t   P e+a e+ ++l 
   AJA92636.1 298 MKDMEKVIeiaqKNNFKVVTEsfPLEQANEVLERLK 333
                  444444432213255555554447777777766665 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.5   0.00029      0.37      52     184 ..     187     337 ..     175     342 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                 TTSHHHHHHHHHH--SEEEEE.......E-.....-HHHHHHHHHHHHHHHHHHHHTTB----EEEESS-STT-HHHHHHGGG-SEEEE.....--T.T CS
        DOT1  52 GvGnvvlqaalevgcklsvGv.......Ei.....mdnaselaekqkeelkkrlklfGkklakiefirksFvenekveeiieeadvilv.....NNf.a 132
                 GvG++ +q a   gc+  +G+        +     ++++ +++e+q+e+l+k  + +G   a++ f+ ++ v++  ++++ +  +vi+       Nf a
  AJA92636.1 187 GVGHMAIQFAKVEGCE-VTGIsrkkehlNVaeklgAEKTFQFTESQEEFLTKVKDDYGYFDAAVVFAPSDMVTDTAIKSVKKGGTVIIAtvgkiPNFlA 284
                 7888888888888887.56662222111111112234556789999**********************************9999999853333345426 PP

                 --H.HHHHHHHHHHTT--TT-EEEESS-SS-TT----SSSTT-GGGGEEEEEE CS
        DOT1 133 Fda.elnkqlkellqdlkegtkiislkslvpskykinsrnledivnilkveel 184
                 F++ ++  +l   ++d+ +   i   +++   + +   +++++++++lk + +
  AJA92636.1 285 FEEkTVRGTLIGSMKDMEKVIEIAQKNNFKVVTESFPLEQANEVLERLKNSDI 337
                 76514666677777777777777777778777777777788888887777665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0002      0.25       6      80 ..     176     264 ..     175     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
  NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleagakvtvvapevkeele........elvkla..eeel....ekdlegad.lviaatddrelneriae 80 
                    k+kk+ + G G v+   ++    +g++vt ++ +  e l+        ++++++  +ee+    ++d   +d  v+ a++d    ++i  
     AJA92636.1 176 KNKKIAIYGIGGVGHMAIQFAKVEGCEVTGISRKK-EHLNvaeklgaeKTFQFTesQEEFltkvKDDYGYFDaAVVFAPSDMVTDTAIKS 264
                    689*******************************4.333344455555444443224444344366665566666777777666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2397.10
//
Query:       AJA92637.1  [L=293]
Description: protoheme IX farnesyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-51  175.1  21.6      2e-51  174.7  21.6    1.1  1  UbiA           UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.28   11.0   0.0       0.28   11.0   0.0    3.5  4  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7  21.6   2.2e-55     2e-51       2     246 ..      22     269 ..      20     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 2.2e-55
        UbiA   2 lipalvglalaa...ggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgl 97 
                 +i+a+ ++ +a+   g+ +d++ l+ +++++ la+a++ alN+y+Dr+iD +mert  RP++sGri+p+ +li+++   +++++ +al ln ++a++++
  AJA92637.1  22 VITAVTSMYAASkliGPELDTWGLIHIIIAGGLASAGSSALNHYYDRDIDPLMERTSTRPIPSGRIKPNSVLIYGLTVSVISVVYGALALNYVSAFFIA 120
                 56666664444411134455588888888888******************************************************************* PP

        UbiA  98 lallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaaril..la 193
                 l++++y ++Yt  +lKr    ++v+gg+a+  ++++gw a+tgs+++l +l++++vf++t +++++ +++ ++++ +a +++lpv++G +++  +  + 
  AJA92637.1 121 LGIFFYvIIYT-AWLKRLNSSNIVIGGFAGSAAAMAGWSAATGSMDILGFLIGFLVFVWTPSHFWCLAMKMKDEYSAAKVPMLPVLIGMQKTSKYilI- 217
                 ***********.6***************************************************************************9999995332. PP

        UbiA 194 lllavllla..llllllalllllylllalllaalallraarlvrrrdakkaakff 246
                      l+l+   l+l++++++l+y+++a+++++l+l+++++l++  +++ a+k++
  AJA92637.1 218 ---NTLILLpySLMLYAFGMGLVYTAIAAASGGLMLVYHYKLTKEPTSDFAWKAY 269
                 ...2222223466899*******************************99999998 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.1e-05      0.28     140     202 ..      18      80 ..       7      97 .. 0.79
   2 ?    5.4   0.6    0.0016        14     118     179 ..      74     131 ..      70     143 .. 0.68
   3 ?   -2.1  10.5       0.3   2.7e+03      99     168 ..     113     187 ..     103     191 .. 0.65
   4 ?    0.1   0.6     0.063   5.7e+02     148     187 ..     222     255 ..     202     278 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
  FA_desaturase 140 wlllllawlglwlalllllglalllwlvplllllfllalvl.nyveHyggdwgerqvetsasir 202
                    ++ll+++++   +a++ l g+ l  w++ +++++  la      ++Hy+ d + ++++ ++s+r
     AJA92637.1  18 VVLLVITAVTSMYAASKLIGPELDTWGLIHIIIAGGLASAGsSALNHYY-DRDIDPLMERTSTR 80 
                    455666667777777777777777*************99999******9.88888888888777 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0016
  FA_desaturase 118 lrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfllalv 179
                    + r   r+ ps +++ + +l++ l + +  + +++++l+l+ +++  ++++l +++ ++ + 
     AJA92637.1  74 MERTSTRPIPSGRIKPNSVLIYGLTVSV--ISVVYGALALNYVSA--FFIALGIFFYVIIYT 131
                    6677778888888888888888888888..888888888888874..444444444433333 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.3
  FA_desaturase  99 lllgllvlg..wllalvlglwlrrlarrrapsksrrrk......wrllawlllllawlglwlalllllglalllwlvp 168
                    +++ ++ +   +++      wl+rl      + +++        w   +  + +l++l+++l++++ +++   +w ++
     AJA92637.1 113 YVSAFFIALgiFFYVIIYTAWLKRLNSSNIVIGGFAGSaaamagWSAATGSMDILGFLIGFLVFVWTPSH---FWCLA 187
                    3333333334555555555577777777777777777777777777788888888778888888887777...77765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.063
  FA_desaturase 148 lglwlalllllglalllwlvplllllfllalvlnyveHyg 187
                    l+ + ++l+++g++  l++ +++++   l     +v+Hy 
     AJA92637.1 222 LLPYSLMLYAFGMG--LVYTAIAAASGGL----MLVYHYK 255
                    33344444444444..2222222222222....5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2066.49
//
Query:       AJA92638.1  [L=358]
Description: PF05982 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-101  340.2  23.4   1.2e-101  340.0  23.4    1.0  1  Sbt_1     Na+-dependent bicarbonate transporter superfamily
     0.0014   19.0   4.6      0.037   14.3   1.5    2.6  2  DUF1772   Domain of unknown function (DUF1772)


Domain annotation for each model (and alignments):
>> Sbt_1  Na+-dependent bicarbonate transporter superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.0  23.4  1.4e-105  1.2e-101       1     306 [.      14     337 ..      14     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: 340.0 bits;  conditional E-value: 1.4e-105
       Sbt_1   1 PvvlffilGllaallksdLeiPealykllslyLLlaiGlkGGvelaeselsaelllallaavvlgllipllaflilrkltkldkvdaaaiAalYGsvSa 99 
                 P+vlff++G++aa +ksdL++Pea++++l +yLL aiGl+GG+e++++++ +e+l+++l+a+ l+ll++l ++ ilr+l k++ +d+ a+A++YG+v a
  AJA92638.1  14 PIVLFFLFGIIAARIKSDLKMPEAISEFLPIYLLAAIGLHGGIEMRKTGF-EEMLVPMLVAIGLSLLFTLNHYQILRRLGKFNIFDSYALASTYGAVGA 111
                 99************************************************.************************************************ PP

       Sbt_1 100 vtfaaalavlesqgiayegymvallalmeipaivvalllakllkkkkkkese...................lkevlkeallnksvvlLlggliiGlltg 179
                 vtf ++l++l++qg++ egy++a+la++e  a ++a++l++++ +k+ ++++                   l++vlke++++k++v+Llg+++iG+++g
  AJA92638.1 112 VTFSVGLSFLKNQGVSSEGYLAAILAVLEPVAFILAIFLTNMAVSKQIRTKKqsisddeeldigmkqtktkLSQVLKESITGKAIVILLGSIVIGYIIG 210
                 *****************************************9999988777789999*************9**************************** PP

       Sbt_1 180 ekgleklepffedlFkgvLalfLLemGlvaarrlkelrkvglflilfailaplvnallgillakllglsaGgavllavLaaSaSyIavPaalrlaiPeA 278
                 ++g+e ++ +f++lF+g++++f++emG++a++rl++++kvg+fl +f+i++p +n+++g+l++++lgls Ggav++  L aSaS+Ia+Pa+lr+aiP+A
  AJA92638.1 211 KEGFEPISIVFDELFTGAIVIFMIEMGIIAGQRLEDIKKVGIFLTSFSIIIPTINGIIGVLVSTALGLSLGGAVMFGLLLASASFIAAPAVLRHAIPQA 309
                 *************************************************************************************************** PP

       Sbt_1 279 npslyltaslgitfpfniligiPlYlal 306
                 npsly+t++lgitfp+ni++ +P+ +++
  AJA92638.1 310 NPSLYITSALGITFPYNIIVLLPIMFTI 337
                 ***********************98876 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.1    0.0028        25      37      95 ..     104     162 ..      62     205 .. 0.55
   2 !   14.3   1.5   4.2e-06     0.037      35      96 ..     281     341 ..     251     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0028
     DUF1772  37 avfpplallsalafayla......araasrgarllylaaaallllsivpyTllvmvPtN....nkLaal 95 
                 +++++++++        +      + + +  ++  y +aa+l++l  v + +l++  tN    +++ ++
  AJA92638.1 104 STYGAVGAV--------TfsvglsFLKNQGVSSEGY-LAAILAVLEPVAF-ILAIFLTNmavsKQIRTK 162
                 222222222........1333333445566666666.4455544222222.222223342221333333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.2e-06
     DUF1772  35 g.kavfpplallsalafa.ylaaraasrgarllylaaaallllsivpyTllvmvPtNnkLaalk 96 
                 g +++f++l++ ++  +a ++ ++a  ++++ ly++ +al +  ++py ++v  P+ +++ ++ 
  AJA92638.1 281 GgAVMFGLLLASASFIAApAVLRHAIPQANPSLYIT-SALGI--TFPYNIIVLLPIMFTISTWV 341
                 448999998888888888677799999999999955.66656..6**********998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2517.17
//
Query:       AJA92639.1  [L=693]
Description: hypothetical protein T478_1019 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-15   56.4  25.4    3.4e-09   36.5   0.6    2.9  2  SMC_N            RecF/RecN/SMC N terminal domain
    1.8e-09   38.4  81.4    7.8e-06   26.5  62.0    4.3  1  AAA_23           AAA domain
    2.5e-09   36.8   0.2    4.8e-09   35.8   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
    2.6e-09   37.3  13.5    0.00013   21.9   1.9    3.0  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-08   34.8  57.4    1.3e-05   25.1  29.6    2.3  2  AAA_15           AAA ATPase domain
      4e-07   29.8   0.9      4e-07   29.8   0.9    2.9  3  AAA_27           AAA domain
    1.6e-05   25.0   0.0    3.3e-05   24.0   0.0    1.5  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
       0.01   16.3   0.0       0.01   16.3   0.0    4.8  1  ABC_tran         ABC transporter
      0.012   15.6   7.2      0.013   15.5   0.0    3.5  3  RsgA_GTPase      RsgA GTPase
      0.017   15.5   7.2      0.017   15.5   7.2    6.2  4  Snapin_Pallidin  Snapin/Pallidin
       0.57   10.5   2.7        2.3    8.6   0.0    3.2  2  AAA_16           AAA ATPase domain
        3.9    7.2  12.8       0.61    9.9   0.1    3.7  4  MukB             MukB N-terminal
        4.5    7.4   8.5       0.24   11.5   0.1    3.1  3  MMR_HSR1         50S ribosome-binding GTPase
          7    7.0   8.4        3.1    8.1   0.6    3.2  3  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.6   2.7e-12   3.4e-09       1      89 [.       1      78 [.       1     129 [. 0.76
   2 !   23.6  18.2   2.3e-08     3e-05      57     206 ..     378     674 ..     222     688 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.7e-12
                EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk 89
                +++++e+ +F     ++++l+fs+  t+ vG+NG+GKs+++dAi F L  +++    +++ ++li +      ++k  v++ f+ ++k+
  AJA92639.1  1 MIHSIELIDFLAH--HNTKLDFSNDATVFVGQNGAGKSSIIDAITFSLFGAHT----RKNNKSLIRR-----GANKSLVKVDFSANGKN 78
                5788999999877..7999***************************9875555....4566788887.....55556666666666655 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 2.3e-08
                 TCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................... CS
                 xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
       SMC_N  57 rseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske................... 135
                 ++ +l+d i k ++e +++++a++++  +n + +++ e+   +i+ +vk+ ++  ++in                    +                   
  AJA92639.1 378 KQVELEDSIEKvNDELREAENADIKLKTHNISTETELEQIAATIKEKVKKIKDIPITINSG------------------Qlleassidahakmkyekil 458
                 3444555555555555666666666666666666666666666666666666666666544..................04444444444444444445 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
       SMC_N 136 ................................................................................................... 135
                                                                                                                    
  AJA92639.1 459 qiekttsgfnqdefllkkkdliqnrdrlrqidqefgatsnrienaeqqlernriildelhnvrkyvieleniqknvysidgpvakslrswaldiiseka 557
                 55899999******************************************************************************************* PP

                 .....................................CS-HHHHHHHHHHHHHH...HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH......HCT CS
                 .....................................xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxx RF
       SMC_N 136 .....................................lLSgGektLvalaLlfA...iqkvkpaplyllDeidaaLDeknvkkvaellke......ksk 188
                                                      +LSgGe+  +al+L++    +  ++   +++lDe   +LD +++k+++ +l +      ++ 
  AJA92639.1 558 seylerlntkiqrislsqktrdvnitcyarstmleleSLSGGEQVSIALSLRLGmahLLGASNLNFMILDEPTTHLDSERRKALVGVLSQlasirgEEA 656
                 ****************************************************9955556678889******************9988775111111456 PP

                 TSEEEEE-SSHHHCCC-S CS
                 xxxxxxxxxxxxxxxxxx RF
       SMC_N 189 naQfivislreemlekad 206
                 ++Qfi+is+++e++e+++
  AJA92639.1 657 SMQFIIISHDAEIFEDSS 674
                 7*************9873 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5  62.0   6.1e-09   7.8e-06       1     167 [.       4     261 ..       4     431 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-09
      AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks..grgfeksdveiesegkvkayveltfenkdgrytrsiererels 97 
                 ++++  f  ++++++dFs+  t+++G+NGaGK++i+dAi++ L+g  +r ++ks  +rg++ks v++ +++++k+y +++  + +g+      +  e++
  AJA92639.1   4 SIELIDFLAHHNTKLDFSNDATVFVGQNGAGKSSIIDAITFSLFGAHTRKNNKSliRRGANKSLVKVDFSANGKNYRTVRQIDAKGTL---TAQFLEKN 99 
                 688999***************************************99888888899999*******9999999999888877777743...22334445 PP

      AAA_23  98 kkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke........................................... 153
                  ++   + + ++++++++  ++++++ lg++++ l++ ++ +q++ + + ++++ke                                           
  AJA92639.1 100 GEDFIPIAEGERKQFGES-MTEEVEKVLGINFEKLKIASIVQQGELNSIIKAKPKEfkellntiigidrldvavesmkevlkefrkdiqtkhgfddtqi 197
                 555555555556666555.56888888888888888888888888555555555555555556666666666666666666666666666677777766 PP

      AAA_23 154 ..................................................rleelekeleeled 167
                                                                   +l+ele+++eel  
  AJA92639.1 198 ellenrmnefqneitnskpmmkkleeekqvretkiiqieqevekdsvkeiQLRELEDQKEELVS 261
                 6666644444444444444444444444444444444444444444444444444444433322 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.2   3.7e-12   4.8e-09       3      57 ..       4      57 ..       2      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.7e-12
      AAA_29  3 rlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfNka 57
                +++l++    ++++++++ ++at+++G++G+GKS+++DAi++ L +a++++ Nk+
  AJA92639.1  4 SIELIDFLAHHNTKLDFS-NDATVFVGQNGAGKSSIIDAITFSLFGAHTRKNNKS 57
                788888888888999998.447**************************8888875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.9     1e-07   0.00013       2      84 ..      25     116 ..      24     225 .. 0.62
   2 !   20.0   3.7   3.7e-07   0.00048     110     302 ..     477     670 ..     372     671 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1e-07
      AAA_21   2 nvliGpNgsGKSnLLdaldllarl........drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv.e 84 
                 +v++G Ng+GKS+++da+ +  +             +g + +l +    +   ++ + ++++ +++++  +++++g ++  +++ er+q+ e
  AJA92639.1  25 TVFVGQNGAGKSSIIDAITFSLFGahtrknnkSLIRRGANKSLVKVDFSANGKNYRTVRQIDAKGTLTAQFLEKNGEDFIPIAEGERKQFgE 116
                 8*****************98654367777775444444444444444555555666666667777777777777777777777777777753 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.7e-07
      AAA_21 110 vfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                 ++  + r+   +++ +  ++++++e  ++q +++++ +++ ++            r+ + ++ +   + +++ + + + +rs+ l+ i   ++++ e+l
  AJA92639.1 477 KDLIQNRDRLRQIDQEFGATSNRIENAEQQLERNRIILDELHNV-----------RKYVIELENIQKNVYSIDGPVAKSLRSWALDIISEKASEYLERL 564
                 44444555555555555555566666666665555555555555...........77777888888888899999999999999999999999999999 PP

      AAA_21 209 iasvderlrer...gvvflengdgqelparelSdGtkrllalltallralkkg....sllliDEpEngLHPkllrrllellkelsr.....ngaQvilt 295
                 ++++++ ++     +v +  + +   l + +lS G +  +al + l  a+  g     + ++DEp ++L+ ++ + l+++l++l++        Q+i+ 
  AJA92639.1 565 NTKIQRISLSQktrDVNITCYARSTMLELESLSGGEQVSIALSLRLGMAHLLGasnlNFMILDEPTTHLDSERRKALVGVLSQLASirgeeASMQFIII 663
                 99999888888888888888888888999999*************************************************7777777787889***** PP

      AAA_21 296 THSplll 302
                 +H+ ++ 
  AJA92639.1 664 SHDAEIF 670
                 ***9885 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1  29.6   9.8e-09   1.3e-05       1     262 [.       1     295 [.       1     339 [. 0.45
   2 !   10.2  26.1   0.00034      0.44      91     368 ..     344     669 ..     300     670 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.8e-09
      AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl.Flnnkekkn.............kkvikiekedleifeniseskdik..Idvef 83 
                 M I++i++  F ++ ++++d+s++ tv++G N++GKSsi++a+ + ++   ++kn             +   k++ +   ++  + + +d k  ++ +f
  AJA92639.1   1 M-IHSIELIDFLAHHNTKLDFSNDATVFVGQNGAGKSSIIDAITFsLFGAHTRKNnkslirrgankslV---KVDFSANGKNYRTVRQIDAKgtLTAQF 95 
                 7.99***************************************864444445666799*****974441...333333333333333333221155555 PP

      AAA_15  84 .aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklek..ekeelkidkedlkklikklees 179
                  +  ++ ++++ +++ ++k++ + ++++ e+  +  i+ +klk+ ++  + e  s+ k       pke +e l++   ++ l++  e++k+++k++++ 
  AJA92639.1  96 lE--KNGEDFIPIAEGERKQFGESMTEEVEK--VLGINFEKLKIASIVQQGELNSIIKA-----KPKEFKELLNTiiGIDRLDVAVESMKEVLKEFRKD 185
                 20..333333333333333333333333333..22222222222222222222222222.....22222222222112344444466666666666666 PP

      AAA_15 180 lkkee........elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl....eeelteklkeiqeklkeidkklaeelk..... 261
                 ++ +         +l+n +++++ ++   +   +  +e++++ ++ ++++ ++  +++++e +    e++++e  +  +e +k+i+ ++ ee+      
  AJA92639.1 186 IQTKHgfddtqieLLENRMNEFQNEITNSKPMMKKLEEEKQVRETKIIQIEQEVEKDSVKEIQlrelEDQKEELVSYAKETIKKIQRDVMEEERkvnec 284
                 666666666666533333333333333333333333344444444444444444444444433333444444444444444444444443333344333 PP

      AAA_15 262 ..........k 262
                            
  AJA92639.1 285 kgcfsivskrG 295
                 22222222231 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
      AAA_15  91 eyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid...kedlkklikkleeslkkee.. 184
                 ++ +  +  +  +++  l+++++ l+  i + k k  + e+s ek+++e +++++ + k+k+++  +e e  +i    ke++kk+ +  +++ +++   
  AJA92639.1 344 VCDSKVDHLNPLFQKEHLEEEIKTLDRKISQTKEKQVELEDSIEKVNDELREAENADIKLKTHNISTETELEQIAatiKEKVKKIKDIPITINSGQLle 442
                 222333333344444556777777778888888888888888888888888888888888888777666666666667888888888444444444488 PP

      AAA_15 185 ................elknvlksaiiklllisakRnvsd.edsekkssllgklkekileealqekl............eeelteklkeiqeklkeidk 254
                                 ++++  + + ++  l ++k  +++ ++  +++  +g++ ++i e+a  ++l              +   +l++iq+++  id+
  AJA92639.1 443 assidahakmkyekilQIEKTTSGFNQDEFLLKKKDLIQNrDRLRQIDQEFGATSNRI-ENAE-QQLernriildelhnVRKYVIELENIQKNVYSIDG 539
                 8888888888777777666666665555555555555555255555555555555555.4433.33358999999999866889999999999999999 PP

      AAA_15 255 klaeelkkilkkkidkikkfnykgkkneeieik..............ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpq 339
                  +a++l ++  ++i++  ++   + +    +i+                + l+l+  + G q  + l+l + +a+      ++ ++ +++EP +hL  +
  AJA92639.1 540 PVAKSLRSWALDIISEKASEYLERLNTKIQRISlsqktrdvnitcyaRSTMLELESLSGGEQVSIALSLRLGMAHLL--GASNLNFMILDEPTTHLDSE 636
                 9999999888888877444444444444444447788888889**********************************..99****************** PP

      AAA_15 340 aqkvlikllkelandnkt....QviitTHSphi 368
                   k l+  l  la+        Q ii +H   i
  AJA92639.1 637 RRKALVGVLSQLASIRGEeasmQFIIISHDAEI 669
                 *************999889999*******8766 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.9   3.1e-10     4e-07       3     195 ..       2     209 ..       1     220 [. 0.68
   2 ?   -1.6   0.0       1.3   1.6e+03     133     162 ..     286     315 ..     237     341 .. 0.74
   3 ?   -0.7   0.4       0.7   8.9e+02     163     201 ..     359     397 ..     333     412 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.1e-10
      AAA_27   3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdnflhd..akkLrigavleeadgeelefaRrkgrkktlldadd 99 
                 +++++L  +    +++ldfs   +d ++ +G N AGKs++++Ai+  lfG ++r++++ l    a+k  ++  + +a+g++ + +R+   k tl+++  
  AJA92639.1   2 IHSIELIDFLAHHNTKLDFS---NDATVFVGQNGAGKSSIIDAITFSLFGAHTRKNNKSLIRrgANKSLVKVDF-SANGKNYRTVRQIDAKGTLTAQFL 96 
                 6778899999999******9...788999**************************9998775114566677777.99999*******999999987654 PP

      AAA_27 100 q.......alpeevlaallggldretFealFgLdherLr.....eGG..ealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskk.... 180
                 +       +++e   +++ +++++e  e++ g++ e+L+     + G  +++++a+ +  + L++   G+ +l   +e++++  +e+ k+ ++k+    
  AJA92639.1  97 EkngedfiPIAEGERKQFGESMTEE-VEKVLGINFEKLKiasivQQGelNSIIKAKPKEFKELLNTIIGIDRLDVAVESMKEVLKEFRKDIQTKHgfdd 194
                 4344465556677777776666655.5888888887775222224442347888888888888888888877766666555555444333333321111 PP

      AAA_27 181 rainealeeleeakk 195
                 ++i   +++++e ++
  AJA92639.1 195 TQIELLENRMNEFQN 209
                 445555555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
      AAA_27 133 GGealleaegelgqlLfeasaGlaslrevl 162
                 G  ++++++ge+ + Lf+ +  l+++++ l
  AJA92639.1 286 GCFSIVSKRGEIESRLFKLEEELQTITKEL 315
                 556677777777777777665555544433 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.7
      AAA_27 163 eaLeaeadelfkprkskkrainealeeleeakkelreaq 201
                 e+Le+e ++l ++ +++k++  e ++++e+++ elrea+
  AJA92639.1 359 EHLEEEIKTLDRKISQTKEKQVELEDSIEKVNDELREAE 397
                 456666666666555555555556666666666555553 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.6e-08   3.3e-05      29      89 ..     592     646 ..     570     647 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.6e-08
     SbcCD_C  29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                 + ++lSGGe+ + ++l l +++a+l++ +     +l +++LDE    lD+e++++l+++l 
  AJA92639.1 592 ELESLSGGEQ-VSIALSLRLGMAHLLGAS-----NLNFMILDEPTTHLDSERRKALVGVLS 646
                 6789******.*****************5.....8********************998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.0   8.1e-06      0.01      12      32 ..      23      43 ..      14     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.1e-06
                SEEEEEESTTSSHHHHHHHHT CS
                xxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 12 ekvaivGenGaGKStLlklla 32
                  +++vG+nGaGKS+++ +++
  AJA92639.1 23 DATVFVGQNGAGKSSIIDAIT 43
                45679*************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   9.9e-06     0.013      97     120 ..      20      43 ..      11      70 .. 0.85
   2 ?    1.0   1.0      0.27   3.4e+02      46     101 ..     379     425 ..     341     431 .. 0.60
   3 ?   -0.6   0.1      0.83   1.1e+03      52      80 ..     473     501 ..     455     524 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.9e-06
                  CTTSEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinall 120
                  ++++ +v+vGq G+GKS++i+a++
   AJA92639.1  20 FSNDATVFVGQNGAGKSSIIDAIT 43 
                  67889***************9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                  T-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
  RsgA_GTPase  46 giepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                  ++e+   +         e++++   e e++++++ + + +t+++le++++ +k+k+
   AJA92639.1 379 QVELEDSI---------EKVNDELREAENADIKLKTHNISTETELEQIAATIKEKV 425
                  22222222.........244555555556666666666667777777777777665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.83
                  EEE-GGG--HHHHHHHHHHHHHHTTSEEE CS
  RsgA_GTPase  52 vlnKiDlleeeeeleelkeelealgyevl 80 
                  +l K Dl++++++l+++ +e+ a+  ++ 
   AJA92639.1 473 LLKKKDLIQNRDRLRQIDQEFGATSNRIE 501
                  78999999999988888887766655544 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.3      0.52   6.7e+02      31      83 ..     167     222 ..     141     227 .. 0.76
   2 ?   15.5   7.2   1.4e-05     0.017      10      51 ..     360     401 ..     358     439 .. 0.77
   3 ?    7.3   0.9     0.005       6.4      15      76 ..     479     538 ..     472     545 .. 0.84
   4 ?   -1.4   0.1       2.5   3.2e+03      35      51 ..     560     576 ..     554     584 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
  Snapin_Pallidin  31 eLleqldrlnekLkeleeaqe.aevlpdlkeya..kKLvnikkrmsslnerlqklk 83 
                       L   +++++e Lke++++ + +  + d++  +  ++++++++++++ +  ++kl+
       AJA92639.1 167 RLDVAVESMKEVLKEFRKDIQtKHGFDDTQIELleNRMNEFQNEITNSKPMMKKLE 222
                      67788889999999999988877777765554444888888888888877777776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.4e-05
  Snapin_Pallidin  10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                      +le ++++ld k+++++++Q eL +++++ n++L+e+e+a+ 
       AJA92639.1 360 HLEEEIKTLDRKISQTKEKQVELEDSIEKVNDELREAENADI 401
                      7999*******************************9998765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.005
  Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssln 76 
                      l + +++l+++ q+  + ++++++  ++L++++ + +   l ++++y+  L ni+k++ s+ 
       AJA92639.1 479 LIQNRDRLRQIDQEFGATSNRIENAEQQLERNRIILD--ELHNVRKYVIELENIQKNVYSID 538
                      5566677777777778888999***********9999..89****************99885 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.5
  Snapin_Pallidin  35 qldrlnekLkeleeaqe 51 
                       l+rln+k+++++  q+
       AJA92639.1 560 YLERLNTKIQRISLSQK 576
                      46666666666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0018       2.3      26      52 ..      24      56 ..       7     192 .. 0.60
   2 ?   -0.6   1.7       1.2   1.5e+03      99      99 ..     512     512 ..     330     681 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
      AAA_16 26 lvllsGesGvGKsslvrellralekd......g 52
                +++++G+ G GKss+++++  +l ++      +
  AJA92639.1 24 ATVFVGQNGAGKSSIIDAITFSLFGAhtrknnK 56
                67899*************998888773333330 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
      AAA_16  99 e 99 
                  
  AJA92639.1 512 I 512
                 1 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00047      0.61       7      67 ..       3      63 ..       1      77 [. 0.85
   2 ?   -0.6   0.8      0.74   9.5e+02     127     159 ..     225     259 ..     192     318 .. 0.65
   3 ?   -2.2   0.0       2.4     3e+03     125     160 ..     361     397 ..     343     444 .. 0.55
   4 ?    4.0   0.4      0.03        39     112     161 ..     490     539 ..     465     549 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                EEEEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT----------- CS
        MukB  7 ksltlinWnGffartfdldelvttlsGgnGaGksttmaafvtaliPdlsllhfrntteaGa 67
                +s+ li++      + d+ +  t + G nGaGks ++ a+  +l    ++ + + +   Ga
  AJA92639.1  3 HSIELIDFLAHHNTKLDFSNDATVFVGQNGAGKSSIIDAITFSLFGAHTRKNNKSLIRRGA 63
                6788888889999999999********************9999998888877776666666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.74
                 TT--HHHHHEE--SSS--EE--..HHHHHHHHHTS CS
        MukB 127 edvkltdvlleklddkkarvre..lnelkekleel 159
                 ++v+ t+++  +++ +k+ v+e  l el ++ eel
  AJA92639.1 225 KQVRETKIIQIEQEVEKDSVKEiqLRELEDQKEEL 259
                 23334444444444444444431144555554443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.4
                 --TT--HHHHHEE--SSS--EE-.-HHHHHHHHHTST CS
        MukB 125 leedvkltdvlleklddkkarvr.elnelkekleele 160
                 lee++k  d  +++ ++k+ ++  +++++ ++l e e
  AJA92639.1 361 LEEEIKTLDRKISQTKEKQVELEdSIEKVNDELREAE 397
                 5555554444444444433332212333333333322 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.03
                 TT-EEEEEEEEES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT CS
        MukB 112 dkkvdikpfalqgleedvkltdvlleklddkkarvrelnelkekleeleg 161
                 d+    ++  +++ e++++ + ++l++l++ ++ v+el+++++++ +++g
  AJA92639.1 490 DQEFGATSNRIENAEQQLERNRIILDELHNVRKYVIELENIQKNVYSIDG 539
                 555667888999********************************998877 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00019      0.24       3      56 ..      26      90 ..      24     189 .. 0.65
   2 ?   -1.5   0.1         2   2.5e+03      63      84 ..     271     292 ..     215     325 .. 0.62
   3 ?   -1.3   1.1       1.7   2.2e+03      65     103 ..     388     427 ..     320     437 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                EEEESTTSSHHHHHHHHH....TSTEEESSSTTSSSSEEEEEEE.......ETT.EEEEEEECGGC CS
    MMR_HSR1  3 aivGrpNvGKStLinalt....gekaivsdkpgtTrdinegrvk.......lkg.keielvDtpGl 56
                ++vG+  +GKS++i a+t    g++ + ++k    r  n+  vk       + + + ++ +D  G 
  AJA92639.1 26 VFVGQNGAGKSSIIDAITfslfGAHTRKNNKSLIRRGANKSLVKvdfsangK-NyRTVRQIDAKGT 90
                79***************95555223333333333333333333322222222.2366777777775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                 HHHHHHHHHHHHCTSEEEEEEE CS
    MMR_HSR1  63 ekglgkaflaleeadlillvvd 84 
                 ++++ ++ ++++e++  + +v+
  AJA92639.1 271 QRDVMEEERKVNECKGCFSIVS 292
                 2344455555556666666665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.7
                 HHHHHHHHHHCTSEEEEEEETT.TTCSHHHHHHHHHHHHH CS
    MMR_HSR1  65 glgkaflaleeadlillvvdas.eeklkpldeeleellee 103
                 ++++++++ e+ad+ l   ++s e++l+++  +++e  ++
  AJA92639.1 388 KVNDELREAENADIKLKTHNIStETELEQIAATIKEKVKK 427
                 3555555556666666666666323466665655555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.4   5.1e+02      10      48 ..      22      60 ..      16     113 .. 0.74
   2 ?    8.1   0.6    0.0024       3.1      54     113 ..     171     240 ..     144     261 .. 0.77
   3 ?    0.2   1.0      0.69   8.9e+02      77     116 ..     439     522 ..     295     531 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.4
      AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                ++  + ++  G GK+ ++ +i   l  ++++k ++ l+ 
  AJA92639.1 22 NDATVFVGQNGAGKSSIIDAITFSLFGAHTRKNNKSLIR 60
                5566778999*********99998888888877777665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0024
      AAA_19  54 AakelrerlaalgaeatTiHrlal..........ldfddlltealelleeaeeekklqeeellivDEfqd 113
                 A++ ++e l+++ ++++T H++             +f++++t+   ++++ eeek+++e++++ +    +
  AJA92639.1 171 AVESMKEVLKEFRKDIQTKHGFDDtqiellenrmNEFQNEITNSKPMMKKLEEEKQVRETKIIQIEQEVE 240
                 999*****************99668889988888888888888888888999999997777887764444 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.69
      AAA_19  77 l..................................ldfddlltealelle............eaeeekklqeeellivDEfqdvde 116
                                                    l+ +dl+++   l +             ++ e++l e++ +i DE  +v +
  AJA92639.1 439 QlleassidahakmkyekilqiekttsgfnqdeflLKKKDLIQNRDRL-RqidqefgatsnrIENAEQQL-ERNRIILDELHNVRK 522
                 044444444444455555555555555555555553333333222222.234444445555433566777.788899999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2457  (0.137041); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 1.11u 0.34s 00:00:01.45 Elapsed: 00:00:00.54
# Mc/sec: 3844.14
//
Query:       AJA92640.1  [L=53]
Description: hypothetical protein T478_0457 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 401.03
//
Query:       AJA92641.1  [L=590]
Description: putative adenine deaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-43  148.3   0.0    5.1e-43  146.3   0.0    1.9  2  Adenine_deam_C  Adenine deaminase C-terminal domain
    1.5e-13   50.8   0.0      1e-12   48.0   0.0    2.0  1  Amidohydro_1    Amidohydrolase family
    7.5e-06   25.7   1.2     0.0063   16.0   0.3    2.1  2  Amidohydro_3    Amidohydrolase family
     0.0042   16.3   2.1       0.24   10.6   0.0    3.2  3  DUF2099         Uncharacterized protein conserved in archaea 
  ------ inclusion threshold ------
      0.044   13.0   0.1      0.094   11.9   0.1    1.5  1  IF-2B           Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.28     1e+03      88     104 ..     356     372 ..     351     374 .. 0.85
   2 !  146.3   0.0   1.4e-46   5.1e-43       2     168 ..     414     580 ..     413     581 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                     TSEEEEEETTEEEEEEE CS
  Adenine_deam_C  88 gGGivvvedgkvlaelp 104
                      GG +vv++gk++a++ 
      AJA92641.1 356 LGGKIVVSNGKIVAKIH 372
                     599*********99875 PP

  == domain 2  score: 146.3 bits;  conditional E-value: 1.4e-46
                     SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHHHHHHHHHHTTSEEEEEET CS
  Adenine_deam_C   2 liTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedmalAvnrvielgGGivvved 96 
                     ++Tk+++++l+v++ +v+a+ +kd++k+a ++R  ++++ +vgf+++fg + gA+As+++  ++++iv+G+n++dma A+n++ + +GG++vv+d
      AJA92641.1 414 IVTKKSSADLDVTNSNVTASYDKDIWKVAALDRTFGSKTKTVGFLENFGADIGAFASTWSFHENDMIVIGSNESDMADACNKLTKSQGGLIVVKD 508
                     89********************************************************************************************* PP

                     TEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSSEEEETTSEEETTTT CS
  Adenine_deam_C  97 gkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPelkltdkGlvdvkkf 168
                     gk+la+lp +++G++S++p+++v +++++++++l + g+k+++p +   fl ++ +P++++   G+vdvk++
      AJA92641.1 509 GKTLASLPFQLGGILSTDPIDKVTKNFTKINDVLVDSGCKFKKPHLMPLFLPFLALPDIRILYSGIVDVKSR 580
                     *******************************99999*********************************986 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.0   2.9e-16     1e-12       2     344 .]      77     361 ..      76     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.9e-16
                   EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHH CS
  Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsldrgsaetskasr 98 
                   v+P ++D H+H+            +++p e+++  l +g++ ++ + + +v  +g+    g++  l+++e+lp+ +   ++++ +  +++++ k++ 
    AJA92641.1  77 VCPSFVDPHIHID----------HFVTPAEFVKKSLLHGVTSLFPDSIDIVSVCGYR---GFKEFLRQTENLPMRFFHTIPGGLPVDRKFSHGKTLS 160
                   79**********4..........3449*****************************6...************9999999998888766666555554 PP

                   HHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEE CS
  Amidohydro_1  99 eklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHa..letkgevedaeaafgetiehgthlevaeslglldeiklil 192
                    k +++a   i  + ++vv   ++  +  ++  d    + lk  ++ +  +  H+  ++ k+ ++++  ++ + +e   +  v+e           l
    AJA92641.1 161 IKEEKQA---I--DLRSVVGlGEVFSWTKVTKRDPKTIKSLKQMHENNCIINGHTagASGKKLNSYIASGIFSCHEPINYDQVLER----------L 242
                   4444443...2..33344443333333333333334445677899**********9999999999999999988888777777777..........* PP

                   HCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSC....EEEEEECT........TSSCCGGHHHHHHHHHHHHHHCCTTTTH CS
  Amidohydro_1 193 ahgvhltpteaellkerlkeagvahcpfsnsilrsgrealrkaldeGvk....vglgtDga........asgnslnlleelrlalklqrgllyedee 277
                     g++++                      + ++r ++  + +++ + ++     ++++Dg+        ++++ +     +r  +           +
    AJA92641.1 243 RLGMWVMIR--------------------EGSIRRDLKEIVPLVLSKKIynnrLMFCSDGVdpfdisniGHIDHC-----VRESI-----------K 303
                   *******77....................455778888888888884445888******9988776666666666.....78888...........9 PP

                   CHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
  Amidohydro_1 278 gglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                    g+ + +a+++a+ n  +++++ ++ G i +Gk AD+ ++          + k+ ++ kvi++Gk+v
    AJA92641.1 304 LGMNPIDAISIASRNCFDYYKMGSDFGGIGPGKVADILIL---------DDYKKIKINKVILGGKIV 361
                   99**************************************.........666677777777777776 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   1.8e-06    0.0063       1      25 [.      68      92 ..      68     113 .. 0.80
   2 !    8.5   0.0   0.00035       1.3     430     473 .]     328     362 ..     306     369 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
  Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                  +v D k+++v P FvD+H+H++   
    AJA92641.1 68 KVLDVKNKHVCPSFVDPHIHIDHFV 92
                  689*****************88765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00035
  Amidohydro_3 430 rkGtLevGadADlvvldadpldvdppelaearvrltvvdGrvvy 473
                     G++++G+ AD+ +ld d  +++        + +++ +G++v+
    AJA92641.1 328 DFGGIGPGKVADILILD-DYKKIK--------INKVILGGKIVV 362
                   449*************8.555555........556666666664 PP

>> DUF2099  Uncharacterized protein conserved in archaea (DUF2099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.027        97     166     209 ..     183     222 ..     153     229 .. 0.79
   2 ?    0.9   0.4     0.058   2.1e+02       9      58 ..     358     406 ..     351     431 .. 0.72
   3 !   10.6   0.0   6.6e-05      0.24     100     144 ..     501     545 ..     469     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.027
     DUF2099 166 iavtvaeaedakklrelekeegvkilifavhttgiskeeaeelv 209
                   vt  +++++k+l+++++    + +i+  ht+g s ++ ++++
  AJA92641.1 183 TKVTKRDPKTIKSLKQMHE----NNCIINGHTAGASGKKLNSYI 222
                 5577777777788887776....8999999*****999887766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.058
     DUF2099   9 arvvvkdgkvv.evgepkikyCPlfkklrgikeitkeaikkniefrikefG 58 
                  ++vv++gk+v ++  pk+ +   +kk+ +i +++ ++ + + ++ ++++ 
  AJA92641.1 358 GKIVVSNGKIVaKIHTPKVPT--WMKKTVKIPKLQPKSFNVTSKNNVETVN 406
                 49******9763688998854..4566888888888777666666666555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.6e-05
     DUF2099 100 aGtvivtnpelvqglggrisGlveTePieevierieeeggivldk 144
                  G ++v++ + + +l  ++ G+++T+Pi++v ++  + + +++d+
  AJA92641.1 501 GGLIVVKDGKTLASLPFQLGGILSTDPIDKVTKNFTKINDVLVDS 545
                 3678899****************************9999888875 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.6e-05     0.094     176     202 ..     350     376 ..     338     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                 TESEEEEEXSEEETTSEEEEETTHHHH CS
       IF-2B 176 evdkvivGAdrilenGaiankiGTssl 202
                 +++kvi+G + +++nG+i++ki T ++
  AJA92641.1 350 KINKVILGGKIVVSNGKIVAKIHTPKV 376
                 79********************88766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3813.80
//
Query:       AJA92642.1  [L=54]
Description: PF06348 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-08   34.9   0.1    1.5e-08   34.7   0.1    1.0  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   8.3e-13   1.5e-08       1      50 [.       1      49 [.       1      52 [. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 8.3e-13
     DUF1059  1 mkefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelveki 50
                m ++ C+D g++C +ei++e e+ v+ + ++H  ++Hg++  p++l + i
  AJA92642.1  1 MAKITCRDYGFECHYEIEGEVEN-VIDEYRKHSTEEHGIEYSPEALTQVI 49
                7789*************887776.**************888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 417.25
//
Query:       AJA92643.1  [L=386]
Description: hydroxymethylglutaryl-CoA reductase, degradative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.9e-104  348.0   7.5   6.7e-104  347.8   7.5    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  347.8   7.5  3.8e-108  6.7e-104       4     367 .]      16     379 ..      13     379 .. 0.94

  Alignments for each domain:
  == domain 1  score: 347.8 bits;  conditional E-value: 3.8e-108
                  HHHHHHHH...S-HHHHHHH..TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHHHHHHHTT-B.EEEE----E CS
  HMG-CoA_red   4 eRrkllee...lteeeleel..keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrgakainesgGvkttvlkdgmt 96 
                  e+++++ +   l+++el++l  ++++ld e a+kmiEn iG+++lPlG+a++++in+ +ylvPm++eE+s++A+as++ak+++ +gG+ t+ ++ ++ 
   AJA92643.1  16 EKLDIICNfsdLNDDELNHLknATGGLDFEYANKMIENAIGTFSLPLGIATNFKINNVDYLVPMVIEEPSVIAAASKAAKIAKLHGGF-TAKVDGNIS 112
                  56666644444999999**95555999*************************************************************.9999999** PP

                  EEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-...SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEE CS
  HMG-CoA_red  97 raqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla...grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeel 187
                  ++q+++l +v+ ++e  + i +++++++elan+ ++t  + g g+k++++  ++   +++++++l +d+gDAmGaN++n+++e +a+lie+ +g+++l
   AJA92643.1 113 IGQIQVL-DVD-IQESISTInSNSDQIIELANSSSKTlpKLGKGAKEVKCkEIKtpsSSMLIVELMIDVGDAMGANVTNTMCETVAPLIEKLTGGKTL 208
                  *******.555.555555565*****************************999988888*************************************** PP

                  EEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT. CS
  HMG-CoA_red 188 lsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa. 284
                  l+ilsN++t+++++a+++++++++        ge+vv++++ a ++a  d++ra  +t+nkG+       +Ng  +v+ AtGqD +a+e+++ha+a+ 
   AJA92643.1 209 LRILSNYSTKRMVTATATFDKDAV-------GGEQVVNDMISAFDFADNDVYRA--VTHNKGV-------MNGAISVANATGQDSRAIEAAAHAYASh 290
                  ******************999888.......9**********************..*******.......**************************** PP

                  ......SEEE...TTTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
  HMG-CoA_red 285 ......leev...edgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                        l+++   +dg+l+g+ ++P l VG+vGG+t+ +p a+l+ k+l++k+ +   eL+ iia++gLAq+++a+rALa+eg+qkgHmklh+
   AJA92643.1 291 tgryrsLTQWskdNDGHLVGKFEIP-LSVGIVGGVTNNHPIAKLCtKILNLKNVQ---ELSCIIASTGLAQNFAAMRALATEGIQKGHMKLHA 379
                  ******99999766777********.***************************99...*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2908.49
//
Query:       AJA92644.1  [L=519]
Description: GDSL-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-06   26.4   0.2    1.3e-05   25.3   0.2    1.6  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase
    9.4e-06   26.1   0.0    1.5e-05   25.5   0.0    1.4  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family


Domain annotation for each model (and alignments):
>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   1.4e-09   1.3e-05      34     200 .]     139     298 ..      83     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.4e-09
                  GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCTTSEEEEE--CTCC-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCH. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
  Lipase_GDSL  34 aldrianignkgasdnelqqllnkyplkseqlkalhpdlviislGtNDsnlgkkstdaakkeaeeyiknlreaikelkeegapkaivvlvsppglgp. 130
                  +   i n+g  ga+++ + +ll      + +  +l p +vi++ G ND+        +a+ ++e + kn ++  k +  ++ ++ +v+++ p+  ++ 
   AJA92644.1 139 YPIEIINAGVQGADSFTELNLL------KTKITNLSPNMVIVYDGWNDL--------RAQHSVETISKNWESICK-IGLQN-NFDVVIMLQPIAGFGn 220
                  4446788899999999999999......88999****************........*****************9.88777.7888888888888888 PP

                  ..........CTCCCCHCCHHHHHHHHHHHHHHHHHHHHHCTEEEECHHHHHHHTHCCGCHCHTSSSB-HHHHHHHHHHH CS
                  ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Lipase_GDSL 131 ..........qeekdakklgekgnefvgeynqrlndlaekdgfavvDlydelqglsgieqlkaDglHpsekgyeklaell 200
                             e  +++++  ++n + ++ n   n ++  +   v Dl +++  +   + +++D+ H s+kg+ ++++++
   AJA92644.1 221 kpltnqelkyVETGTNYNEFPLINSLNEYENYAQNLVLLSSCTHVSDLRNIFDTN--SDAIYWDQGHVSDKGNNIISKAI 298
                  99998888887777777777777777777777666666699999***********..789999************99986 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-09   1.5e-05       2     156 ..     107     274 ..     106     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-09
                    EESHHHHTCTTBCCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H....HHHHHHHHCTGGG-TSEEEEE--CCCCCTT--HHHHHHH..HHH CS
  Lipase_GDSL_2   2 lGDSiTaGygadgggrsypaylarllaarl...gldvvnnlgvsGatt..allrllerlrdllrlkpdlvtiliGtNDlgrgvpaaaaaandnlee 92 
                    lG S + G ga++ + + p+yl++ +  +    + + +n +gv Ga +   l  l  +    + l+p+ v++  G+NDl ++++++++ +n   e+
     AJA92644.1 107 LGGSTMFGHGATSDQTTIPGYLEKIFLTSEekyPIEIIN-AGVQGADSftELNLLKTK---ITNLSPNMVIVYDGWNDLRAQHSVETISKN--WES 196
                    8***********************997777555777777.******997444444444...559**************************9..999 PP

                    HHHHHCCC...GEEE..............CEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT-EEE-HHHHHHH CS
  Lipase_GDSL_2  93 lidalraaapgaril..............vlgplpptpeaaadarelnaviaaynealrevaaeegvpfvDlhdalad 156
                    + +   + + ++ i+              +   ++ t+ ++++ +  n+ +++ n a++ v      ++ Dl++++  
     AJA92644.1 197 ICKIGLQNNFDVVIMlqpiagfgnkpltnQELKYVETGTNYNEFPLINSLNEYENYAQNLVLLSSCTHVSDLRNIFDT 274
                    999777777888777666666655555554444444444445555455555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3986.99
//
Query:       AJA92645.1  [L=374]
Description: hypothetical protein T478_1340 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.002   17.6   0.0     0.0033   16.8   0.0    1.4  1  Glyco_hydro_42   Beta-galactosidase
  ------ inclusion threshold ------
      0.073   13.1   0.0       0.18   11.9   0.0    1.6  1  Phage_int_SAM_6  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.7e-07    0.0033      15      77 ..      64     131 ..      55     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-07
                     HHHHHHHHT--EEEE-TT-HHHH-SBTTB---HHHHHHHHHHHCTT-EEEEE-S......TTS--HHHH CS
  Glyco_hydro_42  15 dirlmkeagvnvvrlgefaWaklePeegkydFewLdevldllekagikviLatp......taapPaWlv 77 
                      +++  + gv  ++  ++ W+ lePe+g++d+ + d +++l ek ++k  L  +       +  P W+ 
      AJA92645.1  64 SYKIASTSGVGRTN-LYVYWSDLEPEKGNFDWRVTDIMMKLNEKYNLKTTLFFSvinadrLGPFPLWMG 131
                     55555566666666.4788****************************9998766665555566677765 PP

>> Phage_int_SAM_6  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      20      72 ..      29      80 ..      18      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
  Phage_int_SAM_6 20 skltsLsnkqvkdkealakviqelkkgvksieelekivkeaRniGliGintya 72
                       ++s sn+ + ++e+++ vi++++   ksi++le+  k a   G+   n y+
       AJA92645.1 29 VETNSFSNQPISQNEKISLVINTINPP-KSIDDLEESYKIASTSGVGRTNLYV 80
                     56899*******************988.9**************9999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2926.88
//
Query:       AJA92646.1  [L=368]
Description: thiolase, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-12   47.9   0.3    3.3e-11   43.1   0.3    2.3  1  Thiolase_N       Thiolase, N-terminal domain
    1.5e-12   47.2   0.1    2.6e-12   46.5   0.1    1.4  1  Thiolase_C       Thiolase, C-terminal domain
      0.002   17.7   0.5     0.0048   16.5   0.0    1.9  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
       0.03   14.3   1.4        3.5    7.7   0.0    3.1  3  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
      0.043   13.8   0.1       0.23   11.5   0.1    2.0  2  RT_RNaseH_2      RNase H-like domain found in reverse transcr


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.3   9.1e-15   3.3e-11       1     188 [.       4     166 ..       4     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 9.1e-15
                 EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCT.TSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHH CS
  Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekag.vdpeevdevivGnvlqa.gegqniarqaalkagipeevpavtvnkvcsSglkavalaaq 97 
                 v+iv++  t++ k      d  +e+Ll e  k++++++   +p++v+ v v++  ++   g++++      +gi ++ +++ ++++csSg +a++ +  
  AJA92646.1   4 VAIVGTGQTKFSK-----DDGDVEKLLFESTKNCIQSVRnCEPKDVEGVLVSTNNNSkYLGAILSET----MGI-QPKISHSIEHLCSSGTNALISGYA 92 
                 78999******99.....99999**************988**********99887776778776665....566.666699****************** PP

                 HHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHH CS
  Thiolase_N  98 siaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaq 188
                  i +g ad++++ GvEs +n  +  + d         +  + +              + + ++ + +k++i+ ee++ + +k+h++a +++
  AJA92646.1  93 YIFSGLADIILISGVESATNPGQILEWDK-----SRGSFEHPIY------------WASMLTKSYKRKFQITEEELAIVSAKNHKQAMDNP 166
                 *****************999877776332.....2222233333............33577778999999999999999999999999886 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   7.2e-16   2.6e-12      26     109 ..     247     346 ..     228     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7.2e-16
                 HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G................GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCTTSEEEEE CS
  Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl................ekvNvnGGaialGHPlGasGaRivvtllselkkeggklgvaa 108
                  a+k + k a +  +d+++ E+++AF++  L+++ +l++ +                + +N +GG i  GHPlGa+G  +++ ++++l+ + +k  ++ 
  AJA92646.1 247 IAAKTAYKMAKIGPNDVNVAEVHDAFSVCELMAISELGITAsdksgefvrdlfntenRMINPRGGLIGAGHPLGATGISQTIEIATQLQGKSEKRQISN 345
                 5888999999******************************99**************999*****************************98877655554 PP

                 E CS
  Thiolase_C 109 l 109
                 l
  AJA92646.1 346 L 346
                 4 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-06    0.0048     150     218 ..      54     123 ..       7     130 .. 0.83
   2 ?   -3.7   0.1         2     7e+03     130     159 ..     333     360 ..     320     363 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                    STTHHHHHHHHHHT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
  ketoacyl-synt 150 lanviagrisyalglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                    ++ ++ +++s ++g++   s++++  CsS+  a+   +  + sg ad++l  Gve +++p+++  +++ +
     AJA92646.1  54 NSKYLGAILSETMGIQPkISHSIEHLCSSGTNALISGYAYIFSGLADIILISGVESATNPGQILEWDKSR 123
                    56667777777777775248899999****99999999*************************9999987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2
                    HHHHHHTTGGGSCTTHHHHHSTTHHHHHHH CS
  ketoacyl-synt 130 aaldedgsevkaspkavgavlanviagris 159
                    +++  + +++++s   +g  ++n+ a+  s
     AJA92646.1 333 QLQG-KSEKRQISNLKTGL-IHNMSAAGTS 360
                    3333.33356666656665.7777776555 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00097       3.5      23      51 ..     242     270 ..     222     274 .. 0.78
   2 ?    4.0   0.0     0.014        49      88     108 ..     316     336 ..     314     346 .. 0.89
   3 ?   -0.2   0.1      0.27   9.8e+02      77     102 ..     340     365 ..     331     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00097
                      HHHHHHHHHHHHHHHT--GGGEEEEE-SS CS
  Ketoacyl-synt_C  23 geaqaraiekalaeagvdpedvdyveahg 51 
                       e+ + a + a+++a++ p+dv++ e h+
       AJA92646.1 242 IESTRIAAKTAYKMAKIGPNDVNVAEVHD 270
                      455566799*******************8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                      -B-GGGHHHHHHHHHHHHHHH CS
  Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalkh 108
                      GH ++A G+ ++i ++ +l+ 
       AJA92646.1 316 GHPLGATGISQTIEIATQLQG 336
                      9**************999985 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.27
                      TSEEE-THHHH-B-GGGHHHHHHHHH CS
  Ketoacyl-synt_C  77 plavgSvKsniGHleaAaGvaelikv 102
                      +  ++  K+ + H  +AaG+ + + v
       AJA92646.1 340 KRQISNLKTGLIHNMSAAGTSSSVVV 365
                      45788999999999999999988766 PP

>> RT_RNaseH_2  RNase H-like domain found in reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.49   1.8e+03       9      49 ..      26      65 ..      20      77 .. 0.67
   2 ?   11.5   0.1   6.5e-05      0.23      43      87 ..     114     158 ..     108     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
  RT_RNaseH_2  9 feklkealtsapvLahpdpdkpfiletDaSdtgigavLsqe 49
                 fe+ k++++s    ++ d  + + ++t+  ++ +ga+Ls +
   AJA92646.1 26 FESTKNCIQSVRNCEPKD-VEGVLVSTNNNSKYLGAILSET 65
                 555666666555444444.3456677778888889988865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
  RT_RNaseH_2  43 gavLsqedddgk.erpiafaSrklskaernysttekellAivwalk 87 
                  g +L  +++ g+ e+pi+ aS  +++ +r+ ++te e lAiv a +
   AJA92646.1 114 GQILEWDKSRGSfEHPIYWASMLTKSYKRKFQITEEE-LAIVSAKN 158
                  66777777888889*********************99.78988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2582.38
//
Query:       AJA92647.1  [L=379]
Description: 3-hydroxybutyryl-CoA dehydrogenase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-66  222.4   2.3    3.8e-66  222.4   2.3    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    2.8e-37  127.2   0.2    8.8e-26   90.4   0.0    3.3  3  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    2.9e-06   27.5   0.1      7e-06   26.3   0.1    1.7  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    3.1e-06   27.2   1.2      7e-06   26.1   1.2    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0007   20.1   0.5     0.0033   18.0   0.5    2.2  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0058   16.6   0.1      0.017   15.1   0.1    1.8  1  DUF1803         Domain of unknown function (DUF1803)
  ------ inclusion threshold ------
      0.011   16.1   0.5      0.021   15.2   0.5    1.4  1  DUF4078         Domain of unknown function (DUF4078)
      0.045   13.3   0.2      0.085   12.4   0.2    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.12   12.8   0.6       0.32   11.4   0.6    1.7  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
       0.13   11.8   0.0       0.28   10.7   0.0    1.5  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
       0.14   11.5   0.7       0.26   10.5   0.2    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.14   11.4   0.1       0.24   10.6   0.1    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
        1.2    8.7   4.5         54    3.3   4.5    2.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.4   2.3   2.8e-69   3.8e-66       1     179 [.       5     185 ..       5     186 .. 0.99
   2 ?   -1.7   0.0       1.7   2.3e+03      87     121 ..     294     327 ..     244     333 .. 0.72

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 2.8e-69
                 EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-SEEEE-S-SSHHHHHHHHH CS
     3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dadlviEavvEnlelKrkvfa 98 
                 +++v+G+G+mG+gia+v a ag++Vvl di++e+l+ka+eki+ sl+k+v k+k+++ee++ + +ri++  dl+eav da++viE v+E ++lK++v+a
  AJA92647.1   5 NITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEFLDKAMEKIKWSLDKMVTKEKISKEEADGIYSRITPIVDLNEAVkDAEMVIEVVPEIMDLKKQVYA 103
                 69************************************************************************************************* PP

                 HHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHTT-EEEEE.CS CS
     3HCDH_N  99 elekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvatvvelakkigktpvvv.kd 179
                 el+k+akp++i+asnTS+l+i+e+a++++rpe++ig+HFfnPp+lmkLvEv++gekT++e+++ ++e++k+++k++v + kd
  AJA92647.1 104 ELDKAAKPEVIFASNTSTLPITEIANTTSRPEKFIGIHFFNPPQLMKLVEVIPGEKTAQEITELTQEFVKSVNKQAVLCrKD 185
                 *******************************************************************************777 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                 -SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHH CS
     3HCDH_N  87 vEnlelKrkvfaelekiakpdailasnTSslsise 121
                  E+l+ K + ++ +++i+++ a l++n  s +i+e
  AJA92647.1 294 SEELAEKCNPIQLVANILNNAAWLITNGAS-DIEE 327
                 456666666667777777777777777543.4555 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.06        83      42      96 ..      17      69 ..       4      70 .. 0.72
   2 !   90.4   0.0   6.3e-29   8.8e-26       1      97 []     188     283 ..     188     283 .. 0.95
   3 !   29.3   0.0   7.3e-10     1e-06       7      80 ..     306     378 ..     305     379 .] 0.93

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.06
                CHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-.HHHHHHHHTT--BGGGTBSSSB CS
       3HCDH 42 Gpfelldlvgldvakkilevlaeelgerayaps.plleklveagrlgrktgkgfyk 96
                G+ +++ ++g +v+++ ++   +e+ ++a ++    l+k+v ++++++++ +g+y 
  AJA92647.1 17 GIAQVSATAGYNVVLRDIK---QEFLDKAMEKIkWSLDKMVTKEKISKEEADGIYS 69
                7777777777777766555...5555553333304599***************995 PP

  == domain 2  score: 90.4 bits;  conditional E-value: 6.3e-29
                 TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGGGTBSSSBC CS
       3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlgrktgkgfyky 97 
                 GF+ nR+++p++ ea+ l ++ +a+ e+iD+a++ +lG+pmG+fel+d +g+dv +k++  ++ + ++   +p++ +ek++++++lg+k+g+g+yky
  AJA92647.1 188 GFIINRLFIPMVHEACYLQDRTNATLEEIDSAVKFKLGFPMGIFELADFTGMDVIHKATVEMHLRDKKV-INPHKTVEKMFDEKKLGQKSGEGYYKY 283
                 9**********************************************************8888775555.6679**********************9 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 7.3e-10
                 HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHH CS
       3HCDH   7 vlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspllekl 80 
                 ++a +ln+a +l+ +g  ++e+i++a++lglGl+   fe++ ++g+    + l+ laee+ge  y+p plle++
  AJA92647.1 306 LVANILNNAAWLITNGASDIEEIEKACKLGLGLKKPLFETAKEIGIKNIVDELNKLAEEHGEF-YKPDPLLESM 378
                 57899*****************************************999999999****9998.7889999998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   5.1e-09     7e-06       1      95 [.       5     124 ..       5     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.1e-09
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHHHCSEEEE-SSSHHHHH.H CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelvasldvvitmvkagkavd.e 71 
                    +i ++G GvMG+ +a+  + agy+v++ + ++e +++++++                         ++++ +++e+v+++++vi +v++  + + +
     AJA92647.1   5 NITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEFLDKAMEKIkwsldkmvtkekiskeeadgiysrITPIVDLNEAVKDAEMVIEVVPEIMDLKkQ 100
                    6899***********************************99789999******************************************9998625 PP

                    HHHSHCCC--TT-EEEE-S---HH CS
  NAD_binding_2  72 viegllealkkgdilidgstsspe 95 
                    v+ +l +a+k++ i+   +++ p 
     AJA92647.1 101 VYAELDKAAKPEVIFASNTSTLPI 124
                    677788888888888776665544 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   1.2     5e-09     7e-06       1     141 [.       5     166 ..       5     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 5e-09
                     -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H............HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH.. CS
  NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree............elieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa.. 81 
                     +i+vlG+G  G  +A+v a +g +v+l   ++             l + + +e+  ++  +g  + + ++   dl+ea+k+a++++ vvP  +  
      AJA92647.1   5 NITVLGSGVMGHGIAQVSATAGYNVVLRDIKQefldkamekikwSLDKMVTKEKISKEEADG--IYSRITPIVDLNEAVKDAEMVIEVVPEIMdl 97 
                     59*************************99998899966655543333333344444444444..6789**********************85422 PP

                     HHHHHHHHCCC--TT-EEEE---SE....ET.TTEEHHHHHHHHH-S--.....EEEEESS--HHHHHT CS
  NAD_Gly3P_dh_N  82 lrevlkklkgllkkkailvsliKGi....eegtlkllsevieeelkeek.....vavlsGpslAeEvak 141
                      ++v ++l++  k+++i++s +  +     ++t+ + ++ i  ++ + +     v v+ G   A+E+++
      AJA92647.1  98 KKQVYAELDKAAKPEVIFASNTSTLpiteIANTTSRPEKFIGIHFFNPPqlmklVEVIPGEKTAQEITE 166
                     789999999999999999998888866654467777777777766665567777888888888888865 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5   2.4e-06    0.0033       2      70 ..       6      92 ..       5     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.......................-EEECECHHHHHHH-SEEEE-S- CS
  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.......................vkvtavdneeaaeeadvvvlavk 70
                   i ++G+G mg+++a+  ++ag   +++v   + ++e ++++ e+++                       ++ +  d +ea+++a++v+  v+
     AJA92647.1  6 ITVLGSGVMGHGIAQVSATAG---YNVV-LRDIKQEFLDKAMEKIKwsldkmvtkekiskeeadgiysrITPIV-DLNEAVKDAEMVIEVVP 92
                   89*******************...****.5599************99999999999999999999998666666.99999999999987666 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.2e-05     0.017      26      74 ..      28      80 ..      23     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
     DUF1803 26 dviLRelkkeFadq..kkldrlldelidaglikRenkr..Yklnlpifeieea 74
                +v+LR++k+eF d+  +k+  +ld+++ ++ i++e+    Y+   pi +++ea
  AJA92647.1 28 NVVLRDIKQEFLDKamEKIKWSLDKMVTKEKISKEEADgiYSRITPIVDLNEA 80
                79*********8752279999************99864338888888775544 PP

>> DUF4078  Domain of unknown function (DUF4078)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   1.5e-05     0.021      12      53 ..     258     299 ..     248     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
     DUF4078  12 satppeevhYdaekEvRtkGvgfyaFskDeeeRkkqmeeLee 53 
                 ++++  e+ +d++k   + G g+y++s D+ eR +  eeL+e
  AJA92647.1 258 NPHKTVEKMFDEKKLGQKSGEGYYKYSDDKYERVELSEELAE 299
                 45566788899999999*********************9987 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.2e-05     0.085       2      81 ..       5      88 ..       4     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                    EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT.S-SS--TTHHHHHHHHCHT...TTEEEES-HHHHHHC-SEEE CS
  UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsg.kipiyepgLeelvkkaves...grlsfttdvekaveeadvif 81
                    +i+v+G+G +G   a v a +g +v++ Di +e  dk  ++ k ++     +e + k+ ++   +r++   d+++av++a++++
      AJA92647.1  5 NITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEFLDKAMEKiKWSLDKMVTKEKISKEEADgiySRITPIVDLNEAVKDAEMVI 88
                    8*******************************9988744331333333332222222222211145555566666666666666 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00023      0.32      37      97 ..      51     115 ..      33     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                     -SSTHHCCCCHHGG...BTCCEEES-CHHHHTT-SEEEE-S--.GGGGGS-HHHHHHCCSS-EEE CS
  UDPG_MGDP_dh_C  37 DPkvkeeaveaele...ekgvevvdsleealkgadaivilteh.defkeldlaklkelmkpavvf 97 
                     D +v++e++++e +   + +++ + +l+ea+k+a++++ +++   ++k++ +a+l +  kp+v+f
      AJA92647.1  51 DKMVTKEKISKEEAdgiYSRITPIVDLNEAVKDAEMVIEVVPEiMDLKKQVYAELDKAAKPEVIF 115
                     7788888887766689988999999*************99966489999999***9999999998 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.28       6      53 ..      14      62 ..      10      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                  HHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSH CS
  adh_short_C2  6 IGraiAkalaeeGaevvltdlneea.kkrveelaeelgaevlecDVtde 53
                  +G++iA+  a +G++vvl d+++e  +k++e+++ +l++ v +  +++e
    AJA92647.1 14 MGHGIAQVSATAGYNVVLRDIKQEFlDKAMEKIKWSLDKMVTKEKISKE 62
                  799**********************999999999888877766655555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00019      0.26      30      78 ..       5      63 ..       2     102 .. 0.71
   2 ?   -2.8   0.0       2.3   3.2e+03      65     124 ..     162     181 ..     154     188 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                 EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE..........H CS
  AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev..........l 78
                 +++v+G Gv G   +++++  g +V++ D++++ l +  + ++ + ++            
   AJA92647.1  5 NITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEFLDKAMEkIKWS-LDKmvtkekiskeE 63
                 689****************************99887765543333.33312224444440 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                  HHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEE CS
  AlaDh_PNT_C  65 eqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVi 124
                  +++ +l +                                        e vks ++++V+
   AJA92647.1 162 QEITELTQ----------------------------------------EFVKSVNKQAVL 181
                  33333333........................................445555544443 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00017      0.24     143     198 ..       4      59 ..       1     116 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00017
                  SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGv 198
                  k+i+v G+G+ G  +A++ a +g++v+l +  +++l +  ++++  l + ++ke++
   AJA92647.1   4 KNITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEFLDKAMEKIKWSLDKMVTKEKI 59 
                  67889999999999999999999999998888888855556666666666666554 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   4.5     0.039        54       5      70 ..       4      93 ..       1     118 [. 0.57

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.039
                S-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-...................HHHHHHHHTT-E.....EEEHHHHHHT-SEEEE-S-H CS
        IlvN  5 kkiaviGyGsqGhaqalnlrdsgldvvvglregs...................ksvkkAkeegfe.....vltvaeavkkadvvmiliPD 70
                k+i+v+G G  Gh  a+    +g +vv+   +++                   ++++k +++g+      +++++eavk+a++v+ ++P+
  AJA92647.1  4 KNITVLGSGVMGHGIAQVSATAGYNVVLRDIKQEfldkamekikwsldkmvtkEKISKEEADGIYsritpIVDLNEAVKDAEMVIEVVPE 93
                778888888888888888888888887766665544444444444444444332333333344321111145666777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2504.13
//
Query:       AJA92648.1  [L=131]
Description: hypothetical protein T478_1402 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.24   11.8   4.1        1.9    8.9   4.1    2.4  1  Lar_restr_allev  Restriction alleviation protein Lar
        2.4    8.7  10.5       0.73   10.4   4.8    2.2  2  zf-CHY           CHY zinc finger


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.1   0.00021       1.9       6      41 ..      28     108 ..       1     128 [. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00021
  Lar_restr_allev   6 CPfCggravlersqrvvaeigq.............................................cvyCadCga..stpwf 41 
                      C fC + + +++++++  +  q                                             + +C+dCg   +++++
       AJA92648.1  28 CGFCSKNGLKHTDELWEIH--QlplkqirrgekisyiqigfgpktparvekwpmhnpdwhqvdfvpiYLHCKDCGLalGGDEV 108
                      7788888877777777654..35699999999999999*************************************96554544 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.8   8.1e-05      0.73      21      50 ..       3      34 ..       1      41 [. 0.71
   2 ?    1.7   0.3     0.041   3.6e+02      21      47 ..      95     121 ..      83     130 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.1e-05
      zf-CHY 21 aCreCHeeledhelerl..evkevlcllCete 50
                 C+ CH+++e+h+ + +  ++++ +c +C+++
  AJA92648.1  3 MCQICHKDSEEHSQKLWesHQQKQICGFCSKN 34
                6*****88777755444226667789999986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.041
      zf-CHY  21 aCreCHeeledhelerlevkevlcllC 47 
                 +C+ C  +l  +e++ ++  ++ cl C
  AJA92648.1  95 HCKDCGLALGGDEVDYADLLSCFCLDC 121
                 466665555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 943.42
//
Query:       AJA92649.1  [L=210]
Description: 2-phospho-L-lactate guanylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.0   5.5    1.4e-25   89.8   5.5    1.0  1  CofC          Guanylyl transferase CofC like
    1.5e-07   31.9   0.0    1.9e-07   31.6   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0011   18.9   0.7     0.0017   18.3   0.7    1.3  1  CTP_transf_3  Cytidylyltransferase
  ------ inclusion threshold ------
      0.044   13.7   1.9      0.081   12.8   1.9    1.4  1  GatB_Yqey     GatB domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   5.5   3.1e-29   1.4e-25       2     185 ..       4     193 ..       3     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3.1e-29
        CofC   2 kviiPvsainsaktrlseilseeerkellkamlldvidalkr...ld.vlvvsedeevleyaldelgvevvkekekdlntaveka...feeieekevii 93 
                  viiPv+++++ ktrl   lsee  + l +++l +vi++++    +d  +vv+++e+v +   +    ++  e+e  +n+av+ a   +++ e+ + i+
  AJA92649.1   4 SVIIPVKTFQKSKTRL--HLSEEKTNSLCRLLLEEVIKTIHDsklIDkTIVVTNEEQVTDIIEKYDCQKIQDEHETSVNDAVKLAekyLIDNEFTHSIV 100
                 79*************9..5*******************99765678999999********99867777777777********9888778899******* PP

        CofC  94 ipsdiPlikkedvkdllelekradvviaParg.GGtnllllr.ksalevkyedfsflkhleearkrglkvkiydsfylsvdinteedlgeillh 185
                 +p d+P+ + ed+++ll+ +    v++ P+r   Gtn ll    +++  +y+++s+   +e a+k ++k++i   + l +di+++edl   ++ 
  AJA92649.1 101 LPLDVPFFDSEDLEKLLKFSVDNSVIVVPSRHfDGTNALLRSpINSMTPRYDEGSYSFQIESAQKNDVKISIGLIYRLMLDIDNSEDLE-FVIK 193
                 ******************************9857****99886799*****************************************95.4443 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.3e-11   1.9e-07      25     126 ..      32     134 ..      11     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.3e-11
                   CHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHH..H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
  NTP_transf_3  25 pllervldalraag.vdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalra..aadadavlvlacDmPlltpelverllaaaaasgadv 118
                    lle v++++++++ +d+ +vv+++e+v++ +++++++ ++de +++    +++ a +    ++ ++ +vl+ D+P++++e +e+ll+    +++ +
    AJA92649.1  32 LLLEEVIKTIHDSKlIDKTIVVTNEEQVTDIIEKYDCQKIQDE-HETSVNDAVKLAEKYliDNEFTHSIVLPLDVPFFDSEDLEKLLKFS-VDNSVI 126
                   79***********867**************************8.5899999999999996444999**********************75.688889 PP

                   EEEESSSE CS
  NTP_transf_3 119 vvptyege 126
                   vvp++  +
    AJA92649.1 127 VVPSRHFD 134
                   99987655 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   3.7e-07    0.0017      26     112 ..      33     117 ..      31     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                   HHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TTS...EEEEE-TT-TT--HHHHHHHH CS
  CTP_transf_3  26 liayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmsenee...iivnlqGdnPllqeevikkai 112
                   l++ v++ + +sk+++k+iv T +e++ ++++++   +  ++ ++e+  +  ++  +++l++ ne    i++ l  d P+ ++e+++k++
    AJA92649.1  33 LLEEVIKTIHDSKLIDKTIVVTNEEQVTDIIEKY--DCQKIQDEHETSVNDAVKLAEKYLID-NEFthsIVLPL--DVPFFDSEDLEKLL 117
                   7899******************************..67778888888888888999999999.44455455555..69999999998876 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   1.8e-05     0.081      36      93 ..      17      76 ..       7      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                TCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH..HHTXXHHHHHHHCTXXXXXXSSX CS
   GatB_Yqey 36 eelkltpeqlaellkliaegkIskkiakevleell..eegkspeeiieekgLkqisdeee 93
                ++l l++e+ + l +l+ e+ I   +  +++++ +  ++++++ +iie+++ ++i+de+e
  AJA92649.1 17 TRLHLSEEKTNSLCRLLLEEVIKTIHDSKLIDKTIvvTNEEQVTDIIEKYDCQKIQDEHE 76
                55678999999************9999999977666788******************776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1264  (0.0705003); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1582.18
//
Query:       AJA92650.1  [L=271]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-98  327.0   1.4      9e-98  326.8   1.4    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    0.00022   20.8   3.1      0.016   14.7   0.3    1.8  2  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.8   1.4    1e-101     9e-98       3     259 .]       4     252 ..       2     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 326.8 bits;  conditional E-value: 1e-101
  Pantoate_transf   3 tvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvvadlPfgsyeaskeqal 96 
                      tv+d+ +mk++ eki++lT yd t+A+l+d++  dviLVGDs+gmv+lgy++t +vt+++mi++t aV+++++++l+vadlP+ sy +++++a+
       AJA92650.1   4 TVNDIIQMKSR-EKITVLTGYDSTMATLCDKV--DVILVGDSAGMVMLGYDDTRDVTMDDMIRFTTAVKNAKTDSLIVADLPINSY-ENEDSAI 93 
                      899******87.******************97..*************************************99*************.8999*** PP

  Pantoate_transf  97 enAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaeklledakaleeaGafalvlEavpaelake 190
                      +n+ rl+++ ga+avKlegg+e+ +++ka+v++gipVmgH+Gl Pq+++    y vq+k++++a +lleda+ le+aG+f++v+E+v++++ak 
       AJA92650.1  94 TNSKRLVQA-GAHAVKLEGGKEIEKIIKAVVDSGIPVMGHLGLLPQTAE---KYSVQAKKSSDAVNLLEDARILEKAGVFSIVFEMVTRDVAKI 183
                      ********9.************************************776...58**************************************** PP

  Pantoate_transf 191 iteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieeavkaYaeevkegsFPae 259
                      ite++++ptIGIG+G++cdGqvlv+hD+lg++ek kpkf+k+y++l+e+i++a+++Y+++vke++FP+e
       AJA92650.1 184 ITESVKVPTIGIGSGKNCDGQVLVVHDMLGMFEKIKPKFAKRYLNLSEDIRNAINSYVKDVKEEKFPEE 252
                      *******************************************************************85 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.8e-06     0.016      30     107 ..      34     112 ..       9     121 .. 0.78
   2 !   13.9   0.2   3.1e-06     0.027      44     179 ..      48     113 ..      43     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-06
  PEP_mutase  30 fkalatsSlavaaslGvpDgeelpleellaavraiaevv.slPlivDle.dGygespeevaetvrrliaaGvvgvniEDk 107
                 ++ + ++  a   +lG++D+ +++++ +++ + a+ ++  +  + +Dl  + y++  ++   + +rl++aG+ +v +E  
  AJA92650.1  34 VDVILVGDSAGMVMLGYDDTRDVTMDDMIRFTTAVKNAKtDSLIVADLPiNSYEN-EDSAITNSKRLVQAGAHAVKLEGG 112
                 456666666667899***************9999998753777889*97478877.77888899*************976 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.1e-06
  PEP_mutase  44 lGvpDgeelpleellaavraiaevv.slPlivDle.dGygespeevaetvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraaaeeagfvi 140
                 lG++D+ +++++ +++ + a+ ++  +  + +Dl  + y++  ++   + +rl++aG+ +v +E                                   
  AJA92650.1  48 LGYDDTRDVTMDDMIRFTTAVKNAKtDSLIVADLPiNSYEN-EDSAITNSKRLVQAGAHAVKLEGG--------------------------------- 112
                 67777777777777777777766542555566775356655.555566667777777777777755................................. PP

  PEP_mutase 141 nARtdalllsagagleeaieRaraYaeAGAdgvfvpglq 179
                                                       +
  AJA92650.1 113 --------------------------------------K 113
                 ......................................3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2024.12
//
Query:       AJA92651.1  [L=116]
Description: hypothetical protein T478_1265 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 838.17
//
Query:       AJA92652.1  [L=368]
Description: succinate-CoA ligase, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-46  158.6   0.6    2.9e-46  157.6   0.6    1.5  1  ATP-grasp_2  ATP-grasp domain
    6.4e-17   61.8   0.5    1.7e-16   60.4   0.5    1.7  1  Ligase_CoA   CoA-ligase
    5.8e-15   55.3   0.1    1.6e-14   53.9   0.1    1.7  2  ATP-grasp_5  ATP-grasp domain
    1.2e-06   28.1   0.0    2.3e-06   27.3   0.0    1.5  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
     0.0003   20.4   0.0    0.00083   19.0   0.0    1.7  1  ATP-grasp    ATP-grasp domain
  ------ inclusion threshold ------
      0.087   12.2   0.5       0.77    9.1   0.1    2.2  2  DUF4152      Protein of unknown function (DUF4152)


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6   0.6   9.7e-50   2.9e-46       2     201 ..       3     188 ..       2     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 9.7e-50
                  E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE CS
  ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekvlvee 99 
                  l Eyqake+++++g+++p +   ++ e+ ++ ak+lg    v+K Qv +GGRGKagG++ ++s +e++ +  +ll+++++       G+k  ++l+e+
   AJA92652.1   3 LLEYQAKELFKEFGIRTPPSISSKDIEKGRKDAKELGYPF-VIKVQVPVGGRGKAGGIQKCSSDDEFELKYPQLLNMSIK-------GEKTRAILLEK 92 
                  89***********************************998.***************************************.......*********** PP

                  ---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEE CS
  ATP-grasp_2 100 aldikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqareiakklglekelvkkaakiikklyklfveldatlvEi 197
                  + di+kElYls+ l r+++++++iaSseGGv+iE v +++  ++         +++ ++a+e+a+++gl++++ ++++++++kl kl +e++a+l+Ei
   AJA92652.1  93 MADIEKELYLSLFLNRSKRCYTIIASSEGGVEIESVKNQTIREVGL------GDVDAQTAKEVANEIGLKDSQEEQFVEMLQKLSKLTIEKEAELAEI 184
                  ************************************9887555544......45567789************************************** PP

                  EEEE CS
  ATP-grasp_2 198 NPLv 201
                  NPL+
   AJA92652.1 185 NPLA 188
                  ***8 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.5   5.7e-20   1.7e-16       3     146 ..     247     358 ..     245     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 5.7e-20
                 SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHHHH CS
  Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkaike 101
                 nG++L + + dl++++              g+++++++d+G++a+t          ++++eal+ + ++++vk+il+++ +G+++++++a+++++a+++
  AJA92652.1 247 NGAGLVMSTFDLVTDN--------------GGKPATFLDVGGGATT----------ESVYEALTLISKMSRVKGILVNLYGGIVKTTTVAEAFIQAYNN 321
                 89**************..............***************6..........******************************************* PP

                 TT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHH CS
  Ligase_CoA 102 akaegrelpvvarvaGteadpqelseqakaleeagveiasskaqa 146
                       +lpv ar++Gte d     +++++l++ + ++ +s ++a
  AJA92652.1 322 NL---IDLPVFARLMGTESD-----KAKEMLKDTKTKMFDSIEEA 358
                 *9...***************.....88888888888877776665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   5.5e-18   1.6e-14      10     220 ..       3     202 ..       1     203 [. 0.90
   2 ?   -2.9   0.0       1.3   3.8e+03     145     164 ..     331     350 ..     324     353 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 5.5e-18
  ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspeariegvlVqemak 107
                  L e++akel++ +gi++++++  ++ e+  + a+e+gyp v+K+++p +  + ++gG++   ++++e + ++ ++l+   +   +++ + +l+++ma+
   AJA92652.1   3 LLEYQAKELFKEFGIRTPPSISSKDIEKGRKDAKELGYPFVIKVQVP-VGGRGKAGGIQK-CSSDDEFELKYPQLLNMSIK---GEKTRAILLEKMAD 95 
                  889*******************************************9.899********9.9**************98655...8899*********9 PP

  ATP-grasp_5 108 r.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldin 204
                    ++  l + +++ +    +i+  +GG+++e +k+ +++ + l + +a+ +      +++++++  +  ++ ++++e+l++ls+L ++ +e +  +in
   AJA92652.1  96 IeKELYLSLFLNRSKRCYTIIASSEGGVEIESVKNQTIREVGLGDVDAQTA------KEVANEIGLK-DSQEEQFVEMLQKLSKLTIE-KEAELAEIN 185
                  555556666677889999*******************99999999999865......4455555555.77889***************.999****** PP

  ATP-grasp_5 205 Pllveeeg.vvalDari 220
                  Pl + ++g ++alD+++
   AJA92652.1 186 PLAILKDGtLMALDGKV 202
                  ******999*****987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
  ATP-grasp_5 145 alpplnstlareliertkas 164
                  +l+  +s +a+e+++ tk++
   AJA92652.1 331 RLMGTESDKAKEMLKDTKTK 350
                  67778899999999999875 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   7.7e-10   2.3e-06       4      97 ..       7     102 ..       5     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7.7e-10
                  HHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTE....EEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEE CS
  CPSase_L_D2   4 sakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGm....rvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEv 97 
                  +ake+ k++++++ ps +   +++e+  + ake+gyP +ik  + +GG+G     + +++++e++  + + l+++     ++ +l+ek+ +  ke+ +
   AJA92652.1   7 QAKELFKEFGIRTPPSISS--KDIEKGRKDAKELGYPFVIKVQVPVGGRGKaggiQKCSSDDEFELKYPQLLNMSIKGEKTRAILLEKMADIEKELYL 102
                  68999**************..***************************98533224588999999999999999998889999999999888777655 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.8e-07   0.00083       2     129 ..      13     153 ..      12     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.8e-07
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC............GTTCEEEEE----SEEE..EEEEEEET CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal............keekvivEefvpfekEl..svlvvrsa 86 
                 ++ g+++p+ +  ++ e+ ++ a+elg+p+v+K  ++   G+G+    ++ + ++ +e              k + +++E++++ ekEl  s+   rs+
  AJA92652.1  13 KEFGIRTPPSISSKDIEKGRKDAKELGYPFVIK-VQVPVGGRGKAGGIQKCSSDDEFELKypqllnmsikgeKTRAILLEKMADIEKELylSLFLNRSK 110
                 7899*****************************.8888888887643333333333333334557888999899999***********64488899999 PP

                 TC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHH CS
   ATP-grasp  87 eGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakki 129
                 +  t +    + v+ + + ++ +    + + ++++a+e+a++i
  AJA92652.1 111 RCYTIIASSEGGVEIESVKNQTIREVGLGDVDAQTAKEVANEI 153
                 9988888888888888888888888888888888888888766 PP

>> DUF4152  Protein of unknown function (DUF4152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00026      0.77      57     116 ..      95     153 ..      70     184 .. 0.84
   2 ?    1.0   0.0     0.078   2.3e+02     135     208 ..     289     363 ..     273     367 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00026
                 HHHHHHHHHHHHHHHH--SEEEESS-SSS-BGGG--HHHHHTSSS-HHHHHHHHHHHHHH CS
     DUF4152  57 airdevllavelarkvkpdvvhldstlggielrkldeptiealgisdkgkevwkelskdl 116
                  i  e +l++ l r  +   + + s+ gg+e+  + + ti  +g+ d   +  ke+++++
  AJA92652.1  95 DIEKELYLSLFLNRSKRCYTI-IASSEGGVEIESVKNQTIREVGLGDVDAQTAKEVANEI 153
                 588999******999877766.67889*******************99888888887765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.078
                 GGG-.HHHHHHHHHHHHHHHHH.HHCTTTTSSEEEEEESTTEEEEEETTEEEEEES-GGGTS-EEEEE----TT-E CS
     DUF4152 135 gkss.vpvriaeiyagiysakw.aieyvekegkllvglprymevdikdgkiigesldpregglygkievsvtegvk 208
                  k+s v   + ++y gi  +   a  +++   + l+ lp + ++   + +   e l   +  ++ +ie  + +gv 
  AJA92652.1 289 SKMSrVKGILVNLYGGIVKTTTvAEAFIQAYNNNLIDLPVFARLMGTESDKAKEMLKDTKTKMFDSIE-EAINGVV 363
                 45442445567889998765540455677788889999999999888888888899888899999998.5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2768.90
//
Query:       AJA92653.1  [L=321]
Description: TIM-barrel protein, nifR3 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-76  255.7   0.0    5.8e-76  255.5   0.0    1.0  1  Dus           Dihydrouridine synthase (Dus)
     0.0058   16.0   0.0      0.012   14.9   0.0    1.5  1  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
     0.0058   15.8   0.1      0.038   13.2   0.0    2.1  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
     0.0083   15.9   0.0        0.2   11.4   0.0    2.4  2  SOR_SNZ       SOR/SNZ family
  ------ inclusion threshold ------
      0.073   12.4   0.0       0.15   11.3   0.0    1.6  1  TMP-TENI      Thiamine monophosphate synthase
      0.096   12.1   0.0       0.22   11.0   0.0    1.7  2  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.5   0.0     2e-79   5.8e-76       2     304 ..      13     318 ..      12     321 .] 0.88

  Alignments for each domain:
  == domain 1  score: 255.5 bits;  conditional E-value: 2e-79
                 E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGT.......SCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEE CS
         Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeee.......tplavQlggsdpallaeaAklvadlgadeIdlNvGCPskk 93 
                 laPmagv+d ++R +++++ga+ Lvvte+ +++aiv ++++  ++ ++  e        +pl+vQl+gsd a l +aAk+v++   d Id N+GCP++ 
  AJA92653.1  13 LAPMAGVSDPALRIMCKKMGAG-LVVTELTSVNAIVAKHEQLESQSKNITEFiefsekeRPLSVQLFGSDIAALEKAAKIVEP-HFDMIDYNMGCPAPH 109
                 8*********************.*****9999998877555444333222223333444************************.*************** PP

                 ETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS.TTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS CS
         Dus  94 vtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid.deeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGd 191
                 +t+++aG aLl+++dl  qi +++v+av+ P+++k+rig+  +++   l++aki+e++G+ ++t+H Rt  q+y+g+adw+ Ik++kq+vs+pv++NGd
  AJA92653.1 110 ITKQMAGGALLQNADLTRQIFRTLVNAVKKPISLKMRIGVTeENNSLFLDIAKIAEQEGIGMMTLHPRTVSQGYSGHADWDMIKKLKQNVSVPVVGNGD 208
                 ****************************************956666679************************************************** PP

                 --SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHHH CS
         Dus 192 IkdaedaqaileetGadgvmigrgalgnPwlfae.stavktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrrele 289
                 I+++e a+++l++t +d +migrga gnP++f++ + +++ g ++ + +l +++e++   l+ +e+      ++ +i ++     kg  +  +lr+ l+
  AJA92653.1 209 ITSPEIAKKVLDYTECDYLMIGRGAMGNPFIFEQiNDYLESGVYK-KYTLTDRLEAFVTYLELTEKYH---IRFANIKQQAIRFTKGTVGGGQLRNRLS 303
                 **********************************66666666555.5566999999998887766655...7888888888899999999999999999 PP

                 HHHHHHCCHHCHH.H CS
         Dus 290 evsdkeealenleea 304
                 + ++ ++ +e l ++
  AJA92653.1 304 AATNTDDLKELLLQK 318
                 999998888777655 PP

>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     4e-06     0.012     282     339 ..     190     247 ..     144     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                   HHHHHHCCCHSSEEEE-SS--SHHHHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCT CS
  Oxidored_FMN 282 kntefvkevwkkplitvgriadeekaaeivaegeadLvamgRefladpdlveklkkgl 339
                      +++k+ +++p+++ g i+++e a++++   e d   +gR  + +p++ e+++  l
    AJA92653.1 190 DMIKKLKQNVSVPVVGNGDITSPEIAKKVLDYTECDYLMIGRGAMGNPFIFEQINDYL 247
                   5679**********************************************99998765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.14   4.3e+02      95     121 ..      15      41 ..       6      66 .. 0.81
   2 !   13.2   0.0   1.3e-05     0.038     106     173 ..     162     230 ..     114     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.14
                 EEEE-SSHHHHHHHHHTT-SEEE-TTT CS
        NanE  95 lmaDistleeglvakklGvdivGttls 121
                  ma +s     +++kk+G+ +v t l 
  AJA92653.1  15 PMAGVSDPALRIMCKKMGAGLVVTELT 41 
                 599999999999999999999988775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                 HHHHHTT-SEEE-TTTTSSTTS-..SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT-.-SEEEE- CS
        NanE 106 lvakklGvdivGttlsGytkeeek.aepDfalvkalsea.glkviaeGrintPekakkaieiG.vdavvvG 173
                 ++a++ G+ ++  tl   t ++    + D++++k+l+++  + v+ +G i +Pe akk+++    d +++G
  AJA92653.1 162 KIAEQEGIGMM--TLHPRTVSQGYsGHADWDMIKKLKQNvSVPVVGNGDITSPEIAKKVLDYTeCDYLMIG 230
                 55566665554..566555544443789********8752678****************996424555555 PP

>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.014        43      60      96 ..     128     163 ..     112     171 .. 0.78
   2 !   11.4   0.0   6.8e-05       0.2      23      95 ..     158     226 ..     136     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.014
                 HHHHHHHHH-SS-EEEEEETT-HHHHHHHHHTT-SEE CS
     SOR_SNZ  60 klikeikeavsipvmakvriGhfveaqilealgvdyi 96 
                 ++ + +++av+ p+  k+riG + e + l  l++  i
  AJA92653.1 128 QIFRTLVNAVKKPISLKMRIGVTEENNSL-FLDIAKI 163
                 56788999*************99998765.3555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.8e-05
                 HHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HHHH.HHHHHTT-SE CS
     SOR_SNZ  23 aeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfvea.qilealgvdy 95 
                  + akiae+ G + +m+l+  p  +    g +  +d ++ik++k+ vs+pv+    i     a ++l+  + dy
  AJA92653.1 158 LDIAKIAEQEG-IGMMTLH--PRTVS--QGYSGHADWDMIKKLKQNVSVPVVGNGDITSPEIAkKVLDYTECDY 226
                 46799999999.6789887..66654..588999******************9988876544425777777776 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.2e-05      0.15      87     165 ..     135     215 ..     131     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
    TMP-TENI  87 aearellgpdliiGlSvhslee.aeeaealgadYigvGpifpTdtKkda.eplgleglkelaealeiPvvaiGGitlenva 165
                 + +++ +  ++ iG++ ++ +  +  a+ +    ig+ +++p +  ++    ++++ +k+l++++++Pvv  G+it  ++a
  AJA92653.1 135 NAVKKPISLKMRIGVTEENNSLfLDIAKIAEQEGIGMMTLHPRTVSQGYsGHADWDMIKKLKQNVSVPVVGNGDITSPEIA 215
                 567777888999999999999954444445557888888899888888889************************987665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   5.5e+03     112     154 ..      24      65 ..       9      71 .. 0.63
   2 ?   11.0   0.0   7.2e-05      0.22      59     118 ..     186     246 ..     137     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                   HHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHH CS
  His_biosynth 112 ikelaekfgsqkivvaiDarrgykvaikgwreetgldavelak 154
                   ++ +++k+g+  +v  + + +   va ++  e+++ +++e+++
    AJA92653.1  24 LRIMCKKMGAGLVVTELTSVNA-IVAKHEQLESQSKNITEFIE 65 
                   5667777777666666666665.67777777776666666665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.2e-05
                   HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT.-SEEEESHHHHH-THHHHHHHHH CS
  His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleag.adkviigtaavknpelikelaek 118
                    a+ d+++++ ++v++pv   G I s e ++++l+   +d+++ig  a+ np +++++ + 
    AJA92653.1 186 HADWDMIKKLKQNVSVPVVGNGDITSPEIAKKVLDYTeCDYLMIGRGAMGNPFIFEQINDY 246
                   567799************88888***********9765**************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2211.61
//
Query:       AJA92654.1  [L=139]
Description: prefoldin, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-21   74.5   4.5    6.3e-21   74.5   4.5    1.7  2  Prefoldin        Prefoldin subunit
     0.0004   20.4  13.9      0.017   15.2   3.0    2.0  2  DHR10            Designed helical repeat protein 10 domain
     0.0005   20.0  12.6     0.0052   16.7   2.7    2.1  2  Prefoldin_2      Prefoldin subunit
     0.0056   16.6   1.2     0.0056   16.6   1.2    2.0  2  RF-1             RF-1 domain
  ------ inclusion threshold ------
      0.016   15.2   8.5       0.31   11.0   0.8    2.2  2  Laminin_II       Laminin Domain II
      0.019   15.3   3.5        0.5   10.7   0.4    2.2  2  kleA_kleC        Uncharacterized KorC regulated protein A
      0.028   14.8   1.0      0.028   14.8   1.0    2.1  2  DASH_Dad2        DASH complex subunit Dad2
      0.036   13.3  10.8      0.045   13.0  10.8    1.0  1  Phage_HK97_TLTM  Tail length tape measure protein
      0.045   14.4   3.9      0.078   13.6   0.2    2.2  2  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
      0.051   13.4   0.3      0.051   13.4   0.3    1.9  2  PhoQ_Sensor      PhoQ Sensor
      0.069   13.2   0.6      0.069   13.2   0.6    2.2  2  DUF3848          Protein of unknown function (DUF3848)
      0.069   13.2  10.1       0.14   12.3  10.1    1.5  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.079   13.1  10.2       0.11   12.6   0.4    2.1  2  RasGAP_C         RasGAP C-terminus
       0.17   11.8   9.2        2.3    8.2   3.1    2.4  2  Sec20            Sec20
       0.45   10.4   2.9       0.42   10.5   0.3    1.9  2  DEDD_Tnp_IS110   Transposase
       0.46   10.7  13.1       0.75   10.1   3.4    2.4  2  WXG100           Proteins of 100 residues with WXG
       0.49   10.9   6.0       0.39   11.2   0.9    2.1  2  SecD-TM1         SecD export protein N-terminal TM region
       0.94    9.5  10.3       0.86    9.6   0.9    2.1  2  DUF1664          Protein of unknown function (DUF1664)
        2.3    8.6  21.2       0.63   10.4   6.3    2.1  2  OmpH             Outer membrane protein (OmpH-like)
        2.6    7.4  12.5       0.16   11.4   3.6    2.0  2  Flagellar_rod    Paraflagellar rod protein
        2.6    8.5  11.2       0.78   10.2   2.1    2.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
        2.7    8.1   7.2        1.5    8.9   0.9    2.1  2  DUF2120          Uncharacterized protein conserved in archaea
          3    8.1  13.1       0.75   10.0   2.7    2.3  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
          3    8.0   8.1          2    8.6   1.7    2.3  2  KIP1             KIP1-like protein
        3.3    7.9   8.8       0.46   10.6   2.4    2.6  2  TRPM_tetra       Tetramerisation domain of TRPM
        3.3    7.5  12.8       0.64    9.8   3.6    2.0  2  SKA1             Spindle and kinetochore-associated protein 1
        4.6    7.4  12.5       0.55   10.4   5.2    2.1  2  PilO             Pilus assembly protein, PilO
        5.3    6.7  14.6        6.7    6.4   2.1    2.1  2  DUF745           Protein of unknown function (DUF745)
        6.3    7.2  11.3        5.5    7.4   2.8    2.1  2  CLZ              C-terminal leucine zipper domain of cyclic n
        6.5    5.5  16.5        1.2    7.9   5.2    2.0  2  Spc7             Spc7 kinetochore protein
        7.2    6.6  10.7        1.9    8.5   1.3    2.2  2  Med10            Transcription factor subunit Med10 of Mediat
        7.5    6.9  13.3        4.9    7.5   2.7    2.3  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        8.5    6.2  12.9        2.2    8.1   2.1    2.0  2  DUF724           Protein of unknown function (DUF724)
        9.5    6.5  14.2         11    6.3   2.7    2.2  2  Spc24            Spc24 subunit of Ndc80


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.7      0.82   4.3e+02     105     118 ..       4      17 ..       1      25 [. 0.43
   2 !   74.5   4.5   1.2e-23   6.3e-21       2     120 .]      17     134 ..      16     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.82
                 HHHHHHHHHHHHHH CS
   Prefoldin 105 dqittleanlaqly 118
                 +q++++ +++++l 
  AJA92654.1   4 EQAQQMLQQMQMLE 17 
                 33344444444332 PP

  == domain 2  score: 74.5 bits;  conditional E-value: 1.2e-23
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkkleelekqlekleeel 100
                 + + ++l ++ +++k  i++ +++++ ++++k+ + + e lvp+g g ++k ++++++k++v++Gag+++ek+ + A  +l+ k++ele +l++ + + 
  AJA92654.1  17 ENMYTELSQKENSIKNIIRDADSAIKSIQEIKA-NPDSESLVPVGMGTFIKTKHIPNEKIVVNVGAGVAIEKDHDSALSYLESKIKELEVALQETNSQR 114
                 67889999*************************.999************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHH CS
   Prefoldin 101 eklkdqittleanlaqlyqk 120
                 +++++++++  ++++q+ q+
  AJA92654.1 115 QQIAANLEQGKQQMQQIMQQ 134
                 ****************9885 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   3.0   3.1e-05     0.017       2      47 ..       4      49 ..       3      55 .. 0.94
   2 !   11.1   3.3   0.00058      0.31      50     102 ..      84     136 ..      74     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
       DHR10  2 eslaeekeelaelErkarelqakidalqvvekdlrsciklleeiea 47
                e+++++ +++++lE+ + el++k ++++++ +d  s+ik ++ei+a
  AJA92654.1  4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIKA 49
                799*****************************************87 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00058
       DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                 a +++ ++ l+ l+ +++e+e  l+e +++++++   le+ ++++++  +q++
  AJA92654.1  84 AIEKDHDSALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQSQ 136
                 55777888888889999999999999999999999999999999998888875 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   2.5    0.0028       1.5       1      42 [.       7      48 ..       7      58 .. 0.93
   2 !   16.7   2.7   9.8e-06    0.0052      47     105 ..      75     134 ..      68     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
  Prefoldin_2  1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelld 42
                 q+++ ++q l++  ++l q+ +++++ +++++++++ +++++
   AJA92654.1  7 QQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIK 48
                 89**********************************999876 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 9.8e-06
                  EEEEET.TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS- CS
  Prefoldin_2  47 vyklvG.dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkklqq 105
                  +  +vG +v +++d +++++ Le ++++le  +++ ++q +++ ++le+ k++ q+ +qq
   AJA92654.1  75 IVVNVGaGVAIEKDHDSALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQ 134
                  5555553577899*******************************************9997 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.9         1   5.3e+02      59      84 ..       4      31 ..       1      56 [. 0.43
   2 !   16.6   1.2   1.1e-05    0.0056      34     101 ..      65     131 ..      59     139 .] 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                HHHHHHHHHH..HHHHHHHHCCCCCHTT CS
        RF-1 59 ekAlerLkak..lkekeleeekeeekkr 84
                e+A ++L+++  l+++  e +++e++ +
  AJA92654.1  4 EQAQQMLQQMqmLENMYTELSQKENSIK 31
                5566666543113222222222222222 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.1e-05
                 EEEEETTTTEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCHTTTTT-.S.-S---S..--EC CS
        RF-1  34 VrlthlptgvivvecqeeRsqekNrekAlerLkaklkekeleeekeeekkrrvkkekkkigtgs..seki 101
                 ++  h+p+++ivv++      ek  + Al+ L++k+ke e++ ++ + +++++ +   ++++g+   ++i
  AJA92654.1  65 IKTKHIPNEKIVVNVGAGVAIEKDHDSALSYLESKIKELEVALQETNSQRQQIAA---NLEQGKqqMQQI 131
                 66789*******************************9977777777777666666...333333212222 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00059      0.31      65     110 ..       3      45 ..       2      61 .. 0.83
   2 ?    8.3   1.5     0.004       2.1       4      38 ..      99     133 ..      84     137 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                 --TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHT-- CS
  Laminin_II  65 eklapqLldklkelkqleeassslsdniseikelIaqARkaAnkik 110
                 e++a+q+l++++ l++   +   ls++ + ik++I  A +a  +i+
  AJA92654.1   3 EEQAQQMLQQMQMLENMYTE---LSQKENSIKNIIRDADSAIKSIQ 45 
                 78999*****9999999999...*************9999999997 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.004
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinr 38 
                 +++e +  ++e+ +q +++++nle+ k+++++i +
  AJA92654.1  99 KIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQ 133
                 34444444555555555555555555555555544 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.039        20       9      46 ..      13      50 ..       5      57 .. 0.86
   2 ?   10.7   0.4   0.00095       0.5       9      40 ..     100     131 ..      96     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.039
   kleA_kleC  9 iDeLpevatdlvarRdkiAaklaeAeeLvrqaeeLRak 46
                +  L++  t+l  + + i + +++A+   + ++e++a+
  AJA92654.1 13 MQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIKAN 50
                56799**********************99999998775 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00095
   kleA_kleC   9 iDeLpevatdlvarRdkiAaklaeAeeLvrqa 40 
                 i eL+ + ++  ++R++iAa l++ ++ ++q+
  AJA92654.1 100 IKELEVALQETNSQRQQIAANLEQGKQQMQQI 131
                 67898888****************99998886 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.0   5.4e-05     0.028      19      63 ..       4      48 ..       2      56 .. 0.92
   2 ?    2.9   3.0      0.29   1.5e+02       4      40 ..      96     133 ..      93     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-05
   DASH_Dad2 19 dlsdslakqleeLeeklstladgteavasVlanWqnvlraismas 63
                ++++++ +q++ Le+ +++l++  ++++++++  ++ +++i+  +
  AJA92654.1  4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIK 48
                6799*************************************9766 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.29
   DASH_Dad2   4 iaeKraELe.aLkqlrdlsdslakqleeLeeklstlad 40 
                 +++K +ELe aL++ +++ +++a +le+ +++++++ +
  AJA92654.1  96 LESKIKELEvALQETNSQRQQIAANLEQGKQQMQQIMQ 133
                 67888888867999999999999999999999888765 PP

>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  10.8   8.4e-05     0.045      60     177 ..       6     128 ..       2     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
  Phage_HK97_TLTM  60 vkeklkklsl.eevadekdklkeslkeqnklvkeaeqkveelkkeldkyq...vsingylvnkldskeeaik.laeatdklsesqsaleavtkk 148
                       ++ l+++++ e++  e ++ ++s+k+  ++++ a + ++e+k + d      v +  +++ k +++e+ +  + +      + +sal+ ++ k
       AJA92654.1   6 AQQMLQQMQMlENMYTELSQKENSIKNIIRDADSAIKSIQEIKANPDSESlvpVGMGTFIKTKHIPNEKIVVnVGAGVAIEKDHDSALSYLESK 99 
                      56778899861556778899999********************999998888899***********9998877999999999************ PP

  Phage_HK97_TLTM 149 skeiqsaLtsveadrvrlirqqaaeqnkv 177
                       ke + aL++ +++r ++  +    ++++
       AJA92654.1 100 IKELEVALQETNSQRQQIAANLEQGKQQM 128
                      *****************998833333333 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   0.00015     0.078      27      68 ..       2      41 ..       1      59 [. 0.73
   2 ?    1.9   0.5      0.64   3.4e+02      37      68 ..      99     129 ..      89     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00015
  5_3_exonuc 27 GektAakLlkeygsleeilenldelkekklkekLeenkeear 68
                +e +A+++l++++ le+++ +l++ ke+++k+ +++ +++a 
  AJA92654.1  2 SEEQAQQMLQQMQMLENMYTELSQ-KENSIKNIIRD-ADSAI 41
                5789****************9986.44455554444.54443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.64
  5_3_exonuc  37 eygsleeilenldelkekklkekLeenkeear 68 
                 ++++le  l+++++ ++++++++Le++k++++
  AJA92654.1  99 KIKELEVALQETNS-QRQQIAANLEQGKQQMQ 129
                 45666777776654.34678888888888765 PP

>> PhoQ_Sensor  PhoQ Sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   9.8e-05     0.051      97     167 ..       7      77 ..       2      86 .. 0.92
   2 ?    0.6   0.2      0.84   4.4e+02      88     121 ..      95     129 ..      81     138 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
  PhoQ_Sensor  97 ekkikkeWlkkeglyeldtdvktssallknnpeaqkklkkldddedeelthsvavnryaateklPaltivv 167
                  ++++++  + ++ + el+ + ++ ++++++  +a k+ ++++ + d+e    v + ++ +t+++P+  ivv
   AJA92654.1   7 QQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIKANPDSESLVPVGMGTFIKTKHIPNEKIVV 77 
                  566777778889999***************************99999999*****************9998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.84
  PhoQ_Sensor  88 WrqrevpelekkikkeWlkkegl.yeldtdvktss 121
                  + ++++ ele ++++   +++++  +l+  +++ +
   AJA92654.1  95 YLESKIKELEVALQETNSQRQQIaANLEQGKQQMQ 129
                  34444444444444433333332123333333333 PP

>> DUF3848  Protein of unknown function (DUF3848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   0.00013     0.069      51      86 ..       2      37 ..       1      45 [. 0.92
   2 ?    0.7   0.3         1   5.5e+02      38      55 ..     114     131 ..     102     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
     DUF3848 51 sdeqakaLlksenpLddvyeewekrddsymedlrqt 86
                s+eqa+ +l++ + L+++y e +++++s  + +r++
  AJA92654.1  2 SEEQAQQMLQQMQMLENMYTELSQKENSIKNIIRDA 37
                799******************************986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
     DUF3848  38 kedilmsleeeelsdeqa 55 
                 +++i+  le+ +++ +q+
  AJA92654.1 114 RQQIAANLEQGKQQMQQI 131
                 566666666655554443 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  10.1   0.00026      0.14       3      95 ..       1     139 []       1     139 [] 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
       Mod_r   3 lSkeeLqelledeeklealvktlpe....vkqlkeekeellaenesla.........................................eknlsl.epe 55 
                 +S e+ q++l++ + le+++++l++    +k++  + ++++++++++                                          ++ ls  e +
  AJA92654.1   1 MSEEQAQQMLQQMQMLENMYTELSQkensIKNIIRDADSAIKSIQEIKanpdseslvpvgmgtfiktkhipnekivvnvgagvaiekdhDSALSYlESK 99 
                 689999***************77555677999999************9**************************************9998888887999 PP

       Mod_r  56 leelrselqekleelkelekefeekeqeldellqkfspda 95 
                 ++el   lqe+ ++ +++ +++e+ +q++++++q+ +p++
  AJA92654.1 100 IKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQSQPQS 139
                 ***********************************99985 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   0.00021      0.11      43      85 ..       4      45 ..       1      75 [. 0.82
   2 ?    4.8   4.0     0.057        30      46      90 ..      94     138 ..      84     139 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
    RasGAP_C 43 rlrekrkeElesleetlktLseknnylesqlesYkayienvle 85
                ++ +++ +++++le+ +++Ls+k+n +++ +++ ++ i+++ +
  AJA92654.1  4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSI-Q 45
                67899************************999999999865.4 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.057
    RasGAP_C  46 ekrkeElesleetlktLseknnylesqlesYkayienvleqlkkk 90 
                  + ++ ++ le +l++ +++++++   le+ k+ ++++++q++ +
  AJA92654.1  94 SYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQSQPQ 138
                 455566777778888888888888888888888888888888765 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4    0.0097       5.1      24      54 ..       2      32 ..       1      68 [. 0.53
   2 ?    8.2   3.1    0.0043       2.3       1      25 [.     112     136 ..     112     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0097
       Sec20 24 Seenleeldastkslekleeeykqvedvlsr 54
                See ++++ ++ + le++  e+ q e++++ 
  AJA92654.1  2 SEEQAQQMLQQMQMLENMYTELSQKENSIKN 32
                5666666666666666655555555444432 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0043
       Sec20   1 sqakqiTeslraisqllsqevqqSe 25 
                 sq +qi ++l +++q+++q +qqS+
  AJA92654.1 112 SQRQQIAANLEQGKQQMQQIMQQSQ 136
                 6899*******************97 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.3   6.8e+02     112     139 ..      10      37 ..       3      47 .. 0.56
   2 ?   10.5   0.3    0.0008      0.42     119     155 .]     101     137 ..      88     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
  DEDD_Tnp_IS110 112 lrplklddeayaeLrqltrqredlvker 139
                     l+++++ ++ y+eL+q  ++ ++++++ 
      AJA92654.1  10 LQQMQMLENMYTELSQKENSIKNIIRDA 37 
                     4455555555556655555555555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0008
  DEDD_Tnp_IS110 119 deayaeLrqltrqredlvkertrlknrlralLdqvfp 155
                     +e  ++L++ ++qr+++++++ + k++++++++q  p
      AJA92654.1 101 KELEVALQETNSQRQQIAANLEQGKQQMQQIMQQSQP 137
                     566789**************************99765 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.4    0.0014      0.75      50      86 .]       3      39 ..       2      39 .. 0.94
   2 ?    5.9   2.3     0.028        15      60      83 ..     107     130 ..      89     137 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
      WXG100 50 qaefeewkqaaqklvdaLeeisealkqaanafedaDe 86
                +++ +++ q++q l ++++e+s++ ++++n  +daD+
  AJA92654.1  3 EEQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADS 39
                57889******************************95 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
      WXG100  60 aqklvdaLeeisealkqaanafed 83 
                 +q+ + + ++i+ +l+q ++++++
  AJA92654.1 107 LQETNSQRQQIAANLEQGKQQMQQ 130
                 333333333333333333333332 PP

>> SecD-TM1  SecD export protein N-terminal TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.36   1.9e+02      45      74 ..      11      40 ..       2      52 .. 0.71
   2 ?   11.2   0.9   0.00074      0.39      25      86 ..      68     129 ..      55     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.36
    SecD-TM1 45 vdeatlskveqaLkeagievksielenesl 74
                 + ++l+++++ L++++ ++k+i  +++s 
  AJA92654.1 11 QQMQMLENMYTELSQKENSIKNIIRDADSA 40
                445677888888888888888888887764 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00074
    SecD-TM1  25 PnlygedpavqisaakatlkvdeatlskveqaLkeagievksielenesllvrfestdqqlk 86 
                   + +e+  v++ a  a  k +++ ls++e+++ke +++ ++++ +++++ + +e+ +qq++
  AJA92654.1  68 KHIPNEKIVVNVGAGVAIEKDHDSALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQ 129
                 5666788899999998888999999***********************************97 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.7     0.054        28      80     121 ..       4      45 ..       1      50 [. 0.71
   2 ?    9.6   0.9    0.0016      0.86      62     103 ..      94     135 ..      75     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.054
     DUF1664  80 eiskeikeevtevredlseigedvesvkeaveglesklerie 121
                 e ++++ ++++ +++  +e++++ +s+k+++++ +s +++i+
  AJA92654.1   4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQ 45 
                 556677777777777777777777777777777777777776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0016
     DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                   L+s+i++++  l+e++   ++i++++++ ++++++i +++
  AJA92654.1  94 SYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQS 135
                 458899999999999999999999999999999999998776 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.0     0.076        40      62     106 ..       3      45 ..       1      49 [. 0.77
   2 ?   10.4   6.3    0.0012      0.63       8      80 ..      73     136 ..      66     139 .] 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  62 eqelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikeva 106
                 e++ q++ q++q  +++ + el +k++ + + i+  ++ aik + 
  AJA92654.1   3 EEQAQQMLQQMQM-LENMYTELSQKENSIKN-IIRDADSAIKSIQ 45 
                 5567888888888.88888999999988555.9999999999875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                 HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH CS
        OmpH   8 qkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka 80 
                 +ki+ +  +g a++++ ++  + l+ +++++e +lq+   + q+ a++         l++ +q++qq +qq +
  AJA92654.1  73 EKIVVNVGAGVAIEKDHDSALSYLESKIKELEVALQETNSQRQQIAAN---------LEQGKQQMQQIMQQSQ 136
                 677777777777777777777777777777777777666666644444.........3333333333333333 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.6      0.31   1.6e+02      59      82 ..       5      28 ..       1      51 [. 0.39
   2 ?   11.4   3.6    0.0003      0.16      31      81 ..      85     135 ..      80     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.31
  Flagellar_rod 59 qqeklvreieelereLqklaeerr 82
                   q ++++++++ le+   +l+++ +
     AJA92654.1  5 QAQQMLQQMQMLENMYTELSQKEN 28
                   333333333333333333332221 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0003
  Flagellar_rod  31 eaaadekqrkrykaqreesdkflqeneeqqeklvreieelereLqklaeer 81 
                    ++++++ + +  + + +e + +lqe ++q++++  ++e+ ++++q+++++ 
     AJA92654.1  85 IEKDHDSALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQS 135
                    678999999999************************************985 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.9      0.24   1.2e+02       3      35 ..      17      49 ..       3      52 .. 0.75
   2 ?   10.2   2.1    0.0015      0.78       5      41 ..      96     132 ..      93     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.24
   FlaC_arch  3 delEnklsklsteletvkkeneelsksveelke 35
                +++ ++ls+ + +++++ ++ ++  ks++e+k 
  AJA92654.1 17 ENMYTELSQKENSIKNIIRDADSAIKSIQEIKA 49
                445567777777888888888888888888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
   FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdll 41 
                 lE+k+++l++ l+   ++ +++  ++e+ k++ ++++
  AJA92654.1  96 LESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIM 132
                 9***************************999999988 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9    0.0028       1.5      54      89 ..      20      55 ..       1      69 [. 0.73
   2 ?    3.2   0.8      0.17        88      35      82 ..      86     132 ..      61     138 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0028
     DUF2120 54 aeevdleseeakkliekldesireveeieeevdafg 89
                  e+  +++ +k++i   d+ i++ +ei++++d+ +
  AJA92654.1 20 YTELSQKENSIKNIIRDADSAIKSIQEIKANPDSES 55
                3456667789**********************9875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.17
     DUF2120  35 keeleeleskleellekldaeevdleseeakkliekldesireveeie 82 
                 +++++   s+le+ +++l++   +++s+  +++ ++l++  +++++i+
  AJA92654.1  86 EKDHDSALSYLESKIKELEVALQETNSQ-RQQIAANLEQGKQQMQQIM 132
                 3446666666676666666665555555.3344444444333333333 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.8      0.15        76      37      80 ..       5      48 ..       1      55 [. 0.45
   2 ?   10.0   2.7    0.0014      0.75      30      69 ..      92     131 ..      84     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                  HHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHH CS
  Seryl_tRNA_N 37 krrelqveleelqaerNelskeIgkakkkkedaeeliaevkelk 80
                  + +++ ++++ l +   els++  ++k+   da++ i++++e+k
    AJA92654.1  5 QAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIK 48
                  33333333333333333344433333333345555555555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-T CS
  Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkkeda 69 
                   +l  l++k +el+v+l+e +++r +++++ ++ k++ +++
    AJA92654.1  92 ALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQI 131
                   4667999*************************99986443 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.7    0.0039         2       7      44 ..       7      43 ..       4      54 .. 0.83
   2 ?    3.1   0.6       0.2   1.1e+02      19      55 ..      92     128 ..      85     137 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0039
        KIP1  7 hisskqskwLqetlseldekvkemlklieedadsfakr 44
                ++  +q + L++  +el +k +++ ++i  dads  k 
  AJA92654.1  7 QQMLQQMQMLENMYTELSQKENSIKNII-RDADSAIKS 43
                55678999********************.778877654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
        KIP1  19 tlseldekvkemlklieedadsfakraemyykkrpeL 55 
                  ls l++k+ke+   ++e + + ++ a +  + ++++
  AJA92654.1  92 ALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQM 128
                 5666777777766555544444444444434444443 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.4   0.00088      0.46      12      47 ..      17      49 ..       1      51 [. 0.80
   2 ?   -0.6   0.5       2.8   1.5e+03      13      38 ..     102     127 ..      93     135 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00088
  TRPM_tetra 12 EnmsmkveevneKenlikaSLqsldfrLgkLedlsa 47
                Enm+    e+++Ken+ik+ + + d+ ++ ++++ a
  AJA92654.1 17 ENMY---TELSQKENSIKNIIRDADSAIKSIQEIKA 49
                4444...489***********************986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
  TRPM_tetra  13 nmsmkveevneKenlikaSLqsldfr 38 
                 ++ + ++e n   + i a+L +  ++
  AJA92654.1 102 ELEVALQETNSQRQQIAANLEQGKQQ 127
                 44444555555555555555444444 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.8      0.11        60      20      62 ..       8      49 ..       1      59 [. 0.69
   2 ?    9.8   3.6    0.0012      0.64      29      72 ..      90     134 ..      81     139 .] 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        SKA1 20 llkedlskieaevsaleellnklkkelqeeeeaikklkkeiea 62
                 + + ++ +e+  ++l ++ n++k ++++  +aik+++ ei+a
  AJA92654.1  8 QMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQ-EIKA 49
                33456667777777777888888888888888888777.6655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXX CS
        SKA1  29 eaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqh 72 
                 ++++s le+++++l+ +lqe +++ +++ +++e+  +q ++ +q+
  AJA92654.1  90 DSALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQiMQQ 134
                 566778888888888888888888888888888777666655554 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.7      0.58   3.1e+02      16      42 ..       7      33 ..       2      53 .. 0.55
   2 ?   10.4   5.2     0.001      0.55       5      38 ..     101     134 ..      97     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.58
        PilO 16 eekkekaanLeklkkqleeleeeleel 42
                ++  ++ + Le++ ++l + e++++++
  AJA92654.1  7 QQMLQQMQMLENMYTELSQKENSIKNI 33
                333444444444444444444444443 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
        PilO   5 eakekeLkkefeekkekaanLeklkkqleeleee 38 
                 ++ e  L+++ ++++++aanLe+ k+q++++ ++
  AJA92654.1 101 KELEVALQETNSQRQQIAANLEQGKQQMQQIMQQ 134
                 667899************************9887 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.1     0.013       6.7      96     136 ..       3      43 ..       1      53 [. 0.77
   2 ?    6.1   4.9     0.016       8.5      64     106 ..      93     135 ..      83     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.013
      DUF745  96 akaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                 ++ a+q+ qq+++l++++ + +++ ++++++   a + +++
  AJA92654.1   3 EEQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKS 43 
                 56788888899999999999888888888888888776665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
      DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqql 106
                 +  le++++e e ++qe +++ q+  an++  ++ ++q+ qq 
  AJA92654.1  93 LSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQS 135
                 5679999**************************9999999986 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.4      0.06        32       3      44 ..       4      45 ..       2      49 .. 0.73
   2 ?    7.4   2.8      0.01       5.5      28      64 ..      95     131 ..      84     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.06
         CLZ  3 ekGreILlKdglLDeeaakagaeqkeleekverLessLeaLq 44
                e  +++L+++ +L++   + +++++++++ ++  +s+++++q
  AJA92654.1  4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQ 45
                556788888888888877777788888887777777766665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
         CLZ  28 eleekverLessLeaLqtrlarLlaeyessqrkLkqR 64 
                  le+k+++Le +L+  + + +++ a++e+ +++++q 
  AJA92654.1  95 YLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQI 131
                 689*******************************995 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.5     0.047        25     210     252 ..       4      46 ..       1      55 [. 0.46
   2 ?    7.9   5.2    0.0023       1.2     207     249 ..      92     134 ..      87     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.047
        Spc7 210 elkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                 e+ +++ +++++l+++ ++l ++e++i+++    +++ + i+e
  AJA92654.1   4 EQAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQE 46 
                 3444444444444444444444444444443333333333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0023
        Spc7 207 elaelkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                 +l+ l+++i+e++  l+e ++q++++++++e+ k+q+++++++
  AJA92654.1  92 ALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQ 134
                 6778899999999999999999999999999999999999887 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.3    0.0036       1.9       6      62 ..       5      61 ..       2      82 .. 0.76
   2 ?    3.6   2.4      0.12        63      16      50 ..     105     136 ..      76     139 .] 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0036
                HHHHHHHHHHHHHHS--TT.S-TTHHHHHHHHHHHHHHHHHHHHH..HH--EEEHHH CS
       Med10  6 eviqsllelgvqvsdydenessqevlaqklktlvesLqelsktaskllqdikiPlel 62
                +  q l ++++  + y+e +++++ +++ +++ +++++++++ ++++ ++  +P+ +
  AJA92654.1  5 QAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEIKANPDSESLVPVGM 61
                556778888888899999889999999999999999999999999996666666543 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                 HHHHS--TT.S-TTHHHHHHHHHHHHHHHHHHHHH CS
       Med10  16 vqvsdydenessqevlaqklktlvesLqelsktas 50 
                 v+    +e++s+++++a +l++  +++q++ ++++
  AJA92654.1 105 VAL---QETNSQRQQIAANLEQGKQQMQQIMQQSQ 136
                 333...33335677777777777777777766655 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.7    0.0094       4.9      14      56 ..       5      47 ..       1      54 [. 0.69
   2 ?    4.9   3.1     0.061        32      39      69 ..      96     126 ..      87     136 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0094
     BLOC1_2 14 eleatvedyklLeklNeaasekykklkdvaaslekkleklnek 56
                + +   +++++Le++ ++ s+k +++k+++ ++ + ++ ++e 
  AJA92654.1  5 QAQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQEI 47
                5555667777777777777777777777777777777777665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.061
     BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidq 69 
                 l++++++le+ l+++n++ ++++ +l+q +q
  AJA92654.1  96 LESKIKELEVALQETNSQRQQIAANLEQGKQ 126
                 4556666666666666666666665554333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   3.4     0.079        42     104     144 ..       6      46 ..       1      56 [. 0.47
   2 ?    8.1   2.1    0.0042       2.2     130     173 ..      91     134 ..      73     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.079
      DUF724 104 qtklleerkklekkieeeesekrkleeeidelekkileler 144
                  +++l++++ le+  +e +++++++++ i++ +++i+ +++
  AJA92654.1   6 AQQMLQQMQMLENMYTELSQKENSIKNIIRDADSAIKSIQE 46 
                 33444444444444444444444444444444444444443 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
      DUF724 130 eeidelekkilelerqlallkekkeaadkeiarlkseaekleee 173
                 + ++ le+ki+ele  l+ + +++++ ++++ + k++++++ ++
  AJA92654.1  91 SALSYLESKIKELEVALQETNSQRQQIAANLEQGKQQMQQIMQQ 134
                 45555666666666666666666666666666666555555554 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.7     0.021        11      17      54 ..       3      41 ..       1      56 [. 0.75
   2 ?    5.9   3.9     0.028        15       9      43 ..      96     130 ..      87     138 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
       Spc24 17 eselesleselaelkeeleeleeeseekeserve.detl 54
                e++++++ ++ + l+++++el++++++ ++ + + d+++
  AJA92654.1  3 EEQAQQMLQQMQMLENMYTELSQKENSIKNIIRDaDSAI 41
                778899999999999999999999999444443446665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
       Spc24   9 iakelsdleselesleselaelkeeleeleeesee 43 
                 +  ++++le +l++ +s+ ++  ++le+ +++ ++
  AJA92654.1  96 LESKIKELEVALQETNSQRQQIAANLEQGKQQMQQ 130
                 45667777777777777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2754  (0.153606); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 985.18
//
Query:       AJA92655.1  [L=358]
Description: alcohol dehydrogenase, catalytic domain, GroES-like family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-25   89.2   0.0    3.4e-25   88.5   0.0    1.3  1  ADH_zinc_N     Zinc-binding dehydrogenase
    5.5e-20   71.3   0.1    8.9e-20   70.6   0.1    1.3  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    9.6e-19   68.7   0.1    1.5e-18   68.1   0.1    1.3  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.037   13.3   0.0       0.06   12.6   0.0    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.27   11.4   0.8       0.73   10.0   0.4    1.9  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   9.4e-29   3.4e-25       1     124 [.     184     313 ..     184     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 9.4e-29
                 HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET......TTC.HHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC. CS
  ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadeviny......kea.dlverikeltg.gegvdvvfecvGsgatleaalkllkpgGrlvvvGg. 90 
                 gvG++a+q+Ak +++ via++s + kl+++ +lGad+++++      k+  +++++i++  g   g+d++f+++G ++ ++  l+llk+g +lv +G+ 
  AJA92655.1 184 GVGSFAIQIAKLYNCDVIATASPD-KLDKCLELGADHAVDHrqedwsKQVfKISKEIAKTKGqAPGIDLSFDHIG-ETHFNKQLQLLKYGATLVSCGAt 280
                 9******************98766.8***************777776666667777777777688**********.**********************7 PP

                 .TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHH CS
  ADH_zinc_N  91 .gkgeeefdlrnlllkeksilGsllgslreefkea 124
                  g++ + +dlr++++k +++lGs+ g+ + e+ e 
  AJA92655.1 281 tGYDAK-IDLRHIFFKGINVLGSTQGT-KAELDEG 313
                 444444.*****************999.7777665 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.1   2.5e-23   8.9e-20       1     107 [.      31     139 ..      31     141 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.5e-23
                 TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG-TTBEETTTS...S-SSSB CS
       ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlCeeakllgvs...ldGgfa 96 
                 p+ev+   ka++++  D++ ++g   +  +lp + G +++G v +vg++vk++kvGdrVv + + +c  C+aC++g+e  C++++++g++   l+G+++
  AJA92655.1  31 PDEVVFTNKASALNYNDIWGMRG-VPIAIPLPHVSGSDVAGDVIAVGEDVKGFKVGDRVVSHSNLACRVCSACTSGREFDCTRRQVWGFQtgpLWGAYS 128
                 578999999**************.8************************************************************************** PP

                 SEEEECGGGEE CS
       ADH_N  97 eyvvvpekklv 107
                 e v +pe ++ 
  AJA92655.1 129 EEVHLPEVNVS 139
                 ******98875 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.1   4.3e-22   1.5e-18       1     133 []     215     353 ..     215     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4.3e-22
                   TT-SEEEETTSTTHH............HHH-T..T-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG... CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe............aatgg..egvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmka 83 
                   lGAd+++d+r+ed+             +  +g   g+D+ +d +g +++  + l++l+ g++lvs g++    +  + + + +   +k   ++  ++
    AJA92655.1 215 LGADHAVDHRQEDWSkqvfkiskeiakT--KGqaPGIDLSFDHIGETHF-NKQLQLLKYGATLVSCGAT----TGYDAKIDLRHIFFKGINVLGSTQ 304
                   8**********************99652..443368*********9988.99999**887999**9963....222222223333334333333445 PP

                   -.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2  84 saqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                   + +a+ l+e + ++ +Gk++  vd+v+++e+aaeAh ++ sg+ +GKi l
    AJA92655.1 305 GTKAE-LDEGLYWMGQGKIKAAVDSVYTFEQAAEAHTKMLSGKFFGKILL 353
                   53555.******************************************86 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05      0.06       5      73 ..     150     218 ..     147     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                  HHHHCSCGCTSEEETTCEETCB---.EEEEESTSH.HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
  AlaDh_PNT_C   5 aakalekffggkgtlaGgvpgvepa.kvlviGgGv.aGlqAiatakglgakVtvlDvrparleqleslgak 73 
                  aa a     ++  +l+G+ + ++p+ +vlv+GgG  +G  Ai++ak  + +V ++  +p++l +  +lga 
   AJA92655.1 150 AAAASMTILTSWHMLVGRAK-ITPGqTVLVMGGGSgVGSFAIQIAKLYNCDVIAT-ASPDKLDKCLELGAD 218
                  66677777788889999999.55552699*****769**************9887.456666666666666 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4    0.0002      0.73      49      82 ..     153     186 ..     146     193 .. 0.84
   2 ?   -2.5   0.0       1.7     6e+03      65      81 ..     267     283 ..     260     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
                    GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTE CS
  ACP_syn_III_C  49 saasiplaLdeaveegklkpgdlvllvgfGaGlt 82 
                    ++ +i+   + +v + k+ pg++vl++g G G+ 
     AJA92655.1 153 ASMTILTSWHMLVGRAKITPGQTVLVMGGGSGVG 186
                    57788889999****************9999975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                    SS-TT-EEEEEEEETTT CS
  ACP_syn_III_C  65 klkpgdlvllvgfGaGl 81 
                     lk g +++ +g+  G+
     AJA92655.1 267 LLKYGATLVSCGATTGY 283
                    67889999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2749.49
//
Query:       AJA92656.1  [L=110]
Description: hypothetical protein T478_0721 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        2.3    8.3   5.7        1.5    8.9   0.2    2.5  2  Sigma70_r1_1  Sigma-70 factor, region 1.1


Domain annotation for each model (and alignments):
>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   8.2e-05       1.5      30      51 ..       9      30 ..       5      32 .. 0.89
   2 ?    1.0   1.2     0.026   4.6e+02       9      30 ..      81     104 ..      75     110 .] 0.57

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 8.2e-05
                  CCSS--HHHHHHHHHHHHCCT- CS
  Sigma70_r1_1 30 pddeldseqiediiemLedmgI 51
                  ++del+++qi +i ++++dm +
    AJA92656.1  9 SKDELSEDQINKIKSYFSDMPV 30
                  5799***************965 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.026
                   HHHHHHHHHSC..EEHHHHHHHGC CS
  Sigma70_r1_1   9 eLikkgKkkGy..LtyeEindaLp 30 
                    +ik  +k+Gy   t + i + L+
    AJA92656.1  81 LMIKNYRKRGYsyPTISRIKKLLQ 104
                   567777777764444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 797.89
//
Query:       AJA92657.1  [L=333]
Description: reversibly glycosylated polypeptide [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-25   88.0   0.1    8.4e-25   87.7   0.1    1.2  1  RGP       Reversibly glycosylated polypeptide


Domain annotation for each model (and alignments):
>> RGP  Reversibly glycosylated polypeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.1   4.7e-29   8.4e-25      70     337 ..      55     329 ..       5     332 .. 0.78

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 4.7e-29
         RGP  70 ksisfsgsscryfGylvs.kkky..ivsidddcvpakdekGllvdavaqhiknlktPatPfffntlydPyreGad..f..vrGyPfslreGvetalslG 161
                 ks  f+ ++ r fG+  + +++y  +v +dddc+p  ++        ++hi+ lk+ +   +fn l       +d  f   rG+P s+ +  ++++  G
  AJA92657.1  55 KSWIFNRHTKRNFGFAYAlQQNYdaVVNLDDDCFPKSNT------YFTDHIERLKSSSHD-YFNILNAYSNIPSDvfFhgARGHPTSITKKSQVVVNQG 146
                 46679999*******877244556699********8765......4789*****998876.56777433333333113335****************** PP

         RGP 162 lwlnladydapt..qlvkaee.......rntryvdavltvPkkallpvsGinlafdrelvGpalfealklagegklryetledlwaGlcvkvicdhlgl 251
                 lw    d+ a t  +++ +++        n+  v   + +Pk+ + +v+G+n +f +e++ +  ++  + +g g +ry+   d+w+Gl +k i d+l+ 
  AJA92657.1 147 LWECDLDLPARTisNILSSKDgkipeplCNQSKVLQDFVIPKNQFTTVCGMNTSFLKEVIPAFPYTYQEPDGFGVARYD---DIWSGLFIKKILDKLDK 242
                 **9977776666323443332112222246677777789**********************999**9************...***************** PP

         RGP 252 GvktGlPyvlrkeasnale.slkkeweGvklmeevvpffqslklsktavtvedcvlelakavkeklgkvd..pvfakaadamvewvkaw 337
                  + +G+P v +++ + +++  +k e +G ++   +   +  l+   ++++   c+le+a+   +   +++    f+k+a++m  w+k  
  AJA92657.1 243 RMSAGFPIVSHEKGTRDVNiDVKFEDKGDTMNSFLWNNLSDLT--LETNDYTSCFLEIADWLGKTSKNNNslKFFEKVAESMYGWIKFL 329
                 ***********98776654278889999888666655555555..56778889*******987665555512579***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2313.36
//
Query:       AJA92658.1  [L=103]
Description: hypothetical protein T478_0832 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.01   16.3   0.1      0.028   14.9   0.0    1.6  2  TetR_C_28  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> TetR_C_28  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.14   2.5e+03      31      52 ..       5      25 ..       1      33 [. 0.45
   2 ?   14.9   0.0   1.6e-06     0.028      15      55 ..      50      91 ..      38      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.14
                HHHHHHHHHHHHHHS--TTGG- CS
   TetR_C_28 31 pellepwrewyrrwlerleadg 52
                +el + + +++++  e+l++d 
  AJA92658.1  5 EEL-AQIMKFVSEYWEKLKNDP 25
                333.344444444446666552 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-06
                ..-HHHHHHHHHGGGSHHHHHHHHHHHHHHS--TTGG-HH.H CS
   TetR_C_28 15 eerallaallaalaedpellepwrewyrrwlerleadgld.p 55
                ++++++++ +++ +ed+e+ + +re+++rw+++ +++++d p
  AJA92658.1 50 KTTKGRWVTTLMYLEDEEMEKSFREVLARWQAKGQQTATDlP 91
                457788999999*********************999998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 761.79
//
Query:       AJA92659.1  [L=423]
Description: collagen triple helix repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-43  144.7 162.7      5e-10   39.0  28.4    5.3  4  Collagen  Collagen triple helix repeat (20 copies)


Domain annotation for each model (and alignments):
>> Collagen  Collagen triple helix repeat (20 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5  34.0   1.6e-13   2.9e-09       1      58 [.     132     189 ..     125     189 .. 0.66
   2 !   24.7  36.2     8e-10   1.4e-05       7      58 ..     174     225 ..     168     237 .. 0.40
   3 !   39.0  28.4   2.8e-14     5e-10       1      59 [.     228     286 ..     222     287 .. 0.86
   4 !   10.7  65.0   1.8e-05      0.33       1      59 [.     324     382 ..     281     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.6e-13
                 XXXXXXXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB--X CS
    Collagen   1 GppGepGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGapg 58 
                 GppG+pG++G++G +G++G+pG++G++G+kG +G+kG++G +G+pG +G kG++G++g
  AJA92659.1 132 GPPGQPGPEGDKGDKGDKGAPGDKGPTGQKGVTGDKGDKGDKGPPGLKGDKGDKGEKG 189
                 6666666666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 8e-10
                 XXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB--X CS
    Collagen   7 GepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGapg 58 
                 G+pG +G +G++Ge+G +G kG+kG++G +G  G +G +G++G++G++G +g
  AJA92659.1 174 GPPGLKGDKGDKGEKGLTGDKGDKGEQGGRGLIGDKGGTGPQGPSGDKGLTG 225
                 4444444444444444444444444444443333333333333333333333 PP

  == domain 3  score: 39.0 bits;  conditional E-value: 2.8e-14
                 XXXXXXXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB--XX CS
    Collagen   1 GppGepGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGapge 59 
                 G++Ge+G+ GppG +G++G pG+ Ge+G+kG +G+ G++G++G++G++GekG+ G +g+
  AJA92659.1 228 GDKGEKGPTGPPGVQGDKGVPGSVGERGDKGVTGPMGEKGPTGPQGPQGEKGKIGITGP 286
                 78899999999999999999999999999999999999999999999999999998885 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 1.8e-05
                 XXXXXXXXXXXXXXXXXX-----XXXXEEEE-TTSS-----------------BB--XX CS
    Collagen   1 GppGepGepGppGppGkrGepGeaGekGekGpaGekGppGaaGkpGapGekGeaGapge 59 
                 GppG +Ge+Gp+Gp+G +G++Ge+G++G +Gp+G+kG++G++G+ G++G++G++G+pge
  AJA92659.1 324 GPPGLTGEKGPRGPQGIQGPQGEQGKQGLQGPPGDKGSQGPQGSVGEKGPRGPPGPPGE 382
                 55555555555555555555555555555555555555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3023.48
//
Query:       AJA92660.1  [L=411]
Description: cytochrome C biogenesis protein transmembrane region [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-57  194.8  16.3    1.4e-45  155.8  10.3    2.1  2  DsbD           Cytochrome C biogenesis protein transmembrane 
    1.4e-10   41.1   0.0    2.3e-10   40.4   0.0    1.3  1  AhpC-TSA       AhpC/TSA family
      6e-10   39.0   0.0    9.8e-10   38.3   0.0    1.3  1  Redoxin        Redoxin
    3.3e-08   33.7  15.2    1.2e-07   31.9  12.8    2.0  2  DsbD_2         Cytochrome C biogenesis protein transmembrane 
    1.6e-07   31.6   0.0    3.7e-07   30.4   0.0    1.6  1  Thioredoxin_8  Thioredoxin-like
     0.0017   17.8   9.0      0.004   16.6   7.4    1.9  2  SfLAP          Sap, sulfolipid-1-addressing protein
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.21   11.6   0.0    1.5  1  Thioredoxin    Thioredoxin
       0.55    9.6   9.4       0.17   11.3   0.2    2.9  3  TMEM43         Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.3   2.6e-14   5.8e-11       1      35 [.     138     172 ..     138     178 .. 0.92
   2 !  155.8  10.3   6.2e-49   1.4e-45      36     213 .]     203     380 ..     190     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.6e-14
        DsbD   1 aflaGllsflsPCilpliPaylsyisgvsvedvkt 35 
                 af aGllsflsPC+lpliPay s+i+g+s+ d  +
  AJA92660.1 138 AFAAGLLSFLSPCVLPLIPAYASFITGMSLRDLSN 172
                 699***************************99876 PP

  == domain 2  score: 155.8 bits;  conditional E-value: 6.2e-49
        DsbD  36 ekkkv..kvllkallFvlGlslvfvslglsaaflgqllkdvkevirrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalg 132
                 +k ++   vl k llFvlG+s++fv lg +++ +g+++ + + +++r++g++ i +Glh++g++k++ l+++k++ + ++++  + +g+l +G++F++g
  AJA92660.1 203 SKFRIqtMVLSKGLLFVLGFSIIFVILGSAVSYAGTMFDEATLWVERIGGIVLITFGLHLIGILKLNKLNMQKSMNFQNRST--KNIGSLFVGMAFGAG 299
                 34455547999****************************************************************7744444..46************* PP

        DsbD 133 wsPCigPvlasvlalaaskeslakgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGvllll 213
                 w+PCigP+la +l++aa++ s   g++ll++y+ Glaipf++ +l ++++  +++++k++  ++e  +g+ll+ +G lll+
  AJA92660.1 300 WTPCIGPILAGILTMAATSSSWGAGTSLLIAYSAGLAIPFIISALAIDRFMTFFNKIKRWIGWIERGSGILLIGIGGLLLT 380
                 *****************************************************************************9986 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0     1e-13   2.3e-10      29     121 ..       1      88 [.       1      91 [. 0.92

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1e-13
                 EEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH..HHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBE CS
    AhpC-TSA  29 vlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe..shkkfiekeslnfpllsDeegkvakaygvlkeekglalratfvidkegki 121
                 +l+++++ wc  C +e+p l++l++e+   g++ + vs+d+     +k+f+++ +++ ++ +D+ +++ +++ ++        + t +i+ +g +
  AJA92660.1   1 MLNVWAT-WCIECLEEMPYLNELNKEYSPSGLKTLSVSIDTISpdIVKEFADDMDMTTEIWYDPRNNATREFRMM------GPPITLLINGNGEL 88 
                 699****.********************************87766******************************......67888888888876 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   4.4e-13   9.8e-10      32     133 ..       1      94 [.       1     104 [. 0.94

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 4.4e-13
                 EEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEE CS
     Redoxin  32 vvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf..vkefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvv 128
                 ++n++++ +c  C +e+pyl++l+++++ +g + + v++d+ ++  vkef+++ + +  + +D+  + t+++   ++       + p + +i+ +g ++
  AJA92660.1   1 MLNVWAT-WCIECLEEMPYLNELNKEYSPSGLKTLSVSIDTISPdiVKEFADDMDMTTEIWYDPRNNATREFR--MM-------GPPITLLINGNGELI 89 
                 58*****.*****************************************************************..65.......99**********999 PP

                 EEEES CS
     Redoxin 129 yleve 133
                 +  ++
  AJA92660.1  90 HEWKG 94 
                 87555 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.077   1.7e+02     113     140 ..     131     158 ..     104     168 .. 0.63
   2 !   31.9  12.8   5.2e-11   1.2e-07      34     198 ..     214     376 ..     195     377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.077
      DsbD_2 113 kklkslasalllGllnGllpCgl.vysal 140
                 ++  s   a+++Gll  l pC l + +a+
  AJA92660.1 131 DQ-LSIGVAFAAGLLSFLSPCVLpLIPAY 158
                 33.37778999999999999987444444 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 5.2e-11
      DsbD_2  34 alllynlGRilsYallGalvgllgsvlqlageleglrallgvllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGlln..Gl 130
                 + ll+ lG  + +++lG +v ++g ++  a+   +++++ g++l++++l     l+   ++lkl++l+ + s  +++ +    +  ++l++G+++  G+
  AJA92660.1 214 KGLLFVLGFSIIFVILGSAVSYAGTMFDEAT--LWVERIGGIVLITFGLH----LI---GILKLNKLNMQKSMNFQNRST---KNIGSLFVGMAFgaGW 300
                 5899***********************8776..57788887777777665....44...345667777655555555544...567778888876337* PP

      DsbD_2 131 lpC..glvysalllalasgsaleGalvmlaFgLGTlpalllfglllgllskklr......kkllrlagvllillgl 198
                  pC  +++  +l++a++s+s+  G  +++a++ G  +++++ +l++ ++ + ++        + r +g+lli +g+
  AJA92660.1 301 TPCigPILAGILTMAATSSSWGAGTSLLIAYSAGLAIPFIISALAIDRFMTFFNkikrwiGWIERGSGILLIGIGG 376
                 ****777999*********************************999999775554434446677888888888886 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.7e-10   3.7e-07       6      94 ..       2      87 ..       1      88 [. 0.92

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.7e-10
                   EEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE-TT-B CS
  Thioredoxin_8  6 LyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvkaiPtlvvldknge 94
                   L ++a+wc +c + +p l+el ++++ + +++ ++vs+d    +  k +++++   +++ +d   rn   +++++++ P +++++ nge
     AJA92660.1  2 LNVWATWCIECLEEMPYLNELNKEYS-PSGLKTLSVSIDTISPDIVKEFADDMDMTTEIWYD--PRNNATREFRMMGPPITLLINGNGE 87
                   899**********************9.9***********99999999999997788888888..67888899***************97 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.19   4.3e+02     104     125 ..     128     149 ..     110     168 .. 0.61
   2 !   16.6   7.4   1.8e-06     0.004      31     208 ..     215     379 ..     210     383 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.19
       SfLAP 104 srleslleggalwvAlvlglls 125
                 s++++l++g a++++l+ +l  
  AJA92660.1 128 SQMDQLSIGVAFAAGLLSFLSP 149
                 4555555555555555544433 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.8e-06
       SfLAP  31 llaFlvgwlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrrpkassrselprllsrleslleggalwvAlvlgllsakpl 129
                 +l+F++g  +  v+lg +v  ++ ++          a  +++ + G++l+ ++++      k ++   ++++  + +s+++ g+l v++++g++  + +
  AJA92660.1 215 GLLFVLGFSIIFVILGSAVSYAGTMFD--------EATLWVERIGGIVLITFGLHLIGIL-KLNKLNMQKSMNFQNRSTKNIGSLFVGMAFGAGWTPCI 304
                 455555555555555555555555554........5566777788888888888877777.444444455555555599999*************999* PP

       SfLAP 130 llylaalaaigasgasvgtqvvalvvFvvvalavveipllaylvapertqavlerlkdwlrsnrrlilavilgvvGlll 208
                  + la +++++a   s g+  ++l++++    a ++ip +  ++a +r  ++ +++k+w+   +r   +++ g+ Glll
  AJA92660.1 305 GPILAGILTMAATSSSWGAGTSLLIAYS----AGLAIPFIISALAIDRFMTFFNKIKRWIGWIERGSGILLIGIGGLLL 379
                 ***********99999888888888875....7799*************************999999999999998887 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.3e-05      0.21      23      60 ..       2      40 ..       1      56 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-05
                 EEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTT CS
  Thioredoxin 23 veFyApwCghCkalaPeleklaeelkd.kvklakvdvde 60
                 ++ +A+wC  C +  P l++l +e++   +k + v +d+
   AJA92660.1  2 LNVWATWCIECLEEMPYLNELNKEYSPsGLKTLSVSIDT 40
                 568**********************98755555555554 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.2      0.42   9.4e+02     191     223 ..     212     241 ..     183     257 .. 0.60
   2 ?    3.0   0.5     0.024        55     185     204 ..     244     263 ..     238     274 .. 0.90
   3 ?   11.3   0.2   7.5e-05      0.17     178     217 ..     353     392 ..     337     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
      TMEM43 191 llGfllmflglllllsplsvlvslipllgelvg 223
                 l   ll++lg+++++ +l   vs++     +  
  AJA92660.1 212 LSKGLLFVLGFSIIFVILGSAVSYAGT---MFD 241
                 344577788888888888877775544...444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.024
      TMEM43 185 ltwllRllGfllmflgllll 204
                 + w+ R++G++l+ +gl l+
  AJA92660.1 244 TLWVERIGGIVLITFGLHLI 263
                 68**************9886 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 7.5e-05
      TMEM43 178 eksenklltwllRllGfllmflglllllsplsvlvslipl 217
                   + ++++ w+ R  G+ll+ +g lll+  lsvl+s++p 
  AJA92660.1 353 FNKIKRWIGWIERGSGILLIGIGGLLLTGSLSVLASYFPN 392
                 566788999*****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2942.21
//
Query:       AJA92661.1  [L=1080]
Description: carbamoyl-phosphate synthase, large subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.1e-102  339.0   0.1    2.5e-74  249.4   0.2    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    2.2e-36  124.9   0.0    5.3e-36  123.7   0.0    1.7  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.3e-19   70.4   0.3    1.3e-09   37.9   0.0    2.4  2  ATP-grasp        ATP-grasp domain
    1.8e-15   57.1   4.1    1.1e-07   31.6   0.0    2.7  3  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    2.7e-14   53.1   0.1    2.7e-13   49.9   0.0    2.9  3  MGS              MGS-like domain
    1.2e-11   44.5   0.0    7.6e-06   25.7   0.0    2.6  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    5.9e-11   42.5   0.6    7.4e-05   22.6   0.0    2.6  2  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    2.8e-07   30.7   0.6     0.0027   17.7   0.0    2.5  2  ATP-grasp_3      ATP-grasp domain
      2e-06   27.5   1.7      0.035   13.7   0.0    2.6  2  ATP-grasp_4      ATP-grasp domain
     0.0064   16.1   0.1      0.035   13.6   0.1    2.3  2  ATP-grasp_2      ATP-grasp domain
  ------ inclusion threshold ------
      0.019   14.5   0.0       0.46    9.9   0.0    2.5  2  ATP-grasp_5      ATP-grasp domain
      0.045   14.0   0.0       0.33   11.2   0.0    2.5  2  TrkA_N           TrkA-N domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.4   0.2   1.6e-77   2.5e-74       1     210 [.     128     333 ..     128     334 .. 0.99
   2 !   87.5   0.0   5.8e-28   8.7e-25       1     209 [.     671     872 ..     671     874 .. 0.91

  Alignments for each domain:
  == domain 1  score: 249.4 bits;  conditional E-value: 1.6e-77
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEve 98 
                  D++ +k+ +k+++vpv +s+++  ++ e+a ++a+e++yPvii+ a++lGG+G+++a+ne el+e+v+++ ++++      qvlve+++ ++k+iE+e
   AJA92661.1 128 DRQLFKDSMKEAGVPVLKSKTV--TNFEDAKKVAEELSYPVIIRVAYTLGGRGGGIAHNEIELHEIVERGCKASM----VGQVLVEEYIGHWKQIEYE 219
                  9*******************99..**************************************************7....89***************** PP

                  EEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS-- CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGld 194
                  v++D +gn ++vc++en+l +  +t++ i+vAPsqt++++e+++lr+aa++++++vg+vg+++++++ld++s++y+ iE+N+Rls++sala+kaTG++
   AJA92661.1 220 VMQDYDGNNVIVCNMENVLSMkvHTGDNIVVAPSQTINNHEYHMLRTAALRATKHVGIVGECNIQYALDADSDRYVAIEINPRLSRSSALASKATGYP 317
                  ******************99999*************************************************************************** PP

                  HHHHHHHHHTT--GCG CS
  CPSase_L_D2 195 lvkeaakialgekLee 210
                  l++++aki+lg++L+e
   AJA92661.1 318 LAYMSAKIGLGYNLSE 333
                  **************97 PP

  == domain 2  score: 87.5 bits;  conditional E-value: 5.8e-28
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEve 98 
                  D++++++ l+k++++  + +a   ++l+ea ++a+++g+Pvi+++++ l G  m+v+++++el+  vk+a++ ++    ++ v + k++    e++v+
   AJA92661.1 671 DRSKFSAELDKLHIQQPKWQAF--SNLNEARNFAQDVGFPVIVRPSYVLSGAAMKVVWSQDELKTYVKEATDVSP----DHPVVISKFMLDSLEVDVD 762
                  8999*******99999988888..**************************************************6....9****************** PP

                  EEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS-- CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGld 194
                   ++  k+ vi     e ++    + ++ +   P   L++++ ++++  + k++ + +v+g  +++fl++  +++ yviE+N R s++ +  +k    +
   AJA92661.1 763 GISNGKEVVIGA-IVEHIDSAgvHSGDAMMCIPPWRLSNKTIETINDYTKKIALTFNVKGPFNLQFLIH--DDHVYVIELNIRASRSMPFVSKLVKTN 857
                  999998877743.3444444445**********************************************..599********************9999 PP

                  HHHHHHHHHTT--GC CS
  CPSase_L_D2 195 lvkeaakialgekLe 209
                  l+  a k  l ++L+
   AJA92661.1 858 LISLASKAILDKPLP 872
                  999998877777776 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7   0.0   3.5e-39   5.3e-36       2     122 .]     425     542 ..     424     542 .. 0.96

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 3.5e-39
  CPSase_L_D3   2 elkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaelleeeeeeevrelrkklgilp 99 
                  +l++ +d+ ++ +a  l+ g+sv++i+el+ idpwF+ek++++v++e++lk+++  l+e++lr+akk+GfsD+qia++ +e++ +evr++rk+ gi p
   AJA92661.1 425 KLSHHDDQILYNVAIGLKMGISVNRIYELSAIDPWFIEKIKNIVNVESNLKESE--LNESVLRNAKKMGFSDNQIARV-KEKTPDEVRKIRKDFGIIP 519
                  688999999******************************************996..9*********************.5688899************ PP

  CPSase_L_D3 100 vykrvDtcAaeFeaetpYlYstY 122
                  ++k++Dt+Aae++a t+YlY tY
   AJA92661.1 520 AVKQIDTLAAEWPAVTNYLYLTY 542
                  **********************9 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.3   2.2e-10   3.3e-07       2     159 ..     137     302 ..     136     309 .. 0.83
   2 !   37.9   0.0   8.7e-13   1.3e-09       2     160 ..     680     843 ..     679     846 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.2e-10
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvv 96 
                 +++g+pv +  +v++ e+++++aeel +pv+++       G+G  + ++e +l++++e        ++v+vEe++   k +   v+++ +G+ +++  +
  AJA92661.1 137 KEAGVPVLKSKTVTNFEDAKKVAEELSYPVIIR-VAYTLGGRGGGIAHNEIELHEIVERGckasMVGQVLVEEYIGHWKQIEYEVMQDYDGNNVIVCNM 234
                 7899*****************************.899999*************99998776777889*************************7777777 PP

                 EEEEETTEE...EEEEECEE-SCH.HHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT.EEEEEEESS CS
   ATP-grasp  97 etvqedgil...rlsvapaevsek.aqkkaeeiakkiveeLggvGvfavElFvledge.llvnElapR 159
                 e+v + ++    +++vap++  ++ + +  ++ a ++++++g+vG   +   + +d++  ++ E+ pR
  AJA92661.1 235 ENVLSMKVHtgdNIVVAPSQTINNhEYHMLRTAALRATKHVGIVGECNIQYALDADSDrYVAIEINPR 302
                 76655554422257778877665515555666666**********99999988888887677788888 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 8.7e-13
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvv 96 
                 +kl+++ p+++a ++ +e++++a+++g+pv+v+ +    +G   +vv s+++l++ ++++     +++v++ +f+  + E+ v ++ + +  +++ ++v
  AJA92661.1 680 DKLHIQQPKWQAFSNLNEARNFAQDVGFPVIVR-PSYVLSGAAMKVVWSQDELKTYVKEAtdvsPDHPVVISKFMLDSLEVDVDGISNGKE-VVIGAIV 776
                 7899*****************************.99999*******************999998899*******************98775.99999** PP

                 EEEEE....TTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS- CS
   ATP-grasp  97 etvqe....dgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRp 160
                 e++ +    +g+  +++ p ++s+k  +++++++kki+ ++++ G f + + +  d++++v El  R 
  AJA92661.1 777 EHIDSagvhSGDAMMCIPPWRLSNKTIETINDYTKKIALTFNVKGPFNLQFLIH-DDHVYVIELNIRA 843
                 **9971111456789**********************************97777.888*****99885 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.4   3.9e-09   5.8e-06      10     174 ..     144     301 ..     136     311 .. 0.77
   2 ?   -3.8   0.1       5.2   7.7e+03      74      96 ..     467     489 ..     462     502 .. 0.76
   3 !   31.6   0.0   7.3e-11   1.1e-07      11     173 ..     688     840 ..     679     844 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.9e-09
                      --EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEE..TSSCEE CS
  Dala_Dala_lig_C  10 vpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlg..neklev 98 
                       + +++++        e  +kv eel+ypv+++ a +    G   +++e el+e +e+  k     +vlvEe+i + ++ie  v++  ++++ +
       AJA92661.1 144 LKSKTVTN------F-EDAKKVAEELSYPVIIRVAYTLGGRGGGIAHNEIELHEIVERGCKASmvGQVLVEEYIgHWKQIEYEVMQdyDGNNVI 230
                      44333332......2.345789*************98777888889***********9987652279*******999*********44344444 PP

                      EEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTE.EEEEEEES CS
  Dala_Dala_lig_C  99 sevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteege.ivlnEvNt 174
                          e v++ ++      +++d++ +    ++++++++ ++++al+a k +++ G + + + l+++ +  v  E+N+
       AJA92661.1 231 VCNMENVLSMKV------HTGDNIVVAPSQTINNHEYHMLRTAALRATKHVGIVGECNIQYALDADSDrYVAIEINP 301
                      444444444433......2568888999999********************************77655055579985 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.2
                      CEEEEE--ESEEEEEEEEETSSC CS
  Dala_Dala_lig_C  74 kvlvEeaiegreievavlgnekl 96 
                       v vE +++  e++ +vl n k 
       AJA92661.1 467 IVNVESNLKESELNESVLRNAKK 489
                      57799999999999999998764 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 7.3e-11
                      -EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEEEEEETSSCEE.EE CS
  Dala_Dala_lig_C  11 pyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreievavlgneklev.se 100
                      +++++ +        +  ++  + +g+pv+V+p+   S   ++ v s++elk +++ea     d+ v++ +++ +  e++v  + n+k  v   
       AJA92661.1 688 KWQAFSNL-------NEARNFAQDVGFPVIVRPSYVLSGAAMKVVWSQDELKTYVKEATDVspDHPVVISKFMlDSLEVDVDGISNGKEVViGA 774
                      44444332.......33457799***********************************76434999*****99899999998888887554044 PP

                      EEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEE CS
  Dala_Dala_lig_C 101 vgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvN 173
                      ++e++ + g+      +s+d++++  p +l++++ e+i+++ +k+  + +++G   + f+++ ++++++ E+N
       AJA92661.1 775 IVEHIDSAGV------HSGDAMMCIPPWRLSNKTIETINDYTKKIALTFNVKGPFNLQFLIH-DDHVYVIELN 840
                      5555555554......57788999999********************************998.8999999999 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         5   7.4e+03      51      69 ..      32      50 ..      12      59 .. 0.70
   2 ?   -2.3   0.0       3.6   5.4e+03      25      46 ..     135     156 ..     133     194 .. 0.72
   3 !   49.9   0.0   1.8e-16   2.7e-13       2      95 .]     955    1048 ..     954    1048 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5
                HHHHHHHTTSCCEEEEE-- CS
         MGS 51 eildaikngeidlvintly 69
                + l+ai++ +i+ v ++++
  AJA92661.1 32 QCLKAIHEDGIKSVLINPN 50
                7889999999997777765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                 HHHHTT--EEECCCCHSTGSGG CS
         MGS  25 llkeagipvtevvektgegerl 46 
                  +keag+pv +   +t++++  
  AJA92661.1 135 SMKEAGVPVLKSKTVTNFEDAK 156
                 5789999999988888888433 PP

  == domain 3  score: 49.9 bits;  conditional E-value: 1.8e-16
                  HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH....CHHHHHHHHHHHTTSHEE CS
         MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva....kdgykirraaenidIplp 94  
                  l++ + klk+lgf++lAT+ Ta++++e+  + +e+v+k++e+er     +i d++ +++id++in++++++  +     +d+y+irr  ++ +Ip+ 
  AJA92661.1  955 LLPSIAKLKQLGFKILATEHTAEFFEEKVGD-IEIVHKISEPERKP---NISDLLYEKKIDFIINIPSTLSLEKYvgmlDDEYQIRRKSLELGIPVL 1047
                  788999********************99888.99********9988...8*******************998887899*****************98 PP

                  S CS
         MGS   95 t 95  
                  t
  AJA92661.1 1048 T 1048
                  7 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     5e-06    0.0074      49     119 ..     264     337 ..     251     347 .. 0.78
   2 !   25.7   0.0   5.1e-09   7.6e-06      47     120 ..     804     878 ..     745     886 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
  ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveep 119
                   l  +a r ++++g+ g  n+Q+  d+d   ++ +EiNpR s      s ++G  l+y+++k  lg + +e ++ 
    AJA92661.1 264 LRTAALRATKHVGIVGECNIQYALDADSdrYVAIEINPRLSRSSAlASKATGYPLAYMSAKIGLGYNLSELVNR 337
                   45678899**************99888776889*******96555156777**********9999866666555 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 5.1e-09
  ATPgrasp_Ter  47 eelielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllgleteeveepe 120
                   e + ++++++a +f+++g +n+Q+  ++d+ +++E N Ras  +  +s l   nl++la k++l+++ ++v+e +
    AJA92661.1 804 ETINDYTKKIALTFNVKGPFNLQFLIHDDHVYVIELNIRASRSMPfVSKLVKTNLISLASKAILDKPLPKVPENK 878
                   56778999************************************8468999**************8666665544 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2     2e-06    0.0029       4     105 ..     130     229 ..     127     247 .. 0.84
   2 !   22.6   0.0   4.9e-08   7.4e-05      10     107 ..     679     772 ..     673     844 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                 HHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE--...-SEEEEEEEE CS
      GARS_A   4 sfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEell...eGeEvsllal 99 
                 +  kd +k+ag+p  + +++t+ e+ak++ ee++ ++ +++ +   +g+g  +a++e e  ++v+   +    G    +v++Ee++   + +E  ++  
  AJA92661.1 130 QLFKDSMKEAGVPVLKSKTVTNFEDAKKVAEELSYPV-IIRVAYTLGGRGGGIAHNEIELHEIVERGCKASMVG----QVLVEEYIghwKQIEYEVMQD 223
                 667999*******************************.999998999************999999999988888....9****9973223455555555 PP

                 ECTTEE CS
      GARS_A 100 vdgktv 105
                  dg++v
  AJA92661.1 224 YDGNNV 229
                 566655 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 4.9e-08
                 HHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE-.--SEEEEEEEEECTTEEEE CS
      GARS_A  10 lkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEel.leGeEvsllalvdgktvkp 107
                 l+k +i+ ++++af++ +ea+++ +++++++ +v+++ + +g  ++v+ s++e  ++vke  +     +  + vvi ++ l+  Ev +  +++gk+v+ 
  AJA92661.1 679 LDKLHIQQPKWQAFSNLNEARNFAQDVGFPV-IVRPSYVLSGAAMKVVWSQDELKTYVKEATD----VSPDHPVVISKFmLDSLEVDVDGISNGKEVVI 772
                 57899**************************.9***************************997....45689999988648999***********9975 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.3   0.00022      0.33       9     159 ..     134     304 ..     126     306 .. 0.70
   2 !   17.7   0.0   1.8e-06    0.0027       2     158 ..     670     843 ..     669     846 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                  HHHTTT.S---.........-EESS--..SSSEEEEESS-------B--SS--TTE...............EEEE---S.EEEEEEEEE.SSSEEEEE CS
  ATP-grasp_3   9 kkLkeagvkvP.....tkleaeeleee..ekklvvKprdGaggesvrvveekeeaeaaieeve........lvqefieG.kplSvsllsdgekvlvla 90 
                  + +keagv+v      t+ e+++   e   +++++  ++  gg +  +++++ e+++++e  +        lv e+i   k++  +++ d   + v++
   AJA92661.1 134 DSMKEAGVPVLksktvTNFEDAKKVAEelSYPVIIRVAYTLGGRGGGIAHNEIELHEIVERGCkasmvgqvLVEEYIGHwKQIEYEVMQDYDGNNVIV 231
                  556666555556665544554444433558999*******************999999999889999999999***9543889999999999999999 PP

                  EEEEEEET....TEEEEE...EES----H...HHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEE.EEEESS-- CS
  ATP-grasp_3  91 vnrqliekaekefvyaGn...vtpietel...keevvelaeevvekleglaGyvGvDlvlkd.eepyv.iEvNPRlt 159
                  +n + +       v +G    v+p++t +    + ++++a ++++++ g++G   +   l   ++ yv iE+NPRl 
   AJA92661.1 232 CNMENVLSM---KVHTGDnivVAPSQTINnheYHMLRTAALRATKHV-GIVGECNIQYALDAdSDRYVaIEINPRLS 304
                  998877542...44444322244555444111555667777777777.888888888777655555555******96 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.8e-06
                  TSHHHHHHHHTTT.S---.........-EESS--.......SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEE CS
  ATP-grasp_3   2 sdKlktykkLkeagvkvP.....tkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvs 78 
                  +d  k+  +L++  ++ P     ++l++     +         +++v p++   g ++ vv  ++e+++ ++e +         + + ++++ ++ v+
   AJA92661.1 670 EDRSKFSAELDKLHIQQPkwqafSNLNE-----ArnfaqdvGFPVIVRPSYVLSGAAMKVVWSQDELKTYVKEATdvspdhpvvISKFMLDSLEVDVD 762
                  7888899999999999997766644433.....22233344899**************99999999999888888999*****66677799******* PP

                  EEE.SSSEEEEEEEEEEEET....TEEEEEEES-..---HHHHHHHHHHHHHTTST...T--EEEEEEEEESS.SEEEEEEESS- CS
  ATP-grasp_3  79 llsdgekvlvlavnrqliekaekefvyaGnvtpi..etelkeevvelaeevvekle...glaGyvGvDlvlkdeepyviEvNPRl 158
                   +s+g++v++ a+ + +        v +G  +    + +l+++++e++++ ++k+    +++G +   ++++d+  yviE N R 
   AJA92661.1 763 GISNGKEVVIGAIVEHIDSA----GVHSGDAMMCipPWRLSNKTIETINDYTKKIAltfNVKGPFNLQFLIHDDHVYVIELNIRA 843
                  *****999888877665544....777887654411345799999999999999988889999999****************985 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.3   6.6e-05     0.098      46     151 ..     197     302 ..     178     308 .. 0.77
   2 !   13.7   0.0   2.3e-05     0.035       2     150 ..     706     841 ..     705     846 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.6e-05
  ATP-grasp_4  46 keevveeesflvEeyieG.eEfavdayfdeeGepvilnilkkefaseedvsdrlyvtsakvieetleal.eellkevnallglknfpvHiElrvsedg 141
                  k+++   +++lvEeyi   + +  ++  d +G++vi+  ++   +++ ++ d + v +++ i+++++++  ++  ++ +++g+  + + i   +++d+
   AJA92661.1 197 KASM--VGQVLVEEYIGHwKQIEYEVMQDYDGNNVIVCNMENVLSMKVHTGDNIVVAPSQTINNHEYHMlRTAALRATKHVGIV-GECNIQYALDADS 291
                  3344..489*******64378899999*********************************999999998556666777788875.3444555554444 PP

  ATP-grasp_4 142 .kiipiEvnpl 151
                   + + iE+np+
   AJA92661.1 292 dRYVAIEINPR 302
                  378889***95 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
  ATP-grasp_4   2 slPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGep.vilnilkkefaseedvsdrl 98 
                   +Pv+++Ps   +   + ++ +++e+k  v++       ++   +++ v  ++f++    +  E+ vd+    +G++ vi +i+++  +   +  d +
   AJA92661.1 706 GFPVIVRPSYVLSGAAMKVVWSQDELKTYVKEAT----DVS---PDHPVVISKFML----DSLEVDVDGIS--NGKEvVIGAIVEHIDSAGVHSGDAM 790
                  5899999999999999999988888888554444....223...333343466665....5569*****98..5655167799999999998888888 PP

  ATP-grasp_4  99 yvt.sakvieetlealeellkevnallglknfpvHiElrvsedgkiipiEvnp 150
                   ++ + +++++t+e++++++k+++  +++k +p+   + +++d ++++iE+n 
   AJA92661.1 791 MCIpPWRLSNKTIETINDYTKKIALTFNVK-GPFNLQFLIHDD-HVYVIELNI 841
                  6651679*****************888875.9*********98.8******96 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   2.4e-05     0.035       9      60 ..     134     182 ..     130     220 .. 0.78
   2 ?   -3.5   0.0       4.2   6.2e+03      13      52 ..     681     720 ..     679     737 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                  HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEE CS
  ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvk 60 
                  + +++ gv+v +++ +++ e+a+++a++l+  + +++     GGRG  gG+ 
   AJA92661.1 134 DSMKEAGVPVLKSKTVTNFEDAKKVAEELSYPV-IIRVAYTLGGRG--GGIA 182
                  568999*************************99.99*********9..5553 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
                  CTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSST CS
  ATP-grasp_2  13 kygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGG 52 
                  k  ++ p+ +  ++ +ea++ a+++g  ++v  + vl G+
   AJA92661.1 681 KLHIQQPKWQAFSNLNEARNFAQDVGFPVIVRPSYVLSGA 720
                  6678888888899999999999999999988777787775 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00031      0.46      19      54 ..     136     171 ..     105     174 .. 0.90
   2 ?    1.5   0.0      0.11   1.7e+02      19      51 ..     679     711 ..     670     714 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
  ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvlKiv 54 
                  ++  g+pv++++ +++ e+a ++aee+ ypv ++++
   AJA92661.1 136 MKEAGVPVLKSKTVTNFEDAKKVAEELSYPVIIRVA 171
                  5678****************************9975 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
  ATP-grasp_5  19 leaygipvvetrlassaeeaveaaeeigypvvl 51 
                  l+ ++i+ ++ +  s+ +ea + a+ +g+pv +
   AJA92661.1 679 LDKLHIQQPKWQAFSNLNEARNFAQDVGFPVIV 711
                  6788999***********************987 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.33      16      83 ..     584     652 ..     578     678 .. 0.85
   2 ?   -2.2   0.0       3.3   4.9e+03      85     115 ..     981    1015 ..     967    1016 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                 HHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHH CS
      TrkA_N  16 eLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavlla 83 
                  L+e g+k+v+v+  ++e+v +  +  ++ +  + t+e +L+  + e+ ++vi+++g  +an l+  la
  AJA92661.1 584 GLQEnGEKNVSVVNCNPETVSTDYDICTRLYFEELTQERLLDISDFENPKGVITCVGGQTANNLTPGLA 652
                 578856689************************************************999988776666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.3
                  HHTSSSEEEEEESSGGG....HHHHHHHTTSEEEE CS
      TrkA_N   85 elnpkkkiiaraqdpeh....aellkklgadvvis 115 
                  e  ++++i+ ++++pe+     +ll++  +d +i+
  AJA92661.1  981 EKVGDIEIVHKISEPERkpniSDLLYEKKIDFIIN 1015
                  34445889999999999777777888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1080 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 6964.91
//
Query:       AJA92662.1  [L=420]
Description: phosphoribosylamine--glycine ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-76  256.4   0.3    2.2e-76  256.0   0.3    1.2  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    5.9e-32  110.3   0.1    1.2e-31  109.4   0.1    1.5  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
    3.7e-30  104.0   0.0    8.4e-30  102.9   0.0    1.6  1  GARS_C           Phosphoribosylglycinamide synthetase, C doma
    3.8e-07   29.8   0.0    6.6e-07   29.0   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    7.3e-07   29.0   0.1    1.6e-06   27.8   0.1    1.5  1  RimK             RimK-like ATP-grasp domain
    9.8e-07   29.0   0.0    1.7e-06   28.2   0.0    1.3  1  ATP-grasp_3      ATP-grasp domain
    7.6e-06   25.6   0.1    1.3e-05   24.8   0.1    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    0.00018   21.1   0.1     0.0003   20.4   0.1    1.2  1  ATP-grasp_2      ATP-grasp domain
    0.00053   19.6   0.0      0.001   18.7   0.0    1.4  1  ATP-grasp_4      ATP-grasp domain
    0.00091   18.5   0.2      0.002   17.4   0.2    1.6  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
  ------ inclusion threshold ------
      0.029   13.9   0.0      0.046   13.2   0.0    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      0.075   12.9   0.1       0.16   11.8   0.1    1.5  1  DUF448           Protein of unknown function (DUF448)


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.0   0.3   1.5e-79   2.2e-76       1     194 []      98     290 ..      98     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.0 bits;  conditional E-value: 1.5e-79
                 HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEEEEEE CS
      GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEvsllal 99 
                 +sK +ak+++k+  ipta++e f+d+++ak+++++ ++++ V+KadglaagKgviv+k+++ea +a++ il kk+fG+ag+k++iEe+++G E s +al
  AJA92662.1  98 SSKIWAKEFMKRNSIPTADFEIFDDAQKAKDFVKSYEKPV-VIKADGLAAGKGVIVCKNKDEANDAIDTILIKKSFGDAGSKIIIEERIDGVEASYIAL 195
                 59**************************************.********************************************************** PP

                 ECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
      GARS_A 100 vdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                 +dgk  +p++++qdhkrv+++D+gpnTGGmGaysp+p++ e+l ++i+e+i+++t++++++eg +fkG+Lyag+m+ +  p+vle+nvR gDpe+
  AJA92662.1 196 CDGKIGIPMATSQDHKRVFDNDEGPNTGGMGAYSPTPIIDEKLGTEIQEKIIDKTIHAMRDEGFEFKGFLYAGIMIKDGIPYVLEYNVRMGDPEC 290
                 ****************************************************************************8888**************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.1   7.7e-35   1.2e-31       2      90 .]       3      97 ..       2      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 7.7e-35
                EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG........TTHHHHHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHHT-EEES--CCCCHHH CS
      GARS_N  2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt........edlealvefakeekidlvvvGpeapLvaGvadaleeekgikvfGpskeaAqlE 90
                +vLvvG GGRehal wkl+ s+k+++vy+apgN+gt        +d+e l++fa+e+++ ++vvGpe+pL++G++da+ e+ g+++fGp+k+aA+lE
  AJA92662.1  3 NVLVVGAGGREHALSWKLSTSEKIDQVYAAPGNGGTlqnvelsvTDIEGLAKFAQEKNC-FTVVGPEDPLATGIVDAFVEK-GLPIFGPTKNAAKLE 97
                8**************************************999999999*******9995.99****************777.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.0   5.6e-33   8.4e-30       1      80 []     326     415 ..     326     415 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 5.6e-33
                 EEEEEEEETTTTSS--ST-EEBS.....TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE--STTTHH CS
      GARS_C   1 avgvvlaskGYPgsyekgkeitg.....egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikfeglfyRkDIGar 80 
                 +v+vvlaskGYP+sy++g+eitg     +++ vfhagtk     + ++GGRvl+v+a+g++l++A+++ay+a+++i+++++++R+DIG++
  AJA92662.1 326 SVCVVLASKGYPSSYPTGDEITGfenisSDAFVFHAGTKkqddkIKSNGGRVLGVTALGSSLQDAINNAYDACNHIHWTNKYHRTDIGKK 415
                 69**************************8889******999**9********************************************85 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.4e-10   6.6e-07       2      73 ..     108     186 ..     107     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.4e-10
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE--- CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvp 73 
                 +++ +p+++f + ++++++++++++ + pvv+K + +   GkG  v+++++++++a++++        ++ k+i+Ee+++
  AJA92662.1 108 KRNSIPTADFEIFDDAQKAKDFVKSYEKPVVIK-ADGLAAGKGVIVCKNKDEANDAIDTIlikksfgdAGSKIIIEERID 186
                 57889****************************.566668******************9999*99999899******997 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   1.1e-09   1.6e-06       4      72 ..     100     168 ..      94     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.1e-09
                 HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH..G CS
        RimK   4 KlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea..l 72 
                 K+ + + + ++ i++  +++  d ++a+++++ +  + Pvv+K      G +v+++k+++++++ +++  +
  AJA92662.1 100 KIWAKEFMKRNSIPTADFEIFDDAQKAKDFVKSY--EKPVVIKADGLAAGKGVIVCKNKDEANDAIDTilI 168
                 555666778889**********************..6***************************9998652 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.1e-09   1.7e-06       7     158 ..     103     285 ..      98     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                  HHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---SEEEEEEEEE.SSS CS
  ATP-grasp_3   7 tykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefieGkplSvsllsdgek 85 
                    +++k++++++         +  ++ +++ ek++v+K    a+g++v v ++k+ea+ ai+++             ++ e i+G ++S  +l+dg+ 
   AJA92662.1 103 AKEFMKRNSIPTAdfeifddAQKAKDFVKSYEKPVVIKADGLAAGKGVIVCKNKDEANDAIDTILikksfgdagskiIIEERIDGVEASYIALCDGKI 200
                  555566664444466555422222223344499*****9999*******************9988999****************************** PP

                  EEEEEEEEEEEET........TEEEEEE..ES----H..HHHHHHHHHHHHTTST....T--EEEEEEEEESS.SEEEEEEESS- CS
  ATP-grasp_3  86 vlvlavnrqliekaeke....fvyaGnv..tpietel..keevvelaeevvekle....glaGyvGvDlvlkdeepyviEvNPRl 158
                    ++a+++ +     ++        G    tpi  e+  +e  ++++ +++++++    + +G++   +++kd+ pyv+E N R+
   AJA92662.1 201 GIPMATSQDHKRVFDNDegpnTGGMGAYspTPIIDEKlgTEIQEKIIDKTIHAMRdegfEFKGFLYAGIMIKDGIPYVLEYNVRM 285
                  *****998876654444556644444441255555656655555566677777766667999**999***************997 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   8.6e-09   1.3e-05       3      91 ..     101     187 ..      99     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.6e-09
                  HHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST..S-EEEEE--SS CS
  CPSase_L_D2   3 esakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn..kqvlvekslkg 91 
                    ake +k+  +p+++ ++   +++++a +++k++  Pv+ika     GkG  v++n++e ++++ + l +   +fg+  +++ +e+ ++g
   AJA92662.1 101 IWAKEFMKRNSIPTADFEIF--DDAQKAKDFVKSYEKPVVIKADGLAAGKGVIVCKNKDEANDAIDTILIKK--SFGDagSKIIIEERIDG 187
                  56889999999999998888..******************************************99988777..57753368899988876 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1     2e-07    0.0003       7     111 ..     103     195 ..     100     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2e-07
                  HHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEEEE---EC CS
  ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekvlveealdik 104
                  ake ++++ ++++ +e+ ++a++a++ +k+ ++ + v+Ka  la G+    Gv ++k+k+ea++a++++l k+         G   +k+++ee++d  
   AJA92662.1 103 AKEFMKRNSIPTADFEIFDDAQKAKDFVKSYEKPV-VIKADGLAAGK----GVIVCKNKDEANDAIDTILIKKSF-------GDAGSKIIIEERIDGV 188
                  89****************************88877.****9999876....6*****************988877.......8888899999999988 PP

                  EEEEEEE CS
  ATP-grasp_2 105 kElYlsi 111
                  +  Y+++
   AJA92662.1 189 EASYIAL 195
                  8888775 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.7e-07     0.001       3      72 ..     135     196 ..     133     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.7e-07
  ATP-grasp_4   3 lPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayf 72 
                   PvviK    ++  GV++++n++e ++a+++i      +k+ + ++   ++++++Ee i+G E +  a+ 
   AJA92662.1 135 KPVVIKADGLAAGKGVIVCKNKDEANDAIDTIL-----IKKSFGDA---GSKIIIEERIDGVEASYIALC 196
                  7*****************************999.....56777774...88************9876666 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.4e-06     0.002      20      85 ..      98     159 ..      89     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
  ATPgrasp_ST  20 ddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                   +K+  ke+++r+ +++ +    ++  ++++++++fvk++e+ vviK+    +GkG++v+++++++
   AJA92662.1  98 SSKIWAKEFMKRNSIPTAD----FEIFDDAQKAKDFVKSYEKPVVIKADGLAAGKGVIVCKNKDEA 159
                  4677888888888888888....77779999*********999*****************885443 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.046       2      92 ..     107     196 ..     106     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                      HHHTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHH......TT-SCEEEEE--ESEEEEEE CS
  Dala_Dala_lig_C   2 lkaaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeaf......kydekvlvEeaiegreieva 89 
                      +k++ +p++++++++ +++ ++        +++   pv++K+  +    Gv  +++++e ++ai++ +         +k+++Ee i+g e    
       AJA92662.1 107 MKRNSIPTADFEIFDDAQKAKDF-------VKSYEKPVVIKADGLAAGKGVIVCKNKDEANDAIDTILikksfgDAGSKIIIEERIDGVEASYI 193
                      78899999999999988776665.......899999***************************9876521111234589*******99987654 PP

                      EEE CS
  Dala_Dala_lig_C  90 vlg 92 
                       l 
       AJA92662.1 194 ALC 196
                      444 PP

>> DUF448  Protein of unknown function (DUF448)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00011      0.16      18      62 ..     129     173 ..     123     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
      DUF448  18 vvrtpegevvlDltgklpGRGaYvcpseeclekaikkkaleralk 62 
                 +v++ e+ vv+  +g + G+G+ vc++++  + ai +  +++++ 
  AJA92662.1 129 FVKSYEKPVVIKADGLAAGKGVIVCKNKDEANDAIDTILIKKSFG 173
                 57776767999999***********************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2992.68
//
Query:       AJA92663.1  [L=580]
Description: transporter, small conductance mechanosensitive ion channel MscS family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-29  100.9   0.1    1.3e-28  100.0   0.1    1.5  1  MS_channel   Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.23   11.0   5.5       0.48    9.9   1.5    2.1  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.1   1.4e-32   1.3e-28       2     206 .]     301     534 ..     300     534 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.4e-32
                 .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE-SSEEEEEETTS.EEEEEEH CS
  MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVediglrttkirtfdg.rivtiPn 98 
                 ++l ili+v +++ v s++ v++  l ++ G l++++glalk++++n+++ i++  +k +k GD+v+++ +  G+V +i+ r+t ir   + ++ +iP+
  AJA92663.1 301 QVLPILIFVGVVIGVVSWWQVDLIVLATATGGLAFGVGLALKETLENYFSYILIRKDKVVKEGDRVQLQsGYNGYVHKITPRVTYIRHGLNeSVAIIPT 399
                 67778999999999******************************************************99*****************9755167799** PP

                 HHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.............................TS-EEEEEEEE-SSSE CS
  MS_channel  99 sslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.............................dkellvvldefgdssl 168
                 ++lv+++i+N+++e + + ++v++gv y  ++ ++  +l ++ + ++ + ++ k                               ++ v++d+f dssl
  AJA92663.1 400 RQLVSAEIINYTKEIKLVPAVVNVGVSYLNNPRQVTSILVKVGKRAMIEARDAKgrhlvrqnrcpyleenkpscgcdkdihvdVTQPVVRFDKFNDSSL 498
                 *******************************99999999999999999999999****************************9999************* PP

                 EEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
  MS_channel 169 nfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                 +f  +v+v++  ++ +++++s+ +l + +++++ +i+i
  AJA92663.1 499 DFSMWVYVRD--YGAQFKTKSDMRLIMYEEFKKYDIRI 534
                 **********..***********************987 PP

>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1    0.0086        77     232     257 ..      28      53 ..       4     127 .. 0.63
   2 ?    9.9   1.5   5.3e-05      0.48      34      70 ..     305     341 ..     299     343 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0086
  Sulf_transp 232 vlvlGiilGaflaallsgefkleapk 257
                  + v+G+i+G ++ +++ ++f++ ++ 
   AJA92663.1  28 LAVIGLIIGIIIISVVYRKFSFWVKT 53 
                  23455555555555555555544332 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.3e-05
  Sulf_transp  34 vgfqllaaaglidlpksafpvvglivGGllFGvGMal 70 
                  +++++    g++ +++  + v++++ GGl FGvG+al
   AJA92663.1 305 ILIFVGVVIGVVSWWQVDLIVLATATGGLAFGVGLAL 341
                  677888889999**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4021.57
//
Query:       AJA92664.1  [L=557]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-15   57.0   0.2    2.9e-15   57.0   0.2    2.5  3  Radical_SAM  Radical SAM superfamily
    2.2e-06   27.8   0.0    2.2e-06   27.8   0.0    1.9  2  Fer4_14      4Fe-4S single cluster domain
    4.1e-06   27.1   0.0      1e-05   25.8   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.1      0.53   3.1e+03       7      18 ..      94     105 ..      93     110 .. 0.87
   2 !   57.0   0.2   4.9e-19   2.9e-15       1     165 [.     113     273 ..     113     275 .. 0.86
   3 ?   -2.0   0.0      0.66     4e+03      50      83 ..     452     478 ..     439     514 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.53
                  ESS--TTTSCCT CS
                  xxxxxxxxxxxx RF
  Radical_SAM   7 CnlrCsfCarpe 18 
                  C+++C  C+++ 
   AJA92664.1  94 CPNNCGLCSNHL 105
                  *********985 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 4.9e-19
                  EEEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG..H CS
                  xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpd..e 91 
                  ++vt+ C l C++C ++ +    ++  + + + +v+  ++ +++   ++  ++ + ++ggep+l+ d+++l++ ++++     +i + tng+++   +
   AJA92664.1 113 MIVTNRCDLTCWYCFFYVKkgleGAYMYEPNHDQVRGMMKTLRSE--RPIpGNSMQITGGEPMLREDIADLIKIMKEE--GVEHIQMNTNGIRHAmdP 206
                  579****************86666666666666666666666666..4445**************************9..9***************** PP

                  HHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                  e  ++ + +g++ ++l+ + ++ +     +n+++ +e +  al+++r+ g   vv++ ++++  nd+el  +++
   AJA92664.1 207 EAGREVRMAGCNNLYLSFDGVTAR-----TNPKNHWE-IPYALDTCRKTGTT-VVFVPTVIKSINDHELGGIIR 273
                  ***********************9.....86755555.559********999.**************9977665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.66
                  EEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  50 vilgggepllypdfvellerlaklavpgiritve 83 
                  ++lg++   +++++ e+lerl +++     i+++
   AJA92664.1 452 LFLGMM--HFQDKYNEDLERLQRCD-----IHYV 478
                  555555..34455666666666663.....2222 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.0   4.2         3   1.8e+04       7      18 ..      93     104 ..      91     107 .. 0.83
   2 !   27.8   0.0   3.8e-10   2.2e-06       4      92 ..     115     202 ..     113     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: -7.0 bits;  conditional E-value: 3
     Fer4_14   7 gCnlsCkgCdnk 18 
                 +C+ +C  C n+
  AJA92664.1  93 SCPNNCGLCSNH 104
                 69999*9**875 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 3.8e-10
     Fer4_14   4 rlsgCnlsCkgCd......nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                  +++C l C  C+       + +++ e ++ q++ ++ + l   +++ i  + + +tGGeP++    +++ +l+k +kee+   +i+++tng  +
  AJA92664.1 115 VTNRCDLTCWYCFfyvkkgLEGAYMYEPNHDQVRGMM-KTL--RSERPIPGNSMQITGGEPMLR---EDIADLIKIMKEEG-VEHIQMNTNGIRH 202
                 589**********776655455566677777777777.444..4667777899*********55...99************.568******9755 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.7e-09     1e-05       3      94 ..     107     200 ..     105     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.7e-09
     Fer4_12   3 GeGvrlslfvsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesi...egltllGGEPllpenaeallelvkevkeekpekdiwlytgy 94 
                 + G+  ++ +++C+l C +Cf    +  ++   ++  ++  + +++ l  e+    + + ++GGEP+l   +e++++l+k +kee++e   + ++g 
  AJA92664.1 107 HSGLANMIVTNRCDLTCWYCFFYVKKGLEGAYMYEpnHDQVRGMMKTLRSERPipgNSMQITGGEPML---REDIADLIKIMKEEGVEHIQMNTNGI 200
                 6788889999***********8777777777777444677777788887655467889**********...99999999999999998888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3875.80
//
Query:       AJA92665.1  [L=361]
Description: putative spore coat polysaccharide biosynthesis protein SpsC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-96  321.5   0.0    9.8e-96  321.2   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.7e-08   34.1   0.0    3.3e-08   33.2   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
    9.1e-07   28.4   0.0    1.8e-06   27.4   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    5.3e-05   22.1   0.2    6.2e-05   21.8   0.2    1.1  1  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas
    0.00028   19.5   0.0    0.00044   18.9   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.025   14.4   0.0       0.73    9.8   0.0    2.4  2  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
      0.027   13.4   0.0       0.04   12.9   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
      0.034   12.9   0.0      0.073   11.8   0.0    1.5  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.2   0.0   4.4e-99   9.8e-96       9     360 ..      19     357 ..      13     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: 321.2 bits;  conditional E-value: 4.4e-99
                      HHHHHHTSS-SSS...SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB CS
  DegT_DnrJ_EryC1   9 aveevlksgwlts...gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyni 99 
                       + ++l+s+++ s     +v++FE++f++y+ ++ ++av+sGtaAl laL+ +++  ++eVI ps++Fv+ta+a++e+g kp+fvD++p++++i
       AJA92665.1  19 VLLKTLDSKFWASgsgSGNVQKFESKFKKYVSADSCVAVNSGTAALNLALSLFNIR-NKEVILPSMSFVSTAHAIVENGGKPIFVDIEPKSLCI 111
                      5678999**99996644589***********************************9.99*********************************** PP

                      -GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHH CS
  DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGavvtndeelaek 193
                      dp++i+ +i ++t aI+pVh+ G ++++d++ +ia+k gl vieDaAhA+G+++  kk+G++g+a +fSF+p Knl++  GG++  n ++  + 
       AJA92665.1 112 DPEKIKDKISKNTIAIMPVHFGGMPCNLDKILKIAKKNGLHVIEDAAHAVGTKFGKKKIGSHGTAVCFSFHPVKNLAMPTGGLIAINHKDSTKF 205
                      *************************************************************************************998887766 PP

                      HHHH...HBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHC CS
  DegT_DnrJ_EryC1 194 arvl...rnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlvee 284
                       ++l   r +G+  +++  y  +  lG ny ++e++A igl+qL++ld++++ R++ia+ y +++   + ++++ ++++    ++hly +lv+ 
       AJA92665.1 206 QKLLfsrRWCGITDRNDTDYDVKE-LGWNYYMNEFSAGIGLEQLKKLDKFNEIRKKIAKQYFNKI---NIESKMSFNEK---CSYHLYWILVK- 291
                      6654333889*9988888888888.*********************************9996655...54445555555...57*********. PP

                      CHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
  DegT_DnrJ_EryC1 285 eaevkrdelvealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                          +r+++ e+l ++gi+t +hy +p+h++++y+++      +lp +e++ ++++++p++p+l++ +++++++++
       AJA92665.1 292 ----NRQRFREKLYKNGIETGTHY-KPIHLMSMYKKNI-----SLPETESVGKKIVTIPIHPNLKKSEIKKIIDTI 357
                      ....89******************.7*********994.....58****************************987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.5e-11   3.3e-08      31     216 ..      35     216 ..      30     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.5e-11
                      -HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE-HHHHHHHS--S-T CS
  Beta_elim_lyase  31 dktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea.Gkmdlekleaaikevga 123
                      + +v+++e ++++++ ++  + v +GtaA +++l+++  r++evi+   +  +  ++ ai+e +g k++ ++++ +   +d+ek++++i ++ +
       AJA92665.1  35 SGNVQKFESKFKKYVSADSCVAVNSGTAALNLALSLFNIRNKEVILP--SMSFVSTAHAIVENGG-KPIFVDIEPKsLCIDPEKIKDKISKNTI 125
                      668999********************************9*****985..5567777888877744.3555554443389***********9333 PP

                      TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESS..STT--SS-EEEEE-HH.. CS
  Beta_elim_lyase 124 heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslk..KdllanvGgvlafrddel 215
                               +   ++  gG +     l+++ +iakk+g++++ D+A     a+  +   k++ s+   v++s+   K+l ++ Gg++a+++++ 
       AJA92665.1 126 --------AIMP-VH-FGGMPCN---LDKILKIAKKNGLHVIEDAAH----AVGTKFGKKKIGSHGTAVCFSFHpvKNLAMPTGGLIAINHKDS 202
                      ........3322.33.4899885...6678899************96....5678899999****99999999666****************87 PP

                      .............. CS
  Beta_elim_lyase 216 .............e 216
                                    
       AJA92665.1 203 tkfqkllfsrrwcG 216
                      55555555555550 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     8e-10   1.8e-06      48     194 ..      40     163 ..      27     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 8e-10
                    HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHH CS
  Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeap 143
                    ++e++  k+++        +++ v v sG+ al+ al  +    + +e+++p+ ++ s  +++  +gg+ + + ++ +++  +d e++++++++  
     AJA92665.1  40 KFESKFKKYVS--------ADSCVAVNSGTAALNLALSLFNI--RNKEVILPSMSFVSTAHAIVENGGKPIFVDIE-PKSLCIDPEKIKDKISK-- 122
                    67777777777........88789999999999998888775..8889**************************88.99**************9.. PP

                    CTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
  Aminotran_1_2 144 egnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                      n      +   p +  G  ++l+++ k+   akk++l+++ D a+a++ 
     AJA92665.1 123 --NT-----IAIMPVHFGGMPCNLDKILKI---AKKNGLHVIEDAAHAVGT 163
                    ..33.....344588999************...**************9875 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   2.8e-08   6.2e-05      74     339 ..      51     305 ..      41     361 .] 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.8e-08
                 HHEECCCSS-H.HHHHHHHHHHHHHHCC--CCEEEEEETCHHHHHHHCTT-EEEEE-EEECTTEEEEHHHHHHHHHHCCTCCCEEEEEECSSTTTTB-- CS
     SepSecS  74 vknafvvPlat.GlslaLClsalrkrskakkviwvridekSslkavelaGleialvekvlegDelitdvedveeiiekkreevilavlstlsffaprsp 171
                 + ++++v   t  l laL l  +r     k+vi + +   S+  a+   G +++ v+  +e+ +l +d+e+++++i k    +++a++       + +p
  AJA92665.1  51 ADSCVAVNSGTaALNLALSLFNIR----NKEVILPSMSFVSTAHAIVENGGKPIFVD--IEPKSLCIDPEKIKDKISK----NTIAIMPVH---FGGMP 136
                 568999976662578888888888....89**************************9..6899************998....456676554...45566 PP

                 --HHHHHHHHHCCT--EEEEGCCCCT-HHHHHHHHHHHHHTTC-EECCCHCHCCCEECCHCCCCE.SSCHCCCCC..HCCCHCHCTSCHCCCCCCCHHH CS
     SepSecS 172 DdvkeiakiCaeydvPhlvNgAYaiqsekyieklkkalkvGRvdvvvksldknllvpvGgaiiaa.sdesfikei..skeypgrasaapskdvlislll 267
                  ++++i ki ++ ++  +  +A a+  +   +k+      G    +     knl +p Gg i    +d ++ +++  s+ + g+  ++ + + +++   
  AJA92665.1 137 CNLDKILKIAKKNGLHVIEDAAHAVGTKFGKKKIGSH---GTAVCFSFHPVKNLAMPTGGLIAINhKDSTKFQKLlfSRRWCGITDRNDTDYDVKE--- 229
                 6677999999999*9999999****777667776543...33334444556*********986550555667875459*******99988877665... PP

                 CCHHHCCHHHHHHH..HHHHHHHHHHHHHHHCCCEEESSSTT-SSEEEEE-CCCHCCCC...THHHHHHHHHHHTTE CS
     SepSecS 268 lGskaykkllkeqk..esfkllreklkklaeeveekllevpeNpissaltletldeikk...karldlaseLfsrkv 339
                 lG + y + +      e  k+l +k +++ +++ ++  ++ + +  + ++ +  +       k+r  + ++L++  +
  AJA92665.1 230 LGWNYYMNEFSAGIglEQLKKL-DKFNEIRKKIAKQYFNKINIESKMSFNEKCSYHLYWilvKNRQRFREKLYKNGI 305
                 6778887777665411333333.456677777777777777777777777776665444555788888888887777 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-07   0.00044      50     177 ..      34     160 ..      19     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-07
                      --HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHH.HHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEE CS
  Cys_Met_Meta_PP  50 gnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrll.kkvlkklgievkfvdt.sdleelekaikentklv 141
                      g  +++ +e++  +  ++++++av+sG+aA+++a+  +    +e+++ +  + +t + + ++  k + ++++      d+e+++ +i++nt ++
       AJA92665.1  34 GSGNVQKFESKFKKYVSADSCVAVNSGTAALNLALSLFNIRNKEVILPSMSFVSTAHAIvENGGKPIFVDIEPKSLcIDPEKIKDKISKNTIAI 127
                      55667899***********************8888888888999*****9999997665155556677777766543799***********999 PP

                      EEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTT CS
  Cys_Met_Meta_PP 142 ylEtptnpllkvvDiekiaklakkagvlvvvDntfa 177
                           +   +    + ki+k+akk+g+ v+ D++ a
       AJA92665.1 128 MPVHFGGMPC---NLDKILKIAKKNGLHVIEDAAHA 160
                      8666666555...57899999999999999887765 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.1   2.3e+02      13      25 ..      36      48 ..      33      52 .. 0.87
   2 ?    9.8   0.0   0.00033      0.73      22      41 ..     317     336 ..     314     338 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.1
                     HHHHHHHHHHHHH CS
  Surfac_D-trimer 13 GklqrLqnafsqY 25
                     G++q+++  f +Y
       AJA92665.1 36 GNVQKFESKFKKY 48
                     99********999 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                      HHHHHHHHHTTTEEEETTEE CS
  Surfac_D-trimer  22 fsqYkKavLFPdGqsVGeKI 41 
                      +s YkK +  P+  sVG KI
       AJA92665.1 317 MSMYKKNISLPETESVGKKI 336
                      799****************9 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05      0.04      45     182 ..      38     163 ..      31     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                  HHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBE.TTSCBEGGGHHHH--TTEE CS
  Aminotran_5  45 veearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipld.eegeldldelekllnektk 141
                  v++ ++k+++ + a+s    + + ++t a+nl++  +     + +e+++ ++   ++    +++ +  g  + ++ ++ +   +d+++++++++++t 
   AJA92665.1  38 VQKFESKFKKYVSADS---CVAVNSGTAALNLALSLF---NIRNKEVILPSMSFVSTA---HAIVENGGKPI-FVDIEpKSLCIDPEKIKDKISKNTI 125
                  5677788888888887...899999999****99999...456778889999888887...56665667777.444440556799***********97 PP

                  EEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
  Aminotran_5 142 lvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                  +++  h     G+   +++i k+akk+g  v+ Daa avg 
   AJA92665.1 126 AIMPVHF---GGMPCNLDKILKIAKKNGLHVIEDAAHAVGT 163
                  6666664...689999********************99975 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05     0.073      76     212 ..      46     165 ..      12     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                 HHHCT-SEEEEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHHHHHHHHHSTTTGSESEEEE CS
    OKR_DC_1  76 arvfgadksyfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeetlkekikevpdakaprlavi 174
                  +   ad    v  GT++ n ++      ++  v+++     S +ha+v +g +P+++  e   l         ++++e +k ki++ + a +      
  AJA92665.1  46 KKYVSADSCVAVNSGTAALNLALSL-FNIRNKEVILPSMSFVSTAHAIVENGGKPIFVDIEPKSL---------CIDPEKIKDKISKNTIAIM------ 128
                 3334555555566677666666555.55567778889999*****************99876554.........4455777777776554433...... PP

                 ESS-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGG CS
    OKR_DC_1 175 tnsTYdGvlynakeivdkleklsdrilfDeAwvgyeqf 212
                     + G+  n+++i + ++k + ++  D A+ + ++f
  AJA92665.1 129 -PVHFGGMPCNLDKILKIAKKNGLHVIEDAAHAVGTKF 165
                 .3446677788888888888888888888888777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2644.41
//
Query:       AJA92666.1  [L=318]
Description: hypothetical protein T478_1408 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.018   14.6   0.0        2.4    7.7   0.0    2.2  2  DUF2201_N  Putative metallopeptidase domain
      0.037   14.1   0.3        0.2   11.7   0.3    2.1  1  Toprim_N   DNA primase catalytic core, N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2201_N  Putative metallopeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00027       2.4     224     261 ..      36      72 ..      25      82 .. 0.79
   2 ?    4.7   0.0    0.0021        19     229     256 ..      85     114 ..      83     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00027
   DUF2201_N 224 lkpkipWeklLrtlldraladkpdySwsrParryiAak 261
                 +++k++   +L++ ld+ ++++ ++S+++P+ ++i  k
  AJA92666.1  36 PETKTDF-YILARDLDDETEREFKISYKKPSYSFIENK 72 
                 5666665.5899**********************9733 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0021
   DUF2201_N 229 pWeklLrtlldraladkpdySw..srParr 256
                 +W ++L++++ ++  ++ ++ w  +rP+  
  AJA92666.1  85 DWSEILKSQISQTNTEQENIHWmkKRPNEH 114
                 9*******************9966688865 PP

>> Toprim_N  DNA primase catalytic core, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.3e-05       0.2      12      54 ..      38      80 ..      26     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                HHHHHHHHCTT--HHHHHHCT-EEE-SHSCHHHHHHHHCT-HH CS
    Toprim_N 12 ekaleYLkkRglseetiekFqlGyapkswdnllkllkkkkvse 54
                +k   Y+  R l++et ++F++ y + s ++++++++ ++++ 
  AJA92666.1 38 TKTDFYILARDLDDETEREFKISYKKPSYSFIENKIQPHRIRM 80
                45667999******************99777777666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2349.10
//
Query:       AJA92667.1  [L=394]
Description: abhydrolase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-18   65.6   0.0      4e-17   62.6   0.0    2.0  1  Abhydrolase_7  Abhydrolase family
    4.5e-05   22.8   0.0    0.00013   21.4   0.0    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.086   13.0   0.0        5.3    7.3   0.0    2.4  2  DUF5062        Domain of unknown function (DUF5062)
       0.48   11.1   6.8          1   10.1   5.9    2.1  1  DUF3139        Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> Abhydrolase_7  Abhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   8.8e-21     4e-17      33     345 ..      60     371 ..      37     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 8.8e-21
                    ---TT---TT--HH.HHHHHHHHHHHHHHHHH----------..-EEEEEEEETTEEEEEEEE--STTB-EEEEEEEETT--S-EEEEEEE--TT- CS
  Abhydrolase_7  33 lkPayafrpdltak.efkkwqkevrkameelmkfPelkklpa..pvcvkteqrdgyrlekwefyPlpkavstflvliPdnvkkpvpavlciPGsgk 125
                       +++f++++++k  f  w++++ ++ +el   P+ ++l++    ++++e++ +y++ k  +  ++     ++ liP++++k+++av+ +PGsg+
     AJA92667.1  60 NSLQLSFKNNVQNKnSFLPWKNKLITKFQELHDLPNFQDLQVnsLNIINSEKKLNYNVTKLSTIAQDGDTIILYELIPKKINKNTSAVFIVPGSGN 155
                    55678999999865269*******************998765115789**********************************************98 PP

                    -HHHHCT---SSGCG--STTSTTT-HHHHHHTTTSEEEEE--TTSGGG-.SSCCCTTTTS--HHHHHHHHHHTT--HHHHHHHHHHHHHHHHCT-T CS
  Abhydrolase_7 126 tkeelaGepevseklteeskeekaamalnlvkkGyiavavdnaaageas.dleklakgssydydvvsrillelgwsylGytsyldkqvldwmktqs 220
                    +  + +   ++++++++++   ++ +a ++v++Gyi  +++n + ge   d+ +     + d    s  +le + + lG+   ++ q++d ++t +
     AJA92667.1 156 QGAKDVI--NMNSEISDNYY--QQGIAEQIVNEGYIVYVIENRGWGERKiDVGSIC--DQSDI-FCSGEFLERQIKNLGFD-LINLQIIDTLQTIK 243
                    7554443..35566666664..67899*******************9752665555..34443.46778899999****96.7899******9999 PP

                    TEEEEEEEEEEEGGGHHHHHHHHHH-TT--EEEEES-B--HHHHHHHB----TTS----SS-GGG--TTCCCC--HHHHHHTTTTS-EEESS-B-H CS
  Abhydrolase_7 221 lirkdriivsGfslGteplmvlGaldesiyafvyndflcrtqeralvltkPdekgrrpfPnsirhliPdfwkkfdfPdivaalaPrPvilteGGld 316
                     +  ++ i        + l  lG       a+    fl + +   l  +    ++  +f n  +h   +f+k+fd Pd+v +laP+P+ l+ G  +
     AJA92667.1 244 SLESNKKI------TFNNLFLLGITHGGKIALRSSLFLPELKGLLLSSSLFSTENFGTFGNGYNH---GFLKYFDNPDLVITLAPKPLYLAWGQNE 330
                    99988876......45799************************9999999**************9...9********************9988654 PP

                    ....H.......HHHHHHHHHHHTT-GGG.EEE---GGG-S CS
  Abhydrolase_7 317 ....r.......dldlvkkayelagkpen.veihhykkyad 345
                        r        + lvk+ay+l +  +n v i h +k ++
     AJA92667.1 331 nppqRyeaqslhTFTLVKNAYRLLNSEKNiVGIVHDQKINS 371
                    22222222222268899999998877666256788877665 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.8e-08   0.00013      20     114 ..     173     291 ..     166     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.8e-08
  Hydrolase_4  20 yae.laeaLaaqGfavyalDhrGhGrse......................gkrghvpsfddyvdDlaafvekvkeehpel..plfllGhSmGGliall 92 
                  y++ +ae+ +++G+ vy + +rG+G+ +                       k   ++ ++  + D  + ++ ++++++ +  +lfllG   GG ial+
   AJA92667.1 173 YQQgIAEQIVNEGYIVYVIENRGWGERKidvgsicdqsdifcsgeflerqIKNLGFDLINLQIIDTLQTIKSLESNKKITfnNLFLLGITHGGKIALR 270
                  66679**************************************999855544444555666666666666666666666699**************** PP

  Hydrolase_4  93 yllrypdkvaglilsaPalkik 114
                    l  p+ ++gl ls+++++ +
   AJA92667.1 271 SSLFLPE-LKGLLLSSSLFSTE 291
                  *******.*********99765 PP

>> DUF5062  Domain of unknown function (DUF5062)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0012       5.3      17      46 ..      23      53 ..      14      88 .. 0.85
   2 ?    3.1   0.0     0.023     1e+02      38      59 ..     347     368 ..     338     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
     DUF5062 17 ekyAkkrGyaefdktdsakekveaiYr.lLv 46
                  y kkrG++++ k  s+k+    iY+ +L+
  AJA92667.1 23 SVYIKKRGINHLAKNLSTKNSHSNIYKkFLI 53
                5799**********************63555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.023
     DUF5062  38 veaiYrlLvqdKliqplpedke 59 
                 v+  YrlL ++K i+++ +d++
  AJA92667.1 347 VKNAYRLLNSEKNIVGIVHDQK 368
                 6778*************99986 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.9   0.00022         1       4      62 ..       5      58 ..       2      75 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
     DUF3139  4 iiiililliillvivkvflglvgskpikkylankkldkylqekgykeddIks..ikpkyds 62
                +iii +l+++++++v+vf  ++++  i      ++l k l + + + ++I +    p+ ++
  AJA92667.1  5 YIIISFLILSISINVAVFSVYIKKRGI------NHLAKNL-STKNSHSNIYKkfLIPEIYT 58
                89*****************99999999......6777777.44444556665453344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2773.78
//
Query:       AJA92668.1  [L=40]
Description: hypothetical protein T478_0750 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 300.16
//
Query:       AJA92669.1  [L=317]
Description: 4Fe-4S dicluster domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-07   31.4  15.7    0.00023   20.8   2.8    2.3  2  Fer4        4Fe-4S binding domain
    4.8e-06   27.1   4.8    1.3e-05   25.7   5.0    1.7  1  Fer4_7      4Fe-4S dicluster domain
    5.5e-05   23.2   5.6    0.00012   22.1   5.5    1.7  1  Fer4_10     4Fe-4S dicluster domain
    8.9e-05   22.6   4.0    0.00017   21.6   4.0    1.5  1  Fer4_9      4Fe-4S dicluster domain
    0.00011   22.3   5.1    0.00018   21.6   5.1    1.4  1  Fer4_21     4Fe-4S dicluster domain
     0.0018   18.7   1.6     0.0045   17.4   1.6    1.7  1  Fer4_8      4Fe-4S dicluster domain
     0.0022   18.1   0.5     0.0047   17.0   0.5    1.5  1  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore
  ------ inclusion threshold ------
      0.018   13.0   0.1      0.025   12.5   0.1    1.2  1  Tenui_PVC2  Tenuivirus PVC2 protein
      0.039   14.9   8.6          4    8.4   2.7    2.9  2  Fer4_16     4Fe-4S double cluster binding domain
       0.12   12.8   0.0       0.23   11.9   0.0    1.5  1  GLTSCR1     Conserved region of unknown function on GLTSCR pr
       0.43   10.8  10.1       0.52   10.5   0.7    2.4  2  Fer4_2      4Fe-4S binding domain
       0.74   10.9  13.7        1.7    9.7   4.9    2.3  2  Fer4_3      4Fe-4S binding domain
        1.1    9.5  14.3        0.3   11.2   2.4    2.3  2  Fer4_6      4Fe-4S binding domain
        2.4    8.9   6.6        8.1    7.2   0.3    2.3  2  Fer4_4      4Fe-4S binding domain
        3.6    8.2   6.7         23    5.6   2.1    2.5  2  Fer4_17     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   2.8   1.9e-07   0.00023       2      22 ..     252     272 ..     251     274 .. 0.90
   2 !   16.2   5.2   5.5e-06    0.0066       7      24 .]     295     312 ..     293     312 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                 EEETTTSSS-THHHHHSTTTE CS
        Fer4   2 videekCigCGaCvevCPvgA 22 
                  +d + C++ GaC+++CPv +
  AJA92669.1 252 SVDFDICVADGACIDACPVAV 272
                 69****************976 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.5e-06
                 TSSS-THHHHHSTTTEEE CS
        Fer4   7 kCigCGaCvevCPvgAIt 24 
                 +Ci+C aC+ vCP  AI+
  AJA92669.1 295 DCIFCLACEGVCPPKAIK 312
                 6***************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   5.0   1.1e-08   1.3e-05       2      51 ..     258     309 ..     257     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.1e-08
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgt.ekveid.pekClgCgaCvavCPtg 51 
                 C+  gaC +aCpv + e+ e++ ++   +k+ ++ + +C++C aC+ vCP +
  AJA92669.1 258 CVADGACIDACPVAVYEFVEFSGNAASdKKPLMSkEPDCIFCLACEGVCPPK 309
                 77779**************9876664436666651559************76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   5.5     1e-07   0.00012       2      56 .]     251     307 ..     250     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
     Fer4_10   2 vvidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk.kvekCtgcgaCveaCP 56 
                 v +d d C+  g+C +aCP+ + + v+ +g a  +++    k  +C++c aC  +CP
  AJA92669.1 251 VSVDFDICVADGACIDACPVAVyEFVEFSGNAASDKKPLMsKEPDCIFCLACEGVCP 307
                 56899***************7774444444444444444447789***********9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   4.0   1.5e-07   0.00017       2      51 .]     258     311 ..     256     311 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-07
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkgai 51 
                 C+  gaC++aCp  v++  ++ + a+ +++       +Ci+C aC+ +Cp +ai
  AJA92669.1 258 CVADGACIDACPVAVYEFVEFSGNAASDKKPLmskePDCIFCLACEGVCPPKAI 311
                 666689**********9999999999877666899989************9987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   5.1   1.5e-07   0.00018       3      58 ..     253     312 ..     251     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-07
     Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvl.....kvvedeCvGCnlCssvCPvedcie 58 
                 +d d C+  g C+ aC+ + ++ +e+++++          e +C+ C  C  vCP  ++i+
  AJA92669.1 253 VDFDICVADGACIDACPVAVYEFVEFSGNAASdkkplMSKEPDCIFCLACEGVCP-PKAIK 312
                 78899*******************887665432222145688*************.68876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.6   3.8e-06    0.0045       2      63 ..     255     308 ..     254     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-06
      Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                 ++ C+  gaC +aCpv+  +  +++ +a  +++    +++          C  c aC+ vCp 
  AJA92669.1 255 FDICVADGACIDACPVAVYEFvEFSGNAASDKKP-LMSKEP--------DCIFCLACEGVCPP 308
                 6779999********9888888999999999888.666555........7************5 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.5   3.9e-06    0.0047      43      91 ..     261     312 ..     248     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                 S-THHHH-TTS-EEEEE...TTTTSSEEEEE-CCC--S--HHHHH-TT--EE CS
      ETF_QO  43 agpeqryCPagvyeive...deeakekklqinaqnCvhCktCdikdpsqnie 91 
                 +g +   CP +vye+ve   ++ +++k l     +C+ C +C+   p + i+
  AJA92669.1 261 DGACIDACPVAVYEFVEfsgNAASDKKPLMSKEPDCIFCLACEGVCPPKAIK 312
                 5667778*********965434567788999999********9887777765 PP

>> Tenui_PVC2  Tenuivirus PVC2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.1e-05     0.025     428     473 ..     241     286 ..     212     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
  Tenui_PVC2 428 dgthsiwgestslsfdycvtdfhifsycpayhynwkrieyeptssr 473
                 +    +wge  s+ fd cv+d   +  cp   y++     + +s +
  AJA92669.1 241 NAIMGVWGEFVSVDFDICVADGACIDACPVAVYEFVEFSGNAASDK 286
                 456689*************************999977766666655 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   8.7     0.017        21       2      65 ..     258     307 ..     257     309 .. 0.67
   2 ?    8.4   2.7    0.0034         4       2      18 ..     296     312 ..     295     317 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
     Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                 C+  g+C+++CP+++ +   e++ +  +       +kk l  +e      +++++C +C+ vCP
  AJA92669.1 258 CVADGACIDACPVAVYEFV-EFSGN--AA-----SDKKPLMSKE------PDCIFCLACEGVCP 307
                 7778999999999998888.22322..22.....2333444443......4577*********9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0034
     Fer4_16   2 CgtCgkCaevCPtnaik 18 
                 C+ C +C  vCP +aik
  AJA92669.1 296 CIFCLACEGVCPPKAIK 312
                 999**********9998 PP

>> GLTSCR1  Conserved region of unknown function on GLTSCR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.23      38      77 ..     119     158 ..      66     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
     GLTSCR1  38 edlekadeefekvaeellkrfqklenkfrklllkeakres 77 
                 +d+ k+ ++f k++++++ r + le+kfr++l+k +k ++
  AJA92669.1 119 KDYRKKADHFAKMVTDTILRNTILEEKFRAALMKTEKISE 158
                 34445689**************************999333 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   0.00043      0.52       3      21 ..     251     269 ..     249     270 .. 0.87
   2 ?    4.5   3.0     0.037        44       7      21 ..     294     307 ..     288     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00043
      Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                 v vd d+C++ gaC++aCP
  AJA92669.1 251 VSVDFDICVADGACIDACP 269
                 568999**988******** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.037
      Fer4_2   7 tdrCigCgaCvsaCP 21 
                 +d Ci C aC  +CP
  AJA92669.1 294 PD-CIFCLACEGVCP 307
                 55.999********9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.5     0.019        23       5      13 ..     262     270 ..     258     271 .. 0.78
   2 ?    9.7   4.9    0.0015       1.7       1      15 []     296     310 ..     296     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
      Fer4_3   5 gaCvevCPv 13 
                 gaC ++CPv
  AJA92669.1 262 GACIDACPV 270
                 79******7 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0015
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ C aC+ vCP++A
  AJA92669.1 296 CIFCLACEGVCPPKA 310
                 *************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.4   0.00025       0.3       2      23 ..     251     272 ..     250     273 .. 0.86
   2 ?    3.7   4.2     0.062        74       9      24 .]     296     311 ..     292     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
      Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                 v +d d C+  g+C+++CP ++
  AJA92669.1 251 VSVDFDICVADGACIDACPVAV 272
                 6778899************876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
      Fer4_6   9 CigCgdCvrvCPegai 24 
                 Ci C +C+ vCP +ai
  AJA92669.1 296 CIFCLACEGVCPPKAI 311
                 888*********8887 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0068       8.1       4      16 ..     258     270 ..     255     277 .. 0.84
   2 ?    4.3   1.3     0.058        69       4      15 ..     296     307 ..     289     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0068
      Fer4_4   4 CigCgsCvaaCPq 16 
                 C+  g+C++aCP+
  AJA92669.1 258 CVADGACIDACPV 270
                 666689******5 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
      Fer4_4   4 CigCgsCvaaCP 15 
                 Ci C +C+ +CP
  AJA92669.1 296 CIFCLACEGVCP 307
                 88899******9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.052        62      44      58 ..     256     270 ..     238     273 .. 0.84
   2 ?    5.6   2.1     0.019        23      44      57 ..     294     307 ..     273     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.052
     Fer4_17  44 slCieCgeCerkCPq 58 
                 + C+  g C  +CP 
  AJA92669.1 256 DICVADGACIDACPV 270
                 679999999999995 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
     Fer4_17  44 slCieCgeCerkCP 57 
                  +Ci C  Ce +CP
  AJA92669.1 294 PDCIFCLACEGVCP 307
                 58999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2191.22
//
Query:       AJA92670.1  [L=504]
Description: isopropylmalate/citramalate/homocitrate synthases [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-89  298.0   0.1    1.3e-88  297.0   0.1    1.5  1  HMGL-like     HMGL-like
    1.5e-27   96.1   1.8    2.6e-27   95.3   1.8    1.4  1  LeuA_dimer    LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
      0.067   12.6   0.0       0.14   11.6   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.0   0.1   2.1e-92   1.3e-88       2     264 .]       3     263 ..       2     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 297.0 bits;  conditional E-value: 2.1e-92
                 -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES- CS
   HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiats 100
                 ++i+dttLRDGeq+++++ls e+kl+iak+Ld++gvd+iE+gfp+ s ++ e v+ i+ ++ ka++++l+r ++kdi+aav+    +g + +h+fiats
  AJA92670.1   3 IRIFDTTLRDGEQSPGVSLSPEKKLNIAKKLDQLGVDAIETGFPVISDGEKEGVKLIVGEGLKAELCGLARTNKKDIDAAVD----CGLNYIHTFIATS 97 
                 89********************************************************************************....************* PP

                 HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB CS
   HMGL-like 101 elhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcH 199
                 ++hl++klk++r+e+++ka eav++ +s+g +ve+s+eda+rtd efl +v  a+++aGa+ri i+DtvG+ tP+ ++e+ +   e+ k  +++svHcH
  AJA92670.1  98 DIHLEHKLKMTRDEALEKAIEAVEYGKSRGLQVEFSAEDATRTDREFLKKVFGAVANAGADRIDIPDTVGYSTPQYIGEITKDAIEVSK--LPISVHCH 194
                 ***********************************************************************************999999..******** PP

                 -TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB-BHHHHHHHHHHTT....-B----HHHHHHHHHHH CS
   HMGL-like 200 ndlGlAvantlaAveaGadrvdgtvnGlGeraGnaaleelvaalealg....vdtgldlqklrsiaalv 264
                 nd+GlAvan++ +v+aGa+   +t+nG+GeraGna+lee+v+al+ l+    ++t+++++ ++++++++
  AJA92670.1 195 NDFGLAVANAISGVQAGASCAHVTINGIGERAGNASLEEFVMALHSLEfenkWETNINTKLIYETSRYI 263
                 ***********************************************99999*************9986 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   1.8   4.3e-31   2.6e-27       1     132 [.     358     493 ..     358     494 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4.3e-31
                 XXXXXXXXXXXXXXXXXXX..--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH...T-EEEEEEEE--TT-TT--E CS
  LeuA_dimer   1 evtdedlealvkdelleae..erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv...dikLldYsvhaitegtdaqa 94 
                 +vt+ +l ++++++++e++  + ++l  ++vs+g ++++ a vkl+v dg+e +a+  G+GpvdA+lnA++k++++   +++L++Y++++i++g++a+ 
  AJA92670.1 358 QVTEVELLSMANEVIGENKlkRIVQLAGFSVSTGVGTMPYAFVKLNV-DGQEFSATDYGVGPVDAALNAIQKITSQvtdEVRLKEYKLDSISGGANALC 455
                 58999999999****9988757789**********************.**************************9999999****************** PP

                 EEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
  LeuA_dimer  95 evrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                 ev+V++e   g+++s  +v +div+ S++A+++++nr+
  AJA92670.1 456 EVTVKVEDARGNIISSKSVGEDIVTTSVQAMVDGINRI 493
                 *******888999***********************98 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.4e-05      0.14      19     124 ..      15     127 ..       7     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                   CSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.............HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGH CS
  AP_endonuc_2  19 lvpvselsdeelrelrkaldelglriaslslftrfgypded.............erearreesvdalkraielaaaLGapllvlhpGtagagpkgse 102
                   + p ++ls+e+   ++k ld+lg+   ++++     +++e              e++       +  k+ i++a ++G  ++++++ t + + +   
    AJA92670.1  15 QSPGVSLSPEKKLNIAKKLDQLGVD--AIETGFPVISDGEKegvklivgeglkaELCGL----ARTNKKDIDAAVDCGLNYIHTFIATSDIHLEHKL 105
                   5555666888999999999999999..88888888888888889999998888877777....8999********************9666666666 PP

                   HHHHHHHHHHHHHHHHHHHHHT CS
  AP_endonuc_2 103 eeawerlaeslneladyaekeg 124
                   + +++ + e+  e+++y++ +g
    AJA92670.1 106 KMTRDEALEKAIEAVEYGKSRG 127
                   6666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3756.22
//
Query:       AJA92671.1  [L=323]
Description: hypothetical protein T478_0263 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00012   22.1  10.6    0.00018   21.5  10.6    1.3  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)
  ------ inclusion threshold ------
       0.14   12.3   0.8         11    6.1   0.0    3.4  3  Cuticle_1    Crustacean cuticle protein repeat
       0.41   11.2  22.3       0.84   10.2  22.3    1.4  1  TonB_N       TonB polyproline region


Domain annotation for each model (and alignments):
>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  10.6     3e-08   0.00018      67     109 ..     136     178 ..      91     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3e-08
  Trypan_PARP  67 pepepepepepepetepeeep..epepepepepepepepepepep 109
                  p p pep p pep    ee     +epep    epepepepep+ 
   AJA92671.1 136 PPPPPEPTPVPEP--VIEEPVpvIEEPEPIAIVEPEPEPEPEPQA 178
                  3334444444444..222222002333333333444443344433 PP

>> Cuticle_1  Crustacean cuticle protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.12   7.1e+02       5      13 ..      71      79 ..      71      83 .. 0.85
   2 ?    1.4   0.0     0.057   3.4e+02      29      38 ..     183     192 ..     181     193 .. 0.80
   3 ?    6.1   0.0    0.0018        11      12      37 ..     215     241 ..     214     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.12
   Cuticle_1  5 iitpDGtnv 13
                i++pDG+ v
  AJA92671.1 71 IVSPDGNIV 79
                899***987 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.057
   Cuticle_1  29 GaVlsdGknv 38 
                 G V++dGk v
  AJA92671.1 183 GTVMKDGKCV 192
                 7788888876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0018
   Cuticle_1  12 nvqfthgva.nivliGpSGaVlsdGkn 37 
                 +vqf ++   n v+++ SG  +  G n
  AJA92671.1 215 QVQFLREIRdNTVMNTQSGTTFMTGFN 241
                 79******************9999865 PP

>> TonB_N  TonB polyproline region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  22.3   0.00014      0.84      27      74 ..     136     177 ..     130     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00014
                 X....XXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXX..XXXXXX CS
      TonB_N  27 PapaaaepePapePavepePePePEvvPePpapvviekPkPePkPkPk 74 
                 P p+ +ep+P peP++ +eP P+ E   eP +p++i  P+PeP+P P+
  AJA92671.1 136 P-PPPPEPTPVPEPVI-EEPVPVIE---EP-EPIAIVEPEPEPEPEPQ 177
                 3.45677778888877.55555444...44.56788888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2367.58
//
Query:       AJA92672.1  [L=173]
Description: hypothetical protein T478_0296 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1239.72
//
Query:       AJA92673.1  [L=482]
Description: tRNA-splicing ligase RtcB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.5e-166  554.7   0.2   1.7e-166  554.5   0.2    1.0  1  RtcB          tRNA-splicing ligase RtcB
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.034   13.9   0.1    1.2  1  DUF3492       Domain of unknown function (DUF3492)
      0.042   13.9   0.2       0.23   11.6   0.1    2.0  2  Complex1_LYR  Complex 1 protein (LYR family)


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.5   0.2  2.8e-170  1.7e-166       1     412 []      48     482 .]      48     482 .] 0.99

  Alignments for each domain:
  == domain 1  score: 554.5 bits;  conditional E-value: 2.8e-170
                 HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHHHS-------------HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelekavpvglgskkkvklskkel 95 
                 q+ nv++lpgi++h++++PD H G+g+p+G+V+a++   g+i+P++VG+DI CGvrll+tnlt+e++++kl++lv++l+k++p+g+gsk++v+l+++el
  AJA92673.1  48 QAVNVSTLPGIQEHSIVLPDGHEGYGFPVGGVAAMDaeeGMISPGGVGYDInCGVRLLRTNLTEEQVRPKLNDLVNDLFKSIPSGVGSKGAVRLTQSEL 146
                 899************************************************************************************************ PP

                 HHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB  96 eevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhq 194
                 +evl +g++wa+++g+g+++d + +ee+g++++ad++kvs+ka++r+ +qlG+lGsGNHF+Evq v+ei deeaak++g+eeg+++v++H+GSRg+Ghq
  AJA92673.1 147 DEVLVKGVSWAIDNGYGTNDDANVCEENGQMANADPNKVSDKARKRGLPQLGSLGSGNHFLEVQRVQEIHDEEAAKRMGIEEGTITVLIHCGSRGFGHQ 245
                 *************************************************************************************************** PP

                 HHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x... RF
        RtcB 195 iaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d... 289
                 +++dyl+i ++  +k+ i+l dr+La++p +seeg++Y kam aa n+A+ NRq+it+++r+++e+v++++++dl+++lv+dvaHNiak E+h+ d   
  AJA92673.1 246 VCSDYLRISEQVQEKYDINLADRELACVPNTSEEGESYRKAMFAALNFAWSNRQMITHWTRKSFERVFSQSESDLDMKLVYDVAHNIAKVEKHRiDgkq 344
                 **********99999*******************************************************999*********************96688 PP

                 EEEEEEEES-EE-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE----- CS
                 xxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB 290 ekvlVhRKGAtrA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkeg 373
                 +kv+VhRKGAtrA             + gqpv++pGsmgt+S+i+ G++n++  sfgSt+HGAGR+msR+ka+++f+ +evkk+l+++gi +++ +++g
  AJA92673.1 345 KKVVVHRKGATRAfpanmdevpskyrDLGQPVLVPGSMGTGSWILLGNENSMsaSFGSTAHGAGRMMSRSKARRNFTESEVKKSLNDKGIFIKSLTRDG 443
                 *************************************************************************************************** PP

                 -------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        RtcB 374 vleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                 v+eE+p+aYKd+d+Vv++ ++ g++++va+l p++v+kg
  AJA92673.1 444 VVEETPQAYKDVDSVVNVSHNLGIATKVAKLVPIGVIKG 482
                 **************************************8 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.7e-06     0.034      23      85 ..     298     358 ..     294     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-06
     DUF3492  23 hqlitklpeveFavlfigsdeeeygelkyelPenVveveevylveeeeaskapasrkgekaaa 85 
                  q+it+    +F+ +f +s+++  ++l+y++ +n+ +ve++ ++ +++  k +++rkg ++a+
  AJA92673.1 298 RQMITHWTRKSFERVFSQSESDLDMKLVYDVAHNIAKVEKHRIDGKQK--KVVVHRKGATRAF 358
                 48*******************************************954..4555788887776 PP

>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.8e-05      0.23       7      36 ..     283     311 ..     283     325 .. 0.89
   2 ?   -0.9   0.0       0.3   1.8e+03      23      36 ..     409     422 ..     401     434 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
  Complex1_LYR   7 YRalLRearkfpdyntreyfrrriRdeFrk 36 
                   YR+ + +a  f + n r+ + +++R++F++
    AJA92673.1 283 YRKAMFAALNFAWSN-RQMITHWTRKSFER 311
                   9**************.*************9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
  Complex1_LYR  23 reyfrrriRdeFrk 36 
                   r+ +r+++R  F +
    AJA92673.1 409 RMMSRSKARRNFTE 422
                   888999***99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3194.28
//
Query:       AJA92674.1  [L=92]
Description: PF04472 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-11   42.7   0.3    5.6e-11   42.6   0.3    1.1  1  SepF         Cell division protein SepF
     0.0025   17.4   0.0     0.0027   17.3   0.0    1.1  1  Herpes_IE68  Herpesvirus immediate early protein
      0.008   16.1   0.0      0.012   15.5   0.0    1.2  1  H_kinase_N   Signal transduction histidine kinase
  ------ inclusion threshold ------
       0.08   12.7   0.1       0.26   11.1   0.1    1.7  2  DRTGG        DRTGG domain


Domain annotation for each model (and alignments):
>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.3   1.2e-14   5.6e-11       3      72 .]      12      84 ..      10      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.2e-14
                EEE-SSGGGHHHHHHHHHTT-EEEEE-CCCTC...HHHHHHHHHHHHHHHHCT-EEEEECTTEEEEE-TT-EE CS
        SepF  3 vveprsfedaqeiadalkegkiVilnledldk...eeakrivdflsgvvyaldGdiqkvgkkvflitPknvdi 72
                ++++r+ +d   i++++k+g ++il ++ l +   e+++++v++l  ++   ++di+++g++ +++tP+nv+i
  AJA92674.1 12 AITIRDPSDLHSIKEDIKKGMVLILRVTPLAQkdvEKLRKVVEELYVIARNAEADIARLGEERIIVTPPNVKI 84
                789*****************************99*************************************98 PP

>> Herpes_IE68  Herpesvirus immediate early protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     6e-07    0.0027      30      74 ..      19      63 ..       3      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6e-07
  Herpes_IE68 30 ldlarlvedinklFrcilraalnstgsanrLRrlvlDiylmGrtr 74
                  dl+ + edi k    ilr+++ ++++ ++LR++v ++y++ r  
   AJA92674.1 19 SDLHSIKEDIKKGMVLILRVTPLAQKDVEKLRKVVEELYVIARNA 63
                 599*********9999*************************9865 PP

>> H_kinase_N  Signal transduction histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-06     0.012       4      37 ..      34      67 ..      33      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                HHHHH----HHHHHHHHHHHHHTHHHHHHHTSEE CS
  H_kinase_N  4 llaehtdlseadiewLhalvgdwqllAdlsfaDl 37
                l+ + t l ++d+e+L+++v+++ ++A  ++aD+
  AJA92674.1 34 LILRVTPLAQKDVEKLRKVVEELYVIARNAEADI 67
                6778899**************************8 PP

>> DRTGG  DRTGG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.19   8.4e+02      31      46 ..      21      36 ..       3      41 .. 0.82
   2 ?   11.1   0.1   5.8e-05      0.26      16      47 ..      47      79 ..      33      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                HHHHHHHHHTSEEEEE CS
       DRTGG 31 venmlerlkegdlviv 46
                ++++ e +k+g+++i 
  AJA92674.1 21 LHSIKEDIKKGMVLIL 36
                6888899999998885 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.8e-05
                .SS--.E-EEEE-SS-HHHHHHHHHTSEEEEEE CS
       DRTGG 16 eelrr.vekvvvgamsvenmlerlkegdlvivp 47
                e+lr+ ve+++v+a+++e+ + rl e++++++p
  AJA92674.1 47 EKLRKvVEELYVIARNAEADIARLGEERIIVTP 79
                556667**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 700.63
//
Query:       AJA92675.1  [L=240]
Description: putative proteasome subunit alpha [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-51  174.8   0.8    1.6e-51  174.5   0.8    1.1  1  Proteasome      Proteasome subunit
    2.4e-11   43.1   0.8    1.7e-10   40.4   0.2    2.5  2  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.5   0.8   1.8e-55   1.6e-51       1     188 [.      29     210 ..      29     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 1.8e-55
                 HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHC CS
  Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrs 99 
                 vk+Gt ++Gi +k+g+vla++ ++     l+ +   +Kif++ddhigva+aG ++Dar+ v+ ar+  q+ +l+y++p+ +e++++++a++ ++ tq+s
  AJA92675.1  29 VKRGTLAIGIMTKEGIVLAVEEKTR---ALQVEGITQKIFQVDDHIGVAAAGYIPDARVQVDNARYFSQSNKLTYDEPVDIETVAKHLADQNHQFTQYS 124
                 799******************8888...44455557*************************************************************** PP

                 TTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
  Proteasome 100 grrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknieva 188
                 g+rpfgv+l+iag+d++g   +y idpsG+y ++ +a+aiG+gs+++ ++lek+yke lt +ea  la+ a++  +e +k++ + i++ 
  AJA92675.1 125 GVRPFGVALIIAGIDRKG-VNVYVIDPSGTYNSY-SAIAIGTGSDEVNEFLEKNYKEGLTIDEAASLAIAAINLKSE-EKSGIEHIKMS 210
                 ***************999.8**************.6************************************98888.66777777765 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.2   1.9e-14   1.7e-10       1      22 [.       6      27 ..       6      27 .. 0.97
   2 ?    0.2   0.0     0.071   6.3e+02      13      18 ..      63      68 ..      63      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-14
  Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmk 22
                    YD + t++SPdGR++QVEYA++
      AJA92675.1  6 YDMTPTMYSPDGRIYQVEYALE 27
                    9*******************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.071
  Proteasome_A_N 13 RLfQVE 18
                    ++fQV+
      AJA92675.1 63 KIFQVD 68
                    79***7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1702.75
//
Query:       AJA92676.1  [L=154]
Description: cupin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-06   27.3   0.0    1.7e-05   24.4   0.0    2.0  1  Cupin_2   Cupin domain
    3.9e-06   26.6   0.0    4.5e-06   26.4   0.0    1.1  1  Auxin_BP  Auxin binding protein
    9.4e-06   25.3   0.0    1.1e-05   25.1   0.0    1.1  1  Cupin_1   Cupin


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.8e-09   1.7e-05       2      62 ..      44     117 ..      43     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.8e-09
                 EEEEETTEEEEEECSSSEEEEEEEEESEEEEEEC.....TE.........EEEEETTEEEEE-TT-EEEEEE-SS CS
     Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvd.....ge.........eveleaGdsvyfpagtpHrfrNtgd 62 
                 +v+++ G+ ++ h H+   ++++V +G+g l +      g           + l++Gd+v++pa++ H+++ t +
  AJA92676.1  44 HVTFKNGARTKLHFHDAG-QTLIVTKGKGSLVMYkkigtGTknfkikkleSMNLNKGDCVHIPAKRLHTHGSTKK 117
                 689999************.************9553666611556666677********************98765 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.5e-10   4.5e-06      45     132 ..      41     133 ..      13     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.5e-10
                 EEEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE-....-SSSSS--S-EE.EEE-TTEEEEE-TT--EEEE---SSS-EEEEEEEESSS-- CS
    Auxin_BP  45 evwlqtlapgsrtpihrhsceevfvvlkgkgtlyla....sssskypgkpqe.lpifanstlsipvndahqvkntgehedlqvlviisrppvk 132
                 +++  t+  g rt +h h   + ++v kgkg+l++       ++++  k  e +++ +   ++ip +  h    t++ ed+  + i s p  k
  AJA92676.1  41 KIYHVTFKNGARTKLHFHDAGQTLIVTKGKGSLVMYkkigTGTKNFKIKKLEsMNLNKGDCVHIPAKRLHTHGSTKKSEDFAHVAINSFPKKK 133
                 57889****************************9852222567889888776367888899********************999999988655 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.8e-09   1.1e-05      37     118 ..      44     131 ..      15     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-09
                 EEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.........EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEESSST CS
     Cupin_1  37 rvdlepgglllPhyhpnateiayvlqGegrvgfvvpgng........nrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfdtnnp 118
                  v ++ g+   +h+h  a + ++v++G+g   ++  + g        +++++ +l++Gd + +Pa   h + ++ +++ +a v++++ ++
  AJA92676.1  44 HVTFKNGARTKLHFH-DAGQTLIVTKGKGS-LVMYKKIGtgtknfkiKKLESMNLNKGDCVHIPAKRLHTHGSTKKSEDFAHVAINSFPK 131
                 56668899999****.**************.55555555798888877777777******************************998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1186.93
//
Query:       AJA92677.1  [L=270]
Description: PF04402 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-39  135.4   3.5    4.3e-39  135.1   3.5    1.1  1  SIMPL     Protein of unknown function (DUF541)
  ------ inclusion threshold ------
       0.11   12.3   0.2       0.29   11.0   0.2    1.8  1  DUF4307   Domain of unknown function (DUF4307)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   3.5   4.7e-43   4.3e-39       1     200 []      58     265 ..      58     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 4.7e-43
       SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy..engknkitgyeasqsltvkfrdldklg 97 
                 I+V+Gsa+++ +pD+ ++ l+v se+k+a+e  +++++ +nav+++l + gi+e+diqts+++++p y+   +++k+ + gy++s+ l+++++++d++g
  AJA92677.1  58 ISVSGSATASSEPDTLIVVLGVDSEAKTANESLSQNSNSLNAVISSLTNSGISEDDIQTSNFRIYPLYDFsdSKDKQILIGYRVSNMLSIQTDKIDSAG 156
                 89**********************************************98********************99999999********************* PP

       SIMPL  98 evldaavka.aneingvsfslsde..delrdeareeAvkdArakAealAkalgvklgkvvsise...sgsnp..yappapamaaaaaaaasaatpfepg 188
                 +v+d av++ an++++vsf+lsde  ++ +d+++  A+ dA +kAe++   l++++ +v+s+ +   +   p  ++p++++ a++a+++++ + p+ +g
  AJA92677.1 157 NVIDIAVSSgANRVDNVSFQLSDEksQKISDDLISNAILDATQKAEKALVPLKQQIVGVKSVIIhdnA-M-PfyDSPMRSSFAGMAMESSMKSAPIMSG 253
                 **********************886666688*************************999666664332.2.24344444445555555999999999** PP

       SIMPL 189 eievtasVtvvf 200
                 + e++ +V+vvf
  AJA92677.1 254 DEEIRTDVSVVF 265
                 99*********9 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   3.3e-05      0.29       6      51 ..       5      48 ..       2      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
     DUF4307  6 villvvlvvvalalvawigysqgsadvsaevvgfevvddstvevtf 51
                + ++v+++vv++++ a+++++++++   +++++fe+ +d+ ++ ++
  AJA92677.1  5 INIAVIVGVVFVLAFAVTLTQYENQ-AVSQDAEFEI-SDELMTHWI 48
                6789999999999999999999555.5569999999.777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2027.50
//
Query:       AJA92678.1  [L=339]
Description: anthranilate phosphoribosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-78  262.3   0.1      6e-78  261.9   0.1    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    4.6e-08   32.8   0.2    1.6e-07   31.1   0.0    2.1  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
  ------ inclusion threshold ------
        1.4    8.5   6.1       0.57    9.8   1.8    2.2  2  Snf7             Snf7


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.9   0.1     1e-81     6e-78       3     252 ..      68     318 ..      66     319 .. 0.99

  Alignments for each domain:
  == domain 1  score: 261.9 bits;  conditional E-value: 1e-81
                      TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHSSSSHHHHHHHHHH CS
  Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfapeyhkamkhvapvrr 96 
                       l+D++gTGGd+ +tfNiStaa++v+A+aG +vakhgnrsvs  sGsaD+ e +g++l+ +p  ve+++e+ g+gf+fap++h+amk+vap+r+
       AJA92678.1  68 TLIDVCGTGGDNLQTFNISTAASFVIAGAGGNVAKHGNRSVSGISGSADIFEYFGFDLNSEPWMVEEMIEKIGIGFMFAPKFHPAMKNVAPARK 161
                      689******************************************************************************************* PP

                      HHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEES CS
  Glycos_transf_3  97 elgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakttvaelkdgeiteytlepedfglkraele 189
                       +g rT fnlLGPL+npa+v++q++gv++++ +e +a+++++  +  +l v + dG+de+s+++k+    lk++eite+ ++p++ +l++ +l 
       AJA92678.1 162 IIGKRTAFNLLGPLCNPAKVRHQMIGVFADNYIERIAKIMQKNFSDTVLTVRSdDGMDELSTTSKNKACLLKNEEITEFIIDPSKYNLEKGNLA 255
                      ******************************************999************************************************* PP

                      HHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHHHHHHTSHH CS
  Glycos_transf_3 190 aleggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakaeevidsGkA 252
                      +++  + ke+++   +vl+++++++  ++++lna+  l++ g  ++ +e v+ a++++++GkA
       AJA92678.1 256 DIQISTKKEAIDSFVKVLNNTSNKTMKEITILNAAGGLLVGGFSNKFEECVELAKQTVNNGKA 318
                      **************************************************************9 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.7e-11   1.6e-07      11      61 ..       6      56 ..       1      58 [. 0.92
   2 ?   -1.8   0.1      0.49   2.9e+03      16      24 ..     235     243 ..     232     261 .. 0.47

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.7e-11
                     .---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
  Glycos_trans_3N 11 eeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmre 61
                     ++Lt +e+  ++++il+g+ +d +ia fL  l  kGet eE+ a+ + m e
       AJA92678.1  6 GDLTFDEMSSVMSEILNGRNNDEEIAEFLRDLSNKGETNEELRAMFTKMNE 56
                     69****************************************999988865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
                      HHHHHHHHH CS
  Glycos_trans_3N  16 eeirfaihg 24 
                      eei ++i +
       AJA92678.1 235 EEITEFIID 243
                      666666643 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.8   9.5e-05      0.57      94     144 ..       1      49 [.       1      57 [. 0.87
   2 ?   -0.0   0.1     0.096   5.7e+02      41      61 ..     303     323 ..     255     338 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.5e-05
                 HHHHHHCTCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-GGTTHHHHHH CS
        Snf7  94 mkamnkkvdidkidklmdeiedqmekaeeisEalsrslddadeedEeelea 144
                 mk++n  +  d+   +m ei +   + eei E l +  +    e  eel a
  AJA92678.1   1 MKKINGDLTFDEMSSVMSEILNGRNNDEEIAEFLRDLSNK--GETNEELRA 49 
                 9*********************************998864..666666665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.096
                 HHHHHHHHHHHHHHHHHHHHH CS
        Snf7  41 dralllLKqkkryekqldqld 61 
                 + +  l+Kq ++  k  ++l+
  AJA92678.1 303 EECVELAKQTVNNGKAFEKLK 323
                 333334443333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1259  (0.0702214); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2434.66
//
Query:       AJA92679.1  [L=416]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2880.42
//
Query:       AJA92680.1  [L=334]
Description: daunorubicin resistance ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-31  108.0   0.0    1.1e-30  106.9   0.0    1.6  1  ABC_tran  ABC transporter
    7.2e-10   39.2   0.7    1.3e-05   25.2   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.1e-06   29.3   1.2    1.1e-06   29.3   1.2    1.9  2  DUF4162   Domain of unknown function (DUF4162)
      4e-05   23.5   4.6     0.0085   15.8   0.2    3.0  3  AAA_15    AAA ATPase domain
    0.00073   20.1   5.4     0.0024   18.4   5.4    2.0  1  AAA_23    AAA domain
     0.0012   18.4   1.9     0.0012   18.3   0.2    1.8  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.004   16.9   0.2     0.0093   15.7   0.2    1.6  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.11   12.3   1.9       0.38   10.5   0.1    2.2  2  MukB      MukB N-terminal
        0.7   10.0   2.9         19    5.4   0.1    2.5  2  MMR_HSR1  50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   5.8e-34   1.1e-30       1     136 [.      19     162 ..      19     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 5.8e-34
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeie 86 
                 ++n+sl+++ege+ +++G+nGaGKSt +++l+ llkpt+G+  + g+d+ + + + +rk+ig+++qe  +++ lt+ren             + +++ie
  AJA92680.1  19 VDNISLSVEEGEIFGFLGPNGAGKSTTMMILTTLLKPTSGNASVYGHDVIT-NPSNVRKNIGFVQQEIGIDEYLTARENlqfqckisqipkeQTQKRIE 116
                 58***********************************************99.8899*********************************998888889* PP

                 HHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  87 kalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 ++++ ++l+e++d+       ++SgG+++r+ +a+ l+ +pk+l+lDEpt
  AJA92680.1 117 EVIDLVELTEKQDEQS----ITFSGGMRKRLDIACGLIHRPKVLFLDEPT 162
                 ****999999777777....9****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   7.5e-05      0.15       2      22 ..      32      52 ..      31      64 .. 0.83
   2 !   25.2   0.0   6.5e-09   1.3e-05     165     298 ..      79     194 ..      59     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
      AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                 ++ GpNg+GKS+ + +l  l
  AJA92680.1 32 FGFLGPNGAGKSTTMMILTTL 52
                6789*************9766 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 6.5e-09
      AAA_21 165 rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllli 263
                  + +++i +d++  a+e+ ++q  ++++ +     + ++                 + ++e +  q+ ++  +S G+++ l ++  l+ ++   ++l++
  AJA92680.1  79 GFVQQEIGIDEYLTARENLQFQCKISQIPKEQTQKRIEE----------------VIDLVELTEKQDEQSITFSGGMRKRLDIACGLIHRP---KVLFL 158
                 666777777777777777777777777777776666665................445555566666666778*******99999899888...9**** PP

      AAA_21 264 DEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                 DEp  gL+ +  r+++e + k++++ g  ++++TH 
  AJA92680.1 159 DEPTVGLDIQTRRKIWEYIrKIHKEFGMTIFVSTHY 194
                 *******************666666**********5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.4   6.8e+03      21      21 ..     112     112 ..      73     137 .. 0.54
   2 !   29.3   1.2   5.5e-10   1.1e-06       3      80 ..     219     307 ..     218     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                 - CS
     DUF4162  21 a 21 
                 +
  AJA92680.1 112 Q 112
                 1 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 5.5e-10
                 HHHHHTTS-SSEEEEE.....-------.....--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHH CS
     DUF4162   3 leeiKrsygknrieve.....adaeellee...pg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiek 80 
                 +e  K+++ +++i+ +     +++e++ +     +  + ve +g++++++ ++ +++ +++++a  + g++i sF +++P+L+d+Fi  
  AJA92680.1 219 PESMKNKLETDMITFSiipdeNKQEQFINKiksFElTKNVEINGNNMVVQSSNsTQVIPKIFQASsEFGISIDSFVLNKPTLDDVFISH 307
                 6788999999**999988765333333333222222555577779999999999***********779*******************86 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   4.3e-06    0.0085      14      83 ..      19     103 ..       5     141 .. 0.61
   2 !    7.2   0.1    0.0017       3.5     323     364 ..     152     193 ..      87     195 .. 0.86
   3 ?    1.0   0.7      0.14   2.7e+02     195     279 ..     231     257 ..     204     324 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.3e-06
      AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn...............kkvikiekedleifeniseskdikIdvef 83 
                  ++++++++e  +  + G+N++GKS+ +++l  +l+ + + n                k i + ++++ i e+     +++ +++ 
  AJA92680.1  19 VDNISLSVEEGeIFGFLGPNGAGKSTTMMILTTLLKPT-SGNasvyghdvitnpsnvRKNIGFVQQEIGIDEYLTARENLQFQCKI 103
                 3444444444478889********************88.44468888778888877744455555555555555555555555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0017
      AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                 ++++l+++EP + L +q  + ++++++++ ++  + ++++TH
  AJA92680.1 152 RPKVLFLDEPTVGLDIQTRRKIWEYIRKIHKEFGMTIFVSTH 193
                 4678************************************** PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.14
      AAA_15 195 iklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgk 279
                 i++ +i+++++                                                           +++i+kik+f+  ++
  AJA92680.1 231 ITFSIIPDENK----------------------------------------------------------QEQFINKIKSFELTKN 257
                 22222222222..........................................................2222222222222222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   5.4   1.2e-06    0.0024      17     123 ..      24     130 ..      10     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
      AAA_23  17 F...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese..gkvkayvelt......fenkdgrytrsiererelskkkgktt 104
                 +   +  ++ + GpNGaGK+T +  ++  L   +++ s         +dv  + +  +k+ ++v+ +      ++       ++++++++ s+  +++t
  AJA92680.1  24 LsveEGEIFGFLGPNGAGKSTTMMILTTLLKPTSGNASV------YGHDVITNPSnvRKNIGFVQQEigideyLTA-----RENLQFQCKISQIPKEQT 111
                 444555799********************9986544444......3333333333122222233333221121333.....356999999999999999 PP

      AAA_23 105 kkaklelleideleqfise 123
                 +k ++e ++  el+++ +e
  AJA92680.1 112 QKRIEEVIDLVELTEKQDE 130
                 9999999999666665444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2     6e-07    0.0012       8     207 ..      11     200 ..       3     211 .. 0.69
   2 ?   -2.9   0.1       1.8   3.6e+03     103     116 ..     250     263 ..     223     278 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6e-07
                 ESETTE.ECEEEEEETTSS.EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                 xxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N   8 enFksy.agktvilpfsks.ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                 +nFk+  a ++++l ++++ +   +GpNG+GKs  +  +  +L  +s     s   +d+i++  ++ + + + v+  +  ++  +  e+ +++ + + +
  AJA92680.1  11 KNFKNStAVDNISLSVEEGeIFGFLGPNGAGKSTTMMILTTLLKPTSG--NASVYGHDVITN-PSNVRKNIGFVQQEIGIDEYLTARENLQFQCKISQI 106
                 5666431334555555554145689***********999888875544..5677789****9.677777777777777666666668888899999999 PP

                 TTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 105 rkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                  k++++ +i++      ++ el e+++ ++ ++SgG ++ + +a  +     +p+ l +lDe    LD + ++k+ e++++ +k++ + +  ++++ +e
  AJA92680.1 107 PKEQTQKRIEE-V---IDLVELTEKQDEQSITFSGGMRKRLDIACGL---IHRPKVL-FLDEPTVGLDIQTRRKIWEYIRKIHKEFGMTI-FVSTHYME 196
                 99998888864.3...45555556666666679***98865555432...2456655.68*********************999855433.33344455 PP

                 C-SC CS
                 xxxx RF
       SMC_N 204 kadk 207
                 +ad+
  AJA92680.1 197 EADS 200
                 5554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                 EETTSEEEEEETTE CS
                 xxxxxxxxxxxxxx RF
       SMC_N 103 vkrkgeseykingk 116
                 ++ + + +++ing+
  AJA92680.1 250 KSFELTKNVEINGN 263
                 22222223333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   4.7e-06    0.0093      16      50 ..      23      57 ..      14      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.7e-06
      AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                ++++++ +++ + Gp+G+GKST +  +++lL p++
  AJA92680.1 23 SLSVEEGEIFGFLGPNGAGKSTTMMILTTLLKPTS 57
                455664448899**********9999999999976 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00019      0.38      32      52 ..      35      55 ..      28      61 .. 0.87
   2 ?    0.7   0.1      0.19   3.8e+02     123     161 ..      95     132 ..      81     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                HS--SHHHHHHHHHHHHHHS- CS
        MukB 32 sGgnGaGksttmaafvtaliP 52
                 G nGaGksttm+ + t l P
  AJA92680.1 35 LGPNGAGKSTTMMILTTLLKP 55
                599**********99999877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                 ES--TT--HHHHHEE--SSS--EE--HHHHHHHHHTSTT CS
        MukB 123 qgleedvkltdvlleklddkkarvrelnelkekleeleg 161
                 ++l+ + k+ ++  e+ +++ ++v++l el ek +e ++
  AJA92680.1  95 ENLQFQCKISQIPKEQTQKRIEEVIDLVELTEKQDE-QS 132
                 5788889999999999999999********999988.44 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.017        33       3      21 ..      33      51 ..      31     133 .. 0.85
   2 ?    5.4   0.1    0.0094        19      25      99 ..     179     248 ..     168     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
                EEEESTTSSHHHHHHHHHT CS
    MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                +++G   +GKSt +  lt 
  AJA92680.1 33 GFLGPNGAGKSTTMMILTT 51
                799*********9999986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0094
                 EESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS.HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHH CS
    MMR_HSR1  25 ivsdkpgtTrdinegrvklkgkeielvDtpGlie.gaseek.glgkaflaleeadlillvvdaseeklkpldeelee 99 
                 ++ ++ g T+ + ++ +++ +    l+D +G+i+ g + +  +  ++++++ e+d+i + +   +e  +++++ +++
  AJA92680.1 179 KIHKEFGMTIFVSTHYMEEAD---SLCDRVGIIDyG-KIQIvDTPESMKNKLETDMITFSII-PDE--NKQEQFINK 248
                 677788999999999898443...899999988733.3333478888888888899888884.312..222233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 2508.30
//
Query:       AJA92681.1  [L=564]
Description: type III restriction enzyme, res subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-18   67.7   0.5    1.7e-17   64.1   0.0    2.4  2  Helicase_C_2  Helicase C-terminal domain
    5.2e-12   46.1   2.7    7.8e-12   45.5   0.3    2.5  3  ResIII        Type III restriction enzyme, res subunit
    3.3e-05   23.6   5.5    0.00019   21.1   1.3    2.4  2  DEAD_2        DEAD_2
    8.7e-05   22.3   1.8       0.12   12.2   0.0    3.3  4  DEAD          DEAD/DEAH box helicase
     0.0011   19.3   0.1     0.0085   16.5   0.0    2.3  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.019   14.6   0.2      0.054   13.1   0.2    1.8  1  DUF4978       Domain of unknown function (DUF4978)
      0.023   15.0   0.7        8.6    6.6   0.0    2.9  3  AAA_22        AAA domain
      0.033   14.6   0.0      0.072   13.5   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.083   12.3   0.2        1.9    7.9   0.0    2.7  3  PhoH          PhoH-like protein


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.23   4.6e+02       7      51 ..     161     204 ..     155     217 .. 0.78
   2 !   64.1   0.0   8.4e-21   1.7e-17       5     153 ..     398     533 ..     395     549 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.23
  Helicase_C_2   7 vvpggvlvffpSyklleevverlkeeleskkieifveekeesrek 51 
                    v  + +    Sy ++ +  ++ ++e+ +kk+ if+e  ++ +++
    AJA92681.1 161 LVSSHSIWNYASYFQMMKYQKEKYAEYLNKKVAIFDE-AHRIEDQ 204
                   56666677788999999999999999999******99.5554444 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 8.4e-21
  Helicase_C_2   5 levvpggvlvffpSyklleevverlkeeleskkieifvee..keesrekvleeykekkkkgaillavcrGklsEGidfsddllraviivglPfpnpk 99 
                   +++  ++ l++++S +   e+ e l++e  +k+i+i ++   + +++++v++e+ e  + + +ll++    l+EG+d+++d+ r  i+ + P+p ++
    AJA92681.1 398 TKYSDKKGLILTSSKSRCFEILENLSAEN-KKRIRICHSFnaNGKTQDQVVQEHAE--SANGVLLSSS---LWEGVDLKEDMSRFQIVAKAPYPMLS 488
                   667788999****************9997.4777666544448999**********..9999999996...9************************9 PP

  Helicase_C_2 100 dpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDe 153
                   + ++++k++         ++  wy+ +a+ ++ Q++GR iR+  D++  ++lD+
    AJA92681.1 489 ETRTKIKMQ---------KYPLWYKAQAIMKLLQGFGRSIRDYGDWADTYVLDS 533
                   999888864.........5678******************************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.3   3.9e-15   7.8e-12       2     147 ..      15     204 ..      14     232 .. 0.74
   2 ?   -1.9   0.0       1.4   2.8e+03     153     169 ..     320     336 ..     266     338 .. 0.66
   3 ?   -1.7   0.1       1.2   2.5e+03      47      61 ..     395     409 ..     361     460 .. 0.51

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.9e-15
                 -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG.......................... CS
      ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef.......................... 74 
                 +++r+ Qe+ ie++ ek++  + k +l+ ++TG GK+l+aa+++ ++ ++      +++  +k+l +q  +++                          
  AJA92681.1  15 FTPRPLQEKLIEEIQEKIN-SGAKVVLLSAPTGIGKSLIAASVAGYFGSS------FVVTASKHLQDQYTKDMpwfkpnkgmpnfachkmmekhgidlt 106
                 789***************9.**********************99999886......88999************77777777777777666666666666 PP

                 ...............GGGTGG....GEEEESSS-B--...................-SEEEEEHHHHHHTH....................HHHTTT-S CS
      ResIII  75 ...............kkflseaykeigkkvsgdkkka............kekdstnkkilvttiqsldadseee............eeeseellrdrfd 134
                                ++f ++++k            +             +++++++ +++ ++qsl ++                 ++++ ++  +++
  AJA92681.1 107 ekdfavqnkwtcdmgTCFDKKTKK------------EcnykpklsdvaeGKIKQDDCLYYLQKYQSLVSSH--SiwnyasyfqmmkYQKEKYAEYLNKK 191
                 544444444444443222222222............133334666666666788999999*******9998..33589999999866666666677777 PP

                 EEEEETGGGTTS. CS
      ResIII 135 viiiDEaHrlgak 147
                 v i+DEaHr+ ++
  AJA92681.1 192 VAIFDEAHRIEDQ 204
                 **********995 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                 HHHT---SEEEEEESS- CS
      ResIII 153 ilekfkeavllglTATp 169
                 +   f++ +++ ++AT+
  AJA92681.1 320 VSTFFDHPIQIFMSATI 336
                 34566777888888886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                 HH-S.....-EEEEE CS
      ResIII  47 rllkkgkeekflflv 61 
                 ++++k++ +k l+l 
  AJA92681.1 395 EIMTKYSDKKGLILT 409
                 222222222333333 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.3   9.4e-08   0.00019      70     175 ..     105     217 ..      85     218 .. 0.67
   2 ?    4.1   0.2     0.016        31      12      70 ..     389     444 ..     380     484 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.4e-08
                 H.........TTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH.T..GCGCEEEECTCCC CS
      DEAD_2  70 k.........eekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk.gislknsivilDEAhN 158
                           + +C++ + +   +k++k+  +    + d+ e   k+  C Yyl +         i  Y+  ++    ++ k    l++++ i+DEAh 
  AJA92681.1 105 LtekdfavqnKWTCDMGTCF---DKKTKKECNYKPKLSDVAEGKIKQDDCLYYLQKYQSLVSSHSIWNYASYFQMMKYQKEKyAEYLNKKVAIFDEAHR 200
                 23333444336677776544...44455666667788999999999999******8766666555555655444433333332346999********** PP

                 HHHHHHHCC-EEEECHH CS
      DEAD_2 159 iedvceeaasveisees 175
                 ied +++ + ++i e++
  AJA92681.1 201 IEDQIIQFVGIDIFERN 217
                 **********9998776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.016
                 HHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH CS
      DEAD_2  12 vvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek 70 
                 v+k +++++   +k ++ k +iL+S k  C +   + + ++k+  ++C++ +++ +++ 
  AJA92681.1 389 VIKKIDEIM---TKYSDKKGLILTSSKSRCFEILENLSAENKKRIRICHSFNANGKTQD 444
                 555555554...4456789***********77444434455666689999998886653 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.9e-05      0.12       2      32 ..      19      54 ..      18      81 .. 0.84
   2 !    6.7   0.1    0.0029       5.7      96     137 ..     156     207 ..     125     245 .. 0.67
   3 ?   -3.6   0.0       3.9   7.9e+03     162     171 ..     329     338 ..     315     341 .. 0.76
   4 ?    0.6   0.0      0.21   4.1e+02      39      87 ..     396     443 ..     377     461 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                HHHHHHHHHHH.....TTCEEEEEESTTSSHHHHHH CS
                xxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
        DEAD  2 diQaeaiplil.....gggdvlvaaeTGsGKTlafl 32
                + Q++ i++i      g + vl++a+TG GK+l+++
  AJA92681.1 19 PLQEKLIEEIQekinsGAKVVLLSAPTGIGKSLIAA 54
                679999999995555444899***********9875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0029
                 TTCSEEEEEHHHHHHHH........HCTSSHCTTEEEEEEETHHHHHHT..T CS
                 xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxx..x RF
        DEAD  96 ngvdivvgtpgrlddll........stgklnlsqvrflVlDEadrlldq..g 137
                 ++++ +v+ ++ +            ++++ ++ + ++ ++DEa+r+ dq  +
  AJA92681.1 156 QKYQSLVSSHSIWNYASyfqmmkyqKEKYAEYLNKKVAIFDEAHRIEDQiiQ 207
                 5555555555444443234444554444556778899***********9442 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.9
                 EEEEESSBSH CS
                 xxxxxxxxxx RF
        DEAD 162 vivlSATlpk 171
                  i++SAT+ k
  AJA92681.1 329 QIFMSATIDK 338
                 4899***974 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.21
                 HHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET..TSSH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
        DEAD  39 vyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig..gvaa 87 
                 ++  ++ + +k li++ +++ + ++l+nl+   k+ ++r++  ++  g+++
  AJA92681.1 396 IM--TKYSDKKGLILTSSKSRCFEILENLSAENKK-RIRICHSFNanGKTQ 443
                 33..46677899*****************988886.355553333113333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.3e-06    0.0085       1      41 [.      39      79 ..      39      83 .. 0.92
   2 ?   -0.5   0.0      0.78   1.6e+03      57      71 ..     181     202 ..     157     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-06
                EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTH CS
         AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvge 41
                vll+ p G+GK+l+a +va  +g++f+ +  + l ++y ++
  AJA92681.1 39 VLLSAPTGIGKSLIAASVAGYFGSSFVVTASKHLQDQYTKD 79
                79*************************99999999888776 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.78
                 S.......TSEEEEEETGGGHH CS
         AAA  57 a.......kpsilfiDEidala 71 
                 +       ++++ ++DE++++ 
  AJA92681.1 181 KekyaeylNKKVAIFDEAHRIE 202
                 233456666799999**99984 PP

>> DUF4978  Domain of unknown function (DUF4978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.7e-05     0.054      46      74 ..     201     229 ..     183     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
     DUF4978  46 sggtnidfvGvdiyktnakkvkgelsaya 74 
                  + + i fvG+di++ n ++ k ++++y 
  AJA92681.1 201 IEDQIIQFVGIDIFERNLNECKIDVENYD 229
                 45688********************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0043       8.6       3      25 ..      34      56 ..      25      69 .. 0.89
   2 ?    5.6   0.0    0.0093        19      78     115 ..     176     213 ..     140     232 .. 0.71
   3 ?   -2.5   0.0       2.8   5.6e+03      51      70 ..     409     428 ..     386     452 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0043
      AAA_22  3 ktagilvvtGesGtGKTtllrrl 25
                ++a+++++ +++G+GK++ ++ +
  AJA92681.1 34 SGAKVVLLSAPTGIGKSLIAASV 56
                68999*************99876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0093
      AAA_22  78 ll.ealeqalraravielliiDEaqhlrseealeeL.rsl 115
                 ++  + e++++   + ++ i DEa+++ ++++++++  ++
  AJA92681.1 176 MMkYQKEKYAEYLNK-KVAIFDEAHRI-EDQIIQFVgIDI 213
                 333666666666667.9**********.655555544333 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.8
      AAA_22  51 tsskdllrellralglelka 70 
                 tssk+ + e+l++l  e+k+
  AJA92681.1 409 TSSKSRCFEILENLSAENKK 428
                 46677777777777777666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.6e-05     0.072      12      62 ..      25      74 ..      15      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
      AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdq 62
                ++++ e+++sg   +vlls + G+GKs ++ +++ ++  + +++ ++ + ++
  AJA92681.1 25 IEEIQEKINSGA-KVVLLSAPTGIGKSLIAASVAGYFGSS-FVVtASKHLQD 74
                456666778887.8********************888877.55524444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00098       1.9       9      40 ..      21      57 ..      16      63 .. 0.82
   2 ?    0.0   0.1      0.25   4.9e+02     118     170 ..     188     245 ..     186     268 .. 0.68
   3 ?   -0.6   0.0      0.38   7.5e+02      50      98 ..     291     343 ..     284     359 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00098
                HHHHHHHHH.....H-SEEEEE--TTSSTTHHHHHHH CS
        PhoH  9 Qkeylealk.....kndivfaiGpaGtGKtylavala 40
                Q++++e ++       ++v   +p+G GK+++a ++a
  AJA92681.1 21 QEKLIEEIQekinsGAKVVLLSAPTGIGKSLIAASVA 57
                77788887765445567****************9887 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.25
                 B-SEEEEE-SGGG--HHHHHHHHT....TB-TT-EE.EEEE--------------THH CS
        PhoH 118 lndafvilDEAQnttkeqmkmflt....RlGenskv.vvtGdvtqidlpkgkksGlae 170
                 ln+++ i+DEA  ++ + ++ + +    R  +++k+ v + d++ id  ++ ++Gl+e
  AJA92681.1 188 LNKKVAIFDEAHRIEDQIIQFVGIdifeRNLNECKIdVENYDLQDIDDVMKLSDGLSE 245
                 7889999999999999998876441111555566663335566666666666666655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.38
                 SEEEEEE-S--TT...----SS---------TTT.HHHHHHHTTTS-TTCHHH CS
        PhoH  50 kriiltrpaveag...eelGflpgdleekvdpyl.rplydaLkdllgaekvek 98 
                 +++il +p  + g   ++l + p d++++v+ ++ +p+   ++ ++++e++ +
  AJA92681.1 291 ENFILNKPYYDEGgkfRSLSVKPLDISKYVSTFFdHPIQIFMSATIDKESFCE 343
                 679999999977423358999********998773678888888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4086.31
//
Query:       AJA92682.1  [L=409]
Description: hypothetical protein T478_0939 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0041   17.4   0.3        5.2    7.4   0.1    3.0  2  DUF4883   DOmain of unknown function (DUF4883)
     0.0042   17.2   0.0     0.0094   16.0   0.0    1.6  1  DUF4366   Domain of unknown function (DUF4366)
  ------ inclusion threshold ------
       0.05   14.2   0.4       0.18   12.4   0.4    1.9  1  ACT_4     ACT domain
       0.13   11.9   0.0       0.18   11.5   0.0    1.2  1  Stk19     Serine-threonine protein kinase 19


Domain annotation for each model (and alignments):
>> DUF4883  DOmain of unknown function (DUF4883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0012       5.2       6      47 ..      62     103 ..      57     112 .. 0.86
   2 !    6.8   0.0    0.0017       7.8      90     112 ..     339     361 ..     326     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
     DUF4883   6 yYtnllakklksnkklklsvldtnlykeievdkeeieiiknf 47 
                  +t++l+kk++ n+k++  v+ +  +  i v++ee+ i+ nf
  AJA92682.1  62 KFTDELIKKINDNEKIRAIVFTNAGECVIGVTSEEQCIMINF 103
                 58*******************999988899999888887776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0017
     DUF4883  90 isvypwDgkykkdyidiknipas 112
                 + + pwDg+ +  + ++++ip++
  AJA92682.1 339 VEIGPWDGNSELSFYSVEDIPQN 361
                 6799*****************86 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-06    0.0094      97     144 ..     359     408 ..     334     409 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
     DUF4366  97 pepekeaepee....peeepekksnnglllvvlavaligggaayyfkvlkpk 144
                 p++eke+ + +     ++e+++++++ ++l++++v++ig +a++y+k +kpk
  AJA92682.1 359 PQNEKEEYQ-SiedfGKKESSDDESQYAVLAIIIVIGIG-AAIFYLKGYKPK 408
                 333333222.13345455555555677777777777777.88899******9 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4     4e-05      0.18      20      60 ..     202     242 ..     195     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
       ACT_4  20 LaditqviseekanivsvnaktrkkdglaeikitveVkdve 60 
                 + di++ +s+++++i s+++ ++ +++l+ +k+t e+kdv+
  AJA92682.1 202 FYDISKKLSKNDGSIISISIIKTGDENLFMFKVTNEIKDVA 242
                 58********************999**************96 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     4e-05      0.18      25      91 ..      39     109 ..      25     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4e-05
       Stk19  25 lrrs.lPplvtvahlhsllaqsptkvereleelirkgklrklvingrgkdisklg...evlvltedyekli 91 
                 + ++    +vt   l ++++q+ ++++  +++  ++ k+r +v +++g+ + ++    +++++  dy++l 
  AJA92682.1  39 YDQQySNSVVTSIGLETISNQEIKFTDELIKKINDNEKIRAIVFTNAGECVIGVTseeQCIMINFDYQQLK 109
                 4444355899999***********************************99876556669****99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2766.70
//
Query:       AJA92683.1  [L=180]
Description: putative methylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-09   36.4   0.0      1e-08   34.9   0.0    1.7  1  MTS              Methyltransferase small domain
    5.7e-07   29.5   0.0    1.1e-06   28.6   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      6e-07   30.0   0.0    9.8e-07   29.3   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    2.5e-06   28.1   0.1    4.4e-06   27.3   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    5.6e-06   26.2   1.4    1.3e-05   25.0   1.4    1.6  1  Methyltransf_31  Methyltransferase domain
    5.8e-05   22.2   0.0    6.6e-05   22.0   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    0.00018   22.2   0.2    0.00037   21.2   0.2    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00043   19.5   0.0     0.0006   19.0   0.0    1.1  1  DREV             DREV methyltransferase
     0.0027   17.5   0.0     0.0036   17.1   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0033   17.4   0.0      0.005   16.8   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0074   15.7   0.1       0.01   15.2   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.17   12.0   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
        0.1   12.9   0.1       0.41   11.0   0.0    1.9  2  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
       0.11   11.5   0.2       0.29   10.1   0.0    1.7  2  RrnaAD           Ribosomal RNA adenine dimethylase
       0.14   11.7   0.0       0.21   11.2   0.0    1.2  1  NodS             Nodulation protein S (NodS)
       0.15   11.7   0.0       0.21   11.2   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0     9e-12     1e-08      21     148 ..      18     146 ..      15     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 9e-12
                 HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STT.......... CS
         MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfha.......... 109
                  +L++ l++ + +++lD+GcG G+l+  l ++ +   v+ +d++++ l  +++n++++++ + ++  d+l   +  +fdli++N P+ a          
  AJA92683.1  18 FFLADRLKDLRGKSALDIGCGSGYLTDILNSNFQL--VVGTDISFNTL--CTQNYKTQNA-ICCHSADAL---N-LQFDLIICNLPYLAtdeiidvatd 107
                 689999**999999************999987766..99******986..5667776664.556666655...3.569********9761111111111 PP

                 TCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH CS
         MTS 110 gkatelavaeeliaeAkeaLkegGeLliVanrklgyesl 148
                 g +  l++  e+i +A  +L+++G++l+V+++  +y  l
  AJA92683.1 108 GGKDGLEIPLEIISSALPHLDKNGKFLFVTSSLSDYMGL 146
                 34445678889******************9998887665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     1e-09   1.1e-06      13      89 ..      17      92 ..       5     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-09
  Methyltransf_23 13 lerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq...eaaepqgkfdlIvlr 89
                     + +l+++  + +g++ LdiGcG+G+l+++l  n+  v+g D+s++          ++ +  +++   +a+  + +fdlI+++
       AJA92683.1 17 TFFLADRlkDLRGKSALDIGCGSGYLTDILNSNFQLVVGTDISFNTLCT------QNYKTQNAIcchSADALNLQFDLIICN 92
                     55566554477899****************99999999******85553......2222222333335555777*****997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   8.7e-10   9.8e-07       1      68 [.      33      92 ..      33     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.7e-10
                     EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
  Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68
                     Ld+GcG+G+l+  l +++  vvg+D+s ++l  + +++++++  + ++ ada +l     +fDl++++
       AJA92683.1 33 LDIGCGSGYLTDILNSNFQLVVGTDISFNTL--CTQNYKTQNA-ICCHSADALNL-----QFDLIICN 92
                     8*****************************9..8888888874.77778888776.....56777765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1     4e-09   4.4e-06       2      80 ..      33      99 ..      32     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4e-09
                     EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
  Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80
                     Ld+GcG+G lt  l  ++  + v+g+Dis + l + + +   ++  + ++ +da +l+     fDl++++  l +l  +
       AJA92683.1 33 LDIGCGSGYLTDILNSNF--QLVVGTDISFNTLCTQNYKT--QN-AICCHSADALNLQ-----FDLIICN--LPYLATD 99
                     9****************9..9********99986555554..33.6888888888885.....8999995..5665544 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   1.4   1.2e-08   1.3e-05       4     116 ..      29     141 ..      26     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.2e-08
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl............ 84 
                      g++ lD+GCG+G+lt  l+++     + vvG Dis + +  +++n + ++   +  + +d+ +l+       fDli++n +             
       AJA92683.1  29 GKSALDIGCGSGYLTDILNSN----FQlVVGTDISFNTL--CTQNYKTQNA--ICCHSADALNLQ-------FDLIICNLPYlatdeiidvatd 107
                      6789***************64....344********976..6666554443..334457777766.......*******444444555577788 PP

  Methyltransf_31  85 ...naladpdkileeiervlkpggilliedprlla 116
                         + l  p +i+ ++   l ++g +l  + + l+
       AJA92683.1 108 ggkDGLEIPLEIISSALPHLDKNGKFLFVTSS-LS 141
                      88899999999999999999999999988887.44 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   5.9e-08   6.6e-05     109     181 ..      22      97 ..      19     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.9e-08
                     GGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHH..HHHHHCCTTT..TSSEEEE---GGGS-T-- CS
  Methyltransf_9 109 phlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliq..feavrkllge..dqrahllplgieqlpele 181
                       l dl+g++ ld+Gcg+Gy l  ++  + +lvvG d s   l++  +++ + +  +  d  + ++ l i +lp l+
      AJA92683.1  22 DRLKDLRGKSALDIGCGSGY-LTDILNSNFQLVVGTDISFNTLCTqnYKTQNAICCHsaDALNLQFDLIICNLPYLA 97 
                     5789***************9.568999*********99988877522555555444300334444455666666654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   3.3e-07   0.00037       1      73 [.      33      92 ..      33     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.3e-07
  Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73
                     L+iGcG+G l++ l  +  +  ++g+Dis + +    +  + +++    +   +al+l       +fDl++++
       AJA92683.1 33 LDIGCGSGYLTDILNSN--FQLVVGTDISFNTL--CTQNYKTQNA--ICCHSADALNL-------QFDLIICN 92
                     8***********99999..88888*********..2222222222..22333444443.......89999997 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.3e-07    0.0006      92     157 ..      26      91 ..      10      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.3e-07
        DREV  92 dqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkkkynvlsalelqetdvkldlilc 157
                 d + k  ld+G G G +t ++++ f+ v  t++s +     + k  n +     +  ++++dli c
  AJA92683.1  26 DLRGKSALDIGCGSGYLTDILNSNFQLVVGTDISFNTLCTQNYKTQNAICCHSADALNLQFDLIIC 91 
                 5567889***************************99999999999999999999999*******99 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.2e-06    0.0036      73      96 ..      28      51 ..       3      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                TT-EEEEES-TTSHHHHHHHHHHC CS
        PCMT 73 kgarvLevGsGsGyltavlarlvg 96
                +g+++L++G+GsGylt +l   ++
  AJA92683.1 28 RGKSALDIGCGSGYLTDILNSNFQ 51
                6899************99987665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.5e-06     0.005      26      60 ..      29      59 ..      13      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.5e-06
  Methyltransf_32 26 altvvDvGaGkgYLsfvlalkekeyklkvvgidak 60
                      ++ +D+G+G gYL+ +l++   +++  vvg d++
       AJA92683.1 29 GKSALDIGCGSGYLTDILNS---NFQ-LVVGTDIS 59
                     56779***************...322.35555554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.4e-06      0.01     161     234 ..      28      93 ..      17     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
        PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaNI 234
                 +g++ lD+G+GSG L+   +  + + vv++Di   ++  +++  ++N +        s+++l+  ++d+i++N 
  AJA92683.1  28 RGKSALDIGCGSGYLT-DILNSNFQLVVGTDISFNTL-CTQNYKTQNAICC-----HSADALN-LQFDLIICNL 93 
                 6789***********8.566778899******87765.3333333444433.....4577877.89******96 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00015      0.17      21     147 ..      28     149 ..      12     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                 TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHH.....CCCC CS
        FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealserkvdlvvsDgapdvsgvhdldeylq.....sqLl 114
                 +gk ++D+g++ G  +++l+ ++   + vv+ D+  +++  +    q  i  +++  + +      ++dl+++ + p     + +d ++      +++ 
  AJA92683.1  28 RGKSALDIGCGSGYLTDILNSNF---QLVVGTDISFNTLCTQNYKTQNAICCHSADALNL------QFDLIICNL-PYLATDEIIDVATDggkdgLEIP 116
                 7899******************8...57******99866644444444444443333333......377777777.46666677777776777776677 PP

                 HHHHCCHCCCCECCCEEEECCCHCCCHHHHHHH CS
        FtsJ 115 laalelalkllkpggtfvlkifrgeeteallkq 147
                 l  ++ al  l+++g f++ +   ++  +l+++
  AJA92683.1 117 LEIISSALPHLDKNGKFLFVTSSLSDYMGLVNF 149
                 777777777777777777666665555555555 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.41      60      89 ..      30      59 ..      19      74 .. 0.84
   2 ?   -0.7   0.0       1.6   1.7e+03      76      91 ..     150     165 ..     132     179 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
  AdoMet_MTase 60 tsfvdvgcgngllvyvlaaegykgygidlr 89
                  +s  d+gcg g l  +l+++     g d+ 
    AJA92683.1 30 KSALDIGCGSGYLTDILNSNFQLVVGTDIS 59
                  6789**************998888888875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
  AdoMet_MTase  76 laaegykgygidlrkr 91 
                   ++++g++   id +k 
    AJA92683.1 150 VNSKGFQAKIIDKKKL 165
                   4555555554444432 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.29      34     124 ..      32     107 ..      21     122 .. 0.84
   2 ?   -2.8   0.2       2.4   2.7e+03      11      37 ..     148     175 ..     147     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                 EEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHH CS
      RrnaAD  34 vleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlle 124
                  l+ig G G lT +L+  ++ vv    d ++  l +++ + ++ +    +D+l+ ++               ++ nlPy ++ ++++  ++
  AJA92683.1  32 ALDIGCGSGYLTDILNSNFQLVVG--TDISFNTLCTQNYKTQNAICCHSADALNLQFDL-------------IICNLPYLATDEIIDVATD 107
                 59***************9987765..688999999998889999999999999999988.............8889999888888876665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                 -EE--HHHHHHHHHHH-GG.TTSEEEEE CS
      RrnaAD  11 nflknkkvineIldklnle.ekltvlei 37 
                 nf+++k   ++I+dk +l  e+l ++e+
  AJA92683.1 148 NFVNSKGFQAKIIDKKKLFfEELIIVEV 175
                 7889999999999999998788888875 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.21      44     113 ..      29      92 ..      15     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
        NodS  44 iadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivva 113
                   +al++Gc +G lt+ l    + +   d+  +++   + ++++   i  + +d      + +fdli++ 
  AJA92683.1  29 GKSALDIGCGSGYLTDILNSNFQLVVGTDISFNTLCTQNYKTQN--AICCHSADAL----NLQFDLIICN 92 
                 5689******************9999999999999887777777..8999999964....5689999985 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.21      97     133 ..      66      97 ..      57     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                 HHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
     UPF0020  97 ekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
                 ++++ ++ i   +ada +L+     +d+i++n+PY  
  AJA92683.1  66 QNYKTQNAICCHSADALNLQ-----FDLIICNLPYLA 97 
                 78888888999999998888.....9*********74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1294.89
//
Query:       AJA92684.1  [L=110]
Description: dUTP diphosphatase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.8e-19   68.6   6.0    1.8e-14   54.2   0.4    2.0  2  dUTPase_2  dUTPase
    9.5e-05   22.8   0.1    0.00012   22.5   0.1    1.1  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
      0.073   13.9   0.1      0.095   13.6   0.1    1.3  1  DUF469     Protein with unknown function (DUF469)


Domain annotation for each model (and alignments):
>> dUTPase_2  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.4     3e-18   1.8e-14       2      89 ..       5      87 ..       4      90 .. 0.86
   2 !   20.9   0.6   5.3e-08   0.00032     139     166 .]      83     110 .]      79     110 .] 0.93

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 3e-18
                HHHHHHHHHHHHHHHSTTH.....HH-HHHHH....HHHHHHHHHHHTTS.---SSSSTT---HHHHHHHHHHHHHHHHHHHHCHHCT CS
   dUTPase_2  2 lksllelQkeLderiekkwnlkkkrkklsdwleekllAllvElaElanetrsfKyWknkkksdlekvleElvDilHFllslalelkde 89
                l s++ +Qk+L+++++ +   k+++ k+s      ++A++ E+ El   t  +K+Wk+ ++   ++ +eEl+Di+HF++   lel+ +
  AJA92684.1  5 LDSIFSMQKGLENMMNLDRYPKDTEGKVS----ALCTAIMHEAVELQRTT-NWKWWKTPTEFSEAEAREELIDIWHFVVQASLELNLT 87
                789*************9994444444443....446**********9999.*****************************99999876 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.3e-08
                 HHTS-...HHHHHHHHHHHHHHHHHTTT CS
   dUTPase_2 139 llgfneeelvkaYvaKnelNlkRqengY 166
                  l+++ +++ k+Y +Kne+N +Rq+ gY
  AJA92684.1  83 ELNLTPDDILKEYERKNEINRQRQKDGY 110
                 589999*********************9 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.9e-08   0.00012      20      83 .]      28      99 ..      16      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.9e-08
                -HHHHHHHHHHHHHHHHHHHHHT-SC........HHHHHHHHHHHHHHHHHHHHHHCT--CHHHHHHHHHHH CS
      PRA-PH 20 taelaslraaligEEavElleaaseg........dlaeladelaDllYvtygllvllGidldavfeevhran 83
                t+ ++s ++++i+ EavEl+ +++ +        + ae  +el+D++ ++  +  +l++++d++++e +r+n
  AJA92684.1 28 TEGKVSALCTAIMHEAVELQRTTNWKwwktptefSEAEAREELIDIWHFVVQASLELNLTPDDILKEYERKN 99
                5556666999*************97788888888*********************************99987 PP

>> DUF469  Protein with unknown function (DUF469)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.6e-05     0.095      60     101 .]      33      75 ..       5      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
      DUF469  60 glvclaklgsvteedreaveawlkarsevkevev.seLvDawy 101
                 + +c+a + ++ e +r++  +w+k+ +e++e+e+ +eL+D+w+
  AJA92684.1  33 SALCTAIMHEAVELQRTTNWKWWKTPTEFSEAEArEELIDIWH 75 
                 347899999999********************99458*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 798.49
//
Query:       AJA92685.1  [L=603]
Description: UDP-N-acetylglucosamine 2-epimerase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-05   23.4   0.0    3.9e-05   22.7   0.0    1.3  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.2e-09   3.9e-05     137     284 ..     396     532 ..     312     540 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.2e-09
                  HHHTT--GGGEEE---HHHHHHHHHHHHHH...T-HHHHHH.--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHHH CS
  Epimerase_2 137 LlkegeeeerifvvGntviDalllskeeieeklkaseilke.lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrll 233
                  + +  +++++i   Gn+v+D+l+ + ++ ++++    i ++  + k++v+     ++     + l+ei+++l++l+k+    v++  h  p  +++ l
   AJA92685.1 396 VENFRISKDKIQDLGNPVFDQLFDHNDNTSNEF--ILI-ATsPPMKDFVIDNTVNVQINY-YSILNEICDFLTKLNKK----VIIKPH--PSLEDKNL 483
                  56677899**************88888888777..233.333577777776555555555.679*************8....899999..99999999 PP

                  HHHHH-TTEEEE----HHHHHHHHHC-SEEEE.S-H.HHHHHHHHCT--EEES CS
  Epimerase_2 234 eeleelenvtlieplgyldflsllknaklvlt.dSg.GiqeEapslgvpvvnl 284
                  e ++++env +i++    d++ l+k+++l++t d + +i  E+ +l++pv+ +
   AJA92685.1 484 ENFKHFENVEIIKN---GDIIPLIKKCELLITfDLStTIL-ESQILKKPVLSI 532
                  99999999999887...57899**********98776999.*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3825.02
//
Query:       AJA92686.1  [L=185]
Description: phosphodiesterase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-28   97.6   0.2    9.8e-28   97.4   0.2    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    5.6e-09   36.8   3.7    1.7e-07   32.0   1.1    2.2  2  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.043   13.3   0.1      0.056   12.9   0.1    1.2  1  SpoIIP         Stage II sporulation protein P (SpoIIP)


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.2   1.6e-31   9.8e-28       1     164 [.       9     177 ..       9     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 1.6e-31
  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela....pvlaVrGNnDeevveedvlreaaelgtdl.peeaelelag 91 
                    Mk++iiSD+H+ +  ++++++++++ +v  +ih+GD+  ++p v+ e+++l     +++ V GNnD   +e+ + +e+++++++l +e  ++++++
     AJA92686.1   9 MKIGIISDTHDDILNTNKAIDIFSQNNVSIVIHVGDF--VAPPVVTEFKRLSkdgvKIIGVLGNND--GEEQGLKEEFEGINGELfKEIGKIKIDN 100
                    *************************************..************9**************..778999999***99999459999***** PP

  Metallophos_2  92 ekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvv.nPGsvgep....rdgdpe........tyaildtde 164
                     k++++Hg+   ++++ ++++++  ++ dv+++GHtH++e   ++++++v nPG +  p                  t++i+dt++
     AJA92686.1 101 LKFGIYHGT---DAKKRQKMIDS--KKFDVCIFGHTHQKENYVDEKTVIVlNPGTAHYPvkmnY----ThdryfgesTIMIFDTND 177
                    ********9...78888899988..7778**********988888775555*****99954431....233356666888888876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   1.1   2.8e-11   1.7e-07       1      87 [.       9      88 ..       9     112 .. 0.71
   2 !    5.7   0.2    0.0031        19     186     203 ..     116     133 ..      99     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.8e-11
                 EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS....CHHHHHHHHHHH CS
  Metallophos  1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe....gfeeellnkygy 87
                 ++i +i+D+H      ++ +++k++d + ++ ++ +v+++GD+v   +     +  +++l k +++++ +lGN +    g++ee +  +g+
   AJA92686.1  9 MKIGIISDTH-----DDILNTNKAIDIFSQN-NVSIVIHVGDFVAPPV-----VTEFKRLSKDGVKIIGVLGNNDgeeqGLKEEFEGINGE 88
                 89********.....**********999777.**************94.....44456667777779********5555333333333222 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0031
                  HHHHHTTESEEEEESSSS CS
  Metallophos 186 dllkkygvdlvisGHtHv 203
                  +  + ++ d++i+GHtH+
   AJA92686.1 116 KMIDSKKFDVCIFGHTHQ 133
                  55667889*********7 PP

>> SpoIIP  Stage II sporulation protein P (SpoIIP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.3e-06     0.056      64      94 ..     110     141 ..      70     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-06
      SpoIIP  64 dseeeeekldkskpevlIY.htHttEsYlpll 94 
                 d +++++ +d++k +v I+ htH++E+Y++++
  AJA92686.1 110 DAKKRQKMIDSKKFDVCIFgHTHQKENYVDEK 141
                 567778899*********99********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1412.22
//
Query:       AJA92687.1  [L=422]
Description: MiaB-like tRNA modifying enzyme, archaeal-type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-17   64.8   0.0      2e-17   64.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    6.2e-15   55.0   0.1    6.2e-15   55.0   0.1    1.7  2  UPF0004      Uncharacterized protein family UPF0004
    0.00078   19.4   0.1      0.002   18.1   0.1    1.7  1  TRAM         TRAM domain
     0.0025   18.0   0.6       0.01   16.0   0.0    2.4  3  TRAM_2       TRAM domain
     0.0071   17.2   0.5      0.019   15.8   0.5    1.7  1  zf-PARP      Poly(ADP-ribose) polymerase and DNA-Ligase Zn-fi


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   5.7e-21     2e-17       1     167 []     139     311 ..     139     311 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 5.7e-21
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTC.CCTEEEEEEECSSCHG.. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.. RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlakla.vpgiritvetngtlpd.. 90 
                  v++  gC   C+fC+++    + g+ +s  v +i+++vk     +g+ ev+l++ +   y     +d+ el+   +++  +  +r+ +  + ++p+  
   AJA92687.1 139 VEIASGCMSECTFCQTKI---SKGDLQSYRVGDIVRQVKTE-LADGCCEVWLTSTDNGCYgfdinSDLPELVNTVSQIPeKFFMRVGMMNPMYMPRir 232
                  57899************8...7*******************.78899999999777777777777788888888888854455555555555555594 PP

                  HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                  xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                  e  l+ +     +  +++++++++d+ vl+ m+rght + + ++ + +re+ + +   ++d+ivg+p e++e+++ +++ll
   AJA92687.1 233 EGLLKSFESSKvFKFLHVPVQSGSDK-VLNDMKRGHTAKTFRDVAQQFREK-FGKftiSTDIIVGFPTETEEDFQMTMQLL 311
                  55555555555***************.************************.66669********************9986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.1   1.7e-18   6.2e-15       1      93 [.       3      90 ..       3      94 .. 0.91
   2 ?   -3.9   0.1         4   1.4e+04      74      80 ..     142     148 ..     137     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.7e-18
                XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-HHHHHHH-TTS CS
     UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrekeellkeepev 93
                k+ +e +GC+   +dse++ +l+ + g++l+e++e++d+ ++ TC+v++++ +k+i+++ + +++      +vv+GC++++ek ++ k ++++
  AJA92687.1  3 KIWVEAYGCSASYSDSEMISGLIVNGGHTLAENSEDSDLNVIVTCSVKDATADKMIRKIMDSSSK-----PLVVAGCLPKAEKTKVEKFAENA 90
                6889******************************************************9887765.....49************999877764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4
                 EEEHHHH CS
     UPF0004  74 vlGCmaq 80 
                 + GCm++
  AJA92687.1 142 ASGCMSE 148
                 6899987 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   5.5e-07     0.002      24      61 ..     384     420 ..     356     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.5e-07
                 EEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEE CS
        TRAM  24 GrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGel 61 
                 Gr+ ++k++fv+  +p+IGd+ +V+It+++ ++L G++
  AJA92687.1 384 GRNFAYKPIFVNE-EPKIGDVRTVEITDATVHSLIGKI 420
                 666679*******.9********************997 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.3   8.2e+03      43      55 ..      41      53 ..      30      59 .. 0.59
   2 ?   -2.2   0.0       1.3   4.7e+03       1      10 [.      98     107 ..      98     115 .. 0.79
   3 !   16.0   0.0   2.8e-06      0.01      32      64 .]     392     421 ..     366     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                .T-EEEEEEEEEE CS
      TRAM_2 43 vGdfvkvkItdad 55
                   +v++ ++da+
  AJA92687.1 41 LNVIVTCSVKDAT 53
                4456666666665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                 BTSEEEEEEE CS
      TRAM_2   1 iGktvevlvd 10 
                 iGkt++v+  
  AJA92687.1  98 IGKTLQVIQS 107
                 9*****9965 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.8e-06
                 EEEES---T...T-EEEEEEEEEETTEEEEEE- CS
      TRAM_2  32 vyvtgaeklskvGdfvkvkItdadeyDLiGevv 64 
                 ++v+++ k   +Gd+ +v+Itda+ + LiG+++
  AJA92687.1 392 IFVNEEPK---IGDVRTVEITDATVHSLIGKII 421
                 67775443...7*******************98 PP

>> zf-PARP  Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   5.4e-06     0.019       1      30 [.     140     172 ..     140     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                 EE-S-S--B-SSS--B--SSSE...EEEE-... CS
     zf-PARP   1 EyAksgrakCkkCkkkIakgel...Rlgkkvei 30 
                 E+A+  +++C  C++kI+kg+l   R+g +v+ 
  AJA92687.1 140 EIASGCMSECTFCQTKISKGDLqsyRVGDIVRQ 172
                 89999*****************88888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2873.45
//
Query:       AJA92688.1  [L=58]
Description: PF06348 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-09   37.3   0.0    2.5e-09   37.2   0.0    1.1  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.4e-13   2.5e-09       3      47 ..       4      47 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.4e-13
     DUF1059  3 efkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelv 47
                e++C+D g+dC+f +++e+ e v+r+  +H+ ++Hgl   ++e +
  AJA92688.1  4 ELACRDYGYDCDFVARGEDSEYVMREFGKHVDEEHGL-WYSDESL 47
                689*********************************5.4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 427.80
//
Query:       AJA92689.1  [L=160]
Description: putative DNA-binding protein Alba [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-08   33.3   0.2    4.4e-08   32.8   0.2    1.3  1  Alba            Alba
    6.5e-05   22.9  17.1    8.5e-05   22.6  17.1    1.2  1  Trypan_PARP     Procyclic acidic repetitive protein (PARP)
  ------ inclusion threshold ------
       0.07   13.8   8.1      0.089   13.5   8.1    1.2  1  Pex14_N         Peroxisomal membrane anchor protein (Pex14p) 
       0.14   11.2   4.6       0.16   11.0   4.6    1.2  1  Roughex         Drosophila roughex protein
       0.37   10.2   0.1       0.37   10.2   0.1    1.7  2  UPF0524         UPF0524 of C3orf70
       0.55   10.4   3.6       0.84    9.8   3.6    1.3  1  DUF3408         Protein of unknown function (DUF3408)
       0.94    9.5   3.4        1.4    9.0   3.4    1.2  1  DUF4366         Domain of unknown function (DUF4366)
        1.9    8.9   7.4        2.8    8.3   7.4    1.3  1  CCDC53          Subunit CCDC53 of WASH complex
        4.3    5.7   7.1        5.9    5.3   7.1    1.2  1  Neisseria_TspB  Neisseria meningitidis TspB protein


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   2.2e-11   4.4e-08       3      65 ..      77     136 ..      75     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.2e-11
                 EEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCT.T.EEEEEEEE CS
        Alba   3 iyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgk.glyqvnvlts 65 
                 i V+  +p+ +yv+ +l++L  ++ ++V++ka+G+ I+ Av+v + + +r+   g y + ++ +
  AJA92689.1  77 ILVGV-KPLVTYVNSTLTQL--STLPTVTIKARGQRITQAVDVSQFIMKRMHSiG-YRISDVRI 136
                 67888.9*************..***********************9999994344.77766665 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6  17.1   4.2e-08   8.5e-05      59     109 ..      19      65 ..       2      83 .. 0.47

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-08
  Trypan_PARP  59 pepepepepepepepepepepetepeeepepepepepepepepepepepep 109
                   +pe +pe +pe +pe++pe ++    e++pe++pe +pe++pe ++e +p
   AJA92689.1  19 KKPEAQPEAQPEAQPEAQPEAQP----EAQPEAQPEAQPEAQPETKSEKKP 65 
                  23333333333333333333333....333333333333333333333322 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   8.1   4.5e-05     0.089      40     126 ..      12     101 ..       2     121 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-05
     Pex14_N  40 eeaLkraereeeasesavaassaseqaqeesasssatpqpqaasqtsqsspsps.ppaqqqqqqy.......rpPivtypefltkppkppppPlr 126
                 +e L++++++e++ e++ +a+++++ +++ +a+++a+p++q+++q++++s++++   +++++  +       ++P+vty +   ++     +P +
  AJA92689.1  12 DEILEDSKKPEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPETKSEKKPfV-PEEKP--TrklilvgVKPLVTYVNSTLTQLS--TLPTV 101
                 67777755554444321112222222233334444444444444454444444421.22222..145688999999999554433333..45555 PP

>> Roughex  Drosophila roughex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.6   8.3e-05      0.16     271     340 ..      12      83 ..       2     132 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-05
     Roughex 271 epdlpdqnkeedkdeqeqqaeqeeqaqqqaeeapvss..distalketnppaepivgernppeksiissltp 340
                 +  l d +k e + e + +a+ e q + q+e  p +       a+ et    +p v e +p  k i+  + p
  AJA92689.1  12 DEILEDSKKPEAQPEAQPEAQPEAQPEAQPEAQPEAQpeAQPEAQPETKSEKKPFVPEEKPTRKLILVGVKP 83 
                 3345566666655554444444444445555554432115667999***9****************999887 PP

>> UPF0524  UPF0524 of C3orf70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.8       2.2   4.4e+03     144     144 ..      43      43 ..      18      68 .. 0.45
   2 ?   10.2   0.1   0.00018      0.37      53      93 ..      86     126 ..      82     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
     UPF0524 144 k 144
                  
  AJA92689.1  43 A 43 
                 1 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
     UPF0524  53 kyvyqpltsveqlpstavpaapsektdtidlsislaerflk 93 
                  yv ++lt+++ lp+ ++ a+++  t+++d+s  +++r+  
  AJA92689.1  86 TYVNSTLTQLSTLPTVTIKARGQRITQAVDVSQFIMKRMHS 126
                 69******************************999988765 PP

>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.6   0.00042      0.84      13      57 ..      19      65 ..       6      92 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00042
     DUF3408 13 kkiplksk..peeeetpakeekeeakeeeeeeaeeeeekekkekkkr 57
                kk+  + +  pe++ ++++e++ ea+ e++ ea++e ++e+k +kk 
  AJA92689.1 19 KKPEAQPEaqPEAQPEAQPEAQPEAQPEAQPEAQPEAQPETKSEKKP 65
                22222222344444444444444444444444444444444444443 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.4   0.00069       1.4      55     111 ..       6      63 ..       2      89 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00069
     DUF4366  55 deaDLl.alleedeeaakeeeevcactekcaagkvntdcpveepepekeaepeepeee 111
                 d +D l ++le++++ + ++e++  ++ + + ++  ++ p ++pe+++ea+pe+++e+
  AJA92689.1   6 DASDILdEILEDSKKPEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPETKSEK 63 
                 5566541455544444444444433333333333333334444444444444332211 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.4    0.0014       2.8      68     110 ..      21      63 ..       2      89 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0014
      CCDC53  68 arkgppppppsseaaaaaaqaeeasqaeesaeeeaeeqeeses 110
                  +++p+++p+++++a+ +aq+e +++a+ +a++ea+ +++se+
  AJA92689.1  21 PEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPEAQPETKSEK 63 
                 2222222222222222222222222222333333322223322 PP

>> Neisseria_TspB  Neisseria meningitidis TspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.1    0.0029       5.9     344     398 ..      21      70 ..       4      76 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0029
  Neisseria_TspB 344 pevspaenpannpdpdenpgtrpnpepdpdlnpdanpdt..dgqpgtrpd.spavpdr 398
                     pe  p  +p  +p+         +pe +p+ +p+a+p++  + qp t+ +  p vp+ 
      AJA92689.1  21 PEAQPEAQPEAQPEA--------QPEAQPEAQPEAQPEAqpEAQPETKSEkKPFVPEE 70 
                     333333333332222........23333333444433331134555544314666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1248.29
//
Query:       AJA92690.1  [L=289]
Description: putative fructokinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-69  234.7   0.2    1.7e-69  234.6   0.2    1.0  1  ROK             ROK family
    0.00012   21.8   0.1     0.0002   21.1   0.1    1.3  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
     0.0021   17.6   0.1     0.0098   15.4   0.1    2.0  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.012   14.6   1.2      0.052   12.5   1.2    1.9  1  Glucokinase     Glucokinase
       0.16   11.8   0.0       0.22   11.4   0.0    1.3  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.6   0.2   4.7e-73   1.7e-69       2     290 ..       4     289 .]       3     289 .] 0.96

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 4.7e-73
                 EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGCGCC.CCTTHHHHHHHHHTS- CS
         ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpnitw.enfdlvekleerlnvp 99 
                 ig+d+Ggtki+ +l+de+ ++  r++++t +++ ++ + ++i++l++e+ ++ ++ +++g++ pG + + s++++++ n +    +dl+++l++ l   
  AJA92690.1   4 IGVDLGGTKIEGILTDENYKTITRKRIPTNQDEGYNSILESIKNLIQELVKESNNKVSIGVCTPGAL-SLSSGLIKNSNTQClIGKDLQNDLKNILHYN 101
                 8******************************************************************.777778888898888**************** PP

                 EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGGSBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC.CGTTS-H CS
         ROK 100 vevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGHiqldpegekcgCGnqgClEtlasgralekraqq.kgeklea 197
                 v +enD+n++alaEa++ga  + + v+ +++gtGvG+G+ii+gk+++Gr+ +age+GH  l+peg  c+CGn+gC+Et++sg+alek++++ + ++ ++
  AJA92690.1 102 VSIENDANCFALAEAKLGAGRNSNLVFGIIMGTGVGGGIIIDGKIHHGRTNIAGEWGHHCLHPEGNTCYCGNKGCVETYISGPALEKKWSElTSQNQPL 200
                 ****************************************************************************************99989999999 PP

                 HHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHHH CS
         ROK 198 keiiklaekgdevaeevverlaeylakaiadlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllGaaaL 290
                  eiik   +  ++  +  +++ +  + ++a++i ++dp++ivlgGgvs+ d l+ + ++++++ +++    ++  i++ +lgd+ag+ Ga +L
  AJA92690.1 201 PEIIKSSDN--PNFPNWKKSFLDDFGSSLANVIDILDPDVIVLGGGVSNIDFLYSEGKNSTHEKVFSDIVDTP--ITKNELGDSAGVFGACML 289
                 999887666..6777788899*********************************999****************..9**************986 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   5.6e-08    0.0002       1      56 [.       3      59 ..       3      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.6e-08
  Hydant_A_N  1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesipr.tsk 56
                rig+D GGT +  +++de+ ++++  ++++++d+  + i+e+++++++e  ++ ++k
  AJA92690.1  3 RIGVDLGGTKIEGILTDENYKTITRKRIPTNQDEGYNSILESIKNLIQELVKEsNNK 59
                79*****************999999*********************99987754444 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.7e-06    0.0098       1      57 [.       4      58 ..       4     159 .. 0.84
   2 ?    0.1   0.0      0.13   4.5e+02     217     265 ..     236     288 ..     222     289 .] 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
                 EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HHH.........HHHHHHHHHHT- CS
  BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesvrfeaaekvleealtealerage 57
                 +G+D+G+T++  +l de+ + ++r    +++   ++ +   +++++ ++e+++++  
   AJA92690.1  4 IGVDLGGTKIEGILTDENYKTITRKRIPTNQD--EGYNSILESIKNLIQELVKESNN 58
                 7*******************999877655444..46677888888888888887655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                  SS.EEEESGGGG-HHHHHHH.........HHHH-S-EE--GGGGGHHHHHHHH CS
  BcrAD_BadFG 217 tdevtltGGvakneaavkelrkl....vkenygevkininpdsiytgalGAal 265
                  +d ++l GGv++   ++ e ++     v +++ + +i  n   + +g+ GA +
   AJA92690.1 236 PDVIVLGGGVSNIDFLYSEGKNSthekVFSDIVDTPITKNELGDSAGVFGACM 288
                  45689999999988777766555111155555666777777777888888865 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.2   1.4e-05     0.052       4     166 ..       7     165 ..       4     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
  Glucokinase   4 DiGGTkarlalveaeeeelelleiekyasadyasleealqaflaeaeaevkrpks..avlAvAgpvegdeveltNlpWviseeelakelg.le..ave 96 
                  D+GGTk    l + + ++++ ++i + + + y+s+ e +++ ++e  +e ++  s  ++   A  ++ + ++  N +  i  ++l+++l+ +   +v+
   AJA92690.1   7 DLGGTKIEGILTDENYKTITRKRIPTNQDEGYNSILESIKNLIQELVKESNNKVSigVCTPGALSLSSGLIKNSNTQCLIG-KDLQNDLKnILhyNVS 103
                  9*******999999999999************************9866666655434555555578899999999998887.6677766532236899 PP

  Glucokinase  97 liNDfeavayaiplleaedlvqlgggkkdaeapiavlGaGTGLGvallipe..kerrvvlasEGGhvdfape 166
                  + ND ++ a+a + l+a    +l           ++   GTG G +++i    +++r+ +a+E Gh  + pe
   AJA92690.1 104 IENDANCFALAEAKLGAGRNSNL--------VFGII--MGTGVGGGIIIDGkiHHGRTNIAGEWGHHCLHPE 165
                  99999999998776655433333........23334..4666666666654115777899999999877776 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.2e-05      0.22       1      57 [.       4      69 ..       4     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.2e-05
  DEDD_Tnp_IS110  1 vGiDvakdkhdacvidaegkvllservpnde........egleallek.laakagevlvvveatgh 57
                    +G+D + +k++  ++d++ k++ ++r+p+++        e+++ l+++ ++++  +v ++v   g 
      AJA92690.1  4 IGVDLGGTKIEGILTDENYKTITRKRIPTNQdegynsilESIKNLIQElVKESNNKVSIGVCTPGA 69
                    7*************************9998743444444477788888666777888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2136.81
//
Query:       AJA92691.1  [L=297]
Description: methionine aminopeptidase, type II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-31  108.6   0.1      4e-31  108.3   0.1    1.2  1  Peptidase_M24  Metallopeptidase family M24
  ------ inclusion threshold ------
      0.049   13.8   0.1       0.13   12.3   0.0    1.7  2  GIT1_C         G protein-coupled receptor kinase-interacting 
      0.057   12.7   0.1      0.086   12.1   0.1    1.3  1  CTP_synth_N    CTP synthase N-terminus
      0.062   13.5   0.0        2.4    8.4   0.0    2.3  2  HSR            HSR domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.1     9e-35     4e-31       2     191 ..       5     196 ..       4     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 9e-35
                    HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC..S.SSB--TTEEEEEEEEEEETTEEEEEEE CS
  Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp..n.drvlkegdlvlidagaeydgyasDitr 94 
                    ++ ka++ia +++e+v +    g t +e+++ +e + +k+  + ++afp  v +++n+ ++hyt+  n + ++ e+dlv+id+ga++dgy++D+++
     AJA92691.1   5 DYIKAGKIAGEVRENVRKTDWVGKTVYEICEHVEGE-IKK-RGAKCAFP--VNTSINEVAAHYTAepNdEMTITEDDLVKIDLGAQIDGYIADTAV 96 
                    5679************65444689**********99.555.556899**..9999999999**5544525559*********************** PP

                    EEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS.SSSEE..EEEESSSTTCSSB--TTBEEEEE CS
  Peptidase_M24  95 TvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl.evhde..gpsvsresndgrkleeGmvftiE 187
                    Tv+    +pe + l++ ++ a+++a++++k G++ s++++++++++++ gl  ++ ++ GH++ +  +h +  +p++++    +      + f++E
     AJA92691.1  97 TVCY---NPEFDTLVQGAESALKNAMSMMKTGIKSSDVGRTIEKTIKELGL-IPIANLSGHSLEQyTIHAGksVPNIWS--IGSFNFPSEQAFACE 186
                    ****...8999***************************************9.899*********98***7655777883..468899999****** PP

                    E......EEE CS
  Peptidase_M24 188 p......giy 191
                    p      g+ 
     AJA92691.1 187 PfvttgdGLG 196
                    *555544222 PP

>> GIT1_C  G protein-coupled receptor kinase-interacting protein 1 C term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.13       9      60 ..      20      71 ..      15      86 .. 0.89
   2 ?   -3.6   0.0       2.6   1.2e+04      45      66 ..     203     225 ..     202     234 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
      GIT1_C  9 vrkteqitkriqeLlqaaqeekkesfvpcaerIqsaVqdlvalfpenlseet 60
                vrkt+ + k + e+ + ++ e k++ ++ca  +++ +++++a ++ ++++e 
  AJA92691.1 20 VRKTDWVGKTVYEICEHVEGEIKKRGAKCAFPVNTSINEVAAHYTAEPNDEM 71
                79*******************************************9888774 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.6
      GIT1_C  45 Vqdlvalfp.enlseetlrtaLk 66 
                 V+++ al + +++++++  + L+
  AJA92691.1 203 VKNIFALASrKKTKDKEADEMLN 225
                 45555555533333344444455 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.9e-05     0.086      86     128 ..       6      49 ..       1      75 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                  EEEHHHHHHHHHHHHHTTTTTT---.-CCCHHHHHHHHHHHHHH CS
  CTP_synth_N  86 nittGkiyksviekerrGdylGktv.qviphvtdeikeriekva 128
                   i +Gki  +v e+ r+ d+ Gktv +++ hv  eik+r  k+a
   AJA92691.1   6 YIKAGKIAGEVRENVRKTDWVGKTVyEICEHVEGEIKKRGAKCA 49 
                  6889*********************55789*******9876665 PP

>> HSR  HSR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.033   1.5e+02      43      72 ..      15      44 ..       4      55 .. 0.83
   2 ?    8.4   0.0   0.00054       2.4      61      90 ..     241     270 ..     215     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
         HSR 43 esleacrnlvpvqkvvYnvLseLektfsls 72
                e+ e+ r+++ v k vY++ +++e + ++ 
  AJA92691.1 15 EVRENVRKTDWVGKTVYEICEHVEGEIKKR 44
                78899999***************9887765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00054
         HSR  61 vLseLektfslsllealfsevnlkeYpdLk 90 
                 +L++ e+++ + +le+l ++  +++Yp L 
  AJA92691.1 241 LLEKWEEKDAKRILEILVKKKAVHAYPVLV 270
                 79999**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2286.32
//
Query:       AJA92692.1  [L=580]
Description: membrane protein, PF09843 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   8.2e-121  404.0   0.5   1.1e-120  403.7   0.5    1.0  1  DUF2070    Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
          3    7.8   5.3          4    7.4   0.4    2.3  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.7   0.5  1.2e-124  1.1e-120       5     554 ..      14     568 ..      10     577 .. 0.93

  Alignments for each domain:
  == domain 1  score: 403.7 bits;  conditional E-value: 1.2e-124
     DUF2070   5 skyifrlPswk.vsllliillalligllaflssk.lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsall..qa 98 
                 +++   +Ps + +sl+++i +a lig+ +   +   ++ l+f   a++a+l+ +++l+il  +  +y++sl+++l+ + ++++ +l+++ +  l+    
  AJA92692.1  14 YTLSLINPSSHyISLAASIAIAGLIGAFTASTYLgSTE-LIFPTLAVIAALVGTQFLDILFAKhREYSKSLHVSLFGNGLFFVSTLIGYGAMGLFekDG 111
                 555555899999************99988666553333.4444446666666666666665555*******************************8666 PP

     DUF2070  99 lvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly...fspesfllllllslifalavylfivvvdrplkrnlgvsaldllsaF 194
                 l l+++ +++++ +++r+ +++++ ++sl+ka+++a+iqp++++l+lv+    +s+ + + ++l+  +f+ ++ ++ ++ d+ +++ l  s+++l++a+
  AJA92692.1 112 LDLFYVTMGMVVFASFRIGIFTTILGASLKKAWAVAFIQPMAMYLVLVPSdmwISSLTNPWIILFGGAFLGLATAWSYLTDKAGRPGL-KSTHELIQAY 209
                 666777788********************************************999999999************************99.9********* PP

     DUF2070 195 lahileg.skelEeffeeigeeadvpvkvlsfrredg.ekallvvPniHPGPlgeiGGsnLpkilaerldelvlvlHgtatHdfNlvserevekiveav 291
                 + +++++    lEe+ e+ ++e++v+++ l+f+ +d+ +++++v+P+iHPGP++ iGGsn+  ++++++d+ ++v+H+++ Hd+Nl++++ev+++++++
  AJA92692.1 210 VTSMSRKdPAPLEEIIEKSSTESTVSTSQLKFQSTDKdNDFRIVLPDIHPGPFHPIGGSNITGLIYKEMDSTAMVMHSISNHDLNLPTQKEVQNYLQSL 308
                 *************************************************************************************************** PP

     DUF2070 292 kealeeleysskaskpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevlpgsedaeeliraa 390
                 ++++++ +    +++pv+v+ ++++  g+ f+ ++ll+++ +p+g++D+p +v  +i++ a++++fe+vl+VD HN++++e +     +ed+e+l+ aa
  AJA92692.1 309 QQSKSKQN-GAVCTEPVSVTMNKARASGLLFDRTALLFLSLSPHGMEDLPPNVRSEIEQFAENRNFEQVLIVDTHNAMGKEIS-----KEDSEDLLLAA 401
                 ****9988.899******************************************************************99977.....8********** PP

     DUF2070 391 ekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealke.vdlevevmTTDtHvvngvsl...g 485
                 ++ l++l+++e +++k+g+ +se ++l++ +++ +++i++l+le++++++++ ++D+NNme+g+re+i+  + + +++ +e++T+DtH+     +   g
  AJA92692.1 402 KSTLDTLKTKESHSFKFGFENSEKMNLNQ-NDIAEGRIATLCLEINNKNYFLGWADANNMENGVREQIVTHFANnGYELIEICTSDTHYTASGARnrnG 499
                 ************************98876.8******************************************99999**********998877789** PP

     DUF2070 486 ynpvGekvskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvstvnsvvsvakilaa 554
                 y ++G   ++++l++++lel ++A +++++ ++++ +++++vkv+g+++f+++++++++ +s++k  ++
  AJA92692.1 500 YFQLGMVSKPNDLANWYLELAKNAESKIKEGTFEVLEHQTNVKVMGPTIFSDYSKVMDKTMSITKWCLL 568
                 **************************************************************9997665 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6     0.018   1.6e+02      79     117 ..      37      75 ..      29     110 .. 0.73
   2 ?    7.4   0.4   0.00044         4      62     117 ..     139     194 ..     134     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.018
   RseC_MucC  79 ilgallgsallgssellaalgallglvlgflivrllskr 117
                 ++ga+ +s+ lgs+el+   +a++++++g  ++ +l  +
  AJA92692.1  37 LIGAFTASTYLGSTELIFPTLAVIAALVGTQFLDILFAK 75 
                 455555555558999998888888888888888754333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00044
   RseC_MucC  62 sllkaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskr 117
                 sl ka +++++ P+++ ++ +   ++++  ++ + +l++ ++l l+  + +l +k 
  AJA92692.1 139 SLKKAWAVAFIQPMAMYLVLVPSDMWISSLTNPWIILFGGAFLGLATAWSYLTDKA 194
                 6778999********99999999999999999************999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4010.59
//
Query:       AJA92693.1  [L=159]
Description: transferase hexapeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-24   83.1  20.6    7.7e-10   38.1   0.3    4.1  5  Hexapep    Bacterial transferase hexapeptide (six repeats)
    3.4e-16   58.7  11.8    1.8e-09   37.1   3.8    4.5  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3   8.6e-14   7.7e-10       2      32 ..      10      40 ..       9      44 .. 0.92
   2 !   28.7   1.1     8e-11   7.1e-07       2      34 ..      28      60 ..      28      62 .. 0.93
   3 !   11.6   0.1     2e-05      0.18       3      18 ..      65      80 ..      63      81 .. 0.79
   4 !   31.8   4.3   8.2e-12   7.3e-08       1      36 []      91     126 ..      91     126 .. 0.96
   5 ?   -2.5   0.1      0.55   4.9e+03      30      35 ..     130     135 ..     128     136 .. 0.46

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.6e-14
                EEEETTEEE-TTEEEETTEEE-TTEEEETTE CS
     Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagv 32
                ++IG+n++I++fa++g++++IG++vkIg+ +
  AJA92693.1 10 AKIGENTKIWHFAYVGDDTEIGNGVKIGSLA 40
                79**************************955 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 8e-11
                EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                t IG++v+Ig+ a++  +VkIG+n+ I+  v+i
  AJA92693.1 28 TEIGNGVKIGSLAHVDYDVKIGNNTMIEGLVYI 60
                68**************************98887 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 2e-05
                EEETTEEE-TTEEEET CS
     Hexapep  3 vIGsnvlIgpfavigg 18
                +IG+nv+Igp a + +
  AJA92693.1 65 RIGNNVFIGPSASLTN 80
                6999999999888866 PP

  == domain 4  score: 31.8 bits;  conditional E-value: 8.2e-12
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                 +++I +n++Ig+ avi ++V+IG+n++++ g+v+++
  AJA92693.1  91 GVTIKDNAIIGSRAVIKAGVTIGENSVVAMGAVVTK 126
                 589*******************************86 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 0.55
                 TTEEEE CS
     Hexapep  30 agvvig 35 
                 a++v+g
  AJA92693.1 130 ANTVVG 135
                 344444 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   4.5e-05      0.41       3      27 ..      11      37 ..       9      38 .. 0.90
   2 ?    2.7   0.1     0.012   1.1e+02       2      10 ..      46      54 ..      45      56 .. 0.78
   3 !   10.5   0.0   4.4e-05      0.39       3      14 ..      65      76 ..      65      79 .. 0.90
   4 !   37.1   3.8   2.1e-13   1.8e-09       2      34 .]      92     126 ..      90     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.5e-05
                EE-TT-EE-TT-EES..EEE-TT-EE- CS
   Hexapep_2  3 iIGdnCliGanagiG..vslGdncvvg 27
                +IG+n+ i  +a++G  +++G+++++g
  AJA92693.1 11 KIGENTKIWHFAYVGddTEIGNGVKIG 37
                8*************777********98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.012
                EEE-TT-EE CS
   Hexapep_2  2 viIGdnCli 10
                v+IG+n++i
  AJA92693.1 46 VKIGNNTMI 54
                788888876 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 4.4e-05
                EE-TT-EE-TT- CS
   Hexapep_2  3 iIGdnCliGana 14
                +IG+n++iG++a
  AJA92693.1 65 RIGNNVFIGPSA 76
                6*********98 PP

  == domain 4  score: 37.1 bits;  conditional E-value: 2.1e-13
                 EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
   Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvita 34 
                 v+I dn +iG++a+i  Gv++G+n+vv++G v+t+
  AJA92693.1  92 VTIKDNAIIGSRAVIkaGVTIGENSVVAMGAVVTK 126
                 7888**********999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1189.67
//
Query:       AJA92694.1  [L=465]
Description: FeS assembly protein SufD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-59  199.7   1.3      7e-59  199.1   1.3    1.3  1  UPF0051   Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
        3.7    7.8   5.4        1.5    9.1   1.3    2.2  2  zf-C4H2   Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.1   1.3   7.8e-63     7e-59       4     218 .]     181     404 ..     178     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 199.1 bits;  conditional E-value: 7.8e-63
     UPF0051   4 ertlivveegaevtiieey.......agc...gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegae 92 
                  r++i+ve++a++++++e+         +     +++ +g+n++l+++++q  +++++n+st+  ++++d+k++++ + +g+ l+r +++ +l+g ga 
  AJA92694.1 181 SRNIIIVEDNAKANLVQELyspqngkQ-QaylELLNTSIGANSSLDVTSLQMMDQSSINFSTRSSHLAQDSKINWYLGLFGAMLSRYRIDYHLNGTGAV 278
                 79**************88888875551.15569****************************************************************** PP

     UPF0051  93 aelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGk 191
                 a+ +++++++++q +d++t v+hn++ t+++++ k++lk+++++ f+g+ik++++a++++++ + r++ll+++a++d+iP lei ++dvka+H A+v +
  AJA92694.1 279 ATDSEVVFGNNEQSFDLNTIVNHNEQSTEGKVVEKSILKNKSKSLFKGMIKINENAAHSNSFLSGRSILLDKDAKSDAIPGLEILTNDVKATHSASVAQ 377
                 *************************************************************************************************** PP

     UPF0051 192 ideeqlfYLmsRGlseeeArrlivrgf 218
                 +deeqlfYL +R ls+ eA+r+iv+gf
  AJA92694.1 378 MDEEQLFYLGTRCLSKPEAERIIVEGF 404
                 **************************9 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.3   0.00016       1.5      11     120 ..       4     113 ..       1     161 [. 0.66
   2 ?   -2.2   0.1      0.47   4.2e+03     110     131 ..     302     327 ..     288     383 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
     zf-C4H2  11 eleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeksl.ekakklyeeykklkeevnelrselglekl 108
                  l+++++ l +e++++++e + l+ey+k+   + +E  a v  L    +D ++++  + +   + + +l +  +k +ee+kk    ++ + ++++  +l
  AJA92694.1   4 TLSSIQSSLVEEISSSKNEPQWLKEYRKNSLSIYNELPAEVSPLYGKYTDAKRMDPEMVSLSINSNSKLpDFLSKRVEEVKKENGLIQ-VGTNIISTNL 101
                 68999*************************************************9988888877776651455666666666544443.2233333334 PP

     zf-C4H2 109 edleeeeeellk 120
                 +d  +++  +++
  AJA92694.1 102 SDELKSKGVVIS 113
                 444444443333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.47
     zf-C4H2 110 dleeeeeellkeeifekqklk....a 131
                 + +++e ++++++i++++ ++    +
  AJA92694.1 302 NEQSTEGKVVEKSILKNKSKSlfkgM 327
                 33455555555555554443333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3183.08
//
Query:       AJA92695.1  [L=486]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3390.63
//
Query:       AJA92696.1  [L=159]
Description: nuclease-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-05   24.6   0.0    3.7e-05   24.2   0.0    1.2  1  SNase     Staphylococcal nuclease homologue


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.1e-09   3.7e-05       1      72 [.      66     132 ..      66     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.1e-09
                 EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEETTEEHHHHHHHT CS
       SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvylnkknineeLvke 72 
                 ++rL+ ++aPe        +p g+e+k f++++++  +  v +ld+ +k + gr ++ v+++++++ne Lv++
  AJA92696.1  66 RIRLALVNAPELT------EPGGDESKLFVESQCSAGSESVFILDRgQKPSFGREVGLVFCSETSLNELLVEN 132
                 79***********......999************************9************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1260.65
//
Query:       AJA92697.1  [L=68]
Description: hypothetical protein T478_1409 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 526.66
//
Query:       AJA92698.1  [L=189]
Description: hypothetical protein T478_1354 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   14.4   0.1      0.092   13.4   0.1    1.5  1  P-II      Nitrogen regulatory protein P-II


Domain annotation for each model (and alignments):
>> P-II  Nitrogen regulatory protein P-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.1e-06     0.092       1      97 [.       4      99 ..       4     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-06
                EEEEEEGGGHHHHHHHHHHTTGGCEEEEEEEEEESTCCEEEECTTEEEEEEEEEEEEEEEEEEGGGHHHHHHHHHHHH-SSSTTSEEEEEEEESEEE CS
        P-II  1 ieaiirpekleevkeaLekagvkgltvtevkGrGkqkghtelyrgaeyevellpkvkleivvsdedvekvveaiikaaktgeiGDGkiFvlpveevi 97
                ieaii  +++  ++++L+ +g++ +   + +      ++t+   g +   +     k+e++++d+d+ +v+e+i k          kiFv++++e++
  AJA92698.1  4 IEAIINRKNYPMIRTELDVLGIEIIDKRNLEDSKFITKSTGSRAGGTGVRS-TMLAKIELAMQDKDARAVLEMISKLSGLPPNMPQKIFVFDMNEMV 99
                89*********************9999999886666666665555554444.55567889999*************998888888899999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1412.60
//
Query:       AJA92699.1  [L=654]
Description: peptidase, S8/S53 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-57  193.2   0.2    8.6e-57  192.7   0.2    1.2  1  Peptidase_S8  Subtilase family
    1.8e-12   47.1   0.2    9.2e-12   44.8   0.0    2.3  3  PA            PA domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.7   0.2   9.6e-61   8.6e-57       1     285 [.      28     417 ..      28     429 .. 0.89

  Alignments for each domain:
  == domain 1  score: 192.7 bits;  conditional E-value: 9.6e-61
                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB-SSTTSEEEEEE-S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeegekngvapgakilsvkvl 97 
                   gkg++++v+DtG++ shpd+ +++++ r l      +g++f+++d+ +      +d ng    HGt v Gi+aa     g+ +g+ap a+i s++v 
    AJA92699.1  28 GKGIKIGVIDTGINLSHPDFFNQDETSRFL------KGYDFVDNDTVP------QDTNG----HGTQVTGIIAAD----GQLKGIAPMAEIFSYRVS 104
                   89*****************99443332222......344444444333......34457....************....*****************9 PP

                   STTSB-HH..HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8  98 dtsggsmetgteliraieeaaedkvdvinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayt 194
                   ++ +  + ++  +i+ai++a+ed+vd+in+slg     +k +   e  a+n+a+ k+g++vv++aGN+g      ++ s++g+p+   n+itvga+ 
    AJA92699.1 105 SDGE--SVPSNLIIKAINQAVEDRVDIINISLGVNMTHNKID---E--AVNNAI-KQGIVVVAAAGNSG------PDKSTIGSPAKNPNAITVGATY 187
                   5544..445599*********************444444444...3..9*****.9*************......9999****************99 PP

                   ................................................................................................. CS
                   ................................................................................................. RF
  Peptidase_S8 195 ................................................................................................. 194
                                                                                                                    
    AJA92699.1 188 nnrdssmvstlevedtqfqvlpmlgtdtisdpisaeivfgkysrendfdgidvrgkivlaerggeapdeivffsdkeifasnngakglivynnqpgi 284
                   9************************************************************************************************ PP

                   ...............................................TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE CS
                   ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_S8 195 ...............................................tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsm 244
                                                                   ++ +a+fSsrGp+s   lkpd+vapG+  v t s ++        y+  
    AJA92699.1 285 ffgeliheyvsedyyptiptvsmtreeglelkkilesetsgtlnvfnHPDFLATFSSRGPVSPFYLKPDLVAPGVF-VNTTSLKNF-------YNIT 373
                   ***********************************************9999************************8.666666662.......99** PP

                   -SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE.... CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
  Peptidase_S8 245 sGTSmAsPnaagaaAlllsalpkltpetvraallntAqdl...g 285
                   sGTS A+P+++ga+Alll+++p++tp++++++l++t +++   +
    AJA92699.1 374 SGTSYAAPHVSGAIALLLEKNPNFTPHEIKSILVTTSDIItdeY 417
                   *************************************8775542 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.1     1e+04      51      53 ..     156     158 ..     142     186 .. 0.51
   2 !   44.8   0.0     1e-15   9.2e-12       2      89 .]     221     315 ..     220     315 .. 0.83
   3 ?   -1.8   0.0      0.37   3.3e+03      46      53 ..     385     392 ..     355     413 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
          PA  51 iiv 53 
                 ++v
  AJA92699.1 156 VVV 158
                 333 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 1e-15
          PA   2 tgplVyscfagygisadfegvdvkGkivLvqr.........tfaeKarnAqaaGAagviivndge...lgaatgasgnegepdgitiPavgvsredgea 88 
                 ++++V   f  y +++df+g+dv+GkivL +r          f +K   A ++GA+g+i++n+++    g+  ++     e+   tiP+v+ +re+g +
  AJA92699.1 221 SAEIV---FGKYSRENDFDGIDVRGKIVLAERggeapdeivFFSDKEIFASNNGAKGLIVYNNQPgifFGELIHEYVS--EDYYPTIPTVSMTREEGLE 314
                 68999...99********************9999888888888******************77777873333333334..44459************87 PP

          PA  89 l 89 
                 l
  AJA92699.1 315 L 315
                 6 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.37
          PA  46 GAagviiv 53 
                 GA+++++ 
  AJA92699.1 385 GAIALLLE 392
                 44444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4544.32
//
Query:       AJA92700.1  [L=186]
Description: non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-41  142.6   0.0    1.5e-41  142.4   0.0    1.0  1  Ham1p_like  Ham1 family
     0.0088   16.6   0.0       0.02   15.5   0.0    1.5  1  ETM         ECORI-T site


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4   0.0   1.6e-45   1.5e-41       1     187 []       7     181 ..       7     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 1.6e-45
                 EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTBGGGTTTTTHTTCHHHHHHHH CS
  Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglPGvysarfagegaedeenlak 97 
                 ++f+++N +K++e+k+il++ +le++ +    ++ +eE+q +++ e+a+ Ka +a+   ++pv+++D gL++d L+g+PG+ys+++ ++ ++  +++ +
  AJA92700.1   7 LFFVSSNTHKFEEAKRILSNLGLEINLF----KTTLEEIQsNSIGEIAKRKALDAFSkLEKPVIIEDDGLFIDSLGGFPGPYSSYVYDTIGN--KGIMR 99 
                 68****************9988888744....45678****************999636788************************865544..67777 PP

                 HHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
  Ham1p_like  98 lleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeegektfaelskeeknaiShRgkAlekllef 187
                 lle++    e r+Arfv+++a++++ +++++lfe ++ G+i   + +egg GyDpiF+p++++kt+a +s   k+++ShR+ +l+k+ ++
  AJA92700.1 100 LLENI----ELRNARFVAMIAYCNG-TDNVKLFESSIPGKISL-SIEEGGWGYDPIFIPDGESKTYANVS--DKDKFSHRAASLKKFSDW 181
                 77777....369************8.7777***********76.8999***********87678****98..6999***********886 PP

>> ETM  ECORI-T site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.2e-06      0.02      29      85 ..      85     141 ..      80     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-06
         ETM  29 tsftfdcahdnrkvncleivglrrneyvcmgkiingdkiicvhensvngkiivpved 85 
                 +s+++d   ++  +  le + lr   +v+m    ng   + ++e s+ gki + +e+
  AJA92700.1  85 SSYVYDTIGNKGIMRLLENIELRNARFVAMIAYCNGTDNVKLFESSIPGKISLSIEE 141
                 588999999999999************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1536.37
//
Query:       AJA92701.1  [L=227]
Description: putative uridylate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-30  105.1   0.9    7.2e-30  104.3   0.9    1.3  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.9     4e-34   7.2e-30       1     241 []       3     203 ..       3     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 4e-34
                 TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHHTT CS
   AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrdalaslgerlvaallaag 97 
                 k++V+K+ G++++ ++ + l+++a+ + ++ ++ +++++V Ggg+++++++++   sg +++ l                 d+l++  +rl+a+ll ++
  AJA92701.1   3 KKIVIKFSGKVFAMENVKLLKDYARFLVKI-SKTYQPIIVAGGGKIARHYITHarSSGADESTL-----------------DELGIEISRLNAKLLIYA 83 
                 689**********776789***********.999*******************54444444444.................99**************** PP

                 HGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTT CS
   AA_kinase  98 lpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpda 196
                 l+++ ++  +++++                  + ++ +++g +++ +g+     +g+    s+  +aal+Ae+++A++ +++tdV+G+yd+dp+k+++a
  AJA92701.1  84 LKDKAYPHPPTTLR------------------EAKHAVDSGLIVIAGGLH----PGQ----STNGTAALIAEKVNAEQFLNATDVSGIYDSDPNKNKKA 156
                 *******9999965..................5667*****999999987....999....9999********************************** PP

                 CECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
   AA_kinase 197 rllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvItn 241
                 +l+++i+ +++++  +++  + gG   ++  al++++r++i++++++
  AJA92701.1 157 KLFKTIEMKSLKKllIHEDSVAGGYDLMDIVALKIIERSKIRTRVIK 203
                 ********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1710.61
//
Query:       AJA92702.1  [L=387]
Description: 2-methylcitrate synthase/citrate synthase II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.8e-126  421.4   0.0   3.2e-126  421.3   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.15   12.4   0.1       0.31   11.3   0.1    1.5  1  DUF2811       Protein of unknown function (DUF2811)


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.3   0.0  3.5e-130  3.2e-126       1     361 []       7     365 ..       7     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 421.3 bits;  conditional E-value: 3.5e-130
                   GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHCSSTTS-HHHHHHHHHHH CS
  Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealealpkdahpmavlraavsa 97 
                   glr++++++t+is +dgekg+l+YRG+d+ +L  ++s+fee ++lLl+ +lP++ e++ef+ +l+ear++pe++++++++++k+ahpm+vl+a v+a
    AJA92702.1   7 GLRNIPIADTKISLIDGEKGKLIYRGFDVLDLT-KNSNFEECCFLLLHDHLPNRIEFNEFTTKLKEARAIPEQMQKNMKNWRKNAHPMDVLQAFVAA 102
                   899******************************.8************************************************************** PP

                   HHHHSTT.CTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHH CS
  Citrate_synt  98 lsaddee.seakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarv 193
                   l+ +++e +++ke s+++a++    li+k+pti+a + r+r+++ep++pd++ls+a+nflyml+g+kpd+e+++++d++l+lhaDH +naSTfaar 
    AJA92702.1 103 LAGYYDEqGSEKEISQQRAIN----LISKVPTIIASWERVRNDKEPIQPDPELSHASNFLYMLTGNKPDKEMERVFDVCLILHADHTFNASTFAARE 195
                   *****9855555556665555....*************************99********************************************* PP

                   HHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHH CS
  Citrate_synt 194 vaStladlysaiaagigalkGplhgganeavlkmleeigsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllkl 290
                   vaSt+a++ysa++a++gal+G+lhggan +v+kml +i++++ ++ ++++++++k+ +r++G+GH+vyk+ DpR  +lk l ++l+e k+  p++++
    AJA92702.1 196 VASTRAHMYSAVSAAVGALSGELHGGANYEVMKMLLDIKDEN-NATNWVKSRIEKG-DRIMGMGHAVYKTVDPRSMVLKGLSKKLSE-KTGLPWYNI 289
                   **************************************8888.***********96.***************************988.58888**** PP

                   HHHHHHHHHHHHHCHHGCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH.HT--....----E CS
  Citrate_synt 291 aeeleevapevlkekeeknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql.adnk....iiRPr 361
                    +++ee ++e++k+++e++++pNvD+ys+ +y++l+ip +l t++faisRv Gw Ah++e++ a+      ++RP+
    AJA92702.1 290 TKKVEETTSEIMKNRKERDIFPNVDLYSASVYYMLNIPMDLNTPIFAISRVSGWAAHVIEEKfAEAApkpmLYRPK 365
                   **************99********************************************9765533446688885 PP

>> DUF2811  Protein of unknown function (DUF2811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   3.5e-05      0.31       5      45 ..      74     114 ..      72     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
     DUF2811   5 eipeeLheslkkflethpnWDqdrllqaALslFLlqngssd 45 
                  ipe++++ +k++ ++    D  + + aAL+++  ++gs++
  AJA92702.1  74 AIPEQMQKNMKNWRKNAHPMDVLQAFVAALAGYYDEQGSEK 114
                 59**************999**************88887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2816.65
//
Query:       AJA92703.1  [L=179]
Description: GTP cyclohydrolase I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-66  221.2   0.2    7.2e-66  221.0   0.2    1.0  1  GTP_cyclohydroI  GTP cyclohydrolase I
     0.0046   17.1   0.0       0.01   16.0   0.0    1.6  2  QueF             QueF-like protein


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.2     8e-70   7.2e-66       2     178 ..       7     176 ..       6     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 8e-70
                      HHHHHHHHHHTT--TTSTTTTTHHHHHHHHHHHHTGGGGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEEEEEEEE-TTEEE-H CS
  GTP_cyclohydroI   2 eeavreiLealgedpereglketpkRvakayeelfkgleedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigkahvaYiPkkkviGl 95 
                      ++ vre++ ++gedp+reglk+tp+R+a+ay e+f+g+++d+    l+ +f+ e +emv+ k+i+f+S+CeHH+lpf+g++++aYiP+++v+G+
       AJA92703.1   7 KKLVRELIIEIGEDPTREGLKDTPRRIADAYTEIFSGYDSDS---ELSVQFS-EDSEMVVAKNIQFYSMCEHHMLPFYGTIQIAYIPNGRVFGI 96 
                      6789*************************************9...3666676.699************************************** PP

                      HHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHHHSSTT--TT-EEEEEEEEEHHHH-HHHHHHHHHHH CS
  GTP_cyclohydroI  96 SklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCmtmrgvkkkesktvtsalrGefkedaalreefleli 178
                      Skl+R+v+ +++rlq+QEr+t+++ad++ ++ + kgvav+ e+ehlCm+mrgv++ ++++++sa+rG+f ed++++ee+l+ i
       AJA92703.1  97 SKLVRVVEKFSKRLQIQERITKNVADEIYAQ-GVKGVAVMAEGEHLCMKMRGVRN-DAQMTSSAFRGVF-EDQKTKEELLKAI 176
                      ****************************987.99*******************75.6788899******.999*****99987 PP

>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.7   1.5e+04       7      25 ..      51      69 ..      49      70 .. 0.61
   2 !   16.0   0.0   1.1e-06      0.01       1      50 [.      78     127 ..      78     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.7
        QueF  7 virYvpdkkvvelkslklY 25
                 +++  d+++v  k ++ Y
  AJA92703.1 51 SVQFSEDSEMVVAKNIQFY 69
                5666666666766666655 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-06
        QueF   1 PDfatlvirYvpdkkvvelkslklYlisfrnrgifhEevvnrilddlvea 50 
                 P ++t++i Y+p+ +v     l + +  f +r + +E ++++++d+++++
  AJA92703.1  78 PFYGTIQIAYIPNGRVFGISKLVRVVEKFSKRLQIQERITKNVADEIYAQ 127
                 669******************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1259.07
//
Query:       AJA92704.1  [L=342]
Description: putative NAD(P)-dependent glycerol-1-phosphate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-71  241.6   0.6    1.3e-71  241.2   0.6    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    6.5e-23   81.1   0.2    6.8e-22   77.8   0.2    1.9  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    6.5e-06   25.5   0.3     0.0002   20.6   0.3    2.7  1  DHQ_synthase  3-dehydroquinate synthase
     0.0082   16.0   0.1       0.03   14.2   0.1    2.0  2  PASTA         PASTA domain
  ------ inclusion threshold ------
      0.012   15.2   2.4      0.015   14.8   0.4    2.1  2  AIRC          AIR carboxylase
      0.055   13.6   0.2       0.12   12.5   0.2    1.5  1  DUF531        Protein of unknown function (DUF531)


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.6   4.5e-75   1.3e-71       2     250 .]       9     264 ..       8     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 4.5e-75
    Fe-ADH_2   2 igegaleklgellkelel.kkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsakln 99 
                 +ge  + ++ge+l++l++ kkv +++++n+kk++g+++ eslk+++i + v++  +++++++e + +++++++++ d+++++GgG+ +Diak+++++l+
  AJA92704.1   9 VGEKNIGQVGEFLRSLSNpKKVSIISGKNVKKIIGKEIDESLKNSKIMA-VWH-LAKSNQVKETATIQKKVKSTKSDIIIGLGGGRSVDIAKLCAFNLK 105
                 78999***********8549*************************8877.465.78999**************************************** PP

    Fe-ADH_2 100 vpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklan........evseplaklsaamvq 190
                 +p+vs+pT+aS+DG+asp++s++ d+   ++  a+aPl+v++Dld++++APr+llasG+GDl++k+ta++dw+l++        ++s+ la +sa+++ 
  AJA92704.1 106 KPFVSIPTSASHDGIASPFVSVRGDK-PHSL-VATAPLGVFVDLDIIKKAPRKLLASGCGDLMAKVTAVHDWELGRdkvgeyygRYSANLASMSAEILI 202
                 *************************7.6677.799****************************************99999999999************* PP

    Fe-ADH_2 191 eaaeklvedkketeal.eelleal.alsgigisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                 e+ae++ +++ +++++ e+l++a  a +++g+srp+SG+EHl+SHa+d l+    lHGe++G
  AJA92704.1 203 ESAENFSKKNIDVRVIvEALISAGvASCIAGSSRPCSGAEHLFSHAIDHLEFGIGLHGEKCG 264
                 ******998777665527777775377777889*****************99*********8 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.2   2.3e-25   6.8e-22       1     333 [.       4     298 ..       4     332 .. 0.75

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 2.3e-25
                 -SEEEEETTGGGGHHHHHTTT-...EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHH CS
      Fe-ADH   1 Ptrivfgkgaleelgellkklg.akralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtAK 98 
                 P++iv g+  + ++ge l++l   k++ i+ +k++  k  + +++ esl++++i  + ++  ++  +++e + + + +++++ d++i++GGG ++D+AK
  AJA92704.1   4 PRQIVVGEKNIGQVGEFLRSLSnPKKVSIISGKNV--KKIIGKEIDESLKNSKIMAV-WHLAKS-NQVKETATIQKKVKSTKSDIIIGLGGGRSVDIAK 98 
                 899******************5489*********5..4559********99999888.454444.4678888999999********************* PP

                 HHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHH CS
      Fe-ADH  99 aialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayv 197
                 + a+ l+                   p++ iPT a+ +  ++p+  +   ++    s++   + P  ++vD +++ ++P++++a++ +D +a++     
  AJA92704.1  99 LCAFNLK------------------KPFVSIPTSASHDGIASPFVSVR-GDKP--HSLV--ATAPLGVFVDLDIIKKAPRKLLASGCGDLMAKVTAVHD 174
                 *******..................79*****************9999.4443..4555..579******************************98854 PP

                 HH........T---TTSSB--HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHSS---.HHHHHHHHHHC..CGGG.GGS-HHHHHHHHH.. CS
      Fe-ADH 198 sk........kanplsdalaleairliaknleravadgedl.eareqmllastlaglafsnaglg.avHalahalga.lfgip.hglanaillpavlrf 284
                  +            +s  la  ++++++++ e+  ++  d     e+++ a + + +a s+  ++ a H ++ha+    fgi  hg+ ++i    + + 
  AJA92704.1 175 WElgrdkvgeYYGRYSANLASMSAEILIESAENFSKKNIDVrVIVEALISAGVASCIAGSSRPCSgAEHLFSHAIDHlEFGIGlHGEKCGIGSIMIAKL 273
                 43455556558888999999999999999999999886444455566666666666666666665599******9994458889999999843333322 PP

                 ........HHHHHHT.......T--HHHHHHHHHHHHHTT---SHHHHT CS
      Fe-ADH 285 naeaaperlaqlaralggesdeeaaeeliealrellkelglptsLselg 333
                 +     +                      +++ + lk+ g+pt+ +e+g
  AJA92704.1 274 QG----Q--------------------NWKEIVKTLKKSGAPTTAKEIG 298
                 22....2....................2333334444444444444444 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3   6.5e-08    0.0002      15     255 ..      66     308 ..      58     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.5e-08
                   HHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS-HH CS
  DHQ_synthase  15 tlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktLper 111
                   ++++  +   + k ++++++i lGGG   D+a + A  +++   fv +Pt+  a  D      +++  ++   l+   + P  v++dl+++k  p++
    AJA92704.1  66 QVKETATIQKKVKSTKSDIIIGLGGGRSVDIAKLCAFNLKK--PFVSIPTS--ASHDGIASPFVSVRGDKPHSLVA--TAPLGVFVDLDIIKKAPRK 156
                   445555555667789*********************99997..8******9..78888888888888888888887..58***************** PP

                   HHHHHHHH.HHHHHHHT-HHHHHHHHHHHHHHHC............TTTHHHHHHHHHHHHHHHHHH..HHHCCTTTTGGGGGGTTHHHHHHHHHHH CS
  DHQ_synthase 112 elraGlaE.viKyalikdeelfelleenaeallk............eeeeealeeliarsievkaev..veeDekekglralLnlGHtigHaiEall 193
                    l++G+++ + K+++++d el +    +     +            e+ e+  ++ i   + v a +    +     + r +    H ++Hai++l 
    AJA92704.1 157 LLASGCGDlMAKVTAVHDWELGRDKVGEYYGRYSanlasmsaeiliESAENFSKKNIDVRVIVEALIsaGVASCIAGSSRPCSGAEHLFSHAIDHLE 253
                   *******94469****9988865443333333233445566666663334444444443333333220022234557788889999*******9886 PP

                   TTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT..-HHHHHHHH CS
  DHQ_synthase 194 gyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkel.leveelleal 255
                        lHGe   iG ++ a+l         ++ ++++k+lkk g p++ ke  l++++l++a+
    AJA92704.1 254 FG-IGLHGEKCGIGSIMIAKLQ-------GQNWKEIVKTLKKSGAPTTAKEIgLKPKTLAKAM 308
                   55.89*************9998.......345789************9999877888888877 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1     1e-05      0.03       6      47 ..     273     316 ..     269     328 .. 0.84
   2 ?   -2.6   0.0       1.8   5.4e+03       9      23 ..     327     341 ..     325     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                 TTTSBHHHHHHHHHHTT--CCCEEE..ECTCCGTTBEEEECS-T CS
       PASTA   6 vtGmsvdeAkatLkalGlkiktvee..tsddvpeGtVisQsPea 47 
                 + G++++e ++tLk++G + + +e   ++++ ++  Vi+Qs  +
  AJA92704.1 273 LQGQNWKEIVKTLKKSGAPTTAKEIglKPKTLAKAMVIAQSLRP 316
                 78****************444444466**************877 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                 SBHHHHHHHHHHTT- CS
       PASTA   9 msvdeAkatLkalGl 23 
                 m+ ++A +++k  G+
  AJA92704.1 327 MTEKDALKLAKTTGV 341
                 9999***99999886 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4   5.2e-06     0.015       1      95 [.      29     122 ..      29     139 .. 0.84
   2 ?   -0.9   0.1      0.36   1.1e+03      41      75 ..     199     234 ..     189     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-06
                 EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEES.S--HHHHHHHHSSS-EEEEEE--STTCCHHH CS
        AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGg.aahLpgvvaslttlPVigvPvkskalkglds 95 
                 kV ii G +    + k++ e lk+ ++    + +    + +e++++ +++++ + ++iI   Gg + +++ ++a + + P +++P+++ + +g+ s
  AJA92704.1  29 KVSIISGKNVKKIIGKEIDESLKNSKIMAVWHLAKS-NQVKETATIQKKVKSTKSDIIIGLGGGrSVDIAKLCAFNLKKPFVSIPTSA-SHDGIAS 122
                 588999999999999999999999999887777655.56688999**************9887779********************99.5556554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.36
                 HHHHHHHHHCHTTTEEE.EEEEEESS--HHHHHHHH CS
        AIRC  41 eelleyaeeaeerglkv.iIagAGgaahLpgvvasl 75 
                 e l+e ae+ ++++++v +I+ A  +a +++ +a+ 
  AJA92704.1 199 EILIESAENFSKKNIDVrVIVEALISAGVASCIAGS 234
                 556778888888888884455666688888888875 PP

>> DUF531  Protein of unknown function (DUF531)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2     4e-05      0.12      53     144 ..       6     103 ..       2     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
      DUF531  53 dvvaekttiGesGkylkelaeknrllvldlpkkgfpaqfGevvattskpdekkai.........tpeevaeeilrkksvllliGlGrkGlPkellklak 142
                 ++v+ +  iG+ G++l++l + ++++++    k+ +  +G+ +  + k ++  a+         +++  +++ ++++   ++iGlG  G   ++ kl+ 
  AJA92704.1   6 QIVVGEKNIGQVGEFLRSLSNPKKVSIIS--GKNVKKIIGKEIDESLKNSKIMAVwhlaksnqvKETATIQKKVKSTKSDIIIGLGG-GRSVDIAKLCA 101
                 5788999********************99..99999999999887777665444322111110043333334444455568899984.66666766666 PP

      DUF531 143 yh 144
                 ++
  AJA92704.1 102 FN 103
                 65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2362.07
//
Query:       AJA92705.1  [L=339]
Description: wyosine biosynthesis protein TYW1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-20   73.4   0.0    5.2e-20   72.5   0.0    1.4  1  Radical_SAM   Radical SAM superfamily
    8.8e-19   67.6   0.1    2.1e-18   66.4   0.1    1.7  1  Wyosine_form  Wyosine base formation
  ------ inclusion threshold ------
      0.013   15.7   0.4       0.58   10.3   0.4    2.9  1  Fer4_14       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   8.7e-24   5.2e-20       7     159 ..      77     252 ..      72     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 8.7e-24
                  ESS--TTTSCCTT.........................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                  xxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   7 CnlrCsfCarpet.........................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                  C +rC++C+rp                            r+  +g++ ++ + +++++e    +  ++ i+++gep++yp++ +l++ l+ l+ +  +
   AJA92705.1  77 CENRCVYCWRPMEfydslemdeqkvaepkdimsklmeeRRKLIVGHFGDPSQDKQKIEESL-TP-SHYAISLSGEPTMYPKLPDLIKYLKSLE-ATKS 171
                  ***********98999999988888888888888888888888888888888888888884.44.8888888********************7.**** PP

                  EEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                  xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  80 itvetngtlpdeeklerllelg..vdrvslgleaaddekvlklmn..rghtfeevlealeklreagikrvvdrivglpGendee 159
                  i+++tng    +++++rl++ +  +++++l+ +a d++ +lk+++    ++++++ ++le+l++++ + +v r+++++ +nd+e
   AJA92705.1 172 IFLVTNGQE--PDMIQRLADENalPTQLYLSTNASDYDSFLKINRpkYDDSWQRWNKTLEMLADLDTR-TVLRVTLIKDWNDSE 252
                  *********..69*******99****************9999999889999*****************.*************97 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   3.5e-22   2.1e-18       2      63 .]     265     326 ..     264     326 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 3.5e-22
                   HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
  Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                   ++++F+E+K+y+++G s++rL+ +n+ ++ +v++f++++ +++ ++e+++e++ Sr+v+l++
    AJA92705.1 265 SNAHFIELKSYMHIGRSTNRLEYENMVEMNDVRKFSEKIVEKSDRFEVMDESEVSRIVVLQN 326
                   689********************************************************986 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   9.7e-05      0.58      32      92 ..     127     181 ..      74     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.7e-05
     Fer4_14  32 elleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                  + +q ++ +l+ s+++   ++l+ GeP +y   ++l +l+k+lk    +k+i l tng   
  AJA92705.1 127 SQDKQKIEeSLTPSHYA---ISLS-GEPTMY---PKLPDLIKYLKSLEATKSIFLVTNGQEP 181
                 33333333356777773...5565.7***9*...555555555555555679*****99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2430.26
//
Query:       AJA92706.1  [L=320]
Description: membrane protein, PF03706 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-33  114.9  17.0    6.1e-33  114.6  17.0    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  17.0   3.4e-37   6.1e-33       1     301 []       8     298 ..       8     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 3.4e-37
  LPG_synthase_TM   1 illglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfvnnvtPgalgGevvr 94 
                      il+g+++s+++  +++  +d+++++++l ++   +l  +l l++  +ll  lrW+lll+ lg+++++ +   ++++++++  +tP+++ G+++r
       AJA92706.1   8 ILIGIVCSIIFYSFIIFVTDFSKIQEQLLNFKIEYLPIILSLIFSGMLLVFLRWHLLLKNLGFNLPIKS-NLVTFLSTLALGMTPVRA-GDLFR 99 
                      6889999955555555557**********************9999999*9****************976.56888888*********9.***** PP

  LPG_synthase_TM  95 ayllkrkegvslskalasvvverlldllalvllgllallllggllaegaavllllalallllavla.....lllllllrrrlarlarvlkrlar 183
                         lk +++++++k +  v+ver++d+l+ v++  + + ++   l+    ++++l++++++++v+      +  ++   ++ ++++++++ l+ 
       AJA92706.1 100 SEILKNRHDLPRTKTAPLVIVERFYDILGAVIVASACISFFEPALY----IMAVLSIFIITAFVIFsskniFKKIINKLKKIKFISKFFEPLLD 189
                      *****************************99988777777666543....44444444444444445555577777777777777777777777 PP

  LPG_synthase_TM 184 llarfarklasakrklvlasprrlllafllslliwllealtlylllralgvd.vslallllillaltlvgalpplPgGlGvrEaalalllallG 276
                          + +++++          +  l++++ls+ +w++    +y++l a++++ + +++++ i+l +++vga++++PgGlGv E++la  l+l+ 
       AJA92706.1 190 SYDVIHQSTRG----------KISLISIFLSISHWIVISISVYFILLAYDITnIGILEIIPIYLSSVVVGAVSFIPGGLGVTEGSLAGFLNLFI 273
                      76666665554..........5589*************************9878999999*********************************6 PP

  LPG_synthase_TM 277 vsaaealaaallyrlitlylllllG 301
                       + + al++++++r++tl++++ +G
       AJA92706.1 274 NDISIALSLSIIIRIFTLWVSVMVG 298
                      6779******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1261  (0.070333); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2084.40
//
Query:       AJA92707.1  [L=146]
Description: succinate dehydrogenase/fumarate reductase transmembrane subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   41.5   1.5    1.8e-10   40.9   1.5    1.3  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   1.5   9.8e-15   1.8e-10      12     101 ..      19     107 ..      14     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 9.8e-15
     Sdh_cyt  12 qlyrlplgawlsilhritGvallvglllllvwlllalslsspesfarvvallas.piklilllllllallyHllnGiRhllwDlglgl.ele 101
                 +++++ ++ ++++l+r+tG++ll  +++ +++ + + +l +++++++  +  +   + l+l +l++   ++H+ nGiR+++ ++g+g  + e
  AJA92707.1  19 KIGKFGIERLAWLLMRLTGLGLLA-YFIGHIYET-SHILDGKAVWDKSLEMTQTtEGHLFL-ALVIGMCVFHTGNGIRLMVAQMGYGIgKAE 107
                 5789999*****************.666666555.77788999999997777776677777.888888888************877765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1066.02
//
Query:       AJA92708.1  [L=956]
Description: leucine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-62  209.8   3.2    7.1e-61  206.2   3.2    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    6.2e-24   84.7   1.2    1.5e-23   83.4   1.2    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.1e-23   82.7   0.2    2.1e-11   43.2   0.1    2.7  2  tRNA-synt_1g   tRNA synthetases class I (M)
    2.5e-12   46.7   0.0    6.4e-12   45.4   0.0    1.6  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    1.2e-10   41.2   5.8      4e-07   29.7   0.1    3.0  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.029   14.2   1.2      0.068   13.0   1.2    1.5  1  DUF659         Protein of unknown function (DUF 659)
       0.17   10.9   1.8       0.33   10.0   1.8    1.4  1  Poty_PP        Potyviridae polyprotein


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   3.2   2.8e-64   7.1e-61       2     600 ..      12     660 ..      11     662 .. 0.84

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 2.8e-64
  tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai...eakve...kklgakekkerk 93 
                  +  kW+e++ f+++    +ek++  +++  Py +   HiGh  + tl d+  r++rmkG++vl+ +G+   G ++    + +e   k++  ++ ++ +
   AJA92708.1  12 WRTKWHEAKDFETN---PNEKPKKFITVAYPYPNSPQHIGHGRTYTLADVHARFYRMKGYNVLFPMGFHYTGTPVlgmAKRIEageKEI-LDGLRNIY 105
                  6689********99...555555556777899999*************************************99822223333111232.22333444 PP

  tRNA-synt_1  94 klgreefrekvr..ewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv...eykdkkda 186
                  ++ ++ ++  v   +++++++eei++ + ++G s+D+ re  T+ +++++ +++ +  l d++ i +g+++v w++  + ++s+ ++        +d 
   AJA92708.1 106 HVPEDVIKTFVEpiKIADYFHEEIKSGMIEMGYSIDWRREFTTIVPGYQKFIEWQISTLRDNDRIIQGSHPVGWCPVDQNPVSQHDTmgdVEPKINDE 203
                  4544444444432257899*****************************************************************99965444556799 PP

  tRNA-synt_1 187 lihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiadd 281
                   + v+f+l++     + i T +PeTl+g t + vnp+  y    +++ek+i+ +   ++l    +e +i+ d++g+e++gk+++ p ++++ipi + +
   AJA92708.1 204 NYLVKFKLDEY---VFPITTLRPETLFGITNLWVNPNTIYKkikADDEKWIVSQECAEKLKFFGKEITIEGDIKGTEIIGKFAKTPHTEQEIPIFEAE 298
                  99999999764...569*********************999998999*********99999999999******************************* PP

  tRNA-synt_1 282 yvdkeaGtGvVkiaPahdedDyev.....gkkynl....evinildedgtlteea......................................aefeg 332
                  +v++ +GtG+V   Pah + Dy++     +k+++l    e+i i+ ++g  +  a                                      ++f  
   AJA92708.1 299 FVESGMGTGLVMSVPAHAPKDYQAlmdlkSKNHELaskiEPIPIIVTEGYGNIPAkdvcerlgvtdqvdakleeateelylkefvngklnekcGDFVN 396
                  ***********************84444467788898886666665555554444557899999999999999999*************9999***** PP

  tRNA-synt_1 333 lkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleniqdWciSRqrwWG 428
                   kv+  r+kv + lk+k++l +  + +     c  + + ++  + +qWf +  +   ++ a + ++ +++ p++ ++++++ ++  ++ +  Rq+  G
   AJA92708.1 397 EKVEFGRNKVRDWLKDKNQLESFPTLQNAPIRCRCGCECVVKVLNNQWFLNYGDeeWKKLARNCLDGMNILPNKIKTEFHDVINWLHERACARQQGLG 494
                  *****************999988877766556666778899999******9865336666777777******************************** PP

  tRNA-synt_1 429 hripl...fvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleG 523
                  +++p    ++ ++  + v+      + +  + e+++ ++l+ke+ d l         d+  l +  sS+     +++   + ++e++ f+p d   +G
   AJA92708.1 495 TKLPWdkdWIVESLSDSVIYMAYYTISRFVNDETVKPENLTKEFFDYL-------FLDKGDLGTVASSANLSEDVIN---TMKKEFQYFYPVDARHSG 582
                  ****75557777777777766666666666677777777777777777.......444445778889**99999999...5589************** PP

  tRNA-synt_1 524 lDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdin 600
                   D ++  ++  +l   a+++++ + ke++v+g v+  +G KmSKs+gN+i   + i+ +gad +Rl++i +++ ++d +
   AJA92708.1 583 RDLVQNHLSFFVLNHAAIFEEKLWpKEIVVNGSVM-MDGAKMSKSMGNIIPLRTAIQDHGADPIRLAIIsSAELLQDAD 660
                  ******************99995548999999888.58*******************************7778888866 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   1.2   5.9e-27   1.5e-23       1     150 [.     695     829 ..     695     832 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 5.9e-27
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelwqreeeelgk 98 
                  d+wils++++ ++evtea e++r+++a++++   f  dl +wy + v+ +  ++       ++ +l+ + ++ + +l+Pf+P+++Ee+w    e+lg+
   AJA92708.1 695 DKWILSKTQSKISEVTEAVEKMRLREALHDILFTFESDL-SWYQKRVQAKKRDD-------VSGILHQINSARVAMLSPFAPHVAEEMW----EKLGN 780
                  9**************************************.***99998876433.......56**************************....9**** PP

  Anticodon_1  99 kesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                  +e +++++wpe ++++ +     ++ el   + ++i+++ ++lk+ + s++k+
   AJA92708.1 781 SELVSKSSWPEySSDKVDVSV-IQAEEL---LKSTIEDISNILKVTKISPKKI 829
                  **********97776665555.678888...5566666666666666666555 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   8.2e-15   2.1e-11       2      69 ..      33     100 ..      32     115 .. 0.91
   2 !   36.8   0.0   7.5e-13   1.9e-09     269     377 ..     567     672 ..     518     683 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.2e-15
                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHH CS
  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvek 69 
                   ++t+a pY+n+++H+Gh +++  aD++aR+ r++g++vlf  g    Gtp+   A++ +   +e+ + 
    AJA92708.1  33 FITVAYPYPNSPQHIGHGRTYTLADVHARFYRMKGYNVLFPMGFHYTGTPVLGMAKRIEAGEKEILDG 100
                   79*************************************************99999888877777665 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 7.5e-13
                   SGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS- CS
  tRNA-synt_1g 269 eekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkD 363
                   +++++ ++     v++    g+d ++ H  f+     +  +e   pk++v+++ ++++g+K+SkS g+++  ++a++   ad +R  ++++a+  +D
    AJA92708.1 567 KKEFQYFYP----VDAR-HSGRDLVQNHLSFFVLNHAAifEEKLWPKEIVVNGSVMMDGAKMSKSMGNIIPLRTAIQDHGADPIRLAIISSAELLQD 658
                   556776662....3333.359***********9988888888889**************************************************** PP

                   EEE-HHHHHHHHHH CS
  tRNA-synt_1g 364 ldfswedfvervNs 377
                   +df++e++    N+
    AJA92708.1 659 ADFNMESVSGIKNK 672
                   *****999877774 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.5e-15   6.4e-12      12     127 ..     207     321 ..     202     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.5e-15
  tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapehplveklaekkke..laafieevkkksesereletkekeGv.ftglkaihPitgekipiwvan 104
                    ++fk++e    + + t rp+tlfG+t + + p+  + +k+++++++  +++ ++e  k   +e ++e  + +G    g +a  P t+++ipi+ a+
     AJA92708.1 207 VKFKLDEYV--FPITTLRPETLFGITNLWVNPN-TIYKKIKADDEKwiVSQECAEKLKFFGKEITIEG-DIKGTeIIGKFAKTPHTEQEIPIFEAE 298
                    566776654..78899**************997.5888885555541133333333333334444444.45666589******************* PP

  tRNA-synt_1_2 105 yvlmeygtgavmavPahdqrDfe 127
                    +v ++ gtg vm+vPah  +D++
     AJA92708.1 299 FVESGMGTGLVMSVPAHAPKDYQ 321
                    *********************97 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.6e-05     0.042      23      50 ..      45      72 ..      34     111 .. 0.92
   2 !   29.7   0.1   1.6e-10     4e-07     208     294 ..     576     664 ..     564     671 .. 0.85
   3 ?   -1.7   1.1      0.57   1.5e+03      41     138 ..     808     906 ..     797     935 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                  -BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
  tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYdvqf 50
                   h+Gh+R++   D+ +r+ +++gY+v f
    AJA92708.1 45 QHIGHGRTYTLADVHARFYRMKGYNVLF 72
                  7*************************98 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-10
                   EEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS.S-TTS-EEE-HH CS
  tRNA-synt_1e 208 idihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls.ahyrsqldfkee 294
                   +d    G DL+  h    +  + a f+ k + k  + ng ++++g kmsks++n+i ++ +++ + +  +Rl+++s a+  +  df+ e
    AJA92708.1 576 VDARHSGRDLVQNHLSFFVLNHAAIFEeKLWPKEIVVNGSVMMDGAKMSKSMGNIIPLRTAIQDHGADPIRLAIISsAELLQDADFNME 664
                   67777899******************978899****************************************98751556666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.57
                   HHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB.--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG- CS
  tRNA-synt_1e  41 lqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptl.eprvsekvdeiielvekliekgyaYavsdgdvyfdvskk 136
                   l+++  d++ +  vt i  k i   +++++  +++  k+ + +    +++++   +l     +   +++ ++v+k+i+  ++ + s  +++++ +++
    AJA92708.1 808 LKSTIEDISNILKVTKISPKKIVIYVNSDSVKSKIYRKILNIMVGGQNNMGIVMKELiADPETIDAKKMPDYVQKVIKDLHSESESIKKMKLESESF 904
                   5555667777788888888888888888888888888888888888888887654440333455567899999999999888777777777766655 PP

                   TT CS
  tRNA-synt_1e 137 ee 138
                   +e
    AJA92708.1 905 NE 906
                   44 PP

>> DUF659  Protein of unknown function (DUF 659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   2.6e-05     0.068       8      92 ..     805     890 ..     803     901 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
      DUF659   8 gtlLqeeveeikkkvkeikkswektgcsillDgwtdkkgrslinflvscpkG.tvFlksvdassekktaeylaelldkvieevgae 92 
                 ++lL++++e+i++ +k  k s +k ++ + +D+ ++k  r+++n++v  ++   + +k + a+ e  +a+++ ++++kvi+++ +e
  AJA92708.1 805 EELLKSTIEDISNILKVTKISPKKIVIYVNSDSVKSKIYRKILNIMVGGQNNmGIVMKELIADPETIDAKKMPDYVQKVIKDLHSE 890
                 689*********************************************99975688888889999999999*********998765 PP

>> Poty_PP  Potyviridae polyprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.8   0.00013      0.33     139     244 ..     806     913 ..     793     919 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
     Poty_PP 139 kvtavnvskiAlklstdeksvgrtlliveelLveerskleqlkhlv..sesvgsylvgilalnyclraryakdrveenievLenvrsqleefsvvsdkd 235
                 ++ ++ ++ i   l++ + s +++++ v+   v+++  +  l+ +v  ++++g  +  ++a   ++ a+   d+v++ i+ L+   +++++++  s++ 
  AJA92708.1 806 ELLKSTIEDISNILKVTKISPKKIVIYVNSDSVKSKIYRKILNIMVggQNNMGIVMKELIADPETIDAKKMPDYVQKVIKDLHSESESIKKMKLESESF 904
                 67788999999********************************99833455677889999999************************************ PP

     Poty_PP 236 eleellien 244
                 +++e+l+ +
  AJA92708.1 905 NEKEFLMSE 913
                 *****8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (956 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.49
# Mc/sec: 5890.77
//
Query:       AJA92709.1  [L=220]
Description: hypothetical protein T478_0427 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1571.87
//
Query:       AJA92710.1  [L=261]
Description: 3-deoxy-7-phosphoheptulonate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-49  167.2   0.0    5.2e-49  167.0   0.0    1.0  1  DeoC        DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.063   12.7   0.0       0.14   11.6   0.0    1.5  1  PEP_mutase  Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   5.8e-53   5.2e-49       3     235 .]      20     232 ..      18     232 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 5.8e-53
                 EEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEEE CS
        DeoC   3 ilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvdevasveeakalGAdavkvvv 101
                  +++D++++n+++++       e++  ++ +  + g  ++ +++g+i    +  +  +++l++++++t l+  ++r+++   sv+ea++lGAd v++++
  AJA92710.1  20 CIPMDHGISNGPIEGL------EKPHDVIYKCENHGLTSIIINKGIIKTLPRPTK--VGILAHFSSSTALSLAPNRKML-TGSVKEAIRLGADGVSLHI 109
                 689*************......8***************************99988..**********************.******************* PP

                 EEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEE CS
        DeoC 102 yyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvv 200
                 ++   g +ee ++++++++++e+che+  pl++++y+r+e++kd + dp++va+ ar++ae+GaDi+K+ ++        +d+++fk+v++++pvp vv
  AJA92710.1 110 NI---GGKEEPEMVEQLGKISEECHEWNVPLLAMMYPRGENVKDPH-DPEVVAHTARIGAECGADIVKTLYT--------GDIDSFKKVTESIPVP-VV 195
                 **...*****************************************.*************************........****************.** PP

                 EETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
        DeoC 201 lsGGv...seedfletvedAvkeagasGvlsGRaifqk 235
                 ++GG+   ++ d+l++ edA+ +aga Gv +GR+if++
  AJA92710.1 196 IAGGPkskTDLDILQMTEDAM-AAGAKGVTYGRNIFAH 232
                 *****976677889*******.**************86 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05      0.14      90     227 ..      93     233 ..      86     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
  PEP_mutase  90 tvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraaaeeag....fvinARtdalllsagagleeaieRaraYaeAGAdgvfvpglqkdaei 184
                  v+++i++G+ gv +  +    ++++  ++ e++ ki++  ++    +     +   R +++      + e   + ar  ae GAd v      + ++ 
  AJA92710.1  93 SVKEAIRLGADGVSLHIN---IGGKEEPEMVEQLGKISEECHEW---NvpllAMMYPRGENVKD--PHDPEVVAHTARIGAECGADIVKTLYTGDIDSF 183
                 588888888888888766...33444445555555555554444...43347778888888763..444444455566668****************** PP

  PEP_mutase 185 aelvaavdvplnvvplkgt.......lsvaelaelGvarislgnhllraa 227
                 +++++ ++vp+++  ++++         +++  ++G++ +++g ++++  
  AJA92710.1 184 KKVTESIPVPVVIAGGPKSktdldilQMTEDAMAAGAKGVTYGRNIFAHK 233
                 *************996433358999767788999*********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1936.01
//
Query:       AJA92711.1  [L=152]
Description: endoribonuclease L-PSP [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-33  115.1   0.0    3.3e-33  114.9   0.0    1.0  1  YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endori
    1.1e-18   67.3   0.0    1.7e-18   66.8   0.0    1.2  1  Ribonuc_L-PSP    Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> YjgF_endoribonc  YjgF/chorismate_mutase-like, putative endoribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   3.7e-37   3.3e-33       2     147 ..       4     149 ..       3     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 3.7e-37
                      HHHHHTT---------SSSS-SEEEETTEEEE--B--EETTEE--BS-BTTTB-HHHHHHHHHHHHHHHHHHHHHHHSSGGG-SEEEEEEEEE- CS
  YjgF_endoribonc   2 srlvalGlelpkvaaalGayepyaivasflttsfqlpylqekllyvGllGddvsvseGiaaarlaalnalaqlkeaaGelarvkrlirleGvln 95 
                       +l  l +elp +++  G+y p    ++    s+q+p +++k+ + G++ d+ s +e   aa+++ +n+laqlk   G+l ++ +++r+ G +n
       AJA92711.1   4 DKLRELSIELPTPPSPAGSYIPVVTTGNLAFVSGQIPMKEGKVVFEGKVPDKQSLDEARDAAKICIINGLAQLKANLGSLDKITKFVRISGFVN 97 
                      56778999************************************************************************************** PP

                      B-TT---HHHHHHHHHHHHHHHHGGGG--EEEEEE-SS-GGGBSEEEEEEEE CS
  YjgF_endoribonc  96 vtqdyiempkvldaasdlllevlGeaGrhartiltnhvmplnalvllylfae 147
                       + ++ e+pkv++aasdll e++G+  +h+r++++   +pln+ v + +  e
       AJA92711.1  98 SNPEFTEQPKVINAASDLLVEIFGDMAKHSRIAVGVASLPLNSTVEIDMVVE 149
                      ********************************************98887765 PP

>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   1.9e-22   1.7e-18       5     120 ..      17     149 ..      14     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.9e-22
                    TTTSSS-BSEEEETTEEEEEEE-SB-T....TTSCB..-SSHHHHHHHHHHHHHHHHHHTT--GGG......EEEEEEEESSGGGHHHHHHHHHHH CS
  Ribonuc_L-PSP   5 paaaapYsqavkagnlvyvsGqlpldp....etgelv.egdveeqtrqalenlkavLaaagaslsd......vVkvtvFladiedfaevnevyaea 89 
                    p++a++Y ++v++gnl +vsGq+p+++     +g++  ++++ e   +a  ++ + La+  a+l++       V+++ F+++ ++f+e+ +v++ a
     AJA92711.1  17 PSPAGSYIPVVTTGNLAFVSGQIPMKEgkvvFEGKVPdKQSLDEARDAAKICIINGLAQLKANLGSldkitkFVRISGFVNSNPEFTEQPKVINAA 112
                    789**********************9755555555554445555556677799999999999999888988899********************** PP

                    SSSS......TS--EEEEEE-SBSGGG-SEEEEEEEE CS
  Ribonuc_L-PSP  90 fdel......keaParsaveVaaLpkgakvEIeaiav 120
                    +d l      +  + r av+Va+Lp +  vEI+++++
     AJA92711.1 113 SDLLveifgdMAKHSRIAVGVASLPLNSTVEIDMVVE 149
                    ***9999995378*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1091.62
//
Query:       AJA92712.1  [L=690]
Description: proton-translocating NADH-quinone oxidoreductase, chain L [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-60  203.0  33.3    2.8e-54  184.3  27.9    2.9  3  Proton_antipo_M  Proton-conducting membrane transporter
    1.4e-12   47.5   1.8    1.4e-12   47.5   1.8    3.0  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
     0.0017   18.0   0.1       0.35   10.5   0.0    2.4  2  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
  ------ inclusion threshold ------
      0.035   13.7   6.8      0.084   12.5   0.1    4.0  4  Oxidored_q2      NADH-ubiquinone/plastoquinone oxidoreductase
       0.65    9.3   2.6       0.63    9.3   0.4    1.9  2  ApoL             Apolipoprotein L


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.2       1.5   5.4e+03     116     152 ..      89     124 ..      84     131 .. 0.55
   2 !   20.8   0.0     5e-08   0.00018       1      31 [.     138     168 ..     138     174 .. 0.92
   3 !  184.3  27.9   7.7e-58   2.8e-54      32     293 .]     188     463 ..     177     471 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.5
  Proton_antipo_M 116 vsallAatlvkagvlllirlllllavssneisqllli 152
                       s++++ ++  ++ l+++  +  ++  +++i+ ++++
       AJA92712.1  89 LSVIMSNVVGWISFLIMCYSTGYMK-GDKDITRFWFW 124
                      5666655555555555554333333.55555555555 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5e-08
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpks 31 
                      +++Ll++++g+E+v+l++y Li +w++++k+
       AJA92712.1 138 SDNLLQVFFGWEGVGLASYALISFWYRDKKK 168
                      79************************99886 PP

  == domain 3  score: 184.3 bits;  conditional E-value: 7.7e-58
  Proton_antipo_M  32 leAslklflltllgsliLLlgilllynltgtlefeelskal...elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.A 121
                      ++A++k+f++t +g++++L g+lll+ ++gt  f+el+  +     + ++  l+ +++ll+ g++ Ksaq+pl+ Wl +a + +Pt+vsal+ A
       AJA92712.1 188 THAGMKAFIMTKVGDVMMLSGMLLLFMFAGTFGFRELVGDTawaVEMSAQGLLVPAFVLLFGGAMGKSAQFPLNEWLLEA-MTGPTAVSALIhA 280
                      68***********************************98876776777777888899***********************.************* PP

  Proton_antipo_M 122 atlvkagvlllirllllla...vssneisq...lllilaiismllgslvalaqtdiKrllAySsishlGymlialav.....atqygveaaiih 204
                      at+vkagv+l++r+ ++++    ++  + q   +++++++i++ll ++ +++  +iK++lAyS+ s++Gym++al+v     + ++g++a ++h
       AJA92712.1 281 ATMVKAGVFLVARIGPIVFalaAAGILADQffeIVAWVGAITALLLATQGMVNPEIKKVLAYSTGSQIGYMMLALGVaglshQYVDGYTAGFFH 374
                      *************9888776654444445511156788999**********************************99554444468******** PP

  Proton_antipo_M 205 llthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPpt.agFlskfliLeaavavslillvlavvasvlt 293
                      l++ha+fka+lF++ags+ +  + +r ++++ggL k m  +++ +  + l+l+G P+  +gF+sk++i++ +++ +  +++ +++ +vlt
       AJA92712.1 375 LISHAMFKASLFMAAGSLLH-VVGSRFMTDMGGLKKQMKKTYAFMWAAGLGLMGAPFItTGFWSKDAIFATVYESGNEWALPLFIIAVLT 463
                      *****************955.569********************************9669*************99888777665555554 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   1.8   3.9e-16   1.4e-12       4      57 ..      74     125 ..      72     126 .. 0.89
   2 ?   -1.8   0.2      0.95   3.4e+03      25      43 ..     350     368 ..     346     375 .. 0.80
   3 ?   -3.1   0.1       2.4   8.7e+03      29      41 ..     593     605 ..     593     606 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 3.9e-16
  Proton_antipo_N   4 WlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                      W++   + ++ g+l D+ls++m  vv ++s+l++ YS+gYM++d+ ++RF + +
       AJA92712.1  74 WID--AIGLKAGVLADPLSVIMSNVVGWISFLIMCYSTGYMKGDKDITRFWFWM 125
                      444..445899***************************************8765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.95
  Proton_antipo_N  25 mllvvtfvsllvhlYSigY 43 
                      ++++  +v+ l h Y  gY
       AJA92712.1 350 YMMLALGVAGLSHQYVDGY 368
                      6788888999999888888 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.4
  Proton_antipo_N  29 vtfvsllvhlYSi 41 
                      v fv + + +YS+
       AJA92712.1 593 VKFVNSNIFFYSM 605
                      6799999****97 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0051        18      76     115 ..     428     467 ..     406     482 .. 0.83
   2 !   10.5   0.0   9.7e-05      0.35      82     125 ..     485     529 ..     469     549 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0051
  Proton_antipo_C  76 rsfititefenkktlsyPhEsdntmlfpllvLvlftlfvG 115
                       +fit+   ++ + + + +Es n   +pl++++++t ++ 
       AJA92712.1 428 APFITTGFWSKDAIFATVYESGNEWALPLFIIAVLTAIIT 467
                      578888888888899*********************9885 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.7e-05
  Proton_antipo_C  82 tefenkk.tlsyPhEsdntmlfpllvLvlftlfvGliGipfnqeg 125
                      +++e+ + + +  hE++++m +p  +L+++t+ +GliG + ++e 
       AJA92712.1 485 KHIEKMEsEGHHIHEAPKSMWIPYGILAVLTIGIGLIGLSAEEEL 529
                      45555332447779************************9877543 PP

>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.3e-05     0.084       7      48 ..     124     166 ..     119     198 .. 0.86
   2 ?   -2.2   0.1      0.87   3.1e+03      32      47 ..     204     219 ..     192     248 .. 0.64
   3 ?    2.2   0.1     0.039   1.4e+02      55      81 ..     446     472 ..     375     488 .. 0.76
   4 ?   -1.2   0.0      0.44   1.6e+03       4      19 ..     510     525 ..     507     531 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                  HHHHHHHHHHHHH.SSCCHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Oxidored_q2   7 allfliGlygvll.rrnllkvliglelisnavnlllvlagvft 48 
                   ++f+iG + +++ ++nll+v++g e +++a + l+  + + +
   AJA92712.1 124 WMMFFIGSMQLIIlSDNLLQVFFGWEGVGLASYALISFWYRDK 166
                  57899999988888*******************9998876654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.87
                  HHHHHHHHHHHHHHHH CS
  Oxidored_q2  32 lisnavnlllvlagvf 47 
                  ++++++ ll++ ag f
   AJA92712.1 204 MMLSGMLLLFMFAGTF 219
                  4455555555555544 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.039
                  .......TTSCGGHHHHHHHHHHHHHH CS
  Oxidored_q2  55 tnpatefadplpqalvLtaivigaaet 81 
                   ++ +e a pl  + vLtai  ++ +t
   AJA92712.1 446 YESGNEWALPLFIIAVLTAIITAFYTT 472
                  456677788888888899988887766 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.44
                  HHHHHHHHHHHHHHHH CS
  Oxidored_q2   4 lliallfliGlygvll 19 
                  +l++l ++iGl+g+ +
   AJA92712.1 510 ILAVLTIGIGLIGLSA 525
                  6788999999999875 PP

>> ApoL  Apolipoprotein L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.32   1.1e+03     217     264 ..     378     425 ..     375     426 .. 0.90
   2 ?    9.3   0.4   0.00018      0.63     118     139 ..     561     582 ..     554     588 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
        ApoL 217 rlvakakrllttgrisaqsakqvqkafggtalamtkgarilgaatagv 264
                 + + ka+ ++++g++    +++  + +gg + +m+k   ++ aa+ g+
  AJA92712.1 378 HAMFKASLFMAAGSLLHVVGSRFMTDMGGLKKQMKKTYAFMWAAGLGL 425
                 66789999*****************************99999998886 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00018
        ApoL 118 aLAPvtaGlSLvLsatGlgLGa 139
                 +L Pv+ G+SLv  atG+gLG 
  AJA92712.1 561 GLNPVALGASLVAFATGFGLGY 582
                 599******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4606.08
//
Query:       AJA92713.1  [L=217]
Description: putative endonuclease III [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-25   89.1   0.1    3.5e-25   88.6   0.1    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    5.9e-09   35.4   0.0    1.7e-08   33.9   0.0    1.9  1  HHH            Helix-hairpin-helix motif
     0.0015   17.9   1.4     0.0046   16.3   1.4    1.8  1  AGOG           N-glycosylase/DNA lyase
     0.0023   18.5   0.6          1   10.0   0.0    2.4  2  HHH_5          Helix-hairpin-helix domain
     0.0054   16.7   0.0      0.018   15.1   0.0    1.7  2  DUF2400        Protein of unknown function (DUF2400)
  ------ inclusion threshold ------
      0.043   13.7   0.1      0.057   13.3   0.1    1.3  1  DUF5092        Domain of unknown function (DUF5092)
      0.088   12.9   0.0        7.5    6.7   0.0    2.3  2  HHH_2          Helix-hairpin-helix motif
       0.26   11.7   3.4       0.44   10.9   3.4    1.4  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.1   1.6e-28   3.5e-25       1     107 [.      39     173 ..      39     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.6e-28
                 HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH...............................S- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............................xx RF
     HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv...............................gk 68 
                 +++ils++t+de+++ri+++lf+ ++  ++ +l +a   +++++i+++Gfy+ Ka++i+e+A+i+                                ++
  AJA92713.1  39 IGTILSARTKDESTTRIVKDLFKVYK--NARQLSKAKLRDVEKIIKSIGFYHVKAERIIEVAKIIDskykgkvpddleklialpgvgrktancvlvyAY 135
                 789*********************99..*********************************************************************99 PP

                 SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  69 pdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                   ++i+vD+hv+ri +rl+++k+ kt++++e++l+e ++
  AJA92713.1 136 EIPAIPVDIHVHRISNRLGLVKT-KTPEETEFALMEKIP 173
                 99*********************.6***********987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   7.8e-12   1.7e-08       1      30 []     104     133 ..     104     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 7.8e-12
                 SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
         HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                 +++g +p+++e L alPGVG+ktA+++l y
  AJA92713.1 104 KYKGKVPDDLEKLIALPGVGRKTANCVLVY 133
                 589************************976 PP

>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.4   2.1e-06    0.0046     157     212 ..     126     181 ..      41     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                 HHTS-----TTS-.----HHHHHHHHHTTS-SS-HHHHHHTHCCHCS.HHHHHHHHH CS
        AGOG 157 algeeiplpfeip.iPvDvRiakltktsglielknekklarkelvqeevieaWkevs 212
                 +++    ++ eip iPvD  +++++   gl+++k+ ++ ++  l++++++++W +v 
  AJA92713.1 126 TANCVLVYAYEIPaIPVDIHVHRISNRLGLVKTKTPEE-TEFALMEKIPKKYWLDVN 181
                 55566789999998*******************99988.7788999*******9986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.2    0.0062        14      24      56 ..      64      99 ..      53     100 .. 0.71
   2 !   10.0   0.0   0.00046         1      33      48 ..     112     127 ..     105     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0062
                -SHHHHHHS...-HHHHHTSTTS-HHHHHHHHHHHH CS
       HHH_5 24 esvedlaaa...dveeLakipGiGkktAeriilelk 56
                +   +l +a   dve++ k  G+   +Aerii+ +k
  AJA92713.1 64 KNARQLSKAklrDVEKIIKSIGFYHVKAERIIEVAK 99
                3344444444459***99999***********9876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00046
                 -HHHHHTSTTS-HHHH CS
       HHH_5  33 dveeLakipGiGkktA 48 
                 d e+L ++pG+G ktA
  AJA92713.1 112 DLEKLIALPGVGRKTA 127
                 5677888888888887 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.73   1.6e+03      77     100 ..      52      75 ..      27     118 .. 0.60
   2 !   15.1   0.0   7.8e-06     0.018     173     195 ..     140     162 ..     136     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.73
     DUF2400  77 llallkalkelleksgsLeeaflk 100
                 ++ ++k l +++++  +L +a l+
  AJA92713.1  52 TTRIVKDLFKVYKNARQLSKAKLR 75 
                 444444444444444444444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.8e-06
     DUF2400 173 iPlDvHvarvarklgllkrkqad 195
                 iP+D+Hv+r++++lgl+k+k+ +
  AJA92713.1 140 IPVDIHVHRISNRLGLVKTKTPE 162
                 8****************999865 PP

>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.5e-05     0.057      48     104 ..      54     109 ..      51     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
     DUF5092  48 elnkvlFevvieserrllhrkkvkdPlnnmkIkqvyyYkltveel...dralveyffkea 104
                  + k lF+v   ++ r+l+  k++d   ++ Ik + +Y+++ e +   ++++ ++++ ++
  AJA92713.1  54 RIVKDLFKV--YKNARQLSKAKLRD--VEKIIKSIGFYHVKAERIievAKIIDSKYKGKV 109
                 68899****..9*************..78899*********9875111556666665554 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.026        58      17      40 ..      57      80 ..      53      99 .. 0.84
   2 ?    6.7   0.0    0.0033       7.5      33      53 ..     112     132 ..     110     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.026
       HHH_2 17 klLakrFksldaLkkasleeLlev 40
                k+L k +k+  +L+ka+l +  ++
  AJA92713.1 57 KDLFKVYKNARQLSKAKLRDVEKI 80
                7899*************9999875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
       HHH_2  33 sleeLlevddiGeeiAqsive 53 
                 +le+L++++++G ++A+ +  
  AJA92713.1 112 DLEKLIALPGVGRKTANCVLV 132
                 589*************99975 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.4    0.0002      0.44       1      17 []     192     208 ..     192     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                    C++ +P Ce C +++ C
     AJA92713.1 192 CKPISPMCEVCKIRNGC 208
                    *************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1664.17
//
Query:       AJA92714.1  [L=189]
Description: KH domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   40.8   9.2    6.3e-06   25.9   2.6    2.3  2  KH_1      KH domain
  ------ inclusion threshold ------
       0.12   11.9   0.0       0.17   11.3   0.0    1.1  1  Pox_M2    Poxvirus M2 protein
       0.22   11.3   4.5       0.37   10.6   0.6    2.4  2  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   2.6   1.1e-09   6.3e-06       4      52 ..       7      49 ..       4      65 .. 0.83
   2 !   18.8   0.5   1.8e-07     0.001      11      65 ..     107     153 ..      99     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
                EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE CS
        KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG 52
                i +P + +g iIGk G++ ++I++++ +  +++ se       ev i+ 
  AJA92714.1  7 IRIPVDRIGVIIGKSGKTKHQIEKKCHVDLNID-SET-----GEVIITS 49
                68**********************888888866.544.....5677765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.8e-07
                 HHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
        KH_1  11 vgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                  griIG +G    ++++ tgakI v  +       r+v i+G+p++   A+++i+
  AJA92714.1 107 KGRIIGENGTARLNMENLTGAKISVY-G-------RTVGIIGEPNQLRMAVDAIS 153
                 69**********************87.4.......89***************997 PP

>> Pox_M2  Poxvirus M2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.17      16      81 ..      16      81 ..      13      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
      Pox_M2 16 lviGlnydiketieeeckideryidknstivltGyGleinltitevtkrlvaaaeGvgkdnklsil 81
                ++iG + + k+ ie++c++d + + ++ ++++t   ++ n+   +  + + a   G+  +n l +l
  AJA92714.1 16 VIIGKSGKTKHQIEKKCHVDLNIDSETGEVIITSDKIDGNISPFKAVEIVSAMGRGFSPENSLRLL 81
                5789999999***************************99999988888899999999999998765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   6.2e-05      0.37      34      58 ..      12      36 ..       7      55 .. 0.79
   2 ?    1.8   0.2     0.035   2.1e+02      36      45 ..     107     116 ..     104     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.2e-05
                SCHHHHHTGGGHHHHHHHHHHHHHH CS
        KH_2 34 sqpgivIGkgGsnikkigkelrkdi 58
                 + g++IGk G++  +i+k+   d+
  AJA92714.1 12 DRIGVIIGKSGKTKHQIEKKCHVDL 36
                589***************9976666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.035
                 HHHHHTGGGH CS
        KH_2  36 pgivIGkgGs 45 
                 +g++IG +G 
  AJA92714.1 107 KGRIIGENGT 116
                 8999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1317.39
//
Query:       AJA92715.1  [L=249]
Description: phosphoribosyl transferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-08   34.6   0.0    2.1e-08   33.8   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    5.8e-05   22.5   0.1    7.9e-05   22.0   0.1    1.2  1  PRTase_3      PRTase ComF-like
    0.00012   21.7   0.1    0.00018   21.1   0.1    1.2  1  PRTase_2      Phosphoribosyl transferase
     0.0091   15.5   0.1      0.015   14.7   0.1    1.5  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.7e-12   2.1e-08      39     119 ..     149     241 ..     147     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.7e-12
                   TTHHHHHHHHHHS......TT-EE-EEEEEE-TTT--EE..............EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEE CS
  Pribosyltran  39 gGvpfakiladeL......evplayvrkvkyrpdgseeaargssdes......rlledpagkkVliVDDildtGgTllaalelLkekgpeevr 119
                    ++ fa+++++ L      +  l+ + k+k+ + ++ ++ + +s+          ++++ gkk+l+VDD l++G+T  + +elLk+ g+e+v 
    AJA92715.1 149 NAYAFANEIHRILqnegheTKLLDCIKKTKKIKIQKLTTEEEISEAVndlfavDEETNLTGKKILLVDDNLTSGNTAGKCAELLKNNGAEIVW 241
                   5899*********999876555888888888888888887666655599*****************************************885 PP

>> PRTase_3  PRTase ComF-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.1   1.8e-08   7.9e-05      77     174 ..     150     244 ..     103     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.8e-08
    PRTase_3  77 reyfvaeLnryLaaenakpvlkvklhraatksedygslsaedreklilndkyhidke.rlkgktlifldDiritgshedkirkslkeeklendivflYl 174
                  ++f +e+ r L +e+ ++ l   + +  tk+ +  +l +e+  +   nd + +d+e +l+gk ++  dD  ++g+++ k  ++lk++++  +iv +++
  AJA92715.1 150 AYAFANEIHRILQNEGHETKLLDCIKK--TKKIKIQKLTTEEEISEAVNDLFAVDEEtNLTGKKILLVDDNLTSGNTAGKCAELLKNNGA--EIVWVFV 244
                 567889999999888877765444443..5677888999999999999*******86479**************************9998..6666655 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   3.9e-08   0.00018      79     147 ..     168     235 ..     149     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-08
    PRTase_2  79 alylhtTRekvagveelleFeEeHSHAtdhllyaedeellaaakelvLvDDEistGktalnliralqek 147
                 +++l   +++ + + + l+ eEe S A++ l+   +e+ l++ k+++LvDD +++G+ta + ++ l+++
  AJA92715.1 168 TKLLDCIKKTKKIKIQKLTTEEEISEAVNDLFAVDEETNLTG-KKILLVDDNLTSGNTAGKCAELLKNN 235
                 555555555555556778889*********999888887776.569*************9998887766 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   3.4e-06     0.015      79     154 ..     164     242 ..      61     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-06
     UPRTase  79 egmeealrellpearvghl.glqreeetlepveyynkLPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekI 154
                 eg+e +l++++++ + +++ +l +eee  e+v  +  + ++   + +++ll+D  + +G++a ++ +lLk++g++   +
  AJA92715.1 164 EGHETKLLDCIKKTKKIKIqKLTTEEEISEAVNDLFAVDEETnlTGKKILLVDDNLTSGNTAGKCAELLKNNGAEIVWV 242
                 488899999998874444413455555555665555555555558889***********************99864444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1221  (0.068102); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1800.13
//
Query:       AJA92716.1  [L=96]
Description: ribosomal protein S26e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-22   80.2   2.4    1.6e-22   80.0   2.4    1.0  1  Ribosomal_S26e   Ribosomal protein S26e
  ------ inclusion threshold ------
       0.03   14.3   1.9       0.18   11.9   0.1    2.0  2  zinc_ribbon_11   Probable zinc-ribbon
      0.053   13.5   0.1        2.7    8.0   0.0    2.4  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
      0.064   13.6   0.3       0.97    9.9   0.1    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   2.4   3.6e-26   1.6e-22       1      97 [.       1      93 [.       1      95 [. 0.94

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.6e-26
                    X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTTSS----TTTTS--S- CS
  Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihskvvrvRsredrknrep 97
                    m+ KR ++gr k g+g+  +v+C nc+ +vpkdKa k +   ++ve++ +++l+ + +y   + Pk+  ++ yc+scaih kv++ Rs+++r+ +++
      AJA92716.1  1 MPLKRASRGRRKGGKGSSGTVQCVNCGGTVPKDKAKKVTSRVSLVEHQLAKELRAQGAYI--SAPKV--TKWYCISCAIHFKVLKIRSADQRRRHTK 93
                    99******************************************************9985..57996..789********************98875 PP

>> zinc_ribbon_11  Probable zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2     0.022        97      23      43 ..      15      35 ..       6      49 .. 0.76
   2 ?   11.9   0.1   3.9e-05      0.18      88     111 ..      58      81 ..      31      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.022
  zinc_ribbon_11 23 klnrqdvlcvscgctltlqrg 43
                    k + + v cv cg t+  ++ 
      AJA92716.1 15 KGSSGTVQCVNCGGTVPKDKA 35
                    56678999*****99876655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.9e-05
  zinc_ribbon_11  88 adyalpkvrkwycvlcdedyegkk 111
                     a  + pkv kwyc+ c  +++  k
      AJA92716.1  58 AYISAPKVTKWYCISCAIHFKVLK 81 
                     344689**********98877655 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00061       2.7       2      18 ..      17      35 ..      16      40 .. 0.77
   2 ?    3.1   0.1      0.02        90      26      31 ..      69      74 ..      66      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00061
  zf-dskA_traR  2 iygs..CeeCGEpIpeaRl 18
                  + g+  C  CG ++p  + 
    AJA92716.1 17 SSGTvqCVNCGGTVPKDKA 35
                  5677789999999998876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.02
  zf-dskA_traR 26 lCveCq 31
                  +C++C+
    AJA92716.1 69 YCISCA 74
                  8****8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00022      0.97      16      37 ..       9      35 ..       3      56 .. 0.60
   2 ?    3.3   0.0     0.024   1.1e+02      11      35 ..      40      74 ..      39      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
  Lar_restr_allev 16 ersqrvvaeigq....cvyCadCga......s 37
                     +r++++     +    +v+C +Cg       +
       AJA92716.1  9 GRRKGG-----KgssgTVQCVNCGGtvpkdkA 35
                     333333.....34445********95443330 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.024
  Lar_restr_allev 11 gravlersqrvvaeigq.............cvyCadCg 35
                     +r  l+++q+ ++ ++q             c++C    
       AJA92716.1 40 SRVSLVEHQLAKELRAQgayisapkvtkwyCISC---A 74
                     5677888888888888888888888885556666...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 691.29
//
Query:       AJA92717.1  [L=354]
Description: putative chlorophyll synthesis pathway protein BchC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-31  107.2   0.5    5.9e-31  106.6   0.5    1.3  1  ADH_N            Alcohol dehydrogenase GroES-like domain
    6.4e-28   97.3   0.1    9.5e-28   96.8   0.1    1.2  1  ADH_zinc_N       Zinc-binding dehydrogenase
    1.8e-11   45.2   0.0    2.9e-11   44.6   0.0    1.3  1  ADH_zinc_N_2     Zinc-binding dehydrogenase
    8.1e-08   32.0   0.1    2.7e-07   30.3   0.1    1.7  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
    0.00023   20.9   0.1    0.00043   20.0   0.1    1.3  1  Urocanase        Urocanase Rossmann-like domain
  ------ inclusion threshold ------
      0.013   16.2   0.4      0.044   14.4   0.4    2.0  1  PglD_N           PglD N-terminal domain
      0.019   14.3   0.2      0.029   13.7   0.2    1.2  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.053   13.1   0.2       0.08   12.5   0.2    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.06   13.1   0.2      0.091   12.5   0.2    1.2  1  Methyltransf_16  Lysine methyltransferase
      0.077   13.2   0.0       0.13   12.4   0.0    1.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.12   11.9   0.1        0.2   11.2   0.1    1.3  1  MTS              Methyltransferase small domain
       0.13   12.2   0.0        2.7    7.9   0.0    2.5  2  SIS              SIS domain


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.5   3.9e-34   5.9e-31       2     104 ..      29     143 ..      28     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.9e-34
                 TEEEEEEEEEEE-HHHHHHHTTS..........TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE..-SSSHHHHTT-GGG-TTBEETT CS
       ADH_N   2 gevlikvkaagiCgsDlhilkgg..........kelevklplilGHEivGeveevgpevkklkvGdrVvveplis..cgeCaaCkegeenlCeeakllg 88 
                 +evlikv ++g+C+sDlh+++gg          ++  vk+p+++GHE+vG++e++g++v+++k+Gd+V+v+p+i     eC +Ck+g++nlCe+ + lg
  AJA92717.1  29 TEVLIKVISTGVCHSDLHLWEGGydtgdgfmkvTDRGVKFPVTPGHEVVGTIEKIGDSVQDVKIGDNVLVYPWIGpkNCECTSCKKGDTNLCETPQSLG 127
                 69*******************************9****************************************94456699***************** PP

                 TSS-SSSBSEEEECGG CS
       ADH_N  89 vsldGgfaeyvvvpek 104
                 v +dGg+ae++++p+ 
  AJA92717.1 128 VFQDGGYAEKIIIPDY 143
                 ************9964 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.1   6.4e-31   9.5e-28       1     128 [.     189     316 ..     189     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 6.4e-31
                 HHHHHHHHHHH.HTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEEEE CS
  ADH_zinc_N   1 gvGlaavqlAk.alGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeeefd 98 
                 g+Gl++vqlA  ++++++i++d+++ekl+ ak+lGa+ vin+ke d +++i ++++++gvd ++++v+++ t++  l++++++G + +vG+++g  +++
  AJA92717.1 189 GLGLMGVQLAShMAKCKIICADIDDEKLKTAKELGATDVINTKESDASQKIMSICNEKGVDSIVDFVNAPPTVKLDLSVIRKRGNIILVGLFGGSVDLP 287
                 89*********67788**************************777**********************************************999999** PP

                 HHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
  ADH_zinc_N  99 lrnlllkeksilGsllgslreefkealdll 128
                 l  + lk ++i+G   g+  +++ e+++l+
  AJA92717.1 288 LVSVPLKAITIQGAYTGN-YKDMVELIELA 316
                 ******************.78888899886 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.9e-14   2.9e-11       1     133 []     222     352 ..     222     352 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-14
                   TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHH CS
  ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileel 93 
                   lGA+ vi+ ++ d+     +  +++gvD ++d v+ + +++  l+v++++G ++ +g    s +l+ ++     ++++++     + +  +d + el
    AJA92717.1 222 LGATDVINTKESDASqkimSICNEKGVDSIVDFVNAPPTVKLDLSVIRKRGNIILVGLFGGSVDLPLVSV--PLKAITIQGAY--TGN-YKD-MVEL 312
                   8******99988888799888889***********88888*******999***99984223333333333..34455555555..345.899.**** PP

                   HHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2  94 aalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                    +l ++G ++p v+++++l+ea  A+++l++++  G+ V+
    AJA92717.1 313 IELAKQGVINPIVSKHYTLDEATGALDDLKNRKILGRAVI 352
                   *********************************9999886 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   1.8e-10   2.7e-07      18     201 ..     166     340 ..     154     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.8e-10
  Glu_dehyd_C  18 elaeasrsafewepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.dsretpvd.eipe..aseemdlvvEaTGsa 111
                     +a+++a   +pes l++GaG lGL+  ++l+++  + + + + +    +d +++  +elGat v +++e++ + +i +   ++ +d +v+   ++
   AJA92717.1 166 TAYTAIKKALVNNPESILIVGAGGLGLMG-VQLASHMAKCK-IICAD---IDDEKLKTAKELGATDViNTKESDASqKIMSicNEKGVDSIVDFVNAP 258
                  556778899999*****************.55655434443.55555...678899999******76355544333134331146789********** PP

  Glu_dehyd_C 112 khafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfed 201
                  + +   ++ ++  G ++L+G+  +s v++   +    + l+   + G   a + +++  v+ ++ +++ +++ +v+k ++lde++ A +d
   AJA92717.1 259 PTVKLDLSVIRKRGNIILVGLFGGS-VDLPLVS----VPLKAITIQG---AYTGNYKDMVELIELAKQGVINPIVSKHYTLDEATGALDD 340
                  *********************9887.4444333....3355666666...5667789999999999999999999999999999999876 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.9e-07   0.00043      15     100 ..     169     252 ..     164     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                 HHHHHHST.T--TT-EEEEE.--STTGGGHHHHHHHTT-EEEEEES-HHHHHHHHHTTS-SEEES-HHHHHHHHHHHHHCT--EEEE CS
   Urocanase  15 naarkklgkgdlkgklvvta.GlGgMsgaQplAatiagavalvvevdesriekrleqgyvdevaddldealalikeakkekealsig 100
                  a +k l  ++ +  l+v a GlG M+  Q lA ++a++ ++++++d++++++  e g  d + ++  +a ++i +  +ek + si 
  AJA92717.1 169 TAIKKALV-NNPESILIVGAgGLGLMG-VQ-LASHMAKCKIICADIDDEKLKTAKELGATDVINTKESDASQKIMSICNEKGVDSIV 252
                 56666666.677788888762577776.45.9****************************************999999999988886 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   2.9e-05     0.044       2      46 ..     182     230 ..     181     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
      PglD_N   2 ivIiGaGGhgkvvadiieangeyeiig.flDdnk.kt.eveg.ypvlgk 46 
                 i+I+GaGG g +  +++ ++ + +ii+  +Dd+k kt ++ g   v+ +
  AJA92717.1 182 ILIVGAGGLGLMGVQLASHMAKCKIICaDIDDEKlKTaKELGaTDVINT 230
                 99*********************99974688876222122232444433 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.9e-05     0.029      27      84 ..     178     234 ..     163     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                  ---EEEEESTSHHHHHHHHHHHHT.T-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHH CS
  AlaDh_PNT_C  27 epakvlviGgGvaGlqAiatakgl.gakVtvlDvrparleqleslgakfvevlksqeel 84 
                  +p  +l++G+G  Gl  ++ a+ + + k+   D++ ++l+  ++lga+   v++ +e+ 
   AJA92717.1 178 NPESILIVGAGGLGLMGVQLASHMaKCKIICADIDDEKLKTAKELGATD--VINTKESD 234
                  67889*****************993469999*************99984..33333333 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.4e-05      0.08       3      41 ..     182     221 ..     180     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.4e-05
                     EEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCT CS
  UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeig.hevigvDideekvdklns 41 
                     i ++G+G +Gl+   + +++   ++i+ Did+ek ++ ++
      AJA92717.1 182 ILIVGAGGLGLMGVQLASHMAkCKIICADIDDEKLKTAKE 221
                     889****99998766666665789**********998775 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.1e-05     0.091      46      81 ..     178     214 ..     156     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.1e-05
  Methyltransf_16  46 sklsvlELGsGt.GlvGlavaellpeakviltDleel 81 
                      ++ s+l +G+G+ Gl+G+ +a+++ ++k+i +D+++ 
       AJA92717.1 178 NPESILIVGAGGlGLMGVQLASHMAKCKIICADIDDE 214
                      6778999999755*********************984 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.6e-05      0.13       3      71 ..     186     250 ..     184     274 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.6e-05
                    EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHH CS
  NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavde 71 
                    g  GlG MG ++a++++k  +k+++ + + ek++++ + ga+ + + +e  as +  i+ + ++k vd+
     AJA92717.1 186 GAGGLGLMGVQLASHMAK--CKIICADIDDEKLKTAKELGATDVINTKESDASQK--IMSICNEKGVDS 250
                    667*************86..67888888888888888888554444443332222..223333344444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00013       0.2      34     101 ..     181     251 ..     163     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                 EEEEET-.TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEE CS
         MTS  34 kvlDlGc.GaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdli 101
                 ++l +G+ G G++g++la++  + ++ + d+d + l+ ake  ++  ++   +   + +++  +ek +d i
  AJA92717.1 181 SILIVGAgGLGLMGVQLASHMAKCKIICADIDDEKLKTAKELGATDVINtkESDASQKIMSICNEKGVDSI 251
                 4666777369*****************************98776666543222233334444445555555 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0018       2.7       4      40 ..     178     214 ..     175     223 .. 0.89
   2 ?    1.2   0.0      0.21   3.1e+02      61      84 ..     301     324 ..     287     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                 TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEH CS
         SIS   4 kakriyvlGaGtsyaiakelalkleeiggivveveda 40 
                 + ++i+++GaG  + ++  la ++++ + i+++++d+
  AJA92717.1 178 NPESILIVGAGGLGLMGVQLASHMAKCKIICADIDDE 214
                 5679***********************9999998876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.21
                 ESSSHHHHHHHHHHHHHHTTSEEE CS
         SIS  61 sfsgetkdlvaaaelakergakii 84 
                 +++g+ kd+v+++elak+   ++i
  AJA92717.1 301 AYTGNYKDMVELIELAKQGVINPI 324
                 599**************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2419.50
//
Query:       AJA92718.1  [L=115]
Description: hypothetical protein T478_0802 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.036   12.8   0.0      0.041   12.6   0.0    1.0  1  Herpes_UL21  Herpesvirus UL21


Domain annotation for each model (and alignments):
>> Herpes_UL21  Herpesvirus UL21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-06     0.041     346     414 ..      34     104 ..      20     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-06
                  HHHHHHHHHHHHXXBXTTXSHHHHHHHHHHHHHHHXXXXXX...TTSXXHHHHHHHHHHHHHHHHHHHHHHH CS
  Herpes_UL21 346 plqklvvlqyilsreralncydvieeLvdrytsrielevPs...pDdtvlaDainsLlrevlflGtaaeill 414
                   ++k+ +l y + +++ l +y++i  Lvd     ie    +    Dd +l D +n L++++++ G +   l+
   AJA92718.1  34 EIKKIELLEYKINKDQNLGTYSIITALVDTDQGLIEILYDEgyrGDD-ALNDSANMLIQNLGLSGLILRSLI 104
                  578999***********************999999887665554677.9*************9998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 669.20
//
Query:       AJA92719.1  [L=372]
Description: hypothetical protein T478_0044 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0094   16.0   0.1      0.028   14.5   0.1    1.8  1  Yopt      Hypothetical protein Yopt
  ------ inclusion threshold ------
       0.13   12.4   2.1       0.49   10.5   0.1    2.6  2  KH_8      Krr1 KH1 domain


Domain annotation for each model (and alignments):
>> Yopt  Hypothetical protein Yopt
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.1e-06     0.028      29      66 ..      87     124 ..      66     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-06
                 HHHHHHTTTT-SEEEEE-TTS-EEEEEEEEEEEEEEEE CS
        Yopt  29 vtricenlllskevsflkadGsvenfklsdmeyeitnt 66 
                 v  i  nlll  e  ++kadG  + f + d+e   t t
  AJA92719.1  87 VGEISSNLLLKGEKFYVKADGNPKGFVIKDLELASTST 124
                 678999*************************9887766 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   5.5e-05      0.49       3      46 ..       6      51 ..       4      61 .. 0.87
   2 ?    0.2   0.2      0.09     8e+02      13      43 ..     321     353 ..     318     367 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.5e-05
        KH_8  3 fevlfpk.yrekylkeveekikklleekklkl.evdlkerslkvsT 46
                ++v++p  + e+ +++  e+ikk+l+ kklk+ ++ +++  ++++ 
  AJA92719.1  6 LVVVYPSlFAENKINQLIENIKKILKIKKLKFaKITRDDFLICIQA 51
                68999976899********************846999999999986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.09
        KH_8  13 kylkeveekikkll..eekklklevdlkerslk 43 
                 ky+ ++e+ +k+ l  ++ klk + +  ++++k
  AJA92719.1 321 KYVPKIEKFLKSNLikSKSKLKNNEKTMKKIIK 353
                 566666666665553233333333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2225.69
//
Query:       AJA92720.1  [L=698]
Description: putative acetyl coenzyme A synthetase (ADP forming), alpha domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-78  263.6   0.6    2.1e-78  262.8   0.6    1.4  1  ATP-grasp_5    ATP-grasp domain
    2.7e-53  179.5   0.6      6e-53  178.4   0.6    1.6  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    7.9e-23   81.2   0.4    3.9e-22   78.9   0.1    2.3  3  CoA_binding_2  CoA binding domain
    1.3e-06   28.2   2.2    2.8e-06   27.0   2.2    1.6  1  ATP-grasp_2    ATP-grasp domain
    2.8e-06   27.9   0.7    1.6e-05   25.5   0.7    2.4  1  CoA_binding    CoA binding domain
    0.00072   18.7   0.1      0.002   17.3   0.1    1.7  1  Dak1_2         Dihydroxyacetone kinase family
  ------ inclusion threshold ------
       0.13   11.8   0.4        1.1    8.8   0.1    2.2  2  ATP-grasp      ATP-grasp domain
       0.23   11.6   4.0       0.62   10.2   0.1    3.3  3  DUF2540        Protein of unknown function (DUF2540)


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.8   0.6   9.4e-82   2.1e-78       2     221 ..     477     697 ..     476     698 .] 0.98

  Alignments for each domain:
  == domain 1  score: 262.8 bits;  conditional E-value: 9.4e-82
  ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkekspearieg 99 
                  a++++r+ L e+e +e+l+ayg+p++ ++la+s++eav+a ++igypvvlKi+sp+i+hK+d+gGv++nl++a++v++a+++i++++k+++++a i+g
   AJA92720.1 477 AKKQKRSALLEEEGQEILRAYGFPLPASKLAKSKKEAVAASKKIGYPVVLKIASPQIIHKSDAGGVKVNLQNAKDVENAFDTIIKNAKKYNKKADIKG 574
                  78999********************************************************************************************* PP

  ATP-grasp_5 100 vlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpe 197
                  vlV+em+k gg E+i+g++ +p FGpv+++G+GG++vevlkdv+++l+p+++ +a ++i+++k++k+l+gvrgek++d+++l+e+++rlsqLv+d+ e
   AJA92720.1 575 VLVVEMVK-GGKEMIIGSKLEPGFGPVVMLGMGGIYVEVLKDVTFRLAPMTNIEADDMISSIKTKKILEGVRGEKPSDIKKLSECIQRLSQLVSDFNE 671
                  ********.***************************************************************************************** PP

  ATP-grasp_5 198 IreldinPllvee..egvvalDarir 221
                  I+eld+nP+lv e  +g+ +lD+ri 
   AJA92720.1 672 IKELDMNPVLVMEknKGCKVLDVRIG 697
                  ***********886566*******96 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4   0.6   2.7e-56     6e-53       2     138 .]     154     292 ..     153     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 2.7e-56
  Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark..kpvvvlksGrseaga 96 
                   G+ial+sqSGa+++al++ a+++g+gfs v+s+Gn+ad+++ d+l++lae+++tkvi++ylE++++g++fl++++ ++rk  kpv+vlksGrs++ga
    AJA92720.1 154 GEIALVSQSGAICAALVEDASAQGIGFSAVISMGNKADMSEIDILKMLAEHKQTKVIVIYLEDMGNGQEFLKVCKDITRKkkKPVLVLKSGRSPEGA 250
                   99****************************************************************************88889************** PP

  Succ_CoA_lig  97 raaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                   +aa+shtgal+gsd+++da+++q+G++rvd++eelfd+a+++
    AJA92720.1 251 KAAMSHTGALMGSDEIYDALLKQSGAIRVDTMEELFDYATAF 292
                   **************************************9986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.1   1.8e-25   3.9e-22       1     114 [.      10     134 ..      10     135 .. 0.95
   2 ?   -2.3   0.0       2.8   6.3e+03      66      80 ..     164     178 ..     149     214 .. 0.62
   3 ?   -3.7   0.0       7.5   1.7e+04      68      98 ..     223     253 ..     199     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.8e-25
                    --EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT...... CS
  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpg...... 88 
                    ++ia++Gasd++g+ g+ +++++ +  +g +++p+ p++e+++ +k+y+s+ + p++vdl++v+t+ +++p++++e+++++ +++++  +      
     AJA92720.1  10 KSIAIIGASDKEGSVGRAITNNIMKgyKG-TIYPISPTRETVFDKKAYKSVLDVPGKVDLAVVVTKNTIVPAVLEECGKKKLRGAIVITAgfkevd 104
                    79***********************9999.**********************758**********************99998888777777***** PP

                    ....---HHHHHHHHHTT-EEE.ES-HHHH CS
  CoA_binding_2  89 ....sedeeaaelaeeagirvvgdrCilve 114
                          ++++ ++a++++++++g++C++v+
     AJA92720.1 105 eegaKLEQKLKDIAKKYKLQIIGPNCLGVM 134
                    ****************************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                    HHHGGGHHHHHHH-- CS
  CoA_binding_2  66 eatpeivkealalga 80 
                    ++++++v++a+a+g+
     AJA92720.1 164 AICAALVEDASAQGI 178
                    455555555555543 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.5
                    HGGGHHHHHHH--SEEEE-TT---HHHHHHH CS
  CoA_binding_2  68 tpeivkealalgakavwlqpgsedeeaaela 98 
                     +++ k++ +++ k v +  + +++e a++a
     AJA92720.1 223 FLKVCKDITRKKKKPVLVLKSGRSPEGAKAA 253
                    4555566666666666666666666655555 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   2.2   1.3e-09   2.8e-06       2     200 ..     485     680 ..     484     682 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.3e-09
                  E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEE.E--SSSTCCCTTCEEEE.SSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--EEE CS
  ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvK.aQvlaGGRGKagGvklv.kskeeakeaakellgkelvtkqtgkeGkkvekvlv 97 
                  l E +++eil+ yg + p +++a+s++ea +a kk+g  + v+K a  ++  +  agGvk+  ++++++++a ++++ +        ++   ++ vlv
   AJA92720.1 485 LLEEEGQEILRAYGFPLPASKLAKSKKEAVAASKKIGYPV-VLKiASPQIIHKSDAGGVKVNlQNAKDVENAFDTIIKNAK----KYNKKADIKGVLV 577
                  678899********************************99.77746666777999*****961555556655555554443....45667899***** PP

                  EE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHHHHHCT--C.HHHHHHHHHHHHHHHHHHHT.TEE CS
  ATP-grasp_2  98 eealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqareiakklglek.elvkkaakiikklyklfvel.dat 193
                   e+++  kE+ ++  l+    ++vv++  +GG+ +E + + +      ++i++   +++ ++++i++ ++ ek + +kk+++ i++l +l+ +  + +
   AJA92720.1 578 VEMVKGGKEMIIGSKLEPGF-GPVVML-GMGGIYVEVLKDVTFRLAPMTNIEADDMISSIKTKKILEGVRGEKpSDIKKLSECIQRLSQLVSDFnEIK 673
                  ****************8765.566666.58******9999999999999******************9877664789*************99852678 PP

                  EEEEEEE CS
  ATP-grasp_2 194 lvEiNPL 200
                   +++NP+
   AJA92720.1 674 ELDMNPV 680
                  8888886 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.7   7.1e-09   1.6e-05       3      96 .]       9      99 ..       8      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.1e-09
                 TEEEEEETTTSHHHHHH.HHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESST CS
  CoA_binding  3 dtkviviGagglgiagl.yhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviiteg 96
                 ++++++iGa+ +++ ++   + + +k g k  +++++p+   ++v + ++yksv +++ k  vd av+++ ++ + ++ +e+ +++ +g+++it+g
   AJA92720.1  9 PKSIAIIGASDKEGSVGrAITNNIMK-GYKgTIYPISPT--RETVFDKKAYKSVLDVPGK--VDLAVVVTKNTIVPAVLEECGKKKLRGAIVITAG 99
                 579***********999556666555.5555********..*******************..*******************************986 PP

>> Dak1_2  Dihydroxyacetone kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1     9e-07     0.002     113     212 ..     176     280 ..     144     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9e-07
      Dak1_2 113 kslgvdevieggqtmnPstedllkaiekvnakeviv..Lpnnkniilaaeqaaelaedk.n.vvviptktivqGlaallvfdper.sleenveamaeaa 206
                 ++ g++ vi+ g++++ s  d+lk + + ++ +viv  L +  n  + ++ +++++++k + v v+++   ++G  a++++  +    +e  +a+ ++ 
  AJA92720.1 176 QGIGFSAVISMGNKADMSEIDILKMLAEHKQTKVIViyLEDMGNGQEFLKVCKDITRKKkKpVLVLKSGRSPEGAKAAMSHTGALmGSDEIYDALLKQS 274
                 67899*************99*************99855678889999999999999988767*****************99988867777777777777 PP

      Dak1_2 207 kavktg 212
                 +a++++
  AJA92720.1 275 GAIRVD 280
                 777665 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00051       1.1       3      36 ..     496     529 ..     494     564 .. 0.72
   2 ?    1.6   0.1     0.081   1.8e+02      94     145 ..     531     582 ..     528     593 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                 TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEES CS
   ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKar 36 
                 + g+p+p   +++sk+e+ +a +++g+pvv+K +
  AJA92720.1 496 AYGFPLPASKLAKSKKEAVAASKKIGYPVVLKIA 529
                 67899***************************43 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.081
                 -EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEE CS
   ATP-grasp  94 pvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFv 145
                 p++ ++ + g ++++++ a+  e+a  ++ + akk  ++ ++ Gv+ vE+  
  AJA92720.1 531 PQIIHKSDAGGVKVNLQNAKDVENAFDTIIKNAKKYNKKADIKGVLVVEMVK 582
                 66677777888888999999889999999999*****************965 PP

>> DUF2540  Protein of unknown function (DUF2540)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.93   2.1e+03      28      45 ..     390     408 ..     386     421 .. 0.77
   2 ?   10.2   0.1   0.00028      0.62      25      59 ..     464     498 ..     460     502 .. 0.94
   3 ?   -0.2   0.2      0.49   1.1e+03      13      41 ..     542     570 ..     532     574 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                 HHHHHHHH.HS---EEEEE CS
     DUF2540  28 vetlkkak.eaekktkktl 45 
                  ++l++++    kk+kkt+
  AJA92720.1 390 YDKLAEVIvSMSKKYKKTM 408
                 5778775427899***997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00028
                 ---HHHHHHHHHS---EEEEEE--HHHHHHHHHHG CS
     DUF2540  25 nvdvetlkkakeaekktkktltLsdeEkkIvkklG 59 
                 nv+ +t+kk+ ++ kk k++  L +e ++I++ +G
  AJA92720.1 464 NVKKNTVKKILDNAKKQKRSALLEEEGQEILRAYG 498
                 78999**************************9998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.49
                 HHHHHHHGGG-----HHHHHHHHHS---E CS
     DUF2540  13 lRYllHklenlenvdvetlkkakeaekkt 41 
                 ++  l   +++en    ++k+ak+ +kk 
  AJA92720.1 542 VKVNLQNAKDVENAFDTIIKNAKKYNKKA 570
                 55566677888888888899999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.79u 0.33s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 4082.08
//
Query:       AJA92721.1  [L=195]
Description: 3-isopropylmalate dehydratase, small subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-35  121.5   0.0    4.3e-35  120.9   0.0    1.3  1  Aconitase_C    Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.014   15.1   0.0       0.25   10.9   0.0    2.1  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus
       0.21   11.4   2.0       0.31   10.8   0.2    1.9  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   7.2e-39   4.3e-35       1     128 [.       1     121 [.       1     124 [. 0.94

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 7.2e-39
                  CCCCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHH CS
  Aconitase_C   1 mekllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSRehAAkalr 98 
                  m+ + k + + t+ +k+nvdtd++ipkqf++ i++ g+g+ l++++r+n++ ++    k d++++  +y+  +++++v   +nfG+GSSRehA +al+
   AJA92721.1   1 MKPFSKINSIITPFDKANVDTDQIIPKQFLKLITKSGFGKFLFYDWRFNHDGKE----KDDFILNDLHYQ--NSQILVTN-ENFGCGSSREHAVWALK 91 
                  67788999999*************************************998875....66**********..88999888.***************** PP

                  HTTEEEEEES-B-HHHHHHHHHTT-EEEEE CS
  Aconitase_C  99 llGikaviaeSFerIfennliknglLplef 128
                  ++G+ ++i++SF++If++n +kng+Lp+ +
   AJA92721.1  92 DFGFDVIISPSFADIFYSNCFKNGVLPIIL 121
                  ***************************965 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.2e-05      0.25      46     140 ..      60     146 ..      48     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.2e-05
                    HHHHHTTSS-EEEEEEEEEES---THHHHHHHHHHSEEETTEEEEEE--EEEEEEE-HHHHHHHHHTT-EEEE---TT--T....T-EEEEETTTT CS
  Aconitase_2_N  46 ieelkkkgvplayvgdvvGtGssRksavnsvlWtigedipyvPnkraggvvlGgkiaPiFfntvedsGalpieadvsklet....Gdvieikpkeg 137
                    +++l+ +  ++   ++  G GssR  av    W++++            v++  + a iF++ +   G lpi +d++++++     d ie++ +++
     AJA92721.1  60 LNDLHYQNSQILVTNENFGCGSSREHAV----WALKDF--------GFDVIISPSFADIFYSNCFKNGVLPIILDIENIKKllkfKDKIELDLQSQ 143
                    6677777788888888888888888775....665532........2257899999*****************99998764111156666666666 PP

                    EEE CS
  Aconitase_2_N 138 kik 140
                    +i+
     AJA92721.1 144 TIN 146
                    665 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   5.2e-05      0.31      21      56 ..     124     160 ..     120     165 .. 0.90
   2 ?   -0.5   0.1      0.18   1.1e+03      21      42 ..     169     190 ..     168     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                    CHHHHCHCCCCCHH.HHCCCCHHHHHHHHHHHHHHHH CS
  Synaptobrevin  21 eNidkvlergekld.eLvdktenLqssaqqFkkqark 56 
                    eNi+k+l+ ++k++ +L+++t n  s++ +F+  +++
     AJA92721.1 124 ENIKKLLKFKDKIElDLQSQTINFGSESINFQIDSHR 160
                    9*************56****************98876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.18
                    CHHHHCHCCCCCHHHHCCCCHH CS
  Synaptobrevin  21 eNidkvlergekldeLvdkten 42 
                    ++id  l+ + k+++ ++ +++
     AJA92721.1 169 DDIDLTLKEDGKIENFEKNSSR 190
                    6788889999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1189.59
//
Query:       AJA92722.1  [L=216]
Description: phosphoserine phosphatase SerB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-12   48.2   0.0    3.1e-12   47.3   0.0    1.5  1  HAD          haloacid dehalogenase-like hydrolase
    9.8e-10   39.1   0.2    1.7e-08   35.0   0.2    2.1  1  Hydrolase    haloacid dehalogenase-like hydrolase
      3e-07   30.4   0.3    4.2e-05   23.4   0.1    2.6  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
    0.00098   18.7   0.0     0.0013   18.3   0.0    1.3  1  S6PP         Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0     7e-16   3.1e-12      47     187 ..      41     167 ..       3     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 7e-16
         HAD  47 lrldraglaelleallagls.eelaaelerfvaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelg 143
                 +++ ++gl + +e ll+g + e +++ ++ +        ++  ga+e+++  + aG++v  vSgg+ +++ +l +el+ d+v+ +el ++d +l+g   
  AJA92722.1  41 SINWEEGLIKRVE-LLKGIDfETCKQVADSLP-------IM-TGAREACQTLKNAGWKVMAVSGGFTIMTDRLKEELNLDHVYTNELIFKDgKLDGV-- 128
                 4444444444444.677777666666666666.......56.9******************************************************.. PP

         HAD 144 legkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                    k+  +++k+++ r   + e+++ + +e+v++ D+ +D++l+
  AJA92722.1 129 ---KINVDSDKAKSARV--KIEEWNVPKDEIVVIVDGANDIKLF 167
                 ...44444455566666..6699******************986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   3.8e-12   1.7e-08     109     204 ..      64     165 ..       1     168 [. 0.77

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.8e-12
                 HHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES.......STTTSHHHHHHHHHHHTSTGGGEEEEESS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 109 avftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet.......vakpspegkvaaireLqgkpeevamVGDg 199
                     +ad+l+++ +a+ea+++Lk ag++v  ++g++  + +r+ ++l+ d+ + +++   + +       v   + +  + +i+e ++++ e++++ Dg
  AJA92722.1  64 K--QVADSLPIMTGAREACQTLKNAGWKVMAVSGGFTIMTDRLKEELNlDHVYTNELIFKDGKldgvkinVDSDKAKSARVKIEEWNVPKDEIVVIVDG 160
                 3..4556666**************************************95555555555555523333336666************************* PP

                 HHHHH CS
                 xxxxx RF
   Hydrolase 200 vnDaa 204
                 +nD++
  AJA92722.1 161 ANDIK 165
                 ***97 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.57   2.5e+03     170     186 ..      22      38 ..      11      39 .. 0.62
   2 !    4.3   0.0    0.0062        28      20      57 ..      76     113 ..      68     130 .. 0.88
   3 !   23.4   0.1   9.3e-09   4.2e-05     185     245 ..     133     192 ..     128     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                  EEEEESTTEEEEEETT- CS
  Hydrolase_3 170 titssskgyleimpkgv 186
                  + ++ +k +++i++kg+
   AJA92722.1  22 EKVNKEKEIWDITKKGI 38 
                  44566667777777766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0062
                  HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
  Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                  ++ea++ lk++g kv+  +G  + ++ ++ eel+ld  
   AJA92722.1  76 AREACQTLKNAGWKVMAVSGGFTIMTDRLKEELNLDHV 113
                  789*******************************9944 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 9.3e-09
                  T-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
  Hydrolase_3 185 gvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                  + +K+++ +  ++e+n++++e++++ Dg NDi+++  ++lg+A   a++ vk  A+ + + 
   AJA92722.1 133 DSDKAKSARVKIEEWNVPKDEIVVIVDGANDIKLFDISNLGIAY-RAQDLVKDLATTTLEE 192
                  679****************************************7.5999999999987765 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     3e-07    0.0013     132     207 ..     100     177 ..      57     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-07
                 HHHHHHHHHHTTTS-EEEEEETTTEEEE..EETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-T CS
        S6PP 132 vlkeleqlLekreldvkviyssgkdlDv..lPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVg 207
                 +++ l+++L+  ++ ++ ++  +  lD   +  +++k+++ r   + ++++ ++i+v  d  nD++l+  ++lg+  +
  AJA92722.1 100 MTDRLKEELNLDHVYTNELIFKDGKLDGvkINVDSDKAKSARVKIEEWNVPKDEIVVIVDGANDIKLFDISNLGIAYR 177
                 567888888888888877777778888613467899********************************9999998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1344.61
//
Query:       AJA92723.1  [L=113]
Description: hypothetical protein T478_0042 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.5   0.2    0.00035   20.8   0.0    1.5  2  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
    0.00075   19.0   0.2       0.15   11.6   0.0    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.052   13.1   0.0    1.3  1  zf-C2H2_12      Zinc-finger C2H2-type
       0.04   13.8   0.6        5.2    7.0   0.1    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
      0.045   14.0   0.8       0.25   11.7   0.0    2.2  2  Ribosomal_L32p  Ribosomal L32p protein family


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.1   7.6e+03      56      56 ..      12      12 ..       3      28 .. 0.51
   2 !   20.8   0.0   9.7e-08   0.00035      33      77 ..      51      95 ..      39     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                - CS
        Rpr2 56 i 56
                i
  AJA92723.1 12 I 12
                2 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 9.7e-08
                HHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E..... CS
        Rpr2 33 kkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkk 77
                +  +++l+p+ k+ +Ck+Cg + + ++ +++r + ++k++ k+ k
  AJA92723.1 51 MGFVMKLDPATKHFICKRCGLYATREQVSDIRYKLSRKESTKSDK 95
                55689****************************865544444433 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0     0.004        14       3      11 ..       4      12 ..       2      28 .. 0.73
   2 !   11.6   0.0   4.2e-05      0.15      13      27 ..      57      71 ..      43      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.004
                  ETTTTCEEC CS
  TF_Zn_Ribbon  3 CPnCgstnl 11
                  CP+C s+++
    AJA92723.1  4 CPECVSREI 12
                  ****99987 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.2e-05
                  EETSTTCEEESSSSB CS
  TF_Zn_Ribbon 13 eDpergelvCtdCGl 27
                  +Dp++  ++C++CGl
    AJA92723.1 57 LDPATKHFICKRCGL 71
                  79************8 PP

>> zf-C2H2_12  Zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.052      11      42 ..      52      83 ..      49      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
  zf-C2H2_12 11 eyLmdydpqrrglvCmvCgeslaslklstikr 42
                 + m +dp+ +  +C  Cg      ++s+i+ 
  AJA92723.1 52 GFVMKLDPATKHFICKRCGLYATREQVSDIRY 83
                699**************************985 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0014       5.2       2      18 ..       3      19 ..       2      22 .. 0.88
   2 ?    5.0   0.1    0.0061        22      24      35 ..      59      70 ..      58      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
     TFIIS_C  2 kCpkCgsreayffqlQt 18
                 Cp+C sre+    +Q+
  AJA92723.1  3 NCPECVSREIAKRKKQL 19
                6*********9999985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0061
     TFIIS_C 24 pmtvfykCtkCg 35
                p+t  + C+ Cg
  AJA92723.1 59 PATKHFICKRCG 70
                89999******8 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.22   7.9e+02      26      39 ..       1      14 [.       1      17 [. 0.74
   2 ?   11.7   0.0   6.9e-05      0.25      37      53 ..      61      77 ..      58      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
                    EEEETTTCCEECTT CS
  Ribosomal_L32p 26 lvecpncgelklpH 39
                    +v+cp+c +  +++
      AJA92723.1  1 MVNCPECVSREIAK 14
                    58999997766655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.9e-05
                    CTTC-BTTTTBSSSBXS CS
  Ribosomal_L32p 37 lpHrvcpscGyYkgrev 53
                      H +c+ cG Y  re 
      AJA92723.1 61 TKHFICKRCGLYATREQ 77
                    68********9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 714.08
//
Query:       AJA92724.1  [L=290]
Description: GDSL-like lipase/acylhydrolase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-08   32.6   0.1    2.2e-07   31.4   0.1    1.7  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
     0.0012   18.8   1.6      0.029   14.3   1.6    2.2  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase
  ------ inclusion threshold ------
      0.059   13.8   2.0      0.077   13.5   1.1    1.6  2  DUF2779        Domain of unknown function(DUF2779)


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.1   3.7e-11   2.2e-07       2     140 ..      37     181 ..      36     271 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.7e-11
                    EESHHHHTCTTBCCHCHHCCCCCCCHHHTT...-EEEEE...EEHCCH-H..HHHHHHHH.CTGGG-TSEEEEE--CCCCCTT--HHHHHHH..HH CS
  Lipase_GDSL_2   2 lGDSiTaGygadgggrsypaylarllaarl...gldvvnn..lgvsGattallrllerlr.dllrlkpdlvtiliGtNDlgrgvpaaaaaandnle 91 
                    +G S   G+ga++ +++ p+y+++ + +++   +   + +  +g++ a +     +e +  +l  ++pdl++i  G+NDl++   + +       +
     AJA92724.1  37 VGGSTVFGVGATSDNHTIPGYIQQFFDKQFpdeD---IEIinAGIPKAYS--STEAEFIKnSLVNYNPDLIVIYDGWNDLNHSYKQFESIDSSPTD 127
                    799***************************6544...44445******77..444455558999***************98888887776666344 PP

                    HHHHHHCCC......GEEECEEEEE-TTT-TTSTCC..HHHHHHHHHHHHHHHH CS
  Lipase_GDSL_2  92 elidalraa...apgarilvlgplpptpeaaadare..lnaviaaynealreva 140
                    eli+++ +     p++ i +  +++ t+ +  d ++    ++++ + + l+e +
     AJA92724.1 128 ELIRMINRSdylTPKVLIQQYFNYQRTSTDIMDFDSsyISEKVNLWKNNLEETC 181
                    444444444322444433333333333333333333223333333333344444 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.6   4.9e-06     0.029      20     200 .]      58     276 ..      34     276 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                  HCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHHHHHCTTSEEEEE--CTCC.-EECSSCTTTCEEHHHHHHHHHHHHHHHHHHHHT CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Lipase_GDSL  20 iqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseqlkalhpdlviislGtNDs.nlgkkstdaakkeaeeyiknlreaikelkeegap 116
                  iq  ++k ++  d     i n+g+ +a +  +++ +      ++ l ++ pdl++i+ G ND+          +k+ ++   +  +e+i+ ++++   
   AJA92724.1  58 IQQFFDKQFPDED---IEIINAGIPKAYSSTEAEFI------KNSLVNYNPDLIVIYDGWNDLnH-------SYKQFESIDSSPTDELIRMINRSDYL 139
                  4444445555443...46677777777777777777......78899****************63.......33333333333444444444444444 PP

                  TEEEEEEE-SSTCH............................................................CTCCCCHCCHHHHHHHHHHHHHHH CS
                  xxxxxxxxxxxxxx............................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
  Lipase_GDSL 117 kaivvlvsppglgp............................................................qeekdakklgekgnefvgeynqrl 154
                   ++v++  + +  +                                                             e+ d+k++ + +   ++  n+++
   AJA92724.1 140 TPKVLIQQYFNYQRtstdimdfdssyisekvnlwknnleetcknsevqnlktviilqpllgtgnkilseeemhyHEHYDSKTMIKYYESYAENLNDLI 237
                  45555555555555555555555566666666666666666666666666666666666666779999988888666666666666655555555555 PP

                  HHHHHHCTEEEECHHHHHHHTHCCGCHCHTSSSB-HHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Lipase_GDSL 155 ndlaekdgfavvDlydelqglsgieqlkaDglHpsekgyeklaell 200
                  n+  +  ++ + D++d  ++       + D  H s+ g++++a+++
   AJA92724.1 238 NSCNK--TIDLRDVFDPYEQT-----VYYDAGHISDFGNKIVASEI 276
                  55555..44455555555555.....222888*******9999976 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   7.7e+03      83     112 ..      90     116 ..      71     135 .. 0.62
   2 ?   13.5   1.1   1.3e-05     0.077      28     114 ..     154     253 ..     139     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
     DUF2779  83 lkelaqlfpeykeelkqiienlvDlldlfk 112
                 +k+ +    +y+ +l  i++   Dl +  k
  AJA92724.1  90 IKNSLV---NYNPDLIVIYDGWNDLNHSYK 116
                 444333...455555555555555555444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
     DUF2779  28 fSlhilqeegev..ehkeflaespntdpreelieeLikiieke...........gsvvvynksfEksrlkelaqlfpeykeelkqiienlvDlldlfkk 113
                  S +i++ +++   e+ +  +++ ++ +++  +++L++ i  +              + y++++  +++ + ++ ++e  ++l + +++++Dl d+f  
  AJA92724.1 154 TSTDIMDFDSSYisEKVNLWKNNLEETCKNSEVQNLKTVIILQpllgtgnkilsEEEMHYHEHYDSKTMIKYYESYAENLNDLINSCNKTIDLRDVFDP 252
                 4777777655556566788889999999999******9998888999999999988899999999999999999888888899999999*******986 PP

     DUF2779 114 s 114
                 +
  AJA92724.1 253 Y 253
                 5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1934.63
//
Query:       AJA92725.1  [L=150]
Description: hypothetical protein T478_1251 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.085   13.0   0.0        1.3    9.2   0.0    2.3  2  Phage_holin_3_3  LydA holin phage, holin superfamily III


Domain annotation for each model (and alignments):
>> Phage_holin_3_3  LydA holin phage, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.022   3.9e+02      28      42 ..      16      30 ..       7      48 .. 0.65
   2 ?    9.2   0.0   7.3e-05       1.3       3      51 ..      51     104 ..      50     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.022
  Phage_holin_3_3 28 ikellleivvSgfvG 42
                     + ++l ++++S++++
       AJA92725.1 16 FLGFLASVIISAVAA 30
                     455666666666655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.3e-05
  Phage_holin_3_3   3 iivlAllGGlvsylmrakk....g.rrrfsikellleivvSgfvGllvfllcee 51 
                      +++++++GGl  + +r+k     g r    +k+ l+ i++S+ +G +v+ ++ +
       AJA92725.1  51 AVFFSVFGGLYYFDNRKKYvldnGqRDNTLLKSDLIKIISSLGIGEVVYTIVRW 104
                      689******998888887677753577777888************999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1112.43
//
Query:       AJA92726.1  [L=94]
Description: hypothetical protein T478_0524 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.04   13.8   0.0      0.043   13.7   0.0    1.1  1  Dak2       DAK2 domain
      0.057   12.0   0.1      0.068   11.7   0.1    1.0  1  LANC_like  Lanthionine synthetase C-like protein


Domain annotation for each model (and alignments):
>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.8e-06     0.043      27      92 ..      22      88 ..       6      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-06
                -SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC......TT---HHHHHHHHHHHHHHHH-- CS
        Dak2 27 easlaevlkalakallsgagGtsGvlysqflralakalke.keeldaedlaaalkaaleaiqavgka 92
                 +s  +++k+  +   s+   + Gv+++++ +a+ +a+++ + e++ +d++++ + + ++i +++ka
  AJA92726.1 22 ADSYNQFAKEYNEFSNSKREIAFGVIIGTVYSAFLQAYSNqQLEVKLDDIQEFHELMRDNIDKITKA 88
                56677777778888888888899***************99777899999***999999***999998 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.6e-06     0.068     125     204 ..       7      84 ..       2      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.6e-06
                 GHHHHHHHHHHHHHHHCHHCCTTTCHSCHH-BTTBEB-STTTSH.HH.HHHHHHCCCHT.-HHHHHHHHHHHHHHHHHTS-T CS
   LANC_like 125 eedllkqilkylvelgiksenqvswsplmyepegesnlGlAHGl.sG.ialallalykgtksekllelikkllkylkslkfk 204
                 ++++l+ +l+y ++      +++ ++ ++y++ ++s   +A G+  G ++ a+l++y +++ e  l++i++  ++++ + +k
  AJA92726.1   7 NKKFLEDLLQYYIDQA----DSYNQFAKEYNEFSNSKREIAFGViIGtVYSAFLQAYSNQQLEVKLDDIQEFHELMRDNIDK 84 
                 3555555555555555....99999***99999**********63699****************************999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1581  (0.0881812); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 674.15
//
Query:       AJA92727.1  [L=56]
Description: putative DNA/RNA-binding protein AlbA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.7   0.2      0.095   12.5   0.0    1.7  2  Alba      Alba


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.3e-06     0.095      38      65 ..       2      29 ..       1      31 [. 0.86
   2 ?   -1.0   0.1     0.092   1.6e+03       2       8 ..      48      54 ..      39      56 .] 0.57

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.3e-06
                HHHHHHHHHHHHHHHTCTT.EEEEEEEE CS
        Alba 38 aIskAvsvaeilkrrfgkglyqvnvlts 65
                +I +Av+va+i+ r+ +++ y + ++ +
  AJA92727.1  2 SIGRAVDVAQIISRKTENSGYMIGNISI 29
                699*************998898888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.092
                EEEE-ST CS
        Alba  2 eiyVssk 8 
                ei+V+++
  AJA92727.1 48 EIEVKRN 54
                3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 408.23
//
Query:       AJA92728.1  [L=267]
Description: TIGR00268 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-09   36.9   0.6    3.2e-08   33.3   0.1    2.5  3  QueC             Queuosine biosynthesis protein QueC
    2.9e-09   37.0   0.0    4.8e-09   36.3   0.0    1.3  1  Asn_synthase     Asparagine synthase
    2.3e-08   33.3   0.2    2.3e-05   23.3   0.2    2.2  2  tRNA_Me_trans    tRNA methyl transferase
    6.6e-08   32.0   0.0    1.4e-07   30.9   0.0    1.5  1  NAD_synthase     NAD synthase
    9.4e-05   22.2   0.3     0.0027   17.5   0.3    2.2  1  ATP_bind_3       PP-loop family
  ------ inclusion threshold ------
      0.017   14.7   0.1      0.062   12.9   0.1    2.0  1  ThiI             Thiamine biosynthesis protein (ThiI)
      0.018   14.3   0.1      0.032   13.5   0.1    1.3  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.1   1.3e-11   3.2e-08       1      65 [.      16      80 ..      16      90 .. 0.89
   2 ?    0.6   0.0      0.13   3.4e+02     154     185 ..     139     174 ..     132     182 .. 0.76
   3 ?   -1.7   0.0      0.67   1.7e+03      33      67 ..     179     218 ..     166     240 .. 0.60

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.3e-11
                EEEEE--SSHHHHHHHHHHHHH.-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGG CS
        QueC  1 kavvllSGGlDSttvlalakke.gkevealtfdYgqrhkkeleaakkiakelgveehkildldllk 65
                k++v lSGG+DS+ v++ a+k+ gk+ +a+t dY+   ++el++ak++a+e+g+  h i++ + l+
  AJA92728.1 16 KVLVSLSGGVDSALVAYAANKKlGKNAIAVTADYKTLSSEELDSAKSVAHEIGI-THSIIEYSELE 80
                57999***********9997762699****************************.99999887654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                 EE-TTT..T--HHHHHHHHHHTT..HHHHH-B-STT CS
        QueC 154 ieaPli..dlsKaeivklgkelg..vpleetlsCYe 185
                 i+ Pl+  +++K+++ k++k++g  +  + + sC +
  AJA92728.1 139 IRSPLLevKFTKENVRKIAKNVGlsIYDKPSNSCLA 174
                 77888611568************6555577899976 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.67
                 SS-TTSHH....HHHHHHH.HHHT--.-EEEEE-GGGGGG CS
        QueC  33 Ygqrhkke....leaakki.akelgveehkildldllkel 67 
                 +gqr ++e    +e  +ki  +++gv++ ++ d++ l+++
  AJA92728.1 179 WGQRVTAEklarIELSEKIiKQKIGVQQVRVRDINGLARI 218
                 5666444411113333343034566766666666666655 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.9e-12   4.8e-09      19      82 ..      16      79 ..      12     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.9e-12
  Asn_synthase 19 pvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvltee 82
                  +v + LSGG+DS+l+a+ a++++ +++ ++++++++ +s+e++ ak va ++g+ h  ++++e 
    AJA92728.1 16 KVLVSLSGGVDSALVAYAANKKLGKNAIAVTADYKTLSSEELDSAKSVAHEIGITHSIIEYSEL 79
                  57789*****************************99********************88776654 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   9.1e-09   2.3e-05       2      72 ..      16      78 ..      15      89 .. 0.80
   2 !    7.7   0.0   0.00051       1.3     170     192 ..     147     169 ..     137     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.1e-09
  tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfek 72
                   kv+v lSgGVDS+++a+  +++ g++ i+v+   +           ++e+l  a++va+++gi ++++++++
     AJA92728.1 16 KVLVSLSGGVDSALVAYAANKKlGKNAIAVTADYK---------TLSSEELDSAKSVAHEIGITHSIIEYSE 78
                   8***************9987762677777764433.........34678899****************9987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00051
  tRNA_Me_trans 170 eltKeevrkiAkeaglavaekkd 192
                    ++tKe+vrkiAk+ gl++ +k+ 
     AJA92728.1 147 KFTKENVRKIAKNVGLSIYDKPS 169
                    579***************99984 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   5.6e-11   1.4e-07      19      83 ..      15      78 ..       8     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.6e-11
                  SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
  NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                  ++v++ lSGGvDS+lva+ a k lg +n++a+    ++ s e++  a+ +a+++gi    i+ ++
    AJA92728.1 15 DKVLVSLSGGVDSALVAYAANKKLG-KNAIAVTADYKTLSSEELDSAKSVAHEIGITHSIIEYSE 78
                  6899********************5.6899*****99999****************998887655 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   1.1e-06    0.0027       1      68 [.      16      78 ..      16     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H CS
  ATP_bind_3  1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv 68
                kvlv +SgG+DS +  ++++k+   lg +++a++ d+++   s ee +  k+++++++i + i + + 
  AJA92728.1 16 KVLVSLSGGVDSALVAYAANKK---LGKNAIAVTADYKTL--SSEELDSAKSVAHEIGITHSIIEYSE 78
                689*********9988888777...556889999999875..44555566777777777776666553 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.4e-05     0.062       4     116 ..      15     119 ..      13     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
        ThiI   4 gkvlaLlSgGiDSpVaaylllkR.GcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekltivllkrkmlriAe 101
                 +kvl+ lSgG+DS   ay + k+ G ++ +v+ + + + s e+ +  +++a+ +        ++  ++++ e+ +e   k +++ ++  ++  +     
  AJA92728.1  15 DKVLVSLSGGVDSALVAYAANKKlGKNAIAVTAD-YKTLSSEELDSAKSVAHEIG-------ITHSIIEYSELENENFVK-NDNKRCFYCRDELSTELI 104
                 799***************9987659999999987.55555555555555555443.......333466777766665544.455667777777766666 PP

        ThiI 102 kvaeeegakalvtGe 116
                 k+ +  +++++v+G 
  AJA92728.1 105 KLSDSLKINTIVDGT 119
                 677777777777775 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.032       3      59 ..      20      77 ..      18      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
  Arginosuc_synth  3 aysGGlDtsviikllkeklgeeviavavdvGq.eeedldevkekalklgavksvvvDa 59
                     + sGG+D + +    ++klg++ iav++d     +e+ld++k+ a+++g ++s++  +
       AJA92728.1 20 SLSGGVDSALVAYAANKKLGKNAIAVTADYKTlSSEELDSAKSVAHEIGITHSIIEYS 77
                     68*******999999**************8753679*************987766543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1948.45
//
Query:       AJA92729.1  [L=430]
Description: glutamyl-tRNA(Gln) amidotransferase, subunit D [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-55  185.2   0.1    1.3e-54  184.7   0.1    1.2  1  Asparaginase    Asparaginase, N-terminal
    1.9e-27   95.7   0.0    4.7e-27   94.5   0.0    1.7  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    6.5e-21   73.4   4.6    9.6e-21   72.9   3.6    1.9  2  GatD_N          GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.7   0.1   2.2e-58   1.3e-54       1     182 [.      94     282 ..      94     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 2.2e-58
                   EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEEEE--STTHHHHHHHHH CS
  Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfVvlhGTDTlaytAsaLs 96 
                   k+l+l+tGGTias++d+++ga++palsa+el+ea+pe++kia++++e+l++  S+n++p++wl++a+++++  e+ y g++++hGTDT++yt+s+Ls
    AJA92729.1  94 KILLLSTGGTIASKVDYRTGAVTPALSASELYEAVPEIAKIANVDAEVLFSEYSENLQPQHWLEIAKKLDSMAESdYTGIIIAHGTDTMHYTSSFLS 190
                   79***********************************************************************555********************* PP

                   HHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEETTTEEE-BSSSSS-EEETTT--SEEEETTE CS
  Asparaginase  97 lmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llranrvtKvhtssldaFespnlgplaevegsk 182
                   ++l +++ p+ l+Gsqr++++++sD++ Nl++A ++ ++s + +g++v++++        +++++rv+K hts++ aFe++  +p   ++++k
    AJA92729.1 191 FALSGFPIPIALVGSQRSSDRPSSDAALNLITATKFLTES-KTKGIYVIMHNDsnddaiaCHKGTRVRKNHTSKRGAFETVGGNPAFIISDDK 282
                   ***************************************9.9*************************************99988887775555 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   7.9e-31   4.7e-27       1     114 []     306     419 ..     306     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 7.9e-31
                     -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHTEEE-TT--HHHHHH CS
  Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlgvisaddmtpeaari 95 
                     +V+++k hpg d+  +k l + g  ++++egtG G++ ++++e++k+ak++g  + +tsqc++g+vs+++y++g++l +lg++  ++m pe+a +
      AJA92729.1 306 KVALVKYHPGYDPRQIKDLADLGFGAIIFEGTGLGHVGNTMYEVIKNAKEQGLFLGMTSQCIDGRVSMTVYDSGRDLLELGIVPLENMIPETALV 400
                     7********************************************************************************************** PP

                     HHHHHCTT---HHHHHHHH CS
  Asparaginase_C  96 kLmlllgkgldpaevrklf 114
                     k m+++g+  + +e+++l+
      AJA92729.1 401 KAMWAYGNSSNADEIKELM 419
                     *****************98 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   3.6   1.6e-24   9.6e-21       1      55 []      20      73 ..      20      73 .. 0.96
   2 ?   -3.1   0.0      0.85   5.1e+03      13      23 ..     167     177 ..     164     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.6e-24
                --TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
      GatD_N  1 ievGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                i+vGDl+kv++ + +y+GilmPr+e++d+++ivlKL++GYNiGi++e+iekie++
  AJA92729.1 20 IKVGDLVKVTS-ELTYSGILMPRYESGDENHIVLKLKSGYNIGIEVEKIEKIEKI 73
                689*****975.79***************************************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.85
                 S-EEEEEE--- CS
      GatD_N  13 greyeGilmPr 23 
                 +++y+Gi++ +
  AJA92729.1 167 ESDYTGIIIAH 177
                 57899999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3049.64
//
Query:       AJA92730.1  [L=276]
Description: thiazole biosynthesis enzyme [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-65  219.8   0.0    3.3e-65  219.6   0.0    1.0  1  Thi4            Thi4 family
    9.7e-13   48.0   0.3    6.1e-06   25.6   0.0    3.0  3  FAD_binding_2   FAD binding domain
      3e-08   33.4   0.0    8.4e-08   32.0   0.0    1.7  1  FAD_oxidored    FAD dependent oxidoreductase
    8.3e-08   32.3   0.0    1.6e-07   31.4   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    6.2e-07   28.9   0.0      8e-07   28.6   0.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.2e-06   27.2   0.0    3.5e-06   26.5   0.0    1.3  1  FAD_binding_3   FAD binding domain
    3.3e-06   26.1   0.0    4.8e-06   25.5   0.0    1.2  1  HI0933_like     HI0933-like protein
    4.3e-06   26.5   0.5    0.00021   21.0   0.2    2.2  2  DAO             FAD dependent oxidoreductase
    8.3e-05   22.0   0.1    0.00012   21.4   0.1    1.2  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00023   20.3   0.2     0.0071   15.4   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
     0.0015   17.7   0.1     0.0022   17.1   0.1    1.2  1  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.018   13.9   0.0        1.9    7.2   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
      0.024   14.9   0.0      0.053   13.8   0.0    1.6  1  TrkA_N          TrkA-N domain
      0.031   12.8   0.0      0.047   12.2   0.0    1.2  1  GDI             GDP dissociation inhibitor
      0.044   14.4   0.0        0.1   13.1   0.0    1.7  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.064   12.6   0.0       0.14   11.4   0.0    1.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.6   0.0   2.9e-68   3.3e-65       1     235 []      23     249 ..      23     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: 219.6 bits;  conditional E-value: 2.9e-68
                 HHHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT---EEESSEEEESEHHHH CS
        Thi4   1 sraiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelgikyedegdyvvvkdaalf 99 
                 +rai ++ ++ l++ aesD++i+GaG++GLta++ l+   + kv+++e++  +GGG wlGG + + + vr pa+++ delgi+y++ g++++      +
  AJA92730.1  23 TRAIAKEFYDVLQDRAESDIIIIGAGPAGLTASRELSLM-GYKVLVIEQNNYLGGGYWLGGYMMNPVTVRAPAQKIWDELGIPYKKVGEGLYLTPGPHA 120
                 79************************************9.*********************************************************** PP

                 HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HH CS
        Thi4 100 tstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGhdgeivavvvkkikleakiekvkgeksldae 198
                 +s+l+ ++++ a+vk ln +  +Dl++r+  +vaG+v+nw+ v+    + +cvDP  ++ak+++da+Ghd+    v+vk++++ +   + kg+ ++++e
  AJA92730.1 121 VSKLIGAACD-AGVKFLNLTKFDDLVMRH-GRVAGIVVNWMPVSALPRNITCVDPVALEAKMIIDASGHDS----VAVKRLVDRQ-LVEWKGMNPMWVE 212
                 **********.******************.8***************999*********************6....7889999888.55789******** PP

                 HHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
        Thi4 199 kaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                  +e+++v+kt e++p+l++aGm v+e +g+ RmGp+f
  AJA92730.1 213 DGEEHVVHKTGEIYPGLVAAGMSVTETHGLARMGPTF 249
                 ************************************9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   5.4e-09   6.1e-06       1      36 [.      41      76 ..      41      97 .. 0.93
   2 !   16.5   0.0   3.2e-06    0.0035     136     201 ..     113     187 ..     103     206 .. 0.85
   3 ?    2.7   0.0     0.048        54     383     413 ..     217     246 ..     212     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.4e-09
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                   D+i+iG+G AGL+A+ e++  G kv+v+e+ ++ gg
     AJA92730.1 41 DIIIIGAGPAGLTASRELSLMGYKVLVIEQNNYLGG 76
                   9******************************99887 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.2e-06
                    ...HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE---- CS
  FAD_binding_2 136 tlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatgG 201
                     l++g++ +  l+ +a +agv+f++ t+ d+L+++ grv G+vv+ +         +    v+++ak +++a+g 
     AJA92730.1 113 YLTPGPHAVSKLIGAACDAGVKFLNLTKFDDLVMRHGRVAGIVVNWMpvsalprniTCVDPVALEAKMIIDASGH 187
                    5789****************************************9888998776666666668899999999886 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.048
                    BESTTEEESSBTEEE-STCEESSSSTTS--T CS
  FAD_binding_2 383 rvldadgqpipGLYAaGevaaggvhganrlg 413
                    +v  ++g++ pGL AaG    +  hg  r+g
     AJA92730.1 217 HVVHKTGEIYPGLVAAGMSV-TETHGLARMG 246
                    678999***********999.9****99987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   7.5e-11   8.4e-08       1     145 [.      41     187 ..      41     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.5e-11
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl.vatdignkaeeqvvtgiareflerlrqrggarlkkrskw..ntfepevakavle 94 
                   D++++G+gpaG++A      +G kvl++e++++lGG    g+ ++++++ +   + +++i++e+    ++ g+            t  p+++ +++ 
    AJA92730.1  41 DIIIIGAGPAGLTASRELSLMGYKVLVIEQNNYLGGGYWLGGyMMNPVTVR---APAQKIWDELGIPYKKVGE--------GlyLTPGPHAVSKLIG 126
                   9*********************************99765444034444433...5567777777666544111........112368999******9 PP

  FAD_oxidored  95 emlaeagvtvllntrlvevekeg..............kriesvtveskegrktirAkvfiDATgd 145
                   + ++  gv+ l  t++++ +++                  + +t+ +     +++Ak++iDA+g 
    AJA92730.1 127 AACDA-GVKFLNLTKFDDLVMRHgrvagivvnwmpvsALPRNITCVD---PVALEAKMIIDASGH 187
                   99987.9*********9999986233334443333321123333332...788999999999986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   1.5e-10   1.6e-07       1      33 [.      44      76 ..      44     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.5e-10
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                   I+GaG +Gl+a ++L+  g++vl++e++++lGG
     AJA92730.1 44 IIGAGPAGLTASRELSLMGYKVLVIEQNNYLGG 76
                   9*******************************7 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   7.1e-10     8e-07       2      43 ..      41      81 ..      40     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 7.1e-10
                 SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggclls 43
                 d+++iG+GpAGl+a+++l+  g+kv+++ ++++ l+gg +l 
   AJA92730.1 41 DIIIIGAGPAGLTASRELSLMGYKVLVI-EQNNYLGGGYWLG 81
                 89**************************.6666666655553 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.1e-09   3.5e-06       2      33 ..      40      71 ..      39      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.1e-09
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                    d++I+GaGpaGl+++++Ls  G +v+++e+ 
     AJA92730.1 40 SDIIIIGAGPAGLTASRELSLMGYKVLVIEQN 71
                   689***************************86 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.3e-09   4.8e-06       2      36 ..      41      75 ..      40      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.3e-09
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 d+i+iG+G+AGl a+ +++  g +Vl++e+++ lg
   AJA92730.1 41 DIIIIGAGPAGLTASRELSLMGYKVLVIEQNNYLG 75
                 89*****************************9887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.8e-07   0.00021       1      35 [.      41      76 ..      41      98 .. 0.91
   2 ?    3.9   0.0     0.029        32     147     222 ..     119     205 ..      94     275 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.8e-07
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                d++iiG+G +Gl++ +eL+  g  V+++e+++ +g g
  AJA92730.1 41 DIIIIGAGPAGLTASRELSLMGykVLVIEQNNYLG-G 76
                8******************999*********9999.4 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.029
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..........EECTEEEE.......EEEE..EEE--GGGHHHHHTTCTT.TSEEEEEEE CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve..........rttpgend.......aada..vVnaaGawsdllgllkel.dlpispvrg 222
                 +++  l  aa ++Gv++l+ t+  +l  + g+v+g+           r   ++ +       +  a  ++ a G+ s  +   k+l d++++  +g
  AJA92730.1 119 HAVSKLIGAACDAGVKFLNLTKFDDLVMRHGRVAGIVvnwmpvsalpR---NI-TcvdpvalE--AkmIIDASGHDSVAV---KRLvDRQLVEWKG 205
                 56778899999999******9999986677899999886666533221...33.133455333..244888888887555...4443444444444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   1.1e-07   0.00012       1      31 [.      43      72 ..      43      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                 iIiGaGPaGl+a  el  +g  ++l++E++n
   AJA92730.1 43 IIIGAGPAGLTASRELSLMGY-KVLVIEQNN 72
                 8********************.7*****987 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.3e-06    0.0071       1      34 [.      41      72 ..      41     102 .. 0.92
   2 ?    2.7   0.0     0.048        54     114     143 ..     160     189 ..     142     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                   D+++iGaGpAgl    +l  + +g kv++ie  +
     AJA92730.1 41 DIIIIGAGPAGLTASREL--SLMGYKVLVIEQNN 72
                   9*****************..**********9765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.048
  Lycopene_cycl 114 eeeageslvvleggrkirarlvvdarglas 143
                    +++a  + +++ + + ++a++++da+g  s
     AJA92730.1 160 PVSALPRNITCVDPVALEAKMIIDASGHDS 189
                    555556789******************544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     2e-06    0.0022       1      31 [.      41      71 ..      41      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                d+i+iG+G AG+ A+ +++ +G+kvl i ++
  AJA92730.1 41 DIIIIGAGPAGLTASRELSLMGYKVLVIEQN 71
                79************************99665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0017       1.9       1      34 [.      41      71 ..      41      75 .. 0.91
   2 ?    4.6   0.0     0.011        12     196     226 ..     174     204 ..     161     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                    +i+i+G+G+aG +a   l+ ++   ++v+++e++
      AJA92730.1 41 DIIIIGAGPAGLTASRELSLMG---YKVLVIEQN 71
                    69****************9999...889999976 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                     -EEE-SEEEE-SGGG-IIIIIIT---EEE-T CS
  Trp_halogenase 196 reveadlfiDcsGfrgllieqaLktgfedws 226
                       +ea ++iD+sG+ +  +++ ++ +  +w+
      AJA92730.1 174 VALEAKMIIDASGHDSVAVKRLVDRQLVEWK 204
                     5799************999998888888876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.7e-05     0.053       1      30 [.      42      71 ..      42      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                iiiiG+G  G +  +eLs  g+ +v+vi+++
  AJA92730.1 42 IIIIGAGPAGLTASRELSLmGY-KVLVIEQN 71
                8******************889.5*****98 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.2e-05     0.047       4      41 ..      39      76 ..      36      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                EECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCG CS
         GDI  4 eydvivlGtGlkecilsGllsvdgkkvlhldrndyyGg 41
                e d+i++G+G      s  ls  g kvl++++n+y Gg
  AJA92730.1 39 ESDIIIIGAGPAGLTASRELSLMGYKVLVIEQNNYLGG 76
                78**********************************98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.3e-05       0.1       2      35 ..      42      75 ..      41      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                ++++G+G  gl +  +l+ +g kV v+e ++ l 
  AJA92730.1 42 IIIIGAGPAGLTASRELSLMGYKVLVIEQNNYLG 75
                89**************************999887 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.14      28      60 ..      39      71 ..      33      74 .. 0.90
   2 ?   -3.9   0.0       5.9   6.7e+03     128     162 ..     128     160 ..     124     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                 --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
  AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                 ++ +++iG+G aGl A +  + +g kV v++ +
   AJA92730.1 39 ESDIIIIGAGPAGLTASRELSLMGYKVLVIEQN 71
                 5789************************99987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.9
                  TGGGT-SBTT--TBBTTSEEEEETTEEEEEBSTGG CS
  AlaDh_PNT_C 128 AidqGGnvetsrltthgepvveekgvvhygvanlp 162
                  A+d+G  +   +lt+ ++ v+++  v  + v+ +p
   AJA92730.1 128 ACDAGVKFL--NLTKFDDLVMRHGRVAGIVVNWMP 160
                  666666555..778888888887777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1964.09
//
Query:       AJA92731.1  [L=297]
Description: hypothetical protein T478_0913 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00053   20.0   1.4      0.001   19.1   1.4    1.5  1  DUF4366          Domain of unknown function (DUF4366)
     0.0087   16.2   2.2      0.013   15.6   2.2    1.2  1  Podoplanin       Podoplanin
  ------ inclusion threshold ------
      0.043   12.6   1.1      0.062   12.0   1.1    1.1  1  Ureide_permease  Ureide permease
        0.2   11.5   0.0       0.33   10.8   0.0    1.2  1  PMP22_Claudin    PMP-22/EMP/MP20/Claudin family
        2.5    7.8   7.7        3.5    7.3   7.7    1.1  1  Band_3_cyto      Band 3 cytoplasmic domain


Domain annotation for each model (and alignments):
>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.4   2.9e-07     0.001      71     137 ..      91     174 ..      76     177 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.9e-07
     DUF4366  71 keeeevcactekcaagkvntdcpveepepekeaepee................peeepekksn....nglllvvlavaligggaayy 137
                  ++e+++++++  ++  +++ ++v++ ep+ke+  ++                ++++++   n     g+++ ++av++ig+gaay+
  AJA92731.1  91 ATSEKTKSEETTSENPYIKSTAEVKKSEPQKEELASKeptieekfiehvekdrSTTKKS---NkgkvVGIIIGIIAVIVIGVGAAYM 174
                 33444555555556666666666644444433222222344455566655444333333...23446999999*********99986 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.2   3.6e-06     0.013      59     145 ..      85     167 ..      43     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                 XXXXXXXXXXXXXXXX-----GGG-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Podoplanin  59 pyesglttlvptstesvtdlrledlptaestvkakeesqstttlnvvtshstekvgeetettvekdGLatvtLvgiivGvllaigfi 145
                 + ++ ++t   t+ e++t+++   ++tae+   + ++ + ++   ++  + +e+v+++ +tt + +      +vgii+G++  i  i
  AJA92731.1  85 KITEVKATSEKTKSEETTSENPYIKSTAEVKKSEPQKEELASKEPTIEEKFIEHVEKDRSTTKKSN---KGKVVGIIIGIIAVIV-I 167
                 2222333333455555666666666666666666666666666666677777******99996654...3445666666543332.2 PP

>> Ureide_permease  Ureide permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1   1.7e-05     0.062     131     211 ..      85     168 ..      75     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
  Ureide_permease 131 klskskseekeetkeeekkeeesekkkee.kdleege.kaaekakagtaeflieleekra.ikvlgkstllGlaivlfaGvcfs 211
                      k++++k++++++++ee+++e+   k++ e k+ e ++ + a+k  +   +f+ ++e+ r+  k  +k +++G+ i ++a ++++
       AJA92731.1  85 KITEVKATSEKTKSEETTSENPYIKSTAEvKKSEPQKeELASKEPTIEEKFIEHVEKDRStTKKSNKGKVVGIIIGIIAVIVIG 168
                      55555555544444444444333332222233333331445555666789*******99835889999*******999988775 PP

>> PMP22_Claudin  PMP-22/EMP/MP20/Claudin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.1e-05      0.33      53     102 ..     129     178 ..     124     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                    S-SBE-B--S---SSTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHTGGGT CS
  PMP22_Claudin  53 gklsckqidslleeedalqavqalmilsiilgilslivavlqlkclkkge 102
                     ++++k i+++ ++ ++++  ++  +++ii+gi+++iv+ ++   +  ++
     AJA92731.1 129 PTIEEKFIEHVEKDRSTTKKSNKGKVVGIIIGIIAVIVIGVGAAYMGSSS 178
                    57889999*******************************99988887665 PP

>> Band_3_cyto  Band 3 cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.7   0.00098       3.5      48     162 ..      24     143 ..      16     153 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00098
                  HHHHCHCCCTTSS-HHHHHHHHHHHTS-EE-CCHHHHHT-EEE-EE-TTS---------.........-EE--SSS-SS-HHHHHHTTTTTSS--... CS
  Band_3_cyto  48 drvvdqlviedqlkeedreevlraLLlkhrHqneekekgvllptvrslssigsllsekk.........kaskellskqssleteeakaseslskssse 136
                  +++++ +  ++ ++ +dr+ v +aL  +   +++++ ++ ++p +r+ +++ + +++++         ++s++++s++++ e+   k++++   ++++
   AJA92731.1  24 KQIIESFQKRSMISMQDRKYV-DALVEQYLTPRHRQMTSKMKPSERQKTNFPRIRKTTEssfkitevkATSEKTKSEETTSENPYIKSTAE---VKKS 117
                  6899999999*******9987.355555555555444555555555555555544444422222111133332222222222222222222...2233 PP

                  .......--SSTTGGGCCGGGS-TT- CS
  Band_3_cyto 137 eslsssleeekkkkkekilkkipega 162
                  e+++++l++++ + +ek+++++ ++ 
   AJA92731.1 118 EPQKEELASKEPTIEEKFIEHVEKDR 143
                  44555555556666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1909  (0.106476); expected 358.6 (0.02)
Passed bias filter:                      833  (0.046461); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2090.39
//
Query:       AJA92732.1  [L=52]
Description: ribosomal L39 protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-18   65.5   6.9    2.6e-18   65.3   6.9    1.1  1  Ribosomal_L39  Ribosomal L39 protein
     0.0047   16.0   1.2     0.0048   16.0   1.2    1.0  1  Ter            DNA replication terminus site-binding protein 


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   6.9   2.9e-22   2.6e-18       1      41 [.       9      49 ..       9      50 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 2.9e-22
  Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                   +K+rL+K++kq ++vPaWv+lkt+r vr+npk R WRrt+ 
     AJA92732.1  9 RKIRLIKKQKQASAVPAWVILKTKRSVRTNPKARAWRRTDV 49
                   7**************************************85 PP

>> Ter  DNA replication terminus site-binding protein (Ter protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.2   5.4e-07    0.0048     202     237 ..      11      46 ..       2      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.4e-07
         Ter 202 ekveqeiqdvkslPekakLkikRpvkvqPiarvwya 237
                  ++ +++++ +++P+ + Lk kR v+++P ar w +
  AJA92732.1  11 IRLIKKQKQASAVPAWVILKTKRSVRTNPKARAWRR 46 
                 55667888999**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 410.23
//
Query:       AJA92733.1  [L=436]
Description: phosphoglycerate mutase (2,3-diphosphoglycerate-independent), archaeal form [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-42  144.8   0.0    3.3e-42  144.2   0.0    1.3  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    3.9e-30  105.0   0.5    4.8e-30  104.7   0.5    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0006   19.5   0.0      0.014   15.0   0.0    2.1  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2   0.0   5.6e-46   3.3e-42       1     170 []      51     241 ..      51     241 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 5.6e-46
                   HHTSEEEEEE-----------TCHHHHTT--.HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-..-TTHHHHHHHT-EE CS
  PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGyd.pkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragri.steeakeLikalnee 95 
                   Ak+G++G + +v +giap+Sd+A++++lGy+  +  y GRG++EA+g+G+++k+gd+a+R+n+ t+d e+++iidrragr+ ++e+a ++ ++++e+
    AJA92733.1  51 AKNGKMGEVISVGKGIAPESDIAVFNMLGYKfHHADYAGRGVIEAIGTGMDFKDGDLALRGNFSTLD-ERDVIIDRRAGRHiEREDALAVSREIEEK 146
                   89*****************************56778******************************8.58899999999877*************** PP

                   E....TTEEEEEEE-STTEEEEEE.....--S-B--S--..SSTTS...........------BS..SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
  PhosphMutase  96 l..e.egvevkfypgveyrhllvl.....lsdkitdtdpphdkegk...........eikellpl.kseeaketaellnelieksqeiLedhpvN 170
                   l  + + ++v + p++++r+++ +     ls +it+tdp++ +++            +i+++lpl +++ ak  a+l+ne++eks +iL+d + N
    AJA92733.1 147 LkfSnPLAKVAVTPTIGHRVIVRIrdehpLSPNITNTDPAYSRVDGmgvakavgdflKIERCLPLdETDTAKLSADLVNEFTEKSLQILKDSETN 241
                   *9955889*********************************999999******************888999********************9988 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.5     8e-34   4.8e-30       2     237 ..      16     420 ..      15     430 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 8e-34
                    EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH........................... CS
                    xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
  Metalloenzyme   2 kvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel........................... 67 
                    k+v v+lDG+G+ p  + +    ++ AktP++dkL+k+       +++g+   + +++ + s+++ +++                           
     AJA92733.1  16 KIVYVLLDGVGDLPHPDIENktpLQAAKTPNMDKLAKN-------GKMGEVISVGKGIAPESDIAVFNMlgykfhhadyagrgvieaigtgmdfkd 104
                    57889*********987777789***************.......789******************9999************************** PP

                    ................................................................................................ CS
                    ................................................................................................ RF
  Metalloenzyme  68 ................................................................................................ 67 
                                                                                                                    
     AJA92733.1 105 gdlalrgnfstlderdviidrragrhieredalavsreieeklkfsnplakvavtptighrvivrirdehplspnitntdpaysrvdgmgvakavg 200
                    ************************************************************************************************ PP

                    ..........................................HHHHTT-----EEEEEE.EE-S---SSHHHHHT--EEEE--SHH.......... CS
                    ..........................................xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
  Metalloenzyme  68 ..........................................lrisetvkfahvtffwn.ggrsgyfnpleereeipsdtvitfdl.......... 110
                                                              +r s+++k  + +++++ g+++++++++++++ ++  +++ + +          
     AJA92733.1 201 dflkierclpldetdtaklsadlvneftekslqilkdsetnkKRNSKGKKLLNSILLRDaGNKYPKVETINKKYSMNFSCIVDMPVeigisnvlem 296
                    ******************************************99*********9999973678899*******************9********** PP

                    .....STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS....... CS
                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Metalloenzyme 111 .....qpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqplT 200
                            ++++e+a  a++ ++    + ++v++k +D+ GH+gd+ ++++ ie++De   + +l++i+ ++  +++ ADH ++   ++       
     AJA92733.1 297 kaysaGGLTDYEEKATVAAKSMET--ENAIYVHLKGPDEFGHDGDAIGKMKNIEEIDErFFGTLLKNIDTNKVAVMISADHATPCINKG------- 383
                    **9998999999999999999944..59******************************6689*************************99....... PP

                    .-----EEEEEESTT----S--S.SHHHHTT-TTEEEE CS
                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
  Metalloenzyme 201 sHtlepVPilivgkglapdkvke.gakfrekggLanva 237
                     H+ +pVP+li g+g+++d +++ +++f++kg+++ ++
     AJA92733.1 384 -HSDDPVPVLISGDGITNDGSERfTEEFAKKGEIGLLE 420
                    .*****************99999999999999877655 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.016        97       5      39 ..      21      61 ..      17      64 .. 0.69
   2 !   15.0   0.0   2.3e-06     0.014     157     237 ..     305     380 ..     239     409 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                  EETT-B....TTHHHHHG.S..TSHHHHHHHHHSEEESEEE- CS
  Phosphodiest  5 slDGlr....adlldrla.e..llpnlaaLakegvsapnlrp 39
                  +lDG+     +d+ ++   +  ++pn+++Lak+g  ++ +++
    AJA92733.1 21 LLDGVGdlphPDIENKTPlQaaKTPNMDKLAKNGKMGE-VIS 61
                  56666666665555555555569***********8887.666 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-06
                   HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHH.HHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
  Phosphodiest 157 ldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvD.kaigdLlealderglsaetniilvSDHGmadv 237
                    d ++++ v++k++e+ + ++v+l ++D +gH    d     ++++++D ++ g Ll+ +d +    ++++++++DH    +
    AJA92733.1 305 TDYEEKATVAAKSMETENAIYVHLKGPDEFGHDG--DAIGKMKNIEEIDeRFFGTLLKNIDTN----KVAVMISADHATPCI 380
                   55666777778888******************66..7777889******5579********99....**********77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3090.43
//
Query:       AJA92734.1  [L=219]
Description: RecA-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-28   98.3   0.3    7.1e-28   97.6   0.3    1.5  1  Rad51         Rad51
    5.1e-11   42.4   2.0      5e-10   39.1   2.0    2.1  1  ATPase        KaiC
      1e-05   25.1   0.0    1.4e-05   24.7   0.0    1.3  1  RecA          recA bacterial DNA recombination protein
    0.00032   20.7   1.7    0.00065   19.7   0.5    2.1  2  AAA_14        AAA domain
    0.00043   20.0   0.1    0.00056   19.6   0.1    1.2  1  Zot           Zonular occludens toxin (Zot)
    0.00066   19.5   0.1     0.0013   18.5   0.1    1.4  1  AAA_24        AAA domain
     0.0018   17.7   0.4     0.0055   16.1   0.1    1.8  2  DnaB_C        DnaB-like helicase C terminal domain
     0.0043   17.3   0.2     0.0079   16.5   0.0    1.5  1  AAA_22        AAA domain
     0.0052   16.5   0.2      0.072   12.8   0.1    2.5  2  IstB_IS21     IstB-like ATP binding protein
     0.0079   15.7   0.1      0.018   14.5   0.0    1.6  2  PhoH          PhoH-like protein
  ------ inclusion threshold ------
      0.011   16.3   0.6      0.026   15.1   0.6    1.7  1  AAA_18        AAA domain
      0.011   15.2   0.2      0.021   14.2   0.2    1.5  1  TniB          Bacterial TniB protein
      0.013   16.0   0.4      0.024   15.0   0.4    1.5  1  AAA           ATPase family associated with various cellular 
      0.015   14.8   0.0       0.09   12.3   0.0    2.0  1  AAA_25        AAA domain
      0.065   13.1   1.6      0.065   13.1   1.6    1.3  1  Palm_thioest  Palmitoyl protein thioesterase
       0.07   13.3   0.4       0.56   10.4   0.4    2.4  1  AAA_33        AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.3   6.3e-31   7.1e-28      25     200 ..       8     172 ..       1     216 [. 0.84

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 6.3e-31
                 HHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHH CS
       Rad51  25 klDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqq 123
                 +lD++ +GG++ g itei G  ++Gktql+ ++++    p      ++k+++idt   frper +++ +  +l ++++len  + R+  + +q e+l++
  AJA92734.1   8 SLDKIFSGGLQNGIITEISGLRGTGKTQLALQFAIE---P---LSNNKKILFIDTTVEFRPERFLQMLQSRNL-PASLLENLHVSRVTDTHKQIEILKT 99 
                 79***************************9888775...4...4579*********************99888.6789*******************86 PP

                 THHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------- CS
       Rad51 124 aaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsad 200
                     l ++ f+lli+D +t l+  ++s ++ l ++++++g+++ +L+++++  ++ ++itnq+ ++ + + + ++a+
  AJA92734.1 100 ----LDKNYFSLLIIDNITDLFAFEYSKKEHLIEKNTNFGNYMINLSQITQSEDIPIIITNQIFSHDEINYQRMHAQ 172
                 ....56788******************************************************98855544444443 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   2.0   4.5e-13     5e-10       2      79 ..       3      81 ..       2     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.5e-13
      ATPase  2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfv..tveepaedlrenakslGwdleklee 79
                ++ I  lD+i++gG+ +g ++ i+G  GtGKt +alqF+i+ +++ +++ +f+  tve ++e + +  +s       le+
  AJA92734.1  3 SSQIGSLDKIFSGGLQNGIITEISGLRGTGKTQLALQFAIEPLSN-NKKILFIdtTVEFRPERFLQMLQSRNLPASLLEN 81
                577999************************************999.******9878899999988877776555555555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.4e-05      40     143 ..       8     116 ..       1     160 [. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                 HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEES......S----HHHHHHTT--.GGG-EEE--SSHHHHHHHHHHHHTTT- CS
        RecA  40 aldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafida......ehaldpkyakklGvd.idellvsqpdtGeqaleiadalvrsga 131
                 +ld  +  GGl +G i+ei G   +Gkt lal+   e   +++ + fid+      e  l+   +++l    +++l vs+     + +ei+++l + + 
  AJA92734.1   8 SLDKIF-SGGLQNGIITEISGLRGTGKTQLALQFAIEPLSNNKKILFIDTtvefrpERFLQMLQSRNLPASlLENLHVSRVTDTHKQIEILKTLDK-NY 104
                 566655.4*****************************************8333333556666778999876369*******99999*****99855.67 PP

                 -SEEEEE-TTT- CS
        RecA 132 idlivvdsvaal 143
                   l+++d ++ l
  AJA92734.1 105 FSLLIIDNITDL 116
                 899999998876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.5   5.8e-07   0.00065       4      86 ..      22     126 ..      19     154 .. 0.64
   2 ?   -1.4   0.0         2   2.3e+03      51      59 ..     172     180 ..     141     194 .. 0.48

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-07
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpekllelilek..lke................ekktylflDEiqevpewe 80 
                 i  i+G+R +GKT l+ q++ e l ++++il+i+   e       ++ ++++l+  +le+  +++                +  ++l++D i  +  +e
  AJA92734.1  22 ITEISGLRGTGKTQLALQFAIEPLSNNKKILFIDTTVEFRperfLQMLQSRNLPASLLENlhVSRvtdthkqieilktldkNYFSLLIIDNITDLFAFE 120
                 56699***************9999999****99866533333333333333444444443221113445555566666532333448888888776666 PP

      AAA_14  81 kalksl 86 
                    k+ 
  AJA92734.1 121 YSKKEH 126
                 655554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
      AAA_14  51 kllelilek 59 
                 +l+++i +k
  AJA92734.1 172 QLENYIHQK 180
                 233333333 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     5e-07   0.00056       6     104 ..      26     136 ..      22     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5e-07
         Zot   6 tGapGsgKtsgavkkdllpalkegRkii..tnidGlrlerieqvlgekvs.tarliridnpegaetlkefakwatidkg..allviDEcqeifpvrake 99 
                  G  G+gKt  a+++ + p + + ++++  t ++ +r er+ q+l+     +  l +++      t k++++ +t dk+  +ll+iD    +f  +  +
  AJA92734.1  26 SGLRGTGKTQLALQFAIEPLSNNKKILFidTTVE-FRPERFLQMLQSRNLpASLLENLHVSRVTDTHKQIEILKTLDKNyfSLLIIDNITDLFAFEYSK 123
                 5889***************998877776235899.********9998877576788888777788888888888888665589**********999985 PP

         Zot 100 grkd.........p 104
                  ++          +
  AJA92734.1 124 -KEHliekntnfgN 136
                 .4334666555541 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.1e-06    0.0013       7      97 ..      25     133 ..      20     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
      AAA_24   7 iyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie................swedfldevvel.aaeladyktlviDtideleelc 81 
                 i G  g+GKT la+++        +k+lfidt     +  + +f ++                  ++d  ++++ l   +++ ++ l+iD+i++l  ++
  AJA92734.1  25 ISGLRGTGKTQLALQFaieplsnNKKILFIDTTV---EFRPERFLQMLqsrnlpasllenlhvsRVTDTHKQIEILkTLDKNYFSLLIIDNITDL--FA 118
                 56889*************************9977...4444444444444577778899998888888888888884446667799*********..88 PP

      AAA_24  82 laevirqnekaesked 97 
                 +++ ++ + + e+++ 
  AJA92734.1 119 FEYSKKEHLI-EKNTN 133
                 9999999988.44433 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.9e-06    0.0055       2     118 ..       2     122 ..       2     149 .. 0.58
   2 ?    1.0   0.1       0.2   2.3e+02     126     178 ..     101     158 ..      63     171 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-06
                 BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEE..ESSSXHHHHHHHHHHHHHTXXHHHHHHTTSX.HHHHHHHHHHH CS
                 xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
      DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavf..slemsaeqlvqRllsseaeidskklrtgklk.eedweklteai 96 
                 +s++  +LDk++s Glq+g ++ i +  ++Gkt lal++a +    ++++++++   +e   e+ +q l s   +++++ l++ +++  +d++k  e +
  AJA92734.1   2 ISSQIGSLDKIFSgGLQNGIITEISGLRGTGKTQLALQFAIEPLS-NNKKILFIdtTVEFRPERFLQMLQSR--NLPASLLENLHVSrVTDTHKQIEIL 97 
                 5678889**998637*************************77654.34455554115566666655544333..3333333333332222333333333 PP

                 HHHHH...SEEEEEEXSSXCHHHHH CS
                 xxxxx...xxxxxxxxxxxxxxxxx RF
      DnaB_C  97 eelse...aklfiddtpaltvseir 118
                 ++l +   + l+id+ ++l   e  
  AJA92734.1  98 KTLDKnyfSLLIIDNITDLFAFEYS 122
                 3333311134555555555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.2
                 HHTTEEEEEEEEGGGTB.TS.CS.SS..CCCHHHHHHHHHHHHHHHHCTSXEEEEEEX CS
                 xxxxxxxxxxxxxxxxx.xx.xx.xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C 126 kekglgliviDyLqlme.gs.ee.ke..nreqevseisrsLkalakelnvpvialsqL 178
                  ++  +l++iD +  +   + ++ ++  +++++  +   +L ++ +  ++p+i+  q+
  AJA92734.1 101 DKNYFSLLIIDNITDLFaFEySKkEHliEKNTNFGNYMINLSQITQSEDIPIIITNQI 158
                 3377788899988644422222222234677888888888999999999999988886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     7e-06    0.0079       8     106 ..      23     124 ..      18     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellr.alglelkaerlsseell.ealeqalrarav...ielliiDEaq 101
                 + + G  GtGKT l+ +++ +          +++++f++ +++  ++ +l++l + +l  +l + +l  +++  ++ +  + ++ +    +lliiD++ 
  AJA92734.1  23 TEISGLRGTGKTQLALQFAIEPLSN------NKKILFIDTTVEFRPERFLQMLQSrNLPASLLE-NLHVSRVTdTHKQIEILKTLDknyFSLLIIDNIT 114
                 5689***********9999998664......99999*************999985267777777.67777776666666555555568889*******9 PP

      AAA_22 102 hlr....s.e 106
                  l+    s +
  AJA92734.1 115 DLFafeySkK 124
                 9876766232 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   6.5e-05     0.072      52      84 ..      25      57 ..      17     148 .. 0.86
   2 ?   -1.2   0.0       1.3   1.5e+03     112     147 ..     159     196 ..     137     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.5e-05
   IstB_IS21 52 llGpsGvGKshlaialgveavraglsvlfvrve 84
                + G  G+GK+ la  ++ e   +++++lf+ ++
  AJA92734.1 25 ISGLRGTGKTQLALQFAIEPLSNNKKILFIDTT 57
                67999************************8764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
   IstB_IS21 112 lilDdlgllpldqaeaellfe..viekryerrsiiits 147
                    D++ ++ +  + ++++ +   +ek  ++++  i+s
  AJA92734.1 159 FSHDEINYQRMHAQLENYIHQkiYLEKINNKNTCTISS 196
                 44577777777777777777622235555555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.6e-05     0.018      18      57 ..      19      56 ..       5      73 .. 0.78
   2 ?   -3.9   0.0       6.7   7.5e+03       8      21 ..     178     191 ..     175     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE- CS
        PhoH 18 kndivfaiGpaGtGKtylavalavealkkkkvkriiltrp 57
                +  i+ + G  GtGKt la++ a+e l+++k  +i+++  
  AJA92734.1 19 NGIITEISGLRGTGKTQLALQFAIEPLSNNK--KILFIDT 56
                5557888999****************99864..5555544 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.7
                 HHHHHHHHHHH-SE CS
        PhoH   8 eQkeylealkkndi 21 
                 +Qk yle +++++ 
  AJA92734.1 178 HQKIYLEKINNKNT 191
                 69999999996554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.6   2.3e-05     0.026       3      96 ..      25     127 ..      24     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-05
      AAA_18   3 ltGtpGvGKttlakeL.....skrlgf.............gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghl 83 
                 ++G  G+GKt+la        s   ++              ++  ++++ ++l  +  ++ l+ s++ d++k+ ++l++l++n+      + l+id + 
  AJA92734.1  25 ISGLRGTGKTQLALQFaieplS---NNkkilfidttvefrPERFLQMLQSRNLPASLLEN-LHVSRVTDTHKQIEILKTLDKNYF-----SLLIIDNIT 114
                 89***********998443331...33666889998888888888888888888888888.**********************97.....999*****9 PP

      AAA_18  84 aeleseaakdikk 96 
                   + +e+ k+ + 
  AJA92734.1 115 DLFAFEYSKKEHL 127
                 9999999988776 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   1.9e-05     0.021      41     144 ..      26     129 ..      22     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
        TniB  41 vGdsnnGKtmivekFarlhppekd......edaekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDEihnlla 133
                  G   +GKt+++ +Fa +  ++++      ++ e +p   +q+    + ++l a++Le+l +    r + ++++ ++l++l++    +LiiD i +l a
  AJA92734.1  26 SGLRGTGKTQLALQFAIEPLSNNKkilfidTTVEFRPERFLQM---LQSRNLPASLLENLHVS---RVTDTHKQIEILKTLDKNYFSLLIIDNITDLFA 118
                 6677889999999998776555431221112233334444444...45678889999999887...4455566777899******************** PP

        TniB 134 gsarkqrefln 144
                  +++k++++++
  AJA92734.1 119 FEYSKKEHLIE 129
                 *****998876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.2e-05     0.024       4     126 ..      26     171 ..      24     176 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                 ESSTTSSHHHHHHHHHHH........HTHE...........EEEEETTTCSSS.................STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
         AAA   4 yGppGtGKTllakavake........lgve...........fleisgsellsk.................yvgesekkirelfkeakekakpsilfiDE 66 
                 +G  GtGKT la + a e        l              f        l++                  v ++ k+i+ ++k++ ++   s l+iD+
  AJA92734.1  26 SGLRGTGKTQLALQFAIEplsnnkkiL--FidttvefrperF--------LQMlqsrnlpasllenlhvsRVTDTHKQIE-ILKTLDKNY-FSLLIIDN 112
                 7999**************754333330..0222222223332........222444555556766666655556666665.555666665.6******* PP

                 GGGHHHHH.TTCCC..HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
         AAA  67 idalaksr.sgses..eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                 i  l+  + s++e+  e++++  n +++ l++ +++e+  i i++tn++ + d+    +R+  
  AJA92734.1 113 ITDLFAFEySKKEHliEKNTNFGNYMIN-LSQITQSED--IPIIITNQIFSHDEINY-QRMHA 171
                 *****99974443311444444555555.444555445..88999999999888888.77765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.1e-05      0.09      19     154 ..       6     116 ..       2     130 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.1e-05
      AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarl.lvldlagveslpL 116
                 + ++++++ g l  g ++ + G +gtGKt lal+ a++ ++             k l++++       ++R+ ++++ ++++a l   l++ +v     
  AJA92734.1   6 IGSLDKIFSGGLQNGIITEISGLRGTGKTQLALQFAIEPLSNN----------KKILFIDTTVEF--RPERFLQMLQSRNLPASLlENLHVSRV----- 87 
                 5567788888889999999*****************9888644..........266666644443..346666666665444433112222111..... PP

      AAA_25 117 fakdrggtlltadvdaleaaieevegvrlvviDplsra 154
                        t +  ++ ++ +++++ +   l++iD+++ +
  AJA92734.1  88 -------TDTHKQI-EILKTLDK-NYFSLLIIDNITDL 116
                 .......1122333.45556666.44666666666665 PP

>> Palm_thioest  Palmitoyl protein thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.6   5.8e-05     0.065     129     169 ..     159     203 ..      15     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
  Palm_thioest 129 vqkslvqaqywrdpekleeYlkknkFLpdiNnerdha......knet 169
                     +     +y r   +le+Y+ +  +L +iNn++++       +n++
    AJA92734.1 159 FSH--DEINYQRMHAQLENYIHQKIYLEKINNKNTCTisspfiQNTK 203
                   333..356799999999*****************9985555554444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4    0.0005      0.56       3      88 ..      24     167 ..      22     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0005
      AAA_33   3 llvGlpGsGKstlaerl.lkklg....avllssdt.....................................................lrrrlfgtdqq 43 
                 ++ Gl G+GK++la +  +++l       ++++ +                                                      ++ lf+ +  
  AJA92734.1  24 EISGLRGTGKTQLALQFaIEPLSnnkkILFIDTTVefrperflqmlqsrnlpasllenlhvsrvtdthkqieilktldknyfslliidNITDLFAFEYS 122
                 567***********9974222224435555666558888888888888888888777776666666666666666666666666655544444444444 PP

      AAA_33  44 sktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarf 88 
                 +k+ +++ ++++ + + +l ++++s+ +++i+ +  +s++e    
  AJA92734.1 123 KKEHLIEKNTNFGNYMINLSQITQSEDIPIIITNQIFSHDEINYQ 167
                 444666666666666667888888888888888877777776444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1607.98
//
Query:       AJA92735.1  [L=186]
Description: TATA-box-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-55  184.3   0.0    4.5e-27   93.8   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    8.6e-08   32.2   0.0     0.0018   18.4   0.0    2.4  2  DUF3378   Domain of unknown function (DUF3378)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0     5e-31   4.5e-27       2      84 ..       8      88 ..       7      89 .. 0.96
   2 !   88.8   0.0   1.9e-29   1.7e-25       2      83 ..      99     178 ..      98     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 5e-31
                EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHHH CS
         TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilkk 84
                + i+Nvvasa++++++dL+ + +k    ++eY p++fpglv+rl++pk++ liF+sGk+v+tGakse+ +++a+k+++++l+k
  AJA92735.1  8 ISIENVVASATVDQKMDLNDITKKF--PDVEYHPDQFPGLVFRLKSPKTATLIFTSGKMVCTGAKSEQMSKNAVKTVVEKLRK 88
                579******************7665..******************************************************97 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 1.9e-29
                 EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
         TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83 
                 ++iqN+vas+nlg +++Le+ a+++    + Yepe+fpgl+ r+ +pk+++l+FssGk+v+tGak+ee++++ ++++  +l+
  AJA92735.1  99 VTIQNIVASINLGGRIHLEQAARTL--PRSMYEPEQFPGLIHRMLDPKTVILLFSSGKLVCTGAKKEEDVYRSVNNLHALLE 178
                 68*******************9887..************************************************9999886 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     2e-07    0.0018      12      61 ..      26      76 ..      17      90 .. 0.83
   2 !   11.7   0.0   2.5e-05      0.22      24      59 ..     130     165 ..     123     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-07
     DUF3378 12 kkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61
                + +++++ +      + p+ vf+ k+++t   ++tSgK +  G++ e+ ++
  AJA92735.1 26 NDITKKFPDVeYHPDQFPGLVFRLKSPKTATLIFTSGKMVCTGAKSEQMSK 76
                55666665543567789****************************999775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.5e-05
     DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                  ++ p+ + +  +++t+I ++ SgK++  G++ e++
  AJA92735.1 130 PEQFPGLIHRMLDPKTVILLFSSGKLVCTGAKKEED 165
                 568899999999******************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1351.10
//
Query:       AJA92736.1  [L=266]
Description: ATPase, AAA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-25   88.3   0.1    6.1e-25   87.8   0.1    1.2  1  AAA_5            AAA domain (dynein-related subfamily)
    3.8e-13   49.4   0.0    5.4e-13   48.9   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    3.2e-08   34.1   0.0    5.3e-08   33.4   0.0    1.4  1  AAA              ATPase family associated with various cellul
    3.3e-07   30.4   0.1    6.5e-07   29.4   0.1    1.5  1  AAA_14           AAA domain
    4.5e-06   26.3   0.0    7.4e-06   25.6   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
    8.9e-06   26.2   0.1    1.8e-05   25.2   0.1    1.7  1  AAA_16           AAA ATPase domain
    3.7e-05   23.5   0.1    7.2e-05   22.6   0.1    1.4  1  Sigma54_activat  Sigma-54 interaction domain
    5.6e-05   23.2   0.3    0.00014   21.8   0.1    1.7  2  ATPase_2         ATPase domain predominantly from Archaea
    9.9e-05   22.9   0.0    0.00023   21.7   0.0    1.6  1  AAA_18           AAA domain
    0.00022   21.2   0.0    0.00033   20.6   0.0    1.4  1  Rad17            Rad17 P-loop domain
    0.00025   21.3   0.1    0.00046   20.5   0.1    1.6  1  AAA_22           AAA domain
     0.0004   20.6   0.0    0.00073   19.7   0.0    1.4  1  CbbQ_C           CbbQ/NirQ/NorQ C-terminal
    0.00073   18.7   0.0     0.0013   17.8   0.0    1.4  1  MCM              MCM P-loop domain
    0.00079   19.3   0.0     0.0013   18.6   0.0    1.2  1  AAA_11           AAA domain
     0.0008   19.5   0.0     0.0017   18.5   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
    0.00081   19.2   0.3      0.018   14.8   0.3    2.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0017   18.5   0.1     0.0033   17.6   0.1    1.6  1  AAA_33           AAA domain
     0.0039   16.6   0.0     0.0053   16.1   0.0    1.2  1  ATPase           KaiC
      0.004   17.4   0.0      0.013   15.8   0.0    1.9  1  AAA_28           AAA domain
     0.0043   16.1   0.0      0.022   13.7   0.0    2.0  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0044   16.2   0.0     0.0061   15.8   0.0    1.3  1  NB-ARC           NB-ARC domain
     0.0049   16.3   0.1        2.2    7.6   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0056   16.4   0.5      0.036   13.8   0.5    2.1  1  AAA_30           AAA domain
     0.0076   16.8   0.6      0.035   14.6   0.1    2.1  2  ABC_tran         ABC transporter
     0.0088   16.0   0.0      0.017   15.1   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.027   13.9   0.0    1.6  1  TniB             Bacterial TniB protein
      0.014   15.1   0.0      0.025   14.3   0.0    1.4  1  AAA_24           AAA domain
      0.015   15.5   0.1      0.028   14.6   0.1    1.4  1  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.016   15.3   0.6      0.059   13.5   0.6    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.02   14.6   0.0      0.039   13.7   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.024   14.4   0.0      0.034   13.9   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.028   14.3   0.0      0.073   13.0   0.0    1.6  1  RsgA_GTPase      RsgA GTPase
      0.032   13.8   0.1      0.058   13.0   0.1    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.034   13.4   0.7       0.17   11.2   0.0    2.0  2  Septin           Septin
      0.035   13.4   0.0       0.16   11.2   0.0    1.8  2  KAP_NTPase       KAP family P-loop domain
      0.037   14.0   0.0      0.068   13.1   0.0    1.4  1  NACHT            NACHT domain
      0.037   14.4   0.0      0.076   13.4   0.0    1.6  1  RNA_helicase     RNA helicase
      0.053   12.3   0.0      0.086   11.6   0.0    1.3  1  AAA_32           AAA domain
      0.083   11.9   0.0       0.16   11.0   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.084   12.6   0.0       0.14   11.8   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
        0.1   12.9   0.2        0.3   11.4   0.0    1.8  1  AAA_19           AAA domain
       0.12   12.1   0.0       0.45   10.3   0.0    1.9  1  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.15   11.6   0.0       0.37   10.4   0.0    1.6  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.1   1.5e-27   6.1e-25       2     138 .]      28     162 ..      27     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.5e-27
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSE.EE..-S CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerr.llleeg 99 
                 vl++Gp+GtgK++l++++a+    ++e ++++ +t+e++l+g+ ++++g+ ++ +++l ++++eg +l+lDE++ ae +vl +L   l++rr + l e+
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTRESHLVGSKSLSEGNIQFDEGILIKSMKEGNMLYLDEINAAEADVLLRLDEALDDRRqVVLKES 126
                 799*************************************************************************************99873667888 PP

                 SSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
       AAA_5 100 gelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                 g+++  +n++    + viat npl+  + +el p+l+sRf
  AJA92736.1 127 GGEIVTANKS----WFVIATINPLNhVGTKELPPQLLSRF 162
                 9999999987....*************************9 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.3e-15   5.4e-13       2     129 ..      28     162 ..      27     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-15
       AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfa.....nllladeinrappktqsalleameer.qvtve 94 
                 vl+ g  G++kt+lv+++ak+ +++++ i f      s ++G++ ++e   +++f +G +++     n+l  dein a++ +   l ea+++r qv ++
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTRESHLVGSKSLSEG--NIQFDEGILIKsmkegNMLYLDEINAAEADVLLRLDEALDDRrQVVLK 124
                 7899999************************************998765..66777787765333337899*******************985277776 PP

       AAA_3  95 ...gethklpepflvlatqnPieqeGtyplpeaqldrf 129
                    ge  + ++ ++v+at nP+++ Gt +lp   l rf
  AJA92736.1 125 esgGEIVTANKSWFVIATINPLNHVGTKELPPQLLSRF 162
                 111455677999********************999999 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.3e-10   5.3e-08       1     130 [.      28     168 ..      28     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.3e-10
                 EEEESSTTSSHHHHHHHHHHHHT.....HEE.EEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelg.....vef.leisgsell.skyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                 vl++Gp+GtGKT+l++  ak+ +     ++f l++  s l+ sk ++e++ ++ e +  +k++++   l +DEi a   +            +  L ++
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSmklesINFsLRTRESHLVgSKSLSEGNIQFDEGI-LIKSMKEGNMLYLDEINAAEADV-----------LLRLDEA 114
                 79*******************752222244446666666666667777777777666.346665448********996665...........3333333 PP

                 HHHTTTS............SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEET CS
         AAA  93 ldgvkkk............eskvivigatnr.....pdkldpallrgRfdrkiei 130
                 ld+ ++             ++  +vi++ n       ++l+p+ll +Rf +++++
  AJA92736.1 115 LDDRRQVvlkesggeivtaNKSWFVIATINPlnhvgTKELPPQLL-SRFPIRLRM 168
                 333333333333333333355567777766677778889999999.999988876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.6e-09   6.5e-07       4      90 ..      27     118 ..      24     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-09
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd.....kkladpe...kllelileklkeekktylflDEiqevp.ewekalkslvdeg 90 
                  +++ G++ +GKTtl+++++k++   k + + ++l + +      k+l+  e   +++e il k ++ + ++l+lDEi  ++ ++   l + +d++
  AJA92736.1  27 FVLVIGPKGTGKTTLVREFAKKQS-MKLESINFSLRTREShlvgsKSLS--EgniQFDEGILIKSMK-EGNMLYLDEINAAEaDVLLRLDEALDDR 118
                 5899******************99.556666666666555555542222..2345677888887556.8999******998524666666666666 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.8e-08   7.4e-06      25      78 ..      17      67 ..       9     109 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.8e-08
       AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql 78
                +le+  +++  vl++Gp+GtGKt++++++ kk +   ++  +infs +t  ++l
  AJA92736.1 17 ILEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQS---MKLESINFSLRTRESHL 67
                57788899999******************99877...88889999999987766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   4.2e-08   1.8e-05      17      50 ..      19      51 ..      11     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.2e-08
      AAA_16 17 ervrsgrpelvllsGesGvGKsslvrellralek 50
                e++++++   vl++G++G+GK++lvre+++  + 
  AJA92736.1 19 EKAHEQG-IFVLVIGPKGTGKTTLVREFAKKQSM 51
                5555544.58*******************84333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   1.7e-07   7.2e-05      10     146 ..      13     147 ..       7     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-07
                      HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHH.HHT.TTSEEEEET CS
  Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlf.eka.dgGtlfLDe 101
                      +++e ++k+ ++ + vl+ G +GtGK++l r   ++++    ++ ++n +    +  es+L G ++ +  G  +  +G + ++  +g +l+LDe
       AJA92736.1  13 NAFEILEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQS---MKLESINFS---LRTRESHLVGSKSLS-EGNIQFDEGILiKSMkEGNMLYLDE 99 
                      6778899999999***************9998765444...445566654...455689999987766.66677777766144425679***** PP

                      GGGS-HHHHHHHHHHHHHSE...EESBTSSSEEE--EEEEEEESS-HH CS
  Sigma54_activat 102 igelplelQekLlrvlqege...vervGsskeikvdvriiaatnedle 146
                      i+  ++++  +L ++l++++   ++  G++  +  +  ++ at + l+
       AJA92736.1 100 INAAEADVLLRLDEALDDRRqvvLKESGGEIVTANKSWFVIATINPLN 147
                      ********9999999998862223444666556666666666665554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   3.4e-07   0.00014      12     114 ..      18     115 ..      12     124 .. 0.67
   2 ?   -1.7   0.0       5.4   2.2e+03      48      82 ..     207     237 ..     196     263 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.4e-07
    ATPase_2  12 eeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk.eksklvfkaiell 109
                 +e + + +  ++++ Gp+g GKt+L++e++++++ k + + +    re+ +   ++    +e + ++++ ++i+  k     +l  ++++ +++ + l 
  AJA92736.1  18 LEKAHE-QGIFVLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTRESHLVGSKSL---SEGNIQFDEGILIKSMKEGN--MLYlDEINAAEADVLLR 110
                 444444.56678889******************998888888888888777766666...67777777777777776554..23335555555555444 PP

    ATPase_2 110 lekik 114
                 l++  
  AJA92736.1 111 LDEAL 115
                 44444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5.4
    ATPase_2  48 dkyviyyialreesiskldefieeeeekkklekal 82 
                 + + +yy++  +e i++++      +++ + +ka+
  AJA92736.1 207 SVEELYYSPSLRETIAYAKLI----DKDMSPKKAA 237
                 446677777777777777776....2222222222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   5.6e-07   0.00023       1      59 [.      28     118 ..      28     148 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.6e-07
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf...............................gvnlrdvakenglllevdpe.aldeskrldedkldk 59 
                 +l+ G+ G+GKttl +e +k+  +                               g+ ++++   n+l+l++ ++ + d  +rlde  +d+
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSMklesinfslrtreshlvgskslsegniqfdeGILIKSMKEGNMLYLDEINAaEADVLLRLDEALDDR 118
                 799*****************97668888889998888888888877777777777777777777777777777776444444444444333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     8e-07   0.00033      38      86 ..      16      64 ..       4     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8e-07
       Rad17 38 dvLesrkkr..iLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepd 86
                ++Le+++++   +L+ GP G gk+t v++ +k+ ++kl+    ++  +  +
  AJA92736.1 16 EILEKAHEQgiFVLVIGPKGTGKTTLVREFAKKQSMKLESINFSL--RTRE 64
                679999888988899********************9996543333..3333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.1e-06   0.00046       7      30 ..      27      50 ..      21     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
      AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                +++v+G++GtGKTtl+r+++++  
  AJA92736.1 27 FVLVIGPKGTGKTTLVREFAKKQS 50
                789*****************9974 PP

>> CbbQ_C  CbbQ/NirQ/NorQ C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.8e-06   0.00073       1      62 [.     176     239 ..     176     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-06
                 HHHHHHHHH.T--HHHHHHHHHHHHHHHTTBTT.TBSS---HHHHHHHHHHHTTT--HHHHHHH CS
      CbbQ_C   1 Eaeivares.gldeevakkLVklAneiRnlkeg.gLeegvSTRlLvyaAkLiasglpareacra 62 
                 E eiv++   + ++e+ ++ +klAn++R+     +L   +S R  ++ AkLi + +++++a+++
  AJA92736.1 176 ELEIVKEHVpEASNETLQRGIKLANTLRQAASVeELYYSPSLRETIAYAKLIDKDMSPKKAAEI 239
                 78999999999*****************8877637*************************9975 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.2e-06    0.0013      57     217 ..      25     181 ..      15     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                 S-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS..SSSSSHSSSEEEEESSSSSEEEEETHHHHT..TTSEEEEESGGGSTCHHHHHHHHHHHH..SE CS
         MCM  57 dinvllvgdpgtaKsqlLkyveklapravytsgk..gssaagLtaavvrdeetgefvleaGalvla..dkGvcciDefdkmkeedrsalhEamEq..qt 149
                  i vl++g  gt+K++l+++ +k  +           + ++ L+ +  ++ ++g++ ++ G l+ +  ++ ++++De++  + +    l Ea+++  q 
  AJA92736.1  25 GIFVLVIGPKGTGKTTLVREFAKKQSMKLESINFslRTRESHLVGS--KSLSEGNIQFDEGILIKSmkEGNMLYLDEINAAEADVLLRLDEALDDrrQV 121
                 589****************998765554433333003445556555..8889999*********7632456899*******************962134 PP

                 EEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHH CS
         MCM 150 isiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeela 217
                 +    +G ++t n    v+a +np +         +   +l+++lLsrF + + +   ++e++ e + 
  AJA92736.1 122 VLKESGGEIVTANKSWFVIATINPLNH--------VGTKELPPQLLSRFPIRLRMDYPPEEKELEIVK 181
                 444445666666777779******872........233478999999998876664444444444444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     3e-06    0.0013      10      76 ..      18     113 ..      11     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3e-06
      AAA_11  10 iksalseseitliqGPPGtgKTktivellsqll..............sr...............rkseeeksakpriLvCapSNaAvDellerllr 76 
                 +++a ++  ++l+ GP GtgKT+ + e+ ++                s+               +    + +++ ++L+  + NaA  ++l+rl +
  AJA92736.1  18 LEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQSmklesinfslrtreSHlvgskslsegniqfdEGILIKSMKEGNMLYLDEINAAEADVLLRLDE 113
                 578888999********************9996555555555544441144444555555544322455667777777777777777777777765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     4e-06    0.0017      12      96 ..      16     131 ..      11     169 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-06
                      HHHHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H................HHHHHHT......TTSEEEEEE-TT--H CS
  Sigma54_activ_2  12 erLeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp................ldlleqa......kggtLylkdiadlsk 83 
                      e Le+a ++   v+++G+kG+gk++  r ++k+++ +le  ++     +                       +      +g +Lyl +i+  ++
       AJA92736.1  16 EILEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTREShlvgskslsegniqfdEG----IliksmkEGNMLYLDEINAAEA 105
                      5699*********************9999999998888777774333322345654444444443322....1333355899************ PP

                      HHHHHHHHHHHH.............H CS
  Sigma54_activ_2  84 aeqkeLlellak.............a 96 
                      + + +L e+l+               
       AJA92736.1 106 DVLLRLDEALDDrrqvvlkesggeiV 131
                      ******99999855666555555542 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   4.3e-05     0.018      34     117 ..      26     124 ..      14     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.3e-05
      RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa...............lltnleekdvlfideihrlsraveevlysamedfrldivi 117
                   vl++Gp G Gkttl +  ak+  +kl++       +++ l++               l+++++e+++l++dei   +  v   l  a++d r  ++ 
  AJA92736.1  26 IFVLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTRESHLVGskslsegniqfdegiLIKSMKEGNMLYLDEINAAEADVLLRLDEALDDRRQVVLK 124
                 579**************9999987777666555444444444431111111111122225667888888888888888888888888888887655554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   7.9e-06    0.0033       2      24 ..      28      50 ..      27     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.9e-06
      AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                vl++G++G+GK+tl+++ +kk+ 
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKKQS 50
                899***************99976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05    0.0053      16      46 ..      22      52 ..      14     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
      ATPase 16 ipegrvvlitGepGtGKtifalqFlikgaek 46
                  +g  vl+ G  GtGKt+++ +F+ k+ +k
  AJA92736.1 22 HEQGIFVLVIGPKGTGKTTLVREFAKKQSMK 52
                5677789********************9776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-05     0.013       2      22 ..      28      48 ..      27      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-05
      AAA_28  2 ivitGgestGKTtlleaLaar 22
                + ++G+ +tGKTtl++++a++
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKK 48
                789***************976 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.3e-05     0.022      22     157 ..      15     160 ..      12     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-05
       AAA_6  22 yltltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyksl...gkifkGlaqs..Ga.WgCfdeFnrielevL.Svvaqqiktiqq 113
                 +  l +A +  +   + Gp gtGKt  v+++ak+ ++ +  +n s +   + l   + + +G +q   G+    + e n + l+ + ++ a  +  + +
  AJA92736.1  15 FEILEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRTRESHLvgsKSLSEGNIQFdeGIlIKSMKEGNMLYLDEInAAEADVLLRLDE 113
                 6667888999999999******************99999999988766655542223556676664224313456666666664440344555666667 PP

       AAA_6 114 alkekkkkfvfe..gkeiklnksvgifitmnp.gyagrteLPdnLka 157
                 al ++++ +  e  g+ ++ nks  ++ t+np +  g +eLP  L +
  AJA92736.1 114 ALDDRRQVVLKEsgGEIVTANKSWFVIATINPlNHVGTKELPPQLLS 160
                 77666655544322556677788888888888667788888887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-05    0.0061      11      47 ..      17      52 ..      11     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCC CS
      NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqilnksdev 47
                 L + +e + ++v + G  G GKttl+++  +k ++ 
  AJA92736.1 17 ILEKAHEQG-IFVLVIGPKGTGKTTLVREFAKKQSMK 52
                455555555.99*****************99996543 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1      0.01       4.2      24      42 ..      27      45 ..      12      57 .. 0.82
   2 !    7.6   0.0    0.0052       2.2     106     158 ..      91     145 ..      47     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
  Mg_chelatase 24 nlllvGppGsGKtmlakrl 42
                   +l++Gp G+GKt l + +
    AJA92736.1 27 FVLVIGPKGTGKTTLVREF 45
                  5899**********99865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0052
  Mg_chelatase 106 hnGvLfLDElpefkrkvlevLRePledge.vtisrakakv.efparfqlvaamNp 158
                   +  +L+LDE+   +++vl  L e l+d++ v+++ +  ++ +   +  ++a++Np
    AJA92736.1  91 EGNMLYLDEINAAEADVLLRLDEALDDRRqVVLKESGGEIvTANKSWFVIATINP 145
                   33499********************987615555555554144445667778888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.5   8.6e-05     0.036      11      43 ..      19      50 ..      15     124 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
      AAA_30 11 ealltsgdrvavltGpAGtGKttalkalreawe 43
                e+++++g  ++++ Gp GtGKtt++++ ++   
  AJA92736.1 19 EKAHEQG-IFVLVIGPKGTGKTTLVREFAKKQS 50
                5555555.6999*************99876544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   8.5e-05     0.035      10      45 ..      24      59 ..      18      84 .. 0.81
   2 ?    0.0   0.0       2.7   1.1e+03     105     134 ..      69      99 ..      51     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.5e-05
                TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 10 egekvaivGenGaGKStLlkllagllkpteGeilld 45
                +g  v ++G+ G+GK+tL++ +a++ + + ++i++ 
  AJA92736.1 24 QGIFVLVIGPKGTGKTTLVREFAKKQSMKLESINFS 59
                6778999****************9999888888554 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 2.7
                 TSGGS-HHHHH.HHHHHHHHHHTSSEEEEES CS
                 xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
    ABC_tran 105 spssLSgGqkq.rvalarallkkpkllllDE 134
                 + +sLS+G  q    +    +k+ ++l lDE
  AJA92736.1  69 GSKSLSEGNIQfDEGILIKSMKEGNMLYLDE 99 
                 3478888887755668888888888999988 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     4e-05     0.017      18      53 ..      22      58 ..       9      65 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4e-05
                H..TEEEEEEESTTSSHHHHHHHHHHHTT------TTT CS
        TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgveevkSPTF 53
                   g ++l  G+ G+GKTtlvr++ak+  + + +S  F
  AJA92736.1 22 HeqGIFVLVIGPKGTGKTTLVREFAKKQSM-KLESINF 58
                2335569999***************99866.4555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.6e-05     0.027      38      61 ..      28      51 ..      14      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.6e-05
        TniB 38 lllvGdsnnGKtmivekFarlhpp 61
                +l++G+  +GKt++v++Fa++++ 
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKKQSM 51
                79*****************99865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     6e-05     0.025       5      23 ..      28      46 ..      24      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
      AAA_24  5 iliyGpsgiGKTtlakelg 23
                +l++Gp g+GKTtl++e+ 
  AJA92736.1 28 VLVIGPKGTGKTTLVREFA 46
                79***************93 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   6.7e-05     0.028       2      36 ..      28      62 ..      28      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-05
                EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEE CS
         Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdf 36
                v+++G +g+GKt+l+++f +++  + e+  +++ +
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKKQSMKLESINFSLRT 62
                689****************9988776655555544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.6   0.00014     0.059       6      94 ..      28     106 ..      23     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00014
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.........EEEEETGGG-------------HH CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.........ivllDEidKihpkessgadvSreg 94 
                 +l++gp+g+Gkt l ++ a+ +++    kl  ++ s  +     e+ +   +  ++g+++++eg          +++lDEi  + +           +
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSM----KLESINFSLRTR----ESHLVGSKSLSEGNIQFDEGIliksmkegnMLYLDEINAAEA-----------D 106
                 789********************9....666666665555....333334444556777777766777777778*******98887...........4 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.2e-05     0.039      19      39 ..      21      42 ..       7      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.2e-05
      AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                 +++g ++l++Gp G+GK+Tl+
  AJA92736.1 21 AHEQGiFVLVIGPKGTGKTTLV 42
                56788999************97 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.1e-05     0.034       5      82 ..      32     108 ..      28     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.1e-05
  Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegk....pklpnlsvrtvdsflmalvks.tkgkililDEylllhaGyilll 82 
                      G  G GK+tl+r++++++ ++l ++  ++ l+t+ +    +k+ ++ +  +d+    +  s ++g+ l lDE+ +++a   ++l
       AJA92736.1  32 GPKGTGKTTLVREFAKKQsMKLESI--NFSLRTREShlvgSKSLSEGNIQFDEGILIK--SmKEGNMLYLDEINAAEA---DVL 108
                      5569*************66555444..4566666667787666666666666544443..3468********988773...544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00018     0.073      92     131 ..      17      57 ..       9      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                  HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
  RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                   l+++ ++  +++++G+ G GK+tL+ +++ ++++k +++ 
   AJA92736.1  17 ILEKAHEQgIFVLVIGPKGTGKTTLVREFAKKQSMKLESIN 57 
                  555555552456678*****************999998886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00014     0.058       3     101 ..      28     138 ..      26     152 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                 EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCHCC..CT.EEEETTTTECCHCTT-HHHHHHHHHHHH............TT-SEEE CS
        cobW   3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellret..gveivelenGciCctlredllkelealeere............erldvil 87 
                 +++ G+ G+GKTtL+++  ++ +++kl  i   +     +++l+ ++  ++  +++ +G +  +++e  +  l+++ + e            +r +v+l
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKK-QSMKLESINFSLR--TRESHLVGSKslSEGNIQFDEGILIKSMKEGNMLYLDEINAAEadvllrldealdDRRQVVL 123
                 5788*************9965.7777777755555..55666665552333366666666666666666666666665555666666677777777888 PP

                 EEECT.TTTHHHHHT CS
        cobW  88 iEttG.laePapvaf 101
                  E++G +++++ ++f
  AJA92736.1 124 KESGGeIVTANKSWF 138
                 888888777776644 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.17       5      36 ..      26      57 ..      22      81 .. 0.79
   2 ?    0.4   0.1      0.74   3.1e+02     158     234 ..     176     255 ..     173     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                EEEEEEEBTTSSCCCCCCTTSSSS-------- CS
      Septin  5 ftlmvvGesglGkttlintlfetdlieeekle 36
                + ++v+G +g+Gkttl++ + +++ ++ e+++
  AJA92736.1 26 IFVLVIGPKGTGKTTLVREFAKKQSMKLESIN 57
                5689****************999988876554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.74
                 HHHHHHHHH...HHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEE.SSSEEEEEEE.TTEEEETT- CS
      Septin 158 ElkefKkki...reeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliek.kgkkvrgRky.pWGvveven 234
                 El+ +K+++    +e  +  ik+ +   + ++   e    s +l+e++ +a +  +++  k  ++ v g  y +WG +e++ 
  AJA92736.1 176 ELEIVKEHVpeaSNETLQRGIKLANTLRQAASV--EELYYSPSLRETIAYAKLIDKDMSPKkAAEIVFGNVYaQWGNIELQK 255
                 566666665221334455667777733333333..346778899999999976666666554888899999956**999876 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038      0.16      10      75 ..      16     160 ..      11     206 .. 0.86
   2 ?   -0.1   0.0         1   4.4e+02      13      30 ..     231     249 ..     219     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
  KAP_NTPase  10 dilseptlatpivvgLygkWGsGKssllnklede..lkefa.......................................................... 48 
                 +il + + +++i v + g+ G+GK++l+ ++ ++  +k ++                                                          
  AJA92736.1  16 EILEKAH-EQGIFVLVIGPKGTGKTTLVREFAKKqsMKLESinfslrtreshlvgskslsegniqfdegiliksmkegnmlyldeinaaeadvllrlde 113
                 6777777.999*******************976511666669********************************************************* PP

  KAP_NTPase  49 ....................kpvrflfaefnawsfkggddavaella 75 
                                     ++  f++a++n++   g+ ++  +ll+
  AJA92736.1 114 alddrrqvvlkesggeivtaNKSWFVIATINPLNHVGTKELPPQLLS 160
                 *******************98899999*****999998877666555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
  KAP_NTPase  13 septlatpivvg.LygkWG 30 
                 ++p+ a +iv+g +y++WG
  AJA92736.1 231 MSPKKAAEIVFGnVYAQWG 249
                 3344488999977*****9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00016     0.068       3      23 ..      28      48 ..      27      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                EEEEC-TTTCHHHHHHHHHHH CS
       NACHT  3 vilqGeaGsGKTtLlqklala 23
                v++ G+ G GKTtL++++a +
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKK 48
                799*************99976 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00018     0.076       1      28 [.      28      55 ..      28      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00018
  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklkl 28
                  +++ Gp+g+GK+tl++e+ak+ + kl++
    AJA92736.1 28 VLVIGPKGTGKTTLVREFAKKQSMKLES 55
                  5799*************99998866633 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021     0.086      20      57 ..      15      52 ..      11      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
      AAA_32 20 lefglkikkkgYNifvlGesgtGrttlvkrlleeiakk 57
                +e+  k +++g  + v+G++gtG+ttlv+++ ++++ k
  AJA92736.1 15 FEILEKAHEQGIFVLVIGPKGTGKTTLVREFAKKQSMK 52
                555556788999999*****************998765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.16     120     147 ..      16      43 ..       8      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
       T2SSE 120 evlrkavrerglilvsGgTgsGKttlly 147
                 e+l+ka ++   +lv G+ g+GKttl+ 
  AJA92736.1  16 EILEKAHEQGIFVLVIGPKGTGKTTLVR 43 
                 78999955566789***********985 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.14      50     131 ..      28     109 ..      17     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
   IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlf...vrvedLveelkrarrdgklar..alkrllkvdllilDdlgllpldqaeaellf 131
                 ++++Gp G+GK+ l   ++++   +  s+ f   +r + Lv + ++ +++ ++ +   +k++ + ++l lD++       aea +l+
  AJA92736.1  28 VLVIGPKGTGKTTLVREFAKKQSMKLESINFslrTRESHLVGSKSLSEGNIQFDEgiLIKSMKEGNMLYLDEIN-----AAEADVLL 109
                 6899****************999999999995444667788777777777777653256778888999999874.....44445555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00071       0.3      11      32 ..      26      47 ..      16      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00071
      AAA_19 11 kvllvtaGpGtGKTrvlkhiva 32
                  +lv+++ GtGKT+++++  +
  AJA92736.1 26 IFVLVIGPKGTGKTTLVREFAK 47
                357889999******9998665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0011      0.45       4      24 ..      28      48 ..      26      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
   PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                +l+iG+ g+GKttL +++ ++
  AJA92736.1 28 VLVIGPKGTGKTTLVREFAKK 48
                799************998664 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00088      0.37      31      51 ..      23      43 ..      16      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00088
      AAA_25 31 pagelallaGapgtGKttlal 51
                  g ++l++G+ gtGKttl+ 
  AJA92736.1 23 EQGIFVLVIGPKGTGKTTLVR 43
                57899*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 2047.84
//
Query:       AJA92737.1  [L=334]
Description: oxidoreductase, aldo/keto reductase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-52  179.0   0.2    1.3e-52  178.8   0.2    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.2   7.3e-57   1.3e-52       1     293 [.      15     317 ..      15     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 7.3e-57
                   .EEEE-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE........--SSSTTSSSS-HHHH CS
  Aldo_ket_red   1 elglGtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv........dlrdaeiksglskeni 86 
                   e+g+G+w++      +ei+++ea ++l++a+++Ginff t+++Ygkg+se+l+Gea+k+   +r evii+tK         + +  e ++++ ++  
    AJA92737.1  15 EIGFGAWTIALNwwgKEIDEDEAKRMLKKAYDCGINFFETGDMYGKGKSERLIGEAFKD---MRNEVIISTKYgydfeqvkQVGHTELPQQFDEKFT 108
                   69********9999*********************************************...***********9988888888888888888888** PP

                   HHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEE.....S--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHH CS
  Aldo_ket_red  87 resleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvS.....nfsveqlekakkkkkvkivavqveynllreleeegllel 178
                   r++l +sl rL+tdyvD++ lH+p++ + +   ++ +l+ l++e ki+ + ++     +++ e le++   k   ++avq  +n+l++   ++ll  
    AJA92737.1 109 RKALTNSLDRLKTDYVDMYGLHNPKMHHIKDDSIFNTLDSLIEEEKIKTYQIAlgpaiGWTEEGLESM---KRKNVTAVQTVFNILEQTPGNELLNS 202
                   *****************************************************999999999999988...88999********************9 PP

                   HHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHG CS
  Aldo_ket_red 179 ckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednld 275
                     +++v++ +  p ++G+ltgk++ +++ ++k++r++ ++ e+++  l+++eel+ +a  +g s+ +la++++ls+++ ++v p + + e++++  d
    AJA92737.1 203 GIENNVGILVRVPDASGILTGKVNADTKIDEKDHRSV-RKGEWIKASLKKVEELKPIADRNGLSIKELAIKFILSKEGISSVFPTVISEEEIQTFSD 298
                   9999*************************99998887.466******************************************************** PP

                   GGG-.---HHHHHHHHHHH CS
  Aldo_ket_red 276 alel.klseeevaeldell 293
                     +   l++++++e+d+l+
    AJA92737.1 299 MSNGgYLNNSDMKEIDQLY 317
                   **999***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2726.90
//
Query:       AJA92738.1  [L=592]
Description: ATP synthase alpha/beta chain, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-93  310.0   0.0      1e-92  309.6   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.4e-43  146.9   0.0    4.1e-43  146.1   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    5.9e-14   52.3   0.2    1.5e-13   51.0   0.2    1.8  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.051   13.8   0.0       0.11   12.8   0.0    1.5  1  AAA_22           AAA domain
       0.11   11.1   0.2       0.17   10.5   0.2    1.2  1  DUF853           Bacterial protein of unknown function (DUF85
       0.19   11.7   0.7        9.8    6.2   0.2    3.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.6   0.0   3.4e-96     1e-92       1     213 []     214     437 ..     214     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.6 bits;  conditional E-value: 3.4e-96
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEEEEEEETTS-HHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtvlvantsnepvaareasiy 91 
                  G+rv+D++fp+++G++  ipgafg+Gktv +++++k+++s+ +++y+g+Gergne++evl efpe      g+ +m+rtvlvantsn+pvaareasiy
   AJA92738.1 214 GQRVIDTFFPLAKGGTGSIPGAFGTGKTVTLHQIAKWADSQ-VVVYIGCGERGNEMTEVLVEFPElkdprtGKpLMDRTVLVANTSNMPVAAREASIY 310
                  9************************************9999.***********************999876337************************ PP

                  HHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  92 tgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagka.....pdrtGsvtivaavspaggDfsdpvttatl 184
                  tg+t+AEy+rd+g++v+l+ads+srwaeAlre+s+rl+empa++gyp+yl+++la++yERag++     p+r Gsv+ v avsp+ggDf++pvtt+t+
   AJA92738.1 311 TGVTIAEYYRDMGYDVVLVADSTSRWAEALREMSGRLEEMPAEEGYPSYLASRLAEFYERAGRVrakgsPERDGSVSLVGAVSPSGGDFTEPVTTHTM 408
                  ****************************************************************99999999************************** PP

                  HHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 185 gitdgfivLdkklaqrkhfPainvlvSvS 213
                  +++++f+ Ld +la ++h+P+in+++S+S
   AJA92738.1 409 RFIKTFWALDASLAYSRHYPSINWMNSYS 437
                  ****************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.1   0.0   1.4e-46   4.1e-43       1     120 [.      85     204 ..      85     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 1.4e-46
                      EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-.EEEEEEE--EEEE-TTSECEEE CS
  ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkv.egkvkeiaeegeytvedtiaev 93 
                      yDGiqrpL+++a+ksgsfi rG++++++d ek+++f+p+v+vgd+v++g+i+Gtv+et+liehki+vpp+   gk+++i+ eg+y++e+ ia+v
       AJA92738.1  85 YDGIQRPLKDLAAKSGSFIGRGITTTPVDMEKQYHFSPSVAVGDEVEAGNIIGTVPETSLIEHKILVPPDHkGGKITNIVAEGDYALETEIATV 178
                      9********************************************************************772678******************* PP

                      CETT.ECEEEESSEEEETTS---ESEE CS
  ATP-synt_ab_Xtn  94 eteegkekeltllqkwPvrkprpvkek 120
                      e+++ ++  l++++kwPvr+prp+ ++
       AJA92738.1 179 EKDG-QSFPLKMYHKWPVRQPRPYLKR 204
                      *776.7******************987 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.2     5e-17   1.5e-13       1      69 []       7      69 ..       7      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5e-17
                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                   iv ++Gp v+++++ +   ++y+ ++v+  e  ++l+g++++l +d++ ++v++st+Gl++G++V+ TG
     AJA92738.1  7 IVWISGPAVKADGMAD--AKMYETVSVG--E--SKLIGEVIRLTGDVAFIQVYESTSGLKPGEPVVGTG 69
                   56699***********..**********..9..***********************************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05      0.11       6      51 ..     228     265 ..     225     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                 g + + G  GtGKT++l ++++++d         ++vv ++ + + +
  AJA92738.1 228 GTGSIPGAFGTGKTVTLHQIAKWAD---------SQVVvYIGCGERG 265
                 678899*****************95.........4444377776665 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   5.5e-05      0.17      24      50 ..     230     255 ..     223     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.5e-05
      DUF853  24 GliaGatGtGktvtLqvlaeslseaGv 50 
                 G i Ga GtGktvtL+++a+  ++  v
  AJA92738.1 230 GSIPGAFGTGKTVTLHQIAKW-ADSQV 255
                 7899**************974.44444 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.063   1.9e+02      45      75 ..      28      58 ..      20      60 .. 0.90
   2 ?    6.2   0.2    0.0033       9.8      43      63 ..     121     141 ..     108     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.063
      RnfC_N 45 lvkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                 v+vg+  l G++i  ++ +   +v+ s+sG
  AJA92738.1 28 TVSVGESKLIGEVIRLTGDVAFIQVYESTSG 58
                799**************99999********9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0033
      RnfC_N  43 kplvkvgdkVlkGqkiaeaeg 63 
                 +p v+vgd+V+ G++i++  +
  AJA92738.1 121 SPSVAVGDEVEAGNIIGTVPE 141
                 789*************98744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4093.01
//
Query:       AJA92739.1  [L=162]
Description: hypothetical protein T478_0433 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.049   13.7   0.0      0.088   12.8   0.0    1.4  1  HTH_Tnp_Tc5  Tc5 transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_Tnp_Tc5  Tc5 transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.9e-06     0.088      12      36 ..      74      99 ..      71     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-06
                 HHHHC-CT---SCHHHHHHHHHHH.H CS
  HTH_Tnp_Tc5 12 irqlrergipitgelirekAqela.s 36
                 i ++ ++ +p  +e+i+ekA+e++  
   AJA92739.1 74 IIDMEKKRFPMDREIIKEKALEILgD 99
                 788999*****************741 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.52
# Mc/sec: 937.54
//
Query:       AJA92740.1  [L=290]
Description: PF01882 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-21   76.1   0.0    3.4e-21   75.3   0.0    1.4  1  DUF58     Protein of unknown function DUF58
    9.1e-07   29.5   0.1      5e-05   23.9   0.0    2.4  2  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.15   11.5   0.0       0.26   10.7   0.0    1.3  1  DUF3047   Protein of unknown function (DUF3047)
       0.23   11.9   1.8        2.8    8.4   0.6    2.4  2  DUF5104   Domain of unknown function (DUF5104)


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   7.7e-25   3.4e-21       1      86 []      38     122 ..      38     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.7e-25
       DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqlldegdrvgl 86 
                 g++f+++ReYv gD++r+IdW++tARt++l+v+ef +er+ +v++++d s+++ +g   ++k     ++aas++ ++++++d+vgl
  AJA92740.1  38 GIEFSEVREYVLGDDIRHIDWNVTARTNKLHVKEFVEERDLRVYVMFDYSASNEFGFM-KSKKSIGHEVAASIIFSAMKNNDNVGL 122
                 78**************************************************999885.58888889*****************97 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.1e-08     5e-05      27     105 ..     106     183 ..      80     185 .. 0.77
   2 ?    3.3   0.0     0.029   1.3e+02      32      87 ..     223     285 ..     211     290 .] 0.78

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.1e-08
       VWA_2  27 aveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleak...gggtnlaaaLqlarkalkkrrkgekrvivlitD 105
                 a++ +++++ ++d+vgl  f ++ e+++p  k++++ l+ lr l a+   + +t++++ L +++ +l +      +v+++i+D
  AJA92740.1 106 AASIIFSAMkNNDNVGLGIFTNKLEHFVPARKGRKHSLSLLRTLLAYkpkSAQTDIESSLLQLHHILGQH-----SVVFIISD 183
                 3333455553699*******************************9999999****************955.....69999999 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.029
       VWA_2  32 lkslp.gdrvglvtfsdgpevliplt..kdkakilnalrnleak....gggtnlaaaLqlark 87 
                 l+++  g ++++ t +++ +  ++ +  ++++ki+n +++l+ +    + +  +++aL++ ++
  AJA92740.1 223 LEDIEsGEQLMVNTSDESFRNAFTKNslESHEKIKNDIKKLKVEmvnvSEQIPFDTALRQFFN 285
                 555544777777777778887887766789************999998888999999987766 PP

>> DUF3047  Protein of unknown function (DUF3047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.8e-05      0.26      56     134 ..      57     138 ..      51     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
     DUF3047  56 rWkvekllakaderekagdDyaariyvvfdddkdklslvertkka.ge..aLnYvWssslpkgtvvpnaytdrvrmiv.vesg 134
                  W+v++  +k+ ++e  ++   +r+yv+fd+ +++   + ++kk+ g+  a   ++s+ +++++v    +t++ +++v  ++g
  AJA92740.1  57 DWNVTARTNKLHVKEFVEE-RDLRVYVMFDYSASNEFGFMKSKKSiGHevAASIIFSAMKNNDNVGLGIFTNKLEHFVpARKG 138
                 6999999999977775544.448**********99888888887777779999999*99999999999999887776614455 PP

>> DUF5104  Domain of unknown function (DUF5104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.059   2.7e+02      82     103 ..     104     125 ..      43     127 .. 0.82
   2 ?    8.4   0.6   0.00061       2.8       6      36 ..     233     263 ..     231     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.059
     DUF5104  82 viaievvlkdeknednvGiysi 103
                 ++a  ++ +  kn+dnvG+ ++
  AJA92740.1 104 EVAASIIFSAMKNNDNVGLGIF 125
                 5666778888899999998765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00061
     DUF5104   6 lenkDkeaikklFskkalkesddldeeidel 36 
                 + n   e++++ F+k++l++++++ ++i++l
  AJA92740.1 233 MVNTSDESFRNAFTKNSLESHEKIKNDIKKL 263
                 6677889*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2089.90
//
Query:       AJA92741.1  [L=151]
Description: ribosomal protein L19e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-39  135.4   9.8    1.6e-39  135.3   9.8    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
       0.12   12.2   0.2        1.2    9.1   0.0    2.2  2  EF-hand_8       EF-hand domain pair
       0.14   12.6   0.7       0.39   11.2   0.1    1.8  2  CelTOS          Cell-traversal protein for ookinetes and spor


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   9.8   2.7e-43   1.6e-39       1     142 [.       4     144 ..       4     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 2.7e-43
                     -THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S-HHHHS-HHHHHHH CS
  Ribosomal_L19e   1 dlklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkGtkeaRlpekelWik 95 
                     +lk++krla+++++vG+nr++ld+++l+++a+Aitr+dir+li+ ++I+ k+ +g+s++ra++++ +k+k r +++G++kG+k+aR+ +k+++++
      AJA92741.1   4 NLKSKKRLASRIVGVGVNRIRLDNDHLDDVADAITRDDIRSLITANTITIKSFTGTSHGRAQAKRIQKAK-RGTKQGSKKGRKGARVGKKTVYVN 97 
                     5899**********************************************************99999886.77889******************* PP

                     HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
  Ribosomal_L19e  96 riRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                     ++RalR lLk  +++k+i+++ ++++Y+k+ G++++nka+L+++i +
      AJA92741.1  98 KVRALRYLLKISKDRKEITNESFKSIYKKIGGNTIRNKAHLRTVIAE 144
                     *******************************************9987 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.079   4.7e+02       4      14 ..      36      46 ..      34      56 .. 0.80
   2 ?    9.1   0.0    0.0002       1.2       3      18 ..     113     128 ..     111     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.079
   EF-hand_8  4 kItreelrril 14
                 Itr++ r+ +
  AJA92741.1 36 AITRDDIRSLI 46
                69****99966 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0002
   EF-hand_8   3 gkItreelrrilrilg 18 
                  +It e++++i++++g
  AJA92741.1 113 KEITNESFKSIYKKIG 128
                 68**********6554 PP

>> CelTOS  Cell-traversal protein for ookinetes and sporozoites
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.5e-05      0.39      26      70 ..      27      71 ..       3      78 .. 0.76
   2 ?   -0.5   0.0      0.26   1.6e+03      22      40 ..     109     127 ..      91     148 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.5e-05
      CelTOS 26 dskgdelvdlian.dlekelqknslvaasfLqsgfdvkkkaKeiiK 70
                ++  d+++d i++ d+ + +  n ++  sf  ++   +++aK+i K
  AJA92741.1 27 NDHLDDVADAITRdDIRSLITANTITIKSFTGTS-HGRAQAKRIQK 71
                5788*******963699999***********999.66788888766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.26
      CelTOS  22 radldskgdelvdliandl 40 
                 ++d +++++e    i + +
  AJA92741.1 109 SKDRKEITNESFKSIYKKI 127
                 4444444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1111.55
//
Query:       AJA92742.1  [L=111]
Description: hypothetical protein T478_0652 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.0   0.8        7.2    6.9   0.0    2.3  2  PPR_2     PPR repeat family


Domain annotation for each model (and alignments):
>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2    0.0025        44       2      25 ..      37      60 ..      36      62 .. 0.88
   2 ?    6.9   0.0    0.0004       7.2      31      45 ..      82      96 ..      80      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0025
       PPR_2  2 dvvtyNtlIsglckkgkveeAfkl 25
                ++ +y   Is+l+k++   +Af l
  AJA92742.1 37 NTESYKKFISYLLKNNLQLKAFNL 60
                7889999*********99999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0004
       PPR_2 31 krglePnsyTysili 45
                +++  Pn+ Ty+i +
  AJA92742.1 82 EKNSNPNAATYTIKL 96
                67889*******966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 770.63
//
Query:       AJA92743.1  [L=341]
Description: PF06849 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-73  246.9   0.2    1.4e-73  246.5   0.2    1.2  1  DUF1297      Domain of unknown function (DUF1297)
    6.4e-48  161.8   0.0    1.1e-47  161.0   0.0    1.4  1  DUF1246      Protein of unknown function (DUF1246)
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.028   14.4   0.0    1.7  2  ATP-grasp_3  ATP-grasp domain
       0.14   12.0   0.3       0.29   11.0   0.3    1.4  1  SCAN         SCAN domain


Domain annotation for each model (and alignments):
>> DUF1297  Domain of unknown function (DUF1297)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.5   0.2     3e-77   1.4e-73       1     188 []     156     341 .]     156     341 .] 0.98

  Alignments for each domain:
  == domain 1  score: 246.5 bits;  conditional E-value: 3e-77
                 HHHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEEEEEEEE-GGGHHHHH CS
     DUF1297   1 efeekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvGnipvvlREsllekvf 99 
                 ++++k ++l+++g+i+++  ++ +i+ey +G+ ++l++fyspl++e+e++g+d+R+es+++gl r+p+++ql+ ++ p+++v+Gn p+vlREsll++v+
  AJA92743.1 156 DYNTKRNQLISEGVISKD--ETLYIQEYAAGVLAYLQFFYSPLTGELEFFGVDQRHESDIEGLGRIPSEQQLKSKKVPSFNVIGNSPLVLRESLLDEVY 252
                 799************555..569**************************************************************************** PP

                 HHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT--CCHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
     DUF1297 100 elgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvymegspyskllfgeplsmGrrialEikeaiekdrleeivt 188
                 ++ge+fveaak++v+pG++GpFc+++v++++++++ f++saRiv+gtn+ym+gspy  llf+e++smG+ria+E+k a ek+++e+ivt
  AJA92743.1 253 TMGENFVEAAKRIVSPGMNGPFCIEGVYDENAKFTSFEFSARIVAGTNIYMDGSPYYSLLFNENMSMGKRIAREVKIAEEKNEIEKIVT 341
                 ****************************************************************************************8 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   2.4e-51   1.1e-47       1     120 [.       4     123 ..       4     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 2.4e-51
                 EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHHC-SS-EES-TTHHH CS
     DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfveYvgiekieelkvpifGnrkllr 99 
                 iatl+SH++lq+lkgAk+egf+t++vcek+reklY++fk+ide+i+++kf++il++e+qekl++++ail+Phg++++ ++ e+ie+++vpifGn+ +lr
  AJA92743.1   4 IATLGSHCSLQVLKGAKDEGFKTILVCEKKREKLYRRFKFIDELIIVEKFSEILNQEIQEKLKQQDAILIPHGTLIAQMSSEEIESITVPIFGNKWILR 102
                 89************************************************************************************************* PP

                 HHCSHHHHHHHHHHTT-BB-- CS
     DUF1246 100 wEerrekkrkyLekAgiriPk 120
                 wE++r++k+k++++A +++Pk
  AJA92743.1 103 WESDRTMKEKLMREATLPMPK 123
                 ********************8 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.1   9.3e+03      72      94 ..       8      32 ..       8      44 .. 0.61
   2 ?   14.4   0.0   6.4e-06     0.028       4      68 ..     107     167 ..     104     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                 SEEEEEEEEE.SSS..EEEEEEEEE CS
  ATP-grasp_3 72 GkplSvsllsdgek..vlvlavnrq 94
                 G+++S+++l  +++  ++++ v+++
   AJA92743.1  8 GSHCSLQVLKGAKDegFKTILVCEK 32
                 7788888886554311555655554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-06
                  HHHHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE.......EEEE CS
  ATP-grasp_3   4 KlktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieevelvqe 68 
                       k ++ea +++P     +e++  ek ++vK   +agg++ +++ ++e+ ++  + ++l++e
   AJA92743.1 107 RTMKEKLMREATLPMP--KPVTEPKDIEKLVIVKRQGAAGGKGYFMAANEEDYNT--KRNQLISE 167
                  5555566777799999..7788999*********************999977664..44445555 PP

>> SCAN  SCAN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   6.4e-05      0.29      41      68 ..      41      68 ..      30      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
        SCAN 41 keqilellvLEQFltilpeelqawvrer 68
                ++ i el++ E+F +il +e+q  ++++
  AJA92743.1 41 FKFIDELIIVEKFSEILNQEIQEKLKQQ 68
                56689******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2515.01
//
Query:       AJA92744.1  [L=122]
Description: hypothetical protein T478_0844 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.2   11.8   6.0       0.09   12.9   3.2    1.9  2  DMPK_coil  DMPK coiled coil domain like


Domain annotation for each model (and alignments):
>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.2     5e-06      0.09      33      61 .]      19      49 ..      13      49 .. 0.82
   2 ?   -2.2   0.0      0.25   4.5e+03      48      54 ..      69      75 ..      63      86 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-06
   DMPK_coil 33 kLke..aEkknreLeeeleqLkkemEelrar 61
                kL+e   Ekkn e +e+l++Lkke+E l+++
  AJA92744.1 19 KLREleLEKKNTEDKEKLNNLKKEIEILQSD 49
                56641168********************985 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.25
   DMPK_coil 48 leqLkke 54
                +e++ +e
  AJA92744.1 69 MEKMSEE 75
                4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2182  (0.121702); expected 358.6 (0.02)
Passed bias filter:                      771  (0.043003); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 938.74
//
Query:       AJA92745.1  [L=79]
Description: hypothetical protein T478_0623 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 612.98
//
Query:       AJA92746.1  [L=357]
Description: hypothetical protein T478_1154 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2895.48
//
Query:       AJA92747.1  [L=128]
Description: hypothetical protein T478_1460 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0065   16.4   3.0     0.0068   16.4   2.2    1.4  1  DER1           Der1-like family
  ------ inclusion threshold ------
       0.04   14.4   4.2      0.056   13.9   4.2    1.3  1  MerC           MerC mercury resistance protein
       0.05   13.5  12.7      0.072   13.0  12.7    1.2  1  7TMR-DISM_7TM  7TM diverse intracellular signalling
        2.3    8.0  12.7        2.9    7.7  12.7    1.1  1  DUF5373        Family of unknown function (DUF5373)
        7.7    4.7  13.0        8.9    4.5  13.0    1.0  1  DUF2070        Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DER1  Der1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.2   1.9e-06    0.0068       1      96 [.      26     121 ..      26     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
        DER1   1 iPavTRllltatvvltllgrlelispaklvlsyelvvkkvQiwRlltsllyfsstgfsflinlyfiyqysskLEegsfrgrsadyvylllflavli 96 
                 iP++   +l a     ++ ++ +i  a l     +  kk  + R+l s + f++++f   + +y+ +   s LE+ s +++  d+ +l++  ++++
  AJA92747.1  26 IPLIVNQILQADFFHVVIHQISFILAAFLTIMAGIGYKKSKMARMLFSSFGFAALAFGQAVFMYVKIFEESDLENVSASESILDFSILIMTILFAV 121
                 78888888888888889999999*99***************************************9999****************99888776665 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.2   1.6e-05     0.056      17      85 ..      18     102 ..      12     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
        MerC  17 llPvllallpllglsflasellhqvllil.vvaigllalvvgy.rrhrktsvlvlgalGllillvalflg..............t 85 
                 +  v++++ pl+   +l++  +h+v+  + +++ ++l+++ g   +  k+  ++   +G+++l+++  +               +
  AJA92747.1  18 IGSVVILSIPLIVNQILQADFFHVVIHQIsFILAAFLTIMAGIgYKKSKMARMLFSSFGFAALAFGQAVFmyvkifeesdlenvS 102
                 5568899999999999**********99878888999999998777778888888889999888877776566665554444322 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  12.7     2e-05     0.072      99     201 ..      11     122 ..       4     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
  7TMR-DISM_7TM  99 lllllavllsllllllpll.pyteslslaq..llallvillllligikaw.rkgnkparyfl..iawlllligvlidilsllgllpsn.....fft 183
                     ++l++++ s+++l++pl+  +  +  +++  +  +++il ++l++++ + +k+ k ar+++  +++++l++g  +++  ++++++ +       +
     AJA92747.1  11 SIFLITIIGSVVILSIPLIvNQILQADFFHvvIHQISFILAAFLTIMAGIgYKKSKMARMLFssFGFAALAFGQAVFM--YVKIFEESdlenvSAS 104
                    577888999999999999975556666777667777888888888888889**********95555555555555544..5554444420011333 PP

  7TMR-DISM_7TM 184 eyllqigvllevlllsla 201
                    e +l +++l+  +l++++
     AJA92747.1 105 ESILDFSILIMTILFAVG 122
                    366666888877777776 PP

>> DUF5373  Family of unknown function (DUF5373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  12.7   0.00081       2.9      29     137 ..      21     125 ..       4     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00081
     DUF5373  29 vlllqilalvlqivwllaeetskvllllkivsivltaf.tvavfivenkiLmrahyysalifllvplavlvlliilaflkilflnleaielksvlslvv 126
                 v++l i  +v qi      +++   ++++ +s +l+af t+ + i  +k+ m   ++s+  f  ++++  v++ + +f +  + n++a+e    +s+ +
  AJA92747.1  21 VVILSIPLIVNQI-----LQADFFHVVIHQISFILAAFlTIMAGIGYKKSKMARMLFSSFGFAALAFGQAVFMYVKIFEESDLENVSASESILDFSILI 114
                 3444444555555.....56778889999999999999789999************************99*******9999999977776665566777 PP

     DUF5373 127 aliilcvyivY 137
                  +i++ v ++Y
  AJA92747.1 115 MTILFAVGVFY 125
                 78888888888 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  13.0    0.0025       8.9      72     168 ..      10     123 ..       2     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0025
     DUF2070  72 lflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly...............fspesfl 155
                 + + l+t + +v+i+ +++++  +lqa +++ ++  +++++a  l ++  ++ ++ + a ++ +   ++a+++ +++               +++es+l
  AJA92747.1  10 YSIFLITIIGSVVILSIPLIVNQILQADFFHVVIHQISFILAAFLTIMAGIGYKKSKMARMLFSSFGFAALAFGQAVfmyvkifeesdlenvSASESIL 108
                 455566666677777888888888888888888888888888777777776665555444444444455554444444568888999998884444444 PP

     DUF2070 156 ll..lllslifalav 168
                  +  l+++++fa++v
  AJA92747.1 109 DFsiLIMTILFAVGV 123
                 440034444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1093  (0.0609627); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 943.98
//
Query:       AJA92748.1  [L=258]
Description: rhodanese-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.4e-40  135.8   0.1    2.8e-19   69.6   0.0    2.0  2  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   1.6e-23   2.8e-19       4     105 ..       7     113 ..       4     115 .. 0.94
   2 !   64.5   0.0   6.2e-22   1.1e-17       3     106 ..     144     250 ..     143     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.6e-23
   Rhodanese   4 elkellekgkvallDvRppeeYekghIpgAvnv...skdtlsrakkseapllelpeellel.gidnkktvvvycdgggr.aaaaaallkklGyknvsvl 97 
                 +l+++ ++++v ++D+R+  +Y+k+hIpgAv++   s+ ++ +++k   ++ e   ++l++ g+d++k++++y+++ g  aa+  ++  +  +++v+ l
  AJA92748.1   7 DLAKIYKDDSVLIIDARSYKDYSKSHIPGAVSLdlfSFHWADTSEKGLISFGEHMRKILSYaGVDENKKIIFYDNTTGMlAARGVWMCLYFSHPDVQML 105
                 677888889999*******************************************************************8999999999999899**** PP

   Rhodanese  98 dGGfkawk 105
                 dGG+++w 
  AJA92748.1 106 DGGLSNWT 113
                 *******7 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 6.2e-22
   Rhodanese   3 kelkellekgkvallDvRppeeY.......ek.ghIpgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaaaaallkklGyk 92 
                 +el e+++k    ++D+R+pee+       ++ ghIp A n+      +++ +++  l+  eel++l +id+++++v+yc+g+ raa+++  lkk G+k
  AJA92748.1 144 EELNENIGKV--TIIDARSPEEFdgttpraARgGHIPTAKNI----DWNNNLDDSGKLKSDEELESLyQIDKETEIVTYCQGAYRAANSYLSLKKIGFK 236
                 6888999665..5***************99555*********....66778888888888888888899****************999999******** PP

   Rhodanese  93 nvsvldGGfkawke 106
                 n++v+ G++ +w +
  AJA92748.1 237 NIKVYLGSWGEWGN 250
                 ************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1969.14
//
Query:       AJA92749.1  [L=211]
Description: ribosomal S3Ae family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-57  192.6   8.7    6.2e-57  192.5   8.7    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.01   15.6   0.2      0.015   15.1   0.2    1.2  1  DUF1481         Protein of unknown function (DUF1481)


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.5   8.7   6.9e-61   6.2e-57       2     201 ..       4     193 ..       3     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.5 bits;  conditional E-value: 6.9e-61
                     S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHH.HHTCSHTSSSEEEEEEEEEEESSEEEEEEEEEEE-HH CS
  Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaD.LtndekeqafrklklkieevqgknaltnFkgmeltrD 95 
                     k++k++Dk+k+K+W++v aP+ f++++iG++++       ++ e++kgr++ev+l D L++d+ +q+++k++++i+ev++++a+t Fk  e++++
      AJA92749.1   4 KARKIKDKWKEKKWVNVVAPDSFNNVNIGYVPI-------TDDENAKGRILEVTLWDiLKGDP-SQHQYKIIFQIDEVNDTKAKTVFKRYEYSKE 90 
                     6789*****************************.......*****************889**9.556**************************** PP

                     HHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEE CS
  Ribosomal_S3Ae  96 klrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlkelvkklipeslgkeiekeakkIyplrn 190
                     +lrsl+r++ss++++++d++tkD+y++r++++a+T+++   +++s+++++r +++++++++++++d++ +v++ +  +++++i  +akk++ lr+
      AJA92749.1  91 FLRSLIRRGSSKVNFNIDIQTKDNYIFRIKMIALTHRQ---LNTSRQRQLRLIAKDVIEKTVPTMDIDGFVQATCYGKINSDIMAAAKKVIKLRH 182
                     **************************************...***********************************77***************** PP

                     EEEEEEEEEE- CS
  Ribosomal_S3Ae 191 veirKvkvlkk 201
                     v  +Kvk++k+
      AJA92749.1 183 VGLEKVKLIKT 193
                     *********97 PP

>> DUF1481  Protein of unknown function (DUF1481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.6e-06     0.015      35     108 ..      77     148 ..      49     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-06
     DUF1481  35 gketevteYrwqegkLreikregegkkpesvqlRfdkeGevvfmqrqldgrkeplsedqlalyqfeAkrllels 108
                 + +t+ ++Y+++++ Lr++ r+g++k+++++ +  +++ + +f+ + ++ + ++l+     ++++ Ak+++e++
  AJA92749.1  77 KAKTVFKRYEYSKEFLRSLIRRGSSKVNFNIDI--QTKDNYIFRIKMIALTHRQLNTSRQRQLRLIAKDVIEKT 148
                 4678999*****************999998887..67889***************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1531.55
//
Query:       AJA92750.1  [L=237]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   75.7   8.1    7.3e-05   22.4   0.0    5.6  6  TPR_1            Tetratricopeptide repeat
    1.9e-19   68.1   3.1     0.0047   16.9   0.0    5.0  5  TPR_2            Tetratricopeptide repeat
    9.5e-14   51.5   0.0    0.00093   19.4   0.0    3.5  3  TPR_12           Tetratricopeptide repeat
      1e-13   50.6   4.5    0.00031   20.9   0.1    4.9  4  TPR_17           Tetratricopeptide repeat
    1.4e-12   47.9   2.4    3.8e-06   27.3   0.2    3.4  4  TPR_19           Tetratricopeptide repeat
    2.3e-12   46.1   4.2      0.046   13.9   0.0    5.2  5  TPR_8            Tetratricopeptide repeat
    3.5e-12   46.0   0.1     0.0047   17.6   0.0    5.0  5  TPR_14           Tetratricopeptide repeat
    7.4e-12   44.8   2.9     0.0001   21.9   0.0    3.8  4  TPR_11           TPR repeat
    2.4e-11   42.8   0.7      0.099   12.7   0.0    4.9  5  TPR_7            Tetratricopeptide repeat
    5.7e-11   41.9   0.3        0.5   10.3   0.0    5.3  5  TPR_10           Tetratricopeptide repeat
    1.2e-07   32.2   0.0      0.084   13.5   0.0    3.3  4  TPR_16           Tetratricopeptide repeat
    1.5e-07   31.3   3.3       0.13   12.4   0.0    4.8  5  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    5.5e-07   29.7   0.0      0.051   13.7   0.0    3.0  3  TPR_9            Tetratricopeptide repeat
      1e-06   28.9   4.9    0.00046   20.4   0.4    2.8  3  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    2.4e-06   27.7   0.1          1    9.4   0.0    4.2  3  DUF3856          Domain of Unknown Function (DUF3856)
    1.7e-05   24.4   4.7      0.036   13.5   0.4    3.0  3  Coatomer_E       Coatomer epsilon subunit
    3.2e-05   24.2   3.3      0.014   15.7   0.1    3.4  3  TPR_20           Tetratricopeptide repeat
    0.00086   19.8   0.6        1.4    9.3   0.1    3.1  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0018   18.2   1.5      0.025   14.5   0.1    2.7  3  DUF4919          Domain of unknown function (DUF4919)
     0.0026   18.3   3.6        5.2    7.9   0.0    4.4  5  TPR_6            Tetratricopeptide repeat
     0.0034   17.4   1.1       0.39   10.8   0.0    3.8  3  MIT              MIT (microtubule interacting and transport) 
     0.0089   16.5   0.1         11    6.5   0.0    3.3  4  BTAD             Bacterial transcriptional activator domain
  ------ inclusion threshold ------
      0.015   14.1   0.1      0.039   12.7   0.1    1.6  2  COPI_C           Coatomer (COPI) alpha subunit C-terminus


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.6   4.3e-06    0.0033      11      34 .]      16      39 ..      15      39 .. 0.93
   2 !   13.2   0.1   7.6e-05     0.059       9      33 ..      48      72 ..      40      73 .. 0.88
   3 ?    2.5   0.0      0.19   1.4e+02      10      25 ..      83      98 ..      82     105 .. 0.91
   4 !   22.4   0.0   9.3e-08   7.3e-05       2      34 .]     109     141 ..     108     141 .. 0.94
   5 !   20.5   0.0   3.7e-07   0.00029       2      34 .]     143     175 ..     142     175 .. 0.95
   6 ?   -2.8   0.0       8.9   6.9e+03      10      20 ..     185     195 ..     184     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-06
                HHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 11 yfklgkydeAleyyekALelnPnn 34
                +f  +k+d A+e+++k Le +Pn+
  AJA92750.1 16 LFDAKKFDAAIEFCQKLLEKDPND 39
                57889*****************97 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.6e-05
                HHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1  9 nayfklgkydeAleyyekALelnPn 33
                 ay+  g y++ +++ +kALe +Pn
  AJA92750.1 48 TAYYIVGAYEDSIKCSDKALEKDPN 72
                79**********************9 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.19
                HHHHTT-HHHHHHHHH CS
       TPR_1 10 ayfklgkydeAleyye 25
                a+ kl+ +d+ le++e
  AJA92750.1 83 ALEKLELHDQVLECCE 98
                7899***********8 PP

  == domain 4  score: 22.4 bits;  conditional E-value: 9.3e-08
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +al  +G a+ k g++++Al  y+ ALel+ +n
  AJA92750.1 109 DALVTKGIALNKTGNHEDALTLYDLALELDKTN 141
                 78999*************************887 PP

  == domain 5  score: 20.5 bits;  conditional E-value: 3.7e-07
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +al n+++++ +l++y+e + yy+ + ++ P++
  AJA92750.1 143 DALMNMAVTLSYLERYQESIPYYDTVQQIMPDF 175
                 89**************************99986 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 8.9
                 HHHHTT-HHHH CS
       TPR_1  10 ayfklgkydeA 20 
                 a+ klg+ d+A
  AJA92750.1 185 AFKKLGREDDA 195
                 67899988877 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   2.4e-05     0.019      11      34 .]      16      39 ..      14      39 .. 0.93
   2 !   16.6   0.0     8e-06    0.0063       2      33 ..      41      72 ..      40      73 .. 0.95
   3 ?   -2.4   0.0       9.6   7.5e+03      10      31 ..      83     104 ..      82     107 .. 0.67
   4 !   16.9   0.0   6.1e-06    0.0047       2      34 .]     109     141 ..     108     141 .. 0.92
   5 !   16.2   0.0   1.1e-05    0.0084       2      33 ..     143     174 ..     142     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
       TPR_2 11 yyklgdyeeAleafekAleldPnn 34
                ++ +++++ A+e+++k le dPn+
  AJA92750.1 16 LFDAKKFDAAIEFCQKLLEKDPND 39
                68899*****************97 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8e-06
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                 al nl  ayy  g ye+ +++ +kAle dPn
  AJA92750.1 41 IALQNLSTAYYIVGAYEDSIKCSDKALEKDPN 72
                7999***************************8 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 9.6
       TPR_2  10 ayyklgdyeeAleafekAleld 31 
                 a++kl  +++ le++e  l+ +
  AJA92750.1  83 ALEKLELHDQVLECCEILLSKN 104
                 5666666777788888777766 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 6.1e-06
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +al   G a+ k g++e+Al +++ Aleld +n
  AJA92750.1 109 DALVTKGIALNKTGNHEDALTLYDLALELDKTN 141
                 67888999999*******************987 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.1e-05
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                 +al+n++  + +l +y+e + +++ + ++ P+
  AJA92750.1 143 DALMNMAVTLSYLERYQESIPYYDTVQQIMPD 174
                 799**************************998 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.9e-05      0.03      26      73 ..      22      68 ..      16      72 .. 0.90
   2 !   19.4   0.0   1.2e-06   0.00093      23      76 ..      87     139 ..      86     140 .. 0.89
   3 !   13.5   0.0   8.4e-05     0.065       5      33 ..     144     172 ..     141     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-05
      TPR_12 26 lekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73
                +++a+e +++ll++  p+  ++l+nL+++y+  g ye+ ++   +al+
  AJA92750.1 22 FDAAIEFCQKLLEK-DPNDPIALQNLSTAYYIVGAYEDSIKCSDKALE 68
                78999999999965.799***********************9999997 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.2e-06
      TPR_12  23 lellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 lel++++le ++ ll + ++  + +l + g+++ ++g++e+Al l+  al++++
  AJA92750.1  87 LELHDQVLECCEILLSK-NDKDVDALVTKGIALNKTGNHEDALTLYDLALELDK 139
                 68999******877765.5699****************************9976 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 8.4e-05
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleia 33 
                 al n+a++l +l+ry+e++ +++++ +i+
  AJA92750.1 144 ALMNMAVTLSYLERYQESIPYYDTVQQIM 172
                 5679******************9998875 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1     4e-07   0.00031       2      31 ..      29      58 ..      28      62 .. 0.88
   2 ?    2.0   0.1      0.43   3.4e+02       3      11 ..      64      72 ..      62      74 .. 0.90
   3 ?    6.9   0.0     0.012       9.1       5      33 ..     100     128 ..      94     129 .. 0.89
   4 !   18.7   0.1   2.1e-06    0.0016       1      31 [.     130     160 ..     130     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4e-07
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmt 31
                ++k le+dPn++ a++nL ++++  G +++
  AJA92750.1 29 CQKLLEKDPNDPIALQNLSTAYYIVGAYED 58
                89********************99886655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.43
      TPR_17  3 lkaleldPn 11
                 kale+dPn
  AJA92750.1 64 DKALEKDPN 72
                59******9 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.012
      TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                  l ++ +++da+  ++ +l k G++++A+
  AJA92750.1 100 LLSKNDKDVDALVTKGIALNKTGNHEDAL 128
                 6788999*******************996 PP

  == domain 4  score: 18.7 bits;  conditional E-value: 2.1e-06
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                 ly  aleld++n+da+ n+A++l+ + ++++
  AJA92750.1 130 LYDLALELDKTNVDALMNMAVTLSYLERYQE 160
                 6889********************9999987 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   4.9e-09   3.8e-06       1      61 [.      16      77 ..      16      84 .. 0.91
   2 !   10.1   0.2    0.0011      0.89      18      64 ..     101     145 ..      91     149 .. 0.66
   3 !   15.7   0.1     2e-05     0.016       5      60 ..     122     177 ..     118     179 .. 0.89
   4 !    7.4   0.0    0.0079       6.2       5      44 ..     156     195 ..     154     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.9e-09
      TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61
                l++++++++A+++ +++l++dp+++ a+ +L  a++  g +++ +++ d+++e+dp++  ++
  AJA92750.1 16 LFDAKKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDSIKCSDKALEKDPNEeHAV 77
                6899*****************************************************64555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
      TPR_19  18 lqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                 l+++ k+ +a+    +al ++g+ ++A  l d ++e d+   ++ +L
  AJA92750.1 101 LSKNDKDVDALVTKGIALNKTGNHEDALTLYDLALELDKT--NVDAL 145
                 5566667777777777777777777777777777766665..44444 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2e-05
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60 
                 g++++Al l+  al+ d  n +a++++A  l  l +++e +   d++++  pd +r
  AJA92750.1 122 GNHEDALTLYDLALELDKTNVDALMNMAVTLSYLERYQESIPYYDTVQQIMPDFSR 177
                 99************************************999888888888777655 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0079
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeA 44 
                 ++y+e ++++  + q  p+ ++a +   +a  +lg+ d+A
  AJA92750.1 156 ERYQESIPYYDTVQQIMPDFSRASIEKSKAFKKLGREDDA 195
                 5899**********************************99 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0032       2.5      12      34 .]      17      39 ..      16      39 .. 0.88
   2 !    9.1   0.1    0.0022       1.7       3      33 ..      42      72 ..      41      73 .. 0.93
   3 !   13.9   0.0   5.9e-05     0.046       2      34 .]     109     141 ..     108     141 .. 0.93
   4 !   11.3   0.0   0.00041      0.32       2      30 ..     143     171 ..     142     175 .. 0.88
   5 ?   -0.2   0.0         2   1.5e+03       6      20 ..     181     195 ..     176     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0032
                HHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8 12 lklgdyeeAkeyyekaleldpdn 34
                ++ +++++A+e+++k le dp++
  AJA92750.1 17 FDAKKFDAAIEFCQKLLEKDPND 39
                56799*************99885 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  3 ayynlgsiylklgdyeeAkeyyekaleldpd 33
                a++nl+ +y   g ye ++++  kale dp+
  AJA92750.1 42 ALQNLSTAYYIVGAYEDSIKCSDKALEKDPN 72
                6899**********************98886 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5.9e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                 +a++ +g ++ k+g++e A   y  aleld++n
  AJA92750.1 109 DALVTKGIALNKTGNHEDALTLYDLALELDKTN 141
                 688999************************975 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00041
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekalel 30 
                 +a++n++ +++ l++y+e++ yy  + ++
  AJA92750.1 143 DALMNMAVTLSYLERYQESIPYYDTVQQI 171
                 799********************987766 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2
                 HHHHHHHHTT-HHHH CS
       TPR_8   6 nlgsiylklgdyeeA 20 
                  ++++ +klg+ + A
  AJA92750.1 181 EKSKAFKKLGREDDA 195
                 67889999*999877 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   8.4e-05     0.066      12      41 ..      17      46 ..      14      49 .. 0.89
   2 !    7.9   0.0    0.0078       6.1       3      38 ..      42      77 ..      40      84 .. 0.83
   3 ?    2.9   0.0      0.32   2.5e+02      10      38 ..      83     111 ..      80     114 .. 0.89
   4 !   17.6   0.0     6e-06    0.0047       3      42 ..     110     149 ..     108     152 .. 0.91
   5 ?    0.3   0.0       2.3   1.8e+03      11      37 ..     152     178 ..     148     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
      TPR_14 12 lalGdpdeAiallrralalaPddaeawlll 41
                + + ++d+Ai+ ++++l+++P+d+ a+  l
  AJA92750.1 17 FDAKKFDAAIEFCQKLLEKDPNDPIALQNL 46
                67889*******************999877 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0078
      TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeaw 38
                al+ l  a++  G ++++i++ ++al+++P+++ a 
  AJA92750.1 42 ALQNLSTAYYIVGAYEDSIKCSDKALEKDPNEEHAV 77
                66778889999*******************987654 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.32
      TPR_14  10 allalGdpdeAiallrralalaPddaeaw 38 
                 al+ l+ +d+ +++++ +l+++ +d +a+
  AJA92750.1  83 ALEKLELHDQVLECCEILLSKNDKDVDAL 111
                 7889999***************9998876 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 6e-06
      TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                 al   + al   G++++A++l++ al+l+ ++ +a++ +a
  AJA92750.1 110 ALVTKGIALNKTGNHEDALTLYDLALELDKTNVDALMNMA 149
                 67777899****************************9998 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 2.3
      TPR_14  11 llalGdpdeAiallrralalaPddaea 37 
                 l  l++++e+i +++ + +  Pd+ +a
  AJA92750.1 152 LSYLERYQESIPYYDTVQQIMPDFSRA 178
                 666889999*****9999998998877 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   4.7e-05     0.036       4      39 ..      16      51 ..      14      54 .. 0.93
   2 !   10.0   0.2   0.00068      0.53       3      26 ..      49      72 ..      48      76 .. 0.94
   3 !   21.9   0.0   1.3e-07    0.0001       3      37 ..     117     151 ..     115     153 .. 0.91
   4 ?   -1.4   0.0       2.5   1.9e+03       9      31 ..     157     179 ..     154     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39
                +++  k+++Aie  +k l+ dP+++ a+ nL  ayy
  AJA92750.1 16 LFDAKKFDAAIEFCQKLLEKDPNDPIALQNLSTAYY 51
                78999**************************99998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00068
      TPR_11  3 ayyeqGkyeeAieaYkkAlkldPd 26
                ayy  G ye++i++  kAl+ dP+
  AJA92750.1 49 AYYIVGAYEDSIKCSDKALEKDPN 72
                79999******************8 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.3e-07
      TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                 a+ + G+ e+A++ Y  Al+ld +n++a+ n++++
  AJA92750.1 117 ALNKTGNHEDALTLYDLALELDKTNVDALMNMAVT 151
                 67889*************************99876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.5
      TPR_11   9 kyeeAieaYkkAlkldPdnaeay 31 
                 +y e+i  Y +  ++ Pd+ +a 
  AJA92750.1 157 RYQESIPYYDTVQQIMPDFSRAS 179
                 77888877877777777765555 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0025         2      14      35 ..      21      40 ..      16      41 .. 0.90
   2 ?    4.3   0.0     0.063        49       1      34 [.      42      73 ..      42      74 .. 0.86
   3 ?   -0.6   0.0       2.3   1.8e+03      10      26 ..      85     101 ..      82     109 .. 0.67
   4 !   11.2   0.0    0.0004      0.31       6      30 ..     115     139 ..     110     142 .. 0.80
   5 !   12.7   0.0   0.00013     0.099       1      23 [.     144     166 ..     144     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
       TPR_7 14 dyeeAielyeqsLaltkdpeda 35
                +++ Aie++++   l+kdp+d+
  AJA92750.1 21 KFDAAIEFCQK--LLEKDPNDP 40
                79*********..*****9986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.063
       TPR_7  1 aLlnLarlysrlGdyeeAielyeqsLaltkdped 34
                aL nL  +y  +G ye+ i++  +  al+kdp++
  AJA92750.1 42 ALQNLSTAYYIVGAYEDSIKCSDK--ALEKDPNE 73
                57777788888999**********..*****987 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
       TPR_7  10 srlGdyeeAielyeqsL 26 
                 ++l  +++ +e++e +L
  AJA92750.1  85 EKLELHDQVLECCEILL 101
                 56667888999998855 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.0004
       TPR_7   6 arlysrlGdyeeAielyeqsLaltk 30 
                 + +  + G++e+A++ly  +L+l+k
  AJA92750.1 115 GIALNKTGNHEDALTLYDLALELDK 139
                 6677789************888776 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.00013
       TPR_7   1 aLlnLarlysrlGdyeeAielye 23 
                 aL n+a++ s l +y+e i +y 
  AJA92750.1 144 ALMNMAVTLSYLERYQESIPYYD 166
                 799*******************6 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.053        41      17      41 ..      15      38 ..      11      40 .. 0.76
   2 !    6.6   0.0    0.0096       7.5       4      30 ..      42      68 ..      41      69 .. 0.90
   3 ?    4.2   0.0     0.055        43      20      38 ..      85     103 ..      85     106 .. 0.88
   4 !   10.3   0.0   0.00064       0.5       9      31 ..     115     137 ..     109     140 .. 0.90
   5 !    9.9   0.0   0.00088      0.69       4      26 ..     144     166 ..     142     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.053
      TPR_10 17 rydeAealleealairrrllGpdHP 41
                ++ +A ++ + a++ +++ll+ d+ 
  AJA92750.1 15 KLFDAKKF-DAAIEFCQKLLEKDPN 38
                56667777.899********98864 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0096
      TPR_10  4 slnNLanalrqrgrydeAealleeala 30
                +l NL+ a++ +g y+++ +  ++al+
  AJA92750.1 42 ALQNLSTAYYIVGAYEDSIKCSDKALE 68
                689**************9999888886 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.055
      TPR_10  20 eAealleealairrrllGp 38 
                 e ++l++++l++++ ll  
  AJA92750.1  85 EKLELHDQVLECCEILLSK 103
                 6899**********99975 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00064
      TPR_10   9 analrqrgrydeAealleealai 31 
                 ++al ++g++++A+ l++ al++
  AJA92750.1 115 GIALNKTGNHEDALTLYDLALEL 137
                 89*****************9986 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00088
      TPR_10   4 slnNLanalrqrgrydeAealle 26 
                 +l N+a++l+ + ry+e+  +++
  AJA92750.1 144 ALMNMAVTLSYLERYQESIPYYD 166
                 899***************99986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00011     0.084       7      67 ..      16      73 ..      13      74 .. 0.91
   2 !   10.9   0.0   0.00072      0.56      22      64 ..      99     138 ..      94     144 .. 0.87
   3 !   12.9   0.0   0.00018      0.14       9      61 ..     120     169 ..     113     174 .. 0.88
   4 ?    3.6   0.0      0.14   1.1e+02       7      56 ..     152     198 ..     146     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
      TPR_16  7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                +++a+++d+A++  + +l++d   P ++ Al +l  a++  g +++ +   ++al+ +p++
  AJA92750.1 16 LFDAKKFDAAIEFCQKLLEKD---PNDPIALQNLSTAYYIVGAYEDSIKCSDKALEKDPNE 73
                789********999*******...99999*****************999888888888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00072
      TPR_16  22 aalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64 
                 ++l ++     +++Al  +g a+ + g++++A+ ly+ al+ +
  AJA92750.1  99 ILLSKN---DKDVDALVTKGIALNKTGNHEDALTLYDLALELD 138
                 566777...77999*************************9765 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00018
      TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                 + g+ +dA+ +++ al++d     +++Al++ ++ +  + r++e + +y+  +
  AJA92750.1 120 KTGNHEDALTLYDLALELD---KTNVDALMNMAVTLSYLERYQESIPYYDTVQ 169
                 679****************...88999*******************9999865 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.14
      TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaal 56 
                 + ++ +y++ +++++++       Pd  +A+ ++  a+ ++gr ++A  +
  AJA92750.1 152 LSYLERYQESIPYYDTVQQIM---PDFSRASIEKSKAFKKLGREDDAFLA 198
                 667899*********999999...99999999999999999999999733 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0051         4      15      34 ..      20      39 ..      17      44 .. 0.88
   2 !   12.4   0.0   0.00016      0.13       6      35 ..      45      74 ..      42      78 .. 0.90
   3 ?   -0.8   0.0       2.2   1.7e+03      13      31 ..      86     104 ..      82     111 .. 0.77
   4 ?    6.6   0.0     0.011       8.2       9      37 ..     116     144 ..     114     148 .. 0.89
   5 ?    1.4   0.0      0.43   3.4e+02      13      37 ..     154     178 ..     143     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0051
                T-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPen 34
                ++++ A ++++ lLe++P+ 
  AJA92750.1 20 KKFDAAIEFCQKLLEKDPND 39
                68999*************86 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00016
                HHHHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C  6 ylAlGhyklgeYseArryvdalLeiEPenr 35
                 l+ ++y +g Y+++ ++ d  Le++P+ +
  AJA92750.1 45 NLSTAYYIVGAYEDSIKCSDKALEKDPNEE 74
                5999***********************976 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.2
                 HHT-HHHHHHHHHHHHHHT CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiE 31 
                 kl  +++ +++++ lL++ 
  AJA92750.1  86 KLELHDQVLECCEILLSKN 104
                 6777788899999999875 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.011
                 HHHHHHT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEPenrQa 37 
                 ++  k g++++A+ + d  Le++  n  a
  AJA92750.1 116 IALNKTGNHEDALTLYDLALELDKTNVDA 144
                 77889*****************9998766 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.43
                 HHT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPenrQa 37 
                  l +Y+e+  y d++ +i P+++ a
  AJA92750.1 154 YLERYQESIPYYDTVQQIMPDFSRA 178
                 5889*************99999766 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.6e-05     0.051       8      65 ..      19      76 ..      16      85 .. 0.93
   2 !   11.1   0.0   0.00044      0.35       8      65 ..      87     144 ..      80     148 .. 0.89
   3 !    7.5   0.0    0.0058       4.5      10      61 ..     123     174 ..     120     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
       TPR_9  8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                ++++++a++ ++ ll  +P+dp  +     +++ +G+++  +++ + +l+++p+ + a
  AJA92750.1 19 AKKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDSIKCSDKALEKDPNEEHA 76
                789**************************************************87766 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00044
       TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapda 65 
                  e +++ l+++e ll  + +d++ +   G++l + G+ + Al   + +l+l+  + da
  AJA92750.1  87 LELHDQVLECCEILLSKNDKDVDALVTKGIALNKTGNHEDALTLYDLALELDKTNVDA 144
                 578999************************************9999999998877766 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0058
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                 ++e al  +++ l l+   ++ ++  ++ l  l+++++ +   ++  ++ pd
  AJA92750.1 123 NHEDALTLYDLALELDKTNVDALMNMAVTLSYLERYQESIPYYDTVQQIMPD 174
                 6899***********************************9999988887775 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00068      0.53       3      56 ..      20      74 ..      18      94 .. 0.82
   2 !   20.4   0.4   5.9e-07   0.00046       4      76 ..      89     162 ..      75     168 .. 0.94
   3 ?   -1.9   0.1       5.3   4.2e+03      31      31 ..     200     200 ..     182     230 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00068
                T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H CS
      ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl 56
                ++++ Ai ++ +ll++++++p ++  l+ ++y  g y+  ++  +ka +++++ +
  AJA92750.1 20 KKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDSIKCSDKAlEKDPNEE 74
                68999**********************************9999999966655554 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.9e-07
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                  ++  + ++e ll+++ ++ +++  ++ +l ++g+++ A++l++ a +l++++  +++ +A +l  L++y+e i
  AJA92750.1  89 LHDQVLECCEILLSKNDKDVDALVTKGIALNKTGNHEDALTLYDLAlELDKTNVDALMNMAVTLSYLERYQESI 162
                 6788899******999999999999***********************************************87 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.3
                 H CS
      ANAPC3  31 l 31 
                 +
  AJA92750.1 200 Q 200
                 3 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0044       3.5      51      83 ..      36      68 ..      13      72 .. 0.88
   2 !    9.4   0.0    0.0013         1     100     129 ..     108     137 ..      98     142 .. 0.90
   3 ?    4.2   0.0     0.052        40     101     122 ..     177     198 ..     144     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0044
                HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
     DUF3856 51 eGfdalchaglsealaklgrydealesadkalr 83
                +  d ++   ls a+  +g y+++++++dkal+
  AJA92750.1 36 DPNDPIALQNLSTAYYIVGAYEDSIKCSDKALE 68
                566889999**********************96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
     DUF3856 100 iaavfsravaleelGrkdealkafrmagem 129
                 + a+++++ al+++G++++al  +  a e+
  AJA92750.1 108 VDALVTKGIALNKTGNHEDALTLYDLALEL 137
                 67899*******************999886 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.052
                 HHHHHHHHHHHHTT-HHHHHHH CS
     DUF3856 101 aavfsravaleelGrkdealka 122
                 +a +++++a+++lGr+d+a+ a
  AJA92750.1 177 RASIEKSKAFKKLGREDDAFLA 198
                 5667899999999999999855 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0018       1.4     215     254 ..      20      59 ..      16      62 .. 0.88
   2 ?    4.4   0.1     0.027        21     215     253 ..      54      92 ..      50      97 .. 0.82
   3 !   13.5   0.4   4.6e-05     0.036     198     255 ..     105     162 ..      96     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                 T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHH CS
  Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaev 254
                 +++++A +  ++ L+kd++d+ +L Nl +a   +g  +++
  AJA92750.1  20 KKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDS 59 
                 789************************9999888876665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                 T-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HH CS
  Coatomer_E 215 gryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdae 253
                 g ye+  +   +aL+kd+++e +  N + a ++l+  ++
  AJA92750.1  54 GAYEDSIKCSDKALEKDPNEEHAVKNKMLALEKLELHDQ 92 
                 5678888888899************99999988876655 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 4.6e-05
                 ---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHH CS
  Coatomer_E 198 kstplllngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevs 255
                 ++  + l  k ++  ++g++e+A +l   aL+ d+ + ++L+N+ v+   l++ +e++
  AJA92750.1 105 DKDVDALVTKGIALNKTGNHEDALTLYDLALELDKTNVDALMNMAVTLSYLERYQESI 162
                 55556667777777889******************************99999887765 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.8e-05     0.014       8      67 ..      26      84 ..      19      95 .. 0.88
   2 ?    6.6   0.0     0.013       9.8      14      43 ..     100     129 ..      87     133 .. 0.89
   3 ?    0.9   0.0      0.76   5.9e+02      15      42 ..     135     162 ..     130     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
      TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllki 67
                ++  ++ l+++p+d  a  +l++a++  g ye++++   + l++d ++ + a+++++l++
  AJA92750.1 26 IEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDSIKCSDKALEKDPNE-EHAVKNKMLAL 84
                66678899************************************9998.88999999875 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
      TPR_20  14 alaanpddldarldlAlallaagryeeAle 43 
                  l +n +d+da +    al++ g++e+Al+
  AJA92750.1 100 LLSKNDKDVDALVTKGIALNKTGNHEDALT 129
                 57899***********************96 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.76
      TPR_20  15 laanpddldarldlAlallaagryeeAl 42 
                 l+ +++++da +++A  l   +ry+e++
  AJA92750.1 135 LELDKTNVDALMNMAVTLSYLERYQESI 162
                 6678899999999999999888888875 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0018       1.4      74     118 ..      11      55 ..       9     103 .. 0.84
   2 ?    6.9   0.1     0.011       8.3      68     123 ..     107     162 ..      67     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                      HHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
  Alkyl_sulf_dimr  74 ekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgy 118
                      +++k+ ++++++ +a+e++++l+++dp++  a + +  a+  +g 
       AJA92750.1  11 TELKKLFDAKKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGA 55 
                      578999*******************99997666666666555554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                      SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
  Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                      +++++++k  +  k g+ + a++l + +++ d++n +a    a +l  l + +es 
       AJA92750.1 107 DVDALVTKGIALNKTGNHEDALTLYDLALELDKTNVDALMNMAVTLSYLERYQESI 162
                      6788999999999**********************************999999986 PP

>> DUF4919  Domain of unknown function (DUF4919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.2e-05     0.025      62     112 ..      11      61 ..       2      69 .. 0.82
   2 ?    1.3   0.0      0.38     3e+02      73     109 ..      56      92 ..      53     119 .. 0.85
   3 ?    1.5   0.1      0.32   2.5e+02      67     121 ..     118     172 ..     100     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
     DUF4919  62 kldkkelseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeaki 112
                 ++ kk  ++++++++i++ +++l+k+P d+ +l++l+ ay   g  e + +
  AJA92750.1  11 TELKKLFDAKKFDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDSIK 61 
                 4568999********************999999999999988887765544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.38
     DUF4919  73 lkeiislaeealkknPfdlkqlnllayaykalgkkee 109
                 +++ i+ + +al+k+P + ++ ++ + a+++l+ +++
  AJA92750.1  56 YEDSIKCSDKALEKDPNEEHAVKNKMLALEKLELHDQ 92 
                 788899999*******999999999999988876655 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.32
     DUF4919  67 elseeelkeiislaeealkknPfdlkqlnllayaykalgkkeeakiyskrlnkll 121
                   ++ + +++++l   al+ +  ++ +l+++a  ++ l++ +e+  y++ +++++
  AJA92750.1 118 LNKTGNHEDALTLYDLALELDKTNVDALMNMAVTLSYLERYQESIPYYDTVQQIM 172
                 5566778888888888999999999999****99999999999999999998886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0067       5.2      13      32 ..      19      38 ..      14      39 .. 0.87
   2 ?   -1.3   0.0       5.7   4.4e+03      14      32 ..      54      72 ..      42      72 .. 0.63
   3 ?    4.4   0.0     0.086        67       1      25 [.     109     133 ..     109     137 .. 0.83
   4 ?    3.3   0.0       0.2   1.5e+02       1      28 [.     143     170 ..     143     174 .. 0.86
   5 ?   -2.0   0.0       9.4   7.3e+03       9      20 ..     185     196 ..     183     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0067
                HHHHHHHHHHHHHHHHH-TT CS
       TPR_6 13 lgdtdkAlealerlikeYPd 32
                +++ d+A+e  ++l+++ P+
  AJA92750.1 19 AKKFDAAIEFCQKLLEKDPN 38
                5699***************9 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.7
                HHHHHHHHHHHHHHHH-TT CS
       TPR_6 14 gdtdkAlealerlikeYPd 32
                g ++++++  ++ +++ P+
  AJA92750.1 54 GAYEDSIKCSDKALEKDPN 72
                4778888887888888876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.086
                 HHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealer 25 
                 dAl   + ++ k+g++++Al++++ 
  AJA92750.1 109 DALVTKGIALNKTGNHEDALTLYDL 133
                 67777899999999********975 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.2
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                 dAl+++a  +  l ++++++ +++ + +
  AJA92750.1 143 DALMNMAVTLSYLERYQESIPYYDTVQQ 170
                 89*****9999977******99998865 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 9.4
                 HHHHHHHHHHHH CS
       TPR_6   9 syrklgdtdkAl 20 
                 +++klg+ d+A 
  AJA92750.1 185 AFKKLGREDDAF 196
                 677788888885 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.84   6.5e+02      26      49 ..      55      77 ..      22      86 .. 0.67
   2 !   10.8   0.0    0.0005      0.39       7      33 ..     111     137 ..     110     137 .. 0.94
   3 ?    1.4   0.0      0.43   3.4e+02       7      28 ..     145     166 ..     144     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.84
         MIT 26 lYkealelLlqalkekneerrell 49
                +Y+++++   +al  k+++   ++
  AJA92750.1 55 AYEDSIKCSDKALE-KDPNEEHAV 77
                46666666666664.455555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0005
         MIT   7 lvkkAveeDnagnyeeAlelYkealel 33 
                 lv+k + + + gn e+Al lY  alel
  AJA92750.1 111 LVTKGIALNKTGNHEDALTLYDLALEL 137
                 899*********************996 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.43
         MIT   7 lvkkAveeDnagnyeeAlelYk 28 
                 l ++Av +   + y+e + +Y 
  AJA92750.1 145 LMNMAVTLSYLERYQESIPYYD 166
                 6788999999999999999996 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.51     4e+02      78     115 ..      22      59 ..      13      64 .. 0.84
   2 ?    6.5   0.0     0.014        11      65     109 ..      43      87 ..      38      95 .. 0.86
   3 ?    4.9   0.1     0.043        33      74     122 ..      86     134 ..      75     141 .. 0.71
   4 ?    2.8   0.0      0.18   1.4e+02      56     116 ..     136     196 ..     132     211 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.51
                 HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHH CS
        BTAD  78 aeealaelealvaehPlrErlhrqlmrAlarsGrqaeA 115
                  ++a++  ++l++++P +  + + l +A++ +G  ++ 
  AJA92750.1  22 FDAAIEFCQKLLEKDPNDPIALQNLSTAYYIVGAYEDS 59 
                 5678888999********************99987776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHT CS
        BTAD  65 lealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlars 109
                 l+ l  a   +G +e+ ++  +++++++P  E +++  m+Al ++
  AJA92750.1  43 LQNLSTAYYIVGAYEDSIKCSDKALEKDPNEEHAVKNKMLALEKL 87 
                 5566666777899****************************9775 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.043
                 HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
        BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerl 122
                 +l+ ++++l+  e l+++++ + ++      Al ++G+ ++AL+ Y+ +
  AJA92750.1  86 KLELHDQVLECCEILLSKNDKDVDALVTKGIALNKTGNHEDALTLYDLA 134
                 5556667777777777777777777777778999999999999999865 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.18
                 HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
        BTAD  56 rleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                 +l++  ++al  +a  +++l+r++e +++++   +  P   r+  +  +A  ++Gr+ +A 
  AJA92750.1 136 ELDKTNVDALMNMAVTLSYLERYQESIPYYDTVQQIMPDFSRASIEKSKAFKKLGREDDAF 196
                 5788899999999999**************9999999988888888888888888888885 PP

>> COPI_C  Coatomer (COPI) alpha subunit C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     5e-05     0.039     288     319 ..      13      44 ..       7      50 .. 0.89
   2 ?   -0.9   0.0      0.66   5.1e+02     283     323 ..      42      81 ..      40      93 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                 HHHHHHHTBHHHHHHHHHHHHHH---HHHHHH CS
      COPI_C 288 lnlffKlknfktaasfarrLLelgpkeevaqq 319
                 l+ +f +k+f++a +f+++LLe +p++ +a q
  AJA92750.1  13 LKKLFDAKKFDAAIEFCQKLLEKDPNDPIALQ 44 
                 567899********************988866 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                 HHHHHHHHHHHHTBHHHHHHHHHHHHHH---HHHHHHHHHH CS
      COPI_C 283 aLrsAlnlffKlknfktaasfarrLLelgpkeevaqqarkv 323
                 aL++  + ++ +  ++ + + + + Le +p+ee+a + + +
  AJA92750.1  42 ALQNLSTAYYIVGAYEDSIKCSDKALEKDPNEEHAVKNK-M 81 
                 6777777888888999999999999*****999998754.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1678.61
//
Query:       AJA92751.1  [L=223]
Description: fibrillarin-like rRNA/tRNA 2'-O-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-85  285.5   0.1    2.4e-85  285.3   0.1    1.0  1  Fibrillarin     Fibrillarin
    0.00075   19.3   0.0    0.00092   19.0   0.0    1.1  1  GCD14           tRNA methyltransferase complex GCD14 subunit
     0.0036   17.1   0.0     0.0056   16.5   0.0    1.5  1  PCMT            Protein-L-isoaspartate(D-aspartate) O-methylt
     0.0076   16.4   0.1      0.012   15.7   0.1    1.2  1  Disulph_isomer  Disulphide isomerase


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.3   0.1   5.3e-89   2.4e-85       8     223 ..       5     220 ..       1     222 [. 0.97

  Alignments for each domain:
  == domain 1  score: 285.3 bits;  conditional E-value: 5.3e-89
                  TTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
  Fibrillarin   8 egvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                  ++ ++ + +g+ +l t+n++pg++vY+Ekl++ ++ EyR W+pfrsKlaa+i++gl+e+p+++ s+vLYlG+++Gtt+sH+sDivg++g++++ve+s+
   AJA92751.1   5 RNYFWFNLDGERKLFTENFSPGKQVYKEKLLDKKGVEYRNWEPFRSKLAACIMNGLEEFPFEEKSSVLYLGVSTGTTISHISDIVGPKGIIFGVEHSS 102
                  5778999899999************************************************************************************* PP

                  HHHHHHH.HHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTE CS
  Fibrillarin 106 rvlreli.evakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeegl 202
                  rv r+++ +va  RknivPi++DA+kP +Y ++ +kvDv+++D+aqpdq++i++ n+k++lk++g+l+++ik+rsidvtkep+++ +ee++kl++ ++
   AJA92751.1 103 RVARDFLdRVAIYRKNIVPIIQDAKKPDQYFSVFSKVDVVYVDIAQPDQTKIAIANCKMYLKKKGMLFLVIKSRSIDVTKEPNQIINEEIKKLQS-DF 199
                  ******97799**********************************************************************************86.6* PP

                  EEEEEEE-TTTSTTEEEEEEE CS
  Fibrillarin 203 kvleqvklepyekdhalvvgk 223
                  ++l+ ++l+p++kdha+++++
   AJA92751.1 200 EILQRIDLKPFDKDHAMIIAR 220
                  ******************996 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-07   0.00092      42     142 ..      69     170 ..      54     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-07
       GCD14  42 svvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel.sqlvtvthrDvckeGfdeevsgkvDavfLDlPaPwe...aiphaakalk 136
                 s v+  G  +g+  + i+  v+P+G +f +e h +r+  ar+ + +  +  +++    +D+ k      v +kvD v++D+ +P++   ai + +  lk
  AJA92751.1  69 SSVLYLGVSTGTTISHISDIVGPKGIIFGVE-HSSRV--ARDFLDRVAIyRKNIVPIIQDAKKPDQYFSVFSKVDVVYVDIAQPDQtkiAIANCKMYLK 164
                 56677787888888889*************9.67775..56666666774557877889999766667999*************975557888888888 PP

       GCD14 137 keggrl 142
                 k+g  +
  AJA92751.1 165 KKGMLF 170
                 777655 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-06    0.0056      61     124 ..      52     118 ..      15     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                 HHHHHHHHTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
        PCMT  61 mvalalelle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                 + a +++ le   ++++++vL +G  +G     ++ +vg+kg + ++e++ +++++   ++     +
  AJA92751.1  52 LAACIMNGLEefpFEEKSSVLYLGVSTGTTISHISDIVGPKGIIFGVEHSSRVARDFLDRVAIYRKN 118
                 6677777777788999***********************************9998877777554433 PP

>> Disulph_isomer  Disulphide isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.6e-06     0.012      54     130 ..     116     194 ..     112     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                     HHHHHHHHHH-S--SEEEEEETTTSHHHHHHHHHTSTTS---SSEEEEEETTEEEEEE-GGGTTTS.-H.HHHHHHHHH CS
  Disulph_isomer  54 RpavklalekekkpdklvtvFagqdkeatakareylegyppsSPsiallkdgelvhlierheiegr.ea.eeiaeelke 130
                     R  ++  ++ +kkpd++++vF+ +d   ++ a+   ++++ +   + l k+g l  +i+ ++i+ + e+ + i ee+k+
      AJA92751.1 116 RKNIVPIIQDAKKPDQYFSVFSKVDVVYVDIAQPDQTKIAIANCKMYLKKKGMLFLVIKSRSIDVTkEPnQIINEEIKK 194
                     77788889999************************************************99998541341445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1680.42
//
Query:       AJA92752.1  [L=221]
Description: putative translation initiation factor eIF-6 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-57  193.3   2.5    3.4e-57  193.0   2.5    1.0  1  eIF-6     eIF-6 family
  ------ inclusion threshold ------
      0.044   12.5   0.1       0.44    9.2   0.0    1.8  2  HlyD_2    HlyD family secretion protein
      0.068   12.2   0.0       0.11   11.5   0.0    1.3  1  MBA1      MBA1-like protein


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   2.5   5.6e-61   3.4e-57       1     196 [.       5     200 ..       5     201 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 5.6e-61
                 .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHHHHH---EEE--SS--HHH CS
       eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklkeslkleverleekltAlGN 99 
                 +++i++ ++iG++++++++++++p+g+++ + ++++e L+v+ +e+++a+ r++G+l+v N++g+l+pst+++ e++++ke+++l+ve+l+ k +AlGN
  AJA92752.1   5 KYDIYSGPNIGIYSTVNDEFIFLPRGFADGKSEKLSEYLEVKPLEVSVANARVLGVLMVVNNHGMLLPSTCSEGEFNHFKENTDLNVEILDVKNNALGN 103
                 578999********************************************************************************************* PP

                 HEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS- CS
       eIF-6 100 vilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkateeeleeleellkveveagTvNrGsklvgsglvaNdkg 196
                 ++ +N+k+ +v+p + ke  ++i+dvL++ev +++iag ++vG +++ ++kg +vhp+++ee+++++++ll+ ++ea+T+N G ++v+sg++aN+++
  AJA92752.1 104 MMSVNNKGGIVSPLIPKEDLQKIQDVLDIEVLQSKIAGFQQVGAVMATSEKGTVVHPETDEEDMKTISNLLGGNIEAATINGGIPFVSSGILANNNS 200
                 **********************************************************************************************986 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   7.4e-05      0.44     259     314 ..      60     115 ..      58     143 .. 0.73
   2 ?    2.1   0.0     0.011        66     364     398 ..     137     170 ..     117     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 7.4e-05
      HlyD_2 259 ifkivnnqkwYlvtlvekeevkslkegkkvkvkvddeeinakvykiykedeksvvi 314
                 ++ +vnn+ + l +++++ e +++ke+ ++ v++ d + na    ++ +++  +v 
  AJA92752.1  60 VLMVVNNHGMLLPSTCSEGEFNHFKENTDLNVEILDVKNNALGNMMSVNNKGGIVS 115
                 5679******************************9999888666666665555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.011
      HlyD_2 364 sgvakFkeikeilgedekyvivdykkneiekvktv 398
                 s++a F++++ ++ ++ek ++v   + ++e++kt+
  AJA92752.1 137 SKIAGFQQVGAVMATSEKGTVVH-PETDEEDMKTI 170
                 67899*****************8.77777788876 PP

>> MBA1  MBA1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.9e-05      0.11      57     106 ..      81     137 ..      74     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.9e-05
        MBA1  57 alfrlqtglkpsflewknkAietyvkvNka.......fAareleqleelvslwvkea 106
                   f+ +t+l++++l +kn+A+ + + vN+        + +++l+++++++ ++v ++
  AJA92752.1  81 NHFKENTDLNVEILDVKNNALGNMMSVNNKggivsplIPKEDLQKIQDVLDIEVLQS 137
                 579*************************85333333356778888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1572.97
//
Query:       AJA92753.1  [L=215]
Description: YjeF family N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-45  153.7   0.0    4.9e-45  153.5   0.0    1.0  1  YjeF_N      YjeF-related protein N-terminus
  ------ inclusion threshold ------
      0.094   12.1   0.1       0.14   11.5   0.1    1.2  1  Thiolase_N  Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.0   5.5e-49   4.9e-45       3     171 .]      24     188 ..      22     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 5.5e-49
      YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv.llleeeekldedaeralellkka.ggkvveekpeedleekls 99 
                  +menag+ +++ l +++ +s+++k+v++++G gnnGgdg ++ArhLa ++a+Vtv ll ++++  +e+  ++++ll+k+  +k+v+ ++++ +     
  AJA92753.1  24 FMMENAGAVAVRRLVEKF-GSVDSKNVVIFIGMGNNGGDGQVMARHLAGHNANVTVvLLGTPDKIKTEESSWNWSLLEKMpSVKLVTGNSTDFDF---- 117
                 69**********888888.6************************************55566677999************9446777777777664.... PP

      YjeF_N 100 apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadvtvtfgapkrg 171
                  ++d++iD++lG+g++g++re++a++i+ +n+++ + +avD+PSG+d++tG+ ++   k+d+tvtf+ +k+g
  AJA92753.1 118 -KPDIIIDGILGTGINGDIREPYASAINFINQTNCYKFAVDVPSGMDPQTGETASLFTKCDMTVTFHKMKQG 188
                 .6********************************************************************98 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   1.5e-05      0.14      13      68 ..      16      71 ..       7      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.5e-05
                ETTSTTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCTTSTSCHHHHHHH CS
  Thiolase_N 13 kfggslkdlsaeeLlaealkallekag.vdpeevdevivGnvlqagegqniarqaal 68
                + +g lk++++e+ +a a+++l+ek g vd+++v  +++G+  ++g+gq +ar++a 
  AJA92753.1 16 HDMGFLKKFMMENAGAVAVRRLVEKFGsVDSKNV-VIFIGMGNNGGDGQVMARHLAG 71
                56799**********************9**9999.4888999999********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1651.61
//
Query:       AJA92754.1  [L=182]
Description: hypothetical protein T478_0660 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-09   35.8   0.0    8.7e-09   35.4   0.0    1.2  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory domain
  ------ inclusion threshold ------
      0.066   13.5   1.0       0.28   11.5   0.1    2.3  3  DUF1828   Domain of unknown function DUF1828


Domain annotation for each model (and alignments):
>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   9.7e-13   8.7e-09       1     160 [.      15     164 ..      15     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.7e-13
        MEDS   1 dHvclfyedeeellealvpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakaladgy 99 
                 +Hv+lf ++ ee  +  + fik+gl++g+ ++y ++  +++++++++++ g++  +   ++ l+i++     +++     e   +++ ++++   ++  
  AJA92754.1  15 THVVLFHDGNEEKKQTEYGFIKKGLDKGQHCFYTTQ--NRQKILDEMKQFGIEDGE--SNELLHIVE-----IPEKF---EDYSDMILDKVEGLPEE-- 99 
                 6********************************665..*********887774444..444445555.....44444...44577788888886666.. PP

        MEDS 100 aglrvigemtwalrspaereelleyEallneliadepvtalClYdrrrfsae....vladvlrtH 160
                 a++rv+    + ++s+++ ++++e E+ +++ +++ +   +C ++ +++++e     l ++l++H
  AJA92754.1 100 AKIRVVSTHYFDFDSEEKTDRMAEIEQCVDDGFEKINGNFVCSFEVKQINEElrdrFLNQLLESH 164
                 9********************************************88888883333577777777 PP

>> DUF1828  Domain of unknown function DUF1828
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.2e-05      0.28      26      70 ..      30      74 ..       9      90 .. 0.75
   2 ?   -1.0   0.0      0.24   2.2e+03      41      79 ..     111     150 ..     105     162 .. 0.53
   3 ?   -0.3   0.0      0.14   1.3e+03      45      61 ..     150     166 ..     136     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
     DUF1828 26 tDdGltlmdLsysgidldlskkRkellesilakfgvtl.edgelsv 70
                t++G +   L++ +  + ++++R+++l+++ ++fg+++ e +el  
  AJA92754.1 30 TEYGFIKKGLDKGQHCFYTTQNRQKILDEM-KQFGIEDgESNELLH 74
                6666666777766555666**********9.7******99998864 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.24
     DUF1828  41 dldlskkRkellesil..akfgvtledgelsvkvteenlaa 79 
                 d+d s+++++ + +i      g ++ +g+++++ + +++ +
  AJA92754.1 111 DFD-SEEKTDRMAEIEqcVDDGFEKINGNFVCSFEVKQINE 150
                 444.4444444444432123444445666666666666554 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.14
     DUF1828  45 skkRkellesilakfgv 61 
                 ++ R+++l+++l+++++
  AJA92754.1 150 EELRDRFLNQLLESHKA 166
                 66788899999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1314.77
//
Query:       AJA92755.1  [L=422]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-101  340.1   0.1   1.9e-101  339.8   0.1    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin
  ------ inclusion threshold ------
      0.041   13.3   0.1      0.077   12.4   0.1    1.4  1  vATP-synt_E    ATP synthase (E/31 kDa) subunit
      0.053   13.7   0.2         33    4.7   0.0    3.4  3  Clp_N          Clp amino terminal domain, pathogenicity islan
       0.13   11.7   0.0       0.21   10.9   0.0    1.3  1  NMT1_3         NMT1-like family


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.8   0.1  4.3e-105  1.9e-101       4     417 .]       9     414 ..       7     414 .. 0.94

  Alignments for each domain:
  == domain 1  score: 339.8 bits;  conditional E-value: 4.3e-105
                    SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHHTT-GGGGGGHHHHH CS
  EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelvldlgnsgtalrlLt 99 
                    +++l+g+++ p++ks+++ra+ lAaL++g+s ++++L+s+D+ s+++a+r +g+e++++  e++v+i++  + s+ ++   ++d+gnsgt++r+ +
     AJA92755.1   9 KSKLNGRITCPSNKSYTHRAIFLAALSDGKSIVKKILRSNDTMSTINACRGFGVEVEEV--EDKVTINNT-IDSTVEN--SMIDAGNSGTTIRIAI 99 
                    579**************************************************999888..456666665.6666665..69************** PP

                    HHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEETSSTTHHHHHHHHHHHTTSBS.EEEEES.-TTHH CS
  EPSP_synthase 100 allalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveikaevsSqqvtsllllaallaeg.ttelee.lasep 192
                    a+++l +g++ LtGdes+rkRP++++ld+L+ +G+e e  ++++k+p++++g  ++++++ik+++sSq++++l+++ + l +g t+ +e+ l+s+p
     AJA92755.1 100 AIAGLSGGNTKLTGDESLRKRPMQPILDSLETMGVETE--SDDGKPPVHINGkIEGNEISIKGDISSQFISALMIIGPRLPDGlTINVEGeLVSKP 193
                    ***********************************999..5567**************************************************** PP

                    HHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSE CS
  EPSP_synthase 193 siddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedas 288
                    ++d t+ ++kkfg++++ ++++++  ++  +  + t++++++D s+ a +l+a ++ g   t+e    +  qGd +++d ilek+g+++t e+d +
     AJA92755.1 194 YVDLTIAIMKKFGVDVKIEEEYKKYLIRH-QIYKPTTFSIPSDFSNLALLLAANVLLGDGLTIEINLGDMPQGDEAIVD-ILEKLGVNVTLEDDII 287
                    ******************99999777775.665555***************************999999999**77777.*************999 PP

                    EEEEETTS--BEEEEEBGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTT CS
  EPSP_synthase 289 ivvgpsglklkdvdietlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRia 384
                    ++++ps lk+ + d+++ pd++p++a+la+ +e   ++ ++++ r+ketdr+a +  eL+k+G +vee+edg+i +++e  +++ae++s  DhR+ 
     AJA92755.1 288 TTESPSLLKGGKFDLSDTPDLLPAVAILALKSEKPIELFNVKHARYKETDRIAILSRELKKIGLHVEEKEDGMILKKPEE-VHSAELDSESDHRLF 382
                    999999********************************************************************999985.*************** PP

                    HHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
  EPSP_synthase 385 malalaglvaegeveiddiectdksfpefeekL 417
                    mal+++g +  g+ ++ d++ +++s+pef+ +L
     AJA92755.1 383 MALSIVG-MFVGDCTVSDPDSVKVSYPEFISDL 414
                    *******.56666****************9865 PP

>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.7e-05     0.077     147     184 ..      41      82 ..      28      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                  -SEEEEESSEB...TTSSS.EEEECCSSSCEEECCCHHHCHH CS
  vATP-synt_E 147 vevagdeedfl...edvlG.GvvleaadgkikvnnTlearLe 184
                  v+++  ++d +   + + G Gv++e+ ++k+ +nnT+++ +e
   AJA92755.1  41 VKKILRSNDTMstiNACRGfGVEVEEVEDKVTINNTIDSTVE 82 
                  44444444444444889999*******************987 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0073        33      18      36 ..      29      47 ..      27      49 .. 0.91
   2 ?    0.5   0.0      0.15   6.6e+02      32      44 ..     200     211 ..     197     219 .. 0.73
   3 ?    3.8   0.0     0.014        65      25      41 ..     264     280 ..     262     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0073
                HHHHHHHSCTSHHHHHHHH CS
       Clp_N 18 LLlALleeddGlaarlLkk 36
                ++lA l++++++ +++L+ 
  AJA92755.1 29 IFLAALSDGKSIVKKILRS 47
                78999************85 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                 HHHHHTTSSHHHH CS
       Clp_N  32 rlLkkaGvdldal 44 
                  ++kk+Gvd+ ++
  AJA92755.1 200 AIMKKFGVDV-KI 211
                 589******5.55 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.014
                 SCTSHHHHHHHHTTSSH CS
       Clp_N  25 eddGlaarlLkkaGvdl 41 
                 ++d ++ ++L+k+Gv++
  AJA92755.1 264 QGDEAIVDILEKLGVNV 280
                 6778999********95 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.8e-05      0.21     114     198 ..     257     337 ..     252     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.8e-05
      NMT1_3 114 vsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldgaalvaGvPvsavtqlaasedikliplddeqldkll 198
                 +++G+   G e +  +ile lg++   ++l  ++ ++es ++lk g+ d   +++ +P+ a+  l  +++i+l++++ +  ++ +
  AJA92755.1 257 INLGDMPQGDE-AIVDILEKLGVN---VTLEDDIITTESPSLLKGGKFDLSDTPDLLPAVAILALKSEKPIELFNVKHARYKETD 337
                 67777777777.7889******97...344467889****************************************998877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2769.89
//
Query:       AJA92756.1  [L=350]
Description: mRNA surveillance protein pelota [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-20   71.7   1.2    9.8e-20   70.9   1.2    1.4  1  eRF1_1    eRF1 domain 1
    2.8e-10   40.6   0.7    1.5e-09   38.3   0.2    2.3  2  eRF1_3    eRF1 domain 3
    0.00015   22.1   0.1     0.0004   20.7   0.0    1.8  1  eRF1_2    eRF1 domain 2


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   1.2   1.6e-23   9.8e-20      13     120 ..       8     117 ..       2     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.6e-23
                 CCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......-.-CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEGGGG.--TTSEEEEEE-TTSE CS
      eRF1_1  13 sgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsre.servklkLtikvekvdfdkdagvlrisGkvieeneh.vklgafhtldlelkrp 109
                 +++++L+ped++dl ++  +++ +d++   t+r ++++++    +  erv+++L ikvek+ +d+  +++r+ G++ e+n++ v+ g++h++++++ + 
  AJA92756.1   8 ENTISLMPEDSDDLLTIRRILKIDDKIIGETTRVIKQDKEYARPDkGERVHVRLAIKVEKISLDNVLDRIRVGGTILESNNEsVPHGTHHSFTIKIDEG 106
                 679********************************995443333348*****************************9998777**************** PP

                 EEEEECEESHH CS
      eRF1_1 110 ftiikeewdsf 120
                 f++ k++w+ +
  AJA92756.1 107 FNLVKKKWSGV 117
                 ********976 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.33     2e+03      11      32 ..     183     204 ..     177     208 .. 0.80
   2 !   38.3   0.2   2.5e-13   1.5e-09       3     113 .]     254     348 ..     252     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                 HHHHHHCTCSSEEESHHHHHHH CS
      eRF1_3  11 fleelakdtgkavYGveevlka 32 
                   + ++kd+  +v+G  e++k 
  AJA92756.1 183 ISSVVEKDNFVIVFGPGETKKK 204
                 56678999999*******9986 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.5e-13
                 HHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHH CS
      eRF1_3   3 qekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesgakveiisseseeGeqlvka 101
                 + +++++e++   +k+++k   G+ee++ka+e gA+e L+ se+  +++d+           +e    i +++++ve+ g++++ + s  ++G ++ ++
  AJA92756.1 254 KVSQIIDEVMFLANKQSKKFSMGIEETKKANEAGAIESLVFSEKAIQDSDE-----------QE----IIDFLNDVESKGGEIFSVDSTIDAGLRV-SG 336
                 66789999999999*****************************99998643...........33....67799***********************.** PP

                 TTTEEEEESS-- CS
      eRF1_3 102 fgGiaaiLRykv 113
                 +gGi+ +LR+++
  AJA92756.1 337 LGGIISLLRFPL 348
                 **********85 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   6.6e-08    0.0004       2     121 ..     131     235 ..     130     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.6e-08
                 EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHHHHHHHHH CS
      eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiilagpgfvkeefldkdllda 100
                 ++li +d g + ig lkg+  ++l ++ +   +K+ +   s+         k+e+f++ v+ a+++    v+kd+   +i+ gpg++k++f+++   + 
  AJA92756.1 131 FILIAIDTGDCGIGRLKGTHLHLLPNMYSGSSGKRYK---SSF--------KIEKFFDDVVGAISSV---VEKDN--FVIVFGPGETKKKFYNYVSKKP 213
                 6678888888888888888888888888888888864...444........689************9...77887..599**************99999 PP

                 HHHTCCEE.EEE-S-TSCHHHH CS
      eRF1_2 101 elkkkvik.lvdvsyggesgln 121
                  + k ++k +  + +gge g++
  AJA92756.1 214 IADKCKFKvIEGIDSGGEDGIH 235
                 9999777745568889999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2523.01
//
Query:       AJA92757.1  [L=171]
Description: hypothetical protein T478_0587 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0018   18.3   0.0     0.0027   17.8   0.0    1.2  1  DprA_WH         DprA winged helix domain
     0.0037   17.1   0.9     0.0059   16.5   0.9    1.5  1  TFIIE_alpha     TFIIE alpha subunit
     0.0043   17.4   0.0     0.0076   16.6   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0058   16.3   0.1     0.0083   15.8   0.1    1.3  1  DUF4423         Domain of unknown function (DUF4423)
     0.0062   16.7   0.0      0.011   16.0   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.017   15.0   0.0    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.051   13.7   0.0       0.11   12.7   0.0    1.4  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.062   13.3   0.2       0.07   13.2   0.2    1.2  1  DUF1676         Protein of unknown function (DUF1676)
      0.067   13.4   0.0       0.11   12.7   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.091   13.1   4.0       0.59   10.5   0.7    2.2  2  CLZ             C-terminal leucine zipper domain of cyclic nu
       0.13   12.3   0.5       0.22   11.6   0.5    1.4  1  BLACT_WH        Beta-lactamase associated winged helix domain
       0.14   12.6   1.5       0.21   12.0   1.3    1.4  1  Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
       0.18   11.7   0.5        4.2    7.3   0.1    2.2  2  Chordopox_L2    Chordopoxvirus L2 protein


Domain annotation for each model (and alignments):
>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     2e-06    0.0027      12      56 ..       5      49 ..       2      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
     DprA_WH 12 dlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                  e  vL a++   + +D ++++t +++  + a+L  LE +Gl++
  AJA92757.1  5 NKETVVLGAISRGVTKFDKISQETNVEPKDLEAILQKLENSGLIR 49
                56888*************************************997 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.9   4.3e-06    0.0059      13      64 ..       5      55 ..       1     109 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-06
                 HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
  TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd 64
                 ++   vl ++  +g+++ + +++e++++++ l  +L +L + +l+ +  ++ 
   AJA92757.1  5 NKETVVLGAIS-RGVTKFDKISQETNVEPKDLEAILQKLENSGLIRVDEKKG 55
                 44555666665.9********************************8766554 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.5e-06    0.0076      26      57 ..      19      50 ..       9      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-06
                B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 26 vsseeiaerqnispsylekilakLrkaglvks 57
                 + ++i++++n++p+ le il+kL+++gl+++
  AJA92757.1 19 TKFDKISQETNVEPKDLEAILQKLENSGLIRV 50
                67899*************************86 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     6e-06    0.0083      34      96 ..      16      76 ..       8      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
     DUF4423 34 dfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtekslttssevkseavrs 96
                 +  + +++++ ++  +  ++ e++l+ L+++gl++ de++ +  t+  ++ ++e   e+ r+
  AJA92757.1 16 RGVTKFDKISQETN--VEPKDLEAILQKLENSGLIRVDEKKGWLGTKIEINPTEEGYREFERQ 76
                55567889******..**********************************9888877776665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.6e-06     0.011      16      78 ..      20      82 ..      11      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.6e-06
      HTH_34 16 dfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78
                +f ++++++++    L + l+kLe+ g i vd ++     ++ ++ T+eG  +f++ +k+L++
  AJA92757.1 20 KFDKISQETNVEPKDLEAILQKLENSGLIRVDEKKGWLGTKIEINPTEEGYREFERQLKILQE 82
                7999***************************998888888999999**************986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.2e-05     0.017      19      58 ..      15      54 ..       8      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
        TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                ++g  + d+i++e++v+      +L++Le+ Gl+++ +++
  AJA92757.1 15 SRGVTKFDKISQETNVEPKDLEAILQKLENSGLIRVDEKK 54
                6788899****************************99876 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.7e-05      0.11      18      48 ..      17      48 ..      14      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.7e-05
  B-block_TFIIIC 18 GitqsdLa.keskqdprslfyrlksLekkgLI 48
                    G+t  d + +e++ +p++l  +l++Le++gLI
      AJA92757.1 17 GVTKFDKIsQETNVEPKDLEAILQKLENSGLI 48
                    7888887779*********************9 PP

>> DUF1676  Protein of unknown function (DUF1676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   5.1e-05      0.07     109     149 ..      83     133 ..      16     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
     DUF1676 109 e.........egRkkk..kkkkklkkmllplllalklklklLlplalgllal 149
                 +         +g  k+  ++k k  k++lp +++  +  ++++ +++ +++ 
  AJA92757.1  83 KwnqlentykSGN-KQelEQKLKEDKSFLPSMMMFGIVDMMMFSMMFSMIGA 133
                 0333444444666.44477777888***********9999999****99986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     8e-05      0.11      19      59 ..      15      55 ..       8      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-05
                    HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
  Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                    +++v k  +++++ nv+p      l+kLe+ G++ +  +kg
      AJA92757.1 15 SRGVTKFDKISQETNVEPKDLEAILQKLENSGLIRVDEKKG 55
                    78899999****************************99998 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.054        75      17      39 ..      23      45 ..      19      57 .. 0.82
   2 ?   10.5   0.7   0.00043      0.59      28      65 ..      65     103 ..      50     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.054
         CLZ 17 eeaakagaeqkeleekverLess 39
                +  ++ + e+k+le  +++Le+s
  AJA92757.1 23 KISQETNVEPKDLEAILQKLENS 45
                44556678999999999999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
         CLZ  28 eleekverLessLeaLqtrlarLlaeyessq.rkLkqRi 65 
                  +ee  +++e +L++Lq + ++L + y+s + ++L+q++
  AJA92757.1  65 PTEEGYREFERQLKILQEKWNQLENTYKSGNkQELEQKL 103
                 5789999********************996515677766 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00016      0.22      25      47 .]      35      56 ..      33      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
    BLACT_WH 25 vlahLeKLeeeGkVkregdkgkW 47
                + a+L+KLe+ G+++ +++ + W
  AJA92757.1 35 LEAILQKLENSGLIRVDEK-KGW 56
                689*************996.888 PP

>> Myb_DNA-bind_4  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   0.00015      0.21      47      77 ..      71     101 ..      38     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                     HC----HHHHHHHHHHHHHHHHCSSSSSS-- CS
  Myb_DNA-bind_4  47 rgykrspeqCkeKienLkkrYkkekerekgs 77 
                     r+++r+ + ++eK+++L+++Yk  +++e ++
      AJA92757.1  71 REFERQLKILQEKWNQLENTYKSGNKQELEQ 101
                     467899999**************99987655 PP

>> Chordopox_L2  Chordopoxvirus L2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0031       4.2       5      32 ..      19      46 ..      18      52 .. 0.89
   2 ?    2.5   0.1     0.091   1.3e+02      38      56 ..     112     131 ..      98     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0031
  Chordopox_L2  5 dklrsieeenkanekfldaiitevesqq 32
                   k ++i +e +++ k l+ai++++e++ 
    AJA92757.1 19 TKFDKISQETNVEPKDLEAILQKLENSG 46
                  6899********************9975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.091
  Chordopox_L2  38 pllrL.lfDlLilvivviil 56 
                   +++ + ++D++++++ ++++
    AJA92757.1 112 SMMMFgIVDMMMFSMMFSMI 131
                   55554499*****9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1317  (0.0734564); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                       137  (0.00764125); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1304.02
//
Query:       AJA92758.1  [L=77]
Description: hypothetical protein T478_0964 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   13.9   0.6      0.053   13.3   0.5    1.4  1  DUF1351   Protein of unknown function (DUF1351)


Domain annotation for each model (and alignments):
>> DUF1351  Protein of unknown function (DUF1351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   2.9e-06     0.053      10      54 ..       5      51 ..       2      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-06
     DUF1351 10 eIei.nfeeleaaveeivkkYeglvvtedsvkdaKk.eraeLnklkk 54
                ++e+ n  + e++v+ei++ Y++++++  +v   K   +a L ++ +
  AJA92758.1  5 NLETeNVNNAEEWVNEIANVYADMEISDVNVSGNKIsFKAGLSGMDD 51
                5678899999******************9999999525677776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 602.07
//
Query:       AJA92759.1  [L=83]
Description: hypothetical protein T478_1316 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 576.98
//
Query:       AJA92760.1  [L=46]
Description: hypothetical protein T478_1122 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.43
# Mc/sec: 321.48
//
Query:       AJA92761.1  [L=60]
Description: hypothetical protein T478_0282 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0085   14.0   0.2     0.0085   14.0   0.2    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.028   14.7   3.8       0.04   14.2   3.8    1.2  1  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
      0.029   13.8   2.4        2.4    7.7   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.036   14.1   1.7      0.044   13.8   1.7    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.096   11.4   0.3      0.081   11.7   0.3    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.22   11.5   2.5       0.54   10.3   0.1    2.2  2  DUF3565         Protein of unknown function (DUF3565)
       0.51   10.3   4.2        6.9    6.7   0.8    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.85    9.7   9.2        3.6    7.8   0.9    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        2.5    8.3   6.6         13    6.0   6.6    1.9  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   4.3e-06    0.0085     610     641 ..      26      57 ..      10      60 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-06
    PolC_DP2 610 geieveiarrkCkkCgketlearCeeCgekte 641
                 g+ +v   + kCkkCg+et   +C++C++  +
  AJA92761.1  26 GKNDVIGYSSKCKKCGEETNGLKCPKCESVKK 57 
                 44555556778888888888888888887654 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   3.8     2e-05      0.04       4      21 ..      38      55 ..      35      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
     zf-C6H2  4 seCgkeassLqCptClkl 21
                ++Cg+e++ L+Cp+C + 
  AJA92761.1 38 KKCGEETNGLKCPKCESV 55
                69*****99******765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0032       6.4      18      24 ..      36      42 ..      34      44 .. 0.81
   2 ?    7.7   0.2    0.0012       2.4       4      16 ..      48      59 ..      46      60 .] 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0032
  zf-ribbon_3 18 vCpyCGt 24
                 +C++CG+
   AJA92761.1 36 KCKKCGE 42
                 8*****7 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
  zf-ribbon_3  4 rCPnCGaplssdd 16
                 +CP+C ++ ++d+
   AJA92761.1 48 KCPKCESV-KKDW 59
                 69999887.7776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.7   2.2e-05     0.044      69      96 ..      33      56 ..      23      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                -EEEETTTS-EEECHHHHHS-TTTSSS- CS
        HypA 69 vkvrCreCgkefeleekalrCpkCgsad 96
                 + +C++Cg+e++     l+CpkC+s +
  AJA92761.1 33 YSSKCKKCGEETN----GLKCPKCESVK 56
                5789*****8887....358****9965 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   4.1e-05     0.081     507     528 ..      34      55 ..       9      60 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                 EEEETT.--EESSSB-TTT--B CS
        NRDD 507 idvCnecgykgeiekCpkCgse 528
                 ++ C++cg +    kCpkC+s 
  AJA92761.1  34 SSKCKKCGEETNGLKCPKCESV 55 
                 689******888888****965 PP

>> DUF3565  Protein of unknown function (DUF3565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00027      0.54      37      56 ..      23      42 ..      19      44 .. 0.90
   2 ?    1.2   0.3      0.18   3.7e+02      48      56 ..      46      54 ..      43      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
     DUF3565 37 teegResmlGkelnCkkcde 56
                t++g+++ +G++ +Ckkc e
  AJA92761.1 23 TKTGKNDVIGYSSKCKKCGE 42
                899***************87 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.18
     DUF3565 48 elnCkkcde 56
                 l+C kc++
  AJA92761.1 46 GLKCPKCES 54
                599****86 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.012        24       3      12 ..      35      44 ..      29      45 .. 0.81
   2 ?    6.7   0.8    0.0035       6.9       4      10 ..      48      54 ..      47      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
  PhnA_Zn_Ribbon  3 pkCplCaSey 12
                    +kC +C+ e+
      AJA92761.1 35 SKCKKCGEET 44
                    7999998665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0035
  PhnA_Zn_Ribbon  4 kCplCaS 10
                    kCp+C S
      AJA92761.1 48 KCPKCES 54
                    8****98 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.9    0.0045         9       2       9 ..      35      42 ..      35      45 .. 0.86
   2 ?    7.8   0.9    0.0018       3.6       3      10 ..      48      55 ..      47      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0045
      zf-ACC  2 tKCpsCge 9 
                +KC +Cge
  AJA92761.1 35 SKCKKCGE 42
                6******9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0018
      zf-ACC  3 KCpsCgem 10
                KCp+C+++
  AJA92761.1 48 KCPKCESV 55
                9****975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   6.6    0.0067        13       7      34 ..      36      54 ..      32      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0067
  Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                 +C++Cg+e + l          CP+C s
   AJA92761.1 36 KCKKCGEETNGLK---------CPKCES 54
                 8*****8888665.........****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1235  (0.0688828); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 449.13
//
Query:       AJA92762.1  [L=119]
Description: cupin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-10   40.1   0.0    3.1e-10   39.6   0.0    1.2  1  Cupin_2          Cupin domain
    1.3e-06   28.1   0.0    1.7e-06   27.7   0.0    1.1  1  Cupin_1          Cupin
    8.7e-06   25.7   0.0    9.2e-06   25.6   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    2.5e-05   24.2   0.0    3.3e-05   23.8   0.0    1.2  1  AraC_binding     AraC-like ligand binding domain
     0.0019   17.5   0.1     0.0034   16.7   0.1    1.4  1  GPI              Glucose-6-phosphate isomerase (GPI)
     0.0048   17.1   0.0     0.0053   16.9   0.0    1.1  1  Ectoine_synth    Ectoine synthase
  ------ inclusion threshold ------
      0.055   13.1   0.0        0.1   12.3   0.0    1.5  1  Auxin_BP         Auxin binding protein
      0.086   13.1   0.0       0.12   12.6   0.0    1.2  1  CENP-C_C         Mif2/CENP-C like
       0.11   12.6   0.0       0.48   10.6   0.0    2.1  1  Cupin_5          Cupin superfamily (DUF985)


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   1.6e-13   3.1e-10       2      71 .]      39     107 ..      38     107 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 1.6e-13
                 EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEEE CS
     Cupin_2   2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvvy 71 
                 +++++pG s+++h  + + e++y+l+G g +++++e+ ++++ +++++p+     ++N+g++++  l+++
  AJA92762.1  39 HCTIAPGNSSKPHKMKTS-EIYYILQGSGIMHIEEEQKVVKKNETIFVPPMSKQFIENNGEGDLIALCIV 107
                 689***********9999.************************************************995 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   8.5e-10   1.7e-06      14     114 ..      17     108 ..       5     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 8.5e-10
                 TEEEEEESTTTSTTTHSSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEE CS
     Cupin_1  14 ggrvteansenlpglntlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivv 112
                 g +++++ s +  + nt + s+a   ++pg  + Ph   +++ei y+lqG+g   + +++     ++k++++ +++ vP+   +f+ n+g+ ++ a+ +
  AJA92762.1  17 GTQIRQIFSPE-DTANTTRYSLAHCTIAPGNSSKPHKM-KTSEIYYILQGSGI--MHIEE-----EQKVVKKNETIFVPPMSKQFIENNGEGDLIALCI 106
                 55665555555.3589*********************9.**************..33333.....4688*********************777666665 PP

                 EE CS
     Cupin_1 113 fd 114
                 +d
  AJA92762.1 107 VD 108
                 55 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.6e-09   9.2e-06      58     146 ..      30     117 ..       5     119 .] 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.6e-09
  MannoseP_isomer  58 degeryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqsGsylgeddi 146
                       ++ ry + + t+ Pg+     + +  +e + +++G   +++++e+ ++k+ne++++p  +   +en G+ +l  + +   ++ +ed++
       AJA92762.1  30 ANTTRYSLAHCTIAPGNSS-KPHKMKTSEIYYILQGSGIMHIEEEQKVVKKNETIFVPPMSKQFIENNGEGDLIALCIVDPAWKQEDEV 117
                      56789***********964.44456789******************************************9999988888888888876 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.7e-08   3.3e-05      11      65 ..      43      97 ..      35     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                  STT-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-T CS
  AraC_binding 11 ypdhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesds 65
                  +p+ s +ph   + +i y+++G+g+ ++++++  +++++ +++pp    ++e  +
    AJA92762.1 43 APGNSSKPHKMKTSEIYYILQGSGIMHIEEEQKVVKKNETIFVPPMSKQFIENNG 97
                  6888999**************************************9887777665 PP

>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.7e-06    0.0034      81     144 ..      53     107 ..      45     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
         GPI  81 strPEvYevlkGealmlLekPeglkvddvivvevkartvvivPPnygHvsinigeedLvmanlv 144
                  +  E+Y+ l+G ++m +e+ +          +vk++++++vPP       n ge+dL+ + +v
  AJA92762.1  53 MKTSEIYYILQGSGIMHIEEEQK---------VVKKNETIFVPPMSKQFIENNGEGDLIALCIV 107
                 56789***********9999888.........7899**********************987654 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.7e-06    0.0053      32     112 ..      32     112 ..       1     118 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                    SSSSEEEEEEE-TT--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS.-EEEEEEEES--X CS
  Ectoine_synth  32 gmGfslhettikagtetelkYknHleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakk.elrlvcvFnPplt 112
                       +sl + ti  g++ + +  +  e  y+++G+g + ++e+ ++   k+ t+++     + + +  + +l  +c+ +P+ +
     AJA92762.1  32 TTRYSLAHCTIAPGNSSKPHKMKTSEIYYILQGSGIM-HIEEEQKVVKKNETIFVPPMSKQFIENNGEgDLIALCIVDPAWK 112
                    3569******************************965.55666777779999***99999998877667*********9865 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05       0.1      49      84 ..      40      75 ..      32     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                EEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSS CS
    Auxin_BP 49 qtlapgsrtpihrhsceevfvvlkgkgtlylassss 84
                 t+apg+ +  h+    e++ +l+g+g +++ + ++
  AJA92762.1 40 CTIAPGNSSKPHKMKTSEIYYILQGSGIMHIEEEQK 75
                59**************************99986543 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     6e-05      0.12      23      76 ..      46      98 ..      31     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6e-05
                CCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SS CS
    CENP-C_C 23 aeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNkln 76
                ++ k+++  k++ ++y++qG   + +++++ v+ k  +  vP +++  ieN+++
  AJA92762.1 46 NSSKPHKM-KTSEIYYILQGSGIMHIEEEQKVVKKNETIFVPPMSKQFIENNGE 98
                44444443.455679************************************765 PP

>> Cupin_5  Cupin superfamily (DUF985)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.48      42      82 ..      35      74 ..      15     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                -EEEEEEEETTBEEEEEEESSEEEEEEEEES-EEEEEESTT CS
     Cupin_5 42 sTaIyylltsgevsalhrvksdevwhyhaGrpLrlvllhad 82
                ++  +  + +g+ s+ h++k+ e+++  +G++  +++ +++
  AJA92762.1 35 YSLAHCTIAPGNSSKPHKMKTSEIYYILQGSG-IMHIEEEQ 74
                45556677789999999999999999999999.44443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 915.73
//
Query:       AJA92763.1  [L=175]
Description: hypothetical protein T478_0070 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1343.73
//
Query:       AJA92764.1  [L=146]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.027   14.9   0.0      0.057   13.9   0.0    1.5  1  MG2            MG2 domain
       0.18   11.7   0.0       0.29   11.0   0.0    1.3  1  EMP24_GP25L    emp24/gp25L/p24 family/GOLD
       0.23   12.0   2.2       0.32   11.6   0.6    1.8  2  Cadherin-like  Cadherin-like beta sandwich domain


Domain annotation for each model (and alignments):
>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.5e-06     0.057      31      94 ..      40     103 ..      24     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                 ---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE-..-TT--SEEEEEEEEECSTTT-EEEEEE CS
         MG2  31 laklplkltirdpdgkevkelplatdetggaesefal..peaaklGeysvelsadsaeeslssgsf 94 
                   ++p+++ +  p+g++v+  +++ d++g++ s++ +  p   + G ys+++++ sa+ + s+  +
  AJA92764.1  40 SSNTPVTIMVLAPNGNVVSIDQINPDSDGSFTSTIGVggPMWKQDGVYSITAQQGSASINKST--V 103
                 4569******************************99955667899*******44444444444..3 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.9e-05      0.29      19     102 ..      27     114 ..      17     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.9e-05
  EMP24_GP25L  19 kkgtlltgsyqvtdggaaldvdlsvkdpdgngerlvkkkdresegdfsftak.........esgeykvCfdnsfstksskkvsfdievgseas 102
                  +  t++t++ ++t+ +    v + v    +ng+++  ++++ ++ d sft++         ++g y++  +  +++ ++ +v+++i  g+ ++
   AJA92764.1  27 EGSTTITITGHATSSN--TPVTIMVL--APNGNVVSIDQINPDS-DGSFTSTigvggpmwkQDGVYSITAQQGSASINKSTVEVEIADGAVVP 114
                  4478899999999988..9*******..7777988888777666.788888778*******************************99887655 PP

>> Cadherin-like  Cadherin-like beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   5.3e-05      0.32      24      85 ..      14      74 ..      12      77 .. 0.82
   2 ?   -0.5   0.0      0.31   1.8e+03      36      47 ..      99     110 ..      83     137 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
  Cadherin-like 24 edvdsvtitataedsvatvtvngvaveegstetkdvsLneGrnkieikvtaedgsttrtYtl 85
                   ++ d +tita a +  +t+t+ g a+ ++++ t  v    G n++ i  ++ d + + t t+
     AJA92764.1 14 HASDGLTITADAVEGSTTITITGHATSSNTPVTIMVLAPNG-NVVSIDQINPDSDGSFTSTI 74
                   677899*******999************9999999999999.99888887777655555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
  Cadherin-like  36 edsvatvtvngv 47 
                    ++s+++v++ + 
     AJA92764.1  99 NKSTVEVEIADG 110
                    234444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1078.35
//
Query:       AJA92765.1  [L=338]
Description: DegT/DnrJ/EryC1/StrS aminotransferase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-52  179.1   0.0    1.2e-35  123.6   0.0    2.0  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.0   1.1e-18     2e-14       4      95 ..      15     107 ..      12     121 .. 0.91
   2 !  123.6   0.0   6.4e-40   1.2e-35     142     360 ..     132     332 ..     130     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.1e-18
                      HHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTT.TT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TT CS
  DegT_DnrJ_EryC1   4 eeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvg.pgdeVIvpsltFvatanavlelgakpvfvDvdpd 95 
                      e e+++v+++l+++ l + ++v+eFE++f++++g++++i+++sGt+Al l+L+ l  + + + + +p +  + +a a ++++ kp++vDv ++
       AJA92765.1  15 EYEKKQVNKILNADYLNEHKTVREFERKFSEFVGARYCITCTSGTTALYLGLKSLTEKnNFKSINIPDYAGIFSAYATIQTNVKPILVDVGKN 107
                      67899*************************************************888835677779************************765 PP

  == domain 2  score: 123.6 bits;  conditional E-value: 6.4e-40
                      EEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS.-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCS..S---B-B-BHHHHHHHHH CS
  DegT_DnrJ_EryC1 142 ieDaAhAlGatykgkkvGalgdaavfSFyptKnl.ttGeGGavvtndeelaekarvlrnhGlkrkaekryvgev..elGynyrlteiqAAigla 232
                      ieD+A+A+  + k+       +++++SF  tK++ t G GGav  +d+e+ +++++l+  G++ +++ + +++     G+n++ te+qAA gla
       AJA92765.1 132 IEDCAQAISHHTKN-------SISCYSFASTKHItTGGQGGAVCCDDKETFDILSRLKDLGRNDRQKLKPMSDNfeFWGFNSKFTEVQAAFGLA 218
                      8*******999998.......9************7789***********************99744444444436779**************** PP

                      HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCC CS
  DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeeas 326
                      qL++l + ++r ++++++++eeL++ +    +++ +e+     +++ +lv+     k d ++e+lk+ gi+ r +y +plh+qp++++++ +++
       AJA92765.1 219 QLKKLPSRLKRLKKMYKTISEELKNEN----VEFFEEEP---TWYIDMLVK-----KPDVFLERLKNLGIQGRRFY-KPLHKQPYFRKNFPSKK 299
                      ************************955....55666665...244555555.....5689****************.7***********98865 PP

                      HC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
  DegT_DnrJ_EryC1 327 gdlpnaerlaervlsLplypelteedvdrVveal 360
                       d++n+++l++r ++Lp++ +lt++dv+r+++++
       AJA92765.1 300 -DFKNSNNLYSRGIWLPSTTNLTDADVNRIIKSI 332
                      .9*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2409.45
//
Query:       AJA92766.1  [L=136]
Description: CoA-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-40  137.1   0.1    4.1e-40  136.9   0.1    1.0  1  CoA_binding_2   CoA binding domain
    1.5e-06   28.8   0.0    2.5e-06   28.1   0.0    1.3  1  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.032   13.4   0.0    1.3  1  Glyco_hydro_57  Glycosyl hydrolase family 57
       0.14   13.0   0.2       0.62   10.9   0.1    2.0  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.1   9.1e-44   4.1e-40       1     115 [.      18     132 ..      18     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 9.1e-44
                    --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT---HHHHH CS
  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgakavwlqpgsedeeaae 96 
                    +++aVvG+s+np+k++++v++yl+++g++++pVnp+++ il +++y ++++ p +vd+vdvf+p++ + +i+kea+++++k++wlq+g+ +eea +
     AJA92766.1  18 KKVAVVGMSKNPDKAAHYVPKYLHDNGYDITPVNPNADVILKKQCYDEITDVPDDVDIVDVFRPSDQVMPIIKEAIKKKPKVIWLQEGIHNEEAEK 113
                    689***********************************************758******************************************* PP

                    HHHHTT-EEE.ES-HHHHH CS
  CoA_binding_2  97 laeeagirvvgdrCilveg 115
                    la++agi+vv +rC+l e+
     AJA92766.1 114 LARDAGIDVVYNRCMLAEH 132
                    ****************998 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   5.5e-10   2.5e-06       2      91 ..      16     101 ..      15     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.5e-10
                  TTEEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEE CS
  CoA_binding   2 kdtkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiv 91 
                  k++kv+v+G++++  + + y+ k   + g   + +vnp+  ++ +l  ++y+++++++++  vd+  ++ P++++  +++e+++++ k+i+
   AJA92766.1  16 KMKKVAVVGMSKNPDKAAhYVPKYLHDNG-YDITPVNPN--ADVILKKQCYDEITDVPDD--VDIVDVFRPSDQVMPIIKEAIKKKPKVIW 101
                  689***************77766666655.5689*****..*******************..99999*********************998 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.1e-06     0.032     163     198 ..      88     123 ..      83     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-06
                     HHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EE CS
  Glyco_hydro_57 163 lyeeyfgqePrgfwlpElavspeileilaelGfeyl 198
                     +++e + ++P+++wl E + ++e +++ +++G++++
      AJA92766.1  88 IIKEAIKKKPKVIWLQEGIHNEEAEKLARDAGIDVV 123
                     689999***************************987 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00014      0.62      49      90 ..      61     100 ..       9     101 .. 0.78
   2 ?   -0.7   0.0      0.55   2.5e+03      35      51 ..     107     123 ..     105     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                   EEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
  GFO_IDH_MocA  49 eaysdleelladpeidavivatpngtheelakaaleagkhvl 90 
                   ++y+++ ++++  ++d+v v  p+++ + ++k+a++++++v+
    AJA92766.1  61 QCYDEITDVPD--DVDIVDVFRPSDQVMPIIKEAIKKKPKVI 100
                   46777777777..9*************************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.55
                   SHHHHHHHHHHTTHEEE CS
  GFO_IDH_MocA  35 daeraeavaesfgveay 51 
                   ++e+ae++a+  g++++
    AJA92766.1 107 HNEEAEKLARDAGIDVV 123
                   67788888888888743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 939.13
//
Query:       AJA92767.1  [L=191]
Description: hypothetical protein T478_1098 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.0   0.0       0.14   10.8   0.0    1.1  1  GATase_2  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     8e-06      0.14      39     118 ..      72     153 ..      38     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-06
                 SSBSEEEEEEE--HHHHHHHHHHTT-----GGG-EEEEEEE-SSHHHHHHHHHHHHHHHHHTT-E..EEEEEE--B-GGGS- CS
    GATase_2  39 ktGDGaGillqiPdeflrkeakekgielpeageyavgmlflpkdeekaeeakkileeiveeegle..vlgwRevpvdksvlg 118
                 + GDG  + l++P+e+  + +++++ +++ +ge+ ++  +l++  ++++++  ++e+i++++g++  +l  R   + ++vl 
  AJA92767.1  72 QIGDGLSLKLKKPWEMHVRLFSNTENSISIQGEVEISRDYLQHLFSQRTAVIYEIESILKKNGIKydILNKRISKYVNKVLD 153
                 67***********************************************************986422777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1452.67
//
Query:       AJA92768.1  [L=642]
Description: hypothetical protein T478_0572 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0021   18.4   8.1       0.32   11.4   0.0    3.5  4  DUF1771      Domain of unknown function (DUF1771)
  ------ inclusion threshold ------
       0.01   15.1   0.1       0.02   14.1   0.1    1.5  1  DLP_helical  Dynamin-like helical domain
      0.013   14.5   2.0      0.022   13.8   2.0    1.3  1  DEC-1_N      DEC-1 protein, N-terminal region
      0.014   14.9   0.4      0.028   13.9   0.4    1.4  1  CAP_N        Adenylate cyclase associated (CAP) N terminal
       0.13   10.5   0.0       0.22    9.8   0.0    1.2  1  OATP         Organic Anion Transporter Polypeptide (OATP) fam


Domain annotation for each model (and alignments):
>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   8.8e-05      0.32      16      36 ..      75      95 ..      69      99 .. 0.88
   2 ?   -0.9   0.1      0.62   2.2e+03      20      41 ..     182     203 ..     179     210 .. 0.84
   3 !   10.0   0.0   0.00024      0.86      16      38 ..     394     416 ..     388     420 .. 0.85
   4 ?   -4.2   0.7         5   1.8e+04      20      32 ..     475     489 ..     471     493 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.8e-05
     DUF1771 16 nelfekAaeAyrrGdgaaAke 36
                 e+++kA++ y+ Gd ++Ak 
  AJA92768.1 75 MECYDKAKQNYQDGDNKQAKL 95
                59*****************95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.62
     DUF1771  20 ekAaeAyrrGdgaaAkelseqG 41 
                 e+A   y++ d   Ak+++ +G
  AJA92768.1 182 EEALIKYNEDDTYGAKKYAYEG 203
                 677888999*********9988 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00024
     DUF1771  16 nelfekAaeAyrrGdgaaAkels 38 
                 ++l+  A++Ay++Gd   A+el+
  AJA92768.1 394 DRLLITAQAAYANGDADLAHELV 416
                 567778***************97 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 5
     DUF1771  20 ekAaeAyrrGd..ga 32 
                 + A++A ++G   +a
  AJA92768.1 475 KTAQAAIASGPapKA 489
                 678888888874333 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.6e-06      0.02      75     174 ..     357     456 ..     322     488 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-06
  DLP_helical  75 qlpeaeerleelekevekleesakriekelaelkkeieearielreelkayfsdLilqvkglsletieeFlereiGdegivvgtkleneferqlekis 172
                  ++ ++ ++++e++  v++l+ +a +  ++l  + + i +  i+++   ++   dL  ++ g++  +  eFle  iG+ ++++ +++e +++++l +++
   AJA92768.1 357 KISTVLKQADEATLTVKNLQANAGEGGANLGGYFETIDRLLITAQAAYANGDADLAHELVGTAYLDNYEFLEAPIGEVDNKLMKTIEDDMRENLRNMI 454
                  67889999***********************************************************************************9999877 PP

  DLP_helical 173 ee 174
                   +
   AJA92768.1 455 TS 456
                  64 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.0     6e-06     0.022     114     151 ..     482     516 ..     441     577 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-06
     DEC-1_N 114 Gaaapapalaaapp.papapvpddpapapaapqaaafaf 151
                   + pap  aaa p p+pap+   papapaa ++   ++
  AJA92768.1 482 A-SGPAPKAAAAAPaPTPAPT---PAPAPAAQETQQISL 516
                 2.4678766555444777775...677777776663333 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   7.8e-06     0.028     201     264 ..     440     512 ..     436     523 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.8e-06
                 HHHHHHHHHHHHHHSTTS----TT.......SBE...............SSC--XXXXXXX.....XXXXXXXX.....X CS
       CAP_N 201 lqilkeLqaYvkeyhttGltWnkk.......Gkdaeealk........aaaaaasaaaaggppp.PpPpPppasvfeees 264
                 ++i +++++ ++++ t+G ++n+                +         a+ +a++aaa++p+p P+P P+pa++++e++
  AJA92768.1 440 KTIEDDMRENLRNMITSGSSYNDVeshilmiN-------NdlktaqaaIASGPAPKAAAAAPAPtPAPTPAPAPAAQETQ 512
                 56678888889999999999997634444442.......24444432322333333333333332444444544333322 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   6.1e-05      0.22     145     176 ..     100     131 ..      73     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 6.1e-05
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 145 GatpiytlGisYidDnvkkknsplylgilyal 176
                  +  iytlG+  ++D v+k+ns+ y+ ++  +
  AJA92768.1 100 QEKSIYTLGMVMMEDAVSKNNSAAYIDWVDIV 131
                 56789*********************988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4527.17
//
Query:       AJA92769.1  [L=74]
Description: hypothetical protein T478_1420 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 538.90
//
Query:       AJA92770.1  [L=207]
Description: ATP-dependent protease La (LON) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-08   32.6   0.0    7.9e-08   32.4   0.0    1.0  1  LON_substr_bdg  ATP-dependent protease La (LON) substrate-bin
  ------ inclusion threshold ------
        0.1   12.1   0.1       0.14   11.7   0.1    1.1  1  DUF1002         Protein of unknown function (DUF1002)


Domain annotation for each model (and alignments):
>> LON_substr_bdg  ATP-dependent protease La (LON) substrate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   8.8e-12   7.9e-08      60     207 ..      26     201 ..       1     202 [. 0.75

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 8.8e-12
  LON_substr_bdg  60 iselysvGtvarIvqil..rlddgrikvvlegleRvkikkleke............................keegylvaeveiieddsepedsd 124
                      +  y++Gt+a+I  +    + +g + v ++g ++++i +l ++                            +++ y++ae+e i     + d++
      AJA92770.1  26 WQAPYDIGTLAKISDCKdvDSTSGHLFVNVRGRRKFRIIRLIPPslkktddydpftidgvkmvdqlhendgiDKKMYIQAEIEMI----SEIDES 116
                     34449***********844444699*************99944469999*9999999999999999999999999999****999....556666 PP

  LON_substr_bdg 125 slqkelkalvqeiiekikkslarellkllleielllkyedlenpyr..LadlvaailpfsneekqelLeeldvedRlkkvlelLk 207
                        +  + lv    +kikks+  + l ++  +  l++y+  ++++    + +++a+ +  + ++q +Le  ++e+ l++ ++lL+
      AJA92770.1 117 ISLEDWENLVDLWKNKIKKSAGNSELTSYQLDHVLEQYYLKTETPTmeYVHSLCALASETPLDLQPILECTNLEQLLERSTKLLE 201
                     66678888888888888886455555555444445555555555544788999999999999********************997 PP

>> DUF1002  Protein of unknown function (DUF1002)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.6e-05      0.14     131     212 ..     101     181 ..      93     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
     DUF1002 131 eaAneeLvttselaekigsekaaelvaevkeevakeklkteeeikkiveevanelninlsdeqiqqivnllkkiqkldldlk 212
                    ++e+++ se++e+i+ e+ ++lv+  k+++ k  + ++e  +  ++ v++++ ++ +  +++ + +l+   +++ ldl+
  AJA92770.1 101 MYIQAEIEMISEIDESISLEDWENLVDLWKNKIKKS-AGNSELTSYQLDHVLEQYYLKTETPTMEYVHSLCALASETPLDLQ 181
                 55689****************************997.567777777889999999999999999999999988888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1438.00
//
Query:       AJA92771.1  [L=315]
Description: asparagine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-36  126.1   0.0    1.8e-22   80.5   0.0    2.1  2  Asn_synthase    Asparagine synthase
    0.00011   21.8   3.3     0.0002   21.0   3.3    1.4  1  zinc_ribbon_2   zinc-ribbon domain
    0.00025   21.0   2.9    0.00025   21.0   2.9    1.6  2  DZR             Double zinc ribbon
      0.003   18.3   2.8     0.0058   17.4   2.8    1.5  1  zinc_ribbon_15  zinc-ribbon family
     0.0047   17.0   1.2     0.0047   17.0   1.2    1.9  2  UPF0547         Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
      0.022   13.9   0.0      0.029   13.5   0.0    1.3  1  NAD_synthase    NAD synthase
      0.069   12.9   0.0       0.12   12.1   0.0    1.4  1  ATP_bind_3      PP-loop family
      0.077   12.5   0.0        0.2   11.1   0.0    1.7  2  QueC            Queuosine biosynthesis protein QueC
      0.097   11.4   0.0       0.17   10.6   0.0    1.4  1  tRNA_Me_trans   tRNA methyl transferase
       0.12   12.4   0.0       0.25   11.4   0.0    1.5  1  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
       0.35   10.4   2.4       0.69    9.4   2.4    1.5  1  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   1.1e-25   1.8e-22      23     142 ..      25     142 ..      12     174 .. 0.88
   2 !   43.7   0.0   1.7e-14   2.7e-11     236     312 ..     172     252 ..     163     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 1.1e-25
  Asn_synthase  23 lLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee..pfadrsaiplyllsrlakrk 117
                    LSGGlDSS++a+l + q +   +t +i +++    ++ +a+ +a+hlg++   ++++ e++ld + ++i++l +   + +r +i  y+    +k+k
    AJA92771.1  25 ALSGGLDSSILAHLRKDQKP---QTMTIITKDFLGTDLTFAQIIAKHLGLNLSLIQVSMEDVLDSINETIKILGNynDIEIRNSIVPYIYLTTLKKK 118
                   6*************999877...677777777799*****************************************98899999999********** PP

  Asn_synthase 118 gvkvvLsGeGaDElfgGYpyfykaa 142
                   gv  v++G+GaDE+f+GY+ f  ++
    AJA92771.1 119 GVDSVITGDGADEVFAGYN-FLLKK 142
                   *******************.54443 PP

  == domain 2  score: 43.7 bits;  conditional E-value: 1.7e-14
  Asn_synthase 236 EaRvPflDhrlvevalrlppelklrg....gieKyiLRealegylPeeileRpKegfsapvgewklkgelrelaeellsds 312
                    + +Pfl  +l+++   + ++ k++     + +K+iLRe +e+ylP++i++R+K+++++++g+++l+g  +  + + +  +
    AJA92771.1 172 KVETPFLNEELIKFSDDIEISKKINVkdggKFGKWILRETFEKYLPNNITWREKSPMQDGSGTNNLTGLFNTIITDDIFTQ 252
                   5567********************9999999*********************************88877766666555544 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.3   1.2e-07    0.0002       1      20 [.     291     310 ..     291     311 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCG 20 
                    +Cp C +e+ +n++FC  CG
     AJA92771.1 291 RCPDCNYEIAPNSRFCRMCG 310
                    6******************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.3   5.4e+03       3      16 ..       7      20 ..       6      22 .. 0.57
   2 !   21.0   2.9   1.5e-07   0.00025      18      49 .]     276     310 ..     267     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.3
         DZR  3 qCgeelppdarfCs 16
                qC++ l++  + C+
  AJA92771.1  7 QCMRILTNAVNECK 20
                56666666555554 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.5e-07
         DZR  18 Cgtklkavaa...edrCpsCgekvdpearfCpeCG 49 
                 C  k ++v++    +rCp C++++ p++rfC  CG
  AJA92771.1 276 CFRKTNSVKKsdsDNRCPDCNYEIAPNSRFCRMCG 310
                 544444333344599*******************9 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.8   3.5e-06    0.0058      55      86 .]     279     310 ..     252     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
  zinc_ribbon_15  55 keiekkessekkeCknCgkeveeefkyCpkCg 86 
                     k+ + k+s + ++C++C+ e+ +++++C  Cg
      AJA92771.1 279 KTNSVKKSDSDNRCPDCNYEIAPNSRFCRMCG 310
                     22333344559********************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.3   2.1e+03       5      17 ..       7      19 ..       7      21 .. 0.88
   2 !   17.0   1.2   2.9e-06    0.0047       2      21 ..     291     310 ..     291     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
     UPF0547  5 eCeakvPvaaqfC 17
                +C +++  a+ +C
  AJA92771.1  7 QCMRILTNAVNEC 19
                7999999999999 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.9e-06
     UPF0547   2 vCPeCeakvPvaaqfCphCG 21 
                 +CP C  +++ + +fC+ CG
  AJA92771.1 291 RCPDCNYEIAPNSRFCRMCG 310
                 6******************9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.029       6      91 ..       9      90 ..       4     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                  HHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE--..-HHHHHHHHHH CS
  NAD_synthase  6 vdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid..ikpivrafeqe 91
                  + +l++ v++++++   + lSGG+DSs+ a l ++   k + ++++   +     d++ a+ +a++lg++   i+  +++++ +++++
    AJA92771.1  9 MRILTNAVNECKSDW--IALSGGLDSSILAHLRKDQ--KPQTMTIIT--KDFLGTDLTFAQIIAKHLGLNLSLIQvsMEDVLDSINET 90
                  567788888887665..569************9985..467777775..777789999999999999988765540055565555554 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.3e-05      0.12       4      28 ..      24      48 ..      22     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-05
                EE--SCHHHHHHHHHHHHHCTTTTT CS
  ATP_bind_3  4 vAvSgGlDSmaLllllaklkkklgi 28
                +A+SgGlDS +L +l +++k ++ +
  AJA92771.1 24 IALSGGLDSSILAHLRKDQKPQTMT 48
                8***************999887654 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012       0.2       5      95 ..      25     108 ..      23     139 .. 0.76
   2 ?   -3.3   0.0       3.1     5e+03     147     160 ..     166     179 ..     148     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                 E--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-----------...--------T CS
        QueC   5 llSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeeievpkeeleeeelpntfVp 95 
                  lSGGlDS++++ l k++  +  ++t+  +    ++l  a+ iak+lg+ +   ++++ ++++ +s  ++e+i++   ++++ e++n++Vp
  AJA92771.1  25 ALSGGLDSSILAHLRKDQKPQ--TMTIITKDFLGTDLTFAQIIAKHLGL-NLSLIQVS-MEDVLDS--INETIKILG-NYNDIEIRNSIVP 108
                 69**********999998644..334444444678999**********9.89999998.6776665..556666655.6777788888887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.1
                 HHTS--EEE-TTTT CS
        QueC 147 gedkkieieaPlid 160
                 +++ ++++e+P+++
  AJA92771.1 166 ATSLNMKVETPFLN 179
                 46667888888765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.17       5      34 ..      24      53 ..      22      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
  tRNA_Me_trans  5 valSgGVDSsvaaallkeqgyevigvflkl 34
                   +alSgG DSs+ a+l k+q  +++ ++ k 
     AJA92771.1 24 IALSGGLDSSILAHLRKDQKPQTMTIITKD 53
                   79******************9998887654 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.25       4     129 ..      24     149 ..      22     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                  EE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-E.EEEEE-SCHHHHHHHHHH-S-THHHC.HHHHHHTHHHHHHHHHCTT CS
  PAPS_reduct   4 vsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglr.lkvyepeeevaekinaekhgsslyee.aaeriaKveplkkaLekld 99 
                  ++ sgG ds++l hL  k +kp +++ + t++   + ++f + +++++gl+   + +++e+v ++in+  +   +y++ ++++ +  +    +L+k +
   AJA92771.1  24 IALSGGLDSSILAHLR-KDQKP-QTMTIITKDFLGTDLTFAQIIAKHLGLNlSLIQVSMEDVLDSINETIKILGNYNDiEIRNSIVPYIYLTTLKKKG 119
                  689***********95.55555.589999999999999**********99955567788888888888887888888876665555555666788888 PP

                  ECEEE----CCCTTTTTTSSSEEECTTT-S CS
  PAPS_reduct 100 edalltGaRrdesksraklpiveidedfek 129
                   d ++tG  +de ++  +  + + de++ +
   AJA92771.1 120 VDSVITGDGADEVFAGYNFLLKKSDEEIGE 149
                  889999988888877666666666666655 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.4   0.00042      0.69       3      24 ..     290     311 ..     288     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00042
  zf-ribbon_3   3 vrCPnCGa.plssddnvCpyCGt 24 
                  +rCP C+  + ++  ++C  CG+
   AJA92771.1 290 NRCPDCNYeI-APNSRFCRMCGK 311
                  59******77.***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2217.35
//
Query:       AJA92772.1  [L=280]
Description: putative formyltetrahydrofolate deformylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-46  158.2   0.1    2.4e-46  157.8   0.1    1.2  1  Formyl_trans_N  Formyl transferase
    3.1e-06   27.1   0.1    1.1e-05   25.3   0.0    2.0  2  ACT_6           ACT domain
  ------ inclusion threshold ------
       0.14   12.6   1.1          9    6.8   0.1    2.4  2  Streptin-Immun  Lantibiotic streptin immunity protein
       0.16   11.6   2.0          1    9.0   0.2    2.2  2  CotE            Outer spore coat protein E (CotE)
       0.43   11.2   2.4       0.69   10.5   0.1    2.5  3  ACT_4           ACT domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.1   6.7e-50   2.4e-46       1     181 []      87     262 ..      87     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 6.7e-50
                     -EEEEEESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SEEEEES--S---HH CS
  Formyl_trans_N   1 kkivvlisgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadlivlagymkllpke 95 
                     k+i+v++++++++lq+l+ a+  ++l++++++v++ ++++ g+  a++a+ p+ +++ek+ ++   +e +++++ k++ +dli la ym++l+++
      AJA92772.1  87 KNIAVFVTKEPHCLQTLIRAQTRKELKGKIAVVIGTENTLSGM--AKKAKLPFVLINEKNQDK---AEAKIIQVCKKYDVDLIALARYMRILTPN 176
                     69***************************************76..567899*****9997665...599************************** PP

                     HHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  96 lvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalveal 181
                     +v +++++i+niHpSLLP+f+Ga a+ +a+e+G k  Gvt h+v+e+lD+G+i++q++  + +e t+e++++  +++e ++l++a+
      AJA92772.1 177 FVWRYPNRIINIHPSLLPAFPGAMAYAQAFERGTKIIGVTSHYVTENLDQGPIIFQDSFSVKPEHTLESIKRAGQKLEAEVLLKAV 262
                     *********************************************************************************99886 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   3.1e-09   1.1e-05       5      74 ..       8      78 ..       4      80 .. 0.90
   2 ?   -2.5   0.1       1.5   5.2e+03      55      71 ..     250     266 ..     243     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.1e-09
       ACT_6  5 itvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgped.alarlekaLlflakelgltve 74
                itv+G+d+ G++a +t  + e + n+  ++q vi g +   l  s  ++ +++r  ++L++l k+l ++v 
  AJA92772.1  8 ITVVGKDKEGIVANFTNFVFERKGNLERVNQNVIKGLFGMYLEASFTKKiDIKRFDSDLEKLGKQLHMEVN 78
                9***********************************88777777776666*****************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
       ACT_6  55 larlekaLlflakelgl 71 
                  ++le+++l +a ++ l
  AJA92772.1 250 GQKLEAEVLLKAVRMHL 266
                 56889999999888766 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0025         9      47      78 ..      52      83 ..      32      95 .. 0.85
   2 ?    4.3   0.1     0.015        53      14      50 ..     128     168 ..     117     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
  Streptin-Immun 47 nltesvtleqiekeieklqnelskkideyeel 78
                     +t+ + +++ ++++ekl ++l+ +++ + e+
      AJA92772.1 52 SFTKKIDIKRFDSDLEKLGKQLHMEVNTHHES 83
                    57999*********************988765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
  Streptin-Immun  14 kiatlnkmaevlvnlksedeetrrla....kydfsklnlte 50 
                      +a+  k+  vl+n k++d+ + ++     kyd++ + l++
      AJA92772.1 128 GMAKKAKLPFVLINEKNQDKAEAKIIqvckKYDVDLIALAR 168
                     5677788899*********9988764233378888777765 PP

>> CotE  Outer spore coat protein E (CotE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   0.00028         1      84     118 ..      72     106 ..      67     126 .. 0.82
   2 ?    1.0   0.1     0.078   2.8e+02      38      62 ..     139     163 ..     134     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00028
        CotE  84 kvklklkdkktlsdeeeiivrvlkqPncvevkise 118
                 +++++++++++ +++++i v v+k+P+c+++ i+ 
  AJA92772.1  72 QLHMEVNTHHESNSQKNIAVFVTKEPHCLQTLIRA 106
                 678999999999*****************998873 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.078
        CotE  38 vINhkfeakkkgdkvevkGsydvni 62 
                 +IN k + k + + ++v  +ydv++
  AJA92772.1 139 LINEKNQDKAEAKIIQVCKKYDVDL 163
                 59999999999999********986 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00019      0.69       8      50 ..       7      47 ..       2      60 .. 0.87
   2 ?   -1.9   0.0       1.5   5.4e+03      11      31 ..     104     124 ..      95     127 .. 0.82
   3 ?   -1.9   0.1       1.5   5.4e+03      15      35 ..     144     164 ..     140     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
       ACT_4  8 rleveaedrkglLaditqviseekanivsvnaktrkkdglaei 50
                 ++v+++d+ g++a+ t+ + e k+n++ vn    k  gl+ +
  AJA92772.1  7 GITVVGKDKEGIVANFTNFVFERKGNLERVNQNVIK--GLFGM 47
                799****************************98864..56655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
       ACT_4  11 veaedrkglLaditqviseek 31 
                 + a+ rk l ++i+ vi  e+
  AJA92772.1 104 IRAQTRKELKGKIAVVIGTEN 124
                 678889999999999988775 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.5
       ACT_4  15 drkglLaditqviseekaniv 35 
                 +++++ a+i+qv+++ ++++ 
  AJA92772.1 144 NQDKAEAKIIQVCKKYDVDLI 164
                 566666899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2118.96
//
Query:       AJA92773.1  [L=267]
Description: hypothetical protein T478_0485 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.5   2.3       0.04   14.5   2.3    2.9  3  M         M protein repeat
       0.77   10.2  19.5       0.17   12.3  10.3    2.3  2  CCDC53    Subunit CCDC53 of WASH complex
        1.4    9.5  10.4       0.54   10.8   2.4    2.2  2  Striatin  Striatin family


Domain annotation for each model (and alignments):
>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.3   6.7e-06      0.04       3      20 ..      14      31 ..      12      32 .. 0.94
   2 ?   -1.7   0.6       1.3   7.6e+03       7      12 ..     205     210 ..     200     212 .. 0.63
   3 ?   -3.5   0.1         3   1.8e+04       4       6 ..     231     233 ..     227     239 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.7e-06
           M  3 kkeLEaelqeLeeelqaL 20
                kk+LEa+ ++Le++l +L
  AJA92773.1 14 KKDLEAKIADLEAKLNKL 31
                9***************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
           M   7 Eaelqe 12 
                 Ea+++e
  AJA92773.1 205 EAKKAE 210
                 566665 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3
           M   4 keL 6  
                 k+ 
  AJA92773.1 231 KTT 233
                 333 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  10.3   2.9e-05      0.17      24     103 ..       8      92 ..       3     126 .. 0.53
   2 ?    3.3   1.7     0.017        99      72     111 ..     196     235 ..     141     259 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
      CCDC53  24 vevekrlqrleitlalLEakLsSipgleeveaeaaeastsddn.....aarkgppppppsseaaaaaaqaeeasqaeesaeeeae 103
                 ++ ++  ++le+++a LEakL+    ++++++++++ + ++++     a+++++p+p++++++ + a++a+e+++ae+  e++++
  AJA92773.1   8 TRKSTTKKDLEAKIADLEAKLNKLAAAQDAKPAETAPKPAETApepkpAETAPEPKPAETAPEPKPAETAPEPKPAETAPEPKPA 92 
                 5566677899************777777777775444444333233332222222222222222222222222222222222222 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.017
      CCDC53  72 ppppppsseaaaaaaqaeeasqaeesaeeeaeeqeesesk 111
                 p+p++++ ++a++a++++ea   +  ++e++++++++ s+
  AJA92773.1 196 PAPKAEKPAEAKKAESKPEAGGGPHGHDEKPKTEAKTTSA 235
                 2222222222333333333333333333333333333222 PP

>> Striatin  Striatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.4     9e-05      0.54      43     117 ..       9      84 ..       3     129 .. 0.64
   2 ?    3.4   1.1     0.018   1.1e+02      78     125 ..     194     239 ..     170     259 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9e-05
    Striatin  43 gaenlkkdlvrrikmLEyalkqerakylklkegtsaa.kenkkkekeeeeaeeeekseeeskskekksakeslkks 117
                 ++  +kkdl  +i  LE +l++  a + +   +t+++  e++ ++k  e+a e +++e+ ++ k++++a+e   ++
  AJA92773.1   9 RKSTTKKDLEAKIADLEAKLNKLAAAQDAKPAETAPKpAETAPEPKPAETAPEPKPAETAPEPKPAETAPEPKPAE 84 
                 567899**************99987755543333333033444444455555555555555555555555554433 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.018
    Striatin  78 aakenkkkekeeeeaeeeekseeeskskekksakeslkkseaeeeses 125
                 +a++ k +++ e +++e++++++   + ++++ k+++k+++a+  +++
  AJA92773.1 194 DAPAPKAEKPAEAKKAESKPEAGGGPHGHDEKPKTEAKTTSAD--TAK 239
                 3333444455555555555555555566666666655554222..111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 1874.71
//
Query:       AJA92774.1  [L=211]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-41  139.6  25.7    6.7e-22   77.2   4.9    2.4  3  UPF0126   UPF0126 domain
  ------ inclusion threshold ------
        9.7    5.5  18.3        1.7    8.0   1.9    2.2  2  ThrE      Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   4.9   7.5e-26   6.7e-22       2      77 ..      14      88 ..      13      89 .. 0.96
   2 !   72.5   8.4   2.1e-24   1.9e-20       3      76 ..     101     173 ..      99     175 .. 0.96
   3 ?   -3.2   0.1      0.88   7.9e+03      10      23 ..     182     195 ..     180     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 7.5e-26
                HHHHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHHH CS
     UPF0126  2 ildaiGlaafavsGalvAlkkgldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvlla 77
                +ld++G++afav+Ga +A++++ d++g+++l+++T+v+GG++RDv+lg++ P  l++ + y++++++ a+v++ll+
  AJA92774.1 14 VLDLFGTMAFAVTGAFKAIEHKADIVGIIILATITGVAGGTIRDVILGKSLPNSLID-PSYVIITVVSAIVIFLLH 88
                89*****************************************************86.8**************987 PP

  == domain 2  score: 72.5 bits;  conditional E-value: 2.1e-24
                 HHHHHHHHHHHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHHHHHHTTSSSSGHHHSSTCHHHHHHHHHHHHHHH CS
     UPF0126   3 ldaiGlaafavsGalvAlkk.gldllgvvvlGvvTAvgGGvlRDvllgrevPvvllreelyataallgalvvvll 76 
                 +daiGl++f+v+Ga  A +  g+++l++v+ G++TA+gGG+lRDv++ + +P+v+++e lya+a++lga v++l+
  AJA92774.1 101 FDAIGLGVFTVIGATFAYNMfGMNFLVIVLSGMLTAIGGGILRDVFVSQ-TPIVFVKE-LYASASFLGASVFFLV 173
                 8******************99***************************6.*****987.*************986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.88
                 HHHHHHHHHHHHTT CS
     UPF0126  10 afavsGalvAlkkg 23 
                 a ++sG l A   +
  AJA92774.1 182 AGTISGLLLATGLR 195
                 55677777776655 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.9   0.00019       1.7     112     180 ..      20      89 ..      15     107 .. 0.79
   2 ?    2.7   9.2    0.0077        69     113     193 ..     108     189 ..     100     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00019
        ThrE 112 vlaaglaaaafallfggdwidf.lvaflagllggllrlllakrglnsfvleavaaflasllallavslgl 180
                 ++a+++ +a+ a+  ++d++ + ++a+++g+ gg +r ++  ++l++ ++    ++++ + a++++ l+ 
  AJA92774.1  20 TMAFAVTGAFKAIEHKADIVGIiILATITGVAGGTIRDVILGKSLPNSLIDPSYVIITVVSAIVIFLLHS 89 
                 67888888888888888887651568899999999****************9999999999999888753 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0077
        ThrE 113 laaglaaaafallfggdwidflvaflagll.ggllrlllakrglnsfvle..avaaflasllallavslglglnpdaiiigsil 193
                 ++  + a +   +fg ++++++++ +++++ gg+lr ++   + + fv e  a a+fl + + +l+++  + +++ a++i+++l
  AJA92774.1 108 VFTVIGATFAYNMFGMNFLVIVLSGMLTAIgGGILRDVFVSQTPIVFVKElyASASFLGASVFFLVIY--VTNDVYAGTISGLL 189
                 44455555555677****99999877766615678888899999999998334455565555555555..45778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1563.43
//
Query:       AJA92775.1  [L=1115]
Description: DNA-directed RNA polymerase subunit B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   9.5e-127  423.3   0.6   1.3e-126  422.8   0.6    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    1.7e-47  161.6   0.0      3e-47  160.8   0.0    1.3  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
      6e-29  100.3   0.0    1.3e-28   99.2   0.0    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.7e-28   98.6   0.1    4.4e-28   97.3   0.1    1.8  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    5.6e-25   88.1   0.0    1.2e-24   87.0   0.0    1.6  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    9.4e-18   64.3   0.2    2.1e-17   63.1   0.2    1.7  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    7.9e-08   32.7   1.2    4.8e-07   30.3   1.2    2.2  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.037   14.1   0.1    1.5  1  DUF2318         Predicted membrane protein (DUF2318)
       0.12   12.3   1.3       0.51   10.3   1.3    2.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.21   11.8   0.5       0.46   10.7   0.5    1.5  1  Ribosomal_L37e  Ribosomal protein L37e


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.8   0.6  7.3e-130  1.3e-126       2     390 .]     645    1018 ..     644    1018 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.8 bits;  conditional E-value: 7.3e-130
                      HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEEEBBBS--TTTTTT CS
  RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqnavVAvmsyeGYniE 94  
                      a+++p++eh+qspr+++++am+kq+lg+ +  + + +  + +++ ++q+P+v+t+ ++++++        ++e ++G n++VAv++++GYniE
      AJA92775.1  645 ASIIPYPEHNQSPRNTYESAMAKQSLGFSTPMMNTSTYVRQHFMLYPQTPIVSTR-AMNLLG--------MEERPAGVNCTVAVLPFDGYNIE 728 
                      889************************9998888888899999************.******........*********************** PP

                      T-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.......-SS-GGGS-TTSB--SS-EEETT-EEE---..B-----...- CS
  RNA_pol_Rpb2_6   95 Daiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.......seealkkLdedGivrvgaevkegdilvgkvtkgeteltpeek 180 
                      Dai+ln+++vdr++f++++++ y++ea+++++g ++ ++ ++ +       +e+a++ L++dGiv  ++ v  gdil+gk+  ++ ++++e k
      AJA92775.1  729 DAIVLNRSSVDRGLFRTFFYRIYDTEAKQYPGGMRDNFEVPNADdnvrgykGEKAYRMLEDDGIVATESGVDGGDILIGKT--SPPRFMEEYK 819 
                      ********************************998877766665889***9*****************************8..8888886665 PP

                      ----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS-- CS
  RNA_pol_Rpb2_6  181 llraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGiv 273 
                      +    f++++   +dts+ v+++e+gvVd+v +       ++++++ k++k++v++ R +++GDKfasrhGqKGv++++++qeD+P++e+Gi+
      AJA92775.1  820 E----FETSGPYRRDTSVGVRPSEHGVVDTVVM-------TQSNEGGKMYKIRVRDMRIPEIGDKFASRHGQKGVLGILAKQEDLPYTEQGIQ 901 
                      5....566666789*******************.......89999************************************************ PP

                      -SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CC CS
  RNA_pol_Rpb2_6  274 vDivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlve 366 
                      +D+++NP+++PSRmt+g+++E+++gkaaal+gk++d+++F g+k + +ke L+++g+++sGke +ydGrtG+ +e + f+Gv+Yy+kL+h+v+
      AJA92775.1  902 PDVLINPHAFPSRMTVGMMMESVCGKAAALRGKQFDGSAFVGEKMDIVKEILDKQGFKYSGKEKMYDGRTGKAFEVDTFIGVVYYQKLHHMVS 994 
                      *******************************************99************************************************ PP

                      CS----SS--B-TTT--B-SCGGG CS
  RNA_pol_Rpb2_6  367 dKihaRstGpyslltqQPlgGkaq 390 
                      dKihaR++G++++lt+QP++G+a+
      AJA92775.1  995 DKIHARARGQVQMLTKQPTEGRAR 1018
                      **********************96 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   1.7e-50     3e-47       2     187 ..      21     376 ..      20     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 1.7e-50
                     TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCC CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsaplyvklklvvyekdnke 96 
                     +++q+l SF++f+++ l+ ii+e  +ie+e+ +    + +++++++i+l++P + e d+s ++++P earlrn++Y ap++++   v     +++
      AJA92775.1  21 IARQHLTSFDEFLDNGLQSIIQEVGQIEIENAE----YPYKIQLGKIKLQQPRMMELDGSITHVTPAEARLRNISYVAPIMMEASVVE----DGK 107
                     679*************************99985....68*****************************************99988888....899 PP

                     EEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.................................... CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
  RNA_pol_Rpb2_1  97 eikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek.................................... 155
                     + + + v iG++P+M++s+ac+l+  ++++l++++E+p d+GGyFiinG+e+v+v +e+                                    
      AJA92775.1 108 TLETRFVHIGDMPVMVKSHACILNTFTDQKLIDHQEDPRDPGGYFIINGSERVVVGLEDlsynkiivdaekvggkivhkakvyssiigyraklel 202
                     *********************************************************************************************** PP

                     ............................................................................................... CS
                     ............................................................................................... RF
  RNA_pol_Rpb2_1 156 ............................................................................................... 155
                                                                                                                    
      AJA92775.1 203 imkddgmivakipgspvdipvvtlmralglesdkdiagavslvdeiqdhlegsfekagdvptskdaivyiskriapgmleefqikraetlldwgl 297
                     *********************************************************************************************** PP

                     ...............................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                     ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb2_1 156 ...............................................laGeLlaslfrvllkklerdvkerlqkslekl 187
                                                                     aG++la+lfr+++++l+rd+k +l++s +k 
      AJA92775.1 298 lphlgkhpenrkekahfmgeaackllelklgwidpddkdhygnkvikFAGQMLADLFRTAFRNLVRDMKYQLERSGQKR 376
                     ************************************************************************9986654 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   7.5e-32   1.3e-28       1      86 [.    1020    1111 ..    1020    1112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 7.5e-32
                      BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEEEEES CS
  RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlqeLqslgialklll 86  
                      GGlrfGEMErd+liayGa++lLk+rl+++SD++++ +c++c+l+ + +       C  + +++ i++v++ +afklLlqe+ sl+ia++l+l
      AJA92775.1 1020 GGLRFGEMERDCLIAYGASMLLKDRLLDESDKTDILLCEKCGLTGYHDarkrkfVCAQCGENAPISSVSVAYAFKLLLQEILSLNIAPRLKL 1111
                      9*********************************************999***************************************9976 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.1   2.5e-31   4.4e-28       1      67 [.     412     475 ..     412     476 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 2.5e-31
  RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                     q+ldr+n+ls++shlrrv+s+   ls+++ ++e+Rdlh++h+GriCp+eTPEG+ncGlvk+Lal+a 
      AJA92775.1 412 QLLDRTNYLSTISHLRRVQSP---LSRTQPNFEARDLHSTHFGRICPSETPEGSNCGLVKNLALSAI 475
                     89*******************...****************************************985 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   6.7e-28   1.2e-24       3     189 ..     170     343 ..     168     344 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 6.7e-28
                     SCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHHHHHHHHHHHHHHCT CS
  RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsedsqlleelleeleekee 95 
                     n+i+v +ek   ki  +a+v ss+i +r+++  + kd++ +++  +    +ip+v +++Algl sd++I  +++     +++++ l  + e++ +
      AJA92775.1 170 NKIIVDAEKVGGKIvhKAKVYSSIIGYRAKLELIMKDDGMIVAKIPGSPVDIPVVTLMRALGLESDKDIAGAVS---LVDEIQDHLEGSFEKAGD 261
                     99************99999*******************************************************...6999************** PP

                     SSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEE CS
  RNA_pol_Rpb2_2  96 iqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkrlkaqdilymidrLlslklgrrevDDiDhlgnkRv 189
                     ++t ++a+ yi k++a +  ee ++++a+ +l         +   l+ hlg++ +  +   ka++ ++++ +Ll+lklg +++DD+Dh+gnk +
      AJA92775.1 262 VPTSKDAIVYISKRIAPGMLEEFQIKRAETLL---------DWGLLP-HLGKHPENRK--EKAHFMGEAACKLLELKLGWIDPDDKDHYGNKVI 343
                     *****************************999.........566777.******9444..6*******************************66 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.2   1.2e-20   2.1e-17       1      62 []     511     577 ..     511     577 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.2e-20
                     EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT.....T--EEEE-SSEEB-EEEEE-S CS
  RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek.....qkevkiatDgGRvcRPliiVe 62 
                     Vfv+G+l+G+++d+++lv+++Re+RR+ ki+++v i++++      ++++++++++GRv+RPl+i++
      AJA92775.1 511 VFVDGKLIGFHKDGQNLVDQMREFRRTSKIHPHVGISIHKPeeegaTQRLYVNCNAGRVLRPLVIIK 577
                     9*************************************99966777777****************96 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   1.2   2.6e-10   4.8e-07       1      55 [.     598     634 ..     598     637 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                     HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEE CS
  RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcE 55 
                     w+dL+r gv+E+lDa+EEe++++  + ++++k                   TH+E
      AJA92775.1 598 WNDLVRMGVIELLDANEEENCYVTFDDKNTKKF------------------THME 634
                     ***********************9988887665..................4444 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.1e-05     0.037      32      67 ..    1052    1088 ..    1040    1091 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
     DUF2318   32 valdaCevCekkgYv.qegeelvCknCgvrfaldsig 67  
                  + +  Ce C+ +gY+  ++ + vC +Cg++  ++s+ 
  AJA92775.1 1052 TDILLCEKCGLTGYHdARKRKFVCAQCGENAPISSVS 1088
                  55668**********8999**********99998875 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00028      0.51      31      55 ..    1057    1081 ..    1055    1083 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
  OrfB_Zn_ribbon   31 CseCgsknkealsgrtfkCpnCgfe 55  
                      C +Cg +++++  +r+f+C +Cg  
      AJA92775.1 1057 CEKCGLTGYHDARKRKFVCAQCGEN 1081
                      **********************975 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00025      0.46      17      38 ..    1055    1079 ..    1048    1083 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
  Ribosomal_L37e   17 ilCrrCgkrsyhvqkkt...CascG 38  
                       lC++Cg + yh  +k+   Ca+cG
      AJA92775.1 1055 LLCEKCGLTGYHDARKRkfvCAQCG 1079
                      58**********65543333****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 7254.72
//
Query:       AJA92776.1  [L=1176]
Description: RecF/RecN/SMC N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-51  174.4  23.8    7.2e-30  104.1   0.1    4.3  3  SMC_N          RecF/RecN/SMC N terminal domain
    1.6e-18   67.9  11.6    1.6e-18   67.9  11.6    6.5  5  AAA_23         AAA domain
    1.1e-16   61.2   0.1    6.3e-16   58.7   0.0    2.5  2  SMC_hinge      SMC proteins Flexible Hinge Domain
      4e-08   33.4  22.9      9e-06   25.7   0.7    4.4  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      1e-07   32.0  15.0      1e-07   32.0  15.0    4.4  4  AAA_15         AAA ATPase domain
    5.3e-06   26.1   0.0    1.5e-05   24.7   0.0    1.7  1  AAA_29         P-loop containing region of AAA domain
     0.0086   16.5   5.0     0.0086   16.5   5.0    8.8  8  KELK           KELK-motif containing domain of MRCK Ser/Thr p
  ------ inclusion threshold ------
      0.031   14.7   0.8       0.16   12.4   0.1    2.7  2  AAA_16         AAA ATPase domain
       0.95   10.0  94.4      0.036   14.6   3.4    8.0  8  APG6_N         Apg6 coiled-coil region
        1.2    9.4  86.7        2.3    8.4   7.2    6.8  6  ATG16          Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.1     4e-33   7.2e-30       2     130 ..       4     134 ..       3     147 .. 0.96
   2 ?  -11.5  13.9        10   1.8e+04      91     137 ..     290     338 ..     260     650 .. 0.74
   3 !   81.4  20.0   3.4e-26   6.2e-23      47     218 ..     694    1159 ..     683    1161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 4e-33
                 EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevs 98 
                 +k++ei +Fks+  k++i++f++++ +i GpNGSGKsn+ldAi F LGe+  k +r+ +l+ l+h    ++++  k a+ +++fdn d+k++++++ v+
  AJA92776.1   4 VKKVEIFGFKSFGFKNTIVDFEPGLVSISGPNGSGKSNILDAITFALGENRPKVMRAPNLRGLMHDveGAARRGPKMARTSVHFDNLDRKIPVDSDIVT 102
                 89****************************************************************87788999************************* PP

                 EEEEEETTSEEEEEETTEEE-HHHHHHHHHCT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  99 isrrvkrkgeseykingkevtkkevsellesa 130
                 i+r++  kg++ y++n+k+v ++++ +l+e a
  AJA92776.1 103 ITREMNDKGDNIYYLNKKKVIRSKILDLMEIA 134
                 **************************999855 PP

  == domain 2  score: -11.5 bits;  conditional E-value: 10
                 SSSSSCEEEEEEEETTS..EEEEEETTEEE-HHHHHHHHHCTT-STTCS CS
                 xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  91 kiekeevsisrrvkrkg..eseykingkevtkkevsellesagiskelL 137
                 + +k+e++++ ++ r++  e +  i+ ++ + +e+   l+s++i+ ++L
  AJA92776.1 290 NKSKSEIETKLSMHRQKfdEADSLIKTSTNRLTEIDTNLPSHKIDLDNL 338
                 3344444444333333311355677777777788888888888777643 PP

  == domain 3  score: 81.4 bits;  conditional E-value: 3.4e-26
                  HCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........ CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
       SMC_N   47 vLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske........ 135 
                  +     +kk r++kl+ l+++   +++++  ev +    +++  + ++ +  is+   +k++ e +in+ + t++ +s+ l + + + e        
  AJA92776.1  694 TVT---KKKNRAKKLDLLVNN--YEKRLSLSEVGMNT--TSN--SLSELKSRISQISNNKKSFETRINQLTRTQERISRELTNRKSHLEslesqikl 781 
                  444...345699999999997..78899999999952..222..356788999999999999*******************99999999999***** PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  AJA92776.1  782 vrdnyaepqmdrianeiklvneqileqdkklepiqndlkkkerhlaelmahdtkitgerknlrhtvssmdqekyhlevdirrltkekettetelvtl 878 
                  ************************************************************************************************* PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  AJA92776.1  879 rddeqklistsgtsveqmtefdnsleslnskerdstkeitlrerntdalnrdltdlrqkeskitsllatfgfdisievfdvestitsleseqnrikn 975 
                  ************************************************************************************************* PP

                  ................................................................................................. CS
                  ................................................................................................. RF
       SMC_N  136 ................................................................................................. 135 
                                                                                                                   
  AJA92776.1  976 slnagaplqyveisngyksssskknmlekerntivafiesvekdkrqtfldafdtvdtqvkdafskmtggsawleleneddifnsglnyliqfpgkp 1072
                  ************************************************************************************************* PP

                  .....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEETTE CS
                  .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  136 .....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkvengv 218 
                       ++SgGektL+a  +++A+qk +p+p+y++De+da+LD+ n +k+++++ke+s+ +Qfi++sl++ ++eka+ ++gv+  ++gv
  AJA92776.1 1073 krestSISGGEKTLAATVFVLALQKLNPSPFYMFDEVDAHLDAPNAEKLSNIIKERSEGSQFIMVSLKDSVVEKARLIYGVFP-KHGV 1159
                  *********************************************************************************99.5555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9  11.6     9e-22   1.6e-18       1     198 [.       6     264 ..       6     301 .. 0.62
   2 ?   -4.1  20.3        10   1.8e+04      88     199 ..     290     405 ..     265     406 .. 0.67
   3 ?   -2.7   7.4         4   7.2e+03     145     197 ..     423     473 ..     411     504 .. 0.73
   4 ?   -6.5  23.9        10   1.8e+04      77     196 ..     693     823 ..     606     832 .. 0.44
   5 ?  -18.8  26.8        10   1.8e+04     101     192 ..     848     941 ..     802    1041 .. 0.48

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 9e-22
      AAA_23   1 kLkienfrsf..rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve.iesegkvkayveltfenkdgry...trsiere 93 
                 k++i +f+sf  +++ +dF++gl+ I+GpNG+GK+ ildAi++aL++  p+  r  + +   +dve  + +g ++a  ++ f n d++     ++++ +
  AJA92776.1   6 KVEIFGFKSFgfKNTIVDFEPGLVSISGPNGSGKSNILDAITFALGENRPKVMRAPNLRGLMHDVEgAARRGPKMARTSVHFDNLDRKIpvdSDIVTIT 104
                 68999*****999999*******************************9999999885555555665233446666777777777666444442222222 PP

      AAA_23  94 relskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer........................feefelkdkke.............rl 155
                 re ++k  + ++ +k+     +  + +i +l+++ ++ ln+i   +q+                         f+e++++++k+             ++
  AJA92776.1 105 REMNDKGDNIYYLNKK-----KVIRSKILDLMEIANAGLNQINNVQQGTvtrisemtseekriviedliglsaFDEKKKEAEKQltdadhkleiamaKM 198
                 2222222222222222.....222233333444444444444444444444443333333444444444444344444444444677888555666644 PP

      AAA_23 156 eelekeleeledekkllekl..............................eqekekekeleeleeeleeilke 198
                  e++k ++ele+       +                               ++ +k k+l+ l++e++ +++e
  AJA92776.1 199 GEVKKRIDELEE-------ErnkklrydilerelnryraisaasslksiqSEKVSKDKTLNSLNSEIKHLEEE 264
                 444444444444.......433333335656567888888888887776545555666888888888877776 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 10
      AAA_23  88 rsiererelskkkgkttkkaklellei.deleqfisellgskkiilnlilflgqerfeefel.kdkkerleelekeleeledekkllekl..eqekeke 182
                  + + e+e++ ++ +++ +++ +l+++ +++  +i+++l s ki l++++++++ ++  ++  k++ + ++e ek+++e+++  + ++++  +++ +  
  AJA92776.1 290 NKSKSEIETKLSMHRQKFDEADSLIKTsTNRLTEIDTNLPSHKIDLDNLQIQKSFSESQISYfKTEINNIRETEKSFDEKTKNLRIQKTEamKKQSQVI 388
                 334555666666677777778888877666678899999999997766655444333222223677899999999999999977766666446666666 PP

      AAA_23 183 keleeleeeleeilkel 199
                  +  ++ ++++ +++++
  AJA92776.1 389 TQKRDVDQKIQRLTDKI 405
                 69999999999888887 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4
      AAA_23 145 efelkdkkerleelekeleeledekkllekleqekekekeleeleeeleeilk 197
                 +++l++ +e+ ++l ++l++le++k +le+ +  ++ +  ++e++ ++++ ++
  AJA92776.1 423 KEKLSSNQEKFNSLVNSLDTLEQQKIKLERII--ENHKHSISEINLRIKKFTD 473
                 55667777888888888888888888888775..4566666666666666544 PP

  == domain 4  score: -6.5 bits;  conditional E-value: 10
      AAA_23  77 ltfenkdgry......trsiererelskkkgkttkkaklellei.......deleqfisellgskki...ilnlilflgqer.feefelkdkkerleel 158
                 lt+++k++r         + e + +ls+               +       +el+ +is++ ++kk+   ++n++   ++       el ++k+ le+l
  AJA92776.1 693 LTVTKKKNRAkkldllVNNYEKRLSLSEVG-------------MnttsnslSELKSRISQISNNKKSfetRINQLTRTQERIsR---ELTNRKSHLESL 775
                 222222222122222212222222222222.............11122222444444444333333322222222222222221...112222222222 PP

      AAA_23 159 ekeleeledekkllekl.................eqekekekeleeleeeleeil 196
                 e +++   d       +                 eq++e+ k+le ++++l++ +
  AJA92776.1 776 ESQIKLVRD-------NyaepqmdrianeiklvnEQILEQDKKLEPIQNDLKKKE 823
                 222222222.......133333334444455555666777777777777777765 PP

  == domain 5  score: -18.8 bits;  conditional E-value: 10
      AAA_23 101 gkttkkaklellei....deleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekl.....eqekekekeleelee 190
                 ++  +++   +++i    +e+e + +el++ ++++ +li+  g + +++ e  + +e l++ e++  ++ + ++   +               l ++e+
  AJA92776.1 848 SSMDQEKYHLEVDIrrltKEKETTETELVTLRDDEQKLISTSGTSVEQMTEFDNSLESLNSKERDSTKEITLRERNTDAlnrdlT-------DLRQKES 939
                 2333333333333333322222222223334444444444444444444444433333333333322222222211111111120.......1111111 PP

      AAA_23 191 el 192
                 ++
  AJA92776.1 940 KI 941
                 11 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.8   1.4e+04      38      79 ..     107     147 ..     103     169 .. 0.63
   2 !   58.7   0.0   3.5e-19   6.3e-16       3     116 ..     527     638 ..     525     639 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.8
   SMC_hinge  38 eetakkiieflkkknagratflpldrikqknkadgandknsg 79 
                 +++    i +l kk+  r  +l l +i     +  +n ++ g
  AJA92776.1 107 MNDKGDNIYYLNKKKVIRSKILDLMEIANAGLNQINNVQQ-G 147
                 5555566678888888888888887777766666665555.3 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 3.5e-19
   SMC_hinge   3 gvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgavplidlvevddelrkalryll 101
                 g+ G + + ++ d++ye A  a++ n ++a+vv+d e+  ++ ef+ +k++ ++ ++pl++i q + +  +++     + l+d+v+++++++ + ++l+
  AJA92776.1 527 GIEGLVYEILSWDKKYERASLAVCSNWIKAVVVKDFESLISLAEFVTDKKLPKLKIIPLESIPQVKIECPKQTG--VLGILSDYVKCENKFSSLKNFLF 623
                 6789*************************************************************999888776..7********************** PP

   SMC_hinge 102 gdtlvvdsldeAeel 116
                 g++++v+s   A +l
  AJA92776.1 624 GNVVLVESRNIAINL 638
                 *********999987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.0   1.4e-07   0.00025       5      26 ..      32      60 ..      28     325 .. 0.79
   2 ?   -0.8   1.8       0.6   1.1e+03     119     190 ..     331     407 ..     305     493 .. 0.54
   3 ?   -3.0   0.2       2.9   5.1e+03     118     141 ..     757     780 ..     711     845 .. 0.49
   4 !   25.7   0.7     5e-09     9e-06     127     296 ..     968    1138 ..     864    1138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
      AAA_21  5 iGpNgsGKSnLLdaldllarl.......d 26
                 GpNgsGKSn+Lda+ ++ +        +
  AJA92776.1 32 SGPNGSGKSNILDAITFALGEnrpkvmrA 60
                5****************987555555551 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.6
      AAA_21 119 rggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.....rigllnifadyfgfakekrllqrlvr 190
                 +++  ++ ++++s se+++ +f+  +++i+++  s+ +   +lr       ++  + i ++    +k++rl+++ + 
  AJA92776.1 331 HKIDLDNLQIQKSFSESQISYFKTEINNIRETEKSFDEKTKNLRIQkteamKKQSQVITQKRDVDQKIQRLTDKITA 407
                 55555555666666666666666666666666666666554444444443333333333333333333333333333 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.9
      AAA_21 118 irggvsvfslkelsvsepndlqfg 141
                 + + +s +    +s  e+ + q +
  AJA92776.1 757 TQERISRELTNRKSHLESLESQIK 780
                 222222222222222222222222 PP

  == domain 4  score: 25.7 bits;  conditional E-value: 5e-09
      AAA_21  127 lkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer..gv 221 
                  + +  ++++ +   + ++++i++ + s+ + +++l k + ++  +f++ + ++k++++l+ +     +v +  s+++ g+   ++++e+++++    
  AJA92776.1  968 SEQNRIKNSLNAGAPLQYVEISNGYKSSSSKKNMLEK-ERNTIVAFIESVEKDKRQTFLDAFDTVDTQVKDAFSKMTGGSAWLELENEDDIFNsgLN 1063
                  3333344444444444445555555555555554444.44444444444444444444444444444444444444444444444444444448899 PP

      AAA_21  222 vflengdgqelparelSdGtkrll.alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                  ++   ++  ++ ++++S G k l+  ++++ l+ l +++++ +DE++++L+    ++l  ++ke s+ g+Q+i+++
  AJA92776.1 1064 YLIQFPGKPKRESTSISGGEKTLAaTVFVLALQKLNPSPFYMFDEVDAHLDAPNAEKLSNIIKERSE-GSQFIMVS 1138
                  999999999**************647777777777777*****************************.*****986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0  15.0   5.8e-11     1e-07       4     261 ..       5     305 ..       3     319 .. 0.58
   2 ?  -13.1  39.2        10   1.8e+04      87     262 ..     290     483 ..     279     534 .. 0.54
   3 ?    0.9  22.6      0.17     3e+02      46     278 ..     615     857 ..     609     875 .. 0.64
   4 ?    0.8  12.6      0.18   3.2e+02     100     360 ..     867    1135 ..     854    1138 .. 0.52

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.8e-11
      AAA_15   4 kkikikNFRs..lkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn.................................kkvikiekedlei 67 
                 kk++i  F+s  +k++ +d+++ l  + G+N+sGKS+il+a+ + l ++++k                                  + +i ++++ + i
  AJA92776.1   5 KKVEIFGFKSfgFKNTIVDFEPGLVSISGPNGSGKSNILDAITFALGENRPKVmrapnlrglmhdvegaarrgpkmartsvhfdnlDRKIPVDSDIVTI 103
                 89999999984469****************************9999988666699*******************9999887777773333333333333 PP

      AAA_15  68 feniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidk 166
                 +++ +  k   I +    k+k +    +  ++ ++   +++++ ++ ++++i + + +  k  ++ + i +    +kk+  +++  +++++ e    + 
  AJA92776.1 104 TREMND-KGDNIYYLN--KKKVIRSKILDLMEIANAGLNQINNVQQGTVTRISEMTSEE-KRIVIEDLIGLSAFDEKKKEAEKQLTDADHKLEIAMAKM 198
                 322222.222222222..24444444566777788888888888888888887766664.566666666655555555444444444444444444455 PP

      AAA_15 167 edlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.................eeelteklkeiqek 248
                  ++kk i++lee  +k+     +l+ ++  ++ isa  + ++ +sek   +++k+++++++e++   l                 + +  ++ +  +++
  AJA92776.1 199 GEVKKRIDELEEERNKKL-RYDILERELNRYRAISAASSLKSIQSEK--VSKDKTLNSLNSEIKH--LeeerasirkdaseiraqKTKFMDEVNAYNKS 292
                 555555555666555555.4555666666667776666666655555..3344444444444221..11132233334333333333333333333333 PP

      AAA_15 249 lkeidkklaeelk 261
                  +ei+ kl+++ +
  AJA92776.1 293 KSEIETKLSMHRQ 305
                 3333333333333 PP

  == domain 2  score: -13.1 bits;  conditional E-value: 10
      AAA_15  87 ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee. 184
                 +k+k++++t+ s  ++k d + + +++   +++++ +++l++ +++ ++ +++k  s+ ++  +k+e ++ +++e ++d ++++  i+k e  +k+++ 
  AJA92776.1 290 NKSKSEIETKLSMHRQKFD-EADSLIKTSTNRLTEIDTNLPSHKIDLDNLQIQKSFSESQISYFKTEINNIRETEKSFDEKTKNLRIQKTEAMKKQSQv 387
                 4566666666655555555.6677777888899999999999999999999999999999999999999999999999999999999988888888885 PP

      AAA_15 185 ..............................elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl...eeelteklkeiqeklk 250
                                                                     s++ +ek ss+ +k  +  ++      l   +++l++++++ + +++
  AJA92776.1 388 itqkrdvdqkiqrltdkitatklavgefesA---------------------STNGKEKLSSNQEKFNSLVNSLDT---LeqqKIKLERIIENHKHSIS 462
                 5555544432222222222222222222220.....................222222222221111111111111...01123333333333333333 PP

      AAA_15 251 eidkklaeelk.........k 262
                 ei+  +++ +           
  AJA92776.1 463 EINLRIKKFTDdkkrsehdiH 483
                 333333222223322222221 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.17
      AAA_15  46 FlnnkekknkkvikiekedleifeniseskdikIdvef..........aekekake..yektlkskekkkadlllkkkesdlkktikdkklklkknels 132
                 F + k   + +v+ +e+ ++ i+ ++s +k+i +  e+          +  +++k+    k+ +++++      l++ +s+l  t+++kk   kk +l 
  AJA92776.1 615 FSSLKNFLFGNVVLVESRNIAINLSKSGFKTITLSGEYfeakttsvviD--NNSKIskLTKIINMSDS---VEGLQQMISALRLTVTKKKNRAKKLDLL 708
                 45555444467999************************55444433321..22222001122222211...1245666777777777777777777777 PP

      AAA_15 133 dekisvekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkee..elknvlksaiiklllisakRnvsdedsekkssllgklkekile 227
                 +++++     s++  ++ +++ +e+++   +i   k++ +  i+   + +   +     ++ + ++ +  l s  + v d+  e + + + + ++  +e
  AJA92776.1 709 VNNYEKRLSLSEVGMNTTSNSLSELKSRISQISnnKKSFETRIN---QLTRT-QerISRELTNRKSHLESLESQIKLVRDNYAEPQMDRIANEIKLVNE 803
                 77766666666666666666666666666655521222222222...22222.2333456666778888888888888888888888888888888888 PP

      AAA_15 228 ealqekleeelteklkeiqeklkeidkklaeelk.........kilkkkidkikkfnykg 278
                 +      ++e+ +kl+ iq++lk+++  lae  +         k+l   ++++++++y  
  AJA92776.1 804 Q------ILEQDKKLEPIQNDLKKKERHLAELMAhdtkitgerKNLRHTVSSMDQEKYHL 857
                 7......88999999999999999999998888777778888877777777777777755 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.18
      AAA_15  100 ekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks.....kkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlk 191 
                  ek+ ++++l  +++d +k+i +  + +++    d++ +  + k+     +  l + +++ l+ + ++l  + +++++l+ ++   ++      +v+ 
  AJA92776.1  867 EKETTETELVTLRDDEQKLISTSGTSVEQMTEFDNSLESLNSKErdstkEITLRERNTDALNRDLTDLRQKESKITSLLATFGFDISI-----EVFD 958 
                  3444444555555555555555555555544444444433333322322222222222222222223333333333333333333322.....2233 PP

      AAA_15  192 saiiklllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelk...........kilkkkidkikkfnyk 277 
                   +++ + l s+++ ++++++      + ++ + ++++        +++  l++  + +  +++ +++++              +k+ ++k+  + + 
  AJA92776.1  959 VESTITSLESEQNRIKNSLNAGAPLQYVEISNGYKSS-------SSKKNMLEKERNTIVAFIESVEKDKRqtfldafdtvdTQVKDAFSKMTGGSAW 1048
                  3333333333333333333333222222222222222.......22222233333333333333333333333333444444445556666666666 PP

      AAA_15  278 gkkneeieik...........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360 
                   + ++e++i+            + + + +  + G + l   ++ ++  + +     ++ +++++E +ahL   + + l + +ke ++ +  Q i
  AJA92776.1 1049 LELENEDDIFnsglnyliqfpGKPKRESTSISGGEKTLAATVFVLALQKLN-----PSPFYMFDEVDAHLDAPNAEKLSNIIKERSEGS--QFI 1135
                  6666666666888888888899999999999************99999999.....**************9999999999999888777..666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.2e-09   1.5e-05      12      46 ..      17      50 ..       5      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.2e-09
      AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                f+++ +++++   + ++Gp+GsGKS +lDAi++ L
  AJA92776.1 17 FKNTIVDFEPG-LVSISGPNGSGKSNILDAITFAL 50
                67778888854.69*****************9887 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.0   4.8e-06    0.0086      23      70 ..     170     217 ..     148     224 .. 0.85
   2 ?    1.4   4.0      0.25   4.4e+02       4      33 ..     253     282 ..     250     332 .. 0.71
   3 ?    2.3   6.6      0.13   2.3e+02       6      63 ..     346     403 ..     341     412 .. 0.89
   4 ?   -4.1  10.4        10   1.8e+04       6      59 ..     367     423 ..     364     462 .. 0.49
   5 ?   -5.5   9.8        10   1.8e+04       3      76 ..     745     823 ..     729     828 .. 0.70
   6 ?   -5.6   9.6        10   1.8e+04       8      69 ..     797     858 ..     771     870 .. 0.72
   7 ?   -1.2   4.6       1.6   2.8e+03       3      41 ..     841     882 ..     839     925 .. 0.51
   8 ?   -3.1   0.1       6.3   1.1e+04       9      33 ..     999    1022 ..     987    1024 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
        KELK  23 laeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqklsR 70 
                 l+ + E+ k+ +k+L da ++ ++am+ + ev++++ el ++++k  R
  AJA92776.1 170 LSAFDEKKKEAEKQLTDADHKLEIAMAKMGEVKKRIDELEEERNKKLR 217
                 45678*************************************999887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
        KELK   4 eLekqlrllkqEkeelqkelaeaqErlksq 33 
                 +L+ ++++l++E+ ++ k+ +e++ +  + 
  AJA92776.1 253 SLNSEIKHLEEERASIRKDASEIRAQKTKF 282
                 688888999999999999888876544333 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
        KELK   6 ekqlrllkqEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrs 63 
                 e q+  +k E +++    + + E+ k+   +  +a++++  ++++ ++v++k++ l  
  AJA92776.1 346 ESQISYFKTEINNIRETEKSFDEKTKNLRIQKTEAMKKQSQVITQKRDVDQKIQRLTD 403
                 6788999999999999999999999999999999999999999999999999988865 PP

  == domain 4  score: -4.1 bits;  conditional E-value: 10
        KELK   6 ekqlrllkqEkeelqkelaeaqErlk..sqk.keLkdaisqrklamqefsevnekls 59 
                 +++ + l+  k e+ k+ +++  + +   qk + L d i+  kla+ ef+ ++   +
  AJA92776.1 367 DEKTKNLRIQKTEAMKKQSQVITQKRdvDQKiQRLTDKITATKLAVGEFESASTNGK 423
                 555555555554444443333332221112213455666666666666655543322 PP

  == domain 5  score: -5.5 bits;  conditional E-value: 10
        KELK   3 keLekqlrllkqEkeelqkelaeaq...ErlksqkkeLkd..aisqrklamqefsevneklselrsqkqklsRqlrdke 76 
                 k++e ++ +l++ +e +++el++ +   E l sq k  +d  a  q +  ++e + vne++ e  ++ + +  +l+ ke
  AJA92776.1 745 KSFETRINQLTRTQERISRELTNRKshlESLESQIKLVRDnyAEPQMDRIANEIKLVNEQILEQDKKLEPIQNDLKKKE 823
                 6788888888888888888887765111444445555556335567777888888888888877777666666666665 PP

  == domain 6  score: -5.6 bits;  conditional E-value: 10
        KELK   8 qlrllkqEkeelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqkls 69 
                 +++l+++   e  k+l+ +q+ lk++++ L + +++      e +++   +s++ ++k  l 
  AJA92776.1 797 EIKLVNEQILEQDKKLEPIQNDLKKKERHLAELMAHDTKITGERKNLRHTVSSMDQEKYHLE 858
                 55555555566678888888888888888888888888888888888888888888887775 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 1.6
        KELK   3 keLekqlrllkqEkeelq...kelaeaqErlksqkkeLkdai 41 
                 k+L +++ +++qEk  l+   + l+  +E   ++   L+d  
  AJA92776.1 841 KNLRHTVSSMDQEKYHLEvdiRRLTKEKETTETELVTLRDDE 882
                 566666666777777666333333333344444444445443 PP

  == domain 8  score: -3.1 bits;  conditional E-value: 6.3
        KELK    9 lrllkqEkeelqkelaeaqErlksq 33  
                    +l++E++ +   + e+ E+ k q
  AJA92776.1  999 KNMLEKERNTIV-AFIESVEKDKRQ 1022
                  344455555443.355555666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   8.7e-05      0.16      20      52 ..      22      61 ..      17     271 .. 0.84
   2 ?   -1.7   0.1       1.9   3.4e+03     116     156 ..     997    1040 ..     897    1047 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
      AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd.......g 52
                 + +p+lv +sG+ G+GKs +++++  al ++        
  AJA92776.1 22 VDFEPGLVSISGPNGSGKSNILDAITFALGENrpkvmraP 61
                566899*******************988888855444440 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
      AAA_16  116 a.....srllellkrllallsrderplvlvlDdlqwadeaslqlla 156 
                  +     +  ++++ ++++  ++ ++    +lD ++ +d++  ++++
  AJA92776.1  997 SkknmlEKERNTIVAFIESVEK-DK-RQTFLDAFDTVDTQVKDAFS 1040
                  1333334444455555555555.33.56777777777777776665 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   8.2       2.4   4.3e+03      56     100 ..     170     214 ..     139     227 .. 0.59
   2 ?   11.1  15.4   0.00024      0.44      14     129 ..     201     317 ..     198     326 .. 0.79
   3 ?    5.2  11.9     0.016        29      44     131 ..     348     445 ..     310     446 .. 0.79
   4 ?    1.0   6.4      0.32   5.7e+02      50     117 ..     420     487 ..     396     502 .. 0.72
   5 ?   14.6   3.4     2e-05     0.036       8      86 ..     706     781 ..     705     790 .. 0.93
   6 ?    6.9  11.0    0.0048       8.7      13      98 ..     807     889 ..     790     900 .. 0.83
   7 ?    3.8  10.7     0.043        78      13      98 ..     863     945 ..     861     979 .. 0.77
   8 ?    0.3   0.1      0.52   9.3e+02      19      43 ..    1000    1024 ..     993    1054 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
      APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                 l++ +++++e++++L +++++ e   a++ + ++  ++leee ++
  AJA92776.1 170 LSAFDEKKKEAEKQLTDADHKLEIAMAKMGEVKKRIDELEEERNK 214
                 445555555555555555555555555555555555555555444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00024
      APG6_N  14 ldkqleqaekerd...aYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelq 109
                 ++k+++++e+er+    Y   +++l++++  +    ++l++++ e    +k+ ++l +e+k le+er++++++ +++++++ +  +e +++ ++ +e +
  AJA92776.1 201 VKKRIDELEEERNkklRYDILERELNRYRAISA--ASSLKSIQSEKVSKDKTLNSLNSEIKHLEEERASIRKDASEIRAQKTKFMDEVNAYNKSKSEIE 297
                 566677777776622268888999999977765..7899999999999999999999999999999999999999999999999999999999999999 PP

      APG6_N 110 lelleleeeldsleaqyeha 129
                 ++l+ + ++ d  ++ ++  
  AJA92776.1 298 TKLSMHRQKFDEADSLIKTS 317
                 99998888888777666655 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.016
      APG6_N  44 k..........qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyehaqn 131
                 +           +e +++ +e+ ++l+ ++ e++++  ++ +++++++++++ l+ +  a +    +f +   + + +l++ +e+ +sl ++++  ++
  AJA92776.1 348 QisyfkteinnIRETEKSFDEKTKNLRIQKTEAMKKQSQVITQKRDVDQKIQRLTDKITATKLAVGEFESASTNGKEKLSSNQEKFNSLVNSLDTLEQ 445
                 144444444445677789999999********************************************999999999*******99999999887766 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.32
      APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                  + +e+l+  +++ ++l++ L+ le+++ +le+ +++ +   ++++   ++f  + +  +++  el e
  AJA92776.1 420 TNGKEKLSSNQEKFNSLVNSLDTLEQQKIKLERIIENHKHSISEINLRIKKFTDDKKRSEHDIHELSE 487
                 44466788888888888999999999999999998888888888888888887776666655555544 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 2e-05
      APG6_N   8 dlLleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86 
                 dlL+++++k+l+ +e  +++ ++ l++lk++ ++ +   ++ ++ e ++ +l +++e+  +eL + +++ e+le++++ 
  AJA92776.1 706 DLLVNNYEKRLSLSEVGMNTTSNSLSELKSRISQIS---NNKKSFETRINQLTRTQERISRELTNRKSHLESLESQIKL 781
                 89*****************************99987...6899*********************************986 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0048
      APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                 e dk+le  +++ ++ e+ l++l +++++ +    e+++l++ ++ +++e+  l+  +++l ke+e  e el +l+  +++l    
  AJA92776.1 807 EQDKKLEPIQNDLKKKERHLAELMAHDTKIT---GERKNLRHTVSSMDQEKYHLEVDIRRLTKEKETTETELVTLRDDEQKLISTS 889
                 6788999999999999999999999988876...6899999999999999999999999999999999999999999999887655 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.043
      APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeee 98 
                 +l+k+ e++e e  ++++ ++kl +++ +   + e++ e +++le l+++e++  +e+   e++ ++l+++l +l+++++++    
  AJA92776.1 863 RLTKEKETTETELVTLRDDEQKLISTSGT---SVEQMTEFDNSLESLNSKERDSTKEITLRERNTDALNRDLTDLRQKESKITSLL 945
                 45555566666666666666666666555...4689999***************************************99987665 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 0.52
      APG6_N   19 eqaekerdaYeeflkklkkekkeee 43  
                  + +eker++  +f + ++k+k+++ 
  AJA92776.1 1000 NMLEKERNTIVAFIESVEKDKRQTF 1024
                  5678999999999999999987765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.0      0.17   3.1e+02      95     134 ..     175     214 ..     169     224 .. 0.87
   2 ?    8.4   7.2    0.0013       2.3      98     175 ..     224     301 ..     220     315 .. 0.89
   3 ?    7.0  10.9    0.0034       6.1      69     175 ..     314     420 ..     291     425 .. 0.88
   4 ?    4.2  14.3     0.024        43      54     158 ..     373     473 ..     353     494 .. 0.80
   5 ?    6.1  11.9    0.0067        12      74     177 ..     679     782 ..     653     802 .. 0.56
   6 ?    6.3  19.4    0.0058        10      17     163 ..     802     934 ..     790     947 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
       ATG16  95 ksrgelaqrllelneelqkleeklkedeerlaeleaeraa 134
                  ++ e +++l+++  +l+   +k+ e ++r++ele+er++
  AJA92776.1 175 EKKKEAEKQLTDADHKLEIAMAKMGEVKKRIDELEEERNK 214
                 57899999**************************999875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
       ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklr 175
                 + + +r +++ ++l+  +++  +++++l++l++e+++le+++++ ++   e ++   ++ DE++a +   + +E kl 
  AJA92776.1 224 ELNRYRAISAASSLKSIQSEKVSKDKTLNSLNSEIKHLEEERASIRKDASEIRAQKTKFMDEVNAYNKSKSEIETKLS 301
                 557889999999*****************************************************9999999999886 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0034
       ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlql 167
                  +++++++++ +++l +++ +l +l+ +++ +++++   ++e+   +e+ k+ +e+ ++l+ ++++  +k ++   + r+ ++ +q l D ++a +l++
  AJA92776.1 314 IKTSTNRLTEIDTNLPSHKIDLDNLQIQKSFSESQISYFKTEINNIRETEKSFDEKTKNLRIQKTEAMKKQSQVITQKRDVDQKIQRLTDKITATKLAV 412
                 4567789999***************************************************************************************** PP

       ATG16 168 nqaEeklr 175
                    E+++ 
  AJA92776.1 413 GEFESAST 420
                 99998765 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.024
       ATG16  54 skksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                  + +++e  +    ++s+  ++  + +qk+++l +  +++  + ge+++  ++ +e+l+  +ek ++  ++l+ le+++ +le+ ++++++ + e +  
  AJA92776.1 373 LRIQKTEAMK----KQSQVITQKRDVDQKIQRLTDKITATKLAVGEFESASTNGKEKLSSNQEKFNSLVNSLDTLEQQKIKLERIIENHKHSISEINLR 467
                 2222222222....334577888999*****************************************************************99998888 PP

       ATG16 153 vqdlqD 158
                 ++++ D
  AJA92776.1 468 IKKFTD 473
                 877776 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0067
       ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEe 172
                 ++++ l+q +++lr  +++   +  +l   +++ ++ l+  e  +++ +++l el++++++++ + k+ e ++++++++ + +  El+  + +l+++E+
  AJA92776.1 679 DSVEGLQQMISALRLTVTKKKNRAKKLDLLVNNYEKRLSLSEVGMNTTSNSLSELKSRISQISNNKKSFETRINQLTRTQERISRELTNRKSHLESLES 777
                 555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

       ATG16 173 klrkl 177
                 + + +
  AJA92776.1 778 QIKLV 782
                 54322 PP

  == domain 6  score: 6.3 bits;  conditional E-value: 0.0058
       ATG16  17 faeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkle 115
                 +        ++l++ ++le  +  l+k+  +  +   +++++k + +++     + +++++s++q+ + l  +   l k+++++++ l++l +  qkl 
  AJA92776.1 802 N-------EQILEQDKKLEPIQNDLKKKERHLAE--LMAHDTKITGERK-----NLRHTVSSMDQEKYHLEVDIRRLTKEKETTETELVTLRDDEQKLI 886
                 3.......35555555555555555444333333..2222222222222.....235678999999999999999999999999999999999999999 PP

       ATG16 116 eklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaL 163
                 +++ +  e++ e  ++ ++l+ k +d ++e+  +e+  ++l  +l+ L
  AJA92776.1 887 STSGTSVEQMTEFDNSLESLNSKERDSTKEITLRERNTDALNRDLTDL 934
                 999999999999999999999999999999888888877777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2554  (0.142451); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        73  (0.00407162); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 2.11u 0.34s 00:00:02.44 Elapsed: 00:00:00.65
# Mc/sec: 5484.86
//
Query:       AJA92777.1  [L=143]
Description: bifunctional nuclease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-08   34.1   0.0    2.3e-08   33.8   0.0    1.1  1  DNase-RNase  Bifunctional nuclease
  ------ inclusion threshold ------
       0.12   12.6   0.4        1.4    9.1   0.4    2.3  1  Skp1_POZ     Skp1 family, tetramerisation domain


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.5e-12   2.3e-08       7     122 ..      22     136 ..      15     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.5e-12
                  EETTTTEEEEEEEETTSSEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEEEEET---.EEEEE-HHHH CS
  DNase-RNase   7 ldassqspvvlLreeegrrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdledgtfyAelvlrkeeee.leidaRpSDa 103
                  +d+  ++ +v+L+++++r++       +  ++ia  l++ + + P+ + +l +++ea ++ + +v I++  d    A+l+l+ + ++ +  + R+SDa
   AJA92777.1  22 VDPYGNEGLVILHSDDKREFHMRAFSGEVSRHIASFLDDDHDTVPTIYKMLEDICEANELLLVKVKIYESGD-ALRANLYLTGK-KDlVLRNYRASDA 117
                  56666777888888888654444445555789************************************9877.57*******95.44477899***** PP

                  HHHHHHHT--EEEEHHHHH CS
  DNase-RNase 104 iaLAlrtgapIyveeevle 122
                  +aLA+ +++pI+v  ++l+
   AJA92777.1 118 VALAVYYKIPILVRSNMLK 136
                  **************99987 PP

>> Skp1_POZ  Skp1 family, tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4   0.00016       1.4      23      43 ..      65      83 ..      29      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                SHHHHHHHHCTCCCGTTCEEE CS
    Skp1_POZ 23 Sktikhmiedlgdddkpripl 43
                 +ti +m+ed+++ ++   +l
  AJA92777.1 65 VPTIYKMLEDICEANE--LLL 83
                579**********998..555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 971.67
//
Query:       AJA92778.1  [L=456]
Description: anthranilate synthase component I, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-97  324.9   0.1    5.8e-95  317.7   0.0    2.6  3  Chorismate_bind  chorismate binding enzyme
    2.8e-23   82.7   0.5    5.2e-20   72.1   0.1    2.7  3  Anth_synt_I_N    Anthranilate synthase component I, N termina
  ------ inclusion threshold ------
      0.024   14.4   0.0       0.06   13.1   0.0    1.7  1  DUF3090          Protein of unknown function (DUF3090)


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0058        35      37      76 ..      18      69 ..       9      93 .. 0.73
   2 ?   -0.5   0.0      0.12   7.1e+02     183     215 ..      87     119 ..      77     123 .. 0.90
   3 !  317.7   0.0   9.7e-99   5.8e-95       2     258 .]     190     443 ..     189     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0058
                     -B-HHHHHHHHHCTBSSSEEEEE.....EETTEEEEEEESSEEE.......E CS
  Chorismate_bind 37 avdplalyralrarnpapysfll.....eledsellgaSPElll.......k 76
                     + +p+++y+++ +++++++ f       el +++++g+ PEl++       +
       AJA92778.1 18 ETQPFDVYNKISRNYTHSFLFESlegpdELAETSIMGFDPELIVtgyfdkiT 69
                     6789**********999999877766665555899********955555441 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.12
                      SEESHHHHHHHHHHHSSS--TTTTSEEEEEETT CS
  Chorismate_bind 183 tGaPkkrameiidelEearRgvYaGavgyldad 215
                      t +P ++  ++i++ + ++ ++ +Gavg +d d
       AJA92778.1  87 TDTPLEEIKKLIKKTDDMSYRYLGGAVGNIDYD 119
                      6799999*********************99876 PP

  == domain 3  score: 317.7 bits;  conditional E-value: 9.7e-99
                      HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEEEECEEEEEEHS CS
  Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrrietepiaGTrarg 95 
                      +e++++ v+k+ke++++gd+++vvlsrr+++e  a+ d l++y++lr+ np+py+f l++++  ++g+SPE+ll+v g+  +et piaGTr+ +
       AJA92778.1 190 KEQFEQIVNKAKEYVHSGDVFQVVLSRRFSFE--AKGDYLRVYEKLRELNPSPYMFHLKMDENVIIGSSPEMLLRVTGR-DVETFPIAGTRKIT 280
                      799*****************************..99999************************9*************55.************** PP

                      SSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEEEESTT--HHHHHHHCSS-CCCSEESHHH CS
  Chorismate_bind  96 ktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstiegelkedvslldllkalfPtgavtGaPkkr 189
                      +++e++e+l++ell+deKe+aEh m+vdl rnd+g+v+  g+vkv+el++++r+s+v+h+v+++ g+l+e+ ++ d+++a+fP+g+v+GaPk r
       AJA92778.1 281 EDEEKNEKLKNELLNDEKELAEHTMLVDLGRNDIGRVCDYGTVKVKELMEIKRFSHVQHIVTHVVGKLNEKNDMYDAFEAVFPAGTVSGAPKVR 374
                      ********************************************************************************************** PP

                      HHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEEEEEEETT--HHHHHHHHHHH CS
  Chorismate_bind 190 ameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlgaGaGIvadSdpeaEyeEtlaK 258
                      ameii+elE+++R+ YaGavgy++++g +++a++IR+++v++++  ++aGaGIv dS +e+E++Et++K
       AJA92778.1 375 AMEIIQELEPTQRETYAGAVGYFSFNGCCDFAIAIRSIFVNKERGFVQAGAGIVFDSIAENELKETEHK 443
                      *******************************************************************99 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.1   8.7e-24   5.2e-20       4     141 ..      20     157 ..      17     158 .. 0.87
   2 ?   -1.8   0.0      0.57   3.4e+03      34      55 ..     251     272 ..     225     320 .. 0.66
   3 !    8.2   0.0   0.00045       2.7      32     102 ..     319     401 ..     292     433 .. 0.70

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 8.7e-24
  Anth_synt_I_N   4 tplsvylklaeee.hkflLeSaeneggegrySfigldpfle.......lkskngevevegpegeeleeeepldalrellerfrsaedseptelpfv 91 
                    +p  vy k++ +  h+fl+eS e+  + ++ S++g+dp l        ++++n++ ++e+ + e  ++ +pl+ +++l+++ ++       + +  
     AJA92778.1  20 QPFDVYNKISRNYtHSFLFESLEGPDELAETSIMGFDPELIvtgyfdkITIQNRDGKTETIQTETIQTDTPLEEIKKLIKKTDD------MSYRYL 109
                    899********99*********977777**********88844444444477777777777788888888*************3......45789* PP

  Anth_synt_I_N  92 gGlvGylgYDlvreieklpksakddlnlpdarlilydtlivfDhkerrly 141
                    gG+vG + YD++r +e++p   k+dl+ p +++ +y++ i++D+k+++ +
     AJA92778.1 110 GGAVGNIDYDAIRLFENIP--GKKDLQKPIMEFGIYNDGILYDNKKKQFF 157
                    *******************..699**********************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
  Anth_synt_I_N  34 Sfigldpflelkskngeveveg 55 
                     +ig +p + l++ +++ve+  
     AJA92778.1 251 VIIGSSPEMLLRVTGRDVETFP 272
                    4777777777777777777665 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00045
  Anth_synt_I_N  32 rySfigldpflelk..skngevevegpegeeleeeepldalrellerfrsaedse............ptelpfvgGlvGylgYDl 102
                     y  + +++ +e+k  s+ + + +++  g+  e++++ da ++++     ++ +             pt+   + G+vGy++++ 
     AJA92778.1 319 DYGTVKVKELMEIKrfSHVQHIVTHV-VGKLNEKNDMYDAFEAVFPAGT-VSGAPkvrameiiqelePTQRETYAGAVGYFSFNG 401
                    55556666666666543333333333.5677777778888888887777.3344457777888888899999**********986 PP

>> DUF3090  Protein of unknown function (DUF3090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05      0.06      71     154 ..     126     208 ..      69     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
     DUF3090  71 elkdeepLeepveeeFrvgtlalawDeetervviealaleeeeedeeldeeeeeeeaealrvrltreqarafakrarevvaaGr 154
                 + + ++ L++p+  eF + + ++ +D+++++++   ++ + +++ +++de+ ++ e + +++ l++eq  +++++a+e v++G 
  AJA92778.1 126 NIPGKKDLQKPIM-EFGIYNDGILYDNKKKQFFYFYYDEDRKDKIKKTDEDVGTFEMSDIKINLNKEQFEQIVNKAKEYVHSGD 208
                 4566789999995.7********************9998888887777999999999***********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3196.35
//
Query:       AJA92779.1  [L=140]
Description: universal stress family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-28   99.1   0.0    3.5e-28   98.9   0.0    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   0.0     2e-32   3.5e-28       2     141 .]       3     140 .]       2     140 .] 0.95

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 2e-32
                 -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHH. CS
         Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeileva. 99 
                 +krIlV++Dgs++s++ +e+A++la + + +++ l+v +++ ++    +   ae+ +l++    ++++    ++e+ +vk   ++ +gd++ +i+++a 
  AJA92779.1   3 IKRILVPLDGSKNSERGIEMAVDLANDAKRTIVGLYVKPTSVNSIKYGELFNAEQNRLMEITFHSAKT----KCEKYDVKFIEETIVGDAKSSIVKYAn 97 
                 69*****************************************************9999999999865....6************************95 PP

                 .HHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
         Usp 100 .eeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                  +++++dli++G+rgr++++ +++GSvs+ vl+++++pVlvV+
  AJA92779.1  98 dNSRKIDLIIMGARGRGSVKAAFMGSVSNHVLNKSKIPVLVVK 140
                 56789*************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1048.93
//
Query:       AJA92780.1  [L=241]
Description: adenosylcobinamide-GDP ribazoletransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-41  142.6  12.6      2e-41  142.4  12.6    1.0  1  CobS       Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.4  12.6   1.1e-45     2e-41       2     204 .]       9     236 ..       8     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 142.4 bits;  conditional E-value: 1.1e-45
        CobS   2 lsflTrlPvp.....elaralaffPlvGlllGlll.llallllllll.llaallavaalvlltgglHlDGlaDtaDglgsgrdrerrleImkDsrvGaf 93 
                 +sflT++P       ++a+ +++fP+vG+++Gl++  l + l+l l  l+ +l++va l+++tg++H DGlaD+aDgl++++++e++ ++mkD +vG+ 
  AJA92780.1   9 FSFLTIIPTSnsdlnSIAKNMYLFPIVGIVIGLVIgSLGYGLSLYLEpLVVSLVVVASLAVITGIHHTDGLADFADGLMTKGTKEKKRKAMKDLSVGSA 107
                 89*******8665544588***************988888888877755577777888899*****************9999***************** PP

        CobS  94 Gvlalvlvlllkvaalaala........lllapvlsRlaallaiallpyaeeglgalfaeaqkk....lv..llal...........avlllllall.. 165
                 G++++vl+ +  ++al +l+        +ll++++++++++l++ l+++a+ g  ++f+++ k     lv  +  +                       
  AJA92780.1 108 GIFSIVLYAIGVIIAL-SLSsgmelfkiILLSEIMAKFSMVLMAGLGNSASIGSNSPFMDSMKDkkrlLVagI--ItiipfiilgemN--------Gfi 195
                 *************996.222244566877799****************9988888998874333355422231..1223433333331........022 PP

        CobS 166 ..laallvalllrrlarrklggvtGDvlGavieltellvll 204
                   +  +++ ++l  l+ +++gg+tGDv+Ga++elt+l  ll
  AJA92780.1 196 vfASGIVLTMFLVGLSTKSFGGITGDVMGASNELTRLSSLL 236
                 2222222333445577777*****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1855.38
//
Query:       AJA92781.1  [L=421]
Description: glutamyl-tRNA reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-37  129.0   0.0    2.2e-37  128.0   0.0    1.5  1  GlutR_N        Glutamyl-tRNAGlu reductase, N-terminal domain
    2.9e-29  101.9   0.1    6.6e-29  100.7   0.0    1.7  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
    9.1e-20   70.9   1.2    2.6e-19   69.5   1.2    1.8  1  GlutR_dimer    Glutamyl-tRNAGlu reductase, dimerisation domai
    0.00077   20.0   0.0     0.0023   18.5   0.0    1.9  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0085   15.5   0.0      0.027   13.8   0.0    1.9  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
  ------ inclusion threshold ------
      0.023   15.2   1.2         13    6.4   0.0    3.7  3  ATP-cone       ATP cone domain


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.0   7.5e-41   2.2e-37       3     146 .]      12     156 ..      11     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 7.5e-41
     GlutR_N   3 inhktapvelreklafseee.lkellkeleekvkeaviLsTCNRtEiylsaeeeeeaseellellaevs...leelkeklyvlegeeavrHlfrVasGL 97 
                 +++k+ p++++e++++ ++e + + +k+  ++++e+viL+TCNR+Ei+ s ++    +ee+++++a+ s   +++++++l+  +++++ +Hl++++sGL
  AJA92781.1  12 VTFKKSPIHVLERFSLGDSEnAYKSFKDH-TGLSECVILQTCNRVEIFGSGNNF--DREEIKKTWASLSgleENSFNDNLEWSQNSDVYEHLLKLTSGL 107
                 689*************6554355555554.5999**************644443..444455554444344499999********************** PP

     GlutR_N  98 dSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                 dS+v+GE+qI++Q+k++++ ak+ +++g+ L++lf+kai+v+ rvrt+t
  AJA92781.1 108 DSMVVGEEQIMTQIKDSIQSAKKLKVSGESLNTLFDKAIRVGTRVRTST 156
                 ***********************************************97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   2.2e-32   6.6e-29       1     137 [.     171     303 ..     171     304 .. 0.98
   2 ?   -3.3   0.0         3   8.9e+03      50      72 ..     377     398 ..     368     411 .. 0.62

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 2.2e-32
                   HHHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHHHHC CS
  Shikimate_DH   1 elakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekeevee 97 
                   +la+++++++k+kk+lliG+Ge a+lvak L ++g+   ++  Rt+er  ++ + ++ge    ++++++ +  +++d+v++at ++ ++++ e++++
    AJA92781.1 171 KLAEENVDEMKSKKILLIGTGEAATLVAKSLKKRGYP-FFISSRTVERSTSFSKTVGGE---PVDFNSILTGFENYDIVFVATTAPYFLVTFERIQK 263
                   599********************************99.******************999...*********************************** PP

                   CHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
  Shikimate_DH  98 alkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                   al+ +++ ++++D+++PR v+++vael++++l+++D + e
    AJA92781.1 264 ALETKHSGMMILDLSNPRTVDEKVAELRGIKLMNIDQIAE 303
                   **9999******************************9976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3
                   HHHHHHHT.ET-EEEEGCGHHHH CS
  Shikimate_DH  50 kelaeelkgeeiealkleelkel 72 
                   +el +++ +e+i  +++++l++ 
    AJA92781.1 377 EELTKSV-AENIMSTPMNNLRKE 398
                   5566666.444777777777665 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   1.2   8.7e-23   2.6e-19       2      96 ..     319     415 ..     318     416 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 8.7e-23
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S...--------TTHHHHHHHHHHHHHHHHHHSS.-TTTTHHHHHHHHH.. CS
  GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkkla.ldgedreelekltrslvnkllheptarLkea.edeeeellealrrlFn 96 
                  Ae+iI+ee+  +ea +k+le++p++k++ +++++ir +ele+a++ l+ l++ +++ +e+lt+s+   ++ +p+++L+++ e+ ++++++a+++lFn
   AJA92781.1 319 AEEIIKEELPVLEATMKRLEAEPIVKDVFKSTDAIRVKELEKAFSMLGeLNDSQKKIIEELTKSVAENIMSTPMNNLRKEtEHGNSDVINAASKLFN 415
                  9*******************************************************************************555555**********8 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   7.8e-07    0.0023       1      81 [.     184     261 ..     184     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.8e-07
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav.dneeaaeeadvvvlavkpedveevlsel 81 
                    ki +iG+G+ +  +a+ l ++g   + + +  sr+ e+ +++ +++g +     +  +  e+ d+v++a    ++  + + +
     AJA92781.1 184 KILLIGTGEAATLVAKSLKKRG---YPFFIS-SRTVERSTSFSKTVGGEPVDFnSILTGFENYDIVFVATTAPYFLVTFERI 261
                    6789******************...999956.**************944444203566678********9988877777776 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     9e-06     0.027      28      98 ..     174     248 ..     154     287 .. 0.78
   2 ?   -1.8   0.0      0.56   1.7e+03     134     160 ..     258     284 ..     254     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                   CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHH...HH-SEEEE- CS
  2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleell...aesDivslh 98 
                   +    e++ k++ +iG+G+ ++ vak lk+ g   ++ +r+ ++++   +++g e v+++ +l   ++ Div+++
    AJA92781.1 174 EENVDEMKSKKILLIGTGEAATLVAKSLKKRGYPFFISSRTVERSTsFSKTVGGEPVDFNSILtgfENYDIVFVA 248
                   5567899*********************************99988744455555777777765111566666654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.56
                   HHHHHHHHHTTSCCEEEES--SSSSSG CS
  2-Hacid_dh_C 134 eeaLleaLksgkiagaalDvfeeeplp 160
                    e + +aL+ ++ +++ lD  ++  ++
    AJA92781.1 258 FERIQKALETKHSGMMILDLSNPRTVD 284
                   567889999999999999987766555 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.3   8.8e+02      22      78 ..     158     214 ..     151     219 .. 0.77
   2 ?    4.3   0.2      0.02        60      20      65 ..     259     309 ..     255     328 .. 0.69
   3 ?    6.4   0.0    0.0045        13      54      86 .]     376     419 ..     331     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.3
                 HHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHHH CS
    ATP-cone  22 iekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaayi 78 
                 i+k   ++  ++ ++aee ++e+++++   i t e  +lv+k l++ +++ ++ ++ 
  AJA92781.1 158 ISKGSISVGSMAVKLAEENVDEMKSKKILLIGTGEAATLVAKSLKKRGYPFFISSRT 214
                 555555566778888889889998888888999999999999999999987776665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
                 HHHHHHHHH........-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHH CS
    ATP-cone  20 raiekAceg........seeeideiaeeveaevrkrlrdgisteeIqdlvektl 65 
                 ++i+kA+e         ++ + + + e+v   ++ r+ + +++++I ++v k+ 
  AJA92781.1 259 ERIQKALETkhsgmmilDLSNPRTVDEKV---AELRGIKLMNIDQIAEMVDKNM 309
                 56777777756556766555566665555...3447888899999999997765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0045
                 HHHHHHHHHHHHH...........HSS-HHHHHHHHHHHHHHHH CS
    ATP-cone  54 teeIqdlvektli...........ehpdyavaaayilyrnlrke 86 
                 +ee+ + v+++++           eh++ +v+ a++  +n++ke
  AJA92781.1 376 IEELTKSVAENIMstpmnnlrketEHGNSDVINAASKLFNFKKE 419
                 899999999999999999999***************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1283  (0.07156); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 2659.38
//
Query:       AJA92782.1  [L=261]
Description: hypothetical protein T478_0504 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0021   18.4   0.0     0.0077   16.6   0.0    1.8  1  Copper-bind      Copper binding proteins, plastocyanin/azurin
     0.0031   17.6   0.0     0.0049   17.0   0.0    1.4  1  Cupredoxin_1     Cupredoxin-like domain
  ------ inclusion threshold ------
      0.059   11.7   2.6      0.074   11.4   2.6    1.1  1  PTPS_related     6-pyruvoyl-tetrahydropterin synthase related
        9.4    5.8  16.7         89    2.6  16.8    2.1  1  DUF998           Protein of unknown function (DUF998)


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.7e-06    0.0077      13      98 ..     181     256 ..     169     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                  EEESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEETTTTTTTSEEEEEE CS
  Copper-bind  13 qFetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCsPHaaagMkgkvtv 98 
                   +++ e  v +g  +++vn ++m+H    + d   + +         +t l  +Ge++++  +  + g+Y+++C  H    M+ ++++
   AJA92782.1 181 DYDPDEALVPQGHIIEWVNDDAMSHTATSSVDFG-ETF---------DTGLLNAGETYKLDTNklDLGEYEYMCIVHP--WMVSTIII 256
                  5777777777788888888888887766666653.223.........34566779***99999777788********9..58999876 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-06    0.0049      31     103 ..     181     255 ..     133     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
  Cupredoxin_1  31 gfePskievkagekvklkiknkdktpeefe.sedlgee...kvlapgktttitiaplkpGeYeftcdmhmdakGkli 103
                    ++P++  v++g    ++++n+d+ +++ + s d+ge      l+ g+t++++ ++l+ GeYe+ c  h+ +  ++i
    AJA92782.1 181 DYDPDEALVPQGH--IIEWVNDDAMSHTATsSVDFGETfdtGLLNAGETYKLDTNKLDLGEYEYMCIVHPWMVSTII 255
                   699*********9..68999999998544403444443222779***********************9997777777 PP

>> PTPS_related  6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   1.7e-05     0.074     182     320 ..      12     148 ..       2     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.7e-05
  PTPS_related 182 sevlksltvpltvaLdPllrlsnggfyfGlaivllilagvllakkrktpglvaliiylvltvgialallk...llPlsqllldiRflpfaavlllll 275
                   ++++ s++  +++++d +  l    f fGl+i+ + l+  +++++++t+++v  i+++ l++g +   l    +lPl+  +     l ++a+ ++++
    AJA92782.1  12 AGLVTSYSGIAHTFIDGMHALTGLLFMFGLIILAAGLLEGGISTSNRTKATVLTIVSISLGFGTFATTLTensTLPLFAGF-----LIMIAIPAIVI 103
                   6777788888888888888888889**********************************9999988887611155555544.....55555444444 PP

  PTPS_related 276 valllwk.vlkravavllalllai..livdslisfnyvgyeakkltev 320
                   + +++   v  +    + ++++++    ++  ++f +v++ +  + + 
    AJA92782.1 104 SYFAMKIpVYAK---PVGVIFIIAfgTGIGLYVAFGFVSPDQYMVATE 148
                   433332213344...333333333233444444555555544444444 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  16.8      0.02        89      79     182 ..       4     102 ..       1     138 [. 0.74

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.02
      DUF998  79 aglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwllaaaldgslllGlaerllvlaita 177
                 +gl +++ + + t+ +g + ++ + +H+l+++++ ++l++ ++ l   ++    + ++++++++++++ ++++ + ++    +    l+ ++++l+++a
  AJA92782.1   4 GGLTAIGLAGLVTSYSGIAHTFIDGMHALTGLLFMFGLIILAAGLL--EGGISTSNRTKATVLTIVSISLGFGTFATT---LTENSTLPLFAGFLIMIA 97 
                 6788888888888888888888889**********99999999777..455555666666666666666666666666...555555555555555555 PP

      DUF998 178 wllal 182
                  ++++
  AJA92782.1  98 IPAIV 102
                 55444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1858.61
//
Query:       AJA92783.1  [L=354]
Description: glycosyltransferase, group 1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-21   76.4   0.1    7.6e-21   74.4   0.0    2.0  2  Glycos_transf_1  Glycosyl transferases group 1
    5.3e-18   65.8   0.0    1.5e-17   64.3   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.7e-09   36.5   0.0    8.4e-09   35.7   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
     0.0004   19.3   0.0       0.11   11.3   0.0    2.2  2  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0015   18.5   0.0      0.005   16.8   0.0    1.8  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.022   14.8   0.0       0.13   12.2   0.0    2.1  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.36   1.1e+03       4      26 ..      53      75 ..      50      94 .. 0.70
   2 !   74.4   0.0   2.5e-24   7.6e-21      36     171 ..     196     327 ..     161     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.36
                     HHHHHTTTTTT-EEEEEESS-TT CS
  Glycos_transf_1  4 kkrkklgknekkkiilsvgrlek 26
                     +k++k+ + e k+ i++v r ++
       AJA92783.1 53 NKKFKNLIEEFKPDIIFVDRTRH 75
                     56667777777777777776554 PP

  == domain 2  score: 74.4 bits;  conditional E-value: 2.5e-24
                      HHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHC CS
  Glycos_transf_1  36 afallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpa 128
                      + + l ++  pnv +  aG+g +++++  l e++e+    ++lg ++ ++++ e+l+  d++ l s  +  +++l EA    +pvia+n+gg++
       AJA92783.1 196 LPEIL-EK-MPNVEFYWAGDGVYRDKILPLLEKYEN---FHWLGSLEyPDKVREFLTEIDVYTLISGIDMSPLTLQEAQLMEKPVIATNVGGIP 284
                      44444.44.79*******************999998...******************************************************* PP

                      HHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
  Glycos_transf_1 129 evvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                      e+ kdgetG+l+++n+ ++l e++  ll++ e+++++g+++++
       AJA92783.1 285 ELMKDGETGFLIEKNSSKELFEKLSTLLNNLEDANKMGKKGKE 327
                      ****************************************987 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   5.5e+03      17      28 ..      56      68 ..      50     107 .. 0.57
   2 !   64.3   0.0     5e-21   1.5e-17      24     134 .]     196     314 ..     180     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                     HHHHHHHH.HHHH CS
  Glyco_trans_1_4 17 vdllleav.pllr 28
                     ++ l+e++ p + 
       AJA92783.1 56 FKNLIEEFkPDII 68
                     5555555555443 PP

  == domain 2  score: 64.3 bits;  conditional E-value: 5e-21
                      HHHHH.H..HEEEEEES---...HHHHHHHTT-T.TEEEE---...THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT-- CS
  Glyco_trans_1_4  24 vpllrkk..dvrlvivGdgp.rpeeleelaagleerveftGfv...edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv 109
                      +p++++k  +v+++ +Gdg  r+ ++  l++++ e+++++G +   ++++e+l + dv+ + s     +l+l Ea  +++pv+at+vggi+e++
       AJA92783.1 196 LPEILEKmpNVEFYWAGDGVyRD-KILPLLEKY-ENFHWLGSLeypDKVREFLTEIDVYTLISgiDMSPLTLQEAQLMEKPVIATNVGGIPELM 287
                      4777777635*********9776.555577666.7********99555***************98889************************** PP

                      ..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4 110 ..gengllvppgdpealaeailrLled 134
                        ge+g+l++++++++l e++ +Ll++
       AJA92783.1 288 kdGETGFLIEKNSSKELFEKLSTLLNN 314
                      **********999************87 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   2.8e-12   8.4e-09      15      91 ..     265     343 ..     251     344 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.8e-12
  Glyco_trans_1_2  15 lfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhraeqll 91 
                      l Ea  +  +++++   g++el ++g++++l+e  + +el ek+  ll+n e++++++++++e+v++++++d+  +++l
       AJA92783.1 265 LQEAQLMEKPVIATNVGGIPELMKDGETGFLIEknSSKELFEKLSTLLNNLEDANKMGKKGKEFVENNFNWDKICNDFL 343
                      568888999*****99*********************************************************999998 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0014       4.2      57      98 ..      54      92 ..      20      97 .. 0.90
   2 !   11.3   0.0   3.8e-05      0.11     207     334 ..     196     329 ..     129     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0014
                 HHHHHHHHHH--SEEEEESSSHHHHHHHHHHHHTT-E.EEEET CS
  Epimerase_2 57 igleevleeekpDlvlvlGDtnetlagalaAfklrip.vaHve 98
                 +++++++ee kpD+++v  D++  +a  l A+k +ip v+H+ 
   AJA92783.1 54 KKFKNLIEEFKPDIIFV--DRTRHFA--LEASKTNIPlVIHLR 92
                 68999***********9..9999998..9*******9567876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.8e-05
                  HHHHHHH.H--EEEEE--..HHHHHHHHHHHHH-TTEEEE----HHH....HHHHHHC-SEEEE.S-H..HHHHHHHHCT--EEESSSS-S-THHHHT CS
  Epimerase_2 207 lkalake.kdvevvvpvhnnprtrkrlleeleelenvtlieplgyld....flsllknaklvlt.dSg..GiqeEapslgvpvvnlReeteRpegvea 296
                  l ++ ++ ++ve+ +        r+++l  le++en++ + +l+y d    fl  +   +l+ + d +  ++q Ea ++++pv+   + +  pe ++ 
   AJA92783.1 196 LPEILEKmPNVEFYWAGD--GVYRDKILPLLEKYENFHWLGSLEYPDkvreFLTEIDVYTLISGiDMSplTLQ-EAQLMEKPVIAT-NVGGIPELMKD 289
                  445555546676666666..88999*******************98721114444444455544665559999.***********9.99********9 PP

                  TSEEE.-T.T-HHHHHHHHHHHCT-..--......--TT- CS
  Epimerase_2 297 gtnvl.vg.tdkeeIvaaleklledkkelekmanaknpYg 334
                  g+  + ++ ++++e+ ++l++ll++ ++ +km ++ + + 
   AJA92783.1 290 GETGFlIEkNSSKELFEKLSTLLNNLEDANKMGKKGKEFV 329
                  98765565166899*********99888888888777765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06     0.005      48     169 ..      40     163 ..      13     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
  Glyco_transf_4  48 lpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye........krllkarlkplsrllralerrllrra 134
                      +++++ ++ + + +++++l++++kpD++ +     +  al a++  ++iplV+++ g           + +  a +k + + + ++ +  ++ +
      AJA92783.1  40 GFPSRKVKNWFNSNKKFKNLIEEFKPDIIFVDRTRHF--ALEASK--TNIPLVIHLRGDHWaemimakeTLYKSAGKKIAINKWDEIGEICFNDS 130
                     34445555555666799************99887766..444555..8*******887777777998753333344444444444555666999* PP

  Glyco_transf_4 135 drviavSeatadelrerygvppekitVipnGvDle 169
                     + ++ +++++ +  ++ry+  ++ i++ + G++ +
      AJA92783.1 131 KMIFPICNYLSEVTKKRYK--KKSIETMYQGINSD 163
                     9**999**********888..56799999999876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.5e-05      0.13      14      87 ..      16      77 ..       2     112 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
  Glyco_trans_4_2 14 lrlakeLakrgyeVhvitpkkgakdeleaegihvhrl.kvd......rkgpleylk.afklkklikkikPDvvhahyakpyg 87
                     +++ak                     le++gi+++ + ++d      ++   ++++  +k+k+li+++kPD++ +  +   +
       AJA92783.1 16 KEFAKN--------------------LEEKGITCKVIlDSDyadgfpSRKVKNWFNsNKKFKNLIEEFKPDIIFVDRTRHFA 77
                     444444....................445555555553222333333455556677256**************987766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2469.12
//
Query:       AJA92784.1  [L=312]
Description: thaumarchaeosortase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-06   26.6  26.5    6.4e-06   25.9  26.5    1.4  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
     0.0072   15.9   5.9     0.0072   15.9   5.9    3.1  3  DUF998           Protein of unknown function (DUF998)
  ------ inclusion threshold ------
        3.3    7.9   0.0        3.3    7.9   0.0    4.5  4  SdpI             SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9  26.5   1.1e-09   6.4e-06      26     253 ..      61     291 ..       6     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-09
  Exosortase_EpsH  26 shgllvpllalyllwdrwrralaasasll.gllllllglfllallgelsrvlllsalslvlillglvllllGlralrlllf.......plllll 111
                       + + +pl+al +           + sl  g++ ++++l+ ++ + e+s++ l++   +++++++ + +l+G++++r+            ++l 
       AJA92784.1  61 RFFYCIPLIALTIT---------YFVSLQfGVRDYIMSLVDVFGVLEYSWEWLFDFAVMAIFVTASLAILFGRKWIRIGPAgpiflagNAIILA 145
                      22222333322222.........1111222344445666448***********************************99998333333333333 PP

  Exosortase_EpsH 112 lalPlpavlvaqlslpLqllvaavagfllsllg...ip.vereGnviql.ptg...qveVaeaCsGlrsllallalglllallfrrrlwkrkll 197
                      l   +p  ++     pLq +v  ++++ ++++    +  +++ +n++ l ++     ++V    +G++s++   ++ +++++ +r   + rk++
       AJA92784.1 146 LDSFFPYDTLG----PLQYIVPYFVQANVWVITvldLGvATARDNLMFLnGDFgpfALQVFWPSAGVHSIIIYSLVMMAFLIKMRIPRN-RKII 234
                      33334444444....899999888877777766322443366666666645446667*************9988877776666666666.66** PP

  Exosortase_EpsH 198 lllaavpiaflaNlvRilll..vllayhygpeaaegllHeiaGwllfgvalllllgll 253
                       ++++++ ++++N++Ri+ l  + l  +++pea  + +H +aG ++f+ +l+++l+++
       AJA92784.1 235 YFVIGILGTIFVNMIRIFSLsvYALKVTTDPEAW-EEFHSVAGEIMFLPWLFIFLLVV 291
                      ********************44445577899**9.89*************87777765 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2     0.066   3.9e+02      36      49 ..      35      48 ..       5      61 .. 0.47
   2 !   15.9   5.9   1.2e-06    0.0072       8      95 ..      70     156 ..      63     199 .. 0.77
   3 ?    0.2   0.4     0.079   4.7e+02      99     116 ..     266     283 ..     204     300 .. 0.46

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.066
      DUF998 36 gpggwlfnaglvll 49
                g gg+lf+a+++++
  AJA92784.1 35 GRGGFLFAAAFIAA 48
                23333333333332 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-06
      DUF998   8 lavilaaallrpgy.dplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavaglglvlagvfptdpgg 95 
                 +++i++ + l+ g+ d + + +   g    +  w + +++ +++++v+a +++l+ +++ r+g ag+++la  ++ l+l+ +fp d+ g
  AJA92784.1  70 ALTITYFVSLQFGVrDYIMSLVDVFGV--LEYSWEWLFDFAVMAIFVTASLAILFGRKWIRIGPAGPIFLAGNAIILALDSFFPYDTLG 156
                 455555555545544555555555555..6666777788899999999988889899*****************************986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.079
      DUF998  99 slsglvHglasavaflal 116
                       H +a+ ++fl  
  AJA92784.1 266 EAWEEFHSVAGEIMFLPW 283
                 333445555555555533 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.6   5.3         3   1.8e+04      39      39 ..      51      51 ..       5     123 .. 0.61
   2 ?    0.4   0.9      0.13   7.5e+02      29      45 ..     132     166 ..      98     183 .. 0.68
   3 ?   -0.8   1.9      0.29   1.7e+03      34      57 ..     212     242 ..     196     254 .. 0.59
   4 ?    7.9   0.0   0.00055       3.3      17      42 ..     263     288 ..     260     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: -4.6 bits;  conditional E-value: 3
        SdpI 39 i 39
                i
  AJA92784.1 51 I 51
                1 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
        SdpI  29 agklwiiaGlilllla..................l 45 
                 ag++++++  i+l+l                   +
  AJA92784.1 132 AGPIFLAGNAIILALDsffpydtlgplqyivpyfV 166
                 56777777777666667777777666554444331 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.29
        SdpI  34 iiaGlilllla..........lgavvlvllvlvl 57 
                 ii +l+++++           +    +++++++ 
  AJA92784.1 212 IIYSLVMMAFLikmriprnrkI---IYFVIGILG 242
                 6667777777778887774331...222222222 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.00055
        SdpI  17 kseetWrkahrfagklwiiaGlilll 42 
                  + e+W+  h +ag ++++  l ++l
  AJA92784.1 263 TDPEAWEEFHSVAGEIMFLPWLFIFL 288
                 589***********877544333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2194.09
//
Query:       AJA92785.1  [L=402]
Description: threonine ammonia-lyase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-84  284.3   0.3    1.3e-84  284.1   0.3    1.1  1  PALP            Pyridoxal-phosphate dependent enzyme
    0.00053   20.5   1.1     0.0025   18.4   0.8    2.1  2  ACT_4           ACT domain
  ------ inclusion threshold ------
      0.091   12.5   0.0       0.22   11.3   0.0    1.7  1  Thr_dehydrat_C  C-terminal regulatory domain of Threonine deh


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.1   0.3   2.2e-88   1.3e-84       4     294 .]      18     303 ..      15     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 284.1 bits;  conditional E-value: 2.2e-88
                 CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT- CS
        PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGa 102
                  i++T l  ++ +sk +g+++flK+E+ ++tgSfK+Rga+y +++l+ +++ k+vv+as+GNh +++A+a++  ++++tiv+p++asp+kva+++ +Ga
  AJA92785.1  18 IIRKTNLEFSETFSKICGAKVFLKNEYEQKTGSFKIRGAYYKIKSLTDEQKSKGVVAASAGNHSQGVAFASSIENIPCTIVMPKTASPAKVAATKGYGA 116
                 6899*****************************************99999************************************************* PP

                 EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTC CS
        PALP 103 evvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalars 201
                 +vv+ g++yde+ ++a+++ +e ++a++++ fd+p+vi+g+g iglEi+eql +++d ++vp+GgGgl+aGi  ++ke++p+vr+igve++  +++ +s
  AJA92785.1 117 KVVLEGSTYDESWEYAQKISSE-TNATIIHAFDDPHVIAGQGVIGLEIMEQL-PNVDEIYVPIGGGGLVAGIILAVKEKNPNVRIIGVESSSYPSMKES 213
                 **********************.*****************************.6********************************************* PP

                 CS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
        PALP 202 lragrrvtvpvsdtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                 +++++ +tv+  +tiadg++v++p+  +f +++ ++deivtv+d +++ am ll +r + vvep++a+ala +    + + + g++vv il+g
  AJA92785.1 214 FEKKSLQTVKGNSTIADGISVKTPGKITFGVVRHQIDEIVTVDDSDIINAMFLLMERSKAVVEPAGAVALAYI---LKHKPESGKTVVPILCG 303
                 *************************************************************************...6666666667**99998 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.71   4.3e+03      18      40 ..     181     203 ..     178     210 .. 0.76
   2 !   18.4   0.8   4.1e-07    0.0025       8      70 ..     327     392 ..     322     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.71
       ACT_4  18 glLaditqviseekanivsvnak 40 
                 gl+a i+ +++e++ n++ + ++
  AJA92785.1 181 GLVAGIILAVKEKNPNVRIIGVE 203
                 89999999999997777655444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.1e-07
       ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLr 70 
                 +++v  +d++g+L+++++ is+ ++niv+v  +  ++    g a ++i++e +d ++ +++i+ L+
  AJA92785.1 327 KISVLLKDKPGALKELVDEISSINVNIVEVIHDRLSTdvsAGSAGVTISLETEDQNQSNELINHLQ 392
                 799**************************9766555545589*********************997 PP

>> Thr_dehydrat_C  C-terminal regulatory domain of Threonine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.7e-05      0.22      13      79 ..     328     399 ..     317     402 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                     XXXXXXXXXXXXXXXXXXXXXXX..XXX.XXXXXXXX.XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX CS
  Thr_dehydrat_C  13 lavefpeqpGaLkkFlellggrnd.iTl.feYrkage.kngkvLvgvevsqaee..ldelierleklgykve 79 
                     ++v + ++pGaLk+ ++++++ n  i + ++ r   + + g++ v ++++ + +  ++eli++l+ +++k+e
      AJA92785.1 328 ISVLLKDKPGALKELVDEISSINVnIVEvIHDRLSTDvSAGSAGVTISLETEDQnqSNELINHLQGKDIKFE 399
                     5677889**************9844555157788878899998888888765543489*******9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2745.59
//
Query:       AJA92786.1  [L=108]
Description: RNA polymerase Rpb4 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-09   36.1   4.4    9.3e-09   35.7   4.4    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4
     0.0087   16.2   0.6        1.6    8.9   0.2    2.2  2  Mrr_N         Mrr N-terminal domain
  ------ inclusion threshold ------
      0.015   15.1   0.4      0.015   15.0   0.4    1.2  1  DUF421        Protein of unknown function (DUF421)
      0.018   15.0   0.6      0.026   14.5   0.4    1.5  1  Blo-t-5       Mite allergen Blo t 5
      0.038   14.0   0.3       0.22   11.5   0.1    2.0  2  Integrase_Zn  Integrase Zinc binding domain
       0.04   13.9   0.0      0.079   13.0   0.0    1.5  1  DUF3895       Protein of unknown function (DUF3895)


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   4.4   3.1e-12   9.3e-09      28     121 ..      14     106 ..       1     107 [. 0.84

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.1e-12
                   CCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHHHHHH CS
  RNA_pol_Rpb4  28 ddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfedeqleeiLdelke 121
                   + k+  k++ ++n+++i++ t +y+++  s l+ +++ +   +l+k  ++t+ E++ l+n++P+++ el++     ++ +  e+le+iL+++k+
    AJA92786.1  14 EVKELLKNQDPENMDQIQRWTFDYVSK-VSTLEASSAKKMKQQLVKDCNITEEEAVELINICPQTMSELRSFTFGWKKLILTETLEKILKIIKD 106
                   3346689999****************9.****96666666666778999*******************************************96 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.2   0.00054       1.6      25      72 ..       2      49 ..       1      53 [. 0.90
   2 !    8.3   0.0   0.00085       2.5      17      57 ..      46      89 ..      42     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00054
       Mrr_N 25 ervaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespkr 72
                e+v+++  +s  e++ell++  +  +++  +W   y +k   le ++ 
  AJA92786.1  2 EEVKKKQAVSLSEVKELLKNQDPENMDQIQRWTFDYVSKVSTLEASSA 49
                68899999999**********9******************99999875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00085
       Mrr_N 17 ehrlkeirervaerfglseeeraell...psgkqtrfknrvgWa 57
                +++ k++++++ ++++++eee  el+   p+  + + +  +gW 
  AJA92786.1 46 ASSAKKMKQQLVKDCNITEEEAVELInicPQTMSELRSFTFGWK 89
                566799******************99665555556666666665 PP

>> DUF421  Protein of unknown function (DUF421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   5.2e-06     0.015      21      85 ..       5      66 ..       1     102 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.2e-06
      DUF421 21 lkklrltvddLleqLRqqgifslsdVkyailEtnGqlsvllkeekkpvtklplplivdGkiqken 85
                 kk+ ++++++ e L++q+ ++++++++ +++   ++s l+ +++k+++   ++l+ d +i +e+
  AJA92786.1  5 KKKQAVSLSEVKELLKNQDPENMDQIQRWTFDYVSKVSTLEASSAKKMK---QQLVKDCNITEEE 66
                48999***************************************99887...*******999875 PP

>> Blo-t-5  Mite allergen Blo t 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.4   8.7e-06     0.026      15      66 ..      14      65 ..       2      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.7e-06
                XXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHH--SSHHHHHHHHHHHHHH CS
     Blo-t-5 15 efDrllieeleekleklekallklseqvkelektkskelkeqilreltialn 66
                e   ll ++  e+++++ +  +    +v+ le + +k++k+q++++ +i+++
  AJA92786.1 14 EVKELLKNQDPENMDQIQRWTFDYVSKVSTLEASSAKKMKQQLVKDCNITEE 65
                56678889999***********************************999874 PP

>> Integrase_Zn  Integrase Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.34     1e+03      16      31 ..       5      20 ..       2      21 .. 0.83
   2 ?   11.5   0.1   7.3e-05      0.22      14      35 ..      55      76 ..      53      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.34
  Integrase_Zn 16 rkkFgitrkqAreIVq 31
                  +kk+ +++++ +e ++
    AJA92786.1  5 KKKQAVSLSEVKELLK 20
                  789999****999876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.3e-05
  Integrase_Zn 14 aLrkkFgitrkqAreIVqsCpt 35
                   L k+++it ++A e ++ Cp+
    AJA92786.1 55 QLVKDCNITEEEAVELINICPQ 76
                  599*****************96 PP

>> DUF3895  Protein of unknown function (DUF3895)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.7e-05     0.079       2      36 ..      28      65 ..      27      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
     DUF3895  2 selqkaileyvksa...elisAkelaeyLvrkgkasne 36
                +++q+  ++yv      e  sAk + ++Lv+++++++e
  AJA92786.1 28 DQIQRWTFDYVSKVstlEASSAKKMKQQLVKDCNITEE 65
                678888999998664568889**************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 752.26
//
Query:       AJA92787.1  [L=97]
Description: hypothetical protein T478_0311 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.01   16.0   0.3      0.017   15.3   0.3    1.5  1  CdAMP_rec  Cyclic-di-AMP receptor
      0.063   12.9   0.6      0.078   12.6   0.6    1.2  1  NAT        NAT, N-acetyltransferase, of N-acetylglutamate syn


Domain annotation for each model (and alignments):
>> CdAMP_rec  Cyclic-di-AMP receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   1.9e-06     0.017      17      65 ..       4      51 ..       1      87 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                HHHHHHTT-EEEEEEEEETTT-SEEEEEEEEEEGGGHHHHHHHHHHC-- CS
   CdAMP_rec 17 vdalteknfkatklattGGflkeGnttlliGvedekvdevlsiikekck 65
                v+ +t+++++a kla+   f+keGn t++  + d    e++  ik+k+ 
  AJA92787.1  4 VEIVTDDKYEAQKLASL-IFVKEGNETFITEIIDVFETEIVISIKDKSV 51
                567899*********97.6**********99998877777777777654 PP

>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   8.7e-06     0.078       5      80 ..      20      94 ..      16      97 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-06
                HHHSSSTSSEEEE---XEEEESSCCCSSXCCHHHHHHTTSTTTSSXHHHHHHHHHTSXEEEEEETTXSEEEEE... CS
         NAT  5 elftdsgagtlirrGlkvitvkslkelidlekLksliedsfkrkldvkdYldrlkgkiakiyiaedyeglAivtwe 80
                 +f ++g+ t+i + + v +++   ++   + ++s++ +++++ ++  d+++++ +k+aki+  +  egl+ + +e
  AJA92787.1 20 LIFVKEGNETFITEIIDVFETEIVISI-KDKSVHSIVLKDKEQVTKFTDFMQSIIEKKAKIIGTSTNEGLVEIFKE 94
                578999999999999999988888887.88899999999999**************************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 749.19
//
Query:       AJA92788.1  [L=279]
Description: 8-oxoguanine DNA glycosylase, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-12   47.9   3.3    6.6e-07   29.5   0.1    2.9  3  OGG_N        8-oxoguanine DNA glycosylase, N-terminal domain
    8.5e-11   42.3   0.0    1.4e-10   41.6   0.0    1.3  1  HhH-GPD      HhH-GPD superfamily base excision DNA repair pro
     0.0012   18.6   0.0      0.013   15.3   0.0    2.5  2  HHH          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.049   14.3   0.0        1.5    9.5   0.0    2.8  3  HHH_5        Helix-hairpin-helix domain
      0.051   14.0   0.2       0.26   11.7   0.0    2.1  3  Terminase_2  Terminase small subunit
       0.16   12.2   0.7         16    5.7   0.0    2.7  2  PYRIN        PAAD/DAPIN/Pyrin domain


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.1e-07    0.0015       8      45 ..       6      41 ..       1      50 [. 0.87
   2 !   29.5   0.1   2.2e-10   6.6e-07      74     120 ..      48      93 ..      43      94 .. 0.93
   3 ?   -1.7   0.1      0.96   2.9e+03      17      29 ..     260     272 ..     255     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.1e-07
                S--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEE CS
       OGG_N  8 eldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqe 45
                e++++ t+++GQ F Wkk +++ ++g+ g++++ L+ +
  AJA92788.1  6 EVNIDDTINSGQVFLWKKFDSK-WYGINGKEILILE-D 41
                79********************.**********998.3 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 2.2e-10
                 HTHHHHTTTTS-HHHHHHHHTT.SHHHHHHHCCTTT-------HHHH CS
       OGG_N  74 eilrdYfnLdvdleelykewskkdplfkksadkftGiRllrqdpwEc 120
                 + ++++f+ d d +++ k++sk d+ +kk++++f G+R+lrqdp+ c
  AJA92788.1  48 KNIHNFFRFDDDFQKIKKQLSK-DDIMKKAIKNFPGMRILRQDPFQC 93 
                 5699****************99.888*******************98 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.96
                 SSS-SSEEE-TTS CS
       OGG_N  17 cGQsFrWkktekt 29 
                  GQ+F +k++++ 
  AJA92788.1 260 YGQQFLFKNERES 272
                 59******99765 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.5e-14   1.4e-10       1     101 [.      95     241 ..      95     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.5e-14
                 HHHHHHTTS-HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH..................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
     HhH-GPD   1 vsailsqqtsderanriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelArilv..................... 66 
                 +s+i+s++ ++ ++ +  ++l ++fg            fp+pe+la+a+ +++ ++    G++ ++ ky+k++A ++                      
  AJA92788.1  95 ISFIVSSNSNIPNIQTRLQKLSRKFGekrtiddkelflFPKPEKLANASITDITKC----GLG-YRSKYVKKAAIAVSegtidfsslkkqdyqeardsl 188
                 79******************************************************....***.*************9********************* PP

                 ...................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHH CS
                 ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  67 ...................gkpdvlivvDvhvrrilkrlrsikekktkkkvekk 101
                                    +k + +++ D +v ril++++s + + ++k +++k
  AJA92788.1 189 cqvfgigkkvadcillfslDKLE-AVPLDRWVLRILQKYYSKEFQISTKTITEK 241
                 ******************97777.8888*************9999555555444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.39   1.2e+03       3      15 ..     137     149 ..     135     150 .. 0.84
   2 !   15.3   0.0   4.3e-06     0.013      10      30 .]     185     205 ..     177     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.39
                 HHHHTSSHHHHHT CS
         HHH   3 eglipasreeLla 15 
                 e l +as+ ++++
  AJA92788.1 137 EKLANASITDITK 149
                 78999***99998 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.3e-06
                 HHHHHTSTT-SHHHHHHHHHH CS
         HHH  10 reeLlalPGVGpktAeaIlsy 30 
                 r+ L+++ G+G+k+A++Il +
  AJA92788.1 185 RDSLCQVFGIGKKVADCILLF 205
                 899***************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.22   6.7e+02      24      40 ..     134     150 ..     129     155 .. 0.84
   2 ?    9.5   0.0   0.00049       1.5      13      53 ..     161     204 ..     160     208 .. 0.71
   3 ?   -3.5   0.0       5.7   1.7e+04      25      42 ..     242     259 ..     238     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.22
                 -SHHHHHHS-HHHHHTS CS
       HHH_5  24 esvedlaaadveeLaki 40 
                   +e+la+a++ +++k 
  AJA92788.1 134 PKPEKLANASITDITKC 150
                 5689**********996 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00049
                 HHHHHHHTTT--SHHHHHHS-....HHHHHTSTTS-HHHHHHHHH CS
       HHH_5  13 ktAlallsaGiesvedlaaad....veeLakipGiGkktAeriil 53 
                 k A+a+ ++    +  l+++d    ++ L+++ GiGkk A+ i+l
  AJA92788.1 161 KAAIAVSEG-TIDFSSLKKQDyqeaRDSLCQVFGIGKKVADCILL 204
                 556666665.556777877653322777************98876 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.7
                 SHHHHHHS-HHHHHTSTT CS
       HHH_5  25 svedlaaadveeLakipG 42 
                 ++++l ++ ve + k  G
  AJA92788.1 242 TYDELHDKIVEHFGKYAG 259
                 777887777777666555 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.6   7.6e+03      58      71 ..      63      76 ..      46      81 .. 0.65
   2 ?   11.7   0.0   8.8e-05      0.26      42     129 ..     105     194 ..      96     212 .. 0.86
   3 ?   -1.1   0.0      0.79   2.4e+03      67     101 ..     222     253 ..     217     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
  Terminase_2 58 ertiieadeVlqel 71
                  ++++++d+++++ 
   AJA92788.1 63 IKKQLSKDDIMKKA 76
                 45666666666655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.8e-05
  Terminase_2  42 kpkIkkaIreakaereertiieadeVlqel..lkiaraeitdevervklkdseevdkeilrevkegkegvkvklkDklkAlellakhlgl 129
                   p+I+ +++++  +  e++ i+ +e++      k+a+a itd+++     +s+ v+k++++  ++  +  ++k +D ++A + l++++g+
   AJA92788.1 105 IPNIQTRLQKLSRKFGEKRTIDDKELFLFPkpEKLANASITDITKCGLGYRSKYVKKAAIAVSEGTIDFSSLKKQDYQEARDSLCQVFGI 194
                  599********************9998766669************77778888888888888888888999999********99999877 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.79
  Terminase_2  67 Vlqellkiaraeitdevervklkdseevdkeilre 101
                  +lq+++++ +   t +++    k+++e+ ++i+++
   AJA92788.1 222 ILQKYYSKEFQISTKTIT---EKTYDELHDKIVEH 253
                  677776665555544444...46666666666655 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.019        57      11      36 ..      57      85 ..      57      93 .. 0.74
   2 ?    5.7   0.0    0.0055        16       4      56 ..     205     258 ..     202     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.019
                HHHHHHHHHHH.HH...--SSSHTTHCCH CS
       PYRIN 11 eeelkkFKslL.kee..eeglksiprgel 36
                +++++k+K +L k+   +++ k++p +++
  AJA92788.1 57 DDDFQKIKKQLsKDDimKKAIKNFPGMRI 85
                699********633367888888886665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0055
                 CCCCCC-HHHHHHHHHHH.HH.--SSSHTTHCCHCT-SHHHHHHHHHHHHTCCC CS
       PYRIN   4 lyLeeLseeelkkFKslL.keeeeglksiprgelekadrvdladlLvehygeda 56 
                   L++L++  l +   +  +++ ++  +i+++ + +++  +l d++veh+g++a
  AJA92788.1 205 FSLDKLEAVPLDRWVLRIlQKYYSKEFQISTKTITEKTYDELHDKIVEHFGKYA 258
                 55666666666654443324444444699999999999*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2128.91
//
Query:       AJA92789.1  [L=322]
Description: transketolase, pyridine binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-33  114.9   0.0    4.2e-33  114.5   0.0    1.1  1  Transket_pyr     Transketolase, pyrimidine binding domain
    5.3e-31  107.1   0.0    9.6e-31  106.2   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
     0.0023   18.2   0.0     0.0052   17.1   0.0    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   7.1e-37   4.2e-33       4     176 ..       7     176 ..       6     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 7.1e-37
                   EHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGG...HHGGHHHHH CS
  Transket_pyr   4 awrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdFangA...qiyadqair 97 
                   ++r+a+++al+el+++d ++v++gaD++ +  +  +g+ +++   r++++gi+E++++ +a+G+a +g  ++ +  +++ F+ g    qi+++ a  
    AJA92789.1   7 DMRTAYGKALNELGEQDRNIVVLGADTTDSLKTSGFGKNFPD---RFFNVGIAEANLVSVAAGLAYSG--KTSFASTYAIFLPGRcvdQIRNSIAYP 98 
                   79****************************************...***********************..9***********8656*********** PP

                   CHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC CS
  Transket_pyr  98 sgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrlpksllr 176
                   s   k++l+v+ v+ + +++vg dG +hq +e++a++r ip++kv+ P+d++ + +l +  ++    +P ++r+ +s+++
    AJA92789.1  99 SRGEKKGLNVKlVTSHGGLSVGPDGGSHQTIEDIAIMRVIPNMKVLIPADAVAVSKLTKNIAQI--YGPFYMRMARSKVP 176
                   ************************************************************9995..47********9986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   1.6e-34   9.6e-31       1     120 [.     188     307 ..     188     311 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.6e-34
                      TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSS CS
  Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdglda 94 
                      gk+ +lr+g+d t+ a+G +v++al+Aa++L++ gis++V+d++t+kp+Dk+ +++++++tg +v+ ee++++gG+gs+v+++++e    + ++
       AJA92789.1 188 GKGITLRDGNDCTIAATGITVKMALDAADKLQQAGISCRVIDCFTIKPIDKDILEKAARETGGIVTCEEHNVMGGFGSAVTEVVSE----SYPV 277
                      78899*********************************************************************************....9*** PP

                      EEEEEEE-SS.SSSSGHH...HHHHHTT-S CS
  Transketolase_C  95 pvkrvggpdv.iepgsae...elekafgld 120
                      p++r+g+ d  +e++      +l++ +g++
       AJA92789.1 278 PIRRIGAQDKfGESARDNeipQLLEKHGIT 307
                      **********99999855555666666665 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.8e-07    0.0052       2      79 ..     198     275 ..     197     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.8e-07
                 SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTG CS
     PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalk 79 
                 +  i a+G++++ a +a+d+l++ gi+  ++   t+ P  ++ l+++++++  +v+ +  + +g  G  v+ev +  +
  AJA92789.1 198 DCTIAATGITVKMALDAADKLQQAGISCRVIDCFTIKPIDKDILEKAARETGGIVTCEEHNVMGGFGSAVTEVVSESY 275
                 667999*****************************************************999**99******988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2511.32
//
Query:       AJA92790.1  [L=524]
Description: PF09369 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.096   12.4   0.4       0.16   11.6   0.4    1.3  1  DUF2291         Predicted periplasmic lipoprotein (DUF2291)
       0.11   12.4   0.0       0.42   10.5   0.0    1.9  2  PriA_3primeBD   3′ DNA-binding domain (3′BD)
       0.13   11.8   5.5       0.47   10.0   1.3    3.1  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.21   11.7   9.2       0.13   12.4   0.5    3.2  3  Zn-ribbon_8     Zinc ribbon domain
        1.3    9.0   6.1         14    5.7   5.6    2.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        3.9    7.5  10.0       0.96    9.5   1.4    3.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
        4.4    7.0   9.5        3.5    7.3   1.5    3.3  3  RecR            RecR protein
          6    6.9  10.2    3.1e+02    1.5  10.2    2.7  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> DUF2291  Predicted periplasmic lipoprotein (DUF2291)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   7.3e-05      0.16     117     172 ..     285     341 ..     264     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
                 SEEEES---TTHHHHHH-S--.GGG-SSHHHHHHHHHHHHHHHHHCTHHHHHTTC-- CS
     DUF2291 117 kvqiGpvikGtaiRDalgfid.fndFknqidfaqvgtalnkrvkeevlspldrealk 172
                 +vq   vi+Gt+  Da+++ + f  F++  + ++++  ln+ v + +l  +d+++l+
  AJA92790.1 285 QVQNNDVIFGTTTYDATSVPNlFRKFNRSENQNEYSVYLNQTVGKGILVRFDKKKLT 341
                 689999*************98689****************************99886 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.4   3.1e+03      52      74 ..      70      98 ..      19     101 .. 0.45
   2 ?   10.5   0.0   0.00019      0.42      14      78 ..     319     382 ..     313     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.4
  PriA_3primeBD 52 eeklkpieevld......eepllteelle 74
                   + k  +i++++        +pl+++e+++
     AJA92790.1 70 PTKQTKIQALMAtysqssAKPLIKKEQIR 98
                   33333333333211122235666666655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
  PriA_3primeBD  14 YrvpeelevkiGsrVlVpfgkrklvGiVvalkeeseveeeklkpieevlde.epllteellelaew 78 
                    Y+v   l++++G+ +lV f k+kl+ iV+++  ++e++  +  +ie+ l + e + ++e+ e++ w
     AJA92790.1 319 YSV--YLNQTVGKGILVRFDKKKLTSIVLQFLIKQELSGTDKAQIEKFLGDiETASESEINEMYSW 382
                    444..568899*************************999999999999976244445555566666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2     0.053   1.2e+02       3      14 ..     116     127 ..     114     132 .. 0.73
   2 ?   10.0   1.3   0.00021      0.47       2      35 ..     134     164 ..     133     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.053
                   ETTTTCEECHEE CS
  TF_Zn_Ribbon   3 CPnCgstnlveD 14 
                   C+ Cg+++++++
    AJA92790.1 116 CKRCGHYEILNP 127
                   999999987655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00021
                   EETTTTCEECHEETSTTCEEESSSSBEEEECCCC CS
  TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVlednsid 35 
                   kCP+C+  +l+  p    + C +CG+V +  s +
    AJA92790.1 134 KCPICKQNELEQIPR--YFSCNKCGNVKD-VSPM 164
                   8******98777677..9********953.5555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   5.7e-05      0.13       8      38 ..     116     145 ..     114     147 .. 0.79
   2 ?    3.6   0.4     0.032        72       6      18 ..     150     164 ..     148     178 .. 0.70
   3 ?   -2.4   0.1       2.4   5.4e+03      23      34 ..     202     214 ..     197     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.7e-05
  Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evrr 38 
                  C++Cg  +e+l + +++ + +CP C++ e+++
   AJA92790.1 116 CKRCG-HYEILNP-DKKTDWKCPICKQnELEQ 145
                  *****.9****97.3344555*****988876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
  Zn-ribbon_8   6 YrCeeCghefe..vl 18 
                  + C++Cg++ +  ++
   AJA92790.1 150 FSCNKCGNVKDvsPM 164
                  78*****98884444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.4
  Zn-ribbon_8  23 daplta.CPeCgs 34 
                  ++p    C  C++
   AJA92790.1 202 EDPVMGfCQVCKA 214
                  5566666888876 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.6    0.0063        14      22      56 ..     125     159 ..     116     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0063
  OrfB_Zn_ribbon  22 vnpay.TSktCseCgsknkealsgrtfkCpnCgfea 56 
                      np   T  +C+ C ++  e + +r f C++Cg + 
      AJA92790.1 125 LNPDKkTDWKCPICKQNELE-QIPRYFSCNKCGNVK 159
                     5555557889****999999.99*********9875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   0.00043      0.96      61      98 ..     104     144 ..      70     146 .. 0.66
   2 ?    1.6   2.2      0.12   2.7e+02      64      84 ..     143     163 ..     140     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                 EEEEEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS-EE CS
        HypA  61 eLeieevpvkvrCreCgkefelee..k.alrCpkCgsadve 98 
                 + ++e  p  + C++Cg+   l+   k + +Cp C+++++e
  AJA92790.1 104 VAHLECFPKGLNCKRCGHYEILNPdkKtDWKCPICKQNELE 144
                 33478889999******6544444323677******99876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                 EEEE--EEEETTTS-EEECHH CS
        HypA  64 ieevpvkvrCreCgkefelee 84 
                 +e++p  + C++Cg+  +++ 
  AJA92790.1 143 LEQIPRYFSCNKCGNVKDVSP 163
                 688888999999996555443 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.5    0.0016       3.5      19      36 ..     116     140 ..     114     142 .. 0.70
   2 ?    3.1   0.1     0.032        72      19      28 ..     152     161 ..     149     163 .. 0.85
   3 ?   -0.9   0.1      0.57   1.3e+03      17      23 ..     207     213 ..     205     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                 -TTT--EESSS.......S-CCCCS CS
        RecR  19 CsrCgnlteed.......lCaICsd 36 
                 C+rCg++   +        C+IC+ 
  AJA92790.1 116 CKRCGHYEILNpdkktdwKCPICKQ 140
                 *******544433344567****86 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.032
                 -TTT--EESS CS
        RecR  19 CsrCgnltee 28 
                 C +Cgn+ + 
  AJA92790.1 152 CNKCGNVKDV 161
                 ******9986 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.57
                 EE-TTT- CS
        RecR  17 rhCsrCg 23 
                 ++C++C 
  AJA92790.1 207 GFCQVCK 213
                 6899995 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  10.2      0.14   3.1e+02      14      44 ..     109     156 ..     103     158 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
  Zn_Tnp_IS1595  14 rWpngfvCPhCgsrkayrikt....................rglfqCkeCr 44 
                    ++p g  C +Cg   +y+i +                    +++f C++C+
     AJA92790.1 109 CFPKGLNCKRCG---HYEILNpdkktdwkcpickqneleqiPRYFSCNKCG 156
                    666777777777...444444444444444444444444455677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3765.69
//
Query:       AJA92791.1  [L=507]
Description: hypothetical protein T478_0027 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.037   13.7   4.7        0.5   10.0   1.1    2.2  2  DUF4131      Domain of unknown function (DUF4131)
      0.076   13.2   4.1        1.9    8.7   0.0    3.3  3  Pox_A28      Poxvirus A28 family
        0.2   11.5   8.7      0.076   12.9   2.5    2.3  2  EptA_B_N     Phosphoethanolamine transferase EptA/EptB
       0.37   10.5   5.1       0.61    9.8   5.1    1.3  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.1   0.00011       0.5       9      67 ..      48     102 ..      37     106 .. 0.67
   2 ?    6.3   0.2    0.0015       6.6       5      59 ..     101     162 ..      99     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
     DUF4131   9 llalllllllllllllrr...rprrrvllllllllllallgfalrapqpnandlsqllesgq 67 
                 + + +++ + l      r     ++  l++ l++ll++ +g  +  +q n++d+sq++  ++
  AJA92791.1  48 AAIGFVFWISL------RvflGGKKAGLIASLFILLFVIYGNIHNILQSNSSDISQFIG-SN 102
                 11122222222......23447888889999999999999999**************97.44 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
     DUF4131   5 lalvllalllllllllllllrrrprrrv.........llllllllllallgfalrapqpnandl 59 
                 ++lvl  ++l++ +l +++++  ++r           +++++++ l+ +l+f +++ ++ ++++
  AJA92791.1 101 SNLVLGPIFLVIGILGIIFFK--KTRASselnsifniIAIAMIAVLITTLMFSYSTNWNDVDSI 162
                 566777777777777777764..33333466777776777777777777788777777776655 PP

>> Pox_A28  Poxvirus A28 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.036   1.6e+02      16      39 ..      70      93 ..      58     100 .. 0.85
   2 ?    0.7   0.8      0.12   5.5e+02       5      33 ..     131     159 ..     128     168 .. 0.73
   3 ?    8.7   0.0   0.00042       1.9      37      93 ..     225     281 ..     220     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.036
     Pox_A28 16 vcllllqlyaiyenydnikefnda 39
                ++ l++ l+ iy n +ni++ n+ 
  AJA92791.1 70 IASLFILLFVIYGNIHNILQSNSS 93
                56678889***********99976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
     Pox_A28   5 sillivlataavcllllqlyaiyenydni 33 
                 si+ i+ +++  +l++  ++++  n++++
  AJA92791.1 131 SIFNIIAIAMIAVLITTLMFSYSTNWNDV 159
                 57777777777777777788888888766 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00042
     Pox_A28  37 ndahsaleysksigvlalDrrvfDpnDevldvkqkWrCvkyenkyvsvskfGfksee 93 
                 n  hs l ++ ++++ +lD  v+D++ +  d +   r +  ++ +     +G+k + 
  AJA92791.1 225 NYPHSFLSFASTLNMGYLDELVEDVDPNSKDFQLFIRYTDQNKVFRIFDSYGYKVSV 281
                 667999***************************************9999***99765 PP

>> EptA_B_N  Phosphoethanolamine transferase EptA/EptB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4     0.056   2.5e+02       5      42 ..      24      61 ..      18      67 .. 0.86
   2 ?   12.9   2.5   1.7e-05     0.076      46     121 ..      82     156 ..      67     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.056
                HHHHHHHH--TTTHHHHHHHHHHHHHHHHHHHHHS--- CS
    EptA_B_N  5 lllllsllslryllkpllilllllsaaasYfmdtYgvv 42
                +l+lls+ s   +++ +l+ +l+ +a+ ++f+ +  v+
  AJA92791.1 24 VLFLLSINSGELTAQDALVPILISAAIGFVFWISLRVF 61
                7899999999999**************99999887776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.7e-05
                 HHHHHHHH--HHHHHTT--HHHHHHHHHHTHHHHHHHHH-EE----HHHHHHHHHHHHHHHHHHHHHHHHTTHHHH CS
    EptA_B_N  46 dMirNvleTdvaEasellslklllyllllgvlPallllrvkikrksllkellkrlalllvallvivlvallfykdy 121
                 + i+N+l+ +++ +s+++  +l+l  ++l++  + ++++ k + +s l+++  +++ +++ +++i  ++++++ ++
  AJA92791.1  82 GNIHNILQSNSSDISQFIGSNLVLGPIFLVIGILGIIFFKKTRASSELNSI-FNIIAIAMIAVLITTLMFSYSTNW 156
                 5599**************888888766654444444444444545555655.455555555566666666666666 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.1   0.00014      0.61      13     119 ..      69     167 ..      48     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                  XXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHH.. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  13 wligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcig..alkenkcllltfsllllvlfllelaagilgfvfsdkar 108
                  +++++++l + ++ ++      ++ l+s+s+  ++++    +v+G +++++g+lG+i     + +  l  +f+++ + +++++++  ++ +       
   AJA92791.1  69 LIASLFILLFVIYGNI------HNILQSNSSDISQFI-GSNLVLGPIFLVIGILGIIFfkKTRASSELNSIFNIIAIAMIAVLITTLMFSYST--N-W 156
                  4667777777777733......333444445555555.6789*************77622555566788888887777777777655544433..3.3 PP

                  ......HHHHH CS
                  xxxxxxxxxxx RF
  Tetraspanin 109 gkvseiinnai 119
                  ++v +i+ n +
   AJA92791.1 157 NDVDSILSNFV 167
                  45555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3024.56
//
Query:       AJA92792.1  [L=220]
Description: TIGR00153 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-16   58.9   9.4    5.1e-16   58.7   9.4    1.0  1  PhoU_div      Protein of unknown function DUF47
     0.0067   16.3   0.5      0.028   14.3   0.1    2.2  2  WD40_alt      Alternative WD40 repeat motif
  ------ inclusion threshold ------
      0.037   12.8   0.5      0.059   12.1   0.1    1.7  2  TSA           Type specific antigen
       0.21   11.9   3.9       0.41   11.0   0.1    3.2  3  TSC22         TSC-22/dip/bun family
       0.21   11.9   6.1        2.3    8.6   0.4    2.6  2  Syntaxin_2    Syntaxin-like protein
       0.51   10.5   5.1       0.93    9.6   0.4    3.0  3  MYO10_CC      Unconventional myosin-X coiled coil domain
        0.8    9.5   7.4        5.2    6.8   0.3    2.9  2  MCPsignal     Methyl-accepting chemotaxis protein (MCP) signa
        1.2    9.4   6.7        2.1    8.5   0.4    2.8  2  Cnn_1N        Centrosomin N-terminal motif 1
        1.6    9.0   9.8         13    6.0   4.3    2.4  2  zf-C4H2       Zinc finger-containing protein
        2.3    6.6   7.9       0.29    9.5   3.3    1.7  2  S6OS1         Six6 opposite strand transcript 1 family
        3.3    7.8   9.9        6.7    6.9   0.3    3.9  4  DUF1192       Protein of unknown function (DUF1192)
        7.6    7.2   6.6         12    6.6   0.6    3.0  2  BST2          Bone marrow stromal antigen 2


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   9.4   3.4e-19   5.1e-16      11     211 ..      20     216 ..      12     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.4e-19
    PhoU_div  11 kslqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvlediamlvtlrkvef. 108
                 + lqd ++ + ++   l +l + ++++d   +   +++i +lE+e  +++r+i + ++    l   Re+ll+ +  +Dei+ ++  ia+ ++ +k +  
  AJA92792.1  20 AVLQDEINRILNAGRSLSQLPELIVKKDKAGIKDAMEQITSLEEEVESLRRKITRDVADVGGLILNRENLLNTAYTMDEIAGYITGIAFKLSNIKASTl 118
                 5577777788888888888889999999999***************************9777778***************************9999872 PP

    PhoU_div 109 .peelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdraedvad 206
                    +l+ ++ +l++ +v+ i++l+e+i++l+ + +++++   +++  ++lE eiD+ +rk+    ++  + s + e+ll+++ ie +e+++d+ ++v+d
  AJA92792.1 119 kSSKLDGDLTELIELVVDEIYKLNEIIRSLNSDSAKSIE---LAQDTQKLEREIDIKYRKM---VLKALEISTTSEMLLMKDTIEGIEEMADKCQEVSD 211
                 245799*************************98888888...9************866655...555566899************************** PP

    PhoU_div 207 risii 211
                  + ++
  AJA92792.1 212 SFILL 216
                 98765 PP

>> WD40_alt  Alternative WD40 repeat motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   2.5e+03      19      29 ..      18      28 ..      11      32 .. 0.77
   2 !   14.3   0.1   1.9e-05     0.028      19      39 ..      57      78 ..      45      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
    WD40_alt 19 rvseLeeEVrt 29
                 v+ L++E++ 
  AJA92792.1 18 AVAVLQDEINR 28
                57889999875 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.9e-05
    WD40_alt 19 rvseLeeEVrtLr.KInkdLfd 39
                +++ LeeEV++Lr KI +d  d
  AJA92792.1 57 QITSLEEEVESLRrKITRDVAD 78
                799*********559***9755 PP

>> TSA  Type specific antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     4e-05     0.059     341     383 ..      24      65 ..       7     116 .. 0.82
   2 ?   -2.2   0.0      0.91   1.4e+03     344     371 ..     145     173 ..     142     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
         TSA 341 aaavrllngsdslkdlykdlvklrrhagikkamekladqeeed 383
                     r+ln   sl +l   +vk + +agik ame++++ eee 
  AJA92792.1  24 DEINRILNAGRSLSQLPELIVK-KDKAGIKDAMEQITSLEEEV 65 
                 34579***********987777.678**********9999875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.91
         TSA 344 vrllngs.dslkdlykdlvklrrhagikk 371
                 +r ln +  +  +l +d +kl+r   ik 
  AJA92792.1 145 IRSLNSDsAKSIELAQDTQKLEREIDIKY 173
                 67787641345689999999999999984 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.7   2.5e+03      13      28 ..      16      31 ..      12      42 .. 0.68
   2 ?   11.0   0.1   0.00027      0.41      20      48 ..      48      76 ..      43      79 .. 0.87
   3 ?    0.1   0.3      0.71   1.1e+03      25      37 ..     157     169 ..     128     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.7
       TSC22 13 rEeVevLkekIkeLee 28
                r  V vL+++I   ++
  AJA92792.1 16 RKAVAVLQDEINRILN 31
                6778888888875554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00027
       TSC22 20 kekIkeLeernseleeENslLkalaspeq 48
                k  Ik+ +e+++ leeE + L++ ++ ++
  AJA92792.1 48 KAGIKDAMEQITSLEEEVESLRRKITRDV 76
                6679999***************9999875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.71
       TSC22  25 eLeernseleeEN 37 
                 eL ++ ++le+E 
  AJA92792.1 157 ELAQDTQKLEREI 169
                 7777778888775 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4    0.0015       2.3       3      63 ..      24      86 ..      22     133 .. 0.72
   2 ?    5.6   0.8     0.014        20       3      36 ..     136     170 ..     134     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
  Syntaxin_2  3 snlqkinsnvstleklvkqLgtkkd..teelreklhelieeinelikktnellkklsqldnss 63
                +++ +i +  ++l +l + + +k     ++  e++ +l ee+  l +k+++++ ++  l+ + 
  AJA92792.1 24 DEINRILNAGRSLSQLPELIVKKDKagIKDAMEQITSLEEEVESLRRKITRDVADVGGLILNR 86
                678888888888888888888874456788889999999999999999999999987776554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.014
  Syntaxin_2   3 snlqkinsnvstleklvkq.Lgtkkdteelreklh 36 
                 ++++k+n+ +++l++   + ++ ++dt++l ++++
  AJA92792.1 136 DEIYKLNEIIRSLNSDSAKsIELAQDTQKLEREID 170
                 68999********9876666**********97774 PP

>> MYO10_CC  Unconventional myosin-X coiled coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00062      0.93       6      25 ..      55      74 ..      52      90 .. 0.85
   2 ?   -1.4   0.0       1.7   2.5e+03      36      50 ..     128     142 ..     120     146 .. 0.78
   3 ?    1.6   0.1       0.2     3e+02      11      17 ..     164     170 ..     162     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
    MYO10_CC  6 mEEILRLErEIerLqrqked 25
                mE I  LE E+e L+r+   
  AJA92792.1 55 MEQITSLEEEVESLRRKITR 74
                9**************98655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
    MYO10_CC  36 qelqrlRdeelkrLe 50 
                 +el++l  +e+++L 
  AJA92792.1 128 TELIELVVDEIYKLN 142
                 677778888888886 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.2
    MYO10_CC  11 RLErEIe 17 
                 +LErEI+
  AJA92792.1 164 KLEREID 170
                 79****8 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0035       5.2      88     155 ..      55     121 ..      15     127 .. 0.73
   2 ?    5.1   1.8     0.012        18      90     154 ..     126     190 ..     118     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0035
                 HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                  ++i++l +e++    + ++ + ++   + +  e   +t+ ++ ei+  ++ +a  +++i+a++ + s
  AJA92792.1  55 MEQITSLEEEVESLRRKITRDVADVGGLILN-RENLLNTAYTMDEIAGYITGIAFKLSNIKASTLKSS 121
                 4444444444444444444444444444443.3445578899999**999999999999999987666 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                 HHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MCPsignal  90 eiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                 ++++li+ ++ ei +  e++ + ++  +++ el+++t++  +ei  +  ++     ei+++se +
  AJA92792.1 126 DLTELIELVVDEIYKLNEIIRSLNSDSAKSIELAQDTQKLEREIDIKYRKMVLKALEISTTSEML 190
                 66778888888888888888888888888888888888888888877777777777777777643 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0014       2.1      32      60 ..      45      73 ..      19      77 .. 0.82
   2 ?    3.6   0.6     0.051        77      43      65 ..     153     175 ..     131     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
      Cnn_1N 32 klseeqkeellkenielkveveslqkelk 60
                k+++  +++++++ + l++evesl++++ 
  AJA92792.1 45 KKDKAGIKDAMEQITSLEEEVESLRRKIT 73
                4555899*******************986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
      Cnn_1N  43 kenielkveveslqkelkekkkl 65 
                 ++ iel ++ ++l++e++ k ++
  AJA92792.1 153 AKSIELAQDTQKLEREIDIKYRK 175
                 5579************9855443 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3      0.01        15      91     136 ..      21      67 ..       9     100 .. 0.58
   2 ?    6.0   4.3    0.0087        13      52     126 ..     129     198 ..     112     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
     zf-C4H2  91 klkeevnelrse.lglekledleeeeeellkeeifekqklkaaavel 136
                  l++e+n++++    l++l++l  +++++  ++ +e+ ++ +++ve+
  AJA92792.1  21 VLQDEINRILNAgRSLSQLPELIVKKDKAGIKDAMEQITSLEEEVES 67 
                 55666666666656666666665555555555554544433333332 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0087
     zf-C4H2  52 eeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglekledleeeeeellkeeifek 126
                 e + l+ + i +l ++i++ +++  ks+e a    ++ +kl +e++   +++ l+ le  +++e  l+k +i e 
  AJA92792.1 129 ELIELVVDEIYKLNEIIRSLNSDSAKSIELA----QDTQKLEREIDIKYRKMVLKALEISTTSEMLLMKDTI-EG 198
                 567788889999***********99999877....5789******************998888887777766.44 PP

>> S6OS1  Six6 opposite strand transcript 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.57   8.6e+02      10      30 ..      11      31 ..       9      56 .. 0.84
   2 ?    9.5   3.3    0.0002      0.29     156     233 ..     135     212 ..     127     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.57
       S6OS1 10 kikEkkkeilklkeninksde 30
                +++ k+k ++ l+++in++ +
  AJA92792.1 11 EVQAKRKAVAVLQDEINRILN 31
                578899999*******98755 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
       S6OS1 156 vnlRlktediLklAetltkkslelkkeadelEikin.ylkkqiarllesknlsevleeknkelekrkelkerifeedeh 233
                 v+  +k ++i++  ++ + ks+el ++++ lE++i+  ++k + + le  ++se+l  k+ ++e   e+ ++  e ++ 
  AJA92792.1 135 VDEIYKLNEIIRSLNSDSAKSIELAQDTQKLEREIDiKYRKMVLKALEISTTSEMLLMKD-TIEGIEEMADKCQEVSDS 212
                 55568999**********************99998734677899************9998.899999998888777766 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.063        95      28      40 ..      18      30 ..      10      35 .. 0.84
   2 ?    6.9   0.3    0.0045       6.7      22      47 ..      51      76 ..      47      79 .. 0.83
   3 ?    1.7   0.2      0.18   2.7e+02      24      45 ..     126     147 ..     125     156 .. 0.85
   4 ?   -1.9   0.0       2.4   3.6e+03      24      36 ..     157     169 ..     152     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.063
     DUF1192 28 rIalLeaEIaRle 40
                 +a L++EI R+ 
  AJA92792.1 18 AVAVLQDEINRIL 30
                5899*******85 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
     DUF1192 22 veELeerIalLeaEIaRleaaiakkk 47
                +++  e I+ Le+E++ l+++i++  
  AJA92792.1 51 IKDAMEQITSLEEEVESLRRKITRDV 76
                5566789***************9865 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.18
     DUF1192  24 ELeerIalLeaEIaRleaaiak 45 
                 +L+e I+l  +EI +l + i++
  AJA92792.1 126 DLTELIELVVDEIYKLNEIIRS 147
                 89999*********99988865 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.4
     DUF1192  24 ELeerIalLeaEI 36 
                 EL +  ++Le EI
  AJA92792.1 157 ELAQDTQKLEREI 169
                 7777778899998 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.008        12      55      87 ..      45      77 ..      10      80 .. 0.86
   2 ?    2.7   0.4      0.13     2e+02      52      78 ..     146     172 ..     138     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.008
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2 55 ekekaqsqkqqakvqelqgeikkLnqkLqdaea 87
                +k+ka  +++ +++  l++e+++L  k+    a
  AJA92792.1 45 KKDKAGIKDAMEQITSLEEEVESLRRKITRDVA 77
                7889999999999***********999987665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.13
                 HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BST2  52 asLekekaqsqkqqakvqelqgeikkL 78 
                  sL+ + a+s +  +  q+l++ei   
  AJA92792.1 146 RSLNSDSAKSIELAQDTQKLEREIDIK 172
                 688889999999999999999999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1174  (0.0654805); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1253.60
//
Query:       AJA92793.1  [L=47]
Description: hypothetical protein T478_1014 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.0   0.3      0.014   15.0   0.3    1.1  1  DUF3098   Protein of unknown function (DUF3098)


Domain annotation for each model (and alignments):
>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3     8e-07     0.014       6      28 ..      10      32 ..       6      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-07
     DUF3098  6 nyillliglaviilGfiLmsGgg 28
                 ++++++gl+ ii+G +L+ G+ 
  AJA92793.1 10 GFMFVVVGLVTIIVGSFLLRGNM 32
                699****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 343.20
//
Query:       AJA92794.1  [L=76]
Description: RNA polymerase Rpb3/Rpb11 dimerization domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-11   42.6   0.1    4.1e-11   42.5   0.1    1.0  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
       0.15   11.6   0.0       0.16   11.5   0.0    1.1  1  DUF3201      Protein of unknown function (DUF3201)


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.1   4.6e-15   4.1e-11       5      73 ..       2      68 ..       1      70 [. 0.92

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 4.6e-15
                 EEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
  RNA_pol_L_2  5 eingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdele 73
                  i++ D   + +++h+llk+++++fag  i+HPl++++ +r++ k   +p++ +  a+++ ++++ +l+
   AJA92794.1  2 AIKDADIGALYIIQHELLKDKNTDFAGVIIKHPLTNEIWMRVNSK--SKPITQISAAADTAISEVANLQ 68
                 58899999999********************************98..59**********9999998886 PP

>> DUF3201  Protein of unknown function (DUF3201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.8e-05      0.16     106     140 ..      24      58 ..       9      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.8e-05
                 -EEEE..TTS---HHHHHHHHTSS-SEEEEEEE-T CS
     DUF3201 106 edvynclresplseevidrivesdekviqfevdld 140
                  d+  ++ ++pl++e++ r+   ++ + q+ +  d
  AJA92794.1  24 TDFAGVIIKHPLTNEIWMRVNSKSKPITQISAAAD 58 
                 6888999*************999999999887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 502.77
//
Query:       AJA92795.1  [L=80]
Description: transcription factor Pcc1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      5e-05   23.3   0.0    6.1e-05   23.1   0.0    1.1  1  Pcc1        Transcription factor Pcc1
  ------ inclusion threshold ------
      0.039   13.9   0.1      0.039   13.9   0.1    1.1  1  IQ_SEC7_PH  PH domain


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   6.8e-09   6.1e-05       3      73 ..       8      79 ..       6      80 .] 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.8e-09
                EEEEE-SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEES.SHHHHHHHHHHHHHHHHHHHHHH CS
        Pcc1  3 tisvpfpterlAsialrtLqvDkelsplavkrslslegnvLqveykAt.tnrmLRvavngfleslglvletm 73
                +i +   ++++A+++ ++L++D+   p+  + ++  ++n L+  ++ + ++r+L  +v+ +le+++l +e++
  AJA92795.1  8 EIAINNISREKAKVIEKALEPDNVNFPKGLSLTINEKKNQLVFCFSNEgDLRKLISTVDEVLEHVNLSMEVI 79
                6777778999************8888877999*************99549********************98 PP

>> IQ_SEC7_PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.4e-06     0.039      76     124 ..      29      73 ..       7      80 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-06
  IQ_SEC7_PH  76 eneyypygielvsavpgaeskvlitfnakneedrkkfvedlkesilEve 124
                 +n ++p g++l+     +e+k +++f+ +ne d +k+++ + e +  v+
  AJA92795.1  29 DNVNFPKGLSLTI----NEKKNQLVFCFSNEGDLRKLISTVDEVLEHVN 73 
                 5778999999965....589**********************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 554.81
//
Query:       AJA92796.1  [L=203]
Description: hypothetical protein T478_0390 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1463.94
//
Query:       AJA92797.1  [L=594]
Description: putative metal-binding domain in RNase L inhibitor, RLI [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-39  134.2   1.0    2.5e-19   70.1   0.2    2.5  2  ABC_tran     ABC transporter
    7.3e-11   41.9   1.4    0.00025   20.5   0.1    2.8  2  SMC_N        RecF/RecN/SMC N terminal domain
    1.1e-10   41.2   2.8    1.1e-10   41.2   2.8    1.8  1  RLI          Possible Fer4-like domain in RNase L inhibitor, 
    3.2e-09   36.2  12.0    8.2e-09   34.9   6.2    2.6  2  Fer4         4Fe-4S binding domain
    1.1e-08   34.8  13.7    1.7e-07   31.0   5.3    2.4  2  Fer4_6       4Fe-4S binding domain
    2.4e-06   27.3   2.2    2.4e-06   27.3   2.2    2.4  2  Fer4_2       4Fe-4S binding domain
    5.5e-06   26.4  12.6    9.3e-06   25.7  12.6    1.4  1  Fer4_21      4Fe-4S dicluster domain
    5.7e-06   26.3   4.3       0.78    9.5   0.4    4.4  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.7e-05   24.8  11.9    3.4e-05   23.9   1.1    2.4  2  Fer4_10      4Fe-4S dicluster domain
    2.7e-05   24.7  10.0    5.5e-05   23.7  10.0    1.6  1  Fer4_7       4Fe-4S dicluster domain
    0.00016   21.5   1.4       0.17   11.6   0.1    2.5  2  AAA_15       AAA ATPase domain
    0.00081   19.1   0.1       0.14   11.9   0.0    3.3  3  AAA_29       P-loop containing region of AAA domain
     0.0023   17.1   0.5       0.55    9.4   0.1    2.5  2  NB-ARC       NB-ARC domain
     0.0025   18.7   9.6     0.0055   17.6   1.0    2.7  2  Fer4_16      4Fe-4S double cluster binding domain
     0.0041   17.0   0.4      0.087   12.7   0.0    2.6  2  RsgA_GTPase  RsgA GTPase
     0.0074   16.0   0.0      0.012   15.3   0.0    1.3  1  His_Phos_1   Histidine phosphatase superfamily (branch 1)
     0.0081   16.6   0.2        1.1    9.6   0.1    2.8  2  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.019   15.1  10.4      0.057   13.6  10.6    1.7  1  Fer4_9       4Fe-4S dicluster domain
      0.019   15.0   0.0       0.68   10.0   0.0    2.6  2  MMR_HSR1     50S ribosome-binding GTPase
      0.025   14.8   0.4         14    6.0   0.0    2.8  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.029   14.9   1.8      0.029   14.9   1.8    2.3  2  Fer4_4       4Fe-4S binding domain
       0.03   13.6   0.1      0.081   12.2   0.1    1.7  1  RE_XcyI      XcyI restriction endonuclease
      0.031   15.2   4.9      0.031   15.2   4.9    2.3  2  Fer4_3       4Fe-4S binding domain
      0.033   13.0   0.6       0.78    8.5   0.1    2.2  2  DLIC         Dynein light intermediate chain (DLIC)
      0.085   12.8   0.1       0.59   10.0   0.0    2.1  2  Rad17        Rad17 P-loop domain
       0.33   11.4   7.0        3.4    8.1   1.3    3.2  2  AAA_23       AAA domain
        1.3    9.6   8.4        0.2   12.3   1.0    2.4  2  Fer4_17      4Fe-4S dicluster domain
        2.2    8.8   7.9        0.4   11.2   1.1    2.0  2  Fer4_8       4Fe-4S dicluster domain
        7.3    7.4  11.5       0.57   11.0   4.0    2.6  1  Fer4_15      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0   1.1e-19     7e-17       9     136 ..      98     241 ..      96     242 .. 0.79
   2 !   70.1   0.2   4.1e-22   2.5e-19       7     137 .]     364     486 ..     362     486 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.1e-19
                 ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH............HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxx RF
    ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeigvlpqepqlfpeltvren............esd 82 
                 k+ge+v+++G+nG GKSt++++l+g lkp+ G+             ++g++lk   ++++  + + ++ pq+ +   +                  +++
  AJA92797.1  98 KKGEVVGLLGRNGMGKSTVVNILSGILKPNLGNYeqppewdeilkYYKGTELKAhfEKIKNGEIKASIKPQQVHTIAD-----AfdgtgkelldkfDQR 191
                 79***************************9999988888888887677888877555555555555555665333332.....2333466789844444 PP

                 TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                     +++++lgl++  ++++    ++LSgG+ qr+++a a  ++++++++DEp+
  AJA92797.1 192 GTSRELVKQLGLENSLEQNL----KELSGGELQRLSVATAASRESDFYFFDEPS 241
                 44999999***999999999....*****************************7 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 4.1e-22
                 EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......HHHTCHHHHHHHSTTGGTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxx RF
    ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvren......esdeeiekalsklglkelk 98 
                 ++++ge+++i+G n  GK+t++k++ag +kpt G++  d + ++++        + ++l+ +  +    +v e+      e ++e e++l+ l+lk+l 
  AJA92797.1 364 TVRKGELLGIMGANALGKTTMMKMIAGVEKPTDGSV--DkKIKISY--------KPQYLSNDIDVEVI-SVLEKangstiEGSAEEEQILDPLKLKKLY 451
                 789*********************************..21222222........22222222111111.1222244555688999999*********** PP

                 CBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  99 dtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                 ++ v    ++LSgG+ q+va+a +ll+k +l+ lDEp+a
  AJA92797.1 452 NKSV----KNLSGGELQKVAIASCLLQKVDLYALDEPSA 486
                 ****....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   4.1e-07   0.00025       9     202 ..      85     276 ..      78     291 .. 0.71
   2 !   19.3   0.1     1e-06   0.00062      48     206 ..     371     525 ..     356     537 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.1e-07
                 SETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N   9 nFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkg 107
                 ++ s++  +  +p + ++  ++G+NG GKs +++ ++ +L  +  +  +  + ++++++   k    ka+ e + +n + k++i+ ++v +   ++ + 
  AJA92797.1  85 GMNSFRLYKLPTPKKGEVVGLLGRNGMGKSTVVNILSGILKPNLGNYEQPPEWDEILKY--YKGTELKAHFEKI-KNGEIKASIKPQQVHTIADAFDGT 180
                 45555555688888899999****************99999888877778889999988..4444455665553.666666778888876666666554 PP

                 EEEE.EETTEEE-HHHHHHHH...HCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHH CS
                 xxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
       SMC_N 108 esey.kingkevtkkevsell...esagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreem 201
                   e     +++ t++e+ ++l   +s + + ++LSgGe +     L +A+ + + + +y++De  +  D  +++ va++++   ++   ++v+ ++ ++
  AJA92797.1 181 GKELlDKFDQRGTSRELVKQLgleNSLEQNLKELSGGELQ----RLSVATAASRESDFYFFDEPSSYNDVFQRTGVARVIHGLAEEgKSVMVVEHDLTL 275
                 433213334566666666666222344556779*****87....4556788999***************************877664677777776665 PP

                 C CS
                 x RF
       SMC_N 202 l 202
                 l
  AJA92797.1 276 L 276
                 5 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1e-06
                 CTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHH CS
                 xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
       SMC_N  48 LGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske...lLSgGek 142
                 LG   a++l ++++ ++i   +k  + +   +++i ++ +  +     +++ +++  + ++ +  +i+g+ ++++++ + l+ ++++ +   +LSgGe 
  AJA92797.1 371 LGIMGANALGKTTMMKMIAGvEKPTDGSVDKKIKISYKPQYLS-----NDIDVEVISVLEKANGSTIEGS-AEEEQILDPLKLKKLYNKsvkNLSGGEL 463
                 5555566777777777777632223333333334433332222.....3333333333333333456664.4555666666666665433339*****9 PP

                 HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-S CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
       SMC_N 143 tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekad 206
                 + va+a        ++  ly lDe  a LD + + +va++l++   +     i+i ++ +++  ++
  AJA92797.1 464 QKVAIASC----LLQKVDLYALDEPSAFLDVEDRIAVAKFLQKFVRSfgKSAIIIDHDLQLMDLVS 525
                 99988766....467778***********************9866553356777777777776664 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   2.8   1.7e-13   1.1e-10       2      33 ..       4      32 ..       3      34 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.7e-13
                -EEEES---------TTHHHHHTTSEEEESS- CS
         RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                r+A+ d++ C+PKKC   +c+++cpv  +++g
  AJA92797.1  4 RVAVLDKELCQPKKCGL-ECIKYCPV--NKSG 32
                9****************.********..**98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3      0.07        43      13      21 ..      21      29 ..      20      29 .. 0.91
   2 !   34.9   6.2   1.3e-11   8.2e-09       2      24 .]      46      68 ..      45      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.07
                HHHHHSTTT CS
        Fer4 13 aCvevCPvg 21
                +C++ CPv+
  AJA92797.1 21 ECIKYCPVN 29
                6******98 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.3e-11
                EEETTTSSS-THHHHHSTTTEEE CS
        Fer4  2 videekCigCGaCvevCPvgAIt 24
                +ide+ C gCG+Cv+vCP++AIt
  AJA92797.1 46 TIDEDICNGCGICVKVCPFDAIT 68
                79********************7 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   1.3    0.0031       1.9       5      22 ..       9      29 ..       5      33 .. 0.84
   2 !   31.0   5.3   2.8e-10   1.7e-07       1      24 []      44      67 ..      44      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0031
      Fer4_6  5 dpdkCi..gCgd.CvrvCPeg 22
                d+++C    Cg  C++ CP +
  AJA92797.1  9 DKELCQpkKCGLeCIKYCPVN 29
                99***9888*999******74 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.8e-10
      Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                +++id+d C+gCg Cv+vCP++ai
  AJA92797.1 44 KATIDEDICNGCGICVKVCPFDAI 67
                689*******************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.3      0.28   1.7e+02       3      21 ..       6      27 ..       4      28 .. 0.73
   2 !   27.3   2.2   3.8e-09   2.4e-06       3      21 ..      45      63 ..      43      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
      Fer4_2  3 vvvdtdrC.i.gCg.aCvsaCP 21
                +v d + C    Cg  C++ CP
  AJA92797.1  6 AVLDKELCqPkKCGlECIKYCP 27
                5677777743249999****** PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.8e-09
      Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                + +d+d+C+gCg+Cv++CP
  AJA92797.1 45 ATIDEDICNGCGICVKVCP 63
                679**************** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7  12.6   1.5e-08   9.3e-06       1      58 [.       6      68 ..       6      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.5e-08
     Fer4_21  1 AridedkCi..gCg.kCliaCe..dtshqaieidaktvl.kvvedeCvGCnlCssvCPvedcie 58
                A++d++ C   +Cg +C++ C+  +++ ++i ++++t+  ++ ed C GC +C++vCP  d+i+
  AJA92797.1  6 AVLDKELCQpkKCGlECIKYCPvnKSGADCIVLNEETKKaTIDEDICNGCGICVKVCPF-DAIT 68
                5677777743379845*****7335799***998776551667999************7.9997 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.4    0.0013      0.78       2      24 ..     103     125 ..     102     157 .. 0.75
   2 ?    5.2   0.1     0.025        15     217     268 ..     169     242 ..     129     243 .. 0.68
   3 ?    6.0   0.0     0.014       8.9       3      83 ..     372     441 ..     370     457 .. 0.70
   4 ?    4.0   0.0     0.061        38     236     280 ..     457     505 ..     454     521 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
      AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                  +l G+Ng GKS++  +l+++  
  AJA92797.1 103 VGLLGRNGMGKSTVVNILSGILK 125
                 689***************99853 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
      AAA_21 217 rer.........................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                 +                            v +l  ++  e ++ elS G ++ l ++ta  r     +++++DEp +
  AJA92797.1 169 QVHtiadafdgtgkelldkfdqrgtsreLVKQLGLENSLEQNLKELSGGELQRLSVATAASRES---DFYFFDEPSS 242
                 4444444444444444444455555555777777788888899999******999999999988...9******965 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.014
      AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersqv 83 
                 ++ G+N+ GK++ ++ + ++            ++++g+  +ki  ++ + + + ++  e++ +l++ +  + +   e++q+
  AJA92797.1 372 GIMGANALGKTTMMKMIAGV-----------EKPTDGSVDKKIKISYKPQYLSNDIDVEVISVLEKANGSTIEGSAEEEQI 441
                 688**************887...........46666667777777777777777777777766666666666666666666 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.061
      AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHP.......kllrrlle 280
                 +lS G ++    ++++l +    +l+++DEp ++L+        k+l ++++
  AJA92797.1 457 NLSGGELQK-VAIASCLLQKV--DLYALDEPSAFLDVedriavaKFLQKFVR 505
                 578888888.45555555444..9***********98655555544444444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.7     0.026        16       3      23 ..       7      30 ..       5      45 .. 0.74
   2 !   23.9   1.1   5.5e-08   3.4e-05       2      27 ..      45      71 ..      44      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
     Fer4_10  3 vidddtC..irCg.kCvkaCPadl 23
                v+d++ C   +Cg +C k CP++ 
  AJA92797.1  7 VLDKELCqpKKCGlECIKYCPVNK 30
                78999996669**9********33 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 5.5e-08
     Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvg 27
                + id+d C +Cg Cvk+CP+d+ t v+
  AJA92797.1 45 ATIDEDICNGCGICVKVCPFDAiTIVN 71
                689*****************8852222 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7  10.0   8.8e-08   5.5e-05       4      52 .]      17      66 ..       8      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.8e-08
      Fer4_7  4 gCg.aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                +Cg  C ++Cpv+    d    +++t+k++id++ C gCg Cv+vCP++a
  AJA92797.1 17 KCGlECIKYCPVNKSGADCIVLNEETKKATIDEDICNGCGICVKVCPFDA 66
                68889******999988887777889*********************997 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00027      0.17      25      83 ..     102     177 ..      85     244 .. 0.71
   2 !    8.5   0.2    0.0024       1.5      13     124 ..     352     450 ..     351     484 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
      AAA_15  25 ltvliGkNnsGKSsilealdlFlnnk.ekkn..................kkvikiekedleifeniseskdikIdvef 83 
                 +  l G+N+ GKS+++++l  +l+ +    n                   k+++++ ++ ei+ +i++ +   I+  f
  AJA92797.1 102 VVGLLGRNGMGKSTVVNILSGILKPNlG--NyeqppewdeilkyykgteLKAHFEKIKNGEIKASIKPQQVHTIADAF 177
                 56688***************99998742..134678888888888888844556666666666668888777777777 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
      AAA_15  13 slkdveidlsee......ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkad 105
                 +++++++++++       l  + G+N+ GK++ ++++    + +                   + s +k+ikI ++ ++ +++++ e+++  ++++ ++
  AJA92797.1 352 KYDSFSVSIEPGtvrkgeLLGIMGANALGKTTMMKMIAGVEKPT-------------------DGSVDKKIKISYKPQYLSNDIDVEVISVLEKANGST 431
                 66777777777777777788899**************5444443...................333333333333321113333333333333333333 PP

      AAA_15 106 lllkkkesdlkktikdkkl 124
                 ++   +e+++ + +k kkl
  AJA92797.1 432 IEGSAEEEQILDPLKLKKL 450
                 3333333333333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00023      0.14      19      49 ..      96     127 ..      83     132 .. 0.81
   2 ?   -0.8   0.0       2.1   1.3e+03      20      39 ..     248     268 ..     242     269 .. 0.82
   3 ?    2.5   0.1       0.2   1.2e+02      24      39 ..     370     385 ..     359     394 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
      AAA_29  19 idlkg.atlltGpsGsGKSTllDAiqalLvpa 49 
                    kg ++ l G++G GKST++  ++ +L p+
  AJA92797.1  96 TPKKGeVVGLLGRNGMGKSTVVNILSGILKPN 127
                 5556778889***********98888888776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
      AAA_29  20 dlkg.atlltGpsGsGKSTll 39 
                 ++ g a ++ G  + GKS ++
  AJA92797.1 248 QRTGvARVIHGLAEEGKSVMV 268
                 5567778999********986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
      AAA_29  24 atlltGpsGsGKSTll 39 
                    ++G++  GK+T++
  AJA92797.1 370 LLGIMGANALGKTTMM 385
                 55599*********98 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.014       8.7      21      37 ..     101     117 ..      90     133 .. 0.83
   2 !    9.4   0.1   0.00089      0.55      22      91 ..     370     439 ..     364     475 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                 EEEEEEESTTSSHHHHH CS
      NB-ARC  21 lvvalvGmgGvGKttla 37 
                  vv+l G+ G+GK+t++
  AJA92797.1 101 EVVGLLGRNGMGKSTVV 117
                 49*************86 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00089
                 EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS CS
      NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves 91 
                 +++++G   +GKtt++k i    + ++g  d  + ++   ++ s++i  +++ +L++++  + e + +e+
  AJA92797.1 370 LLGIMGANALGKTTMMKMIAGVEKPTDGSVDKKIKISYKPQYLSNDIDVEVISVLEKANGSTIEGSAEEE 439
                 689******************99********************************999877766655543 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.9       0.1        64       3      35 ..      16      46 ..      13      51 .. 0.71
   2 !   17.6   1.0   8.9e-06    0.0055       2      20 ..      52      70 ..      51      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
     Fer4_16  3 gtCgk.CaevCPtnaikekkekeiearecisynt 35
                ++Cg  C++ CP+n   ++   +i  +e+++++t
  AJA92797.1 16 KKCGLeCIKYCPVNKSGAD---CIVLNEETKKAT 46
                579988******9987666...555555555544 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8.9e-06
     Fer4_16  2 CgtCgkCaevCPtnaikek 20
                C +Cg C++vCP +ai+  
  AJA92797.1 52 CNGCGICVKVCPFDAITIV 70
                999************9855 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00014     0.087      97     124 ..      98     125 ..      75     160 .. 0.87
   2 ?    1.2   0.1      0.49   3.1e+02      99     131 ..     368     400 ..     362     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                  CTTSEEEEECSTTSSHHHHHHHHCTT-- CS
  RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpele 124
                   k++++ l+G  G+GKSt++n l + l+
   AJA92797.1  98 KKGEVVGLLGRNGMGKSTVVNILSGILK 125
                  5678999***************988655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.49
                  TSEEEEECSTTSSHHHHHHHHCTT-----S--- CS
  RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevs 131
                  +++  ++G    GK+t+++++++ ++   g+v 
   AJA92797.1 368 GELLGIMGANALGKTTMMKMIAGVEKPTDGSVD 400
                  4667799*************9997666655555 PP

>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-05     0.012      59     157 ..     193     281 ..     190     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                 HHHHHHHCTT--EEE-GGGS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHH..HHHHHHHHHHHTTTSEEEEEE-HHHHHHHH CS
  His_Phos_1  59 TaeliaealglpveldegLrEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaR..vaaaleelaarhegetvlvVsHggvirall 155
                 T + + ++lgl+  l+++L+E++ G+++ l+ a++a++  +++  ++++p         s++dv +R  va++++ la++ ++  v+vV H  ++  +l
  AJA92797.1 193 TSRELVKQLGLENSLEQNLKELSGGELQRLSVATAASRESDFY--FFDEP--------SSYNDVFQRtgVARVIHGLAEEGKS--VMVVEHDLTLLDFL 279
                 8889999***********************8888888733322..34444........59*******5556777777777665..******99886666 PP

                 HH CS
  His_Phos_1 156 ar 157
                 ++
  AJA92797.1 280 SD 281
                 55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0017       1.1      24      52 ..     100     150 ..      89     254 .. 0.57
   2 ?    3.7   0.0      0.12        74      20     107 ..     366     475 ..     360     532 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
      AAA_16  24 pelvllsGesGvGKsslvrellralekd......................g 52 
                 +e+v l G  G+GKs++v+ l   l+ +                      +
  AJA92797.1 100 GEVVGLLGRNGMGKSTVVNILSGILKPNlgnyeqppewdeilkyykgtelK 150
                 38899*************999876666665555555555555554333332 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
      AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy.sa.laqalareellrqlldeaesaeleawrekleeala.......... 106
                 r+g  el+ + G+ + GK++++++++  +ek     + g  d+   +i+y  + l + ++ e +   ++++ ++ e +a  e++++ l+          
  AJA92797.1 366 RKG--ELLGIMGANALGKTTMMKMIA-GVEKP----TDGSVDKK-IKISYkPQyLSNDIDVEVISVLEKANGSTIEGSAEEEQILDPLKlkklynksvk 456
                 444..788899***********9999.56666....44444443.444443223444444433333334444444455555555555555555556555 PP

      AAA_16 107 ..................a 107
                                    
  AJA92797.1 457 nlsggelqkvaiascllqK 475
                 5555555444444444441 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6  10.6   9.1e-05     0.057       4      51 .]      17      67 ..      12      67 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-05
      Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                +Cg +C++ Cp +    d+     + ++a    + C gCg Cv++Cp +ai
  AJA92797.1 17 KCGlECIKYCPVNKSGADCIVLNEETKKATIdeDICNGCGICVKVCPFDAI 67
                58756999997666655554444443332224458************9987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0011      0.68       2      22 ..     103     123 ..     102     200 .. 0.86
   2 ?    2.3   0.0      0.27   1.7e+02       3      22 ..     372     391 ..     370     427 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                 EEEEESTTSSHHHHHHHHHTS CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                 v+++Gr   GKSt++n l+g 
  AJA92797.1 103 VGLLGRNGMGKSTVVNILSGI 123
                 89****************984 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                 EEEESTTSSHHHHHHHHHTS CS
    MMR_HSR1   3 aivGrpNvGKStLinaltge 22 
                 +i+G    GK+t+++ + g 
  AJA92797.1 372 GIMGANALGKTTMMKMIAGV 391
                 899************99873 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.023        14      21      49 ..     202     229 ..     186     241 .. 0.80
   2 ?    5.7   0.1     0.028        17      26      47 ..     451     472 ..     440     502 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.023
     SbcCD_C  21 gkekelsrssgtlSGGekqflaylalaaa 49 
                 g e +l+++ ++lSGGe q  +++a aa+
  AJA92797.1 202 GLENSLEQNLKELSGGELQ-RLSVATAAS 229
                 55677999**********5.556777665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.028
     SbcCD_C  26 lsrssgtlSGGekqflaylala 47 
                  ++s+++lSGGe q++a    +
  AJA92797.1 451 YNKSVKNLSGGELQKVAIASCL 472
                 67999*******9987765554 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.9      0.24   1.5e+02       2      17 .]      11      29 ..      10      30 .. 0.77
   2 ?   14.9   1.8   4.6e-05     0.029       3      16 ..      51      64 ..      47      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.24
      Fer4_4  2 erCi..gCg.sCvaaCPqg 17
                e C+   Cg  C+ +CP++
  AJA92797.1 11 ELCQpkKCGlECIKYCPVN 29
                66766689956******75 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.6e-05
      Fer4_4  3 rCigCgsCvaaCPq 16
                 C+gCg Cv +CP+
  AJA92797.1 51 ICNGCGICVKVCPF 64
                5************7 PP

>> RE_XcyI  XcyI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013     0.081      81     142 ..     142     203 ..     139     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
     RE_XcyI  81 elyrgdkglgkfkklekkGkiakasep.eiedlvvaliesaeklldslekdsiteellddltl 142
                 ++y+g +   +f+k+ + G+i+   +p +++++  a+  +++ lld +++   ++el+++l l
  AJA92797.1 142 KYYKGTELKAHFEKIKN-GEIKASIKPqQVHTIADAFDGTGKELLDKFDQRGTSRELVKQLGL 203
                 6899998889*****88.99988777637******************************9987 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   3.2      0.12        76       3      14 ..      17      29 ..      13      31 .. 0.80
   2 ?   15.2   4.9     5e-05     0.031       1      15 []      52      66 ..      52      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.12
      Fer4_3  3 gCg.aCvevCPvg 14
                 Cg  C + CPv+
  AJA92797.1 17 KCGlECIKYCPVN 29
                59966******96 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5e-05
      Fer4_3  1 CtgCgaCvevCPvgA 15
                C+gCg Cv+vCP +A
  AJA92797.1 52 CNGCGICVKVCPFDA 66
                ************998 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.082        51      21      52 ..      93     127 ..      88     131 .. 0.78
   2 ?    8.5   0.1    0.0013      0.78      30      57 ..     373     400 ..     365     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.082
        DLIC  21 klPsgks...vlvlGedgsGkttliaklqGveeek 52 
                 klP+ k+   v +lG +g Gk+t++  l G+ +++
  AJA92797.1  93 KLPTPKKgevVGLLGRNGMGKSTVVNILSGILKPN 127
                 6776553332679*****************97766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
        DLIC  30 vlGedgsGkttliaklqGveeekkGrGl 57 
                 ++G ++ Gktt++  + Gve++  G+  
  AJA92797.1 373 IMGANALGKTTMMKMIAGVEKPTDGSVD 400
                 89********************999865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00095      0.59      46      97 ..     101     154 ..      80     166 .. 0.78
   2 ?   -0.3   0.0       1.4   8.8e+02      43      66 ..     366     389 ..     358     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
       Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn..qksdfkglte 97 
                 +++ + G  G gkstvv++Ls +l ++l ++  p +  e     + +++k+ +e
  AJA92797.1 101 EVVGLLGRNGMGKSTVVNILSGILKPNLGNYEQPPEWDEILKyyKGTELKAHFE 154
                 3777889*******************9999988877666433346666666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
       Rad17  43 rkkriLLisGPsGCgkstvvkvLs 66 
                 rk ++L i G    gk+t++k+++
  AJA92797.1 366 RKGELLGIMGANALGKTTMMKMIA 389
                 4556999**************987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.3    0.0054       3.4      21      48 ..     102     129 ..      79     244 .. 0.54
   2 ?    4.6   0.4     0.064        39      20      40 ..     369     389 ..     351     475 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0054
      AAA_23  21 ltlItGpNGaGKTTildAiklaLygetp 48 
                 ++ + G NG GK+T+++ +  +L    +
  AJA92797.1 102 VVGLLGRNGMGKSTVVNILSGILKPNLG 129
                 66789************99988865433 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.064
      AAA_23  20 gltlItGpNGaGKTTildAik 40 
                  l  I G N  GKTT +  i 
  AJA92797.1 369 ELLGIMGANALGKTTMMKMIA 389
                 47789**********998875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   9.5      0.19   1.2e+02      45      57 ..      51      63 ..      14      66 .. 0.70
   2 ?   12.3   1.0   0.00032       0.2       2      17 ..      52      67 ..      51      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
     Fer4_17 45 lCieCgeCerkCP 57
                 C++Cg C+++CP
  AJA92797.1 51 ICNGCGICVKVCP 63
                4555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00032
     Fer4_17  2 CiqCgyClpeCpsyea 17
                C++Cg C+++Cp+ ++
  AJA92797.1 52 CNGCGICVKVCPFDAI 67
                9999999999997554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   8.8     0.028        17       8      63 ..      18      64 ..      13      67 .. 0.82
   2 ?   11.2   1.1   0.00065       0.4       5      17 ..      52      64 ..      48      93 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
      Fer4_8  8 Cg.aCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63
                Cg  C + Cpv ++ ++ +  +++ +++   +e+          C++cg C++vCp 
  AJA92797.1 18 CGlECIKYCPVNKSGADCIVLNEETKKA-TIDEDI---------CNGCGICVKVCPF 64
                7756999999999888888888888777.666666.........9999999999996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00065
      Fer4_8  5 CieCgaCqsaCpv 17
                C++Cg C + Cp+
  AJA92797.1 52 CNGCGICVKVCPF 64
                8888888888883 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.0   0.00092      0.57       2      19 ..      46      63 ..      45      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00092
     Fer4_15  2 vvDrdaCigcglCvaeap 19
                ++D+d C gcg Cv+++p
  AJA92797.1 46 TIDEDICNGCGICVKVCP 63
                79**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3836.93
//
Query:       AJA92798.1  [L=128]
Description: hypothetical protein T478_0646 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.16   12.1   2.1       0.42   10.8   2.1    1.7  1  Pentapeptide_4  Pentapeptide repeats (9 copies)


Domain annotation for each model (and alignments):
>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.1   2.4e-05      0.42       5      38 ..      16      49 ..      12      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.4e-05
  Pentapeptide_4  5 rcsfnncklsnvnFsearlrdcnFtecrlsnvnF 38
                    ++ ++n +++n++F +++l+d+n + + ++++n 
      AJA92798.1 16 NSNYENEDFDNFTFDAVYLKDSNSVLITFDDTNQ 49
                    6778888999999999999999998888877772 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 967.18
//
Query:       AJA92799.1  [L=170]
Description: hypothetical protein T478_0145 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1310.02
//
Query:       AJA92800.1  [L=441]
Description: signal peptide-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-69  232.0   0.3    9.4e-69  231.0   0.3    1.5  1  SRP54            SRP54-type protein, GTPase domain
    1.2e-25   89.9   2.9    1.2e-25   89.9   2.9    2.5  1  SRP_SPB          Signal peptide binding domain
    2.3e-18   66.1   3.8    3.9e-18   65.4   0.8    2.7  2  SRP54_N          SRP54-type protein, helical bundle domain
    6.3e-06   26.3   0.0    1.9e-05   24.7   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    7.7e-05   23.1   0.6    0.00028   21.3   0.1    2.2  2  AAA_17           AAA domain
     0.0001   21.4   0.2    0.00054   19.0   0.2    2.1  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0003   20.2   0.0     0.0006   19.2   0.0    1.5  1  6PF2K            6-phosphofructo-2-kinase
    0.00037   20.5   0.3     0.0019   18.2   0.3    2.1  1  AAA_31           AAA domain
    0.00037   20.4   0.5     0.0014   18.5   0.2    2.1  2  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00073   19.3   0.8       0.59    9.9   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
    0.00094   18.5   0.8       0.13   11.5   0.8    2.3  1  MipZ             ATPase MipZ
     0.0016   18.0   0.0     0.0031   17.0   0.0    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
     0.0018   18.2   0.2      0.005   16.7   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
     0.0025   17.9   0.5      0.011   15.8   0.5    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0026   17.9   0.0     0.0058   16.8   0.0    1.6  1  AAA_33           AAA domain
     0.0027   17.3   0.9     0.0069   16.0   0.9    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.003   18.1   0.1      0.016   15.7   0.1    2.4  1  AAA_18           AAA domain
     0.0033   16.7   0.0     0.0057   15.9   0.0    1.4  1  Zeta_toxin       Zeta toxin
     0.0072   15.6   0.0      0.015   14.6   0.0    1.4  1  VirC1            VirC1 protein
  ------ inclusion threshold ------
       0.01   15.8   0.8      0.032   14.1   0.7    2.0  1  NTPase_1         NTPase
      0.013   14.7   0.6       0.42    9.7   0.1    2.3  2  DUF4317          Domain of unknown function (DUF4317)
      0.013   14.7   0.0      0.023   13.9   0.0    1.5  1  G-alpha          G-protein alpha subunit
      0.014   15.4   0.2      0.078   13.0   0.1    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
      0.015   14.8   0.8      0.039   13.4   0.1    2.1  2  KTI12            Chromatin associated protein KTI12
      0.015   15.0   0.6       0.05   13.3   0.2    2.1  1  Thymidylate_kin  Thymidylate kinase
      0.016   15.7   1.2       0.16   12.4   0.1    3.0  2  AAA              ATPase family associated with various cellul
      0.016   14.9   0.1      0.045   13.5   0.0    1.8  2  AAA_30           AAA domain
      0.018   14.5   0.2       0.12   11.9   0.1    2.2  2  Arf              ADP-ribosylation factor family
      0.028   14.2   0.2        2.5    7.9   0.2    2.7  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.032   13.7   0.6        2.6    7.4   0.2    2.5  2  SRPRB            Signal recognition particle receptor beta su
      0.034   14.5   0.1      0.073   13.5   0.1    1.7  1  AAA_16           AAA ATPase domain
      0.052   13.1   0.1        0.1   12.1   0.1    1.4  1  AAA_7            P-loop containing dynein motor region
      0.053   13.8   0.1       0.28   11.4   0.0    2.2  2  AAA_22           AAA domain
      0.057   13.1   0.0       0.14   11.9   0.0    1.7  1  AAA_24           AAA domain
      0.067   14.2   0.0       0.29   12.1   0.1    2.1  1  LytR_C           LytR cell envelope-related transcriptional a
      0.076   13.5   0.9       0.29   11.6   0.1    2.1  2  ABC_tran         ABC transporter
       0.12   12.2   0.6        2.1    8.1   0.6    2.6  1  AAA_26           AAA domain
       0.13   12.0   0.0       0.31   10.8   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.19   11.8   0.4       0.53   10.4   0.4    1.8  1  CaM_bdg_C0       Calmodulin-binding domain C0 of NMDA recepto
       0.34   10.1   5.7        2.2    7.4   0.4    3.2  3  ArsA_ATPase      Anion-transporting ATPase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.0   0.3   2.1e-71   9.4e-69       3     196 .]     101     294 ..      99     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.0 bits;  conditional E-value: 2.1e-71
                 EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHH CS
       SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndkel 101
                  +l++G+qG+GKTt  +KLa+ l+k+g++v  + aDt+R++A+ QL+t+ ek +v+v+++++++d+a+++k++++++++++idvvl+DTaGr++++k+l
  AJA92800.1 101 KVLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGALVQLRTNCEKSNVEVYGEENNKDSAEIVKNGLKHFENSNIDVVLIDTAGRHKEEKDL 199
                 689************************************************************************************************ PP

                 HHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
       SRP54 102 meelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                 ++e+++i+kv +pd  llv+d+t+gq+ ++qa+aF++ v ++g+++tklD++akgG+al+++a+++  ++++g+Ge+i+dle+f+p+r+v rllg
  AJA92800.1 200 LDEMTEISKVSNPDLALLVIDGTIGQQCFSQAEAFNKIVPVGGIVITKLDSSAKGGGALAASAATGAQVMYVGTGERIDDLEQFSPTRFVGRLLG 294
                 *********************************************************************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   2.9   2.8e-28   1.2e-25       2      99 .]     325     423 ..     324     423 .. 0.94

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 2.8e-28
                 SCTHHHHHHHHHHHCCCCCCHHHHCCC.......H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
     SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae..akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRiArGsGtsvqevnellkqfeqmk 96 
                 ++++d+  ql++++k+G+l++l++ +Pg+s +  +  +  e  e++++++ +ii+SM  +E+++p+ ll++sR++RiArGsG   +ev+el+k++++ k
  AJA92800.1 325 MNMEDFFYQLEEVTKVGSLQSLMETMPGLSGMvkE--DqlEVMEQRMDKWRYIIQSMNTKEKADPD-LLNSSRIKRIARGSGWPEHEVKELIKNYKNSK 420
                 79**************************9999643..3358889**********************.899***************************** PP

                 HHT CS
     SRP_SPB  97 kmm 99 
                 +mm
  AJA92800.1 421 SMM 423
                 **8 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.8   8.8e-21   3.9e-18       1      75 []       5      82 ..       5      82 .. 0.96
   2 ?   -0.1   0.1       2.6   1.1e+03      44      72 ..     409     436 ..     408     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 8.8e-21
                HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
     SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                L+++l++a+kk+ ++s idee+++e+ k+++++Ll++DV+vk+v ++++n++++ ++e     l++k++++ki++deL
  AJA92800.1  5 LKDGLRTAIKKIVSSSGIDEELIKELAKDVQRSLLQSDVNVKLVLEITKNLQERCINETPppgLSRKDHIVKILYDEL 82
                6899*************************************************9999555*****************8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.6
                 HHHHHHHHHHHHHCTTSS-HHHHHHHHHH CS
     SRP54_N  44 vkklienvkkkavgekklkpkqqvkkivk 72 
                 vk+li+n k+++    k ++++q++ +++
  AJA92800.1 409 VKELIKNYKNSKSM-MKASKGRQMQGMLR 436
                 8999****886655.77899999988776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   4.3e-08   1.9e-05       9      86 ..     109     250 ..     106     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.3e-08
                 TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH............HTTEB-HHHH......................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxx......................................... RF
        CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai............leglendiep......................................... 54 
                 G+GKTt++ +La+ l ++g+rV ++ aD+ ++ + +            ++g en+++                                          
  AJA92800.1 109 GSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGALVqlrtnceksnveVYGEENNKDSaeivknglkhfensnidvvlidtagrhkeekdlldemteis 207
                 99***************************9999887666555544444444444444477777777777777777777777777777777777777777 PP

                 .......................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS CS
                 .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 .......................dlkrllellealgkkkalllkiagvvlnrvdg 86 
                                                 ea+ k     + + g+v+++ d+
  AJA92800.1 208 kvsnpdlallvidgtigqqcfsqA--------EAFNKI----VPVGGIVITKLDS 250
                 777777766666543222111110........222222....4556666666655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       8.3   3.7e+03      55      68 ..      24      37 ..       7      63 .. 0.55
   2 !   21.3   0.1   6.3e-07   0.00028       1     108 [.     105     218 ..     105     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.3
                HHHHHHHHHHHHHH CS
      AAA_17 55 kelqkeaaekiaee 68
                +el ke+a+++++ 
  AJA92800.1 24 EELIKELAKDVQRS 37
                33333333333333 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.3e-07
                 EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC.....TSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE-SEEEETTEEEESS CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr.....klpleekkelqkeaaekiaeea..kkkgvlvdghprikeqagfldgl 92 
                 lG+ GsGK+t+++kl++ +  + +  G +  ++ ++g l++ r + +        +e +k+  +++++ +++ +  + + vl+d+  r ke++++ld++
  AJA92800.1 105 LGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGALVQLRTNCEksnveVYGEENNKDSAEIVKNGLKHFEnsNIDVVLIDTAGRHKEEKDLLDEM 203
                 79***************9988888888888888888877777766662222123555556666666666655432144679*****************9 PP

                 HHHHHHHH..SEEEEE CS
      AAA_17  93 pkevleelkpdaiill 108
                 ++ + +  +pd+ +l+
  AJA92800.1 204 TE-ISKVSNPDLALLV 218
                 95.7888889887765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.2e-06   0.00054      24      74 ..      94     141 ..      83     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                 GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------- CS
        MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGG 74 
                  k+G+ ++v + G+ G+Gk t+ ++l+  l+++G+rv+ +  D    +  G
  AJA92800.1  94 FKSGKINKVLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADT---YRPG 141
                 579999********************************998884...4445 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.3e-06    0.0006      15     120 ..     101     205 ..      89     231 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS...---GGGGSTT-HHHHHHHHHHHHHHHHHHHHHHHTS--SEEEEES---SHH CS
       6PF2K  15 vivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska...lsdaeffrpdneealklreklalaalkdllaylneeegqvaifDAtNttre 110
                  ++++G+   gKt++s+kl ++l   g+r     +  yr  a  +   + + + ++   ee++k      ++ +k+ l+++++ + +v + D     +e
  AJA92800.1 101 KVLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGALVQlrtNCEKSNVEVYGEENNK----DSAEIVKNGLKHFENSNIDVVLIDTAGRHKE 195
                 488************************************9887774332222333333333333....3334444555566777778888887777777 PP

                 HHHHHHHHHH CS
       6PF2K 111 rRklilefve 120
                 +++l+ e++e
  AJA92800.1 196 EKDLLDEMTE 205
                 7777766654 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   4.2e-06    0.0019      12      91 ..     109     185 ..     106     211 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.2e-06
      AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenldlipssidLa 91 
                 G GKTT s +la++l+k+g++v  + +D+    +  +++ ++++ek+ +ev  ee+n ++a i  k+   ++  s+id++
  AJA92800.1 109 GSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGAL-VQL-RTNCEKSNVEVYGEENNKDSAEI-VKNGLKHFENSNIDVV 185
                 99**************************9877665.333.44455555555433333333333.1112224444444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.2e-06    0.0014       4      33 ..     104     133 ..     101     139 .. 0.91
   2 ?   -1.3   0.0       4.2   1.9e+03      43      73 ..     160     189 ..     151     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-06
        MobB   4 ivgksgsGKTtLleklipelkarglrvgti 33 
                 + g +gsGKTt  +kl + l+++g+rvg+i
  AJA92800.1 104 MLGIQGSGKTTVSSKLAKFLTKQGYRVGAI 133
                 6799************************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
        MobB  43 dkpgkDsyrhrkAGAkevlvaskerlalike 73 
                 ++++kDs ++ k G k+    s+  + li  
  AJA92800.1 160 EENNKDSAEIVKNGLKHFE-NSNIDVVLIDT 189
                 5667777777777766543.34444444444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3    0.0075       3.4       2      22 ..     100     120 ..      99     128 .. 0.89
   2 !    9.9   0.0    0.0013      0.59      37     103 ..     183     252 ..     174     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0075
   PduV-EutP   2 kkilliGkvgsGKttLtqalk 22 
                 +k+l++G  gsGKtt++ +l 
  AJA92800.1 100 NKVLMLGIQGSGKTTVSSKLA 120
                 69**************99986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
   PduV-EutP  37 sdeviDtPGeylenrklysalivts..aeadvialvqdateeesvfppgfasvfnkeviGi.itkidlae 103
                    +iDt G + e++ l   ++ +s   + d+  lv d t  ++ f+++ a     +v Gi itk+d + 
  AJA92800.1 183 DVVLIDTAGRHKEEKDLLDEMTEISkvSNPDLALLVIDGTIGQQCFSQAEAFNKIVPVGGIvITKLDSSA 252
                 4567***************999887325789****************9766666668888637***9874 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.8    0.0003      0.13      11     113 ..     109     195 ..     102     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                 TSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHTTS-HHHHHHHHHHHHHH.HHHH-SEEEEE-- CS
        MipZ  11 GsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalseaeeaeveeeeeaevaeleelvad.leaeldfividtP 108
                 GsGk+t++  +a  L+k+G rv+ai  d+ +      ++ r++  e++++++   e            ++++e+     ++ +++  ++++d+++idt 
  AJA92800.1 109 GSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGA--LVQLRTNC-EKSNVEVYGEEN----------NKDSAEIV----KNGLKHfENSNIDVVLIDTA 190
                 99***********************999855432..23333332.223333332222..........11222222....22222202456777777777 PP

                 SS--H CS
        MipZ 109 Gsdsa 113
                 G++++
  AJA92800.1 191 GRHKE 195
                 77765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     7e-06    0.0031      13      47 ..     108     142 ..      99     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7e-06
        ParA  13 GGVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47 
                  G GK+tv+++lA  L+k+g++vg + aD y p  
  AJA92800.1 108 QGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGA 142
                 589**************************997754 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05     0.005       5      46 ..     102     143 ..      99     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                 EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTT CS
  APS_kinase   5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLn 46 
                 v++ G+ gsGK+t++ +l+k L+++g++v  +  d+ R g  
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGAL 143
                 6788*************************9999999987755 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   2.4e-05     0.011       2      86 ..     102     222 ..     101     245 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-05
                 EEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSE.EEEEEEETTEE...............................EEEEECGGCSSHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltg....ekaivsdkpgtTrdi.negrvklkgke...............................ielvDtpGliegaseek 64 
                 v+ +G   +GK+t+ ++l +    +  +v+++   T  +    +++++ ++                               ++l+Dt+G  +  +eek
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKfltkQGYRVGAIGADTYRPgALVQLRTNCEKsnvevygeennkdsaeivknglkhfensnidVVLIDTAG-RH--KEEK 197
                 7788999999999999997644423567888888787775444444221112344444555556666666666666667777********.54..4555 PP

                 HHHHHHHHHHC...TSEEEEEEETT CS
    MMR_HSR1  65 glgkaflalee...adlillvvdas 86 
                 +l +++ ++ +    dl+llv+d +
  AJA92800.1 198 DLLDEMTEISKvsnPDLALLVIDGT 222
                 555555554443217********44 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0058       2      72 ..     102     183 ..     102     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg.....avllssdtlrr.rlfg.....tdqqsktdytrvldrlyqilnelarkalsagrn 72 
                 vl+ G +GsGK+t++ +l+k l+     +  +  dt+r  +l+      ++ + + +  + +++  +i+++ ++    ++++
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTkqgyrVGAIGADTYRPgALVQlrtncEKSNVEVYGEENNKDSAEIVKNGLKHFENSNID 183
                 79****************9888888544344778886654444333222222222233334444555555555555555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   1.5e-05    0.0069       5     155 ..     104     253 ..     101     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                 EEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEEECT.TTTHHHHH CS
        cobW   5 ltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeereerldviliEttG.laePapva 100
                 + G  GsGKTt+ ++l     ++g+++  i  + +  +   +l ++++++ ve+         +e + + l+++e+ +  +dv+li t G   e + ++
  AJA92800.1 104 MLGIQGSGKTTVSSKLAkfLTKQGYRVGAIGADTYRPGALVQLRTNCEKSNVEVYGEENNKDSAEIVKNGLKHFENSN--IDVVLIDTAGrHKEEKDLL 200
                 56899*******9999998899*************8888888888888889998755555555666666677777666..**********878888886 PP

                 TTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCH CS
        cobW 101 fteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDllde 155
                  + +e+++  + d  + v+D+  +  ++  ++ +a +++     +v++K D   +
  AJA92800.1 201 DEMTEISKVSNPDLALLVIDG-TI-GQQCFSQAEAFNKIVPVGGIVITKLDSSAK 253
                 6699*****************.44.466667777777888888899999997655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.6e-05     0.016       2      81 ..     103     189 ..     102     238 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-05
      AAA_18   2 lltGtpGvGKttlakeLskrl.gf................gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidg 81 
                 l  G++G+GKtt++  L+k l +                  v+lr ++ +++ + + +++  ++s +++++     l+ +e+++      ++++id 
  AJA92800.1 103 LMLGIQGSGKTTVSSKLAKFLtKQgyrvgaigadtyrpgaLVQLRTNCEKSNVEVYGEEN-NKDSAEIVKNG----LKHFENSNI-----DVVLIDT 189
                 678**************9876433567766666666666655555555555555555555.44555555544....344444333.....4444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05    0.0057      19     105 ..     102     192 ..      85     205 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
  Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvv.rldpDdlRe..lhPeyeeilkadpkkaseltqkdaselvekllqeaiengynii.vegtlr 105
                 +l+ G +G+GK++++++l++ l++qg  v  + +D++R+  l     +++k +++ + e  +kd+ e+v++ l++  +  ++++ ++++ r
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQGYRVgAIGADTYRPgaLVQLRTNCEKSNVEVYGEENNKDSAEIVKNGLKHFENSNIDVVlIDTAGR 192
                 89999******************76655538*******63244444566667888888888888888888888888888888762455555 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.4e-05     0.015      12      96 ..     109     194 ..     103     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-05
       VirC1  12 GaGkttalmglcsalasdgkrvalfeadenrP..ltkwkenalrkgawddacevfvadelplleaayeeaegeGfdyaladtrgGss 96 
                 G+Gktt    l   l+ +g rv+   ad  rP  l + + n  +++  +   e  + d   ++ +  +++e +  d++l+dt g   
  AJA92800.1 109 GSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPgaLVQLRTNCEKSN-VEVYGEENNKDSAEIVKNGLKHFENSNIDVVLIDTAGRHK 194
                 89*****************************977788888877655.6888999999*************************98665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   7.2e-05     0.032       2      39 ..     102     139 ..     101     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                 EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                 v++ G +G+GKtT+ +k+++ l ++g++vg + +  +r
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYR 139
                 667799***********************988777666 PP

>> DUF4317  Domain of unknown function (DUF4317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.099        44     284     320 ..      11      46 ..       9     101 .. 0.82
   2 ?    9.7   0.1   0.00095      0.42     249     311 ..     358     420 ..     353     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.099
     DUF4317 284 keikkiLeesgveeeklekiekafeeafgedtelkae 320
                 ++ikki ++sg++ee ++++ k  ++++  ++ ++++
  AJA92800.1  11 TAIKKIVSSSGIDEELIKELAKDVQRSL-LQSDVNVK 46 
                 5789999999999999999999988877.44444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00095
     DUF4317 249 eelekevvkeiqeelnemieekkeeeeeepltldkkeikkiLeesgveeeklekiekafeeaf 311
                 +e++ ev+++  ++ + +i++ +++e+ +p  l++++ik+i + sg +e++++++ k+++++ 
  AJA92800.1 358 KEDQLEVMEQRMDKWRYIIQSMNTKEKADPDLLNSSRIKRIARGSGWPEHEVKELIKNYKNSK 420
                 567778888889999999*999999999*******************************9875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.023      22      61 ..      98     140 ..      79     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                 .EEEEEEEESTTSSHHHHHHHHH.HHCS----HHHH.HC.CHH CS
     G-alpha  22 revkllllGqseSGKsTilkqlk.llykkgfseeel.at.wra 61 
                 ++ k+l+lG ++SGK+T+  +l  +l k+g++   + a  +r+
  AJA92800.1  98 KINKVLMLGIQGSGKTTVSSKLAkFLTKQGYRVGAIgADtYRP 140
                 4669**************8777637777878776555444555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00017     0.078       2      36 ..     102     137 ..     101     159 .. 0.86
   2 ?   -0.6   0.0       2.8   1.2e+03     104     124 ..     357     383 ..     304     397 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                 EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT- CS
       AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt 36 
                 vl++G +G+gK++++ +la++l ++ + + ++ +dt
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLtKQGYRVGAIGADT 137
                 89********************88877777777666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
                 E---............-EEEEEESS-- CS
       AAA_5 104 kakndd.ller.....frviatanpld 124
                  ++ +   +e+      ++i ++n+ +
  AJA92800.1 357 VKEDQLeVMEQrmdkwRYIIQSMNTKE 383
                 222222233334555677777777776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.7e-05     0.039       4      41 ..     102     139 ..     101     188 .. 0.84
   2 ?   -2.8   0.1       7.4   3.3e+03     111     145 ..     389     424 ..     364     426 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-05
                 EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
       KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                 v++ G+  sGK+t++++Lak l++++++v  i  ++++
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYR 139
                 7899999**********************999999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.4
                 HHHHHHHHT.T-S..S-HHHHHHHHHH---TTSS-G CS
       KTI12 111 vlvkwneer.eekeeyekelldaLiqRyeePdsknr 145
                  l + + +r +  +++++  +++Li+ y + +s+++
  AJA92800.1 389 LLNSSRIKRiARGSGWPEHEVKELIKNYKNSKSMMK 424
                 333333222022334999999999999988877765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00011      0.05       3      26 ..     106     129 ..     105     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                      ESTTSSHHHHHHHHHHHHHHTTE. CS
  Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik 26 
                      G+ G+GKtt++ +l++ l+++g++
       AJA92800.1 106 GIQGSGKTTVSSKLAKFLTKQGYR 129
                      99********************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00037      0.16       1      70 [.     102     193 ..     102     293 .. 0.70
   2 ?    0.7   0.2       1.5   6.6e+02      90     127 ..     362     398 ..     295     401 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00037
                 EEEESSTTSSHHHHHHHHHHHHTHE..................EEEEETTTCS.SSSTTHHHHHHHHHHHHH.HHTS..TSEEEEEETGGGH CS
         AAA   1 vllyGppGtGKTllakavakelgve..................fleisgsell.skyvgesekkirelfkea.keka..kpsilfiDEidal 70 
                 vl+ G  G GKT++ + +ak l  +                   l++++ +   + y +e++k+ +e++k+  k+ +  +  +++iD + + 
  AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQgyrvgaigadtyrpgalvQLRTNCEKSNvEVYGEENNKDSAEIVKNGlKHFEnsNIDVVLIDTAGRH 193
                 7999*****************8433333444445555556654455555555545577777777777777742222243579***9977665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.5
                 HHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEE CS
         AAA  90 lteldgvkkkeskvivigatnrpdkldpallr.gRfdrk 127
                 l+++++  +  +   +i   n+ +k dp ll  +R++r+
  AJA92800.1 362 LEVMEQRMD--KWRYIIQSMNTKEKADPDLLNsSRIKRI 398
                 333333333..2336777778899999999988888775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0    0.0001     0.045      22      98 ..     103     191 ..      93     217 .. 0.70
   2 ?   -2.8   0.0       9.5   4.3e+03     116     123 ..     265     272 ..     252     327 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.0001
      AAA_30  22 vltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLaeelgieastiakllkrlk...........grarlepgtllivDEag 98 
                 ++ G  G+GKtt+ ++l++ ++++g+rv  + A t +  + ++  ++ e s+++ + ++++           ++ + ++ +++++D ag
  AJA92800.1 103 LMLGIQGSGKTTVSSKLAKFLTKQGYRVGaIGADTYRPGALVQLRTNCEKSNVEVYGEENNkdsaeivknglKHFENSNIDVVLIDTAG 191
                 678999**********************7245677776666666666666666666655556666666665422222333666666665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.5
      AAA_30 116 gakvilvG 123
                 ga+v+ vG
  AJA92800.1 265 GAQVMYVG 272
                 55555554 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00026      0.12      10      35 ..      95     120 ..      87     129 .. 0.85
   2 ?   -0.6   0.0       1.8     8e+02      79     120 ..     177     218 ..     172     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                 T.TTEEEEEEEESTTSSHHHHHHHHH CS
         Arf  10 lkkkelrilllGLDnaGKtTilkklk 35 
                 ++ k  ++l+lG+ ++GKtT+  kl 
  AJA92800.1  95 KSGKINKVLMLGIQGSGKTTVSSKLA 120
                 4567789**************99986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.8
                 CTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCT..TSEEEE CS
         Arf  79 fektdavifvvDsadreRleeakeeLkalleeeelk..evallv 120
                 fe+ +  + ++D+a   R +e k+ L++++e ++++  + allv
  AJA92800.1 177 FENSNIDVVLIDTAG--RHKEEKDLLDEMTEISKVSnpDLALLV 218
                 777777788888875..667889999999998887733455555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0056       2.5      25     129 ..     130     207 ..     106     240 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0056
      CLP1_P  25 pvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpslylalvkelareveekleenkkakasgliIntpGwvkglgaelll 123
                 +  +                +  ++  + v+  ++++++ v  +G+++ +d+     ++vk  ++++e       +++ ++++I+t G  k + ++ll 
  AJA92800.1 130 VGAIG---------------ADTYRPGALVQLRTNCEKSNVEVYGEENNKDSA----EIVKNGLKHFE-------NSNIDVVLIDTAGRHK-EEKDLLD 201
                 54444...............444444444555556666666666666655544....56666666666.......3456777777777555.3445555 PP

      CLP1_P 124 elieal 129
                 e++e+ 
  AJA92800.1 202 EMTEIS 207
                 554444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0059       2.6       4      26 ..     100     122 ..      97     133 .. 0.84
   2 ?    4.0   0.0     0.064        29      45     102 ..     178     237 ..     149     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                 -EEEEE-STTSSHHHHHHHHHHS CS
       SRPRB   4 pavllvGlsdsGKTslftrLttd 26 
                 ++vl++G++ sGKT++  +L + 
  AJA92800.1 100 NKVLMLGIQGSGKTTVSSKLAKF 122
                 79**************9999765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.064
                 ..GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE...EEEEEETTS-HHHHHHHHHHHHHH CS
       SRPRB  45 sekgskltliDfPGheklrqklleklkaksslkg...lvfvvDStidpkevkevAEllyei 102
                 ++ +  + liD  G +k  ++ll+++ + s++      + v+D ti ++   + AE + +i
  AJA92800.1 178 ENSNIDVVLIDTAGRHKEEKDLLDEMTEISKVSNpdlALLVIDGTIGQQCF-SQAEAFNKI 237
                 66788899***************9998887765433268899**9988654.557776666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   0.00016     0.073      21      63 ..      96     153 ..      68     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
      AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd..............ggif.lrgkcdql 63 
                 sg  + vl  G +G+GK+++  +l++ l+k+              g+++ lr++c+++
  AJA92800.1  96 SGKINKVLMLGIQGSGKTTVSSKLAKFLTKQgyrvgaigadtyrpGALVqLRTNCEKS 153
                 455588999**********************554444444444444444444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00023       0.1      34     100 ..     100     164 ..      92     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
       AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggk 100
                 ++vl+ G +G+GKt++ ++l k l k+ y +  i    +   + +q  +  + ek + +vyg  ++k
  AJA92800.1 100 NKVLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRPGALVQ--LRTNCEKSNVEVYGEENNK 164
                 589**************************99999877777766666..7888888888888877776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.1   4.1e+03     110     135 ..      28      57 ..      11      60 .. 0.61
   2 ?   11.4   0.0   0.00063      0.28      11      97 ..     105     219 ..     101     234 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
      AAA_22 110 eeL.rsllnl.......srkgvqliLvGtpelrk 135
                 +eL +    +       s+ +v+l+L +t +l++
  AJA92800.1  28 KELaK----DvqrsllqSDVNVKLVLEITKNLQE 57 
                 33332....2222244477788888877777776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00063
      AAA_22  11 tGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsst.sskdllrellralglelka........erlsseellea 81 
                  G  G+GKTt+  +l++ l+++ +                      e++ v  +   + + +s+++ ++ l+ +++++ +        + +++++ll+ 
  AJA92800.1 105 LGIQGSGKTTVSSKLAKFLTKQGYRVGaigadtyrpgalvqlrtncEKSNVEVYGEEN-NkDSAEIVKNGLKHFENSNIDvvlidtagRHKEEKDLLDE 202
                 5889***************766553334455554444444444332222211222222.1233344443333333333335555555444444455555 PP

      AAA_22  82 leqalrarav.iellii 97 
                 +++ ++      +ll+i
  AJA92800.1 203 MTEISKVSNPdLALLVI 219
                 54444444444444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0003      0.14       3      76 ..     100     192 ..      98     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0003
      AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfi.......................dtekGlksldadkfpdieswedfldevvel.....aaeladyktlviDt 73 
                 +k+l+ G +g+GKTt+ ++l  k+l                         ++ek+  ++++ + +   s e        +       e+++++++ iDt
  AJA92800.1 100 NKVLMLGIQGSGKTTVSSKL-AKFLTKqgyrvgaigadtyrpgalvqlrtNCEKSNVEVYGEENN-KDSAEI-------VknglkHFENSNIDVVLIDT 189
                 5899****************.66665555555555666666666666666666666666666644.223333.......14455555888899999999 PP

      AAA_24  74 ide 76 
                 ++ 
  AJA92800.1 190 AGR 192
                 876 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00066      0.29       9      80 ..     109     185 ..     107     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00066
      LytR_C   9 gtgvsGlAarvadaLeerGftvgevgnagnadee.............ttivy.reaaaaaakalaaalglgelqedsvkdasvtvv 80 
                 g+g++ + +++a+ L+++G++vg++g+ + +  +              + vy +e+++++a+ +++ l+  e       +++++vv
  AJA92800.1 109 GSGKTTVSSKLAKFLTKQGYRVGAIGADTYR--PgalvqlrtnceksNVEVYgEENNKDSAEIVKNGLKHFE-------NSNIDVV 185
                 899999******************8853333..134666887888743333444433457777777665444.......4445555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00065      0.29       6      80 ..      92     177 ..      88     220 .. 0.59
   2 ?   -0.4   0.1       3.4   1.5e+03      39      96 ..     354     420 ..     342     440 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00065
                 EEEETTS..EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG......B-HHHCCHCEEEE-SS--S-TTSBHHHH....H CS
                 xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
    ABC_tran   6 lklkege..kvaivGenGaGKStLlkllagllkpteGeilldgkdlke......qeleslrkeigvlpqepqlfpeltvren....e 80 
                 +++k g+  kv ++G  G+GK+t+ + la+ l+++  ++   g+d+ +       +++  +++++v+ +e++ ++   + +n     
  AJA92800.1  92 FHFKSGKinKVLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIGADTYRpgalvqLRTNCEKSNVEVYGEENNKDSAE-IVKNglkhF 177
                 5555554227999****************999996656644455444444444344445555555555553333333.444445551 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                 EEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........HHHTCHHHHHHHSTTGG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxx RF
    ABC_tran  39 eGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.........esdeeiekalsklglke 96 
                 +G ++ d+ ++ eq++ ++r  i+ +  +++ +p+l + ++         + + e++++++++++++
  AJA92800.1 354 SGMVKEDQLEVMEQRMDKWRYIIQSMNTKEKADPDLLNSSRikriargsgWPEHEVKELIKNYKNSK 420
                 5666666666666777777777777777777777775555577777777744444444444444333 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.6    0.0046       2.1      10      33 ..     108     131 ..     106     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0046
      AAA_26  10 tgvGKTvvslgLvralkrkgvkvg 33 
                 +g+GKT+vs  L++ l+++g++vg
  AJA92800.1 108 QGSGKTTVSSKLAKFLTKQGYRVG 131
                 589*************99999987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00069      0.31      32     117 ..      98     186 ..      91     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
      RuvB_N  32 aldhvllyGpPGlGkttlakiiakelgvk.lkits.gPvlekagdlaalltnleekdvlfi.deihrlsraveevlysamedfrldivi 117
                 +++ vl+ G  G Gktt+++ +ak l  +  ++ + g    ++g l+ l tn e+++v    +e  + s ++     + +e+ ++d+v+
  AJA92800.1  98 KINKVLMLGIQGSGKTTVSSKLAKFLTKQgYRVGAiGADTYRPGALVQLRTNCEKSNVEVYgEENNKDSAEIVKNGLKHFENSNIDVVL 186
                 6789********************9977625554327778899********99999995440444444444433344556666677665 PP

>> CaM_bdg_C0  Calmodulin-binding domain C0 of NMDA receptor NR1 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4    0.0012      0.53       9      29 .]     357     377 ..     356     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
  CaM_bdg_C0   9 rkqKqlELArhAaDkWRgniq 29 
                  k+ qlE +    DkWR  iq
  AJA92800.1 357 VKEDQLEVMEQRMDKWRYIIQ 377
                 6999*************9887 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0049       2.2       4      36 ..     102     134 ..      99     138 .. 0.84
   2 ?   -0.5   0.0       1.2   5.5e+02     114     133 ..     171     190 ..     159     193 .. 0.85
   3 ?    2.9   0.6      0.11        50     152     205 ..     331     383 ..     317     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0049
                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
  ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllis 36 
                  +l+ G  G GKttvs+ +a  l+++g++v  i 
   AJA92800.1 102 VLMLGIQGSGKTTVSSKLAKFLTKQGYRVGAIG 134
                  667788899*****************9986665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                  HHHHHHHHCSSSSEEEEESB CS
  ArsA_ATPase 114 eellkyvkeeeydvvvlDta 133
                  ++ lk+ ++++ dvv++Dta
   AJA92800.1 171 KNGLKHFENSNIDVVLIDTA 190
                  55679999***********9 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.11
                  HHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT CS
  ArsA_ATPase 152 leklvklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpe 205
                  + +l ++  k+++l + +  + gl g+  e++le +e+++++ + + + ++ +e
   AJA92800.1 331 FYQLEEV-TKVGSLQSLMETMPGLSGMVKEDQLEVMEQRMDKWRYIIQSMNTKE 383
                  3333333.36888899999999999999999**********9999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 3138.04
//
Query:       AJA92801.1  [L=318]
Description: replication factor C C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-17   62.3   1.1    1.9e-12   47.2   0.5    2.4  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    2.5e-12   47.3   0.1    5.7e-12   46.2   0.1    1.6  1  AAA              ATPase family associated with various cellul
    3.9e-08   33.6   0.3    1.6e-07   31.6   0.2    2.1  1  Rep_fac_C        Replication factor C C-terminal domain
    1.8e-07   31.1   0.0    6.9e-07   29.1   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.7e-05   24.9   0.3    4.6e-05   23.4   0.1    1.8  2  Rad17            Rad17 P-loop domain
    0.00013   22.4   0.3    0.00093   19.6   0.3    2.4  1  AAA_16           AAA ATPase domain
    0.00023   21.2   0.2    0.00055   20.0   0.2    1.8  1  AAA_14           AAA domain
    0.00026   21.3   0.1    0.00064   20.0   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0009   19.1   0.6     0.0019   18.0   0.1    1.7  2  DNA_pol3_delta   DNA polymerase III, delta subunit
     0.0026   17.6   0.0     0.0044   16.9   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0047   16.3   0.0       0.21   10.9   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0089   16.3   0.2      0.041   14.2   0.2    2.1  1  MAP              MAP domain
  ------ inclusion threshold ------
      0.011   16.1   2.5       0.91    9.8   0.1    2.9  3  AAA_22           AAA domain
      0.011   15.2   0.1        2.4    7.6   0.0    2.5  2  PhoH             PhoH-like protein
      0.014   15.4   0.4       0.11   12.5   0.4    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
       0.02   13.9   0.1        0.3    9.9   0.0    2.1  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.023   14.5   0.6       0.62    9.8   0.1    2.6  2  DEAD             DEAD/DEAH box helicase
      0.024   14.3   0.0        3.1    7.5   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.025   13.6   0.0      0.052   12.6   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.027   14.6   0.0      0.067   13.3   0.0    1.6  1  PTPlike_phytase  Inositol hexakisphosphate
      0.036   14.3   0.0       0.18   12.1   0.0    2.1  2  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
      0.041   13.9   0.0      0.093   12.7   0.0    1.5  1  Ribosomal_S6e    Ribosomal protein S6e
      0.046   13.6   0.5          3    7.7   0.2    2.6  2  NACHT            NACHT domain
      0.047   13.8   7.0        2.1    8.5   0.1    3.5  4  Arc_PepC         Archaeal Peptidase A24 C-terminal Domain
      0.058   13.4   0.3        1.3    9.0   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
      0.074   12.9   0.0       0.34   10.8   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
      0.079   12.5   0.0       0.16   11.4   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.082   12.3   0.2        2.4    7.5   0.0    2.3  2  TniB             Bacterial TniB protein
       0.13   12.6   0.7        2.3    8.5   0.1    2.6  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   7.1e-05     0.044       2      47 ..      23      68 ..      22      79 .. 0.87
   2 !   47.2   0.5   3.1e-15   1.9e-12      85     162 ..      84     164 ..      68     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.1e-05
  DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                     q+++   ls  lk+++    +Lf+G++g+gk ++al++++++l ++
       AJA92801.1 23 QKDIKGSLSALLKNQEEMPHLLFSGSAGVGKTTMALCISQEILGDK 68
                     56677789999999999999********************998776 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 3.1e-15
  DNA_pol3_delta2  85 ldqirelieelsrkp...reskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfspl 162
                      ++ +re  +++sr +   +e   kiii+++a++mt+ A+ al +++E+  +   fiLi+++ +k++++i+SRc ++kfs++
       AJA92801.1  84 INMVRERVKKFSRFAgldTEIPFKIIILDEADEMTSDAQTALRRIIEDTAKFCRFILIANNISKIINPIQSRCAVFKFSQI 164
                      55555555555554311145678*******************************************************986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.1   9.2e-15   5.7e-12       1     126 [.      43     158 ..      43     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 9.2e-15
                 EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsell.skyvgesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlte 92 
                 +l++G  G+GKT++a  + +e+     + + le+++s+ +  ++v e+ kk++ +     ++  p +i+++DE+d+++++            + +L + 
  AJA92801.1  43 LLFSGSAGVGKTTMALCISQEIlgdkwKDYTLELNASDERgINMVRERVKKFSRFAGL-DTEI-PfKIIILDEADEMTSDA-----------QTALRRI 128
                 699******************6665557999*********555666666666555443.4444.78***********9999...........******* PP

                 HHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
         AAA  93 ldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                 +++  k    + +i+++n+++k+ +++  +R+ +
  AJA92801.1 129 IEDTAKF---CRFILIANNISKIINPIQ-SRCAV 158
                 ******5...99****************.9*986 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   2.6e-10   1.6e-07       4      87 ..     231     311 ..     229     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.6e-10
                 HHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHH.HHHHHHHHHHHCTH-HHHHHHHHHH CS
   Rep_fac_C   4 teieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleil.ellgeiekrlveGasehlqlsalla 87 
                 +++e++l+ + +g++++ ++k+ el+  +G+s +d l+ + + +++ +    +  le l + ++ +++r++ G+++++qlsa+la
  AJA92801.1 231 NDVEDVLKLAVSGKIQDSRNKMIELVKVYGMSESDFLKYINQALFSAK----YDNLEELsQIIAKYDYRILVGSNPEIQLSAMLA 311
                 68999*****99**********9788888****************963....445555535589*******************98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.1e-09   6.9e-07       2      57 ..      13      64 ..      12      75 .. 0.91
   2 ?   -2.7   0.0       7.1   4.4e+03      85     111 ..     106     132 ..      90     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.1e-09
      RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                rPk+++e + q+++k +l+ ++    k +e++ h+l++G+ G+Gktt+a  i++e+
  AJA92801.1 13 RPKKISEIVNQKDIKGSLSALL----KNQEEMPHLLFSGSAGVGKTTMALCISQEI 64
                9***************998776....56899**********************997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
      RuvB_N  85 kdvlfideihrlsraveevlysamedf 111
                  +++ +de   +++ ++  l   +ed 
  AJA92801.1 106 FKIIILDEADEMTSDAQTALRRIIEDT 132
                 467888999999988888888888885 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   7.5e-08   4.6e-05       8     116 ..       7     113 ..       4     150 .. 0.71
   2 ?   -2.6   0.0       7.2   4.4e+03      94      94 ..     268     268 ..     226     308 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.5e-08
       Rad17   8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLsk.elgiklrewlnpvslkepdnqksdfkgltekesrf..l 103
                  W+eky+P+k  e+       +++k  l a   ++++   LL sG +G gk+t+   +s+ +lg k +++   ++  + +   + ++  ++k+srf  l
  AJA92801.1   7 MWVEKYRPKKISEIVNQ----KDIKGSLSALLKNQEEMPHLLFSGSAGVGKTTMALCISQeILGDKWKDYTLELN-ASDERGINMVRERVKKFSRFagL 100
                 6************9644....4788888775555555559*************8887776258999999887777.44444666778888888888443 PP

       Rad17 104 sqiesfkeleLkd 116
                      fk + L +
  AJA92801.1 101 DTEIPFKIIILDE 113
                 3333455555554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.2
       Rad17  94 g 94 
                  
  AJA92801.1 268 K 268
                 2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.3   1.5e-06   0.00093      18      89 ..      32     113 ..      22     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-06
      AAA_16  18 rvrsgrp..elvllsGesGvGKsslvrellralekd...............ggiflrgkcdqlesaipysalaqalareellrqllde.........a 89 
                 ++ ++++  + +l+sG +GvGK++++ ++ +++ +d               g+  +r++ +++                + ++ l++e         +
  AJA92801.1  32 ALLKNQEemPHLLFSGSAGVGKTTMALCISQEILGDkwkdytlelnasderGINMVRERVKKF----------------SRFAGLDTEipfkiiildE 113
                 4444444469************************99564444444333332122233333333................3333333332222222222 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2     9e-07   0.00055       6     106 ..      44     149 ..      19     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9e-07
      AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev.pewekalkslvdeg.knldvivtG 99 
                 + +G   vGKTt++  + +e l    k+ +l++n  der  ++  ++ k  + +  + +e   ++++lDE+ e+ +++++al+++++++ k +++i+  
  AJA92801.1  44 LFSGSAGVGKTTMALCISQEILgdKWKDYTLELNASDERGINMVRERvKKFSRFAGLDTEIPFKIIILDEADEMtSDAQTALRRIIEDTaKFCRFILIA 142
                 6678889******9998888888877888999999999987655442222333333333334578******987368**********996778998876 PP

      AAA_14 100 Snsklls 106
                  n + + 
  AJA92801.1 143 NNISKII 149
                 6665555 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1     1e-06   0.00064       4      41 ..     181     223 ..     178     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                  .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......X CS
  AAA_assoc_2   4 klkleddalealaeladGDaRkaLnlLElaaeaaeak.....e 41 
                  k k +++ l+ +a +a+GD R a+nlL++aa++ + +     +
   AJA92801.1 181 KGKADEKGLKEIAGYAGGDLRHAINLLQTAASTGDITqdsvkA 223
                  66889999*********************99987654333321 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.1e-06    0.0019      59     170 ..     107     208 ..     104     210 .. 0.91
   2 ?   -2.8   0.0       7.7   4.8e+03      82      85 ..     274     277 ..     247     293 .. 0.45

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.1e-06
                     EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHH CS
  DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealel 153
                     +i++l+ +      +  + + +++L ++++++ + + +ilia+ +++   k++  ++++  v+++++ +e+e+ + +++++++++ k +++ l++
      AJA92801.1 107 KIIILDEA------DEMTSDAQTALRRIIEDTAKFCRFILIAN-NIS---KIINPIQSRCAVFKFSQIDEKEITTHLKAVLKKEKGKADEKGLKE 191
                     56666666......668889999********************.777...8999***************************************** PP

                     HHHHHTT-HHHHHHHHH CS
  DNA_pol3_delta 154 Llelvennlsaikqele 170
                     ++ + +++l+ + + l+
      AJA92801.1 192 IAGYAGGDLRHAINLLQ 208
                     *********99988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.7
                     HHHH CS
  DNA_pol3_delta  82 eLee 85 
                      +++
      AJA92801.1 274 LFSA 277
                     2222 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.2e-06    0.0044       1      88 [.      42     131 ..      42     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.2e-06
       AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkG...pvfanllladeinrappktqsalleamee 88 
                 h+l+ g  G++kt+++  +++ +  +     +t +l  sd  G+++++e+ k+f+  +G    +  ++++ de +  ++ +q+al  ++e+
  AJA92801.1  42 HLLFSGSAGVGKTTMALCISQEILGDK-WKDYTLELNASDERGINMVRERVKKFSRFAGldtEIPFKIIILDEADEMTSDAQTALRRIIED 131
                 99******************9886654.458******************998888777644379999*****************9887765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00035      0.21      24      59 ..      42      78 ..      17      96 .. 0.82
   2 ?    3.2   0.0      0.08        49     109     133 ..     108     132 ..     106     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
  Mg_chelatase 24 nlllvGppGsGKtmlakrlp.sllpplseeealevak 59
                  +ll+ G++G GKt +a +++ ++l +  ++ +le ++
    AJA92801.1 42 HLLFSGSAGVGKTTMALCISqEILGDKWKDYTLELNA 78
                  89**************999526888888877777665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.08
  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                   +++LDE+ e+++++  +LR+ +ed+
    AJA92801.1 108 IIILDEADEMTSDAQTALRRIIEDT 132
                   689*****************99985 PP

>> MAP  MAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   6.6e-05     0.041       6      49 ..     144     187 ..     141     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.6e-05
         MAP   6 avngisalilselkfsnkskisykdlsskvKsvlksdrGiteed 49 
                 ++ +i ++i+s   + + s+i  k++++++K+vlk+++G ++e+
  AJA92801.1 144 NISKIINPIQSRCAVFKFSQIDEKEITTHLKAVLKKEKGKADEK 187
                 688999*********************************88765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.039        24       7      23 ..      42      58 ..      37      68 .. 0.84
   2 ?    9.8   0.1    0.0015      0.91      77     128 ..      82     141 ..      59     149 .. 0.65
   3 ?   -1.1   0.0       3.3   2.1e+03      50      80 ..     260     287 ..     221     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
      AAA_22  7 ilvvtGesGtGKTtllr 23
                +l+  G +G+GKTt + 
  AJA92801.1 42 HLLFSGSAGVGKTTMAL 58
                78899*********975 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
      AAA_22  77 ellealeqalrarav.........ielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                 + ++++++ +++ ++          +++i+DEa+ + + +a + Lr++ ++  k +++iL+
  AJA92801.1  82 RGINMVRERVKKFSRfagldteipFKIIILDEADEM-TSDAQTALRRIIEDTAKFCRFILI 141
                 444555555555555555566777789*********.877777776666644555555555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.3
      AAA_22  50 stsskdllrellralglelkaerlsseelle 80 
                 ++s +d+l+ + +al + + +   ++eel +
  AJA92801.1 260 GMSESDFLKYINQALFSAKYD---NLEELSQ 287
                 335667777777777766666...5555554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0039       2.4      21      44 ..      42      65 ..      20      72 .. 0.75
   2 ?    5.1   0.1     0.022        14     121     146 ..     107     131 ..     104     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                EEEEE--TTSSTTHHHHHHHHHHH CS
        PhoH 21 ivfaiGpaGtGKtylavalaveal 44
                 +   G+aG GKt +a+++  e+l
  AJA92801.1 42 HLLFSGSAGVGKTTMALCISQEIL 65
                56678************9887666 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                 EEEEE-SGGG--HHHHHHHHTTB-TT CS
        PhoH 121 afvilDEAQnttkeqmkmfltRlGen 146
                 +++ilDEA ++t+   ++ l R+ e+
  AJA92801.1 107 KIIILDEADEMTSD-AQTALRRIIED 131
                 58*********986.56777777554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   0.00017      0.11       1      91 [.      42     131 ..      42     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                 EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH.HH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHS CS
       AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteed.lkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlsllee 91 
                 ++l  G  G+gK+++a  +++ + ++++  + l  + + e  + + r   ++ ++++  +  +     +i++lDE +++ s+++ +L +++e+
  AJA92801.1  42 HLLFSGSAGVGKTTMALCISQEIlGDKWKDYTLELNASDERgINMVR---ERVKKFSRFAGLDTEIPFKIIILDEADEMTSDAQTALRRIIED 131
                 68999***************999966666666655444443033333...3445555544444445999*********************997 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00049       0.3       9      33 ..      34      58 ..      28      70 .. 0.85
   2 ?    2.0   0.0      0.12        77      62     105 ..     143     185 ..     105     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00049
  TrwB_AAD_bind  9 lpkeretqhilivGttGsGKtqale 33
                   l++++e  h+l+ G++G GKt+++ 
     AJA92801.1 34 LKNQEEMPHLLFSGSAGVGKTTMAL 58
                   56788999**************976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
  TrwB_AAD_bind  62 egkdillnPlDaRsaaWsvfaeikeksdfaeiAaalipedggss 105
                    ++   ++nP+ +R+a  + f  i+ek+  +++ a l  e+g+ +
     AJA92801.1 143 NNISKIINPIQSRCAVFK-FSQIDEKEITTHLKAVLKKEKGKAD 185
                    4557899*******9986.5667777666666666666655444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.26   1.6e+02      16      38 ..      42      64 ..      27     100 .. 0.78
   2 ?    9.8   0.1     0.001      0.62     123     150 ..     107     133 ..     103     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                EEEEEESTTSSHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 16 dvlvaaeTGsGKTlaflipvlqi 38
                ++l ++  G GKT+++l    +i
  AJA92801.1 42 HLLFSGSAGVGKTTMALCISQEI 64
                56788999*****9987655444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.001
                 EEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 123 rflVlDEadrlldqgfsdfinrilnqlp 150
                 ++++lDEad++ ++  +  ++ri++ ++
  AJA92801.1 107 KIIILDEADEMTSD-AQTALRRIIEDTA 133
                 789**********8.9999999998874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.005       3.1       7      45 ..      25      63 ..      20      83 .. 0.73
   2 ?    4.4   0.0     0.043        27      96     119 ..     108     131 ..      98     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                     HHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
  Sigma54_activat  7 alkelleqikkvaktdlsvlitGesGtGKellaraihea 45
                      +k  l+ + k  +   ++l  G  G+GK+++a +i ++
       AJA92801.1 25 DIKGSLSALLKNQEEMPHLLFSGSAGVGKTTMALCISQE 63
                     5555555566666666899**************999874 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.043
                      EEEEETGGGS-HHHHHHHHHHHHH CS
  Sigma54_activat  96 tlfLDeigelplelQekLlrvlqe 119
                      ++ LDe  e++ ++Q+ L r++++
       AJA92801.1 108 IIILDEADEMTSDAQTALRRIIED 131
                      689*****************9987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.4e-05     0.052     104     154 ..      16      65 ..       8      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.4e-05
       T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                 ++++++ +++ k  ++++l++  +e   +l+sG  g GKtt++  + +ei 
  AJA92801.1  16 KISEIVNQKDIKGSLSALLKNQ-EEMPHLLFSGSAGVGKTTMALCISQEIL 65 
                 5788999999999999999999.9999***************999999885 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.067     116     151 ..      24      60 ..      17      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                      HHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHH CS
  PTPlike_phytase 116 edfdalvsilkea.pektalvfnCqmGrgRTTtamvi 151
                      +d++  +s+l+++ +e + l+f+ ++G+g+TT+a++i
       AJA92801.1  24 KDIKGSLSALLKNqEEMPHLLFSGSAGVGKTTMALCI 60 
                      5666555555555499******************998 PP

>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       8.6   5.3e+03       4      36 ..      24      38 ..      14      46 .. 0.55
   2 ?   12.1   0.0   0.00029      0.18      32      76 ..      78     123 ..      57     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.6
                    SS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCC CS
  Shikimate_dh_N  4 npikhSlSPaihnaafkalglngsyeafeveed 36
                    ++ik SlS ++                   +++
      AJA92801.1 24 KDIKGSLSALL------------------KNQE 38
                    34445555444..................4444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                     E-SCCTHHHHHHHHHH.TTESEEEE-TTSCCHHHGGSSEE-HHHHH CS
  Shikimate_dh_N  32 eveedelekaveelra.lglaGlnvTiPfKeaviplldelseeAka 76 
                     + +e  ++ + e++++ + +aGl   iPfK  +++ +de++++A+ 
      AJA92801.1  78 ASDERGINMVRERVKKfSRFAGLDTEIPFKIIILDEADEMTSDAQT 123
                     4456677778888888899*************************86 PP

>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.093      30      65 ..      55      89 ..      49     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                   BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TT CS
  Ribosomal_S6e 30 rigeevdgdalGeelkgyvlkitggsdkqGfpmkqg 65
                    ++  ++ ++lG+++k+y+l++  +sd+ G+ m ++
     AJA92801.1 55 TMALCISQEILGDKWKDYTLELN-ASDERGINMVRE 89
                   58889999**************9.99****999764 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0049         3       4      24 ..      44      64 ..      42      79 .. 0.82
   2 ?    3.7   0.0     0.084        52      84     116 ..     100     132 ..      69     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0049
                EEEC-TTTCHHHHHHHHHHHH CS
       NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                +  G aG+GKTt++  + +++
  AJA92801.1 44 LFSGSAGVGKTTMALCISQEI 64
                678**********98888876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.084
                 E........EEEE-STT-SS-TCH.........HHHHHCTT CS
       NACHT  84 L........lilDglDelvtdlgqkekqpvrtlLselirkk 116
                 L        +ilD +De+ +d +          L+++i+ +
  AJA92801.1 100 LdteipfkiIILDEADEMTSDAQT--------ALRRIIEDT 132
                 1555555559*********97777........666666663 PP

>> Arc_PepC  Archaeal Peptidase A24 C-terminal Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.4   8.5e+02      37      63 ..     103     129 ..     100     149 .. 0.87
   2 ?    6.2   0.4     0.018        11      53     107 ..     164     217 ..     160     220 .. 0.85
   3 ?    8.5   0.1    0.0033       2.1      85     109 ..     223     248 ..     220     250 .. 0.87
   4 ?   -2.0   0.0       6.4   3.9e+03      54      80 ..     262     288 ..     254     292 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
    Arc_PepC  37 diladiilekeddevtvddksllkrlk 63 
                 +i+ +ii+ +e de+t d +  l r+ 
  AJA92801.1 103 EIPFKIIILDEADEMTSDAQTALRRII 129
                 688899999999******999999985 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.018
    Arc_PepC  53 vddksllkrlkealktgdvskietk.gkvlvsdlaeGLtkediellkkLvsegKie 107
                 +d+k+++  lk +lk ++ +k   k  k++++  a G     i+ll+   s g i+
  AJA92801.1 164 IDEKEITTHLKAVLK-KEKGKADEKgLKEIAGY-AGGDLRHAINLLQTAASTGDIT 217
                 799************.77777777867999999.8888889999999999998886 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0033
    Arc_PepC  85 laeGLtk.ediellkkLvsegKiede 109
                  a+GLtk +d+e + kL   gKi+d+
  AJA92801.1 223 AAAGLTKtNDVEDVLKLAVSGKIQDS 248
                 599**98469**************96 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 6.4
    Arc_PepC  54 ddksllkrlkealktgdvskietkgkv 80 
                  ++++lk +++al +++ +++e   ++
  AJA92801.1 262 SESDFLKYINQALFSAKYDNLEELSQI 288
                 578899999999988888888843555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0022       1.3      17      52 ..      32      68 ..       9      77 .. 0.71
   2 ?    1.8   0.0      0.34   2.1e+02     133     162 ..     106     137 ..      76     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                ......TTS..EEEEEESTTSTHHHHHHHHHHHH-S.. CS
      ResIII 17 eklkskrdk..rglikmaTGtGKTlvaaklierllkkg 52
                + lk ++++  ++l+    G+GKT +a+ + +++l  +
  AJA92801.1 32 ALLK-NQEEmpHLLFSGSAGVGKTTMALCISQEILGDK 68
                3333.4444669***************99998887655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.34
                 -SEEEEETGGGTTS...TTTHHHHHT---SEE CS
      ResIII 133 fdviiiDEaHrlgak..kswreilekfkeavl 162
                 f++ii DEa  ++++  ++ r+i+e   ++++
  AJA92801.1 106 FKIIILDEADEMTSDaqTALRRIIEDTAKFCR 137
                 569*******9999744599999887766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00054      0.34      80     122 ..      20      63 ..       6      94 .. 0.67
   2 ?   -1.8   0.0       4.1   2.5e+03      87     106 ..     279     299 ..     250     312 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                  EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                  ++ +++ k +l++l ++ ++    ++ G+ GvGK+t+   + +e
   AJA92801.1  20 IVNQKDIKGSLSALLKNQEEmPHLLFSGSAGVGKTTMALCISQE 63 
                  4445555566666666666657889***********98777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.1
                  HTTHHHHHHHCTT.SEEEEEC CS
  RsgA_GTPase  87 kegleelkellkd.ktsvlvG 106
                   ++leel++ +++ +  +lvG
   AJA92801.1 279 YDNLEELSQIIAKyDYRILVG 299
                  334444444444433444443 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.16      32      72 ..      39      79 ..      18      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
       AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                +  ++l+ G++G+GKt+++  + +++  +k++  t++++a+
  AJA92801.1 39 EMPHLLFSGSAGVGKTTMALCISQEILGDKWKDYTLELNAS 79
                34578**************9999999999999998888875 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0039       2.4      17      51 ..      24      56 ..      13      62 .. 0.83
   2 ?    2.4   0.0      0.15        93     116     141 ..     102     127 ..      84     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
        TniB 17 keilerLeeLleypkrkrmpnlllvGdsnnGKtmi 51
                k+i  +L +Ll++  +++mp+ll+ G   +GKt++
  AJA92801.1 24 KDIKGSLSALLKN--QEEMPHLLFSGSAGVGKTTM 56
                5666777777765..678***************96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
        TniB 116 relkvrvLiiDEihnllagsarkqre 141
                  e+  +++i+DE +++ +  +++ r+
  AJA92801.1 102 TEIPFKIIILDEADEMTSDAQTALRR 127
                 57789*********998766555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0037       2.3      10      63 ..      40      92 ..      31     142 .. 0.77
   2 ?   -2.2   0.0       7.6   4.7e+03      15      38 ..     221     244 ..     208     258 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
      AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerla 63
                 ++ll  + +G GKT++  +i ++++  + +k  ++ l a  +r  + +rer++
  AJA92801.1 40 MPHLLFSGSAGVGKTTMALCISQEILGDK-WKDYTLELNASDERGINMVRERVK 92
                567888999********999998887776.555777777777777777777774 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.6
      AAA_19  15 vtaGpGtGKTrvlkhivallvelg 38 
                 v a +G  KT  ++ +++l+v+ +
  AJA92801.1 221 VKAAAGLTKTNDVEDVLKLAVSGK 244
                 667788888887777777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2205.51
//
Query:       AJA92802.1  [L=272]
Description: putative 3'(2'),5'-bisphosphate nucleotidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-49  168.1   0.4    3.5e-49  167.7   0.4    1.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.7   0.4     2e-53   3.5e-49      14     255 ..      22     250 ..      17     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 167.7 bits;  conditional E-value: 2e-53
                 HHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEE CS
  Inositol_P  14 akagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigl 112
                  kage++ e+++ ++++ e+k    +  ++t+ad +++++++e+l e+    ++l+ee+ ++ +  +l+e+  +wivDP+DGT+ Fv+++  +++++gl
  AJA92802.1  22 EKAGEKILEVYE-TDFSTEKKD---DDSPITQADIESNKILKEVLGETG--ITVLSEEDTDDKK--RLSEE-KVWIVDPLDGTTDFVNRTGEFTIMVGL 111
                 589********9.*****9887...889****************99987..999********99..88888.9************************** PP

                 EETTEEEEEEEEETTTTEEECEETTTEEEETC...EEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTST CS
  Inositol_P 113 lvegkpvlGviaqPllgqlysaakgkGaflng...eklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgssalklaavaeGka 208
                 ++++k vlG+i+ P+++++y a  gkGaf+ +   +k+++s  ++i++++ +    ++++ + +e+ ll+ +e  v +     +  s lk+  +a+G+a
  AJA92802.1 112 VEKQKSVLGLIYWPIKKKMYLAESGKGAFCHNeewKKIEVSMMSEIQNCHALV---SRHHLSEREKKLLDEMEISVVTN----I-GSSLKVTEIASGDA 202
                 ******************************99788889999999998887633...44444444445666665555555....5.5669********** PP

                 SEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSCSSSTTSSEEEEES CS
  Inositol_P 209 daylefg.rekkWDhAAGeaileeaGGvvtdakgegrlllargiiaan 255
                 ++y++ + ++k WD++A ++i+ eaGG++td++g++ ++++ ++  +n
  AJA92802.1 203 EIYMTTTnKMKQWDTCASNCIISEAGGKMTDISGKEMVYNTESVNHEN 250
                 *******9***************************7777776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2255.22
//
Query:       AJA92803.1  [L=221]
Description: hypothetical protein T478_0057 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-06   26.6   6.2    5.8e-06   26.0   6.2    1.3  1  Snf7         Snf7
  ------ inclusion threshold ------
      0.012   13.7   3.5       0.49    8.3   0.0    2.0  2  Prominin     Prominin
       0.02   14.9   0.6      0.045   13.8   0.6    1.6  1  Serine_rich  Serine rich protein interaction domain
       0.02   14.7   2.2        0.3   10.9   0.1    3.0  3  DASH_Duo1    DASH complex subunit Duo1
      0.032   14.4   0.3       0.62   10.3   0.3    2.4  2  SesA         N-terminal domain on NACHT_NTPase and P-loop NTP
      0.042   14.2   6.0       0.53   10.7   2.0    2.6  2  Flagellin_C  Bacterial flagellin C-terminal helical region
       0.11   12.5   1.1        1.9    8.5   0.6    2.5  2  DASH_Dad4    DASH complex subunit Dad4
       0.11   12.8   4.2       0.48   10.8   2.0    2.2  2  OmpH         Outer membrane protein (OmpH-like)
       0.21   11.9   1.5        2.2    8.6   0.1    2.5  2  Rx_N         Rx N-terminal domain
       0.27   11.7   6.3        7.4    7.1   2.1    3.0  2  NPV_P10      Nucleopolyhedrovirus P10 protein
       0.75   10.1   8.4        8.2    6.8   0.5    3.5  3  DUF948       Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   6.2   3.6e-09   5.8e-06       2     172 ..      37     204 ..      31     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.6e-09
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
        Snf7   2 airsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnkevlnamkqgakamkamnkk 100
                 a  +L+ ++ k+d    +le++ ++l + +    +  +k +  +l +++ + +k +++l + + +leqv+l + + ++  + + a + +  +mk+ ++ 
  AJA92803.1  37 AVNKLQAQTSKMDTMLGKLEQRDQQLFQRVVTAVQNHDKSASTVLSNELAEVRKVKKMLGGARMSLEQVQLRLSTIHDLGDAMVAIGPAMGTMKSLQSS 135
                 56789999999999999999999999999999999999***********************************************************99 PP

                 TCCHHHHHHHHHHHHHH.HHHTCHHHHHHHHHTT-..GGTTHHHHHHHHHHHHHHHHHCSH.HHHHHHHTXXXST CS
        Snf7 101 vdidkidklmdeiedqm.ekaeeisEalsrsldda..deedEeeleaeLdaLeqelgdeelldesvklpevPsee 172
                 +      k m e   ++ ++ + ++  + +s+ ++   + + +   +e +a++qe  +  +++ + k p+vPs e
  AJA92803.1 136 LG-----KFMPEADSELnAMTQTLNGLMVDSI-SGdsFNMESDASSEETNAILQEASAVAEQQIGDKFPSVPSLE 204
                 88.....9999997665055566788888888.44434444566789999999998887777899*******965 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.6    0.0028       4.6     663     714 ..      35      87 ..      24     101 .. 0.68
   2 ?    8.3   0.0    0.0003      0.49     232     316 ..     103     184 ..      88     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0028
    Prominin 663 qelvlplessvkklkksvkklde.ensdlqesikkllaaveraenflkkngse 714
                 q+ v +l+++++k+   + kl++ +++ +q+ ++ + ++ ++a   l ++ +e
  AJA92803.1  35 QNAVNKLQAQTSKMDTMLGKLEQrDQQLFQRVVTAVQNHDKSASTVLSNELAE 87 
                 67788888888888888888888445555666666666656666666555544 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0003
    Prominin 232 snvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldq 316
                 ++v   L++++ l++++ ++  ++ ++++l+++L k + +  + l+++ + ln ++ ++++    ++++ ++++ + +t++ l++
  AJA92803.1 103 EQVQLRLSTIHDLGDAMVAIGPAMGTMKSLQSSLGKFMPEADSELNAMTQTLNGLMVDSIS---GDSFNMESDASSEETNAILQE 184
                 566889*************************************************999777...566666666666666666533 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   2.7e-05     0.045      37     114 ..      33     113 ..      11     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
  Serine_rich  37 nleanlqeirlavdrlrtslrefleFarga...lanaaklsdknlqtkLrkqlqkledsdqilqetsqeLdsceWsleala 114
                  ++++ +++++++++++ t l ++ +  ++    +++a++ +dk+ +t L+++l ++++ +++l  ++ +L++ + +l++++
   AJA92803.1  33 RIQNAVNKLQAQTSKMDTMLGKLEQRDQQLfqrVVTAVQNHDKSASTVLSNELAEVRKVKKMLGGARMSLEQVQLRLSTIH 113
                  5677888888888888888888887766542226899**********************************9988888765 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.092   1.5e+02      16      35 ..      34      53 ..      28      74 .. 0.70
   2 ?   10.9   0.1   0.00019       0.3       2      34 ..      81     113 ..      80     119 .. 0.94
   3 ?   -1.6   0.1       1.4   2.3e+03      35      46 ..     173     184 ..     145     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.092
   DASH_Duo1 16 ienviesLkkaksniervke 35
                i+n +++L++ +s+++++  
  AJA92803.1 34 IQNAVNKLQAQTSKMDTMLG 53
                56666666666666666544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
   DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervk 34 
                 L +El ++rk+ +++ + + sL++++  +++++
  AJA92803.1  81 LSNELAEVRKVKKMLGGARMSLEQVQLRLSTIH 113
                 889***********************9999998 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
   DASH_Duo1  35 etvestntLLdk 46 
                  + e+tn++L++
  AJA92803.1 173 ASSEETNAILQE 184
                 456777777765 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00038      0.62      61     105 ..      33      75 ..      16      87 .. 0.78
   2 ?    2.0   0.0      0.14   2.3e+02      20      58 ..      87     118 ..      76     152 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
        SesA  61 aikpvlesckekatkleeifekvapapadsrleryrkavrslgkg 105
                  i++++++ +++  k+++++ k+ ++++++ ++r+++av++  ++
  AJA92803.1  33 RIQNAVNKLQAQTSKMDTMLGKL-EQRDQQLFQRVVTAVQN-HDK 75 
                 39*********************.67777777*******99.333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.14
        SesA  20 dikglpeaFrevgkrLplvqetLedaksqlesskldedt 58 
                 ++       r+v+k L   +  Le+++ +l++ ++  d+
  AJA92803.1  87 EV-------RKVKKMLGGARMSLEQVQLRLSTIHDLGDA 118
                 44.......444444444555555555555555544444 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.0   0.00033      0.53      19      73 ..      28      82 ..      18      95 .. 0.92
   2 ?    4.9   0.1     0.021        35       3      37 ..     121     155 ..     119     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                 HHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Flagellin_C 19 GavqnRlesaitnlkaqsenlkaaesrledvDpaeestrvtklqiliqasyalla 73
                 Ga + R+++a+++l+aq++ +++  ++le+ D       vt+ q +  +++++l+
   AJA92803.1 28 GALKPRIQNAVNKLQAQTSKMDTMLGKLEQRDQQLFQRVVTAVQNHDKSASTVLS 82
                 89999***************************99999999999999999999887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.021
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Flagellin_C   3 ivdeaitdldkvrselGavqnRlesaitnlkaqse 37 
                  +++ a+ ++++ +s+lG  +   +s  ++++++ +
   AJA92803.1 121 AIGPAMGTMKSLQSSLGKFMPEADSELNAMTQTLN 155
                  68899************999888888888777654 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0012       1.9       9      59 ..      27      78 ..      25      84 .. 0.80
   2 ?    6.8   0.2    0.0039       6.3       6      39 ..      56      90 ..      54      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
   DASH_Dad4  9 qsalLsRIiknvekLnesvvelnkeleeinkkNknv.elvsqlwenYqrnvq 59
                q al  RI + v+kL  +  +++++l + +++ +++ + v + ++n  +++ 
  AJA92803.1 27 QGALKPRIQNAVNKLQAQTSKMDTMLGKLEQRDQQLfQRVVTAVQNHDKSAS 78
                6778889999****************99999998863567777777777765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
   DASH_Dad4  6 eeqqsalLsRIiknvekLnesvve.lnkeleeink 39
                e++ ++l++R+++ v++  +s  + l +el+e+ k
  AJA92803.1 56 EQRDQQLFQRVVTAVQNHDKSASTvLSNELAEVRK 90
                899**************999875437888888876 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.0    0.0003      0.48      64     100 ..      31      72 ..       8     104 .. 0.65
   2 ?    2.2   0.0      0.13   2.1e+02      16      49 ..     128     161 ..     119     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                 H..HHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
        OmpH  64 e..lqkkeqelqqkqqqka...qelqkkqqellkpildkink 100
                 +  +q+ +++lq++ ++     ++l+++ q+l+++++  +++
  AJA92803.1  31 KprIQNAVNKLQAQTSKMDtmlGKLEQRDQQLFQRVVTAVQN 72 
                 134666666666633333366677777777777777766665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  16 egkaaqeqlekkfkklqaeleakekelqklqeel 49 
                  +k+ q+ l k   + + el+a+ + l+ l+ + 
  AJA92803.1 128 TMKSLQSSLGKFMPEADSELNAMTQTLNGLMVDS 161
                 5677777777777777788888887777654432 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0013       2.2       7      49 ..      18      60 ..      15      77 .. 0.90
   2 ?    1.7   0.1      0.19   3.1e+02      10      39 ..      78     107 ..      69     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
        Rx_N  7 qkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqi 49
                +k  d l+ + +l   +++ ++kl+ + ++++ +L + e+r++
  AJA92803.1 18 DKFRDTLKPQGALKPRIQNAVNKLQAQTSKMDTMLGKLEQRDQ 60
                677899999*******************************986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
        Rx_N  10 adllaeeakllkgvkeeleklkdeLesiqa 39 
                 +++l++e + +++vk+ l   +  Le++q 
  AJA92803.1  78 STVLSNELAEVRKVKKMLGGARMSLEQVQL 107
                 678889999999999999888888888875 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.1    0.0045       7.4      23      60 ..      34      72 ..      31      75 .. 0.85
   2 ?    5.3   0.1     0.017        28      28      64 ..      79     115 ..      64     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0045
     NPV_P10 23 lqqqvddvqenlpdvtelnekLdaqsaqL.aeletkven 60
                +q++v+++q++  +++ +  kL++  +qL + + t+v+n
  AJA92803.1 34 IQNAVNKLQAQTSKMDTMLGKLEQRDQQLfQRVVTAVQN 72
                89**********************999984566666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
     NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                 + ++++l +v ++++ L +   +L++++  +++I+d+
  AJA92803.1  79 TVLSNELAEVRKVKKMLGGARMSLEQVQLRLSTIHDL 115
                 567888999************************9985 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   1.1     0.053        86      40      86 ..      32      79 ..       9      82 .. 0.65
   2 ?    6.8   0.5     0.005       8.2      25      84 ..      60     119 ..      50     123 .. 0.85
   3 ?    4.6   0.3     0.024        39      23      61 ..     142     190 ..     125     221 .] 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.053
      DUF948 40 kqvdpilkevedllakvnelledvneklekv.dplteavadlgesvse 86
                 ++++ ++++++ ++k+ ++l  ++++ +++ +++++av++  +s s+
  AJA92803.1 32 PRIQNAVNKLQAQTSKMDTMLGKLEQRDQQLfQRVVTAVQNHDKSAST 79
                455566666666666777777777776666546777888777777665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.005
      DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                 +++++++ +++++  k +  +l +  + ++kv+++l + +  le+v+   + ++dlg+++
  AJA92803.1  60 QQLFQRVVTAVQNHDKSASTVLSNELAEVRKVKKMLGGARMSLEQVQLRLSTIHDLGDAM 119
                 67788888889999999999988888899**************************99875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.024
      DUF948  23 klkktldeaaatieele..........kqvdpilkevedllakvnelle 61 
                 ++ + l+++++t+++l+           + d+ ++e++++l+++ +++e
  AJA92803.1 142 EADSELNAMTQTLNGLMvdsisgdsfnMESDASSEETNAILQEASAVAE 190
                 4455566666777777688888888877778888888888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1348  (0.0751855); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 1806.51
//
Query:       AJA92804.1  [L=717]
Description: phosphoribosylformylglycinamidine synthase II [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-46  158.5   0.1    3.3e-26   92.3   0.2    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    3.7e-38  130.1   0.3    1.2e-18   67.6   0.4    2.4  2  AIRS            AIR synthase related protein, N-terminal doma
    3.4e-08   33.9   1.6    1.3e-07   32.0   1.7    2.1  2  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.071   12.9   0.0        8.4    6.1   0.0    3.1  3  TPP_enzyme_M    Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.2   7.4e-30   3.3e-26       4     149 ..     189     332 ..     186     337 .. 0.90
   2 !   63.9   0.0   3.9e-21   1.7e-17       4     147 ..     550     682 ..     548     687 .. 0.89

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 7.4e-30
                 EEEEEEET....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHH CS
      AIRS_C   4 dvliltgs....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifd 98 
                 d+++l+g+    +G+gg+        ++ eg+d+savq+ d++ e+  i++ +++  + + ++a++D++gGGL++a++e a+  g+g+e+d+++v +++
  AJA92804.1 189 DLVLLIGGstgrDGVGGSQ----FASDALEGEDRSAVQIPDPFIEKLIIEAILECRDE-NCINAMKDLGGGGLSCAISETAESLGIGIELDVKNVHLRE 282
                 7777777776666666666....4445677777889*********9999999999997.**************************************** PP

                 HHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
      AIRS_C  99 elesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                    sp e+++se+++r+lv+ ++++  ++ +i+++ ++ +++vIG+v +++
  AJA92804.1 283 SDLSPDEIMISESQERMLVISSSDNLSKIEKICDKFRI-QCSVIGKVKEDK 332
                 **************************************.7*******9986 PP

  == domain 2  score: 63.9 bits;  conditional E-value: 3.9e-21
                 EEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHH CS
      AIRS_C   4 dvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdel 100
                 dv++l+g+  + lgg+ +++  + +     +     ++d    ++ ++ +++l+ + +lvk+ahD++ GGL+ a++e++  +++g  ++l     +   
  AJA92804.1 550 DVILLVGEtkDELGGSEYYEYIHNFIGGIAP-----KVDFSESQKNMKSVLSLISK-NLVKCAHDCSKGGLAIAISELCVFGKLGCDVNLT--SSL--- 637
                 9****************99977666666665.....89999999999999999997.**********************************..444... PP

                 HHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
      AIRS_C 101 esplemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                  s ++ml+se+  r+l++v++++ d+++++l+e+++  ++++G   +
  AJA92804.1 638 -SSEKMLFSESHSRYLLVVDKNNLDEIKSLLSEHDCI-FSELGIFSG 682
                 .4579*******************************5.999997665 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.4   2.6e-22   1.2e-18       5      92 ..      73     173 ..      60     175 .. 0.93
   2 !   59.9   0.0   6.5e-20   2.9e-16       6      94 .]     433     536 ..     420     536 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 2.6e-22
                 EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC..........HHHHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEE CS
        AIRS   5 vvvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp..........wleevvrglaeaaeelgvplvgGdtsfsne....ptisvt 89 
                 v+v+++shn+p++vep+ + +a++v+++++D+++ G rP+al++ l ++           ++++v+g+a+++++lg+p++gG+++f+++     ++ v+
  AJA92804.1  73 VTVHIESHNHPSAVEPFGG-AATGVGGVIRDILSAGTRPIALFDGLRFGdiendaharwLFKNAVSGIADYGNCLGIPTIGGEVEFDTCytnyALVDVA 170
                 57899**************.**************************************999*************************9998999889999 PP

                 EEE CS
        AIRS  90 avG 92 
                 avG
  AJA92804.1 171 AVG 173
                 998 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 6.5e-20
                 EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEEEEEEEESS.......EEEEE CS
        AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvplvgGdtsfsne.......ptisv 88 
                  v++d+++++++++p+++ +  +  +++++++++GA+P+++++ l ++         ++ e ++g+ + a+ l+vp vgG++sf+ne       pt+ +
  AJA92804.1 433 SVKIDGNPKHCYIDPRQG-AIGCFEEACRNVVCTGATPMGMVDHLQFGnpedpeifwTFMESIEGITDFAKFLNVPCVGGKVSFYNEtsngpikPTPLI 530
                 689***************.**************************************9***************************999*********** PP

                 EEEEEE CS
        AIRS  89 tavGlv 94 
                 +++Gl+
  AJA92804.1 531 GVLGLI 536
                 **9985 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   1.7     3e-11   1.3e-07      16      50 .]       7      38 ..       1      38 [. 0.78
   2 ?   -2.9   0.0       2.3     1e+04      22      40 ..     668     681 ..     656     682 .. 0.63

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3e-11
  FGAR-AT_linker 16 EidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                    E   ++   ++++r+ t +El+++a+ wSEHC++K
      AJA92804.1  7 EKLHIE---KNVKRELTSTELQILAAEWSEHCSYK 38
                    333344...459**********************9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
  FGAR-AT_linker  22 eafeklgrnPtdvElemfa 40 
                     +       +  + El++f+
      AJA92804.1 668 SE-----HDCIFSELGIFS 681
                     33.....567778888887 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.25   1.1e+03      72      90 ..     182     200 ..     169     223 .. 0.69
   2 ?    2.4   0.0     0.027   1.2e+02      60     103 ..     530     573 ..     521     601 .. 0.69
   3 ?    6.1   0.0    0.0019       8.4      48      83 ..     640     675 ..     623     708 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                   HHHHHH-SEEEEES-SSST CS
  TPP_enzyme_M  72 nealeeaDlvlalGarfdd 90 
                   + +++  Dlvl++G     
    AJA92804.1 182 KNHANINDLVLLIGGSTGR 200
                   5555668999999976544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.027
                   EEESGGGSCHHHHHHH.HH-SEEEEES-SSSTCCCTTTTTTTTTT CS
  TPP_enzyme_M  60 lgmlglhgskaaneal.eeaDlvlalGarfddirttgsepefape 103
                   +g+lgl+ +++       + D++l++G   d+   ++++ e+  +
    AJA92804.1 530 IGVLGLIENSPLVPTTpSNNDVILLVGETKDE-LGGSEYYEYIHN 573
                   5889999988888888788********77666.333333355544 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0019
                   GTTSS-TTSTTEEEESGGGSCHHHHHHHHH-SEEEE CS
  TPP_enzyme_M  48 gkgvipedhplylgmlglhgskaanealeeaDlvla 83 
                    k +++e+h +yl +++    ++ + +l e+D+++ 
    AJA92804.1 640 EKMLFSESHSRYLLVVDKNNLDEIKSLLSEHDCIFS 675
                   499*******************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5069.54
//
Query:       AJA92805.1  [L=145]
Description: polyketide cyclase/dehydrase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-06   26.5   0.0    7.8e-06   26.1   0.0    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    1.8e-05   25.0   0.0    2.1e-05   24.8   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   8.7e-10   7.8e-06       3     129 ..      12     136 ..      10     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 8.7e-10
                     S-HHHHHHHHTTTGGCCSCCCCEE.EEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEEEEECTECCEEECEEEE CS
  Polyketide_cyc   3 apadqvyalvadvesypeflphcs.svevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfkslegkWtieslppnsggtrtk 96 
                      + d+ +a+ +d+e+++e+lp++  + +++e++++ +++  ++ f g t + t++ + ++p++  +k+ +g  k      + e++     g++tk
      AJA92805.1  12 IDRDKFFAISTDYERFTEILPEYFlELKIVERDGNTTKIFETLRFLGKTVNVTTEHVIEKPDRHIVKMLDGQAKGTTFDEKYEKV-----GDKTK 101
                     5678889***************9978*********999999************99999999995666666554444444444444.....55555 PP

                     EEEEEEE..E-SSCHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc  97 valevdf..kfaspllgalvgqvaervldellaal 129
                     v++evdf   ++ ++lg++++  +e+  + +l+++
      AJA92805.1 102 VTIEVDFvlSGGLKILGMFAKSKIESSMKMVLDEF 136
                     55555554488999999998887777777666665 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.4e-09   2.1e-05       2     141 ..       2     139 ..       1     141 [. 0.73

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.4e-09
                      EEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEE.EEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSE.EEEEE CS
  Polyketide_cyc2   2 vkvtvsvviaappekVwalvsdfenwprWhpeva.rveleggggpargvegtvrvggrgtvreelvevdpegrllsyrivkpvpvany.vatwt 93 
                       k++ ++ ++ + +k +a+ +d+e + +  pe+  + ++++++g+++ + +t+r+ g +tv  + + v +++ ++  ++    + a++ +   +
       AJA92805.1   2 PKFSFTKLVDIDRDKFFAISTDYERFTEILPEYFlELKIVERDGNTTKIFETLRFLG-KTVNVTTEHVIEKPDRHIVKML--DGQAKGtTFDEK 92 
                      57888999*********************995554889888777776666****999.4433333333233444444442..233333256789 PP

                      EEECCETEEEEEEEEEEE.E--TT--HHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  94 vtpdgggtrvtwtgefda.gplggpfekpaaakavkgdleagLerLkar 141
                       + +g+ t+vt++++f   g+l   + + +a++ +++ ++  L+ ++  
       AJA92805.1  93 YEKVGDKTKVTIEVDFVLsGGL--KILGMFAKSKIESSMKMVLDEFANY 139
                      999*********9999964444..445788*************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1086.16
//
Query:       AJA92806.1  [L=79]
Description: hypothetical protein T478_0602 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 587.40
//
Query:       AJA92807.1  [L=412]
Description: enolase, N-terminal domain / enolase, C-terminal TIM barrel domain multi-domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.4e-59  199.1   1.1    1.3e-58  198.6   1.1    1.2  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    3.3e-20   72.6   0.2    1.1e-19   70.9   0.2    2.0  1  Enolase_N  Enolase, N-terminal domain
    6.8e-06   25.8   0.0    1.9e-05   24.3   0.0    1.7  2  MR_MLE_C   Enolase C-terminal domain-like


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.6   1.1   2.2e-62   1.3e-58       4     279 ..     133     402 ..     130     408 .. 0.94

  Alignments for each domain:
  == domain 1  score: 198.6 bits;  conditional E-value: 2.2e-62
                 E-EE-EEEEE-GGGSS.SS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHHHHHHHHHHHHCT-TC..TB CS
   Enolase_C   4 lPvPalnvinGGshag.nklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkealdliveaiekaGykg..kv 99 
                 +P P+ n++ GG hag ++ ++qe +++ +ga++++e++ +  +v+++lk+++ k+  + +   GdeGG+aP+++ n+eald+ v+aie+ G++   +v
  AJA92807.1 133 FPFPLGNILGGGAHAGpGTPDIQEILVASIGAKTVRESIDTNLQVHKELKKLILKNDPTFTNGRGDEGGWAPKFN-NEEALDISVKAIENLGFTLgkEV 230
                 799************95678*********************************99999999999*********96.89***************98889* PP

                 EEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHC CS
   Enolase_C 100 kialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiek 198
                  +++d ass  ++e++kky  d  + e+d+ +        ++  +++++y ++  ed++ e+ ++  +++t++   +  i Gddltvtn k+l++a+e 
  AJA92807.1 231 GLGVDFASSTQWNEEKKKYVYDRAGFENDSGE------QIEFASKIIENYKLIYAEDAVHEEAFDDMAEITKKFP-NSMITGDDLTVTNNKILTKAVEA 322
                 **********************9996666543......357999******************************9.6679******************* PP

                 T--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHH CS
   Enolase_C 199 kaanalllkvnqiGsltesleavklakeagygvvvshrsGetedttiadlavglsaGqiktGaparserlakynqllriee 279
                 k++na +lkvnq Gsl ++le +k+a+++    + shrsGe+ d+ i+++ +g+ +  +k G +   er+ k n+l+ri e
  AJA92807.1 323 KSCNAAILKVNQAGSLYDALEFAKVANQNNIKLITSHRSGESSDSHISHIGIGTGSKLLKVGIV-GGERVEKVNELIRISE 402
                 **************************************************************76.68************87 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.2   1.9e-23   1.1e-19       1     131 []       4     125 ..       4     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 1.9e-23
                 EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBTT-HHHHHHHHHHHH-STT CS
   Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldvtdqeeiDkllielDgten 99 
                 I+ + +r  ++SrG++T+ev+vtt+ +  gr ++psGaS+g++ea+         + +++ e++++  n++  ++ ig+d +d +++ +++ ++D+t+n
  AJA92807.1   4 ITAISGRVLYNSRGSKTIEVDVTTDGKYQGRVCAPSGASVGKFEAVS--------FPNNSPEESLSLLNQNS-DKFIGIDSSDLKQVHDVIHSIDETDN 93 
                 899*********************99999*****************5........55568899999888775.6677********************** PP

                 -TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
   Enolase_N 100 ksklGaNailavSlAvakaaAkakelplyryl 131
                  +k+G+  ++a+++A+ + aAk ++ ++++ +
  AJA92807.1  94 YAKIGGACAFAITIAATESAAKVENKQFFQMI 125
                 *************************9999875 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.2     7e+03      87     110 ..      91     116 ..      86     125 .. 0.67
   2 !   24.3   0.0   3.2e-09   1.9e-05      27     154 ..     212     357 ..     191     374 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.2
                 HHHHHHHHH.HH.SSEEEESTTSSSH CS
    MR_MLE_C  87 leglaelra.ra.sipiaagEslysr 110
                  +++a++    a  i iaa Es++ +
  AJA92807.1  91 TDNYAKIGGaCAfAITIAATESAAKV 116
                 56677777653356788888887665 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.2e-09
                 HHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..................BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHHHH.SSEEEEST CS
    MR_MLE_C  27 vaedvervravreavgpgddvdlmvDanqaw..................dlatAirvarelee.ldllwlEEPvppeddleglaelrara.sipiaagE 105
                 ++  v+ ++ +  ++g+  +v l vD+  +                   d  + i++a ++ e ++l + E+ v+ e   +++ae++ ++ +   ++g 
  AJA92807.1 212 LDISVKAIENLGFTLGK--EVGLGVDFASSTqwneekkkyvydragfenDSGEQIEFASKIIEnYKLIYAEDAVHEE-AFDDMAEIT-KKfPNSMITGD 306
                 56667777777777844..669999988884448888888999999998999*********666***********95.6********.77777888888 PP

                 TS..SSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEE CS
    MR_MLE_C 106 sl..ysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvap 154
                 +l  ++ + + +++ea+ + ++ ++v+++g +  a+++a++a +++++++ 
  AJA92807.1 307 DLtvTNNKILTKAVEAKSCNAAILKVNQAGSLYDALEFAKVANQNNIKLIT 357
                 651156999*************************************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2929.60
//
Query:       AJA92808.1  [L=311]
Description: hypothetical protein T478_1300 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2266.54
//
Query:       AJA92809.1  [L=773]
Description: valine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     5e-106  355.3   0.3   6.9e-105  351.6   0.3    2.0  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    8.1e-32  110.3   3.4    1.9e-31  109.1   1.1    2.3  2  Anticodon_1    Anticodon-binding domain of tRNA
    7.4e-22   77.6   2.8    4.1e-13   48.8   0.0    3.6  4  tRNA-synt_1g   tRNA synthetases class I (M)
     0.0016   18.0   0.0      0.089   12.3   0.0    2.8  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
        0.1   13.7   0.2        1.5    9.9   0.0    2.7  2  DUF1773        Domain of unknown function


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.6   0.3  1.9e-108  6.9e-105       2     594 ..      18     563 ..      17     571 .. 0.94

  Alignments for each domain:
  == domain 1  score: 351.6 bits;  conditional E-value: 1.9e-108
  tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGsl.HiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgre 98 
                  +++kW++e++++ +     + +++++  +PPy  G++ HiG a + +  d++ r++rm+Gk+v + +G+D  Gl++e   ekk g++ +    +  r 
   AJA92809.1  18 ILKKWDDEKLHDFK----LQDENYTIDTPPPYPSGRPwHIGAASHYAQIDMIARTARMNGKNVYFPIGIDRNGLPVELYTEKKHGIRMR----ETERG 107
                  78999999997766....45789************977*********************************************999997....88999 PP

  tRNA-synt_1  99 efrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEveykdkkdalihvafplad 196
                  ef + +++  +   +e+ + +k lG s Df++ y T ++e+ + ++e+f  l +kg+iy ++++ n+++ + t+++++E+ y d    l++++f ++d
   AJA92809.1 108 EFLNLCKNALDDLEAEMIQIMKSLGLSGDFKNYYRTDSEEYRKFTQETFIDLWKKGVIYLATRPNNYDWVSGTTIADAEIVYDDLPTKLVYMKFIVKD 205
                  ************************************************************************************************** PP

  tRNA-synt_1 197 keevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVki 294
                  +e+ +++ia T+Pe l + ++v vnp+                               der+++L+gk++  pl+n+++ i     ++ e+G+G+V +
   AJA92809.1 206 EEK-EIIIASTRPELLCACKTVIVNPD-------------------------------DERYSNLIGKNLVVPLTNKEVEITPHHSAKIEFGSGAVMV 271
                  ***.***********************...............................9*************************************** PP

  tRNA-synt_1 295 aPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaal 392
                    + d++D ++ ++ +le + ++  dg++te a++++glk ++ar k++e+l++ +l  k+e+i+h  p++ersk pi+    e ++ ++k+  +++ 
   AJA92809.1 272 CSYGDQNDVALFRELQLEEVIAIGLDGRMTEAAGNYQGLKPKQARTKIIEDLENANLVEKIEEISHRTPLSERSKIPIEIVPMEEYYLKQKDSIEKMK 369
                  ************************************************************************************************** PP

  tRNA-synt_1 393 kavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdkl.kkekgelekdedvlD 488
                  k  ++++f+p+++++  ++wle i+ dW iSR r++G+ ip+++ +e  e  v e  k            + + ++   +k  k+++ e++ ++ ++D
   AJA92809.1 370 KLGSEIEFYPNMHKQILMNWLESISiDWPISRRRFYGTEIPIWYCNECSEPFVPEPGK----------YYRPWKDSCPAQKCeKCGNTEFTGEDRTFD 457
                  ***********************977*********************99998833333..........33333333333444478999********** PP

  tRNA-synt_1 489 vWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadal 586
                  +W +S+ +p  + ++     e +kk++p+ +  +  Di+r W++  +l   +ltg++P+ e  v g  +de+G KmSKs+gN idpl vi+k gad  
   AJA92809.1 458 TWMDSSVSPLFVTKFNRD-DEFFKKTYPTGIRPQAKDIVRTWLYYTLLRCEKLTGQKPWSEAWVMGYGLDEKGMKMSKSKGNAIDPLPVIQKSGADTF 554
                  **************8776.8899*************************************************************************** PP

  tRNA-synt_1 587 Rltli.lsd 594
                  R++ + + +
   AJA92809.1 555 RFWSAsEIN 563
                  ***874444 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   4.4e+02      82     118 ..       3      32 ..       1      76 [. 0.55
   2 !  109.1   1.1   5.3e-35   1.9e-31       1     148 [.     607     749 ..     607     753 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
  Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpekaeelekel 118
                  P itE++w  e ++    e+ +l +w  +++ ++ +l
   AJA92809.1   3 PKITEKAW--EPKL----EDAILKKWD-DEKLHDFKL 32 
                  889*****..4544....666688898.554443322 PP

  == domain 2  score: 109.1 bits;  conditional E-value: 5.3e-35
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra.aqevllevletllrllaPfmPfitEelwqreeeel 96 
                  d+wilsel+kl++ ++e y +y+f   a+al ef+wn ++  y+e++k r y+   +d+ r  a  +l++vl+t+l+llaP++PfitE+lw    ++l
   AJA92809.1 607 DKWILSELDKLISVCNEGYSKYNFFIPATALREFTWNIFAAQYIEMAKARAYGIGFDDDeRDgAIFTLHKVLSTILKLLAPITPFITEHLW----QTL 700
                  9****************************************************9999999999****************************....999 PP

  Anticodon_1  97 gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpssel 148
                   +k+si++++ p+ ++    +++  ++ +++ e ++ + + +++++++ +  +
   AJA92809.1 701 YSKNSIHKEQLPKiEN---IEDM-TNMTQVIVEFNSKVWNEKKQNNLSLKDSI 749
                  ************6443...2223.34555545555555556777777766655 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.2e-16   4.1e-13       2     135 ..      38     187 ..      37     191 .. 0.83
   2 !    8.3   0.1   0.00023      0.83     177     238 ..     350     410 ..     316     428 .. 0.83
   3 !   18.6   0.1   1.8e-07   0.00065     317     372 ..     520     576 ..     450     589 .. 0.79
   4 ?   -3.6   0.1      0.97   3.5e+03     100     131 ..     693     724 ..     692     742 .. 0.73

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.2e-16
                   EEEE--B--SS--.-HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH.TTS-HHH........HH....HHHHHHHHHHHHHTT-- CS
  tRNA-synt_1g   2 lvttalpYangkl.HlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek.egvtpee........lv....ekvheeikelfkklnis 84 
                    + t+ pY++g++ H+G + ++ + D++aR  r++g++v+f  g D  G p+el  ek +g+  +e        l+    ++ ++e+ +++k+l++s
    AJA92809.1  38 TIDTPPPYPSGRPwHIGAASHYAQIDMIARTARMNGKNVYFPIGIDRNGLPVELYTEKkHGIRMREtergeflnLCknalDDLEAEMIQIMKSLGLS 134
                   688999****9755***************************************98765267766542223322255111145677888899999997 PP

                   ..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
  tRNA-synt_1g  85 ..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                     f +y+rt+see ++++qe f  l +kg iy  +    y+   +++++d ++
    AJA92809.1 135 gdFKNYYRTDSEEYRKFTQETFIDLWKKGVIYLATRPNNYDWVSGTTIADAEI 187
                   5588****************************************999999887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00023
                   EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
  tRNA-synt_1g 177 evketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                   e+   e++++k ++  +k+k+   +e +  ++  k+i+ +wl++   d+ isr+  +G ++P
    AJA92809.1 350 EIVPMEEYYLKQKDSIEKMKKLG-SEIEFYPNMHKQILMNWLESISIDWPISRRRFYGTEIP 410
                   55567899***********9999.555569999999********999**************9 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.8e-07
                   EE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHH CS
  tRNA-synt_1g 317 ahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfv 372
                   + +y l  +g K+SkS+g+++++  ++++  ad++R++ a+e ++  D+  s++++ 
    AJA92809.1 520 VMGYgLDEKGMKMSKSKGNAIDPLPVIQKSGADTFRFWSASEINQGYDFRCSEQKIE 576
                   4555466789********************************999999999888765 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 0.97
                   HHHHHHHHHHTT-EEEEEEEEEEETTTTEEE- CS
  tRNA-synt_1g 100 vqeifkklkekgliyekeieqlycpkderflp 131
                   +++++++l++k+ i +++  ++   +d + ++
    AJA92809.1 693 TEHLWQTLYSKNSIHKEQLPKIENIEDMTNMT 724
                   78999999999999998876665555555555 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.021        75      11      46 ..     198     233 ..     195     242 .. 0.88
   2 !   12.3   0.0   2.5e-05     0.089      86     142 ..     240     294 ..     231     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
  tRNA-synt_1_2  11 eiefkveeseeklevfttrpdtlfGvtfvalapehp 46 
                     ++f v+++e+++ +  trp+ l   + v + p+ +
     AJA92809.1 198 YMKFIVKDEEKEIIIASTRPELLCACKTVIVNPDDE 233
                    689***********************9999999876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.5e-05
  tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikp 142
                    g + + P+t+++++i       +e+g+gavm +   dq+D +  ++ +l  ++vi+ 
     AJA92809.1 240 GKNLVVPLTNKEVEITPHHSAKIEFGSGAVMVCSYGDQNDVALFRELQL--EEVIAI 294
                    667889***********************************98887665..555553 PP

>> DUF1773  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.46   1.6e+03       7      55 ..     332     378 ..     328     378 .. 0.68
   2 ?    9.9   0.0   0.00042       1.5      31      53 ..     707     727 ..     700     728 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.46
     DUF1773   7 nldfskrksgysassvpflngeepedeePLLpdigsilDinvLS.QlsfF 55 
                  +++s r   ++ s++p + +    ++   L ++ si+    L  ++ f+
  AJA92809.1 332 IEEISHRTPLSERSKIPIEIVPME-EYY--LKQKDSIEKMKKLGsEIEFY 378
                 566666665555566666644333.777..********999997788887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00042
     DUF1773  31 edeePLLpdigsilDinvLSQls 53 
                  +e+  Lp+i++i+D ++++Q++
  AJA92809.1 707 HKEQ--LPKIENIEDMTNMTQVI 727
                 4789..***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 4580.20
//
Query:       AJA92810.1  [L=172]
Description: putative ferritin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-30  103.9   1.3      8e-30  103.6   1.3    1.1  1  Ferritin      Ferritin-like domain
    0.00016   22.1   0.5    0.00028   21.3   0.5    1.5  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.063   13.3   0.0        0.1   12.7   0.0    1.3  1  ANAPC8        Anaphase promoting complex subunit 8 / Cdc23


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   1.3   1.3e-33     8e-30       2     141 ..       9     144 ..       8     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.3e-33
                 HHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS.CSSHHHHHHHHHHHHHHHHHHH CS
    Ferritin   2 kaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke.fgsveevleaalehekkvtesl 99 
                 kaLn+q+ +e +aa+ yl+ a++++ +g++g a+ff  qa+ee +h+ k+ ++++          a ++ +++p++ ++s+e++ + al  e+ vt+++
  AJA92810.1   9 KALNKQIEMEANAANAYLSAASWCDITGYDGAAKFFHAQAQEEHQHMLKFVNFVNGQCM-----SAIIPGVKQPPKtYKSLEAICKIALSNEQGVTKAI 102
                 89***********************************************9999986666.....888899999999899******************** PP

                 HHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin 100 relielaeeegDpatadfledfleeqeeheweleallekler 141
                 + +++la + +D+ t  fl+ f++eq e+e+++e++l+k+++
  AJA92810.1 103 NHMVDLATKDKDHNTITFLQFFVNEQIEEEQQFEDILQKFNL 144
                 **************************************9976 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.5   4.7e-08   0.00028       2     110 ..      10     112 ..       9     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.7e-08
                   HHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHHHHHHHHHHHHHH CS
  Rubrerythrin   2 iLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakpkflttaknLeeaiegayaee 96 
                    L+k i +E  a + Y + a+  +  gy   a++F++ A+eE++H  ++ ++++    +     vk+  ++y   ++  ++   n +    g +++ 
    AJA92810.1  10 ALNKQIEMEANAANAYLSAASWCDiTGYDGAAKFFHAQAQEEHQHMLKFVNFVNGQCMSAIiPGVKQPPKTYKSLEAICKIALSNEQ----GVTKAI 102
                   69999****************************************998888887755555535555555555555444444444444....333333 PP

                   HCHHHHHHHHHHHT CS
  Rubrerythrin  97 eemyrfyeelaeke 110
                        ++ +la k 
    AJA92810.1 103 ----NHMVDLATKD 112
                   ....3333333333 PP

>> ANAPC8  Anaphase promoting complex subunit 8 / Cdc23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.7e-05       0.1      64     107 ..      12     121 ..       4     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                 HHHHHHHHHTHHHHHHHHHHHHTT-HHHHHHH..................................................................T CS
      ANAPC8  64 peeaaleakeldkYllAkslFDckEfdrcaav..................................................................l 96 
                 +++ ++ea+ +++Yl A s+ D+  +d +a++                                                                  +
  AJA92810.1  12 NKQIEMEANAANAYLSAASWCDITGYDGAAKFfhaqaqeehqhmlkfvnfvngqcmsaiipgvkqppktyksleaickialsneqgvtkainhmvdlaT 110
                 567789*************************97777666666666666666666666666666666666666666666666555555555555555555 PP

                 TT--SHHHHHH CS
      ANAPC8  97 kdelsqkslFL 107
                 kd+ ++   FL
  AJA92810.1 111 KDKDHNTITFL 121
                 55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1248.03
//
Query:       AJA92811.1  [L=715]
Description: hypothetical protein T478_0678 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.37   11.3   0.0    1.4  1  ZapB      Cell division protein ZapB


Domain annotation for each model (and alignments):
>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     2e-05      0.37      12      43 ..     572     603 ..     570     617 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2e-05
        ZapB  12 kiqkaidtitlLqmeieeLkeeneelkeenre 43 
                 k++ +i++i++L  ei eLk++ +e ++ n+ 
  AJA92811.1 572 KYDGLITKISELNTEITELKKRLSEHAQPNNP 603
                 8999*******************999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 5067.97
//
Query:       AJA92812.1  [L=46]
Description: hypothetical protein T478_1403 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 352.59
//
Query:       AJA92813.1  [L=291]
Description: ribose-phosphate diphosphokinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-24   85.3   0.3    1.1e-23   83.4   0.0    2.1  3  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    2.7e-14   53.6   6.3    1.2e-13   51.6   1.6    2.9  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    5.7e-14   51.9   1.2    5.7e-14   51.9   1.2    2.4  3  Pribosyltran    Phosphoribosyl transferase domain
    1.3e-05   24.7   0.0    2.2e-05   24.0   0.0    1.5  1  UPRTase         Uracil phosphoribosyltransferase
      0.003   17.1   0.1     0.0055   16.2   0.1    1.4  1  PRTase_2        Phosphoribosyl transferase
     0.0035   17.2   0.0     0.0054   16.6   0.0    1.4  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.0   3.7e-27   1.1e-23       3     116 .]       6     119 ..       4     119 .. 0.97
   2 ?   -1.3   0.0      0.66     2e+03      13      53 ..     125     165 ..     121     183 .. 0.70
   3 ?   -2.0   0.0       1.1   3.3e+03      45      57 ..     209     221 ..     173     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 3.7e-27
  Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgysrqdrk 97 
                     ++ g ss +La++ia++++++ +k++ + f+dgE k++i++  +++ v+++qs+ +pv+ nl+ell +++ ++ +  +++ aViPy+gy+rqdr+
      AJA92813.1   6 VVGGDSSSDLAKRIARKIKSPYIKTEKKVFPDGESKITINQIPKKSIVVVVQSTYPPVDSNLLELLSIVSKVQ-KFSSKVYAVIPYMGYARQDRE 99 
                     7899********************************************************************7.66699**************** PP

  Pribosyltran_N  98 .ksrepisaklvaklLeaaG 116
                         e i+  +v klL+aaG
      AJA92813.1 100 fLGGEIITIGVVGKLLKAAG 119
                     999***************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.66
  Pribosyltran_N  13 aekiakrlgvelgkakvsrfadgEikveieesvrgkdvfii 53 
                       +i+++l ++  +++ ++ +  E+ v+  ++++ k+ +++
      AJA92813.1 125 TVDIHSKLALKELRISSENVSAMEVLVKHFKKMKMKNPVVV 165
                     55677777777777777777777777776666665555554 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
  Pribosyltran_N  45 vrgkdvfiiqsls 57 
                     v+++d++++ ++ 
      AJA92813.1 209 VKDRDLILVDDMI 221
                     4455555444443 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1     0.067     2e+02     141     172 ..     107     138 ..      82     152 .. 0.67
   2 ?    0.5   0.0      0.17   5.2e+02       2      29 ..     159     186 ..     158     202 .. 0.82
   3 !   51.6   1.6   3.9e-17   1.2e-13      80     157 ..     208     285 ..     189     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.067
                     EESSS--HHHHHT-TTEEEE--HHHHHHHHHH CS
  Pribosyl_synth 141 vtntipheiqklrcskiktvdislllaeairr 172
                         + + ++ +  +ki tvdi   la    r
      AJA92813.1 107 TIGVVGKLLKAAGVKKILTVDIHSKLALKELR 138
                     44455555566666777777776555544334 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                     GGGEEEEESSGGGHHHHHHHHHHTT-EE CS
  Pribosyl_synth   2 yrnavivakspgsakkatsyaerlrlgl 29 
                     ++n v+v+ + g  ++a  ++e l+   
      AJA92813.1 159 MKNPVVVSPDLGGKERAVKFSELLKTDF 186
                     699999*9999999***99999998654 PP

  == domain 3  score: 51.6 bits;  conditional E-value: 3.9e-17
                     --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-TTE CS
  Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcski 157
                     dv+ r  i+vdd+i    s+++a++ lk++   +++v +th ll +da+++++++ + +++ tntip e  k+  sk+
      AJA92813.1 208 DVKDRDLILVDDMISTGGSIIKATQFLKKQKCRRVFVACTHALLVNDAAKKIKNAGVSQIISTNTIPGESAKVDVSKV 285
                     899999****************************************************************99999887 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.29   8.5e+02      44      93 ..      16      56 ..      11      57 .. 0.58
   2 ?   -1.4   0.0       0.5   1.5e+03     105     126 ..     110     131 ..     107     145 .. 0.76
   3 !   51.9   1.2   1.9e-17   5.7e-14      17     145 ..     148     273 ..     133     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.29
                  HHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE CS
  Pribosyltran 44 akiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliV 93
                  ak++a++++ p+    ++k+ pdg ++++           +p++++V++V
    AJA92813.1 16 AKRIARKIKSPYIK-TEKKVFPDGESKIT--------INQIPKKSIVVVV 56
                  55555555544322.33445555555555........5678999999988 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.5
                   HHHHHHHCC-BSEEEEEEEEE- CS
  Pribosyltran 105 aalelLkekgpeevriavlvdk 126
                    + +lLk++g++++ ++ ++ k
    AJA92813.1 110 VVGKLLKAAGVKKILTVDIHSK 131
                   57889******99877666655 PP

  == domain 3  score: 51.9 bits;  conditional E-value: 1.9e-17
                   ETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC CS
  Pribosyltran  17 rlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkek 113
                   + + +++++ + k++vvv ++ gG  +a + +  L+   +++  +k r+ +++++++ s        d++++  ++VDD+++tGg++++a+++Lk++
    AJA92813.1 148 EVLVKHFKKMKMKNPVVVSPDLGGKERAVKFSELLK--TDFIALKKQRDRKTGKVKILS-----GKVDVKDRDLILVDDMISTGGSIIKATQFLKKQ 237
                   566777888899***********************9..566666666666666665544.....788****************************** PP

                   -BSEEEEEEEE...E-HHHHHHHHHH-TTS...... CS
  Pribosyltran 114 gpeevriavlv...dkpateeevdknakrvfsls.p 145
                   ++ +v +a+ +    + a ++ + +++  ++s++ +
    AJA92813.1 238 KCRRVFVACTHallVNDAAKKIKNAGVSQIISTNtI 273
                   ********9997765555555666666666666655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   7.5e-09   2.2e-05      93     158 ..     185     246 ..     133     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.5e-09
     UPRTase  93 rvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvls 158
                  ++ l+ qr+ +t + ++   k+   +++r  +l+D +i+TGgs+++a q Lk++ ++  +++v++
  AJA92813.1 185 DFIALKKQRDRKTGKVKILSGKVD--VKDRDLILVDDMISTGGSIIKATQFLKKQKCR--RVFVAC 246
                 566788889998888766666654..579*************************7765..555443 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.8e-06    0.0055     120     165 ..     210     255 ..     200     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
    PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslvdwrsee 165
                 +++ l+LvDD istG ++++  + l+++  r+ +v ++   +++++
  AJA92813.1 210 KDRDLILVDDMISTGGSIIKATQFLKKQKCRRVFVACTHALLVNDA 255
                 6789**********************99999887777654444444 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06    0.0054     170     216 ..     225     271 ..     131     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                   HHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHH CS
  Asp_Glu_race 170 railkllerlaergadaviLGCTelplllekaealekeksvpvidpt 216
                     i+k+ + l+++++ +v+++CT+  l+ ++a++++++   ++i+++
    AJA92813.1 225 GSIIKATQFLKKQKCRRVFVACTHALLVNDAAKKIKNAGVSQIISTN 271
                   45677777788***********************9998766677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2062.94
//
Query:       AJA92814.1  [L=386]
Description: thiolase, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.2   0.0    2.4e-20   73.0   0.0    1.7  1  Thiolase_N       Thiolase, N-terminal domain
    2.2e-11   43.5   0.6    1.1e-10   41.3   0.1    2.4  3  Thiolase_C       Thiolase, C-terminal domain
    8.1e-05   22.3   0.8       0.03   13.9   0.4    2.9  3  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0079   16.0   0.0       0.39   10.6   0.0    2.5  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
  ------ inclusion threshold ------
       0.15   12.1   1.2        1.4    9.0   0.6    2.7  2  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   6.6e-24   2.4e-20       8     259 ..      13     223 ..       6     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 6.6e-24
                 EE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHS CS
  Thiolase_N   8 rtpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagipeevpavtvnkvcsSglkavalaaqsiaagead 105
                  t+ gk      d s++++  +a  +++e+ag++p+e++  +++nv   ++ q  +   ++ ++gi  e p+  ++ +c+Sg  +  +a  ++aag +d
  AJA92814.1  13 STKYGK-----LDDSISDITLQASVGAIESAGIEPKEIEAGYISNVFGVADKQVhLGPVVMSNLGI-SECPSLSIESACGSGSVSFREAFANVAAGFYD 105
                 555555.....456788888999999***********************9999979999999****.9******************************* PP

                 EEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEE CS
  Thiolase_N 106 vvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkg 204
                 +v++ G+E+ +++ t+ +t+  s       + +d+  ++g a a+     +  a+ ++++++++ e+++++Avk+h++++ ++ka+ ++++i       
  AJA92814.1 106 AVLVTGTEKVTHTGTDWTTTYFS-------YCSDFF-YEGQAGASFPGLFASMARAYLHEFDATEEDLASVAVKNHENGVLNPKAH-LRKKI------- 188
                 *************9999855543.......333333.23333334444667889********************************.99989....... PP

                 SSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
  Thiolase_N 205 kkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqisDGaaavllmse 259
                        + d+ ++s v+a +L+ +             ++++ sDGa+ v+l++e
  AJA92814.1 189 -------SIDDVMDSAVVASPLKLY-------------DCCPFSDGASSVILCNE 223
                 .......89****************.............***************98 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.92   3.3e+03      27      47 ..      30      50 ..      27      60 .. 0.65
   2 ?   -2.1   0.0      0.77   2.8e+03      44      54 ..      89      99 ..      47     116 .. 0.59
   3 !   41.3   0.1   2.9e-14   1.1e-10      18     115 ..     252     369 ..     241     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.92
                HHHHHHHHHT--GGGESEEEE CS
  Thiolase_C 27 aikkvlkkagltvedidlfEi 47
                a+  +++ ag++ ++i++  i
  AJA92814.1 30 ASVGAIESAGIEPKEIEAGYI 50
                455567777777777766554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.77
                EEEE--SBHHH CS
  Thiolase_C 44 lfEinEAFaaq 54
                 + + EAFa +
  AJA92814.1 89 SVSFREAFANV 99
                45566777765 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 2.9e-14
                 GGGGGHHH..HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHHHHHHHHHHHH CS
  Thiolase_C  18 eilglgPa..yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasGaRivvtllse 96 
                 e+l++ P    a++++ k ag+t +d+d+ E+++ F++  ++  ++l++ +                    +N  GG  + GHP+Ga+G+ +vv + ++
  AJA92814.1 252 EQLTTIPStrIAAEAAYKMAGITAKDVDFAEVHDCFTVAEVVDSEDLGFFEkgtgataarngdtklngsISINPSGGLKSKGHPIGATGVGQVVEAFEQ 350
                 5566666522588999*********************************999**************99889**************************** PP

                 HHHCTTSEEEEEEEETTTE CS
  Thiolase_C  97 lkkeggklgvaalCigggq 115
                 l+ + g+ +v  + ig  q
  AJA92814.1 351 LTGKSGERTVNDAKIGLTQ 369
                 **99998888877777665 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0     0.004        14      88     123 ..      23      58 ..      11      71 .. 0.85
   2 !   13.9   0.4   8.5e-06      0.03     166     207 ..      76     117 ..      67     122 .. 0.91
   3 ?   -1.0   0.0       0.3   1.1e+03      27      58 ..     248     279 ..     246     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.004
                    HHHHHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESS CS
  ketoacyl-synt  88 qqrllleaawealedagltpeeldgsrvgvfiGvga 123
                     + + l+a+  a+e+ag++p+e++   + ++ Gv+ 
     AJA92814.1  23 ISDITLQASVGAIESAGIEPKEIEAGYISNVFGVAD 58 
                    566789*****************9988999888875 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.5e-06
                    SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
  ketoacyl-synt 166 GpsvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                     ps+++++AC S+ v    a  ++ +g  d++l+ G+e  ++
     AJA92814.1  76 CPSLSIESACGSGSVSFREAFANVAAGFYDAVLVTGTEKVTH 117
                    69***********************************98776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.3
                    HTT---EEES-TTSSCGTTSBTSSTTEEE-BS CS
  ketoacyl-synt  27 legrdaiselpadrwdadklydpparaagkik 58 
                    l+gr+  +++p++r  a++ y+ +  +a++++
     AJA92814.1 248 LQGREQLTTIPSTRIAAEAAYKMAGITAKDVD 279
                    57888888999988888887766666666554 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00011      0.39       3      45 ..      81     124 ..      79     140 .. 0.88
   2 ?    2.6   0.0     0.033   1.2e+02      49      64 ..     208     223 ..     197     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                  EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG.CS-TTT CS
  ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlsk.ilDwkd 45 
                  +++aC +  +    A a +++g +  vLv g+e++++  +Dw+ 
   AJA92814.1  81 IESACGSGSVSFREAFANVAAGFYDAVLVTGTEKVTHtGTDWTT 124
                  6789999999999999********************98999975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.033
                  HTTB-EEEEEEEEEEE CS
  ACP_syn_III  49 avlfGDGAgAvvleas 64 
                  +  f+DGA  v+l ++
   AJA92814.1 208 CCPFSDGASSVILCNE 223
                  677*********9876 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.7   2.5e+03      32      45 ..      33      46 ..      26      62 .. 0.82
   2 ?    9.0   0.6   0.00039       1.4      28      54 ..     262     288 ..     238     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.7
                     HHHHHHT--GGGEE CS
  Ketoacyl-synt_C 32 kalaeagvdpedvd 45
                      a+++ag++p++++
       AJA92814.1 33 GAIESAGIEPKEIE 46
                     68899999999986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00039
                      HHHHHHHHHHT--GGGEEEEE-SS-SS CS
  Ketoacyl-synt_C  28 raiekalaeagvdpedvdyveahgtgt 54 
                       a e+a+++ag++++dvd  e h+  t
       AJA92814.1 262 IAAEAAYKMAGITAKDVDFAEVHDCFT 288
                      46899******************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2778.01
//
Query:       AJA92815.1  [L=102]
Description: translation initiation factor Sui1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-18   65.1   0.1    8.1e-18   64.7   0.1    1.2  1  SUI1          Translation initiation factor SUI1
  ------ inclusion threshold ------
      0.058   13.3   0.0      0.082   12.8   0.0    1.3  1  DUF3877       Domain of unknown function, E. rectale Gene des
      0.068   13.5   0.1        0.2   12.0   0.0    1.7  2  PG_binding_2  Putative peptidoglycan binding domain
       0.12   12.7   0.0       0.14   12.5   0.0    1.3  1  Img2          Mitochondrial large subunit ribosomal protein (


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   1.8e-21   8.1e-18       3      76 ..      25      94 ..      23      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.8e-21
        SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                ++i irle+r+ +Kk T ++gl+++  +l+++akelk k ac+g+  k+g   i +QGd+r+ ++e+L++  g+
  AJA92815.1 25 SQIIIRLETRRFKKKGTMIEGLDPKINNLESVAKELKGKYACGGTA-KEG--YIFLQGDHRDTIKEALVKL-GF 94
                6899*****************************************6.888..8****************97.76 PP

>> DUF3877  Domain of unknown function, E. rectale Gene description (DUF3877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.082       8      28 ..      81     101 ..      74     102 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
     DUF3877   8 lidvikEeqlKlGyrkekirl 28 
                   d+ikE+ +KlG+++eki+l
  AJA92815.1  81 HRDTIKEALVKLGFSEEKIEL 101
                 579****************98 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.76   3.4e+03      53      58 ..      50      55 ..      49      62 .. 0.72
   2 ?   12.0   0.0   4.4e-05       0.2       8      32 ..      72      96 ..      68     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.76
  PG_binding_2 53 veNFEn 58
                  ++N+E 
    AJA92815.1 50 INNLES 55
                  799996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.4e-05
  PG_binding_2  8 eeervlaedvaeevqaaLsrLGyyd 32
                  e +  l++d  + +++aL++LG+ +
    AJA92815.1 72 EGYIFLQGDHRDTIKEALVKLGFSE 96
                  6788899****************44 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.2e-05      0.14      51      80 .]      65      94 ..      18      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.2e-05
        Img2 51 lvkvnevtgkieikGdrveevkkfLeskgF 80
                ++  + ++g i ++Gd+++ +k+ L ++gF
  AJA92815.1 65 ACGGTAKEGYIFLQGDHRDTIKEALVKLGF 94
                355666999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 777.80
//
Query:       AJA92816.1  [L=588]
Description: BNR repeat-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-11   43.8   0.0    1.7e-10   40.7   0.0    2.2  1  BNR_2     BNR repeat-like domain
  ------ inclusion threshold ------
       0.01   15.2   0.5       0.01   15.2   0.5    2.8  2  BNR_4     BNR repeat-containing family member
        1.3    9.3  20.0       0.83    9.9   0.3    6.3  6  BNR       BNR/Asp-box repeat


Domain annotation for each model (and alignments):
>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   2.8e-14   1.7e-10      17     258 ..     192     470 ..     185     515 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.8e-14
                 EEEEEEEEETTEEE.EEEEEE-TTS-...BTTEEEEEEEEEEETTTEEEEEEEEEETT--HH........T----E.....EEESSTTSS----E...H CS
       BNR_2  17 dvaiwvsvsdkgsneWsapqvvadreqsrearkklgNPvlfqdpsgtliLfykvgvsvggwa........gskitr.....vtSkDdGktWsapr...r 99 
                 ++ i +  + +g+n+W+ p++v +   +  + +  g  +l + p+g+++  y  g s+++ +        g    +      +S+D+GktW   +   +
  AJA92816.1 192 ETNILFTSTYDGGNTWTDPTIVNEPG-KASRPHMAGGAMLQVGPDGEIYALY--GHSIKNQKvmdegfghG----YtytilARSDDGGKTWPMHTligD 283
                 5666666678999************9.8888899999999999********9..55555555557777652....0234569*********98886652 PP

                 HHGGEEEEEE-SS--..EE--....T--EEEE...EE..SS--...EEEEEEEESSTTSS-EE----S.SSEEEEEEEE.EEETTEEEEEEEE...... CS
       BNR_2 100 lpkspflnisgpvknkpiqla....dGrlilP...sshelagk...wrallelsddggktWkkgrvve.qisgeiqpsilvekdgslvalaRs...rka 184
                   ++    ++g+++ k ++      dGr+ ++   s+++ +g+    ++ +++sd +g + +k+ +v+ +   ++   i  ++ g+  + +R+   +  
  AJA92816.1 284 PNTHYHDAANGMMHSKTFESFsirdDGRVYVAwldSRGQQNGGyttGQVRMQYSDTNGESFSKSVIVKnKVCPCCATDICSKTTGETFVQYRNivgN-Y 381
                 2222445689999998854335667*******999777744443336789**********999999985566789999***************9853.3 PP

                 ......EEEEEEESSTTSS-EEE-EEEEE----.......---SEEEEEE...EE--..........SSEEEEEEESTT-GGG----EEEEEE CS
       BNR_2 185 ......aileseSedgGetWskveltslpnpnsgidavtlkdgrlllvyN...hesa..........pRkpLtvalskdngkswkevltLekg 258
                        i++s+S d G+ W+++el     ++   +a t+++  ++l +N   h  a          +   L  a+skd++++w+ +l  + +
  AJA92816.1 382 gepnyrDIVVSKSDDHGAVWNPPELVGDDGYETNGCAHTVSS--MALDSNgylH--AawytggrsnaEGPGLYYAVSKDDAETWSYPLKVWGE 470
                 5889999*****************887777776666666544..5555554331..1234443333345568889999999999988877765 PP

>> BNR_4  BNR repeat-containing family member
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   3.1     0.025   1.5e+02      92     144 ..     165     215 ..     131     351 .. 0.60
   2 ?   15.2   0.5   1.7e-06      0.01     101     195 ..     364     462 ..     360     489 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.025
                 SSEEEEEEEE-GGG-.EEEEEEE-TTSS-EEEEEEEETTTTEEEEEES-.SB-- CS
       BNR_4  92 ssvTYPrflstedgk.LllsyRdgksgngnavlneYdektdkwktlgekqlldg 144
                 + + YP ++ + d + + ++y d+  g++n+    + ++ d  +t+ + ++++ 
  AJA92816.1 165 DGMAYPGVVIDGDRSaVHVTYADTVNGETNIL---FTSTYDGGNTWTDPTIVNE 215
                 44555544444333325555555555555554...2222222345555444444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-06
                 E-GGG-EEEEEEE-T..TSS-EEEEEEEETTTTEEEEEES-.SB--T.....TT-EEEEEE.EE-TTS-EEEEEEEE-SSSGGGEEEEEEEEESSTTSS CS
       BNR_4 101 stedgkLllsyRdgk..sgngnavlneYdektdkwktlgekqlldgee....gqrnaYlkglsygkdgrihvtwtwretpdaetnhdlyYaysddggrt 193
                 s+  g+ ++ yR++   +g+ n +    ++++d+   +++   l g +    ++    ++ +  + +g +h +w +++  ++++   lyYa+s+d++ t
  AJA92816.1 364 SKTTGETFVQYRNIVgnYGEPNYRDIVVSKSDDHGAVWNPP-ELVGDDgyetNGCAHTVSSMALDSNGYLHAAWYTGG-RSNAEGPGLYYAVSKDDAET 460
                 56678888999986533666666667788999999999996.66665667754555557788999*************.77777779************ PP

                 -B CS
       BNR_4 194 we 195
                 w 
  AJA92816.1 461 WS 462
                 94 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.1     0.059   3.5e+02       3      11 ..     200     208 ..     199     209 .. 0.89
   2 ?    9.9   0.3   0.00014      0.83       2      10 ..     267     275 ..     266     275 .. 0.93
   3 ?    1.1   0.1      0.11   6.8e+02       1      12 []     335     346 ..     335     346 .. 0.89
   4 ?    4.9   0.0    0.0064        38       3      11 ..     394     402 ..     393     403 .. 0.90
   5 ?   -3.0   0.2       2.5   1.5e+04       8      11 ..     459     462 ..     459     463 .. 0.80
   6 ?   -1.9   0.0         1   6.3e+03       3      10 ..     496     503 ..     495     505 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.059
                 ESSTTSS-E CS
         BNR   3 StDgGktWs 11 
                 ++DgG tW+
  AJA92816.1 200 TYDGGNTWT 208
                 78******7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                 EESSTTSS- CS
         BNR   2 yStDgGktW 10 
                  S+DgGktW
  AJA92816.1 267 RSDDGGKTW 275
                 59******* PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.11
                 EEESSTTSS-EE CS
         BNR   1 yyStDgGktWsk 12 
                 +yS+ +G+++sk
  AJA92816.1 335 QYSDTNGESFSK 346
                 79999*****96 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0064
                 ESSTTSS-E CS
         BNR   3 StDgGktWs 11 
                 S+D+G  W+
  AJA92816.1 394 SDDHGAVWN 402
                 9*******7 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2.5
                 SS-E CS
         BNR   8 ktWs 11 
                 +tWs
  AJA92816.1 459 ETWS 462
                 69*8 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 1
                 ESSTTSS- CS
         BNR   3 StDgGktW 10 
                 + DgG  +
  AJA92816.1 496 TVDGGAVY 503
                 78***765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4073.47
//
Query:       AJA92817.1  [L=136]
Description: hypothetical protein T478_0857 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   15.2   0.4        7.7    6.4   0.0    3.1  2  Ribosomal_S14  Ribosomal protein S14p/S29e
       0.16   11.9   0.7       0.16   11.9   0.7    4.6  4  Prok-RING_4    Prokaryotic RING finger family 4
       0.29   11.2  14.9          4    7.6   1.9    3.3  3  PHD_4          PHD-finger


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0013       7.7      11      25 ..      48      62 ..      40      69 .. 0.78
   2 ?    5.2   0.3    0.0031        18      14      38 ..      95     128 ..      86     135 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0013
                   .CTTT---SSS--SS CS
  Ribosomal_S14 11 ptrirnrCrvtGrpr 25
                    + i+ +C+v+G++ 
     AJA92817.1 48 DSNIKAKCVVCGKQS 62
                   57899*******986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0031
                    TT---SSS--SSSEE-.....GGG-....EHHHH CS
  Ribosomal_S14  14 irnrCrvtGrprGvir.....kfgL....sRicf 38 
                     +  C+++ +  G+ir     ++++    +R+c+
     AJA92817.1  95 KKEFCVLCNKKMGFIRynpkpEWKIkgqlCRVCW 128
                    566799*******998333333444444466665 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.036   2.2e+02      32      41 ..      10      19 ..       4      26 .. 0.63
   2 ?    2.8   1.6     0.018   1.1e+02      21      39 ..      35      61 ..      33      68 .. 0.60
   3 ?   11.9   0.7   2.6e-05      0.16      19      40 ..      79     106 ..      77     109 .. 0.82
   4 ?    4.8   0.3    0.0042        25      20      30 ..     123     133 ..     122     136 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.036
  Prok-RING_4 32 sCPlCqrris 41
                  C +C+++ +
   AJA92817.1 10 ICTVCKKETK 19
                 5666666643 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.018
  Prok-RING_4 21 CkeCfdsk.dls.......sCPlCqrr 39
                 C +C+ +k + s        C +C ++
   AJA92817.1 35 CGDCYMDKmKESydsnikaKCVVCGKQ 61
                 788876664222334466677777665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 2.6e-05
  Prok-RING_4  19 lvCkeCfdskdls......sCPlCqrri 40 
                  l+Ck+Cfd+k+         C lC++++
   AJA92817.1  79 LLCKTCFDNKEADfktkkeFCVLCNKKM 106
                  79*******95555577779****9985 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0042
  Prok-RING_4  20 vCkeCfdskdl 30 
                  +C+ C+d+++ 
   AJA92817.1 123 LCRVCWDEQKA 133
                  7******9875 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.9   0.00066         4       5      36 ..       9      38 ..       6      45 .. 0.66
   2 ?    7.2   3.0   0.00087       5.2       4      39 ..      52      87 ..      50     103 .. 0.88
   3 ?    2.2   0.7     0.032   1.9e+02       5      38 ..      97     129 ..      93     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00066
       PHD_4  5 aaCivCgedgkedevveeesetpsslmeCsvC 36
                a+C+vC+++ k++++++  +e + +   C  C
  AJA92817.1  9 AICTVCKKETKHKHKAK--KEWYVESPLCGDC 38
                89*********995332..3444333334444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00087
       PHD_4  4 taaCivCgedgkedevveeesetpsslmeCsvCyei 39
                +a C+vCg++ k  +  e + +   + + C+ C++ 
  AJA92817.1 52 KAKCVVCGKQSKITDLWEPRWQWDMKGLLCKTCFDN 87
                799*********99999888999999999****986 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.032
       PHD_4   5 aaCivCgedgkedevveeesetpsslmeCsvCye 38 
                 + C++C+++    +  + + e + +   C vC++
  AJA92817.1  97 EFCVLCNKKMGFIRY-NPKPEWKIKGQLCRVCWD 129
                 568888776554433.333566666667888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1052.81
//
Query:       AJA92818.1  [L=70]
Description: hypothetical protein T478_0956 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 529.53
//
Query:       AJA92819.1  [L=292]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-16   59.2   0.0    1.2e-15   58.3   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   6.6e-20   1.2e-15       2     155 ..      21     176 ..      20     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.6e-20
                  EEESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESST.GGGSTTHHHHHHHHHHTC.CCTEEEEEEECSSCHG...HH CS
                  xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xx RF
  Radical_SAM   2 vvtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekg.vkevilggge.pllypdfvellerlakla.vpgiritvetngtlpd...ee 92 
                   vt gC+++ CsfC+ ++     + + +++++e++ e++ +++ +  +  ++l  g+  +l  ++ ++++++++++ ++  ri++ + ++ +    +e
   AJA92819.1  21 QVTLGCSFNqCSFCDMYR----SKEYSERTWDEVKGEIDMMAKIMPdTQRIFLADGDaINLSTEYMVKILEYIREKfSSIERISCYAMPMNLLrktPE 114
                  5899****99*******5....8*******************555559999999666156678888888888888776666666665555555788** PP

                  HHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  93 klerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                   l++l ++g++ ++lg+e+++d + +k + +g t + +++a+ k++++g+k ++ +i+gl G 
   AJA92819.1 115 DLQKLHNAGLNMLYLGIESGSDIVLRKVT-KGATSKTIIKACNKAKDVGFKLSCMVILGLGGK 176
                  ***********************555555.99*******************988888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1914.00
//
Query:       AJA92820.1  [L=68]
Description: hypothetical protein T478_0634 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.013   15.5   0.0    1.1  1  DUF2714   Protein of unknown function (DUF2714)


Domain annotation for each model (and alignments):
>> DUF2714  Protein of unknown function (DUF2714)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   7.5e-07     0.013      84     131 ..      15      63 ..      12      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.5e-07
     DUF2714  84 eainlsssndeklnkflkslNklikkll.ekkklveilpniilfvsket 131
                  +i l+ss d + +  l+ +N   ++ l +++ ++  +++++lfvs+ +
  AJA92820.1  15 FSIGLISSADAHPHVSLELMNTHSHEILtSQDFVIHTFEQVVLFVSQLQ 63 
                 689999**********************99999************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 509.59
//
Query:       AJA92821.1  [L=444]
Description: adenosylmethionine-8-amino-7-oxononanoate transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-92  308.3   0.0    8.2e-92  307.9   0.0    1.0  1  Aminotran_3      Aminotransferase class-III
    5.7e-05   22.5   0.0    0.00011   21.7   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.052   13.9   0.0        3.1    8.2   0.0    2.6  2  DUF2183          Uncharacterized conserved protein (DUF2183)


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.9   0.0   1.4e-95   8.2e-92      12     403 ..      25     434 ..      16     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 307.9 bits;  conditional E-value: 1.4e-95
                  EEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHHHHHHH CS
  Aminotran_3  12 vitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAlKlark 109
                   i  a+G++l+d  g ++lD v+s++ +  Gh+  ++v  + +q + l+h+ + +lt+ +a+kl++kll+l pk +  vf+ ++Gs A+e A+K+a +
   AJA92821.1  25 EIVSAKGMWLYDSKGGKMLDGVASMWCNVWGHSKSELVSEIIKQTKILQHTPLFNLTHPSAEKLSKKLLQLNPK-MKSVFFSDNGSTAMEIAIKIALQ 121
                  57789*********************************************************************.*********************** PP

                  HHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HH..HHHHHHHHHHHHHH..CHTCCCEEEEEE-S.CE CS
  Aminotran_3 110 yarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkene..eeeaalleeleale..kkkkdevaAvivEp.iq 202
                  y r++++++kt++ ++++++HG+t+ga+sv+   ++  ++f + l  +++++ p ++++ +n   ++++ ++ +l+++e   +k++ +aA+++E   q
   AJA92821.1 122 YWRNVGENKKTNVATLENGYHGDTFGAMSVGYV-PEFFSKFRSKLFSTIQFPVPRTVIIGSNTkkSSKEYAEYCLSKIEdkLEKDNSIAAFVMESgAQ 218
                  *********************************.9********************99998887546677788889999987789999*********** PP

                  TTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS........B--TT CS
  Aminotran_3 203 gegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs........hgsTf 291
                   +gGv++++++f +++ ++ckk+dvl++ DE++tGfGr G +  +++ + +pD++ ++K+ltgG  +++a+l+t+++++ +  g+        hg+T+
   AJA92821.1 219 MAGGVIIYPKNFQKRISQICKKNDVLFVLDEIATGFGRLGSMIEYQSQNSTPDIVSFGKMLTGGyQTFAATLTTKKINDSF-LGEfsqfkhlfHGHTY 315
                  ****************************************************************8899************9.7777999********* PP

                  TT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC.........HHHHHHHHHCTEE-EEETTT CS
  Aminotran_3 292 gGnplacavalavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke.........keilkkakekGvlilsaGdn 380
                  +Gnp a+a++l+ le+ ++ +l+e++q++++++k++L ++++ +  ++e+R +G++++iel+++++ ++         k ++++++++ ++++++G n
   AJA92821.1 316 TGNPTAAALSLKNLELYKKYHLIEKIQKTSKIFKDRLDDISNLD-LVGEIRHQGMVMGIELVQNKNSNKplssnisinKLVFEEGRKHQIYFRTLG-N 411
                  *****************************************997.*********************999********9889***************.* PP

                  EEEE---TT--HHHHHHHHHHHH CS
  Aminotran_3 381 virllppliitdeeidelleilk 403
                  +i l+ppl i++++++ l++ + 
   AJA92821.1 412 IIMLVPPLDISQKDLNFLIDGTI 434
                  ***************99998765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.8e-08   0.00011      35     167 ..      86     248 ..      81     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-08
                      HHHHHHHHHHTT-SEEE.EES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..................... CS
  Beta_elim_lyase  35 nrLedavaelfgkeaal.fvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..................... 106
                      ++L +++ +l  k + + f  +G  A +i++ki lq + +v  +++ ++ + e+g +    g++ +    +                       
       AJA92821.1  86 EKLSKKLLQLNPKMKSVfFSDNGSTAMEIAIKIALQYWRNVGENKKTNVATLENGYHGDTFGAMSVGYVPEFFskfrsklfstiqfpvprtvii 179
                      5666666666666655516669**************************************99977776665558999***************** PP

                      ...........TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHH.HHHHHHHHHCT-EEEEE CS
  Beta_elim_lyase 107 ...........GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleel.revaaiakkygiplhlD 167
                                  +  l k+e+++++  +  + i++ +++   ++agG ++ +++  +++++i+kk+++ ++lD
       AJA92821.1 180 gsntkksskeyAEYCLSKIEDKLEK--D--NSIAAFVMESGAQMAGGVIIYPKNFqKRISQICKKNDVLFVLD 248
                      *************************..5..67***************99988887367*************99 PP

>> DUF2183  Uncharacterized conserved protein (DUF2183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00052       3.1      48      92 ..      82     126 ..      55     128 .. 0.76
   2 ?    2.6   0.0     0.029   1.7e+02      61      85 ..     170     194 ..     162     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00052
     DUF2183  48 aehKraeiekiletfperkfiliGDsgqkdpeiYaeiakefpeqi 92 
                 +   ++  +k+l+  p++k + + D+g + +ei  +ia ++ +++
  AJA92821.1  82 HPSAEKLSKKLLQLNPKMKSVFFSDNGSTAMEIAIKIALQYWRNV 126
                 4444555579***********************999999987666 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
     DUF2183  61 tfperkfiliGDsgqkdpeiYaeia 85 
                 +fp  + ++iG +++k  + Yae +
  AJA92821.1 170 QFPVPRTVIIGSNTKKSSKEYAEYC 194
                 699999***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 2413.66
//
Query:       AJA92822.1  [L=96]
Description: hypothetical protein T478_1221 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 709.18
//
Query:       AJA92823.1  [L=265]
Description: inositol monophosphatase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-27   95.4   0.0    4.8e-27   95.2   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
     0.0021   17.6   0.0      0.004   16.7   0.0    1.4  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   0.0   5.3e-31   4.8e-27      11     258 ..       9     256 ..       2     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 5.3e-31
                 HHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEE CS
  Inositol_P  11 elaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekseltedgltwivDPiDGTknFvrgipqvaVs 109
                 e+ +++ e++++ +++++++ + +      d+  ++d  +e ++l+ l+e   + ++lgee ++ +   + +++  ++i D iDG +n vrg p ++ s
  AJA92823.1   9 EASRRIFEAVKDMAGTEKAAGDFG-RGAGGDISRNIDITAENTVLDYLKEINFECVVLGEECGRVEL--SDNPK-GFIIMDAIDGSANAVRGVPFFCSS 103
                 333344444444444333333333.356789******************9999********999888..44455.69********************** PP

                 EEEEETTE...EEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTEEEEEESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHH CS
  Inositol_P 110 igllvegk...pvlGviaqPllgqlysaakgkGaflngeklplsrappiseallvtlfavssrkdtseasllekvesavsaegvrsvgssalklaavae 205
                 ++++ e +   ++ Gvi +  +gq+y+++kg+Gafl++++++++++ p+ + + v+ +++ s++ +++   l+ v +++s++  r +g+ al++a+ a+
  AJA92823.1 104 LAFATENRlssITDGVITNLSTGQMYHSTKGNGAFLDDKQISVHKDVPLYKIVGVN-TSGASQEIMKK---LQPVFEHHSHT--RHFGANALEMAMFAQ 196
                 *****765222677*********************************888887766.44444444444...89999999999..*************** PP

                 TSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEEESSSC......SSSTTSSEEEEESCHH CS
  Inositol_P 206 Gkadaylefg.rekkWDhAAGeaileeaGGvvtdakge......grlllargiiaanqke 258
                 G +d++++ + ++ + D+AAG +i++eaGG ++d k +      +++   + i+aanq+ 
  AJA92823.1 197 GLMDVFIDLRdKIRIQDIAAGYIIVKEAGGLLLDSKFNsldadlSYDTRVSFIAAANQEI 256
                 *********99************************9998877544444444444444433 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.4e-07     0.004      30     116 ..       9      92 ..       4      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.4e-07
      FBPase  30 lalkiisskvrk.aelvnllGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                 +a + i ++v+  a+  +  G    +   Gd  +++D+ a++++ + lk+ +  +v+  EE   ++      + k  +++D +DGS+n
  AJA92823.1   9 EASRRIFEAVKDmAGTEKAAGDF-GRGAGGDISRNIDITAENTVLDYLKEINFECVVLGEECGRVELS---DNPKGFIIMDAIDGSAN 92 
                 55555555555413333333333.356789*********************99999999998887665...56666899*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1889.97
//
Query:       AJA92824.1  [L=107]
Description: hypothetical protein T478_0264 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 768.77
//
Query:       AJA92825.1  [L=1268]
Description: DNA-directed RNA polymerase subunit A' / DNA-directed RNA polymerase, subunit A'' multi-domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-93  312.5   0.0    6.3e-93  311.5   0.0    1.5  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    3.5e-83  279.1   2.4    5.8e-83  278.4   1.8    1.6  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    6.3e-72  241.2   0.0    1.2e-71  240.3   0.0    1.5  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.8e-33  115.7   0.2      5e-33  114.3   0.0    1.9  2  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.1e-23   83.3   0.1    1.1e-23   83.3   0.1    2.4  2  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
     0.0047   17.2   0.3       0.62   10.4   0.1    3.3  4  Peptidase_C34   Putative closterovirus papain-like endopeptid


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.5   0.0   2.1e-96   6.3e-93       2     312 .]       7     316 ..       6     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 311.5 bits;  conditional E-value: 2.1e-96
                     E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE-HHHHHHHHHHCTTC CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfhigffklilkilecv 96 
                     k+i+ i+f + sp+eirk+Svve+t++et++e+   + +gGl+D rlg+ +   +C t g++ ++++ghfGhieLa+Pv+hi f++ i+k+l+++
      AJA92825.1   7 KSIEGITFAVWSPQEIRKYSVVEITQPETYDEDG-MAVQGGLMDGRLGVLEPGQKCLTDGNTAARSPGHFGHIELAEPVLHIAFVDNIYKLLQST 100
                     89******************************95.99********************************************************** PP

                     ETTTTEBSS-TTSH....HHHHHHCSSSCC...CCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTH CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1  97 ckecskllldeekkkllsklkkrekleelk...krlkaieelckkinlcekCgavqpkleeegeklkaalkkskeeekeklsaekvkkllkried 188
                     c++c+++ +++e+ k +sk+k+r++   +    +  ++i+e+ kk ++c +Cg  ++++e  + k ++ ++k++   ++ l + ++++ l+ i+d
      AJA92825.1 101 CRTCGRIKMSPEDIKEFSKIKERQASYTVLsqkRIPDQIQEKAKKQKDCPHCG--KSQYELIFTKPTTFVEKTEI-GENRLLPITIRERLSIIPD 192
                     ************99999999987765444323367899***************..66788888888887777766.88999************** PP

                     HHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSS CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 189 edvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisgl 283
                     ed+ +lg +++ +rPew++l+ lPVpP+++RPs+ l++g rsedDlt+kl+dii+ N+rLk+ +e+g+p li+++ ++lLQ+hv+t+fdne+sg+
      AJA92825.1 193 EDLALLGYDPKTARPEWFVLQALPVPPVTVRPSIILETGIRSEDDLTHKLVDIIRVNQRLKESKEAGTPPLIVQDLVDLLQYHVTTYFDNEVSGI 287
                     *********************************************************************************************** PP

                     SEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 284 kpatqkskrplkslsqrLkGKeGrfRgnL 312
                     ++a+++s+rplk+l+qrLkGKeGrfRg+L
      AJA92825.1 288 PQAHHRSGRPLKTLTQRLKGKEGRFRGSL 316
                     ***************************98 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         2   5.8e+03     185     222 ..     582     627 ..     464     638 .. 0.73
   2 !  278.4   1.8     2e-86   5.8e-83       1     265 [.     784    1207 ..     784    1209 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2
                     HTTSTT....TBETTTEEES....SHHHHHHHHCHHHHHHHHHHHH CS
                     xxxxxx....xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5 185 vlkvee....vvdageilsn....diaeileilgieaarkallkei 222
                     v+k+ +    v+d++ i ++     ++ i++ +g e+a+ +l +e+
      AJA92825.1 582 VIKNGQlisgVIDKSSIGAEepesVLHRIAKDYGNEKAKIFLNSEL 627
                     3322222223555555555544446677777777777777777775 PP

  == domain 2  score: 278.4 bits;  conditional E-value: 2e-86
                      B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS........................... CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
  RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg........................... 66  
                      GL+  efffh+mggReGL+DtAv+T +sGY+qRrl++ale +  +yd+tvr+ +g+i+qflygedg                           
      AJA92825.1  784 GLSTLEFFFHAMGGREGLVDTAVRTQQSGYMQRRLINALEHIKLEYDGTVRDPHGHIIQFLYGEDGidvaksdhgeafnvdrliesesivdsg 876 
                      99******************************************************************************************* PP

                      .......................................................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSS CS
                      .......................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5   67 .......................................................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknv 104 
                                                                               epG+avGi+ aQSiGePgTQ+tl+TFHfaG+a++nv
      AJA92825.1  877 kaatkdeiapiikkytsefnprltnavsnslensklskqgvekvakkglslynnaKAEPGQAVGIVTAQSIGEPGTQMTLRTFHFAGIAERNV 969 
                      ********************************************************************************************* PP

                      SSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE............................................... CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
  RNA_pol_Rpb1_5  105 tlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek............................................... 150 
                      tlG+prl e++++ k+  ++++ ++l  +++++++k+ +v+++i +                                               
      AJA92825.1  970 TLGLPRLIELVDARKKPVTPTMDIYLSGDAKTDQAKTVEVARNILQttvndlildadtdyktkitlnlnerkltdrgctlddvkaalesnkkf 1062
                      ******************************99999988999888889999******************************************* PP

                      .....................................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHH CS
                      .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5  151 .....................................gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeil 206 
                                                           g+++i r+ ++     k++ +e+v++t g nls+vl+ve+ +d++++ +n++ ei+
      AJA92825.1 1063 kmednginsvvlnlvdeeadapavivvrnkvlkttvkGVPDIARVTIV-----KKN-DEYVIQTTGSNLSKVLEVEG-IDKNNVRTNNVSEIA 1148
                      **********************99999999999988888888888877.....222.5789****************.*************** PP

                      HHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_5  207 eilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265 
                      e+lgieaar+al++e++++++ qg++v++r l+l+ d+m+ +g++ +++r+Gi  ++ s
      AJA92825.1 1149 ETLGIEAARNALINELSNTLEDQGLEVDQRYLMLVSDLMCHRGYMQQIGRHGIAGTKDS 1207
                      *****************************************************987765 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.3   0.0     4e-75   1.2e-71       1     166 []     318     485 ..     318     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 240.3 bits;  conditional E-value: 4e-75
                     SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC..HHCCTTTTSEEEE CS
  RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk..lakelekgdiver 93 
                     Gkrvd+s+R+vispdpnl+l evgvP +vakklt+peivt++ni+kl+klv+ngp++ Pg +y++r dg + +l   +++  +a++le+g  ver
      AJA92825.1 318 GKRVDFSSRTVISPDPNLDLSEVGVPETVAKKLTIPEIVTDWNIEKLKKLVINGPSTFPGVNYITRPDGVKIRLDFVEDRslIADSLEIGFLVER 412
                     9**************************************************************************99886579************ PP

                     E--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHHCSBT CS
  RNA_pol_Rpb1_2  94 hvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEaeelllv 166
                     h++dgd+vl+NRqPsLh++simah+v+vl++kt+rl+ sv+ +yNaDFDGDemnlh+pqseear+Ea  l+ v
      AJA92825.1 413 HLMDGDIVLFNRQPSLHQMSIMAHYVRVLPGKTFRLHPSVCPPYNADFDGDEMNLHVPQSEEARSEAILLMRV 485
                     *********************************************************************9975 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   1.7e-36     5e-33       1     157 []     488     646 ..     488     646 .. 0.92
   2 ?   -2.8   0.1       1.7   5.2e+03      54     103 ..    1083    1128 ..    1039    1161 .. 0.43

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.7e-36
                     CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHCCCCEEEE...SSSS.... CS
  RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpneinyerk...neek.... 88 
                     +++sp+ g P+ig  +D+++G+yl+Tk+++ ++ +e+ +l + g ++    ++++p  +k + l+tgkq+fs +lp+++ny  +   +  k    
      AJA92825.1 488 QLISPRFGGPIIGGLRDFITGAYLMTKDGTTLSSQEFANLAMLGGFT---GQLPEPENKKEN-LYTGKQLFSIFLPEDFNYVMTskwS--Kgtkg 576
                     689*****************************************665...457777777776.******************9976441..25577 PP

                     .STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
  RNA_pol_Rpb1_3  89 .dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigigDt 157
                      +++v+ikng+li+Gvidk+ +g+++ +s++h +ak+yg ++++ fl+s   ++ ++++++gf+ g+gD+
      AJA92825.1 577 kEKDVVIKNGQLISGVIDKSSIGAEEPESVLHRIAKDYGNEKAKIFLNSELIVIKQFITHYGFSYGYGDL 646
                     89******************************************************************95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                      SSSSBESSSEBEEHHHHHHCCCHC..CCCEEEESSSSSTSEEECSSEEEES- CS
  RNA_pol_Rpb1_3   54 lrpailkpkelwtgkqtfsrilpn..einyerkneekdgkvlikngelikGv 103 
                       ++ i+++  ++++k+t+  +  +  ++ + +k   +d++v+   g  ++ v
      AJA92825.1 1083 APAVIVVR--NKVLKTTVKGVP-DiaRVTIVKK---NDEYVIQTTGSNLSKV 1128
                      33333333..234444443221.1112222221...1444555555554444 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.1   3.5e-27   1.1e-23       4     108 .]     673     777 ..     670     777 .. 0.96
   2 ?   -2.8   0.3         2   5.8e+03      12      50 ..     886     930 ..     877     932 .. 0.51

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 3.5e-27
                     HCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS--SSTSCSSTTSSSS CS
  RNA_pol_Rpb1_4   4 aerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkripkgfsgrtlphfkki 98 
                     +e++g l+ + g++++e++ea i + l k rd+a ++a+ sl+++N  +iM+ +Ga+Gs +n+ q+ag lGqq+ +g+r +kg+++r+l hf+++
      AJA92825.1 673 QEKKGTLKATRGMTTQETLEAYIVNNLGKLRDRAATAANLSLDDDNAGKIMATTGARGSSLNVGQMAGALGQQARRGNRLNKGYNNRVLTHFEEH 767
                     56779**************************************77************************************************** PP

                     ESSTTTSSEE CS
  RNA_pol_Rpb1_4  99 despesrGFv 108
                     +++p ++GFv
      AJA92825.1 768 ENDPDAHGFV 777
                     *********8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2
                     HHTTHCHHHHHHHHHHHHHHHHHHH......HHHHHHHCSTTTSH CS
  RNA_pol_Rpb1_4  12 dlpgksleelfeakinkilnkardk......agkiaskslaasNs 50 
                     ++++k ++e+   ++n ++n  +++      ++k+a+k l+ +N+
      AJA92825.1 886 PIIKKYTSEFNPRLTNAVSNSLENSklskqgVEKVAKKGLSLYNN 930
                     455555555555555555554444444445566666666664455 PP

>> Peptidase_C34  Putative closterovirus papain-like endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.6   4.9e+03      67      87 ..     731     751 ..     688     753 .. 0.80
   2 ?    2.8   0.0     0.047   1.4e+02      16      89 ..     884     962 ..     876     965 .. 0.70
   3 !   10.4   0.1   0.00021      0.62      11      64 ..    1013    1068 ..    1003    1076 .. 0.73
   4 ?   -3.9   0.0       5.9   1.8e+04      19      49 ..    1109    1139 ..    1104    1142 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
  Peptidase_C34  67 glvevgsiglslgrlllrgnh 87 
                     +++vg++  +lg+   rgn 
     AJA92825.1 731 SSLNVGQMAGALGQQARRGNR 751
                    468999999999999999997 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.047
  Peptidase_C34  16 laeliskkpeevmlkvpnvldrcisn.....kgcslddlkaiceayeikvevegdcglvevgsiglslgrlllrgnhfs 89 
                    +a +i+k + e   +  n +   + n     +g +    k +    + k e     g+v   sig +  +++lr  hf+
     AJA92825.1 884 IAPIIKKYTSEFNPRLTNAVSNSLENsklskQGVEKVAKKGLSLYNNAKAEPGQAVGIVTAQSIGEPGTQMTLRTFHFA 962
                    67777777777766666655555555111004555445555555567899999999*********************96 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00021
  Peptidase_C34   11 clfsslaeliskkpeevmlkv.pnvldrcisnkgcslddlkaic.eayeikveveg 64  
                      l +++ +li   + +   k+ +n+ +r ++++gc ldd+ka   ++ ++k+e +g
     AJA92825.1 1013 ILQTTVNDLILDADTDYKTKItLNLNERKLTDRGCTLDDVKAALeSNKKFKMEDNG 1068
                     566777888877666666554168889*************9865156778888766 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 5.9
  Peptidase_C34   19 liskkpeevmlkvpnvldrcisnkgcslddl 49  
                     +++k++e v+ ++   l + +   g + +++
     AJA92825.1 1109 IVKKNDEYVIQTTGSNLSKVLEVEGIDKNNV 1139
                     5666666677777777888887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 7858.63
//
Query:       AJA92826.1  [L=360]
Description: hypothetical protein T478_0032 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
        1.7    9.6  17.6        1.1   10.1   2.1    4.3  4  DUF5339         Family of unknown function (DUF5339)


Domain annotation for each model (and alignments):
>> DUF5339  Family of unknown function (DUF5339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.32   5.8e+03      15      35 ..      34      55 ..      23      61 .. 0.56
   2 ?   10.1   2.1   6.3e-05       1.1      13      67 ..      94     145 ..      89     148 .. 0.84
   3 ?    5.1   1.3    0.0024        42       9      38 ..     153     181 ..     153     185 .. 0.93
   4 ?    2.5   0.0     0.015   2.7e+02       6      51 ..     210     250 ..     209     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.32
     DUF5339 15 liakaekq.pgtktqadaikkq 35
                +++ aek     k+++d+++++
  AJA92826.1 34 MLKIAEKAkRYIKHNIDEMENN 55
                4444444323445556666555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.3e-05
     DUF5339  13 dkliakaekqpgtktqadaikkqleqsKkqilalpkeqQ.eaaCkqgldalkqlkq 67 
                 + +i+ +    ++ +q++++ +q+ ++K+q ++lp+  Q  +  ++  ++l+q+ +
  AJA92826.1  94 EHFISSM----SKIKQISQMLNQIAETKAQDASLPDHSQiIKRYEMNFQKLQQISD 145
                 6678888....4489************************88888888888888766 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0024
     DUF5339   9 Fkevdkliakaekqpgtktqadaikkqleq 38 
                 F+e+++l+  a kq+++++q d+ k+ ++q
  AJA92826.1 153 FSEMKNLLTLA-KQNNQQGQSDKAKQTIDQ 181
                 89999****99.8899**********9997 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.015
     DUF5339   6 ekYFkevdkliakaekqpgtktqadaikkqleqsKkqilalpkeqQ 51 
                 ekY +++++li +a     ++  +  + k+le sK q+ +     Q
  AJA92826.1 210 EKYVDRINTLIVQA-----KTSGLLDYVKMLENSKIQLISSNSTSQ 250
                 799999********.....566666777789999999887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2202  (0.122818); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2297.52
//
Query:       AJA92827.1  [L=333]
Description: adenylosuccinate synthase-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-81  273.9   0.3    1.5e-39  136.1   0.0    3.0  3  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.1   1.2e-37   2.2e-33       1     142 [.       4     138 ..       4     145 .. 0.91
   2 !  136.1   0.0   8.4e-44   1.5e-39     190     331 ..     144     283 ..     138     287 .. 0.93
   3 !   19.4   0.0   2.2e-08    0.0004     377     419 .]     287     329 ..     284     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 1.2e-37
                      .EEEE-SSS-S-HHHHHHHHHTT..-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHHTTSS-TT..... CS
  Adenylsucc_synt   1 vvvvGaqwGDEGKGkivDllaee..advvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEieeleakgvelsk 92 
                      ++v+G  +GDEGKGki+ +la++   ++vvR   G nAGHt+  ++k++k+++lpSG ln++ + +iG+gvvv+p+++l+Ei+++  +      
       AJA92827.1   4 TIVIGGFFGDEGKGKIISYLAQKddPTIVVRGGAGPNAGHTIKDGDKTFKVRMLPSGFLNKNSRVMIGPGVVVNPDVFLKEINDFGTD------ 91 
                      68******************9953389********************************************************99764...... PP

                      .TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT- CS
  Adenylsucc_synt  93 erllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarr 142
                      +r ++++++ ++ ++h + D+       k+kiG+T++G Gpa a++++r+
       AJA92827.1  92 GRSFLDNNCGIIEKHHLEDDSKGRL---KEKIGSTGSGTGPANAERAMRT 138
                      4789******999999888876665...369***************9996 PP

  == domain 2  score: 136.1 bits;  conditional E-value: 8.4e-44
                      HHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHH CS
  Adenylsucc_synt 190 yaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdev 283
                        + l++y++d+  ++n+al++++++L+EG qgt+l+++hGtYPfvT+  +ta+g+++  g++pk+id+v+ v+K+y trvG+Gp+  el  ++
       AJA92827.1 144 EIDSLQKYIIDVPLEINNALDRNENILIEGTQGTHLSLWHGTYPFVTTKDVTASGICADVGIGPKRIDDVIVVFKSYLTRVGTGPMAGEL--SA 235
                      5678999**********************************************************************************9..44 PP

                      HHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGG CS
  Adenylsucc_synt 284 geklrekGkEfgtttgrpRrcGwlDlvllryavrvngvtelaltklDv 331
                      +e+ ++  +Efgt+tgr Rr   +D  l+ +a+++++++++ +tklDv
       AJA92827.1 236 EETSQKGWEEFGTVTGRLRRAAEFDFELASRAIMLSSANQISITKLDV 283
                      344555557**************************************9 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 2.2e-08
                      --TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
  Adenylsucc_synt 377 disgvrsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                      d++g++s+++l ++ak++++ ie+ lgv+v++i++G + +++i
       AJA92827.1 287 DCAGAQSLDELGADAKSFIKNIEDKLGVKVTLIGTGAGVNDII 329
                      567899*******************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2403.73
//
Query:       AJA92828.1  [L=43]
Description: hypothetical protein T478_1369 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1634  (0.0911373); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 317.15
//
Query:       AJA92829.1  [L=319]
Description: oxidoreductase, NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-26   93.5   0.0    2.6e-26   92.8   0.0    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    7.1e-07   29.2   0.0    1.3e-06   28.4   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.054   13.9   0.0       0.11   12.9   0.0    1.6  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
        0.1   12.0   0.0       0.16   11.3   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   5.8e-30   2.6e-26       2     120 .]      10     125 ..       9     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 5.8e-30
                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEEEESSS-SS CS
  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagkhvllEKPlatt 98 
                   +v  iG+G  g++h r l e   +  + a++d + era+++ e+++v+ y+ leel++++e da++++tp++th ela++++e++khv++EKP++  
    AJA92829.1  10 KVIQIGTGGWGKNHCRVLSE---FGVLSAICDMNYERAKEFGEKYNVNYYKTLEELFENEEFDAAFICTPTSTHSELALQLIEKKKHVFVEKPMTYL 103
                   6778***********65555...5899********************************************************************** PP

                   HHHHHHHHHHHHHHTS-EEEE- CS
  GFO_IDH_MocA  99 veeakelvelaekkgklvsvgy 120
                    e+ ++lve a+kk+++++ gy
    AJA92829.1 104 SEDGERLVEEAKKKKVILTCGY 125
                   *****************99887 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.9e-10   1.3e-06      32      99 ..     156     220 ..     150     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.9e-10
                     CGGSH..HCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEEEEEEEEEETTEEEE CS
  GFO_IDH_MocA_C  32 wkrrk..kksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaavmsvlnlekgsgevi 99 
                     ++r++   k+ G+ +d ++HdiD ++wLf + p vv+a     q+++  ed+ +     l + ++++++i
      AJA92829.1 156 EHRMPlhIKDVGIIYDTSVHDIDTAMWLFDETPQVVFAKS--GQINHEHEDFATI---MLGFKDSRIATI 220
                     55555666788****************************8..7999888888776...666666666555 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05      0.11       6      94 ..      15      95 ..      10     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                    TTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
  Semialdhyde_dh  6 GatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelapklaeagvkvi 94
                    G tG  G++  r+L+e   ++ ++ +  +r   k++ e+++ ++++   ++e+    e +e d +f ++p ++++ela +l+e++ +v+
      AJA92829.1 15 G-TGGWGKNHCRVLSEFGVLSAICDMNYER--AKEFGEKYN-VNYY--KTLEE--LFENEEFDAAFICTPTSTHSELALQLIEKKKHVF 95
                    5.6666666666666633333333333222..444444444.1122..22233..4556889*******************99998875 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.5e-05      0.16      34      93 ..       6      67 ..       1      93 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
                  GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH-S CS
  2-Hacid_dh_C 34 lsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelvsleellaesD 93
                  + +++v  iG+G  G++  ++l++fg+   + d + ++ +   e+ +  ++ +leel+++ +
    AJA92829.1  6 VLKMKVIQIGTGGWGKNHCRVLSEFGVLSAICDMNYERAKefGEKYNVNYYKTLEELFENEE 67
                  556778889******************8888877666555444444444788******8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2305.62
//
Query:       AJA92830.1  [L=194]
Description: O-methyltransferase, TylF family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-22   79.9   0.1    2.3e-22   79.6   0.1    1.0  1  TylF             Macrocin-O-methyltransferase (TylF)
    1.5e-08   35.6   0.0    2.1e-08   35.1   0.0    1.2  1  Methyltransf_24  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TylF  Macrocin-O-methyltransferase (TylF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.1   2.5e-26   2.3e-22      75     240 ..      24     179 ..      20     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 2.5e-26
        TylF  75 edvleegv..pGdliEtGvWRGGaailmrgvLkaegvedRkvwvaDsFeglPkp.deeklaedagdklkeleevlavseeevrenFrrygLlddqvrfl 170
                 +++++ ++  +Gd+ E+Gv+ GG+a      L  e+ ++++++++D+F glPk  d +++  ++++ ++++++   +s e++++  ++y    ++v+++
  AJA92830.1  24 HSIVRTQIalDGDMAEVGVYQGGSAK-----LICEAKKEKELYLFDTFTGLPKLsDDDTHFGEKHWYENQFNN---TSIESIKKLLSKY----KNVHII 110
                 55555555337************986.....667889999************971445556666666666666...9************....59**** PP

        TylF 171 kGwFkdtLptapieklallRlDgdlyestldaleaLYdkvskGGfviiDDyaaveecreavedfreakgi 240
                 kG F  + +++  +k+  + lD dly+st+d+l+  ++k+ +GG ++i Dy+  +++++a ++f +++ +
  AJA92830.1 111 KGEFPSSGEKIINKKFCFVHLDVDLYKSTIDSLRFFFPKMIRGGIILIHDYHS-DGIQKAFKEFMDENYL 179
                 ****************************************************9.**********998765 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.3e-12   2.1e-08       2     106 .]      39     161 ..      38     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.3e-12
  Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.....................aeeaaalare.........aglddrvrlikadseealasl 65 
                      E+Gvy+G s+ ++++a ++ +   l+ +d++ g                              +         +   ++v++ik+++++  ++ 
       AJA92830.1  39 EVGVYQGGSAKLICEAKKEKE---LYLFDTFTGlpklsdddthfgekhwyenqfN--------NtsiesikklLSKYKNVHIIKGEFPSSGEKI 121
                      9*************9877766...8999999999999888777776554422221........1233345534333344*************99 PP

  Methyltransf_24  66 aagsiDllfiDgghaaeavledleallprlapggvvlfdDi 106
                       ++++ ++++D +  ++++++ l+ + p++ +gg++l++D+
       AJA92830.1 122 INKKFCFVHLDVD-LYKSTIDSLRFFFPKMIRGGIILIHDY 161
                      99***********.8*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1458.79
//
Query:       AJA92831.1  [L=368]
Description: deoxyhypusine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-78  263.7   0.0    2.2e-78  263.5   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.5   0.0   1.2e-82   2.2e-78       1     286 [.      24     320 ..      24     322 .. 0.91

  Alignments for each domain:
  == domain 1  score: 263.5 bits;  conditional E-value: 1.2e-82
          DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLrekgi 99 
                 el+e y+++gf+a++lgea+++++km  +e++ti+l++++++++ G+ +ii++l ++++vd+ivtT++++ ++ + a+g  + +g+fe+dd+ L+ek+i
  AJA92831.1  24 ELIEIYANSGFNARQLGEAAKLYQKM-IHENATICLTVAGAMTPVGFGGIIKTLLEKGFVDWIVTTGANVYHEDHFAWGLPVKQGHFEVDDNILYEKEI 121
                 699***********************.57899******************************************************************* PP

          DS 100 nRignllvpnenyckfedwvre.ildkleeeqkvwspselikelGkein.....deeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkld 192
                  Ri +++v+  +  ++ed + + ++++  + +k+++++e+++ lGk  +      e+S+l++Ay+ d+pv++++l D+sl+++l++++   ++k ++ld
  AJA92831.1 122 VRIRDVYVKFYETLELEDNIIQnMFKDKFS-EKSFTTAEFCNVLGKISKekskfPEKSFLTTAYELDVPVYVSTLKDSSLAMNLAVHR-L-KNKPFNLD 217
                 *********999988887665525555444.5789**********98877777888**************************666555.5.5566**** PP

          DS 193 ivkDirelndialkakktgaiilGGGvpKhhilnanlm........rngadyavyittaqefdGslsgatldEavSwgkikaea.ksvkvyaDaTivlP 282
                  v++i e ++i++++kk+g++ lGGGvpK+ ++++  +        + g dy+++it a++ +G+lsgatl+E++Swgk+++++ + ++vy+D+Ti++P
  AJA92831.1 218 FVREIIEQAAIVYNSKKSGILELGGGVPKNTAQQTGPLldqilrkdHGGQDYIIQITDARPDTGGLSGATLQEGKSWGKVQDSHeDLITVYTDSTIAFP 316
                 ************************************6669***987569********************************9654889*********** PP

          DS 283 Llva 286
                 Ll+ 
  AJA92831.1 317 LLAL 320
                 **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2718.08
//
Query:       AJA92832.1  [L=503]
Description: capsule polysaccharide biosynthesis protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-07   31.0   0.1    2.9e-07   30.2   0.1    1.4  1  Capsule_synth  Capsule polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.1   1.6e-11   2.9e-07      96     257 ..     237     388 ..     183     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.6e-11
  Capsule_synth  96 ilqhklpkYkrHrilnalaelkgsilkrvaykvedreadkvtrllaekkkriflvplQvedDsqvrihsafgsersallevLesfaeeapadaeli 191
                     ++ ++  Y r r +  l+e+k   l r ++ + d+++ k    + +k+ +++ +pl +e+ + + i ++f  ++    e+++  ++  p + +li
     AJA92832.1 237 TNKTHYTYYGRKRSKVVLNEIKKNNLVRNRKSFIDKKLLK----KIPKNYKLVYYPLHIEQERNLLIAAPFYINQ---IELIRNIVQSLPIEYKLI 325
                    3567788888888888888887555555555444554444....79************************76433...3455666666788889** PP

  Capsule_synth 192 iKtHPldeglikyrrvikgyltelaalkkrvllvedvnlpsLldqvdgvvvvnStaGleALlhgkp 257
                    +K+HP  e   + +r i +y     +++++ l+  +v +  +l+++  v+++  t+GleA   + p
     AJA92832.1 326 VKEHPAQET--REWRNISEYEEI-MDIPNVFLMHPEVSSNEILKKSSLVITIGGTSGLEANFYQIP 388
                    *****9986..56799**99766.6**********************************9766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3760.91
//
Query:       AJA92833.1  [L=97]
Description: hypothetical protein T478_0547 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 728.15
//
Query:       AJA92834.1  [L=324]
Description: porphobilinogen synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.2e-137  458.3   0.9   1.4e-137  458.1   0.9    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.1   0.9  7.8e-142  1.4e-137       2     316 ..       7     322 ..       6     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 458.1 bits;  conditional E-value: 7.8e-142
                 --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-SS-BSS-GGGGSTTSHHHHHHH CS
        ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvpeekdeegsealnedglvqrair 100
                 +rlrrlr+++++r+lv+e ++s++dli+p+fv+eg e+k++i+smp ++rl+++e+v+ev+++ +lgi+a++lFg+p+ekd+eg++a+ e+g+vq+ai+
  AJA92834.1   7 TRLRRLRTNQKMRDLVQEVSISPKDLICPVFVEEGIEAKKQINSMPAMERLPLSEVVNEVNTISELGIPAIMLFGIPSEKDDEGTSAFVEHGIVQKAIS 105
                 79************************************************************************************************* PP

                 HHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGH CS
        ALAD 101 aikeev.pelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYg 198
                 ++++++ +++v+++Dvclc+yt++Ghcg ++++++dnd++l +l k+avsqa+aG+d+v+pS mmDg+v+air+aLd++gf++vai+s+saK+ S+fY 
  AJA92834.1 106 EVRKNFgDKIVIMADVCLCQYTTSGHCGHIHDNKIDNDSSLITLGKIAVSQAKAGVDVVSPSAMMDGQVKAIRKALDDEGFTDVAIMSHSAKHRSNFYS 204
                 ******777****************************************************************************************** PP

                 HHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHH CS
        ALAD 199 PFrdaaesapsfgdrktYqmdpansrealreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEslls 297
                 PFrdaae+ap+f+dr+tYq++++n rea+reve+d++eG Divm+KPal+ylD+i+e++++f++pvaay+vSGEYa++k aa +gw+de++++ E l s
  AJA92834.1 205 PFRDAAECAPQFSDRRTYQVPFTNPREAMREVETDVNEGVDIVMIKPALTYLDLISETRRRFNVPVAAYSVSGEYALVKGAAMQGWIDEDEMTKEILYS 303
                 *************************************************************************************************** PP

                 HHHTT-SEEEETTHHHHHH CS
        ALAD 298 ikRAGadliltYfakevak 316
                 ikRAGad+i+tYfak++a+
  AJA92834.1 304 IKRAGADMIVTYFAKHIAE 322
                 ****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2367.64
//
Query:       AJA92835.1  [L=202]
Description: ribosomal RNA large subunit methyltransferase J [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-51  172.8   0.0    8.3e-51  172.6   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
    0.00022   21.1   0.0    0.00028   20.8   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    0.00046   20.0   0.1      0.004   17.0   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
     0.0018   17.9   0.0     0.0025   17.4   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.002   18.8   0.1     0.0053   17.4   0.1    1.9  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   0.0   2.3e-54   8.3e-51       1     177 []      20     195 ..      20     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 2.3e-54
                 CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS CS
        FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealserkvdlvvsDgapdv 99 
                 yrsR++yKL ei++ ++++ pg  v+Dlg+aPGgw qv+ q  g++gkv+++Dl  ++ lpgv++i+g+i dp+  e+i  +++ rk+d v++D++p+v
  AJA92835.1  20 YRSRASYKLKEINKSYRIIGPGSYVLDLGCAPGGWLQVARQISGNQGKVLGIDLSFVEDLPGVEIIRGNIEDPDILEEIMSFFN-RKIDSVICDLSPNV 117
                 9******************************************999**********************************9996.5************* PP

                 -CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEEEEEEEE-SS--CCG-EEEEEEEEC CS
        FtsJ 100 sgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFekvsvvkPkssrsesseeflvcrgf 177
                 sg++++d+++q++L   a +l+ k+l+++g+ ++k+f+ge ++++++++kk+F k ++ kPk+sr++sse + +c g+
  AJA92835.1 118 SGNWSVDHAVQISLNYTAEKLMEKTLSNKGNALFKVFDGEYSAEFYEFVKKKFIKTKLLKPKASRKSSSELYCICMGY 195
                 ***************************************************************************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   7.8e-08   0.00028      21      55 ..      39      76 ..       8     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7.8e-08
  Methyltransf_23 21 raggrvLdiGcGtGillevlren.gf..svtgvDlspe 55
                      +g+ vLd+Gc+ G +l+v+r+  g   +v g+Dls++
       AJA92835.1 39 GPGSYVLDLGCAPGGWLQVARQIsGNqgKVLGIDLSFV 76
                     46779***************875333459******986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-06     0.004       4      37 ..      41      74 ..      38      76 .. 0.92
   2 ?    1.0   0.0      0.09   3.2e+02      62      84 ..      93     115 ..      80     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
  Methyltransf_31  4 glrvlDlGCGtGeltfelaeelgpkaevvGiDis 37
                     g +vlDlGC+ G  + ++ +  g +++v GiD s
       AJA92835.1 41 GSYVLDLGCAPGGWLQVARQISGNQGKVLGIDLS 74
                     779*****************9999********86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.09
  Methyltransf_31  62 dieelekl.ledekfDlilsnevl 84 
                      di e  ++ ++ +k+D ++++   
       AJA92835.1  93 DILEEIMSfFN-RKIDSVICDLSP 115
                      55565555555.899999998333 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     7e-07    0.0025       8      80 ..      35     110 ..      28     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7e-07
        MetW   8 aelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdld.....kdlenfedksfdyvv 80 
                  ++i pgs vldlGc  G  l++ ++  + +g+ l +d + v +    G+++i+g+++     +++  f +++ d v+
  AJA92835.1  35 YRIIGPGSYVLDLGCAPGGWLQVARQISGNQGKVLGIDLSFVEDL--PGVEIIRGNIEdpdilEEIMSFFNRKIDSVI 110
                 5899**********************9999999999999999875..6888888887622222455566666666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.5e-06    0.0053       1      31 [.      44      75 ..      44     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                     EEEET-TTSHHHHHHHCTST.SSEEEEEESSH CS
  Methyltransf_25  1 vLdlGcGtGrltlalakrlg.kakvtgvDise 31
                     vLdlGc +G +++ + +  g ++kv+g+D+s 
       AJA92835.1 44 VLDLGCAPGGWLQVARQISGnQGKVLGIDLSF 75
                     9********9988777666559********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1481.73
//
Query:       AJA92836.1  [L=353]
Description: 23S rRNA (adenine(2503)-C(2))-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-19   68.5   0.2    2.7e-18   66.9   0.2    1.9  2  Radical_SAM    Radical SAM superfamily
    7.4e-05   22.9   0.0    0.00021   21.4   0.0    1.8  1  Fer4_14        4Fe-4S single cluster domain
     0.0099   16.2   0.1      0.017   15.4   0.1    1.4  1  Fer4_12        4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.027   14.1   0.1        1.1    8.8   0.0    2.9  2  Peptidase_C71  Pseudomurein endo-isopeptidase Pei


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.2     6e-22   2.7e-18       2     165 ..     114     281 ..     113     288 .. 0.85
   2 ?   -1.1   0.0      0.47   2.1e+03      92     148 ..     282     331 ..     277     332 .. 0.60

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 6e-22
                  EEESEESS--TTTSCCTT......HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTEEEEEEECSSCH CS
                  xxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpet......vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpgiritvetngtlp 89 
                  +++ gC+++C+fCa++++      ++ + +++++  eei+e+ ke      ++ v++g+gep++++d+   + ++           ++it++t g++ 
   AJA92836.1 114 STQIGCAMGCTFCATGQMgfetnlKAEHIVAQVVHFEEIIEQKKEHI----TNLVFMGMGEPMANYDEMIRAVKILTDPrgfgLGQRHITISTIGIK- 206
                  6788************9877777777777777777777777777776....99**************999999999999******************. PP

                  GHHHHHHHHHTT.-SEEEEEEBSSSHH..HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  90 deeklerllelg.vdrvslgleaadde..kvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleelle 165
                    e +e+l++      ++++l+a+++e  k l ++  +++++e+++a  ++ ++ ++rv++ + +++G+nd+  +++++
   AJA92836.1 207 --EGIEKLADEDlQIGLAISLHAPNNElrKKLVPTATKDSVKEIIDAGHYYFKKTGRRVTFEYALMEGVNDS--RDTAQ 281
                  ..6*******99***************6666666668888888888888888888888*************6..34443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
                  HHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEE CS
                  xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  92 eklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdr 148
                  e +e+l+  g  v+++ ++  a+d +       r ++ ++v e  ++l+eag++ +++r
   AJA92836.1 282 ELAELLRGNGshVNVIPINPTAGDFK-------R-PSKSRVFEFKRILNEAGVN-CTIR 331
                  56666666666666666666666665.......3.4555666666666666666.5555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.7e-08   0.00021       7      76 ..     118     187 ..     113     222 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.7e-08
     Fer4_14   7 gCnlsCkgCd.nketwks..elgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlke 76 
                 gC + C++C   +  ++   +++++ ++ +  +++   ++++ +i +lv++G GeP+  +n +e+++ vk l +
  AJA92836.1 118 GCAMGCTFCAtGQMGFETnlKAEHIVAQVVHFEEI--IEQKKEHITNLVFMGmGEPM--ANYDEMIRAVKILTD 187
                 8*********5344444411444444444444444..5666677789**********..888888888887765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.9e-06     0.017      12      77 ..     116     183 ..     104     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.9e-06
     Fer4_12  12 vsgCnlsCkgCfnketw...sfksgkeft.kelleeiiedlkkesiegltllG.GEPllpenaeallelvk 77 
                   gC + C +C   ++    + k+++ +      eeiie+ kke+i+ l+++G GEP++  n++++++ vk
  AJA92836.1 116 QIGCAMGCTFCATGQMGfetNLKAEHIVAqVVHFEEIIEQ-KKEHITNLVFMGmGEPMA--NYDEMIRAVK 183
                 469********98888655566777777624445677766.69****************..9888877665 PP

>> Peptidase_C71  Pseudomurein endo-isopeptidase Pei
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.061   2.7e+02      59     127 ..      43     115 ..      36     131 .. 0.73
   2 ?    8.8   0.0   0.00026       1.1      25      81 ..     243     300 ..     230     344 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.061
  Peptidase_C71  59 dasqlfkkvleal...Gyev...kiehvrvrcndgkwyGhyllrvkgkeladgtvwdyvsavktGrslgapccsa 127
                    d  ql kk++ ++   Gy +   k +  rv  +dg     +ll +++ +  +    +y s   +G + ++ c s+
     AJA92836.1  43 DIKQLPKKMIAEMveaGYTIgsaKEI-HRVTSEDGD-TTKLLLNLTNDKSVETVLMQYESEKENGLPRSTVCVST 115
                    66677777766554557876321223.377777887.78899999999999899999999999999988877665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00026
  Peptidase_C71  25 ekvkkrckykyyyndkvpnreaikkivtdGin.ctdasqlfkkvlealGyevkiehvr 81 
                    + vk+  + ++yy +k+  r++ +    +G+n   d++q + ++l + G +v+++ + 
     AJA92836.1 243 DSVKEIIDAGHYYFKKTGRRVTFEYALMEGVNdSRDTAQELAELLRGNGSHVNVIPIN 300
                    5677788889*********************94579*************999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2520.72
//
Query:       AJA92837.1  [L=100]
Description: putative ribonuclease P protein component 4 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-14   54.1   0.2    1.7e-14   53.8   0.2    1.1  1  Rpr2         RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.008   16.0   0.6      0.013   15.4   0.6    1.3  1  C1_1         Phorbol esters/diacylglycerol binding domain (C1
  ------ inclusion threshold ------
      0.053   14.1   0.3      0.081   13.5   0.3    1.3  1  PRESAN       Plasmodium RESA N-terminal
      0.086   12.3   0.9        4.6    6.8   0.1    2.2  2  zf-ribbon_3  zinc-ribbon domain
        1.4    8.7   9.0       0.24   11.1   1.4    2.4  2  zf-C2H2_10   C2H2 zinc-finger


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.2   4.9e-18   1.7e-14       1      90 []      12      91 ..      12      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 4.9e-18
                HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
        Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                r+++L++ a l +a+++p+l++  a  ++ +s+k ++ +pp++++++CkkC+++++p+++++vr+ + ++         +++ +tC  C+
  AJA92837.1 12 RMEILFNNALL-NARNNPELAQKQALLIKGISMKFKIAIPPEIRSSFCKKCKKFIVPNISSRVRLGQGNS---------KSISITCSFCN 91
                89*********.99***************************************************65332.........2467******6 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   3.5e-06     0.013      11      38 ..      55      94 ..      52      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                --B-TTT-SB-...........-S.SSS-EEEETTT--EE CS
        C1_1 11 ptfCkhCgefl...........wg.kekqglkCswCkllv 38
                ++fCk+C++f+           +g   +  ++Cs C+ ++
  AJA92837.1 55 SSFCKKCKKFIvpnissrvrlgQGnSKSISITCSFCNHVY 94
                68*******************99989999*******9775 PP

>> PRESAN  Plasmodium RESA N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.2e-05     0.081      12      75 ..       2      66 ..       1      73 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                T-S-SEEEHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
      PRESAN 12 nslneviskkdmyiiwnyvmknekkkyknmikk.Lsnyleelakkynipeeykkklwkeckneit 75
                ++ +++i +k m i++n+ + n++++ +  +k+ L  +  +++ k  ip e++  ++k+ck+ i 
  AJA92837.1  2 KNSKKEIARKRMEILFNNALLNARNNPELAQKQaLLIKGISMKFKIAIPPEIRSSFCKKCKKFIV 66
                56678999******************8888876355556677777777*************9885 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0013       4.6      12      26 .]      51      65 ..      48      65 .. 0.80
   2 ?    4.0   0.1    0.0095        34       3      11 ..      85      93 ..      84      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
  zf-ribbon_3 12 lssddnvCpyCGtkl 26
                 ++ + ++C++C +++
   AJA92837.1 51 PEIRSSFCKKCKKFI 65
                 578899*****9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0095
  zf-ribbon_3  3 vrCPnCGap 11
                 ++C+ C+++
   AJA92837.1 85 ITCSFCNHV 93
                 689999985 PP

>> zf-C2H2_10  C2H2 zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.1     0.066   2.4e+02       7      11 ..      56      60 ..      52      61 .. 0.79
   2 ?   11.1   1.4   6.8e-05      0.24       4      11 ..      85      92 ..      84      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.066
  zf-C2H2_10  7 SYChe 11
                S+C++
  AJA92837.1 56 SFCKK 60
                ***98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.8e-05
  zf-C2H2_10  4 itCSYChe 11
                itCS+C+ 
  AJA92837.1 85 ITCSFCNH 92
                9*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 701.48
//
Query:       AJA92838.1  [L=414]
Description: membrane protein, PF01595 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-49  166.5   0.2    7.2e-49  165.9   0.2    1.3  1  DUF21      Cyclin M transmembrane N-terminal domain
      1e-17   63.9   1.9    2.3e-17   62.8   0.4    2.1  2  CorC_HlyC  Transporter associated domain
    5.7e-16   58.7   0.5    6.6e-07   29.7   0.1    2.7  2  CBS        CBS domain
  ------ inclusion threshold ------
       0.18   12.1   0.1       0.76   10.1   0.0    2.0  2  DUF2889    Protein of unknown function (DUF2889)


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.2   1.6e-52   7.2e-49       2     176 .]       9     185 ..       8     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 1.6e-52
       DUF21   2 iivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellaegalavviatvivtllilvf 100
                 ++v+l++ls+ffsg+E+Alv ++ +++e++++++ k+a+ llkl  np+r+++++ +gn+lvn++++a+at+++ +++++   +++i++ i+t+lilvf
  AJA92838.1   9 LLVVLIGLSGFFSGLEVALVGVRLSKIEQMVKDKVKGASSLLKLKTNPSRMMASVNLGNNLVNVASTAIATDIALKIFGN--DGLAIVIGIMTFLILVF 105
                 5699**************************************************************************75..5999999********** PP

       DUF21 101 gEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil....esesepavseeelkklveeseeegvieeee 176
                 gEi+Pk++++++a kia++++p+l  +++ +yP+v++l++++++i+    +s++ p ++e+e+k +++++ +  +ie++e
  AJA92838.1 106 GEITPKTYCNANAAKIATRYSPVLLAFSYAFYPIVRILEAITKGIIrltgSSDNPPGLTEDEIKGVIDQGLKDKAIEKQE 185
                 *************************************************999************************9987 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.21   9.6e+02      33      53 ..     310     330 ..     299     338 .. 0.68
   2 !   62.8   0.4     5e-21   2.3e-17       4      80 ..     338     413 ..     335     414 .] 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                 SBHHHHHHHHH-S---TT-EE CS
   CorC_HlyC  33 eTlgGlllellgriPkegesv 53 
                  Tl +ll e  g+i +e+++v
  AJA92838.1 310 VTLEDLLEEIVGEIHDEKDTV 330
                 477777777777777777744 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 5e-21
                 CTTEEEEETT-BHHHHHHHHTSTTHH.CT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEEEE- CS
   CorC_HlyC   4 degsylvdGslpldeleeelglelpe.edyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrvekl 80 
                 +++ +l +G++++d+++e++++++pe +dy  l+Gll e+l +iPkeg+++e++  +lr+ ++++++++ +k+r+ek+
  AJA92838.1 338 GNDVILTNGDIEIDKINEIFKTNIPEgDDYSRLNGLLHEKLRDIPKEGDKIEIE--SLRIMIEKVSKNKPDKIRIEKI 413
                 5678899*******************889********************77777..*******************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.4e-09   6.1e-06       2      55 ..     201     257 ..     199     259 .. 0.84
   2 !   29.7   0.1   1.5e-10   6.6e-07       3      56 ..     268     320 ..     266     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.4e-09
                 HHHSBS..SCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
         CBS   2 gdimtr..dvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55 
                 +++mt+  +++t++    l eal ++ ++g+sr+PV  ++++++ Giv+ rD+l+ l
  AJA92838.1 201 RSVMTPrtKMFTLNSKKMLFEALPEINNSGFSRIPVFsENSDNITGIVHVRDVLKTL 257
                 5676665588999999**********8888******9755557***********987 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.5e-10
                 HHSBSSCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHHH CS
         CBS   3 dimtrdvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllrall 56 
                 +im rd+++v+ +  ++++l++m + + +++  VVde g + G vtl+Dll+ ++
  AJA92838.1 268 EIM-RDPIFVSQEKRVSDLLKEM-QGRQTHMaIVVDEFGGVEGCVTLEDLLEEIV 320
                 787.5666***************.55555662389****************9986 PP

>> DUF2889  Protein of unknown function (DUF2889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.68     3e+03      83     104 ..      26      46 ..      25      48 .. 0.87
   2 ?   10.1   0.0   0.00017      0.76      73     117 ..     278     319 ..     234     324 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.68
     DUF2889  83 kLvGltigrgfrravrerlggv 104
                 +LvG+++ ++ ++ v+++++g+
  AJA92838.1  26 ALVGVRL-SKIEQMVKDKVKGA 46 
                 599***9.9999***9999987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
     DUF2889  73 eCpeaaasyqkLvGltigrgfrravrerlggveGCtHLtellrsl 117
                 + +++ + ++++ G +     ++ v +++ggveGC+ L++ll ++
  AJA92838.1 278 QEKRVSDLLKEMQGRQT---HMAIVVDEFGGVEGCVTLEDLLEEI 319
                 55555555666666655...78999****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2723.52
//
Query:       AJA92839.1  [L=159]
Description: ribosomal protein L18e/L15 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-15   56.4   0.6    7.2e-15   55.8   0.6    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.6     4e-19   7.2e-15       2     127 ..      29     137 ..      28     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4e-19
                     GGGTSSTTTTTTTTT-..S--.........S--.........---GGG..---EEEEHHHHHHTTTTGTTS------EEEGGGTTTTSSS....S CS
  Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkkkpg...feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerleladeaeeidleelaeaglikkkdg 91 
                     G++gG G+ G+ k+    v k ++   f  G           G ++ + +  +  +n++dL++l+++   ++ ++++++dle+l          +
      AJA92839.1  29 GHKGGLGRSGHLKHLAstVIK-EDqdhF--GHE---------GTHSPHPSITKVWINIRDLNDLFAKSGKSE-NSKNVLDLESL----------E 100
                     999**********98854333.323468..877.........998545568889*********999987754.589********..........9 PP

                     E.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
  Ribosomal_L27A  92 v.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                     + K+lg g+ +++ ++k+++++++A+ekI++aGG+v+
      AJA92839.1 101 IeKLLGGGQTNTAYTIKVKNATPSAIEKIKQAGGEVI 137
                     99*********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1109.27
//
Query:       AJA92840.1  [L=220]
Description: hypothetical protein T478_1186 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   13.5  10.5      0.061   13.1  10.5    1.2  1  TAF4      Transcription initiation factor TFIID component TAF
       0.19   12.2   0.1       0.19   12.2   0.1    2.3  2  APG6_N    Apg6 coiled-coil region
        0.7    8.6   0.0        0.7    8.6   0.0    2.1  2  FbpA      Fibronectin-binding protein A N-terminus (FbpA)
        1.2    9.7   4.6         38    4.9   0.0    2.6  2  HisKA_3   Histidine kinase


Domain annotation for each model (and alignments):
>> TAF4  Transcription initiation factor TFIID component TAF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.5   1.4e-05     0.061     147     207 ..       7      69 ..       2     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
        TAF4 147 aak.drskgedeeekklkaketakevqkeedekarhraANatAlaavgeprk.Kkyswmsags 207
                  ++ ++++++d+e++k++ak+++k+ + +e++++   +A a+A aa+ +++  K+     +  
  AJA92840.1   7 DSEvKDAPKADKESQKQDAKKSLKASKDAEKAAKAAADAEAAADAAIAKAKElKEAAAKASEE 69 
                 444578999**************9999999888889999999999999555544442222222 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0  13.5      0.26   1.1e+03      46     101 ..      15      70 ..       2      93 .. 0.56
   2 ?   12.2   0.1   4.3e-05      0.19      64     109 ..     167     212 ..     122     216 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.26
      APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                 + + e+ +++ +k  k+ +++++  k++ +++++ +a++a+++e +ea  +  e++
  AJA92840.1  15 KADKESQKQDAKKSLKASKDAEKAAKAAADAEAAADAAIAKAKELKEAAAKASEEE 70 
                 34455555555556666666666666666666666666665555443333333222 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.3e-05
      APG6_N  64 eelleeLkelekereeleaelaaleeelealeeeeerfwreynelq 109
                 +el+++L++l++  e+l ++++++e+ l+ l+   e++    n ++
  AJA92840.1 167 DELQAKLDRLKSDPESLPEQIEQIEQNLSYLDSLHENYYLGMNVFR 212
                 6899********************************9998777665 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7  14.7      0.42   1.9e+03     376     443 ..      19      85 ..      15      95 .. 0.83
   2 ?    8.6   0.0   0.00016       0.7     388     419 ..     172     203 ..     167     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.42
                 ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHHHHHHHHHHTTS-- CS
        FbpA 376 kspsenAqkyfkkykKlkraveaveeqieetkeeleylesveaaleqaesledleeikeELieegylk 443
                  s ++ A+k  k  k +++a++a+  + +++ + +++ +++++a+++a s+e+ ++i++E++ee    
  AJA92840.1  19 ESQKQDAKKSLKASKDAEKAAKAAADAEAAADAAIAKAKELKEAAAKA-SEEEFKAIADEIKEEAPKA 85 
                 5778999999999999******************************99.***********98774333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00016
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        FbpA 388 kykKlkraveaveeqieetkeeleylesveaa 419
                 k  +lk+  e + eqie+ +++l+yl+s+ ++
  AJA92840.1 172 KLDRLKSDPESLPEQIEQIEQNLSYLDSLHEN 203
                 77899**********************99775 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.3     0.014        63      31      59 ..      31      59 ..      20      68 .. 0.82
   2 ?    4.9   0.0    0.0084        38      22      50 ..     167     195 ..     160     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.014
                TTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
     HisKA_3 31 lekdpekaaeqlreieelarealqevRrl 59
                + kd+ekaa++++++e++a+ a++ +++l
  AJA92840.1 31 ASKDAEKAAKAAADAEAAADAAIAKAKEL 59
                367888****************9999887 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0084
                 HHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
     HisKA_3  22 lqlelakrllekdpekaaeqlreieelar 50 
                   l++   +l++dpe + eq+++ie++++
  AJA92840.1 167 DELQAKLDRLKSDPESLPEQIEQIEQNLS 195
                 56777778899**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2452  (0.136762); expected 358.6 (0.02)
Passed bias filter:                      946  (0.0527637); expected 358.6 (0.02)
Passed Vit filter:                       158  (0.00881254); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 1483.59
//
Query:       AJA92841.1  [L=839]
Description: hypothetical protein T478_0643 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-07   29.7   0.2    7.3e-07   29.7   0.2    3.3  4  DUF3892       Protein of unknown function (DUF3892)


Domain annotation for each model (and alignments):
>> DUF3892  Protein of unknown function (DUF3892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.2   4.1e-11   7.3e-07       2      76 .]       9      99 ..       8      99 .. 0.95
   2 ?   -3.6   0.2         1   1.8e+04      16      35 ..     191     206 ..     183     225 .. 0.53
   3 ?   -4.1   2.3         1   1.8e+04       9      45 ..     446     483 ..     441     530 .. 0.52
   4 ?   -2.9   0.0      0.62   1.1e+04      19      45 ..     794     824 ..     782     836 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.1e-11
     DUF3892  2 ItavrkdggnsherItevk....gsntlstgekyskeeaislikngkkagVevvrsk...............dGekYlrtkadgtetdNLlsLp 76
                ++a++k  g++  +I +v+    ++   ++++ ++k ++ s i++g + +V+v +++               dGe Y+rt+++++  dNL+++p
  AJA92841.1  9 VSAIKK--GSGLANISHVQihedLEHGFGSPKLIDKYQLSSKIQKGLT-FVTVHKKNenewavgelirtyvkDGEAYIRTDDNKVDGDNLGHMP 99
                579999..9999*********99999**********************.99999988***********************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1
     DUF3892  16 Itevkgsntlstgekyskee 35 
                 I e+k    +++++++s+e+
  AJA92841.1 191 IKEMK----KKSKQNISREK 206
                 33333....33333344433 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1
     DUF3892   9 ggnsherItevk.gsntlstgekyskeeaislikngkk 45 
                 ++ ++++++ +k ++  +  ++  + +++i++  ++++
  AJA92841.1 446 REQHEKELEQIKiQIMEDARKQAEKEAQIIRDKLQKEI 483
                 55555555555553333333334444444443333333 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 0.62
     DUF3892  19 vk....gsntlstgekyskeeaislikngkk 45 
                 v+     +++++t+e  + + a +++k+g +
  AJA92841.1 794 VDdedsDEEDEKTPEDAKEDYAAKMAKKGAT 824
                 4444444446788888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (839 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4292  (0.239389); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                       582  (0.0324614); expected 17.9 (0.001)
Passed Fwd filter:                       204  (0.0113782); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 5.09u 0.42s 00:00:05.51 Elapsed: 00:00:01.27
# Mc/sec: 2000.31
//
Query:       AJA92842.1  [L=301]
Description: hypothetical protein T478_0430 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1694.22
//
Query:       AJA92843.1  [L=61]
Description: hypothetical protein T478_0500 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.004   17.3   3.3     0.0043   17.2   3.3    1.0  1  ECF_trnsprt     ECF transporter, substrate-specific component
  ------ inclusion threshold ------
      0.058   12.9   2.0      0.062   12.8   2.0    1.0  1  DUF3169         Protein of unknown function (DUF3169)
       0.13   12.2   3.4       0.14   12.0   3.4    1.1  1  DUF378          Domain of unknown function (DUF378)
        0.3   10.4   3.8       0.35   10.2   3.8    1.0  1  Heliorhodopsin  Heliorhodopsin


Domain annotation for each model (and alignments):
>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.3   9.5e-07    0.0043      38      91 ..       2      49 ..       1      59 [. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.5e-07
                 HHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHHHHHCHHHHHHHHH CS
  ECF_trnsprt 38 lggllfGpikGailgiitsvlkailtggtgalssfvpiaflsriligliaglly 91
                 ++g++fG ++G++ + +++++++++      +s+   i f++ +++g+++ + +
   AJA92843.1  2 FIGCIFGSVAGIFPSNLIMFYGFTT----ETFSM--SIPFIVVGVVGVVVCFHF 49
                 5699*********************....45777..888888888888888655 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.0   1.4e-05     0.062      15      79 ..       1      58 [.       1      61 [] 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
     DUF3169 15 gliGgiiGfllgafeaekgleelsaalkelllligskilpllli.iavlvviisvvflrkakkllk 79
                ++iG i+G + g+f ++     l+ +   +  ++++  +p+  i + v+ v++++ f +ka+++++
  AJA92843.1  1 MFIGCIFGSVAGIFPSN-----LIMFYGFTTETFSM-SIPF--IvVGVVGVVVCFHFAHKAENVQS 58
                46777777777777666.....34443333444444.5666..3399*************998876 PP

>> DUF378  Domain of unknown function (DUF378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.4   3.2e-05      0.14      12      59 ..       2      49 ..       1      50 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
      DUF378 12 iiGalNWgliGlfdfdLVaalfggessllsriiYilVglaglylisll 59
                 iG++   + G+f  +L+ +   +++++   i +i+Vg+ g+++++ +
  AJA92843.1  2 FIGCIFGSVAGIFPSNLIMFYGFTTETFSMSIPFIVVGVVGVVVCFHF 49
                6999999999*********99888999999999*********998765 PP

>> Heliorhodopsin  Heliorhodopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.8   7.7e-05      0.35     154     195 ..       6      48 ..       2      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.7e-05
  Heliorhodopsin 154 ifGciagivpWivillyllaa.eseeevPaFvyaivvslfvlf 195
                     ifG++agi p   i++y +++ + + ++P  v+++v +++ + 
      AJA92843.1   6 IFGSVAGIFPSNLIMFYGFTTeTFSMSIPFIVVGVVGVVVCFH 48 
                     8***********9999999986778899988888877665553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 377.67
//
Query:       AJA92844.1  [L=482]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.3e-139  464.3   0.1   4.9e-139  464.2   0.1    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.2   0.1  2.7e-143  4.9e-139       1     450 [.      23     464 ..      23     465 .. 0.98

  Alignments for each domain:
  == domain 1  score: 464.2 bits;  conditional E-value: 2.7e-143
                 HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE CS
     Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkT 99 
                 e + a l+ri+ v+e+++ ++ +++++a+++A+++dkk+a+g++ g  +G Pis+KDni++ g +tt++sk+len++a++ atvv +L++++avi gkT
  AJA92844.1  23 EFTAATLQRIKDVDEDVH-AYLSLNDSAINDAKSIDKKIASGEKIGKCYGFPISIKDNICITGTKTTCASKILENFIAPYTATVVNHLNDEDAVITGKT 120
                 57899*************.89999*************************************************************************** PP

                 --SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHH CS
     Amidase 100 nmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsve 198
                 n+defamg++te s+fgpt+NPw+++ +pGGSSGGsAA vAa+ +++++G+DtGGS+R PAsfc++vGlKPtyg++Sr+g++++++s++++Gp++++v+
  AJA92844.1 121 NLDEFAMGLTTEFSAFGPTKNPWNLDCVPGGSSGGSAASVAANECLASLGSDTGGSVRNPASFCSVVGLKPTYGLISRYGLISYANSIEQIGPMTKNVK 219
                 *************************************************************************************************** PP

                 HHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGC.SS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHHHHH CS
     Amidase 199 dlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedg.vasldpevqravekalkaLeeaGhevvevelpsleealslyylilvaea 296
                 d a+ll  i+g+d +d+t+ +  + + ++ e+ ++  +g++iG++ke+   + l+ ev  a+++a+   e++G+  +ev+lp +++ +++yy+i   ea
  AJA92844.1 220 DSAFLLNIIAGQDANDDTTID--NNDVNYLENIENGIEGKKIGIIKEMTtSDGLSSEVSTATKDAINDFESLGASCEEVTLPTIPYTVAAYYTITSTEA 316
                 *********************..899***********************999*********************************************** PP

                 HHHTTT-SSSSS.---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCH CS
     Amidase 297 ssnlarylgvry.erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdk 394
                 +snlary+++ry ++++   +  + + ++++ ++g+ev+rri+lg+++ sa+  +ky+lka kv++ l+ e++ afe++D l++Ptap +++r gek  
  AJA92844.1 317 GSNLARYDNIRYgYEMDSEGYEYNSYISKSRTKFGPEVTRRIILGGFVPSAGHAGKYFLKALKVKSKLISEINSAFEKFDYLIAPTAPVQPFRFGEKI- 414
                 *************8888888889999999999***************************************************************996. PP

                 HHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
     Amidase 395 tidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                   d++ +l +l+  t   v +nl+g pa+svp+  s+ glP+G+q++++ +qe+ l
  AJA92844.1 415 --DDPVTLMLLDYNT---VTANLTGRPAISVPYRISN-GLPIGMQIMANSLQEKSL 464
                 ..8899999999999...****************996.***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3531.04
//
Query:       AJA92845.1  [L=88]
Description: hypothetical protein T478_1104 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 651.27
//
Query:       AJA92846.1  [L=234]
Description: ribosomal RNA adenine dimethylase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-39  136.1   4.8    1.5e-39  135.7   4.8    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    7.2e-06   25.9   0.0    2.1e-05   24.4   0.0    1.8  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.023   14.1   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
      0.034   14.9   0.0      0.087   13.5   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
       0.11   13.2   0.0       0.25   12.0   0.0    1.6  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   4.8   4.1e-43   1.5e-39       3     229 ..       2     207 ..       1     233 [. 0.87

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 4.1e-43
                 CCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCC CS
      RrnaAD   3 klrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsih 101
                 ++rk++gqnfl++k +++ I+d ++++++  v+eig GkGilT  L + +k+v ++E+d +L+++ + k+sk ++lk++h D+ k   + +        
  AJA92846.1   2 SIRKKLGQNFLNSKLIAKFIVDSAKISKNNIVYEIGIGKGILTPFLCEKSKNVISVEKDVKLYEESKVKFSKIKNLKIIHGDGFKQHEKFD-------- 92 
                 589*******************************************************************************987543332........ PP

                 CEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S-- CS
      RrnaAD 102 qeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpq 200
                    ++v+nlPy  s++ + ++l +++f  +  ++++q  fa++lla+ +  +r+++svl++  +++k+++k++k++f+P+pk+dsa++   rk++ +  
  AJA92846.1  93 ---IFVSNLPYSESKNAIQWML-MEKF--QHGIVMVQYDFAKKLLAEGN--ERKAISVLAQSGFEMKILKKIGKENFTPKPKIDSAIMSFSRKNT-F-- 180
                 ...699************9999.6888..9****************755..9*******************************************.5.. PP

                 S-HHHHHHHHHHHHCTTTSBCCCHCCCTS CS
      RrnaAD 201 kdlkkyesvvrkllnrkrktlstslksll 229
                    k++ + v+ ++  +rk+l++  k+l+
  AJA92846.1 181 --SKELIQSVNLMFSFRRKKLQNIGKKLG 207
                 ..577777788888888888877644443 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.9e-09   2.1e-05      64     139 ..      20      90 ..       3     122 .. 0.84
   2 ?   -1.3   0.0      0.43   1.5e+03      23      57 ..     151     181 ..     136     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.9e-09
                 HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGG CS
        PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyee 139
                 ++++  +++k + v e+G G G+lt  l +   ++ +v+s+e+  +l+ee+k  +k ++++n+++++gDG k +e+
  AJA92846.1  20 FIVDSAKISKNNIVYEIGIGKGILTPFLCE---KSKNVISVEKDVKLYEESK--VKFSKIKNLKIIHGDGFKQHEK 90 
                 556777899999*************98865...566799**********996..7778899*********887665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.43
                 HHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE- CS
        PCMT  23 ealeevdReefvpesfkekaYedaplsigynatiS 57 
                 ++l+++ +e+f p+       + a +s + ++t S
  AJA92846.1 151 KILKKIGKENFTPK----PKIDSAIMSFSRKNTFS 181
                 55666666666666....22233333444444444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.5e-06     0.023       2      63 ..      30      87 ..      29      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.5e-06
                    -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
  Methyltransf_4  2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63
                    + +v eiG GkG ++  l +k  +kn++ +E+ vk+ ++  +k++ +++kNl+i++gd +k+
      AJA92846.1 30 NNIVYEIGIGKGILTPFLCEK--SKNVISVEKDVKLYEE--SKVKFSKIKNLKIIHGDGFKQ 87
                    67999********99999988..69*******9999876..799999***********9765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.087       1      76 [.      33     100 ..      33     117 .. 0.82
   2 ?   -1.7   0.0       1.3   4.8e+03      27      41 ..     124     138 ..     107     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhh 76 
                      v ++G G+G lt  l ++   ++v+ v+ + ++ e+ + ++++  + n+++++gd  + +   ++fD+ vs+  l +
       AJA92846.1  33 VYEIGIGKGILTPFLCEKS--KNVISVEKDVKLYEESKVKFSK--IkNLKIIHGDGFKQH---EKFDIFVSN--LPY 100
                      679*************995..9*******************65..44********87654...689999995..444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                      EESSHHHHHHHHHHH CS
  Methyltransf_25  27 vDiseemleaarera 41 
                       D+++++l++ +er 
       AJA92846.1 124 YDFAKKLLAEGNERK 138
                      555555555555444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05      0.25       2      69 ..      35      98 ..      34     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                     EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES CS
  Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse 69
                     ++G G+G+l+  l ++ ++v+ v+ + ++ + +k k s+ + +++++++d  k   + ++fD+ vs+ 
       AJA92846.1 35 EIGIGKGILTPFLCEKSKNVISVEKDVKLYEESKVKFSKIK-NLKIIHGDGFK---QHEKFDIFVSNL 98
                     79****************************99999999988.59********9...8899***99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1675.92
//
Query:       AJA92847.1  [L=533]
Description: CTP synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.1e-117  390.6   0.8   4.2e-117  390.2   0.8    1.1  1  CTP_synth_N    CTP synthase N-terminus
    7.9e-51  172.5   0.0    1.3e-50  171.9   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    3.4e-11   43.3   0.0    7.8e-11   42.1   0.0    1.6  1  Peptidase_C26  Peptidase C26
     0.0056   16.7   0.0      0.027   14.5   0.0    2.1  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.089   12.6   0.0       0.19   11.5   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.2   0.8  1.2e-120  4.2e-117       1     264 [.       4     267 ..       4     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 390.2 bits;  conditional E-value: 1.2e-120
                  EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT----GGGEEEHHHHHHHHHH CS
  CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikltkennittGkiyksvie 98 
                  k+i+vtGGv+SglGkG++++s+++ll+ ++ kv++ikiDPYln+dagt++p+ hGEvfv+ddG+e+D+D+GnYeRfl++++ k++nitt +iy+svie
   AJA92847.1   4 KFIFVTGGVMSGLGKGVVSSSICKLLQLSDQKVSCIKIDPYLNYDAGTMNPIAHGEVFVTDDGGECDMDIGNYERFLNQDIPKSHNITTAQIYSSVIE 101
                  8************************************************************************************************* PP

                  HHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHH CS
  CTP_synth_N  99 kerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvke 196
                   er+G+ylG++vq+iphvtd+ik+ri+k+a  +e ++++ve gGtvgdieslpflea+rq+++e g+env+++hvtl p l+  ge+ktkptqhsv+e
   AJA92847.1 102 SERKGEYLGACVQIIPHVTDAIKNRIKKIAADEELEILVVECGGTVGDIESLPFLEALRQIRVEEGSENVIFVHVTLAPSLDVVGEQKTKPTQHSVQE 199
                  ******************************9999**************************************************************** PP

                  HHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT CS
  CTP_synth_N 197 lrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesiyevpllleeqglaelileklk 264
                  lr++Giqpd++++r++++l++++++ki++f+nv++++v+s++dv+si++vp +l +qgl ++i +k++
   AJA92847.1 200 LRRIGIQPDLLCVRCSMPLQDKTRNKISMFTNVTNNDVFSCHDVDSIFQVPEILYDQGLVDVIFKKFN 267
                  ***************************************************************99986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.9   0.0   3.5e-54   1.3e-50       2     188 ..     306     527 ..     305     529 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.9 bits;  conditional E-value: 3.5e-54
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH..THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE..... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile..llknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgrkvv..... 93 
                 l D+y sv+++l+ha++++g k+++++id+++ +  +   l++++gilv+gG+g++g eg i+++++are++iP+LGIC+G+Ql+a +f+r+v      
  AJA92847.1 306 LADSYVSVNHALKHAAASIGKKITIDWIDSENING-NvdTLSKYNGILVPGGFGTRGSEGIIKTANFAREQNIPYLGICFGFQLAAVSFARNVCshtda 403
                 78***************************854433.3457***************************************************99999999 PP

                 ..................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT. CS
      GATase  94 ..................kekekehhggtmrlgddet........allyglknevierhrHryevnpk...elepaglevtakseddeelmeiiekkn. 162
                                   ++   +++gg+ rlg++e         +++yg+ +++  rhrHrye+n k   e+ ++g++++++s+++ ++mei e ++ 
  AJA92847.1 404 nsteieqntnnpiidllpEQDGITDMGGSLRLGANEInvkpdtiaNKIYGQ-DKISKRHRHRYEFNTKyleEFAQKGMIFSGESDEG-RRMEILEIPSh 500
                 99999999999999***98888************6669************9.**************99****************887.9*********9 PP

                 T.EEEESSBTTSTTSTTHHHHHHHHHH CS
      GATase 163 p.fvgvQFHPEststpegpellfnfli 188
                 + fvgvQFHPE+ s+p+ pe +f+ + 
  AJA92847.1 501 KfFVGVQFHPEFNSRPGYPEHVFKAFT 527
                 9**********************9886 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   2.2e-14   7.8e-11     101     216 .]     372     511 ..     365     511 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 2.2e-14
  Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.............q.....saashavkvekgsllaellgseeievnslHhqai 178
                    a e+++P lgiC G+ql +v +  ++ ++ +++s++ +   ++             +        + +++v+++++ ++++g+++i+    H+   
     AJA92847.1 372 AREQNIPYLGICFGFQLAAVSFARNVCSHTDANSTEIEQNTNNpiidllpeqdgitDmggslRLGANEINVKPDTIANKIYGQDKISKRHRHRYEF 467
                    6799**************************9977777776666889988886666515666777899********************9*9**9988 PP

  Peptidase_C26 179 ke.....laeelrveAvaeDg..viEaieseeakafvlgvQwHPE 216
                    ++      a++  + +  +D+   +E +e++++k f++gvQ+HPE
     AJA92847.1 468 NTkyleeFAQKGMIFSGESDEgrRMEILEIPSHK-FFVGVQFHPE 511
                    777777766666666666554136********87.*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.7e-06     0.027       7      55 ..      13     242 ..       6     434 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                 STTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
        CbiA   7 kGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................................... 54 
                  +G GK +++ +++++l+    +V  ++ Dp  n +a   g+ n i+                                                    
  AJA92847.1  13 MSGLGKGVVSSSICKLLQLSDQKVSCIKIDPYLNYDA---GTMNPIAHgevfvtddggecdmdignyerflnqdipkshnittaqiyssvieserkgey 108
                 69******************************88887...88888888888888899999998888888888888888888877777777777777777 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        CbiA  55 ................................................................................................... 54 
                                                                                                                    
  AJA92847.1 109 lgacvqiiphvtdaiknrikkiaadeeleilvvecggtvgdieslpflealrqirveegsenvifvhvtlapsldvvgeqktkptqhsvqelrrigiqp 207
                 777777777777666666666666666666666666666666666666555555555555555555555555555555555555555555555555555 PP

                 ..................................C CS
                 ..................................x RF
        CbiA  55 ..................................d 55 
                                                   d
  AJA92847.1 208 dllcvrcsmplqdktrnkismftnvtnndvfschD 242
                 55555555555555555555555555555555550 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.2e-05      0.19      36     112 ..     314     393 ..     283     416 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                 S..TSEEEETTSEEEE-SEEGG......GCTCC.G-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTT CS
   DJ-1_PfpI  36 d..keevkgsrGlkvtvdasld......dvkaa.eyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagv 112
                 +   +    s G k+t+d  +d      +v++  +y+ +++pGG       r +e +++++  + e++ ++  IC g   Laa + 
  AJA92847.1 314 NhaLKHAAASIGKKITIDW-IDseningNVDTLsKYNGILVPGGFG----TRGSEGIIKTANFAREQNIPYLGICFGF-QLAAVSF 393
                 3445555667777777777.334777777766559***********....88899**********************5.4555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3740.36
//
Query:       AJA92848.1  [L=334]
Description: polysaccharide biosynthesis protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-97  325.8   0.1    2.7e-97  325.5   0.1    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.1e-25   90.5   0.0    9.3e-25   87.5   0.0    2.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.3e-20   71.6   0.0    4.1e-17   62.1   0.0    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      1e-16   61.3   0.0      9e-15   54.9   0.0    2.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.3e-13   48.2   0.0    4.1e-11   42.5   0.0    2.1  1  RmlD_sub_bind    RmlD substrate binding domain
    8.3e-12   45.4   0.0    1.1e-11   44.9   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.1e-09   36.9   0.4    7.8e-06   25.2   0.1    3.1  2  NAD_binding_4    Male sterility protein
    1.1e-05   25.0   0.0    2.3e-05   24.0   0.0    1.5  1  adh_short        short chain dehydrogenase
    0.00012   21.7   0.0    0.00033   20.3   0.0    1.8  2  NmrA             NmrA-like family
    0.00016   21.7   0.0    0.00035   20.6   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00018   22.0   0.0    0.00075   20.0   0.0    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00023   21.2   0.0    0.00052   20.0   0.0    1.6  1  KR               KR domain
     0.0047   17.3   0.0      0.065   13.7   0.0    2.4  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
       0.01   15.5   0.2      0.025   14.3   0.2    1.6  1  Polysacc_syn_2C  Polysaccharide biosynthesis protein C-termin


Domain annotation for each model (and alignments):
>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.5   0.1  2.1e-100   2.7e-97       1     291 [.       7     281 ..       7     284 .. 0.96

  Alignments for each domain:
  == domain 1  score: 325.5 bits;  conditional E-value: 2.1e-100
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      +l+tG++Gs+G++l++++l+ +p+ i++++r+E k+ e+e+e+    ++ +l+++    +gdvrd+erl  ale  +vd+vfhaAAlKhVP +e
       AJA92848.1   7 ILITGGTGSLGQALTKKLLSYEPEAIRIFSRNESKQIEMESEF----DNPRLRFF----MGDVRDSERLYYALE--DVDIVFHAAALKHVPKIE 90 
                      89**************************************998....68899999....***************..****************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS-..-EEEEEEE-EETTGTTSSHHHHHHHH CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqalakeseekk..tkfvvvRfGNVlgSrGSviplFkkqi 186
                      +np+e iktNv+g++nvi+ +++++v+kv+++ tDKAv+P n++GatK+l+ekl+++++++ + +k  tkfv+vR+GNV+gS+GSvip+F + i
       AJA92848.1  91 YNPFESIKTNVIGSQNVIDNSLRQNVEKVICVGTDKAVSPLNTYGATKLLMEKLFVSANNYVNPEKhkTKFVAVRYGNVMGSSGSVIPKFIDLI 184
                      ***********************************************************998654455************************** PP

                      HTTSSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE----TT--SS-EEE-GGGG CS
  Polysacc_synt_2 187 keggpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikitGlRpGEklyEeLlieees 280
                      k+++p+t+Td +mtR+ +t++ea +++l+a++ +kg+eif+ +  +++ +  l ++l el+g       + + +i+G+RpGEkl+E+L++++e 
       AJA92848.1 185 KKNKPITITDLKMTRFTITMNEALEFILNATQVGKGSEIFIPEL-KSYDMSTLIESLSELYG-------EAKQEIVGIRPGEKLHETLINHDEI 270
                      ********************************************.************99998.......56789*****************999 PP

                      GGEEE-SSEEE CS
  Polysacc_synt_2 281 veetelekilr 291
                          +++++++
       AJA92848.1 271 LYGWKINQMYM 281
                      98888888776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   7.3e-28   9.3e-25       1     216 [.       7     205 ..       7     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 7.3e-28
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqg 94 
                 il+tG+tG +G+al+k+ll+   e i + +++++++ + + +      ++  +d++d+++l  +++  ++d+v+h+Aa ++v+    +p + i++n++g
  AJA92848.1   7 ILITGGTGSLGQALTKKLLSYEPEAIRIFSRNESKQIEMESEFdnprlRFFMGDVRDSERLYYALE--DVDIVFHAAALKHVPKIEYNPFESIKTNVIG 103
                 8*********************997777777777777777766899********************..89***************************** PP

                 HHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT.....-EEEEEEESEEESTTS-TTSTTSHHHH CS
   Epimerase  95 tlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyg.....lnaiilrlfnlyGprngegevsrvipa 188
                 ++n+++ + +++v++++ ++++           + +       p + Y+a+Kl++ekl  ++++  +     ++++++r+ n++G         +vip+
  AJA92848.1 104 SQNVIDNSLRQNVEKVICVGTD-----------KAV------SPLNTYGATKLLMEKLFVSANNYVNpekhkTKFVAVRYGNVMGSS------GSVIPK 179
                 *********************2...........222......47799************9998543344444**************9......****** PP

                 HHHHHHTTSSSEEEETTST-EEEEEEHH CS
   Epimerase 189 lirkilegkqevtllgdgtalRdflyve 216
                 +i  i+++k ++t+  d++  R  +  +
  AJA92848.1 180 FIDLIKKNK-PITIT-DLKMTRFTITMN 205
                 *********.99985.566666555555 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   3.2e-20   4.1e-17       1     122 [.       8     130 ..       8     132 .. 0.90
   2 !    8.6   0.1   0.00064      0.83     142     224 ..     130     209 ..     123     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.2e-20
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk..viegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGT 96 
                 ++tGg+G lG+al k+L++ e+ + +r++  +es+++ e  s++++    +  gDv+d ++l  ale+vd+v+h a+l  v + +++  e  k nv G 
  AJA92848.1   8 LITGGTGSLGQALTKKLLSYEP-EAIRIFSRNESKQI-EMESEFDNPRlrFFMGDVRDSERLYYALEDVDIVFHAAALKHVPKiEYNPFESIKTNVIGS 104
                 69*******************7.9*****99998887.555555554456********************************9888888999******* PP

   3Beta_HSD  97 rnvleacvkagvrvlvYtSsaevvgp 122
                 +nv++  ++++v++++ + + ++v p
  AJA92848.1 105 QNVIDNSLRQNVEKVICVGTDKAVSP 130
                 ****************9999888876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00064
   3Beta_HSD 142 hqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                 + ++y  +K l Ekl ++aN+ +  +  +   +a+R   + G   +++ +++  ++k++     +  +  ++ ++   N a  
  AJA92848.1 130 PLNTYGATKLLMEKLFVSANNYVNPEKHKTKFVAVRYGNVMGSSGSVIPKFIDLIKKNK---PITITDLKMTRFTITMNEALE 209
                 6789*****************55555558888***********9999999998888887...333334444555555555555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   7.1e-18     9e-15       1     259 [.       8     237 ..       8     269 .. 0.72

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 7.1e-18
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    LiTG++G  G+ l+++Ll+ + e + i  r++s +++  ++         +++l+++ gD++Ds++l  +l++v  d v++ AA +hV++   +P 
     AJA92848.1   8 LITGGTGSLGQALTKKLLSYEPEAIRIFSRNESKQIEMESE-F------DNPRLRFFMGDVRDSERLYYALEDV--DIVFHAAALKHVPKIEYNPF 94 
                    9**************************99999966543333.3......35789******************99..89****************** PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-E.EESTTS-TT CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfn.hesprrget 191
                    + +++nv+G +++++   + ++e   +++ ++t+                ++P + Y+a+Kl  + + v+ ++  +     + +    ++  +g +
     AJA92848.1  95 ESIKTNVIGSQNVIDNSLRQNVE---KVICVGTDK--------------AVSPLNTYGATKLLMEKLFVSANNYVNPEKHKTKFVAvRYGNVMGSS 173
                    **************999888876...667777763..............45666666666666666665555444433333322222455555444 PP

                    SCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCH CS
  GDP_Man_Dehyd 192 fvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefv 259
                         i++++  i+++k   +++ +l+ +R     ++  e + ++ q +k +++ i + +++ + +++
     AJA92848.1 174 --GSVIPKFIDLIKKNK--PITITDLKMTRFTITMNEALEFILNATQVGKGSEIFIPELKSYDMSTLI 237
                    ..446666666666654..4445666666666666666666666666666666666666666665555 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   3.2e-14   4.1e-11       2     186 ..       6     203 ..       5     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.2e-14
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayav 77 
                    kil+tG++G lG++L+k+l + + e++ + ++                      d++d+e++  +l++   d+v +aAA + v k E ++ ++ + 
     AJA92848.1   6 KILITGGTGSLGQALTKKLLSYEPEAIRIFSRneskqiemesefdnprlrffMGDVRDSERLYYALED--VDIVFHAAALKHVPKIEYNPFESIKT 99 
                    89*****************9988888888555599****************99**************9..899*********************** PP

                    HTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH.........H-SSEEEEEE-SEESSSSS-HHHHH CS
  RmlD_sub_bind  78 naeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla.........agkkalivRtswvygekgknfvktm 163
                    n+ +++++ +   + ++  +i v tD               ++sPln+YG+tKl++E+   +         ++ k++ vR + v g++g   + ++
     AJA92848.1 100 NVIGSQNVIDNSLRQNVEkVICVGTD--------------KAVSPLNTYGATKLLMEKLFVSannyvnpekHKTKFVAVRYGNVMGSSGS-VIPKF 180
                    ************99999626666665..............579**************986654666666655668899999999999876.56678 PP

                    HHHHHH-SEEEEESS-EE--EEH CS
  RmlD_sub_bind 164 lrlakereelkvvaDqlgsPTsa 186
                    ++l k+++++++ + ++ + T +
     AJA92848.1 181 IDLIKKNKPITITDLKMTRFTIT 203
                    89999999999998887776665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   8.8e-15   1.1e-11       1     102 [.      11     128 ..      11     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 8.8e-15
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.........HHHH...... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele...aeeglevvegdvtdvedlaealkgadaVvsalggggk.........deeg...... 77 
                     G+tG+ G++l+k+ll+ +  +++++ Rn++k  e+e   ++++l+ + gdv d+e l  al+++d+V+ a++ ++             +      
      AJA92848.1  11 GGTGSLGQALTKKLLSYEPEAIRIFSRNESKQIEMEsefDNPRLRFFMGDVRDSERLYYALEDVDIVFHAAALKHVpkieynpfeS--Iktnvig 103
                     9*****************889*******9999777766688******************************554444444444330..1455678 PP

                     HHHHHHHHHHCT--EEEEEEETTTT CS
  NAD_binding_10  78 aknivdaakeagvkRfvlvsaigvg 102
                      +n++d   +++v+++++v++ ++ 
      AJA92848.1 104 SQNVIDNSLRQNVEKVICVGTDKAV 128
                     *******************987665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   6.1e-09   7.8e-06       1     136 [.       9     124 ..       9     131 .. 0.77
   2 !    7.3   0.0    0.0018       2.3     169     220 ..     127     183 ..     123     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.1e-09
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    +TG+TG LG+ L +kLL+ +pe  i +  R++s+      +       e++s++      r+++  GD+ +++     + +  l e vd+++h aA
     AJA92848.1   9 ITGGTGSLGQALTKKLLSYEPE-AIRIFSRNESK-----QI-------EMESEFD---NPRLRFFMGDVRDSE-----RLYYAL-EDVDIVFHAAA 82 
                    8********************9.77777777766.....44.......5555665...899********9854.....556555.*********** PP

                    S-S.ST.TSS..EEHHHHHHHHHHHHHHHTSSS--.-EEEEEE CS
  NAD_binding_4  97 tvnfde.pyk..ellrvNveGtrevlelakklkklkvllhvST 136
                      ++ + +y+  e +++Nv G ++v++ + + +    ++ v T
     AJA92848.1  83 LKHVPKiEYNpfESIKTNVIGSQNVIDNSLRQNVE-KVICVGT 124
                    988765544422699**********9987754444.6666666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
                    TTTCCCHHHHHHHHHHHHHHHHH.....HHH---EEEEEE-EEE--SSST---TTSH CS
  NAD_binding_4 169 lkglpntYeqsKalaEklvrear.....rrsglpvvivRpsiitgesktGwingsdl 220
                      +  ntY  +K l Ekl  +a+     ++++ ++v vR ++++g+s + +++  dl
     AJA92848.1 127 AVSPLNTYGATKLLMEKLFVSANnyvnpEKHKTKFVAVRYGNVMGSSGSVIPKFIDL 183
                    567789***********998887233333577789999***9999887766665554 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.8e-08   2.3e-05       1     169 [.       5     154 ..       5     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.8e-08
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselse 98 
                 k +l+tG+++ +G+a+ k+l++   + +  ++r+e+k  e+ +e+ +   ++ ++ +Dv+d+e++  ++e++       d++ + A++   + + +++ 
  AJA92848.1   5 KKILITGGTGSLGQALTKKLLSYEPEAIRiFSRNESKQIEMESEFDN--PRLRFFMGDVRDSERLYYALEDV-------DIVFHAAAL---KHVPKIEY 91 
                 689*******************999988779*****99999999997..79*********999888777765.......999999999...34445555 PP

                 HHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGG CS
   adh_short  99 eewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelap 169
                 + +e +i++N+ g  +++   l++    +  +++ v+   +   v  +  Y+A+K  +++l+ s+ + ++p
  AJA92848.1  92 NPFE-SIKTNVIGSQNVIDNSLRQ----NVEKVICVGTDKA---VSPLNTYGATKLLMEKLFVSANNYVNP 154
                 5554.5788988876666666665....5556666665555...555677888888888887777666555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.6e-07   0.00033       1      73 [.       7      82 ..       7     118 .. 0.90
   2 ?   -3.1   0.0       3.7   4.8e+03     110     128 ..     281     299 ..     276     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                EEESSTTSHHHHHHHHHHHH.HT-EEEEEES-S..-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
        NmrA  1 IlviGaTGrqGksvvrallk.aghkvralvRdt..kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                Il++G+TG++G+++++ ll+ +   +r+  R++  + e   ++ +    +  gd+ d e l  al++vd vf + +
  AJA92848.1  7 ILITGGTGSLGQALTKKLLSyEPEAIRIFSRNEskQIEMESEFDNPRLRFFMGDVRDSERLYYALEDVDIVFHAAA 82
                89*****************977889*******9544566778888889999*********************9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                 .SSS---TTTHHHHHHHHH CS
        NmrA 110 naeepavphfdsKaeieey 128
                   + p+ ++f++K   e+y
  AJA92848.1 281 MLANPHYELFNQKNILENY 299
                 5678999999999988877 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.7e-07   0.00035      10     119 ..       2     118 ..       1     128 [. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.7e-07
                   .TT-EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-E.....EEEGCGHHHHHHT-SEEEE-SSSSS.-SB-HHHHHCCH CS
  Shikimate_DH  10 lkekkvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeie.....alkleelkellaeadvvisatasee.pilekeeveeal 99 
                   +k+kk+l+  G+G +++ ++k+Ll+ + +++ ++ R+ ++  e+ +e+++ +++     +++ e l  +l+++d+v+ a a ++ p +e + +e+++
    AJA92848.1   2 FKGKKILITgGTGSLGQALTKKLLSYEPEAIRIFSRNESKQIEMESEFDNPRLRffmgdVRDSERLYYALEDVDIVFHAAALKHvPKIEYNPFESIK 98 
                   578999998458************************************88766422222678889999**********9987763678888888777 PP

                   HH.S..EEEEE--SS-SB-T CS
  Shikimate_DH 100 kkrkkplllvDiavPRdvep 119
                   ++   ++ ++D ++  +ve+
    AJA92848.1  99 TNVIGSQNVIDNSLRQNVEK 118
                   66557777777777777775 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.9e-07   0.00075       4      77 ..       9      89 ..       6     109 .. 0.87
   2 ?   -2.7   0.0       7.5   9.5e+03      77      81 ..     236     240 ..     210     264 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.9e-07
                   EE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
  F420_oxidored  4 ii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvlavkpedveev 77
                   i  G+G++g+al+++ll+    p+ i++  srn++k  e+++e+           v+ ++     a+e+ d+v+ a   ++v+++
     AJA92848.1  9 ITgGTGSLGQALTKKLLSYE--PEAIRIF-SRNESKQIEMESEFDnprlrffmgdVRDSE-RLYYALEDVDIVFHAAALKHVPKI 89
                   4469***************9..99***66.***************9**999997755555.6788999******99999999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                    HHHHC CS
  F420_oxidored  77 vlsel 81 
                    ++++l
     AJA92848.1 236 LIESL 240
                    44333 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     4e-07   0.00052       4      76 ..       8      75 ..       6     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4e-07
                EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
          KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                litGG+G+LG++l++ l++   + + ++sR+++++        e e  + + +++  Dv d++ +  +le+++
  AJA92848.1  8 LITGGTGSLGQALTKKLLSYEPEAIRIFSRNESKQ-----IEMESEFDNPRLRFFMGDVRDSERLYYALEDVD 75
                9******************************3322.....223333345677778888888777777777665 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   5.1e-05     0.065       1      83 [.       6      90 ..       6     149 .. 0.67
   2 ?    1.0   0.0      0.44   5.6e+02       4      29 ..     169     194 ..     168     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                    EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSG..GGTTTECEBEEE..GGGGGCTT-SEEEE-SCHHHHHHHH CS
  Semialdhyde_dh  1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavk..aleegkdlkved..vdeeelkevdivflalpagvskela 83
                    k+ i G+tG  Gq+l + L + +p  e ++++s+++s+  ++++ +    l       v+d      +l++vdivf a+  +   +++
      AJA92848.1  6 KILITGGTGSLGQALTKKLLSyEP--EAIRIFSRNESKQIEMESEFDnpRL-RFFMGDVRDseRLYYALEDVDIVFHAAALKHVPKIE 90
                    57899**********999998577..5566667777666666666663222.22222333322444566*******998766555554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                     EETTTSHHHHHHHHHHHCTSSEEEEE CS
  Semialdhyde_dh   4 ivGatGyvGqellrlLeehpevelvv 29 
                     + G +G v  +++ l++++++++++ 
      AJA92848.1 169 VMGSSGSVIPKFIDLIKKNKPITITD 194
                     7899**************99999875 PP

>> Polysacc_syn_2C  Polysaccharide biosynthesis protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2     2e-05     0.025      13      46 ..     300     333 ..     298     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
  Polysacc_syn_2C  13 eGeekiseledYnShNTerLdveeikelLlkldy 46 
                      +G eki+e e Y S+ +++ + ee+k+++ +l++
       AJA92848.1 300 NGIEKINEMESYSSDVAQKISKEELKKKISELEF 333
                      5889**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2237.34
//
Query:       AJA92849.1  [L=587]
Description: dolichyl-phosphate-mannose-protein mannosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-13   49.0  15.3    7.5e-13   49.0  15.3    3.0  4  PMT_2          Dolichyl-phosphate-mannose-protein mannosyltra
     0.0085   16.0   9.2     0.0085   16.0   9.2    2.4  2  DUF2723        Protein of unknown function (DUF2723)
  ------ inclusion threshold ------
      0.019   15.0   0.3      0.071   13.2   0.0    2.1  2  DUF2973        Protein of unknown function (DUF2973)
       0.12   11.8   0.8       0.17   11.4   0.1    1.6  2  Peptidase_M60  Peptidase M60, enhancin and enhancin-like
          7    6.9   7.6          4    7.7   0.3    3.3  3  Holin_SPP1     SPP1 phage holin


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       4.2   1.5e+04     148     152 ..      20      24 ..      11      36 .. 0.44
   2 !   49.0  15.3   2.1e-16   7.5e-13       3     154 ..      67     216 ..      65     222 .. 0.91
   3 ?    3.7   0.3     0.018        66      45     110 ..     325     368 ..     290     379 .. 0.50
   4 ?   -1.6   0.1      0.78   2.8e+03     139     155 ..     398     415 ..     391     421 .. 0.70

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4.2
       PMT_2 148 lalll 152
                 l++l+
  AJA92849.1  20 LIFLI 24 
                 11111 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 2.1e-16
       PMT_2   3 PPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkyw 101
                 P   a + al+ + f ++ +++ ++s++ g+ +++l y ++r+++ +r+a+l+ l+ a++p +++ s + ++d + +++++l+ly++ +   ++   + 
  AJA92849.1  67 PYGGAIFFALVNSFFDDGFTVMKMISIISGSGSVFLSYYILRNVVRSRTAFLGQLFFAFSPWVGFFSIQAEIDMFPIFFIMLSLYFITKSELSKF--DI 163
                 66778899******************************************************************************999988774..99 PP

       PMT_2 102 llagvlfGlgflsKytaallliaall.yllisarrilkekkpylalllalllfs 154
                 ll++v+++++f+++   +++++++++  +++  +   ++++++l+++l +l +s
  AJA92849.1 164 LLSAVFIAISFMVRTQTIVVIFTIVItLMIFF-KNDYRKNIKFLIIFLSVLFIS 216
                 ***********************999755555.567888888887777777765 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.018
       PMT_2  45 rlfg.kraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkywllagvlfGl 110
                 ++ + ++  +                       + +ll+ l+ +ll  ++     +++l++g++f+l
  AJA92849.1 325 NYKNnHSKNI-----------------------LPLLLLPLVFWLLTSLVNLSAGEQFLVIGISFAL 368
                 4444333344.......................4444444444444444444444444444444443 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.78
       PMT_2 139 ekkpyl.alllalllfsp 155
                 +kk++l +++++l+l+s 
  AJA92849.1 398 NKKKLLiCSIIILILISN 415
                 455555588888888874 PP

>> DUF2723  Protein of unknown function (DUF2723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   9.2   2.4e-06    0.0085      30     164 ..      74     198 ..      69     203 .. 0.81
   2 ?   -0.2   0.1      0.23   8.1e+02      59     162 ..     344     374 ..     325     379 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
     DUF2723  30 fslla.daekvalrvnllsalssaltilflfltitlllrskakkiailgaglvgalafafsdtfWfsaveaeVYalsslftalvlwlilkweeeadekr 127
                 f+l+  ++++  + + ++s +s++ ++++ + ++ +++r          ++++g l fafs  + f +++ae+  + ++f+ l l++i+k e ++ +  
  AJA92849.1  74 FALVNsFFDDGFTVMKMISIISGSGSVFLSYYILRNVVR--------SRTAFLGQLFFAFSPWVGFFSIQAEIDMFPIFFIMLSLYFITKSELSKFD-- 162
                 555555555566677888999999999999999988887........56899**************************************9999987.. PP

     DUF2723 128 sdrwlvliayligLslgvhllnllllpaia..llyyfk.k 164
                     ++l a+ i++s+ v++ ++++++ i+  l+++fk +
  AJA92849.1 163 ----ILLSAVFIAISFMVRTQTIVVIFTIVitLMIFFKnD 198
                 ....9999**********9888877765541156777734 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
     DUF2723  59 fltitlllrskakkiailgaglvgalafafsdtfWfsaveaeVYalsslftalvlwlilkweeeadekrsdrwlvliayligLslgvhllnllllpaia 157
                 f+++                                                                         + l+ Ls g ++l++ + +a++
  AJA92849.1 344 FWLL-------------------------------------------------------------------------TSLVNLSAGEQFLVIGISFALF 369
                 3333.........................................................................4444455555544444444444 PP

     DUF2723 158 llyyf 162
                   ++f
  AJA92849.1 370 SAVFF 374
                 44444 PP

>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3         3   1.1e+04      14      24 ..     168     178 ..     163     190 .. 0.72
   2 ?   13.2   0.0     2e-05     0.071      11      62 ..     406     457 ..     402     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3
     DUF2973  14 aflAvanLirs 24 
                 +f+A++ ++r 
  AJA92849.1 168 VFIAISFMVRT 178
                 47777777775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
     DUF2973  11 tvlaflAvanLirslitlsadsqrkkkskksrtkkvtpHPELLDeaGklikE 62 
                  ++ ++ ++n   s ++  a+++ +  ++ s + +++ HPEL+ ++G++ ++
  AJA92849.1 406 SIIILILISNFGYSYVMYRATTSFQAFENISTEIEYVFHPELVQKRGDVLND 457
                 578888899999*****99999999999999999**************9886 PP

>> Peptidase_M60  Peptidase M60, enhancin and enhancin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.2   4.3e+03     145     158 ..     248     261 ..     245     261 .. 0.84
   2 ?   11.4   0.1   4.7e-05      0.17     180     262 ..     454     565 ..     439     572 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
  Peptidase_M60 145 gwkwvggttEvtnN 158
                    +++w+  +tE+++N
     AJA92849.1 248 TIEWKERVTEIAVN 261
                    57899999*****9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.7e-05
  Peptidase_M60 180 tgadeaanglkgwaretnakeylekgkdlLvffgqlklyf...................gwdfykklleaarkqetlteenkegd........... 245
                    + +d ++   k +++++  ++y+ +++ ++v++gq kl f                   +w+f +k++  +++ + ++ ++++             
     AJA92849.1 454 VLNDIWK---KLEQENNIENSYIMAPQLYFVPYGQSKLLFahfnegpsddtienyitreNWKFTEKFHSNIHSIPADRLDENN-Pipkyivhidrd 545
                    5566666...5566777778999999999****************************99999999999999999999988555.467888888888 PP

  Peptidase_M60 246 ...kqdefmkkasklakkdL 262
                       kq+ef+k   + + +++
     AJA92849.1 546 fgkKQHEFIKILNDPYDENI 565
                    88888888887766666665 PP

>> Holin_SPP1  SPP1 phage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4     0.089   3.2e+02      34      56 ..      11      33 ..       1      39 [. 0.80
   2 ?    7.7   0.3    0.0011         4      38      59 ..     178     199 ..     164     200 .. 0.88
   3 ?   -1.6   0.0       0.9   3.2e+03      47      58 ..     318     329 ..     312     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.089
  Holin_SPP1 34 eealytaitlvftvataivawyK 56
                 +++  ++tl+f+++t+ va+++
  AJA92849.1 11 YKKFSIVLTLIFLIVTSYVAFFE 33
                45677799*********999997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
  Holin_SPP1  38 ytaitlvftvataivawyKNny 59 
                 ++ i+++ft++ +++ ++KN y
  AJA92849.1 178 TQTIVVIFTIVITLMIFFKNDY 199
                 68899***************87 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.9
  Holin_SPP1  47 vataivawyKNn 58 
                 +a  i+  yKNn
  AJA92849.1 318 GAIHIIKNYKNN 329
                 57789999***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3850.56
//
Query:       AJA92850.1  [L=157]
Description: DnaJ domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-20   71.6   1.5    7.9e-20   70.8   1.5    1.4  1  DnaJ      DnaJ domain
  ------ inclusion threshold ------
      0.069   13.3   0.1         17    5.6   0.0    2.6  2  UBA_2     Ubiquitin associated domain (UBA)
      0.073   12.8   0.0       0.11   12.2   0.0    1.3  1  DUF1673   Protein of unknown function (DUF1673)
       0.25   12.0   2.8       0.58   10.8   1.6    2.0  2  AKNA      AT-hook-containing transcription factor


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   1.5   1.8e-23   7.9e-20       4      59 ..      18      72 ..      16      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.8e-23
                HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHH CS
        DnaJ  4 eiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekR 59
                eiLgv+kd+s++eIk+aYrkl+lkyHPDkn  ++++ +kFkei+eAy+ L+  +k 
  AJA92850.1 18 EILGVTKDSSHKEIKQAYRKLSLKYHPDKN-PESNSGKKFKEITEAYQYLKSHRKN 72
                79****************************.66679999***********998875 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0038        17      21      40 ..      17      35 ..       7      38 .. 0.76
   2 ?    4.9   0.0    0.0064        29      30      44 ..      49      67 ..      44      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0038
       UBA_2 21 ieaLekaekskssneIkDAY 40
                 e L   ++s s++eIk AY
  AJA92850.1 17 REILGVTKDS-SHKEIKQAY 35
                4555555666.899****** PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0064
       UBA_2 30 s....kssneIkDAYlLmk 44
                +    k+ +eI +AY+ +k
  AJA92850.1 49 EsnsgKKFKEITEAYQYLK 67
                23356899*******9777 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.11      18      73 ..      95     150 ..      89     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
     DUF1673  18 aletrksispenleadnysrakeenesseenpgwvdkrsnrillvslfftllsllv 73 
                 +++  ++ s+e+l+ +n++++++ n++ ++++ + ++  +++ll+  ++ ++  ++
  AJA92850.1  95 KMGDEMRFSFEELRRENQQFGGDFNQETHNREKPISQKTTHLLLYGGLGVVTLWII 150
                 788999*************************************9765554444333 PP

>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.22   9.8e+02      41      73 ..      49      81 ..      24      91 .. 0.67
   2 ?   10.8   1.6   0.00013      0.58      49      88 ..      91     135 ..      57     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
        AKNA 41 sreleaeIyqlgqrleeLkdqtdqlkqkveefs 73
                +++  ++     + ++ Lk + ++  +k e++s
  AJA92850.1 49 ESNSGKKFKEITEAYQYLKSHRKNQSNKDEQVS 81
                344444444456778888888888777777776 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
        AKNA  49 yqlgqrleeLkdqtdqlkqkveefskdiaqds.....psplqdar 88 
                  q++++ +e++   + l+++ ++f+ d +q++     p++ + ++
  AJA92850.1  91 AQGEKMGDEMRFSFEELRRENQQFGGDFNQEThnrekPISQKTTH 135
                 69****************************986666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1238.90
//
Query:       AJA92851.1  [L=106]
Description: hypothetical protein T478_0452 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.03   14.1   0.4      0.069   12.9   0.2    1.6  1  CAP_assoc_N  CAP-associated N-terminal


Domain annotation for each model (and alignments):
>> CAP_assoc_N  CAP-associated N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.9e-06     0.069       8      44 ..      60      96 ..      57     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-06
  CAP_assoc_N  8 veeklGepkrkdpseygyewwvYnedykeyiqvgved 44
                 v++++  + rk+++e +++ w+++ed+++y  v v+ 
   AJA92851.1 60 VTTTVTYALRKTKQERDVRYWTFHEDKDNYAIVFVSS 96
                 667777889***********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 761.87
//
Query:       AJA92852.1  [L=274]
Description: prephenate dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-54  183.7   0.3    6.3e-54  182.6   0.2    1.6  2  PDT       Prephenate dehydratase
    4.7e-07   29.5   0.0    8.9e-07   28.6   0.0    1.4  1  ACT       ACT domain
  ------ inclusion threshold ------
      0.096   13.3   0.1       0.26   11.9   0.1    1.8  1  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.6   0.2     1e-57   6.3e-54       1     182 [.       4     182 ..       4     183 .. 0.96
   2 ?   -1.8   0.0      0.38   2.3e+03      54      76 ..     243     266 ..     207     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 1e-57
                 EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS....-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEEEEEE---EEEE-TT--TT CS
         PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekge....adyavvPiENsteGsVnetlDlLlkesdlkivgEvvlpiehcLlakpktkle 95 
                 v+y+G +g+ys+ Aa+k+f +e++++i ++s+e+++++ ++++    ++y+++P+ENs+eG+V +++D ++k ++l+ +gEv+l++ehcL+++ +   +
  AJA92852.1   4 VSYQGVQGAYSQSAAKKFF-GEEIDTIGTSSFEDALKSAQNDKtssdVSYSILPVENSIEGTVGQSIDEIVK-TNLHAIGEVYLKVEHCLIGRGEL--D 98 
                 78*****************.*********************9988889************************.89***************988765..* PP

                 T--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHHHTT-EEEECS-SS-S--EEEEEEEEETT CS
         PDT  96 eikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaaelyglkvleeniedkknntTRFlvlakee 182
                 +i+kvyShpqalgQc++f+e+h  +++ v++++ta ++++  ++ ++++aaias++a +ly++ +++e i +++nn+TRFl+ +ke+
  AJA92852.1  99 DITKVYSHPQALGQCSDFIENH--GLKTVPTYDTAGSVEI-IKDLENNCAAIASSLASNLYDVPIIKEGIANNSNNFTRFLIFSKEK 182
                 **********************..****************.66788899***********************************997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.38
                 SSS-B-HHHHHHHHH.S.SEEEEE CS
         PDT  54 steGsVnetlDlLlkes.dlkivg 76 
                 s + +++ +lD+++k++  lki+g
  AJA92852.1 243 SSNSKIKSVLDNIRKNTiFLKIIG 266
                 667778888888888444467766 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.5e-10   8.9e-07       1      63 [.     191     253 ..     191     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.5e-10
                 EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHH CS
         ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealk 63 
                 t+++++v+ +PG+L +++  + d++iN+++ie+r+ + + +++ f+v+  ++++ ++++  l 
  AJA92852.1 191 TSIIFSVKHEPGALYQILKEFNDNDINLTKIESRPNKNTNWEYNFFVDFLGHSSNSKIKSVLD 253
                 5899*********************************************99999999988776 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   4.3e-05      0.26       9      49 ..     193     232 ..     186     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
       ACT_4   9 leveaedrkglLaditqviseekanivsvnaktrkkdglae 49 
                 +   ++ ++g+L +i++ ++++++n+++++++ +k +   e
  AJA92852.1 193 IIFSVKHEPGALYQILKEFNDNDINLTKIESRPNK-NTNWE 232
                 56667889*************************87.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2096.94
//
Query:       AJA92853.1  [L=274]
Description: phosphoribosylaminoimidazolesuccinocarboxamide synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-71  238.9   0.0    7.8e-71  238.6   0.0    1.0  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.6   0.0   4.4e-75   7.8e-71       2     250 ..       4     236 ..       3     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.6 bits;  conditional E-value: 4.4e-75
                  EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH--BSEEEE.....-SSSEEEEE-EEEESEEEEEEEE--HHH CS
  SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklekipnhliksldpeqlegrsmlvkklkmlpvEvvvRgyltGsl 99 
                  l++GKv+dvY++ +dd+ll+ +++r+sA+dv+ ++eip+KGkvl+++++fwfe+l+ ++nh+iks      ++++++vkk++mlp+E+vvRgy  Gsl
   AJA92853.1   4 LNSGKVKDVYDM-GDDTLLFNFSNRVSAYDVKFNDEIPQKGKVLCKFAKFWFEQLD-VENHFIKS-----HSDTEIIVKKMEMLPIECVVRGYFYGSL 94 
                  579********9.899***************************************6.8*****88.....89************************** PP

                  .......HH....HH....T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEE CS
  SAICAR_synt 100 wkeykksgkvcgirlpe..glkegeklpepiftpstKaeegehDeniseeevvealg..teeeaeeieelalavyekaaelaaergiilvDtKlEFGl 193
                  ++ y+++++    +lpe  + + ++klpep+f+p+tK+e   hD +i+++e++++ +  t e++e ++e ++++y+k+a +a++ g il+D KlEFG+
   AJA92853.1  95 VSRYNSGTT----SLPEniDTTLATKLPEPLFDPTTKSE---HDIPITKDEAITQ-NlvTLEDYEWLSEKTIQIYNKMALIADSAGFILADLKLEFGR 184
                  *******99....77772255679*************98...6*****9999855.3479************************************** PP

                  ETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-STHHHHHHHHHH CS
  SAICAR_synt 194 deedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwleeveekwkekle 250
                     +g+++L+D +  pD  R+w++++y++gk qe +DKq++Rdwl+e  ++++++ e
   AJA92853.1 185 L--NGKITLGDSI-GPDEYRLWPKSSYSPGKIQEAYDKQLLRDWLTE--HGYQKQFE 236
                  9..7*********.*********************************..99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2195.49
//
Query:       AJA92854.1  [L=465]
Description: hydroxymethylglutaryl-coenzyme A synthase C-terminal [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-34  120.1   0.3    2.4e-34  119.3   0.3    1.4  1  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    8.9e-28   97.3   0.1    1.5e-27   96.5   0.1    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
      0.027   14.4   0.0       0.18   11.8   0.0    2.3  3  DUF1726         Domain of unknown function (DUF1726)


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.3     4e-38   2.4e-34       2     240 ..     180     428 ..     179     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 4e-38
                     EE-TT--EEEE----SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHH.HHHHHHH.------GGG-SEEEE--SSHHHHHHHHHHHHHHH CS
  HMG_CoA_synt_C   2 vfdrklrashmehayDFykPdlaseYPvvDGklslscYlkaldrcYksyskk.vkkitkd.adkeftlddfdyvifhsPfcklvqkslarllynD 94 
                      fd+k+ ++ +++ yDFy+P +  e P+v G++s   Yl  ++++ + y++k  k+   d ++ +  ld++dy  +h P++ + +k+la l+  +
      AJA92854.1 180 EFDPKVTSTSIKNEYDFYRP-FGKETPIVHGQYSNLLYLIQVKNALNDYKRKaLKTGLIDmKEGQSMLDHIDYFNMHLPYSNMGKKALAYLVRHE 273
                     599****************9.99****************************943333334379999***************************** PP

                     HHH.S-HHH.HHHH..-GGGGGG.....TT--GGGGGT-HHHH..HHHHH..HHHHHHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HH. CS
  HMG_CoA_synt_C  95 flanassdk.eeev..kekleek.....ddlkldesltdkdle..kallk..iakelfkkkvkpsllvptevGnmYtaslyaalasllskvsad. 176
                      ++ ++ ++  +ev  +e + +      +++ +d  ++ kd e  k + k    +e++++kv++sl++++ +Gn+Ytasly  + s l++  ++ 
      AJA92854.1 274 LRNTPKWKEvIAEVgmEEPVPKDprgtiESIIADSEFMTKDSEftKRFAKtnTYQEIYENKVASSLIASKSIGNLYTASLYLGFRSCLEYEFQKg 368
                     99998854312222112222222333346777788777776553266665115689********************************9865543 PP

                     .HHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHHHHTTTTHHHHHHTSEEE-HHHHHHHHHH CS
  HMG_CoA_synt_C 177 .elagkriglfsYGsGlaaslfslrvkqdvsedsildiakvldlkkkLdsRkevtPeefeealel 240
                      +l+gkr g+ sYGsG++a +fs  +k +        i k+++l++++ +R++++ e++ee  e 
      AJA92854.1 369 vNLEGKRFGFASYGSGSSAMVFSGVIKPEHLS-----IVKEMNLETEIGERQKLSLEDYEELHEN 428
                     3899**********************998887.....**********************997654 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   2.6e-31   1.5e-27       5     170 ..       3     173 ..       1     176 [. 0.92

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2.6e-31
  HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgtetiidksksvksvlm.. 97 
                      gi  + iy+p  ++d  ++    g++  k   glg ++m++v+ ++d   l+     k+++++kl+ ++igrl v te+  d sk+++s ++  
      AJA92854.1   3 AGIDDISIYIPRLFMDAGDFAEARGLDPQKLVKGLGVSKMAIVDSNQDPACLAANACLKIMQKNKLSPEQIGRLYVATESSFDESKAMNSYVIgm 97 
                     5999***********************************************************************************99976611 PP

  HMG_CoA_synt_N  98 ..qlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna.rptggagavallig 170
                       q+++  +     gi+   ac  g+ al++  nwi +   + +yalvv+ dia yd g++   t g gava+l+ 
      AJA92854.1  98 leQVYGAGSFQHCGGIECKFACVSGSYALYDNTNWIRAGESEEKYALVVVSDIAKYDLGSSgEMTQGGGAVAMLLN 173
                     11555555667899********************************************98636799*******975 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.92   5.5e+03      20      31 ..      65      76 ..      59      80 .. 0.81
   2 ?   11.8   0.0     3e-05      0.18      21      67 ..     148     194 ..     140     203 .. 0.84
   3 ?   -2.2   0.0      0.67     4e+03      74      82 ..     316     324 ..     303     345 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.92
     DUF1726 20 fealtPnalgrl 31
                 ++l+P+++grl
  AJA92854.1 65 KNKLSPEQIGRL 76
                47899*****98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3e-05
     DUF1726  21 ealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvvepl 67 
                 +++   +lg   e+++GGG++ +ll++  +l +++ +++++ + +++
  AJA92854.1 148 SDIAKYDLGSSGEMTQGGGAVAMLLNDSPRLLEFDPKVTSTSIKNEY 194
                 55566689**************************9999988887777 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.67
     DUF1726  74 rfnkrfirk 82 
                 +f krf ++
  AJA92854.1 316 EFTKRFAKT 324
                 333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3422.96
//
Query:       AJA92855.1  [L=71]
Description: ribosomal protein S14p/S29e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-05   22.5   4.9    0.00015   21.5   5.0    1.6  1  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   5.0   8.3e-09   0.00015       9      52 ..      28      69 ..      21      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.3e-09
                   S..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE CS
  Ribosomal_S14  9 ssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkK 52
                   ++ +r+ + C+ +G     i+k+ L  +R+cfRe A      G+kK
     AJA92855.1 28 KRFGRGARWCKRCGCY-VTIQKYDLmlCRQCFREVATS---LGFKK 69
                   56799*********75.56999*9999***********...99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 555.97
//
Query:       AJA92856.1  [L=135]
Description: NikR C-terminal nickel binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-14   51.9   0.6      1e-13   51.2   0.6    1.3  1  NikR_C    NikR C terminal nickel binding domain
    1.9e-05   24.4   0.0    3.1e-05   23.8   0.0    1.3  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.072   12.8   0.1       0.52   10.0   0.1    2.0  2  DUF1387   Protein of unknown function (DUF1387)


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.6   1.7e-17     1e-13      11      75 ..      69     133 ..      62     135 .] 0.92

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.7e-17
                 TSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEE CS
      NikR_C  11 hqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvklt 75 
                 h  e ++++tdi+h+y+dli++ lh  ++ d+c+e+++lkGe+e + e+++k+   k + +vkl+
  AJA92856.1  69 HNDEYDNQVTDIKHSYEDLITMHLHSKIEGDKCMELFILKGESEPVGEITKKFQINKKMDTVKLV 133
                 455999*********************************************************97 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   5.1e-09   3.1e-05       2      36 ..      12      47 ..      12      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.1e-09
                EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHH CS
       RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlrey 36
                vsi+l +e+l+++d l + +g + rS++IR+ +r +
  AJA92856.1 12 VSISLNDEILKQIDSLQKNLGfSGRSDAIRAGIRSF 47
                8*****************************999876 PP

>> DUF1387  Protein of unknown function (DUF1387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   8.7e-05      0.52     258     279 ..      40      61 ..      37      84 .. 0.88
   2 ?    1.1   0.0     0.046   2.7e+02     184     205 ..      67      88 ..      63      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 8.7e-05
     DUF1387 258 LRadIKhFVseRKyDEeLgraa 279
                 +Ra I++FVse K  E+L+ ++
  AJA92856.1  40 IRAGIRSFVSEEKQKEDLSGSV 61 
                 7*****************8665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.046
     DUF1387 184 vvvkeEvdsSvkkikqtFaelq 205
                 vv ++E d+ v  ik+ +++l 
  AJA92856.1  67 VVHNDEYDNQVTDIKHSYEDLI 88 
                 67799*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1077.45
//
Query:       AJA92857.1  [L=166]
Description: ribosomal protein S11P [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-42  143.9   2.0    3.2e-42  143.4   2.0    1.2  1  Ribosomal_S11  Ribosomal protein S11
      0.002   18.2   0.1     0.0028   17.7   0.1    1.4  1  DUF3898        Domain of unknown function (DUF3898)
     0.0098   16.1   0.1      0.018   15.3   0.1    1.4  1  CBM_25         Carbohydrate binding domain (family 25)


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   2.0   5.3e-46   3.2e-42       1     110 []      44     162 ..      44     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 5.3e-46
  Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pGpGreaalralaraGl 87 
                    G+ahi++s+nntii+itdl+Gae+++ s+Gg  v a+r +ssP+aa++aa+ + e+++ kG + ++++v++        pGpG++aa+ralar G+
     AJA92857.1  44 GIAHIFSSYNNTIIHITDLTGAETVSISSGGHHVNADRyESSPFAAMKAANVVTESAKTKGFTGLHIRVRAvggvgsrvPGPGAQAAIRALARGGF 139
                    9*********************************************************************************************** PP

  Ribosomal_S11  88 kigriedvtPiPhdgirrpkkrr 110
                    kig+i+dvtPiPhd++r+++++r
     AJA92857.1 140 KIGKIDDVTPIPHDTTRKKGGKR 162
                    *******************9987 PP

>> DUF3898  Domain of unknown function (DUF3898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   4.8e-07    0.0028       8      57 ..      16      67 ..       4      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-07
     DUF3898  8 teqvieaaaqiveqkPeielklkl.deievkalladfGek.lhiakvndrYv 57
                te+v+ea++++ve kP+  +k k+ d+  +  +++ + ++ +hi+ + +   
  AJA92857.1 16 TEEVVEATEEVVEAKPQQPTKAKVvDKWGIAHIFSSYNNTiIHITDLTGAET 67
                79*********************648899********987369998877555 PP

>> CBM_25  Carbohydrate binding domain (family 25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   3.1e-06     0.018       8      56 ..      96     144 ..      90     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.1e-06
      CBM_25   8 vyystrkkGftsayihyrpaGGswtavpGvkmrdaeaGyakkdvdlGaa 56 
                 v  s+++kGft  +i  r  GG  + vpG + ++a    a+    +G  
  AJA92857.1  96 VTESAKTKGFTGLHIRVRAVGGVGSRVPGPGAQAAIRALARGGFKIGKI 144
                 556899*****************************98888877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1255.18
//
Query:       AJA92858.1  [L=107]
Description: hypothetical protein T478_1319 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0023   18.0   7.8     0.0031   17.6   7.8    1.2  1  DivIVA        DivIVA protein
  ------ inclusion threshold ------
      0.011   14.0   5.2      0.013   13.8   5.2    1.0  1  Gp58          gp58-like protein
      0.022   14.6   1.5      0.022   14.6   1.5    2.0  2  FAM184        Family with sequence similarity 184, A and B
      0.025   14.5   8.0       0.57   10.1   0.4    2.0  2  Phage_Mu_Gam  Bacteriophage Mu Gam like protein
      0.026   15.1   4.9      0.056   14.1   1.5    2.0  2  DUF883        Bacterial protein of unknown function (DUF883)
      0.027   14.8   5.6      0.034   14.5   5.6    1.2  1  Muted         Organelle biogenesis, Muted-like protein
      0.031   14.3   5.7      0.048   13.7   4.1    1.9  2  Phasin        Poly(hydroxyalcanoate) granule associated prote
      0.045   14.2   8.3       0.24   11.8   8.3    2.3  1  V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
        0.1   13.2   3.4       0.15   12.7   3.4    1.3  1  YabA          Initiation control protein YabA
       0.16   10.5   5.4       0.17   10.4   5.4    1.0  1  Het-C         Heterokaryon incompatibility protein Het-C
       0.17   11.9   5.3       0.32   11.1   1.2    2.0  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.21   11.9   3.1        2.1    8.6   3.1    2.2  1  DUF948        Bacterial protein of unknown function (DUF948)
       0.22   11.6  10.2       0.67   10.0  10.2    1.7  1  ApoLp-III     Apolipophorin-III precursor (apoLp-III)
       0.23   12.5   4.2       0.24   12.5   1.6    2.0  3  RNase_J_C     Ribonuclease J C-terminal domain
       0.24   11.6   9.6        2.2    8.6   9.6    2.0  1  Spc24         Spc24 subunit of Ndc80
       0.25   11.5   6.8       0.39   10.8   6.8    1.4  1  ATP-synt_B    ATP synthase B/B' CF(0)
       0.25    9.7   3.0       0.26    9.6   3.0    1.1  1  DUF2863       Protein of unknown function (DUF2863)
       0.89   10.1   8.3          4    8.1   8.3    2.0  1  YtxH          YtxH-like protein
          1    8.6   6.1        1.1    8.4   6.1    1.1  1  TMPIT         TMPIT-like protein
        1.6    8.8   6.8        2.2    8.3   0.2    2.0  2  DUF1664       Protein of unknown function (DUF1664)
        1.8    9.8   7.0          3    9.0   7.0    1.6  1  Sox_N         Sox developmental protein N terminal
        3.6    8.0  10.2       0.41   11.1   2.7    2.6  2  FlaC_arch     Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   7.8   3.8e-06    0.0031      32     118 ..       3      91 ..       1      96 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.8e-06
                 HHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  32 kdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliike....Aekkaekiveeaeeeakkiaeeiee 118
                 +++  +++  +el+++++  + +l+++k+  +++ +  +  ++  e++++ a+ eae +i+e    Ae +++ki ++ e+++++i+++i++
  AJA92858.1   3 QKVDGIINSLSELESEIDSVNLSLADMKKSLNSIANKEI--ESLLEQTRKMATSEAESMISEskskAESESQKITQDGESKVAEIQQKIDS 91 
                 567778899999******************999988754..7899***************9822224555678999*********999985 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.2   1.6e-05     0.013      70     154 ..       2      91 ..       1     103 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
        Gp58  70 sgestGlfksleealsqlkelnLeLtdtkns..nLWsk.ik..lnnkgmlreyaddeikteivesaegiaerisedtdkklalinetieG 154
                 s++  G+++sl e+ s++ ++nL L d k+s   +  k i   l++   + +   +++ +e  ++ae   ++i++d + k+a i++ i+ 
  AJA92858.1   2 SQKVDGIINSLSELESEIDSVNLSLADMKKSlnSIANKeIEslLEQTRKMATSEAESMISESKSKAESESQKITQDGESKVAEIQQKIDS 91 
                 67889************************873212222232324444444555666777888899*********************9985 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.14   1.1e+02     119     154 ..      12      50 ..       1      56 [. 0.46
   2 ?   14.6   1.5   2.6e-05     0.022      11      50 ..      55      94 ..      51     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
      FAM184 119 faqlqeqle......qekekaLeelrkkhreeveeLlkeqea 154
                 +++l+++++      ++ +k+L+++ +k   e+e+Ll++ ++
  AJA92858.1  12 LSELESEIDsvnlslADMKKSLNSIANK---EIESLLEQTRK 50 
                 4444444443333333333433333333...55555554443 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.6e-05
      FAM184 11 eheaeiqalkeaHeeeiqqilaetrekilqykskveeeld 50
                e e++i++ k   e e q+i+++++ k+ ++++k+++  d
  AJA92858.1 55 EAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFD 94
                7799*******************************99877 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4    0.0007      0.57       2      50 ..       3      51 ..       2      54 .. 0.92
   2 ?    8.0   2.7    0.0031       2.5      13      50 ..      55      92 ..      49      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0007
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH CS
  Phage_Mu_Gam  2 eeanwalrkiaelkreleeieaeaneeiaaikekleaeleplkkeieyl 50
                  ++++  +  + el+ e++ ++  + ++++ ++  +++e+e+l ++  ++
    AJA92858.1  3 QKVDGIINSLSELESEIDSVNLSLADMKKSLNSIANKEIESLLEQTRKM 51
                  57899999**********************************9998776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH CS
  Phage_Mu_Gam 13 elkreleeieaeaneeiaaikekleaeleplkkeieyl 50
                  e++  ++e +++a++e ++i+++ e+++++++++i+  
    AJA92858.1 55 EAESMISESKSKAESESQKITQDGESKVAEIQQKIDST 92
                  66778999**************************9965 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.083        68       2      40 ..      14      52 ..      13      54 .. 0.81
   2 ?   14.1   1.5   6.8e-05     0.056       8      58 ..      50     100 ..      45     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.083
      DUF883  2 eleaeleslladleellkeaadeageeaeelRerleerl 40
                ele+e++s+  +l+++ k+ ++ a++e+e+l e+ ++++
  AJA92858.1 14 ELESEIDSVNLSLADMKKSLNSIANKEIESLLEQTRKMA 52
                688899999999999999999999999998888877765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.8e-05
      DUF883   8 eslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaera 58 
                 +++++++e++++e++++a++e +++ +  e+++++ +++++ + ++++++a
  AJA92858.1  50 KMATSEAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVDNA 100
                 67899*****************************************99987 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.6   4.2e-05     0.034      62     133 ..      25      98 ..       2     105 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
       Muted  62 s...mkenLseln.kkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekve 133
                 s   mk++L+++  k++e +le+++++ + e+e+    se  +++e e+++  ++  ++++e ++++D +f+ +v+
  AJA92858.1  25 SladMKKSLNSIAnKEIESLLEQTRKMATSEAESMI--SESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVD 98 
                 234489999998636699999999999999666665..44445555666666666667788888888888888775 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.18   1.5e+02      65      97 ..      14      46 ..       2      49 .. 0.65
   2 ?   13.7   4.1   5.9e-05     0.048      34      99 ..      38     104 ..      31     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.18
      Phasin 65 svkskveevkekaeeqwdklekafdervakaLs 97
                +++s++++v+  +++  ++l+++ ++ +++ L+
  AJA92858.1 14 ELESEIDSVNLSLADMKKSLNSIANKEIESLLE 46
                556667777777777777777777777766665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.9e-05
      Phasin  34 sklfeaLvkeGeklek.ktkkvaeekleevresvkskveevkekaeeqwdklekafdervakaLsrl 99 
                 +k +e+L ++ +k+   ++++ + e+ ++++++ ++ +++ ++k++e  +k+++ fd+ v +a+s++
  AJA92858.1  38 NKEIESLLEQTRKMATsEAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVDNAVSTI 104
                 6778889988888765267788888888999888899999999999999999999999999998865 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   8.3   0.00029      0.24       9      97 ..      35      88 ..       3     107 .] 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHH CS
  V-ATPase_G_2  9 eLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaeaqavrkraearlqqAvel 97
                  +                                    A++++++l ++ ++  + e + +  e +++ae+e+q++++ +e ++++  ++
    AJA92858.1 35 S-----------------------------------IANKEIESLLEQTRKMATSEAESMISESKSKAESESQKITQDGESKVAEIQQK 88
                  3...................................35555555555555555555555555666666666666666666555554333 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.4   0.00018      0.15       6      72 ..       8      81 ..       3      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........XXXXXXXXXXXXXXXXXXXX CS
        YabA  6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl.........eeeekkekekkkelsegken 72
                ++++l+ele+++++++ +l+++k++l+++ +  +e+e   e+ r++          e+++k+e+e++k +++g+++
  AJA92858.1  8 IINSLSELESEIDSVNLSLADMKKSLNSIAN--KEIESLLEQTRKMAtseaesmisESKSKAESESQKITQDGESK 81
                78999*********************99975..5555555666666644566666544444444444444555555 PP

>> Het-C  Heterokaryon incompatibility protein Het-C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.4    0.0002      0.17     285     372 ..      16     104 ..       6     107 .] 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
       Het-C 285 qsevdeldaaleeaekssssssksalksllsklpgtgddlaeeaeelkaks.eaqeaenasaseskanavpgvspnfdpee...vakkiypi 372
                 +se+d ++ +l++ +ks +s ++++++sll++  ++ ++   eae++ ++s +++e+e+++ +++ +++v++++++ d +    v + +  i
  AJA92858.1  16 ESEIDSVNLSLADMKKSLNSIANKEIESLLEQTRKMATS---EAESMISESkSKAESESQKITQDGESKVAEIQQKIDSTFdsaVDNAVSTI 104
                 79****************99***********99865553...33333333203333444445555555666665555543222255555555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   0.00039      0.32      85     130 ..       3      48 ..       1      55 [. 0.78
   2 ?    3.1   0.2      0.11        89      44      77 ..      68     102 ..      51     107 .] 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
  Baculo_PEP_C  85 neLtnlnsiltnLlssvtNinstLnnllqalnnldlgalsqeleda 130
                   ++ +++ + l++L s++  +n +L+ + ++ln++++ ++++ le++
    AJA92858.1   3 QKVDGIINSLSELESEIDSVNLSLADMKKSLNSIANKEIESLLEQT 48 
                   5677888888889999999999999999999988888888877765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
  Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtllt.nLtdaln 77 
                   e++ +++++d +s +ae+++++d++++ ++++a+ 
    AJA92858.1  68 ESESQKITQDGESKVAEIQQKIDSTFDsAVDNAVS 102
                   44445555555555666666555443213444443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.1    0.0026       2.1      18      61 ..       9      53 ..       5     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0026
      DUF948 18 ivvllklkktldeaaatieelekqvdpil.kevedllakvnelle 61
                i  l +l++ +d+++ ++++++k +++i  ke+e ll+++++++ 
  AJA92858.1  9 INSLSELESEIDSVNLSLADMKKSLNSIAnKEIESLLEQTRKMAT 53
                66788999999***********99999974689999999998543 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  10.2   0.00083      0.67      54     137 ..      13     101 ..       2     106 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00083
   ApoLp-III  54 deleealkevkkkieetadklse.enPevkkkaqelqekvQsgvqslvkesqklaes....lkensqeakeklakaikqayddaveaaq 137
                 +ele+ ++ v+  ++ + ++l++ +n e++  ++++++   s  +s+++es+  aes    + ++ +   ++++++i +  d av++a 
  AJA92858.1  13 SELESEIDSVNLSLADMKKSLNSiANKEIESLLEQTRKMATSEAESMISESKSKAESesqkITQDGESKVAEIQQKIDSTFDSAVDNAV 101
                 56777777777777777777777777777777777777777777777777776666411113333334444555555555555555553 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       1.6   1.3e+03      12      15 ..      38      41 ..       3      52 .. 0.56
   2 ?   -0.1   0.1       2.4   1.9e+03      12      28 ..      38      54 ..      35      57 .. 0.72
   3 ?   12.5   1.6   0.00029      0.24      13      56 ..      54      97 ..      48     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
   RNase_J_C 12 vkes 15
                 ke 
  AJA92858.1 38 NKEI 41
                1222 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.4
   RNase_J_C 12 vkeseeLieeakkvvre 28
                 ke e+L+e+++k++++
  AJA92858.1 38 NKEIESLLEQTRKMATS 54
                57778888888887765 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00029
   RNase_J_C 13 keseeLieeakkvvretieealeekesdwnelkrkirealkkfl 56
                 e+e++i+e k+++++  +++ +++es+ +e+++ki ++  + +
  AJA92858.1 54 SEAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAV 97
                6899********************************99987766 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   9.6    0.0027       2.2       8      44 ..       7      52 ..       1     106 [. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0027
       Spc24  8 riakelsdleselesleselaelkeeleeleeesee.........k 44
                 i+++ls+lese++s++ +la++k+ l+ + +++ e          
  AJA92858.1  7 GIINSLSELESEIDSVNLSLADMKKSLNSIANKEIEslleqtrkmA 52
                5899******************************998876433220 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.8   0.00048      0.39      56     111 ..      45     100 ..      14     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
  ATP-synt_B  56 aeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeIeqekdra 111
                  eq  k A +eA+ +i + k++ae + ++i ++ e +++ ++++   + + + d a
  AJA92858.1  45 LEQTRKMATSEAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVDNA 100
                 46667788999999999999999999999999999999999998766666555555 PP

>> DUF2863  Protein of unknown function (DUF2863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.0   0.00032      0.26      21      91 ..       6      79 ..       1      96 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
     DUF2863 21 lalaqsgsrlEdryWearla.allekllkegeeetldaaLdhlfkadseaydeLaelaEt..lsEslelekegq 91
                 ++ +s s lE +    +l+ a ++k l++ +++++++ L++  k  ++  + ++    +  +sEs +++++g+
  AJA92858.1  6 DGIINSLSELESEIDSVNLSlADMKKSLNSIANKEIESLLEQTRKMATSEAESMISESKSkaESESQKITQDGE 79
                6788999999999999988735799********************99988888887766511566777888876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   8.3    0.0049         4      26      73 ..      48      99 ..       1     101 [. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
        YtxH 26 tRkdlkek....addlkekakelleeakekakekaedlkekvkekadelkek 73
                tRk +  +     +++k ka++  +++ + +++k++++++k+++++d+++++
  AJA92858.1 48 TRKMATSEaesmISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVDN 99
                5555555522224455555555555555555**************9999886 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.1    0.0014       1.1       3      84 ..      11      91 ..       2     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
       TMPIT  3 eweelekefkeleetakeykqkleelsklqskcskei.kkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84
                +++ele+e+++++ +   +k++l+++++ + +  + + ++ k   +e +s++++ k+++++e+++++++ +++++e+++ +++
  AJA92858.1 11 SLSELESEIDSVNLSLADMKKSLNSIANKEIE--SLLeQTRKMATSEAESMISESKSKAESESQKITQDGESKVAEIQQKIDS 91
                44566666666666666666666665543322..2221334455678889999999999999999999999999999988874 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0028       2.2      86     123 ..       2      39 ..       1      40 [. 0.82
   2 ?    2.5   2.6      0.17   1.4e+02      68      99 ..      60      92 ..      38     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
     DUF1664  86 keevtevredlseigedvesvkeaveglesklerieek 123
                 +++v+ + + lse++++++sv+    +++++l++i +k
  AJA92858.1   2 SQKVDGIINSLSELESEIDSVNLSLADMKKSLNSIANK 39 
                 67888888899999999999999999999999988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
     DUF1664 68 idrvdkkld.eqkeiskeikeevtevredlsei 99
                i +  +k + e+++i+++ +++v+e++++++++
  AJA92858.1 60 ISESKSKAEsESQKITQDGESKVAEIQQKIDST 92
                333333333145666777777788887777654 PP

>> Sox_N  Sox developmental protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.0    0.0037         3      11      65 ..      52     106 ..       9     107 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0037
       Sox_N  11 slsesssspagsssdsessgssedlakvgseedkseaeddrfpvcIreAVSqVLk 65 
                 + se++s+ ++s+s++es+ ++  ++ +++  + +++ d  f +++ +AVS +Lk
  AJA92858.1  52 ATSEAESMISESKSKAESESQKITQDGESKVAEIQQKIDSTFDSAVDNAVSTILK 106
                 3455555555555555555444444444444445555667899**********98 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.7    0.0005      0.41       7      40 ..      10      44 ..       4      53 .. 0.53
   2 ?   -0.7   3.2       2.3   1.9e+03      27      27 ..      79      79 ..      39     104 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
   FlaC_arch  7 nklsklsteletvkkeneelsksveel.kenVkdl 40
                n ls+l++e+++v  ++ +++ks++ + +++++ l
  AJA92858.1 10 NSLSELESEIDSVNLSLADMKKSLNSIaNKEIESL 44
                55566666666666666666666555522333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
   FlaC_arch 27 s 27
                +
  AJA92858.1 79 E 79
                2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2746  (0.15316); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 796.82
//
Query:       AJA92859.1  [L=171]
Description: hypothetical protein T478_1137 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.15   12.2   0.1       0.34   11.1   0.1    1.5  1  Pigment_DH  Pigment-dispersing hormone (PDH)


Domain annotation for each model (and alignments):
>> Pigment_DH  Pigment-dispersing hormone (PDH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.9e-05      0.34       2      12 ..     122     132 ..     122     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.9e-05
  Pigment_DH   2 sdLINfLLsLP 12 
                 s+LIN  LsLP
  AJA92859.1 122 SELINNVLSLP 132
                 8********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1246.95
//
Query:       AJA92860.1  [L=70]
Description: hypothetical protein T478_0239 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       854  (0.0476323); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 541.69
//
Query:       AJA92861.1  [L=369]
Description: hypothetical protein T478_0141 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.1   0.1      0.009   15.4   0.1    1.4  1  DUF915    Alpha/beta hydrolase of unknown function (DUF915)


Domain annotation for each model (and alignments):
>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     5e-07     0.009      80     120 ..     208     248 ..     138     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-07
      DUF915  80 aslkkqakwlkkvlseLkkkYnikkfnavGhSmGglaltsY 120
                 +sl+ +   +++ l++L +++ ++ f ++G S Gg + t+Y
  AJA92861.1 208 SSLSYFFTPISITLNYLSENFSFDDFHMIGISGGGWTTTVY 248
                 4667777778999**************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2691.41
//
Query:       AJA92862.1  [L=280]
Description: CobQ/CobB/MinD/ParA nucleotide binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-20   73.5   0.0    2.3e-20   73.0   0.0    1.2  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
    3.6e-19   69.4   0.1    1.2e-17   64.4   0.1    2.2  1  AAA_26    AAA domain
      0.006   16.5   0.0      0.043   13.7   0.0    2.2  2  MobB      Molybdopterin guanine dinucleotide synthesis protei
     0.0096   15.0   0.0      0.014   14.4   0.0    1.2  1  SelA      L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0     5e-24   2.3e-20       1     116 [.       5     229 ..       5     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 5e-24
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 ++i++t++G+GKT l+++L+r++++ g+ V +++ ++++n + i +  e+ +++                                             
  AJA92862.1   5 LMIQGTSSGAGKTILVTALCRIFSDLGYTVSPFKSQNMSNFSYIEKNFEISRAQaiqavaartditpdqnpillkplgnyrssifvngkffkkmhasdy 103
                 69****************************************999999999999********************************************* PP

                 ..............................................................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS CS
                 ..............................................................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
        CbiA  55 ..............................................................dlkrllellealgkkkall.....lkiagvvlnrvdg 86 
                                                                               d++r ++ +++++++++l       ++ g+++n+++g
  AJA92862.1 104 yenfalktglktsmnsfnklsesheivflegagspaeinlqkfditnmkiaqktkspvllvtDIER-GGAFASIVGTMELIekkyqKLVEGFIINKFRG 201
                 **************************************************************6655.45555555554443555558************ PP

                 ...-TTCHHHHHHHHHHCTS-EEEEEE--C CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  87 eneetllkealeelkqrygvpvlgviprde 116
                 +  ++ lk ++++lkq++g+pvlg ip ++
  AJA92862.1 202 D--IEILKPGYRKLKQKTGLPVLGTIPMTD 229
                 *..************************976 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1   2.7e-21   1.2e-17       1     191 [.       3     228 ..       3     233 .. 0.70

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.7e-21
      AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.......ededselikellgldqtyelpeplalsapl...............spel 77 
                 +++++ gt+ g+GKT++ ++L+r++++ g+ v+ fK  +  +        e ++++ i+ ++  ++ + + +p++l+ pl               + ++
  AJA92862.1   3 KSLMIQGTSSGAGKTILVTALCRIFSDLGYTVSPFKSQNMSNFsyieknfEISRAQAIQAVAARTDITPDQNPILLK-PLgnyrssifvngkffkKMHA 100
                 689********************************996433334566666223444444444433334444444443.221100000000000002233 PP

      AAA_26  78 aarqegedidlekiv............kelekdadivvVEGagglgvp..iteellnadiaknlgapvilVarggl.gtinqllltiealrqknvr.vl 160
                 ++  e+                     ++l++ ++iv+ EGag+  +   + ++ +n +ia++ ++pv+lV+ +++ g+++ ++ t+e+  +k  + v 
  AJA92862.1 101 SDYYENF-------AlktglktsmnsfNKLSESHEIVFLEGAGSPAEInlQKFDITNMKIAQKTKSPVLLVTDIERgGAFASIVGTMELIEKKYQKlVE 192
                 3333333.......2445555556788*****************99762255669*******************99569***********987555499 PP

      AAA_26 161 GvilNkvrnp.e....nvetlekksgipvlGvvPyl 191
                 G i+Nk+r + e     +++l++k+g+pvlG++P++
  AJA92862.1 193 GFIINKFRGDiEilkpGYRKLKQKTGLPVLGTIPMT 228
                 *********98355569*****************86 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.5e-06     0.043       4      37 ..       7      41 ..       4      65 .. 0.85
   2 ?    0.2   0.0      0.15   6.7e+02      94     116 ..     189     212 ..     149     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.5e-06
        MobB  4 ivgk.sgsGKTtLleklipelkarglrvgtiKhah 37
                i g+ sg+GKT L++ l +++++ g++v+  K ++
  AJA92862.1  7 IQGTsSGAGKTILVTALCRIFSDLGYTVSPFKSQN 41
                5554389**********************999765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
        MobB  94 vlvEGfkkealp.kievlraelgk 116
                  lvEGf  ++++  ie+l++ ++k
  AJA92862.1 189 KLVEGFIINKFRgDIEILKPGYRK 212
                 599999888775379999987766 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-06     0.014     128     233 ..      83     186 ..      79     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                 HHHHT--TTEEEEEEE---SEEEE.ES-B..---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEE CS
        SelA 128 Dyekainentalllkvhtsnyrie.Gftk..evelaeLvelgkekglpvleDlGsGllvdlseyglskePtvqealaeGvdlvsfsGDkllGgpqaGii 223
                 +y+++i  n  ++ k+h s+y+     ++  + +++ + +l++ ++++ le +Gs + ++l+++ +++  ++ ++ ++ v lv+   D   Gg+ a  i
  AJA92862.1  83 NYRSSIFVNGKFFKKMHASDYYENfALKTglKTSMNSFNKLSESHEIVFLEGAGSPAEINLQKFDITNM-KIAQKTKSPVLLVT---DIERGGAFAS-I 176
                 799999*************88643122221134567899***************************975.66667777788887...6667888886.6 PP

                 EE-HHHHHHH CS
        SelA 224 vGkkeliekl 233
                 vG  eliek 
  AJA92862.1 177 VGTMELIEKK 186
                 8999999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2074.49
//
Query:       AJA92863.1  [L=161]
Description: anaphase-promoting complex, cyclosome, subunit 3 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-17   61.5   7.1    1.2e-06   28.1   0.0    4.9  5  TPR_1            Tetratricopeptide repeat
    1.1e-13   50.6   0.1    4.9e-05   22.9   0.0    3.5  3  TPR_11           TPR repeat
    1.1e-12   47.0   5.0     0.0043   17.1   0.0    4.4  5  TPR_2            Tetratricopeptide repeat
    5.1e-11   41.9   7.8     0.0067   16.6   0.1    4.9  5  TPR_8            Tetratricopeptide repeat
    4.9e-10   39.5   1.0     0.0014   18.9   0.0    3.9  3  TPR_12           Tetratricopeptide repeat
    9.4e-09   35.7   2.0     0.0043   17.5   0.0    3.5  3  TPR_19           Tetratricopeptide repeat
      6e-08   32.6   0.8       0.85   10.1   0.0    4.4  4  TPR_17           Tetratricopeptide repeat
    8.3e-08   32.4   0.0        2.2    9.3   0.0    4.2  4  TPR_14           Tetratricopeptide repeat
    2.7e-06   27.0   2.0        2.2    8.5   0.0    4.2  5  TPR_7            Tetratricopeptide repeat
    1.2e-05   25.8   0.0       0.16   12.7   0.0    2.9  3  TPR_16           Tetratricopeptide repeat
    3.7e-05   23.7   3.1        1.6    8.9   0.5    3.7  3  MIT              MIT (microtubule interacting and transport) 
    0.00013   22.0   0.0      0.074   13.2   0.0    2.2  2  TPR_9            Tetratricopeptide repeat
    0.00018   21.9   1.3         11    6.9   0.1    4.5  5  TPR_6            Tetratricopeptide repeat
    0.00039   20.6   0.8     0.0014   18.8   0.1    2.1  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
     0.0013   17.7   0.4       0.23   10.3   0.0    2.1  2  NARP1            NMDA receptor-regulated protein 1
     0.0023   18.4   0.7       0.02   15.4   0.1    2.0  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
     0.0044   15.8   0.0     0.0055   15.5   0.0    1.1  1  PknG_TPR         Protein kinase G tetratricopeptide repeat
  ------ inclusion threshold ------
      0.012   15.4   0.0         38    4.3   0.0    4.0  4  TPR_10           Tetratricopeptide repeat
      0.072   13.2   0.6         31    4.7   0.0    3.6  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
       0.76    9.3   0.0       0.76    9.3   0.0    3.4  4  SHNi-TPR         SHNi-TPR


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.3    0.0013       1.1      15      33 ..      19      37 ..      12      38 .. 0.90
   2 ?    3.3   0.0      0.09        81       3      34 .]      41      72 ..      39      72 .. 0.89
   3 !   28.1   0.0   1.3e-09   1.2e-06       2      34 .]      74     106 ..      73     106 .. 0.95
   4 !   21.5   0.0   1.6e-07   0.00014       2      34 .]     108     140 ..     107     140 .. 0.93
   5 ?   -1.3   0.1       2.6   2.3e+03      25      30 ..     148     153 ..     148     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                T-HHHHHHHHHHHHHHSTT CS
       TPR_1 15 gkydeAleyyekALelnPn 33
                ++y+eA+  y+k L  +P+
  AJA92863.1 19 QEYEEAILLYDKILDSDPK 37
                68************99997 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  3 alynlGnayfklgkydeAleyyekALelnPnn 34
                al  ++++++++gk  +  + y+  L+ + nn
  AJA92863.1 41 ALLDKAATLQRMGKNSQSFQIYNSILKEDSNN 72
                78889***********9999999999999887 PP

  == domain 3  score: 28.1 bits;  conditional E-value: 1.3e-09
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +al ++G +++ + k+ eA+e+y+ AL++ P +
  AJA92863.1  74 DALIGKGTLLHAKSKFSEAIECYDSALKIKPRF 106
                 6999***************************75 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 1.6e-07
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                  al  +G+ + + g+++ Al +++kAL+++ ++
  AJA92863.1 108 MALACKGMSLGEIGQLKSALSCFKKALTIDKDY 140
                 68999*************************986 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 2.6
                 HHHHHH CS
       TPR_1  25 ekALel 30 
                 +kALel
  AJA92863.1 148 QKALEL 153
                 789987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00047      0.42       6      42 .]      17      53 ..      12      53 .. 0.89
   2 !   22.9   0.0   5.4e-08   4.9e-05       2      32 ..      81     111 ..      80     119 .. 0.87
   3 !   13.7   0.0   4.2e-05     0.037       7      30 ..     120     143 ..     114     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
      TPR_11  6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                e ++yeeAi  Y k l+ dP+   a++  +++++++G
  AJA92863.1 17 EDQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMG 53
                6689*****************9999999999999887 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 5.4e-08
      TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                  +++++ k+ eAie+Y  Alk++P +a a+ 
  AJA92863.1  81 TLLHAKSKFSEAIECYDSALKIKPRFAMALA 111
                 57899*******************9997765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 4.2e-05
      TPR_11   7 qGkyeeAieaYkkAlkldPdnaea 30 
                  G+++ A+ ++kkAl +d d+  a
  AJA92863.1 120 IGQLKSALSCFKKALTIDKDYDLA 143
                 69******************9766 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00024      0.22       8      33 ..      12      37 ..       5      38 .. 0.87
   2 ?   -0.1   0.0       1.5   1.4e+03       4      34 .]      42      72 ..      40      72 .. 0.78
   3 !   17.0   0.0   4.9e-06    0.0044       3      33 ..      75     105 ..      73     106 .. 0.92
   4 !   17.1   0.0   4.8e-06    0.0043       2      33 ..     108     139 ..     107     140 .. 0.92
   5 ?   -2.4   0.1       8.4   7.5e+03      25      30 ..     148     153 ..     148     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
       TPR_2  8 GlayyklgdyeeAleafekAleldPn 33
                +  +++ ++yeeA+ +++k l  dP+
  AJA92863.1 12 ASDLAEDQEYEEAILLYDKILDSDPK 37
                66678899**************9997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.5
       TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                l   +  + ++g+  +  + ++  l+ d nn
  AJA92863.1 42 LLDKAATLQRMGKNSQSFQIYNSILKEDSNN 72
                5667888999999888888888888888776 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.9e-06
       TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                 al   G ++ ++ ++ eA+e+++ Al++ P+
  AJA92863.1  75 ALIGKGTLLHAKSKFSEAIECYDSALKIKPR 105
                 78899999********************996 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 4.8e-06
       TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                  al + G+++ + g+++ Al +f+kAl +d +
  AJA92863.1 108 MALACKGMSLGEIGQLKSALSCFKKALTIDKD 139
                 689999***********************987 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 8.4
       TPR_2  25 ekAlel 30 
                 +kAlel
  AJA92863.1 148 QKALEL 153
                 577776 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.7   1.5e+03      20      33 ..       5      18 ..       2      19 .. 0.80
   2 ?    6.4   0.2     0.013        12      15      33 ..      19      37 ..      15      38 .. 0.91
   3 ?    4.0   0.0     0.078        70       2      33 ..      40      71 ..      39      72 .. 0.88
   4 !   16.0   0.0   1.2e-05      0.01       2      32 ..      74     104 ..      73     106 .. 0.91
   5 !   16.6   0.1   7.4e-06    0.0067       7      33 ..     113     139 ..     109     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.7
                HHHHHHHHHHHHHH CS
       TPR_8 20 Akeyyekaleldpd 33
                 ++ +e+a +l++d
  AJA92863.1  5 FQKMLEQASDLAED 18
                57899999999986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                T-HHHHHHHHHHHHHHHHH CS
       TPR_8 15 gdyeeAkeyyekaleldpd 33
                ++yeeA+  y k l+ dp+
  AJA92863.1 19 QEYEEAILLYDKILDSDPK 37
                58***************97 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.078
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                +a++ ++ +++ +g+  ++ + y+  l+ d +
  AJA92863.1 40 PALLDKAATLQRMGKNSQSFQIYNSILKEDSN 71
                68899999***************999998876 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.2e-05
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                 +a+  +g +++ + ++ eA+e+y  al+++p
  AJA92863.1  74 DALIGKGTLLHAKSKFSEAIECYDSALKIKP 104
                 6788899***********************9 PP

  == domain 5  score: 16.6 bits;  conditional E-value: 7.4e-06
                 HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                 +g+ + + g++++A ++++kal++d+d
  AJA92863.1 113 KGMSLGEIGQLKSALSCFKKALTIDKD 139
                 6899999******************98 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.2   0.00017      0.15      10      72 ..      12      66 ..       5      67 .. 0.72
   2 !   18.9   0.0   1.6e-06    0.0014      28      76 ..      57     104 ..      37     105 .. 0.82
   3 !    8.2   0.0    0.0034       3.1      53      76 ..     115     138 ..     107     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
      TPR_12 10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72
                a+ l++ ++y+eA+ l++k l+          p ++ +l + + +++++g+  +  ++++  l
  AJA92863.1 12 ASDLAEDQEYEEAILLYDKILDS--------DPKLIPALLDKAATLQRMGKNSQSFQIYNSIL 66
                56666666666666666666443........46799999999999999999999999998765 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-06
      TPR_12  28 kaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                 ++ +i++++l +d+ + + +l++ g+l++a  ++ eA+e +  al+i++
  AJA92863.1  57 QSFQIYNSILKEDS-NNLDALIGKGTLLHAKSKFSEAIECYDSALKIKP 104
                 66777777787888.789***************************9975 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0034
      TPR_12  53 rlyralgryeeAlelleealaiae 76 
                 + + + g+++ Al+ +++al i++
  AJA92863.1 115 MSLGEIGQLKSALSCFKKALTIDK 138
                 445567778888888888887765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.3    0.0015       1.3       2      39 ..      16      53 ..      15      58 .. 0.81
   2 !   17.5   0.0   4.8e-06    0.0043       6      57 ..      54     105 ..      49     111 .. 0.88
   3 !    7.1   0.0    0.0086       7.7       5      30 ..     121     146 ..     119     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalg 39
                 +++ y+eA+ l+ ++l+ dpk   a+l+ A  l  +g
  AJA92863.1 16 AEDQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMG 53
                67899999999999999999998888888877776666 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.8e-06
      TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 +  +  +++ ++l+ed +n++a+++   +l a   + eA+++ d +++ +p 
  AJA92863.1  54 KNSQSFQIYNSILKEDSNNLDALIGKGTLLHAKSKFSEAIECYDSALKIKPR 105
                 55566799**************************************999886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0086
      TPR_19   5 gdyaeAlalleqalqedpknaearll 30 
                 g++ +Al+ +++al+ d +++ a ++
  AJA92863.1 121 GQLKSALSCFKKALTIDKDYDLANMG 146
                 899****************9988775 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00095      0.85       1      29 [.      27      55 ..      27      60 .. 0.90
   2 ?    6.8   0.0     0.011        10       2      33 ..      62      93 ..      61      94 .. 0.87
   3 !   10.1   0.0     0.001       0.9       1      33 [.      95     127 ..      95     128 .. 0.95
   4 ?    0.6   0.1       1.1   9.8e+02       1      12 [.     129     140 ..     129     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00095
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdl 29
                ly k l+ dP+  +a+  +A +l + G+ 
  AJA92863.1 27 LYDKILDSDPKLIPALLDKAATLQRMGKN 55
                7***********************99875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.011
      TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                y   l+ d nn da+  +++ll+ + ++ +A+
  AJA92863.1 62 YNSILKEDSNNLDALIGKGTLLHAKSKFSEAI 93
                5667899****************999988887 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.001
      TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 +y  al++ P  a a+  ++  l ++G+l+ A+
  AJA92863.1  95 CYDSALKIKPRFAMALACKGMSLGEIGQLKSAL 127
                 7999************************99886 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.1
      TPR_17   1 lylkaleldPnn 12 
                 +++kal +d+++
  AJA92863.1 129 CFKKALTIDKDY 140
                 799****99986 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.4    0.0075       6.8       7      41 ..      11      45 ..       6      48 .. 0.83
   2 ?    7.0   0.0     0.013        12       3      42 ..      41      80 ..      39      82 .. 0.91
   3 !    9.3   0.0    0.0025       2.2      11      39 ..      83     111 ..      78     116 .. 0.84
   4 ?    5.3   0.0     0.047        42      15      38 ..     121     144 ..     114     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0075
      TPR_14  7 laeallalGdpdeAiallrralalaPddaeawlll 41
                 a+ l++ ++++eAi l++++l+ +P+   a+l  
  AJA92863.1 11 QASDLAEDQEYEEAILLYDKILDSDPKLIPALLDK 45
                577789999*****************987777655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
      TPR_14  3 allalaeallalGdpdeAiallrralalaPddaeawllla 42
                all+ a+ l + G+  ++ ++++ +l+ + ++++a++  +
  AJA92863.1 41 ALLDKAATLQRMGKNSQSFQIYNSILKEDSNNLDALIGKG 80
                78999************************99999987665 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0025
      TPR_14  11 llalGdpdeAiallrralalaPddaeawl 39 
                 l a  ++ eAi++++ al+  P +a a+ 
  AJA92863.1  83 LHAKSKFSEAIECYDSALKIKPRFAMALA 111
                 5566789****************999886 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.047
      TPR_14  15 GdpdeAiallrralalaPddaeaw 38 
                 G+++ A+ ++++al  + d + a+
  AJA92863.1 121 GQLKSALSCFKKALTIDKDYDLAN 144
                 89****************999887 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0027       2.4      10      32 ..      16      36 ..       8      39 .. 0.82
   2 ?   -1.6   0.0       4.3   3.8e+03       2      16 ..      42      56 ..      41      62 .. 0.72
   3 !    8.5   0.0    0.0024       2.2       6      28 ..      80     102 ..      75     111 .. 0.81
   4 !    6.7   0.0    0.0092       8.2      12      31 ..     120     139 ..     114     144 .. 0.84
   5 ?   -2.6   0.0       8.8   7.9e+03      16      23 ..     148     155 ..     148     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
       TPR_7 10 srlGdyeeAielyeqsLaltkdp 32
                 ++++yeeAi ly +   l++dp
  AJA92863.1 16 AEDQEYEEAILLYDK--ILDSDP 36
                5789**********9..666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
       TPR_7  2 LlnLarlysrlGdye 16
                Ll  a + +r+G+ +
  AJA92863.1 42 LLDKAATLQRMGKNS 56
                666678888888765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0024
       TPR_7   6 arlysrlGdyeeAielyeqsLal 28 
                 + l ++  +++eAie+y  +L +
  AJA92863.1  80 GTLLHAKSKFSEAIECYDSALKI 102
                 567778899********996655 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0092
       TPR_7  12 lGdyeeAielyeqsLaltkd 31 
                  G+ + A+++++++L ++kd
  AJA92863.1 120 IGQLKSALSCFKKALTIDKD 139
                 588899*******8888877 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 8.8
       TPR_7  16 eeAielye 23 
                 ++A+el++
  AJA92863.1 148 QKALELLK 155
                 57777776 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0016       1.4       2      31 ..      10      36 ..       9      42 .. 0.80
   2 !   12.7   0.0   0.00017      0.16       2      65 ..      44     104 ..      43     107 .. 0.91
   3 ?   -0.7   0.0       2.7   2.4e+03       4      27 ..     114     137 ..     113     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0016
      TPR_16  2 alaraalragdyddAaaaleaalkrdpssP 31
                ++a ++++ ++y++A+ +++  l++d   P
  AJA92863.1 10 EQASDLAEDQEYEEAILLYDKILDSD---P 36
                68888888888888888888888888...4 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00017
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraap 65 
                 ++a  + r g+  +    ++  lk d   + + +Al ++g ++ +++ + eA++ y++al+  p
  AJA92863.1  44 DKAATLQRMGKNSQSFQIYNSILKED---SNNLDALIGKGTLLHAKSKFSEAIECYDSALKIKP 104
                 6777888889999999999999****...9999***************************9887 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.7
      TPR_16   4 araalragdyddAaaaleaalkrd 27 
                 ++++ + g+   A+  ++ al  d
  AJA92863.1 114 GMSLGEIGQLKSALSCFKKALTID 137
                 566667788888888888887655 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.5    0.0018       1.6       7      29 ..       8      30 ..       6      34 .. 0.89
   2 !    8.4   0.0    0.0025       2.2      11      32 ..      80     101 ..      75     102 .. 0.79
   3 ?    4.5   0.0      0.04        36       5      32 ..     108     135 ..     106     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
         MIT  7 lvkkAveeDnagnyeeAlelYke 29
                ++++A ++ + ++yeeA+ lY +
  AJA92863.1  8 MLEQASDLAEDQEYEEAILLYDK 30
                678999***************86 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
         MIT  11 AveeDnagnyeeAlelYkeale 32 
                  + +  + +++eA+e+Y +al+
  AJA92863.1  80 GTLLHAKSKFSEAIECYDSALK 101
                 555667889***********96 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.04
         MIT   5 lelvkkAveeDnagnyeeAlelYkeale 32 
                  +l+ k + + + g+ + Al+++k+al 
  AJA92863.1 108 MALACKGMSLGEIGQLKSALSCFKKALT 135
                 5666777777777777788888877764 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0069       6.2       7      47 ..      17      57 ..      11      76 .. 0.86
   2 !   13.2   0.0   8.3e-05     0.074       6      61 ..      84     139 ..      79     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0069
       TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsa 47
                + +++e+a+  ++ +l  +P+ +  ++d +  l+++G  s+
  AJA92863.1 17 EDQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMGKNSQ 57
                66889999*****************************8766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.3e-05
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                   + ++++a++++++ l ++P+ +  +   G+ l + G+l+ Al ++  +l ++ d
  AJA92863.1  84 HAKSKFSEAIECYDSALKIKPRFAMALACKGMSLGEIGQLKSALSCFKKALTIDKD 139
                 5678999*****************************************99976654 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.012        11       9      32 ..      14      37 ..       8      37 .. 0.76
   2 ?    5.7   0.0     0.029        26       4      31 ..      43      70 ..      40      72 .. 0.73
   3 ?    2.5   0.0      0.32   2.9e+02       2      28 ..      75     101 ..      74     104 .. 0.73
   4 ?    1.5   0.0      0.65   5.8e+02       7      27 ..     114     134 ..     108     140 .. 0.83
   5 ?    0.6   0.0       1.3   1.1e+03       4      18 ..     123     142 ..     121     156 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                HHHH.HHHHHHHHHHHHHHHHH-TT CS
       TPR_6  9 syrk.lgdtdkAlealerlikeYPd 32
                 + + + ++++A+ ++++++++ P+
  AJA92863.1 14 DLAEdQ-EYEEAILLYDKILDSDPK 37
                445547.**************9996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.029
                HHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6  4 yklalsyrklgdtdkAlealerlikeYP 31
                +  a  ++++g+ +++ +++++++ke  
  AJA92863.1 43 LDKAATLQRMGKNSQSFQIYNSILKEDS 70
                44444455566*************9865 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.32
                 HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                 Al   + ++ +  + ++A+e +++ +k
  AJA92863.1  75 ALIGKGTLLHAKSKFSEAIECYDSALK 101
                 5555666666545999******99876 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.65
                 HHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   7 alsyrklgdtdkAlealerli 27 
                 ++s+ + g+   Al  +++ +
  AJA92863.1 114 GMSLGEIGQLKSALSCFKKAL 134
                 778888679999999999877 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 1.3
                 HHHHHHHHH.H....HHHHH CS
       TPR_6   4 yklalsyrk.l....gdtdk 18 
                 +k als +k +    +d+d 
  AJA92863.1 123 LKSALSCFKkAltidKDYDL 142
                 55666666533555544443 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.6e-06    0.0014       3      80 ..      19      97 ..      17      99 .. 0.94
   2 ?   -0.3   0.0       1.5   1.3e+03       5      18 ..     123     135 ..     119     160 .. 0.55

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
      ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                + y++Ai+l++++l ++++   +++ +A +l ++g+  + ++++++  k++s++l +++ ++  l + +k+ eAi +++
  AJA92863.1 19 QEYEEAILLYDKILDSDPKLIPALLDKAATLQRMGKNSQSFQIYNSIlKEDSNNLDALIGKGTLLHAKSKFSEAIECYD 97
                68************999999999999*******************************99999999999*******9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                 HHHHHHHHHHHH.H CS
      ANAPC3   5 yknAiflaerllaa 18 
                 +k+A+ ++ ++l +
  AJA92863.1 123 LKSALSCFKKAL-T 135
                 444555555544.2 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00026      0.23     204     251 ..      17      64 ..       6      73 .. 0.84
   2 !    5.9   0.1    0.0058       5.2     208     257 ..      89     138 ..      82     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                 HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHH CS
       NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmee 251
                 + +++e+A+ + dk ++++p+l+   l Ka  l+++G  ++  ++ ++
  AJA92863.1  17 EDQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMGKNSQSFQIYNS 64 
                 446788*******************************99988877665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0058
                 SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTT CS
       NARP1 208 rekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDl 257
                  ++A+e+ d+a++ +p +      K+  l   G+lk A ++ ++a  +D+
  AJA92863.1  89 FSEAIECYDSALKIKPRFAMALACKGMSLGEIGQLKSALSCFKKALTIDK 138
                 468******************************************99996 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.2e-05      0.02      70     132 ..       6      68 ..       4      73 .. 0.93
   2 ?    1.4   0.1      0.44     4e+02      81     120 ..     119     158 ..     105     161 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHHHHH CS
  Alkyl_sulf_dimr  70 ekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniYlsg 132
                      +k+le+a++ +++++y+ a+ l ++++ +dp+   a   ka++l+++g+ ++s +  n  l +
       AJA92863.1   6 QKMLEQASDLAEDQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMGKNSQSFQIYNSILKE 68 
                      6899*************************************************9999888765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.44
                      HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH- CS
  Alkyl_sulf_dimr  81 kegdyrwaaellnhlvfadpenaeakelkadaleqlgyqa 120
                      + g+++ a++  +++++ d++ + a   k +ale l  q+
       AJA92863.1 119 EIGQLKSALSCFKKALTIDKDYDLANMGKQKALELLKSQK 158
                      7899999************999999999999999888776 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.1e-06    0.0055     141     231 ..      18     109 ..      10     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.1e-06
                 HT-HHHHHHHHHHHHHHSTT-SHHHHHHHHHHHHHT---TT.-HHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHTS-TTSTTHHHH CS
    PknG_TPR 141 egdyeeAaaeFdevlaalpGEiaPklaLAataElagetdee.kyYrtVwrtdrgvvsAaFGlaRqlaaagdraaAvaaLdeVpatSrhyttA 231
                 +++yeeA+  +d++l+  p  i+  l  Aat  ++g++ ++ + Y+++ + d + + A  G    l a+ + ++A++  d+  +    +++A
  AJA92863.1  18 DQEYEEAILLYDKILDSDPKLIPALLDKAATLQRMGKNSQSfQIYNSILKEDSNNLDALIGKGTLLHAKSKFSEAIECYDSALKIKPRFAMA 109
                 478********************************87765449***********************************99887777777766 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       0.1        90      21      37 ..      18      33 ..       8      36 .. 0.59
   2 ?    0.7   0.0      0.58   5.2e+02       9      25 ..      46      62 ..      41      67 .. 0.82
   3 ?    1.5   0.0      0.33     3e+02       9      31 ..      80     102 ..      73     103 .. 0.83
   4 ?    4.3   0.0     0.043        38       2      31 ..     107     136 ..     106     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.1
      TPR_10 21 AealleealairrrllG 37
                  ++ eea+ ++ ++l 
  AJA92863.1 18 DQEY-EEAILLYDKILD 33
                3333.677666666665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.58
      TPR_10  9 analrqrgrydeAeall 25
                a++l+++g+  ++ +++
  AJA92863.1 46 AATLQRMGKNSQSFQIY 62
                89999999999988886 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.33
      TPR_10   9 analrqrgrydeAealleealai 31 
                 + +l++  ++ eA + ++ al i
  AJA92863.1  80 GTLLHAKSKFSEAIECYDSALKI 102
                 66788888999999999999986 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.043
      TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                 A++l   ++ l + g+++ A+  +++al i
  AJA92863.1 107 AMALACKGMSLGEIGQLKSALSCFKKALTI 136
                 788888999******************987 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.13   1.2e+02      15      33 ..      19      37 ..      18      42 .. 0.92
   2 ?    0.9   0.0      0.54   4.8e+02      13      37 ..      51      75 ..      46      77 .. 0.87
   3 ?    4.7   0.0     0.034        31      16      38 ..      88     110 ..      84     116 .. 0.85
   4 ?   -1.7   0.0       3.6   3.2e+03      15      32 ..     121     138 ..     119     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                T-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPe 33
                +eY+eA  + d +L  +P+
  AJA92863.1 19 QEYEEAILLYDKILDSDPK 37
                69*************9996 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.54
                HHT-HHHHHHHHHHHHHHTTS-HHH CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQa 37
                ++g+ s++ +  + +L+ + +n  a
  AJA92863.1 51 RMGKNSQSFQIYNSILKEDSNNLDA 75
                888899999999*******999987 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.034
                 -HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C  16 eYseArryvdalLeiEPenrQaq 38 
                 ++seA ++ d  L+i P++  a+
  AJA92863.1  88 KFSEAIECYDSALKIKPRFAMAL 110
                 589**************987665 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.6
                 T-HHHHHHHHHHHHHHTT CS
  Fis1_TPR_C  15 geYseArryvdalLeiEP 32 
                 g+ + A+ + +  L i+ 
  AJA92863.1 121 GQLKSALSCFKKALTIDK 138
                 677888888888888775 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1         1   9.2e+02      22      36 ..      19      33 ..      19      35 .. 0.83
   2 ?    9.3   0.0   0.00084      0.76      15      31 ..      87     103 ..      85     105 .. 0.93
   3 ?   -0.3   0.1      0.85   7.6e+02       7      13 ..     117     123 ..     115     136 .. 0.75
   4 ?   -2.1   0.2       3.1   2.7e+03      25      31 ..     148     154 ..     148     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
    SHNi-TPR 22 eDlrkaLeLreqllp 36
                +++++a+ L+ ++l 
  AJA92863.1 19 QEYEEAILLYDKILD 33
                689999999999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00084
    SHNi-TPR  15 enFpqAveDlrkaLeLr 31 
                 ++F++A+e +++aL+++
  AJA92863.1  87 SKFSEAIECYDSALKIK 103
                 89*************98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.85
    SHNi-TPR   7 LGEislE 13 
                 LGEi++ 
  AJA92863.1 117 LGEIGQL 123
                 8888864 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.1
    SHNi-TPR  25 rkaLeLr 31 
                 +kaLeL 
  AJA92863.1 148 QKALELL 154
                 79***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1082.11
//
Query:       AJA92864.1  [L=584]
Description: NLI interacting factor-like phosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-05   22.9   0.1    0.00021   21.1   0.0    2.0  2  NIF             NLI interacting factor-like phosphatase
    0.00045   20.4   0.0      0.001   19.3   0.0    1.6  1  Acetyltransf_1  Acetyltransferase (GNAT) family
    0.00089   19.1   5.1     0.0014   18.5   1.3    2.7  2  Acid_PPase      Acid Phosphatase
     0.0098   15.8   0.0      0.022   14.7   0.0    1.6  1  FR47            FR47-like protein
  ------ inclusion threshold ------
      0.011   15.9   0.9      0.033   14.3   0.1    2.3  2  Acetyltransf_4  Acetyltransferase (GNAT) domain
      0.065   13.1   0.3       0.14   12.0   0.3    1.5  1  RMI1_C          Recq-mediated genome instability protein 1, C
      0.088   13.2   0.0       0.23   11.9   0.0    1.7  1  Acetyltransf_7  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5     4e+03     125     146 ..     139     162 ..     136     169 .. 0.78
   2 !   21.1   0.0   8.3e-08   0.00021       1     117 [.     233     350 ..     233     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
         NIF 125 ipiksf..fsdkkDneLlkllpll 146
                 ++i+++  ++ ++D++ ++l + +
  AJA92864.1 139 LQIPNYspYGIDDDHAVKSLKQAI 162
                 789999777899999999998765 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 8.3e-08
         NIF   1 ktLVLDLDetLvhskleksk..klkvegekvevsvlkRpgldefLkelsklyevvi.fTasseeyaeavidildpekkllshrlyrescv.kkkgeyvK 95 
                 k++VLDLD+tL+  +  + +  ++k+ +++      +   + ef+k+l  l + +i    +s+++ ++ +++++++  ++ ++    +c+  +  + v 
  AJA92864.1 233 KCIVLDLDNTLWGGVIGEDGfdNIKLGDNP------VGRTFVEFQKRLLALNQRGIlLAINSKNNFNDAVEVIQKHPSMVLRE-DDFACMkINWDNKVV 324
                 79**********999733333344444444......5566679****9999888887999****************9854444.333343133335666 PP

         NIF  96 dLsllgr....dlsrvvivDdspdsf 117
                 +L+++ +     l+++v++Dd+p + 
  AJA92864.1 325 NLEKIAEelniGLDSIVFFDDDPINQ 350
                 88888553334788********9875 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.9e-07     0.001      37     117 .]     475     557 ..     438     557 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.9e-07
                     E..EEETTE.EEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE..EEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  37 v..aeedge.liGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl..aveedndaairlYeklGF 117
                         +++++ + G+  + k++d   ++++i+ +  s    g+G+   ++ +++e a++ g+k+i+     ++ n++a ++YeklGF
      AJA92864.1 475 QvnDKFGDNgITGTYIIEKKND---EEWIIDTFLLSCRIIGRGVEEIMISQIIENAKSSGVKRIMGqfIPTAKNKPAENFYEKLGF 557
                     1233333335999999999999...89**********************************998444477788************9 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.3   5.6e-07    0.0014       4     142 ..     233     355 ..     230     364 .. 0.81
   2 ?   -2.4   0.1       1.5   3.8e+03      77     124 ..     374     425 ..     368     427 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.6e-07
                 SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT-G..........GGESEE CS
  Acid_PPase   4 klivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLklleindakekekklldvfddv 102
                 k iv+DLD TLW   +      ++k  ++        g   + + + ++ l +l+++++ la+ S+ +  d  + +++         + +  +d f  +
  AJA92864.1 233 KCIVLDLDNTLWGGVIGEDGFDNIKLGDNP------VG---RTFVEFQKRLLALNQRGILLAINSKNNFNDAVE-VIQKH------PSMVLREDDFACM 315
                 78**********888777777777777776......23...5677788899999************98877544.43332......334567889999* PP

                 EESSS-HHHHHHHHHHHH---GGGEEEEES-HHHHHHHHT CS
  Acid_PPase 103 eiykgsktkhfeklkkktgieyedmlfFDdesrnievesr 142
                 +i   +k+  +ek++++ +i  ++++fFDd   n+e +++
  AJA92864.1 316 KINWDNKVVNLEKIAEELNIGLDSIVFFDDDPINQEYVRE 355
                 **********************************998875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                 HHHHHHTT-G.............GGESEEEESS.S-HHHHHHHHHHHH---G CS
  Acid_PPase  77 relLkllein...dakekekklldvfddveiyk.gsktkhfeklkkktgiey 124
                 + l +++e++    ++e++k+   + ++ +  +  +k+  f+++ k+ +ie 
  AJA92864.1 374 KILTEMIEFDalkITEEDTKRSSMYLGQKKRKElETKIGNFNEFLKQMNIEV 425
                 4444455444443446666667777777444443789999999988888875 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.7e-06     0.022      62      86 .]     542     565 ..     512     565 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.7e-06
                 ETT-HHHHHHHHHHT-EEEEEEEEE CS
        FR47  62 vasNtpsirlyeklGfekieetewv 86 
                  a+N+p++++yeklGf+k  +  wv
  AJA92864.1 542 TAKNKPAENFYEKLGFKKE-NDFWV 565
                 589**************98.66665 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.3   3.3e+03      25      59 ..     170     205 ..     160     227 .. 0.63
   2 ?   14.3   0.1   1.3e-05     0.033      73     140 ..     494     563 ..     427     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.3
  Acetyltransf_4  25 itfeyevssve.efekflealdsekeyvflvae..sdr 59 
                     +++  ++  ++ +f++f++++  +++++f + +  s++
      AJA92864.1 170 FQWSKQHMLLTyDFNQFIQKY--GENNIFNYKQffSGD 205
                     555555544331577888887..556666555444554 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
  Acetyltransf_4  73 akdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiasp..nensiqfhkalGFelvgif 140
                       d+++++ ++l       +g+   +i  +++ +k  ++++++ + + +  n+++ +f+++lGF+++ +f
      AJA92864.1 494 KNDEEWIIDTFLLSCRIIGRGVEEIMISQIIENAKSSGVKRIMGQFIPTakNKPAENFYEKLGFKKENDF 563
                     3677888888886322334444444******************99865544889***********99876 PP

>> RMI1_C  Recq-mediated genome instability protein 1, C-terminal OB-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   5.6e-05      0.14      65     128 ..     374     441 ..     368     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
      RMI1_C  65 evlteligfspaelkeslalkkd....qkkrqklkealkeaqekLidleclmeielnpaskkpvvlel 128
                 ++lte+i f + +++e+   ++     qkkr++l++ + ++ e+L++++   e++ + + + p +++l
  AJA92864.1 374 KILTEMIEFDALKITEEDTKRSSmylgQKKRKELETKIGNFNEFLKQMNIEVEVKKADSFSIPRISQL 441
                 79*********9998888777778999**********************9999999988888888887 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.9e-05      0.23      60      76 .]     543     559 ..     512     559 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                     ETHHHHHHHHHHTTEEE CS
  Acetyltransf_7  60 lnaekaikfYeklGFee 76 
                      ++++a++fYeklGF++
      AJA92864.1 543 AKNKPAENFYEKLGFKK 559
                     233489*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3935.32
//
Query:       AJA92865.1  [L=245]
Description: PF01973 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-35  122.1   0.7    2.5e-35  121.7   0.7    1.1  1  MAF_flag10     Protein of unknown function DUF115
  ------ inclusion threshold ------
       0.01   16.3   0.0        1.5    9.3   0.0    2.3  2  Guanylin       Guanylin precursor
      0.056   13.5   0.1      0.099   12.7   0.1    1.6  1  TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
        0.1   11.9   0.0       0.18   11.1   0.0    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.7   0.7   5.5e-39   2.5e-35       6     169 ..      30     185 ..      27     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 5.5e-39
  MAF_flag10   6 nlkenlk..pslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfkeaekkgdiplvfas 101
                 +l+++lk  +s +++ n ++g k+++i+gaGPSL  +l+++k+  ++++ i ad+a++aLl+++IkPDi v+ lD+   + + ++++ k +  ++v+a+
  AJA92865.1  30 KLNSLLKgkNSKNQFQNMIQG-KTVFIIGAGPSLTRSLKYIKKS-KDVTKIVADGAVRALLEKNIKPDILVTdLDG---DLKSIEKIGKTRIPIIVHAH 123
                 566666665566777777788.*******************988.57777788***********************...99999999999666789*** PP

  MAF_flag10 102 gvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqDlayt 169
                 g+n+e+l+ +k+ k ++ ++  q ++ +    ++++fgG+++++++++lA ++++++I+liG+D++ +
  AJA92865.1 124 GDNYEKLEIVKKLKNVIGST--Q-TSKI---GKSENFGGFTDGDRCVFLAEYFNASKIVLIGMDFGQK 185
                 *******9999999976665..4.3333...23379*****************************975 PP

>> Guanylin  Guanylin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00034       1.5      13      63 ..      25      80 ..      21      91 .. 0.84
   2 ?    4.6   0.0    0.0099        44       7      30 ..     124     148 ..     118     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00034
                SHHHHTTTTXXSSXXXXXSSX.....XXXXSSXSSTTSXGGGHHHHTSTTHHHHHH CS
    Guanylin 13 LesvkkLkdleelqeprlqaq.....savpsvCsepalPeelkpvCkekeaaeilq 63
                L svkkL++l + ++++ q q     ++v ++ + p+l ++lk + k+k+ ++i+ 
  AJA92865.1 25 LISVKKLNSLLKGKNSKNQFQnmiqgKTVFIIGAGPSLTRSLKYIKKSKDVTKIVA 80
                779*******99976655555558888999999**************999999875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0099
                 SSSEEXSHHHHTTTTXXSS.XXXXX CS
    Guanylin   7 gdfsfsLesvkkLkdleel.qeprl 30 
                 gd   +Le vkkLk++  + q++++
  AJA92865.1 124 GDNYEKLEIVKKLKNVIGStQTSKI 148
                 566668*********9988445555 PP

>> TPK_catalytic  Thiamin pyrophosphokinase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.2e-05     0.099       9      54 ..      75     115 ..      66     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
  TPK_catalytic   9 slrvcaDgGanrlyeeekerlellpdvivGDlDSirpevkefyesk 54 
                     ++++aDg+++ l+     +++++pd++v DlD   +++ ++ +++
     AJA92865.1  75 VTKIVADGAVRALL-----EKNIKPDILVTDLDGDLKSIEKIGKTR 115
                    4689**********.....9999***99877776666665555543 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     4e-05      0.18      32      85 ..      46      99 ..      40     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                   ---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE CS
  THF_DHG_CYH_C 32 ielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvv 85
                     ++gk+v+++G++  + ++l+ + ++k+ t  v++ + + l e+  + di+v+
     AJA92865.1 46 NMIQGKTVFIIGAGPSLTRSLKYIKKSKDVTKIVADGAVRALLEKNIKPDILVT 99
                   5689************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1677.04
//
Query:       AJA92866.1  [L=75]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-18   63.6   0.3    1.7e-11   43.4   0.1    2.1  2  TPR_1       Tetratricopeptide repeat
      2e-16   58.7   0.1      2e-09   36.8   0.0    2.1  2  TPR_2       Tetratricopeptide repeat
    5.1e-13   48.5   0.1    4.1e-06   26.4   0.0    2.1  2  TPR_11      TPR repeat
    1.1e-11   43.9   0.1    8.1e-07   28.8   0.0    2.1  2  TPR_8       Tetratricopeptide repeat
    1.7e-10   41.3   0.0    1.9e-10   41.1   0.0    1.1  1  TPR_19      Tetratricopeptide repeat
    2.4e-09   36.9   0.3    2.2e-06   27.6   0.0    2.4  2  TPR_17      Tetratricopeptide repeat
    4.7e-09   35.6   0.1     0.0034   17.3   0.0    2.2  2  TPR_7       Tetratricopeptide repeat
    9.5e-09   35.4   0.1    2.8e-08   33.9   0.1    1.7  1  TPR_12      Tetratricopeptide repeat
    1.1e-08   35.0   0.0    1.3e-08   34.8   0.0    1.1  1  TPR_9       Tetratricopeptide repeat
    1.8e-07   31.7   0.0    2.2e-07   31.4   0.0    1.1  1  TPR_16      Tetratricopeptide repeat
    3.6e-07   30.4   0.2      0.028   15.2   0.0    2.1  2  TPR_14      Tetratricopeptide repeat
    2.1e-05   24.2   0.4      0.012   15.5   0.1    2.3  2  TPR_10      Tetratricopeptide repeat
    0.00036   20.5   0.0       0.31   11.1   0.0    2.1  2  MIT         MIT (microtubule interacting and transport) domai
     0.0061   15.5   0.0     0.0071   15.3   0.0    1.0  1  NARP1       NMDA receptor-regulated protein 1
       0.01   15.3   1.7       0.46   10.0   0.7    2.4  2  SHNi-TPR    SHNi-TPR
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.022   14.2   0.0    1.2  1  Coatomer_E  Coatomer epsilon subunit
      0.024   14.7   0.0      0.053   13.6   0.0    1.5  1  DUF3856     Domain of Unknown Function (DUF3856)
      0.038   14.1   0.2        5.7    7.1   0.0    2.6  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.7e-07   0.00096      13      34 .]      16      37 ..       5      37 .. 0.87
   2 !   43.4   0.1   1.7e-14   1.7e-11       2      34 .]      39      71 ..      38      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.7e-07
                HTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1 13 klgkydeAleyyekALelnPnn 34
                + g++++Al ++e+AL l P++
  AJA92866.1 16 EDGNFEDALSFFEQALLLKPDD 37
                569*****************96 PP

  == domain 2  score: 43.4 bits;  conditional E-value: 1.7e-14
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                + ++n+G a+++lg+ydeA  +y+k Lel+P +
  AJA92866.1 39 DLWNNKGIALRSLGRYDEASYCYNKSLELDPRD 71
                79*****************************75 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.9e-07   0.00039       8      34 .]      11      37 ..       5      37 .. 0.85
   2 !   36.8   0.0     2e-12     2e-09       1      34 []      38      71 ..      38      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.9e-07
       TPR_2  8 GlayyklgdyeeAleafekAleldPnn 34
                G   ++ g++e+Al +fe+Al l P++
  AJA92866.1 11 GVKNLEDGNFEDALSFFEQALLLKPDD 37
                6666789******************97 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 2e-12
       TPR_2  1 aealynlGlayyklgdyeeAleafekAleldPnn 34
                +++++n G a++ lg+y+eA  +++k+leldP++
  AJA92866.1 38 PDLWNNKGIALRSLGRYDEASYCYNKSLELDPRD 71
                579*****************************86 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.1e-08   7.1e-05       7      38 ..      17      48 ..      15      49 .. 0.94
   2 !   26.4   0.0   4.1e-09   4.1e-06       3      27 ..      47      71 ..      45      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.1e-08
      TPR_11  7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                 G++e+A+  +++Al l+Pd++++++n G a+
  AJA92866.1 17 DGNFEDALSFFEQALLLKPDDPDLWNNKGIAL 48
                59***************************985 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4.1e-09
      TPR_11  3 ayyeqGkyeeAieaYkkAlkldPdn 27
                a++++G+y+eA  +Y+k l+ldP +
  AJA92866.1 47 ALRSLGRYDEASYCYNKSLELDPRD 71
                899********************75 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.2e-05     0.062      15      34 .]      18      37 ..      14      37 .. 0.92
   2 !   28.8   0.0   8.1e-10   8.1e-07       2      33 ..      39      70 ..      38      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.2e-05
                T-HHHHHHHHHHHHHHHHH. CS
       TPR_8 15 gdyeeAkeyyekaleldpdn 34
                g++e A +++e+al l+pd+
  AJA92866.1 18 GNFEDALSFFEQALLLKPDD 37
                9*****************96 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 8.1e-10
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                ++++n+g ++++lg+y+eA  +y+k leldp 
  AJA92866.1 39 DLWNNKGIALRSLGRYDEASYCYNKSLELDPR 70
                68*****************************6 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0     2e-13   1.9e-10       2      58 ..      15      71 ..      14      75 .] 0.94

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-13
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58
                l++g++++Al+++eqal  +p++++++ +  +al +lg++deA  + ++ +e dp d
  AJA92866.1 15 LEDGNFEDALSFFEQALLLKPDDPDLWNNKGIALRSLGRYDEASYCYNKSLELDPRD 71
                899*************************************************99995 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   2.3e-09   2.2e-06       1      32 [.      26      57 ..      26      58 .. 0.97
   2 !    7.1   0.0    0.0083       8.2       1      12 [.      60      71 ..      60      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-09
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtA 32
                ++++al l P+++d++nn++ +l+++G++++A
  AJA92866.1 26 FFEQALLLKPDDPDLWNNKGIALRSLGRYDEA 57
                599***************************98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0083
      TPR_17  1 lylkaleldPnn 12
                +y k+leldP +
  AJA92866.1 60 CYNKSLELDPRD 71
                8*********86 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.4e-06    0.0034      11      32 ..      16      37 ..      15      39 .. 0.78
   2 !   16.4   0.1   6.4e-06    0.0064       2      31 ..      41      70 ..      40      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
       TPR_7 11 rlGdyeeAielyeqsLaltkdp 32
                ++G++e+A++++eq+L l  d+
  AJA92866.1 16 EDGNFEDALSFFEQALLLKPDD 37
                68************66666554 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.4e-06
       TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkd 31
                ++n + + ++lG+y+eA  +y +sL+l+ +
  AJA92866.1 41 WNNKGIALRSLGRYDEASYCYNKSLELDPR 70
                7999*******************7777654 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1   2.8e-11   2.8e-08      15      76 ..      16      69 ..       3      70 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.8e-11
      TPR_12 15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76
                + g++++Al+++e+al +      pd p+     +n g+++r lgry+eA + ++++l++++
  AJA92866.1 16 EDGNFEDALSFFEQALLLK-----PDDPD---LWNNKGIALRSLGRYDEASYCYNKSLELDP 69
                68*****************.....**999...5**************************975 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   1.3e-11   1.3e-08       9      64 ..      18      73 ..      14      75 .] 0.94

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.3e-11
       TPR_9  9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64
                 ++e al   e  lll+Pddp+++   G++l  lG++ +A  + +  l+l+p +++
  AJA92866.1 18 GNFEDALSFFEQALLLKPDDPDLWNNKGIALRSLGRYDEASYCYNKSLELDPRDRA 73
                57999***********************************************8875 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   2.2e-10   2.2e-07       8      66 ..      15      70 ..      14      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.2e-10
      TPR_16  8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66
                l+ g+++dA+  +e+al +    Pd+++ ++++g a+  +gr++eA   y++ l+ +p 
  AJA92866.1 15 LEDGNFEDALSFFEQALLLK---PDDPDLWNNKGIALRSLGRYDEASYCYNKSLELDPR 70
                578*****************...99999******************8777777777775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.8e-05     0.028      13      39 ..      16      42 ..      14      46 .. 0.90
   2 !   13.7   0.0   8.5e-05     0.085       8      35 ..      45      72 ..      44      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-05
      TPR_14 13 alGdpdeAiallrralalaPddaeawl 39
                + G++++A+  +++al l Pdd+++w 
  AJA92866.1 16 EDGNFEDALSFFEQALLLKPDDPDLWN 42
                679**********************95 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.5e-05
      TPR_14  8 aeallalGdpdeAiallrralalaPdda 35
                + al+ lG++deA  ++++ l+l+P d+
  AJA92866.1 45 GIALRSLGRYDEASYCYNKSLELDPRDR 72
                6799*********************986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0057       5.7      15      29 ..      17      31 ..      15      39 .. 0.91
   2 !   15.5   0.1   1.2e-05     0.012       6      30 ..      42      66 ..      42      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0057
      TPR_10 15 rgrydeAealleeal 29
                 g++++A+ ++e+al
  AJA92866.1 17 DGNFEDALSFFEQAL 31
                69************8 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
      TPR_10  6 nNLanalrqrgrydeAealleeala 30
                nN ++alr++grydeA   + ++l+
  AJA92866.1 42 NNKGIALRSLGRYDEASYCYNKSLE 66
                899*************999888887 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00031      0.31       7      31 ..       7      31 ..       6      33 .. 0.93
   2 !    7.5   0.1    0.0042       4.2      16      33 ..      50      67 ..      43      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
         MIT  7 lvkkAveeDnagnyeeAlelYkeal 31
                l++  v++ + gn+e+Al+ +++al
  AJA92866.1  7 LIQNGVKNLEDGNFEDALSFFEQAL 31
                7999*******************98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0042
         MIT 16 nagnyeeAlelYkealel 33
                + g y+eA  +Y ++lel
  AJA92866.1 50 SLGRYDEASYCYNKSLEL 67
                5699***********996 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.1e-06    0.0071     207     260 ..      19      72 ..      10      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.1e-06
                 -SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT-H CS
       NARP1 207 srekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaDR 260
                 + e Al++ ++a+  +p   +l+ +K+  l+  G  ++A  + +++ +lD +DR
  AJA92866.1  19 NFEDALSFFEQALLLKPDDPDLWNNKGIALRSLGRYDEASYCYNKSLELDPRDR 72 
                 5679*************************************************9 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.7   0.00046      0.46      11      31 ..      14      34 ..      14      35 .. 0.88
   2 ?    3.8   0.0     0.039        38      16      30 ..      53      67 ..      51      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
    SHNi-TPR 11 slEnenFpqAveDlrkaLeLr 31
                +lE++nF++A++ ++ aL L+
  AJA92866.1 14 NLEDGNFEDALSFFEQALLLK 34
                59*********9999999775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.039
    SHNi-TPR 16 nFpqAveDlrkaLeL 30
                ++++A+  ++k+LeL
  AJA92866.1 53 RYDEASYCYNKSLEL 67
                89999999*****98 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.2e-05     0.022     203     262 ..       6      65 ..       2      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT--HHHHHHHHHHH CS
  Coatomer_E 203 llngkAvvslllgryeeAeslLkeaLdkdakdeetLiNlvvaaqhlgkdaevsernlsql 262
                 +l  + v +l  g++e+A s  ++aL  ++ d++   N  +a   lg+ +e+s  + ++l
  AJA92866.1   6 TLIQNGVKNLEDGNFEDALSFFEQALLLKPDDPDLWNNKGIALRSLGRYDEASYCYNKSL 65 
                 556667889999***********************************9999886655555 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.4e-05     0.053      79     129 ..      21      67 ..      11      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                 HHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
     DUF3856  79 dkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrmagem 129
                 + al +f++   l+ d+  lW     +++ al +lGr+dea   ++++ e+
  AJA92866.1  21 EDALSFFEQALLLKPDDPDLW----NNKGIALRSLGRYDEASYCYNKSLEL 67 
                 68999999999999******9....58****************99998875 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.9   1.9e+03      38      49 ..       2      13 ..       1      17 [. 0.80
   2 ?    4.2   0.0     0.045        45      15      34 ..      18      37 ..      14      40 .. 0.90
   3 ?    7.1   0.0    0.0057       5.7      14      35 ..      51      72 ..      45      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                HHHHHHHHHHHH CS
  Fis1_TPR_C 38 qsLkeliedkik 49
                ++L++li++ +k
  AJA92866.1  2 NELETLIQNGVK 13
                689999998776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.045
                T-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C 15 geYseArryvdalLeiEPen 34
                g++++A+ + ++ L + P+ 
  AJA92866.1 18 GNFEDALSFFEQALLLKPDD 37
                89************999985 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0057
                HT-HHHHHHHHHHHHHHTTS-H CS
  Fis1_TPR_C 14 lgeYseArryvdalLeiEPenr 35
                lg+Y+eA  + +  Le++P+ r
  AJA92866.1 51 LGRYDEASYCYNKSLELDPRDR 72
                9******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 559.56
//
Query:       AJA92867.1  [L=328]
Description: phosphate transporter family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-80  268.7  32.7    3.5e-79  266.3  32.7    1.8  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.3  32.7   1.9e-83   3.5e-79       1     335 [.      19     315 ..      19     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 266.3 bits;  conditional E-value: 1.9e-83
        PHO4   1 iGanDvanafatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselm.lgmlaallgaavwlllatvlglPvStthslvGali 98 
                 +G+nD an++at++g+++l++  Av ++a  +f+G +++G +Va ti+kgiv     +p++++ ++++  l+ga++w +l+t++glP+S +hsl+G+++
  AJA92867.1  19 NGFNDSANSVATVIGTRVLKPIHAVTISAAANFAGPFVFGVAVATTIAKGIV-----SPDDITvYMIIGGLAGAITWSTLCTYFGLPISNSHSLIGGIM 112
                 8***************************************************.....677777589999****************************** PP

        PHO4  99 GaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlvtiailalsilfkgeskkddeeteklfkflqvvsa 197
                 Ga++a  g+e +  ++l+k++++++++P+ g++++++ + l+ ++  +                                 k+   ++++f  lq++s+
  AJA92867.1 113 GAGIAGLGFEKLVYDGLAKVFTGIIVAPIGGMMFGIAATGLIIYFFAR---------------------------------KKPAIVNRTFGRLQIISS 178
                 *****76678998999***********************999999442.................................345557899********* PP

        PHO4 198 alvsfahGanDvanaiGpllaalisiykask.evplwvlllgglaialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStTh 295
                 a ++++hGanD+++++G+++++l+s+  +++ e+plwv+++ ++a++lG+++gG++vikt+G k+t +l+p++Gfaae+++ l+++++  lg+P StTh
  AJA92867.1 179 AWFALTHGANDGQKTMGIIVLILFSVGLIEElEMPLWVIFAAAAAMGLGTFFGGYKVIKTLGVKVT-RLKPYQGFAAETSGGLMLAVFATLGIPASTTH 276
                 *******************8888876657999**********************************.7******************9999********* PP

        PHO4 296 vlvgavvGvGlakkresavnwklvrnivlaWvlTlpvsal 335
                 +++g ++G+G a+ r +av+w++ r+i+++Wv+T+p +a 
  AJA92867.1 277 AITGTIMGAGSAR-RIRAVRWRVSRQIIFSWVITIPGAAG 315
                 *************.9*********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2296.62
//
Query:       AJA92868.1  [L=194]
Description: riboflavin synthase, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-43  146.2   4.9    1.2e-22   79.7   0.1    2.0  2  Lum_binding  Lumazine binding domain


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   1.8     3e-23   5.5e-19       1      86 [.       3      88 ..       3      89 .. 0.91
   2 !   79.7   0.1   6.5e-27   1.2e-22       2      87 .]     103     186 ..     102     186 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 3e-23
                 -S--SEEEEEEEEE.E.CGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEE CS
  Lum_binding  1 tGiVeevgtvesieke.ekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEr 86
                 tGi++++g++++ie++ ++ + ++++++   + + ++ G+s+a+nGvcL  +  ++++++ t+++i eT+++t lg+lkvg+ VN+Er
   AJA92868.1  3 TGIITSTGKIKKIEQNtKNRSAIKVSVDlGKDSKGLKIGQSVALNGVCLSAT--KIAKNTCTFEMIDETMKKTDLGNLKVGSLVNVER 88
                 8************7664677777777778778888899*************9..7999*****************************8 PP

  == domain 2  score: 79.7 bits;  conditional E-value: 6.5e-27
                  S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEEE CS
  Lum_binding   2 GiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEra 87 
                  G+V++v+++++iek+ k  ++ +++p +l+ky+v+kG sia++G++LTVv  +v+++  +v +ip+T+e t+++++++ dk+N+E++
   AJA92868.1 103 GHVDGVAQIKKIEKKPKEVKIWFKIPkNLKKYVVQKG-SIALDGISLTVV--DVKNDLASVCLIPHTIEITNFKTKNIDDKLNIETD 186
                  9***********989888999999999**********.***********9..9********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1427.15
//
Query:       AJA92869.1  [L=250]
Description: GGDN family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-51  174.9   0.0      2e-51  174.7   0.0    1.0  1  GCH_III         GTP cyclohydrolase III
    3.3e-05   24.2   0.8      0.016   15.5   0.0    2.3  2  mCpol           minimal CRISPR polymerase domain
     0.0022   17.7   1.8     0.0032   17.1   0.6    1.9  3  Guanylate_cyc   Adenylate and Guanylate cyclase catalytic dom
  ------ inclusion threshold ------
      0.035   14.3   0.4       0.13   12.4   0.1    2.0  2  IFT20           Intraflagellar transport complex B, subunit 2
      0.097   12.5   0.4       0.57   10.0   0.2    2.4  3  NOG1            Nucleolar GTP-binding protein 1 (NOG1)
        0.4   10.8   4.9       0.64   10.1   0.0    2.9  2  ARL2_Bind_BART  The ARF-like 2 binding protein BART


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   0.0   6.6e-55     2e-51       2     235 ..       5     236 ..       1     244 [. 0.94

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 6.6e-55
                 EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHSSS-EEEEEEEESSHHHHHHHHHH CS
     GCH_III   2 tviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnrypvtvsmgigaaetPldaleaase 100
                 t+++i +YgpWt +++ +re +lq+lq++ly  lq+ ++ ++ lvf  R D   a+tng+ l +h  iq+ +   + ++ sm+ig +e+P+da   a e
  AJA92869.1   5 TIMKITGYGPWTLTLGFDREHELQMLQSKLYNKLQELFSKKNCLVFLNRSDEYFAVTNGLSLDDHVAIQKELESSFDIKLSMSIGYGENPYDANLDAYE 103
                 899************************************************************************************************ PP

                 HHHHH--TT-TT----EEES---SS--EEEEEEEETTHHHHTTTTS-HHHHHHHHHHHHHHHHHHHHTTT---EEEETTEEEEE-TT--HHHHHHHHHH CS
     GCH_III 101 aLreagsaqdeeRkevlsvdelvtegyvqiahiDinnitgtltdivsavrtylevnkvkaklakklekegallqfiGGDnilavcneleeedvldiine 199
                 a +++  +  +e   ++ + +  +e  v++ h+D+ +it    +  s+++t+  + k+   ++++   ++ l++f+GGDn++ v+n   +    d i+ 
  AJA92869.1 104 AKKSQ--KFLNEQYSIFGTLNGHSEHSVTVMHLDVDDITSIRKKSMSPYDTSSLMFKIYSRMSEYFLSKNSLTFFMGGDNFMVVTNSEFKTFAKDFIQI 200
                 97664..4455666667776667899*************9999*******************************************9999999999*** PP

                 HHHHHS--EEEEEEEESSHHHHHHHHHHHHHHHHTT CS
     GCH_III 200 vkekvdvdlkaGiGiadtaedaaaladeaLeeiRgk 235
                  k++ +++l+ GiG a t++da  la e+L++iR  
  AJA92869.1 201 CKDEFQIELNCGIGTASTSRDAVKLATESLDTIREI 236
                 *********************************965 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.4e-06     0.016      36     107 ..      35     108 ..      18     114 .. 0.82
   2 !    7.3   0.1     0.002       5.9      28      96 ..     152     222 ..     129     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-06
       mCpol  36 ikklkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkit..gltvSiGvGktlrealiaLkkAkskg 107
                  +kl++l++++ ++ v  +  D+  a ++  + d+ v +++++++    +l++SiG+G++  +a +    Ak ++
  AJA92869.1  35 YNKLQELFSKK-NCLVFLNRSDEYFAVTNGLSlDDHVAIQKELESSFdiKLSMSIGYGENPYDANLDAYEAKKSQ 108
                 56788888888.9999999*******99876689999999999999899************99988777777655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
       mCpol  28 lskevkeaikklkkllkdelgasvifaaGDsilaksslee.dllvelsrvyqkit..gltvSiGvGktlrea 96 
                 +s+ + +  +++++++ ++ +    f +GD+ ++ ++ e  + + ++ ++ +     +l + iG+  t+r+a
  AJA92869.1 152 TSSLMFKIYSRMSEYFLSK-NSLTFFMGGDNFMVVTNSEFkTFAKDFIQICKDEFqiELNCGIGTASTSRDA 222
                 5666667778888888888.777789*********9866534444444444444445666666666666665 PP

>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.84   2.5e+03      37      65 ..      33      61 ..      24      89 .. 0.60
   2 ?   -2.0   0.0      0.81   2.4e+03      27      47 ..     103     123 ..      97     128 .. 0.76
   3 !   17.1   0.6   1.1e-06    0.0032       6      69 ..     126     195 ..     121     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.84
  Guanylate_cyc 37 elyarfdelldekkvykvktiGdaymvvs 65
                   +ly++++el ++k++       d y +v+
     AJA92869.1 33 KLYNKLQELFSKKNCLVFLNRSDEYFAVT 61
                   67778888888877766666666665554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.81
  Guanylate_cyc  27 spievvklLnelyarfdelld 47 
                    ++++  k+Lne y+ f +l +
     AJA92869.1 103 EAKKSQKFLNEQYSIFGTLNG 123
                    467778999999999988765 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.1e-06
  Guanylate_cyc   6 ydevtilFadIvgftalssahs.pievvklLnelyarfdelldekkvykvktiGdaymvvsglp.....e 69 
                     ++vt++  d+ + t++ +++  p +  +l+ ++y+r+ e   +k+     + Gd +mvv++++     +
     AJA92869.1 126 EHSVTVMHLDVDDITSIRKKSMsPYDTSSLMFKIYSRMSEYFLSKNSLTFFMGGDNFMVVTNSEfktfaK 195
                    678**************987645*************************************9998543331 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.4e-05      0.13       2      45 ..      19      64 ..      18      73 .. 0.93
   2 ?   -0.9   0.0      0.58   1.7e+03      36      50 ..     188     202 ..     170     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
       IFT20  2 lyfDelnkiRvldpevaeeteel..keeckeFvkkinefqklvkel 45
                l fD + ++++l+++ +++ +el  k++c  F+++ +e+ +++++l
  AJA92869.1 19 LGFDREHELQMLQSKLYNKLQELfsKKNCLVFLNRSDEYFAVTNGL 64
                77***********************************999888876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
       IFT20  36 nefqklvkelievle 50 
                 +ef+++ k++i++ +
  AJA92869.1 188 SEFKTFAKDFIQICK 202
                 678888888888765 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00019      0.57      34      58 .]      31      55 ..      27      55 .. 0.95
   2 ?   -1.5   0.0      0.75   2.2e+03      27      46 ..      62      81 ..      60      86 .. 0.85
   3 ?   -2.9   0.0       2.1   6.2e+03      31      42 ..     111     122 ..     106     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
        NOG1 34 QlsLleeikelfankpvivvlnKiD 58
                Q +L+++++elf++k+ +v ln +D
  AJA92869.1 31 QSKLYNKLQELFSKKNCLVFLNRSD 55
                99********************988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
        NOG1 27 cgysleeQlsLleeikelfa 46
                 g sl++ +++ +e+++ f+
  AJA92869.1 62 NGLSLDDHVAIQKELESSFD 81
                68899999999999999997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
        NOG1  31 leeQlsLleeik 42 
                 l+eQ+s++ ++ 
  AJA92869.1 111 LNEQYSIFGTLN 122
                 678999987765 PP

>> ARL2_Bind_BART  The ARF-like 2 binding protein BART
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00022      0.64      10      39 ..      27      56 ..      23      79 .. 0.86
   2 ?   -0.1   2.5      0.33   9.8e+02      47      47 ..     157     157 ..     104     238 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                    HHHTS-HHHHHHHHHHHHHHHHTT--SS-S CS
  ARL2_Bind_BART 10 eeflaspefkspvqeFidencivFddeeen 39
                    +++l+s+ ++++++ F ++nc vF +  ++
      AJA92869.1 27 LQMLQSKLYNKLQELFSKKNCLVFLNRSDE 56
                    799*********************985444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.33
                     H CS
  ARL2_Bind_BART  47 h 47 
                     +
      AJA92869.1 157 F 157
                     1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1782.20
//
Query:       AJA92870.1  [L=286]
Description: putative proteasome endopeptidase complex, alpha subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-51  174.9   0.4    1.7e-51  174.5   0.4    1.2  1  Proteasome      Proteasome subunit
    1.8e-13   49.9   0.1    1.8e-13   49.9   0.1    2.9  3  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.5   0.4   1.8e-55   1.7e-51       1     178 [.      72     244 ..      72     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 1.8e-55
                 HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHC CS
  Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrs 99 
                 v++G  +vG+++k+gv++a++ ++    kl+  +t +Kif+id hig+a+aG ++Dar  ++ ar   q+ +l y++p+ ve++++++a++ q+ytq++
  AJA92870.1  72 VRRGALAVGVRTKNGVIIAVEEKSR---KLQIINTPQKIFQIDYHIGAAAAGYIPDARSQIDTARTFSQSNKLVYDEPVEVETVAKHLADQCQQYTQYG 167
                 578999***************9999...555667779************************************************************** PP

                 TTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHB CS
  Proteasome 100 grrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerd 178
                 g rp+gvsl+i+g+d  g   Ly++dpsGsyi++ +a++iG +s+++ ++lek+yked++l++a  la+ a++ ++e  
  AJA92870.1 168 GARPIGVSLIIGGIDPAG-TNLYMTDPSGSYISY-NAISIGANSDVVNEFLEKNYKEDMSLDDAASLAIAAIYISSETK 244
                 ***************999.7**************.7*************************************999943 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.7         1   9.3e+03       5       9 ..      16      20 ..      16      20 .. 0.89
   2 !   49.9   0.1     2e-17   1.8e-13       1      22 [.      49      70 ..      49      70 .. 0.98
   3 !    3.3   0.1    0.0076        69      13      19 ..     106     112 ..     106     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1
  Proteasome_A_N  5 lttFS 9 
                    +t+FS
      AJA92870.1 16 TTIFS 20
                    79**9 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 2e-17
  Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmk 22
                    YDr++t+FSPdGRL+QVEYA++
      AJA92870.1 49 YDRAITVFSPDGRLYQVEYAIE 70
                    ********************97 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0076
  Proteasome_A_N  13 RLfQVEY 19 
                     ++fQ++Y
      AJA92870.1 106 KIFQIDY 112
                     79***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2213.12
//
Query:       AJA92871.1  [L=277]
Description: PF08643 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-51  172.8   0.0    6.9e-51  172.5   0.0    1.1  1  adh_short     short chain dehydrogenase
    3.8e-38  131.4   0.0    5.9e-38  130.7   0.0    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    6.9e-07   29.4   0.0    1.4e-06   28.4   0.0    1.4  1  KR            KR domain
      4e-06   26.4   0.0    0.00015   21.2   0.0    2.3  1  DUF1776       Fungal family of unknown function (DUF1776)


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.0   1.5e-54   6.9e-51       1     192 [.       3     194 ..       3     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 1.5e-54
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 kv++vtG ssGIG +++ +la+eG+ ++++ r  +k+  +     ee+  + +i++Dv + e++ +++++++++ g++dvLvnNAG    g+ +++s e
  AJA92871.1   3 KVAVVTGSSSGIGFETSLALAREGYVTYATMRDVKKADDIQRITDEENLPLKVIELDVDNDESAGNAIDTIIQEKGRIDVLVNNAGWGIWGTGEDVSIE 101
                 89***********************************999888888899************************************************** PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                 e+++ +e+N+++++ l++ v+p+m kq sG+Ivn+sSvag+ ++++ +aY +sK+a++g+++sl+ el+p gi+v+++ PG+++T++  + r+
  AJA92871.1 102 EFREQFETNFFSIVRLIQKVAPTMRKQGSGDIVNISSVAGRIGFPVSTAYISSKFALEGFSESLRYELQPFGINVIIIEPGVIKTNFFDSMRT 194
                 **************************************************************************************9988776 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   0.0   1.3e-41   5.9e-38       1     191 [.       9     201 ..       9     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 1.3e-41
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE..EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae..vlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   G  sgIG+++  ala+eG+   +t ++ +++++++++++e +    v+e+DV ++e+  ++++++ ++ g++D+lvnnag+     g  +++s eef
    AJA92871.1   9 GSSSGIGFETSLALAREGYVTYATMRDVKKADDIQRITDEENLPlkVIELDVDNDESAGNAIDTIIQEKGRIDVLVNNAGWGIW--GTGEDVSIEEF 103
                   5679**********************************997755338*************************************..999******** PP

                   HHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHH CS
  adh_short_C2  96 draldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelle 190
                   ++ +++n+ s+++l++ ++p m+++  g ivn+ssv++++++p  +ay  +K ale+++ +l +el p gi v  + pg+ikT+  ++++ +++  +
    AJA92871.1 104 REQFETNFFSIVRLIQKVAPTMRKQgsGDIVNISSVAGRIGFPVSTAYISSKFALEGFSESLRYELQPFGINVIIIEPGVIKTNFFDSMRTAKKADN 200
                   ********************999886888******************************************************99888877665544 PP

                   H CS
  adh_short_C2 191 e 191
                    
    AJA92871.1 201 D 201
                   3 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     3e-10   1.4e-06       4     164 ..       6     166 ..       4     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3e-10
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 ++tG   g+G e++  la++g  + + + R+ + ++   + i+++++  +   +v+++Dv + ++  +++++i +e+++i   ++ Ag    ++ e+++
  AJA92871.1   6 VVTGSSSGIGFETSLALAREGYVTYATM-RDVK-KA---DDIQRITDEeNLPLKVIELDVDNDESAGNAIDTIIQEKGRIDVLVNNAGWGIWGTGEDVS 99 
                 89*******************8776554.5523.33...34555555437899********************************************** PP

                 HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalaeyrr 164
                  e++++ ++  +  +  L + +++    +    +v +SS+ag +g +  ++Y +    l+++ e+ r
  AJA92871.1 100 IEEFREQFETNFFSIVRLIQKVAPtmrkQGSGDIVNISSVAGRIGFPVSTAYISSKFALEGFSESLR 166
                 *****999999988888877655545446667799******************99999999988766 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.5e-08   0.00015     106     282 ..      93     253 ..       2     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-08
     DUF1776 106 gpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphnidvtqikLGnldlan 204
                 g  e +++++++++++++++s + ++q+  p +++   q +  iv   s+   +  p +   +    al+ + e+L+ el+p +i+v+ i  G ++   
  AJA92871.1  93 GTGEDVSIEEFREQFETNFFSIVRLIQKVAPTMRK---QGSGDIVNISSVAGRIGFPVSTAYISSKFALEGFSESLRYELQPFGINVIIIEPGVIKTN- 187
                 444999****************************8...8888899999**********999999999***************************9983. PP

     DUF1776 205 gsqsnskiasvagsevlsWsesaralygpnyvsilskaisaksir.rgsslreLhnalfdllegsskkrvvyvGkgarl 282
                    + + + ++++++         + y+++ ++ +s    ++ +   g++ +e+ na++++++++ + + + vG  a++
  AJA92871.1 188 ---FFDSMRTAKKAD-------NDDTYKDITSKVISG---VEMMAeMGTPPKEVANAIINSIKEENPLPRYVVGNDAAM 253
                 ...333333333333.......233344433333332...222224789999999999999988888888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2069.05
//
Query:       AJA92872.1  [L=160]
Description: hypothetical protein T478_0370 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0081   16.1   1.4     0.0097   15.9   0.6    1.5  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
  ------ inclusion threshold ------
      0.094   11.5   0.3       0.11   11.2   0.3    1.1  1  DUF2207    Predicted membrane protein (DUF2207)
       0.17   11.9   0.0       0.23   11.5   0.0    1.2  1  GvpH       GvpH


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   1.6e-06    0.0097      69     121 ..      18      72 ..      12      78 .. 0.75
   2 ?   -3.2   0.0       1.3   7.6e+03      37      52 ..     127     142 ..     122     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
   RseC_MucC  69 lvYllPllllilgallgsall.gssellaalgallglvlgflivrllskr.lkkk 121
                 l Y++P++lli++ l+  + l +++ ++++++  ++lv  +++ r+++k  +++k
  AJA92872.1  18 LNYVVPIILLIFFGLVYAMSLrADNGFVSFILIGIALVTIVYWTRVIKKMvVTQK 72 
                 67******99987777666666888888888888888888888888877623444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
   RseC_MucC  37 ekrleveneigakvGd 52 
                 +k++++e ++++++Gd
  AJA92872.1 127 SKEVQIEGPKEMEIGD 142
                 6788888888899887 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   1.8e-05      0.11     384     434 ..      19      67 ..       4      87 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.8e-05
     DUF2207 384 salglgliilglilillallllvlllvfllilllillliaiivlllfsrll 434
                 ++  ++ iil+++++l+ +++l + + f +++l++++l+ i+++    + +
  AJA92872.1  19 NY--VVPIILLIFFGLVYAMSLRADNGFVSFILIGIALVTIVYWTRVIKKM 67 
                 33..33333333434444444444488888888888888888877665544 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.23     101     167 ..      94     158 ..      81     160 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
        GvpH 101 delvvvadlpGvtdedvdvaletdeqaltlrvdddvverlvlddp.dvaitdltlrnqvlelrlarse 167
                 +e v va++pG  d+   +a+   ++ l +r  +   + + ++ p ++ i d+  rn vl lr+  se
  AJA92872.1  94 NETVFVAEVPGPEDK---IAVRLIDGILYIRGSQGFSKEVQIEGPkEMEIGDFKYRNGVLTLRIRTSE 158
                 57899******8876...4555557******************99569***************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1103.65
//
Query:       AJA92873.1  [L=152]
Description: ribosomal protein L22 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-22   80.2   0.4    1.4e-22   79.8   0.4    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.17   11.8   0.0    1.5  1  RelB           RelB antitoxin
       0.18   11.7   2.9       0.83    9.5   2.9    2.0  1  HTH_ParB       HTH domain found in ParB protein


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.4   2.4e-26   1.4e-22       2     102 ..      20     149 ..      19     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 2.4e-26
                    EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST...........................THHHHHHHHHHHHHHHH..HT-GGGEEEEE CS
  Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk...........................aakfvlklLknaeanaelkgldvdslvIee 68 
                    ++++ ++s+k++re+a++I+g ++e+A +y+    +k++                            a ++lklL n e+nae+kg+d d+l I +
     AJA92873.1  20 SIREKKISHKHARETAKAIKGLTLEKARDYMLSviAKERaipfarfknqvghrsdpgmmsgrypekTAGEFLKLLDNLESNAEYKGMDMDRLKIIN 115
                    567889**************************99766669******************************************************** PP

                    EEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
  Ribosomal_L22  69 iqvnkgpklkrrtyrArGrinpirkspchievvl 102
                    +  +kg  +kr+ +rA+Gr++  +   +h+e+v 
     AJA92873.1 116 ATSHKGVAIKRFIPRAQGRATDKNDILTHVELVA 149
                    *******************************985 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.9e-05      0.17      23      47 ..      39      63 ..      18      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                CT--HHHHHHHHHHHHHHHTS-STT CS
        RelB 23 mGltiSqairlfLekiaktkalPfd 47
                 Glt  +a + +L  iak++a+Pf 
  AJA92873.1 39 KGLTLEKARDYMLSVIAKERAIPFA 63
                49*********************95 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.9   0.00014      0.83       2      39 ..      16      57 ..      15      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00014
    HTH_ParB  2 evqeavsegkiseGHAR....aLlslkdeelqlqlaekiiee 39
                 v+  ++e+kis +HAR    a+++l+ e+ +  ++  i++e
  AJA92873.1 16 HVRASIREKKISHKHARetakAIKGLTLEKARDYMLSVIAKE 57
                58999**********974444777777766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1134.76
//
Query:       AJA92874.1  [L=226]
Description: 4Fe-4S single cluster domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-15   56.9   3.0      5e-15   55.7   0.3    2.3  2  Fer4_14      4Fe-4S single cluster domain
    5.8e-12   46.0   0.9    1.5e-11   44.7   0.0    1.9  2  Fer4_12      4Fe-4S single cluster domain
    3.1e-11   43.9   0.0    5.5e-11   43.1   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.099   13.6   0.7      0.099   13.6   0.7    1.9  2  Lipocalin_4  Lipocalin-like domain


Domain annotation for each model (and alignments):
>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.3   1.1e-18     5e-15       1      92 [.      22     109 ..      22     132 .. 0.75
   2 ?    1.5   0.1     0.071   3.2e+02      71     101 ..     167     199 ..     156     212 .. 0.64

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.1e-18
     Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwletngtle 92 
                 +f+r+++Cnl+C++Cd+k tw+ +    q+e  +   ++  ++   + +i+ lv+tGGePL   ++++l +l++ lk  +    + +etn t+ 
  AJA92874.1  22 IFLRTAQCNLKCTWCDTKYTWDWKNYDFQKEVKE-MTIDevKDAILDLEIKHLVITGGEPL--LQQDDLADLLSFLKPDF---YVEVETNCTIL 109
                 79*****************999866555444333.23331233444666799*********..78***********9888...99999999986 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.071
     Fer4_14  71 vkrlkeey..pekkiwletngtleielektpdl 101
                 +k+ +++y  pe +++l t ++ + e+ + +++
  AJA92874.1 167 IKKFVTKYniPENRVQLMTQASTKEEISMKEKS 199
                 344444444599999***999999888754433 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   3.4e-15   1.5e-11       2      96 ..      11     109 ..      10     128 .. 0.78
   2 ?   -0.2   0.2      0.24   1.1e+03      18      51 ..     141     174 ..     131     211 .. 0.61

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.4e-15
     Fer4_12   2 nGeG.....vrlslfvsgCnlsCkgCfnketwsfk...sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwlyt 92 
                 +GeG       ++l+++ Cnl+C  C  k tw+ k    +ke+++ +++e+ + + + +i+ l+++GGEPll  ++++l++l+  +k  ++  + ++++
  AJA92874.1  11 QGEGpnfgkPAIFLRTAQCNLKCTWCDTKYTWDWKnydFQKEVKEMTIDEVKDAILDLEIKHLVITGGEPLL--QQDDLADLLSFLKPDFY--VEVETN 105
                 667654433347999*****************8774446677778888888888888999************..99999999999988888..456666 PP

     Fer4_12  93 gytl 96 
                  ++l
  AJA92874.1 106 CTIL 109
                 6665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
     Fer4_12  18 sCkgCfnketwsfksgkeftkelleeiiedlkke 51 
                 +C ++f+++  +f +    ++  + ei + + k+
  AJA92874.1 141 ECYYFFANQENCFFKYVVENESDIPEIKKFVTKY 174
                 6777776666655543333333334443333333 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.2e-14   5.5e-11       4      91 ..      26     110 ..      23     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.2e-14
                  ESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGH CS
                  xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   4 trgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpde 91 
                  t  Cnl+C++C++++t         + +++++++e+++ +  l     +k+++++ggepll+ d   +l+   k   p++ + vetn t + +
   AJA92874.1  26 TAQCNLKCTWCDTKYTwdwknYDFQKEVKEMTIDEVKDAILDLE----IKHLVITGGEPLLQQDDLADLLSFLK---PDFYVEVETNCTIL-P 110
                  778**************777777777777777777777777776....**************999777777777...8*********9998.3 PP

>> Lipocalin_4  Lipocalin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       0.6   2.7e+03      47      62 ..      32      46 ..      24      67 .. 0.63
   2 ?   13.6   0.7   2.2e-05     0.099       4      82 ..     120     200 ..     117     203 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.6
                 SS-----EEEEEEEET CS
  Lipocalin_4 47 scneskdesgtytisg 62
                 +c++  d+++t+  ++
   AJA92874.1 32 KCTWC-DTKYTWDWKN 46
                 56666.6666665554 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.2e-05
                  EEE--SS--...STT---E.....EEE-SS...S-EEE----..SS-----EEEEEEEETT..TTEEEET-S--EEEEEEEE CS
  Lipocalin_4   4 tWklteitydgepetldecekgsyitfnan.tttfesyttydggscneskdesgtytisgn..kltitvtdgesketeiiel 82 
                  +W+++  t++   ++l+ ce++  + f an ++ f +y  ++++++ e k+   +y+i +n  +l ++ + +e+ +++  ++
   AJA92874.1 120 QWNVSPKTQNS-GNPLELCENNECYYFFANqENCFFKYVVENESDIPEIKKFVTKYNIPENrvQLMTQASTKEEISMKEKSI 200
                  68888777522.33577777665555555546777788889999*****************554444445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1612.44
//
Query:       AJA92875.1  [L=109]
Description: PF04075 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-08   32.4   0.0    1.2e-07   31.9   0.0    1.3  1  F420H2_quin_red  F420H(2)-dependent quinone reductase
  ------ inclusion threshold ------
      0.015   15.5   0.1      0.016   15.3   0.1    1.1  1  DUF2255          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> F420H2_quin_red  F420H(2)-dependent quinone reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.3e-11   1.2e-07      26     102 ..      11      83 ..       2     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.3e-11
                      EEEEEE-TTT-SEEEEEEEEEEETTEEEEE-SGGGGSSS-HHHHHHHH--EEEEEETTEEEEEEEEE--HHHHHHHH CS
  F420H2_quin_red  26 llLtttGrktgkprktplgfvrdgdsylvvaskgGapkhpswylNlkanPrvevqvgakkldvtAreveddekarlw 102
                      ++L+t Grk+gk  k     v  +d     +       +++w+ N  a+P+v+v+  ++++++ Ar ve+de a+  
       AJA92875.1  11 AILKTKGRKSGKEHKVWAKAVTYNDMIYF-SRRN---PNSDWLKNAIAHPQVKVEFDGNEFSGLARLVEEDELAQKI 83 
                      79***********9988777777665554.4444...59******************************99988643 PP

>> DUF2255  Uncharacterized protein conserved in bacteria (DUF2255)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.8e-06     0.016      21      95 ..      19      91 ..       2     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-06
     DUF2255 21 tlrkpttiWv..VrvdddlyvrsanGraskWyraalaqkagriraggvekdVtfeeeadkelndkidaaYraKYary 95
                + +k  ++W+  V+ +d +y  s +  +s+W ++a+a+ + +++ +g e+      ++++el++ki +    KY + 
  AJA92875.1 19 KSGKEHKVWAkaVTYNDMIYF-SRRNPNSDWLKNAIAHPQVKVEFDGNEFSGLARLVEEDELAQKISN---LKYTEE 91
                677888888533777888886.77889***********************999999999999999987...666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 777.98
//
Query:       AJA92876.1  [L=155]
Description: redoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-26   91.1   0.3      6e-26   90.8   0.3    1.1  1  AhpC-TSA  AhpC/TSA family
    2.7e-13   49.9   0.3    3.4e-13   49.5   0.3    1.1  1  Redoxin   Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.8   0.3   6.7e-30     6e-26       2     123 ..       6     132 ..       5     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 6.7e-30
                 TSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHH.H....HHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHH CS
    AhpC-TSA   2 gdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCtt.e....lpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkv 94 
                 gd a dfel  +dg++++ls yk+ k vvl+fypk++ + C+  +    +++   +y+e+++ +  v+++svds++s+++f++++++++  lsD+++++
  AJA92876.1   6 GDTAEDFELLAHDGKPITLSSYKNsKNVVLCFYPKNHLFACPSkKvfemAKSVISVYPEITATDTVVFAISVDSVDSQADFVKEYEIPYVHLSDQKKTA 104
                 899*******************887****************8523222255666789****************************************** PP

                 HHHTT-EETTTTECSCEEEEE-TTSBEEE CS
    AhpC-TSA  95 akaygvlkeekglalratfvidkegkiry 123
                 +k+y   +  +gla r+tfvidk+g+i+ 
  AJA92876.1 105 CKKYAGTNI-TGLAKRSTFVIDKNGIIQD 132
                 ****99866.5****************96 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.3   3.8e-17   3.4e-13       1     131 [.       4     134 ..       4     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 3.8e-17
                 -TTSBB---ECCEETTCEEEEEHHHHTTSE.EEEEEESTTT-HHHHHTHH.....HHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-T CS
     Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkk.vvvnfvpgafcPtCsaehp.....yleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDg 93 
                 ++gd+a df+l  +a dg++++ls++k+ k vv+ f+p ++   C  + +      +  +++++ + +  v+a+++d+ + + +f+++++++++ lsD+
  AJA92876.1   4 QQGDTAEDFEL--LAHDGKPITLSSYKNSKnVVLCFYPKNHLFACPSKKVfemakSVISVYPEITATDTVVFAISVDSVDSQADFVKEYEIPYVHLSDQ 100
                 589*******8..79**********665554**********99998877666667888899*************************************8 PP

                 TSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEE CS
     Redoxin  94 saaftkalGlrleedaseglrtpryavidedgkvvyle 131
                 ++   k++  +    + +gl+ ++++vid++g +  + 
  AJA92876.1 101 KKTACKKYAGT----NITGLAKRSTFVIDKNGIIQDVM 134
                 88877777733....3456899***********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1167.10
//
Query:       AJA92877.1  [L=92]
Description: hypothetical protein T478_0077 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1532  (0.0854482); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 652.61
//
Query:       AJA92878.1  [L=424]
Description: putative glutamate dehydrogenase (NAD(P)(+)) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-64  218.0   0.6    2.4e-64  217.4   0.6    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.3e-47  160.9   0.0    2.4e-47  160.1   0.0    1.4  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.4   0.6   2.7e-68   2.4e-64       1     243 []     189     421 ..     189     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.4 bits;  conditional E-value: 2.7e-68
                    T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHS CS
  ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelkeerksvkeykkss 96 
                    GGsl+r+ aTglG++y+v+ ++k lk++ l+g++v+ +G+Gn   +a + l+++gak+++ sDs+G i+ p+G+++ +l+e+k++++sv  ++   
     AJA92878.1 189 GGSLARNVATGLGTAYCVRGAAKILKIN-LKGAKVVLQGFGNASTFAGEYLEKMGAKCIGASDSKGSIIVPNGFKVSKLIEHKQKKGSVVGFPG-- 281
                    9***************************.****************************************************************3.. PP

                    TSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT--- CS
  ELFV_dehydrog  97 ekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlsw 192
                        ++++ e +ll++k++il+P A++n+id++ ak +++  ++++ E+AN+pt +eA+ i+ +++++v+pd++aN+GGV +S+lE++qn+++++w
     AJA92878.1 282 ---SKKVSTE-QLLTTKCEILIPGALENQIDAKLAK-KLQ--CRIIGEAANGPTLPEADPIIYNKKIMVIPDILANSGGVCISYLEWVQNNMGYYW 370
                    ...3678886.9************************.777..****************************************************** PP

                    -HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHHCT CS
  ELFV_dehydrog 193 teeevdeklkkimkeifkavveeaeeykqelvkganiagfekvaeamkaqG 243
                    + +ev  k++++  +  k+ ++  ++yk +++ +a+++++++v+ea +++G
     AJA92878.1 371 SFDEVAGKMEANIVRGLKDTHDISKKYKIDMRRAAMVLAVQRVMEAFEHKG 421
                    **********************************************99988 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   0.0   2.6e-51   2.4e-47       1     129 [.      35     169 ..      35     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 2.6e-51
                      -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEE.ETT--HH....HHHHHHHHHHHHHHHTTSS-EEEEEEEES-GG..GS-HHHH CS
  ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRf.hpsvnld....evkaLaalmtyKnalvdlpfGGakggvkidpk..klseeel 87 
                      p++vl+v++pvk+dnG+++v++g+r+qh++ +gP+kGGiR+  p+   +    ev+aL+++mt+K+a+vd+p+GG+kg++ ++pk  klse el
       AJA92878.1  35 PNKVLRVKIPVKMDNGKIRVFTGFRSQHNNDRGPYKGGIRYfDPEGGVQymerEVMALSSWMTWKCAVVDVPLGGGKGAIFVNPKkdKLSEGEL 128
                      899*************************************9444444446667*******************************977799**** PP

                      HHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
  ELFV_dehydrog_N  88 eritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                      er+tr f+ ++  ++iGp++D+pApDv+t+ +em  ++d+++
       AJA92878.1 129 ERLTRGFAYKIG-EIIGPQKDIPAPDVYTTGKEMTQIMDTWS 169
                      ************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2998.71
//
Query:       AJA92879.1  [L=518]
Description: hypothetical protein T478_1365 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        0.1   13.1   6.3       0.42   11.1   1.9    3.0  2  DUF1374      Protein of unknown function (DUF1374)
        1.5    8.5   3.7        2.9    7.5   0.0    2.5  3  LD_cluster3  SLOG cluster3 family


Domain annotation for each model (and alignments):
>> DUF1374  Protein of unknown function (DUF1374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.022     2e+02      49      68 ..      82     101 ..      57     118 .. 0.77
   2 ?   11.1   1.9   4.7e-05      0.42      24      75 ..     168     219 ..     159     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.022
                 EECTTEEEEEEEEE-SSSEE CS
     DUF1374  49 vknnnilideyvYdenddii 68 
                  ++n+ l de+ Y ++ + i
  AJA92879.1  82 FNDNQLLLDEWFYTQDGNLI 101
                 35788899********9998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.7e-05
                 EEEEEEEEEH.HHHHHCC-S-SEEEEEECTTEEEEEEEEE-SSSEEEEEEEEE CS
     DUF1374  24 klkkelivse.nefeeligkpdssnsvknnnilideyvYdenddiikkLiieY 75 
                 +++ ++ v++ + ++e +g+ d  ++vk+    + +++Yd ++++  k+ + +
  AJA92879.1 168 EFEVQVSVTNvKYYQEKVGEKDAEFRVKSYYDKVSNFEYDSKENVA-KISFPF 219
                 444555555515689*************************999976.776655 PP

>> LD_cluster3  SLOG cluster3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.6     0.037   3.3e+02      49      85 ..     167     203 ..     161     216 .. 0.82
   2 ?    7.5   0.0   0.00032       2.9      53      99 ..     255     301 ..     243     307 .. 0.87
   3 ?   -3.0   0.0      0.55     5e+03      62      82 ..     376     396 ..     371     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.037
  LD_cluster3  49 vdyeeavklyqskffkdefpeeneefenvvyteavdk 85 
                  v++e +v +   k++++++ e  +ef+   y ++v++
   AJA92879.1 167 VEFEVQVSVTNVKYYQEKVGEKDAEFRVKSYYDKVSN 203
                  667778999999****************999999976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00032
  LD_cluster3  53 eavklyqskffkdefpeeneefenvvyteavdkdreksllamReeml 99 
                  + + l++s+ f d ++ee ++  + v+ ++  + +++ +++m eem 
   AJA92879.1 255 NGIELFKSSIFIDDYSEEDNRIVHFVLLPDHVRHIKNQMKKMGEEMP 301
                  5699*************999999999888888899999****99995 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.55
  LD_cluster3  62 ffkdefpeeneefenvvytea 82 
                  f +d+f++  ++f++ ++te+
   AJA92879.1 376 FSEDRFAKIGADFTDFTFTEE 396
                  668899999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3795.54
//
Query:       AJA92880.1  [L=151]
Description: WxcM-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-18   66.7   0.2      2e-18   66.4   0.2    1.0  1  FdtA      WxcM-like, C-terminal
     0.0056   16.4   0.0     0.0094   15.6   0.0    1.5  1  Cupin_2   Cupin domain


Domain annotation for each model (and alignments):
>> FdtA  WxcM-like, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.2   2.2e-22     2e-18      11     129 ..      19     143 ..       7     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.2e-22
                 EEET..TEEEEEEEBTTT..BSS--SEEEEEES--TTTEEEEEEESS--EEEEEEES-EEEEEE-SS-E.EEEEE-STT.EEEEE-TT-EEEEE---TT CS
        FdtA  11 ikde..rgnLsvieeeke..vpfeikrvyyvydvpegeerGeHahkkleqllialsGsvevllddgkkk.keilldsps.kglyipkmiWrelinfsed 103
                 + d+  +g+L+vi+++++  ++ ++k+vy+ +  p+ e++G H+hk+++  + +++G++ ++++d+  k +ei+++ ++   + ++++i +++in +e 
  AJA92880.1  19 VIDShiNGELTVIWRDWDniIEDHPKMVYVNSVNPK-EVKGPHLHKNRTTYFACIEGEIILVIKDSDGKfHEITVNPKKpSLVCVKNGIAAAIINPTEK 116
                 4343359**********9999*******98776665.56**************************999889*****99967778999********9999 PP

                 .-EEEEEESS---GGGEE--HHHHHHH CS
        FdtA 104 .avllvlasesydeedYirdyeeflkl 129
                  + +lvla+  ++++d   +  +f+++
  AJA92880.1 117 iSKVLVLADIAWKPNDNEMENVDFVNY 143
                 9***************88888888775 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-06    0.0094       4      37 ..      50      83 ..      47     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-06
                EEETTEEEEEECSSSEEEEEEEEESEEEEEECTE CS
     Cupin_2  4 elppGesapshrHpgedeffyVleGegeltvdge 37
                ++ p e+ ++h H++ + +f ++eGe+ l + + 
  AJA92880.1 50 SVNPKEVKGPHLHKNRTTYFACIEGEIILVIKDS 83
                57899*999*****************99986543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1070.30
//
Query:       AJA92881.1  [L=196]
Description: hypothetical protein T478_1296 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1368.75
//
Query:       AJA92882.1  [L=255]
Description: methionine biosynthesis protein MetW [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-18   65.3   0.0    7.9e-18   64.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      2e-17   63.5   0.0    2.9e-17   63.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-16   60.9   0.0    3.5e-16   59.7   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.3e-16   59.2   0.0      1e-15   58.3   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    6.7e-15   55.5   0.0    1.3e-14   54.6   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    7.8e-10   38.5   0.0    3.4e-09   36.5   0.0    2.0  2  MTS              Methyltransferase small domain
    8.7e-09   34.9   0.0    1.4e-08   34.1   0.0    1.2  1  DREV             DREV methyltransferase
    9.8e-09   34.9   0.0    2.8e-08   33.4   0.0    1.7  2  CMAS             Mycolic acid cyclopropane synthetase
    8.6e-08   31.5   0.0    1.5e-07   30.7   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
    1.3e-07   31.4   0.0    7.9e-07   28.9   0.0    1.9  1  MetW             Methionine biosynthesis protein MetW
    5.9e-06   26.0   0.0    9.1e-06   25.4   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    7.1e-06   25.6   0.0    1.1e-05   25.0   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    2.6e-05   23.8   0.1    4.8e-05   22.9   0.1    1.4  1  TehB             Tellurite resistance protein TehB
    0.00044   20.3   0.1    0.00073   19.5   0.1    1.4  1  Methyltransf_32  Methyltransferase domain
     0.0016   17.9   0.1     0.0044   16.4   0.1    1.6  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0041   16.5   0.0     0.0081   15.5   0.0    1.5  1  Methyltransf_2   O-methyltransferase domain
     0.0092   15.7   0.0      0.014   15.1   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.025   14.3   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.016   15.5   0.0      0.039   14.3   0.0    1.7  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
       0.03   14.4   0.0        1.5    8.9   0.0    2.1  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
      0.059   13.2   0.0       0.12   12.3   0.0    1.5  1  Methyltransf_8   Hypothetical methyltransferase
      0.079   12.1   0.0       0.12   11.5   0.0    1.2  1  N2227            N2227-like protein
      0.087   12.3   0.0       0.37   10.2   0.0    2.0  2  Methyltransf_4   Putative methyltransferase
      0.088   12.3   0.0         12    5.3   0.0    2.3  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.1e-20   7.9e-18       4     114 ..      40     140 ..      38     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.1e-20
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee.leklledekfDlilsnevlnaladpdkil 94 
                      g+++lD+GCGtG+l++ +a++   +++v GiD+s +aie A ++      +  n++ e+ d+ + ++      k+D+i+s ++l ++  p   l
       AJA92882.1  40 GKTILDVGCGTGKLAYMIAKK---GGKVKGIDYSTTAIETALSKY-----ShpNLSYEKVDVSKkIS-----GKYDVIISIGTLEHMDQPYTML 120
                      689****************55...67899**************53.....334999********777.....89******************** PP

  Methyltransf_31  95 eeiervlkpggilliedprl 114
                      ++ ++ lkp g +++++p++
       AJA92882.1 121 KKFKSHLKPRGKIILTSPNW 140
                      ******************92 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.0   3.9e-20   2.9e-17      21     157 ..      38     178 ..       6     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.9e-20
  Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqg...kfdlIvlrevlehvpdppellrqiatllkp 111
                       +g+ +Ld+GcGtG l+  ++++g +v g+D s  a+e a +++  ++ ++  ++ +++++   k+d+I+++ +leh++ p   l++++++lkp
       AJA92882.1  38 WTGKTILDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIETALSKYSHPNLSY--EKVDVSKKisgKYDVIISIGTLEHMDQPYTMLKKFKSHLKP 129
                      4667**********************************9965555555555..44444444555****************************** PP

  Methyltransf_23 112 gGylllseplaslkedrllldwlylvpag...rhi..sffsarslkellee 157
                       G ++l+ p  ++++ r +  +++++  +   ++   ++ +  ++ +++e+
       AJA92882.1 130 RGKIILTSP--NWANPRGFILMTLWALFDapiTLAdlHYLTPVDFIKWAEQ 178
                      *********..5889999888888877665553334466666777666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   4.6e-19   3.5e-16       1      97 []      43     131 ..      43     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 4.6e-19
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLk 94 
                      +Ld+GcGtG+l+ ++ak++  +kv g+D+s +++e+a +++  +++n+++++ d+++    +g++D+++s+g+l+h+++    ++lk+++++Lk
       AJA92882.1  43 ILDVGCGTGKLAYMIAKKG--GKVKGIDYSTTAIETALSKY--SHPNLSYEKVDVSKK--ISGKYDVIISIGTLEHMDQ--PYTMLKKFKSHLK 128
                      8*****************6..9*******************..5789********764..4689******999***995..559********** PP

                      EEE CS
  Methyltransf_25  95 pgG 97 
                      p G
       AJA92882.1 129 PRG 131
                      *98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.3e-18     1e-15       1      99 []      44     133 ..      44     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.3e-18
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L++GcGtG l+ ++++k  + ++ g+D+s+ aie a  k ++ + ++ ++v++ ++ ++      ++D+++++++l+h++++  +l++++++Lk
       AJA92882.1  44 LDVGCGTGKLAYMIAKK--GGKVKGIDYSTTAIETALSKYSHPN-LSYEKVDVSKKISG------KYDVIISIGTLEHMDQPYTMLKKFKSHLK 128
                      8****************..**************66666655544.46666666666544......***************************** PP

  Methyltransf_12  95 pgGrl 99 
                      p G++
       AJA92882.1 129 PRGKI 133
                      ***86 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.7e-17   1.3e-14       1      95 [.      44     134 ..      44     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.7e-17
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                      LdvGcGtG+la  +ak+g++v g+D+s++++++a +k+s ++  +++ + d++k    ++++D+++s  +l+h+++p   lk+++  Lkp G++
       AJA92882.1  44 LDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIETALSKYSHPN--LSYEKVDVSK--KISGKYDVIISIGTLEHMDQPYTMLKKFKSHLKPRGKI 133
                      8**************************************998..89*******8..5678********************************99 PP

                      E CS
  Methyltransf_11  95 v 95 
                      +
       AJA92882.1 134 I 134
                      8 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.4     1e+03     140     166 ..       4      30 ..       2      34 .. 0.88
   2 !   36.5   0.0   4.6e-12   3.4e-09      28     137 ..      36     135 ..      24     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.4
                 ETTSCHHHHHHHHHS--EEEEEESSEE CS
         MTS 140 nrklgyeslleelfgnvevvaktkkfk 166
                 n++++ +++ +++f++ + v +t++fk
  AJA92882.1   4 NQNIKLKKIYDKTFKKKNRVRETDEFK 30 
                 88899999999*********9999997 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 4.6e-12
                 HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHH CS
         MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagkatelavaeeliaeAk 126
                 ++ + +++lD+GcG+G l+ ++ak+  +  v+ +d ++ A+e a   +++ +l  ++ + dv ++++ +k+d+i+s      g+ ++ +   +++++ k
  AJA92882.1  36 DQWTGKTILDVGCGTGKLAYMIAKKGGK--VKGIDYSTTAIETALSKYSHPNL--SYEKVDVSKKIS-GKYDVIISI-----GTLEHMDQPYTMLKKFK 124
                 4447889*****************9999..9*************999999886..77789*******.******984.....44445556788999999 PP

                 HHEEEEEEEEE CS
         MTS 127 eaLkegGeLli 137
                 ++Lk+ G++++
  AJA92882.1 125 SHLKPRGKIIL 135
                 99999999876 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   1.9e-11   1.4e-08      75     187 ..      26     136 ..      21     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.9e-11
        DREV  75 eeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrd.rlkkkkynvlsale...lqetdvkldlilclnlldrcfdplk 169
                  + f+ +l+i+      +++ k++ld+G G G+++ ++a+   +v   + s+t ++  l+k  +  ls  +    ++   k+d+i ++  l+ +++p++
  AJA92882.1  26 TDEFKEVLKID------QWTGKTILDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIEtALSKYSHPNLSYEKvdvSKKISGKYDVIISIGTLEHMDQPYT 118
                 57899999999......5778***********************999999888664268888888887544224456788******************* PP

        DREV 170 lledirsalepngrviva 187
                 +l+  +s l+p+g++i++
  AJA92882.1 119 MLKKFKSHLKPRGKIILT 136
                 ***************985 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.8e-11   2.8e-08      56     166 ..      31     137 ..      13     146 .. 0.80
   2 ?   -1.8   0.0         2   1.5e+03     176     196 ..     218     240 ..     207     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.8e-11
                 TTTT--T..T-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHH CS
        CMAS  56 eklelkp..GmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkkl 152
                 e+l++++  G+t+Ld+GcG G+l+   +++ + kv g+  S+   ++a  +  + +l+  ++v+++  + +++k+d ++s+g +eh+ +    t  kk+
  AJA92882.1  31 EVLKIDQwtGKTILDVGCGTGKLAYMIAKK-GGKVKGIDYSTTAIETALSKYSHPNLSY-EKVDVS--KKISGKYDVIISIGTLEHMDQP--YTMLKKF 123
                 555555433**************9999988.************9999998888887653.345554..68****************9754..4678999 PP

                 HHHS-TT-EEEEEE CS
        CMAS 153 kkllkedGllllht 166
                 k+ lk+ G ++l +
  AJA92882.1 124 KSHLKPRGKIILTS 137
                 99999999988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                 HCTTCCC..HHHHHHTSTTS--- CS
        CMAS 176 aerglkl..kfidkeiFPgGelp 196
                 ++++++l  k+i++ + P  +l 
  AJA92882.1 218 KQQKIDLflKWINQRVVPITQLS 240
                 22333335599999999977765 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0     2e-10   1.5e-07     111     218 ..      35     136 ..      24     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2e-10
                     S.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES-GGG-S-HHHHHHH CS
  Methyltransf_9 111 lsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmGvlyhrrsPldhllq 204
                     + + +g+tildvGcg+G   + m++++   v Gid s+  +    a+ k++  +    ++ +     ++    +d++ s+G l h   P   l +
      AJA92882.1  35 IDQWTGKTILDVGCGTGKLAY-MIAKKGGKVKGIDYSTTAIE--TALSKYSHPNLSYEKVDV----SKKiSGKYDVIISIGTLEHMDQPYTMLKK 122
                     67789************8776.89999999*****9987554..688888877776666633....2332567********************** PP

                     HHCTEEEEEEEEEE CS
  Methyltransf_9 205 lkdqlvkgGelvle 218
                     +k +l+  G+++l 
      AJA92882.1 123 FKSHLKPRGKIILT 136
                     ************96 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.1e-09   7.9e-07      13     163 ..      39     184 ..      26     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.1e-09
        MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkevlde...llrigrraivs 108
                  g ++ld+GcG G+l +++++ k+ + +G++ +++++  +++k  +        d+++  + ++d+++   tl  + +p ++l++    l+   ++i++
  AJA92882.1  39 TGKTILDVGCGTGKLAYMIAK-KGGKVKGIDYSTTAIETALSKYSHPNLSYEKVDVSKKISGKYDVIISIGTLEHMDQPYTMLKKfksHLKPRGKIILT 136
                 4678*************9965.999******************999888888889999999*********************9862226888999**** PP

        MetW 109 fPnfGhWrvrlsllskGrmPvtdalPyeWydtpnihlltikdfvelceelnlkve 163
                  Pn+     r  +l++  +    + P+     +++h+lt  df++ +e+l+lk++
  AJA92882.1 137 SPNWANP--RGFILMT--LWALFDAPI---TLADLHYLTPVDFIKWAEQLELKLN 184
                 ***7643..4344421..222222333...3567788888888888887777766 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.2e-08   9.1e-06      42     153 ..      38     144 ..      16     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.2e-08
        NodS  42 gsiadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdlivvaevlyyiedvaelraavrnlvsllapdg 140
                  +   +l+vGc +G l+ ++a    ++  +d  + ai+ a  +  + +++s+ + dv + + + k+d+i+    l ++++     + ++ + s l+p g
  AJA92882.1  38 WTGKTILDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIETALSKYSH-PNLSYEKVDVSK-KISGKYDVIISIGTLEHMDQ---PYTMLKKFKSHLKPRG 131
                 344578***********************************99998.**********98.56789*****9988866655...55668999999***** PP

        NodS 141 qlvfGsardavcr 153
                 ++++ s+  a+ r
  AJA92882.1 132 KIILTSPNWANPR 144
                 ***9999877755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.4e-08   1.1e-05     161     258 ..      39     135 ..      29     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
        PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellkeekadvivaNILaevl...ielaedikklvkeggl 255
                 +g+++lDvG+G+G La   ak g  kv ++D+   A++ a +  +  +++  k++  +s+++ + +k+dvi++    e +     +++++k+++k+ g 
  AJA92882.1  39 TGKTILDVGCGTGKLAYMIAKKGG-KVKGIDYSTTAIETALSKYSHPNLSYeKVD--VSKKI-S-GKYDVIISIGTLEHMdqpYTMLKKFKSHLKPRGK 132
                 689***************999985.79*************999888777762554..45555.4.69*****966555552224688888999999998 PP

        PrmA 256 lil 258
                 +il
  AJA92882.1 133 IIL 135
                 886 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   6.4e-08   4.8e-05       9     110 ..      17     115 ..       7     138 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.4e-08
                 HHHHHT-----HHHHHHCCCS-.S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSG CS
        TehB   9 fskkynltathsevveavkivk.pgk.vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvvl 105
                 f kk n  +   e +e  ki +  gk +ld+gcg g+ +  ++ +g +v+ +d   ++i+   +  ++ n   +s + +d+   k++ +yd i+s   l
  AJA92882.1  17 F-KKKNRVRETDEFKEVLKIDQwTGKtILDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIETALSKYSHPN---LSYEKVDVS-KKISGKYDVIISIGTL 110
                 3.444555666778888887652355269************************98888776555555555...558899986.58**********8877 PP

                 GGS-G CS
        TehB 106 mflea 110
                   +++
  AJA92882.1 111 EHMDQ 115
                 66654 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   9.8e-07   0.00073      22      70 ..      36      80 ..       8     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.8e-07
  Methyltransf_32 22 kesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekr 70
                     ++ + +t++DvG+G g L+ ++a     ++ kv gid ++  +e+a   
       AJA92882.1 36 DQWTGKTILDVGCGTGKLAYMIAK----KGGKVKGIDYSTTAIETALSK 80
                     456789******************....59**********999998765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   5.8e-06    0.0044      46      94 ..      38      83 ..      24     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.8e-06
                     --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHH CS
  Ubie_methyltran 46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklke 94
                      +g+++lDv +Gtg la+ +++   + gkv+++D++ + ++++  k  +
       AJA92882.1 38 WTGKTILDVGCGTGKLAYMIAK---KGGKVKGIDYSTTAIETALSKYSH 83
                     5899*************99875...6789*******9999988777654 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05    0.0081      63     165 ..      40     136 ..       3     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                     -SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS---.--SEEEEESSGGGS-HHHHHHHHHHHHHH- CS
  Methyltransf_2  63 lkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslP.eaDaillkrvlhDwsdekcvklLkrvkkal 156
                      k+++DvG GtG la +i+++  ++k+i +     +e+A ++     ++++++ + d+  +++  + D+i+    l ++ d+   ++Lk+ k+ l
      AJA92882.1  40 GKTILDVGCGTGKLAYMIAKKGGKVKGIDYSTTA-IETALSK---YSHPNLSYEKVDVS-KKISgKYDVIISIGTL-EHMDQ-PYTMLKKFKSHL 127
                     3799************************998765.5666555...5889*********9.5665377877665555.56654.5789******** PP

                     -TT-EEEEE CS
  Methyltransf_2 157 pagGkvivv 165
                     ++ Gk+i+ 
      AJA92882.1 128 KPRGKIILT 136
                     *******96 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05     0.014      40      87 ..      42      88 ..      11     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                EEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGG CS
        TPMT 40 rvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvke 87
                 +l  +CG +  +  +A++g +v G++ s  A+e + +++  +p++++
  AJA92882.1 42 TILDVGCGTGKLAYMIAKKGGKVKGIDYSTTAIETALSKYS-HPNLSY 88
                556669*****************************866655.477544 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.4e-05     0.025      67     117 ..      31      80 ..      20     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                 HHTT--T..T-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
        PCMT  67 ellelkk..garvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                 e l++++  g+ +L+vG+G+G l+    ++ ++ g+v +i+++   +e+a  +
  AJA92882.1  31 EVLKIDQwtGKTILDVGCGTGKLAY---MIAKKGGKVKGIDYSTTAIETALSK 80 
                 566655333899*********9885...5556788899***999888777555 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.2e-05     0.039      60      88 ..      41      69 ..      29      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
  AdoMet_MTase 60 tsfvdvgcgngllvyvlaaegykgygidl 88
                  +++ dvgcg g l y++a +g k  gid 
    AJA92882.1 41 KTILDVGCGTGKLAYMIAKKGGKVKGIDY 69
                  5678*******************999996 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.002       1.5      12      90 ..      53     141 ..      49     148 .. 0.85
   2 ?    3.4   0.0     0.098        73      57     125 ..     169     244 ..     158     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                 HHHHHHHTT-EEEEEEEEESSSSSS.CEEEEEEEESS.-S...SS--TTSEEEEEES.......SH.HHHHHHGGGEEEEEEEEEECTCGT CS
         POR  12 lakaaaraGyyvqanreygseirGg.hsyshvrisdepiv...psievgeadllval.......da.etlsehldglkpggiiiynseelk 90 
                 la+++a++G +v++ +    +i  + + ysh ++s e +v   + i+ g++d+++         ++ ++l+++ ++lkp g ii+ s+ ++
  AJA92882.1  53 LAYMIAKKGGKVKGIDYSTTAIETAlSKYSHPNLSYE-KVdvsKKIS-GKYDVIISIgtlehmdQPyTMLKKFKSHLKPRGKIILTSPNWA 141
                 7889999999999999999999998677899999997.554667777.9**************87788999**************997765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.098
                 SEEEEEESSHHHHH....HHGGGEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHH...T-EEEEE-HHHHHHHCC CS
         POR  57 eadllvaldaetls....ehldglkpggiiiynseelkpdelkkakeeerelkerl...gvrvygvdatkiakeig 125
                 ++d++   ++ +l+    +  +    g  +i++ ++  p+++k+ k+  +++k  l    ++  +v++t++ +e g
  AJA92882.1 169 PVDFIKWAEQLELKlnwkTIEHSWGGGDKLIADLKQRLPKVFKDMKMNVKQQKIDLflkWINQRVVPITQLSEEGG 244
                 5666666666666544445555566678999999999999999999987777666699878888899999998744 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.12      38     104 ..       7      72 ..       1      94 [. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                     HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHC.TS-TTS-EEEES-TT-HHHHH--S-...EEEEESS-S CS
  Methyltransf_8  38 peafdlyhkgfrsqvkkWPenPldviirklk.kkkdnlvvadlGcGeakiaeavrek.ekvrsfdlvav 104
                      ++ ++y k f++   k  ++  d++ + lk  +   +++ d+GcG  k+a  + +k  kv+ +d  + 
      AJA92882.1   7 IKLKKIYDKTFKK---KNRVRETDEFKEVLKiDQWTGKTILDVGCGTGKLAYMIAKKgGKVKGIDYSTT 72 
                     5566778888875...44566778888888855557789************776554268999887655 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.12      59      89 ..      41      71 ..      21      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                -EEEEET-TT-HHHHHHHHTT-EEEEEE--H CS
       N2227 59 vkilvPGaGlGrlavelatkgyqvegnEfsy 89
                 +il  G+G+G+la+ +a+kg +v+g+++s 
  AJA92882.1 41 KTILDVGCGTGKLAYMIAKKGGKVKGIDYST 71
                568888*********************9986 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005      0.37       3      47 ..      41      83 ..      39      97 .. 0.86
   2 ?   -1.3   0.0       1.8   1.3e+03      98     116 ..     118     136 ..     116     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                    EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHH CS
  Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiea 47
                    +++l++GcG G++   +Akk  +++  Gi+ +++ ++++l+k  +
      AJA92882.1 41 KTILDVGCGTGKLAYMIAKKGGKVK--GIDYSTTAIETALSKYSH 83
                    5799****************99877..999999999999988754 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                     HHHHHHHHHEEEEEEEEEE CS
  Methyltransf_4  98 ellkelarvLkkgGvlela 116
                     ++lk++++ Lk++G + l 
      AJA92882.1 118 TMLKKFKSHLKPRGKIILT 136
                     57999*********99876 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.022        16      32      50 ..      40      58 ..      17      86 .. 0.72
   2 ?    5.3   0.0     0.016        12     122     173 ..      88     135 ..      70     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.022
                SEEEEEES-TTTHHHHHHH CS
        CheR 32 rvriwsagcssGeEpYslA 50
                  +i+ +gc++G+ +Y +A
  AJA92882.1 40 GKTILDVGCGTGKLAYMIA 58
                45799********888776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                 EEE--TTT-SGGG--EEEEEE-SSGGGC-CHHHHHHHHHHHCCEEEEEEEEE CS
        CheR 122 FeklnllekksvlgklDvifcrnvliYfdeetqekvlerfaeklkpgglLll 173
                 +ek ++ +  +++gk Dvi++   l  +d++   ++l++f ++lkp g ++l
  AJA92882.1  88 YEKVDVSK--KISGKYDVIISIGTLEHMDQPY--TMLKKFKSHLKPRGKIIL 135
                 55555555..999***************9985..79************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1763.29
//
Query:       AJA92883.1  [L=41]
Description: hypothetical protein T478_1356 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.034   14.2   0.1      0.049   13.7   0.1    1.4  1  Spectrin_like  Spectrin like domain


Domain annotation for each model (and alignments):
>> Spectrin_like  Spectrin like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.7e-06     0.049      18      38 ..      16      36 ..       7      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-06
  Spectrin_like 18 lamlktmkpeeyrqvlknLel 38
                   l+ +k m pe+y+++l++Lel
     AJA92883.1 16 LEEIKVMFPEDYKKILRDLEL 36
                   67899**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 308.46
//
Query:       AJA92884.1  [L=347]
Description: CorA-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-28   97.5   4.6    1.1e-27   97.1   4.6    1.0  1  CorA           CorA-like Mg2+ transporter protein
     0.0072   16.2   0.1       0.01   15.7   0.1    1.2  1  FA_desaturase  Fatty acid desaturase
  ------ inclusion threshold ------
      0.096   13.4   2.1       0.41   11.4   0.4    2.5  2  PMC2NT         PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   4.6   1.8e-31   1.1e-27       4     291 ..      36     326 ..      34     327 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.8e-31
        CorA   4 fvWldlssptee.eleeLaeelgldelaledlldseerprvedyddylllvlpsveldkseeeeeevplsillgdnflitvrrepleal.......dev 94 
                 ++W+++  ++   e  ++ e+l+++ +   + l s   +++ed +d+l++++p++++ ++  +++++   i++++++++t++++    +       + +
  AJA92884.1  36 LTWIECVVDDIVsETPKILEKLNINMDS--STLLSGYLTEYEDVGDTLGIMVPFIFTGENRTQTSPC--LIFVKKDLIVTIHDDYGGKItklynysNSL 130
                 68999988887669***********444..456677*********************9999999888..**************9944443556666777 PP

        CorA  95 ikrlk.deggkpkspgellyrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddklldded 190
                 +++l    +++ +  + ll+rllde+ +++f +l+++ e+ +++e  l  ++++++++  el++++r+l  +  a++++ +++ r+l+++d ++l+d+d
  AJA92884.1 131 MRKLPqTPENWAERQTMLLFRLLDEVSETNFSALRTIVERAEQIEIDLagSRQIHRDLSTELSNMKRSLLSFLNAVWATHDTV-RNLKYGDPDMLTDDD 228
                 777779888**************************************************************************.************999 PP

        CorA 191 key..lrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTvltaif.lPlTlitGiyGmNfkglPelewsygypfvlllglmallaill 286
                   +  ++ +l  l+r ++m+e++ e+++     +++ ++++l +++  LTv ++++ +P+T +++i+G     +P+le sy++++ +l++++al+ i++
  AJA92884.1 229 DILekFEVILATLDRQIQMAENVMEVISTGITVIQTESTNQLTKLIVWLTVAATAVlVPNT-LATIFG-----IPGLEFSYVWVIPVLIFATALSIIIT 321
                 6555588888888888888888888888888888888888888888888**999988**99.9***98.....89******777777888888888888 PP

        CorA 287 lfwfk 291
                 + w k
  AJA92884.1 322 FRWTK 326
                 88866 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.7e-06      0.01     129     180 ..     268     320 ..     209     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
  FA_desaturase 129 ksrrrkwrllawlllllawlglwlalllllglall.lwlvplllllfllalvl 180
                    ++  +  ++l++++ ++ +  +++ +++ +gl ++ +w++p+l+++++l+++ 
     AJA92884.1 268 NQLTKLIVWLTVAATAVLVPNTLATIFGIPGLEFSyVWVIPVLIFATALSIII 320
                    33333466777777777779999999999999999*************99984 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.18   1.1e+03      70      89 ..      44      63 ..      15      65 .. 0.75
   2 ?   11.4   0.4   6.8e-05      0.41      14      84 ..     177     249 ..     165     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.18
      PMC2NT 70 ksvvdvvDsllEkadtcLDe 89
                +++v    ++lEk ++++D 
  AJA92884.1 44 DDIVSETPKILEKLNINMDS 63
                55666666799999999996 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.8e-05
      PMC2NT  14 Dldfyrsldpefaksldeqserllslinsllklaaskseisas..sklededdveekfksvvdvvDsllEkad 84 
                 Dl+  r ++++++++l + ++ lls +n++   +++ ++ +    + l+d dd+ ekf+ +  ++D  +  a+
  AJA92884.1 177 DLAGSRQIHRDLSTELSNMKRSLLSFLNAVWATHDTVRNLKYGdpDMLTDDDDILEKFEVILATLDRQIQMAE 249
                 777889999*********************9999999999776999999*************99998666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2635.81
//
Query:       AJA92885.1  [L=85]
Description: hypothetical protein T478_0991 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0018   18.1   0.5     0.0023   17.8   0.5    1.2  1  Prok-RING_4   Prokaryotic RING finger family 4
     0.0019   18.0   2.0     0.0028   17.5   2.0    1.2  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.047   13.7   0.2      0.051   13.6   0.2    1.1  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.41   10.2   5.7       0.96    9.0   0.5    2.1  2  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5     5e-07    0.0023      20      39 ..      61      80 ..      47      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5e-07
  Prok-RING_4 20 vCkeCfdskdlssCPlCqrr 39
                 +C +C ++ +++ CP+C r+
   AJA92885.1 61 ICVKCGSKIENKKCPICDRK 80
                 9****************997 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.0   6.2e-07    0.0028      25      46 ..      61      80 ..      58      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.2e-07
                E-HHHHHHHHHTT-B-TTT--B CS
  zf-C3HC4_3 25 lCeeCaekllkrkkkCpiCrrp 46
                +C +C +k+  ++kkCpiC r+
  AJA92885.1 61 ICVKCGSKI--ENKKCPICDRK 80
                8********..9*******986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.1e-05     0.051      64      98 ..      53      83 ..      35      85 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
        HypA 64 ieevpvkvrCreCgkefeleekalrCpkCgsadve 98
                iee   +  C +Cg+++e +    +Cp C++++++
  AJA92885.1 53 IEESVGEGICVKCGSKIENK----KCPICDRKKFK 83
                78888999******999966....7*****98876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5   0.00021      0.96      18      31 ..      58      71 ..      51      73 .. 0.85
   2 ?    4.3   0.6    0.0065        29       2      10 ..      73      81 ..      72      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                  TCEEESSSSBEEEE CS
  TF_Zn_Ribbon 18 gelvCtdCGlVled 31
                  ge +C +CG+ +e+
    AJA92885.1 58 GEGICVKCGSKIEN 71
                  7889********96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0065
                  EETTTTCEE CS
  TF_Zn_Ribbon  2 kCPnCgstn 10
                  kCP+C  ++
    AJA92885.1 73 KCPICDRKK 81
                  8****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 619.91
//
Query:       AJA92886.1  [L=322]
Description: putative pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-97  323.9   3.1    5.3e-97  323.6   3.1    1.1  1  SOR_SNZ       SOR/SNZ family
    6.2e-07   29.0   3.6    1.5e-05   24.4   0.3    2.5  2  ThiG          Thiazole biosynthesis protein ThiG
      1e-06   28.4   0.4     0.0026   17.2   0.0    3.2  2  His_biosynth  Histidine biosynthesis protein
    0.00037   20.0   3.1      0.086   12.2   0.1    2.3  2  NMO           Nitronate monooxygenase
    0.00089   18.5   0.0      0.022   13.9   0.0    2.4  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0025   16.9   1.0        0.6    9.2   0.3    2.3  2  Dus           Dihydrouridine synthase (Dus)
     0.0069   15.6   2.3       0.11   11.7   0.0    3.0  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.015   14.7   0.4      0.025   14.0   0.4    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
       0.06   12.9   1.1        1.3    8.5   0.2    2.6  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.6   3.1  2.7e-100   5.3e-97       2     207 .]      29     238 ..      28     238 .. 0.98

  Alignments for each domain:
  == domain 1  score: 323.6 bits;  conditional E-value: 2.7e-100
                 THHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT-HHHHHHHHHTT-SEEEEET CS
     SOR_SNZ   2 lkvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGhfveaqilealgvdyiDese 100
                  ++k+g+a+mlk+Gv+mdv+++eqa+iaeeaGav+vm+l+++p+d+rk+ggvar++++++i+ei+++v+ipvmak+riGh+ ea++l++ +vd+iDese
  AJA92886.1  29 STLKRGFAHMLKNGVVMDVTTVEQAQIAEEAGAVSVMVLDKLPSDVRKAGGVARTASIRIIEEIMDHVTIPVMAKCRIGHMYEAKVLDETNVDMIDESE 127
                 578************************************************************************************************ PP

                 TS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHHHHHHHHHHTTS....-HHHHHHHHHHHHGGGHHHHHHH CS
     SOR_SNZ 101 vltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrkikeeirklksl....seeelvalakelkaplelvkeva 195
                 vltpade +hi k+++++pfv+Gar+l+ealrr++eGaamirtkGe+gtG+v+ea+ h++k++ee+r++ks+    ++++lv++a+++k++++lv+e+a
  AJA92886.1 128 VLTPADEYHHIWKWDYTTPFVNGARSLAEALRRVEEGAAMIRTKGEPGTGNVAEAIYHIKKVNEELRAIKSIydsdDKQDLVKMARDFKVSYDLVEETA 226
                 *********************************************************************99988888999******************* PP

                 HHTTS-S---T. CS
     SOR_SNZ 196 elgrlpvvnfaa 207
                 + grlpvvnfaa
  AJA92886.1 227 KIGRLPVVNFAA 238
                 **********98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.2    0.0066        13     137     192 ..      53     114 ..      21     133 .. 0.75
   2 !   24.4   0.3   7.7e-09   1.5e-05     175     224 ..     230     281 ..     216     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0066
                 HHHHHHTT-SEBEEB...SSSTTS----S-HHHHHHH...HHH-SS-BEEES---SHHHHHH CS
        ThiG 137 arrleevGcaavmPl...aapiGsglGllnkealkii...ieeakvPvivDAGigspsdaaq 192
                 a+  ee+G+ +vm l    + +  + G++ ++ ++ii   ++++++Pv+    ig+  +a  
  AJA92886.1  53 AQIAEEAGAVSVMVLdklPSDVRKAGGVARTASIRIIeeiMDHVTIPVMAKCRIGHMYEAKV 114
                 555689999999965222788999999998888777522267889****9999998887765 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 7.7e-09
                 SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
        ThiG 175 kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklav 224
                 ++Pv+  A  Gi +p daa  m lG+d++++ + + +a+d  + Ara+ la+
  AJA92886.1 230 RLPVVNFAagGIATPADAAYLMSLGCDGIFVGSGIFKAEDAQERARAVVLAT 281
                 56777543349************************************99986 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.015        29     146     203 ..      46     109 ..       9     124 .. 0.47
   2 !   17.2   0.0   1.3e-06    0.0026      59     132 ..     216     310 ..     206     321 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.015
                   EEEHHHHHHHHHHTT-SEEEEEE.....TTTT.TTSS---HHHHHHHHHHHSSEEEEESS--SH CS
  His_biosynth 146 gldavelakkleelgageilltd.....idrd.GtlsGpdleltkelaeavkipviasGGvgsl 203
                   ++++ve a+ +ee+ga ++++ d     + +  G+     + +++e+ ++v+ipv+a   +g++
    AJA92886.1  46 DVTTVEQAQIAEEAGAVSVMVLDklpsdVRKAgGVARTASIRIIEEIMDHVTIPVMAKCRIGHM 109
                   4555555555555554444332211111332213333344455555555555555555444444 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.3e-06
                   HHHHHHHHHHHHH-SSEE..EEESSSSSHHHHHHHHHCT-S...................EEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
  His_biosynth  59 eanldlveeiaeevfipv..qvGGGIrsledveelleagad...................kviigtaavknpelikelaekfgsqkivvaiDarr 132
                   ++ +dlvee+a+  ++pv     GGI +  d++ l+++g+d                    v+++t   ++p+ +k++ + + + +  +++D+++
    AJA92886.1 216 KVSYDLVEETAKIGRLPVvnFAAGGIATPADAAYLMSLGCDgifvgsgifkaedaqerarAVVLATTFWEEPDKVKDAQKMIDERQSLLGLDVKN 310
                   56677888888877777733467888888888888888855333334444444444444478888888888888888888888888888888887 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.5   0.00082       1.6     139     198 ..      43     102 ..      32     113 .. 0.75
   2 !   12.2   0.1   4.3e-05     0.086     182     232 ..     219     271 ..     206     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00082
         NMO 139 liptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                 +++ +++v++a+++e++Ga ++ v  +     +    v+ +  ++++++++d v iPv+A
  AJA92886.1  43 VVMDVTTVEQAQIAEEAGAVSVMVLDKLPSDVRKAGGVARTASIRIIEEIMDHVTIPVMA 102
                 556799************76555544443333332344446689***************9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.3e-05
         NMO 182 faLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                   Lv++ ++   +Pv+  AaGGi +  + a  ++lG  g+ +g+    +++++
  AJA92886.1 219 YDLVEETAKIGRLPVVnfAAGGIATPADAAYLMSLGCDGIFVGSGIFKAEDAQ 271
                 6788888888889**877**************************999888875 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.049        97      63      88 ..      42      67 ..      39     108 .. 0.87
   2 !   13.9   0.0   1.1e-05     0.022     190     253 ..     213     276 ..     206     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.049
                ESBSS--HHHHHHHHTTT.-SEEEEE CS
        IGPS 63 liredfdpaeiAkkyeeagAsaiSVL 88
                 + +d+  +e+A+  eeagA  + VL
  AJA92886.1 42 GVVMDVTTVEQAQIAEEAGAVSVMVL 67
                5778999************9999988 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.1e-05
                 TTTEE-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
        IGPS 190 ktlevdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                 ++++v+ + +ee ak  +  v+  a  Gi+t++d+  l + g +++ vG+ + ++ed+++  r+
  AJA92886.1 213 RDFKVSYDLVEETAKIGRLPVVNFAAGGIATPADAAYLMSLGCDGIFVGSGIFKAEDAQERARA 276
                 578888888888888777789999*********************************9988775 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.3    0.0003       0.6     139     208 ..      48     121 ..      44     216 .. 0.76
   2 !    6.6   0.0    0.0019       3.7     181     216 ..     230     264 ..     213     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0003
                 .HHHHHHHHHHCT-SEEEEESS....ECCCTT-C.G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--S CS
         Dus 139 nalelakiveaaGaqaltvHgR....traqnyeg.tadweaIkevkqavsipviaNGdIkdaedaqaileetGad 208
                 +++e a+i+e+aGa  ++v       +r+ +  + ta ++ I+e+ ++v+ipv+a   I ++ +a+ +l+et +d
  AJA92886.1  48 TTVEQAQIAEEAGAVSVMVLDKlpsdVRKAGGVArTASIRIIEEIMDHVTIPVMAKCRIGHMYEAK-VLDETNVD 121
                 578999999999999999988878776666666679999999999999999999988888888775.55665555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0019
                 H-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH CS
         Dus 181 avsipviaNGdIkdaedaqaileetGadgvmigrga 216
                 +++++ +a G+I ++ da   ++  G+dg+ +g g 
  AJA92886.1 230 RLPVVNFAAGGIATPADAAYLMSL-GCDGIFVGSGI 264
                 456777899*********999998.********886 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.7     0.061   1.2e+02     124     157 ..      74     110 ..      25     138 .. 0.56
   2 !   11.7   0.0   5.3e-05      0.11     135     182 ..     220     270 ..     206     278 .. 0.73
   3 ?   -1.4   0.0      0.55   1.1e+03      61     103 ..     270     312 ..     265     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.061
                 STTS-...SS--HHHHHHHHHT.T--EEEES---SHH CS
        NanE 124 tkeeek..aepDfalvkalsea.glkviaeGrintPe 157
                 + ++        +++++++++   + v+a  ri    
  AJA92886.1  74 VRKAGGvaRTASIRIIEEIMDHvTIPVMAKCRIGHMY 110
                 3333223233444444444433134455555555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.3e-05
                 HHHHHHHHTT--...EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHH CS
        NanE 135 alvkalseaglk...viaeGrintPekakkaieiGvdavvvGsaitrleei 182
                 +lv++  + g       a G i tP+ a+  + +G d + vGs i + e+ 
  AJA92886.1 220 DLVEETAKIGRLpvvNFAAGGIATPADAAYLMSLGCDGIFVGSGIFKAEDA 270
                 4454444443222224699*************************9988765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.55
                 HTTT-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHH CS
        NanE  61 aaagadiialDatdrerpvtieelikkikekyqllmaDistle 103
                 a++ a  + l +t+ e p ++++  k i e+  ll  D+ +le
  AJA92886.1 270 AQERARAVVLATTFWEEPDKVKDAQKMIDERQSLLGLDVKNLE 312
                 5566667778888889999999999999999999988888877 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   1.3e-05     0.025      39     172 ..      46     179 ..      37     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                   EEEE--HHHHHHHHHH....HHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHH CS
  Phos_pyr_kin  39 evhplpaelveaqlea....vledvkvdavKiGmlasaeiievvaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEae 131
                   +v++++++ +++ + a    vl+ ++ d+ K G +a+++ i+++ e +++     V  PVm+     ++ e+++++  + +++ +++v+tP  +E+ 
    AJA92886.1  46 DVTTVEQAQIAEEAGAvsvmVLDKLPSDVRKAGGVARTASIRIIEEIMDH-----VTIPVMAKCRIGHMYEAKVLDETNVDMIDESEVLTP-ADEYH 136
                   5555666555555443111178999**********************999.....888999999999999999999999999*********.69*** PP

                   HHHT---S..SHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEE CS
  Phos_pyr_kin 132 aLlgekik..teedmkeaakkllklgakaVlikGghlegeeav 172
                   ++ + + +   ++ +++ a++l+++   a +i+ +  +g+ +v
    AJA92886.1 137 HIWKWDYTtpFVNGARSLAEALRRVEEGAAMIRTKGEPGTGNV 179
                   **99666622567999999999998888888866554444433 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.3   2.7e+03       8      29 ..      46      67 ..      35      98 .. 0.59
   2 ?    8.5   0.2   0.00066       1.3     196     224 ..     248     276 ..     151     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                -SSSHHHHHHHHHHHGG.GSSEE CS
   OMPdecase  8 Dvatarelleladkvgp.sivvl 29
                Dv+t  e  ++a+++g+ s++vl
  AJA92886.1 46 DVTTV-EQAQIAEEAGAvSVMVL 67
                55544.33355555555444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00066
                 HHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
   OMPdecase 196 kligiagadiiivGRgIlkagdpveeaer 224
                 +     g+d i vG gI+ka+d +e a++
  AJA92886.1 248 AYLMSLGCDGIFVGSGIFKAEDAQERARA 276
                 44444689999999999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2194.09
//
Query:       AJA92887.1  [L=193]
Description: dTMP kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-34  119.9   0.1    1.1e-34  119.7   0.1    1.0  1  Thymidylate_kin  Thymidylate kinase
     0.0033   16.2   4.3       0.53    8.9   0.7    2.5  3  HPHLAWLY         Domain of unknown function


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.1   1.3e-38   1.1e-34       1     185 []       5     183 ..       5     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 1.3e-38
                      EEESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHH CS
  Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRylfSsl 93 
                      +EG D aGK tq+++l ++l+++++k  ++++++ +t+iG+ i+++l  ++++  q ++ l+aa+r ++ ++ +++a +++ +vi+ Ry  S+l
       AJA92887.1   5 FEGGDQAGKKTQSAMLQRKLRSAKLKvKLFSFPDYTTPIGKEIDRYLHGKRKYPAQVIHCLLAANR-WERANDVIKAHEKNSVVIMNRYRESNL 97 
                      8*************************99**************************************.88887788889999************* PP

                      HHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
  Thymidylate_kin  94 aYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                      +Y   ++g+ ld++ +l e ++ k dl++ ldv+ +++ +R ++++    + e++++f +k+ ++y +lak ++ ++i++as+s+++vh+++
       AJA92887.1  98 VYGI-TNGLKLDWLEKLDEGLP-KSDLVIVLDVPQKESFARKKQNRD---KFEKNKEFSNKISQGYRKLAK-KKGWKIVNASQSKNDVHSDV 183
                      **77.6669***********99.******************999998...7889999*************7.9****************975 PP

>> HPHLAWLY  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   9.1e-05      0.81     245     281 ..       1      38 [.       1      60 [. 0.81
   2 !    8.9   0.7     6e-05      0.53     207     236 ..      78     107 ..      63     154 .. 0.84
   3 ?   -1.6   0.8     0.086   7.7e+02     196     578 ..     136     173 ..     110     183 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 9.1e-05
    HPHLAWLY 245 mLvvhekreqy.rkmqaqmlgaklripsskvkvlsfae 281
                 m++ +e  +q  +k q+ ml+ klr    kvk++sf +
  AJA92887.1   1 MIITFEGGDQAgKKTQSAMLQRKLRSAKLKVKLFSFPD 38 
                 667777776653899********************976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 6e-05
    HPHLAWLY 207 gkyfekksgapkkrvprgkLlYGltntlkL 236
                  k  ek+s    +r +   L+YG+tn lkL
  AJA92887.1  78 IKAHEKNSVVIMNRYRESNLVYGITNGLKL 107
                 4789*************************9 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.086
    HPHLAWLY 196 lkknqvenlkkgkyfekksgapkkrvprgkLlYGltntlkLRLkqtnPdmLvvhekreqyrkmqaqmlgaklripsskvkvlsfaeqsqkphqLpkdky 294
                  kk+  ++++k                                                                                        
  AJA92887.1 136 RKKQNRDKFEK---------------------------------------------------------------------------------------- 146
                 22322333333........................................................................................ PP

    HPHLAWLY 295 lesdasfaensdtskqisvvldessttketklkeatekktvdvkenrtsngsleeivspansivpekltqtnilegkvevkvqspevfqqdavvDrivv 393
                                                                                                                    
  AJA92887.1   - ---------------------------------------------------------------------------------------------------   -
                 ................................................................................................... PP

    HPHLAWLY 394 dkeiddkqvkttdndiltadisenkpsknscsesiselkysddftspcyseDfcttedtsrslqahdsspeaenpkssqytskssetrlsirknsseks 492
                                                                                                                    
  AJA92887.1   - ---------------------------------------------------------------------------------------------------   -
                 ................................................................................................... PP

    HPHLAWLY 493 silsPPfsaGsPvhsykrshisktqdksleeassistsDlsssqwteekenqiDqnsmhnskvikrgqdisvklktrtgcksleks 578
                                                                            n++ +++ ++   kl  + g+k ++ s
  AJA92887.1 147 -----------------------------------------------------------NKEFSNKISQGYRKLAKKKGWKIVNAS 173
                 ...........................................................333333333333444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1373.18
//
Query:       AJA92888.1  [L=464]
Description: replication factor A domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-10   40.2   0.1      0.026   14.5   0.0    3.4  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
    9.2e-06   25.5   0.1       0.04   13.6   0.0    2.4  2  CDC24_OB3        Cell division control protein 24, OB domain 
     0.0015   18.4   0.0        1.6    8.6   0.0    2.8  3  POT1PC           ssDNA-binding domain of telomere protection 


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.4e-06     0.026       1      68 [.      76     153 ..      76     162 .. 0.87
   2 !    8.1   0.0   0.00045       2.7      13      76 .]     210     274 ..     198     274 .. 0.87
   3 !   13.8   0.0   7.4e-06     0.044      17      57 ..     401     440 ..     377     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-06
                      EEEEEEEEEEE........EEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEE CS
  tRNA_anti-codon   1 VtvaGrvtsis........drsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvt.Grvkrrpggelel 68 
                      Vt++ rv +is        d+s+ ++ +i++ D+  +  v l++ ++    +e+lk+Gd++++   +vk++ +g +++
       AJA92888.1  76 VTLESRVLNISptkqftkkDGSSFSLRTITVYDNNSTASVKLWDeKANLPGLEELKPGDLIKIIkAYVKSDLTGAPTI 153
                      7899999999999999988888889999****************6666777999*********99**99986665555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00045
                      EEETTEEEEEEEETT.EEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEEE CS
  tRNA_anti-codon  13 rsggkvifidlrDgt.griqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveeiell 76 
                      ++ +k++ + l+ +    ++vvl+ ++ + l + +  +  v+ +G  +++  + le++ ++ +++
       AJA92888.1 210 GQPSKALKFRLKGENkNLVNVVLWGKDESILPKVIGQDAKVKLFGVRTKTGMQGLEIHGNDATII 274
                      777899999999999889*******88888888899********9999996555******99986 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7.4e-06
                      TEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEE CS
  tRNA_anti-codon  17 kvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGr 57 
                       ++ + ++D++g++ +  +r ++ +l+++ + Gd++ + G 
       AJA92888.1 401 QLSEMFVEDDSGQVWIKGWR-QQADLMDSYTLGDIITILGV 440
                      4556669*************.*****************995 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00012      0.73       1      71 [.      68     142 ..      68     188 .. 0.76
   2 !   13.6   0.0   6.7e-06      0.04      22      70 ..     392     440 ..     368     449 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
   CDC24_OB3   1 DLrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfk.rlrvGhlvllsgLa 71 
                 DL   + +vtL  rv +i     f   ++++  +   + +++ D++++  + lw+e ++l    +l++G+l+ + + +
  AJA92888.1  68 DLYIGAKEVTLESRVLNIsptkqF---TKKDgSSFSLRTITVYDNNSTASVKLWDEKANLPGLeELKPGDLIKIIKAY 142
                 566667789*********774443...333345688889*****************9998776789999999775544 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.7e-06
   CDC24_OB3  22 knsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgL 70 
                 +++++ ++++ + + +eD++G++++  w++ + l ++   +G+++ + g+
  AJA92888.1 392 IQTKSgENIQLSEMFVEDDSGQVWIKGWRQQADLMDS-YTLGDIITILGV 440
                 45555579999*************************9.*****9998776 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00026       1.6      75     109 ..     109     144 ..      74     190 .. 0.80
   2 !    6.8   0.0   0.00095       5.7      75     122 ..     224     267 ..     198     294 .. 0.83
   3 ?   -2.8   0.0      0.85   5.1e+03      84     117 ..     419     450 ..     411     455 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                 BS-EEEEEE-HHHHHHHTTT.--TT-EEEEEEEEEE CS
      POT1PC  75 gkltlqitlydehaefaren.lkpgdfvrLrNvhik 109
                 ++ t+ + l+de a++   + lkpgd++++    +k
  AJA92888.1 109 NNSTASVKLWDEKANLPGLEeLKPGDLIKIIKAYVK 144
                 348999********9996555********9876666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00095
                 BS-EEEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EEEEE- CS
      POT1PC  75 gkltlqitlydehaefarenlkpgdfvrLrNvhiklgrkgsklegflh 122
                 +k +++++l+++  +++++++ +++ v+L  v++k g +g    + +h
  AJA92888.1 224 NKNLVNVVLWGKDESILPKVIGQDAKVKLFGVRTKTGMQG----LEIH 267
                 45689******************************99987....3334 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.85
                 -HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-E CS
      POT1PC  84 ydehaefarenlkpgdfvrLrNvhiklgrkgskl 117
                 + ++a+++ +  + gd++++  v+++ g +g kl
  AJA92888.1 419 WRQQADLMDS-YTLGDIITILGVNARPGLEG-KL 450
                 6677888888.8999****999999877666.45 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3199.24
//
Query:       AJA92889.1  [L=161]
Description: transcriptional regulator, PadR family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-11   42.8   0.0    7.1e-11   41.9   0.0    1.5  1  PadR          Transcriptional regulator PadR-like family
    0.00016   21.6   0.7    0.00042   20.2   0.1    2.0  2  HTH_45        Winged helix-turn-helix
    0.00053   20.1   0.1     0.0048   17.0   0.0    2.3  2  Mrr_N         Mrr N-terminal domain
    0.00076   18.7   2.0     0.0012   18.1   2.0    1.3  1  Hemocyanin_M  Hemocyanin, copper containing domain
     0.0022   18.6   0.7       0.03   15.0   0.0    2.3  2  RTP           Replication terminator protein
  ------ inclusion threshold ------
       0.03   14.1   1.1      0.071   12.9   0.1    2.0  2  DUF4364       Domain of unknown function (DUF4364)
      0.032   13.9   0.0      0.039   13.7   0.0    1.2  1  AphA_like     Putative AphA-like transcriptional regulator


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   2.8e-14   7.1e-11       1      73 [.      22      86 ..      22      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.8e-14
                HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
        PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                iL+ l+eqp  G eii+   e s g +++s+G +Yp+L rL +egl+e++++ +        Y++Td G++ l
  AJA92889.1 22 ILQQLKEQPHTGKEIIDSAIEASAGNWKPSPGLIYPLLGRLLDEGLIEESENGK--------YQITDHGKTIL 86
                8999*************999999999***********************98875........*******9866 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.6e-07   0.00042      40      73 ..      59      93 ..      54      97 .. 0.86
   2 ?   -1.4   0.1      0.94   2.4e+03      36      43 ..     140     147 ..     115     160 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.6e-07
      HTH_45 40 LdmLvekglikk.skekYvlTekGlelleklkele 73
                L  L+++gli++ +++kY++T+ G+ +l +l++ +
  AJA92889.1 59 LGRLLDEGLIEEsENGKYQITDHGKTILTDLEHWK 93
                7789******765899*************999765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.94
      HTH_45  36 lnkYLdmL 43 
                 ++kY ++L
  AJA92889.1 140 IEKYKKFL 147
                 34444444 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.33   8.5e+02       8      29 ..      22      42 ..      19      47 .. 0.77
   2 !   17.0   0.0   1.9e-06    0.0048      61      86 ..      62      87 ..      59      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.33
       Mrr_N  8 lLealadgsehrlkeirervae 29
                +L+ l+++  +  kei++ ++e
  AJA92889.1 22 ILQQLKEQPHTG-KEIIDSAIE 42
                778888777776.999998877 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.9e-06
       Mrr_N 61 LkkagllespkrgvwkiTekGrevlk 86
                L  +gl+e++++g+++iT+ G+++l 
  AJA92889.1 62 LLDEGLIEESENGKYQITDHGKTILT 87
                5578******************9985 PP

>> Hemocyanin_M  Hemocyanin, copper containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.0   4.7e-07    0.0012     154     239 ..      75     159 ..      65     161 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.7e-07
                   TEETTSGGGHHHHHHHHHHHHHHHHHHHHSEE.EETTCEEETTSCHHHHHHHHHHHT-GGSB--TTS--HHHHHHHHHCT----SB CS
  Hemocyanin_M 154 yyeletegnyeklekvedlekrirdaidsgyvltadgkkidLrkpegieilgnilegnvdsidkkfygslevlarkllgdaeepdd 239
                   +y++ t++ +  l+++e++++  ++  d+ + l++ gk++ ++  e + ilgn+l +n+ ++ ++  ++++ + ++ l +++e+d+
    AJA92889.1  75 KYQI-TDHGKTILTDLEHWKMDAQKQMDTMMRLMNMGKFMGMDMLERVTILGNLLSSNASQMTNHEIEKYKKFLQDELEKIKEMDS 159
                   6788.7888899****************************************************9999999998888887777665 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05      0.03       7      75 ..      15      83 ..      12     112 .. 0.75
   2 ?    1.3   0.4       0.2   5.2e+02      86     106 ..     137     157 ..     126     161 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                HHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEB.TSSSSSE CS
         RTP  7 rAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelk.ekaklqe 75
                r F + y+++ ++++++ g +++d+  +      +kP++  iy  l  l+++g+++  ++ k + +++ +
  AJA92889.1 15 RGFSRYYILQQLKEQPHTGKEIIDSAIE-ASAGNWKPSPGLIYPLLGRLLDEGLIEESENGKyQITDHGK 83
                6799********************9755.45666*********************998877733333333 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                 HHHHHHHHHHHHHHHHHHHHH CS
         RTP  86 kekaklykkqvkidldrckkl 106
                 + +++ ykk ++ +l++ k++
  AJA92889.1 137 NHEIEKYKKFLQDELEKIKEM 157
                 578899999999999998876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.8e-05     0.071      39      74 ..      58      90 ..      20     100 .. 0.84
   2 ?   -0.7   0.2      0.41     1e+03      75      97 ..     133     155 ..     119     160 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
     DUF4364 39 alseLvesglieeeekenktlykiTekGketlelfe 74
                 l  L+++gliee   +++  y+iT+ Gk +l  +e
  AJA92889.1 58 LLGRLLDEGLIEE---SENGKYQITDHGKTILTDLE 90
                5789********8...899***********998765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.41
     DUF4364  75 nripksirekideylkenkeelk 97 
                 +++ ++  ek +++l+++ e++k
  AJA92889.1 133 SQMTNHEIEKYKKFLQDELEKIK 155
                 33333444444444444444444 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.039       7     117 ..      13     119 ..       8     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
   AphA_like   7 tpkeavrLvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLveavdGeGmednalLaiteaGrrelqaLltanlrapl..sdlsk 103
                 +p+   r  +L  ++ +p + +e+ ++        + Ps  L++  l  l+ eGL+e        +n +  it+ G+  l++L   ++ a     ++ +
  AJA92889.1  13 VPRGFSRYYILQQLKEQPHTGKEIIDSAIEASAGNWKPSPGLIYPLLGRLLDEGLIEES------ENGKYQITDHGKTILTDLEHWKMDAQKqmDTMMR 105
                 67888889999999**********99999999999**********************98......7999**************9999888741134777 PP

   AphA_like 104 lviaLklrfLdLle 117
                 l    k+  +d+le
  AJA92889.1 106 LMNMGKFMGMDMLE 119
                 77777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1345  (0.0750181); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1216.53
//
Query:       AJA92890.1  [L=327]
Description: multicopper oxidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-16   58.2   0.1    1.5e-07   31.8   0.0    2.3  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    1.1e-12   48.0   0.4    1.9e-05   24.7   0.0    2.6  2  Cu-oxidase_3  Multicopper oxidase
    4.8e-10   39.5   0.0    0.00095   19.2   0.0    2.4  2  Cupredoxin_1  Cupredoxin-like domain
    1.1e-07   31.5   1.4      0.015   14.8   0.1    3.1  2  SoxE          Sulfocyanin (SoxE) domain
    6.1e-07   29.3   0.0      0.012   15.3   0.0    2.6  2  Cu-oxidase_2  Multicopper oxidase
    5.1e-05   23.2   0.0       0.15   12.1   0.0    2.5  2  Cu_bind_like  Plastocyanin-like domain
  ------ inclusion threshold ------
      0.058   13.4   0.1         12    6.1   0.0    2.4  2  CHU_C         C-terminal domain of CHU protein family
       0.22   11.8   0.0         14    6.0   0.0    2.5  3  DUF5599       Domain of unknown function (DUF5599)
       0.86   10.7   7.7        2.5    9.3   0.5    3.0  2  PPC           Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.4e-08   2.8e-05      63      98 ..     155     194 ..     105     195 .. 0.69
   2 !   31.8   0.0   7.5e-11   1.5e-07      17      99 .]     239     327 .]     237     327 .] 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                  EBSTTEEEEEEEE..SSEEEEEEET.T.TTTTTSEEEEEE CS
  Copper-bind  63 liggGekdsvtfd..eagtYkffCs.P.HaaagMkgkvtv 98 
                     +Ge+   +f   e+gtY ++C+ P H+++gM+g+++v
   AJA92890.1 155 PLKPGESGVSEFIptEPGTYYYICTvPgHRMQGMVGEIVV 194
                  356899999999777999********************98 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 7.5e-11
                  SEEEEETTEEEE..EEEE..SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEET.T.TTTTTSEEEEEEE CS
  Copper-bind  17 keitvkkgekvt..fvnl..avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffCs.P.HaaagMkgkvtve 99 
                   ei+v++g+++t  +vn      +  vv + d   + v ++++ a   t+   +Ge+ svtf   ++gtY ++C+ P Ha +gM+g+ +ve
   AJA92890.1 239 PEIRVNSGDEITvtTVNAgkSFHAFGVVSNPDDFTSVVFDSEIAAA--TNPLKPGESGSVTFLagAPGTYYYICTvPgHALQGMQGTFIVE 327
                  6899****97651155555444455688888999888888888885..66789*********999999*******************9986 PP

>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   9.3e-09   1.9e-05      26     115 ..     106     195 ..      92     198 .. 0.85
   2 !   20.6   0.1   1.7e-07   0.00034      26     115 ..     238     327 .]     233     327 .] 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 9.3e-09
                   S-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG........GSCS.GGG-B-TT-EEEEEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE CS
  Cu-oxidase_3  26 gptievregdtvvvnvtNkldentsihwhGlqqrktswmD...Gvpgv.tqcpiqpgesftyrftvkqqagtlwYhshlslqqaaGlaGaiiie 115
                    pti+++ gd+++ +v+N    + s h  G+  +++ ++    G +    + p++pges + +f  ++  gt++Y   + +++++G++G i++ 
    AJA92890.1 106 NPTINANVGDKIIFDVVND---GKSFHAFGVTKDTEGFSNlipGSEVAsMNEPLKPGESGVSEFIPTE-PGTYYYICTVPGHRMQGMVGEIVVT 195
                   7****************96...668888888888877665222555441578****************.***********************97 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.7e-07
                   S-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-....GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE CS
  Cu-oxidase_3  26 gptievregdtvvvnvtNkldentsihwhGlqqr....ktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlslqqaaGlaGaiiie 115
                    p+i+v++gd+++v+ +N+     s h  G+  +    ++++ D     +++p++pges + +f +    gt++Y   + ++  +G+ G++i+e
    AJA92890.1 238 NPEIRVNSGDEITVTTVNAG---KSFHAFGVVSNpddfTSVVFDSEIAAATNPLKPGESGSVTFLAGA-PGTYYYICTVPGHALQGMQGTFIVE 327
                   69**************9985...46666666554111145678999999*****************99.*************99********96 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0028      36     102 ..     108     189 ..     104     194 .. 0.86
   2 !   19.2   0.0   4.8e-07   0.00095      36     104 .]     240     326 ..     233     326 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
  Cupredoxin_1  36 kievkagekvklkiknkdktpeefesed..............lgeekvlapgktttitiaplkpGeYeftcdmhmd.akGkl 102
                   +i+++ g k+ + ++n++k+ + f +++               + ++ l+pg++ + ++ p +pG+Y ++c      ++G++
    AJA92890.1 108 TINANVGDKIIFDVVNDGKSFHAFGVTKdtegfsnlipgsevASMNEPLKPGESGVSEFIPTEPGTYYYICTVPGHrMQGMV 189
                   68889999999999999999999999999999999999999878899*************************7765566543 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.8e-07
  Cupredoxin_1  36 kievkagekvklkiknkdkt..............peefesedlgeekvlapgktttitiaplkpGeYeftcdmhm...d.akGkliV 104
                   +i v++g +++++ +n +k+              ++ f se       l+pg++ ++t+ +  pG+Y ++c       + ++G++iV
    AJA92890.1 240 EIRVNSGDEITVTTVNAGKSfhafgvvsnpddftSVVFDSEIAAATNPLKPGESGSVTFLAGAPGTYYYICTVPGhalQgMQGTFIV 326
                   456666666666666666665555555443332235555555888899***********************9666445668888887 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   7.4e-06     0.015     101     140 ..     157     196 ..     109     203 .. 0.83
   2 !   14.4   0.1   9.7e-06     0.019      95     138 ..     283     326 ..     233     327 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-06
        SoxE 101 ssGqsasGlledlsaGtywlacgilGhaesGmWvdlivss 140
                   G+s +  + +  +Gty+ +c+++Gh  +Gm  +++v++
  AJA92890.1 157 KPGESGVSEFIPTEPGTYYYICTVPGHRMQGMVGEIVVTG 196
                 556665556667789*****************99999865 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.7e-06
        SoxE  95 yavsGissGqsasGlledlsaGtywlacgilGhaesGmWvdliv 138
                  a++ +  G+s s  +   ++Gty+ +c+++Gha +Gm   +iv
  AJA92890.1 283 AATNPLKPGESGSVTFLAGAPGTYYYICTVPGHALQGMQGTFIV 326
                 556677778888888888899*****************876665 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   9.6e-05      0.19      95     134 ..     156     195 ..     109     197 .. 0.90
   2 !   15.3   0.0   6.1e-06     0.012      77     134 ..     270     327 .]     221     327 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                   E-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEEEE CS
  Cu-oxidase_2  95 vppggwvairfkadnpGvwllHCHilwHldqGmalqfvvr 134
                   ++pg+  + +f ++ pG +++ C +  H  qGm++++vv+
    AJA92890.1 156 LKPGESGVSEFIPTEPGTYYYICTVPGHRMQGMVGEIVVT 195
                   5688888999*************************99986 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.1e-06
                   CTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEEEE CS
  Cu-oxidase_2  77 edpksynlenpvrrdtvqvppggwvairfkadnpGvwllHCHilwHldqGmalqfvvr 134
                   +d +s+ ++  +   t  ++pg+   + f a  pG +++ C +  H+ qGm ++f+v+
    AJA92890.1 270 DDFTSVVFDSEIAAATNPLKPGESGSVTFLAGAPGTYYYICTVPGHALQGMQGTFIVE 327
                   334677778889999999*************************************985 PP

>> Cu_bind_like  Plastocyanin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   7.7e-05      0.15      19      84 .]     112     188 ..     107     188 .. 0.75
   2 !    8.8   0.0    0.0008       1.6      51      84 .]     287     320 ..     245     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
  Cu_bind_like  19 rvGDtLlFkydse...vhsvvevs.kkeyekCetskpleeft.......tgsdkvtLtkegsnyFisgvpghCkkGq 84 
                   +vGD ++F+  ++   +h    ++ ++ +++    +++++++       +g ++   t++g+ y+i++vpgh  +G+
    AJA92890.1 112 NVGDKIIFDVVNDgksFHAFGVTKdTEGFSNLIPGSEVASMNeplkpgeSGVSEFIPTEPGTYYYICTVPGHRMQGM 188
                   689999998755411156665565577899888888888888888877766666667899************99887 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0008
  Cu_bind_like  51 pleefttgsdkvtLtkegsnyFisgvpghCkkGq 84 
                   pl+  ++gs +     +g+ y+i++vpgh  +G+
    AJA92890.1 287 PLKPGESGSVTFLAGAPGTYYYICTVPGHALQGM 320
                   44444477777777789************99997 PP

>> CHU_C  C-terminal domain of CHU protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0059        12      61      82 ..     169     190 ..     158     194 .. 0.72
   2 ?    5.1   0.0     0.012        24      63      83 ..     303     323 ..     291     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0059
       CHU_C  61 lpeGtYfYvlkleegekeekkG 82 
                 ++ GtY+Y++++  ++ + + G
  AJA92890.1 169 TEPGTYYYICTVPGHRMQGMVG 190
                 678********95555554555 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
       CHU_C  63 eGtYfYvlkleegekeekkGw 83 
                  GtY+Y++++  +  + ++G+
  AJA92890.1 303 PGTYYYICTVPGHALQGMQGT 323
                 69*******966665556665 PP

>> DUF5599  Domain of unknown function (DUF5599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         5   9.9e+03      10      26 ..     119     135 ..     108     149 .. 0.51
   2 ?    3.0   0.0     0.062   1.2e+02      78      93 .]     203     218 ..     186     218 .. 0.88
   3 ?    6.0   0.0    0.0071        14      30      63 ..     239     271 ..     230     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5
     DUF5599  10 WdvglnkkrlasFvlpk 26 
                 +dv  + k++  F ++k
  AJA92890.1 119 FDVVNDGKSFHAFGVTK 135
                 33333334444444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.062
     DUF5599  78 kkaPtevttgFtvefV 93 
                 + +Pt v+++Ft +fV
  AJA92890.1 203 AAPPTGVSHDFTFDFV 218
                 5689***********9 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0071
     DUF5599  30 gelrlvvGDelrlkykgseaeeWegeghvvkltd 63 
                  e+r+ +GDe+ +  ++++++++++ g v++ +d
  AJA92890.1 239 PEIRVNSGDEITVT-TVNAGKSFHAFGVVSNPDD 271
                 589*********99.6788899**9999987665 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.6     0.084   1.7e+02      37      65 ..     148     175 ..      66     177 .. 0.65
   2 ?    9.3   0.5    0.0012       2.5       8      65 ..     242     307 ..     240     309 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.084
                 -SS-EE-STT-TTS-TTS-EE-SSSEEEE CS
         PPC  37 svaaydansapsgsdeyieftapqaGtYy 65 
                 +va+ + +  p+ s    ef ++++GtYy
  AJA92890.1 148 EVASMNEPLKPGES-GVSEFIPTEPGTYY 175
                 33332223344444.56667789999997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                 EE-TT-EEEEEES-TT..............SEEEEE-TT..-SS-EE-STT-TTS-TTS-EE-SSSEEEE CS
         PPC   8 evpagdsltididggti............dldLylldsngtsvaaydansapsgsdeyieftapqaGtYy 65 
                  v++gd++t+++ + +             d++  ++ds+   +aa++++  p+ s  +++f a ++GtYy
  AJA92890.1 242 RVNSGDEITVTTVNAGKsfhafgvvsnpdDFTSVVFDSE---IAAATNPLKPGES-GSVTFLAGAPGTYY 307
                 689999999998555553566666664434444466666...3333335566666.8899999******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2374.13
//
Query:       AJA92891.1  [L=259]
Description: hypothetical protein T478_0478 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0081   16.0   0.1          4    7.4   0.0    2.3  2  Dioxygenase_N  Catechol dioxygenase N terminus
  ------ inclusion threshold ------
       0.11   13.2   0.1       0.26   12.0   0.1    1.7  1  Glyco_hydro_2  Glycosyl hydrolases family 2


Domain annotation for each model (and alignments):
>> Dioxygenase_N  Catechol dioxygenase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0   0.00089         8      20      40 ..      37      57 ..      24      60 .. 0.84
   2 !    7.4   0.0   0.00045         4       7      41 ..      74     108 ..      72     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00089
                   HHTT--HHHHHHHHHHHHHHH CS
  Dioxygenase_N 20 revdlteeEwwaavdfLtrvG 40
                   +e ++++ E+ ++++fL++ G
     AJA92891.1 37 SERQISQTEFTNGLEFLINEG 57
                   6889*************9866 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00045
                    HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHH CS
  Dioxygenase_N   7 iverlvrhlhdfirevdlteeEwwaavdfLtrvGq 41 
                    i+ + vr++     e ++  +E+ +a+++L+++G 
     AJA92891.1  74 IIPDWVRNTAGWWAEGKIPDSEFVNAMKYLIEIGL 108
                    56666777777778889999*************96 PP

>> Glyco_hydro_2  Glycosyl hydrolases family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.9e-05      0.26      35     109 ..     183     253 ..     170     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                    CEEEEEEEEETTSTEEEEEEEEEEEESTT-EEEEEEEEEES--BBECCCB--EEEEEEEEETTEEEEEEEEEE-B CS
  Glyco_hydro_2  35 evtleteikdaegkkvkeessvlslgngetksiklelevknpklWspetPnLYtlkveldkdgkvidevstrfGf 109
                     v++e+e++++eg  ++++ ++       +   +   + ++  lW     nLYt++v+++ dg++++++++ +G+
     AJA92891.1 183 GVNVEIELYNEEGLIHTSSGTTKDGFFRYQILAR--ETTQDGTLWMIN--NLYTVNVTVSLDGQTTEKIHQFYGI 253
                    5666666666666666665555554444444443..244555788876..8*******************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1948.17
//
Query:       AJA92892.1  [L=47]
Description: hypothetical protein T478_1413 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 361.87
//
Query:       AJA92893.1  [L=157]
Description: putative cytidyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-14   52.1   0.0      1e-13   51.7   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.032   14.1   0.1    1.7  2  FAD_syn          FAD synthetase
      0.072   12.3   0.0        6.2    6.0   0.0    2.1  2  Pantoate_ligase  Pantoate-beta-alanine ligase
       0.14   12.1   0.0       0.28   11.1   0.0    1.6  2  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   2.3e-17     1e-13       1     140 [.      21     146 ..      21     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2.3e-17
                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTTEEEEEEEHH CS
  CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.k.kplasaeeRlemlelakevdevisvdpweltrevlkklkpdklylvigad 92 
                      lagG+FD+iH GH++ l+ akkl++  l+v v++d+++ k  k +pl +a+ R e +  +  vd  i  d+ ++ + +++  kp+  ++++g d
       AJA92893.1  21 LAGGVFDIIHPGHINTLNAAKKLGDI-LVVVVATDKTAVKMkKrEPLHNAQLRQELVSSLNMVDVCIIGDEEDIFK-TVDLVKPQ--IIALGYD 110
                      79************************.99999999998887359*******************************7.99******..******9 PP

                      HHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHH CS
  CTP_transf_like  93 vledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstki 140
                      +  +   +k + e  ++ +l v++ +        + e ++++ Ss+ i
       AJA92893.1 111 QTHQ---EKFITEGCKKINLDVEVAR--------L-ESPRPETSSSSI 146
                      9877...8888888888888888443........3.444455555555 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.1e-06     0.032       3      80 ..      14      85 ..      12      98 .. 0.67
   2 ?   -0.9   0.0       0.3   1.4e+03     119     145 ..     107     133 ..      93     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-06
     FAD_syn  3 eedegavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelg.vdav 80
                +++++ v++ G FD +H GH + l+ a+++    ++ +vvv  ++   ++    k+++ L + + + el+++l+ vd++
  AJA92893.1 14 NSSSKIVLAGGVFDIIHPGHINTLNAAKKLG---DILVVVVATDKTAVKM----KKREPLHNAQLRQELVSSLNmVDVC 85
                56789999************99999888886...4445555444433332....2344466777777777766644544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
     FAD_syn 119 fGkkregdvellkelgaklgfevevvp 145
                 +G++++ + +++ e ++k++++vev++
  AJA92893.1 107 LGYDQTHQEKFITEGCKKINLDVEVAR 133
                 577777777777777777777777665 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0038        17      31      54 ..      28      51 ..       3      66 .. 0.80
   2 ?    6.0   0.0    0.0014       6.2     128     172 ..      94     138 ..      90     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0038
                     S-GHHHHHHHHHHHHHSSEEEEEE CS
  Pantoate_ligase 31 aLHeGHlsLvkaakeendvvvvSi 54
                      +H GH++ ++aak+  d++vv +
       AJA92893.1 28 IIHPGHINTLNAAKKLGDILVVVV 51
                     58****************999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0014
                      HHHHHHHT-SEEEEEGGGHHHHHHHHHHHHHTT-SSEEEEEEEEB CS
  Pantoate_ligase 128 tkLfnivqpdrayfGqKDaqqlavirrlvkdlnlpveivavpivR 172
                       k +++v+p+++ +G     q   i++ +k++nl+ve+  ++  R
       AJA92893.1  94 FKTVDLVKPQIIALGYDQTHQEKFITEGCKKINLDVEVARLESPR 138
                      577899********************************9988766 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.86   3.9e+03      94     134 ..      14      28 ..       6      31 .. 0.51
   2 ?   11.1   0.0   6.3e-05      0.28      70     119 ..      78     124 ..      34     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.86
  Glyco_tran_WecB  94 askpdlllvglGapkqEkwiarlkeelkakviigvGaafdf 134
                      +s+ +                          i+  G++fd+
       AJA92893.1  14 NSSSK--------------------------IVLAGGVFDI 28 
                      33333..........................4455666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.3e-05
  Glyco_tran_WecB  70 glriagthdgykeeeeeaiieainaskpdlllvglGapkqEkwiarlkee 119
                       l+++ ++      +ee+i +++   kp+++ +g     qEk+i +  ++
       AJA92893.1  78 SLNMVDVCII---GDEEDIFKTVDLVKPQIIALGYDQTHQEKFITEGCKK 124
                      4444443333...58999**************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1216.55
//
Query:       AJA92894.1  [L=336]
Description: oxidoreductase, aldo/keto reductase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-52  176.7   0.0    6.4e-52  176.6   0.0    1.0  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.6   0.0   3.6e-56   6.4e-52       2     292 ..      18     317 ..      17     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.6 bits;  conditional E-value: 3.6e-56
                   EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH.....-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHHHH CS
  Aldo_ket_red   2 lglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkk.....srkkreeviiatKvdlrdaeiksglskenireslee 92 
                   +  G+wq+ ++ +ei+ ++a+  +  + e+G+n++D+A++Y  g++e ++G + ++      +++ e++   tK      +++  ++++ +++ +++
    AJA92894.1  18 ILNGMWQVAGGhGEIDHDSAISQMLEYNENGFNTWDMADIY--GPAESFYGDFRNEienkkGKNELEKIQGFTKF----VPNPGPMTRSIVEHYIDQ 108
                   778*******9******************************..***********9999988888999********....999999************ PP

                   HHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEB CS
  Aldo_ket_red  93 slkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqlekakkkkkvkivavqveynllreleeegllelckkkgvpliay 189
                   s++++++d +D++++H++d+++ ++ ++l  l++l++ Gki +++++nf+ e+++ +  +++++++++qv+y++ +++ + +++++ck++++++ ay
    AJA92894.1 109 SMRKMNVDVIDVIQFHWWDYNDANYIDALHQLTKLRDDGKISHLALTNFDTERIQIM-VDNGIQLISNQVQYSIIDQRPNVKMASFCKNHNMKILAY 204
                   *******************************************************88.*************************************** PP

                   STTGGGTTGTTTSS---SSSCCC-------........TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--S..SHHHHHHHHGG CS
  Aldo_ket_red 190 splggGlltgkyqseedkedkeprkdlkrd........ertsknldaaeelselakehgvslaqlalryalsqpavgivipgas..nieqlednlda 276
                   ++l gGllt+ky   +++ +++ +  + ++          +  +++++  l+e+ak+h+v++  +a r++l +pav  +i+g++   ++++e+n + 
    AJA92894.1 205 GTLLGGLLTEKYLGGPKPTQTDLDTYSLQKymnmidawGGWGLFQELLVVLDEIAKKHNVQIPNVATRFVLDRPAVAGTIIGSRlgLSDHIEQNSKT 301
                   *************988776555544444446****************************************************63379********* PP

                   GG----HHHHHHHHHH CS
  Aldo_ket_red 277 lelklseeevaeldel 292
                   ++l+l+++++++++++
    AJA92894.1 302 FSLQLQNDDYEKIKSV 317
                   ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2553.51
//
Query:       AJA92895.1  [L=312]
Description: thiamine-phosphate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   51.2   0.0    2.5e-13   50.5   0.0    1.3  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.0   1.4e-17   2.5e-13       6      94 .]      34     131 ..      21     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-17
                 EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEE CS
        AIRS   6 vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsfsneptisvta 90 
                 +v++d     +lve ++         i +k++   +sD aa G  P +++ s++lp      +++e+ +g+++a++e++++l+gGdt++++e++i+v+ 
  AJA92895.1  34 AVCVD-----TLVESTDIpkgsklsdISRKSIVSSVSDFAAKGIIPKFCIISVTLPktiskkQVQELSKGFSKACKEFKIQLLGGDTNQGTEISIHVVL 127
                 58888.....9999999899999999************************************************************************9 PP

                 EEEE CS
        AIRS  91 vGlv 94 
                 +G v
  AJA92895.1 128 FGNV 131
                 9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1975.24
//
Query:       AJA92896.1  [L=439]
Description: glycine hydroxymethyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-75  252.5   0.1    7.2e-75  252.1   0.1    1.1  1  SHMT             Serine hydroxymethyltransferase
    6.9e-09   35.4   0.0    1.3e-08   34.5   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    2.6e-07   30.1   0.0    6.2e-07   28.9   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
    8.4e-05   21.7   0.3    0.00018   20.6   0.3    1.7  1  Aminotran_5      Aminotransferase class-V
    0.00047   19.3   0.0    0.00074   18.6   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.1   0.1     2e-78   7.2e-75       6     398 ..      10     394 ..       6     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 252.1 bits;  conditional E-value: 2e-78
                 HHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE---SSHHHHHHHHHH CS
        SHMT   6 pevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqplsGsqanlavyt 104
                  +v++ ++k +e  +++i liasen+ s+av ea+ s + n+yaeG+PG+r y Gc ++deve  +++ a++lfk++    +++v++ sG  anla+y+
  AJA92896.1  10 DKVFSSLEKHHEWFENSIPLIASENIPSPAVREAVMSDFGNRYAEGWPGERVYAGCTYIDEVEIQCMELAQKLFKAE----FADVRSVSGVVANLAIYS 104
                 57899999999******************************************************************....****************** PP

                 HHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH-.....-SEEEEE-SST-S---HHHHHHHHHHTT- CS
        SHMT 105 allepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefk.....PklivaGtsaysrlidyarlreiadevga 198
                 a  +pgd +++ ++++GGh++hG k +s   +      ++  +  d+e+ ++d d+ + k ++ k     Pk+ + G s +      + l e  +  g 
  AJA92896.1 105 AYSNPGDVMIASSIPAGGHISHGKKEHS-GTAGLVHGLDIEFFAFDPEEMTLDVDKTKAKVEDLKsqgklPKIAMFGGSVFLFPHPVKELAEFLKGHGM 202
                 ************************9998.444445566888899999999999999988877665555569**************************** PP

                 EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSH CS
        SHMT 199 yllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealep 296
                 ++  d ah+aGl+a+g + +P++  +d +t  thktl Gp+ggl++ +              ee ++ i++a+fPgl    + h ++akava+ eale 
  AJA92896.1 203 HINYDAAHVAGLIAGGKFQDPLREgTDTMTMSTHKTLFGPQGGLVIGS--------------EEHAEPIKKAMFPGLTSSHHIHHMGAKAVAFAEALEF 287
                 *********************975389******************988..............7999******************************975 PP

                 HHHHHHHHHHHHHHHHHHHHHHTT-EEGG...GS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STT....TT-SEEEEESHHHHHTT- CS
        SHMT 297 efkvyqkqvlknakalaealkekgyklvs...gGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksa....lvtsGlrlGtpaltsrgf 387
                   k y++q +knakala++l++ g+k++    g t++h  +v++ + g dG + e+ lek+ni +n+  +Pgd k a    + ++G+rlGt+ +t+ g+
  AJA92896.1 288 G-KDYAEQTIKNAKALASELNNVGFKVLGekrGYTESHQTVVNVLDYG-DGGTIEADLEKANIIVNRQLIPGDlK-AgrhyMHPGGIRLGTSEITRLGM 383
                 4.9************************97332569**********998.8999********************63.334449***************** PP

                 -HHHHHHHHHH CS
        SHMT 388 keedlekvakf 398
                 ke++++++a++
  AJA92896.1 384 KESEMKEIASL 394
                 ********976 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   3.7e-12   1.3e-08      43     289 ..      81     327 ..      51     413 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 3.7e-12
                      HHTT-S.EEEEES-HHHHHHHHHHHH--TTEEEEEETT......-HHHHSSTTHHHHCC--EEE..EE-EBTTTBE-HHHHHHHS--S-TTS-E CS
  Beta_elim_lyase  43 elfgke.aalfvpqGtaAnsillkillqrgeevivtep......ahihfdetgaiaelagvklr..dlknkeaGkmdlekleaaikevgaheek 127
                      +lf +e a +  ++G  An   +++  ++g+ +i+++       +h+     g +  + g       ++ +e  ++d++k +a++++ ++ + k
       AJA92896.1  81 KLFKAEfADVRSVSGVVANLAIYSAYSNPGDVMIASSIpagghiSHGKKEHSGTAGLVHGLDIEffAFDPEE-MTLDVDKTKAKVEDLKS-QGK 172
                      344444334448899999999999999999988887767777777777777777766666554410444444.88888888888888666.566 PP

                      EEEEEEESSBTTTTTB---.HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH....... CS
  Beta_elim_lyase 128 iklisltvTnntagGqvvs.leelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel..... 215
                       + i       + gG v   +  ++e+a++ k +g+++ +D+A +a    + g     + ++ D++tms  K l+ + Gg+++++++++     
       AJA92896.1 173 LPKIA------MFGGSVFLfPHPVKELAEFLKGHGMHINYDAAHVAGLI-AGGKFQDPLREGTDTMTMSTHKTLFGPQGGLVIGSEEHAepikk 259
                      66664......468888651677**********************9866.777777778899*************************7755555 PP

                      ...............................HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEEC CS
  Beta_elim_lyase 216 .............................edylaerveqrkylggglrqagvlaaleagiraleeglaslerdhktaeqlaeklelvrlaiprr 280
                                                   +dy ++ ++ +k+l+++l+++g+++                                     ++r
       AJA92896.1 260 amfpgltsshhihhmgakavafaealefgKDYAEQTIKNAKALASELNNVGFKVL-----------------------------------GEKR 318
                      5555555555555555555555555555555555555555555555555555555...................................2334 PP

                      CGTTCCEEE CS
  Beta_elim_lyase 281 vytqehldy 289
                       yt++h  +
       AJA92896.1 319 GYTESHQTV 327
                      444444333 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.7e-10   6.2e-07     169     306 ..     189     320 ..     138     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-10
                    HHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHH CS
  Aminotran_1_2 169 eleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaa 263
                     +++l+++ k +++++  D a+ ++     ++      + e+++++++++  + fG  G   G ++g+++ ++ ++k+  p+l  s +  ++ a+a
     AJA92896.1 189 PVKELAEFLKGHGMHINYDAAHVAGLIAGGKF---QDPLREGTDTMTMSTHKTLFGPQG---GLVIGSEEHAEPIKKAMFPGLTsSHHIHHMGAKA 278
                    4899********************99998777...7799999*****************...***************9999999788999999999 PP

                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS CS
  Aminotran_1_2 264 lsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgm 306
                    +  a+   ++ ++ +++ +k++k l +eL++ g+kvl+++ g+
     AJA92896.1 279 VAFAEAL-EFGKDYAEQTIKNAKALASELNNVGFKVLGEKRGY 320
                    9998875.6****************************998876 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.3     5e-08   0.00018     156     230 ..     188     266 ..     113     395 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5e-08
                  --HHHHHHHHHHTT-EEEEE-TTTTTTS-....--HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTS CS
  Aminotran_5 156 qpveeigklakkkgalvlvDaaqavghip....idvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggem 230
                  +pv+e+++ +k +g+ +  Daa  +g i      d  + g D +++s+hK l+gP+G G++++++e+ e +++++++g +
   AJA92896.1 188 HPVKELAEFLKGHGMHINYDAAHVAGLIAggkfQDPLREGTDTMTMSTHKtLFGPQG-GLVIGSEEHAEPIKKAMFPGLT 266
                  79*******************998754432222799999******************.****************999982 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.1e-07   0.00074     188     236 ..     212     260 ..     192     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-07
                 GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHS CS
        SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkkn 236
                  gl    ++q+ l+eG d ++ s  k l gpq G+++G  e  e +kk 
  AJA92896.1 212 AGLIAGGKFQDPLREGTDTMTMSTHKTLFGPQGGLVIGSEEHAEPIKKA 260
                 477788899*********************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3003.73
//
Query:       AJA92897.1  [L=114]
Description: hypothetical protein T478_0276 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-10   41.1   0.2    3.5e-10   40.1   0.2    1.5  1  CaMKII_AD  Calcium/calmodulin dependent protein kinase II ass
    2.1e-09   37.7   0.0      3e-09   37.2   0.0    1.2  1  SnoaL_3    SnoaL-like domain
    6.6e-09   36.1   0.0    7.4e-09   36.0   0.0    1.0  1  DUF4440    Domain of unknown function (DUF4440)
     0.0004   21.0   0.0    0.00047   20.8   0.0    1.1  1  SnoaL_2    SnoaL-like domain
      0.001   19.6   0.0     0.0012   19.4   0.0    1.1  1  NTF2       Nuclear transport factor 2 (NTF2) domain
  ------ inclusion threshold ------
      0.016   15.3   0.1       0.37   10.9   0.1    2.0  1  SnoaL_4    SnoaL-like domain
       0.12   12.1   0.0       0.13   12.0   0.0    1.3  1  DUF3225    Protein of unknown function (DUF3225)


Domain annotation for each model (and alignments):
>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.2   1.4e-13   3.5e-10       8     127 ..       1     110 [.       1     111 [. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-13
                 HHHHHHHHHHTT-HHHHHHHEEEEEEEE-GGGTT-EEESSHHHHGGGS...SSSS-SEEEEEESEEEEEESTTEEEEEEEEEEEEE-TTS-EEEEEEEE CS
   CaMKII_AD   8 lletlleaisegdfetytklcdpeltvfepevlgnlveglefhrfyfekllakrkkavrttilnkrvrllgddsAviayvrlltlldknGkkhtrqsee 106
                 +let++e i++ d++++++l++ + ++++ + ++  ++g + +  yfe+ll  +   v ++i  ++ +  +    +ia   l +++  +G  +t++++ 
  AJA92897.1   1 MLETWVEKIKTNDPKQVASLYHAD-GLLLGTFSDIERKGYDLILEYFENLLKAK---VDVEIVTQHKHETES---LIANSGLYNFIV-DG--KTVNARF 89 
                 589*********************.***********************888554...566899999887766...777777777764.35..46799** PP

                 EEEEEEETTEEEEEEEEEE-X CS
   CaMKII_AD 107 trVwekrdgkWkivhvHrSaa 127
                 ++V+ k dg Wki+ +H+S  
  AJA92897.1  90 SFVFIKTDGDWKILSHHSSVL 110
                 ******************975 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.2e-12     3e-09       5     119 ..       2     110 ..       1     112 [. 0.79

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
     SnoaL_3   5 ldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtes..gdvawvtelldvtaaedgtegegqlrlTgv 101
                 l+ + e +++ d +++ +l++ d + +gt +d    g++ +++++++ + +   ++++ ++ + tes     ++++  +      dg++ ++  r+++v
  AJA92897.1   2 LETWVEKIKTNDPKQVASLYHADGLLLGTFSDIERKGYDLILEYFENLLKAKVDVEIVTQHKHETESliANSGLYNFIV------DGKTVNA--RFSFV 92 
                 6789999999*************************************99975555555555555543113555555544......5555555..***** PP

     SnoaL_3 102 lrrtdggWkivhhhlSvp 119
                 +++tdg Wki++hh+Sv+
  AJA92897.1  93 FIKTDGDWKILSHHSSVL 110
                 ****************85 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   2.9e-12   7.4e-09       5     107 .]       2     102 ..       1     102 [. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.9e-12
                 HHHHHHHHHCT-HHHHHHCEEEEEEEE-TTS-E.EEHHHHHHHHHCCH.CEEEEEEEEEEEEEEETTEEEEEEEEEEEECCTTEEEEEEEEEEEEEEEE CS
     DUF4440   5 eealeeafvagdaealaallapdavlvgpsgtv.ldkeellealeagf.aagrslelteeevrvlgdlAvvtgrytfegrgdgepvegrgrftsvwrke 101
                  e++ e +++ d++++a+l+++d +l g + ++ + + +l+  ++++   a+ ++e+ +++ + ++ l + +g y+f +  dg+  ++++rf++v+ k+
  AJA92897.1   2 LETWVEKIKTNDPKQVASLYHADGLLLGTFSDIeRKGYDLILEYFENLlKAKVDVEIVTQHKHETESLIANSGLYNFIV--DGK--TVNARFSFVFIKT 96 
                 5899999***********************99966555555555555515589************************87..664..579********** PP

                 TTEEEE CS
     DUF4440 102 gggWri 107
                 +g+W+i
  AJA92897.1  97 DGDWKI 102
                 ****98 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.8e-07   0.00047       2      99 ..       3     100 ..       2     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.8e-07
                 HHHHHHHHTTCHHHHHHTEEEEEEEEETTSE..EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEEETTSSEEEEEEEEEEEEETTE CS
     SnoaL_2   2 raflaalnagdldalaalfapdvvwedpgge..lrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgtipatgrgvtvrgvdvfrvrdGk 98 
                 + +++ + + d++ +a+l+++d  + +++ +  ++G + i ++f+ l++a+ d+++  ++  + +  +a ++ +      +g++v+ r+  vf   dG 
  AJA92897.1   3 ETWVEKIKTNDPKQVASLYHADGLLLGTFSDieRKGYDLILEYFENLLKAKVDVEIVTQHKHETESLIANSGLYNF--IVDGKTVNARFSFVFIKTDGD 99 
                 678899999*******************66668****************999999999999999999999876664..789999999999999999986 PP

                 E CS
     SnoaL_2  99 i 99 
                 +
  AJA92897.1 100 W 100
                 5 PP

>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   4.6e-07    0.0012       9     102 ..       5      94 ..       1     105 [. 0.70

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.6e-07
                 HHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHHHSSCSCEEEEEEEEEEEETSEGGGCEEEEEEEEEEEETTSCCEEEEEEEEE CS
        NTF2   9 YYaaldagdregllalyaadaslltpegsspvkgreaIteffrslpftrielkittvdaqpdeaslstgvlvmvtGelkvddfkkrrkfsqtfi 102
                  ++ + ++d+++++ ly+ad  ll    + + kg + I e f++l ++++ ++i t   +    +++  +  +    + vd++  + +fs +fi
  AJA92897.1   5 WVEKIKTNDPKQVASLYHADGLLLGTFSDIERKGYDLILEYFENLLKAKVDVEIVTQHKH----ETESLIANSGLYNFIVDGKTVNARFSFVFI 94 
                 66788999****************999999******************865544433333....122333333333444455544466666665 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00014      0.37      20     121 ..       9     100 ..       1     106 [. 0.52

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                 HHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH....-EEE.EE---EEEE........ETTEEEEEEEEEEEEEETTEEEEEE. CS
     SnoaL_4  20 lDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfa....ltqH.llsnpliel........dgdtAtgrayllatlvrdgdggrqvl 105
                 + t+d++++a+l+++d+ +  t + + + +g d i +++++ l++++    +tqH + +  li          dg+t  +r+                 
  AJA92897.1   9 IKTNDPKQVASLYHADGLLLGT-FSDIERKGYDLILEYFENLLKAKVdveiVTQHkHETESLIANsglynfivDGKTVNARF----------------- 89 
                 5577778888888888777666.43455567788888888877555544443333222222222112222234444555554................. PP

                 .EEEEEEEEEEETTEE CS
     SnoaL_4 106 aggryedelvredggW 121
                      +  ++++dg W
  AJA92897.1  90 -----SFVFIKTDGDW 100
                 .....44455555555 PP

>> DUF3225  Protein of unknown function (DUF3225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.13      90     125 ..      77     112 ..       9     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                 EEE-SS-SS-EEEEEEEEEETTEEEEEEEEEEE-.- CS
     DUF3225  90 efrregseriGRqsqtWvrlpegWrivaahvsllde 125
                 +f  +g++   R s ++++++  W+i++ h s+l+e
  AJA92897.1  77 NFIVDGKTVNARFSFVFIKTDGDWKILSHHSSVLPE 112
                 6888999999**********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 828.86
//
Query:       AJA92898.1  [L=78]
Description: hypothetical protein T478_0757 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.023   14.8   7.5      0.025   14.7   7.5    1.1  1  MRP-L28         Mitochondrial ribosomal protein L28
      0.049   12.5   0.5      0.082   11.8   0.1    1.5  2  Dak1            Dak1 domain
      0.066   12.6   9.8      0.065   12.6   9.8    1.1  1  Glycoprotein_G  Pneumovirus attachment glycoprotein G
        0.2   12.6   8.3       0.23   12.4   8.3    1.1  1  AIM3            Altered inheritance of mitochondria protein 3


Domain annotation for each model (and alignments):
>> MRP-L28  Mitochondrial ribosomal protein L28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   7.5   5.5e-06     0.025       8      59 ..       3      58 ..       1      77 [. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.5e-06
                XXXXXXX....XXX.XXXXXXXXXXXXXXXXXXXXXXXXXSXSXXT...TSSTTX. CS
     MRP-L28  8 kkkkvdpqvvkrre.erakkrlekqirkleksakelkPveelivpl...ksvdsak 59
                 kkk++++v+k+++ ++akk  +k  +k +k++ + +P++  iv +    svd+++
  AJA92898.1  3 EKKKTTKKVAKKTTkKVAKKTTKKTTKKSTKNKANSEPLDSGIVIVdddLSVDKES 58
                345555556666551678888999999*************9988551124666554 PP

>> Dak1  Dak1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.11   4.9e+02     219     228 ..      12      21 ..       2      41 .. 0.42
   2 ?   11.8   0.1   1.8e-05     0.082     101     133 ..      33      65 ..      26      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.11
                 HHHHHHHHHH CS
        Dak1 219 veelleklle 228
                 +++ ++k+ +
  AJA92898.1  12 AKKTTKKVAK 21 
                 2222222222 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
                 HHHHHHTT--EEEEEE--B-SSSSSTTCSSSB- CS
        Dak1 101 aekakaegikvetvvvdDDvavedseekagrRG 133
                  +ka++e ++  +v+vdDD +v++++e ++rR+
  AJA92898.1  33 KNKANSEPLDSGIVIVDDDLSVDKESELEERRA 65 
                 567888889999********************7 PP

>> Glycoprotein_G  Pneumovirus attachment glycoprotein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   9.8   1.5e-05     0.065     198     231 ..       4      37 ..       2      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                     XXXXXXXXXXX........XXXXXXXXXXXXXXX CS
  Glycoprotein_G 198 klkttkkdtktlakklkkettikrtsketkkttk 231
                     k kttkk +k  +kk+ k+tt+k t+k tk++ +
      AJA92898.1   4 KKKTTKKVAKKTTKKVAKKTTKKTTKKSTKNKAN 37 
                     3455555555555555555555555555555443 PP

>> AIM3  Altered inheritance of mitochondria protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   8.3   5.1e-05      0.23       9      57 ..       6      59 ..       2      78 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
        AIM3  9 ktagKygykGtksvaKsGyqagKkhykkskekreerdgk..........ddsdeereed 57
                kt+ K++ k tk vaK+  +   k++ k+k+++e  d+           d     +e++
  AJA92898.1  6 KTTKKVAKKTTKKVAKKTTKKTTKKSTKNKANSEPLDSGivivdddlsvD-----KESE 59
                799999999*****998888777777777777776644478876444432.....2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3516  (0.196107); expected 358.6 (0.02)
Passed bias filter:                     1064  (0.0593452); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 550.90
//
Query:       AJA92899.1  [L=508]
Description: PF01935 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-38  131.5   0.5    1.4e-37  130.0   0.5    1.8  1  DUF87         Helicase HerA, central domain
     0.0014   18.1   0.2      0.038   13.4   0.0    2.1  2  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0024   16.5   0.0        0.3    9.6   0.0    2.3  2  DUF853        Bacterial protein of unknown function (DUF853)
      0.004   17.3   0.5      0.013   15.6   0.5    1.9  1  HAS-barrel    HAS barrel domain
  ------ inclusion threshold ------
      0.021   15.3   0.1      0.053   14.0   0.1    1.8  1  ABC_tran      ABC transporter


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.5   3.8e-41   1.4e-37       2     226 ..     129     327 ..     128     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 3.8e-41
       DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsakdkelkinpwsldpe 100
                 +iG+ll +++++ +++lnk+v+rHl+il++TG+GKSn+v++L ++++   ++t++i+D H++Y++++     +k++vi++         kinp++ld e
  AJA92899.1 129 KIGNLLRNQDIDSKINLNKIVSRHLGILAMTGMGKSNLVSLLASKIA-ALSGTVIIFDYHNDYADLD----IPKINVIDA---------KINPRLLDAE 213
                 8**********************************************.*******************....********9.........9********* PP

       DUF87 101 elldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf.snsstdlialllekle 198
                  l ++le+  ++ a++q+++l++a++    +e ke++++ e + +  + +   ++++rk+ + ++ r++dk++d  ++ +++ + ++  ++ l+     
  AJA92899.1 214 TLSEVLEI--REGADIQQRILRKAFT----PEVKESANFWEALDQQVQYIG--SDPERKEERHSADRVQDKIDDARNRFADIlDPDMVYPVGLI----- 299
                 ********..***************9....355666666666665555555..7899999**********************777777778888..... PP

       DUF87 199 kegkitiidlsgvdelaqqlvvsvilrr 226
                 keg+++i+++s+++++++++  +++l++
  AJA92899.1 300 KEGRLNILNVSEFSDKQANVALGYYLQE 327
                 ********************99999876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.024        84      13      59 ..     125     170 ..     120     179 .. 0.77
   2 !   13.4   0.0   1.1e-05     0.038     121     217 ..     327     428 ..     323     444 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.024
                   T---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
  FtsK_SpoIIIE  13 tessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntL 59 
                   +e+ ++ ++l+ + +++++ l+ +++  hl ++  tg GKS+ +  L
    AJA92899.1 125 NEWLKIGNLLRNQDIDSKINLNKIVSR-HLGILAMTGMGKSNLVSLL 170
                   555566666666669999999999999.*************988655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.1e-05
                   HHHHHTT-SSHHHHHHHHHHHHHTT---.B-TT-............................-----------B-----EEEEEEC-HHHHHHHHHH CS
  FtsK_SpoIIIE 121 alfreagvrsiaaydgeiaedpldifgd.vflvlDnyddlaaene......ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapk 210
                   +l+++++++s a+  ++ +++++++f+  +f+++ +   +  ++e        t+++ +g ++g  + v ++r  +++ps++++ ++++ + +++++
    AJA92899.1 327 ELLNDRKAASNAK-SAKSKSKKNYMFNSpIFVIIEEAHVFIPKGEdarakyWATKIAREGRKFGLGLCVVSQRPRNIEPSILSQMGSLAVMKMVQED 422
                   5566666666665.4444444555555415666777777777777888888899******************************************* PP

                   H....HH CS
  FtsK_SpoIIIE 211 dssvlve 217
                   d+   + 
    AJA92899.1 423 DQH-QIA 428
                   *53.333 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0     0.003        11      12      66 ..     142     195 ..     132     220 .. 0.75
   2 !    9.6   0.0   8.4e-05       0.3     282     361 ..     379     452 ..     352     462 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.003
      DUF853  12 elalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiak 66 
                 ++ l  k++ rh  i   tG Gk   + +la ++++   +v++ d   d +++  
  AJA92899.1 142 KINL-NKIVSRHLGILAMTGMGKSNLVSLLASKIAALSGTVIIFDYHNDYADLDI 195
                 4443.4688999888899***************************9999987654 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.4e-05
      DUF853 282 eqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealv 361
                  ++ r  r  G G+  v+q P ++  ++L+q+G+     ++    +dq+ + +a++++ +    d+   +t+L+vG+a++
  AJA92899.1 379 TKIAREGRKFGLGLCVVSQRPRNIEPSILSQMGSLA--VMKMVQEDDQHQIASASESISR----DLIAQLTSLNVGDAVL 452
                 4667778999***********************964..5788899999999999998865....789999******9975 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   3.7e-06     0.013       3      74 ..       5      76 ..       2      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.7e-06
  HAS-barrel  3 evigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgn...selsndlalvlsleeleeangdde 74
                 v+ges ++ +++ + +   + +GeyV+ie + ++++ G+v++ +  +   s+ +n+ + ++s+e +e +  d +
  AJA92899.1  5 FVVGESKPNVVTIQSSR--ALPIGEYVIIEVE-EGKIVGLVETSFVTSaalSDVRNYDEAEESIELAELNKRDKS 76
                46777777666666666..9************.********9977655778999999999988888887777665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.5e-05     0.053      11      80 ..     150     262 ..     140     344 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                 TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
    ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............................. 79 
                 ++ ++i+  +G GKS L++lla +    +G++ + + + ++ +l + + ++   + +p+l +  t+ e                               
  AJA92899.1 150 SRHLGILAMTGMGKSNLVSLLASKIAALSGTVIIFDYHNDYADLDIPKINVIDAKINPRLLDAETLSEVleiregadiqqrilrkaftpevkesanfwe 248
                 567899999***********************6665555555555555555555555666665555555555555555555555555555544444444 PP

                 .............H CS
                 .............x RF
    ABC_tran  80 .............e 80 
                              e
  AJA92899.1 249 aldqqvqyigsdpE 262
                 44444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3697.30
//
Query:       AJA92900.1  [L=182]
Description: hypothetical protein T478_1384 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1380.40
//
Query:       AJA92901.1  [L=61]
Description: hypothetical protein T478_1411 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.05   13.8   6.2      0.052   13.8   6.2    1.1  1  zf-4CXXC_R1  Zinc-finger domain of monoamine-oxidase A repres
       0.11   12.6   5.4       0.13   12.4   5.4    1.1  1  Zf_RING      KIAA1045 RING finger
       0.47   10.8  11.9       0.22   11.9   9.7    1.5  2  DUF2039      Uncharacterized conserved protein (DUF2039)
       0.85    9.5   5.9       0.87    9.4   5.9    1.1  1  DUF2797      Protein of unknown function (DUF2797)


Domain annotation for each model (and alignments):
>> zf-4CXXC_R1  Zinc-finger domain of monoamine-oxidase A repressor R1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   6.2   1.2e-05     0.052       7      51 ..       5      47 ..       1      56 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
  zf-4CXXC_R1  7 ttChqCrqktletktsCkakeCksaklkfCekClkn.Rygeeveev 51
                 + C +C++k+++++ +C  ++C  +  k+C +C+ + +   ++++v
   AJA92901.1  5 SICEFCKKKQATKSFHC--NHCL-KPHKICMSCILKyKTKMNLRKV 47
                 67***************..99*9.899******8641333444444 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.4   2.8e-05      0.13       5      47 ..       4      43 ..       1      54 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
     Zf_RING  5 delCeiCevytaeelypCRvCtkvfHegClrklgylqdesale 47
                  +Ce C+  +a + + C  C k  H+ C+  + + +  ++++
  AJA92901.1  4 SSICEFCKKKQATKSFHCNHCLKP-HKICMSCILKYK--TKMN 43
                679*******************95.99**99854444..3333 PP

>> DUF2039  Uncharacterized conserved protein (DUF2039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   9.7   4.9e-05      0.22      54      87 ..       4      35 ..       1      37 [. 0.91
   2 ?   -1.2   0.0      0.59   2.6e+03      47      57 ..      37      47 ..      35      56 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
     DUF2039 54 kkkCvkCeektvkkaYhkiCkkCakekkvCakCs 87
                ++ C+ C++k+ +k++h  C++C k +k+C  C 
  AJA92901.1  4 SSICEFCKKKQATKSFH--CNHCLKPHKICMSCI 35
                567*************9..**************6 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.59
     DUF2039 47 kYkaltkkkkC 57
                kYk++ + +k 
  AJA92901.1 37 KYKTKMNLRKV 47
                44444443333 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.9   0.00019      0.87      12      59 ..       5      49 ..       1      59 [. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
     DUF2797 12 rrCvnC.grktkksfsqgvCakCfkklaeadecimkpekchahlgtclr 59
                  C  C +++  ksf   +C +C+k    + +ci+k  k++++l +  +
  AJA92901.1  5 SICEFCkKKQATKSF---HCNHCLKPHKICMSCILKY-KTKMNLRKVHK 49
                569999444567888...*****************98.55555555445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 481.31
//
Query:       AJA92902.1  [L=101]
Description: Rieske [2Fe-2S] domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   58.6   0.0    4.7e-16   58.5   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
    9.8e-12   44.7   0.0    1.1e-11   44.6   0.0    1.0  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   5.2e-20   4.7e-16       1      78 [.       2      78 ..       2      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 5.2e-20
                CEEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGG.SEEETT.EEE-TTT--EEE.TTSBEEE CS
      Rieske  1 swvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplse.gkidekgvleCpcHgwayd.adGkvik 78
                +w++va++ d+++g++++++v g++++v++  ++ ++Al+++C+H+  +l+  gki e+  +eCp+H w y+ ++G++ +
  AJA92902.1  2 TWTKVAEKGDIQSGSSKEFEVEGKKIAVFN--QDGFHALDGICQHQDGSLAPkGKI-EGDIVECPLHFWHYNiKTGELMD 78
                69****************************..588***************998***.566****************9876 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.2e-15   1.1e-11       1     103 [.       2      99 ..       2     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.2e-15
                 SEEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-BBSS.-TTSB-BEE-EEEST CS
    Rieske_2   1 ewvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGecle.deevslkvypvrved 98 
                 +w++v++  d+  ++++   v+gk++a+f +  +  +A+d ++  ++ +   +G+++ +    +v++Pl+  ++++ktGe ++  + ++lk y+v v+d
  AJA92902.1   2 TWTKVAEKGDIQSGSSKEFEVEGKKIAVFNQ--DGFHALDGICQHQDGSLAPKGKIEGD----IVECPLHFWHYNIKTGELMDyLKGIKLKKYDVDVRD 94 
                 6****************************98..99**********9999999****988....9*******************4466************ PP

                 SEEEE CS
    Rieske_2  99 gkvev 103
                 + ++v
  AJA92902.1  95 DGIYV 99 
                 **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 752.64
//
Query:       AJA92903.1  [L=373]
Description: N-acetyl-ornithine/N-acetyl-lysine deacetylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-29  102.5   0.2    4.7e-29  101.6   0.2    1.5  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.4e-15   55.2   1.6    6.2e-14   51.8   0.2    2.2  2  M20_dimer      Peptidase dimerisation domain
    1.4e-05   24.3   0.7      0.084   11.9   0.0    2.4  2  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.027   14.2   0.0    1.3  1  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.2   1.1e-32   4.7e-29       1     205 [.      67     362 ..      67     364 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1.1e-32
                    EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEE CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfe 96 
                    +l +H+DvVp     g     + ++e ++l+GrGa+d k+ ++a+l a++++ ++    +gti+++  +dEEg+  G+k+l++   +  +vd+   
     AJA92903.1  67 MLCGHMDVVP-----G---KIKVRIEGDMLHGRGASDAKAPLIAMLFAAASIGEN----EGTITFVGAVDEEGNATGIKNLVK---NTPDVDY--- 144
                    5789******.....4...468899999***********************9999....9************988********...4567777... PP

                    EEEESSSBTCHSTETEEEE............................................................................. CS
                    xxxxxxxxxxxxxxxxxxx............................................................................. RF
  Peptidase_M20  97 lhieepgileagklaigvv............................................................................. 115
                    ++ +ep+  +  k  +++                                                                              
     AJA92903.1 145 AVFGEPSSIQ--K--VTIAykgrlainlrvnvkdsahasapwlaknaieeissvaielknelesgqenktkgmmltatlteirggtshnvtpkecv 236
                    4489999999..3..34446688999999******************************************************************* PP

                    .................................EEEEEEE....EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTE CS
                    .................................xxxxxxx....xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxx RF
  Peptidase_M20 116 .................................kvevell....eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agip 170
                                                     +v    l     + +p+++  +splv+al  ++ ++ +++++li +  g+ d++ +   ++ip
     AJA92903.1 237 atldiripvdmncndieekitkiinemsikreiEV----LysviDETEPFEAAhNSPLVRALTLSILDVEKKRPMLIRKT-GTGDMNVIgnqLKIP 327
                    ***************************99775533....23345999999999***************944336666666.********9555555 PP

                    EEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20 171 tvmifgpgs.glaHspnEyvdledlekgikvlarll 205
                     v+ +gpg+   aH+ +E+v++e+++kgi++l++ l
     AJA92903.1 328 -VITYGPGDpHEAHTIDEKVSIEEFVKGIEILKKSL 362
                    .457****88*********************99866 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.02        91       9      49 ..      79     133 ..      70     174 .. 0.72
   2 !   51.8   0.2   1.4e-17   6.2e-14      15     105 ..     173     264 ..     158     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                 EEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC................. CS
   M20_dimer   9 gkitvkgkagHsgapgagaNAieklarllaeledeegdia..............e 49 
                  k++++g ++H+    ++  ++ ++  + a++ ++eg i+              +
  AJA92903.1  79 IKVRIEGDMLHGRGASDAKAPLIAMLFAAASIGENEGTITfvgavdeegnatgiK 133
                 4666*********9999999**************999888666666655555552 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 1.4e-17
                 -B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCC CS
   M20_dimer  15 gkagHsgapgagaNAieklarllaeledeegdia.eerslprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevleeieeilekea 105
                   ++H++ap  + NAie+ + +  el++e ++ +  +      t ++t+i+gG++ nv+p e+ a++diR++  ++  +++e+i++i+++  
  AJA92903.1 173 KDSAHASAPWLAKNAIEEISSVAIELKNELESGQeNKTKGMMLTATLTEIRGGTSHNVTPKECVATLDIRIPVDMNCNDIEEKITKIINEMS 264
                 4579*************99999999999987777444455669*********************************************9865 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   1.9e-05     0.084       1      25 [.      53      75 ..      53      82 .. 0.93
   2 !   10.6   0.1   4.6e-05      0.21     133     249 ..      94     207 ..      80     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                   S-EEEEEESSTTSSEEEEEEE--B- CS
  Peptidase_M42  1 GnliakkkgkekepkvmiaAHmDei 25
                   Gnlia+k +   epk+m+++HmD +
     AJA92903.1 53 GNLIATKGS--GEPKIMLCGHMDVV 75
                   9******99..9***********76 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.6e-05
                    HHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSSTTS-CEEEEEETTCCSHHHHHHH CS
  Peptidase_M42 133 lDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeaklgkGpvirvkDasgiyhpklrkk 228
                     D +a ++++l ++ ++ e+e   t+++v+ v EE +  G k+++++  pd+  av   +++ ++ +  ++ +l     + vkD+ +   p l k+
     AJA92903.1  94 SDAKAPLIAMLFAAASIGENE--GTITFVGAVDEEGNATGIKNLVKN-TPDVDYAVFGEPSSIQKVTIAYKGRLAINLRVNVKDSAHASAPWLAKN 186
                    588889999999999999987..9**********************9.9******99999999999999999999999***************999 PP

                    HHHHHHHTT--EEEEEESSSS CS
  Peptidase_M42 229 llelAkknnipyqlevlsggg 249
                     +e  ++  i+++ e+ sg  
     AJA92903.1 187 AIEEISSVAIELKNELESGQE 207
                    988888888888776555544 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.1e-06     0.027       2      87 ..      55     140 ..      54     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                    EEEEESTTCESEEEEEEEE--B-TTT.....TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHHHHCC CS
  Peptidase_M28   2 viatlegkatdevlllgAHyDsvgvg.....rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafakakpe 87 
                    +iat  g+  +  ++l++H+D v+ +     +g+     GA D  ++  a+L  a  + +    ++ ++ f+    EE    G k+++k +++
     AJA92903.1  55 LIATK-GSG-EPKIMLCGHMDVVPGKikvriEGDmlHGRGASDAKAPLIAMLFAAASIGE----NEGTITFVGAVDEEGNATGIKNLVK-NTP 140
                    55554.455.568***********999999966666667****************99996....689***********99999999994.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2734.07
//
Query:       AJA92904.1  [L=168]
Description: hypothetical protein T478_0259 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.05   14.1   0.5       0.76   10.3   0.2    2.1  2  SusF_SusE        Outer membrane protein SusF_SusE
      0.056   13.6   0.1      0.078   13.2   0.1    1.2  1  Peptidase_M1_N   Peptidase M1 N-terminal domain
      0.076   12.1   4.0       0.16   11.1   4.0    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
        0.1   12.6   0.0       0.17   11.9   0.0    1.3  1  Thump_like       THUMP domain-like
       0.23   11.4   4.9       0.88    9.6   1.1    2.4  2  Gram_pos_anchor  LPXTG cell wall anchor motif
          2    8.0   5.4        2.5    7.7   0.5    2.3  2  Saf_2TM          SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> SusF_SusE  Outer membrane protein SusF_SusE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.053   1.6e+02      64      89 ..      45      74 ..      23      87 .. 0.62
   2 ?   10.3   0.2   0.00025      0.76      62      83 ..      91     115 ..      65     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.053
                E.....TTCEEE-S-EEEEEEEEEECCCCEE CS
   SusF_SusE 64 r.....dgnfevakaglYlvtvtisveekev 89
                +     d   e++++g+Y v   i+ +e ++
  AJA92904.1 45 QleikaDLDPEINTEGVYAVQT-IEGKEYDI 74
                13344599999*******9987.44444443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00025
                 EEE...TTCEEE-S-EEEEEEEEEE CS
   SusF_SusE  62 vsr...dgnfevakaglYlvtvtis 83 
                 ++r   ++nfe+++ag+Y++++t+s
  AJA92904.1  91 INRnsfEDNFEIEQAGTYTLIITTS 115
                 33367899**************544 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.6e-05     0.078      11      79 ..      50     117 ..      40     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                     EETT.TTEEEEEEEEEEEES..S-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCE CS
  Peptidase_M1_N  11 idlk.ektfkGsvtitlqlk..eatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkes 79 
                      dl+ e   +G   +++      ++s +v+d++++ki++vs+++++  ++     +ieq  +  l+i+++es
      AJA92904.1  50 ADLDpEINTEGVYAVQTIEGkeYDISAVVIDSSEIKIRDVSINRNSFEDNF----EIEQAGTYTLIITTSES 117
                     44443333344444332222245899*****************99999985....55566677788888775 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.0   5.3e-05      0.16      79     190 ..      29     166 ..       8     168 .] 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
  ABC2_membrane_3  79 idgilvipkgfskdll....................................kgesatvtvlinssnlnsskailna.lnsllqqlnasalvlq 135
                      i+g lvi++g  ++l+                                    ++e     v in + ++++ +i++a  +            ++
       AJA92904.1  29 ITGDLVIEEGKVNSLTqleikadldpeintegvyavqtiegkeydisavvidSSEIKIRDVSINRNSFEDNFEIEQAgTY------------TL 110
                      55555665555555555555555555554444444444421111111222221122222222222222222222222222............33 PP

  ABC2_membrane_3 136 seatstsaninvestql...eeelsnvasflvgliliilifitasfiavsiveEkesr 190
                      +++ts+s +i++          ++++v+  +vg+++ii+ +i+++ i ++i+++k+++
       AJA92904.1 111 IITTSESEEIPLVG--GighVPDSTGVTISIVGFFIIISGMIGVAAIGFMIIRQKKNK 166
                      44555555555554..133233447888889999999999999999**********98 PP

>> Thump_like  THUMP domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.5e-05      0.17      26      65 ..      79     117 ..      63     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.5e-05
  Thump_like  26 igkanikkRgfpldpeeLrkklklkdggraatLvlTrvge 65 
                 i + +ik R++ ++   +  ++ + ++g ++tL++T+  +
  AJA92904.1  79 IDSSEIKIRDVSINRNSFEDNFEIEQAG-TYTLIITTSES 117
                 56789*******************9999.********943 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1    0.0003      0.88      15      35 ..       3      24 ..       2      26 .. 0.87
   2 ?    3.1   0.1     0.031        93      19      42 ..     142     166 ..     133     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0003
                     XXXXXXXXXXXXXXXXXXXX.X CS
  Gram_pos_anchor 15 ngnifltaaGllallggllL.l 35
                     n +++l ++G+++++g++lL +
       AJA92904.1  3 NLTKYLVIVGIMIAVGAMLLiY 24
                     6789***************943 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.031
                      XXXXXXXXXXXXXXXX.XXXXXXXX CS
  Gram_pos_anchor  19 fltaaGllallggllL.lvkrRKke 42 
                      f+ +   ++ ++++++  ++ +K++
       AJA92904.1 142 FFIIISGMIGVAAIGFmIIRQKKNK 166
                      5667777777888888555555543 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.5     0.032        95      72      88 ..       8      24 ..       3      31 .. 0.82
   2 ?    7.7   0.5   0.00085       2.5      45      84 ..     111     150 ..     100     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.032
     Saf_2TM 72 lvigvllivvGavllil 88
                lvi  ++i+vGa+lli+
  AJA92904.1  8 LVIVGIMIAVGAMLLIY 24
                78888999999999997 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00085
     Saf_2TM  45 ialklaggslevsfssseipeivlaiilvigvllivvGav 84 
                 i+++++++++ +  ++  +p+ + ++i ++g+++i+ G++
  AJA92904.1 111 IITTSESEEIPLVGGIGHVPDSTGVTISIVGFFIIISGMI 150
                 567777888888888999********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1239.96
//
Query:       AJA92905.1  [L=186]
Description: PF11611 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-08   32.6   0.6    1.4e-07   31.8   0.6    1.4  1  DUF4352   Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.6   7.9e-12   1.4e-07       3     112 ..      37     160 ..      35     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7.9e-12
                 TCEEECCTTEEEEEEEE.EEEEEETTS-CEET...............T-.SEEEEEEEEEEE-SSS-EEEEGGGEEEEETTEEE-BEEESCCCCTTB-- CS
     DUF4352   3 vgetvkvgdlevtVnsv.eytksvgkneylqp...............daggeflivdvtvkNkgkealtvnssqfkLkdgdgkeydadlsasskaddlf 85 
                  ge+v+vgd+ + V+ v +  + ++++e+  +               ++  +++ ++vt +Nkg++ + +   q +L+dg +k++++ + ++ +++ l 
  AJA92905.1  37 FGEPVQVGDVMFDVQYVtNFDFLQKTKEFKLAekaeidrglieasneKPTHTYFQIQVTAENKGNDIVRFTGGQLHLYDGSNKRFSPIFVGYGDNE-LS 134
                 699***********999444455555555555999**********99999*****************************************99986.9* PP

                 EEEE-TT-EEEEEEEEEESTT-CGEEE CS
     DUF4352  86 lgtlnpGkkvtGklvFdvpkgkkkleL 112
                 l +l p k vt +  Fd++ +++ +++
  AJA92905.1 135 LIDLEPQKAVTMTTQFDIEYDEE-MQY 160
                 ******************99988.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1427.93
//
Query:       AJA92906.1  [L=224]
Description: chlorite O(2)-lyase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-55  187.5   0.3    2.3e-55  187.2   0.3    1.0  1  Chlor_dismutase  Chlorite dismutase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.2   0.3   1.3e-59   2.3e-55       2     193 ..      30     213 ..      28     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.2 bits;  conditional E-value: 1.3e-59
                      HHHHHHHHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS-GGGHHHCHHHHS- CS
  Chlor_dismutase   2 eeaveelealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkeedeenkshvearlap 95 
                      ee ++ele++le+a   v++++ys+lGlr+daD+++w+++e++e++qe+ +++  t +gk++ p+  y+s t++s Y     ++k+ +++++ +
       AJA92906.1  30 EESAKELENILENAP--VQSRTYSTLGLRNDADFLIWFMSESIEDIQETISKIYLTVVGKYIMPSIVYFSSTRPSIY-----AQKDRIHSFVGG 116
                      667788888887755..459*********************************************************.....788888888877 PP

                      ---SSSEEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTTEEEEEEE-TTTSSSSEEEEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-E CS
  Chlor_dismutase  96 elpkkkyvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgkVrqiitgsfGldDyEwgvaleaddleefkdlvyelRfdeasakvaeegpfy 189
                       + +kky +vYP+ k+reWYllp e+R+++m+eH+++++kY++V+ ++t+sfG++D+++++a+e+ddl+ f+d+++elR +++sa+v+e++p++
       AJA92906.1 117 LE-AKKYTVVYPFIKTREWYLLPLEQRKAMMDEHIKVSQKYPQVELNTTYSFGIHDQDFMLAFESDDLNVFQDMIMELRGTKVSAYVKEDTPMI 209
                      77.9****************************************************************************************** PP

                      EEEE CS
  Chlor_dismutase 190 vGrr 193
                      v+ +
       AJA92906.1 210 VCVK 213
                      *975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1579.34
//
Query:       AJA92907.1  [L=250]
Description: hypothetical protein T478_0454 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0057   16.7   9.7       0.18   11.8   0.9    2.9  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
  ------ inclusion threshold ------
      0.013   15.7  15.5      0.013   15.7  15.5    4.0  4  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
      0.039   13.7  10.5       0.27   11.1   0.4    3.5  2  DASH_Duo1       DASH complex subunit Duo1
      0.048   13.4  26.5      0.037   13.8  10.6    2.1  2  DUF745          Protein of unknown function (DUF745)
       0.11   12.9   3.2         15    6.1   0.2    3.4  2  UPF0184         Uncharacterised protein family (UPF0184)
       0.14   12.4   3.9       0.15   12.3   1.0    2.5  2  Virulence_fact  Virulence factor
       0.28   11.9   6.6        0.3   11.8   1.4    2.8  2  VWA_2           von Willebrand factor type A domain
       0.31   11.5   2.3         41    4.7   0.1    3.0  3  MtrB            Tetrahydromethanopterin S-methyltransferase s
        1.1    8.1  41.4        1.4    7.7  41.4    1.1  1  DUF812          Protein of unknown function (DUF812)
        1.2    8.7   6.0       0.58    9.7   3.8    1.7  1  DUF3300         Protein of unknown function (DUF3300)
        1.7    9.1   4.5        2.1    8.8   0.2    2.9  2  ACP_PD          Acyl carrier protein phosphodiesterase
        2.6    8.0   7.5        0.7    9.9   2.4    2.5  3  PSDC            Phophatidylserine decarboxylase
        2.8    8.1  23.5       0.86    9.8  13.9    2.5  2  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
        2.9    8.3  21.4        3.7    7.9   9.3    4.0  3  FCH             Fes/CIP4, and EFC/F-BAR homology domain
          3    6.7  41.1      0.057   12.3  18.7    3.0  3  Spc7            Spc7 kinetochore protein
        3.2    6.7  13.0       0.24   10.3   3.4    2.2  2  DUF2333         Uncharacterized protein conserved in bacteria
        3.4    7.5  36.6       0.19   11.5   7.7    3.4  3  Phage_GP20      Phage minor structural protein GP20
        3.7    7.0  29.9       0.22   11.0  10.8    3.2  3  DegS            Sensor protein DegS
        3.8    7.8  10.0        5.5    7.3   0.5    3.1  2  DUF948          Bacterial protein of unknown function (DUF948
        3.8    7.4   6.6        1.9    8.4   0.3    3.4  4  MtrG            Tetrahydromethanopterin S-methyltransferase, 
        5.4    5.5  37.0        3.8    6.0  25.7    2.0  2  AAA_13          AAA domain
        5.5    7.2  33.3       0.63   10.2  12.5    2.5  2  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
        6.7    6.1  34.0        7.4    5.9  13.1    2.2  2  Golgin_A5       Golgin subfamily A member 5
        9.6    6.2  33.8        2.3    8.3  13.6    2.4  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.9    0.0015       1.1      18      89 ..       4      73 ..       1      88 [. 0.82
   2 !   11.8   0.9   0.00024      0.18      36      89 ..     111     163 ..     107     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
  Baculo_PEP_C 18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89
                  L n L+++ +q+++i +++ +  ++  ++++++s + +s+l++ ++r+dt+ ++ +d    l++++  ++++
    AJA92907.1  4 LKNKLKQLTSQKSEI-SKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQKI-AQMES 73
                  8899***********.******************************99998776555444444544.34444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00024
  Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89 
                   l+  ld+i ++++++++++k+  +++++++++++++++++ n++++t+++++++
    AJA92907.1 111 LQYRLDSIISTIEEIKNEIKQ-RTSMEKKFSQAIDEIEKKKNSVSKTIKKNIES 163
                   677899999***********9.788************************99986 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5  11.5       8.1     6e+03      26      75 ..      30      80 ..       2     102 .. 0.45
   2 ?    1.8   9.2      0.37   2.8e+02       5      99 ..      51     145 ..      49     146 .. 0.86
   3 ?   15.7  15.5   1.8e-05     0.013      29     105 ..     127     207 ..     108     210 .. 0.85
   4 ?   -1.3   1.3       3.4   2.5e+03      69      87 ..     222     240 ..     210     249 .. 0.37

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.1
                  HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCC CS
  Seryl_tRNA_N 26 advdell.eldekrrelqveleelqaerNelskeIgkakkkkedaeeliae 75
                  ++v+++  +  +  +++q++++ +++    +++  ++++++ e +++l+  
    AJA92907.1 30 KKVKSISrKYSSSLKSTQKRIDTFKQTAEDVNEILSQKIAQMESIQRLKSA 80
                  222222201223334445555555555555555555555544444444433 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.37
                   HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                   + + +  e v e l ++ ++ + +++l ++ ++r +l+++  e  +     s + +++   +   +++i  ++e+k+e+k+ +  +k+ ++++++
    AJA92907.1  51 DTFKQTAEDVNEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVESEIDFSDTPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDE 145
                   67888999999999999999999999999999999999999888888889999999998888999999999999999999999988888888776 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.8e-05
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS- CS
  Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaeleklllaiP 105
                    e+ +  +  ++  ++++e+ +++N++sk+I+k +++k    + a+   ++ ++ +++++ ++++++ ++a+l k+ +aiP
    AJA92907.1 127 NEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKpelaKLAKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAIP 207
                   45566666667888899*********************88888888888999999**********************9999 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.4
                   TCCCCCCCHHHHHHHHHHH CS
  Seryl_tRNA_N  69 aeeliaevkelkeelkale 87 
                   + +++a+ k+ k + k ++
    AJA92907.1 222 TRKIKAKPKTRKIKAKPKT 240
                   2222222222222222222 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00036      0.27      13      46 ..      33      66 ..      26      77 .. 0.83
   2 ?    6.9   1.6    0.0071       5.3       8      40 ..     114     146 ..     109     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00036
   DASH_Duo1 13 nevienviesLkkaksniervketvestntLLdk 46
                 ++  ++ +sLk++++ i+++k+t e++n++L +
  AJA92907.1 33 KSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQ 66
                444468899**********************975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0071
   DASH_Duo1   8 qLrkinevienviesLkkaksniervketvest 40 
                  L++i+++ie +++++k+ +s  +++++++++ 
  AJA92907.1 114 RLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEI 146
                 799**************9999999999988765 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   9.0     0.027        20      69     165 ..       6     104 ..       1     112 [. 0.77
   2 ?   13.8  10.6   4.9e-05     0.037      68     168 ..     112     212 ..     106     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
      DUF745  69 qelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv..eeLkkqlkearkdlekt 165
                 ++l+   ++ +e++k  ++ e+  k +++++++  ++l++ ++ ++++k+++e+++++ ++  +++++ + l  aA++R+  e+ +k+  e   d+ +t
  AJA92907.1   6 NKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQKIAQMESIQRLKSAAQERLtlETQNKEQVESEIDFSDT 104
                 555555556666777777888999999999999999999999999999999999999999999999999999999999972244555555566666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.9e-05
      DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektk 166
                 +  l    + ++e+k+++++  +  k  ++a ++++++ +++++++k+  e+  ++ ++a+ aqq+l++ ++  e+AkkR  +++ ql+++++   k k
  AJA92907.1 112 QYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAIPKPK 210
                 555566667899******************************************************************************998776666 PP

      DUF745 167 ka 168
                  +
  AJA92907.1 211 PK 212
                 55 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.035        26       4      54 ..       5      55 ..       1     110 [. 0.77
   2 ?    6.1   0.2      0.02        15      26      69 ..     127     170 ..     116     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
     UPF0184  4 kngddnisvedgaeteedefgeeEyeainsmLDqinsaLDalEernDdlns 54
                kn  ++++++ + +++    ge Ey+ + s   + +s L    +r D  + 
  AJA92907.1  5 KNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQ 55
                566667778888888888889999999999999999999888888887654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
     UPF0184  26 eEyeainsmLDqinsaLDalEernDdlnskLrELlesnRqiRle 69 
                 +E+++  sm  + + a+D++E++++++   ++  +es  +  ++
  AJA92907.1 127 NEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKL 170
                 56666678889999******************999998776544 PP

>> Virulence_fact  Virulence factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.7   1.3e+03      53      72 ..      49      68 ..      39     100 .. 0.66
   2 ?   12.3   1.0    0.0002      0.15      16      71 ..     128     181 ..     121     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
  Virulence_fact 53 rygdleeiaeevaeeleaaY 72
                    r +++++ ae+v e l+++ 
      AJA92907.1 49 RIDTFKQTAEDVNEILSQKI 68
                    44444455544444444333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
  Virulence_fact  16 eeearveLperFeqAidraamasdnyiaerkwaeqgvrygdleeiaeevaeeleaa 71 
                     e ++r++++++F+qAid++++++ n + +  +++  + + +l++ a++++++l++a
      AJA92907.1 128 EIKQRTSMEKKFSQAIDEIEKKK-NSVSKTIKKN-IESKPELAKLAKTAQQKLDSA 181
                     5579****************655.5555444444.466778888888888888765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4    0.0004       0.3      21      99 ..      74     156 ..      39     161 .. 0.79
   2 ?    2.0   0.2      0.42   3.1e+02      56      93 ..     172     210 ..     160     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
       VWA_2  21 leaakdaveallk...slpgdrvglvtfsdgpevlipltkdkakilnalrnleak.gggtnlaaaLqlarkalkkrrkgekrv 99 
                 ++++k+a+++ l    +++++  + + fsd+pe + +l    ++i + +++++ + ++ t++++ +++a ++++k++++++++
  AJA92907.1  74 IQRLKSAAQERLTletQNKEQVESEIDFSDTPEEKQSLQYRLDSIISTIEEIKNEiKQRTSMEKKFSQAIDEIEKKKNSVSKT 156
                 445555554444433344555556689**************************99******************9988555554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.42
       VWA_2  56 tkdkakilnalrnleak.gggtnlaaaLqlarkalkkrr 93 
                 ++ ++k+++a ++ e   + +++++a L+++++a++k +
  AJA92907.1 172 KTAQQKLDSASKKFESAkKRESSVTAQLSKVKAAIPKPK 210
                 567788888888888778899999999999999998765 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.07        52      30      62 ..      42      74 ..      31      82 .. 0.88
   2 ?    0.4   0.1       1.2   8.9e+02      24      40 ..     115     131 ..     104     152 .. 0.58
   3 ?    4.7   0.1     0.054        41      29      70 ..     155     196 ..     146     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.07
        MtrB 30 sldpvleeidkLekiaddlvnsLdpetallesy 62
                sl+  +++id  +++a+d+ + L+ + a +es 
  AJA92907.1 42 SLKSTQKRIDTFKQTAEDVNEILSQKIAQMESI 74
                7889999*****************999999885 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
        MtrB  24 edvvllsldpvleeidk 40 
                  d ++ +++++++ei++
  AJA92907.1 115 LDSIISTIEEIKNEIKQ 131
                 34455555555555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.054
        MtrB  29 lsldpvleeidkLekiaddlvnsLdpetallesypgRektlv 70 
                  ++++ +e   +L k+a+   ++Ld  ++  es ++Re++++
  AJA92907.1 155 KTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKKRESSVT 196
                 4455555555689*************************8764 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  41.4    0.0019       1.4     233     453 ..      15     236 ..       3     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
      DUF812 233 asrlteeeykkrkkeklqkrlaeqlrkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaeklqftkeelakkaeteeelkkkreee 331
                 +s+ ++   k + + k  k ++++++++++++++ +   ++ ++d++e+ls+ + + e+ +    + + + +e+l+++++  ++++e+e +     ee+
  AJA92907.1  15 KSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQKIAQMESIQ----RLKSAAQERLTLETQ-NKEQVESEIDFSDTPEEK 108
                 2335555555566888899999999999999999888888999999999999866666644....555556666666555.234666666766666655 PP

      DUF812 332 leelqeqieeleskieeleeeikk...lessikqveeeleeekeen.eelekevklkkktlellpdaeeniekLqalveasaqrlvelakqWekhRvpl 426
                  ++lq +++++ s+iee+++eik+   +e++ +q+ +e+e++k++  ++ +k+++ k  +++l+++a++ +    + +e++++r  ++ +q  k ++++
  AJA92907.1 109 -QSLQYRLDSIISTIEEIKNEIKQrtsMEKKFSQAIDEIEKKKNSVsKTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAI 206
                 .99****************99996333677777777788777766514567899*******************************************99 PP

      DUF812 427 ie...eyrelkesksekekeaerkleeikk 453
                  +   + r+ k + ++++ +a+ k ++ik+
  AJA92907.1 207 PKpkpKTRKIKAKPKTRKIKAKPKTRKIKA 236
                 87555899999999*************996 PP

>> DUF3300  Protein of unknown function (DUF3300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.8   0.00078      0.58      89     126 ..      61      98 ..      31     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00078
     DUF3300  89 daflaqeeevldavQrLRqkAkaagnLksteqqkvtve 126
                 +  l+q+   ++++QrL++ A+++ +L+++++ +v++e
  AJA92907.1  61 NEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVESE 98 
                 5678899999************************9988 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2         1   7.8e+02      38      42 ..      63      67 ..      27     103 .. 0.54
   2 ?    8.8   0.2    0.0028       2.1      59      94 ..     120     155 ..     116     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
      ACP_PD 38 rlqrl 42
                 l++ 
  AJA92907.1 63 ILSQK 67
                22222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
      ACP_PD  59 egieralqrmarrlkrasklaeaieeleenyaelea 94 
                 + ie++ +++++r+++++k+++ai+e+e++++ +++
  AJA92907.1 120 STIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSK 155
                 67999999*********************9998776 PP

>> PSDC  Phophatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.2   8.7e+02      38      60 ..      44      66 ..       6     109 .. 0.66
   2 ?    9.9   2.4   0.00093       0.7       3      53 ..     121     170 ..     119     203 .. 0.77
   3 ?    2.5   0.1      0.18   1.3e+02       5      36 ..     155     186 ..     151     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
        PSDC 38 ptgkkqirdyeellellnhiltt 60
                ++++k+i+++++  e  n+il++
  AJA92907.1 44 KSTQKRIDTFKQTAEDVNEILSQ 66
                33445666666655555555554 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00093
        PSDC   3 vvqelkdliesdprlrmlfssmfeevpskkpykkdptgkkqirdyeellel 53 
                 +++e+k+ i++++++ + fs++++e++ kk+ + ++t kk+i++  el +l
  AJA92907.1 121 TIEEIKNEIKQRTSMEKKFSQAIDEIE-KKKNSVSKTIKKNIESKPELAKL 170
                 799***********************9.55555567777788776666554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.18
        PSDC   5 qelkdliesdprlrmlfssmfeevpskkpykk 36 
                 +++k+ ies+p+l +l++ + ++  s ++  +
  AJA92907.1 155 KTIKKNIESKPELAKLAKTAQQKLDSASKKFE 186
                 578999******99999999888774433332 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   6.4       1.1   8.5e+02      42      94 ..       5      57 ..       2      95 .. 0.51
   2 ?    9.8  13.9    0.0012      0.86      16     117 ..      90     192 ..      75     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.1
      CENP-Q 42 spelhslelLeaeiekeeralerdyeaLreLeknakaeare.rke..klkkehvll 94
                +  l++l   ++ei+k  r+ e +y++ ++  ++ ++  ++ +k+  + k+    +
  AJA92907.1  5 KNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKStQKRidTFKQ---TA 57
                556677777777777777777777777777777777666663333332222...22 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
      CENP-Q  16 qsdggkekeldfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerkeklkkehvllqesdseelslleassdevlg 114
                 q++++ e+e df  + +ek++l+  L+    ++e+ ++ei++   + ++  +a+ e ek+ ++  ++ k++ +++  l++ +++++++l++as+++ ++
  AJA92907.1  90 QNKEQVESEIDFSDTPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKLAKTAQQKLDSASKKFESA 188
                 778899*************************************************************99988888889998889999999999986665 PP

      CENP-Q 115 ea.s 117
                 ++ +
  AJA92907.1 189 KKrE 192
                 5431 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.2      0.57   4.2e+02      27      61 ..      33      57 ..       5      80 .. 0.52
   2 ?   -0.4   0.1       1.9   1.4e+03       9      30 ..      64      88 ..      58      91 .. 0.57
   3 ?    7.9   9.3     0.005       3.7       4      53 ..     110     166 ..     109     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.57
                HHHHHHHHHHHHHHCT----TT-.....HHHHHHH CS
         FCH 27 aeiEkeYakkLqkLakkylkrrkkkseestlvtaw 61
                 +i + Y+ +L+   k+++           ++++ 
  AJA92907.1 33 KSISRKYSSSLKSTQKRIDT----------FKQTA 57
                33333333333333333333..........22222 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                HHHHHHHHHHH...HHHHHHHHHHH CS
         FCH  9 leqgialledl...qeflkeRaeiE 30
                l+q+ia++e +   ++  +eR  +E
  AJA92907.1 64 LSQKIAQMESIqrlKSAAQERLTLE 88
                5566666665511155566666665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.005
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----TT-............. CS
         FCH   4 vlqkrleqgialledlqeflkeRaeiEkeYakkLqkLakkylkrrkkks.........e 53 
                 +lq rl++ i ++e++++ +k+R + Ek ++++ + + kk ++   +k+         e
  AJA92907.1 110 SLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSV--SKTikknieskpE 166
                 68999*********************************998874..2322234554441 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  15.2     0.028        21     150     251 ..       3     100 ..       1     109 [. 0.80
   2 ?   12.3  18.7   7.6e-05     0.057     153     252 ..      59     159 ..      47     166 .. 0.90
   3 ?    0.8   7.7      0.25   1.9e+02     182     260 ..     166     244 ..     159     250 .] 0.50

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.028
        Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkselee 248
                 gl++  ++L++q++e++++  + e+e++++++  +k  +      +++++++ +++++ +++++ +++k +++++ q+ + + +e+++  +++k+++e+
  AJA92907.1   3 GLKNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSS----SLKSTQKRIDTFKQTAEDVNEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVES 97 
                 667777777777777777777777777776666555555....3347999************************************************* PP

        Spc7 249 eia 251
                 ei 
  AJA92907.1  98 EID 100
                 997 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.6e-05
        Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                 + +e L+++ ++++++    ++ +++l+ e ++ ++ + e++ +d +ee ++l+ +l+++ ++iee k+e++++++  ++ +++i+e++++k+++ + i
  AJA92907.1  59 DVNEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVESEIDFSDtPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTI 157
                 3367899999999999999999999*****************9*99****************************************************9 PP

        Spc7 251 ae 252
                 ++
  AJA92907.1 158 KK 159
                 97 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.25
        Spc7 182 eleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                 el+kl + a++  ++ +++ e+++++ +++ a++++ k+ + + + +  ++++k ++ k + +    +i+++ ++++ +
  AJA92907.1 166 ELAKLAKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAIPKPKPKTRKIKAKPKTRKIKAKPKTRKIKAKPKTRKIK 244
                 4444444444444445555555555555555555555555555555555555555555555555555555555555444 PP

>> DUF2333  Uncharacterized protein conserved in bacteria (DUF2333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.4   0.00033      0.24     145     218 ..      25      98 ..      11     118 .. 0.78
   2 ?    1.6   2.1      0.15   1.1e+02     144     227 ..     134     214 ..     122     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
     DUF2333 145 teseYrkgikalerYlkrlsdekekdaqFyaradnLneyleevekRLgslsqrLsasvgkaklntdlagdeeak 218
                  e+eY+k  +  ++Y + l++++++   F + a+++ne l++    ++s+ +  sa+ ++ +l+t+ +++ e +
  AJA92907.1  25 GETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVESE 98 
                 699********************************************999666566666666666655443333 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
     DUF2333 144 steseYrkgikalerYlkrlsdekekdaqFyaradnLneyleevekRLgslsqrLsasvgkaklntdlagdeeakqskeeeeek 227
                 s e+++ ++i+++e+  + +s++ +k+        +L++  ++ +++L+s s++   + ++++  t+  ++ +a+  k++++++
  AJA92907.1 134 SMEKKFSQAIDEIEKKKNSVSKTIKKN---IESKPELAKLAKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAIPKPKPKTR 214
                 778888899999988888888865554...445678888888888899998888877666664444444444444444444444 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   7.7   0.00025      0.19      16      76 ..      22      86 ..       6     100 .. 0.75
   2 ?    8.6   8.1    0.0021       1.6      10      78 ..      90     159 ..      86     165 .. 0.91
   3 ?   -3.4   8.6       9.9   7.4e+03      27      97 ..     171     241 ..     161     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
  Phage_GP20 16 t...kakldeveeerdtlkeqlkdrdkqLedLkkkakdnee.Lqkqieelqaknkkakaeyeaki 76
                    ++++++v++   ++ ++lk  +k ++++k+ a+d++e L ++i++++     ++a  e   
  AJA92907.1 22 RrkgETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEiLSQKIAQMESIQRLKSAAQERLT 86
                2445899*******************************766378999999977666555555444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0021
  Phage_GP20  10 engkdit.kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiad 78 
                 +n++ +  + ++++  ee+++l+ +l+   +++e++k++ k  ++++k++ +   +++k+k+   + i++
  AJA92907.1  90 QNKEQVEsEIDFSDTPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKK 159
                 677778668899999********************************************99999999986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.9
  Phage_GP20  27 rdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLkeakakne 97 
                  +t +++l+ + k+ e  kk    +++   +++    k k +  + +ak + +k+ +  ++   +ak k  
  AJA92907.1 171 AKTAQQKLDSASKKFESAKKRESSVTAQLSKVKAAIPKPKPKTRKIKAKPKTRKIKAKPKTRKIKAKPKTR 241
                 56777777777777777777766666666666666666666666666666666666655555444555554 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.0     0.014        11       5      55 ..       5      55 ..       4      57 .. 0.90
   2 ?   -1.1  13.8       1.6   1.2e+03      25     123 ..      46     148 ..      43     148 .. 0.80
   3 ?   11.0  10.8   0.00029      0.22       5      76 ..     116     190 ..     112     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
        DegS  5 kktietiekskeeifeIaEsarkeverlkkeleelkeevsevikevdklek 55
                k+ ++ +++ k+ei +I  + ++e++++k+  ++  + ++++ k++d++++
  AJA92907.1  5 KNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQ 55
                788999***********************9999999999999999998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
        DegS  25 arkeverlkkeleelkeevsevikevdklekkerkarkrLa.eVskdFkkyseeeikeaYeeakelqvelall..r.ekEkqlrerRdelerrLkklke 119
                 ++k ++  k+  e+++e +s+ i++++++++ +  a++rL+ e + + +  se +  ++ ee ++lq +l       e+ k+ +++R ++e++  ++ +
  AJA92907.1  46 TQKRIDTFKQTAEDVNEILSQKIAQMESIQRLKSAAQERLTlETQNKEQVESEIDFSDTPEEKQSLQYRLDSIisTiEEIKNEIKQRTSMEKKFSQAID 144
                 67788999********************************8244555555688899***********9985431131444677899*****99999888 PP

        DegS 120 tier 123
                  ie+
  AJA92907.1 145 EIEK 148
                 8876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00029
        DegS   5 kktietiekskeeife...IaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyse 76 
                 +++i+tie+ k+ei +   +  +  + +++++k+ + + +++++ i++  +l+k  + a+++L   sk+F++ ++
  AJA92907.1 116 DSIISTIEEIKNEIKQrtsMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKK 190
                 5678888888888854222777888999999999999999999999************************97665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0073       5.5      34      78 ..      31      82 ..       3      91 .. 0.67
   2 ?    3.4   3.2      0.12        90      29      84 ..     137     195 ..     108     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0073
      DUF948 34 tieelekqvdpilkevedllakvnelledvne.......klekvdplteava 78
                 ++++ ++  + lk +++ +++ ++++edvne       ++e++++l +a++
  AJA92907.1 31 KVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEilsqkiaQMESIQRLKSAAQ 82
                4555566666666666666666666666666644443336666666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
      DUF948  29 deaaatieelekqvdpilkevedllakvne...lledvneklekvdplteavadlgesv 84 
                 ++++++i+e+ek+ ++++k +++ ++   e   l++  ++kl++  + +e++++   sv
  AJA92907.1 137 KKFSQAIDEIEKKKNSVSKTIKKNIESKPElakLAKTAQQKLDSASKKFESAKKRESSV 195
                 34455555555555555555555555433333377778888888888888887766665 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.3   1.7e+03      13      37 ..      44      68 ..      40      71 .. 0.78
   2 ?    8.4   0.3    0.0025       1.9       9      37 ..     105     133 ..      99     138 .. 0.90
   3 ?   -1.7   0.0       3.6   2.7e+03      17      28 ..     141     152 ..     134     161 .. 0.63
   4 ?   -0.3   0.0       1.3     1e+03      14      29 ..     173     188 ..     169     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
        MtrG 13 nevkkrLdeieekvefvnsEiaqri 37
                +  +kr+d   ++ e vn  ++q+i
  AJA92907.1 44 KSTQKRIDTFKQTAEDVNEILSQKI 68
                5678999999999999888777776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
        MtrG   9 pddfnevkkrLdeieekvefvnsEiaqri 37 
                 p++ + ++ rLd i  ++e ++ Ei qr+
  AJA92907.1 105 PEEKQSLQYRLDSIISTIEEIKNEIKQRT 133
                 56778899*******************97 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.6
        MtrG  17 krLdeieekvef 28 
                 + +deie+k + 
  AJA92907.1 141 QAIDEIEKKKNS 152
                 556777777544 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.3
        MtrG  14 evkkrLdeieekvefv 29 
                 +++++Ld   +k e +
  AJA92907.1 173 TAQQKLDSASKKFESA 188
                 6799*****9999865 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.0    0.0099       7.4     407     468 ..       4      65 ..       1      69 [. 0.91
   2 ?    6.0  25.7    0.0051       3.8     291     446 ..      70     222 ..      66     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0099
      AAA_13 407 leseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                 l+++l+++++++++++k   k e+e k+ ++  +k+    k  +k++ + k++ae++n++L+
  AJA92907.1   4 LKNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILS 65 
                 5778899999999999999999999*********************************9997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0051
      AAA_13 291 liekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvel.esvkakiesikklvaeineliakhNekvanl 388
                  +e++++ ks ++e+l ++ ++++e+ ++e d ++  +e++ l+ +L+++ + +e+ ++e+ ++ ++ +++++ i++i+k+ +++ ++i+k+ e   +l
  AJA92907.1  70 QMESIQRLKSAAQERL-TLETQNKEQVESEIDFSDTPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMeKKFSQAIDEIEKKKNSVSKTIKKNIESKPEL 167
                 5788899998888899.55556888999**************************************967788899************************ PP

      AAA_13 389 eeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleee..i 446
                 ++ +++a++kl     +++    +  kk  ++++++++k+++++ + + +++k++++   
  AJA92907.1 168 AKLAKTAQQKLDS-ASKKF----ESAKKRESSVTAQLSKVKAAIPKPKPKTRKIKAKpkT 222
                 ***********98.33444....4446677777778888888888777777777776332 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4  13.0      0.23   1.7e+02      55     131 ..       4      86 ..       1     106 [. 0.54
   2 ?   10.2  12.5   0.00085      0.63      49     141 ..     108     200 ..      98     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.23
  Jnk-SapK_ap_N  55 lreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrele......lkaknaadqlsrleekeaelkk 131
                    l+++l+qL++++++  + r++ e e+ ++    ++  + l++  ++ ++ ++  e       +  ++ + ++rl++  +e  +
     AJA92907.1   4 LKNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEdvneilSQKIAQMESIQRLKSAAQERLT 86 
                    8999*******************777666666665555555554444444444440001001111222233333333333322 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00085
  Jnk-SapK_ap_N  49 eaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheret 141
                    ++ l+   + + +  +e ++e ++r   e+++ ++ d++e++++ +++ ++++ e + el + ak a+++l + ++k ++ kk++s+ + + +
     AJA92907.1 108 KQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKKRESSVTAQLS 200
                    444444444444444556667777777778888888888888888888888888888888866777777777777777666666666655444 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  19.2     0.015        11      29     144 ..      10     132 ..       3     134 .. 0.72
   2 ?    5.9  13.1    0.0099       7.4      47     137 ..      99     192 ..      96     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
   Golgin_A5  29 sLkegsgeeglesstalsaeldelkqerdllreelqklnqqieqlrt...elqdleaqqqaeaeslreqlqeleeqleeerkakeeveaele.....rl 119
                 +L +++ +e ++ +++ ++e+ ++k+ +  + ++l++++++i++ ++   +++++ +q+ a++es++   + ++e+l+ e+++ke+ve+e+      + 
  AJA92907.1  10 QLTSQK-SEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQtaeDVNEILSQKIAQMESIQRLKSAAQERLTLETQNKEQVESEIDfsdtpEE 107
                 233222.22334466778889999998888899999999988877762226677778999999*************************99963333356 PP

   Golgin_A5 120 keelryleeelvrskatlqsrikdr 144
                 k+ l+y  +  + + ++++++ik+r
  AJA92907.1 108 KQSLQYRLDSIISTIEEIKNEIKQR 132
                 7778888888888888888888776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0099
   Golgin_A5  47 aeldelkqerdllreelqklnqqieqlrtel...qdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatl 137
                  +++++ +e++ l+  l +  ++ie++++e+     +e+++++ +++++++ +++ ++++++ ++k e+ +  +  +++l+++ +    +k+  
  AJA92907.1  99 IDFSDTPEEKQSLQYRLDSIISTIEEIKNEIkqrTSMEKKFSQAIDEIEKKKNSVSKTIKKNIESKPELAKLAKTAQQKLDSASKKFESAKKRE 192
                 566777899999******************9533369999999999999999999999999999999999999999999998877655444332 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  13.6     0.003       2.3      51     137 ..       5      93 ..       3      96 .. 0.83
   2 ?    3.3  21.6     0.099        74      22     137 ..      64     184 ..      62     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
  CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe..kvqmkeeskaaveeLqtqlke 137
                     k+++++l +++ e+++ +r+ e++ ++++s   +   +l+  q+r+++ +++ ++++++l++k ++   +q  +++ ++   L+tq ke
      AJA92907.1   5 KNKLKQLTSQKSEISKIRRKGETEYKKVKSISRKYSSSLKSTQKRIDTFKQTAEDVNEILSQKIAQmeSIQRLKSAAQERLTLETQNKE 93 
                     778999******************************************************99988722445555555555556666665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.099
  CENP-F_leu_zip  22 LkdkvenLerelemseenqekvileaEtskaevet......lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenll 110
                     L +k+ ++e+      + qe+++le  ++ ++ve+        ee++ l+ +l  + + ++++++e ++ + + +k  + ++e e+ + s+++++
      AJA92907.1  64 LSQKIAQMESIQRLKSAAQERLTLETQNK-EQVESeidfsdTPEEKQSLQYRLDSIISTIEEIKNEIKQRTSMEKKFSQAIDEIEKKKNSVSKTI 157
                     89**********************98775.4444446666678999999999999999999999999999999999999**************** PP

  CENP-F_leu_zip 111 eekEqekvqmkeeskaaveeLqtqlke 137
                     +++ + k ++ + +k+a ++L +  k+
      AJA92907.1 158 KKNIESKPELAKLAKTAQQKLDSASKK 184
                     *********************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4210  (0.234815); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 1.10u 0.30s 00:00:01.40 Elapsed: 00:00:00.54
# Mc/sec: 1386.21
//
Query:       AJA92908.1  [L=215]
Description: putative cyclase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-36  124.3   0.0    4.7e-36  124.0   0.0    1.1  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   0.0   2.6e-40   4.7e-36       1     135 [.       4     156 ..       4     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 2.6e-40
     Cyclase   1 idLshplsedtpvwp...dp.................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvsakaaaedyeiitaedleaal 77 
                 idL++++se++p++p   +p                 + ls+htGTH+Dap+Hf++  ++id++  ++lv++av++ +++    +d++i ++ d+++++
  AJA92908.1   4 IDLTLTISEKIPTFPgspQPnfinwesiekdgynlelLFLSTHTGTHIDAPYHFVKkgQKIDQIVTKRLVTEAVLIKIRKG---SDQAI-SKTDIQKFE 98 
                 8*************6565338899999*********999****************9999*******************775...57755.********* PP

     Cyclase  78 akqgveikpgdivlirTgwskrledkeky..rnpglseeaaewlaekgvkavGvDtlsvD 135
                 +k g +i +g+ ++++Tgw+k+l+ k+ y  +npgl  +aa++la+k++++vG+D +s+D
  AJA92908.1  99 KKFG-KIDDGSTIIFHTGWQKNLN-KKSYfsKNPGLAVSAAKYLASKKINLVGIDSPSID 156
                 ****.***************9965.55565*99**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1582.79
//
Query:       AJA92909.1  [L=255]
Description: sugar-specific transcriptional regulator, TrmB family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-21   75.7   0.0    4.1e-21   74.6   0.0    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
    3.9e-07   29.5   0.0    5.3e-07   29.1   0.0    1.1  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    5.9e-05   22.8   0.0    0.00016   21.4   0.0    1.7  2  HTH_IclR         IclR helix-turn-helix domain
     0.0013   18.3   0.0     0.0028   17.2   0.0    1.6  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0059   16.6   0.0      0.013   15.5   0.0    1.5  1  HTH_29           Winged helix-turn helix
     0.0092   16.3   0.0      0.066   13.6   0.0    2.1  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.033   14.7   0.0    1.7  1  HTH_27           Winged helix DNA-binding domain
      0.019   15.3   0.0       0.05   14.0   0.0    1.7  1  Rrf2             Transcriptional regulator
      0.032   14.2   0.0      0.067   13.2   0.0    1.6  1  PadR             Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   2.1e-24   4.1e-21       1      67 [.      11      77 ..      11      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 2.1e-24
                HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
        TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                L+k+GL++yE+++Y++L+k g+++a+ei++++gvp+sk+Ye+L  Le+kG++   ++rp++Y a  p
  AJA92909.1 11 LEKIGLTSYEIRAYTTLIKDGESNASEISQNSGVPYSKIYEILGTLEEKGWIGSDDSRPTKYFAKAP 77
                789***********************************************************99877 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.7e-10   5.3e-07       2     124 ..     118     245 ..     117     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.7e-10
                     EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GG...GHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EEEEETTTEEE CS
  Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpse...lLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsgapllvivDrkrgv 93 
                     +w + +  +++++i e++e  ++e+++++p+    ++++  ++l++ +++g+++ +li+++ d++  +  + +++v+v  +     +i+D++++v
      AJA92909.1 118 IWFISGAMNIVSKIMEMVEHCREEVMIAVPQAgelIVKQALPKLRQLHDKGIKITILISDEFDKDSIKAISRVADVKVKGGLFGGGIISDKRYVV 212
                     89****************************9755589****************************************9877766679******99 PP

                     EE-SSS-..EEEE--HHHHHHHHHHHHHH.... CS
  Regulator_TrmB  94 vaprevl..rdkeeeyaiifkekelihvlshyF 124
                     +        ++++e  ai+ +   l+ +   yF
      AJA92909.1 213 ILLGPEIssSTSSEIVAIWADHAGLAGFAREYF 245
                     975533347999999999998888877766666 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.1e-08   0.00016      17      51 ..      31      65 ..      28      66 .. 0.89
   2 ?   -3.1   0.0       3.5   6.9e+03       8      20 ..     131     143 ..     129     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.1e-08
                SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                +e + se+++++g+p S+ + +L tL+e G++  d
  AJA92909.1 31 GESNASEISQNSGVPYSKIYEILGTLEEKGWIGSD 65
                66789**************************8665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                 HHCT-CTTBSS-B CS
    HTH_IclR   8 iLdalaeapqelt 20 
                 i+++++++++e+ 
  AJA92909.1 131 IMEMVEHCREEVM 143
                 8999999999875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0028       6      47 ..      21      62 ..      16      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
      HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                ++ + +L k++  + +e+++ +g++ s + + l  Lee+G+I
  AJA92909.1 21 IRAYTTLIKDGESNASEISQNSGVPYSKIYEILGTLEEKGWI 62
                5667789**********************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06     0.013       7      48 ..      27      69 ..      26      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
      HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rr 48
                l+++G+s+ s+i ++ g+ ++++y +l   ee+G+ + +d r+
  AJA92909.1 27 LIKDGESNASEISQNSGVPYSKIYEILGTLEEKGWIGSDDsRP 69
                789**********************************999555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   3.3e-05     0.066      21      86 ..      36      94 ..      16     110 .. 0.74
   2 ?    0.2   0.0      0.46   9.2e+02       6      30 ..     140     164 ..     137     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-05
                     HHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXX CS
  Penicillinase_R 21 kevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfeg 86
                     +    e+++++ + ys +  +l+ L++Kg++ ++   r + Y + +  + +   ++kq  d++f++
       AJA92909.1 36 S----EISQNSGVPYSKIYEILGTLEEKGWIGSDD-SRPTKYFAKAPSNALE--TTKQNADTIFSE 94
                     4....456666778******************987.8999999999887764..456666666653 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                      SHHHHHHHHHS-EEHHHHHHT--GG CS
  Penicillinase_R   6 aevmeilwekgeatvkevveeleee 30 
                      +evm ++ ++ge+ vk+   +l + 
       AJA92909.1 140 EEVMIAVPQAGELIVKQALPKLRQL 164
                      7999999999999999877777654 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.033      11      60 ..      27      70 ..      21      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
      HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrek 60
                li+  ++++ ++++++   v +s i ++l  L+ekG++   g+  d r++
  AJA92909.1 27 LIK--DGESNASEISQNSGVPYSKIYEILGTLEEKGWI---GS-DDSRPT 70
                555..89999****************************...55.466654 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-05      0.05       8      57 ..      18      64 ..      15      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                +y ++a + L k  e    +++ei+++ +++ s +  il +L+++g++ s
  AJA92909.1 18 SYEIRAYTTLIKDGE---SNASEISQNSGVPYSKIYEILGTLEEKGWIGS 64
                566666666666666...579***************************88 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.4e-05     0.067      28      64 ..      43      74 ..      30      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                CTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEE CS
        PadR 28 elseGslYpaLkrLekeglveseweesgegpprkyYr 64
                 + ++++Y +L +Le++g++ s  +     +p+ky++
  AJA92909.1 43 GVPYSKIYEILGTLEEKGWIGSDDS-----RPTKYFA 74
                467899**************99855.....5888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1836.45
//
Query:       AJA92910.1  [L=447]
Description: phosphoglucosamine mutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-40  136.4   0.0    9.6e-40  135.5   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    7.6e-25   87.5   0.0    1.7e-24   86.4   0.0    1.6  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.1e-20   73.9   0.0    2.7e-20   72.7   0.0    1.7  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
      5e-08   33.0   0.0    1.3e-07   31.7   0.0    1.6  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
       0.03   14.3   0.0       0.07   13.1   0.0    1.6  1  CHASE5       Periplasmic sensor domain found in signal transd


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0   2.7e-43   9.6e-40       2     135 ..       3     131 ..       2     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 2.7e-43
                 GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--T CS
   PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaS 100
                 ++fgt+G+Rg+++e+ +t e+v  l++++a ++k+    +k++vG+D+R+ss+ +a+ + + l  +G++ +++gl+ptP + +a++kl++d+g+mitaS
  AJA92910.1   3 KLFGTNGVRGVFSED-FTLEFVNDLVMSLAAHFKQ----GKILVGYDGRHSSPIVAKVVSSALNYSGLDCYMAGLVPTPCLEYATKKLGYDGGLMITAS 96 
                 79***********65.9*****************9....9*********************************************************** PP

                 TS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
   PGM_PMM_I 101 HnppeyngiKvylsnGgpispeveekIeaiiekee 135
                 Hnpp+yngiK + s+G++is+e+e+kIe+i++++ 
  AJA92910.1  97 HNPPQYNGIKPVASDGVEISREDERKIEQIFDEKN 131
                 ******************************99875 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   4.8e-28   1.7e-24       2     103 .]     150     250 ..     149     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 4.8e-28
                 HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEEE CS
  PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDaDRlgvvd 100
                 +Yi+++ + +d++ ik +++kv +d ++Ga + ++k+l++ lg+dv+++n+e ++dfp++ ++p++ ++l++l++lv +++ ++g+afDgD+DR +++d
  AJA92910.1 150 TYIDGIISLIDIDSIKAKKFKVCLDLGNGAQAVTAKKLCENLGCDVHTINEEINGDFPGRGSEPTP-QNLDELSKLVVDTNSNFGIAFDGDGDRSIFCD 247
                 7*****************************************************************.******************************** PP

                 TTE CS
  PGM_PMM_II 101 erG 103
                 e G
  AJA92910.1 248 ETG 250
                 987 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.0   7.5e-24   2.7e-20       2     112 ..     255     363 ..     254     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 7.5e-24
                  HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS--HHHHHHHHHHHHHHH CS
  PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkDGilaallvleilaet 99 
                  gd+ ++ll +yll++   p+ +vv+ + + +++e++++k + ++v+tkvG+  v ++m + +a++G+Ee+g+++f++++  +DG+++ +l+l +l+++
   AJA92910.1 255 GDSSALLLCDYLLQQ-Y-PNSQVVTCLNSGNIIENIVEKTNSHVVRTKVGSVEVSRRMVNDDALVGYEENGGFMFGNHNHVRDGAMTLALMLDLLSKS 350
                  9***********996.5.5556**************************************************************************** PP

                  TS-HHHHHHHHHH CS
  PGM_PMM_III 100 gkslselleellk 112
                  + +ls+ +++l++
   AJA92910.1 351 QLDLSQNIKNLPP 363
                  ******9998876 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   3.5e-11   1.3e-07      14      69 ..     387     438 ..     371     445 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.5e-11
                 EECCCCCTTHHCCCCCCC.CGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHH CS
  PGM_PMM_IV  14 aalaallkvasikeglki.lledGrrlavRpSGTepllrvyvEaksdeelarlaeev 69 
                 +++++     ++++g+ki +++d +++ +RpSGTep +r+y E+ s++ l+ l   +
  AJA92910.1 387 KEFPDS----NTSDGIKIqVDKDNWVM-IRPSGTEPIIRIYGESNSQQNLDSLISNF 438
                 333343....46788887368888888.******************99998876655 PP

>> CHASE5  Periplasmic sensor domain found in signal transduction proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05      0.07       6      67 ..     120     178 ..     116     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
      CHASE5   6 vsriearldeiekatlevLaeslWnlDerllklqLeGlvrLPdidyieikedsdvrvaaGep 67 
                   +ie+ +de + +++ ++++s+   + +++ + ++G++ L did i+ k+  +v +  G+ 
  AJA92910.1 120 ERKIEQIFDEKNWIKASTFGKSFE--ETNVISTYIDGIISLIDIDSIKAKK-FKVCLDLGNG 178
                 56899*****************85..689*******************998.5566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3210.95
//
Query:       AJA92911.1  [L=458]
Description: NADH dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-95  318.6  16.8    5.8e-95  318.0  16.8    1.2  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
        0.8    9.8   2.9        1.2    9.2   0.3    2.6  2  NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.0  16.8   6.4e-99   5.8e-95       9     297 ..      91     442 ..      83     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 318.0 bits;  conditional E-value: 6.4e-99
                 HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT.TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS-SSS...SSS--TTHHHHHH CS
      NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl.GllqplaDalKlllKediipkkadkllfllapvlalilallafaviPfge...vladlnvglllil 103
                 +++l++a ++++eRk+lA++q R+GP ++G++ G+lq+  D+lKl+ Ke iip+kadk lf++apvl + +a + +a+iP+++   v+adl+vgll ++
  AJA92911.1  91 FAALIAAGTIFVERKMLAKLQLRVGPFYCGKVeGILQLAGDGLKLISKEIIIPAKADKPLFWAAPVLFVGTAAAFVALIPVAPggwVVADLDVGLLAVF 189
                 56788889**********************766*************************************************7789************* PP

                 HHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCTT.-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTST CS
      NADHdh 104 alsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqeei.wfillqllafiifliallaetnraPFDlpeae 201
                 a++ + +++++l++w++nsk++++G++R++ qm+s+E++l+lsll+vv+l+g+l+lseive+q++  w+i++ ++++i+f+ ++lae++r+PFDlpeae
  AJA92911.1 190 AVIGFFPIITILSAWSANSKFPFIGGIRALHQMVSFEIPLILSLLGVVILTGTLNLSEIVESQSSFpWIIFM-PIGAIVFFTTMLAELERIPFDLPEAE 287
                 ***************************************************************988786665.************************** PP

                 TSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS.................................................... CS
      NADHdh 202 sELvaGfhtEYsgmkfalfflaeyanmvlvsalavllFlgGwllpfs.................................................... 248
                 sE+vaG+ tE+sgm ++l+ l++y+++++++al+v++FlgGw++p+                                                     
  AJA92911.1 288 SEIVAGWLTEFSGMMYGLVQLGSYLKLYAFAALFVIIFLGGWTGPVFwppldtelitkgtpipnyagdpvltvfapglpifdadpnewvkqqqgelqyt 386
                 *********************************************9999************************************************** PP

                 .......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
      NADHdh 249 .......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                        g++wf+lK++ ++f++++ r ++pR+R+d l+++gw  l+ l+++n+++
  AJA92911.1 387 sgqllisGVFWFVLKTVGVIFFILLPRGVFPRIRLDMLLHIGWYKLIGLSFVNIFI 442
                 ******************************************************98 PP

>> NDUF_B12  NADH-ubiquinone oxidoreductase B12 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00013       1.2      23      47 ..      82     106 ..      77     111 .. 0.81
   2 ?   -1.9   0.2      0.39   3.5e+03      26      39 ..     298     310 ..     289     322 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
    NDUF_B12  23 kraffpGfglavaafaaavgyEhfl 47 
                 + + fpGfg a+ ++a ++ +E  +
  AJA92911.1  82 RIVAFPGFGFAALIAAGTIFVERKM 106
                 44556****************9765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.39
    NDUF_B12  26 ffpGfglavaafaa 39 
                 f  G++++++    
  AJA92911.1 298 F-SGMMYGLVQLGS 310
                 3.899999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3405.99
//
Query:       AJA92912.1  [L=241]
Description: methyltransferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-13   50.5   0.0    4.7e-13   49.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.2e-09   38.1   0.0    1.9e-09   37.5   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    5.8e-08   33.4   0.0    1.1e-07   32.5   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    1.1e-06   28.7   0.0    1.5e-06   28.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    1.4e-06   27.8   0.0    2.2e-06   27.2   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-06   27.1   0.0    2.5e-06   26.9   0.0    1.1  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
    4.1e-06   27.4   0.0    8.8e-06   26.3   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00014   21.4   0.0    0.00022   20.8   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00014   21.3   0.0     0.0009   18.7   0.0    2.0  2  Methyltransf_4   Putative methyltransferase
    0.00065   19.6   0.0    0.00097   19.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00069   19.0   0.0    0.00096   18.5   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
     0.0069   15.5   0.0      0.012   14.8   0.0    1.3  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.02   14.4   0.0    1.3  1  DOT1             Histone methylation protein DOT1
      0.065   12.7   0.0      0.087   12.3   0.0    1.3  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.074   12.7   0.0      0.099   12.3   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
      0.083   12.6   0.0       0.14   11.9   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
       0.13   12.2   0.0       0.41   10.6   0.0    1.9  1  RST              RCD1-SRO-TAF4 (RST) plant domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   4.4e-16   4.7e-13       1      92 [.      44     144 ..      44     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 4.4e-16
                      EEEET-TTSHHHHHHHCTS.T.SSEEEEEESSHHHHHHHHHHHHH.TTT.TEEEEESBCCG..BS..SSTTTEEEEEEEST.GGGSSHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.g.kakvtgvDiseemleaareraee.egl.nvefvqgdaed..lp..fedgsfDlvvssga.lhhlsdedleka 85 
                      ++d+G+GtGr+++al +rl +   k++gv++se ml++a++++++ eg+ ++ef++ d+++  l+  f++g+ ++v++ ++ l +++ e+++++
       AJA92912.1  44 IIDMGAGTGRVIFALDERLqEsTTKFYGVEVSEPMLDYAKQKNQNhEGVsKIEFLKYDLTEpnLSdyFNKGETNIVMCLYNtLGVIPSEKRQQF 137
                      79*****************6359*****************999986777**********884454779*************9************ PP

                      HHHHHHH CS
  Methyltransf_25  86 lkeiarv 92 
                      +++++ +
       AJA92912.1 138 IDNMRCI 144
                      **99865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   1.8e-12   1.9e-09       2     113 ..      39     157 ..      38     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.8e-12
  Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielAre.naqklgldnveFeqgdiee.lekl.ledekfDlilsn.evl..nala 88 
                      +k+ +++D G+GtG+ +f+l e+l +   +++G++ se ++ +A++ n  + g++ +eF + d +e   ++ +++   +++++  ++l      
       AJA92912.1  39 NKNSSIIDMGAGTGRVIFALDERLQEsTTKFYGVEVSEPMLDYAKQkNQNHEGVSKIEFLKYDLTEpNLSDyFNKGETNIVMCLyNTLgvIPSE 132
                      6899*****************966664777****************566667999**********96444555656666666532444555566 PP

  Methyltransf_31  89 dpdkileeiervlkpggilliedpr 113
                        ++++ ++     ++g  +++ ++
       AJA92912.1 133 KRQQFIDNMRCIAGEKGLTILTAFN 157
                      6666666666655555555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0     1e-10   1.1e-07       2      90 ..      46     142 ..      45     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1e-10
  Methyltransf_12   2 eiGcGtGsllrallekl..pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvvas.nvlhhl..kdirev 85 
                      + G+GtG++++al e+l  ++++++gv++s+ +++ ak+k + +e   ++++e+ + dl +   +     +   +v ++ n+l ++  ++++++
       AJA92912.1  46 DMGAGTGRVIFALDERLqeSTTKFYGVEVSEPMLDYAKQKNQNHE--GVSKIEFLKYDLTEPNLSdyfnkGETNIVMCLyNTLGVIpsEKRQQF 137
                      89***************999**************55555555554..456666666666555554555558888899989*******99999** PP

  Methyltransf_12  86 ldnir 90 
                      +dn+r
       AJA92912.1 138 IDNMR 142
                      **998 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.4e-09   1.5e-06       4      92 ..      23     105 ..      21     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.4e-09
  Methyltransf_32   4 heverlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieea 92 
                      +e++ l +l++k++++    +++ +++D+GaG g   f+l  + +e  +k++g++++e + + a++ +++ +  + ++++f + + +e 
       AJA92912.1  23 KEIDILTNLCKKVYDQ----NKNSSIIDMGAGTGRVIFALDERLQESTTKFYGVEVSEPMLDYAKQKNQNHE-GV-SKIEFLKYDLTEP 105
                      5666666666666665....999*******************66669*********************9998.34.6777777666555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0     2e-09   2.2e-06      39     105 ..      32     100 ..      10     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                      HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHH.EEEEEES-HHHHHHHHHHHHH.HTSSTEEEEE- CS
  Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekg.kvvvlDinenmLkvgekklke.egkinieflqa 105
                       +k+  + + ++++D+ +Gtg + f+l + ++e+  k  +++++e mL+ +++k ++ eg+++iefl+ 
       AJA92912.1  32 CKKVYDQNKNSSIIDMGAGTGRVIFALDERLQESTtKFYGVEVSEPMLDYAKQKNQNhEGVSKIEFLKY 100
                      55667778889*****************998876549**************99987538999****975 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   2.3e-09   2.5e-06      43     180 ..      22     155 ..      19     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.3e-09
  Methyltransf_33  43 rtEiaiLqehaaeiaaaipaatlvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealealaaeypsleveglvgdyedglewlaslp 136
                      ++Ei+iL++  +++ ++ +++ ++++G+G+++ +  L e l+  e++++++ ++vse +L+ a ++ ++ +++++   ++ +y+     l++  
       AJA92912.1  22 KKEIDILTNLCKKVYDQNKNSSIIDMGAGTGRVIFALDERLQ--ESTTKFYGVEVSEPMLDYAKQKNQN-HEGVSKIEFL-KYDLTEPNLSDYF 111
                      68**************99999***********9999999996..4589**************9999866.4666544433.3444445666665 PP

  Methyltransf_33 137 eaederrlvlflGssigNlepeeaaafLrklraal.gpgdllLlG 180
                       ++ e ++v+ l +++g ++ e++++f+ ++r    ++g  +L +
       AJA92912.1 112 -NKGETNIVMCLYNTLGVIPSEKRQQFIDNMRCIAgEKGLTILTA 155
                      .378999************************98862445555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   8.3e-09   8.8e-06       2      69 ..      46     123 ..      45     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.3e-09
                      EET-TTSHHHHHHHHTT....SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC..TS..S-TT-EEEEEEES CS
  Methyltransf_11   2 dvGcGtGrlaealakrg....arvvgvDlskemlklakekaseegl..kvefvvadaek..lp..fednsfDlvvsse 69 
                      d+G+GtGr+  al +r     ++ +gv++s+ ml++ak+k+++ +   k+ef++ d+++  l   f+++   +v++  
       AJA92912.1  46 DMGAGTGRVIFALDERLqestTKFYGVEVSEPMLDYAKQKNQNHEGvsKIEFLKYDLTEpnLSdyFNKGETNIVMCLY 123
                      99************6666778****************999988877899*******9982232335555556665555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.1e-07   0.00022      11      92 ..      20     105 ..      18     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-07
                 TTTTS--HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E..EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT CS
         MTS  11 FskdklDkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeae..vtlvdvdarAlesakenleankle..vevvasdvlee 92 
                 + k+++D+ ++l  +  +++++ +++D+G+G+G +  al ++ +e +     v+v+   l+ ak+  ++++    +e+++ d++e 
  AJA92912.1  20 YLKKEIDILTNLCKKVYDQNKNSSIIDMGAGTGRVIFALDERLQESTtkFYGVEVSEPMLDYAKQKNQNHEGVskIEFLKYDLTEP 105
                 56899******************************99999998887734667899999****998777766544899998888775 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.6e-07    0.0009       2      79 ..      41     122 ..      40     125 .. 0.85
   2 ?    0.3   0.0      0.41   4.3e+02      31      65 ..     131     165 ..     121     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.6e-07
                     -EEEEEET-TTSHHHHHHHH..HSTTSEEEEEES-HHHHHHHHHHHHHC.TTSSEEEEES-CCC.HHHHCS-TTSEEEEEEE CS
  Methyltransf_4   2 apvvleiGcGkGeflvalAk..knPdknflGiEirvkvvakvlkkieal.elkNlrilrgdalk.vllelledgslekifil 79 
                     ++ ++++G G G+++ al +  ++ +++f G+E+++++++++ +k +++ +++ ++ l+ d ++  l++++++g+ + ++ l
      AJA92912.1  41 NSSIIDMGAGTGRVIFALDErlQESTTKFYGVEVSEPMLDYAKQKNQNHeGVSKIEFLKYDLTEpNLSDYFNKGETNIVMCL 122
                     6789***********99986337999******************9999879999***9999865369999999988776655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.41
                     EES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHH CS
  Methyltransf_4  31 iEirvkvvakvlkkiealelkNlrilrgdalkvll 65 
                      E+r++ ++++ + +++++l+ l  ++gd ++++ 
      AJA92912.1 131 SEKRQQFIDNMRCIAGEKGLTILTAFNGDEFDFIA 165
                     49999999999999999999999999999888775 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.2e-07   0.00097      19     156 ..      34     212 ..      19     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.2e-07
  Methyltransf_23  19 k...lraggrvLdiGcGtGillevl....rengfsvtgvDlspeaveiaekakkaqkdqfdeq..eaae...........pqgkfdlIvl.rev 91 
                      k   ++++++++d+G+GtG++   l    +e  ++++gv+ s+ + + a+++ +++      +  +  +           ++g ++++ +  ++
       AJA92912.1  34 KvydQNKNSSIIDMGAGTGRVIFALderlQESTTKFYGVEVSEPMLDYAKQKNQNHEGVSKIEflK--YdltepnlsdyfNKGETNIVMClYNT 125
                      344479999**********998888553233455*************9976666666666444330..24444444444477777766551567 PP

  Methyltransf_23  92 lehvpd..ppellrqiatllkpgGylllseplasl.............kedrllldwlylvpag....rhi...sffsarslkelle 156
                      l+ +p+      +++++ +  + G+ +l+ ++ +              +  + ++++ ++v++     +++   ++f+ ++lk +l+
       AJA92912.1 126 LGVIPSekRQQFIDNMRCIAGEKGLTILTAFNGDEfdfiaprlynpmmPMIKQIDENSFDVKNKvfqnGLGfrsQWFTKEELKSMLQ 212
                      888885435567777777777888888888877667777777777777677777777777666555543334478888888888776 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.1e-07   0.00096      23     128 ..      28     141 ..      22     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.1e-07
       Rsm22  23 Ldelaer.vpdflPkslldvgegpgtalwaaselwe.eleevlvidaseelleiskelaadapelkeaa.lrrsvir....ealeleeadLviisyvLl 114
                 L++l ++  ++ +  s++d+g+g+g +++a  e  + ++++ + ++ se++l  +k+  ++ + + +++ l+ ++++    +  +  e+++v++ y  l
  AJA92912.1  28 LTNLCKKvYDQNKNSSIIDMGAGTGRVIFALDERLQeSTTKFYGVEVSEPMLDYAKQKNQNHEGVSKIEfLKYDLTEpnlsDYFNKGETNIVMCLYNTL 126
                 5555443046677889****************99998999*************9998877666555554145555431000344444559***999766 PP

       Rsm22 115 eled.esreklvknl 128
                  + + e+r+++++n+
  AJA92912.1 127 GVIPsEKRQQFIDNM 141
                 666669*******98 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.012      92     153 ..      38     101 ..      23     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
        DREV  92 dqedkklldlGaGdGeitkrvaptfee....vyatelsetmrdrlkkkkyn..vlsalelqetdvkld 153
                 + ++  ++d+GaG G +   + + ++e     y  e+se m d  k+k+ n   +s++e+     k+d
  AJA92912.1  38 QNKNSSIIDMGAGTGRVIFALDERLQEsttkFYGVEVSEPMLDYAKQKNQNheGVSKIEFL----KYD 101
                 457889**********987777777766666***********9888876551156666655....444 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.9e-05      0.02      30      90 ..      27      90 ..      19     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                HHHHHHHHT.T--TT-EEEEES-TTSHHHHHHH..HHH--SEEEEEE--HHHHHHHHHHHHHHH CS
        DOT1 30 flsevldkv.nlkkedvFvDLGSGvGnvvlqaa..levgcklsvGvEimdnaselaekqkeelk 90
                +l+++ +kv + +k++  +D+G G G+v++     l+  + + +GvE+++   ++a+++++  +
  AJA92912.1 27 ILTNLCKKVyDQNKNSSIIDMGAGTGRVIFALDerLQESTTKFYGVEVSEPMLDYAKQKNQNHE 90
                56666666535678999***********987651156667889*************99887665 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.2e-05     0.087      42      99 ..      28      87 ..       2     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.2e-05
  Methyltransf_PK 42 lkklkkeslpgkrevkvaldcGaGiGrvtknl...LlkllskvDlvepvekflekakeela 99
                     l++l k+ + ++++++ ++d+GaG Grv   l   L +  +k   ve+ e +l+ ak++  
       AJA92912.1 28 LTNLCKK-VYDQNKNSSIIDMGAGTGRVIFALderLQESTTKFYGVEVSEPMLDYAKQKNQ 87
                     5566665.6689999*************876622244444555555555555555553332 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.4e-05     0.099      58     159 ..      65     159 ..      27     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
                 TTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEEE--............-TTT---SS-..EEEEEEESSTTTS-GGGHHHHHHHHHHHEEEEEE..EEE CS
        TPMT  58 qgrevvGvelselAvekffeeanlepkvkelsgvke.ysageiellcgdvFtlraeelgkfdliydraalvAlppelreryakslaelLkpdgeglLvt 155
                    +  Gve+se  +  + ++++ ++ v+++++ k   + ++     +d+F+  ++++  + ++y+   l  +p e r+++ ++++ +  ++g ++L  
  AJA92912.1  65 STTKFYGVEVSEPMLDYAKQKNQNHEGVSKIEFLKYdLTEPN----LSDYFNKGETNI--VMCLYN--TLGVIPSEKRQQFIDNMRCIAGEKGLTILTA 155
                 556789**********99888888999********9444444....57**********..777876..78999**************999999988877 PP

                 EE-- CS
        TPMT 156 ldyp 159
                  +++
  AJA92912.1 156 FNGD 159
                 7665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.14      29     125 ..      18     120 ..      14     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
  Methyltransf_16  29 vkylekklake.....lganelsklsvlELGsGtGlvGlavaellpeakviltDleellellkknielnkn.alkskvkvevLdWgeeleedll 116
                      v yl+k++        +  ++ ++ s++++G+GtG v  a++e l+e       +e  +++l +  + n+n    sk+++ + d  e+  +d +
       AJA92912.1  18 VNYLKKEIDILtnlckKVYDQNKNSSIIDMGAGTGRVIFALDERLQESTTKFYGVEVSEPMLDYAKQKNQNhEGVSKIEFLKYDLTEPNLSDYF 111
                      56666655332556554456788999*****************998888888888888888888888877634556777777676776667888 PP

  Methyltransf_16 117 ekeevDlil 125
                      +k e ++++
       AJA92912.1 112 NKGETNIVM 120
                      877777776 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.41      41      59 ..     133     151 ..     106     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
         RST  41 sreefvrklRsivGDklLk 59 
                 +r++f+  +R i+G+k L+
  AJA92912.1 133 KRQQFIDNMRCIAGEKGLT 151
                 69*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1611.96
//
Query:       AJA92913.1  [L=271]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-35  118.1  13.3    9.1e-08   31.6   0.1    6.7  7  TPR_1            Tetratricopeptide repeat
    1.9e-31  105.6   6.6    2.8e-06   27.0   0.3    7.1  7  TPR_2            Tetratricopeptide repeat
      8e-25   87.2   0.0    1.3e-06   28.9   0.1    4.0  4  TPR_16           Tetratricopeptide repeat
    9.9e-25   85.1   4.4    0.00017   21.7   0.1    6.8  7  TPR_17           Tetratricopeptide repeat
    3.7e-24   82.9   7.8    0.00044   20.3   0.4    7.0  7  TPR_8            Tetratricopeptide repeat
    1.1e-22   79.4   7.3    6.4e-05   22.6   0.0    5.8  7  TPR_11           TPR repeat
    1.2e-21   75.5   0.2     0.0037   17.9   0.0    7.0  7  TPR_14           Tetratricopeptide repeat
    1.6e-20   73.4   2.3      9e-07   29.3   0.1    4.1  4  TPR_19           Tetratricopeptide repeat
    6.2e-20   70.4   0.7       0.01   16.4   0.0    7.0  7  TPR_6            Tetratricopeptide repeat
    1.8e-17   63.3   0.1    1.9e-07   31.2   0.0    3.9  4  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.1e-17   62.6   1.6      2e-07   31.2   0.5    5.6  5  TPR_12           Tetratricopeptide repeat
    7.4e-13   48.5   0.0    1.6e-06   28.2   0.0    4.1  5  TPR_9            Tetratricopeptide repeat
    1.6e-10   40.3   0.0      0.053   13.6   0.0    6.1  6  TPR_7            Tetratricopeptide repeat
    3.7e-08   32.7   4.6      0.005   15.8   0.2    3.3  3  NARP1            NMDA receptor-regulated protein 1
    1.4e-07   30.6   0.0    0.00069   18.4   0.0    2.1  2  PknG_TPR         Protein kinase G tetratricopeptide repeat
    1.5e-07   31.0   4.3     0.0004   20.1   0.3    5.4  6  TPR_10           Tetratricopeptide repeat
    7.6e-06   26.2   3.9        1.4    9.3   0.8    4.5  5  TPR_20           Tetratricopeptide repeat
    0.00023   20.3   0.0      0.047   12.7   0.0    2.1  2  Paf67            RNA polymerase I-associated factor PAF67
    0.00025   20.3   0.6      0.013   14.8   0.1    2.5  2  TPR_15           Tetratricopeptide repeat
    0.00029   20.8   1.2      0.022   14.7   0.4    3.1  2  Thioredoxin_6    Thioredoxin-like domain
      0.001   19.2   7.2         24    5.4   0.0    6.3  7  PPR              PPR repeat
     0.0011   18.7   3.2      0.018   14.7   0.4    2.3  2  TPR_21           Tetratricopeptide repeat-like domain
     0.0014   18.2   4.7       0.18   11.2   1.0    2.9  3  Coatomer_E       Coatomer epsilon subunit
     0.0055   16.8   0.4         12    6.0   0.0    4.1  4  DUF3856          Domain of Unknown Function (DUF3856)
     0.0066   16.1   1.5        2.2    7.9   0.0    3.4  4  Ribosomal_S7     Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.023   15.1   2.6        2.3    8.7   0.0    3.1  3  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
       0.05   13.7   0.1         17    5.6   0.0    3.9  4  Rapsyn_N         Rapsyn N-terminal myristoylation and linker 
       0.28   11.3   8.8        3.6    7.7   0.2    5.0  5  MIT              MIT (microtubule interacting and transport) 


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00021      0.14       6      34 .]      15      43 ..      10      43 .. 0.91
   2 !   31.6   0.1   1.4e-10   9.1e-08       2      34 .]      45      77 ..      44      77 .. 0.96
   3 !   26.2   0.4   7.5e-09   4.8e-06       1      33 [.      78     110 ..      78     111 .. 0.94
   4 !   22.1   0.1   1.4e-07   8.9e-05       1      33 [.     112     144 ..     112     145 .. 0.96
   5 !   17.0   0.0   5.7e-06    0.0036       6      34 .]     151     179 ..     148     179 .. 0.92
   6 !   13.0   0.0   0.00011      0.07       3      29 ..     182     208 ..     180     213 .. 0.90
   7 ?   -2.3   0.2       7.2   4.6e+03      13      29 ..     226     242 ..     218     243 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                  +++++++++++ A+  ++k+ +++P+n
  AJA92913.1 15 YQAMTFLEKNQPKAAVSLFKKVTKIDPEN 43
                67899**********************97 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1.4e-10
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALelnPnn 34
                +a+yn G+a+ +l+ky +A+ +++   + nPn+
  AJA92913.1 45 NAWYNQGLALNQLKKYADAITCFDMITQRNPND 77
                79*****************************97 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 7.5e-09
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                 a al+n+G a  +lg+++ A eyyekA++ + +
  AJA92913.1  78 AAALNNRGIAMAELGDPEGAMEYYEKAIKADSS 110
                 78**************************98876 PP

  == domain 4  score: 22.1 bits;  conditional E-value: 1.4e-07
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   1 akalynlGnayfklgkydeAleyyekALelnPn 33 
                 a a+yn+G+++ k+ ++de l+  ++A+e +P+
  AJA92913.1 112 APAYYNKGVLLDKKLEHDESLKVLDEAIEKDPK 144
                 68******************************7 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 5.7e-06
                 HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   6 nlGnayfklgkydeAleyyekALelnPnn 34 
                  +G ++ k+gk++ Al ++e + + nP++
  AJA92913.1 151 YKGIVLGKMGKHELALNCFESVHRANPQH 179
                 79********************9999985 PP

  == domain 6  score: 13.0 bits;  conditional E-value: 0.00011
                 HHHHHHHHHHHTT-HHHHHHHHHHHHH CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALe 29 
                 +++ +G  + +l+++++A+e ++k L 
  AJA92913.1 182 SFFHKGIELAELERHEKAIEVFDKILD 208
                 6889********************986 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 7.2
                 HTT-HHHHHHHHHHHHH CS
       TPR_1  13 klgkydeAleyyekALe 29 
                  +++ +eA +  + A++
  AJA92913.1 226 AMNEVNEAFDLLNLAIK 242
                 67888889888888876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00011     0.068       2      34 .]      11      43 ..      10      43 .. 0.94
   2 !   19.6   0.0     1e-06   0.00067       2      34 .]      45      77 ..      44      77 .. 0.95
   3 !   27.0   0.3   4.4e-09   2.8e-06       1      31 [.      78     108 ..      78     111 .. 0.93
   4 !   17.2   0.0   6.1e-06    0.0039       1      33 [.     112     144 ..     112     145 .. 0.95
   5 !   12.4   0.0   0.00021      0.14       5      34 .]     150     179 ..     147     179 .. 0.94
   6 !   11.4   0.0   0.00045      0.29       4      31 ..     183     210 ..     181     213 .. 0.86
   7 ?    1.3   0.1      0.74   4.7e+02       5      30 ..     218     243 ..     215     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                e l+++++  +++++++ A+ +f+k+ ++dP+n
  AJA92913.1 11 EDLMYQAMTFLEKNQPKAAVSLFKKVTKIDPEN 43
                67899**************************97 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1e-06
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPnn 34
                 a+yn+Gla+ +l++y++A+ +f+   + +Pn+
  AJA92913.1 45 NAWYNQGLALNQLKKYADAITCFDMITQRNPND 77
                69*****************************97 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 4.4e-09
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                 a al+n+G a ++lgd+e A e++ekA++ d
  AJA92913.1  78 AAALNNRGIAMAELGDPEGAMEYYEKAIKAD 108
                 689*************************987 PP

  == domain 4  score: 17.2 bits;  conditional E-value: 6.1e-06
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                 a a+yn G ++ k+ +++e l+ +++A+e dP+
  AJA92913.1 112 APAYYNKGVLLDKKLEHDESLKVLDEAIEKDPK 144
                 569*****************************7 PP

  == domain 5  score: 12.4 bits;  conditional E-value: 0.00021
       TPR_2   5 ynlGlayyklgdyeeAleafekAleldPnn 34 
                 ++ G ++ k+g++e Al++fe + + +P++
  AJA92913.1 150 FYKGIVLGKMGKHELALNCFESVHRANPQH 179
                 789*************************86 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00045
       TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                  +  G  +++l ++e+A+e f+k l   
  AJA92913.1 183 FFHKGIELAELERHEKAIEVFDKILDKH 210
                 5789999****************99765 PP

  == domain 7  score: 1.3 bits;  conditional E-value: 0.74
       TPR_2   5 ynlGlayyklgdyeeAleafekAlel 30 
                 y+ +++ +++++ +eA ++++ A++ 
  AJA92913.1 218 YAKARSKAAMNEVNEAFDLLNLAIKQ 243
                 7778888999999******9999986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.3e-09   2.1e-06       3      67 ..      16      77 ..      16      78 .. 0.92
   2 !   28.9   0.1   2.1e-09   1.3e-06      10      66 ..      57     110 ..      56     112 .. 0.95
   3 !   26.9   0.0   8.6e-09   5.5e-06       6      68 .]      87     146 ..      82     146 .. 0.93
   4 !   18.6   0.0   3.4e-06    0.0022       6      63 ..     155     209 ..     152     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.3e-09
      TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67
                +a+ +l+ +++ +A+ +++ ++k d   P+++ A+++ g+a+ +++ +a+A+  ++   +  p++
  AJA92913.1 16 QAMTFLEKNQPKAAVSLFKKVTKID---PENVNAWYNQGLALNQLKKYADAITCFDMITQRNPND 77
                68899********************...************************9888877777766 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 2.1e-09
      TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                 +++y+dA+  ++  + r+   P +a+Al+++g a +++g+ ++A ++y++a++a+++
  AJA92913.1  57 LKKYADAITCFDMITQRN---PNDAAALNNRGIAMAELGDPEGAMEYYEKAIKADSS 110
                 789***************...*******************************99876 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 8.6e-09
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                 a +++gd++ A +++e a+k+d   +  a A++++g+++ ++ +++e + ++++a++ +p+ p
  AJA92913.1  87 AMAELGDPEGAMEYYEKAIKAD---SSYAPAYYNKGVLLDKKLEHDESLKVLDEAIEKDPKKP 146
                 55789*****************...**********************************9876 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 3.4e-06
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                  + + g+ + A++ +e + +++   P++ ++ +++g  ++++ r+++A++++++ l+ 
  AJA92913.1 155 VLGKMGKHELALNCFESVHRAN---PQHLDSFFHKGIELAELERHEKAIEVFDKILDK 209
                 67789*****************...****************************99865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.5   1.6e+03      16      33 ..      13      30 ..       7      31 .. 0.79
   2 !   21.7   0.1   2.6e-07   0.00017       1      33 [.      32      64 ..      32      65 .. 0.96
   3 !   18.1   0.0   3.8e-06    0.0024       7      32 ..      72      97 ..      66      99 .. 0.89
   4 !   21.0   0.2   4.4e-07   0.00028       1      26 [.     100     125 ..     100     133 .. 0.88
   5 !   14.7   0.0   4.6e-05     0.029       3      32 ..     136     165 ..     134     167 .. 0.93
   6 ?    1.4   0.0      0.84   5.4e+02       8      34 .]     175     201 ..     170     201 .. 0.90
   7 ?    2.1   0.0       0.5   3.2e+02       2      22 ..     203     223 ..     202     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.5
      TPR_17 16 ynnLAelllknGdlmtAr 33
                + + A ++l++++++ A+
  AJA92913.1 13 LMYQAMTFLEKNQPKAAV 30
                567799999999999885 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.6e-07
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                l++k+ ++dP n++a++n + +l +++++++A+
  AJA92913.1 32 LFKKVTKIDPENVNAWYNQGLALNQLKKYADAI 64
                799***************************996 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 3.8e-06
      TPR_17  7 eldPnnadaynnLAelllknGdlmtA 32
                +++Pn+a a+nn++ +++++Gd++ A
  AJA92913.1 72 QRNPNDAAALNNRGIAMAELGDPEGA 97
                78********************9988 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 4.4e-07
      TPR_17   1 lylkaleldPnnadaynnLAelllkn 26 
                 +y+ka++ d ++a+ay+n+++ll k+
  AJA92913.1 100 YYEKAIKADSSYAPAYYNKGVLLDKK 125
                 6**********************865 PP

  == domain 5  score: 14.7 bits;  conditional E-value: 4.6e-05
      TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtA 32 
                  +a+e+dP+ +++ ++++ +l k G+++ A
  AJA92913.1 136 DEAIEKDPKKPNPRFYKGIVLGKMGKHELA 165
                 68************************9988 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.84
      TPR_17   8 ldPnnadaynnLAelllknGdlmtArq 34 
                  +P + d+++ ++  l+++ ++++A++
  AJA92913.1 175 ANPQHLDSFFHKGIELAELERHEKAIE 201
                 599999*******99999999999985 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.5
      TPR_17   2 ylkaleldPnnadaynnLAel 22 
                 + k l++++ n+++ + +A+ 
  AJA92913.1 203 FDKILDKHKGNVNVVYAKARS 223
                 7899************99985 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00013     0.082       8      34 .]      17      43 ..      16      43 .. 0.93
   2 !   16.0   0.0   1.6e-05      0.01       2      33 ..      45      76 ..      44      77 .. 0.87
   3 !   20.3   0.4   6.8e-07   0.00044       2      32 ..      79     109 ..      78     111 .. 0.88
   4 !   13.9   0.1   7.2e-05     0.046       1      33 [.     112     144 ..     112     145 .. 0.94
   5 ?    6.4   0.0     0.019        12       9      33 ..     154     178 ..     152     179 .. 0.84
   6 !    9.9   0.0    0.0014      0.89       2      28 ..     181     207 ..     180     208 .. 0.88
   7 ?    1.0   0.1      0.99   6.3e+02       5      31 ..     218     244 ..     214     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  8 gsiylklgdyeeAkeyyekaleldpdn 34
                +++ l++++ ++A++ ++k++++dp+n
  AJA92913.1 17 AMTFLEKNQPKAAVSLFKKVTKIDPEN 43
                788999*******************86 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.6e-05
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                 a+yn g+++ +l++y  A+ ++   ++ +p+
  AJA92913.1 45 NAWYNQGLALNQLKKYADAITCFDMITQRNPN 76
                69********************9877777766 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 6.8e-07
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                  a++n g +  +lgd e A+eyyeka+++d 
  AJA92913.1  79 AALNNRGIAMAELGDPEGAMEYYEKAIKADS 109
                 578888889999****************997 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 7.2e-05
                 CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 a+ayyn+g +++k+ +++e+ +++ +a+e dp+
  AJA92913.1 112 APAYYNKGVLLDKKLEHDESLKVLDEAIEKDPK 144
                 79**************************98876 PP

  == domain 5  score: 6.4 bits;  conditional E-value: 0.019
                 HHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   9 siylklgdyeeAkeyyekaleldpd 33 
                  ++ k+g++e A  ++e + +++p+
  AJA92913.1 154 IVLGKMGKHELALNCFESVHRANPQ 178
                 57889************98888877 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 0.0014
                 CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                 ++ +++g  + +l+++e+A+e++ k l
  AJA92913.1 181 DSFFHKGIELAELERHEKAIEVFDKIL 207
                 5778999999*************9976 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.99
                 HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                 y +++    +++ +eA   ++ a++ +
  AJA92913.1 218 YAKARSKAAMNEVNEAFDLLNLAIKQS 244
                 788888999999999999999999865 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     1e-07   6.4e-05       4      38 ..      20      54 ..      19      57 .. 0.91
   2 !   18.9   0.1   1.4e-06   0.00087       1      42 []      51      92 ..      51      92 .. 0.97
   3 !   22.5   1.4     1e-07   6.5e-05       6      38 ..      90     122 ..      89     125 .. 0.92
   4 !   17.8   0.0     3e-06    0.0019      10      42 .]     128     160 ..     127     160 .. 0.96
   5 ?    0.8   0.0      0.63     4e+02       7      29 ..     159     181 ..     158     188 .. 0.75
   6 ?    1.2   0.0      0.47     3e+02       4      19 ..     190     205 ..     187     208 .. 0.83
   7 ?   -3.0   0.1       9.4     6e+03       8      23 ..     228     243 ..     225     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-07
      TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38
                + e+++ ++A+  +kk  k+dP+n++a+yn Gla+
  AJA92913.1 20 FLEKNQPKAAVSLFKKVTKIDPENVNAWYNQGLAL 54
                67899999*************************98 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.4e-06
      TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                G a+ ++ ky +Ai+++    + +P++a a++n+G a++++G
  AJA92913.1 51 GLALNQLKKYADAITCFDMITQRNPNDAAALNNRGIAMAELG 92
                88999**********************************998 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1e-07
      TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                 e+G+ e+A+e Y+kA+k d+++a ayyn G+++
  AJA92913.1  90 ELGDPEGAMEYYEKAIKADSSYAPAYYNKGVLL 122
                 68999*************************876 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 3e-06
      TPR_11  10 yeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                  +e+++++ +A++ dP+ ++  +  G ++ k+G
  AJA92913.1 128 HDESLKVLDEAIEKDPKKPNPRFYKGIVLGKMG 160
                 79*****************************98 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.63
      TPR_11   7 qGkyeeAieaYkkAlkldPdnae 29 
                  Gk e A+++++   + +P+  +
  AJA92913.1 159 MGKHELALNCFESVHRANPQHLD 181
                 69********9987777776555 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.47
      TPR_11   4 yyeqGkyeeAieaYkk 19 
                 + e+ + e+Aie++ k
  AJA92913.1 190 LAELERHEKAIEVFDK 205
                 678999******9765 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 9.4
      TPR_11   8 GkyeeAieaYkkAlkl 23 
                 ++ +eA   ++ A+k 
  AJA92913.1 228 NEVNEAFDLLNLAIKQ 243
                 6778887777777775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00037      0.24       2      39 ..      11      48 ..      10      53 .. 0.88
   2 !   17.9   0.0   5.8e-06    0.0037       2      38 ..      45      81 ..      44      85 .. 0.94
   3 !   17.3   0.0   9.1e-06    0.0059       7      41 ..      84     118 ..      83     121 .. 0.88
   4 ?    7.4   0.0     0.014       8.8      16      33 ..     127     144 ..     119     159 .. 0.87
   5 ?    3.9   0.0      0.18   1.2e+02      10      35 ..     155     180 ..     146     188 .. 0.84
   6 !   11.4   0.0   0.00075      0.48      11      43 ..     190     222 ..     180     223 .. 0.89
   7 ?    3.2   0.0      0.32     2e+02       3      33 ..     216     246 ..     214     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00037
      TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawl 39
                e l+  a  +l+  +p++A+ l++++ + +P++  aw+
  AJA92913.1 11 EDLMYQAMTFLEKNQPKAAVSLFKKVTKIDPENVNAWY 48
                566777889999***********************997 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 5.8e-06
      TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeaw 38
                +a++  + al +l ++++Ai++++ + +++P+da+a+
  AJA92913.1 45 NAWYNQGLALNQLKKYADAITCFDMITQRNPNDAAAL 81
                79********************************997 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 9.1e-06
      TPR_14   7 laeallalGdpdeAiallrralalaPddaeawlll 41 
                 ++ a+++lGdp++A++++++a++++ + a a++  
  AJA92913.1  84 RGIAMAELGDPEGAMEYYEKAIKADSSYAPAYYNK 118
                 57899******************999998888766 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.014
      TPR_14  16 dpdeAiallrralalaPd 33 
                 ++de++++l++a++++P+
  AJA92913.1 127 EHDESLKVLDEAIEKDPK 144
                 69***************7 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.18
      TPR_14  10 allalGdpdeAiallrralalaPdda 35 
                 +l   G+++ A+++++ + +++P+++
  AJA92913.1 155 VLGKMGKHELALNCFESVHRANPQHL 180
                 5667899****************986 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.00075
      TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                 l++l+++++Ai++++++l+++ ++  + ++ a+
  AJA92913.1 190 LAELERHEKAIEVFDKILDKHKGNVNVVYAKAR 222
                 7899*******************9988888776 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.32
      TPR_14   3 allalaeallalGdpdeAiallrralalaPd 33 
                 + +a a+  +a  +  eA +ll+ a+++  +
  AJA92913.1 216 VVYAKARSKAAMNEVNEAFDLLNLAIKQSKA 246
                 5688899999999*************98765 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   1.4e-09     9e-07       2      60 ..      21      79 ..      20      83 .. 0.94
   2 !   20.6   0.1   7.1e-07   0.00046       3      58 ..      90     145 ..      88     154 .. 0.93
   3 ?    3.2   0.0       0.2   1.3e+02       3      26 ..     158     181 ..     156     188 .. 0.91
   4 !   17.0   0.2   9.7e-06    0.0062       3      54 ..     192     243 ..     189     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-09
      TPR_19  2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddar 60
                l+ +++ +A++l++++ + dp+n +a+++   al +l+ +++A+ + d + + +p+da+
  AJA92913.1 21 LEKNQPKAAVSLFKKVTKIDPENVNAWYNQGLALNQLKKYADAITCFDMITQRNPNDAA 79
                7889****************************************************865 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 7.1e-07
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                 + gd++ A++++e+a+++d  +a a ++   +l +  + de  ++Ld++ e+dp+ 
  AJA92913.1  90 ELGDPEGAMEYYEKAIKADSSYAPAYYNKGVLLDKKLEHDESLKVLDEAIEKDPKK 145
                 569***************************************************94 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.2
      TPR_19   3 aegdyaeAlalleqalqedpknae 26 
                 ++g+++ Al+ +e++  ++p++++
  AJA92913.1 158 KMGKHELALNCFESVHRANPQHLD 181
                 5899*****************987 PP

  == domain 4  score: 17.0 bits;  conditional E-value: 9.7e-06
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpee 54 
                 + ++++ A++ + ++l++  +n ++ ++ A+   a+++++eA +lL+ + ++
  AJA92913.1 192 ELERHEKAIEVFDKILDKHKGNVNVVYAKARSKAAMNEVNEAFDLLNLAIKQ 243
                 55799*************************************9999988776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012      0.74       3      32 ..      13      42 ..      13      43 .. 0.91
   2 !   16.4   0.0   1.6e-05      0.01       2      32 ..      46      76 ..      45      77 .. 0.96
   3 !   13.2   0.1   0.00017      0.11       5      28 ..      83     106 ..      79     109 .. 0.90
   4 !    8.7   0.0    0.0047         3       2      32 ..     114     144 ..     113     145 .. 0.95
   5 ?    5.8   0.0     0.039        25       4      32 ..     150     178 ..     149     179 .. 0.87
   6 ?    6.4   0.0     0.026        16      10      30 ..     190     210 ..     181     213 .. 0.77
   7 ?    0.2   0.1       2.3   1.5e+03       6      28 ..     220     242 ..     216     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                HHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  3 lyklalsyrklgdtdkAlealerlikeYPd 32
                l+++a+ +++ +++ +A+ +++++ k  P+
  AJA92913.1 13 LMYQAMTFLEKNQPKAAVSLFKKVTKIDPE 42
                6799*****988*************99996 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.6e-05
                HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  2 AlyklalsyrklgdtdkAlealerlikeYPd 32
                A y+++l++ +l+++++A++ ++ + ++ P+
  AJA92913.1 46 AWYNQGLALNQLKKYADAITCFDMITQRNPN 76
                89*********9******************9 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00017
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   5 klalsyrklgdtdkAlealerlik 28 
                 +++ ++ +lgd++ A+e++e+ ik
  AJA92913.1  83 NRGIAMAELGDPEGAMEYYEKAIK 106
                 67999***99***********998 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0047
                 HHHHHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
       TPR_6   2 Alyklalsyrk.lgdtdkAlealerlikeYPd 32 
                 A+y+ + ++ k l ++d++l+ l++ i++ P+
  AJA92913.1 114 AYYNKGVLLDKkL-EHDESLKVLDEAIEKDPK 144
                 99********989.***************996 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.039
                 HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                 ++ +  + k+g+++ Al  +e++ +  P+
  AJA92913.1 150 FYKGIVLGKMGKHELALNCFESVHRANPQ 178
                 66778888999*************99997 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.026
                 HHHHHHHHHHHHHHHHHHHH- CS
       TPR_6  10 yrklgdtdkAlealerlikeY 30 
                 + +l +++kA+e ++++++++
  AJA92913.1 190 LAELERHEKAIEVFDKILDKH 210
                 4555699***********997 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 2.3
                 HHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                  a+s  ++++  +A ++l+  ik
  AJA92913.1 220 KARSKAAMNEVNEAFDLLNLAIK 242
                 58888998999999999988777 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0     3e-10   1.9e-07      19      80 ..       6      68 ..       3      70 .. 0.96
   2 ?    1.6   0.1      0.53   3.4e+02      23      79 ..      75     135 ..      71     138 .. 0.59
   3 !   21.7   0.0   2.7e-07   0.00017       4      81 ..     127     205 ..      97     206 .. 0.96
   4 !   12.8   0.1   0.00016       0.1      37      79 ..     194     237 ..     190     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3e-10
                HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
      ANAPC3 19 etespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                ++e+ped+++ A ++++ +q k A  l++k  k+++++ +++y  + +l +Lkky +Ai++++
  AJA92913.1  6 KKEDPEDLMYQAMTFLEKNQPKAAVSLFKKVtKIDPENVNAWYNQGLALNQLKKYADAITCFD 68
                579*********************************************************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.53
                 HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
      ANAPC3  23 pedayll...AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                 p+da +l   + ++ ++g+ + A+e+++ka k +s+   + y ++  l k  +++e +++L
  AJA92913.1  75 PNDAAALnnrGIAMAELGDPEGAMEYYEKAiKADSSYAPAYYNKGVLLDKKLEHDESLKVL 135
                 5555555455666777889999999999996665555555554444443444556666665 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.7e-07
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                  +++ + +++ + +++++ p+ +++++ +l ++g+++ A++ +++  + n+++l + + ++  l +L+++e+Ai +++k
  AJA92913.1 127 EHDESLKVLDEAIEKDPKKPNPRFYKGIVLGKMGKHELALNCFESVhRANPQHLDSFFHKGIELAELERHEKAIEVFDK 205
                 6888899999999***************************************************************998 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00016
                 T-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
      ANAPC3  37 gqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                 +++++A+e+++k  ++ + + ++ y +A++  ++++++eA ++L
  AJA92913.1 194 ERHEKAIEVFDKIlDKHKGNVNVVYAKARSKAAMNEVNEAFDLL 237
                 67889999999998888999999999999999999999998887 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.085        55      52      76 ..      17      41 ..      14      42 .. 0.90
   2 !   31.2   0.5   3.1e-10     2e-07       4      74 ..      45     107 ..      43     110 .. 0.90
   3 !   10.4   0.0   0.00099      0.63       5      73 ..     114     174 ..     110     178 .. 0.77
   4 !   15.2   0.0     3e-05     0.019      10      73 ..     153     208 ..     148     211 .. 0.91
   5 ?   -0.5   0.0       2.4   1.5e+03       9      33 ..     220     244 ..     213     248 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.085
      TPR_12 52 grlyralgryeeAlelleealaiae 76
                ++++++ +++++A++l++++++i++
  AJA92913.1 17 AMTFLEKNQPKAAVSLFKKVTKIDP 41
                7889999*************99975 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 3.1e-10
      TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                 +a++n +++l++l++y++A+++++      +r   p+    a++l+n g++  +lg++e A e++e+a+++
  AJA92913.1  45 NAWYNQGLALNQLKKYADAITCFDMI---TQRN--PN---DAAALNNRGIAMAELGDPEGAMEYYEKAIKA 107
                 6889**********************...4443..65...6***************************987 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00099
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 a++n +++l +  ++de+l+ l++a+e       p      + ++  g+++ ++g++e Al+ +e + +
  AJA92913.1 114 AYYNKGVLLDKKLEHDESLKVLDEAIEKD-----P---KKPNPRFYKGIVLGKMGKHELALNCFESVHR 174
                 67788888888888888888888883333.....4...4555799999999999999999999998876 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 3e-05
      TPR_12  10 aavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 + vl ++g+++ Al ++e ++++      p+h   + + +  g+ + +l+r+e+A+e + + l+
  AJA92913.1 153 GIVLGKMGKHELALNCFESVHRAN-----PQH---LDSFFHKGIELAELERHEKAIEVFDKILD 208
                 789999**************7777.....999...77*********************999875 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 2.4
      TPR_12   9 laavlrrlgrydeAlellekaleia 33 
                  a   +++ +  eA++ll+ a+ + 
  AJA92913.1 220 KARSKAAMNEVNEAFDLLNLAIKQS 244
                 5666777777888888888777665 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0016         1       7      52 ..      22      67 ..      16      68 .. 0.84
   2 !   28.2   0.0   2.5e-09   1.6e-06       8      59 ..      57     108 ..      54     115 .. 0.91
   3 !    9.2   0.0    0.0021       1.3      11      61 ..     128     178 ..     124     183 .. 0.89
   4 !    9.1   0.0    0.0022       1.4      10      58 ..     161     209 ..     160     227 .. 0.90
   5 ?    2.1   0.0      0.34   2.2e+02       6      58 ..     191     243 ..     186     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
       TPR_9  7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladL 52
                ++++  +a      +  ++P+ +  ++  Gl+l ql  ++ A+ ++
  AJA92913.1 22 EKNQPKAAVSLFKKVTKIDPENVNAWYNQGLALNQLKKYADAITCF 67
                556666677777778899************************9887 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2.5e-09
       TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                  ++++ a+ + +++ + +P+d+  +  RG++ a+lG++++A++  e ++  +
  AJA92913.1  57 LKKYADAITCFDMITQRNPNDAAALNNRGIAMAELGDPEGAMEYYEKAIKAD 108
                 57899*****************************************999655 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0021
       TPR_9  11 weralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                 +++ l+v++  +  +P+ p  r+  G++l ++G  + Al+++e   + +p+
  AJA92913.1 128 HDESLKVLDEAIEKDPKKPNPRFYKGIVLGKMGKHELALNCFESVHRANPQ 178
                 56779999999999****************************988777775 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0022
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                 ++e al + e++   +P++ +  +  G+ la+l++ ++A++ ++  l++
  AJA92913.1 161 KHELALNCFESVHRANPQHLDSFFHKGIELAELERHEKAIEVFDKILDK 209
                 5789************************************999988865 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.34
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylal 58 
                 ++ e++e+a++v + +l  +   +  ++  ++  a ++ +++A + L+ ++ +
  AJA92913.1 191 AELERHEKAIEVFDKILDKHKGNVNVVYAKARSKAAMNEVNEAFDLLNLAIKQ 243
                 56789999999999999999999999999999999999888888877777665 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.086        55       6      34 ..      17      43 ..      13      45 .. 0.84
   2 ?    4.9   0.0     0.048        31       1      24 [.      46      69 ..      46      79 .. 0.84
   3 !   13.6   0.0   8.2e-05     0.053       1      29 [.      80     106 ..      80     110 .. 0.88
   4 ?    3.3   0.0      0.15        98       1      35 [.     114     146 ..     114     147 .. 0.90
   5 ?    1.6   0.0      0.54   3.4e+02       9      24 ..     156     171 ..     150     180 .. 0.80
   6 ?    4.1   0.0     0.085        55      11      26 ..     192     207 ..     190     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.086
       TPR_7  6 arlysrlGdyeeAielyeqsLaltkdped 34
                a ++ + ++ + A++l+++  ++  dpe+
  AJA92913.1 17 AMTFLEKNQPKAAVSLFKK--VTKIDPEN 43
                678899999**********..99888877 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.048
       TPR_7  1 aLlnLarlysrlGdyeeAielyeq 24
                a++n + +  +l +y++Ai+++  
  AJA92913.1 46 AWYNQGLALNQLKKYADAITCFDM 69
                68899999999**********975 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.2e-05
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                 aL+n + +  +lGd e A e+ye+  a+ 
  AJA92913.1  80 ALNNRGIAMAELGDPEGAMEYYEK--AIK 106
                 799999999***************..654 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.15
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                 a++n ++l  +  +++e ++++ +  a++kdp ++
  AJA92913.1 114 AYYNKGVLLDKKLEHDESLKVLDE--AIEKDPKKP 146
                 78999999999999**********..*****9876 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.54
       TPR_7   9 ysrlGdyeeAielyeq 24 
                   ++G++e A+ ++e 
  AJA92913.1 156 LGKMGKHELALNCFES 171
                 5689**********97 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.085
       TPR_7  11 rlGdyeeAielyeqsL 26 
                 +l ++e+Aie++ + L
  AJA92913.1 192 ELERHEKAIEVFDKIL 207
                 6789********9944 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0015      0.96       2      71 ..       8      77 ..       7      84 .. 0.93
   2 !    9.2   0.1   0.00081      0.52     204     256 ..      90     142 ..      83     145 .. 0.92
   3 !   15.8   0.2   7.8e-06     0.005       8     106 ..     150     244 ..     145     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                HHHHHHHHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT- CS
       NARP1  2 eesellLyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpen 71
                e+ e l+y+++ + e+++ + A+  ++++ k   ++++   +++  l +L+++++A + +  + +rnp++
  AJA92913.1  8 EDPEDLMYQAMTFLEKNQPKAAVSLFKKVTKIDPENVNAWYNQGLALNQLKKYADAITCFDMITQRNPND 77
                5668899************************9999********************************986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00081
                 HHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCT CS
       NARP1 204 klgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklD 256
                 +lg+ e A+ey +kai+ + +    y++K+ +l ++ + ++  +v++ea + D
  AJA92913.1  90 ELGDPEGAMEYYEKAIKADSSYAPAYYNKGVLLDKKLEHDESLKVLDEAIEKD 142
                 688999******************************************98777 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 7.8e-06
                 HHHHHHHHHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT..SSS-HHHHHHHHHHTTTS-TT- CS
       NARP1   8 LyknqiieeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekakklskedeeallalydelaekyprs 106
                  yk  ++ + gk+e Al+ +e++++    +l     k+  l +L+r+e+A +++ ++l++ + n +   +  ++    k+ ++++++++d l+ ++++s
  AJA92913.1 150 FYKGIVLGKMGKHELALNCFESVHRANPQHLDSFFHKGIELAELERHEKAIEVFDKILDKHKGNVNVVYAKARS----KAAMNEVNEAFDLLNLAIKQS 244
                 59999*******************************************************99987643333332....233344444444444444444 PP

>> PknG_TPR  Protein kinase G tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06   0.00069      99     220 ..      15     137 ..       5     145 .. 0.83
   2 !   12.9   0.0   5.1e-05     0.032     111     225 ..     129     244 ..     127     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                 HHHHHHHHCT-HHHHHHHHHHHHHHH---HHHHHH.HHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHH.HHHHHHT---TT-HHHHHHHH-TT-H CS
    PknG_TPR  99 aevrahldlGdveearelLdeleeeveedWrldWy.rglaeLlegdyeeAaaeFdevlaalpGEiaPklaLA.ataElagetdeekyYrtVwrtdrgvv 195
                  ++   l+  ++++a++l++++++  +e+    Wy +gla  + ++y+ A+++Fd + +  p ++a       a aEl   + + +yY+   + d ++ 
  AJA92913.1  15 YQAMTFLEKNQPKAAVSLFKKVTKIDPENVN-AWYnQGLALNQLKKYADAITCFDMITQRNPNDAAALNNRGiAMAELGDPEGAMEYYEKAIKADSSYA 112
                 5556678888999999999999887777655.6773588888899*******************997665542468998889999************** PP

                 HHHHHHHHHHHHTT-HHHHHHHHHT CS
    PknG_TPR 196 sAaFGlaRqlaaagdraaAvaaLde 220
                  A +     l ++ + ++ +++Lde
  AJA92913.1 113 PAYYNKGVLLDKKLEHDESLKVLDE 137
                 ****999999999999999999998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.1e-05
                 HHHHHHHHHHHHHH---HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-SHHHHHHHH.HHHHHT---TT-HHHHHHHH-TT-HHHHHHHHHHHHHT CS
    PknG_TPR 111 eearelLdeleeeveedWrldWyrglaeLlegdyeeAaaeFdevlaalpGEiaPklaLAa.taElagetdeekyYrtVwrtdrgvvsAaFGlaRqlaaa 208
                 +e  ++Lde  e+ +++   ++y+g+    +g+ e A ++F++v++a p  +   +   +  aEl  ++++ + ++ +    +g v  ++  aR +aa 
  AJA92913.1 129 DESLKVLDEAIEKDPKKPNPRFYKGIVLGKMGKHELALNCFESVHRANPQHLDSFFHKGIeLAELERHEKAIEVFDKILDKHKGNVNVVYAKARSKAAM 227
                 667788888888888899999******************************9998887763478888888889************************** PP

                 T-HHHHHHHHHTS-TTS CS
    PknG_TPR 209 gdraaAvaaLdeVpatS 225
                 +++++A + L+   ++S
  AJA92913.1 228 NEVNEAFDLLNLAIKQS 244
                 *******9998666655 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.3   8.3e+02       9      23 ..      51      65 ..      49      68 .. 0.85
   2 !   20.1   0.3   6.3e-07    0.0004       2      30 ..      78     106 ..      78     107 .. 0.96
   3 ?    2.7   0.0      0.19   1.2e+02       5      30 ..     115     140 ..     114     141 .. 0.87
   4 ?    2.7   0.0      0.19   1.2e+02       9      28 ..     153     172 ..     152     175 .. 0.89
   5 ?   -0.3   0.0       1.7   1.1e+03      12      32 ..     190     210 ..     187     211 .. 0.75
   6 ?   -1.6   0.0       4.5   2.9e+03      13      25 ..     225     237 ..     221     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
      TPR_10  9 analrqrgrydeAea 23
                + al q+++y++A  
  AJA92913.1 51 GLALNQLKKYADAIT 65
                7899********975 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.3e-07
      TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                 A++lnN ++a  ++g+ ++A++++e+a+ 
  AJA92913.1  78 AAALNNRGIAMAELGDPEGAMEYYEKAIK 106
                 89*************************96 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.19
      TPR_10   5 lnNLanalrqrgrydeAealleeala 30 
                 + N +++l +  ++de+++ l+ea++
  AJA92913.1 115 YYNKGVLLDKKLEHDESLKVLDEAIE 140
                 678888899999************97 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.19
      TPR_10   9 analrqrgrydeAealleea 28 
                 +++l ++g+++ A++ +e +
  AJA92913.1 153 GIVLGKMGKHELALNCFESV 172
                 899************99965 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 1.7
      TPR_10  12 lrqrgrydeAealleealair 32 
                 l ++ r+++A + +++ l+ +
  AJA92913.1 190 LAELERHEKAIEVFDKILDKH 210
                 778889999999888887765 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 4.5
      TPR_10  13 rqrgrydeAeall 25 
                  ++++ +eA +ll
  AJA92913.1 225 AAMNEVNEAFDLL 237
                 5788999999887 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0052       3.3      12      55 ..      34      77 ..      23      82 .. 0.84
   2 ?    2.5   0.1      0.28   1.8e+02      16      55 ..      72     111 ..      69     118 .. 0.89
   3 ?    4.3   0.0     0.078        50       4      45 ..     128     169 ..     125     181 .. 0.87
   4 ?    4.7   0.0      0.06        39      13      53 ..     171     211 ..     166     213 .. 0.89
   5 !    9.3   0.8    0.0022       1.4       5      66 ..     197     258 ..     193     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0052
      TPR_20 12 eaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55
                ++  + +p++++a ++  lal++ ++y++A++ + +i +r+ ++
  AJA92913.1 34 KKVTKIDPENVNAWYNQGLALNQLKKYADAITCFDMITQRNPND 77
                5556789************************9998888888765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.28
      TPR_20  16 aanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                 + np+d +a  +   a ++ g+ e A+e   + +k+d+++
  AJA92913.1  72 QRNPNDAAALNNRGIAMAELGDPEGAMEYYEKAIKADSSY 111
                 579************************9988888888776 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.078
      TPR_20   4 dapelaeleaalaanpddldarldlAlallaagryeeAleqL 45 
                 ++++l+ l++a++++p+  + r+    +l + g++e Al+ +
  AJA92913.1 128 HDESLKVLDEAIEKDPKKPNPRFYKGIVLGKMGKHELALNCF 169
                 6788999*******************************9865 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.06
      TPR_20  13 aalaanpddldarldlAlallaagryeeAleqLleilkrdr 53 
                 + + anp+ ld  +     l++ +r+e+A+e + +il +++
  AJA92913.1 171 SVHRANPQHLDSFFHKGIELAELERHEKAIEVFDKILDKHK 211
                 56789***************************999999987 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.0022
      TPR_20   5 apelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaarkqllk 66 
                 ++ ++ +++ l +++ +++  ++ A+  +a +++ eA+++L   +k+ ++ +  a ++++++
  AJA92913.1 197 EKAIEVFDKILDKHKGNVNVVYAKARSKAAMNEVNEAFDLLNLAIKQSKAIKLWARKEKVFQ 258
                 56777788889999********************************9999877766666665 PP

>> Paf67  RNA polymerase I-associated factor PAF67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.4e-05     0.047     139     192 ..      15      72 ..      13      86 .. 0.77
   2 !    5.7   0.0    0.0099       6.3     155     221 ..     171     237 ..     157     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
       Paf67 139 ttalkvlenidls.kkall...skvpaahvsllYyvGfaylmlrrYkDAirtlsqill 192
                 ++a++ le+ + +   +l+   +k+ + +v++ Y  G+a   l++Y+DAi ++  i++
  AJA92913.1  15 YQAMTFLEKNQPKaAVSLFkkvTKIDPENVNAWYNQGLALNQLKKYADAITCFDMITQ 72 
                 56777777766663334552226667779************************99876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0099
       Paf67 155 llskvpaahvsllYyvGfaylmlrrYkDAirtlsqillyisrtkq.yqsrsyqsdqinkqadrmyaLl 221
                  +++  + h+  +++ G+    l+r + Ai+++ +il   + + + ++++   + ++n+ ++  + Ll
  AJA92913.1 171 SVHRANPQHLDSFFHKGIELAELERHEKAIEVFDKILDKHKGNVNvVYAKARSKAAMNEVNE-AFDLL 237
                 56788899999**************************8887776654345555555555444.34444 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     2e-05     0.013     144     244 ..       8     108 ..       5     121 .. 0.91
   2 ?    3.6   0.0     0.051        32      20     115 ..     158     252 ..     141     271 .] 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
      TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqak 242
                 +++  l++ a   ++++q++aA+ +++++ + +p++ ++  +   +l+ l+++a +        +r  +da+  +  + A++ Lg+p+ A+ey++k  k
  AJA92913.1   8 EDPEDLMYQAMTFLEKNQPKAAVSLFKKVTKIDPENVNAWYNQGLALNQLKKYADAITCFDMITQRNPNDAAALNNRGIAMAELGDPEGAMEYYEKAIK 106
                 5677799999999**************************999999*********98899999999999999999999*******************888 PP

      TPR_15 243 en 244
                 + 
  AJA92913.1 107 AD 108
                 54 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.051
      TPR_15  20 kqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.lydaepkeaarlaekgwrrfrsprlLss 115
                 k g+ + Al+   e + +a+p+  + ++    +LA   +  ++a++   ++l   k++ +   +  +    ++e +ea +l   + ++++  +l+ +
  AJA92913.1 158 KMGKHELALNCF-ESVHRANPQHLDSFFHKGIELAELER-HEKAIEVFDKILDKHKGNVNVVYAKARSkAAMNEVNEAFDLLNLAIKQSKAIKLWAR 252
                 556777888888.56677778888888888888886544.444555555555555554444444444437788888888887777777777777765 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.25   1.6e+02      75      96 ..      32      53 ..      28      64 .. 0.83
   2 !   14.7   0.4   3.5e-05     0.022      72     137 ..     165     226 ..     161     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.25
                   ---SEEE-SHHHHHHHHTSS-- CS
  Thioredoxin_6 75 slplvreltpenaeelfeeglp 96
                    +  v++++pen+++ +++gl 
     AJA92913.1 32 LFKKVTKIDPENVNAWYNQGLA 53
                   57899*************9976 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.5e-05
                    HHH---SEEE-SHHHHHHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETT...G CS
  Thioredoxin_6  72 eknslplvreltpenaeelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladak...s 137
                    + n+++ v   +p+ ++ +f++g+     l    + e++ek+ +++ k+  ++k+++n+++a+a    +
     AJA92913.1 165 ALNCFESVHRANPQHLDSFFHKGIE----LA---ELERHEKAIEVFDKILDKHKGNVNVVYAKARskaA 226
                    579********************99....22...4679************************9984433 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.94     6e+02      13      26 ..      23      36 ..      20      39 .. 0.82
   2 ?   -1.7   0.0       7.1   4.5e+03      12      29 ..      56      73 ..      53      74 .. 0.76
   3 ?    4.3   0.1     0.085        55      10      27 ..      88     105 ..      86     108 .. 0.83
   4 ?    0.1   0.1         2   1.2e+03      15      29 ..     127     141 ..     124     142 .. 0.81
   5 ?    4.7   0.0     0.067        43      10      27 ..     156     173 ..     154     176 .. 0.85
   6 ?    5.4   0.0     0.038        24      13      28 ..     193     208 ..     190     210 .. 0.82
   7 ?   -0.8   0.0       3.8   2.5e+03      14      24 ..     228     238 ..     225     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.94
         PPR 13 nGkleeAlelfkeM 26
                +++++ A++lfk+ 
  AJA92913.1 23 KNQPKAAVSLFKKV 36
                678999*****985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 7.1
         PPR 12 knGkleeAlelfkeMkek 29
                +  k+ +A+ +f+ + ++
  AJA92913.1 56 QLKKYADAITCFDMITQR 73
                677888999999987665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.085
         PPR  10 ycknGkleeAlelfkeMk 27 
                  +  G++e A+e++++ +
  AJA92913.1  88 MAELGDPEGAMEYYEKAI 105
                 5779**********9865 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 2
         PPR  15 kleeAlelfkeMkek 29 
                 +++e l++++e +ek
  AJA92913.1 127 EHDESLKVLDEAIEK 141
                 6899******98876 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.067
         PPR  10 ycknGkleeAlelfkeMk 27 
                 ++k Gk+e Al +f+   
  AJA92913.1 156 LGKMGKHELALNCFESVH 173
                 89************9765 PP

  == domain 6  score: 5.4 bits;  conditional E-value: 0.038
         PPR  13 nGkleeAlelfkeMke 28 
                   ++e+A+e+f+++++
  AJA92913.1 193 LERHEKAIEVFDKILD 208
                 5789********9976 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 3.8
         PPR  14 GkleeAlelfk 24 
                 +++ eA++l++
  AJA92913.1 228 NEVNEAFDLLN 238
                 6789****997 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   2.9e-05     0.018      82     181 ..      16     119 ..      11     130 .. 0.78
   2 ?    4.5   0.1      0.04        25      26     108 ..     167     246 ..     151     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
      TPR_21  82 lAkaaveagdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakkee.afaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                 +A +  e+++ +aA + +++v +    e+++a  +  La  l + kky++A++  +  ++    +a++ + rG ++++ g+ + A + Y++A++a ++ 
  AJA92913.1  16 QAMTFLEKNQPKAAVSLFKKVTKID-PENVNAWYNQGLA--LNQLKKYADAITCFDMITQRnPNDAAALNNRGIAMAELGDPEGAMEYYEKAIKADSSY 111
                 6667777777777777666666555.667*********9..677799********99876515789999*************************99877 PP

      TPR_21 180 a......r 181
                 a       
  AJA92913.1 112 ApayynkG 119
                 65555433 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.04
      TPR_21  26 qgwqdyqeeqaeeAsalYqqlqeaveakdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakd 108
                 + +++ ++++ ++  + +++  e +e + ++ka e ++++ d+++g+    +a   +A+++++ +++++A   L+ +++++k 
  AJA92913.1 167 NCFESVHRANPQHLDSFFHKGIELAELERHEKAIEVFDKILDKHKGNVNVVYA---KARSKAAMNEVNEAFDLLNLAIKQSKA 246
                 55666666666666667777777777888889999999999999999666665...69999**************99999986 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   1.0   0.00028      0.18     140     246 ..      19     123 ..       6     138 .. 0.81
   2 ?    2.5   0.0      0.12        77     216     236 ..     127     147 ..     120     180 .. 0.81
   3 ?    5.5   0.2     0.015       9.9     182     230 ..     195     243 ..     188     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                 HHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHH..HHH-T.THHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-H CS
  Coatomer_E 140 illklhrvdlAekelkkmqdidedatltQLAqawvk..lavgg.ekiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdkdakde 235
                  +l  ++ ++A    kk+ +id +++     +aw +  la    +k+ dA   f+ ++++ ++  + ln + ++   lg++e A +  ++a++ d+ ++
  AJA92913.1  19 TFLEKNQPKAAVSLFKKVTKIDPENV-----NAWYNqgLALNQlKKYADAITCFDMITQRNPNDAAALNNRGIAMAELGDPEGAMEYYEKAIKADSSYA 112
                 57777888888888888888888876.....6776522344445899***************************************************9 PP

                 HHHHHHHHHHH CS
  Coatomer_E 236 etLiNlvvaaq 246
                  +  N  v+  
  AJA92913.1 113 PAYYNKGVLLD 123
                 99999866543 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                 -HHHHHHHHHHHHHH-TT-HH CS
  Coatomer_E 216 ryeeAeslLkeaLdkdakdee 236
                 +++e  ++L ea++kd+k+++
  AJA92913.1 127 EHDESLKVLDEAIEKDPKKPN 147
                 68999************9986 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.015
                 HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
  Coatomer_E 182 kiqdAyyifqelsekykstplllngkAvvslllgryeeAeslLkeaLdk 230
                 + + A  +f+ + +k+k +  +   kA  + ++++ +eA  lL+ a+++
  AJA92913.1 195 RHEKAIEVFDKILDKHKGNVNVVYAKARSKAAMNEVNEAFDLLNLAIKQ 243
                 5678999************************************999876 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.11        70     100     127 ..      44      71 ..      28      76 .. 0.89
   2 ?    6.0   0.0     0.019        12     101     127 ..      79     105 ..      74     110 .. 0.91
   3 ?    1.8   0.0      0.37   2.4e+02     101     133 ..     181     210 ..     171     216 .. 0.78
   4 ?    0.2   0.1       1.1   7.3e+02      97     126 ..     211     240 ..     191     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                 HHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 100 iaavfsravaleelGrkdealkafrmag 127
                 ++a ++++ al++l ++++a+  f m++
  AJA92913.1  44 VNAWYNQGLALNQLKKYADAITCFDMIT 71 
                 567799******************9875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                 HHHHHHHHHHHHTT-HHHHHHHHHHHH CS
     DUF3856 101 aavfsravaleelGrkdealkafrmag 127
                 aa+ +r+ a++elG  + a++++++a 
  AJA92913.1  79 AALNNRGIAMAELGDPEGAMEYYEKAI 105
                 78899******************9985 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.37
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH- CS
     DUF3856 101 aavfsravaleelGrkdealkafrmagemiaer 133
                    f+++  l+el r+++a++ f ++   ++ +
  AJA92913.1 181 DSFFHKGIELAELERHEKAIEVFDKI---LDKH 210
                 567999999***********999764...4455 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.1
                 HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
     DUF3856  97 klWiaavfsravaleelGrkdealkafrma 126
                 k  +++v+ +a++ + +   +ea++ ++ a
  AJA92913.1 211 KGNVNVVYAKARSKAAMNEVNEAFDLLNLA 240
                 444678888888888888888888777665 PP

>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0034       2.2      34      65 ..       5      36 ..       1      47 [. 0.90
   2 ?   -0.8   0.0       1.6     1e+03      66      66 ..     105     105 ..      53     143 .. 0.54
   3 ?    4.8   0.1     0.032        21      44      79 ..     185     220 ..     158     230 .. 0.79
   4 ?    1.3   0.1      0.39   2.5e+02      27      61 ..     214     249 ..     213     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0034
                  TBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHH CS
  Ribosomal_S7 34 GkkslAekivygaldiieektkkdplevleeA 65
                  Gkk+  e ++y+a++ +e+++ k +++++++ 
    AJA92913.1  5 GKKEDPEDLMYQAMTFLEKNQPKAAVSLFKKV 36
                  9****************************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                   H CS
  Ribosomal_S7  66 l 66 
                   +
    AJA92913.1 105 I 105
                   3 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.032
                   HHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEB CS
  Ribosomal_S7  44 ygaldiieektkkdplevleeAlenvkPrvevksrr 79 
                   ++ +++ e + +++++ev+ ++l++ k +v+v   +
    AJA92913.1 185 HKGIELAELERHEKAIEVFDKILDKHKGNVNVVYAK 220
                   45556666667889****************997655 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.39
                   HHHHSBTTBHHHHHHHHHHHHHHHHHHHSS.-HHHH CS
  Ribosomal_S7  27 inklmkdGkkslAekivygaldiieektkk.dplev 61 
                   +n +  + + + A++ v++a+d+++   k+ +++++
    AJA92913.1 214 VNVVYAKARSKAAMNEVNEAFDLLNLAIKQsKAIKL 249
                   678888889999999999999999886433245555 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0036       2.3      68     123 ..       9      64 ..       1      74 [. 0.87
   2 ?   -0.1   0.0       1.9   1.2e+03      86     118 ..     129     161 ..      76     176 .. 0.66
   3 ?    4.7   0.4     0.059        38      50     102 ..     190     247 ..     178     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0036
                      SHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
  Alkyl_sulf_dimr  68 gaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                      + e ++ +a + l++++ ++a++l +++   dpen +a   +  al+ql + a + 
       AJA92913.1   9 DPEDLMYQAMTFLEKNQPKAAVSLFKKVTKIDPENVNAWYNQGLALNQLKKYADAI 64 
                      5677888999999*************************999999999998877665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                      HHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHH CS
  Alkyl_sulf_dimr  86 rwaaellnhlvfadpenaeakelkadaleqlgy 118
                        ++++l+ ++++dp++ + +  k  +l ++g+
       AJA92913.1 129 DESLKVLDEAIEKDPKKPNPRFYKGIVLGKMGK 161
                      345666666666777666666665555555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.059
                      TS---HHHHHHHHHHHT.....TSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT- CS
  Alkyl_sulf_dimr  50 Lnplppeekakrlvelm.....Ggaekvlekakealkegdyrwaaellnhlvfadpen 102
                      L +l+++eka ++ + +     G+++ v +ka+++++ ++++ a  lln ++ + +  
       AJA92913.1 190 LAELERHEKAIEVFDKIldkhkGNVNVVYAKARSKAAMNEVNEAFDLLNLAIKQSKAI 247
                      555566666655544321111289999***********************99876654 PP

>> Rapsyn_N  Rapsyn N-terminal myristoylation and linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.82   5.3e+02      15      34 ..      19      38 ..      13      65 .. 0.84
   2 ?    1.4   0.0      0.54   3.5e+02      11      50 ..      83     122 ..      77     140 .. 0.83
   3 ?    5.6   0.0     0.027        17      11      36 ..     185     210 ..     178     219 .. 0.90
   4 ?   -1.0   0.0       3.1     2e+03      21      31 ..     242     252 ..     222     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.82
    Rapsyn_N 15 klyesndtekalrvWrkvLk 34
                 + e+n+ ++a+ +++kv k
  AJA92913.1 19 TFLEKNQPKAAVSLFKKVTK 38
                5678999******9999976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.54
    Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkktsdregkfrvLGcLi 50 
                 ++G+ + e  d e a++ + k++k  s  +  +   G+L+
  AJA92913.1  83 NRGIAMAELGDPEGAMEYYEKAIKADSSYAPAYYNKGVLL 122
                 6899999999*************99888877777666666 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.027
    Rapsyn_N  11 ekGLklyesndtekalrvWrkvLkkt 36 
                 +kG+ l e    eka++v+ k+L k 
  AJA92913.1 185 HKGIELAELERHEKAIEVFDKILDKH 210
                 69*********************885 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 3.1
    Rapsyn_N  21 dtekalrvWrk 31 
                 ++ ka+++W++
  AJA92913.1 242 KQSKAIKLWAR 252
                 57899999975 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.8   5.2e+02      24      44 ..      57      76 ..      53      85 .. 0.73
   2 ?    7.7   0.2    0.0057       3.6       4      32 ..      78     106 ..      75     107 .. 0.90
   3 ?    0.9   0.1      0.77   4.9e+02       8      32 ..     116     140 ..     111     144 .. 0.79
   4 ?    0.6   0.0      0.91   5.9e+02      25      39 ..     194     208 ..     183     224 .. 0.72
   5 ?    1.7   0.1      0.44   2.8e+02      28      42 ..     231     246 ..     220     260 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.8
         MIT 24 lelYkealelLlqalkeknee 44
                l++Y +a+  + ++ ++ n++
  AJA92913.1 57 LKKYADAITCFDMITQR-NPN 76
                57899999999988884.333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0057
         MIT   4 AlelvkkAveeDnagnyeeAlelYkeale 32 
                 A +l ++ + + + g+ e A+e+Y++a++
  AJA92913.1  78 AAALNNRGIAMAELGDPEGAMEYYEKAIK 106
                 788889999999***************96 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.77
         MIT   8 vkkAveeDnagnyeeAlelYkeale 32 
                  +k v +D++ + +e l+   ea+e
  AJA92913.1 116 YNKGVLLDKKLEHDESLKVLDEAIE 140
                 6788889999999998888777776 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.91
         MIT  25 elYkealelLlqalk 39 
                 e  ++a+e++ ++l 
  AJA92913.1 194 ERHEKAIEVFDKILD 208
                 556777777777775 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.44
         MIT  28 kealelLlqalke.kn 42 
                  ea +lL++a+k+ k+
  AJA92913.1 231 NEAFDLLNLAIKQsKA 246
                 6889999999994232 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1571.58
//
Query:       AJA92914.1  [L=197]
Description: putative proteasome endopeptidase complex, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-46  157.5   0.0    3.3e-46  157.2   0.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   1.8e-50   3.3e-46       4     190 .]       6     184 ..       4     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 1.8e-50
                 S-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCTTT CS
  Proteasome   4 GttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsgrr 102
                 G t+vGi++++gvv+a++kr+ +g+ l+skst +K f i++++g+++aGl+aD++ l  +++a a+ ++++ +r++p+      +a+++++++++++  
  AJA92914.1   6 GATAVGITFDEGVVFASEKRIAYGNFLVSKST-KKTFPITPKVGATCAGLVADMQLLSLQISALAKIRKMDLKRDVPPN----TIAKMMSNMMYERRYF 99 
                 89*************************99996.**********************************************....**************** PP

                 TTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
  Proteasome 103 pfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievavi 190
                 p++ +++++g+   ++p +y++dp Gs++ ++ ++a+G+g+e+a ++l+ ++ke+++++ea +lavka+++a+ rd++sg++i+v v+
  AJA92914.1 100 PLLTQVIVGGMT--DKPVIYTLDPLGSVLPDE-YAAVGTGAEMALGVLDPQFKENMNEKEATDLAVKAVRSATMRDSFSGDGIDVLVV 184
                 ************..66***************6.****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1449.76
//
Query:       AJA92915.1  [L=55]
Description: Sec61beta family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-14   52.7   0.3    3.5e-14   52.5   0.3    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.3     2e-18   3.5e-14       1      40 [.      13      52 ..      13      53 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2e-18
                XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
  Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                S+aGLlr++e++++g+k+dPk+V+ + + +i++ +lL il
  AJA92915.1 13 SGAGLLRFFEDETKGVKVDPKIVVSVPISLIIVSWLLDIL 52
                89************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 411.17
//
Query:       AJA92916.1  [L=207]
Description: ribosomal protein S7 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-35  122.3   0.2      2e-35  121.6   0.2    1.3  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   0.2   1.1e-39     2e-35      17     149 .]      58     207 .]      48     207 .] 0.95

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1.1e-39
                   STTSBHHHHHHHHHSB............TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE-HHHHHHHHH CS
  Ribosomal_S7  17 kynselveklinklmk............dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevrpkRrqalAl 101
                   k + ++ve+l nklm+             Gkk+   +i++ a+dii+ kt+++p+evl++A+en++P+++++++ +GG+ y+v+v+v+p Rr++lAl
    AJA92916.1  58 KGDVHIVERLANKLMHfgkkyakntgrqGGKKQHSLNIIKLAFDIINLKTGQNPVEVLVRAVENSAPNEDTTRIVYGGTVYHVSVDVAPIRRVDLAL 154
                   45679**********************99******************************************************************** PP

                   HHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
  Ribosomal_S7 102 rwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                   r+i++a    ++ + k+++e +ae li Aa+++  + +vkk++e++r+A+a+r
    AJA92916.1 155 RFIADAIkeaTFSNPKPIEEYIAEHLILAANNDpaAPSVKKKNELERVAQASR 207
                   ****99877788999******************88889*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1445.61
//
Query:       AJA92917.1  [L=251]
Description: ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-31  109.5   0.0    3.4e-31  108.6   0.0    1.4  1  ABC_tran      ABC transporter
    1.6e-09   38.1   0.0     0.0005   20.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00063   20.2   0.3     0.0066   16.9   0.3    2.1  1  AAA           ATPase family associated with various cellular 
     0.0014   18.5   0.0      0.052   13.3   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0014   18.6   0.1     0.0044   17.0   0.0    1.8  2  Rad17         Rad17 P-loop domain
     0.0018   17.7   0.3       0.59    9.5   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0041   17.1   0.0     0.0068   16.3   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
     0.0088   16.6   0.2      0.014   15.9   0.2    1.4  1  AAA_23        AAA domain
     0.0099   15.6   0.1       0.02   14.6   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.034   14.4   0.0    1.8  2  AAA_22        AAA domain
      0.011   16.1   0.0      0.029   14.7   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.011   14.5   0.4       0.75    8.5   0.1    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.012   16.0   0.1      0.093   13.1   0.0    2.3  3  RNA_helicase  RNA helicase
      0.018   15.0   0.0       0.14   12.1   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
      0.023   15.3   0.1      0.046   14.3   0.1    1.6  1  AAA_18        AAA domain
      0.031   14.2   0.0      0.058   13.3   0.0    1.4  1  NACHT         NACHT domain
      0.035   14.4   0.0        0.1   12.8   0.0    1.8  2  AAA_28        AAA domain
      0.039   14.1   0.1      0.048   13.8   0.1    1.5  1  AAA_33        AAA domain
      0.043   13.6   0.4       0.91    9.2   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
      0.044   13.5   0.0       0.25   11.1   0.0    2.0  2  AAA_30        AAA domain
      0.051   12.4   0.0       0.81    8.4   0.0    2.2  2  Adeno_IVa2    Adenovirus IVa2 protein
      0.059   13.4   0.1       0.17   12.0   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
      0.069   13.0   0.1       0.24   11.3   0.1    1.9  1  ATPase_2      ATPase domain predominantly from Archaea
      0.087   12.5   0.1       0.21   11.3   0.0    1.6  2  AAA_24        AAA domain
       0.14   11.7   0.1       0.33   10.5   0.0    1.6  2  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.0   4.7e-34   3.4e-31       3     137 .]      25     163 ..      23     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 4.7e-34
                 EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxx RF
    ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeieka 88 
                  v+l+++ ge v ivG++G+GKSt+l++lagl+kp+ Geilldgk+l +     +     +++qe  lfp ltv++n             e+ e  +++
  AJA92917.1  25 GVNLTVNDGEFVCIVGPSGCGKSTFLRILAGLEKPDDGEILLDGKKLVN-----TGPDRIMVFQEGALFPWLTVEDNveyglkvagipekERHEISKRY 118
                 69*****************************************999988.....677777999999********************7542222225556 PP

                 HHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  89 lsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                 l+ ++l++++++      ++LS G+kqrva+aral+ +p++ll+DEp+a
  AJA92917.1 119 LDMMQLSQFANSYT----YQLSTGMKQRVAIARALVMDPDVLLMDEPFA 163
                 66666666555555....*****************************85 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     7e-07    0.0005       1      60 [.      35      82 ..      35     102 .. 0.77
   2 !   16.4   0.0   8.3e-06    0.0059     235     299 ..     133     196 ..      89     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7e-07
      AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                + +++Gp g+GKS++L++l +l            e+++ g+i  + ++l ++ p+  ++f
  AJA92917.1 35 FVCIVGPSGCGKSTFLRILAGL------------EKPDDGEILLDGKKLVNTGPDRIMVF 82
                679****************999............55555555555555555555555555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.3e-06
      AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll...ellkelsrngaQviltTHS.p 299
                 ++lS G+k+  a++ al  ++   ++ll DEp + L+ +    ll   +++ ++++    +i++TH+ p
  AJA92917.1 133 YQLSTGMKQRVAIARALVMDP---DVLLMDEPFAALDSQTRDLLLvemQMIWQKTK--KTIIFVTHNvP 196
                 789*******9***9***999...9*************999999977777755555..79******955 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   9.3e-06    0.0066       1     110 [.      36     193 ..      36     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.3e-06
                 EEEESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCSSS..........................................................ST CS
         AAA   1 vllyGppGtGKTllakavakelgve..fleisgsellsk..........................................................yv 39 
                 v+++Gp G+GK+++ + +a   + +   + ++g++l++                                                           y+
  AJA92917.1  36 VCIVGPSGCGKSTFLRILAGLEKPDdgEILLDGKKLVNTgpdrimvfqegalfpwltvednveyglkvagipekerheiskryldmmqlsqfansytYQ 134
                 689****************99652222355555555555555555555666666666666666666666666666666666666666666666665566 PP

                 THHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
         AAA  40 gesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatn 110
                   + +k r  +++a  +  p +l++DE  a   s+          + + Ll e++   +k++k+i i +t+
  AJA92917.1 135 LSTGMKQRVAIARALVMD-PDVLLMDEPFAALDSQ----------TRDLLLVEMQMIWQKTKKTI-IFVTH 193
                 666666666666666665.9*******88888777..........67788888887777655444.44444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   7.2e-05     0.052      23      44 ..      34      54 ..      21      82 .. 0.83
   2 ?    3.0   0.0     0.092        66     293     365 ..     131     194 ..      94     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
      AAA_15 23 eeltvliGkNnsGKSsileald 44
                e + +++G+ ++GKS++l++l 
  AJA92917.1 34 E-FVCIVGPSGCGKSTFLRILA 54
                2.99***************996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.092
      AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                 + ++ ++G+++ + ++  ++  ++        ++ll++EP a L  q    l   ++ + +++k+ +i+ TH+
  AJA92917.1 131 YTYQLSTGMKQRVAIA--RALVMDP-------DVLLMDEPFAALDSQTRDLLLVEMQMIWQKTKKTIIFVTHN 194
                 5566677777766554..4444444.......99******************************99******7 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.1e-06    0.0044      47      66 ..      35      54 ..      22      63 .. 0.86
   2 ?   -1.2   0.0       2.3   1.7e+03     130     139 ..     183     192 ..     123     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.1e-06
       Rad17 47 iLLisGPsGCgkstvvkvLs 66
                 + i GPsGCgkst +++L+
  AJA92917.1 35 FVCIVGPSGCGKSTFLRILA 54
                67799*************98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
       Rad17 130 rtdkklilve 139
                 +t+k +i+v 
  AJA92917.1 183 KTKKTIIFVT 192
                 4555555553 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00082      0.59      24      41 ..      33      50 ..      19      54 .. 0.84
   2 !    6.5   0.0    0.0071       5.1     136     198 ..     134     194 ..      92     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00082
                SSEEEEEESTTSSHHHHH CS
                xxxxxxxxxxxxxxxxxx RF
       SMC_N 24 ksftaivGpNGSGKsnll 41
                 +f +ivGp G+GKs +l
  AJA92917.1 33 GEFVCIVGPSGCGKSTFL 50
                5799***********986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0071
                 CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH...HHHHHHHCTTSEEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv...aellkeksknaQfivislr 198
                 +LS G k+ va+a  +    ++p  + l+De  aaLD + +  +    +++ +k+k++ ++ ++++
  AJA92917.1 134 QLSTGMKQRVAIARAL---VMDPD-VLLMDEPFAALDSQTRDLLlveMQMIWQKTKKTIIF-VTHN 194
                 6777777777766543...23454.568*************99833347777887665444.4554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.4e-06    0.0068      99     125 ..      32      59 ..       8      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.4e-06
                  T.SEEEEECSTTSSHHHHHHHHCTT--- CS
  RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelel 125
                  d +++++vG+SG GKSt++  l++ ++ 
   AJA92917.1  32 DgEFVCIVGPSGCGKSTFLRILAGLEKP 59 
                  44899***************99986555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     2e-05     0.014      18      39 ..      32      53 ..       3      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
      AAA_23 18 skgltlItGpNGaGKTTildAi 39
                +  +++I+Gp G+GK+T+l+ +
  AJA92917.1 32 DGEFVCIVGPSGCGKSTFLRIL 53
                33588*************9865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   2.8e-05      0.02      17      39 ..      28      50 ..      22      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
      AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                ++++  +++ ++GpsG GKST+l
  AJA92917.1 28 LTVNDGEFVCIVGPSGCGKSTFL 50
                5566444999***********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.8e-05     0.034       5      26 ..      33      54 ..      30      74 .. 0.88
   2 ?   -1.5   0.0         4   2.9e+03      91      99 ..     149     160 ..     107     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
      AAA_22  5 agilvvtGesGtGKTtllrrll 26
                  +++++G+sG+GK+t lr l+
  AJA92917.1 33 GEFVCIVGPSGCGKSTFLRILA 54
                5789*************99776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4
      AAA_22  91 v...ielliiDE 99 
                     + +l+ DE
  AJA92917.1 149 LvmdPDVLLMDE 160
                 122444555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.1e-05     0.029      20      45 ..      31      54 ..      26      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-05
      AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                ++g  e v ++G+sG+GKs+ +r l+
  AJA92917.1 31 NDG--EFVCIVGPSGCGKSTFLRILA 54
                444..789*************99776 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.019        13     241     288 ..      29      80 ..      18      87 .. 0.74
   2 ?    8.5   0.1     0.001      0.75     320     382 ..     132     197 ..     117     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                 EE-SS.EEEEEE-TTSSHHHHHH...HHHHCCSEE-TTSS-TTEEE-TT-EE CS
  ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLe...AlekGvynhvpgDGRefvvtdktavk 288
                  +  G  + IvG+   GKsT L+    lek  +  +  DG+++v t ++ + 
  AJA92917.1  29 TVNDGeFVCIVGPSGCGKSTFLRilaGLEKPDDGEILLDGKKLVNTGPDRIM 80 
                 456676789***********98722256777788888888888888777665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.001
                 ESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HH...HHHHS-GGG--B--HHHCHHH CS
  ABC_ATPase 320 tedASGStsqAanimealeagakllLiDEDtsAtNlmirDer...mqelvskekepitplvdrvre 382
                 t + S  + q ++i++al ++ ++lL+DE  +A     rD +   mq + +k+k++i  +++ v e
  AJA92917.1 132 TYQLSTGMKQRVAIARALVMDPDVLLMDEPFAALDSQTRDLLlveMQMIWQKTKKTIIFVTHNVPE 197
                 555677788999*********************999999964333999999999999877777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.093       1      19 [.      36      54 ..      36      69 .. 0.90
   2 ?   -2.1   0.0       6.9   4.9e+03      78      99 ..      95     116 ..      90     122 .. 0.80
   3 ?   -0.7   0.0       2.6   1.9e+03      66      85 ..     117     136 ..     100     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
  RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                  ++++Gpsg+GKSt+ + La
    AJA92917.1 36 VCIVGPSGCGKSTFLRILA 54
                  689***********99865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.9
  RNA_helicase  78 sstpyplnmasleekgtlftSk 99 
                   ++++y l++a + ek+++  Sk
    AJA92917.1  95 DNVEYGLKVAGIPEKERHEISK 116
                   5788999999999999876665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.6
  RNA_helicase  66 npsdlaelirlvsstpypln 85 
                    + d+++l + ++s++y+l 
    AJA92917.1 117 RYLDMMQLSQFANSYTYQLS 136
                   34488888999999999875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.14       2      21 ..      36      55 ..      35      61 .. 0.91
   2 ?   -0.0   0.0       1.1   7.9e+02      24      85 ..     183     245 ..     170     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                EEEE--SSSSHHHHHHHGGG CS
       AAA_5  2 vlLvGppGtgKselaerlaa 21
                v++vGp+G+gKs++ + la 
  AJA92917.1 36 VCIVGPSGCGKSTFLRILAG 55
                89************999885 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.1
                 S--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG--HHHHHHH CS
       AAA_5  24 nreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEveraesevlnsL 85 
                 +++ +++  t + +e+ ++g+r       s+++s+++++      +++++ ++ + + e+++l++L
  AJA92917.1 183 KTKKTIIFVTHNVPEAAVLGSRVA---VFSHRPSVVKKSLDidykRPRVAEDENLGQFEKQILAAL 245
                 667788888899999999999885...667777777666666666888888888877777777766 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   6.5e-05     0.046       1      21 [.      36      56 ..      36      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
      AAA_18  1 IlltGtpGvGKttlakeLskr 21
                +++ G++G+GK+t+ + L+ +
  AJA92917.1 36 VCIVGPSGCGKSTFLRILAGL 56
                79***************9755 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.1e-05     0.058       2      21 ..      35      54 ..      34      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.1e-05
                CEEEEC-TTTCHHHHHHHHH CS
       NACHT  2 lvilqGeaGsGKTtLlqkla 21
                 v++ G++G+GK+t+l+ la
  AJA92917.1 35 FVCIVGPSGCGKSTFLRILA 54
                589*************9776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014       0.1       2      20 ..      36      54 ..      35      66 .. 0.89
   2 ?   -2.2   0.0       5.8   4.2e+03     101     119 ..     143     162 ..     112     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
      AAA_28  2 ivitGgestGKTtlleaLa 20
                ++i+G++++GK+t l+ La
  AJA92917.1 36 VCIVGPSGCGKSTFLRILA 54
                89**************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.8
      AAA_28 101 eaaarekrydl.vfllppap 119
                 +a+ar+  +d  v+l+++ +
  AJA92917.1 143 VAIARALVMDPdVLLMDEPF 162
                 44555555555444444333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.6e-05     0.048       2      20 ..      36      54 ..      35     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
      AAA_33  2 vllvGlpGsGKstlaerll 20
                v +vG++G+GKst+++ l+
  AJA92917.1 36 VCIVGPSGCGKSTFLRILA 54
                678***********99875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0013      0.91      44      63 ..      30      49 ..      13      62 .. 0.82
   2 ?    2.4   0.1      0.16   1.1e+02     102     151 ..     146     197 ..     111     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
   IstB_IS21 44 iekkenivllGpsGvGKshl 63
                +++ e ++++GpsG GKs +
  AJA92917.1 30 VNDGEFVCIVGPSGCGKSTF 49
                577899***********865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
   IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellf...eviekryerrsiiitsnlpf 151
                 a + ++ +d+l++D+  +  ld++ + ll+   ++i ++ +++ i +t n+p 
  AJA92917.1 146 ARALVMDPDVLLMDEP-FAALDSQTRDLLLvemQMIWQKTKKTIIFVTHNVPE 197
                 3344566799999995.778888888888544478899999999999999885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.25      16      41 ..      31      56 ..      25      68 .. 0.78
   2 ?   -0.4   0.0       1.1   8.2e+02      37      68 ..     176     207 ..     172     231 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
      AAA_30 16 sgdrvavltGpAGtGKttalkalrea 41
                ++  +++++Gp G GK+t l+ l+ +
  AJA92917.1 31 NDGEFVCIVGPSGCGKSTFLRILAGL 56
                444699***************98866 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
      AAA_30  37 alreaweaaggrviglAptgkaAkvLaeelgi 68 
                 +++ +w++ ++++i ++++   A+vL+  + +
  AJA92917.1 176 EMQMIWQKTKKTIIFVTHNVPEAAVLGSRVAV 207
                 67789999999*****9999999999987765 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0011      0.81      90     107 ..      36      53 ..       4      58 .. 0.69
   2 ?    1.5   0.0      0.15   1.1e+02     265     291 ..     112     139 ..      91     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
  Adeno_IVa2  90 GviyGPtGsGksqllrnl 107
                   i GP G+Gks +lr l
  AJA92917.1  36 VCIVGPSGCGKSTFLRIL 53 
                 3589************87 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
  Adeno_IVa2 265 hilsski.apfqlarfvntyakglskdl 291
                 h +s +    +ql++f n+y+ +ls+ +
  AJA92917.1 112 HEISKRYlDMMQLSQFANSYTYQLSTGM 139
                 66777651568**********9998755 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.17       2      21 ..      36      55 ..      35      72 .. 0.89
   2 ?   -1.7   0.0       4.3   3.1e+03      81      81 ..     156     156 ..     103     193 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                EEEEESTTSSHHHHHHHHHT CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                v+ivG +  GKSt+++ l g
  AJA92917.1 36 VCIVGPSGCGKSTFLRILAG 55
                89**************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                 E CS
    MMR_HSR1  81 l 81 
                 l
  AJA92917.1 156 L 156
                 1 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00033      0.24      19      42 ..      32      55 ..      20     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
    ATPase_2 19 pneiyfiYGpegsGKtaLlkeiie 42
                  e++ i Gp g+GK+++l+ ++ 
  AJA92917.1 32 DGEFVCIVGPSGCGKSTFLRILAG 55
                467899************996654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.21       5      22 ..      36      53 ..      33      80 .. 0.88
   2 ?   -2.3   0.0       4.2     3e+03     119     131 ..     182     194 ..     174     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
      AAA_24  5 iliyGpsgiGKTtlakel 22
                ++i+Gpsg GK+t+++ l
  AJA92917.1 36 VCIVGPSGCGKSTFLRIL 53
                79************9877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
      AAA_24 119 qelrknvifiahe 131
                 q+++k++if+ h 
  AJA92917.1 182 QKTKKTIIFVTHN 194
                 4556678887774 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00047      0.33      31      50 ..      31      50 ..      22      55 .. 0.87
   2 ?   -2.9   0.0       6.1   4.4e+03      80      95 ..     108     123 ..     100     172 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
      AAA_25 31 pagelallaGapgtGKttla 50
                  ge++ ++G++g+GK+t++
  AJA92917.1 31 NDGEFVCIVGPSGCGKSTFL 50
                6799**************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.1
      AAA_25  80 EdsedelrrRlravge 95 
                 E  ++e+ +R+  +++
  AJA92917.1 108 EKERHEISKRYLDMMQ 123
                 5566667777766653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1711.63
//
Query:       AJA92918.1  [L=215]
Description: enoyl-(Acyl carrier protein) reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-17   62.4   0.0      7e-16   58.5   0.0    1.9  2  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    2.1e-16   60.0   0.0    5.2e-11   42.4   0.0    2.1  2  adh_short      short chain dehydrogenase
     0.0039   16.5   0.0     0.0098   15.2   0.0    1.7  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.073   12.2   0.0       0.11   11.5   0.0    1.3  1  RmlD_sub_bind  RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.012        53       1      32 [.       8      39 ..       8      52 .. 0.74
   2 !   58.5   0.0   1.6e-19     7e-16      60     231 ..      44     208 ..      35     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.012
                  TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHH CS
  adh_short_C2  1 GaasgIGraiAkalaeeGaevvltdlneeakk 32
                  Ga +gIG+ i  +l++   +v     n+ + +
    AJA92918.1  8 GASRGIGKSISDSLKKLDLDVFSLSSNDIDTS 39
                  899*************9999987666655433 PP

  == domain 2  score: 58.5 bits;  conditional E-value: 1.6e-19
                   HHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHH CS
  adh_short_C2  60 veevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylA 156
                   v++ +++ ++ Dilv n g  p    +f+++s+e++++ ++  + ++  l++ +   +++gg + +++s   +   ++  + +a +aa  ++ + l 
    AJA92918.1  44 VNKFANENNSTDILVLNTGGPPI--IEFEKISKEDWEKYHNQLFVGFCTLLQKI--KINDGGYVFAITSNVIKEPNSKLIISSAYRAAFSSVFKILS 136
                   66777788999***********9..**********************9999988..59************8888888888***************** PP

                   HHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEEST CS
  adh_short_C2 157 velgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDg 231
                   +e++++ +    ++pgpi+T+ ++++    +  ee +++ p++rlg+pee+++ +  ++ +e +y +G ++  Dg
    AJA92918.1 137 KEFAERDVSLINIAPGPINTDRTKELV---DNVEEYADSLPMKRLGKPEEIGDFVSSIVEKEIKYLSGVVINFDG 208
                   ***********************9997...445677789********************************9998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-06    0.0045       1      34 [.       2      35 ..       2      54 .. 0.87
   2 !   42.4   0.0   1.2e-14   5.2e-11      68     193 ..      44     165 ..      35     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCH CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrse 34
                k ++v Gas+GIG+ i++ l k + +v+ +++++
  AJA92918.1  2 KKAIVLGASRGIGKSISDSLKKLDLDVFSLSSND 35
                689************************9988775 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 1.2e-14
                 HHHHHHHHSSESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHH CS
   adh_short  68 vekavkklgkldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslake 166
                 v+k +++  + d+Lv N+G     +f+++s+e+we++ +  ++g   l +     ++ + +G +  ++S++ k+p+  ++  sA  aa  + ++ l+ke
  AJA92918.1  44 VNKFANENNSTDILVLNTGGPPIIEFEKISKEDWEKYHNQLFVGFCTLLQK----IKINDGGYVFAITSNVIKEPNSKLIISSAYRAAFSSVFKILSKE 138
                 56666777889***************************9999998887777....44579*************************************** PP

                 HGGGTEEEEEEEESSBSSHHHHHHCTH CS
   adh_short 167 laptgirvnavaPGlvdTdmakelrek 193
                 +a++ ++ +++aPG+++Td +kel ++
  AJA92918.1 139 FAERDVSLINIAPGPINTDRTKELVDN 165
                 *********************998765 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.2e-06    0.0098      37     101 ..       2      75 ..       1      77 [. 0.74
   2 ?   -3.0   0.0      0.85   3.8e+03      26     112 ..      91     111 ..      86     134 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                    -EEEEE---TTTHHHHHHHHHCTT-EEEEE-TT...SCCHHHH......HCCSSEEEE-SS-TT-B-GGGS-TT CS
  THF_DHG_CYH_C  37 kkvvvvGrsnivgkplallLleknatVtvchsk...tkdlaei......treadivvvavGkpelikaemvkeg 101
                    kk++v+G+s+ +gk+++  L++ +  V  + s+   t++l+++       ++ di+v  +G p +i+ e ++++
     AJA92918.1   2 KKAIVLGASRGIGKSISDSLKKLDLDVFSLSSNdidTSNLDSVnkfaneNNSTDILVLNTGGPPIIEFEKISKE 75 
                    79********************8777766654322266655441111115678**************9999765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.85
                    HHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC CS
  THF_DHG_CYH_C  26 llketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvkegavviDvGinrv 112
                    ll+                                                                  +  +++g  v  +  n +
     AJA92918.1  91 LLQ------------------------------------------------------------------KIKINDGGYVFAITSNVI 111
                    343..................................................................333333333333333333 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.5e-05      0.11       3      53 ..       4      54 ..       1      62 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                   EEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--S CS
  RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpd 53
                    +v+Ga+  +G+ + ++l++ +l+v +l+++++d ++ ++v+++ +e++  
     AJA92918.1  4 AIVLGASRGIGKSISDSLKKLDLDVFSLSSNDIDTSNLDSVNKFANENNST 54
                   6899***************************************99987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1555.37
//
Query:       AJA92919.1  [L=185]
Description: 4Fe-4S binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-10   40.1  14.2    6.1e-05   22.7   3.0    3.2  3  Fer4          4Fe-4S binding domain
    2.3e-08   34.5  26.2    4.1e-06   27.3   8.8    2.0  3  Fer4_7        4Fe-4S dicluster domain
    4.5e-08   33.9  14.6    6.4e-06   27.0   6.1    2.5  3  Fer4_16       4Fe-4S double cluster binding domain
      5e-08   32.9  14.4    5.5e-07   29.6   4.7    2.0  2  Fer4_10       4Fe-4S dicluster domain
    4.1e-07   30.4   1.3       0.01   16.3   0.1    2.3  2  Fer4_8        4Fe-4S dicluster domain
    1.8e-06   28.0   7.7    1.8e-05   24.8   8.1    2.1  2  Fer4_9        4Fe-4S dicluster domain
    7.6e-06   26.0   3.7     0.0033   17.5   0.5    2.3  2  Fer4_21       4Fe-4S dicluster domain
    1.8e-05   25.2   0.4       0.11   13.0   0.1    2.3  2  Fer4_17       4Fe-4S dicluster domain
    0.00016   21.8   4.3    0.00016   21.8   4.3    1.9  2  Fer4_18       4Fe-4S dicluster domain
    0.00025   21.0  12.7      0.041   14.0   4.6    2.5  2  Fer4_6        4Fe-4S binding domain
     0.0015   19.0   8.6       0.32   11.6   0.3    2.5  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0054   17.6   0.6          3    8.7   0.1    2.3  2  Fer4_22       4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.2  10.5      0.019   15.4   1.0    2.7  2  Fer4_4        4Fe-4S binding domain
      0.024   15.5  16.7       0.15   13.0   6.7    2.4  2  Fer4_3        4Fe-4S binding domain
      0.061   13.4  14.4      0.079   13.1   3.0    2.7  2  Fer4_2        4Fe-4S binding domain
       0.18   11.8   2.3         15    5.7   0.0    2.4  2  Adhesin_P1_N  Adhesin P1 N-terminal domain
        3.9    8.3  13.5        2.8    8.8   3.6    2.5  2  Fer4_15       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.31   3.2e+02       2      10 ..       2      10 ..       1      13 [. 0.85
   2 !   22.3   1.3   7.4e-08   7.8e-05       4      22 ..      73      91 ..      70      93 .. 0.91
   3 !   22.7   3.0   5.8e-08   6.1e-05       4      22 ..     135     153 ..     133     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.31
                EEETTTSSS CS
        Fer4  2 videekCig 10
                 i+e+ C g
  AJA92919.1  2 PINEDFCHG 10
                69*****98 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 7.4e-08
                ETTTSSS-THHHHHSTTTE CS
        Fer4  4 deekCigCGaCvevCPvgA 22
                d++ C++ GaC+e+CPv +
  AJA92919.1 73 DWDVCVADGACIEACPVQV 91
                89**************986 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 5.8e-08
                 ETTTSSS-THHHHHSTTTE CS
        Fer4   4 deekCigCGaCvevCPvgA 22 
                  e +Ci+C+aCv+vCP  A
  AJA92919.1 135 REHDCIYCMACVSVCPPQA 153
                 5678************877 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.6   0.00015      0.15      31      52 .]      70      91 ..      31      91 .. 0.68
   2 !   27.3   8.8   3.9e-09   4.1e-06       2      52 .]      77     153 ..      76     153 .. 0.67
   3 !   18.2   2.5   2.6e-06    0.0028       2      25 ..     139     162 ..     138     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
      Fer4_7 31 veidpekClgCgaCvavCPtga 52
                v+ d + C+  gaC+++CP+++
  AJA92919.1 70 VANDWDVCVADGACIEACPVQV 91
                2446678************985 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.9e-09
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..............gtekv................eidpekClgCgaCvavCPtga 52 
                 C+  gaC +aCpv+++++   + ++              g   v                +i++ +C++C aCv+vCP +a
  AJA92919.1  77 CVADGACIEACPVQVFQWYRTD-KDvsgidavkdttewkG---VgetekeerrdftdkadAIREHDCIYCMACVSVCPPQA 153
                 77779************97542.22344444444444441...03334445556666667789999************765 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2.6e-06
      Fer4_7   2 CigCgaCvaaCpvkaieldeeene 25 
                 Ci C aCv++Cp +a+ +d+++ e
  AJA92919.1 139 CIYCMACVSVCPPQAVLVDQSNLE 162
                 9***********999999876544 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.4   5.7e+03      20      33 ..      38      49 ..      31      68 .. 0.54
   2 !   27.0   6.1   6.1e-09   6.4e-06       2      65 ..      77     150 ..      76     152 .. 0.73
   3 !   18.8   1.3   2.2e-06    0.0023       2      30 ..     139     166 ..     138     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
     Fer4_16 20 kkekeiearecisy 33
                +  +e++a ++++ 
  AJA92919.1 38 Q--NEWDASKNEQV 49
                4..56666665544 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 6.1e-09
     Fer4_16   2 CgtCgkCaevCPtnaikek.keke...iearecisy.......ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                 C+  g+C+e+CP+++++   ++k    i+a +++ +       +++e++d+++++ +   + ++++C +C+ vCP
  AJA92919.1  77 CVADGACIEACPVQVFQWYrTDKDvsgIDAVKDTTEwkgvgetEKEERRDFTDKADAIR-EHDCIYCMACVSVCP 150
                 88889***********9552223311234444333378899867777788888888887.889***********9 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.2e-06
     Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearec 30 
                 C+ C +C++vCP +a+  + + ++ea+e+
  AJA92919.1 139 CIYCMACVSVCPPQAVLVD-QSNLEAHEK 166
                 ***************9988.567777665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   4.7   5.2e-10   5.5e-07       3      56 .]      71     150 ..      69     150 .. 0.91
   2 !   15.6   2.1   1.2e-05     0.013       4      25 ..     134     155 ..     131     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.2e-10
     Fer4_10   3 vidddtCirCgkCvkaCPadl..........................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                   d d C+  g+C +aCP+++                          ++ + +  +  ++a+ +   +C+ c aCv++CP
  AJA92919.1  71 ANDWDVCVADGACIEACPVQVfqwyrtdkdvsgidavkdttewkgvgETEKEERRDFTDKADAIREHDCIYCMACVSVCP 150
                 567899*************99************************997777788888888888888*************9 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.2e-05
     Fer4_10   4 idddtCirCgkCvkaCPadlts 25 
                 i +  Ci C +Cv++CP ++  
  AJA92919.1 134 IREHDCIYCMACVSVCPPQAVL 155
                 56778***********995522 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   8.3e-05     0.087      27      65 .]      54      91 ..      30      91 .. 0.70
   2 !   16.3   0.1   9.8e-06      0.01       4      16 ..     138     150 ..     103     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-05
      Fer4_8 27 dargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65
                ++rge++e +    +++ ++ ++ C++ gaC e+Cpv++
  AJA92919.1 54 EKRGEKME-KLGITGTMVANDWDVCVADGACIEACPVQV 91
                34444444.4444444449999**************975 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.8e-06
      Fer4_8   4 kCieCgaCqsaCp 16 
                 +Ci C+aC s Cp
  AJA92919.1 138 DCIYCMACVSVCP 150
                 4666666666665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.4   0.00092      0.97      25      49 ..      68      90 ..      45      92 .. 0.72
   2 !   24.8   8.1   1.7e-08   1.8e-05       2      50 ..      77     153 ..      76     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00092
      Fer4_9 25 karlraaseeaCigCgaCveaCpkg 49
                ++  + +  + C+  gaC+eaCp +
  AJA92919.1 68 TMVANDW--DVCVADGACIEACPVQ 90
                3333333..4599999999999987 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.7e-08
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase............................eaCigCgaCveaCpkga 50 
                 C+  gaC+eaCp +v++  +  + ++   a +                             +Ci C+aCv +Cp +a
  AJA92919.1  77 CVADGACIEACPVQVFQWYRTDKDVSGIDAVKdttewkgvgetekeerrdftdkadaireHDCIYCMACVSVCPPQA 153
                 666689**********99888887776444446788************************99************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0013       1.4      34      54 ..      70      90 ..      59      94 .. 0.79
   2 !   17.5   0.5   3.1e-06    0.0033      35      55 ..     133     152 ..     119     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
     Fer4_21 34 lkvvedeCvGCnlCssvCPve 54
                ++   d Cv+   C++ CPv+
  AJA92919.1 70 VANDWDVCVADGACIEACPVQ 90
                445568899999999999994 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.1e-06
     Fer4_21  35 kvvedeCvGCnlCssvCPved 55 
                 +++e++C+ C  C+svCP  +
  AJA92919.1 133 AIREHDCIYCMACVSVCPP-Q 152
                 4567778888888888873.3 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00061      0.65      40      59 ..      64      90 ..      35      92 .. 0.67
   2 !   13.0   0.1   0.00011      0.11      43      57 ..     136     150 ..      93     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
     Fer4_17 40 e.......ekaslCieCgeCerkCPqg 59
                        + ++ C+  g C ++CP +
  AJA92919.1 64 GitgtmvaNDWDVCVADGACIEACPVQ 90
                03334444899**************76 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00011
     Fer4_17  43 aslCieCgeCerkCP 57 
                  ++Ci C  C+++CP
  AJA92919.1 136 EHDCIYCMACVSVCP 150
                 478888888888888 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.022        23      54      75 ..      70      91 ..      35      93 .. 0.68
   2 !   21.8   4.3   1.5e-07   0.00016       4      74 ..      81     152 ..      78     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
     Fer4_18 54 kekgagdcidcescvkvcPtgi 75
                 +++   c++ ++c++ cP+++
  AJA92919.1 70 VANDWDVCVADGACIEACPVQV 91
                4455566999999999999876 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
     Fer4_18   4 dvcvyvcPyarvqsvlydeet..llvvydakrGekiagrkkekkalkekeerkekgagdcidcescvkvcPtg 74 
                   c+ +cP   +q    d++   + +v d++  +++ g++++++    +++  +  + dci c +cv+vcP +
  AJA92919.1  81 GACIEACPVQVFQWYRTDKDVsgIDAVKDTTEWKGV-GETEKEERRDFTDKADAIREHDCIYCMACVSVCPPQ 152
                 57***********99999886114455555443333.333333444445555667889************965 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.1   0.00022      0.23       8      23 ..      76      91 ..      70      92 .. 0.88
   2 !   14.0   4.6   3.9e-05     0.041       9      23 ..     139     153 ..     133     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
      Fer4_6  8 kCigCgdCvrvCPega 23
                 C+  g+C+ +CP ++
  AJA92919.1 76 VCVADGACIEACPVQV 91
                59999********998 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.9e-05
      Fer4_6   9 CigCgdCvrvCPega 23 
                 Ci C++Cv+vCP +a
  AJA92919.1 139 CIYCMACVSVCPPQA 153
                 999*********987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   0.00031      0.32       4      21 ..      75      93 ..      73     133 .. 0.72
   2 !   10.3   3.1   0.00077      0.81       4      17 ..     137     150 ..     134     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
     Fer4_13  4 dtCiacgaCvelaP.dvFe 21
                d C+a+gaC e++P +vF+
  AJA92919.1 75 DVCVADGACIEACPvQVFQ 93
                78************55665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00077
     Fer4_13   4 dtCiacgaCvelaP 17 
                 + Ci c+aCv+++P
  AJA92919.1 137 HDCIYCMACVSVCP 150
                 67***********9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0076         8      73      95 ..      68      90 ..      30      91 .. 0.72
   2 !    8.7   0.1    0.0029         3       2      14 ..     139     151 ..     115     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0076
     Fer4_22 73 fkekfgesgCvGCgRCieacpvk 95
                ++   +  +Cv  g Cieacpv+
  AJA92919.1 68 TMVANDWDVCVADGACIEACPVQ 90
                344457889************97 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
     Fer4_22   2 ClsCgaCtlvCpt 14 
                 C+ C aC  vCp 
  AJA92919.1 139 CIYCMACVSVCPP 151
                 7777777777774 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.2     0.017        18       2      17 .]      75      90 ..      72      96 .. 0.86
   2 ?   15.4   1.0   1.8e-05     0.019       4      15 ..     139     150 ..     129     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
      Fer4_4  2 erCigCgsCvaaCPqg 17
                + C+  g+C+ aCP++
  AJA92919.1 75 DVCVADGACIEACPVQ 90
                5688889*******75 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.8e-05
      Fer4_4   4 CigCgsCvaaCP 15 
                 Ci C++Cv++CP
  AJA92919.1 139 CIYCMACVSVCP 150
                 999********* PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.3    0.0066       6.9       5      13 ..      81      89 ..      77      91 .. 0.77
   2 ?   13.0   6.7   0.00015      0.15       1      15 []     139     153 ..     139     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0066
      Fer4_3  5 gaCvevCPv 13
                gaC e+CPv
  AJA92919.1 81 GACIEACPV 89
                79******7 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ C+aCv vCP+ A
  AJA92919.1 139 CIYCMACVSVCPPQA 153
                 9***********866 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.9     0.003       3.2       6      21 ..      73      88 ..      69      89 .. 0.79
   2 ?   13.1   3.0   7.5e-05     0.079      10      21 ..     139     150 ..     132     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
      Fer4_2  6 dtdrCigCgaCvsaCP 21
                d d C++ gaC+ aCP
  AJA92919.1 73 DWDVCVADGACIEACP 88
                567888669******* PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.5e-05
      Fer4_2  10 CigCgaCvsaCP 21 
                 Ci C aCvs+CP
  AJA92919.1 139 CIYCMACVSVCP 150
                 ***********9 PP

>> Adhesin_P1_N  Adhesin P1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.014        15      37      56 ..      43      62 ..      36      70 .. 0.84
   2 ?    5.2   0.7      0.02        21      15      35 ..     102     122 ..      98     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.014
  Adhesin_P1_N 37 daKkaeIkaDYnkQakeika 56
                  ++K + + aDY+k  +++++
    AJA92919.1 43 ASKNEQVLADYEKRGEKMEK 62
                  689999*******9998876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
  Adhesin_P1_N  15 aGveVekdatvDkGtaktaee 35 
                   +G++ +kd+t  kG+ +t++e
    AJA92919.1 102 SGIDAVKDTTEWKGVGETEKE 122
                   79***************9987 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.6    0.0026       2.8       3      46 ..      72     118 ..      70     136 .. 0.56
   2 ?    4.9   2.5     0.043        45       6      19 ..     137     150 ..     133     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
     Fer4_15   3 vDrdaCigcglCvaeap.evfeldedglasvl...........lddgeiaegevpd 46 
                  D+d C  +g+C++++p +vf+    ++++             +         v++
  AJA92919.1  72 NDWDVCVADGACIEACPvQVFQWYRTDKDVSGidavkdttewkG---------VGE 118
                 59**************6356665555555433222223222221.........322 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.043
     Fer4_15   6 daCigcglCvaeap 19 
                   Ci c +Cv ++p
  AJA92919.1 137 HDCIYCMACVSVCP 150
                 57***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1383.77
//
Query:       AJA92920.1  [L=310]
Description: 4-phosphoerythronate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-61  206.1   0.0    3.9e-61  205.5   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    7.2e-31  106.6   0.1    8.2e-31  106.4   0.1    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
      0.003   17.7   0.7      0.019   15.1   0.0    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.034   13.9   0.0    1.5  1  LXG            LXG domain of WXG superfamily


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5   0.0   8.7e-65   3.9e-61       1     178 []     109     284 ..     109     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 8.7e-65
                   HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE CS
  2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivsl 97 
                   l+l+l+l+r++++ad+evr+g+w  +k+l+g+el+gk +Gi+GlG+IG+++ ++++a++m++i+yd+ + +ee  +e+g+ +++l +lla+sD+vsl
    AJA92920.1 109 LGLMLSLAREIPRADREVRNGNW-IKKELMGTELRGKYLGIVGLGNIGKRLGRLARALNMNIIGYDVVPIDEEFSSEVGLMKADLGTLLASSDYVSL 204
                   589********************.999*******************************************99988999999**************** PP

                   -S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSSGTCHHHHHSTTEEE-SS-T CS
  2-Hacid_dh_C  98 hlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeeplpedspllelpnviltPHia 178
                   h+pl ++t+hlinae+++ mk+++ +iNt+RGg++deeaL+e Lk+gk++gaalDvfe ep++++ +l++lpn+i tPH++
    AJA92920.1 205 HVPLLDSTKHLINAEKMSTMKNTSRIINTSRGGVIDEEALYEFLKDGKLGGAALDVFEVEPATSN-KLASLPNFISTPHMG 284
                   ***************************************************************66.*************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.4   0.1   1.8e-34   8.2e-31       1     126 [.       7     308 ..       7     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 1.8e-34
                 EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvA 99 
                 vli++++++   e+l+++g++++++ e++ +++lek+++++++ivrs+tk+t++++e+++k+++iar+gvG Dn+D  +ake++i V n+ +   ++vA
  AJA92920.1   7 VLICDQVNPVLNEILEKNGLQITYEPEITPDQILEKIENFEVIIVRSRTKITKDMIEKANKCQIIARVGVGLDNIDQTTAKEKNIRVINAVEGAMNAVA 105
                 799**************999******************************************************************************* PP

                 HHH................................................................................................ CS
                 xxx................................................................................................ RF
  2-Hacid_dh 100 Elt................................................................................................ 102
                 El+                                                                                                
  AJA92920.1 106 ELVlglmlslareipradrevrngnwikkelmgtelrgkylgivglgnigkrlgrlaralnmniigydvvpideefssevglmkadlgtllassdyvsl 204
                 *************************************************************************************************** PP

                 ................................................................................T-BHHHHHHHHHHHHHHHH CS
                 ................................................................................xxxxxxxxxxxxxxxxxxx RF
  2-Hacid_dh 103 ................................................................................aaTeeaqeniaeeaaenlv 121
                                                                                                 a T+eaq+ +a  +ae+++
  AJA92920.1 205 hvplldstkhlinaekmstmkntsriintsrggvideealyeflkdgklggaaldvfevepatsnklaslpnfistphmgAQTKEAQSLAANVIAEKII 303
                 *******************************************************************************999***************** PP

                 HHHTT CS
                 xxxxx RF
  2-Hacid_dh 122 aflkg 126
                 ++l+g
  AJA92920.1 304 QILRG 308
                 *9998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       0.1   4.6e+02      24      97 ..       6      91 ..       1     112 [. 0.65
   2 !   15.1   0.0   4.3e-06     0.019       2     105 ..     146     249 ..     145     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.1
                   EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHS.....HCCC--TT-EEEE-S---HHHH CS
  NAD_binding_2 24 kvavynrtkekveelvaeg.....akaaesieelvasl..dvvitmvkagkavdevieg.....llealkkgdilidgstsspedt 97
                   +v + +  +  ++e+++++      ++  ++ ++++++    vi++ + +k ++++ie+     +++++  g   id +t++ ++ 
     AJA92920.1  6 SVLICDQVNPVLNEILEKNglqitYEPEITPDQILEKIenFEVIIVRSRTKITKDMIEKankcqIIARVGVGLDNIDQTTAKEKNI 91
                   66677777777777777655555545555555666666632233344556777888888888888888888888888888776554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.3e-06
                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---HHH CS
  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealkkgdilidgstssped 96 
                    +g++GlG++G+ + +   + ++++++y++ +   ee+ +e   + +++  l+as d v + v+  + ++++i+   ++++k+ + +i++s   + d
     AJA92920.1 146 LGIVGLGNIGKRLGRLARALNMNIIGYDVVP-IDEEFSSEVGLMKADLGTLLASSDYVSLHVPLLDSTKHLINAeKMSTMKNTSRIINTSRGGVID 240
                    69**************************995.45677777777899999***********************998889999999999999888888 PP

                    HHHHHHHHH CS
  NAD_binding_2  97 trelakelk 105
                     + l++ lk
     AJA92920.1 241 EEALYEFLK 249
                    887777766 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.5e-06     0.034      55     106 ..     201     250 ..     198     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.5e-06
         LXG  55 yadlhlplltslqdlieqyeefLkkikealesvepssngfidedfLeqelen 106
                 y +lh+pll+s+++li+   e+ +++k+    +++s  g+ide++L + l++
  AJA92920.1 201 YVSLHVPLLDSTKHLINA--EKMSTMKNTSRIINTSRGGVIDEEALYEFLKD 250
                 5579*************9..99************************976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2334.09
//
Query:       AJA92921.1  [L=435]
Description: putative UDP-glucose 6-dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-48  163.1   1.2      6e-48  162.9   0.1    1.7  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    2.2e-35  120.7   1.8    4.8e-35  119.7   0.1    2.2  2  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    3.1e-26   91.8   0.7    1.9e-25   89.3   0.5    2.3  3  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    7.5e-07   29.6   1.9     0.0038   17.8   0.1    4.0  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    3.9e-06   27.1   0.1    0.00022   21.4   0.0    2.6  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00072   19.5   0.1     0.0045   16.9   0.0    2.4  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.003   17.8   0.0       0.01   16.1   0.0    2.0  1  TrkA_N          TrkA-N domain
     0.0038   16.6   1.9       0.87    8.9   0.1    3.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.024   13.8   0.0    1.4  1  Sugar-bind      Putative sugar-binding domain
      0.013   15.7   6.0       0.17   12.1   0.2    2.8  3  CRAL_TRIO_2     Divergent CRAL/TRIO domain
      0.016   14.4   0.1       0.18   11.0   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.036   14.0   0.6       0.47   10.4   0.1    3.0  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.1     4e-51     6e-48       1     181 [.       1     182 [.       1     188 [. 0.95
   2 ?   -2.4   0.1       2.1   3.1e+03      44     118 ..     304     321 ..     290     368 .. 0.54

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 4e-51
                     SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB CS
  UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaa 95 
                     mki++iGlG+vGl    vla++g e ig+Did +k +++ +g+ p++ep+Le+ +++ + +++l+ ++d++  v+++d if+aVgTP+k+ + a+
      AJA92921.1   1 MKIAIIGLGFVGLSLTSVLAAKGYETIGIDIDIKKCKEISAGNPPFFEPKLEKTLREGL-KKKLTISNDFSL-VRNCDFIFVAVGTPQKS-NGAI 92 
                     8**********************************************************.7*********99.*****************.8888 PP

                     -THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE------TTSHHHHHHS-S-EEEEESSCHHH CS
  UDPG_MGDP_dh_N  96 Dlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnPEflregsavkdllnpdrvviGveekkae 181
                     Dl+++ + + +i++ + k   ++++ +kSTv +gt+++++ +ile++skkk g++f+++snPEfl+e sa+kd+  p  vv+G+ ++k  
      AJA92921.1  93 DLSMIRKSITKISKSMYKnkkDQIIFIKSTVTPGTMKNVILPILEKNSKKKaGKEFGLISNPEFLQETSAIKDTKFPHAVVLGGYNTKYM 182
                     *************9886656699*************************9999*******************************9998765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                     -SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEE CS
  UDPG_MGDP_dh_N  44 ipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvv 118
                     i+++e++L+ +  k+                                                         + +
      AJA92921.1 304 IKLVEKKLKGISSKR---------------------------------------------------------ITI 321
                     233333333333333.........................................................323 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.1   3.2e-38   4.8e-35       1      93 [.     204     297 ..     204     298 .. 0.98
   2 ?   -0.5   0.1      0.94   1.4e+03       5      29 ..     377     401 ..     375     432 .. 0.87

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 3.2e-38
  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlceal.gidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgleaelleavrevNe 93 
                   +tAE++K+a+N+flatkIsfiN+l+n+c+++ +++++++ +++gld+rig+ fl++g+G+GGsclpkD+kaL++ a++ g++++ll+av+e+N+
    AJA92921.1 204 QTAEMVKYANNSFLATKISFINQLSNICQNIpEANIDDISKTIGLDQRIGKLFLNAGPGYGGSCLPKDMKALINFANDIGVKPSLLNAVEEINT 297
                   59*****************************99************************************************************6 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.94
  UDPG_MGDP_dh   5 liKlaaNaflatkIsfiNelanlce 29 
                   +i+ ++N++ a+ ++++ e++++ +
    AJA92921.1 377 MIRALENSQCAIFMTYWKEFEKINN 401
                   7888999999999999999888765 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   2.1e+03      36      78 ..      47      86 ..      16     105 .. 0.66
   2 ?   -2.8   0.0       5.6   8.3e+03      56      80 ..     181     207 ..     157     230 .. 0.61
   3 !   89.3   0.5   1.3e-28   1.9e-25       1     104 [.     320     420 ..     320     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                    E-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GG CS
  UDPG_MGDP_dh_C 36 yDPkvkeeaveaeleekgvevvdsleealkgadaiviltehde 78
                    ++Pk ++  +e    +k++++ +++ + ++++d i +++  ++
      AJA92921.1 47 FEPKLEKTLREGL--KKKLTISNDF-SLVRNCDFIFVAVGTPQ 86
                    4444444444432..5688888776.78899999988876554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                     EES-CHHHHTT-S..EEEE-S--GGGG CS
  UDPG_MGDP_dh_C  56 vvdsleealkgad..aiviltehdefk 80 
                     +++++++ +++ +   ++i+t+h+  +
      AJA92921.1 181 YMKKAKHFFSKLHpnTAIIITNHQTAE 207
                     444444444444322456666665544 PP

  == domain 3  score: 89.3 bits;  conditional E-value: 1.3e-28
                     EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-E CS
  UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpav 95 
                     +i+G afK++tdD+R+S ++++i++Ll+++a+++iyDPk+ ++ ++     k++++ ds+ +al+++++++ +t ++ef++++ +++ +lmk+++
      AJA92921.1 320 TIMGTAFKPNTDDVRDSISIELIKKLLKMKANITIYDPKAIDNTKKIFD--KKITYEDSMIRALENSQCAIFMTYWKEFEKINNKSI-RLMKRKL 411
                     59***************************************99998854..79*****************************99888.68***** PP

                     EEESSS-CC CS
  UDPG_MGDP_dh_C  96 vfDgrnvld 104
                     ++D+r+++ 
      AJA92921.1 412 IIDCRRIFS 420
                     *****9985 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.6e-06    0.0038       1      71 [.       2      84 ..       2     104 .. 0.85
   2 ?    2.9   0.0      0.11   1.7e+02      37      77 ..     183     227 ..     160     239 .. 0.74
   3 ?    5.5   0.0     0.017        26      14      94 ..     341     415 ..     336     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC................-EEECECHHHHHHH-SEEEE-S-H CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg................vkvtavdneeaaeeadvvvlavkp 71
                   ki+iiG G +g +l+s l+a+g   +e + + + + +k +e+ +                    k+t ++   +++++d++++av +
     AJA92921.1  2 KIAIIGLGFVGLSLTSVLAAKG---YETI-GIDIDIKKCKEISAGNPpffepklektlreglkKKLTISNDFSLVRNCDFIFVAVGT 84
                   7*********************...7777.66888888888876655788888888888999999999999*************965 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                    CCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
  F420_oxidored  37 ekaeelaeelg....vkvtavdneeaaeeadvvvlavkpedveev 77 
                    +ka+++ ++l     + +t  +++e+++ a+  +la k + + ++
     AJA92921.1 183 KKAKHFFSKLHpntaIIITNHQTAEMVKYANNSFLATKISFINQL 227
                    555555555555555888999999************999887765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                    HHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEE CS
  F420_oxidored  14 lasgllaagaqpheivvansrnpekaeelaeelgvkvtav.dneeaaeeadvvvlavkpedveevlselakdalkgklvisv 94 
                    l+++ll+      +i++    +p+ ++ +++ +  k+t   +   a+e++   ++   ++ +e++ ++   ++ k+kl+i++
     AJA92921.1 341 LIKKLLKMK---ANITIY---DPKAIDNTKKIFDKKITYEdSMIRALENSQCAIFMTYWKEFEKINNKS-IRLMKRKLIIDC 415
                    677777777...888866...888888888888877765305678999******************999.9*********97 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.5e-07   0.00022       1      96 [.       2     127 ..       2     140 .. 0.78
   2 ?    3.0   0.1      0.07   1.1e+02      14      63 ..     341     391 ..     339     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..................EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS... CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..................akaaesieelvasldvvitmvkagkavdevieg... 75 
                    ki++iGlG  G ++ + l+++gy++++++ + +k++e+ a +                    ++++  +lv+++d++++ v   ++ +  i+    
     AJA92921.1   2 KIAIIGLGFVGLSLTSVLAAKGYETIGIDIDIKKCKEISAGNppffepklektlreglkkKLTISNDFSLVRNCDFIFVAVGTPQKSNGAIDLsmi 97 
                    79*************************************99999***999999999986522333334689999********99999988877654 PP

                    ......HCCC-......-TT-EEEE-S---HHH CS
  NAD_binding_2  76 ......lleal......kkgdilidgstssped 96 
                          +          kk++i+   st+ p +
     AJA92921.1  98 rksitkI---SksmyknKKDQIIFIKSTVTPGT 127
                    4443333...04446666777777777776665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.07
                    HHHHHHHTT-EEEEE-.SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-S CS
  NAD_binding_2  14 malnllkagykvavyn.rtkekveelvaegakaaesieelvasldvvitmv 63 
                    ++++llk + ++++y+    ++++++ +++++  +s+  ++++ ++ i+m 
     AJA92921.1 341 LIKKLLKMKANITIYDpKAIDNTKKIFDKKITYEDSMIRALENSQCAIFMT 391
                    7889999*********55569***************999999998777763 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     3e-06    0.0045       1      83 [.       2      79 ..       2      84 .. 0.74
   2 ?   -2.2   0.0       2.1   3.2e+03      33      73 ..     187     227 ..     170     243 .. 0.52
   3 ?   -1.9   0.0       1.7   2.6e+03      29      53 ..     294     318 ..     283     352 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEE CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlvi 83
                k+a+iG G +G ++++v+a++g+e+  +di+ ++ ++  +     +e      kl++  +e + +++++++d++ ++++d+++
  AJA92921.1  2 KIAIIGLGFVGLSLTSVLAAKGYETIGIDIDIKKCKEISAGNPPFFEP-----KLEKTLREGLKKKLTISNDFSLVRNCDFIF 79
                69****************************999988877665553333.....333344556666677777777776777766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                 HHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-H CS
     3HCDH_N  33 ealekalekieksleklvekgklkeeeveaalarisfttdl 73 
                 ++  k + + +  + + + ++ +k ++ + ++++isf ++l
  AJA92921.1 187 HFFSKLHPNTAIIITNHQTAEMVKYANNSFLATKISFINQL 227
                 44444444444444444444444444444445555555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.7
                 -S-HHHHHHHHHHHHHHHHCCTTTT CS
     3HCDH_N  29 diseealekalekieksleklvekg 53 
                 +i++++le+  + +ek+l+   +k+
  AJA92921.1 294 EINTKQLEQIIKLVEKKLKGISSKR 318
                 5667777777777777776654433 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.9e-06      0.01       1      42 [.       3      44 ..       3      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.9e-06
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTS CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegl 42
                i+iiGlG vG sl+  L + g+ + ++id d ++++e+++ + 
  AJA92921.1  3 IAIIGLGFVGLSLTSVLAAkGY-ETIGIDIDIKKCKEISAGNP 44
                79*****************777.5*************987665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00058      0.87      38      73 ..       2      37 ..       1     101 [. 0.91
   2 !    5.8   0.2    0.0053       7.9      47     122 ..     337     412 ..     287     415 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00058
                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                  +++iiGlG +G ++  +l+a g + i++d   kk +
    AJA92921.1  2 KIAIIGLGFVGLSLTSVLAAKGYETIGIDIDIKKCK 37
                  799**************************9988655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0053
                   HHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEE CS
  2-Hacid_dh_C  47 IGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDivslhlpltpetrhlinaeelakmkkgai 122
                   I  +++k+l ++++++++yd++  +++ +  +++++++ s+  +l++s++ + ++  ++   + in++++++mk++ i
    AJA92921.1 337 ISIELIKKLLKMKANITIYDPKAIDNTkKIFDKKITYEdSMIRALENSQCAIFMTYWKE--FEKINNKSIRLMKRKLI 412
                   6668899999************98777655555665554999******99887776544..45589999999998766 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.6e-05     0.024     122     170 ..      52     100 ..      39     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                 SHHHHHHHHTSHHHHHHHHHHHT-SEEEEE-EEHCCCCHHHCCTTS-HH CS
  Sugar-bind 122 saelreallaersikevlelakkadvalvGiGsaseeaklvkrgfltee 170
                 +++lre+l+++ +i++ ++l++++d ++v +G++++++ +++  +++++
  AJA92921.1  52 EKTLREGLKKKLTISNDFSLVRNCDFIFVAVGTPQKSNGAIDLSMIRKS 100
                 57899*********************************99999999876 PP

>> CRAL_TRIO_2  Divergent CRAL/TRIO domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00011      0.17      39     133 ..      77     173 ..      49     178 .. 0.82
   2 ?    5.7   0.6     0.011        16      68     124 ..     179     239 ..     176     247 .. 0.81
   3 ?   -3.1   0.0       5.3   7.9e+03      17      41 ..     298     321 ..     291     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
  CRAL_TRIO_2  39 yvlVyfhtglssenkpslswlkkvystlprrykknlkklyi.vhps....tfvktllktvlsafvsskfrkkveyvsrleeLarkidrtqllkslPeg 131
                  ++ V   t  +s+  ++ls ++k + ++++++ kn k  +i + ++    t+  ++l  +l  ++++k +k++  +s+ e L+++  ++    ++P +
   AJA92921.1  77 FIFVAVGTPQKSNGAIDLSMIRKSITKISKSMYKNKKDQIIfIKSTvtpgTMKNVIL-PILEKNSKKKAGKEFGLISNPEFLQETSAIKDT--KFPHA 171
                  55555555555577899******************9988885666688888899999.89999999999***************9999999..99977 PP

  CRAL_TRIO_2 132 vv 133
                  vv
   AJA92921.1 172 VV 173
                  76 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
  CRAL_TRIO_2  68 rrykknlkklyi.vhps...tfvktllktvlsafvsskfrkkveyvsrleeLarkidrtql 124
                   +y k+ k+++  +hp+   + +   +++++++ + s++  k+ ++++l+ + + i  +++
   AJA92921.1 179 TKYMKKAKHFFSkLHPNtaiIITNHQTAEMVKYANNSFLATKISFINQLSNICQNIPEANI 239
                  578899999999999995554444444599999999999**************99998887 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.3
  CRAL_TRIO_2  17 adldkllryvlhtladkivgkeyvl 41 
                  ++l+++++ v ++l + i++k +++
   AJA92921.1 298 KQLEQIIKLVEKKL-KGISSKRITI 321
                  56677777777777.6666666555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.18       2      58 ..       2      99 ..       1     179 [. 0.74
   2 ?    0.8   0.0      0.16   2.3e+02      14      78 ..     340     413 ..     338     430 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                 SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHHHHHHHHHHHHH................................H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxx................................x RF
  Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskallgvaedaeias................................e 58
                 ++++iG G+ Gl++   la++g++++ ++         + g+ +++ + l k+l++  +++ ++s                                +
   AJA92921.1  2 KIAIIGLGFVGLSLTSVLAAKGYETIGIDidikkckeiSAGNPPFFEPKLEKTLREGLKKKLTISndfslvrncdfifvavgtpqksngaidlsmirK 99
                 899*************************8888888889999999999999999999999988888888888888888888776555555544433332 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                  HHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...........HHHHCHHHH.CCCCHCCTCEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx.xxxxxxxxxxxx RF
  Pyr_redox_2  14 aaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...........evvkklnqg.ielllgeevvki 78 
                  ++ ++l + +a++t++ + +++ n + +  k+++   +  + ++           ++++k+n++ i+l+++  ++ i
   AJA92921.1 340 ELIKKLLKMKANITIY-DPKAIDNTKKIFDKKITYEDSMIRALEnsqcaifmtywKEFEKINNKsIRLMKR--KLII 413
                  5677888889999999.999999999999999999999998888999999999999999999995555555..4444 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00032      0.47       1      79 [.       2      84 ..       2     173 .. 0.62
   2 ?   -1.1   0.0       1.1   1.6e+03      59     106 ..     201     248 ..     177     258 .. 0.61
   3 ?   -1.4   0.0       1.4     2e+03      52      95 ..     366     409 ..     356     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                    -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS......SBTTTBTT----TTEEEES-HHHHHTT--EEEE---H CS
  NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineeh......envkyLpgiklpenlvattdlaealkgadiivlvvPs 79
                    kia++G G  G +l  vla +g e+  +  + + ++ei++ +      + +k L++  l ++l++++d+   ++++d+i+++v +
      AJA92921.1  2 KIAIIGLGFVGLSLTSVLAAKGYETIGIDIDIKKCKEISAGNppffepKLEKTLRE-GLKKKLTISNDFSL-VRNCDFIFVAVGT 84
                    79***********************************9986522211123334443.57777777777654.5567777777754 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                     EES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE CS
  NAD_Gly3P_dh_N  59 attdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi 106
                      + + ae +k a+  +l+   +++++  + ++++ +++   +s + G+
      AJA92921.1 201 TNHQTAEMVKYANNSFLATKISFINQLSNICQNIPEANIDDISKTIGL 248
                     344455666666666666666666666666666666666556555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.4
                     ---TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--T CS
  NAD_Gly3P_dh_N  52 klpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkk 95 
                      ++++++ ++ + +al+++++ ++    + ++++ +k   l+k+
      AJA92921.1 366 IFDKKITYEDSMIRALENSQCAIFMTYWKEFEKINNKSIRLMKR 409
                     56788899999999999999999988888888877776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       906  (0.0505327); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3028.51
//
Query:       AJA92922.1  [L=125]
Description: hypothetical protein T478_0667 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 936.17
//
Query:       AJA92923.1  [L=182]
Description: AAA domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-14   53.9   0.5    4.2e-14   53.1   0.2    1.5  1  AAA_17           AAA domain
    3.8e-10   40.4   0.1    6.3e-10   39.7   0.1    1.4  1  AAA_18           AAA domain
      8e-05   22.6   0.7     0.0012   18.7   0.1    2.5  3  NTPase_1         NTPase
    0.00026   21.3   0.1    0.00071   19.9   0.1    1.9  1  AAA_28           AAA domain
    0.00037   20.6   0.4     0.0006   19.9   0.2    1.5  1  ADK              Adenylate kinase
    0.00041   20.8   0.3      0.001   19.5   0.3    1.7  1  AAA              ATPase family associated with various cellul
    0.00041   19.4   0.1    0.00089   18.3   0.1    1.5  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00043   20.0   0.0    0.00066   19.4   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
    0.00066   19.6   0.0     0.0079   16.1   0.0    2.2  2  APS_kinase       Adenylylsulphate kinase
    0.00098   19.3   0.2     0.0029   17.8   0.2    1.8  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.3      0.025   15.0   0.2    1.7  1  AAA_16           AAA ATPase domain
      0.014   14.6   0.1      0.026   13.7   0.1    1.4  1  NB-ARC           NB-ARC domain
      0.014   15.1   0.1      0.021   14.5   0.1    1.4  1  AAA_30           AAA domain
      0.018   15.3   0.7      0.078   13.2   0.7    2.0  1  AAA_22           AAA domain
      0.018   14.3   0.3      0.048   12.9   0.0    1.8  3  Zeta_toxin       Zeta toxin
      0.026   14.6   0.0      0.084   12.9   0.0    1.8  1  AAA_14           AAA domain
      0.033   13.6   0.8      0.081   12.4   0.1    2.0  2  KTI12            Chromatin associated protein KTI12
      0.037   14.1   0.4      0.066   13.3   0.4    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
      0.041   13.6   0.1      0.059   13.1   0.1    1.5  1  AAA_24           AAA domain
      0.053   13.5   0.7       0.26   11.3   0.6    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
      0.072   13.0   0.0       0.09   12.7   0.0    1.3  1  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.078   12.6   0.3        1.1    8.9   0.0    2.1  2  CoaE             Dephospho-CoA kinase
      0.095   12.3   0.6        5.4    6.5   0.3    2.4  2  AAA_25           AAA domain
      0.096   12.4   0.2       0.18   11.6   0.2    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.096   12.4   0.1       0.16   11.7   0.1    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.17   11.8   0.1       0.93    9.4   0.0    2.1  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.2   6.1e-17   4.2e-14       1     129 [.       9     130 ..       9     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 6.1e-17
                 EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHH.....HHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekk.....elqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                 +G+PG+GK+t+++kl+e+ g++ +s Gd +r+eakr++l+++  ++ kl le ++     ++ ++++e+i+e + ++ +++dg  +i e          
  AJA92923.1   9 TGMPGAGKSTIVSKLKED-GYETFSLGDGVRAEAKRQNLEPTGANLGKLMLELREkngpgAIAELLKESIKE-STHQIIIIDGVRSIHE---------I 96 
                 7**************776.***********************999999866666612332445555555554.477889*****99843.........3 PP

                 HHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS CS
      AAA_17  95 evleelkpdaiilleadpeeilerrlkdrtrgrdd 129
                 +vl+e    +++ ++a p++ ++  l++r+r++d 
  AJA92923.1  97 NVLKETGNVKLLAVDAAPDTRFNF-LRERKRSDDP 130
                 4556666679999*****987765.5544444433 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.1   9.1e-13   6.3e-10       1     125 [.       6     137 ..       6     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.1e-13
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkl.dklldaleenssaleegknlvidghlaeleseaak 92 
                 ++ltG+pG+GK+t+   L++  g+     g+ +r  ak  +l+ +  +  +    ++l+e++   ++ ++l+e++ ++  ++ ++idg+++ +e   +k
  AJA92923.1   6 VCLTGMPGAGKSTIVSKLKED-GYetfslGDGVRAEAKRQNLEPTGANLgK--LMLELREKNGpGAIAELLKESI-KESTHQIIIIDGVRSIHEINVLK 100
                 89****************998.56668899999999999888888888853..3333333332045555555555.58999999************999 PP

      AAA_18  93 dikk...vvLtaspeelleRlekRgyeeakik.enee 125
                 + +      ++a p++++  l++R+++++  + e+ e
  AJA92923.1 101 ETGNvklLAVDAAPDTRFNFLRERKRSDDPLTrEKFE 137
                 988899*************999999776544444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.8e-06    0.0012       2      46 ..       6      50 ..       5      61 .. 0.80
   2 ?    4.1   0.0     0.056        39      46     103 ..      27      89 ..      24      96 .. 0.76
   3 ?   -1.9   0.0       3.8   2.6e+03       8      27 ..     144     163 ..     117     170 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.8e-06
                EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------E CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrig 46
                v++TG+pG GK+T+v+k+ e   +     +G+ +e  r++ + +g
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKEDGYETFSLGDGVRAEAKRQNLEPTG 50
                78***************9998876655667888888888776666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.056
                 EEEEEET.T--EEEEEETT.---SSEETTEEE-HHH..HHHHHHHHHHHHH..HHH-EEEE-- CS
    NTPase_1  46 gFkivdlasgeegiLarve.akreprvgkyvvdves..feelalealrkal..seadviviDE 103
                 g++  +l +g +++  r++ ++ ++++gk ++++ +      ++e l++++  s+ ++i+iD 
  AJA92923.1  27 GYETFSLGDGVRAEAKRQNlEPTGANLGKLMLELREknGPGAIAELLKESIkeSTHQIIIIDG 89 
                 788888889999999999888999999999999988542344556666666446778*****6 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.8
                 TTSSHHHHHHHHHHHH...G CS
    NTPase_1   8 pGvGKtTlvkkvlellkssg 27 
                  GvG   +++ + e +++++
  AJA92923.1 144 IGVGLKEIIELADESIENNN 163
                 34444444444444444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     1e-06   0.00071       2      27 ..       6      31 ..       5      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
      AAA_28  2 ivitGgestGKTtlleaLaargypvv 27
                +++tG +++GK+t++++L+++gy+++
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKEDGYETF 31
                89********************9976 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   8.7e-07    0.0006       1      94 [.       8     101 ..       8     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.7e-07
                 EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-..HHHHHHHHHH.HTTSS--HHHHHHHHHHHHHCHGTTTEEEEESB-SSHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgt..elGkeakevm.dkgelvpdevvvklvkeelekedkkkgfllDGfPRtveqaealee 94 
                 l G PgaGK t  +kl+++ g+   s Gd +Rae k++   ++G ++ ++m +  e      + +l+ke+++++ +++  ++DG  R++++ + l+e
  AJA92923.1   8 LTGMPGAGKSTIVSKLKED-GYETFSLGDGVRAEAKRQNlePTGANLGKLMlELREKNGPGAIAELLKESIKES-THQIIIIDGV-RSIHEINVLKE 101
                 679*************887.789999*******9987643378888866552556667778899*******987.8899999*96.77777777776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   1.5e-06     0.001       1      74 [.       6      97 ..       6     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.5e-06
                EEEESSTTSSHHHHHHHHHHH..............HTHEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGG CS
         AAA  1 vllyGppGtGKTllakavake..............lgvefleisgsellsk..................yvgesekkirelfkeakekakpsilfiDEida 69
                v+l+G pG GK+++++ + ++              +              k                    ++++  i+el+ke  +++++ i++iD + +
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKEDgyetfslgdgvraeA--------------KrqnleptganlgklmlelREKNGPGAIAELLKESIKESTHQIIIIDGVRS 92
                79******************9555554444433332..............22333333333333455557888999999999995444459********99 PP

                HHHHH CS
         AAA 70 laksr 74
                +++ +
  AJA92923.1 93 IHEIN 97
                99877 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.3e-06   0.00089      30      51 ..       4      25 ..       2      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                EEEEEEE-TTSSHHHHHHHHHH CS
        MeaB 30 qvvGltGvPGaGkstlvealgl 51
                 vv ltG+PGaGkst+v++l +
  AJA92923.1  4 LVVCLTGMPGAGKSTIVSKLKE 25
                5899***************975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.6e-07   0.00066       3      92 ..       5      90 ..       3     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.6e-07
                EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHH.HHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE- CS
       SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQ.LktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTa 92
                v+ l G+ GaGK t ++KL     ++g+++ +   D  Ra A  Q L+  + +lg  +++ +e++ p a+a+   e+ ke+ ++++++D  
  AJA92923.1  5 VVCLTGMPGAGKSTIVSKLK----EDGYET-FSLGDGVRAEAKRQnLEPTGANLGKLMLELREKNGPGAIAELLKESIKESTHQIIIIDGV 90
                8899**************85....666665.6789*******9888*********88999999999***********************64 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0079       3      46 ..       4      42 ..       2      49 .. 0.83
   2 ?    0.9   0.0      0.55   3.8e+02      14      40 ..      65      91 ..      58     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTT CS
  APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLn 46
                +vv ltG+ g+GKsti  +    L+e+g+++  L Gd vR + +
  AJA92923.1  4 LVVCLTGMPGAGKSTIVSK----LKEDGYETFSL-GDGVRAEAK 42
                6899***********9865....66889999887.999998765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.55
                SHHHHHHHHHHHHHHTT--EEEEEHHH CS
  APS_kinase 14 GKstianalekkLvekgisvylLdGdn 40
                G  +ia+ l+++++e+ ++++++dG  
  AJA92923.1 65 GPGAIAELLKESIKESTHQIIIIDGVR 91
                66799*******************954 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   4.2e-06    0.0029       1     134 [.       5     137 ..       5     144 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.2e-06
      AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdt......lrrrlfgtdqqsktdytrvl.drlyqilnelarkalsagrn.vildatnlsrrerarflkl 91 
                 +v l G+pG+GKst + +l k+ g+++ s  +       r++l++t+ +  +   +++ ++  + ++el+++  ++  + +i+  + +s +e     ++
  AJA92923.1   5 VVCLTGMPGAGKSTIVSKL-KEDGYETFSLGDgvraeaKRQNLEPTGANLGKLMLELReKNGPGAIAELLKESIKESTHqIIIIDGVRSIHEI----NV 98 
                 78999*************6.5888666554442222214445555555544444443314445566666666555544448888888888884....66 PP

      AAA_33  92 arrlgvpvrivvvetdeetlkeRlakRaangddrsevpeeald 134
                 +++ g +v++++v++ ++t    l++R+++ dd+  +++e ++
  AJA92923.1  99 LKETG-NVKLLAVDAAPDTRFNFLRERKRS-DDP--LTREKFE 137
                 67777.777888888888888878777774.555..6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   3.6e-05     0.025      26      46 ..       5      25 ..       2      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
      AAA_16 26 lvllsGesGvGKsslvrellr 46
                +v l+G++G GKs++v +l++
  AJA92923.1  5 VVCLTGMPGAGKSTIVSKLKE 25
                689**************9997 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.7e-05     0.026      20      43 ..       3      26 ..       1      32 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                SEEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC 20 slvvalvGmgGvGKttlakqilnk 43
                +lvv l Gm+G GK+t++++  ++
  AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLKED 26
                589***************998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.1e-05     0.021      18      40 ..       3      25 ..       1      91 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
      AAA_30 18 drvavltGpAGtGKttalkalre 40
                ++v++ltG +G+GK+t++++l+e
  AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLKE 25
                5799**************99865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   0.00011     0.078       5      29 ..       3      27 ..       1     130 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
      AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                + ++++tG +G+GK+t + +l+e  
  AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLKEDG 27
                67899****************9864 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     7e-05     0.048      16      39 ..       3      26 ..       1      32 [. 0.87
   2 ?   -2.8   0.0       4.6   3.2e+03      31      50 ..      68      88 ..      65     106 .. 0.63
   3 ?   -1.9   0.0       2.4   1.7e+03     153     153 ..     135     135 ..      87     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
  Zeta_toxin 16 PklillgGqpGAGKselaellkde 39
                + ++ l G pGAGKs++ ++lk++
  AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLKED 26
                56899***************9986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.6
  Zeta_toxin 31 elaellkdele.rqgnvvrld 50
                ++aellk++++ ++ +++ +d
  AJA92923.1 68 AIAELLKESIKeSTHQIIIID 88
                566666666654444444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.4
  Zeta_toxin 153 l 153
                 +
  AJA92923.1 135 K 135
                 1 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.084       3      79 ..       4      96 ..       2     106 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
      AAA_14  3 kilvitGaRrvGKTtllkqlikell...........vkkesilyinldderd..............kkladpe...kllelileklkeekktylflDEiqe 75
                 ++++tG+  +GK+t++ +l ++ +                      +++++              +   +++    + el++e++ke+ ++++++D +  
  AJA92923.1  4 LVVCLTGMPGAGKSTIVSKLKEDGYetfslgdgvraE---------AKRQNLeptganlgklmlelR---EKNgpgAIAELLKESIKESTHQIIIIDGVRS 92
                6899****************98888664444433331.........222222333334444442222...2224446667777777778899999999988 PP

      AAA_14 76 vpew 79
                + e+
  AJA92923.1 93 IHEI 96
                7765 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012     0.081       4      27 ..       6      29 ..       3      96 .. 0.65
   2 ?   -1.1   0.0       1.5     1e+03     136     155 ..     117     136 ..     115     178 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                EEEE--TTSSHHHHHHHHHHHHHH CS
       KTI12  4 vvltGlPssGKstrakeLakalee 27
                v ltG+P +GKst++++L++   e
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKEDGYE 29
                679***************986555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                 H---TTSS-GGGS-SEEEE. CS
       KTI12 136 RyeePdsknrWDsPlftvls 155
                 R++   ++ r D Pl   + 
  AJA92923.1 117 RFNFLRERKRSDDPLTREKF 136
                 77777888888888866553 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   9.5e-05     0.066       2      21 ..       6      25 ..       5     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                EEEEESTTSSHHHHHHHHHT CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                v++ G+p +GKSt++++l +
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKE 25
                899*************9976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.6e-05     0.059       2      23 ..       3      27 ..       2      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
      AAA_24  2 klkiliyGpsgiGKTtlakel...g 23
                kl ++++G +g+GK+t++++l   g
  AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLkedG 27
                7899****************95433 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00037      0.26       2      21 ..       6      25 ..       5     105 .. 0.69
   2 ?   -2.5   0.0       6.7   4.6e+03       9      35 ..     145     172 ..     143     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                EEEE--SSSSHHHHHHHGGG CS
       AAA_5  2 vlLvGppGtgKselaerlaa 21
                v+L G pG gKs+++ +l++
  AJA92923.1  6 VCLTGMPGAGKSTIVSKLKE 25
                8**************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                 SSSHHHHHHHGGGGB.S--EEEEE--TT CS
       AAA_5   9 GtgKselaerlaaal.nreveyvqltrd 35 
                 G+g  e++e   + + n++v++ q+ ++
  AJA92923.1 145 GVGLKEIIELADESIeNNNVTINQMVES 172
                 7777778888888888888887777664 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013      0.09       3      32 ..       3      33 ..       1      81 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
  Ploopntkinase3  3 arliylvGqPGaGkstlmaelt.kgfdrskv 32
                    + ++ l G PGaGkst++++l  +g++  ++
      AJA92923.1  3 KLVVCLTGMPGAGKSTIVSKLKeDGYETFSL 33
                    5578899*************97246665554 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0016       1.1       1      26 [.       4      29 ..       4      58 .. 0.88
   2 ?    2.1   0.1      0.19   1.3e+02      90     175 ..      69     163 ..      64     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                EEEEEEESTTSSHHHHHHHHHHTT-E CS
        CoaE  1 livgltGgiasGKstvanlfadlgvp 26
                l+v ltG  ++GKst+ + +++ g++
  AJA92923.1  4 LVVCLTGMPGAGKSTIVSKLKEDGYE 29
                589***************99987765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.19
                 HHHHHHHHHHH--SSEEEEE.-TTTTTTTGGGGSSEE..EEEE--HHHHHH..HHHHCC..TSTHHHHHHHHHHS-..-HHHHHHH-SEEEE-.S CS
        CoaE  90 irreikkelakleskyvlld.vPLLvEkqleklierv..lvvdvelelqve..Rlvard..gvseeevkaiiaaQl..seeerlaladvvldNds 175
                 i++ +k+++++ +++++++d v  + E ++ k + +v  l vd+ ++++ +  R  +r+   +++e+ +++ +  +    +e ++lad  ++N++
  AJA92923.1  69 IAELLKESIKESTHQIIIIDgVRSIHEINVLKETGNVklLAVDAAPDTRFNflRERKRSddPLTREKFEERDNREIgvGLKEIIELADESIENNN 163
                 55666666666666555554355555666655555443377888888887522333333226889999888877651156788899999999976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3    0.0078       5.4      35      53 ..       5      23 ..       2      24 .. 0.88
   2 ?    3.7   0.0     0.059        41     121     159 ..      63      98 ..      37     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0078
      AAA_25 35 lallaGapgtGKttlaldl 53
                ++ l+G pg+GK+t+++ l
  AJA92923.1  5 VVCLTGMPGAGKSTIVSKL 23
                6789**********99865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.059
      AAA_25 121 rggtl.ltadvdaleaaieevegvrlvviDplsralggde 159
                 ++g+  +++    l + i+e    + ++iD + ++++ + 
  AJA92923.1  63 KNGPGaIAEL---LKESIKE-STHQIIIIDGVRSIHEINV 98 
                 3443313322...5667777.679**********999865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00026      0.18      25      39 ..       6      20 ..       1      23 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
      AAA_29 25 tlltGpsGsGKSTll 39
                + ltG  G+GKST++
  AJA92923.1  6 VCLTGMPGAGKSTIV 20
                689**********97 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00024      0.16       4      23 ..       9      31 ..       6     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
  Viral_helicase1  4 hGvpGcGKStlirkllrts...l 23
                      G+pG+GKSt++ kl ++     
       AJA92923.1  9 TGMPGAGKSTIVSKLKEDGyetF 31
                     7*********6666555535432 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0014      0.93       2      21 ..       5      24 ..       4      29 .. 0.90
   2 ?   -0.3   0.0       1.3   9.1e+02      80      94 ..      80      94 ..      48     112 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                CEEEEC-TTTCHHHHHHHHH CS
       NACHT  2 lvilqGeaGsGKTtLlqkla 21
                +v+l+G +G GK+t + kl 
  AJA92923.1  5 VVCLTGMPGAGKSTIVSKLK 24
                79**************9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
                CCCEEEEEE-STT-S CS
       NACHT 80 perlLlilDglDelv 94
                 +   +i+Dg+  ++
  AJA92923.1 80 STHQIIIIDGVRSIH 94
                233335666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1147.90
//
Query:       AJA92924.1  [L=473]
Description: multicopper oxidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-05   24.2   0.2    9.1e-05   22.5   0.2    1.9  1  Cu-oxidase_3  Multicopper oxidase


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   5.1e-09   9.1e-05      11     116 ..      92     195 ..      84     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.1e-09
                   TEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TT..... CS
  Cu-oxidase_3  11 ggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlsl..... 102
                   g+ + +++t+ +q+pgpt++v++gd v +++t   de   ++ hG +++++  m   p+  + +++ ge+ +y f ++   g + Yh +  +     
    AJA92924.1  92 GS-TYSAMTFSEQVPGPTLRVTQGDVVHMTLTIPGDE---VTQHGNDMHAS-QMSSKPY--MGAVNIGETGEYCFIAEV-PGVFKYHCSGVNiaamd 180
                   44.4899******************999988754444...45566666666.4444455..789999************.*******8755556788 PP

                   HHH.TT-EEEEEEE- CS
  Cu-oxidase_3 103 qqa.aGlaGaiiied 116
                   q++ +G++G+ i+++
    AJA92924.1 181 QHVlSGMYGITIVDP 195
                   8889********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 3188.64
//
Query:       AJA92925.1  [L=538]
Description: hypothetical protein T478_1359 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3414.49
//
Query:       AJA92926.1  [L=50]
Description: hypothetical protein T478_1470 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 373.42
//
Query:       AJA92927.1  [L=333]
Description: ABC transporter, permease protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-40  137.2  17.2    4.9e-40  137.2  17.2    1.5  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.46   10.5   3.4        7.3    6.6   0.0    2.8  3  MerE          MerE protein
        5.1    7.6  23.4       0.15   12.6   5.6    3.1  3  FtsX          FtsX-like permease family


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2  17.2   8.3e-44   4.9e-40       1     184 [.     127     330 ..     123     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 8.3e-44
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpviillllsaapyvrlirraal 76 
                   gi+lG+ + ++ ++k+d++ +++  + +s+P+ ++++l+++vf                     +il  l+h++lpvi+++l++++++++l+r+ ++
    AJA92927.1 127 GIVLGAASSNKIGSKTDRITSTFAVISSSFPVWWIGMLMIFVFafvyqifparatpsiepddpgYILALLYHMALPVITIVLIGFGAWAYLVRNFMV 223
                   567777777*******************************999****************************************************** PP

  BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvad 173
                    ++++d++ a ++ G sr++i++ ++l+na+ppi+t l+l++ g+lgga+++e ++ wpG+g+l +eai+ +d++ i+ g++++l++++l+ +++ad
    AJA92927.1 224 GIMQEDFISAKKTIGISRKKIVYSHALRNAAPPIVTILALSLSGSLGGAIITEAVFDWPGMGRLYFEAISVMDLPVII-GSTYILTVLFLVSIFIAD 319
                   ******************************************************************************.****************** PP

  BPD_transp_1 174 ilqrlldprvr 184
                   +l+ ++dprvr
    AJA92927.1 320 LLYGYFDPRVR 330
                   **********8 PP

>> MerE  MerE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0012       7.3      29      54 ..     198     223 ..     185     228 .. 0.81
   2 ?    3.7   0.1    0.0098        58      29      50 ..     255     276 ..     249     282 .. 0.88
   3 ?   -3.8   0.2       2.2   1.3e+04      58      67 ..     306     315 ..     300     318 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0012
        MerE  29 PchlpilaivlaGttaGaflgeywvi 54 
                    lp+++ivl G  a a+l+  +++
  AJA92927.1 198 HMALPVITIVLIGFGAWAYLVRNFMV 223
                 4569****************988766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0098
        MerE  29 PchlpilaivlaGttaGaflge 50 
                 P  ++ila+ l+G+  Ga ++e
  AJA92927.1 255 PPIVTILALSLSGSLGGAIITE 276
                 66789***************98 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.2
        MerE  58 altGlfvlsl 67 
                  lt lf++s+
  AJA92927.1 306 ILTVLFLVSI 315
                 4777777775 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.6   2.4e-05      0.15      17      79 ..     112     173 ..     103     185 .. 0.57
   2 ?   -2.2   0.9         1   6.2e+03      27      38 ..     201     212 ..     190     226 .. 0.52
   3 ?    6.7   2.4    0.0017        10       4      84 ..     231     315 ..     228     323 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
        FtsX  17 vlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllll 79 
                 ++ll++t +++i+++++v+G + ++++     d + s +  ++ ++ + +i +l i+v++++ 
  AJA92927.1 112 TILLFTTATIIISIIGIVLGAASSNKIGSK-TDRITSTFAVISSSFPVWWIGMLMIFVFAFVY 173
                 455555555555555555555555555444.33333333336666666666666666666653 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
        FtsX  27 litlvalviGlg 38 
                 l ++   +iG+g
  AJA92927.1 201 LPVITIVLIGFG 212
                 333333333332 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0017
        FtsX   4 igilralGmkkkqvlllllteill...itlva.lviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallag 84 
                 i+  +++G ++k+++    + +++   +t++a +++G + g++++++++d+ +     +e+   +dl  ++    +l++l+l+++
  AJA92927.1 231 ISAKKTIGISRKKIVYSHALRNAAppiVTILAlSLSGSLGGAIITEAVFDWPGMGRLYFEAISVMDLPVIIGSTYILTVLFLVSI 315
                 6677899999999998888887751112333303445777999999999997655332344444444444444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2337.50
//
Query:       AJA92928.1  [L=266]
Description: hypothetical protein T478_1087 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0036   17.2   0.2     0.0079   16.1   0.2    1.6  1  MarR            MarR family
      0.004   17.3   0.2     0.0078   16.4   0.2    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
       0.11   11.8  42.1       0.13   11.6  42.1    1.1  1  CDC27           DNA polymerase subunit Cdc27
       0.79   10.4   2.9        5.8    7.6   2.9    2.2  1  RPA_C           Replication protein A C terminal
        1.3    9.1   7.3        1.6    8.8   7.3    1.1  1  PARM            PARM
        2.2    8.2   6.0         22    5.0   0.0    2.2  2  DUF3558         Protein of unknown function (DUF3558)
        3.7    8.1  14.8        4.8    7.7  14.8    1.1  1  SOBP            Sine oculis-binding protein
        6.8    4.8  19.1        8.3    4.5  19.1    1.2  1  PAT1            Topoisomerase II-associated protein PAT1
        7.6    5.1  16.5        8.6    4.9  16.5    1.0  1  Ndc1_Nup        Nucleoporin protein Ndc1-Nup


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     4e-06    0.0079      20      52 ..     169     201 ..     157     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                 HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR  20 vseLakklgvskstvtrvldrLekkGlieRsks 52 
                 +seL+kkl++++   +r++ rLe++Gli+R+k 
  AJA92928.1 169 QSELWKKLKLNSRDGSRLALRLERRGLISREKI 201
                 89****************************986 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.9e-06    0.0078       7      54 ..     155     202 ..     150     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
  B-block_TFIIIC   7 lLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsii 54 
                     + e+Ia   ++G++qs+L+k +k  +r+   +   Le+ gLI + +i 
      AJA92928.1 155 VCEIIAEFEDKGVLQSELWKKLKLNSRDGSRLALRLERRGLISREKIL 202
                     56899999*************************************994 PP

>> CDC27  DNA polymerase subunit Cdc27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  42.1   6.5e-05      0.13     139     264 ..      13     137 ..       1     178 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
       CDC27 139 plaapaseakektangkkpkaakekaaketssakseskkksaekskdaskettkekaekaasskaaslkkkasaksnimksffkakpaekkkkteakeq 237
                 ++ ++ +e   +  n+kk+   k+kaak+++  k++++k++++++k++++++ ++ ++++   k++ +kk+a+ k++  k++ ka+ a++kk+++a ++
  AJA92928.1  13 QIKKELAELRAQLENQKKS---KKKAAKPKAEKKAAKPKAEKKAAKPKAEKKAAKPKAEKKAAKPKAEKKSAKPKAEKPKKLTKAQIAQAKKDAKAAKE 108
                 5555555555556677666...888888998888888888888888877666666555666677777888999************************** PP

       CDC27 238 kveeeseeekekedkeleddsa..aeeee 264
                 k e+e++++ke+ +++ edd +    +e+
  AJA92928.1 109 KEEAEAKAAKEAAERTPEDDLEeqFSDEQ 137
                 ********************984422222 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.9    0.0029       5.8      10      97 ..     105     196 ..      24     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0029
                 XXXXX......XXXXXXXXXXXX..........XXXXXXXXXXXX....XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTT CS
       RPA_C  10 gssagaagaavavsaggsamgtd..........galsgnqaklan...kgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneG 95 
                 +++++++++a a +                    ++s  q ++++     + +l++ v+++i +   +++Gv  +e+ +kl+l+ +d  + +  L+  G
  AJA92928.1 105 AAKEKEEAEAKAAKE-------AaertpeddleEQFSDEQIRNFQiekMDMDKLTNKVCEIIAE--FEDKGVLQSELWKKLKLNSRDGSRLALRLERRG 194
                 333332222222222.......12222222344677777777777876669*************..8899***************99999998888888 PP

                 SE CS
       RPA_C  96 ii 97 
                 +i
  AJA92928.1 195 LI 196
                 87 PP

>> PARM  PARM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.3   0.00081       1.6      87     209 ..      27     145 ..       2     170 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00081
        PARM  87 etdpssvk.lsstssgveltptpeehssgtpeasvpatgsqspaesptltSpqapasspsslstslppevssasvstnhssaetstkptgapttpespt 184
                 ++++s+ k  ++ ++++  +p  +e++++ p+a+  a++ ++  e+  +  p+a   s ++ +   p + + a+++ ++  a+++ ++++a+ +++  +
  AJA92928.1  27 NQKKSKKKaAKPKAEKKAAKPK-AEKKAAKPKAEKKAAKPKA--EK-KAAKPKAEKKSAKPKAEK-PKKLTKAQIAQAKKDAKAAKEKEEAEAKAAKEA 120
                 3333433303333444444443.6666666666665555444..44.456789999999999998.99**************************99999 PP

        PARM 185 eehssaetptshataepvpeettsq 209
                 +e ++++    + + e + +++  +
  AJA92928.1 121 AERTPEDDLEEQFSDEQIRNFQIEK 145
                 9999998888877777776655544 PP

>> DUF3558  Protein of unknown function (DUF3558)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   5.5     0.095   1.9e+02      14      65 ..      55     110 ..      35     123 .. 0.72
   2 ?    5.0   0.0     0.011        22     107     149 ..     130     173 ..     112     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.095
     DUF3558  14 apaasssassssttsssaapavpldtsgvlfdpCglltddqlaelggd....keke 65 
                 +p+a   a+ + +++++a p+ +++ +++  +  + lt +q+a+++ d    keke
  AJA92928.1  55 KPKAEKKAAKPKAEKKAAKPKAEKKSAKPKAEKPKKLTKAQIAQAKKDakaaKEKE 110
                 4666666677777777777777889999999999**************54332222 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
     DUF3558 107 teerlditieGrpaviardpgdeas.Cevavgvadgqvvvvsvs 149
                  e+++d +i  ++   ++ ++ +++ Ce+ ++++d++v+++ ++
  AJA92928.1 130 EEQFSDEQIRNFQIEKMDMDKLTNKvCEIIAEFEDKGVLQSELW 173
                 23344999999997777766665555**********99987665 PP

>> SOBP  Sine oculis-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  14.8    0.0024       4.8      75     184 ..      29     140 ..       7     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
        SOBP  75 sncrsrsaspaskrsesvspepsksaspssspt..ssnsskplisvassskllaeksqepaslveaplepkkqrkkkpglrkpkqvkagsskssetkag 171
                 +  ++++a+p+++++ ++ ++ +k a p+++    + +++k+  +++ ++k+ ++k ++p++l++a+  + k++ k+++ +++ ++ka +++ ++t+++
  AJA92928.1  29 KKSKKKAAKPKAEKKAAKPKAEKKAAKPKAEKKaaKPKAEKKAAKPKAEKKSAKPKAEKPKKLTKAQIAQAKKDAKAAKEKEEAEAKAAKEAAERTPED 127
                 445677777877555554433333333333322224455566666666777888888888888877777777777777777777777777888888888 PP

        SOBP 172 llqkqqkalplsa 184
                  l++q +  ++ +
  AJA92928.1 128 DLEEQFSDEQIRN 140
                 7777733333333 PP

>> PAT1  Topoisomerase II-associated protein PAT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  19.1    0.0042       8.3     196     314 ..      17     128 ..       2     183 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0042
        PAT1 196 sleEvEaamraqakkkaaqaaaaaaas.qqPaaeqaeqaeaaaqaakaeqaqqapesakeqqqeqeqaaqaqqkkeqgkpvtilqrpqskqakpaepsa 293
                  l E+ a++  q+k+k+++a+ +a+++  +P+ae+++ + +a+++a   ++ +a+++a++ ++e+++a+ + +k+++ ++++i q ++ ++a++++++a
  AJA92928.1  17 ELAELRAQLENQKKSKKKAAKPKAEKKaAKPKAEKKAAKPKAEKKA---AKPKAEKKAAKPKAEKKSAKPKAEKPKKLTKAQIAQAKKDAKAAKEKEEA 112
                 4789999998888777666554444333666655544444333222...22222222222222333333333333333333433333333222222222 PP

        PAT1 294 sseaqeakqqappakvqptqi 314
                 +++a +     ++a+ +p   
  AJA92928.1 113 EAKAAK-----EAAERTPEDD 128
                 222222.....1122222222 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  16.5    0.0043       8.6     341     471 ..      16     137 ..      10     203 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0043
    Ndc1_Nup 341 klikeltqrinergqpapkaapskapknkasapvkelprlsksplkkk....ddeifgnsltaeaspkssssskegvekalsslakspgqspsptarls 435
                 k+++el+ ++++++++++kaa++k +++ka++p+ e++  + + +kk      ++  +++++ ++s+k++ ++++++ ka+ ++ak++           
  AJA92928.1  16 KELAELRAQLENQKKSKKKAAKPK-AEKKAAKPKAEKKAAKPKAEKKAakpkAEKKAAKPKAEKKSAKPKAEKPKKLTKAQIAQAKKD----------- 102
                 578889999999888555555533.333333333333333322222212111111111122222333333333333333333333222........... PP

    Ndc1_Nup 436 prarkllekaksrllskeqkealsestikkkvekel 471
                 ++a+k+ e+a+ ++ + e++e+ +e+  ++++++e 
  AJA92928.1 103 AKAAKEKEEAEAKAAK-EAAERTPEDDLEEQFSDEQ 137
                 3333333333333333.4444444444444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3655  (0.20386); expected 358.6 (0.02)
Passed bias filter:                      989  (0.055162); expected 358.6 (0.02)
Passed Vit filter:                       323  (0.0180155); expected 17.9 (0.001)
Passed Fwd filter:                       100  (0.00557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.12u 0.35s 00:00:01.47 Elapsed: 00:00:00.50
# Mc/sec: 1588.47
//
Query:       AJA92929.1  [L=376]
Description: putative 8-amino-7-oxononanoate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-49  166.7   0.0    9.5e-49  166.5   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
     0.0003   19.4   0.1    0.00047   18.8   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0023   17.3   0.3      0.012   14.9   0.3    2.0  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0055   15.7   0.6     0.0091   15.0   0.6    1.4  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.0   2.1e-52   9.5e-49       2     361 ..      40     364 ..      39     366 .. 0.91

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 2.1e-52
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    +++n++sn+ylg      + ++++++ +    ++++  +g+      le++lak  +        +e+a+++ +G+ a++ +++ +++  ++d i+
     AJA92929.1  40 KLLNFSSNDYLGI----KSGKIKHTQFQ----SSSRLVSGNDASFSLLEKKLAKHKS--------QEQAIIFPTGYMANLGMITSIAT--KHDTIF 117
                    789*********9....77777777755....8889999999999************........888*******************9..****** PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                    ++++++as+ ++++lsg+++  ++       h+++ +le+++++ +     +k++++e++++++G+  +l+e++++    +k++++++vD+a+++f
     AJA92929.1 118 SDELNHASIVEACKLSGSKIKIFK-------HNNIGDLERKVQKTK----GKKILITEGVFSMDGDWSKLNEICQV---SEKHGMITVVDDAHGDF 199
                    ************************.......************943....447***********************...***************** PP

                    BSSSS.HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsl.davatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaa.alsdallkqseleemrqrlqkrrke 287
                    v+g+  + +a+ ++ve++++ l v+slsK +G+ G   Gy++g +++++   + s +f+++s+l+  +++ +l+ ++   s+ e  r++l+k+   
     AJA92929.1 200 VLGKDgKGTANFFDVEKKID-LYVSSLSKGLGSFG---GYVCGRKKLIDLCINTSKTFIYTSALPSSINQySLNRFN---SKREIYREKLWKKINL 288
                    ***66544455*********.**************...**********************77777777761455555...48899*********** PP

                    HHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHH CS
  Aminotran_1_2 288 lrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelve 361
                    ++++L+e++l  ++  s ++++  +++++a+e+sk L+ + g+  ++++++tv   ++r+Ri++   l+++e+e+ ++
     AJA92929.1 289 FHKRLEEIELHTTS-TSQIIPIIIGNEKKAMEFSKFLRIN-GIFAQAIRYPTVkkdQARIRISItGWLSNKEIEYSIQ 364
                    *****999996665.6************************.***************9*******88899999998765 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-07   0.00047      55     175 ..      77     195 ..      53     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-07
                      HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT..TEEEEEEESS CS
  Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike..ntklvylEtp 146
                      s le+++a+ ++ e+a+++++G  A   +i++++++ d i +++  +      + + +k +g ++k++  +++ +le+++++    k++ +E +
       AJA92929.1  77 SLLEKKLAKHKSQEQAIIFPTGYMANLGMITSIATKHDTIFSDELNHA----SIVEACKLSGSKIKIFKHNNIGDLERKVQKtkGKKILITEGV 166
                      679***********************9999999999988877665444....455666677888889999999999999988645678889*** PP

                      -TTTT----HHHHHHHHHHTT-EEEEEGT CS
  Cys_Met_Meta_PP 147 tnpllkvvDiekiaklakkagvlvvvDnt 175
                       +   +   +++i+++  k+g+++vvD +
       AJA92929.1 167 FSMDGDWSKLNEICQVSEKHGMITVVDDA 195
                      ***************************86 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   2.7e-06     0.012      28     215 ..      70     243 ..      66     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-06
                      CT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S CS
  Beta_elim_lyase  28 YgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikev 121
                       g+d ++  Le+++a+    e+a+ +p+G +An  +++ ++ +++ ++ +e +h    e+     l+g+k + +k+++     + +le++++++
       AJA92929.1  70 SGNDASFSLLEKKLAKHKSQEQAIIFPTGYMANLGMITSIATKHDTIFSDELNHASIVEACK---LSGSKIKIFKHNN-----IGDLERKVQKT 155
                      589**************************************99999999999**99999754...5888888888888.....88888888884 PP

                      -TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH...TTSSEEEEESSSTT--SS-EEEEE-H CS
  Beta_elim_lyase 122 gaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemf...syvDsvtmslkKdllanvGgvlafrd 212
                      +      k i++t  + ++ G      +l+e+ ++ +k+g+  ++D A       + g   ++ f   + +D  + sl+K+l+   Gg +++r+
       AJA92929.1 156 KG-----KKILITEGVFSMDGDW---SKLNEICQVSEKHGMITVVDDAHGDFVLGKDGKGTANFFdveKKIDLYVSSLSKGLGS-FGGYVCGRK 240
                      44.....7777777777777765...4566777778899999999988765556555666666665557789999999999887.899999998 PP

                      H.. CS
  Beta_elim_lyase 213 del 215
                      + +
       AJA92929.1 241 KLI 243
                      844 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.6     2e-06    0.0091      85     217 ..     110     242 ..      81     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                  -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT... CS
  Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqa... 179
                    + d+i   e++h + +    e++k  g k+k+++ ++ g l+  +++k  ++  k+++   v ++ G +  ++ei+++  k+g++++vD a +   
   AJA92929.1 110 ATKHDTIFSDELNHASIV----EACKLSGSKIKIFKHNNIGDLE-RKVQK--TKGKKILITEGVFSMDGDWSKLNEICQVSEKHGMITVVDDAHGdfv 200
                  567788888888888877....999999*********9999998.44433..578899*********************************9975221 PP

                  T...TTS---HH..HHTESEEEEETTTTTSSTT-EEEEEEHHH CS
  Aminotran_5 180 v...ghipidvk..klgvDflafsghKllgPtGiGvlyvrkel 217
                  +   g+   ++   + ++D++++s  K lg  G G +++rk+l
   AJA92929.1 201 LgkdGKGTANFFdvEKKIDLYVSSLSKGLGSFG-GYVCGRKKL 242
                  111122222222112356777777777777777.666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2559.69
//
Query:       AJA92930.1  [L=298]
Description: 3-beta hydroxysteroid dehydrogenase/isomerase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-58  197.6   0.0    2.6e-58  197.3   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    8.2e-54  183.2   0.6    4.5e-53  180.8   0.6    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    6.7e-27   94.2   0.2    9.8e-27   93.7   0.2    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-21   77.1   0.1    6.3e-21   74.8   0.1    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.6e-21   75.5   0.0    3.9e-21   75.4   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-14   53.5   0.1      3e-09   36.5   0.0    2.3  2  NAD_binding_4    Male sterility protein
    6.4e-08   32.7   0.0    1.3e-07   31.7   0.0    1.4  1  KR               KR domain
    7.3e-07   29.3   0.0      1e-06   28.7   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.8e-05   24.4   0.1    5.1e-05   23.6   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    0.00024   20.6   0.0    0.00041   19.8   0.0    1.4  1  adh_short        short chain dehydrogenase
     0.0019   17.8   0.1     0.0029   17.2   0.1    1.3  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.025   14.6   0.1    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.022   14.3   0.1      0.043   13.4   0.1    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.039   14.2   0.1        0.2   12.0   0.0    2.2  3  TrkA_N           TrkA-N domain
       0.11   12.3   0.0       0.18   11.7   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   0.0   2.2e-61   2.6e-58       2     241 .]       4     234 ..       3     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 2.2e-61
                 EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHHHH CS
   Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgtln 97 
                 +VtG++Gf+Gs+lvk l +kg++vi++d+l ++++ +++  l   ++ e+d++d ++le++++  ++d v+h Aa   v++s+++p+++ + n++gt n
  AJA92930.1   4 VVTGGAGFVGSYLVKLLVRKGHQVIVIDNLHKGKKDNLESVLskiQFEEIDIRDYASLEKILS--NIDGVFHQAALTVVQDSFDRPEEYHDVNVIGTEN 100
                 7*****************************777777666666*********************..9********************************* PP

                 HHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTT CS
   Epimerase  98 lleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkileg 196
                 ++  a+k++  +++++sSs+vYG ++++p +e++   + +p +pY+ +Kl  e l e+y + +  ++i lr+fn++G++ ++ e ++vi+++i +i+++
  AJA92930.1 101 IFRLAKKNNF-KVVYASSSSVYGHKETMPINEDS---ERNPINPYGQTKLDDEFLFEKYSKMG-AKIIGLRYFNIFGKG-QTLEYAGVITKFIDRINQK 193
                 **********.***********************...77899*****************7766.8**************.9999**************9 PP

                 SSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 197 kqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 + + +++gdgt+ Rdf+yveDv+ ++ll +e     ++   +n+G
  AJA92930.1 194 Q-PPIIFGDGTQIRDFIYVEDVVMMNLLCMES---HKTELLVNVG 234
                 9.*****************************9...4444467776 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   0.6   3.7e-56   4.5e-53       2     272 ..       5     258 ..       4     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 3.7e-56
                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHH CS
  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPey 97 
                    +TG+aGf+Gsyl++lL++kg++v++i+++++  + +++e++ +        ++++ + D++D +sle++l+++  d v++ AA   V+ sf+ Pe+
     AJA92930.1   5 VTGGAGFVGSYLVKLLVRKGHQVIVIDNLHKG-KKDNLESVLS--------KIQFEEIDIRDYASLEKILSNI--DGVFHQAALTVVQDSFDRPEE 89 
                    9************************9998876.5577777763........689****************997..9******************** PP

                    HHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSC CS
  GDP_Man_Dehyd  98 taevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfv 193
                    + +vnv+Gt +++ ++++    ++++++ aS+s vYG+ +  p++E+   +P +PY+ +Kl  +++ ++y +  g  ++  ++fn  +  ++ ++ 
     AJA92930.1  90 YHDVNVIGTENIFRLAKK----NNFKVVYASSSSVYGHKETMPINEDSERNPINPYGQTKLDDEFLFEKYSK-MGAKIIGLRYFNIFGKGQTLEYA 180
                    ****************98....569*********************************************87.8999**************99955 PP

                    CCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EE.E-TT-EEECHHCHHCCHHCCCHHHHH CS
  GDP_Man_Dehyd 194 trkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyv.iatgethsvrefvelaflelgktiew 272
                       it+++ ri++++ + +++G++ ++Rd+ +v+D+v +  l +++ k+e  v ++tg+  s+ e++++ +   g +++ 
     AJA92930.1 181 -GVITKFIDRINQKQ-PPIIFGDGTQIRDFIYVEDVVMMNLLCMESHKTELLVnVGTGDAISILELAKMMIDVSGLEMQP 258
                    .9*********9965.7888*******************99999998877654378889888888888776655554433 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.2   8.2e-30   9.8e-27       1     229 [.       4     222 ..       4     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 8.2e-30
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTrn 98 
                 vvtGgaGF+G++lvk Lvr +  ++v v+D  ++ ++ +  s +  +++ e D++d ++le+ l ++d v+h a+l+ v+   ++ +e+ +vnv GT+n
  AJA92930.1   4 VVTGGAGFVGSYLVKLLVRKG--HQVIVIDNLHKGKKDNLESVLSKIQFEEIDIRDYASLEKILSNIDGVFHQAALTVVQDsFDRPEEYHDVNVIGTEN 100
                 8********************..59*****99988886666667777799*****************************99567889************ PP

   3Beta_HSD  99 vleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl.....lvpl 192
                 +   ++k++ + +vY Ss +v g    +e +   +E+   e ++ ++y ++K   E l  k        g++   + LR   i+G g++l     ++++
  AJA92930.1 101 IFRLAKKNNFK-VVYASSSSVYGH---KETMP-INEDS--ERNPINPYGQTKLDDEFLFEKYSK----MGAK--IIGLRYFNIFGKGQTLeyagvITKF 186
                 ********986.69*********9...44444.44554..5567899*****999988877666....4544..478*********9987222213344 PP

   3Beta_HSD 193 lkqlaklglalfkigdeevlsdrvYvgNvawahilAa 229
                 + + +++++  +  gd  ++ d++Yv+ v+ + +l +
  AJA92930.1 187 IDR-INQKQPPIIFGDGTQIRDFIYVEDVVMMNLLCM 222
                 444.4555588999******************99875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.1   5.2e-24   6.3e-21       2     253 ..       4     258 ..       3     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 5.2e-24
                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHHH CS
  Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlvee 95 
                      +vtG++G +Gs lv+ +++k  + i++ + +  k +++e+ l      +k+++e      d+rd ++lek+l+  ++d vfh AAl  V     
       AJA92930.1   4 VVTGGAGFVGSYLVKLLVRKGHQVIVIDNLHKGKKDNLESVL------SKIQFE----EIDIRDYASLEKILS--NIDGVFHQAALTVVQDSFD 85 
                      69*************999999988888888888889998887......356566....46*************..******************* PP

                      SHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.............GGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG.. CS
  Polysacc_synt_2  96 npleaiktNvlgtenvieaaieagvkkvvliSt.............DKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS.. 174
                       p e  + Nv+gten+ + a++++ k v + S+             D   nP+n +G tK+  e l+ +++k       k++  R+ N++g   
       AJA92930.1  86 RPEEYHDVNVIGTENIFRLAKKNNFKVVYASSSsvyghketmpineDSERNPINPYGQTKLDDEFLFEKYSKMG----AKIIGLRYFNIFGKgq 175
                      ********************9998876554443333333333333388899****************9999987....8899999999998522 PP

                      ...TTSSHHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH.......... CS
  Polysacc_synt_2 175 ...rGSviplFkkqikeg.gpvtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekk 253
                            vi++F ++i+++  p+   d + +R f+ +e+ v + l +++ +k+  +  +  G++++i++lak +i++sgle++ 
       AJA92930.1 176 tleYAGVITKFIDRINQKqPPIIFGDGTQIRDFIYVEDVVMMNLLCMESHKTELLVNVGTGDAISILELAKMMIDVSGLEMQP 258
                      2223569********999467999********************9999988887777899******************98765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   3.3e-24   3.9e-21       1     154 [.       1     173 [.       1     263 [. 0.88

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.3e-24
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHH CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavn 78 
                    mk +vtG+ G +Gs L+k+l ++g++v+ +++                   e+d++d ++++++l+++  d v + AA t v    + +e+ + vn
     AJA92930.1   1 MKYVVTGGAGFVGSYLVKLLVRKGHQVIVIDNLhkgkkdnlesvlskiqfeEIDIRDYASLEKILSNI--DGVFHQAALTVVQDSFDRPEEYHDVN 94 
                    899***************************776799******************************95..56************************ PP

                    THHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH...H-SSEEEEEE-SEESS CS
  RmlD_sub_bind  79 aeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla...agkkalivRtswvyge 154
                    + ++e++ ++a++ + ++++ S+  V+  ++++p +ed+e +P+n YG+tKl+ E   ++    g+k++ +R   ++g+
     AJA92930.1  95 VIGTENIFRLAKKNNFKVVYASSSSVYGHKETMPINEDSERNPINPYGQTKLDDEFLFEKyskMGAKIIGLRYFNIFGK 173
                    *******************************************************998883323334444666666665 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   7.6e-06    0.0091       1      36 [.       5      40 ..       5      59 .. 0.72
   2 !   36.5   0.0   2.5e-12     3e-09      80     240 ..      60     201 ..      40     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksges 36
                   +TG+ GF+G++L++ L+r+  +v ++  +++ ++++
     AJA92930.1  5 VTGGAGFVGSYLVKLLVRKGHQVIVIDNLHKGKKDN 40
                   7******************99874444444444433 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.5e-12
                    HHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTC CS
  NAD_binding_4  80 dlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkgl 172
                    +l+++ +++d ++h aA + ++++ ++     +vNv Gt+++++lakk +    +++ S++ v+g++e+                   +++++++ 
     AJA92930.1  60 SLEKILSNIDGVFHQAALTVVQDSFDRpeeYHDVNVIGTENIFRLAKKNNF--KVVYASSSSVYGHKETM----------------PINEDSERNP 137
                    678999*************9999776544499***************6655..59999999999999943................4677888899 PP

                    CCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES-SB- CS
  NAD_binding_4 173 pntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpeilgd 240
                     n Y q+K   E l +++++  g +++ +R  +i g   +G++ +   +i+ ++  i++++ p i+gd
     AJA92930.1 138 INPYGQTKLDDEFLFEKYSKM-GAKIIGLRYFNIFG---KGQTLEYAGVITKFIDRINQKQPPIIFGD 201
                    9***************99976.88888888888877...34444444455555555555555555555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.1e-10   1.3e-07       3     145 ..       3     125 ..       2     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.1e-10
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 y++tGG+G +G  l++ l++kg + +v+   +    +    + ++le+   ++++ ++D+ d +++e++l++i+       Gv+h A ++    + + +
  AJA92930.1   3 YVVTGGAGFVGSYLVKLLVRKGHQVIVIDNLH----KG---KKDNLESVLSKIQFEEIDIRDYASLEKILSNID-------GVFHQAALT----VVQDS 83 
                 9***********************99997666....23...3478999999******************99886.......****99875....56667 PP

                 HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--TT CS
          KR 102 aedleqvlapKvkGawnLhelledesldffvlfSSiagllgsag 145
                  ++ e+     v G++n+ +l ++   +f v+++S ++++g+++
  AJA92930.1  84 FDRPEEYHDVNVIGTENIFRLAKK--NNFKVVYASSSSVYGHKE 125
                 78888888889**********986..678899999999999875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   8.7e-10     1e-06       1     110 [.       7     130 ..       7     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 8.7e-10
                     TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SEEEES-.........--TCCHHHH...... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleae.eglevvegdvtdvedlaealkgadaVvsal.........ggggkdeeg...... 77 
                     G+ G vG++lvk l+++ gh+v +++ n  + k ++le+  ++++  e+d+ d ++l++ l+++d V+  +             +          
      AJA92930.1   7 GGAGFVGSYLVKLLVRK-GHQV-IVIDNlhKGKKDNLESVlSKIQFEEIDIRDYASLEKILSNIDGVFHQAaltvvqdsfD---R---Peeyhdv 93 
                     99***************.5998.56677334444566655689*************************9996665543221...1...1233555 PP

                     ....HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHH CS
  NAD_binding_10  78 ....aknivdaakeagvkRfvlvsaigvgdevpgefg 110
                         ++ni + ak+++ k +   s+   g++   + +
      AJA92930.1  94 nvigTENIFRLAKKNNFKVVYASSSSVYGHKETMPIN 130
                     6688************966555555544443333333 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   4.2e-08   5.1e-05       5      71 ..       8      69 ..       4      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.2e-08
                     --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSS CS
  Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegd 71
                     GaG+vG+ +++ll+r+++   +++v+d  +++ +  +++   ++++++++d+ +y++ L+++l+  d
       AJA92930.1  8 GAGFVGSYLVKLLVRKGH---QVIVIDNLHKGKKDNLES-VLSKIQFEEIDIRDYAS-LEKILSNID 69
                     88**************97...799999999987777776.7899*************.**9998765 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.5e-07   0.00041       4      72 ..       4      69 ..       2     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.5e-07
                EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
   adh_short  4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekav 72
                +vtG+++ +G  ++k l+++G +v+v+d+  +  +  ++++ +   k+ + ++D++d++++e++++++ 
  AJA92930.1  4 VVTGGAGFVGSYLVKLLVRKGHQVIVIDNLHKGKKDNLESVLS---KIQFEEIDIRDYASLEKILSNID 69
                8***************************998888666666665...6***************9998774 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.4e-06    0.0029       2      73 ..       4      76 ..       3      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                EESSTTSHHHHHHHHHHHHHT-EEEEEES-S...-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE--- CS
        NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt...kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtg 73
                +v+G++G  G+++v+ l+++gh+v + + ++   k+++++s+ ++  ++ + d+ d++sl+++l++ d+vf   +
  AJA92930.1  4 VVTGGAGFVGSYLVKLLVRKGHQVIV-IDNLhkgKKDNLESVLSK-IQFEEIDIRDYASLEKILSNIDGVFHQAA 76
                69*********************966.455523366666665443.566699*******************8665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.1e-05     0.025      17      81 ..       6      73 ..       1      81 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                  EES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHH...HHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
  Shikimate_DH 17 liGaGemaelvakhLlakgvkkvvvaNRtlerakel...aeelkgeeiealkleelkellaeadvvis 81
                    GaG +++ ++k L++kg + +v+ N    + ++l    ++++ eei ++++ +l+++l+++d v+ 
    AJA92930.1  6 TGGAGFVGSYLVKLLVRKGHQVIVIDNLHKGKKDNLesvLSKIQFEEIDIRDYASLEKILSNIDGVFH 73
                  459************************9887776661115666778889999999********99985 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.6e-05     0.043       7      41 ..       8      43 ..       1      72 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                    --STTHHHHHHHHHHCTSEEEEE-S.-HHHHHHHCT CS
  UDPG_MGDP_dh_N  7 GlGYvGlvtaavlaeighevigvDi.deekvdklns 41
                    G+G+vG     +l ++gh+vi++D+  + k d+l+s
      AJA92930.1  8 GAGFVGSYLVKLLVRKGHQVIVIDNlHKGKKDNLES 43
                    9***********************723445555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016       0.2       5      31 ..       8      34 ..       3      67 .. 0.82
   2 ?   -2.9   0.0       6.7     8e+03      26      49 ..      95     117 ..      88     120 .. 0.58
   3 ?   -1.8   0.0         3   3.6e+03      33      51 ..     186     204 ..     182     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                S-SHHHHHHHHHHHHTTEEEEEEESSH CS
      TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkde 31
                G+G vG+ l++ L ++g++v+vid+ +
  AJA92930.1  8 GAGFVGSYLVKLLVRKGHQVIVIDNLH 34
                89*************5558*****965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                 EEESSHHHHHHHHHTTSEEEES-T CS
      TrkA_N  26 vidkdeerveelreeglevvvgda 49 
                 vi + e+ ++ +++++++vv+++ 
  AJA92930.1  95 VIGT-ENIFRLAKKNNFKVVYASS 117
                 5544.4555666666677777665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                 HHHHHHHTTSEEEES-TTS CS
      TrkA_N  33 rveelreeglevvvgdatd 51 
                  ++++ ++  +++ gd+t+
  AJA92930.1 186 FIDRINQKQPPIIFGDGTQ 204
                 56778889999*****996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.18       6      43 ..       8      49 ..       3      81 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                --SCCHHHHHHHHHHTT-EEEEE-S....-HHHHHHHHHHHH CS
     3HCDH_N  6 GaGtmGagiaavfasagleVvlvdi....seealekalekie 43
                GaG +G+ + ++++++g++V ++d     +++ le++l+ki+
  AJA92930.1  8 GAGFVGSYLVKLLVRKGHQVIVIDNlhkgKKDNLESVLSKIQ 49
                9***********************944444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2017.99
//
Query:       AJA92931.1  [L=135]
Description: hypothetical protein T478_1449 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.8   0.6       0.12   12.9   0.2    1.6  2  DUF4369   Domain of unknown function (DUF4369)
       0.17   12.0   0.1       0.32   11.1   0.1    1.4  1  SGS       SGS domain


Domain annotation for each model (and alignments):
>> DUF4369  Domain of unknown function (DUF4369)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.85   7.6e+03      65      76 ..      25      36 ..      11      45 .. 0.54
   2 ?   12.9   0.2   1.4e-05      0.12       3      77 ..      60     126 ..      59     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.85
     DUF4369 65 lengtititidd 76
                +++ t+ ++++d
  AJA92931.1 25 ADSNTTVLSTND 36
                333333333333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.4e-05
     DUF4369   3 IeGtikgladgkkvylsydd.ngvvklDsavv.knGkFtfkgkvdeprlaylliddkggalpfflengtititiddg 77 
                 IeGt+++ a+g  v+l+ ++  ++v+   + v ++G++++k  +   ++  +++  +g+          ++++i ++
  AJA92931.1  60 IEGTVENHAEGYPVILQIYQnDEPVHFAQTNVnEDGTYEYKFRARNLDGNNVVTVYEGN----------YEVKIFKS 126
                 9******9***9999665544889999999998*********99998888777777666..........55555555 PP

>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.6e-05      0.32      46      63 ..      20      37 ..      17      56 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
         SGS 46 mmKSyveSnGtvLstnWe 63
                m  S+ +Sn tvLstn  
  AJA92931.1 20 MSPSFADSNTTVLSTNDG 37
                889************953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 941.68
//
Query:       AJA92932.1  [L=106]
Description: hypothetical protein T478_1181 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00099   18.9   0.2        1.4    8.8   0.0    2.4  2  HNH_5           HNH endonuclease
  ------ inclusion threshold ------
      0.011   16.1   1.0       0.17   12.2   0.1    2.7  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
      0.025   14.3   3.1       0.16   11.7   0.2    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.025   14.5   0.8       0.13   12.2   0.2    2.1  2  Gin             Inhibitor of sigma-G Gin
       0.03   14.2   0.1        1.2    9.1   0.0    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.032   14.6   0.0      0.045   14.1   0.0    1.3  1  SAP30_Sin3_bdg  Sin3 binding region of histone deacetylase co
      0.044   13.4   2.6       0.73    9.5   0.2    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.055   13.7   1.0         10    6.4   0.1    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.11   12.0   1.0       0.71    9.4   1.0    2.1  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.24   11.6   2.4        0.4   10.8   0.2    2.1  2  SR1P            SR1 protein
       0.34   10.6   3.0        1.6    8.5   0.7    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


Domain annotation for each model (and alignments):
>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0017       2.8      32      43 ..      48      59 ..      41      66 .. 0.80
   2 !    8.8   0.0   0.00087       1.4      33      45 ..      86      98 ..      78     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
       HNH_5 32 lvtlCkkCNqkk 43
                l   Ck+CN+++
  AJA92932.1 48 LKHFCKACNSEF 59
                4668******98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00087
       HNH_5 33 vtlCkkCNqkkgq 45
                + +C+kCN+  g+
  AJA92932.1 86 QYICQKCNSTIGE 98
                679******9885 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.3   2.1e+03      20      27 ..       6      13 ..       5      13 .. 0.81
   2 ?   12.2   0.1    0.0001      0.17      11      32 ..      61      93 ..      52      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                    ....S-EE CS
  Prim_Zn_Ribbon 20 kdgrGtwf 27
                     +g+G+w+
      AJA92932.1  6 LQGSGGWV 13
                    5799***7 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0001
                    -TTTEEETT...............S-EEETTTT CS
  Prim_Zn_Ribbon 11 GrDrFrfddkdgr...........GtwfCrqCg 32
                    G ++F +++k++            G ++C++C+
      AJA92932.1 61 GPTGFQIEEKPNEevanglilierGQYICQKCN 93
                    6689999*****99******************5 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.046        75      23      31 ..      51      59 ..      49      60 .. 0.79
   2 ?   11.7   0.2    0.0001      0.16      14      30 ..      79      95 ..      76      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.046
  A2L_zn_ribbon 23 vCieCgasf 31
                   +C+ C+++f
     AJA92932.1 51 FCKACNSEF 59
                   788888876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0001
  A2L_zn_ribbon 14 ilnseqgylvCieCgas 30
                   ++  e+g ++C++C+++
     AJA92932.1 79 LILIERGQYICQKCNST 95
                   555799********986 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.34   5.5e+02      19      26 ..      51      58 ..      47      64 .. 0.80
   2 ?   12.2   0.2   8.1e-05      0.13       9      27 ..      76      96 ..      68     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                EEHHHHHH CS
         Gin 19 ICeeCekk 26
                 C++C+++
  AJA92932.1 51 FCKACNSE 58
                59999875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 8.1e-05
                SSEE-S..SS--EEHHHHHHH CS
         Gin  9 eeGiii..lgkfICeeCekki 27
                 +G+i+  +g++IC++C++ i
  AJA92932.1 76 ANGLILieRGQYICQKCNSTI 96
                34777733589*******988 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.055        90      25      34 ..      50      59 ..      30      61 .. 0.72
   2 ?    9.1   0.0   0.00072       1.2      20      34 ..      82      96 ..      75      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.055
  Zn_ribbon_SprT 25 YrCrrCkgtL 34
                    + C+ C +++
      AJA92932.1 50 HFCKACNSEF 59
                    88****9887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00072
  Zn_ribbon_SprT 20 irrhnYrCrrCkgtL 34
                    i r  Y+C++C +t+
      AJA92932.1 82 IERGQYICQKCNSTI 96
                    56667******9987 PP

>> SAP30_Sin3_bdg  Sin3 binding region of histone deacetylase complex subunit SAP30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.045      19      52 ..      19      54 ..      14      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
  SAP30_Sin3_bdg 19 rpgsskeqLaeaVarHFkaq..pvdEkevitsFlya 52
                      + sk +L+  + +HF a+  ++d ++++ +F++a
      AJA92932.1 19 DEEVSKSKLVPNIDKHFLASleKLDPTKMLKHFCKA 54
                    56889************998645**********987 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.028        45       3      13 ..      50      60 ..      49      63 .. 0.85
   2 ?    9.5   0.2   0.00045      0.73       2      12 ..      86      96 ..      85      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
      zf_UBZ  3 ylCerCgkeip 13
                ++C+ C++e+ 
  AJA92932.1 50 HFCKACNSEFD 60
                69*****9985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00045
      zf_UBZ  2 tylCerCgkei 12
                +y+C++C+++i
  AJA92932.1 86 QYICQKCNSTI 96
                8*******998 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0064        10      50      64 ..      43      57 ..      36      60 .. 0.86
   2 ?    6.2   0.1    0.0076        12      57      70 .]      87     100 ..      82     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0064
  zf-LITAF-like 50 dslkdvehyCpnCga 64
                   d +k  +h+C+ C++
     AJA92932.1 43 DPTKMLKHFCKACNS 57
                   667899*******97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0076
  zf-LITAF-like  57 hyCpnCgallgtyk 70 
                    + C++C++++g y+
     AJA92932.1  87 YICQKCNSTIGEYR 100
                    68*********985 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   0.00044      0.71       3      34 ..      52     101 ..      50     106 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00044
                   ETTTTCEEC..............HEE....TSTTCEEESSSSBEEEECCC CS
  TF_Zn_Ribbon   3 CPnCgstnl..............veD....pergelvCtdCGlVlednsi 34 
                   C+ C+s+++              v +     erg ++C +C + + +  +
    AJA92932.1  52 CKACNSEFDgptgfqieekpneeVANglilIERGQYICQKCNSTIGEYRV 101
                   88888888788888888888888555555589*********776666555 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2      0.59   9.6e+02       6      11 ..      52      57 ..      51      60 .. 0.80
   2 ?   10.8   0.2   0.00024       0.4       5      13 ..      88      96 ..      85      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.59
        SR1P  6 CqtCna 11
                C+ Cn 
  AJA92932.1 52 CKACNS 57
                999995 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
        SR1P  5 vCqtCnatI 13
                +Cq+Cn tI
  AJA92932.1 88 ICQKCNSTI 96
                9*******9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.083   1.4e+02       7      12 ..      52      57 ..      49      68 .. 0.78
   2 ?    8.5   0.7   0.00098       1.6      20      31 ..      85      96 ..      85      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.083
     zf-RRN7  7 CgvCgc 12
                C +C++
  AJA92932.1 52 CKACNS 57
                777776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00098
     zf-RRN7 20 GfyyCrrChtqe 31
                G+y+C+ C + +
  AJA92932.1 85 GQYICQKCNSTI 96
                9*******8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 767.87
//
Query:       AJA92933.1  [L=385]
Description: putative spore coat polysaccharide biosynthesis protein SpsC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.9e-121  405.2   0.0   3.3e-121  405.0   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    9.8e-11   41.4   0.2    1.7e-10   40.6   0.2    1.4  1  Aminotran_1_2    Aminotransferase class I and II
    2.8e-06   26.6   0.4    5.7e-06   25.5   0.4    1.4  1  Aminotran_5      Aminotransferase class-V
    2.5e-05   23.0   0.6    3.8e-05   22.4   0.6    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.048   13.5   0.0    1.6  1  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
      0.034   14.1   0.1       0.95    9.5   0.0    2.8  3  DUF1967          Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.0   0.0  1.1e-124  3.3e-121       3     360 ..      21     381 ..      19     382 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.0 bits;  conditional E-value: 1.1e-124
                      HHHHHHHHHHHHTSS-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT CS
  DegT_DnrJ_EryC1   3 keeeleaveevlksgwltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdt 96 
                       +e+ + + ++lk+ +lt gp+ e+FE++f++y ++k+a+avs++taAlhl+L+alg++++deVI+p ltFva anavl ++akp+ vD++++ 
       AJA92933.1  21 SKEDEKIISKTLKQSMLTLGPQLEKFEADFCKYSKAKYAVAVSNCTAALHLSLKALGIKENDEVIIPDLTFVADANAVLACNAKPIAVDINKEN 114
                      678889999************************************************************************************* PP

                      SSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHH CS
  DegT_DnrJ_EryC1  97 ynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGavvtndeel 190
                      + ++ +++++ it+rtkaI+pVh+yGqv++++++ ++a++ +lkvieD+AhA+G+ +k k+vG++g +++fSFyptKn+tt+eGG+v+tn++++
       AJA92933.1 115 FFLSISNVKKNITKRTKAIIPVHIYGQVCNIEEILDMAKDNNLKVIEDCAHAVGTFHKSKHVGTIGHTGCFSFYPTKNITTAEGGMVTTNSKNI 208
                      ********************************************************************************************** PP

                      HHHHHHHHBTTCECCTCSSCECCS.......S---B-B-BHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESC CS
  DegT_DnrJ_EryC1 191 aekarvlrnhGlkrkaekryvgev.......elGynyrlteiqAAiglaqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhl 277
                      aek+r+lr+hG+ ++ + ry +e        e+Gynyrl+ei +A+g++qL+r++++++ R+++  +y+++L++++g++ + +  +++ h++hl
       AJA92933.1 209 AEKVRQLRSHGMTKSLKSRYSSEYpwvfdivEPGYNYRLDEIRSALGITQLKRIKKINELRKKASFYYHRNLKNIPGIILPDMVRDRS-HSYHL 301
                      **************99*************************************************************98877777777.***** PP

                      EEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
  DegT_DnrJ_EryC1 278 yavlveeeaevkrdelvealkeegigtrvhypnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                      y+++v + ++++r++l ++lke+gi t+v+   p+h++ +y++ ++++  ++ n+ ++++++l+Lpl p+++++++d V++ +
       AJA92933.1 302 YTIRVTKPFKLSRNQLYKKLKENGIRTTVYW-MPIHEYAAYRKFTKKS--NVVNTTKIYDEILALPLFPNISKKHQDAVIKVI 381
                      ********99********************9.7**********97664..69***************************9976 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.2   5.8e-14   1.7e-10      43     212 ..      41     192 ..       6     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.8e-14
                    TTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHH CS
  Aminotran_1_2  43 idglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeea 138
                    ++ l ++e + +k+ +        ++ av v++++ al   l++l  +   de+++pd+t+    n++ ++ ++ + + ++ +e+f l + ++++ 
     AJA92933.1  41 PQ-LEKFEADFCKYSK--------AKYAVAVSNCTAALHLSLKALG-IKENDEVIIPDLTFVADANAVLACNAKPIAVDIN-KENFFLSISNVKKN 125
                    33.4677777777777........777*******************.********************************88.99************ PP

                    HTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.....HGGSTTSTT CS
  Aminotran_1_2 139 lkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat.....ranveeepn 212
                    +++      +tk i+   p +  G+v++ ee+ ++   ak +nl ++ D a+a++ f ++++v t     ++ + +  n
     AJA92933.1 126 ITK------RTKAII---PVHIYGQVCNIEEILDM---AKDNNLKVIEDCAHAVGTFHKSKHVGTightgCFSFYPTKN 192
                    ***......99***9...88889************...*******************9887666666666444444444 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4   1.9e-09   5.7e-06      53     307 ..      48     295 ..      31     330 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.9e-09
                  HHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBET CS
  Aminotran_5  53 aelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsn 150
                  a++ + ++++  + +s++t a+ l +++l+  +k+ de+++ ++   a    ++ +++++ + v++   +e+  l +++++k+++++tk+++  h+  
   AJA92933.1  48 ADFCKYSKAKYAVAVSNCTAALHLSLKALG--IKENDEVIIPDLTFVADA-NAVLACNAKPIAVDIN--KENFFLSISNVKKNITKRTKAIIPVHI-- 138
                  56777777788899***************5..9***************99.6777777767766543..3689999****************9995.. PP

                  TTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS--.....-HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHC CS
  Aminotran_5 151 vtGtiqpveeigklakkkgalvlvDaaqavghipi.....dvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleettfae 243
                    G +  +eei ++ak+++  v+ D a avg  +       +  +g+ f +  +  +  ++G  v   +k++ ek+++l   g    ++sl+++  +e
   AJA92933.1 139 -YGQVCNIEEILDMAKDNNLKVIEDCAHAVGTFHKskhvgTIGHTGC-FSFYPTKNITTAEGGMVTTNSKNIAEKVRQLRSHGM---TKSLKSRYSSE 231
                  .8***************************985443111114566778.555555558999998888999999999999988888...77776666678 PP

                  TTGGGS.SS--HHHHH...HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
  Aminotran_5 244 apskfeaGTpnvagii...glgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                   p+ f          +    ++ al + +   +++i++  k+++ y +  lk++pg+ l +  + +r
   AJA92933.1 232 YPWVFDI--VEPGYNYrldEIRSALGITQLKRIKKINELRKKASFYYHRNLKNIPGIILPD-MVRDR 295
                  9999984..3333333011456788888888999999999999999999999999998743.23333 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.6   1.3e-08   3.8e-05      52     184 ..      41     173 ..      38     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-08
                      HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHH.HHHHHHHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEEE CS
  Cys_Met_Meta_PP  52 ptrsvleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYgg.tqrllkkvlkklgievkfvdt.sdleelekaikentklvy 142
                      p  + +e+  ++  +++ a+avs  +aA+++++ al +k+ de+++ d  +   ++++l   +k + ++++  +   ++++++k i+++tk++ 
       AJA92933.1  41 PQLEKFEADFCKYSKAKYAVAVSNCTAALHLSLKALgIKENDEVIIPDLTFVAdANAVLACNAKPIAVDINKENFfLSISNVKKNITKRTKAII 134
                      677899****************************997899********9997625566777777799999999875899**************6 PP

                      EESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-G CS
  Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqrp 184
                         p  +  +v+ ie+i+++ak++++ v+ D + a + + + 
       AJA92933.1 135 ---PVHIYGQVCNIEEILDMAKDNNLKVIEDCAHAVGTFHKS 173
                      ...999***********************9999888887765 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05     0.048       2      28 ..      30      56 ..      29      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                     HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Surfac_D-trimer  2 aaLrQrveaLeGklqrLqnafsqYkKa 28
                     ++L+Q +  L  +l ++++ f +Y Ka
       AJA92933.1 30 KTLKQSMLTLGPQLEKFEADFCKYSKA 56
                     79************************9 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00032      0.95      49      68 ..      72      91 ..      69      92 .. 0.92
   2 ?   -2.4   0.0       1.6   4.8e+03      38      52 ..     212     226 ..     201     227 .. 0.74
   3 ?    0.9   0.0      0.15   4.4e+02      41      56 ..     312     327 ..     310     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00032
                HHHTTT--TT-EEEETTEEE CS
     DUF1967 49 aLrkaGakeGdtVrIgdveF 68
                 L+++G+ke d+V I d++F
  AJA92933.1 72 SLKALGIKENDEVIIPDLTF 91
                599**************999 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                 HHHHHHTTHHHHHHT CS
     DUF1967  38 arrLkklGvedaLrk 52 
                  r+L++ G+ + L+ 
  AJA92933.1 212 VRQLRSHGMTKSLKS 226
                 578999999999985 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.15
                 HHHTTHHHHHHTTT-- CS
     DUF1967  41 LkklGvedaLrkaGak 56 
                 L ++ + ++L++ G++
  AJA92933.1 312 LSRNQLYKKLKENGIR 327
                 7888999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2792.45
//
Query:       AJA92934.1  [L=106]
Description: Sjogren'S syndrome/scleroderma autoantigen 1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-10   40.4   1.7    3.7e-10   39.8   1.7    1.3  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
  ------ inclusion threshold ------
      0.072   12.6   2.0       0.14   11.7   2.0    1.6  1  TF_Zn_Ribbon   TFIIB zinc-binding
       0.47    9.9   4.9        1.8    8.1   4.7    2.0  1  zf-ribbon_3    zinc-ribbon domain
        0.9    9.9   3.6         16    5.9   0.0    2.3  2  zinc_ribbon_9  zinc-ribbon


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   1.7   8.2e-14   3.7e-10       5      40 .]      11      44 ..       7      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 8.2e-14
  Auto_anti-p27  5 elLlkGwtMLaetCpvC.gvPLmrdrkggkvyCvaCd 40
                   e+Ll G+t+L+e Cp C gv  m+d   g+ +Cv+C+
     AJA92934.1 11 EMLLSGATLLSEPCPYCkGVRVMKD---GDALCVSCG 44
                   89***************99****94...799*****6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.0   3.2e-05      0.14       3      26 ..      24      44 ..      22      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                  ETTTTCEECHEETSTTCEEESSSS CS
  TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCG 26
                  CP+C++ ++  D   g+ +C +CG
    AJA92934.1 24 CPYCKGVRVMKD---GDALCVSCG 44
                  ******887777...********9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.7   0.00041       1.8       5      24 ..      24      45 ..      22      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00041
  zf-ribbon_3  5 CPnCGa..plssddnvCpyCGt 24
                 CP+C+   + +++d  C +CG+
   AJA92934.1 24 CPYCKGvrVMKDGDALCVSCGK 45
                 ****996449***********6 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.8    0.0054        24      20      29 ..      21      29 ..      15      32 .. 0.83
   2 ?    5.9   0.0    0.0035        16      15      29 ..      31      45 ..      28      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0054
  zinc_ribbon_9 20 sdvlCPhCgg 29
                   s++ CP+C+g
     AJA92934.1 21 SEP-CPYCKG 29
                   678.****98 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0035
  zinc_ribbon_9 15 spdedsdvlCPhCgg 29
                   + ++d d+lC +Cg 
     AJA92934.1 31 RVMKDGDALCVSCGK 45
                   457899999****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1431  (0.0798148); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 808.20
//
Query:       AJA92935.1  [L=352]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2521.36
//
Query:       AJA92936.1  [L=228]
Description: rRNA metabolism protein, SBDS family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-20   73.2   0.7    2.5e-20   72.3   0.7    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.7e-16   60.2   0.5    2.6e-16   59.7   0.1    1.5  2  SBDS_C    SBDS protein C-terminal domain
      0.007   16.4   0.0      0.015   15.4   0.0    1.6  1  EFG_C     Elongation factor G C-terminus
  ------ inclusion threshold ------
      0.042   14.1   0.0         10    6.4   0.0    2.1  2  Big_3_2   Bacterial Ig-like domain


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.7   5.6e-24   2.5e-20       2      88 .]       4      90 ..       3      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 5.6e-24
                -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HHHHH CS
        SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsaeerk 88
                v++v+y  + ++Fei+v+++ + +y+ gk  ++s++l s++i+tn+ kG++as++ l k+f+t++ ++i++++++kGe+++++e+rk
  AJA92936.1  4 VTVVKYSYETEKFEILVKPDPAFDYKLGKISEISKILVSDEIYTNSGKGTRASNELLLKVFKTDDTTKIAEIMMQKGELNLTTEQRK 90
                899*********************************************************************************997 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.2   5.3e+03      23      73 ..      69      87 ..      54      93 .. 0.53
   2 !   59.7   0.1   5.8e-20   2.6e-16       2      98 ..      97     191 ..      96     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                -HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE- CS
      SBDS_C 23 tttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcp 73
                tt++ e                                i++++ +l++t +
  AJA92936.1 69 TTKIAE--------------------------------IMMQKGELNLTTE 87
                333333................................4444444444443 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 5.8e-20
                 HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHHHHHHHHHH......S.EE CS
      SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkilklieqvesqk.vaekewe 98 
                 +k+i++++++  v+p+t+ p+++ +Ie+a+++ ++sv++ k+ ++Q+ +++++L+ +ip + ++  l+i++p   ++++ + +  ++s   +++++w+
  AJA92936.1  97 RKQIVTFISKTYVDPRTHLPHPPLRIEQAMTDGRVSVDPFKNPDEQIKDIVEKLRPIIPLKTENLTLEISVP---AQYVAQSYTVLKSTGsLKKEDWQ 191
                 79**********************************************************************...55555555555443212223343 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-06     0.015       8      73 ..     162     226 ..     160     228 .] 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-06
                 EEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEE CS
       EFG_C   8 kveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsm 73 
                 ++ei+vp +yv++ ++ l+s  G +++ + + +g  +   eiP+a   +  ++L ++TkG++++++
  AJA92936.1 162 TLEISVPAQYVAQSYTVLKST-GSLKKEDWQPNGSLKAILEIPAAARPNVIDRLGAITKGTANVEV 226
                 689************888776.555555555589999999**********************9876 PP

>> Big_3_2  Bacterial Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0022        10      17      91 ..      38     116 ..      17     128 .. 0.81
   2 ?    5.7   0.0    0.0037        17      56      94 ..     157     196 ..     153     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
     Big_3_2  17 mvtsgavw..elglgaaskaalrlsGi.tddasGidsaklrvidsdgsvyssvnvsydegqgtvsipv.asakksglfP 91 
                  +++++++  + g g+ + ++l l+ + tdd++ i+++ ++  + + + ++ +++  d+ ++ v+  + +++ + + +P
  AJA92936.1  38 KILVSDEIytNSGKGTRASNELLLKVFkTDDTTKIAEIMMQKGELNLTTEQRKKMTSDKRKQIVTFISkTYVDPRTHLP 116
                 377778788899*************9999************9999*************999999876656666666666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0037
     Big_3_2  56 idsdgsvyssvnvsydegqgtvsipvasakksglfPss.l 94 
                 + ++ +++ sv+++y +++ tv  + +s kk ++ P++ l
  AJA92936.1 157 KTENLTLEISVPAQYVAQSYTVLKSTGSLKKEDWQPNGsL 196
                 567889999***************************9855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1787.16
//
Query:       AJA92937.1  [L=105]
Description: hypothetical protein T478_0934 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 735.97
//
Query:       AJA92938.1  [L=458]
Description: hypothetical protein T478_0018 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00018   21.9   0.1      0.011   16.1   0.1    2.3  2  Radical_SAM  Radical SAM superfamily
     0.0028   17.9   0.0     0.0058   16.9   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
     0.0084   16.2   0.0      0.021   14.9   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.9e-06     0.011       5      64 ..     158     216 ..     155     228 .. 0.77
   2 ?    3.6   0.0     0.013        75      94     143 ..     221     271 ..     217     281 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                  SEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHH CS
                  xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   5 rgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfv 64 
                  + C+  CsfC r+    + +e + +++  +e+++ v+e   e  +  ++++gg+p+  p ++
   AJA92938.1 158 QTCHAYCSFCFRWPQfvGMDEMKFAMKEGDELAQYVREH-PE--ISDILFTGGDPMIMPAKI 216
                  57************7666666666666666666666555.34..***********9887655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                  HHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                  xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  94 lerllelg...vdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                  +++ll++    + ++ +g +a+++ +  k +   ++++e+le++++ +++gi+
   AJA92938.1 221 IDTLLDADlpnLKTIRIGTKALSYWP-YKFV-SDKDYQETLETFRRVNKKGIH 271
                  56666666666777777777777773.4555.5699***************98 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.6e-07    0.0058      12      65 ..     157     211 ..     142     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.6e-07
     Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPll 65 
                  + C   C++Cf         + +f  +  +e+ + + + ++i+++ ++GG+P+ 
  AJA92938.1 157 GQTCHAYCSFCFRWPQFVGMDEMKFAMKEGDELAQYVREhPEISDILFTGGDPMI 211
                 578*********55555555666677899999*9999854999**********98 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.5e-06     0.021       7     106 ..     159     260 ..     155     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-06
     Fer4_14   7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeey.pe.kkiwletngtleiele..ktpdl 101
                  C+  C +C++  ++    + +++ ++ ++   +   ++ +i+ + +tGG+P++    k +   ++ l +   p+ k i++ t ++     +  + +d+
  AJA92938.1 159 TCHAYCSFCFRWPQFVGMDEMKFAMKEGDELA-QYVREHPEISDILFTGGDPMIM-PAKIFSAYIDTLLDADlPNlKTIRIGTKALSYWPYKfvSDKDY 255
                 69********8777755444444444443333.33334444678*********65.7888888888887776555588888888876655552233444 PP

     Fer4_14 102 kekle 106
                 +e+le
  AJA92938.1 256 QETLE 260
                 44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2709.15
//
Query:       AJA92939.1  [L=75]
Description: hypothetical protein T478_0604 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 465.10
//
Query:       AJA92940.1  [L=206]
Description: putative membrane protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-14   53.3  12.2    7.3e-14   51.9  12.2    1.6  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
  ------ inclusion threshold ------
       0.12   12.6   0.4       0.18   12.1   0.4    1.3  1  Orf78       Orf78 (ac78)
       0.16   12.4   1.5       0.28   11.7   1.5    1.4  1  Ets         Ets-domain


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9  12.2   1.2e-17   7.3e-14      22     165 ..      46     198 ..      31     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.2e-17
  EMC3_TMCO1  22 lvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsemmmdqmkpmivtmipqiliffwlnsffsgfvvak 120
                  +gi+  ++ + ++k+++d+ k++++ k  ++ qk+  ++ +++d+ + +  +k+++++++ ++emm++ ++pm++t+ip +lif+ +   +  ++va 
  AJA92940.1  46 GFGIALNVINSGIRKKMVDQVKQRRITKEVRAWQKERMAAFRSKDQARIANANKKSAYMNKMNMEMMQMNIRPMMITIIPLMLIFYFVLPQLFSYTVAL 144
                 5789999******************************************************************************99998888888888 PP

  EMC3_TMCO1 121 lpfpl......tgrfksllqrgl......esldvrfvssiswYflcsfglsqiirkl 165
                  p+pl      +  f+ l+ + +         d +  +   wYfl+s+++s++i kl
  AJA92940.1 145 SPIPLnvipgdW--FE-LTCTAIkveegaYCQDENALYLWAWYFLSSIAFSGLIMKL 198
                 888883333222..33.444445447333223333445668*************987 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   3.1e-05      0.18      42      88 ..      87     134 ..      50     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
       Orf78  42 saaeknditekesn.aaekaqalnillisllavvcvlvllyviyYfvi 88 
                 +++++ +i +++++ a  ++ +++++ + +  +++ ++ l++i+Yfv+
  AJA92940.1  87 RSKDQARIANANKKsAYMNKMNMEMMQMNIRPMMITIIPLMLIFYFVL 134
                 222333333333332344455556666666667777777999999997 PP

>> Ets  Ets-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.5   4.6e-05      0.28      13      62 ..      69     119 ..      60     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
         Ets  13 ps.kssiiaWtdkeegeFklvdpeevarlWgkrknkpkmnyeklsralRyy 62 
                 ++  +++ aW++++   F+ +d++++a+  +k    +kmn+e ++ ++R +
  AJA92940.1  69 RRiTKEVRAWQKERMAAFRSKDQARIANANKKSAYMNKMNMEMMQMNIRPM 119
                 555778889**************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1473  (0.0821574); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1461.28
//
Query:       AJA92941.1  [L=168]
Description: hypothetical protein T478_0526 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.035   13.3   0.3      0.086   12.0   0.2    1.6  2  Phage_HK97_TLTM  Tail length tape measure protein
      0.093   12.8   0.2       0.25   11.4   0.1    1.8  2  Coiled-coil_56   Coiled-coil domain-containing protein 56
       0.13   12.0   0.0       0.23   11.2   0.0    1.3  1  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like


Domain annotation for each model (and alignments):
>> Phage_HK97_TLTM  Tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.031   1.8e+02      26      66 ..      18      56 ..      16      60 .. 0.82
   2 ?   12.0   0.2   1.4e-05     0.086     167     269 ..      51     160 ..      32     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.031
  Phage_HK97_TLTM 26 pGlvilaAGafYllYqkqkqAresAreyAkeieevkeklkk 66
                      G +i++  +fY  Y   +qA+    ++ +ei+ ++e++++
       AJA92941.1 18 IGAIIIGVIVFYF-Y-SADQAKIRGFAFGNEIQTLQEEIQD 56
                     6888888888774.4.57899999999999**999999876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.4e-05
  Phage_HK97_TLTM 167 irqqaaeqnkvkrsllilNeekaesnklldlgNkklaetvkLleeikkveiPvrvkea......evnkkikdllkkseRdlelsklkgeakvir 254
                       ++   eq k   s+   Ne+      ++ +g k l+  ++Ll++ ++ + P    +            ++  ++  e  l   k  +e  +ir
       AJA92941.1  51 QEEIQDEQGKFISSIAKWNEKTISDDEMIRIGEKHLETFNGLLDKYDELHPPDAFIKSvkllrlS----LEYQIESHEHRLGWIKNGDESELIR 140
                      44545568899999999***********************************8755443444440....4555555555555555555555554 PP

  Phage_HK97_TLTM 255 .....eaefeAkDaGlnsdd 269
                           ++ feA+ aGl+s +
       AJA92941.1 141 sqeltQLSFEAEQAGLKSFN 160
                      22222678999999998543 PP

>> Coiled-coil_56  Coiled-coil domain-containing protein 56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.1e-05      0.25      44      78 ..       3      37 ..       1      53 [. 0.88
   2 ?   -2.8   0.0       1.1   6.7e+03      28      42 ..     134     148 ..     115     155 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
  Coiled-coil_56 44 klqkrrrrnlltGlaiGglvlgiygytfysvkqek 78
                    k + ++++n++    iG++++g+  + fys  q k
      AJA92941.1  3 KRKAKKSKNKFPIAIIGAIIIGVIVFYFYSADQAK 37
                    556678899999999*****************988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
  Coiled-coil_56  28 aqlefmrkvelaqlq 42 
                     ++ e++r  el ql 
      AJA92941.1 134 DESELIRSQELTQLS 148
                     456677777777665 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.23      90     149 ..       7      66 ..       2      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
  EMC3_TMCO1  90 dqmkpmivtmipqiliffwlnsffsgfvvaklp.fpltgrfksllqrglesldvrfvssis 149
                 ++ k+++ + i+  +i++++ ++f     ak+  f +  +++ +lq++++++ ++f+ssi 
  AJA92941.1   7 KKSKNKFPIAIIGAIIIGVIVFYFYSADQAKIRgFAFGNEIQ-TLQEEIQDEQGKFISSIA 66 
                 67799*******9999999999999999999999********.889*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      906  (0.0505327); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1178.32
//
Query:       AJA92942.1  [L=179]
Description: hypothetical protein T478_1100 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1282.95
//
Query:       AJA92943.1  [L=196]
Description: PAP2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-24   83.7   1.1    1.5e-23   83.1   1.1    1.2  1  PAP2      PAP2 superfamily
    3.9e-12   46.2   5.3    1.1e-11   44.8   5.3    1.6  1  PAP2_3    PAP2 superfamily
    7.5e-06   26.4   0.8    7.5e-06   26.4   0.8    2.0  2  PAP2_C    PAP2 superfamily C-terminal
  ------ inclusion threshold ------
      0.017   15.2   1.6       0.16   12.0   0.4    2.0  2  DUF1097   Protein of unknown function (DUF1097)
        1.4    8.9   0.0        1.4    8.9   0.0    2.8  4  OppC_N    N-terminal TM domain of oligopeptide transport perm
          2    8.6   6.6       0.74    9.9   3.4    1.9  2  DUF2198   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1   1.1   4.9e-27   1.5e-23       3     127 ..      59     181 ..      57     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 4.9e-27
        PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletses.....keakesfPSgHsafafalalllalllrrkrkkiglvllalillllav 96 
                 ++ll+ l+l+ llt+ +K  v+r RPf  +   +l + v+  +  +s     ++ + +fPSgH+a+++++a++++++l +k+++      + +++++ +
  AJA92943.1  59 MILLILLVLSSLLTGYIKCGVDRDRPFLDWLGSELPFEVEPDS--FSlfcegRSWTAGFPSGHAARSAMFAFVMVYVLSEKFPR-----GVHLIWIYPI 150
                 6889999999999*******************99999865432..33478999999****************************.....899******* PP

        PAP2  97 lvalsRlylgvHflsDvlaGlliGialaala 127
                 l+++sR+y+  H++ Dv++G+++G++la ++
  AJA92943.1 151 LMSFSRIYVLQHYPLDVIGGFVLGVLLAGYV 181
                 ***************************9865 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   5.3   3.8e-15   1.1e-11      40     188 ..      39     178 ..      29     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.8e-15
      PAP2_3  40 hfqvtllvlvllflrrrerlreflttlllatllgllvyalfPaagPrll...eeagfvdtvaaaslagalrdgasravllrgtienglaafPSlHvawa 135
                 ++++++ +++l+++++r+ +  +l++l+l+ ll+  +   + +++P+l    +e  f       +++    d++s  +  +g   +  a fPS H+a +
  AJA92943.1  39 FVMLPFSIILLIIRKTRKIGMILLILLVLSSLLTGYIKCGVDRDRPFLDwlgSELPF-------EVEP---DSFS--LFCEGR--SWTAGFPSGHAARS 123
                 56778888888889********************************55543322222.......2222...2222..222332..44556********9 PP

      PAP2_3 136 llvalalwrlrrkr..llrvlalllnvlmivatvatgnHYlvDviaGvalalvai 188
                  ++a++++++ + +  +   l++++++lm ++ ++   HY +Dvi+G++l+++ +
  AJA92943.1 124 AMFAFVMVYVLSEKfpRGVHLIWIYPILMSFSRIYVLQHYPLDVIGGFVLGVLLA 178
                 99999999999999445556799***************************99865 PP

>> PAP2_C  PAP2 superfamily C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.47   1.4e+03      15      40 ..      41      65 ..      31      75 .. 0.47
   2 !   26.4   0.8   2.5e-09   7.5e-06       8      69 ..     117     178 ..     115     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
      PAP2_C 15 tlavlfileyspkklailkvilllla 40
                +l + +il   +k+ + + +ill+l+
  AJA92943.1 41 MLPFSIILLIIRKTRK-IGMILLILL 65
                3334444444444432.233333332 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 2.5e-09
      PAP2_C   8 SGHtvvltlavlfileyspkklailkvillllallglfliiasrkHYtvDVllglyittlvf 69 
                 SGH++   +++++++++ ++k+    ++++++ +l +f+ i+  +HY +DV+ g+++ +l+ 
  AJA92943.1 117 SGHAARSAMFAFVMVYVLSEKFPRGVHLIWIYPILMSFSRIYVLQHYPLDVIGGFVLGVLLA 178
                 9*********************99999*****************************999875 PP

>> DUF1097  Protein of unknown function (DUF1097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.053   1.6e+02      78     118 ..      39      79 ..      25      93 .. 0.78
   2 ?   12.0   0.4   5.5e-05      0.16      78     144 ..     123     185 ..     108     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.053
     DUF1097  78 lvvgivaflmvllakipllsfiPaiflGlastfatllktav 118
                 +v+  ++++++++ k++++ +i+ i+l l+s ++ + k +v
  AJA92943.1  39 FVMLPFSIILLIIRKTRKIGMILLILLVLSSLLTGYIKCGV 79 
                 37778999999***********9999999999887777555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5.5e-05
     DUF1097  78 lvvgivaflmvllakipllsfiPaiflGlastfatllktavalsnpllavivslllGavf.Gylseal 144
                 +++++++++ vl  k+p   + + +++   + f+ ++     l++  l vi  ++lG+++ Gy+s++l
  AJA92943.1 123 SAMFAFVMVYVLSEKFPR-GVHLIWIYPILMSFSRIYV----LQHYPLDVIGGFVLGVLLaGYVSKRL 185
                 367777777777777777.999************8888....**********************9976 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.9         6   1.8e+04      22      26 ..      46      50 ..      40      51 .. 0.52
   2 ?    8.9   0.0   0.00047       1.4      18      36 ..      57      75 ..      52      86 .. 0.90
   3 ?   -1.8   0.2         1   3.1e+03      15      25 ..     123     133 ..     122     135 .. 0.74
   4 ?   -0.4   0.2      0.39   1.2e+03      17      28 ..     167     178 ..     164     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 6
      OppC_N 22 illll 26
                i+ll+
  AJA92943.1 46 IILLI 50
                33333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00047
      OppC_N 18 vglvilllllliaifaPli 36
                +g+++l+ll+l +++  +i
  AJA92943.1 57 IGMILLILLVLSSLLTGYI 75
                8*************99988 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1
      OppC_N  15 lAvvglvilll 25 
                  A++++v++ +
  AJA92943.1 123 SAMFAFVMVYV 133
                 69999998765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.39
      OppC_N  17 vvglvillllll 28 
                 v+g ++l +ll+
  AJA92943.1 167 VIGGFVLGVLLA 178
                 899999999875 PP

>> DUF2198  Uncharacterized protein conserved in bacteria (DUF2198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.4   0.00025      0.74       7      44 ..      41      76 ..      38      78 .. 0.92
   2 ?   -1.8   0.1       1.1   3.4e+03      56      66 ..     171     181 ..     144     186 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
     DUF2198  7 vlPclLvvlftrvTynhyvGllltvaLivasvykgYtk 44
                +lP+ +++l+ r T+   +G++l ++L++ s++ gY k
  AJA92943.1 41 MLPFSIILLIIRKTR--KIGMILLILLVLSSLLTGYIK 76
                79999*******999..8******************75 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
     DUF2198  56 llaGflyakkm 66 
                  ++G l+a ++
  AJA92943.1 171 FVLGVLLAGYV 181
                 34455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1441.88
//
Query:       AJA92944.1  [L=164]
Description: hypothetical protein T478_0341 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1179.03
//
Query:       AJA92945.1  [L=219]
Description: putative diaminohydroxyphosphoribosylaminopyrimidine reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-48  164.1   0.2    3.8e-48  164.0   0.2    1.0  1  RibD_C       RibD C-terminal domain
  ------ inclusion threshold ------
      0.018   14.6   0.3      0.027   14.0   0.3    1.2  1  DUF2067      Uncharacterized protein conserved in archaea (DU
      0.056   12.0   0.0       0.07   11.7   0.0    1.1  1  Semenogelin  Semenogelin


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.0   0.2   6.4e-52   3.8e-48       1     200 []       8     215 ..       8     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 164.0 bits;  conditional E-value: 6.4e-52
                 -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEEEETTS-S-TTSH.HHHSS CS
      RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvVvdstlrvpldak.vltdd 98 
                 p+v+l +a++lDGk+  ++++   +++++++ +vh+lr+++dailvG +tv +d+p ltvr++k+         ++p+r+++ds+ +++ + k + t +
  AJA92945.1   8 PKVTLSAAITLDGKIGQKNKQIV-LSSKTDKIRVHKLRSKSDAILVGKNTVEQDDPLLTVRYAKG---------KNPIRIILDSHGTIKNNSKiIKTCK 96 
                 89*****************9888.*****************************************.........9******************555556 PP

                 .S-EEEEESSCSCHHHHHHCC.....E......SE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--T.TSBCSSSSST-SS. CS
      RibD_C  99 .aptlvatteeadkekveklk.....v......rvdlkelleeLkergirsllveGGatLagsllraglvDelrlyiaPkllGg.agktlfdgegfka. 183
                   pt+++t+e ++k ++++l+     v      +v++ +ll++L+++gi+++l+eGG+tL++s+l+++l+De+++   P++lG+ ++ +lf+g  f++ 
  AJA92945.1  97 rVPTIIVTSEIISKPNLNRLQklpidVivcgktQVNITKLLSILSKKGIKTVLLEGGGTLNRSFLKKNLIDEMIIALTPYVLGSkNTVSLFEGMSFPEl 195
                 89*******************999772568889*****************************************************************9 PP

                 ...EEEEEEEEEEETTEEEE CS
      RibD_C 184 ...lklklvksealgegvvl 200
                    l lkl+++++ g++++l
  AJA92945.1 196 ktkLPLKLKNVQKSGNEIIL 215
                 99999***********9986 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   4.6e-06     0.027      33     109 ..      73     157 ..      62     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-06
     DUF2067  33 n..rllievyGtekeikdiirrikellre......klkkekrglfkyslsdllreag.apvppdvLvdaLkllGykaelre.envlk 109
                 n  r++ + +Gt k+  +ii++ k++ +         k++  +l+k++++ ++   g ++v++  L  +L+++G+k+ l e +++l 
  AJA92945.1  73 NpiRIILDSHGTIKNNSKIIKTCKRVPTIivtseiISKPNLNRLQKLPIDVIV--CGkTQVNITKLLSILSKKGIKTVLLEgGGTLN 157
                 4557777777777777777776666666566677778899999**********..5559*********************9999886 PP

>> Semenogelin  Semenogelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.2e-05      0.07     524     580 ..      19      75 ..       5      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
  Semenogelin 524 kgksgqsadskqdll.sheqkgrykqesseshnivitehevaqddh.ltqqynedrnpi 580
                   gk gq    kq +l s+ +k r ++  s+s  i++ +  v qdd  lt +y + +npi
   AJA92945.1  19 DGKIGQK--NKQIVLsSKTDKIRVHKLRSKSDAILVGKNTVEQDDPlLTVRYAKGKNPI 75 
                  5777775..577666156789***********************963699********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1600.75
//
Query:       AJA92946.1  [L=115]
Description: hypothetical protein T478_0230 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 823.63
//
Query:       AJA92947.1  [L=138]
Description: polyketide cyclase/dehydrase and lipid transport [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-09   37.0   0.0    4.1e-09   36.8   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.6e-07   30.9   0.0    6.2e-07   29.7   0.0    1.6  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   4.6e-13   4.1e-09       1     143 []       1     137 [.       1     137 [. 0.87

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 4.6e-13
                      EEEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEEETTTTEEEEEEE.SSS-TSEEEEEEE CS
  Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggrgtvreelvevdpegrllsyrivkpvpvanyvatwtv 94 
                      m+++++sv+i+a+ ekVw+++sd +n p+   + ++v+  +++g+  ++ ++++ ++r++   + v++ p + +++  +  + +v  ++  +t+
       AJA92947.1   1 MAEIKTSVTINATQEKVWDVISDIDNEPKFWKGTKEVRNISKNGN--QISREITIAFRDQKCLQDVTIVP-KETIKAVF--TEGVIVGEKILTL 89 
                      78999************************9999999988888999..999*******9555555566669.99999999..5999999****** PP

                      EECCETEEEE..EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc2  95 tpdgggtrvt..wtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                      ++ +  ++++  w++ +   + +g+f ++ ++k +k+  e++L+++k+++e
       AJA92947.1  90 KDMENSCELEalWDVKLS--GKMGMF-TGIIKKHIKSGTEQALQAIKEEVE 137
                      **********77777555..455887.7889****************9998 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.9e-11   6.2e-07       1     128 [.      10     131 ..      10     133 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.9e-11
                     ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEEEEEEEECTECCEEECEEE CS
  Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfkslegkWtieslppnsggtrt 95 
                     ++a  ++v+++++d+++ p+f+++ ++v+ ++++++++s   e+  +   ++   +vt +p e i+  + eg    ++g+  ++  +  ++++++
      AJA92947.1  10 INATQEKVWDVISDIDNEPKFWKGTKEVRNISKNGNQISR--EITIAFRDQKCLQDVTIVPKETIKAVFTEG---VIVGEKILTLKDM-ENSCEL 98 
                     7899*******************************97666..455555556666777667777644444442...2233333333332.234444 PP

                     EEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc  96 kvalevdfkfaspllgalvgqvaervldellaa 128
                     +   +v++ +++++   ++++ +++  ++ l+a
      AJA92947.1  99 EALWDVKLSGKMGMFTGIIKKHIKSGTEQALQA 131
                     444444445666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1040.27
//
Query:       AJA92948.1  [L=296]
Description: GHMP kinase, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.2   0.5    2.2e-09   37.4   0.5    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.095   12.7   0.0       0.26   11.3   0.0    1.8  1  SASP            Small, acid-soluble spore proteins, alpha/bet


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.5   2.5e-13   2.2e-09       7      66 .]      92     151 ..      86     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.5e-13
                     SSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
  GHMP_kinases_N   7 eiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66 
                     ++Pvg G+G SAA+a++l  Al+++lg +l++ + a+ a+      +++ gDv as++Gg
      AJA92948.1  92 DVPVGYGFGCSAAVALSLSIALNDALGCKLSKIQVAQIAHDVEIDCKTGLGDVLASYHGG 151
                     79****************************99999*****77777**************8 PP

>> SASP  Small, acid-soluble spore proteins, alpha/beta type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     3e-05      0.26      43      55 ..     197     212 ..     185     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                 HH...HHHHHHHHHHH CS
        SASP  43 sv...GGemvkklveq 55 
                 s+   GG+mvkkl+e+
  AJA92948.1 197 SInglGGKMVKKLIES 212
                 45566*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2144.55
//
Query:       AJA92949.1  [L=159]
Description: hypothetical protein T478_0029 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0001   21.9   7.5    0.00013   21.6   7.5    1.1  1  HMMR_N         Hyaluronan mediated motility receptor N-termin
    0.00013   21.0   6.8    0.00016   20.7   6.8    1.1  1  Spc7           Spc7 kinetochore protein
    0.00025   21.2  12.0    0.00085   19.5   9.0    2.0  2  Tropomyosin_1  Tropomyosin like
     0.0003   19.6   4.2    0.00037   19.3   4.2    1.0  1  AAA_13         AAA domain
    0.00068   19.0   1.5    0.00086   18.7   1.5    1.2  1  DUF3450        Protein of unknown function (DUF3450)
     0.0012   19.3   4.0       0.08   13.4   2.6    2.2  2  DUF16          Protein of unknown function DUF16
     0.0016   18.5   4.8      0.028   14.4   1.7    2.0  2  DUF1664        Protein of unknown function (DUF1664)
     0.0087   16.3   1.0      0.011   15.9   1.0    1.3  1  ATG16          Autophagy protein 16 (ATG16)
  ------ inclusion threshold ------
      0.019   14.1   1.8      0.022   13.9   1.8    1.1  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
      0.024   14.5   5.8      0.039   13.8   5.7    1.4  1  KASH_CCD       Coiled-coil region of CCDC155 or KASH
      0.026   13.4   1.8      0.032   13.1   1.8    1.2  1  FemAB          FemAB family
      0.026   14.7   1.7      0.039   14.1   1.7    1.3  1  CENP-Q         CENP-Q, a CENPA-CAD centromere complex subunit
      0.034   14.0   7.3      0.068   13.0   7.2    1.6  1  DUF724         Protein of unknown function (DUF724)
      0.083   13.4   2.8       0.18   12.3   2.9    1.6  1  Spectrin       Spectrin repeat
      0.087   13.2   3.0       0.15   12.4   3.0    1.5  1  OmpH           Outer membrane protein (OmpH-like)
      0.096   12.6   4.2          1    9.3   3.2    2.3  2  Prefoldin      Prefoldin subunit
      0.097   12.0   6.7      0.094   12.1   5.3    1.5  1  GAS            Growth-arrest specific micro-tubule binding
      0.097   12.1   7.9       0.19   11.2   7.4    1.7  1  DUF3552        Domain of unknown function (DUF3552)
       0.12   12.8   6.0        1.8    9.1   2.5    2.7  2  FadA           Adhesion protein FadA
       0.31   10.2   2.0       0.41    9.8   2.0    1.3  1  TMPIT          TMPIT-like protein
       0.34   10.9   7.1          2    8.4   2.6    2.4  2  MIP-T3_C       Microtubule-binding protein MIP-T3 C-terminal 
       0.36   10.6   7.5       0.69    9.7   7.0    1.9  1  Mei5           Double-strand recombination repair protein
       0.37   11.0   4.6        2.6    8.2   4.3    1.9  2  Fib_alpha      Fibrinogen alpha/beta chain family
       0.43    9.9   3.1       0.49    9.7   3.1    1.2  1  FAM76          FAM76 protein
       0.78    9.7   8.3         15    5.6   0.1    3.2  3  Nas2_N         Nas2 N_terminal domain
       0.82   10.1   9.6        5.9    7.4   3.1    2.7  3  FlaC_arch      Flagella accessory protein C (FlaC)
       0.87    9.7   6.4        1.6    8.8   6.4    1.6  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
       0.94   10.2   4.0        3.8    8.2   4.0    1.9  1  YabA           Initiation control protein YabA
          2    8.7   8.8        5.5    7.3   3.1    2.3  2  XhlA           Haemolysin XhlA
        6.2    6.7   7.1         12    5.7   5.5    2.2  1  DivIC          Septum formation initiator
          7    7.0  10.3        3.1    8.1   5.4    2.5  3  ABC_tran_CTD   ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   7.5   2.3e-07   0.00013     198     298 ..      55     155 ..      42     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.3e-07
      HMMR_N 198 LeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekek 296
                 ++   + +a+Lkek ++leke +ee  ++++l e   ++s  +++  +  + + q ++ +++++de+ +L ss++ek   ++k ++d  +++    +++
  AJA92949.1  55 IDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDKIIDDEGKRITSFKESR 153
                 55556779************************************9999999***************************************999999998 PP

      HMMR_N 297 ee 298
                 e+
  AJA92949.1 154 EK 155
                 86 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   6.8   2.7e-07   0.00016     157     259 ..      43     141 ..      30     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
        Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255
                  L++++++l+e+ + +    a+l+e+ ++l+++ ee    ++ ++++l+e+l +++  i+e  + ++ l ++++++e++ +e+ + +s+++e+++  ++
  AJA92949.1  43 SLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEE----ESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDK 137
                 68999999999999999999************8887....677899**********************************************9998888 PP

        Spc7 256 vlee 259
                 +++ 
  AJA92949.1 138 IIDD 141
                 8764 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.13        76      28      54 ..      32      58 ..      10      67 .. 0.71
   2 !   19.5   9.0   1.5e-06   0.00085      37     126 ..      62     155 ..      59     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
  Tropomyosin_1 28 qenlekeqeiksLtkknqqleeevekl 54
                     + + +  i+sL +k  +lee ++ +
     AJA92949.1 32 MAQSDSDIGISSLMNKRAKLEEAIDYV 58
                   33334455689**********999865 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.5e-06
  Tropomyosin_1  37 iksLtkknqqleeevekleeklkeakekaeese....kkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerde 126
                    i++L++k  +le+e+e+ + ++k+ kek+ + +    ++    e l++k + +E+e++e  + + +  ekL+ +d+  ++  +++++  ++r++
     AJA92949.1  62 IANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSdyidEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDKIIDDEGKRITSFKESREK 155
                    899*******************9999998665411114555678*****************************************999999886 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   4.2   6.4e-07   0.00037     351     480 ..      28     152 ..      17     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.4e-07
      AAA_13 351 pfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeL 449
                 p +++ +++++  i+s+ ++ a+++e i      +anl+e++++++k++e   v     +++++k+k+ k+++ i + ++ ++  +++ +++e+e+ e 
  AJA92949.1  28 PPQEMAQSDSDIGISSLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESV-----DIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEV 121
                 556566666666679999*******************************99664.....3555555555666666666666666666666666666666 PP

      AAA_13 450 ekqlrdekpaaeeinkeLkafGlgeleLkfe 480
                  + +++ ++  + i k++ + G++  ++k  
  AJA92949.1 122 GTLISSMREKLSGIDKIIDDEGKRITSFKES 152
                 6666666665555555555555555555554 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.5   1.5e-06   0.00086      26     110 ..      49     133 ..      32     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
     DUF3450  26 ekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                 +k  +a   +   i +l++++++l++e+++ +  +++l+ +  ++++++++  + i+ l ++ + +e+ ++e+  l+ +m ++L 
  AJA92949.1  49 AKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLS 133
                 5555555555667899****************************************************************99986 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   0.00062      0.36      45      97 ..      43      95 ..      27      98 .. 0.59
   2 !   13.4   2.6   0.00014      0.08      38     100 ..      78     140 ..      73     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00062
                ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
       DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkink 97
                +l ++ +kle++++  g  i +lk++    ++e+++    ++ + e L k+++
  AJA92949.1 43 SLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSD 95
                55555666666666666666666666666666666555555555555555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                 HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHH CS
       DUF16  38 kieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlD 100
                 +    ++ l+e++ k+ + +++ +  i++l+++ +a ++e ++v+  + ++ e L  i+k +D
  AJA92949.1  78 EESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDKIID 140
                 3444678999********************************999999999999999999887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.7   4.9e-05     0.028      55     123 ..      42     110 ..      30     111 .. 0.92
   2 !    7.5   0.2    0.0071       4.1      62     106 ..     105     149 ..      97     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-05
     DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                 +sl + + +L++ id v+  + + ke  +++++e++e + d+++++e++ +v++ + +    +e++++k
  AJA92949.1  42 SSLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQK 110
                 688999************************************************999988888888776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0071
     DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                 +hLs++ + v+++ de+  ++++++e+++ + + +++ g+ ++s 
  AJA92949.1 105 EHLSQKRNAVENEADEVGTLISSMREKLSGIDKIIDDEGKRITSF 149
                 578888888888888888888888888888877777666666665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0     2e-05     0.011      67     141 ..      38     120 ..       6     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-05
       ATG16  67 q........snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkd 141
                 +        + +k ++ i     ++a l+e  ++l k+ +e +  +++l+e+l k  + + e+++ +++l+++r+a+e + ++
  AJA92949.1  38 DigisslmnKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADE 120
                 24444444444455556666666777777777777777777777777777777777777777777777777777777766544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.8   3.8e-05     0.022      82     153 ..      54     141 ..      21     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.8e-05
       Atg14  82 r.......lqelkdklsqlkkeieekkkklaklsdklk.........kRrsdleslqneleerrkkqiaklqdaikrieqklsslssk 153
                         +++lk+k+++l keiee +  ++ l++kl          +R  ++ s +    e++++++ +l ++++++   ++++ ++
  AJA92949.1  54 AidyvgglIANLKEKRTNLEKEIEEESVDIKNLKEKLMkvsdyideeTRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDKIIDD 141
                 4444555567778888888888888888888888887778888888877788777778888888888888877777555444444444 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.7   6.7e-05     0.039      85     151 ..      64     130 ..      42     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
    KASH_CCD  85 rlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekea 151
                 +lk ++ +leke +  ++ i++L+e+++k+   +de  + ++ L+++++ + ++++e+ +l+++  +
  AJA92949.1  64 NLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMRE 130
                 67889999***************************************************99987544 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.8   5.5e-05     0.032     238     304 ..      63     131 ..      61     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
       FemAB 238 lnlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiekdgee 304
                 +nl+e++++l++++e+ + ++++l+ekl k  +  +++++ ++ l+++ +++e+e +e+  +i++  e+
  AJA92949.1  63 ANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDyiDEETRGIEHLSQKRNAVENEADEVGTLISSMREK 131
                 69******************************999999999*****************99999887776 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.7   6.8e-05     0.039       8     104 ..      23     118 ..      17     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
      CENP-Q   8 r.lpfPpatqsdggkekeldfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerkeklkkehvllqesdseelsl 104
                   +p Pp  q+  + +++  + +l ++ a le   +     ++ L++ +  +e++ e++   +++L+++  +     +e+ +  ++l q+ +  e++ 
  AJA92949.1  23 EsMPEPP--QEMAQSDSDIGISSLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEA 118
                 4489999..999999*****************************************************999999996665566666776443333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   7.2   0.00012     0.068      99     179 ..      64     144 ..      30     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
      DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                 +lk+++t+l++e+++   +i++ +++  k+++ ide  + i +l +++ ++ ++ ++    i++++ + + +++ ++d  +
  AJA92949.1  64 NLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDKIIDDEGK 144
                 578889999999999888899989999999999999999999999999988888888899999999999998888887655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.9   0.00032      0.18      38     103 ..      64     132 ..      44     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00032
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH...HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Spectrin  38 allkkhkaleaelaaqqervkalnelaeklldeghsas...eeieerleelnerWeeLkelaaerkqkL 103
                 +l +k + le+e++++   +k+l+e   k+ d+ ++++   e+++++ +++++  +e+ +l+ ++++kL
  AJA92949.1  64 NLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETrgiEHLSQKRNAVENEADEVGTLISSMREKL 132
                 5677999*****************99999988887777777*************************999 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.0   0.00026      0.15      22      90 ..      63     132 ..      45     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkle..keekeqe.lqkkeqelqqkqqqkaqelqkkqqel 90 
                 ++l++k+++l++e+e++  ++++l+e+l  k ++    +e++  e l +k++++++++++    + + +++l
  AJA92949.1  63 ANLKEKRTNLEKEIEEESVDIKNLKEKLM-KVSD-YidEETRGIEhLSQKRNAVENEADEVGTLISSMREKL 132
                 6899************************7.3333.2445555555788888888885544444444444443 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.2    0.0018         1      74     116 ..      50      92 ..      48     124 .. 0.91
   2 ?    1.5   0.0      0.45   2.6e+02       3      38 ..     109     143 ..     103     152 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                 EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                 +leeAi+++   +++l++ +++le+e+e+ +  i++l ++l +
  AJA92949.1  50 KLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMK 92 
                 5899999999999999999999999999999999999887765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.45
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT CS
   Prefoldin   3 eeleslqaelaqlkeaieelektletlktlkkedeg 38 
                 ++ ++++ e +++ + i++ ++ l+ ++++++ deg
  AJA92949.1 109 QKRNAVENEADEVGTLISSMREKLSGIDKIID-DEG 143
                 44455556666666666666666666666666.554 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.3   0.00016     0.094      54     125 ..      46     121 ..      32     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
         GAS  54 qenkrlkepLkkaeeeveeLrkqlknyek....dkqslknlkarlkelekelkdlkwehevleqrfekvekerdel 125
                 ++  +l+e +  +   +++L+++  n ek    + +++knlk++l ++ +++ + +   e l+q+ ++ve+e de+
  AJA92949.1  46 NKRAKLEEAIDYVGGLIANLKEKRTNLEKeieeESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEV 121
                 5555566666665566666666554444411114567999999999999999999999999999999999999985 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.4   0.00032      0.19      62     154 ..      65     146 ..      60     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
     DUF3552  62 ihklreelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtkeeAkei 154
                 +++ r++leke++e   ++++l ++l++  + +d+ ++ +e    +l++k++        +e++ +e+ +l+++ r++L  i ++  +e k i
  AJA92949.1  65 LKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETRGIE----HLSQKRNA-------VENEADEVGTLISSMREKLSGIDKIIDDEGKRI 146
                 57789999999999999999999999999999998876554....24444444.......555555555555555555555555555555544 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.5    0.0031       1.8      66      94 ..      60      88 ..      33      94 .. 0.92
   2 ?    4.8   0.2     0.066        38      61      94 ..     118     151 ..      87     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
        FadA 66 ellkeyksllkelekeikekekkianfek 94
                 l+ ++k+ +++lekei+e++  i+n+++
  AJA92949.1 60 GLIANLKEKRTNLEKEIEEESVDIKNLKE 88
                68999*********************976 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.066
        FadA  61 kdeYkellkeyksllkelekeikekekkianfek 94 
                  de ++l++++++ l+ ++k i ++ k+i  f++
  AJA92949.1 118 ADEVGTLISSMREKLSGIDKIIDDEGKRITSFKE 151
                 477889999999999999*********9999987 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.0   0.00071      0.41       7      87 ..      44     123 ..      40     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
       TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeves 87 
                 l ++  +lee+ + +   +++l++  +++ kei++++ ++k+lk++l k++  ++ ee + +e+l+++ +  ++  +ev  
  AJA92949.1  44 LMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYID-EETRGIEHLSQKRNAVENEADEVGT 123
                 5556666666666666667777777777777777777777777777777776653.4444555555554444444444333 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.6    0.0035         2     111     147 ..      61      97 ..      41     104 .. 0.82
   2 ?    4.8   0.1     0.043        25      96     138 ..     109     151 ..      98     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
    MIP-T3_C 111 aleplkaqlaeleeaIkdqkekisnvrakilkNeaki 147
                  + +lk++  +le++I+++   i+n+++k++k    i
  AJA92949.1  61 LIANLKEKRTNLEKEIEEESVDIKNLKEKLMKVSDYI 97 
                 567899999*********************9977666 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.043
    MIP-T3_C  96 qqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvra 138
                 q+ +++++e  +    ++ ++++l+ +++ I d+ ++i   ++
  AJA92949.1 109 QKRNAVENEADEVGTLISSMREKLSGIDKIIDDEGKRITSFKE 151
                 56677777888888889999**************999998876 PP

>> Mei5  Double-strand recombination repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.0    0.0012      0.69     101     148 ..      37      92 ..       7     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                 XX.....................XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        Mei5 101 se...ssliln..slkekie...lekkeLeeekakLekqvrekeelLrrLklvkky 148
                 s+   ssl+++  +l+e i+    ++ +L+e+++ Lek+++e++ +++ Lk++ + 
  AJA92949.1  37 SDigiSSLMNKraKLEEAIDyvgGLIANLKEKRTNLEKEIEEESVDIKNLKEKLMK 92 
                 335554444430033444558888999***************99999999887664 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.0     0.017       9.8      82     124 ..      47      89 ..      17      95 .. 0.52
   2 ?    8.2   4.3    0.0044       2.6      30     111 ..      73     153 ..      63     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                 HHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha  82 sskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                  + +lee i ++   i +  ++  +L + +e+ +++i++L+++
  AJA92949.1  47 KRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEK 89 
                 2333443333333333333344444444444444444444443 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0044
                 CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
   Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                 ek+++++  +++n  e++ + +  ++e ++ i++  +++++ +++ d+v + + ++++e+ + +++ id++ ++i   ++  
  AJA92949.1  73 EKEIEEESVDIKNLKEKLMKVSDYIDEETRGIEHLSQKRNAVENEADEVGTLI-SSMREKLSGIDKIIDDEGKRITSFKESR 153
                 22222222334444444444445555556666666667777777555554444.4455588899999999999998887765 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   0.00085      0.49     220     297 ..      61     137 ..       6     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00085
       FAM76 220 avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkevaelsk 297
                  +++Lke+ ++l+k++e+  +++ + + k+ ++ ++ +++e++  e+l++ ++ ++++ +++ + i++++ +++ + k
  AJA92949.1  61 LIANLKEKRTNLEKEIEEESVDIKNLKEKLMKV-SDYIDEETRGIEHLSQKRNAVENEADEVGTLISSMREKLSGIDK 137
                 466777777777777777777777777777654.56667777777777777777777777777777777666665544 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.25   1.5e+02       2      16 ..      42      56 ..      41      63 .. 0.85
   2 ?    4.8   1.6     0.045        26       2      23 ..      63      84 ..      62     101 .. 0.71
   3 ?    5.6   0.1     0.026        15       2      38 ..     105     143 ..     104     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
      Nas2_N  2 keLekkkdeiekeie 16
                ++L++k++++e+ i+
  AJA92949.1 42 SSLMNKRAKLEEAID 56
                68**********997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.045
      Nas2_N  2 keLekkkdeiekeieelsevLe 23
                 +L++k++++ekeiee s  ++
  AJA92949.1 63 ANLKEKRTNLEKEIEEESVDIK 84
                6899***********9876666 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.026
      Nas2_N   2 keLekkkdeiekeieelsevLe..sqnvgmdgplvDeeg 38 
                 ++L++k++++e+e +e+ + ++  ++++   ++ +D+eg
  AJA92949.1 105 EHLSQKRNAVENEADEVGTLISsmREKLSGIDKIIDDEG 143
                 78**************99999955444444456677776 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.5   3.2e+03      22      30 ..      47      55 ..      30      68 .. 0.51
   2 ?    7.4   3.1      0.01       5.9       3      32 ..      70      99 ..      68     109 .. 0.90
   3 ?    6.0   0.2     0.027        16       3      31 ..     112     140 ..     110     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.5
   FlaC_arch 22 eneelsksv 30
                +  +l++ +
  AJA92949.1 47 KRAKLEEAI 55
                333333333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
   FlaC_arch  3 delEnklsklsteletvkkeneelsksvee 32
                 +lE+++++ s+ ++++k+++ ++s+ ++e
  AJA92949.1 70 TNLEKEIEEESVDIKNLKEKLMKVSDYIDE 99
                589***********************9987 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.027
   FlaC_arch   3 delEnklsklsteletvkkeneelsksve 31 
                 + +En+ +++ t +++++++++ + k ++
  AJA92949.1 112 NAVENEADEVGTLISSMREKLSGIDKIID 140
                 679********************999887 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.4    0.0028       1.6      93     164 ..      43     113 ..       8     157 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
     UPF0242  93 elqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklel...eeqLaekqellqeyqetieeqrsv 164
                  l ++  +L+e +d+   ++++lke+  +L+++ e+ + d+++lk +l    + ++e++  ++++    +++r+ 
  AJA92949.1  43 SLMNKRAKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLmkvSDYIDEETRGIEHL----SQKRNA 113
                 33344444444444444444444444444444444444333333322200011122222221111....112222 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.0    0.0065       3.8      11      53 ..      49     108 ..      40     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0065
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.................X CS
        YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl.................e 53 
                 ++lee ++ +   +++lke+ ++l +e +e +++ ++l+e+l                 +
  AJA92949.1  49 AKLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEKLmkvsdyideetrgiehlS 108
                 566666666666666666666666666666666666666666444444433333222221 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.1    0.0095       5.5       8      47 ..      50      89 ..      46      92 .. 0.89
   2 ?    4.6   0.2     0.066        38      13      46 ..     104     137 ..      95     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0095
        XhlA  8 rietkldnleervdkleekaaeaeekiknleedlkklesn 47
                ++e+ +d  +  +  l+ek ++ e++i++   d+k+l++ 
  AJA92949.1 50 KLEEAIDYVGGLIANLKEKRTNLEKEIEEESVDIKNLKEK 89
                678888888888999**********************986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.066
        XhlA  13 ldnleervdkleekaaeaeekiknleedlkkles 46 
                 ++ l+++ + +e+ a+e+ + i ++ e+l+ + +
  AJA92949.1 104 IEHLSQKRNAVENEADEVGTLISSMREKLSGIDK 137
                 5678886699999999999999999999998875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.5     0.021        12      21      63 ..      64     103 ..      39     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXX CS
       DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARs 63 
                  lk++++ l++e+++ + ++++L++++ + +   dyi+e  R 
  AJA92949.1  64 NLKEKRTNLEKEIEEESVDIKNLKEKLMKVS---DYIDEETRG 103
                 5788888999999999999999999888886...999999985 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.4   8.1e+02      31      57 ..      32      55 ..      27      58 .. 0.60
   2 ?    8.1   5.4    0.0054       3.1       9      59 ..      68     120 ..      61     122 .. 0.85
   3 ?   -0.8   0.2       3.2   1.9e+03      11      35 ..     119     143 ..     115     156 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
  ABC_tran_CTD 31 ladpelysdpeklaelsaeleeleaeL 57
                  +a+ +  sd   ++ l+++ ++le+++
    AJA92949.1 32 MAQSD--SDI-GISSLMNKRAKLEEAI 55
                  55555..444.4666666667776665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0054
  ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpek..laelsaeleeleaeLee 59 
                   +  +le+eIe+   +i++l ++l + + y d+e+  +  ls++ +++e+e +e
    AJA92949.1  68 KRTNLEKEIEEESVDIKNLKEKLMKVSDYIDEETrgIEHLSQKRNAVENEADE 120
                   3358*********************99997774457************99887 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.2
  ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpe 35 
                   +e+   I ++ e+++ +++ + d++
    AJA92949.1 119 DEVGTLISSMREKLSGIDKIIDDEG 143
                   5555566666666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1771  (0.0987785); expected 358.6 (0.02)
Passed bias filter:                      888  (0.0495287); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 1190.10
//
Query:       AJA92950.1  [L=267]
Description: imidazoleglycerol phosphate synthase, cyclase subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-83  279.3   0.9    2.4e-83  279.1   0.9    1.0  1  His_biosynth  Histidine biosynthesis protein
    1.6e-07   30.8   0.1    9.3e-05   21.7   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.2e-05   24.9   0.1       0.03   13.7   0.0    2.2  2  NMO           Nitronate monooxygenase
    7.7e-05   22.1   0.4      0.033   13.5   0.0    2.4  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0011   18.3   0.1       0.28   10.5   0.0    2.2  2  TMP-TENI      Thiamine monophosphate synthase
     0.0027   16.6   0.1     0.0045   15.9   0.1    1.3  1  Trp_syntA     Tryptophan synthase alpha chain
     0.0084   15.3   0.1       0.35   10.0   0.0    2.1  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.023   14.2   0.2      0.051   13.0   0.1    1.6  2  PcrB          PcrB family
      0.027   13.9   0.7        1.3    8.5   0.1    2.5  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.1   0.9   1.2e-86   2.4e-83       1     227 [.       6     248 ..       6     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.1 bits;  conditional E-value: 1.2e-86
                   EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S CS
  His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagad 97 
                   riip+lD+ +G+vV   kG +f++ ++agdpv+la++y++egadel+++D++a++e+re+ ++lv++iae ++ip++vGGG++sl++++++l +gad
    AJA92950.1   6 RIIPCLDVANGRVV---KGLNFESIKDAGDPVQLAEKYSNEGADELVFLDITASSEQRETIKSLVKKIAEVIDIPFTVGGGVKSLQHARDILLNGAD 99 
                   8*************...******************************************************************************** PP

                   EEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......C............EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS CS
  His_biosynth  98 kviigtaavknpelikelaekfgsqkivvaiDarr......g............ykvaikgwreetgldavelakkleelgageilltdidrdGtls 176
                   kv i+t avknpe+i+el+e fg+q++vvaiD+rr      g            ++v+i+g+++ tgld++++ kk+eelgageillt+idrdGt++
    AJA92950.1 100 KVAINTGAVKNPEVITELMELFGKQCVVVAIDSRRnynlekGknifsengkqfwFEVFIYGGKKGTGLDVIDWSKKIEELGAGEILLTSIDRDGTKD 196
                   ***********************************7766551677778889**9******************************************* PP

                   ---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTC.SEEEESHHHHTTS CS
  His_biosynth 177 GpdleltkelaeavkipviasGGvgsledlkelksegv.davivgsalyege 227
                   G+d  lt+e+  av ipviasGG+g++ed+ ++++++  +a++++s++++++
    AJA92950.1 197 GYDTLLTNEIVHAVGIPVIASGGCGKPEDMIDIFKNTEvNAALAASIFHYET 248
                   **********************************66555**********975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.7e-08   9.3e-05     141     227 ..      34     119 ..      26     151 .. 0.79
   2 !    7.3   0.0    0.0011       2.2     177     212 ..     205     240 ..     191     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.7e-08
                 HHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HH CS
         Dus 141 lelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.st 227
                 ++la++ +++Ga++l+    t+  + ++t++ + +k++ + + ip+ + G++k+++ a++il + Gad v i  ga +nP ++ e ++
  AJA92950.1  34 VQLAEKYSNEGADELVFLDITASSEQRETIK-SLVKKIAEVIDIPFTVGGGVKSLQHARDILLN-GADKVAINTGAVKNPEVITElME 119
                 6667777777777776666555555555444.46888999999*******************99.*****************987554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                 HHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
         Dus 177 evkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                 e+  av ipvia G++ ++ed+ +i ++t +++ ++
  AJA92950.1 205 EIVHAVGIPVIASGGCGKPEDMIDIFKNTEVNAALA 240
                 6788999*******************9998888665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00032      0.64     179     223 ..      61     105 ..      37     113 .. 0.89
   2 !   13.7   0.0   1.5e-05      0.03     181     208 ..     199     226 ..     170     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
         NMO 179 kglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                 +   +Lv+++++++diP    GG+   +    +L  GA  v+i t
  AJA92950.1  61 ETIKSLVKKIAEVIDIPFTVGGGVKSLQHARDILLNGADKVAINT 105
                 45678*************************************988 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.5e-05
         NMO 181 lfaLvpqvldavdiPviAaGGiidrrgv 208
                  + L ++++ av iPviA GG  + +++
  AJA92950.1 199 DTLLTNEIVHAVGIPVIASGGCGKPEDM 226
                 57899****************8877775 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.6e-05     0.033     134     208 ..      34     108 ..      18     121 .. 0.85
   2 !    6.3   0.1    0.0026       5.2     137     193 ..     173     229 ..     154     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                 HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
        ThiG 134 lvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                 + la++  + G+  ++ l     s +  + k  +k i e +++P  v  G+ s ++a   +  Gad v +nt   
  AJA92950.1  34 VQLAEKYSNEGADELVFLDITASSEQRETIKSLVKKIAEVIDIPFTVGGGVKSLQHARDILLNGADKVAINTGAV 108
                 457888888888888888888889999999999**************************************9644 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0026
                 HHHHHHTT-SEBEEBS.SSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHH CS
        ThiG 137 arrleevGcaavmPla.apiGsglGllnkealkiiieeakvPvivDAGigspsdaaqa 193
                 ++++ee+G+  ++  +    G+  G  +    + i++ + +Pvi   G g+p+d +  
  AJA92950.1 173 SKKIEELGAGEILLTSiDRDGTKDGYDTL-LTNEIVHAVGIPVIASGGCGKPEDMIDI 229
                 67888888866654431456888887665.457788999**************98765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00014      0.28     140     177 ..      65     103 ..      31     107 .. 0.77
   2 !    5.9   0.0    0.0035         7     120     160 ..     179     221 ..     172     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
    TMP-TENI 140 eglkelaealeiPvvaiGGit.lenvaevleagadgvav 177
                 +++k++ae + iP+ + GG++ l+++ ++l  gad va+
  AJA92950.1  65 SLVKKIAEVIDIPFTVGGGVKsLQHARDILLNGADKVAI 103
                 56899999999*********83689999*********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0035
    TMP-TENI 120 igvGpifpTdtKkdaeplglegl..kelaealeiPvvaiGGit 160
                 +g+G i  T+   d +  g ++l  +e+++a+ iPv+a GG  
  AJA92950.1 179 LGAGEILLTSIDRDGTKDGYDTLltNEIVHAVGIPVIASGGCG 221
                 678888888888888777777665599**************85 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.2e-06    0.0045     178     231 ..      55     109 ..      52     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-06
                 TTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHH CS
   Trp_syntA 178 aenavaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvk 231
                 a+++  +++++lv+++ ++ + P  vG G+++ ++++ +  ++ad v +    vk
  AJA92950.1  55 ASSEQRETIKSLVKKIAEVIDIPFTVGGGVKSLQHARDILlNGADKVAINTGAVK 109
                 46778899*******************************99****9988666665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00017      0.35     233     283 ..      66     114 ..      58     121 .. 0.80
   2 ?    3.3   0.0      0.02        40     240     289 ..     209     256 ..     200     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                 HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCH CS
      DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpki 283
                 ++ +++++++  ip    GG++s + a + +  GA  v++ t+ v++  +i
  AJA92950.1  66 LVKKIAEVID--IPFTVGGGVKSLQHARDILLNGADKVAINTGAVKNPEVI 114
                 4566666666..999999*************************97664444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.02
                 HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHH CS
      DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikk 289
                  +   ip+I++GG    eD ++ ++      ++ + +   +  +++++k+
  AJA92950.1 209 AVG--IPVIASGGCGKPEDMIDIFKNTEVNAALAASIFHYETHSVNRVKE 256
                 455..**************9998876555555555554555555555555 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05     0.051     156     210 ..      48     106 ..      41     120 .. 0.75
   2 ?   -2.6   0.0       1.5     3e+03     161     178 ..     216     233 ..     197     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                 EEEEE-TTSSS-HHHHHHHHHHHSS...SEEEEESS--SHHHHHHHHCC.SSEEEE-CH CS
        PcrB 156 liYlEasGaledveevialkkklek...arlivGGGirsaEkAkevvea.ADvivvGnv 210
                 l++l+    +e+ e ++ l+kk+ +   + + vGGG++s  +A++++   AD + + + 
  AJA92950.1  48 LVFLDITASSEQRETIKSLVKKIAEvidIPFTVGGGVKSLQHARDILLNgADKVAINTG 106
                 56777777788888888888887751115578***************999**8765443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                 -TTSSS-HHHHHHHHHHH CS
        PcrB 161 asGaledveevialkkkl 178
                 asG  +++e +i++ k  
  AJA92950.1 216 ASGGCGKPEDMIDIFKNT 233
                 566666666666665544 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00063       1.3     127     167 ..      63     103 ..      61     109 .. 0.90
   2 ?    3.4   0.0     0.023        46     131     160 ..     203     232 ..     198     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00063
                   GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
  G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavst 167
                   +++++k+i + ++ip+  GG +++ ++ +++l +Ga+ v+ 
    AJA92950.1  63 IKSLVKKIAEVIDIPFTVGGGVKSLQHARDILLNGADKVAI 103
                   567899******************************99875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.023
                   HCTSTTS...EEEEESS--SHHHHHHHCTT CS
  G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealka 160
                   ++ei +++ ip+ia+G   + ed+ +++k+
    AJA92950.1 203 TNEIVHAVGIPVIASGGCGKPEDMIDIFKN 232
                   57889999*********9999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2059.10
//
Query:       AJA92951.1  [L=182]
Description: Rieske [2Fe-2S] domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.2e-07   28.9   0.0    1.2e-06   28.4   0.0    1.3  1  Rieske    Rieske [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   6.5e-11   1.2e-06      34      82 ..      89     138 ..      44     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.5e-11
                 S-EEEEESC-TTTT-BC....GGSEEETT.EEE-TTT--EEE.TTSBEEE-TTH CS
      Rieske  34 gevyAlsdvCtHrgapl....segkidekgvleCpcHgwayd.adGkvikgPap 82 
                  +++A+s +C H+ +      +eg++    + eCpcHg+ yd  +G + +gPa 
  AJA92951.1  89 SSFRAYSMICLHLWCVWkywpQEGRM----RGECPCHGSMYDpVTGTAFAGPAS 138
                 5678************6444466777....669*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1458.61
//
Query:       AJA92952.1  [L=86]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-21   75.5   4.8    2.7e-21   75.1   4.8    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.045   14.3   2.6      0.059   14.0   2.6    1.2  1  DoxX         DoxX
       0.21   10.4   0.4       0.22   10.3   0.4    1.1  1  DUF5423      Family of unknown function (DUF5423)
       0.37   11.2   3.6         10    6.6   3.6    2.0  1  DUF3165      Protein of unknown function (DUF3165)


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   4.8   6.1e-25   2.7e-21      10     104 ..       1      82 [.       1      84 [. 0.97

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.1e-25
                  HHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-BCCG-- CS
  Oxidored_q2  10 fliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetavgLallvrlyreygtddvqelr 104
                  ++iG+yg+ ++rn++++l+++e+i na+nl+lv++++f                  +q+l+L+ i+i+aae+avgLal++ +yr y+++d+ ++r
   AJA92952.1   1 MGIGIYGLAVKRNAIRMLFAVEIIVNAANLNLVAFARFM-------------PHSGGQTLALFSIAIAAAEVAVGLALIIVAYRMYKNVDIADFR 82 
                  58************************************9.............8999**********************************99875 PP

>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.6   1.3e-05     0.059       6      61 ..      16      67 ..       7      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
        DoxX  6 RlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllll 61
                R+l++v  i        +++l ++a ++ + g ++ +l+ +++a++E+++gl+l++
  AJA92952.1 16 RMLFAVEII----VNAANLNLVAFARFMPHSGGQTLALFSIAIAAAEVAVGLALII 67
                444444444....44444567799******************************97 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4     5e-05      0.22      30      79 ..      32      80 ..       6      83 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5e-05
     DUF5423 30 ilcivsiilwtqgsglalfaiapalaigalgvtllvsdlaesqkskeiad 79
                +++    +  + g  lalf+ia a a  a+g++l++       k  +iad
  AJA92952.1 32 LVAFARFMPHSGGQTLALFSIAIAAAEVAVGLALIIVAYR-MYKNVDIAD 80
                333334455667889******************9987543.445555655 PP

>> DUF3165  Protein of unknown function (DUF3165)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   3.6    0.0022        10      43      73 ..      46      76 ..       8      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
     DUF3165 43 vlsflkilqlPkeifvgllmillgyfalkdi 73
                +l+++ i     e+ vgl++i+++y   k++
  AJA92952.1 46 TLALFSIAIAAAEVAVGLALIIVAYRMYKNV 76
                5788888888999999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 682.98
//
Query:       AJA92953.1  [L=81]
Description: transcription factor Pcc1 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-09   35.6   0.0    8.4e-09   35.4   0.0    1.0  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   4.7e-13   8.4e-09       2      73 ..       5      76 ..       4      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 4.7e-13
                EEEEEE-SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHH CS
        Pcc1  2 ltisvpfpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvletm 73
                ++ +++f+++++ s++++++  D+e  p++ +k ++sl++  + +e ++  + +LR+ +n+ l++l+   +t+
  AJA92953.1  5 FSAKIQFSSDKENSSIYQSINTDNEFYPENpTKTKISLDK-EIIIELESHHLPHLRANLNSTLRLLQASYDTI 76
                7889**********************************76.99***********************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 611.96
//
Query:       AJA92954.1  [L=109]
Description: ribosomal protein S17P [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-18   66.9   1.9    2.1e-18   66.1   1.0    1.7  2  Ribosomal_S17    Ribosomal protein S17
     0.0046   17.3   0.5     0.0085   16.5   0.1    1.7  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.15   1.4e+03      34      48 ..       6      20 ..       1      21 [. 0.75
   2 !   66.1   1.0   2.4e-22   2.1e-18       1      68 []      38     106 ..      38     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                   EEEEE-TTTS--TT- CS
  Ribosomal_S17 34 kylahdennsvkvGD 48
                    +++  ++++ k+GD
     AJA92954.1  6 GIKVKAPKEEPKEGD 20
                   578889999999999 PP

  == domain 2  score: 66.1 bits;  conditional E-value: 2.4e-22
                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                    G+Vv+ + + Tvv + e  v+ +k+k+y + +++++ah ++n  v++GD+V  +ecrP++k+++fvvve
     AJA92954.1  38 GKVVKSRGKDTVVLQKEANVYFSKFKRYGRSTSRIHAHVPSNLqVNEGDTVIAAECRPIAKSVSFVVVE 106
                    99****************************************99***********************97 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   9.5e-07    0.0085      33      69 .]       2      36 ..       1      36 [. 0.87
   2 ?   -2.3   0.0      0.69   6.2e+03       8      16 ..      53      61 ..      44      76 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.5e-07
                     -----TT----GGGGS-----TTSSSSSS----S-EE CS
  Ribosomal_S17_N 33 vknvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                      +n+g+  k+Pke  ++   DkK PF G+  +rG+++
       AJA92954.1  2 TRNIGIKVKAPKEEPKE--GDKKNPFNGTLPVRGKLF 36
                     689*********86655..4**************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.69
                     --SS----- CS
  Ribosomal_S17_N  8 kQetvflnk 16
                     k  +v+ +k
       AJA92954.1 53 KEANVYFSK 61
                     333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:01.02
# Mc/sec: 323.63
//
Query:       AJA92955.1  [L=170]
Description: adenine phosphoribosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-14   53.7   0.1      2e-14   53.4   0.1    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0078   15.7   0.0     0.0096   15.4   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   2.3e-18     2e-14      24     132 ..      42     156 ..      27     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.3e-18
                   EE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE-SEESSSHHHHHHHHHHHC CS
  Pribosyltran  24 ee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVDDildtGgTllaalelLke 112
                   ++  ++  dv++gi+++G+++a +la + +  +  vrk  + p++  +++ +++          ++  + +g++Vli+DD+l+tGgT +aa++l+++
    AJA92955.1  42 KKfHPNDVDVFAGIESRGFIIACALALKYNKGMILVRKAGKLPGKVVKTSYTLE--YgkatlevQKDVIQEGQRVLICDDLLATGGTAKAAAKLIEK 136
                   334456899************************************999986654..35699*99999999*************************** PP

                   C-BSEEEEEEEE...E-HHHHHH CS
  Pribosyltran 113 kgpeevriavlv...dkpateee 132
                    + ++v++a ++   +      +
    AJA92955.1 137 INGTIVGFAFIIellE---LNGR 156
                   **********994442...3333 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-06    0.0096     116     148 ..     104     138 ..      78     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-06
     UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkerg 148
                 +k++  + ++vl++D ++aTGg+a aa +l+ + +
  AJA92955.1 104 QKDViqEGQRVLICDDLLATGGTAKAAAKLIEKIN 138
                 4444456677******************9999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1257.59
//
Query:       AJA92956.1  [L=436]
Description: aspartate--tRNA(Asn) ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-80  268.2   0.0      1e-79  267.9   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
      2e-10   40.5   1.1    3.7e-10   39.7   0.5    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.081   12.4   0.1       0.21   11.0   0.0    1.6  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
        0.1   13.0   0.1        0.2   12.1   0.1    1.5  1  DraK_HK_N        DraK Histidine Kinase N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.9   0.0   2.3e-83     1e-79       3     312 ..     126     429 ..     124     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 267.9 bits;  conditional E-value: 2.3e-83
                  CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHHHHHHHHHCTHSEEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspqlylellivagidrvfqiara 100
                  ++rl+ r +dlr++ ++k++ +rs  +ka+r+yl +++f+e++tP ++ ++te+ga lF +   +k  e f L+qspqly+e l ++ +++vf+ia+ 
   AJA92956.1 126 DTRLEVRAIDLRRNVLQKIFLARSVTLKALRDYLGKEDFVEVNTPKMIATATEGGAALFPIFYYNK--EAF-LAQSPQLYKEQLTMS-FEKVFEIAPI 219
                  799**********************************************************44433..555.***************.********** PP

                  E--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxx RF
  tRNA-synt_2 101 FRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrltykeaieklnei......gkdldkade 192
                  FRaE srt+rhl+E ++i++e ++++++d+m+ +eel+k+++++v ++  k+   + +    d++++++r++y+e iek++        g+dl  +++
   AJA92956.1 220 FRAEPSRTNRHLSEAISIDFEEAYVDYNDVMDRIEELVKNCISTV-QNFVKEHP-DVEFSVPDVPDKIPRYKYAELIEKMQAAgvkaqwGDDLYPKNL 315
                  *********************************************.55534433.333444799***************9888777766555544433 PP

                  .HHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEE CS
                  .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 193 .ralvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlgl 289
                   ++ +    + ++f++d+P   kpFy + ++dd+k++es+Dl++ ++El +Gs+Rie++ ele+++k+kg++    e f+  l+ +++G+pph+G+g+
   AJA92956.1 316 qKIGL----SGFYFIVDWPMGPKPFYVKVKKDDPKISESFDLMWGDLELSSGSTRIEKKSELEDRMKNKGMK---TEAFDYHLNIFDFGVPPHAGCGI 406
                  03444....59*************************************************************...*********************** PP

                  EHHHHHHHHCT-SSGGGCSSS-X CS
                  xxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 290 GldRlvmlllgsesIrdviaFPk 312
                  Gl+Rl+m l+g+e+Ird++++P+
   AJA92956.1 407 GLERLMMALTGTENIRDTTFYPR 429
                  **********************8 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.5   8.2e-14   3.7e-10       1      75 [.      27     105 ..      27     106 .. 0.95
   2 ?   -3.0   0.0       1.7   7.8e+03      37      68 ..     247     278 ..     241     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 8.2e-14
                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEE CS
  tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiel 75 
                      V+v G+v+++  r++g+++f+++rD+ g+iqv+  +    ++ ++ +++lke + + v G+ ++    p+g +e++ +e+++
       AJA92956.1  27 VVVMGWVVTV--RGHGNIVFATIRDKLGNIQVITKSgecdDDIREKLSHLKEHSSIAVVGKTRKNeksPTG-IEVVPSEMRI 105
                      89********..*****************************************************999999.9999988875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                      HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEE CS
  tRNA_anti-codon  37 eeatklaenlkeGdvvrvtGrvkrrpggelel 68 
                      +++++  e+l ++++  v   vk+ p+ e+++
       AJA92956.1 247 NDVMDRIEELVKNCISTVQNFVKEHPDVEFSV 278
                      56677778888888888888899988877765 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.66     3e+03     103     150 ..     212     258 ..     208     288 .. 0.56
   2 ?   11.0   0.0   4.7e-05      0.21     213     239 ..     403     431 ..     380     435 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.66
                   EEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHH CS
  tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellk 150
                   k++ i  +fR +     +hl e  ++++   +  v  +d++  +eel+k
    AJA92956.1 212 KVFEIAPIFRAEPsRTNRHLSEAISIDF--EEAYVDYNDVMDRIEELVK 258
                   6677777788777445555555544433..2223333333333333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.7e-05
                   EEEEEHHHHHHHHHT-SSGHH..HHTT.H CS
  tRNA-synt_2d 213 afGlGveRlamlkygieDiRe..lvendl 239
                   + G+G+eRl m  +g e+iR+  ++ +d+
    AJA92956.1 403 GCGIGLERLMMALTGTENIRDttFYPRDV 431
                   68******************733555565 PP

>> DraK_HK_N  DraK Histidine Kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.4e-05       0.2       8      53 ..     126     171 ..     120     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                 HHHHHHHHHHHHHHHHHHHHHTS---HHHHTTT-SS-SEEEEE-TT CS
   DraK_HK_N   8 qervesraqrlasivdsrlaagepitaelLeeqvpgdryvvVripg 53 
                   r+e ra  l ++v +++   + +t ++L+++ ++++ v V++p 
  AJA92956.1 126 DTRLEVRAIDLRRNVLQKIFLARSVTLKALRDYLGKEDFVEVNTPK 171
                 679*****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2934.70
//
Query:       AJA92957.1  [L=438]
Description: hypothetical protein T478_1406 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.074   13.4   1.7         13    6.1   0.1    2.8  2  PurL_C    Phosphoribosylformylglycinamidine synthase II C-ter


Domain annotation for each model (and alignments):
>> PurL_C  Phosphoribosylformylglycinamidine synthase II C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0012        21      17      38 ..      15      36 ..      11      62 .. 0.83
   2 ?    6.1   0.1   0.00075        13      16      62 ..      80     127 ..      73     138 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0012
                --GGGHHHHHHHHHHHHHTT-E CS
      PurL_C 17 felerekklWseirklvekgaf 38
                fel  ek++W+ ++klv  g++
  AJA92957.1 15 FELFLEKEVWTMLEKLVRSGTY 36
                89999************98876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00075
                 S--GGGHHHHHHHHHHHHHTT-EEE--T...TSS-HHHHHHHHTT-EEEE CS
      PurL_C  16 dfelerekklWseirklvekgafvvsss...dyskrttlenalkglklnv 62 
                 dfe er k  W+e +k+v    +++      ++ ++t +e+  +++kl+v
  AJA92957.1  80 DFE-ERKKLYWNENKKIVRSPRYLLKILpefSLPHLTEVEQ-EQDVKLEV 127
                 454.899999*********9999776541114555555555.34555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3226.95
//
Query:       AJA92958.1  [L=70]
Description: hypothetical protein T478_1260 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 490.40
//
Query:       AJA92959.1  [L=355]
Description: histidinol-phosphate transaminase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-43  148.3   0.0    3.7e-43  148.1   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II
    3.2e-05   23.0   0.0    4.4e-05   22.5   0.0    1.2  1  Alliinase_C    Allinase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   4.2e-47   3.7e-43       2     359 ..      26     346 ..      25     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 4.2e-47
                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEE CS
  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeil 97 
                    dv++L sne+l  +++ + + +++a+k+     +++    p  g   l + lak+l+        ++  + vg+G++++++++ + + + + ++il
     AJA92959.1  26 DVLKLDSNENLAIKKEFQTELIREAQKR-----SDIRT-YPLGGVENLISSLAKYLK-------VPKNMISVGNGSDQILDLILANF-CTKLTKIL 107
                    78999*****998555666655555555.....45544.56777*************.......667699*****************.8******* PP

                    EEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTC CS
  Aminotran_1_2  98 vpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagf 193
                     +dpt++ +++ ++l+ ++ v++p++  +++ l +e+++++ k+       + +i++ sp+NPtG  ++ ++lekl   +k+    +++DeaY++f
     AJA92959.1 108 TSDPTFGFFEERCKLYSIKQVTIPFS--KNMDLRIEDFIKKAKS-------VDMIYLDSPNNPTGFQFSNKDLEKL---IKSFSGPIIIDEAYGEF 191
                    ************************77..************8886.......58***********************...***************** PP

                    BSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHH.HHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 194 vfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsr.pflsssllqaavaaalsdallkqseleemrqrlqkrrkel 288
                            +++++v+++pn+++v +lsKafGlaG+R+Gy ++++++ +   ++ + p+   +l+ +    a+++++    ++    + ++k+r ++
     AJA92959.1 192 SNS-----SVLSLVKKYPNVILVKTLSKAFGLAGLRIGYMIADKKFTEVFSNVIQyPYPLNTLAIECGILAIEKSK----QIISIFEIIKKQRARI 278
                    **9.....67**********************************88888877765144457777777777777777....678999********** PP

                    HHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS.TTEEEEECTTS-HHHHHHH CS
  Aminotran_1_2 289 rdeLael.glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv.pgrlRitvAglteeeleel 359
                     ++L++   ++v++s+++++l+    a   + ++ +L+e+ g+ +++       +g+lR+t+  +t++++ ++
     AJA92959.1 279 IKNLKKYdAFDVFDSNANFVLFDAKGAD--TRVYNALIEQ-GISIRKLGKLAShKGCLRVTI--GTPDMNSKF 346
                    ****88899*************777766..999*******.******8888889********..666665554 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.9e-09   4.4e-05      67     220 ..      80     242 ..      70     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.9e-09
                  SEEEEECHHHHHHHHHHHHHHHH..SSSSSEEEEE-SS--THHHHHTTTT-BTTEE..EEEE....STT-.--S..S-EEEEEESS-TTT---..... CS
  Alliinase_C  67 ryivvGtGstqLlqalvyalspeasseskpvkvvaavPyysvykeqtslldsklyk..weGd....aaayvkkknpeefielvtsPnnPdgll..... 153
                  + i vG+Gs q+l+ ++  + +      k +k++++ P +  ++e+ +l++ k+    ++ +     ++++kk ++ ++i l  sPnnP g+      
   AJA92959.1  80 NMISVGNGSDQILDLILANFCT------KLTKILTSDPTFGFFEERCKLYSIKQVTipFSKNmdlrIEDFIKKAKSVDMIYL-DSPNNPTGFQfsnkd 170
                  5688999999999877766555......599****************99887765422444411226799999999999976.7******97422222 PP

                  ------TT-EEEEEE-TT-STTTS---...S-B--SEEEEEHHHHHS-GGG-EEEEEES-H...HHHHHHHHH CS
  Alliinase_C 154 reavvkgseakviyDlayYWPhytpit...skadedimLftlskltGhaGsrlGWalvkdk...evakklvey 220
                   e+++k+ ++ +i D ay     + +    +k  + i + tlsk  G aG r+G+ +  dk   ev + +++y
   AJA92959.1 171 LEKLIKSFSGPIIIDEAYGEFSNSSVLslvKKYPNVILVKTLSKAFGLAGLRIGYMI-ADKkftEVFSNVIQY 242
                  36899*************76555555411144455566679*************965.554122566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2675.64
//
Query:       AJA92960.1  [L=478]
Description: menaquinone biosynthesis decarboxylase, TIGR03701 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.4e-146  487.7   0.2   2.9e-146  487.5   0.2    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.5   0.2  1.6e-150  2.9e-146       2     405 ..      11     420 ..      10     421 .. 0.96

  Alignments for each domain:
  == domain 1  score: 487.5 bits;  conditional E-value: 1.6e-150
                 HHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..-............ CS
        UbiD   2 ealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkpp............ 88 
                 e lekagel++i++evd elE+aei+rr++  +gpallFenvkg+  ++pvl+n+fg+ +r++l l+ s++ ei++++a++++++ p            
  AJA92960.1  11 EVLEKAGELKKITTEVDSELELAEILRRTMYDNGPALLFENVKGY--DMPVLGNAFGSMKRLELSLETSDFTEIGQRIADMTKMEIPkgmlnkikklpe 107
                 78***************************99***********866..8***********************************999899********** PP

                 ......---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHC CS
        UbiD  89 ......ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkk 181
                        +p     +++p+  ev+  ++++  +++P+l+++++D+G++it gl++t++petg rnlg+yR+q++d +++ +hwq+hk+gaeh++  k  
  AJA92960.1 108 lskmseSFPSLE--KSGPVT-EVI--KENPTFDDIPILKSFHKDAGKFITFGLTATKHPETGIRNLGVYRIQIVDSTHALMHWQKHKRGAEHHAITKST 201
                 *99999888777..469***.564..589**************************************************************77665555 PP

                 CT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEE CS
        UbiD 182 ggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVta 280
                 +    +va++iG++Pa+++++vap+Pegl++++faG+ r++ +++vkc+t+d+evpa+AEivleG++d ++ ++EGPfgdhtGyy +++++fp+f++t 
  AJA92960.1 202 K---TEVAIIIGGEPATVFSGVAPVPEGLDKYLFAGITRKKGIKMVKCKTIDVEVPANAEIVLEGYVDSSDIRDEGPFGDHTGYY-TPKEPFPTFTLTG 296
                 5...9********************************************************************************.78899******** PP

                 EEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-T CS
        UbiD 281 ithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdv 379
                 ++ Rk+piy ttvvgkp  eda++gk++ ++flp++++  pev+d+ +p++g f+ la++sikkrypg+akkvm++lw+++q l ltK+++vvDedv+v
  AJA92960.1 297 VMQRKNPIYLTTVVGKPILEDAYIGKVIASSFLPMIRMFHPEVVDFEMPAAGWFQGLAIISIKKRYPGQAKKVMMGLWGMGQ-LALTKMFVVVDEDVNV 394
                 **************************************99****************************************88.**************** PP

                 TSHHHHHHHHHHC--CCCCEEEECCC CS
        UbiD 380 rdlkevlwaiatrvdpdrDlviiegt 405
                 +d+++v+wai+tr d++rD++ii+++
  AJA92960.1 395 HDMNDVIWAITTRTDAARDITIIDRA 420
                 ***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3626.80
//
Query:       AJA92961.1  [L=296]
Description: winged helix-turn-helix DNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   21.8   0.0    0.00046   19.9   0.0    1.9  2  HTH_23         Homeodomain-like domain
    0.00055   19.8   0.1     0.0015   18.5   0.1    1.8  1  HTH_11         HTH domain
    0.00057   20.3   0.0    0.00093   19.6   0.0    1.3  1  B12-binding_2  B12 binding domain
    0.00076   19.0   0.1      0.002   17.7   0.0    1.8  2  HTH_24         Winged helix-turn-helix DNA-binding
     0.0018   18.2   0.1        0.4   10.7   0.0    3.0  2  HTH_Mga        M protein trans-acting positive regulator (MGA
     0.0031   17.5   0.0     0.0066   16.4   0.0    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.031   14.2   0.0      0.072   13.0   0.0    1.6  1  MarR           MarR family
      0.051   13.9   0.6        1.9    8.9   0.0    3.0  3  Mnd1           Mnd1 HTH domain
      0.052   13.6   0.0       0.18   11.9   0.0    1.9  2  HTH_29         Winged helix-turn helix
       0.11   12.5   0.0       0.24   11.3   0.0    1.5  1  PAX            'Paired box' domain
       0.11   12.3   0.0       0.23   11.3   0.0    1.5  1  HTH_10         HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.8e-07   0.00046       4      45 ..       8      52 ..       5      56 .. 0.90
   2 ?   -1.7   0.0       1.7   2.7e+03      28      40 ..      93     105 ..      91     109 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.8e-07
      HTH_23  4 ereRlrillllae...GlsvreIAreLgvsrrTvyrwlkryreeG 45
                 + ++r ++ll     G+s  eI+++Lg++r T +++l+++++eG
  AJA92961.1  8 TEVKFRLIKLLHSsksGISGVEISEKLGINRVTMSKYLNKFAAEG 52
                6789999999998889*************************9898 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
      HTH_23  28 gvsrrTvyrwlkr 40 
                 ++++r+v + +k 
  AJA92961.1  93 DCNERHVNNLIKN 105
                 799******9997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     9e-07    0.0015       3      38 ..      12      47 ..      10      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9e-07
      HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIka 38
                + +++lL ++++ isg e++e+L++ r t  +++ +
  AJA92961.1 12 FRLIKLLHSSKSGISGVEISEKLGINRVTMSKYLNK 47
                578999*999999****************9999876 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.7e-07   0.00093       1      62 [.      83     144 ..      83     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.7e-07
  B12-binding_2   1 laerlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvll 62 
                    ++e+++  +++ +++ ++ li+ +++++ + ++++ ++++p++ ++ +lf+ g++   ++ l
     AJA92961.1  83 VQEKFLSHVIDCNERHVNNLIKNCINSKAKMDKIITEIIIPTIPHIQKLFDDGKIGKSEEQL 144
                    57899999*****************88888************************97666655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.2e-06     0.002       4      48 .]      10      55 ..       7      55 .. 0.92
   2 ?   -3.1   0.0       3.7     6e+03      36      43 ..      97     104 ..      97     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
      HTH_24  4 tdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                 ++++++lL   +++is  e++e+lg+ + t +++l+++  eG I+
  AJA92961.1 10 VKFRLIKLLHSsKSGISGVEISEKLGINRVTMSKYLNKFAAEGTIT 55
                6789999999999******************************985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
      HTH_24  36 rrlkrLee 43 
                 r++++L++
  AJA92961.1  97 RHVNNLIK 104
                 899**998 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00025       0.4       7      44 ..      11      48 ..       8      54 .. 0.93
   2 ?    3.9   0.0     0.035        57      39      55 ..      69      83 ..      67      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
     HTH_Mga  7 klkLlelLteneksltldelakeLglseltlqsdiseL 44
                k +L+ lL ++++ ++ +e++++Lg+ ++t  ++++++
  AJA92961.1 11 KFRLIKLLHSSKSGISGVEISEKLGINRVTMSKYLNKF 48
                6789*******************************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
     HTH_Mga 39 sdiseLnelFpeelsiv 55
                +di++Ln  Fp++++ v
  AJA92961.1 69 EDIEQLN--FPDDYFLV 83
                79*****..****9976 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.1e-06    0.0066      25      55 ..      28      58 ..      13      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.1e-06
                HHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
   HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgr 55
                 e+++ lG++r+t+s+ l+++  eg i++++
  AJA92961.1 28 VEISEKLGINRVTMSKYLNKFAAEGTITQKN 58
                5899***********************9554 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.4e-05     0.072       2      48 ..       8      55 ..       8      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-05
                -HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR  2 tltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                t++ f+++ +l+++ + +s  e+ +klg+++ t+++ l +   +G i+
  AJA92961.1  8 TEVKFRLIKLLHSSKSgISGVEISEKLGINRVTMSKYLNKFAAEGTIT 55
                7889**********9989999*********************999886 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011       1.9      23      56 ..      32      65 ..      27      67 .. 0.89
   2 ?    2.0   0.0      0.16   2.6e+02      35      46 ..     127     138 ..      99     141 .. 0.83
   3 ?   -3.6   0.0       9.2   1.5e+04       9      16 ..     246     253 ..     245     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
        Mnd1 23 kekgivsqsVkdvlqsLvdDglveveKiGssnvy 56
                 + gi++ ++  +l++  ++g + ++ iG+ n++
  AJA92961.1 32 EKLGINRVTMSKYLNKFAAEGTITQKNIGNLNLW 65
                3489***************************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
        Mnd1  35 vlqsLvdDglve 46 
                 ++q+L dDg++ 
  AJA92961.1 127 HIQKLFDDGKIG 138
                 69*******985 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.2
        Mnd1   9 kefytlKe 16 
                  +fy++Ke
  AJA92961.1 246 DSFYSVKE 253
                 68999998 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.18       9      63 .]      22      73 ..      15      73 .. 0.85
   2 ?   -2.5   0.0       3.3   5.4e+03      20      34 ..      90     104 ..      88     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
      HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn.rlseeqea 63
                + G s   +i + lg+ r t  ++l+ f ++G   ++ +++ g+++   ++e+ e+
  AJA92961.1 22 KSGIS-GVEISEKLGINRVTMSKYLNKFAAEG---TITQKNIGNLNLwFVDEDIEQ 73
                56775.9*************************...899999999988888887776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
      HTH_29  20 kllglsrrtvyrwlk 34 
                 ++ ++ +r+v++ +k
  AJA92961.1  90 HVIDCNERHVNNLIK 104
                 567889999999998 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.24      25      70 ..      16      61 ..       7      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
         PAX 25 kivelahsgvrpcvisrqlrvshgcvskilgryqetgsirpgvigg 70
                k++  ++sg+  ++is +l + +  +sk l+++   g+i  + ig 
  AJA92961.1 16 KLLHSSKSGISGVEISEKLGINRVTMSKYLNKFAAEGTITQKNIGN 61
                34445678*********************************99996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.23      24      46 ..      25      47 ..      22      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
      HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                ++  e++++lGI + t+s++L+k
  AJA92961.1 25 ISGVEISEKLGINRVTMSKYLNK 47
                56779****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2274.08
//
Query:       AJA92962.1  [L=260]
Description: NAD+ synthetase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-75  251.1   0.1      9e-75  250.9   0.1    1.0  1  NAD_synthase   NAD synthase
    1.6e-05   23.9   0.0     0.0046   15.8   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase
     0.0013   18.3   0.0     0.0061   16.1   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
     0.0083   15.8   0.0      0.018   14.7   0.0    1.5  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.016   15.1   0.5         11    5.9   0.0    3.1  3  HTH_25         Helix-turn-helix domain
      0.021   14.6   0.0      0.037   13.8   0.0    1.4  1  ATP_bind_3     PP-loop family
      0.069   12.7   0.0        1.3    8.6   0.0    2.3  2  ThiI           Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.9   0.1   3.5e-78     9e-75       3     242 .]      19     257 ..      17     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 250.9 bits;  conditional E-value: 3.5e-78
                   HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH-H CS
  NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidikpivrafeqelkeaked 98 
                   +++++ lk++++++++kgv++GlSGG+DS+++a+l+ +++ ke+ la+++P s+ s+e+++ da++++++lg+++k +di++i + f+  l+++   
    AJA92962.1  19 TRIQEGLKQKIEETNSKGVIFGLSGGIDSAVIAYLCNNIV-KEKTLAVIMPdSKISPESETSDAIKIVDELGLDYKLLDINSIHKEFNMVLEPED-- 112
                   578899**********************************.**********9999********************************99998876.. PP

                   HHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-H CS
  NAD_synthase  99 lakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikY 195
                    a gNl+aRiRm+ily++an  nl+ lg ++ksE  +GyfTk+GDgaad++pi +l+Kt+v+eLa++l++ e++++k+ s +L+p+   e+e+g++Y
    AJA92962.1 113 RALGNLRARIRMNILYYYANLKNLVTLGSSDKSEFNIGYFTKFGDGAADVLPIVSLYKTQVRELARHLGIDESIITKKSSPHLWPNHEAEHEIGVEY 209
                   899********************************************************************************************** PP

                   HHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGSSS CS
  NAD_synthase 196 delDeiLk.lvekkkspeeiikekelpaevvekieklvkksehKrklp 242
                   +++D iL+ ++++k s +++++e +++ + veki +++ ksehKr  p
    AJA92962.1 210 EQIDVILHcFIDRKLSLNDTANESQIDIKLVEKIHSMYMKSEHKRINP 257
                   ********9***********************************9765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-06    0.0046       3      75 ..      37     102 ..      35     110 .. 0.75
   2 !    5.9   0.0    0.0018       4.7     165     193 ..     162     192 ..     159     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
  tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeqgye.vigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeyk 75 
                    v+ +lSgG+DS+v a+l ++  +e + +v++  +        + + e++++da ++ ++lg+ ++ +d+++ +k
     AJA92962.1  37 VIFGLSGGIDSAVIAYLCNNIVKEkTLAVIMPDS--------KISPESETSDAIKIVDELGLDYKLLDINSIHK 102
                    899**************99876541444444322........23566788999999999999999999877665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0018
  tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdS 193
                    ++P+ +l K++vr++A++ g++  + +kk S
     AJA92962.1 162 VLPIVSLYKTQVRELARHLGIDesIITKKSS 192
                    79*****************998778888887 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06    0.0061       3      72 ..      38     108 ..      36     142 .. 0.79
   2 ?   -0.9   0.0      0.38   9.8e+02     157     176 ..     164     183 ..     160     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                 EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG CS
        QueC   3 vvllSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkiakelgveehkildldllkelggsaL 72 
                 +  lSGG+DS+++++l ++ +ke ++  +  +++   ++e++ a ki++elg+ + k ld++ +++  +  L
  AJA92962.1  38 IFGLSGGIDSAVIAYLCNNIVKEKTLAVIMPDSKisPESETSDAIKIVDELGL-DYKLLDINSIHKEFNMVL 108
                 6779**************9998877666666666447788888999*******.*******99887655555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                 TTTT--HHHHHHHHHHTTHH CS
        QueC 157 PlidlsKaeivklgkelgvp 176
                 P++ l K+++ +l+ +lg++
  AJA92962.1 164 PIVSLYKTQVRELARHLGID 183
                 99999999999999999954 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.9e-06     0.018      24      74 ..      41      92 ..      32     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-06
  Asn_synthase 24 LSGGlDSSliaalaarqsksplktFsigfee...kgsdeakyakevaehlgteh 74
                  LSGG+DS++ia+l +   k   kt ++ + +      +e++ a +++++lg++ 
    AJA92962.1 41 LSGGIDSAVIAYLCNNIVK--EKTLAVIMPDskiSPESETSDAIKIVDELGLDY 92
                  9***************996..588888883234567777777788888888874 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.54   1.4e+03      19      34 ..      18      33 ..       2      36 .. 0.69
   2 ?    5.7   0.0    0.0053        13      35      60 ..     160     185 ..     150     187 .. 0.81
   3 ?    5.9   0.0    0.0045        11       9      31 ..     222     244 ..     220     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.54
                HSS--HHHHHHHHCT- CS
      HTH_25 19 etkIrkdylealEedd 34
                 t+I++ + +++Ee +
  AJA92962.1 18 STRIQEGLKQKIEETN 33
                5777777777777765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0053
                 -TTSS-HHHHHHHHHHHHHHTT--HH CS
      HTH_25  35 fdalpepvylrgylrnYArlLgldpe 60 
                  d lp     +  +r++Ar+Lg+d++
  AJA92962.1 160 ADVLPIVSLYKTQVRELARHLGIDES 185
                 5667777777889**********985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0045
                 TT--HHHHHHHSS--HHHHHHHH CS
      HTH_25   9 rglsleevaketkIrkdylealE 31 
                 r+lsl + a+e +I  +++e++ 
  AJA92962.1 222 RKLSLNDTANESQIDIKLVEKIH 244
                 89******************995 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.037       2      67 ..      37      98 ..      36     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE-- CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvd 67
                v+ ++SgG+DS ++ +l ++  k+   +l++i+ d ++++es+   ++  +++++l+++++  +++
  AJA92962.1 37 VIFGLSGGIDSAVIAYLCNNIVKE--KTLAVIMPDSKISPESETSDAI--KIVDELGLDYKLLDIN 98
                6789***************99775..5789999999999877665443..4555555555555555 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00051       1.3       6      23 ..      37      54 ..      32     109 .. 0.79
   2 ?    1.8   0.0     0.058   1.5e+02     143     170 ..     164     191 ..     159     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00051
        ThiI  6 vlaLlSgGiDSpVaayll 23
                v+  lSgGiDS V ayl 
  AJA92962.1 37 VIFGLSGGIDSAVIAYLC 54
                66779***********85 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.058
        ThiI 143 PLigldKeeiiklAkeigtyeisieked 170
                 P+++l K ++ +lA+++g  e  i+k+ 
  AJA92962.1 164 PIVSLYKTQVRELARHLGIDESIITKKS 191
                 99****************9887666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1680.93
//
Query:       AJA92963.1  [L=43]
Description: hypothetical protein T478_1352 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 317.95
//
Query:       AJA92964.1  [L=126]
Description: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-18   67.3   0.7    1.3e-18   66.9   0.7    1.2  1  Oxidored_q4      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.071   13.2   0.0    1.4  1  MPS-4            MinK-related peptide, potassium channel acce
       0.54   10.2   0.1       0.54   10.2   0.1    2.1  3  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.7   2.2e-22   1.3e-18       4      93 ..      26     118 ..      12     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2.2e-22
                  HHHHHCHSS---...--HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHHH CS
  Oxidored_q4   4 llllsallgpkk...pnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYewk 93 
                  +ll+s++l+p++   pn+ k+ p EcG  p g  r++f +++y + l+F+iFDv ++fl++w  sl +l  ++++ ++ Fl+i+++++++++ 
   AJA92964.1  26 ALLVSRMLSPENkkqPNPVKTLPMECGQVPSGAGRTHFMMQYYAYVLMFVIFDVMAIFLYAWGSSLLDLPRTATLPIIAFLGIMFAAMAFALY 118
                  5788999987764446677***********************************************99999******************9975 PP

>> MPS-4  MinK-related peptide, potassium channel accessory sub-unit protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.071      20      72 ..      46      96 ..      37     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
       MPS-4 20 ylleeflkrssscnrisystkyfdfllvviisvvslglvylllwievllnsvr 72
                 l  e  +  s   r  +  +y+ ++l+ +  ++ + +++l  w   ll+  r
  AJA92964.1 46 TLPMECGQVPSGAGRTHFMMQYYAYVLMFV--IFDVMAIFLYAWGSSLLDLPR 96
                56667778889999**********998766..578899******999997655 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2      0.98   5.8e+03      22      36 ..      15      29 ..      10      31 .. 0.48
   2 ?   -2.9   0.7       1.2   6.9e+03       2      10 ..      40      48 ..      39      48 .. 0.83
   3 ?   10.2   0.1     9e-05      0.54      19      41 ..     102     124 ..      94     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.98
                     XXXXXXXXXXXXXXX CS
  Gram_pos_anchor 22 aaGllallggllLlv 36
                      +G + ++ + +Llv
       AJA92964.1 15 MFGFACAAMAPALLV 29
                     444444455555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                     EEEBB-XXX CS
  Gram_pos_anchor  2 kkskkkqLP 10
                     + + +k+LP
       AJA92964.1 40 QPNPVKTLP 48
                     678899**9 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 9e-05
                      XXXXXXXXXXXXXXXXXXXXXXX CS
  Gram_pos_anchor  19 fltaaGllallggllLlvkrRKk 41 
                      +  ++G++ ++ +++L+ ++RK+
       AJA92964.1 102 IIAFLGIMFAAMAFALYQSKRKD 124
                      56789****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 976.77
//
Query:       AJA92965.1  [L=429]
Description: phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-23   83.5   0.0    2.8e-23   82.2   0.0    1.7  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    5.7e-16   58.7   0.2    2.2e-15   56.8   0.1    1.9  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.2e-11   45.1   0.0    2.5e-11   44.1   0.0    1.5  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.8e-06   27.0   0.0    7.8e-06   26.0   0.0    1.5  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
       0.13   12.2   0.1        0.3   11.0   0.1    1.6  1  PELOTA_1     PELOTA RNA binding domain
       0.32   11.3   2.9       0.66   10.3   2.9    1.5  1  SirA         Sporulation inhibitor of replication protein Sir


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   9.4e-27   2.8e-23       7     120 ..       6     111 ..       1     128 [. 0.88

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 9.4e-27
                 TCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--TTS-TT CS
   PGM_PMM_I   7 sGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaSHnppe 105
                 sG+Rg++g++ + pe v k+ +++ + +k     +k ++G+DtR +++++++ + a +++ G++v++lg++ptP+v   +++  + agi+it SHnp e
  AJA92965.1   6 SGIRGVYGKD-FFPEDVIKFCNGFSKLIKT----GKCAIGMDTRETGEMIQKLVSATMLERGIDVYNLGIIPTPVVFRKAKE--IGAGIVITSSHNPLE 97 
                 8*******66.9*****************8....9******************************************99999..78************* PP

                 CCCEEEEETTTCE-- CS
   PGM_PMM_I 106 yngiKvylsnGgpis 120
                  ng+K++   G  i+
  AJA92965.1  98 WNGLKFIID-GRGIT 111
                 *****9876.44443 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   3.2e+03      23      50 ..      48      75 ..      37      78 .. 0.79
   2 !   56.8   0.1   7.4e-19   2.2e-15      23      99 ..     251     328 ..     232     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                 EEEEETTS-THHHHHHHHTT-EEEEESS CS
  PGM_PMM_III 23 gvvktvmtslalervakklgiklvetkv 50
                  +++++++ ++ler ++ +++ ++ t+v
   AJA92965.1 48 EMIQKLVSATMLERGIDVYNLGIIPTPV 75
                 4788999999999999999988888886 PP

  == domain 2  score: 56.8 bits;  conditional E-value: 7.4e-19
                  EEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETT.CEEEETTTBSS--HHHHHHHHHHHHHHH CS
  PGM_PMM_III  23 gvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeS.ghiifldeattkDGilaallvleilaet 99 
                  + v ++ +sla+e+++ ++g+k+ ++kvG  +v+++m e++a  GgE S g++i++d++ ++DG+l++ l+++++ ++
   AJA92965.1 251 KFVLSIDSSLAVEKYIIQHGGKVSRSKVGEANVIQMMIENDAEAGGEGSsGGFILKDFNMCRDGLLTSGLIASMIDDE 328
                  58999********************************************9***********************99865 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   8.3e-15   2.5e-11       3      99 ..     139     225 ..     137     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 8.3e-15
                 HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEE CS
  PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDaDRlgvv 99 
                 Yi + ++++  + +k    +v +d ++Ga+++i+++ll+e+g++v ++n+e d+      p+p+   +l +l   v ++  dlg+afD D DR+++v
  AJA92965.1 139 YISDAVKIIG-KLNKT--QQVTVDIGGGAAKTIAPKLLQEIGCQVETINDELDGCSR--GPDPTS-NELTEL---V-SKTKDLGFAFDLDSDRVILV 225
                 6666666666.34444..58**********************************665..589998.445555...4.5667**************99 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.6e-09   7.8e-06      12      72 ..     361     420 ..     348     422 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.6e-09
                 ..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
  PGM_PMM_IV  12 vvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevael 72 
                 +v+++++ +k  s+ +g+ki   d ++  +R S+Te+ +r+  E+ ++e+l ++++e+++ 
  AJA92965.1 361 IVKKIEGKYKI-SQLDGIKISIDDNTWSLIRKSNTEDIIRISTESNDRELLVKIQKEMIKM 420
                 67888888887.999999*9999998888*************************9998865 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001       0.3       5      60 ..     360     416 ..     357     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
    PELOTA_1   5 aaveriaeeygiedinliKPgigEaTRvlLRRvPekvlvrdeee.pdlahlllLake 60 
                 + v++i+ +y+i++ + iK +i + T  l+R+   + ++r  +e +d ++l+++ ke
  AJA92965.1 360 EIVKKIEGKYKISQLDGIKISIDDNTWSLIRKSNTEDIIRISTEsNDRELLVKIQKE 416
                 679*****************************9888777765551555555554444 PP

>> SirA  Sporulation inhibitor of replication protein SirA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.9   0.00022      0.66      18     103 ..     331     423 ..     320     428 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                 T-CHHHHHHHHHHHCS---HHHHHHHHHHHHEE---.HHHHHH......HHHHHCT.TSEEEEETTEEEEE-GGGSEEEEEEEETTEEEEEEE CS
        SirA  18 greskLfklfeeiykakeedkeilykqieqitkplp.klklnk......klkqklsekigykkeknihvinnlkkeevaeltiknsyiklete 103
                 ++   +f+ f +i+   + ++++ +k i++i+k+++ k+k+ +       + ++    i  +++++i++i++++++    ++i++++ik+  +
  AJA92965.1 331 QKDIEFFESFSQIRDKVSIESSLHDKIITEIVKKIEgKYKISQldgikiSIDDNTWSLIRKSNTEDIIRISTESNDRELLVKIQKEMIKMVEN 423
                 567789*****************************74556555332222566777777899****************************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3280.89
//
Query:       AJA92966.1  [L=185]
Description: redoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-22   78.0   0.2    6.9e-22   77.7   0.2    1.1  1  AhpC-TSA       AhpC/TSA family
    3.6e-15   56.0   0.1    4.6e-15   55.6   0.1    1.1  1  Redoxin        Redoxin
    1.8e-05   25.0   0.1      3e-05   24.2   0.1    1.4  1  Thioredoxin_8  Thioredoxin-like
     0.0003   21.2   0.1     0.0005   20.5   0.1    1.3  1  Thioredoxin_2  Thioredoxin-like domain
     0.0089   15.6   0.0      0.014   14.9   0.0    1.3  1  GSHPx          Glutathione peroxidase
  ------ inclusion threshold ------
      0.026   14.5   0.2       0.31   11.0   0.1    2.1  2  Thioredoxin    Thioredoxin
      0.068   13.0   0.0       0.17   11.7   0.0    1.7  1  TraF           F plasmid transfer operon protein
        0.1   12.5   0.0       0.13   12.1   0.0    1.2  1  SCO1-SenC      SCO1/SenC
       0.12   11.6   0.0       0.17   11.1   0.0    1.3  1  T4_deiodinase  Iodothyronine deiodinase


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.2   3.4e-25   6.9e-22       2     122 ..      13     133 ..      12     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 3.4e-25
                 TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH........HHHHHHHH-H.SSEEEE-TTS CS
    AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe........shkkfiekeslnfpllsDeeg 92 
                 gd ap+f+lk  d +  sl+dy++k +++ f+++ +cp+ +++++a+++l+++fk  ++ ++g+++++          s+k+ +++++l++++l De++
  AJA92966.1  13 GDNAPEFNLKGIDDQMHSLNDYSKKGLLVIFMCN-HCPFVKAKIEAIKELHDKFK-DDISIVGINSNDSVkypdddfdSMKAVAKEKGLEIDYLVDETQ 109
                 99********************999999999999.********************.79********66666**************************** PP

                 HHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
    AhpC-TSA  93 kvakaygvlkeekglalratfvidkegkir 122
                 ++ak+yg++      +++  f++d+e+k+ 
  AJA92966.1 110 EIAKKYGAV------CTPDPFLFDSEKKLI 133
                 *********......99********99975 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.1   2.3e-18   4.6e-15       1     131 [.      11     136 ..      11     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 2.3e-18
                 -TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH........HHHHHHHTT-TSEEEE CS
     Redoxin   1 kagdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf........vkefwgkeglkfpvls 91 
                 k gd aP+f+l++   d + +sl ++ +k  +++++ +++cP  +a++ ++++l ++  + ++++v+++++++          +k++++++gl + +l+
  AJA92966.1  11 KTGDNAPEFNLKG--IDDQMHSLNDYSKKG-LLVIFMCNHCPFVKAKIEAIKELHDK-FKDDISIVGINSNDSVKypdddfdsMKAVAKEKGLEIDYLV 105
                 579********88..**********98777.88999999***************999.5667******9998877888888*66666666********* PP

                 -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEE CS
     Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvyle 131
                 D++++++k++G+          +tp  +++d ++k++  +
  AJA92966.1 106 DETQEIAKKYGAV---------CTPDPFLFDSEKKLIFHG 136
                 ***********88.........************998765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.5e-08     3e-05       4      93 ..      39     130 ..      36     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.5e-08
                    EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-.......SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT-SEEEEE-TT CS
  Thioredoxin_8   4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl.......dkkeeefekylkknkkpwlsvpfddkkrnklkkkynvkaiPtlvvldkn 92 
                    +l+ f  ++cp  ka ++ +kel++k+k  +++ iv +++       d + ++++++ k+     l++++  +++++++kky+  + P  ++ d++
     AJA92966.1  39 LLVIFMCNHCPFVKAKIEAIKELHDKFK--DDISIVGINSndsvkypDDDFDSMKAVAKEK---GLEIDYLVDETQEIAKKYGAVCTPDPFLFDSE 129
                    6899***********************9..**********888888777777777777777...99999999999*************99999976 PP

                    - CS
  Thioredoxin_8  93 g 93 
                    +
     AJA92966.1 130 K 130
                    5 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.5e-07    0.0005       5      96 ..      36     134 ..      33     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkd...................ieenvelarkygvrgt 81 
                    +k +lv+f  ++Cp+ k+   +++ +++++++     +k++  + +v i  ++++k   +d                   ++e++e a+kyg   t
     AJA92966.1  36 KKGLLVIFMCNHCPFVKA---KIEAIKELHDK-----FKDD--ISIVGINSNDSVK-YPDDdfdsmkavakekgleidylVDETQEIAKKYGAVCT 120
                    899***********9887...77777777888.....8888..7777777777774.4444555566688899*********************** PP

  Thioredoxin_2  82 Ptivfldgkeivarl 96 
                    P+ +++d + + ++ 
     AJA92966.1 121 PDPFLFDSE-KKLIF 134
                    **8888888.33344 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.1e-06     0.014       4      78 ..      19      93 ..      17     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                BEEEBTTSSEEEGGGGTTSEEEEEEEESSSTTHH.HHHHHHHHHHHHGGGTEEEEEEEE-TTTT---S-GGGHHHT CS
       GSHPx  4 lsakdidgekvkleklrgkvvlivnvaskCglte.qykeleelqkrykdkglvilgfPCnqfgkqepgsdeeikkf 78
                ++ k id ++ +l+ +  k +l++ +  +C + + + + ++el+ ++kd  + i+g   n   k    + + +k +
  AJA92966.1 19 FNLKGIDDQMHSLNDYSKKGLLVIFMCNHCPFVKaKIEAIKELHDKFKD-DISIVGINSNDSVKYPDDDFDSMKAV 93
                77889999*************************999***********95.68899988887666554444445555 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00016      0.31      17      61 ..      35      79 ..      25      90 .. 0.85
   2 ?    1.5   0.0      0.15     3e+02      58      84 ..     105     131 ..      87     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                 TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTS CS
  Thioredoxin 17 ekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvden 61
                 +kk +lv F+ + C+  ka    +++l +++kd++ ++ ++ +++
   AJA92966.1 35 SKKGLLVIFMCNHCPFVKAKIEAIKELHDKFKDDISIVGINSNDS 79
                 68899999*999999999999999**************9998766 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.15
                  TTTSHHHHHHTT-SSSSEEEEEETTEE CS
  Thioredoxin  58 vdenedlakkyevegiPtlklfkngke 84 
                  vde +++akky+  + P   lf ++k+
   AJA92966.1 105 VDETQEIAKKYGAVCTPDPFLFDSEKK 131
                  699999******999999988887774 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.6e-05      0.17     119     177 ..      26      84 ..      18     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.6e-05
        TraF 119 ekeaalkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpn 177
                 ++   l++ +k+  L++F+ ++cp+ +a ++ ++++ dk++ ++ +V ++ + + ++p+
  AJA92966.1  26 DQMHSLNDYSKKGLLVIFMCNHCPFVKAKIEAIKELHDKFKDDISIVGINSNDSVKYPD 84 
                 56778999999999*************************97777777776665544555 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.7e-05      0.13       3      98 ..      18     113 ..      16     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
   SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfi.TvDPerDtpevlkeyleafdpriigltGskeeiak 98 
                 +F+l   d++  + +d+++k  lv f+  hCp v  ++++ ++e+ d+++++   v + +  +v    D+ + +k+ +++ + +i  l ++ +eiak
  AJA92966.1  18 EFNLKGIDDQMHSLNDYSKKGLLVIFMCNHCPFV-KAKIEAIKELHDKFKDDISIVGINSNdSVKYPDDDFDSMKAVAKEKGLEIDYLVDETQEIAK 113
                 78888889999999******************99.789**************655665553599999*********************998888876 PP

>> T4_deiodinase  Iodothyronine deiodinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.7e-05      0.17      73     137 ..      10      71 ..       2      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
  T4_deiodinase  73 vkeGgdaPnsevvrvsgteschildfaqgnrPlvlnfGsatcPpflaklsafkrlveefssvadf 137
                     k+G++aP+ ++  ++ +    + d+   ++ l++ f    cP   ak++a k l ++f+ ++  
     AJA92966.1  10 LKTGDNAPEFNLKGIDDQM-HSLNDYS--KKGLLVIFMCNHCPFVKAKIEAIKELHDKFKDDISI 71 
                    5889999999999999888.8899997..5789999***********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1449.02
//
Query:       AJA92967.1  [L=178]
Description: tRNA-intron endonuclease [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-30  105.2   0.1    2.9e-30  104.2   0.0    1.5  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    1.7e-16   59.6   0.1    2.7e-16   59.0   0.1    1.3  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.66   5.9e+03      41      59 ..      58      76 ..      56      83 .. 0.61
   2 !  104.2   0.0   3.2e-34   2.9e-30       1      85 []      86     170 ..      86     170 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.66
                   SEEEEEEETTSEEEHHHHH CS
  tRNA_int_endo 41 eylVvvvsedeeldwpdls 59
                   ++ +++++++++++ ++++
     AJA92967.1 58 KSKIQIYKNKKKITTKKML 76
                   5556666666666666655 PP

  == domain 2  score: 104.2 bits;  conditional E-value: 3.2e-34
                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85 
                    f++k+ vy+d+r+kGy+v++G+kFG+dF+vYq++p+ +h+ +lV+v++ +e+++ +d++ a+rla svkK++ilai + +++v+y
     AJA92967.1  86 FEKKFQVYKDFRDKGYIVNPGIKFGCDFAVYQKGPGIDHAPFLVQVYNRNENMTSTDIVLAGRLASSVKKQFILAIPSGKDKVDY 170
                    899*****************************************************************************99998 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.1     3e-20   2.7e-16       1      66 [.       1      75 [.       1      76 [. 0.97

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 3e-20
                     EEEEEETTEEEESSHHHHHHHHHTTT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
  tRNA_int_endo_N  1 vegeLsgdrvlvedeeaakrlyekgfYGkp.........lidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                     ++ eL+++r +v++ +++k+l+ +g+YGkp         +i+ pL L+l+E+ YL++k k++++k++++++ +++
       AJA92967.1  1 MKTELLENRLIVWNLDDSKKLFGQGYYGKPigipkpkldEINVPLILDLIEGYYLMSKSKIQIYKNKKKITTKKM 75
                     789*******************************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1404.79
//
Query:       AJA92968.1  [L=586]
Description: AIPR protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-47  162.9  10.4    1.3e-47  162.9  10.4    1.8  2  AIPR      AIPR protein


Domain annotation for each model (and alignments):
>> AIPR  AIPR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1     0.069   1.2e+03     242     282 ..     132     186 ..      62     204 .. 0.59
   2 !  162.9  10.4   7.1e-52   1.3e-47       1     276 [.     229     521 ..     229     550 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.069
        AIPR 242 k.............anivyyilaalrkllkkk.ldllkiweeqkisqelekllek 282
                 k             +++ ++++ +  + ++++ +d  +++ +q+++q+l++ ++k
  AJA92968.1 132 KrdelqilwkilndKKMKVDLVYITDQCVDDYqNDKVRVMGRQQVYQTLWERIKK 186
                 1333333333444433333333333333333343345666666665555555544 PP

  == domain 2  score: 162.9 bits;  conditional E-value: 7.1e-52
        AIPR   1 lekNvReflgttgkvNkgIreTlreepekFflyNNGItitaekiklekkesgseviielenlqIVNGgQTtasIykalkkkldlskvyVqvklikvaed 99 
                 +e+N+R+ lg++g +Nk+I  Tl+++p++Ff  NNGItit+++++++  +++    + l++ qIVNG+QT +sI++++kk+++  ++ V+v++ik+  +
  AJA92968.1 229 FESNIRKHLGGKGSINKKISTTLEDDPHQFFEWNNGITITVDDVSIK--NNE----LYLKGAQIVNGAQTSKSILDKKKKANN-VDAEVLVTVIKT--K 318
                 8*********************************************6..443....56**********************988.99**********..9 PP

        AIPR 100 eedlikeIsraaNsQnkVsdkdlasndefhkrlekllreeqtkvfYerargefdnek.............afk.....pkskkitk.tdlakvlnalfl 179
                 +e+ +++I++++NsQn+V+ kd +s++++++ ++  l+ ++  + +e ++g + n +             + k     + + +i+  + +a+++  +f 
  AJA92968.1 319 DEEHQRKITKYRNSQNAVKGKDYVSLQDYFVSIHHMLA-TRLDYCFEHQQGLWLNLStaekakfqgdemyN-KylpdaKDRCRIKDdSAIASFVS-YFV 414
                 99************************************.9****************999999666655541.05654433333444255666665.*** PP

        AIPR 180 qkPhqaskgkaklekkyekeeekgskyekifkeklt..ykkliasvilfkklekkikke...lkegykanivyyilaalrkllkkk............l 261
                 qkP+++++g ak         ++g kye++f+++l   y+ ++   ++ +++++++       ++++k+++    +a+ +++++k+            l
  AJA92968.1 415 QKPNEVYGGIAK-------YLPNGAKYENVFNDELEcdYRYFLFPHLIREFAKNQLGYDrknTQNKNKRYAQSLFVAVTARIIHKNilakhddfkmdiL 506
                 ************.......67899*******99999997777777777777777666664332223333333333333333333333334677766666 PP

        AIPR 262 dllkiweeqkisqel 276
                 +l+ki+++ ++ +++
  AJA92968.1 507 ELEKIMKNFGLCEKV 521
                 666666666555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 4003.47
//
Query:       AJA92969.1  [L=80]
Description: hypothetical protein T478_0595 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 598.27
//
Query:       AJA92970.1  [L=150]
Description: hypothetical protein T478_1089 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00076   18.5   2.8      0.001   18.1   2.8    1.2  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.15   11.9   4.3      0.068   13.0   1.5    1.7  2  DUF2955   Protein of unknown function (DUF2955)
       0.52    9.9   9.7       0.57    9.8   0.9    3.3  3  DUF3098   Protein of unknown function (DUF3098)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.8   1.7e-07     0.001     212     315 ..       8     121 ..       2     142 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.7e-07
       MFS_1 212 llialllfffgfsglltllply....lqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt........ 297
                 ++++l+l  f+++ +ltl+ ++     ++ +g+  g   ++ +++l+ + + i++ ++  ls+r+g+r   +l++l++++++lg+a++++         
  AJA92970.1   8 AIAGLVLSIFFVAEVLTLFNFMidpsDNDSFGFEaG-PKLYQFISLSIAPATIMMGVSFHLSKRYGSRLNGMLIILSGAIILLGMAYASTMiedlkpsl 105
                 444455554444444444444322225788888895.666666777777777778899*******************************9988655433 PP

       MFS_1 298 ssavllll....vlvliGfglg 315
                             ++ li++gl+
  AJA92970.1 106 V------DssveMVPLISMGLS 121
                 1......122243333444443 PP

>> DUF2955  Protein of unknown function (DUF2955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.28   1.7e+03      74      80 ..      14      20 ..       3      38 .. 0.48
   2 ?   13.0   1.5   1.1e-05     0.068      79     137 ..      58     116 ..      46     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.28
     DUF2955 74 mtllvfl 80
                + ++ ++
  AJA92970.1 14 LSIFFVA 20
                2222222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.1e-05
     DUF2955  79 flllllkfrlmsrgskflfgamlvislsillvfasydttdvedlilsllaalllavvia 137
                  +++ ++f+l +r ++ l g++ ++s++i+l  + y +t +edl  sl+ +++ +v ++
  AJA92970.1  58 TIMMGVSFHLSKRYGSRLNGMLIILSGAIILLGMAYASTMIEDLKPSLVDSSVEMVPLI 116
                 689999********************************************999888765 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9   9.5e-05      0.57      18      58 ..      23      65 ..       5      68 .. 0.83
   2 ?    1.9   1.0     0.028   1.6e+02       6      21 ..      76      91 ..      71      98 .. 0.63
   3 ?    1.9   0.0     0.028   1.7e+02       7      24 ..     115     132 ..     111     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.5e-05
     DUF3098 18 ilGfiLmsGggsddpnvFne..diFsfrRirlAPivvliGfvi 58
                +  f +m+  + +d+  F++  +++ f  + +AP+ +++G+ +
  AJA92970.1 23 LTLFNFMIDPSDNDSFGFEAgpKLYQFISLSIAPATIMMGVSF 65
                44577899999999999997779*****************866 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.028
     DUF3098  6 nyillliglaviilGf 21
                n +l++ + a+i+lG+
  AJA92970.1 76 NGMLIILSGAIILLGM 91
                4555555556666655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.028
     DUF3098   7 yillliglaviilGfiLm 24 
                 +i ++ ++ +ii+G  L+
  AJA92970.1 115 LISMGLSIPIIIVGARLL 132
                 5789999*******8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1101.42
//
Query:       AJA92971.1  [L=188]
Description: monooxygenase subunit B domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-09   35.4   1.1    2.7e-08   33.1   0.2    2.3  2  Monooxygenase_B  Monooxygenase subunit B protein


Domain annotation for each model (and alignments):
>> Monooxygenase_B  Monooxygenase subunit B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1     0.027   4.8e+02     199     223 ..       3      27 ..       2      62 .. 0.59
   2 !   33.1   0.2   1.5e-12   2.7e-08      86     129 ..     111     154 ..      32     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.027
                      HHHHHHHHHHHHHHHHHHHHHHHCC CS
  Monooxygenase_B 199 drkvglvvlvlvllivlvgyavtek 223
                      drkv +  l++v++++++g +v+ +
       AJA92971.1   3 DRKVMAFALATVMVVGVFGPNVATM 27 
                      7777777777777777665544433 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.5e-12
                      T-EEEEEEEEEE-S-EEEEEEEEEEESSS-EEEEEEEEEEEES- CS
  Monooxygenase_B  86 GedYefkvvlkaRrpGtyhvhpmlnvedaGplvGpgkwvtiegd 129
                       +  ++++ ++a  pG yhvh++ln+e  Gp +Gpg+ v +eg+
       AJA92971.1 111 NDVVDYEISARALEPGVYHVHTQLNIEHVGPGLGPGQTVVVEGE 154
                      45569************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1357.05
//
Query:       AJA92972.1  [L=50]
Description: hypothetical protein T478_1469 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 393.38
//
Query:       AJA92973.1  [L=446]
Description: tRNA adenylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-35  120.2   0.1      1e-34  119.2   0.1    1.6  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    2.7e-12   46.8   0.3    7.8e-12   45.3   0.3    1.7  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0002   21.3   0.6    0.00085   19.4   0.1    2.2  2  Polbeta          Polymerase beta, Nucleotidyltransferase
    0.00038   20.7   0.6      0.001   19.3   0.6    1.7  1  SMODS            Second Messenger Oligonucleotide or Dinucleo
  ------ inclusion threshold ------
      0.088   13.0   0.0       0.19   11.9   0.0    1.5  1  DNA_pol_B_palm   DNA polymerase beta palm
       0.13   11.3   0.1        1.5    7.8   0.0    2.2  2  Asparaginase_2   Asparaginase


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.1   3.4e-38     1e-34       1     112 [.     153     259 ..     153     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 3.4e-38
                      HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETTEEEEETTTTS-HHHHH CS
  tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPvDpkRNvaaalslekla 94 
                      d++r+lK flk  g+YG+e+  +GfsGY++E+lv++ gsfe+vl++++k+k++ +i      +  +kf++p+v+iDP+D++RN +aa+s ++++
       AJA92973.1 153 DDIRILKCFLKINGMYGAEIAKQGFSGYVCEVLVYYLGSFENVLKKISKIKNNEMIG-----ESPRKFESPIVIIDPIDRNRNLGAAISIQNVT 241
                      89******************************************************5.....33589*************************** PP

                      HHHHHHHHHHHS--GGGG CS
  tRNA_NucTransf2  95 efilaareflkkpseeff 112
                      +fil ar+flkk s+++f
       AJA92973.1 242 NFILIARNFLKKSSLSYF 259
                      *****************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.3   2.6e-15   7.8e-12       5      85 ..      35     129 ..      32     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.6e-15
                   HHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH..............HHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEE CS
  NTP_transf_2   5 leelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre..............kkeegleklaeiikfleellglevdlvtrekledpllv 85 
                   ++e k+   v++v+  GSya+ t++++  DiD++v +++ +s+               kk++   +++e+++++  + g+ v +v+++ +++ +  
    AJA92973.1  35 NKEAKKQKAVVSVHFGGSYAKETWTPEkIDIDIFVKFKKTTSEKnfekvgkkigfdslKKFKPYVRYSEHPFVEADIDGVGVNVVPCYDIKK-GEW 129
                   566666666********************************988**************888999**************************95.333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.9e-07   0.00085       4      51 ..      35      83 ..      33     105 .. 0.80
   2 ?   -1.6   0.1      0.95   2.9e+03      60      90 ..     283     315 ..     257     317 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
                TTTHHHHHHHHSTTEEEEEE-S----.--EEEEEEEESS---HHHHHHH CS
     Polbeta  4 keilekekeielaylFGSrakgkare.eSDiDlavllkekldleeelel 51
                ++ ++k+k +  +   GS+ak++ ++ + DiD++v +k++ + ++  ++
  AJA92973.1 35 NKEAKKQKAVVSVHFGGSYAKETWTPeKIDIDIFVKFKKTTSEKNFEKV 83
                567899999**************996478***********554444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.95
                 SSSEEEEEE..TTTS-HHHHHHHHHS-EEEES- CS
     Polbeta  60 lgkkvDlvd..lneapplllyeilkegkllysk 90 
                 ++++ D++   +++a + +  +i+keg  ++ +
  AJA92973.1 283 KKRSDDIIYgqIKRAATSIESQITKEGFNVLRS 315
                 344455554336677788888898888777665 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.6   3.3e-07     0.001      17     141 ..      16     132 ..       6     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.3e-07
       SMODS  17 sqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvnevegdepsdlleklkkal....kktyksseirq 111
                 ++ +++++++  +++ + +nk+  + ++++++    GSya++T  +    +    + d+d++v++++++++   +  ek+ k +     k+ k   +  
  AJA92973.1  16 NNVQRKKVDKIANQVFSLVNKEA-KKQKAVVSVHFGGSYAKETWTP----E----KIDIDIFVKFKKTTSE---KNFEKVGKKIgfdsLKKFKPYVRYS 102
                 55566777777788888888888.667789999999*******988....4....6899*******97554...5566777766666677778879999 PP

       SMODS 112 drqvvvvelneikidvvPavenkdgsyeip 141
                 +++ v  +++++ + vvP+   k+g+++ +
  AJA92973.1 103 EHPFVEADIDGVGVNVVPCYDIKKGEWKSA 132
                 99******************9999988765 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.4e-05      0.19       8      60 ..      28      81 ..      18     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                    HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SE..ESSEEEEEEBTTBSTTSS--H CS
  DNA_pol_B_palm  8 ealealvkkaakeldpevevivcGSYRRgaes..sGDvDvlitkkdakseskklk 60
                    +++ +lv+k+ak+ +  v+v  +GSY ++  +    D+D+ +  k+++se++  +
      AJA92973.1 28 NQVFSLVNKEAKKQKAVVSVHFGGSYAKETWTpeKIDIDIFVKFKKTTSEKN-FE 81
                    45566788999999999***********986511579999999999999653.33 PP

>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.059   1.8e+02     239     287 ..      13      59 ..       3      67 .. 0.73
   2 ?    7.8   0.0    0.0005       1.5      84     123 ..     227     266 ..     220     324 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.059
                     HHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETTS-EEEEECS CS
  Asparaginase_2 239 divalmeykglsleeAaekvieeklkrvkgsgGviavdkkGevaaefns 287
                      i   ++   +++++ a++v++  +k++k++ +v+ v   G++a e+ +
      AJA92973.1  13 AIPNNVQ--RKKVDKIANQVFSLVNKEAKKQKAVVSVHFGGSYAKETWT 59 
                     3334444..4788888999999999999999999999999999877655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0005
                     TTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHH CS
  Asparaginase_2  84 ktlraGaVagvkrvknpislArlvmeksehvlLvgegAee 123
                     ++++ Ga +++++v n i +Ar  ++ks+ +++ +++ ++
      AJA92973.1 227 RNRNLGAAISIQNVTNFILIARNFLKKSSLSYFKEKSKDK 266
                     67899***********************999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3304.98
//
Query:       AJA92974.1  [L=338]
Description: galactose-1-phosphate uridyl transferase, N-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-07   31.5   0.0     0.0057   17.4   0.0    2.3  2  HIT              HIT domain
    3.3e-05   24.4   0.1    7.3e-05   23.3   0.0    1.6  2  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    0.00031   20.5   0.0    0.00053   19.7   0.0    1.4  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
     0.0026   18.2   0.0       0.12   12.8   0.0    2.3  2  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0057      21      94 ..      94     168 ..      83     171 .. 0.92
   2 !   11.7   0.0   7.7e-05      0.34       9      92 ..     209     291 ..     206     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                 SS-SSSSEEEEEESS.TGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEE CS
         HIT  21 idpkapghlLvipkk.hlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHvip 94 
                 ++p +  h  +i    ++++l  ++ e  +++ls+v+   + l ++     + ++   g+++g  v+h H+H+++
  AJA92974.1  94 SEPAYGYHYNIIASPdETKTLATIDVEQWGYVLSVVQDRLRWLYTQKGVAYVAIYADSGKNSGTKVQHPHLHMMS 168
                 678889999999999899*************************999999999********************997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.7e-05
                 EEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEE CS
         HIT   9 vyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHv 92 
                 +++++ ++a+    p  p  + ++pkkh++ +++++++e+ +l  + +     l + +k  +++++    ++  +s +++H+Hv
  AJA92974.1 209 ILQTEGFIALSPWAPSHPYEFWICPKKHATSFSKISQKEINDLALILRATLGGLSNSIKDVSFNIAFHLSPEKKNS-KQIHWHV 291
                 77888888999999999999************************************99999999999888888887.8999998 PP

>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.6e-08   7.3e-05      91     175 ..      80     164 ..      72     173 .. 0.89
   2 ?   -3.4   0.0       2.4   1.1e+04     120     137 ..     235     252 ..     233     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.6e-08
  GalP_UDP_transf  91 yikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifENkGaamgvsnphPHg 175
                      +i+te++ ++  + +epayG  + ii s++ ++tla++++++   v++  q++   l  ++++++v i    G   g + +hPH 
       AJA92974.1  80 DIETENTYSEHPLYSEPAYGYHYNIIASPDETKTLATIDVEQWGYVLSVVQDRLRWLYTQKGVAYVAIYADSGKNSGTKVQHPHL 164
                      566666667778889*********************************************************************5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.4
  GalP_UDP_transf 120 kheltladlspkdikavv 137
                      kh ++++++s+k+i++ +
       AJA92974.1 235 KHATSFSKISQKEINDLA 252
                      789999999999998765 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.2e-07   0.00053      34     154 ..     210     323 ..     189     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.2e-07
                    EE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS---EEEEEE---SCCCTTTT--EEEEE--BCSSTTEB CS
  GalP_UDP_tr_C  34 elkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfetsfeysmGlhqaplnaeednswlHaHfevpllrsatvr 129
                     +++ f+a++p+    P+e  + +k++ +s ++++++e +dla il+  +    n  + +  + + +h +p + + ++  +H+ ++++ +      
     AJA92974.1 210 LQTEGFIALSPWAPSHPYEFWICPKKHATSFSKISQKEINDLALILRATLGGLSNSIK-DVSFNIAFHLSPEKKNSKQIHWHVEVYPQTIPWS--- 301
                    45677******************************************98877777664.6777888888888877777777888888888654... PP

                    ----THHHHT-EEESS-HHHHHHHH CS
  GalP_UDP_tr_C 130 kieVGlelLperlrdllaEqaaerl 154
                     +e G+ +    l +l++E+aae l
     AJA92974.1 302 GLELGFGIF---LNELTPEKAAEEL 323
                    356677765...4455556555554 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.032   1.4e+02      36     103 ..     101     170 ..      92     179 .. 0.61
   2 !   12.8   0.0   2.8e-05      0.12      14     100 ..     206     292 ..     195     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.032
                 EEEEEESS.---SGGG--TTTTTHHHHHHHHHHHHH.HHTT-T-EEEEE--SCCCT--S-S--EEEEE.. CS
      DcpS_C  36 hllvipkr.dikslrdLtkehlpllkemrekakkvi.eekynevdaeelrvgvhyqPsvyhlHlHvisld 103
                 h+ +i+   + k+l  ++ e+   + +++++   ++  +k  ++ a     g +   +v+h HlH++s +
  AJA92974.1 101 HYNIIASPdETKTLATIDVEQWGYVLSVVQDRLRWLyTQKGVAYVAIYADSGKNSGTKVQHPHLHMMSFS 170
                 5555555555555555555555554444444333330334444666666778888899********9955 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.8e-05
                 B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT-...-S-S--EEEE CS
      DcpS_C  14 ervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyqP...svyhlHlHvi 100
                  r ++++e+f++l    p  ++ + + pk++ +s  +++++++  l+ + +     +++     +   +++ +h+ P     +++H Hv 
  AJA92974.1 206 PRQILQTEGFIALSPWAPSHPYEFWICPKKHATSFSKISQKEINDLALILRATLGGLSNSI---KDVSFNIAFHLSPekkNSKQIHWHVE 292
                 4678899***************************************999999998887655...7899*********9988999****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2536.44
//
Query:       AJA92975.1  [L=364]
Description: oxidoreductase, aldo/keto reductase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-26   90.9   0.2      7e-22   78.0   0.1    2.5  2  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.1   3.9e-26     7e-22       1     202 [.      33     301 ..      33     313 .. 0.74
   2 !   11.0   0.0   9.5e-06      0.17     241     288 ..     309     357 ..     291     362 .. 0.81

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 3.9e-26
                   .EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH....-TTTGGG-EEEEEE....................... CS
  Aldo_ket_red   1 elglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkk....srkkreeviiatKv....................... 70 
                   ++g+Gt  lg ++  ++e + +++++ +  Gin +DtA  Y+  +se+ +G al++    +  kree++i+tK                        
    AJA92975.1  33 NIGIGTY-LGEPDSQTDEIVKDAVKKSILSGINVIDTAINYRAQKSERSIGTALSElldeNLIKREELFICTKNgyvtndgdikedfmqyimrelgk 128
                   5999999.555569999999999***********************************98889*****************66666555544444444 PP

                   --SSSTTSSSS-HH.................HHHHHHHHHHHHHT-S-EEEEEE-S--TTS-..........HHHHHHHHHHHHHTTSEEEEEEES- CS
  Aldo_ket_red  71 dlrdaeiksglske.................niresleeslkrLgtdyvDllllHrpdpslp.........sieevldaleelvkeGkiraiGvSnf 141
                   +                               ++ +le+slk+L+++++Dl +lH+    +p         ++ +v+++ ee +keGkir +G++ +
    AJA92975.1 129 P------------GiikegdissgyhcmtipYLQDQLERSLKNLNLECIDLMYLHNAVEGHPemsksqfleNLKKVFEFYEEKRKEGKIRFYGLATW 213
                   0............155556666666666666****************************************************************77 PP

                   -..HHHHHHH..............HHTTT--EEEEE-B-BTT.......-HHHHTTHHHHHHH....TT-EEEEBSTTGGGTTGTTTS CS
  Aldo_ket_red 142 s..veqleka..............kkkkkvkivavqveynll.......releeegllelckk....kgvpliaysplggGlltgkyq 202
                   +   +  ++a                 + + + ++q  +nl        +++  eg+ + + +     g+++ +  pl++G l ++ +
    AJA92975.1 214 EcfRATFDNAmflsledvvklaqdVGGNDHGFRFIQLPFNLNfdqamllKNQTVEGIQKSILEsaveFGIGVFTSVPLMQGRLLEWAK 301
                   6422333333455555555555554455555666666666655565555333333333333333442466666666666666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.5e-06
                   --HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HHHHHH CS
  Aldo_ket_red 241 vslaqlalryalsqpavgivipgasnieqlednldalel.klseeevae 288
                    s++   l+++ s p+v  +++g +++ ++e+nl+++++  ++++e++e
    AJA92975.1 309 SSPSVGLLQFIRSTPGVLAPLIGQKSSTHVEENLQVMKInSMNQSEYDE 357
                   46677789999999***********************997777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2635.21
//
Query:       AJA92976.1  [L=469]
Description: 3-isopropylmalate dehydratase, large subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   3.7e-149  497.7   0.0   4.1e-149  497.5   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)
     0.0055   15.5   0.0     0.0079   14.9   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.85    9.7   0.0    2.0  2  THUMP      THUMP domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.5   0.0  6.9e-153  4.1e-149       1     461 []       7     460 ..       7     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 497.5 bits;  conditional E-value: 6.9e-153
   Aconitase   1 ekiwdahlveeeg....iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryefLksaak 95 
                 ekiw++h+v e++    + y+ dr+l+++vt++qa+ +l+  +++vrr++ t+atidh+vp++   d+s          + de+++  +++++L++++k
  AJA92976.1   7 EKIWNSHVVVERKnepsLIYI-DRHLIHEVTSPQAFDGLRVNNRKVRRPDLTVATIDHNVPTT---DRSL--------PMIDETSS--TQIKTLEKNCK 91 
                 79*****99442223557777.*****************************************...8887........67777777..9********** PP

   Aconitase  96 afgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklke..gvtakDlvlavi 189
                 +fgi+++ ++   qGIvH+++++ g++lpg t+v++DSHT++ g++G++a+G+G++e+e+ l++q+l+l++pk+ ++  tGk k+   vt+kD++l +i
  AJA92976.1  92 DFGIKLFGINdpnQGIVHVIGPQLGITLPGSTIVCGDSHTSTQGAFGAFAFGIGTSEVEHTLATQTLWLEKPKTFEILATGKRKNsfAVTSKDIILSII 190
                 **99998777777********************************************************************99874479********** PP

   Aconitase 190 gklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf..elaadedaeydkvleldlst 286
                 ++++++g++g+v+E+ G+++++Ls+e+r+Ti+NM++E+G+++gl+++dekt++YL+  +re+++   ++yd+ ++ +  +l +d++ ++dk +++d+++
  AJA92976.1 191 KQIGTDGGTGHVLEYRGDAISDLSMEQRMTICNMSIEAGSRAGLIAPDEKTYDYLN--NREYTP---KNYDELVDEWknNLMSDPNSKFDKSFTIDVEQ 284
                 ********************************************************..******...899999999965599***************** PP

   Aconitase 287 lepsvagpkrPqdavplselvk.k.efk..eelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsv 380
                 +ep+v+++++P ++ +++++++ + +f   +e++ e+a+kal+y +lk++t + ++++d ++igSCTN+++ed++ aa++++     g++v+++v+++v
  AJA92976.1 285 IEPQVSWGTNPAMVSDVTGKIPtPeDFGqnNEIQIESAKKALSYmDLKPDTAIVEIPIDRVFIGSCTNARLEDLKDAAEIVK-----GKTVNSDVNAMV 378
                 *********************975577622455689999999999*************************************.....************ PP

   Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaSPelvvaaAlaG 461
                 +PGS+ vk ++e+ Gl++i+++a fe++++gCs+C+g n+d l++ge+++s+sNRNFegRqg+++r++L+SP +++a+A+aG
  AJA92976.1 379 VPGSQMVKLEAEKLGLDKIFKDANFEWRESGCSMCLGmNPDILKPGERCASTSNRNFEGRQGSGGRTHLVSPVMAAASAIAG 460
                 *********************************************************************************9 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.3e-06    0.0079     249     365 ..     301     421 ..     292     449 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-06
      DUF521 249 vTPeaetleealgekekaekititkedleevleel...skakeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsre.vkeeaerlglv 342
                 vT + +t e+  +     ++i+i+ ++ +  + +l   ++  e ++d v++G c  + le+l++ ae++kgk+++++v+ +v+ + + vk eae+lgl 
  AJA92976.1 301 VTGKIPTPEDFGQ----NNEIQIESAKKALSYMDLkpdTAIVEIPIDRVFIGsCTNARLEDLKDAAEIVKGKTVNSDVNAMVVPGSQmVKLEAEKLGLD 395
                 5555555444332....344555555555555555444444567899999997899********************988777765543999******** PP

      DUF521 343 eklekaGvkvlsdtCmvv...splik 365
                 ++ ++a+ +  ++ C ++   +p i 
  AJA92976.1 396 KIFKDANFEWRESGCSMClgmNPDIL 421
                 ********998777755434465544 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.22   1.3e+03      82     112 ..     163     193 ..     154     202 .. 0.66
   2 ?    9.7   0.0   0.00014      0.85      19      77 ..     312     368 ..     300     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.22
                 CT-EEEEEEEESSSTS.SSHHHHHHHHHHHHH CS
       THUMP  82 eketFaVrvkrrgkhf.eftsreinrevGkai 112
                 +k tF + ++ ++k+   +ts++i   + k i
  AJA92976.1 163 PK-TFEILATGKRKNSfAVTSKDIILSIIKQI 193
                 33.77777776666644778888766665555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                 EETTEEEEECTEEEEEETHHHHHHHHHTST..........TECEEEEEEEEEESSHHHHHHHHHHHHHH CS
       THUMP  19 agkgrivvelkgekpeedeellkealekar..........giqrvipvcevceadledileaakeivkk 77 
                 +++++i++e+ ++           al++             i+rv+++ ++++a+led+++aa+ ++ k
  AJA92976.1 312 GQNNEIQIESAKK-----------ALSYMDlkpdtaiveiPIDRVFIG-SCTNARLEDLKDAAEIVKGK 368
                 5555555555544...........33333333344456667*******.**************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3327.74
//
Query:       AJA92977.1  [L=258]
Description: putative fumarate reductase iron-sulfur subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-30  105.2   0.1    3.6e-30  104.2   0.1    1.5  1  Fer2_3       2Fe-2S iron-sulfur cluster binding domain
    1.6e-11   44.4   2.7    1.6e-11   44.4   2.7    2.1  2  Fer4_8       4Fe-4S dicluster domain
    2.5e-10   40.3   2.9    2.5e-10   40.3   2.9    2.1  2  Fer4_10      4Fe-4S dicluster domain
    1.9e-08   34.8   3.4    1.9e-08   34.8   3.4    2.4  2  Fer4_7       4Fe-4S dicluster domain
    6.2e-08   32.7   5.6      1e-07   32.0   2.7    2.4  2  Fer4_9       4Fe-4S dicluster domain
    7.2e-08   33.3   3.2    7.2e-08   33.3   3.2    2.1  1  Fer4_16      4Fe-4S double cluster binding domain
    5.8e-07   30.0   4.1    5.8e-07   30.0   4.1    2.7  2  Fer4_17      4Fe-4S dicluster domain
    1.3e-05   24.8   0.8    1.3e-05   24.8   0.8    3.2  3  Fer4         4Fe-4S binding domain
    4.1e-05   23.4   1.0    7.6e-05   22.6   0.1    2.0  2  Fer2         2Fe-2S iron-sulfur cluster binding domain
    0.00014   22.0   6.2       0.08   13.1   0.1    2.8  3  Fer4_18      4Fe-4S dicluster domain
      0.002   18.2   1.8      0.002   18.2   1.8    3.0  3  Fer4_6       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.024   14.7   1.8      0.024   14.7   1.8    3.4  3  Fer4_2       4Fe-4S binding domain
       0.11   13.0   1.3       0.11   13.0   1.3    3.1  3  Fer4_4       4Fe-4S binding domain
       0.32   11.1   3.0         12    6.0   0.7    2.4  2  NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur bin
       0.35   11.0  14.5       0.03   14.4   6.8    2.8  2  Fer4_21      4Fe-4S dicluster domain
       0.97   10.5  21.4       0.39   11.8   4.6    3.2  3  Fer4_3       4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.1   3.2e-33   3.6e-30       2     109 .]      25     129 ..      24     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 3.2e-33
      Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirDL 100
                 +k+kR +p+  ++ +k++++ v+ e+ +tvldaLl +k+++d+++  r+sCr++ CGsc+++inGkp+laC ++i++l++++  +++ep++++pv+rDL
  AJA92977.1  25 VKIKRSNPNV-NADEKFDDFVVPIEKWTTVLDALLDVKSHLDHSVGVRYSCRQASCGSCGMKINGKPALACFTKISELNSDT--VTVEPMDNYPVVRDL 120
                 79******66.5599***************************************************************9875..*************** PP

      Fer2_3 101 vvDidemle 109
                  v++d+m++
  AJA92977.1 121 AVNMDRMIN 129
                 ******985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.5e+03       5       8 ..      79      82 ..      61     143 .. 0.80
   2 !   44.4   2.7   1.5e-14   1.6e-11       2      65 .]     167     240 ..     166     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
      Fer4_8  5 CieC 8 
                C+ C
  AJA92977.1 79 CGSC 82
                3333 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 1.5e-14
      Fer4_8   2 lekCieCgaCqsaCp............vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                 +++Ci+Cg+C+saCp            +l +  + + d r++ +  + + +v +e +++w+C+  g+C++vCp+g+
  AJA92977.1 167 FSSCIKCGLCNSACPtmamdktfvgpqALAQAYRYIADDRDKGK--NKRLKVIDESHGIWRCHFAGSCSQVCPKGV 240
                 789***********955444444444322222244444444433..344555556899***************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.5   1.7e+03      44      51 ..      73      82 ..      61      85 .. 0.63
   2 !   40.3   2.9   2.3e-13   2.5e-10       3      56 .]     164     237 ..     162     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
     Fer4_10 44 kCtg..cgaC 51
                +C +  cg+C
  AJA92977.1 73 SCRQasCGSC 82
                5555445555 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.3e-13
     Fer4_10   3 vidddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 +i+ ++Ci+Cg C++aCP+ +                    +++++k+++ +   +++++++C++ g+C ++CP
  AJA92977.1 164 YIQFSSCIKCGLCNSACPTMAmdktfvgpqalaqayryiadDRDKGKNKRLKVIDESHGIWRCHFAGSCSQVCP 237
                 68899**************88******************9999999999999999999***************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.4         3   3.4e+03      37      41 ..      78      82 ..      49     126 .. 0.79
   2 !   34.8   3.4   1.7e-11   1.9e-08       1      52 []     169     240 ..     169     240 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3
      Fer4_7 37 kClgC 41
                +C +C
  AJA92977.1 78 SCGSC 82
                33333 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 1.7e-11
      Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..............gt.ekv.....eidpekClgCgaCvavCPtga 52 
                 +Ci+Cg C +aCp+ a++ + +  ++              g+ +++      +  ++C + g+C +vCP+g+
  AJA92977.1 169 SCIKCGLCNSACPTMAMDKTFVGPQAlaqayryiaddrdkGKnKRLkvideSHGIWRCHFAGSCSQVCPKGV 240
                 5****************9885332222222223333333322222233343556789************996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.5   5.6e+02      33      39 ..      77      82 ..      27      96 .. 0.76
   2 !   32.0   2.7     9e-11     1e-07       2      49 ..     170     239 ..     169     240 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.5
      Fer4_9 33 eeaCigC 39
                + +C +C
  AJA92977.1 77 A-SCGSC 82
                2.34444 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 9e-11
      Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                 C++Cg C +aCp++++ +  ++  a  +a+++                      ++C++ g+C ++Cpkg
  AJA92977.1 170 CIKCGLCNSACPTMAMDKTFVGPQALAQAYRYiaddrdkgknkrlkvideshgiWRCHFAGSCSQVCPKG 239
                 **************************999999************************************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   3.2   6.4e-11   7.2e-08       2      66 ..     170     238 ..     169     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 6.4e-11
     Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy......ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                 C++Cg C ++CPt a++++  ++  +   ++y      ++++k++  + + + +  +++++ + C +vCP 
  AJA92977.1 170 CIKCGLCNSACPTMAMDKT--FVGPQALAQAYryiaddRDKGKNKRLKVIDESHGIWRCHFAGSCSQVCPK 238
                 *****************99..33333333333335556666666666666777779**************6 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   8.4   0.00016      0.18      32      58 ..     156     182 ..      74     186 .. 0.84
   2 !   30.0   4.1   5.2e-10   5.8e-07       2      61 .]     170     241 ..     169     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
     Fer4_17  32 glleeaekeekaslCieCgeCerkCPq 58 
                 ++ e++ek  ++s+Ci+Cg+C+++CP 
  AJA92977.1 156 QSPENVEKYIQFSSCIKCGLCNSACPT 182
                 56788888899***************6 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 5.2e-10
     Fer4_17   2 CiqCgyClpeCpsyeaydn..epkkllraakl..........glleeaekeekaslCieCgeCerkCPqgld 61 
                 Ci+Cg C  +Cp+++  ++   p+ l++a+++          ++l+ + +++ + +C+  g C+++CP+g+d
  AJA92977.1 170 CIKCGLCNSACPTMAMDKTfvGPQALAQAYRYiaddrdkgknKRLKVIDESHGIWRCHFAGSCSQVCPKGVD 241
                 *************999777446999999988888776665432333344559*****************997 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.9       1.8     2e+03      11      14 ..      79      82 ..      77      84 .. 0.69
   2 !   24.8   0.8   1.2e-08   1.3e-05       2      23 ..     164     185 ..     163     186 .. 0.89
   3 !    6.9   0.8    0.0053         6      12      21 ..     230     239 ..     225     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                -THH CS
        Fer4 11 CGaC 14
                CG C
  AJA92977.1 79 CGSC 82
                7777 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.2e-08
                 EEETTTSSS-THHHHHSTTTEE CS
        Fer4   2 videekCigCGaCvevCPvgAI 23 
                 +i  + Ci+CG+C ++CP+ A 
  AJA92977.1 164 YIQFSSCIKCGLCNSACPTMAM 185
                 677899*************985 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0053
                 THHHHHSTTT CS
        Fer4  12 GaCvevCPvg 21 
                 G C +vCP g
  AJA92977.1 230 GSCSQVCPKG 239
                 99******88 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   6.8e-08   7.6e-05      18      76 ..      56      97 ..      43     109 .. 0.80
   2 ?   -2.2   0.1       3.8   4.2e+03      39      43 ..     172     176 ..     144     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.8e-08
                BHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSE CS
        Fer2 18 tlldaaee.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqti 76
                 lld+  + ++ ++++ysC++++Cg+C  +++            g++      +laC t+
  AJA92977.1 56 ALLDVKSHlDHSVGVRYSCRQASCGSCGMKIN------------GKP------ALACFTK 97
                366666688889******************99............565......4777665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.8
                 SSSTT CS
        Fer2  39 gCgtC 43 
                 +Cg C
  AJA92977.1 172 KCGLC 176
                 37777 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       4.1   4.6e+03      80      91 ..      69      82 ..      56      91 .. 0.57
   2 !   11.4   0.5   0.00024      0.27      36      74 ..     144     183 ..     122     190 .. 0.63
   3 !   13.1   0.1   7.2e-05      0.08      51      83 ..     216     248 ..     184     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.1
     Fer4_18 80 Glqlec..iscllc 91
                G++++c   sc+ c
  AJA92977.1 69 GVRYSCrqASCGSC 82
                44444422234444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00024
     Fer4_18  36 kiagrkkekkalkekeer.kekgagdcidcescvkvcPtg 74 
                 +i  ++  ++ l++ e+  k  + + ci+c+ c + cPt 
  AJA92977.1 144 EIDAESGIREFLQSPENVeKYIQFSSCIKCGLCNSACPTM 183
                 4445555555555555540445678899999999999974 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 7.2e-05
     Fer4_18  51 eerkekgagdcidcescvkvcPtgidirkGlql 83 
                    +++g   c   +sc +vcP g+d   G+ql
  AJA92977.1 216 VIDESHGIWRCHFAGSCSQVCPKGVDPAMGIQL 248
                 23345677789999**************99997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   1.5       4.7   5.3e+03       8      15 ..      78      82 ..      73      85 .. 0.57
   2 !   18.2   1.8   1.7e-06     0.002       7      23 ..     168     184 ..     165     185 .. 0.92
   3 ?    1.6   0.1       0.3   3.4e+02      14      22 ..     231     239 ..     229     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
      Fer4_6  8 kCigCgdC 15
                +   Cg C
  AJA92977.1 78 S---CGSC 82
                4...5555 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.7e-06
      Fer4_6   7 dkCigCgdCvrvCPega 23 
                 ++Ci Cg C ++CP+ a
  AJA92977.1 168 SSCIKCGLCNSACPTMA 184
                 68************987 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.3
      Fer4_6  14 dCvrvCPeg 22 
                  C  vCP g
  AJA92977.1 231 SCSQVCPKG 239
                 6999***87 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.1      0.69   7.8e+02      12      16 ..      76      82 ..      70      85 .. 0.67
   2 ?   14.7   1.8   2.1e-05     0.024       9      22 .]     169     182 ..     163     182 .. 0.90
   3 ?    5.4   0.9     0.019        22      13      21 ..     226     237 ..     224     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.69
      Fer4_2 12 g..CgaC 16
                +  Cg+C
  AJA92977.1 76 QasCGSC 82
                4447777 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
      Fer4_2   9 rCigCgaCvsaCPa 22 
                 +Ci Cg C saCP+
  AJA92977.1 169 SCIKCGLCNSACPT 182
                 7************7 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.019
      Fer4_2  13 C...gaCvsaCP 21 
                 C   g+C ++CP
  AJA92977.1 226 ChfaGSCSQVCP 237
                 65557******9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.9       3.2   3.6e+03       6      10 ..      78      82 ..      72      82 .. 0.70
   2 ?   13.0   1.3    0.0001      0.11       3      16 ..     169     182 ..     167     193 .. 0.91
   3 ?   -0.4   0.9         2   2.3e+03       8      16 ..     230     238 ..     225     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.2
      Fer4_4  6 gCgsC 10
                 CgsC
  AJA92977.1 78 SCGSC 82
                79999 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0001
      Fer4_4   3 rCigCgsCvaaCPq 16 
                 +Ci Cg C +aCP+
  AJA92977.1 169 SCIKCGLCNSACPT 182
                 8************5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2
      Fer4_4   8 gsCvaaCPq 16 
                 gsC  +CP 
  AJA92977.1 230 GSCSQVCPK 238
                 589999996 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.027        30      10      29 ..      74      93 ..      70     134 .. 0.76
   2 ?    6.0   0.7     0.011        12       6      29 ..     161     184 ..     158     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.027
                 HHHH--S--HHHHIIIIHHH CS
  NADH_4Fe-4S 10 yaaesCGkCtpCreGtkrll 29
                 +++ sCG C+    G + l+
   AJA92977.1 74 CRQASCGSCGMKINGKPALA 93
                 8899*****99888877765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                  HHHHHHHH--S--HHHHIIIIHHH CS
  NADH_4Fe-4S   6 llefyaaesCGkCtpCreGtkrll 29 
                  + ++++  sC kC+ C +  + ++
   AJA92977.1 161 VEKYIQFSSCIKCGLCNSACPTMA 184
                  56789999********99888775 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.9       4.2   4.8e+03      11      16 ..      79      84 ..      71     119 .. 0.69
   2 ?   14.4   6.8   2.7e-05      0.03       3      52 ..     165     237 ..     163     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
     Fer4_21 11 CgkCli 16
                Cg+C +
  AJA92977.1 79 CGSCGM 84
                444433 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.7e-05
     Fer4_21   3 idedkCigCgkCliaCedtshqai..................eidaktvlkvved.....eCvGCnlCssvCP 52 
                 i+ ++Ci+Cg+C  aC++ +++                    ++ ++++lkv+++     +C     Cs+vCP
  AJA92977.1 165 IQFSSCIKCGLCNSACPTMAMDKTfvgpqalaqayryiaddrDKGKNKRLKVIDEshgiwRCHFAGSCSQVCP 237
                 67789************99998876777777777777666553344456677755344445777788999999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.3       7.7   8.7e+03       4       7 ..      79      82 ..      74      97 .. 0.56
   2 ?   11.8   4.6   0.00035      0.39       1      13 [.     170     182 ..     170     184 .. 0.93
   3 ?   10.4   1.2   0.00095       1.1       5      14 ..     230     239 ..     224     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.7
      Fer4_3  4 CgaC 7 
                Cg C
  AJA92977.1 79 CGSC 82
                4433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00035
      Fer4_3   1 CtgCgaCvevCPv 13 
                 C+ Cg+C  +CP+
  AJA92977.1 170 CIKCGLCNSACPT 182
                 ************7 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00095
      Fer4_3   5 gaCvevCPvg 14 
                 g C +vCP+g
  AJA92977.1 230 GSCSQVCPKG 239
                 58******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1935.30
//
Query:       AJA92978.1  [L=1066]
Description: isoleucine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     1e-133  446.8   6.0   1.5e-133  446.2   6.0    1.2  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      4e-29  101.6   2.0    1.2e-28  100.0   2.0    1.9  1  Anticodon_1   Anticodon-binding domain of tRNA
    8.6e-25   87.3   2.0    8.3e-10   38.0   0.1    4.2  3  tRNA-synt_1g  tRNA synthetases class I (M)
    2.1e-07   30.6   0.0    1.5e-05   24.5   0.0    2.7  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    7.8e-06   25.0   0.0    6.8e-05   21.9   0.1    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.2   6.0  4.3e-137  1.5e-133       9     600 ..      23     637 ..      16     639 .. 0.94

  Alignments for each domain:
  == domain 1  score: 446.2 bits;  conditional E-value: 4.3e-137
  tRNA-synt_1   9 edvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklg..reefrekv 104
                  +d+ k  +e e++k+e +++ gPP  +G +H Gh   ++ kd+  ry+ ++G++v +  GwD+ Gl++e + ek+lg +++k+  + +   e+ ++++
   AJA92978.1  23 KDISKLIQEDENKKNEIMFIEGPPTMNGIPHAGHLRGRVFKDLWYRYNVLSGNKVIFNAGWDTQGLPVELQAEKELGMENGKSDISSTedIEKLVAEC 120
                  5666667778888999****************************************************************9887766522589***** PP

  tRNA-synt_1 105 rewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeev 200
                  ++ +++y+ ++ +  k +G+s+  d+ y T ++e+ e  ++ +++ +++g++ +g ++v ++++++t+ls  Ev   y  +kd++++ + +la++e+ 
   AJA92978.1 121 KNLVQKYHTKWVEVDKLIGMSFNQDKAYWTYKDEFIEKEWQLMKKAFENGIMTEGFRVVAYCPSCQTSLSHSEVnqGYDMVKDPSLYYKVKLAEEEK- 217
                  **************************************************************************6557889****************. PP

  tRNA-synt_1 201 klviaTTtPeTllgdtavavnpeldyv...itkeklilaeallkslvkke..sekkiledergkeLegkevelpl............vnrkipiiadd 281
                   l+++TT P Tl++d  v vnp ++yv   +++e++++ +++l++++ +   +e++i++++ g+e+egk++++pl            +++  + +a++
   AJA92978.1 218 FLIVWTTMPFTLVTDAMVGVNPKEEYVevlVEDETWVVGKTRLEEFMTEVkiEEYEIKRTFLGSEMEGKKYIHPLldeipklaeiskQDNYHVTVAEN 315
                  *******************************************998876556777*******************************988899999*** PP

  tRNA-synt_1 282 yvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateq 379
                  +vd +aG+G+V+++Pa +e+D+++++k +++v +++d++ ++te+a++++gl v da++k+v+++k++++l+k+ ki+h++p+c+r ++ ++  a   
   AJA92978.1 316 FVDVNAGSGLVHLSPANGEEDNNIAMKRKVTVFCPIDDEVKFTEDAGKYAGLFVRDADEKLVQSVKDRNALVKIGKIKHKYPLCWRCNHGLVWLARRE 413
                  ************************************************************************************************** PP

  tRNA-synt_1 380 WfvrvkeladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelva.greeeeaekkalekeakdkl... 473
                  +f  +++l d+a+ka e+v++  ++ ++r+ +++++ + WciSR+r+WG +ip++  ++ e++ +  + ke+v+ ++e  ++e+ +l++  +dk+   
   AJA92978.1 414 YFYMLDKLGDKAIKAAEDVEYFFDQPKNRFLEIIKEKHPWCISRERYWGCPIPVWKCNDCENTEQLFSRKEIVEsAIELPDGENFELHRPWIDKIkvk 511
                  ********************************************************999998888777777765156778999999********9887 PP

  tRNA-synt_1 474 .kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse..PfkevlvhglvrdeeGrKmSKsl 568
                   k+  g ++++e vlD+W +Sg  p+++l+     +  +k+  pa +++eG+D++rgW ++l++  +  ++ +  P+k+ l +g v+de+G KmSKs+
   AJA92978.1 512 cKECSGLMQREEFVLDTWHNSGAAPIASLD-----EATYKEKIPAPFFTEGIDQTRGWAYTLLIENVIYNNASvsPYKSFLFQGHVLDENGNKMSKSK 604
                  6777889999999****************9.....45667789*********************99998887667*********************** PP

  tRNA-synt_1 569 gNvidpldvikkygadalRltli.lsdvgrdin 600
                  gNv++ +++++ky +d +R++ + +++  + +n
   AJA92978.1 605 GNVLEAKELLEKYPVDLVRFYFMwKASPIEPLN 637
                  *********************997777766665 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   2.0   3.3e-32   1.2e-28       1     148 [.     690     837 ..     690     842 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 3.3e-32
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra..aqevllevletllrllaPfmPfitEelwqreeee 95 
                  d w+ls+l++ ++++te  +++rf++ a+++ +f++n+l++ y+ ++k++l++e++++k r+  ++++l++ l+t+ +l++Pf+Pf++++l+    ++
   AJA92978.1 690 DVWLLSKLQRMIERTTETNDSCRFHESAKSIEDFLINSLSQIYIPIIKSELWDEDDSKKnRRftIYAILAKTLKTINILIHPFAPFTSQYLY----KS 783
                  67***************************************************9998889665556**************************....55 PP

  Anticodon_1  96 l.gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpssel 148
                  +  +ke i+l++wp+ +++  +++  e++++llke+v++  ++r + k+k++++l
   AJA92978.1 784 MfSEKENILLESWPKvDSSLIDEKV-ETSFDLLKETVSVTSAARMKGKLKRRWPL 837
                  55889**********8887777777.99**********************99985 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   2.3e-13   8.3e-10      10     135 ..      48     194 ..      44     198 .. 0.62
   2 !   10.8   0.0   4.1e-05      0.15     167     239 ..     397     469 ..     385     480 .. 0.82
   3 !   33.4   0.0   5.8e-12   2.1e-08     320     374 ..     592     646 ..     572     655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.3e-13
                   -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT........TS-...........HHHHHHHHHHHHHHHHHHTT---.. CS
  tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke........gvt...........peelvekvheeikelfkklnisf.. 85 
                   +ng +H Ghl+  +  D ++Ry+ l+g++v+f +g D+ G p+el+Aeke        +++            ++lv+k+h++  e+ k +++sf  
    AJA92978.1  48 MNGIPHAGHLRGRVFKDLWYRYNVLSGNKVIFNAGWDTQGLPVELQAEKElgmengksDISstedieklvaeCKNLVQKYHTKWVEVDKLIGMSFnq 144
                   79*********************************************98652222222222111111111112334444444444443444444422 PP

                   SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
  tRNA-synt_1g  86 dkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                   dk + t ++e  e   +++kk  e+g ++e+   ++ycp++++ l+ ++v
    AJA92978.1 145 DKAYWTYKDEFIEKEWQLMKKAFENGIMTEGFRVVAYCPSCQTSLSHSEV 194
                   44455555555555666666666666666666666666666666666555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.1e-05
                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..T CS
  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..g 239
                   p +  +++  ++  ++++f+ l+k+ +k  +   e+ +   ++ k+  +e++ke  ++++isr+  wG p+P  +
    AJA92978.1 397 PLCWRCNHGLVWLARREYFYMLDKLGDKAIKAA-EDVEYFFDQPKNRFLEIIKE-KHPWCISRERYWGCPIPvwK 469
                   56677777777777999**********999988.66667888889999999999.79**************9651 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 5.8e-12
                   -EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHH CS
  tRNA-synt_1g 320 yltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfver 374
                    l  +g+K+SkS+g+v  ake+le++++dl+R+y++ +a+  + l+fs+++++ r
    AJA92978.1 592 VLDENGNKMSKSKGNVLEAKELLEKYPVDLVRFYFMWKASPIEPLNFSTKELMSR 646
                   456789********************************************99986 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.018        64       9      50 ..      38      79 ..      29      84 .. 0.78
   2 !   24.5   0.0   4.1e-09   1.5e-05     238     296 ..     583     643 ..     572     646 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                  EEEEEEEE.EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
  tRNA-synt_1e  9 kvtlYvCG.ptvydashlGhaRslvafDilrrilqalgYdvqf 50
                  ++ +++ G pt+    h Gh R  v+ D+  r+   +g +v f
    AJA92978.1 38 EI-MFIEGpPTMNGIPHAGHLRGRVFKDLWYRYNVLSGNKVIF 79
                  33.455552699999*****************99889988876 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 4.1e-09
                   EEEEEEE--E.EETTBE--TTTT---BHHHHHTTS-HHHHHHHHH.SS-TTS-EEE-HHHH CS
  tRNA-synt_1e 238 vkyflhnghl.kiegekmsksLknfitikdvlkkfdprqlRllll.sahyrsqldfkeell 296
                    k fl +gh+   +g+kmsks +n++  k++l+k+    +R++++ +a   ++l+f+ ++l
    AJA92978.1 583 YKSFLFQGHVlDENGNKMSKSKGNVLEAKELLEKYPVDLVRFYFMwKASPIEPLNFSTKEL 643
                   5779999997246689*************************98872455678999988766 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.1   3.6e+02       7      45 ..      24      60 ..      20      84 .. 0.72
   2 !   21.9   0.1   1.9e-08   6.8e-05     274     322 ..     592     641 ..     579     675 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
  tRNA-synt_1f  7 laeklieerkkkkaekdevv.vesGispSGliHiGnlrev 45
                     kli+e ++k   k+e++ +e   +  G +H G lr  
    AJA92978.1 24 DISKLIQEDENK---KNEIMfIEGPPTMNGIPHAGHLRGR 60
                  556788666554...5555505666799*******99954 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.9e-08
  tRNA-synt_1f 274 illkggekmssSkGnvltledwlevaepevlrfl.ilrrkPkkakkldld 322
                   +l+++g+kms+SkGnvl  +++le ++ +++rf+ + ++ P + ++++ +
    AJA92978.1 592 VLDENGNKMSKSKGNVLEAKELLEKYPVDLVRFYfMWKASPIEPLNFSTK 641
                   789999**************************862567788888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1066 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.81u 0.29s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 6599.52
//
Query:       AJA92979.1  [L=473]
Description: DHHA1 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.7   0.0    4.2e-10   40.2   0.0    1.9  1  DHHA1     DHHA1 domain
     0.0066   16.7   0.1      0.014   15.6   0.1    1.6  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   4.7e-14   4.2e-10      55     136 ..     379     461 ..     331     463 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.7e-14
                 HHHHHHHHHHTHGBTTCEEEEEEEECT.EEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHH CS
       DHHA1  55 algiaadklksklkkpvivfvakeegd.kvkvsarskkd...gvdagelakeaaaklgggGGGHdlAaGagipaekleealealee 136
                 +   +a+  k+   +  iv++ +++ + ++k+s r +++    ++++ l++  a+++ g GGGH+ AaGa+i ++kl+ +l+ le+
  AJA92979.1 379 ISSLIAGSPKN---SGKIVILRTDGSEgTIKFSSRKSAScknSINLSQLMRGGAEQFDGIGGGHEAAAGAKITKDKLDGFLDYLES 461
                 33344444455...46666666677677*********99*******************************************9986 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.6e-06     0.014       2      63 ..      26     116 ..      25     156 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                 EEEE-ECSSSHHHHHH.HHHHHHC..................ECS--TCGGCGCCH............HCCCSEEEEEEE-S---SS---SS- CS
                 xxxxxxxxxxxxxxxx.xxxxxxx..................xxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxx RF
         DHH   2 ilivghknpDtDsigS.aialanl..................lvDhneksqavege............akeeaedviiiDHHrlgeefetlap 63 
                 il+    + D+D+i+S ai  ++l                  lvD  +k+                   ++  ++ +++DHH++++e +++++
  AJA92979.1  26 ILV--TTHIDCDGITSgAIISKALirqgakctvrttnefsekLVDKMQKETRDLHVitdlgggfgkllDEKLSDNWLMLDHHEISDEEKDNER 116
                 666..8899*******99888884455555554444444444444333333333335555555566544777888899999999865554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3378.37
//
Query:       AJA92980.1  [L=106]
Description: hypothetical protein T478_1142 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 781.19
//
Query:       AJA92981.1  [L=102]
Description: hypothetical protein T478_0569 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 749.69
//
Query:       AJA92982.1  [L=237]
Description: hypothetical protein T478_0611 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0076   16.2   3.5      0.018   15.0   3.5    1.6  1  TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane p
  ------ inclusion threshold ------
      0.024   15.7   0.1       0.09   13.9   0.1    2.0  1  PPC              Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> TMEMspv1-c74-12  Plectrovirus spv1-c74 ORF 12 transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   3.5     2e-06     0.018      11      30 ..     216     235 ..     211     237 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
  TMEMspv1-c74-12  11 vvivLgiFlyiGLsiyqKik 30 
                      v i+LgiF  iG +iy Kik
       AJA92982.1 216 VGILLGIFGLIGFGIYRKIK 235
                      559****************9 PP

>> PPC  Bacterial pre-peptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     1e-05      0.09       4      68 ..      59     166 ..      57     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                 EEEEEE-TT-EEEEEE.....S-TT....................SEEEEE-TT......-SS-EE-ST.T-TT.................S-TTS-EE CS
         PPC   4 vysfevpagdsltidi.....dggti..................dldLylldsn....gtsvaaydans.apsg.................sdeyieft 57 
                 +y+f+++++d+l  +i     d++ +                     L + d +     +  + yda+  + +g                  +  i+  
  AJA92982.1  59 FYKFDAKKDDRLFSSIvipklDNLENftpslvligpstfldlvdE--LKVMDVDknfdYPIPDGYDAYVfDYNGpipskefyepfgqvtywERQEIDLE 155
                 8**********6655445666777756677777777666643332..3322222111224444455555533336777777777778888855777888 PP

                 -SSSEEEEEEE CS
         PPC  58 apqaGtYyvaV 68 
                   ++GtYy aV
  AJA92982.1 156 IEAPGTYYMAV 166
                 899*****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.51
# Mc/sec: 1406.92
//
Query:       AJA92983.1  [L=278]
Description: NurA domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-19   69.3   0.3    1.1e-18   67.8   0.1    1.8  2  NurA      NurA domain
  ------ inclusion threshold ------
      0.015   14.8   0.1       0.02   14.4   0.1    1.1  1  DUF2608   Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.1     1e+04     122     236 ..      17      32 ..       7      35 .. 0.51
   2 !   67.8   0.1   1.3e-22   1.1e-18       4     242 .]      49     253 ..      47     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.1
                 EEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH CS
        NurA 122 vgvaKsfrskellnllletlligesisDiallgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrleipaevstakdedvlslla 220
                 +++ K  ++++++                                                                                      
  AJA92983.1  17 LSILKGPEYEKII-------------------------------------------------------------------------------------- 29 
                 4444444444444...................................................................................... PP

                 ..TTB-SSSBCCHHHH CS
        NurA 221 sqrlsisGYprpLalA 236
                              ++A
  AJA92983.1  30 -------------QKA 32 
                 .............444 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 1.3e-22
                 EEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEEEEECSHHCCCHHHHHHHHHH CS
        NurA   4 aAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedllllDGsligslvefdelheel 102
                 a++D+S+++ ++ g  l ++ a+++ + g++    +  ++  d+             l  ++E+   a +++ +++dl+l+DGsl+  ++         
  AJA92983.1  49 AGIDSSFNSTKFQGAELWAVTAVSIKSDGEIIADLH--DFGLDT-------NPVLASLASKMEID--ACNMSIDNADLVLMDGSLYSQFM--------T 128
                 678888888888888888888888544444433333..444444.......55666677777777..7788999****************........9 PP

                 HHHHHHHHHHHHTT-TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEE CS
        NurA 103 eyeeylyslsrlleaglnlvgvaKsfrskellnllletlligesisDiallgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrl 201
                  ++ +  s+ ++++++ n+v+v+K++++++ ++ l      g    Di + +  +r+pg+++        ++ + ++ +dk i++ + rl+ + ++ ++
  AJA92983.1 129 RQASLTESMVNAMKKRNNVVFVSKTSNTRKQFEDL------GAIAGDIFYYNHAARTPGFSK--------IFEDEKFGKDKIITSIFARLADSLPLIKV 213
                 999999999999999********************......*******************85........344555555555***************** PP

                 EHHHHHH.CCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHCC CS
        NurA 202 eipaevs.takdedvlsllasqrlsisGYprpLalAhelaki 242
                 e++ +++  + ++ vl++++    sisGYp++L+lAh++ ki
  AJA92983.1 214 ELFGTGYsNDDFKRVLNKIY--KNSISGYPYSLKLAHNNCKI 253
                 *******9************..****************9887 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.2e-06      0.02      63     191 ..      27     155 ..       9     186 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-06
     DUF2608  63 kleclfedlgllyelgkmklvekevpslvnnlqnqgttvlaLTarsptlrtatlreLkslgidfskkaltqe.kveyrftltldkaerevsykkGvlft 160
                 k+  + +++ + y  +k ++v + ++s  n+ + qg+++ a Ta s ++    +  L++ g+d +    +   k+e+ + + +   ++  ++++G l++
  AJA92983.1  27 KIIQKAKENWIDYTPKKQEVVSAGIDSSFNSTKFQGAELWAVTAVSIKSDGEIIADLHDFGLDTNPVLASLAsKMEIDACN-MSIDNADLVLMDGSLYS 124
                 444455666778888999*****************************************9999886554444356666666.55568999********* PP

     DUF2608 161 sglnKGeaLlklLdkigrepksviFiDDkkk 191
                 + +   + L + +    ++ ++v+F+  + +
  AJA92983.1 125 QFMTRQASLTESMVNAMKKRNNVVFVSKTSN 155
                 **************************76554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2012.67
//
Query:       AJA92984.1  [L=202]
Description: copper-binding protein, plastocyanin/azurin family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-06   28.0   0.0    6.2e-06   26.6   0.0    1.7  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    0.00078   19.5   0.0     0.0023   18.0   0.0    1.7  2  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   6.9e-10   6.2e-06      11      99 .]     123     202 .]     116     202 .] 0.82

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.9e-10
                  TSEEESSEEEEETTEEEEEEEESSSSBEEEEET.TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  11 dlqFetkeitvkkgekvtfvnlavmgHNvvldk.dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  d  + ++++++ +g++v + n+++ +H     + dg p+gv ++ + +        gG +++ +f+e+g++ ++C  H    M+g+v+ve
   AJA92984.1 123 DECYIPATLNIPAGTTVIWENNDAAAHLATSGTpDGGPDGVFDSGMIM--------GGATYEYEFSETGEFVYYCLVHP--WMVGTVVVE 202
                  556999*********************665544466666665555555........7**********************..69****996 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.74   6.7e+03      74      88 ..      46      60 ..      42      68 .. 0.75
   2 !   18.0   0.0   2.5e-07    0.0023      29     104 .]     123     201 ..     119     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.74
  Cupredoxin_1 74 ktttitiaplkpGeY 88
                    +t+ +++ k+G Y
    AJA92984.1 46 RDKTAFFEMCKAGNY 60
                  566777888999999 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.5e-07
  Cupredoxin_1  29 dggfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   d+ + P++++++ag+  ++ ++n+d+ ++  +s         +  +  ++ g+t++ ++   + Ge+ ++c  h+ + G+++V
    AJA92984.1 123 DECYIPATLNIPAGT--TVIWENNDAAAHLATSGTpdggpdgVFDSGMIMGGATYEYEF--SETGEFVYYCLVHPWMVGTVVV 201
                   77899*********8..99*********99999888899998777899***********..99************99****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1541.09
//
Query:       AJA92985.1  [L=66]
Description: zinc finger, C2H2 type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-11   42.1   4.4    8.7e-05   22.8   0.2    2.2  2  zf-C2H2        Zinc finger, C2H2 type
    3.3e-09   36.8   3.8    0.00027   21.5   0.4    2.2  2  zf-C2H2_4      C2H2-type zinc finger
    3.4e-07   30.4   3.0     0.0078   16.5   0.1    2.4  2  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
    4.3e-07   29.6   0.4    0.00033   20.3   0.0    2.2  2  zf-C2H2_11     zinc-finger C2H2-type
    6.7e-06   26.0   6.2      0.015   15.3   0.7    2.1  2  zf-C2H2_6      C2H2-type zinc finger
    4.5e-05   23.7   1.8      0.056   13.8   0.1    2.3  2  zf-met         Zinc-finger of C2H2 type
    5.9e-05   23.0   2.8     0.0044   17.0   0.8    2.3  2  zf-BED         BED zinc finger
    7.8e-05   21.4   5.3      0.023   13.3   0.5    2.0  2  DUF629         Protein of unknown function (DUF629)
    0.00016   21.0   6.8      0.011   14.9   0.7    2.0  2  Actin_micro    Putative actin-like family
    0.00022   21.3   1.2       0.19   11.9   0.1    2.1  2  zf_ZIC         Zic proteins zinc finger domain
    0.00045   19.7   3.4       0.38   10.4   0.2    2.2  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
    0.00052   20.3   6.8      0.059   13.7   1.2    2.0  2  zf-C2H2_2      C2H2 type zinc-finger (2 copies)
    0.00056   20.6   0.8          1   10.0   0.0    2.0  2  zf-C2H2_3rep   Zinc finger C2H2-type, 3 repeats
     0.0019   18.4   1.3       0.39   11.1   0.1    2.0  2  zf-C2H2_8      C2H2-type zinc ribbon
     0.0023   18.3  11.7     0.0028   18.0   0.1    3.0  3  zf-H2C2_2      Zinc-finger double domain
     0.0024   18.3   7.8     0.0093   16.4   7.8    1.8  1  zf-C2HE        C2HE / C2H2 / C2HC zinc-binding finger
     0.0088   16.2   4.1      0.019   15.1   4.1    1.5  1  zf-C2H2_aberr  Aberrant zinc-finger
     0.0099   16.5   3.1        2.4    8.8   0.3    2.1  2  FOXP-CC        FOXP coiled-coil domain
  ------ inclusion threshold ------
      0.012   15.2   0.9          4    7.1   0.1    2.1  2  zf_C2H2_ZHX    Zinc-fingers and homeoboxes C2H2 finger domain
      0.016   15.5   4.6      0.033   14.5   4.4    1.6  1  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
      0.046   13.9   2.7       0.69   10.1   0.1    2.4  2  zf-AN1         AN1-like Zinc finger
      0.061   13.1   0.9       0.61    9.9   0.1    2.2  2  zinc_ribbon_5  zinc-ribbon domain
       0.07   13.0   0.7        3.1    7.7   0.1    2.1  2  zf-C2H2_9      C2H2 type zinc-finger (1 copy)
       0.13   12.4   5.9       0.14   12.3   0.5    2.1  2  Zn-ribbon_8    Zinc ribbon domain
       0.14   12.7   4.4       0.31   11.6   0.8    2.0  2  Evr1_Alr       Erv1 / Alr family
       0.14   12.6   2.7        2.4    8.7   0.2    2.0  2  OrsD           Orsellinic acid/F9775 biosynthesis cluster pro
       0.18   11.8   5.6       0.21   11.6   0.2    2.4  2  YhfH           YhfH-like protein
       0.18   12.2   0.6        8.4    6.9   0.1    2.1  2  DUF983         Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   1.4e-07   8.7e-05       2      23 .]       8      30 ..       7      30 .. 0.95
   2 !   21.2   0.7   4.2e-07   0.00027       1      23 []      36      59 ..      36      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.4e-07
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                +C++C+ +Fk++++L++H+++ H
  AJA92985.1  8 PCEKCDLKFKSQEELMQHLQItH 30
                6******************9988 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 4.2e-07
                EEETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                y C++Cg+ F++ +++++H+++ H
  AJA92985.1 36 YDCKECGENFSNMEDMRTHLQRkH 59
                89*******************999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.5e-05    0.0094       2      24 .]       8      30 ..       7      30 .. 0.91
   2 !   21.5   0.4   4.3e-07   0.00027       3      24 .]      38      59 ..      36      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-05
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                +C+ C+  F+s+++L +Hl+  H
  AJA92985.1  8 PCEKCDLKFKSQEELMQHLQITH 30
                7*****************98766 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 4.3e-07
   zf-C2H2_4  3 CpiCgksFsskkaLlrHlkthH 24
                C+ Cg++Fs+ +++++Hl++ H
  AJA92985.1 38 CKECGENFSNMEDMRTHLQRKH 59
                ********************99 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.5   6.3e-05      0.04       4      21 ..       9      26 ..       6      27 .. 0.91
   2 !   16.5   0.1   1.2e-05    0.0078       2      21 ..      36      55 ..      35      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.3e-05
                 BTTTTBBBSSHHHHHCCT CS
  zf-C2H2_jaz  4 CvlCdKyFksenaldnHl 21
                 C+ Cd  Fks++ l +Hl
   AJA92985.1  9 CEKCDLKFKSQEELMQHL 26
                 888**************8 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                 CBBTTTTBBBSSHHHHHCCT CS
  zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                 + C++C   F++++++++Hl
   AJA92985.1 36 YDCKECGENFSNMEDMRTHL 55
                 78*****************8 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.2e-07   0.00033       7      28 ..       9      30 ..       7      30 .. 0.98
   2 !    7.6   0.1    0.0051       3.3       7      23 ..      38      54 ..      36      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.2e-07
  zf-C2H2_11  7 CleCGlcftSqlsLsRHlfIvH 28
                C +C l+f Sq  L  Hl+I+H
  AJA92985.1  9 CEKCDLKFKSQEELMQHLQITH 30
                9********************* PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0051
  zf-C2H2_11  7 CleCGlcftSqlsLsRH 23
                C eCG +f+     + H
  AJA92985.1 38 CKECGENFSNMEDMRTH 54
                ********976555555 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.6     7e-05     0.045       4      24 ..       9      30 ..       8      32 .. 0.93
   2 !   15.3   0.7   2.3e-05     0.015       2      24 ..      36      59 ..      36      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
   zf-C2H2_6  4 CsvCsksFpslqaLggHk.ksH 24
                C  C+  F+s+ +L+ H+ ++H
  AJA92985.1  9 CEKCDLKFKSQEELMQHLqITH 30
                99***************98888 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.3e-05
   zf-C2H2_6  2 heCsvCsksFpslqaLggHk.ksH 24
                + C++C++ F+   ++++H+ + H
  AJA92985.1 36 YDCKECGENFSNMEDMRTHLqRKH 59
                67******************6666 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   8.8e-05     0.056       3      21 ..       9      27 ..       7      28 .. 0.93
   2 !    9.2   0.2    0.0025       1.6       1      21 [.      36      56 ..      36      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.8e-05
      zf-met  3 CelCnvtfnsesqlksHlq 21
                Ce C+ +f+s+  l +Hlq
  AJA92985.1  9 CEKCDLKFKSQEELMQHLQ 27
                777***************8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0025
      zf-met  1 fyCelCnvtfnsesqlksHlq 21
                + C+ C   f++  ++++Hlq
  AJA92985.1 36 YDCKECGENFSNMEDMRTHLQ 56
                67******************8 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.012       7.6      16      43 ..       6      30 ..       4      31 .. 0.86
   2 !   17.0   0.8   6.9e-06    0.0044       6      44 .]      30      60 ..      29      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                --EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED 16 kavCryCgkilsrgggttnLkrHLrrkH 43
                k+ C  C  ++++      L++HL+  H
  AJA92985.1  6 KIPCEKCDLKFKSQ---EELMQHLQITH 30
                67799999999998...99*****8766 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.9e-06
                SS----GGSS--EETTTTEE----SSTHHHHHHHHHS-H CS
      zf-BED  6 yftpvslkeqkavCryCgkilsrgggttnLkrHLrrkHp 44
                +f++++       C+ Cg+++s+      +++HL+rkH+
  AJA92985.1 30 HFKDLP-----YDCKECGENFSNM---EDMRTHLQRKHS 60
                555555.....67*********95...***********6 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.4   0.00013     0.084      59      84 ..       9      34 ..       3      37 .. 0.92
   2 !   13.3   0.5   3.5e-05     0.023      58      82 ..      37      61 ..      35      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
      DUF629 59 CrtCsekfsdaeeckqHlvqeHvakl 84
                C +C+ kf++ ee +qHl   H ++l
  AJA92985.1  9 CEKCDLKFKSQEELMQHLQITHFKDL 34
                **********************9987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-05
      DUF629 58 vCrtCsekfsdaeeckqHlvqeHva 82
                 C++C e+fs++e++++Hl ++H  
  AJA92985.1 37 DCKECGENFSNMEDMRTHLQRKHSY 61
                6**********************75 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.7   1.8e-05     0.011     225     250 ..       6      32 ..       1      35 [. 0.89
   2 !   10.6   0.8   0.00035      0.22     225     252 ..      35      63 ..      31      66 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
  Actin_micro 225 efsCkvCdvkfev.ekiseHllkkHii 250
                  ++ C++Cd kf++ e++++Hl+ +H++
   AJA92985.1   6 KIPCEKCDLKFKSqEELMQHLQITHFK 32 
                  678**********9***********97 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00035
  Actin_micro 225 efsCkvCdvkfev.ekiseHllkkHiike 252
                   + Ck C+ +f+  e++  Hl++kH  k+
   AJA92985.1  35 PYDCKECGENFSNmEDMRTHLQRKHSYKK 63 
                  589********999***********8754 PP

>> zf_ZIC  Zic proteins zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0029       1.9      22      42 ..      10      30 ..       5      31 .. 0.88
   2 !   11.9   0.1   0.00029      0.19      21      42 ..      38      59 ..      32      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                ------BSSHHHHHHHHHCTT CS
      zf_ZIC 22 kpCsktFstmhelVtHltveH 42
                  C+ +F++  el  Hl + H
  AJA92985.1 10 EKCDLKFKSQEELMQHLQITH 30
                67999*************999 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                -------BSSHHHHHHHHHCTT CS
      zf_ZIC 21 kkpCsktFstmhelVtHltveH 42
                 k C+  Fs m ++ tHl   H
  AJA92985.1 38 CKECGENFSNMEDMRTHLQRKH 59
                599***************8877 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.4   0.00061      0.39       3      20 ..       7      25 ..       5      26 .. 0.89
   2 !   10.4   0.2   0.00059      0.38       3      20 ..      36      54 ..      35      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00061
      zf_UBZ  3 ylCerCgkeipes.elqEH 20
                ++Ce+C+ ++ +  el +H
  AJA92985.1  7 IPCEKCDLKFKSQeELMQH 25
                79**********9999999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00059
      zf_UBZ  3 ylCerCgkeipes.elqEH 20
                y C++Cg++++   ++  H
  AJA92985.1 36 YDCKECGENFSNMeDMRTH 54
                89********977688777 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.4   0.00062       0.4      50      75 ..       6      31 ..       1      37 [. 0.71
   2 !   13.7   1.2   9.3e-05     0.059      51      74 ..      36      59 ..      28      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
   zf-C2H2_2 50 kleClyCekefkslealreHmkkkgH 75
                k  C  C+ +fks+e+l++H++  + 
  AJA92985.1  6 KIPCEKCDLKFKSQEELMQHLQITHF 31
                56788888888888888888875544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 9.3e-05
   zf-C2H2_2 51 leClyCekefkslealreHmkkkg 74
                + C  C+++f+++e++r+H++ k+
  AJA92985.1 36 YDCKECGENFSNMEDMRTHLQRKH 59
                57*****************98874 PP

>> zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0019       1.2      34      59 ..       8      33 ..       2      37 .. 0.70
   2 !   10.0   0.0    0.0016         1      34      57 ..      37      60 ..      34      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
  zf-C2H2_3rep 34 qcipcgshfgnaeelwlhvlsvhpsd 59
                   c  c  +f ++eel++h++  h +d
    AJA92985.1  8 PCEKCDLKFKSQEELMQHLQITHFKD 33
                  45566677888888888888777766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
  zf-C2H2_3rep 34 qcipcgshfgnaeelwlhvlsvhp 57
                   c  cg  f+n+e++ +h++  h+
    AJA92985.1 37 DCKECGENFSNMEDMRTHLQRKHS 60
                  588888888888888888888776 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0006      0.39      68      89 ..       8      29 ..       2      33 .. 0.86
   2 ?    7.0   0.1     0.011         7      40      65 ..      38      65 ..      29      66 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
   zf-C2H2_8 68 kcencllrfrthrslfkhlhvc 89
                 ce+c l+f+++  l++hl++ 
  AJA92985.1  8 PCEKCDLKFKSQEELMQHLQIT 29
                5*****************9875 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
   zf-C2H2_8 40 tascaetfpsmqelvah..tklhykpnr 65
                ++ c e f  m+++ +h   k  yk +r
  AJA92985.1 38 CKECGENFSNMEDMRTHlqRKHSYKKDR 65
                568************9933355677766 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.8     0.039        25      15      26 .]       7      18 ..       2      18 .. 0.83
   2 !   18.0   0.1   4.3e-06    0.0028       2      26 .]      22      47 ..      21      47 .. 0.89
   3 ?    0.8   0.3       1.2   7.8e+02       3       9 ..      52      59 ..      50      64 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.039
   zf-H2C2_2 15 yeCplCdkaFkt 26
                  C++Cd +Fk+
  AJA92985.1  7 IPCEKCDLKFKS 18
                58********96 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.3e-06
   zf-H2C2_2  2 LrrHirk.HtgekpyeCplCdkaFkt 26
                L++H+   H ++ py C++C+  F++
  AJA92985.1 22 LMQHLQItHFKDLPYDCKECGENFSN 47
                99**995499**************87 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.2
   zf-H2C2_2  3 rrHi.rkH 9 
                r H+ rkH
  AJA92985.1 52 RTHLqRKH 59
                55652466 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   7.8   1.4e-05    0.0093       6      60 ..       7      57 ..       2      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
     zf-C2HE  6 vpledlpeelekdgeieslseeqskelilktpLkCtrCganfgnkfpkLKeHLee 60
                +p e+ +  l+ + + e +++ q ++  ++ p  C  Cg + ++++ +++ HL+ 
  AJA92985.1  7 IPCEKCD--LKFKSQEELMQHLQITHF-KDLPYDCKECG-ENFSNMEDMRTHLQR 57
                5667777..777777788999999999.***********.999**********85 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   4.1     3e-05     0.019       2      68 ..       6      62 ..       5      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3e-05
  zf-C2H2_aberr  2 kClykaCdlkyssvlglrrhlveykhslytnsefslkCpvrkCsesivelentelleehlekehaak 68
                   k + ++Cdlk++s   l +hl+   h  + +    l    ++C     +++n+e +++hl+++h++k
     AJA92985.1  6 KIPCEKCDLKFKSQEELMQHLQI-TH--FKD----LPYDCKEC---GENFSNMEDMRTHLQRKHSYK 62
                   667899**************975.56..333....44445677...77899999**********986 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2    0.0039       2.5      11      31 ..      11      31 ..       4      35 .. 0.89
   2 !    8.8   0.3    0.0038       2.4      11      33 ..      40      62 ..      37      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
     FOXP-CC 11 gCekvledveeflkhlnseHa 31
                 C+  ++++ee+++hl+ +H 
  AJA92985.1 11 KCDLKFKSQEELMQHLQITHF 31
                59999************9995 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0038
     FOXP-CC 11 gCekvledveeflkhlnseHald 33
                +C + ++++e++  hl+++H+ +
  AJA92985.1 40 ECGENFSNMEDMRTHLQRKHSYK 62
                699*****************976 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0064       4.1       7      24 ..       9      26 ..       6      31 .. 0.88
   2 ?    7.1   0.1    0.0063         4       5      29 ..      36      60 ..      32      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0064
  zf_C2H2_ZHX  7 CveCsfsakkfegLalHN 24
                 C +C+   k+ e+L +H 
   AJA92985.1  9 CEKCDLKFKSQEELMQHL 26
                 99***************5 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0063
  zf_C2H2_ZHX  5 FvCveCsfsakkfegLalHNarsHp 29
                 + C eC+ +  + e++  H  r H+
   AJA92985.1 36 YDCKECGENFSNMEDMRTHLQRKHS 60
                 78*****************999996 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.4   5.2e-05     0.033       3      54 .]       7      60 ..       5      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
     zf-Di19  3 ftCPyCgke.ltvkeLveHvedeHrveskevvCPvCaekvtk..dlvaHltleha 54
                ++C  C  +  +++eL++H++  H ++  ++ C  C e+ ++  d+  Hl+ +h+
  AJA92985.1  7 IPCEKCDLKfKSQEELMQHLQITHFKDL-PYDCKECGENFSNmeDMRTHLQRKHS 60
                577789987256889*********9986.688****99977556*******9995 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3       0.1        66      13      23 ..       6      16 ..       1      18 [. 0.80
   2 ?   10.1   0.1    0.0011      0.69      12      23 ..      34      45 ..      25      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
      zf-AN1 13 pfkCryCgkvF 23
                 + C++C+ +F
  AJA92985.1  6 KIPCEKCDLKF 16
                488****9998 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
      zf-AN1 12 lpfkCryCgkvF 23
                lp++C++Cg++F
  AJA92985.1 34 LPYDCKECGENF 45
                79********99 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00095      0.61       3      15 ..       7      19 ..       6      28 .. 0.80
   2 ?    2.1   0.0      0.26   1.7e+02       5      12 ..      38      45 ..      34      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00095
  zinc_ribbon_5  3 irCpdCdtkFklv 15
                   i C++Cd kFk  
     AJA92985.1  7 IPCEKCDLKFKSQ 19
                   78********965 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
  zinc_ribbon_5  5 CpdCdtkF 12
                   C +C+  F
     AJA92985.1 38 CKECGENF 45
                   88888777 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0048       3.1       4      23 ..       9      28 ..       7      34 .. 0.85
   2 ?    4.1   0.1     0.064        41       4      25 ..      38      59 ..      35      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                -TTT--B-SSHHHHHHHHHH CS
   zf-C2H2_9  4 CPvCevkfnswkdlseHils 23
                C  C +kf+s ++l +H+ +
  AJA92985.1  9 CEKCDLKFKSQEELMQHLQI 28
                889**************944 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.064
                -TTT--B-SSHHHHHHHHHHHT CS
   zf-C2H2_9  4 CPvCevkfnswkdlseHilsaa 25
                C  C  +f +++d+  H+  + 
  AJA92985.1 38 CKECGENFSNMEDMRTHLQRKH 59
                888**************95443 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.5    0.0023       1.5       8      36 ..       9      45 ..       4      48 .. 0.81
   2 ?   12.3   0.5   0.00023      0.14       6      22 ..      36      52 ..      34      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
  Zn-ribbon_8  8 CeeCghefe.......vlqsisdaplta.CPeCgsev 36
                 Ce+C+ +f        +lq  + ++l+  C+eCg++ 
   AJA92985.1  9 CEKCDLKFKsqeelmqHLQITHFKDLPYdCKECGENF 45
                 9999999999999888777555777888899999865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00023
  Zn-ribbon_8  6 YrCeeCghefevlqsis 22
                 Y C+eCg+ f  +  + 
   AJA92985.1 36 YDCKECGENFSNMEDMR 52
                 99********9988776 PP

>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.5     0.076        49      40      55 ..       7      21 ..       1      34 [. 0.68
   2 ?   11.6   0.8   0.00048      0.31      30      63 ..      26      56 ..      17      65 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                SSCHHHHHHHHHHHHH CS
    Evr1_Alr 40 ypCeeCaehfekvlae 55
                +pCe+C  +f++ ++e
  AJA92985.1  7 IPCEKCDLKFKS-QEE 21
                69*******999.333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                HHHHHHHHHHSSCHHHHHHHHHHHHHCH.CCCGS CS
    Evr1_Alr 30 kaflkliakfypCeeCaehfekvlaenppekeve 63
                 ++ ++    y C+eC e+f++ ++++ ++  ++
  AJA92985.1 26 LQITHFKDLPYDCKECGENFSN-MEDMRTH--LQ 56
                4566666777************.8887733..33 PP

>> OrsD  Orsellinic acid/F9775 biosynthesis cluster protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.11        67      14      35 ..       9      31 ..       5      36 .. 0.73
   2 ?    8.7   0.2    0.0037       2.4      87     113 ..      36      59 ..      32      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
        OrsD 14 CreCkyavlp.selerHLrkrhr 35
                C++C       +el +HL+  h 
  AJA92985.1  9 CEKCDLKFKSqEELMQHLQITHF 31
                77777777665678888887765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
        OrsD  87 yrCrakakCkyltrslktlrkHlqkkh 113
                 y C   ++C     +++ +r Hlq+kh
  AJA92985.1  36 YDC---KECGENFSNMEDMRTHLQRKH 59 
                 566...678888888888888888888 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0      0.23   1.5e+02       5      16 ..       1      12 [.       1      21 [. 0.76
   2 ?   11.6   0.2   0.00033      0.21       8      27 ..      31      49 ..      23      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
        YhfH  5 veFfrnLPkKkC 16
                + Ff ++P  kC
  AJA92985.1  1 MKFFAKIPCEKC 12
                578999996666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
        YhfH  8 frnLPkKkCteCGkeieEqa 27
                f+ LP   C eCG+++  ++
  AJA92985.1 31 FKDLPY-DCKECGENFSNME 49
                788887.8*******98886 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.095        61      11      22 ..       9      20 ..       3      23 .. 0.86
   2 ?    6.9   0.1     0.013       8.4       6      21 ..      33      48 ..      28      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.095
      DUF983 11 CeaCgldlshar 22
                Ce+C+l++++++
  AJA92985.1  9 CEKCDLKFKSQE 20
                ********9876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.013
      DUF983  6 kvadaCeaCgldlsha 21
                ++   C++Cg+++s  
  AJA92985.1 33 DLPYDCKECGENFSNM 48
                56779*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 433.91
//
Query:       AJA92986.1  [L=261]
Description: PD-(D/E)XK nuclease domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-07   32.0   0.0    1.8e-05   24.8   0.0    2.2  1  PDDEXK_1   PD-(D/E)XK nuclease superfamily
     0.0047   16.7   0.1       0.23   11.3   0.0    2.2  2  Dna2       DNA replication factor Dna2
  ------ inclusion threshold ------
      0.019   15.3   0.0        0.4   11.1   0.0    2.4  2  DciA       Dna[CI] antecedent, DciA
       0.12   12.1   0.0       0.54   10.0   0.0    1.9  2  DUF1281_C  Ferredoxin-like domain in Api92-like protein


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0     4e-09   1.8e-05     114     219 ..     135     240 ..      82     260 .. 0.56

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4e-09
    PDDEXK_1 114 frpvalel.efg..........gekvrLkGriDrvddkegelriiDyKtgsappkskelaelk.egl..QlllYllalaegeelkeegepagalylrle 198
                 f+ v++el +++          +ek+ + G++D + + +g l iiD+K+++   ++k+  e++ + +  Q ++Y l+++    l+++  +++++ ++  
  AJA92986.1 135 FQNVKSELnKIDnimamefpmiSEKYGFAGKLDVLAEYNGVLSIIDFKSSR---TKKK--EVYcKKWflQEAAYSLLVEDV--LGKP--VGQLVTISA- 223
                 333333311111222333334345566*********************999...4444..333133366**********99..5544..444444444. PP

    PDDEXK_1 199 epkvkdeevvkkmalteeele 219
                      + ++v+  +  ++e+ 
  AJA92986.1 224 ----AEDGTVEVFVKHRDEFL 240
                 ....45566666656666663 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.012        54      83     106 ..     100     122 ..      86     143 .. 0.71
   2 !   11.3   0.0   5.1e-05      0.23     173     202 ..     142     171 ..     131     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
        Dna2  83 skamliGtilHelfqkalleeeld 106
                   a+ +G+++H++ ++ l++e  +
  AJA92986.1 100 HDAIQRGNLFHKICESYLKNEC-T 122
                 567889************8744.3 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.1e-05
        Dna2 173 klsiskvldiEEniwspkyGLKGkiDatve 202
                   +i++++++E  ++s+kyG+ Gk+D+ +e
  AJA92986.1 142 LNKIDNIMAMEFPMISEKYGFAGKLDVLAE 171
                 568***********************9875 PP

>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.9e-05       0.4      24      57 ..      81     114 ..      73     124 .. 0.85
   2 ?    1.3   0.0       0.1   4.6e+02      20      56 ..     198     234 ..     185     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
        DciA  24 rllqaWeeivGpelaahcrpvklrdgtLvveves 57 
                 + l +W++ vG+++a+ +    +++g+L+ + ++
  AJA92986.1  81 DSLDRWRKRVGEDIAKKTLHDAIQRGNLFHKICE 114
                 5588***********************9866555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.1
        DciA  20 lalarllqaWeeivGpelaahcrpvklrdgtLvveve 56 
                 l++a+     e+++G+ + + ++    +dgt  v v+
  AJA92986.1 198 LQEAAYSLLVEDVLGKPVGQLVTISAAEDGTVEVFVK 234
                 566666667899******************9888765 PP

>> DUF1281_C  Ferredoxin-like domain in Api92-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00012      0.54      26      66 ..      24      67 ..      18      71 .. 0.87
   2 ?   -1.3   0.0      0.41   1.8e+03      28      46 ..     108     127 ..     106     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
   DUF1281_C 26 eeiiaaLskky.dvef..eheyaeegiglncGyreyknGeliee 66
                e +++ +s+k+ + ++   +ey+e+  +   G r y+nG+ + +
  AJA92986.1 24 ERWVQMVSRKFtHTSIpqGVEYTEPTVQNIHGSRMYSNGTGVYH 67
                6799999*****99994458********99*********99865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
   DUF1281_C  28 iiaaLskky.dvefeheyae 46 
                 ++ ++++ y + e++ ++++
  AJA92986.1 108 LFHKICESYlKNECTCQFEN 127
                 67899999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1923.60
//
Query:       AJA92987.1  [L=493]
Description: proton-translocating NADH-quinone oxidoreductase, chain N [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-67  227.7  23.3    1.7e-67  227.7  23.3    2.5  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   4.4     0.019   3.4e+02     119     163 ..      81     126 ..      76     128 .. 0.83
   2 !  227.7  23.3   9.6e-72   1.7e-67       1     284 [.     127     414 ..     127     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.019
  Proton_antipo_M 119 llAatlvkagvlllirllllla.vssneisqlllilaiismllgsl 163
                      ++A  ++ +++++++  +  +  +s+++i+  l++l++i+m+l ++
       AJA92987.1  81 FFAIAMLIVSIMAVAGSFNYMRnKSNPAIYFSLILLSSIGMVLIAF 126
                      566668888999998777777789999***************9987 PP

  == domain 2  score: 227.7 bits;  conditional E-value: 9.6e-72
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal.elglnslel.llllllllvgl 92 
                      ++dL++l++++El+++p+y+L+g++kk+p+s+eA++k+fl ++l+s i+++gi+l y++tg++++ +++  + +l  + l + ll++ ++++g+
       AJA92987.1 127 STDLVMLFVAWELMSIPTYILAGYNKKDPSSNEAAIKYFLFGALSSGIIIYGISLAYGITGSTNIGDVIYGFsNLSPDMLPIgLLAIGMFIAGF 220
                      78*****************************************************************99997544444444415566677889* PP

  Proton_antipo_M  93 lvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGy 185
                       +K+++vp+h+Wlpd y++aPtp++allAa + kag  + +r++ + a   + +++  l ++ai++m +g+++a+ q ++ r+lAySsi+h Gy
       AJA92987.1 221 GFKMGLVPFHMWLPDTYEGAPTPITALLAAGTKKAGFAAALRVVIMGAaALNLDWTLALGVIAIMTMTIGNIAAIMQKNLTRMLAYSSIGHAGY 314
                      ****************************8889999999999998888888999***************************************** PP

  Proton_antipo_M 186 mlialav..atqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaava 277
                      +li++++   t  g++a+++h+l ha++k + F+++ +++  +     +++++gL  kmPi+a  l++ ll+laG+Pp+ gF+sk++++ +a++
       AJA92987.1 315 ILIGISLapFTGLGLQASLFHILNHAVMKGAAFIAIAGIV-TTLGIVHLDKIKGLGRKMPITAFGLVISLLALAGVPPLNGFWSKLMLFGSAID 407
                      ******966677899*********************8885.556999********************************************998 PP

  Proton_antipo_M 278 vslillv 284
                      + +++ +
       AJA92987.1 408 ATSVVWW 414
                      8766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3232.60
//
Query:       AJA92988.1  [L=75]
Description: hypothetical protein T478_0023 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 521.77
//
Query:       AJA92989.1  [L=110]
Description: thioredoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-29  102.2   0.0    1.5e-29  102.0   0.0    1.0  1  Thioredoxin    Thioredoxin
    5.4e-10   39.5   0.1    1.9e-06   28.1   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    6.5e-09   36.2   0.1    1.3e-08   35.3   0.1    1.5  1  Thioredoxin_2  Thioredoxin-like domain
    5.5e-06   26.5   0.1    8.3e-06   25.9   0.1    1.3  1  Thioredoxin_7  Thioredoxin-like
    5.7e-06   26.3   0.0    6.8e-06   26.0   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    8.5e-05   22.3   0.0    0.00011   21.9   0.0    1.2  1  Redoxin        Redoxin
    0.00021   21.3   0.0    0.00027   20.9   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
    0.00028   20.7   0.0    0.00031   20.5   0.0    1.1  1  Thioredoxin_9  Thioredoxin
     0.0013   18.1   0.0     0.0014   18.0   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0014   18.5   0.0     0.0016   18.3   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0086   16.0   0.0      0.012   15.6   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
  ------ inclusion threshold ------
      0.024   14.3   0.2      0.066   12.8   0.2    1.9  1  DUF953         Eukaryotic protein of unknown function (DUF953
      0.025   14.5   0.0      0.032   14.1   0.0    1.1  1  Thioredoxin_6  Thioredoxin-like domain
      0.065   13.5   0.0       0.11   12.8   0.0    1.3  1  Glutaredoxin   Glutaredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.0   1.1e-32   1.5e-29       5     102 ..       7     104 ..       3     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 1.1e-32
                  SSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHH CS
  Thioredoxin   5 ltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaaflk 102
                     +++e++v +++k+v+v+F+A+wCg+C+++ P++e+la ++ +kv ++kv+vd+ +++a+ky+v +iPtl+l+++g+ +++ +ga +ke  +++++
   AJA92989.1   7 ADPKSWETDVLNSEKPVFVDFWAQWCGPCRMVGPVVEELAGDYDGKVNFVKVNVDNAQEIAQKYNVFSIPTLLLLNKGEIIAQQVGAGSKEVYQNMID 104
                  56789************************************************************************************999999886 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.5e-09   1.9e-06       2      48 ..      21      65 ..      19      66 .. 0.95
   2 !   12.0   0.0   0.00016      0.21      71      92 ..      63      84 ..      61      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.5e-09
                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HH CS
  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkee 48
                   k v++ f+a wc pc+ + p + el  ++    kv++v v++d+ +e
     AJA92989.1 21 KPVFVDFWAQWCGPCRMVGPVVEELAGDYD--GKVNFVKVNVDNAQE 65
                   889**************************9..***********9876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                   HHHHTT-S--TT-SEEEEE-TT CS
  Thioredoxin_8 71 rnklkkkynvkaiPtlvvldkn 92
                    +++++kynv +iPtl++l+k 
     AJA92989.1 63 AQEIAQKYNVFSIPTLLLLNKG 84
                   6899***************985 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1     1e-11   1.3e-08       4     107 ..      19     101 ..      16     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1e-11
  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldgkeivarlpGy 99 
                    ++kpv+v+f++ +C+ C+    +++el +         ++ +++++ v+++ a+e              a+ky+v++ Pt+++l++ ei+a+ +G+
     AJA92989.1  19 SEKPVFVDFWAQWCGPCRMVGPVVEELAGD--------YDGKVNFVKVNVDNAQEI-------------AQKYNVFSIPTLLLLNKGEIIAQQVGA 93 
                    69*************************222........79999********99987.............6************999999******** PP

  Thioredoxin_2 100 vpaeelea 107
                     ++e ++ 
     AJA92989.1  94 GSKEVYQN 101
                    99987766 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   6.5e-09   8.3e-06      16      82 ..      19      82 ..      15      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.5e-09
                   HT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---....SSEEEEE- CS
  Thioredoxin_7 16 rgkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqg....vPvvafld 82
                   ++kpv+v+f a+wc++C+ +  ++++       +++k+ +++v+v++ ++   +    +    +P++++l+
     AJA92989.1 19 SEKPVFVDFWAQWCGPCRMVGPVVEEL--AGD-YDGKVNFVKVNVDNAQEIA-QK---YnvfsIPTLLLLN 82
                   78**********************877..666.***************9833.43...2334699999997 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   5.3e-09   6.8e-06      24     104 ..      19      97 ..       7     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.3e-09
                 TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETT CS
    AhpC-TSA  24 kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygvlkee 104
                 + kpv + f+++ wc +C+   p  ++l+ +++  +v+ + v+vd+ +++++  +  s++  ll+ + + +a++ g+  +e
  AJA92989.1  19 SEKPVFVDFWAQ-WCGPCRMVGPVVEELAGDYD-GKVNFVKVNVDNAQEIAQKYNVFSIPTLLLLNKGEIIAQQVGAGSKE 97 
                 569*********.*******************9.68************9999999999***************99998665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.9e-08   0.00011      17     102 ..       8      92 ..       3     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.9e-08
                 CEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHHTT CS
     Redoxin  17 dgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftkalG 102
                 d++s +++    +k+v+v f++  +c++C+   p +e+la    ++ v++v v++dn +   +  +  +++ ++l+  +  ++++ G
  AJA92989.1   8 DPKSWETDVlNSEKPVFVDFWAQ-WCGPCRMVGPVVEELAGD-YDGKVNFVKVNVDNAQEIAQKYNVFSIPTLLLLNKGEIIAQQVG 92 
                 556666666556789********.***************999.7888**********998666666666666666666666666655 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.1e-07   0.00027      10      58 ..      32      85 ..      23     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.1e-07
                   STTCHHHHHHHHHHCHCCTCECEEECC..TTHHHH.HHCT-SSSSEE.ECT.TC CS
  Thioredoxin_3 10 CakCpklekavkeaaaekgikaevekv..tdfeei.ekygVmsvPal.vid.gk 58
                   C  C+ +  +v+e+a + + k++++kv   + +ei +ky+V s+P+l +++ g+
     AJA92989.1 32 CGPCRMVGPVVEELAGDYDGKVNFVKVnvDNAQEIaQKYNVFSIPTLlLLNkGE 85
                   999***************877777666558999**************6777555 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.4e-07   0.00031      49     110 ..      28      87 ..       8     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                    --TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--E CS
  Thioredoxin_9  49 tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegee 110
                     ++wCg ++++ Pv++++a ++  ++++  +  d+ +e+ ++y      +iPtl++l+++   
     AJA92989.1  28 WAQWCGPCRMVGPVVEELAgDYDGKVNFVKVNVDNAQEIAQKYN---VFSIPTLLLLNKGEII 87 
                    579****************889999999999************5...59********987444 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0014      46     104 ..      32      83 ..      13     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
   OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfpp 104
                 C +Cr + p +e +a  ++ +       + F+kv++d+++++ qk+++ s+P lll + 
  AJA92989.1  32 CGPCRMVGPVVEELAGDYDGK-------VNFVKVNVDNAQEIAQKYNVFSIPTLLLLNK 83 
                 899999999999999887776.......89*************************9987 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0016     134     212 ..      25      94 ..      17     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
        TraF 134 lfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaG 212
                 + F ++ c+ c++  p+++++a +y  +v +V+v+    +e+++         +++v ++P+l+l ++ +     v+aG
  AJA92989.1  25 VDFWAQWCGPCRMVGPVVEELAGDYDGKVNFVKVNVDNAQEIAQ---------KYNVFSIPTLLLLNKGEIIAQQVGAG 94 
                 5588999*************************999988766666.........**************995444455554 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.1e-06     0.012      49      96 ..      41      87 ..      35      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.1e-06
                HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEE CS
        HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeyl 96
                v+ El   +    + + v+  ++ +++a++++v+  P+ll+l +ge++
  AJA92989.1 41 VVEELAGDYDGKVNFVKVN-VDNAQEIAQKYNVFSIPTLLLLNKGEII 87
                6678888888888888887.888999******************9986 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.2e-05     0.066      36      81 ..      30      75 ..       8      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.2e-05
                BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH CS
      DUF953 36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRk 81
                 WC  C    pv+ee   +    v++v+v+v + +   ++ n f  
  AJA92989.1 30 QWCGPCRMVGPVVEELAGDYDGKVNFVKVNVDNAQEIAQKYNVFSI 75
                5******************************887766665555544 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.5e-05     0.032     117     159 ..      42      82 ..      38      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                    HHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEE CS
  Thioredoxin_6 117 iekvakefkdkinfaladaksfkrpleylglsssdlPvivivd 159
                    +e++a ++ +k+nf+ +++++ +++ + +++   ++P++ +++
     AJA92989.1  42 VEELAGDYDGKVNFVKVNVDNAQEIAQKYNVF--SIPTLLLLN 82 
                    799*****************99*******877..999999998 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.3e-05      0.11       5      46 ..      28      71 ..      23      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.3e-05
                  ESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHHHHHHT CS
  Glutaredoxin  5 tkptCpyCkkakrlLkelg......vkfeeidvdkdeeireelkelsg 46
                    ++C+ C+++  + +el       v+f  ++vd+ +ei ++     +
    AJA92989.1 28 WAQWCGPCRMVGPVVEELAgdydgkVNFVKVNVDNAQEIAQKY----N 71
                  4589***********999988888999********98887766....4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 824.06
//
Query:       AJA92990.1  [L=104]
Description: ribosomal protein L7Ae [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-10   40.7   0.4    1.7e-10   40.5   0.4    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.011   15.8   1.8        2.3    8.4   0.1    2.2  2  Trans_coact     Phage late-transcription coactivator


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.4   1.9e-14   1.7e-10       2      93 ..       5      94 ..       4      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.9e-14
                    HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEES.CHHHHHHHTTSSSECSEEEEEESTTTHH CS
  Ribosomal_L7Ae  2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvk.skkeLGelvgkkrpvsalaikdegdskd 93
                    ++e++lk a k + ++lG+k+v+  +   + klv+l+++v+   ++k +e  +k+ +v  ++ +     LG+l+g++++vsa++ ++  d+++
      AJA92990.1  5 QLEKTLKDAIKEDAYILGTKQVLGNIS--KSKLVLLSKSVPSHISEK-IEDDAKKSNVSTISYDdTSVNLGKLCGLQFRVSAISLTNIADADI 94
                    7899********************996..689***************.************999853499**************9999988876 PP

>> Trans_coact  Phage late-transcription coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3   0.00085       7.6      37      54 ..       2      19 ..       1      25 [. 0.89
   2 ?    8.4   0.1   0.00026       2.3      38      58 ..      39      59 ..      37      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00085
  Trans_coact 37 vpklIskpLkeKikaEAi 54
                 ++k + k+Lk+ ik++A 
   AJA92990.1  2 IKKQLEKTLKDAIKEDAY 19
                 78999***********96 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00026
  Trans_coact 38 pklIskpLkeKikaEAielnl 58
                 +k +++ + eKi+++A + n+
   AJA92990.1 39 SKSVPSHISEKIEDDAKKSNV 59
                 7899************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 712.21
//
Query:       AJA92991.1  [L=451]
Description: DEAD/DEAH box helicase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-49  167.8   0.2    6.3e-48  162.9   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
    2.5e-28   98.6   0.8    1.3e-27   96.3   0.4    2.3  3  Helicase_C     Helicase conserved C-terminal domain
    2.3e-05   24.4   0.0    6.5e-05   23.0   0.0    1.7  1  ResIII         Type III restriction enzyme, res subunit
    0.00014   21.2   0.3    0.00019   20.7   0.3    1.1  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    0.00038   19.9   0.2     0.0036   16.7   0.0    2.3  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
     0.0055   16.4   0.1      0.014   15.2   0.0    1.6  2  AAA_30         AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.036   13.9   0.0    1.7  2  Helicase_RecD  Helicase
      0.074   12.3   0.2       0.14   11.4   0.2    1.4  1  SecA_DEAD      SecA DEAD-like domain
       0.12   12.5   0.0        0.2   11.7   0.0    1.3  1  DUF4839        Domain of unknown function (DUF4839)
       0.14   12.5   0.1       0.26   11.6   0.1    1.5  1  AAA_19         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   0.0   3.5e-51   6.3e-48       1     173 [.      26     188 ..      26     191 .. 0.96
   2 ?    2.9   0.0     0.046        82      44     104 ..     235     295 ..     220     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 3.5e-51
                 -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvd 99 
                 ++iQaeaip +l+g dv+++a+TG+GKT+ f ip+lq++++     g + l+++PtreLa q+ +++kk++ky++++v+ ++gg+    ql++l+++++
  AJA92991.1  26 FPIQAEAIPVLLRGTDVIGQAHTGTGKTATFGIPMLQNILH---GGGIQGLVIAPTRELAMQITEEIKKVGKYTKIKVVTVYGGQGIGVQLDALRRKPE 121
                 58*************************************86...99************************************************999** PP

                 EEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 100 ivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpkdv 173
                 ivv+tpgrl+d+l++g++++++++ +VlDEad +ld+gf ++i+ +l+++       +++r + ++SAT+p ++
  AJA92991.1 122 IVVATPGRLIDHLDNGSIRTDDIKHVVLDEADVMLDMGFIEDIEYVLQKV-------PANRITSLFSATMPPEI 188
                 **************************************************.......67788********9655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.046
                 TSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET...TSSHHHHHHHHH.TTCSEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxx RF
        DEAD  44 gktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig...gvaardqlskld.ngvdivvgt 104
                 ++++ ++++ + t+  +++++++l+k+  +    v++i g   +++++  + k++ n++d++v+t
  AJA92991.1 235 NQNRGQVIVFCSTKIRTRNVARDLQKSRYK----VVAIEGdmsQNKREYSMMKFRkNQADVLVAT 295
                 466778999999999999999999888774....555544111444444444444366*****99 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       4.6   8.3e+03      20      49 ..      73     106 ..      61     118 .. 0.54
   2 ?   -0.9   0.0       1.1   2.1e+03      34      81 ..     166     215 ..     145     217 .. 0.64
   3 !   96.3   0.4   7.4e-31   1.3e-27       2     111 .]     226     333 ..     225     333 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.6
                 EEEESSHHHHHH....HHHHHHHTTSTEEEESTT CS
  Helicase_C  20 lifvntidrlek....vklllekkgikvavlhge 49 
                 l++++t++ + +    +k + +  +ikv++++g 
  AJA92991.1  73 LVIAPTRELAMQiteeIKKVGKYTKIKVVTVYGG 106
                 5556666622222112222222336777666664 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                 HHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT.SSST CS
  Helicase_C  34 lllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvae.rGid 81 
                 ++l+k  + +++ l + +   e ++  +++ ++  ++Li +d+++ +Gid
  AJA92991.1 166 YVLQKVpANRITSLFSATMPPEILRLSDKYLNNPKNILIDSDDLSgEGID 215
                 44333344455555555555555666666667778899999887537777 PP

  == domain 3  score: 96.3 bits;  conditional E-value: 7.4e-31
                 HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHH CS
  Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvts 99 
                 k ++l++++  ++++g++++f+ t+ r  + ++ l +k+ +kv+++ g+++qn+re ++ +f+k++ dvL+atdva+rGid+pkv lV+n+d+p +   
  AJA92991.1 226 KHKYLTDFI--NQNRGQVIVFCSTKIRTRNvARDL-QKSRYKVVAIEGDMSQNKREYSMMKFRKNQADVLVATDVAARGIDVPKVGLVVNYDVPNQDMV 321
                 778899998..89*************997655555.6778*********************************************************** PP

                 HHHHHTTSSSTT CS
  Helicase_C 100 yiqriGRtgRag 111
                 y +riGRt+Rag
  AJA92991.1 322 YFHRIGRTARAG 333
                 **********97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.6e-08   6.5e-05      29     147 ..      44     158 ..      22     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.6e-08
                 EEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--........-SEEEEEHHHHHHTH....... CS
      ResIII  29 ikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.kekdstnkkilvttiqsldadseeeeees 125
                  ++ TGtGKT +  + + +++l+ g++ + l+++p+++l  q  ee+kk+ + ++ ++ +++ g++        + + +i+v+t  +l  ++     ++
  AJA92991.1  44 GQAHTGTGKTATFgIPMLQNILHGGGI-QGLVIAPTRELAMQITEEIKKVGKYTKIKVVTVYGGQGIGVqLDALRRKPEIVVATPGRLIDHL-----DN 136
                 5788*********77777777776665.99********************998876655555544444433334557799999999999988.....66 PP

                 .HHHTTT-SEEEEETGGGTTS. CS
      ResIII 126 eellrdrfdviiiDEaHrlgak 147
                  + + d ++ ++ DEa  + ++
  AJA92991.1 137 GSIRTDDIKHVVLDEADVMLDM 158
                 7777777788888888666666 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   1.1e-07   0.00019      49     131 ..     227     313 ..     215     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
  ERCC3_RAD25_C  49 cefLikyhekrgDkiivfsDnvfaLkeyakklkkp.y....iyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqi 131
                     ++L ++ ++   ++ivf+      +++a+ l+k  y    i G++s+++r   + kf+kn + ++++   v+   iD+P+   ++  
     AJA92991.1 227 HKYLTDFINQNRGQVIVFCSTKIRTRNVARDLQKSrYkvvaIEGDMSQNKREYSMMKFRKN-QADVLVATDVAARGIDVPKVGLVVNY 313
                    47999**9*99*******************9987432333499****************98.6789999***********99888764 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     2e-06    0.0036     179     209 ..     121     151 ..     112     161 .. 0.90
   2 ?    0.0   0.0      0.25   4.4e+02     127     152 ..     239     264 ..     224     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
        CMS1 179 giavGtpgRildLleeeslsvdeLkrivlDa 209
                  i v tpgR++d l+++s++ d++k++vlD 
  AJA92991.1 121 EIVVATPGRLIDHLDNGSIRTDDIKHVVLDE 151
                 68899************************96 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.25
        CMS1 127 PelLvltlaalRaaDlaralkklqtk 152
                  +++v +++ +R  ++ar l+k + k
  AJA92991.1 239 GQVIVFCSTKIRTRNVARDLQKSRYK 264
                 578999**************999877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.6e-06     0.014       6      98 ..      29     153 ..      27     177 .. 0.71
   2 ?   -3.4   0.0       3.7   6.7e+03      59     114 ..     251     260 ..     230     276 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
      AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalk..alreaweaaggrviglAptgkaAkvLaeelg.ieastiakllkrlk.................... 81 
                 Qa+a+  ll ++d  ++ ++  GtGKt + +   l+++++  g + +++Apt + A +++ee+  +  +t  k+++ ++                    
  AJA92991.1  29 QAEAIPVLLRGTD--VIGQAHTGTGKTATFGipMLQNILHGGGIQGLVIAPTRELAMQITEEIKkVGKYTKIKVVTVYGgqgigvqldalrrkpeivva 125
                 9999999999998..99*********9997622679999999******************987733333333444344455566666666666666666 PP

      AAA_30  82 ...........grarlepgtllivDEag 98 
                            g  r ++ + ++ DEa 
  AJA92991.1 126 tpgrlidhldnGSIRTDDIKHVVLDEAD 153
                 6666666666644455555777777775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.7
      AAA_30  59 AkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaek 114
                  ++                                              +++ ++k
  AJA92991.1 251 TRN----------------------------------------------VARDLQK 260
                 333..............................................3333333 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     2e-05     0.036       4      99 ..      46     152 ..      43     175 .. 0.73
   2 ?   -2.1   0.0       1.6   2.9e+03      25      65 ..     237     280 ..     223     307 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
  Helicase_RecD   4 AdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke.............eekkkkaekaelrvrkqrieyiapdell 85 
                    A+ G+GK+a+ G+ + + i +g   + lv ap++e + +++e ++k  + +++k                 ++k+e + +++ ++ i+++   ++ 
     AJA92991.1  46 AHTGTGKTATFGIPMLQNILHGGgIQGLVIAPTRELAMQITEEIKKVGKYTKIKVvtvyggqgigvqlDALRRKPE-IVVATPGRLIDHLDNGSIR 140
                    889**********87776666666********************99988777777777666666655323233333.4455556666666666665 PP

  Helicase_RecD  86 klkeqadllvvDEA 99 
                    +   + + +v DEA
     AJA92991.1 141 TD--DIKHVVLDEA 152
                    54..3588888888 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
  Helicase_RecD  25 gksnilvtapskenvktlfeflakglealglke...eekkkkae 65 
                    ++ +++v   +k  ++++ + l+k+  ++   e   +++k++ +
     AJA92991.1 237 NRGQVIVFCSTKIRTRNVARDLQKSRYKVVAIEgdmSQNKREYS 280
                    44444444444444444433333332222111122222222222 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   7.8e-05      0.14      76     150 ..      23     101 ..       7     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.8e-05
                 xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SecA_DEAD  76 mrhydvQliGglvlhegk..iaemkTGEGKtlvatlpaylnaltgkgvh..vvtvndYLakrdaewmgpvyeflGlsvg 150
                 ++++ +Q  +  vl +g+  i + +TG GKt +  +p++ n l+g g++  v++    La + +e++++v ++  ++v 
  AJA92991.1  23 TTPFPIQAEAIPVLLRGTdvIGQAHTGTGKTATFGIPMLQNILHGGGIQglVIAPTRELAMQITEEIKKVGKYTKIKVV 101
                 7899999999999998865599*************************97668888888999999988888888877775 PP

>> DUF4839  Domain of unknown function (DUF4839)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011       0.2      13      75 ..     223     287 ..     215     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
     DUF4839  13 kdeadeavadFAkkykGrtieFdGsiaalvnhgd..kktrydillgagdydeetakGPaFkfedv 75 
                 + e +++ +dF ++ +G+ i F  + +   n     +k+ry ++   gd+++++ +    kf++ 
  AJA92991.1 223 DREKHKYLTDFINQNRGQVIVFCSTKIRTRNVARdlQKSRYKVVAIEGDMSQNKREYSMMKFRKN 287
                 3467999***************776555554433479*****************99999999863 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.26       3      69 ..      31     100 ..      29     184 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
      AAA_19   3 eave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....a 69 
                 ea+   l+ + ++  a  GtGKT +    +   +  gg    + l++a+t+  a++++e+++++g+      
  AJA92991.1  31 EAIPvLLRGTDVIGQAHTGTGKTATFGIPMLQNILHGG--GIQGLVIAPTRELAMQITEEIKKVGKYtkikV 100
                 566545556666667889******98765444444443..479******************88776544332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2623.30
//
Query:       AJA92992.1  [L=149]
Description: CBS domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-26   90.9   0.5    5.1e-14   52.5   0.0    2.1  2  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   1.8e-13   3.3e-09       1      55 [.      15      68 ..      15      70 .. 0.91
   2 !   52.5   0.0   2.8e-18   5.1e-14       1      56 [.      80     134 ..      80     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.8e-13
                HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                ++dim ++v+t+  d t  +a+++++ek++s l V+ ++gk+ G+++++D +r++
  AJA92992.1 15 IRDIMEKNVITIENDKTAQDAAKIIAEKDISFL-VIMNEGKPQGVLSESDFVRKV 68
                68****************************777.764699***********9987 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 2.8e-18
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 +++im+ ++ +v p+tt+e+a+++m +++++rl+++d +++lvG++t++Dl+++l 
  AJA92992.1  80 ISEIMSYKFRSVGPTTTIEDAIQKMLNNNIRRLLILD-NENLVGVITQTDLASYLR 134
                 589******************************99*6.555************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1063.55
//
Query:       AJA92993.1  [L=60]
Description: hypothetical protein T478_0696 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.6   0.1       0.13   11.4   0.1    1.0  1  DUF2920   Protein of unknown function (DUF2920)


Domain annotation for each model (and alignments):
>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   7.2e-06      0.13     129     159 ..       9      38 ..       2      42 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.2e-06
     DUF2920 129 alnlvdenaklrlsatliPpkgeYqnfGima 159
                  +n ++ +++   +  +iP+ + YqnfGi+ 
  AJA92993.1   9 PQNYIK-KYEKITQIPIIPAVNGYQNFGILC 38 
                 455555.5555668899************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 420.35
//
Query:       AJA92994.1  [L=185]
Description: hypothetical protein T478_1492 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.3   0.2      0.029   13.8   0.2    1.3  1  Beach     Beige/BEACH domain
       0.05   14.2   0.7      0.069   13.7   0.7    1.3  1  DUF2408   Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> Beach  Beige/BEACH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.2e-06     0.029      36      79 ..      15      58 ..       8      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-06
       Beach 36 wvlkdyeseeldledektyRdLskpigalneerleklkeryeel 79
                 v+++++se+++  +++ +R+Ls +ig l++e+ + ++++ +++
  AJA92994.1 15 IVMQEFQSEDIQELNSDFFRNLSSTIGKLKNEEYDGIEKKAKNQ 58
                5899*******99999******************9999999883 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   7.7e-06     0.069      21     113 ..      35     143 ..      14     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-06
     DUF2408  21 sLlslaakskaeeakesee.................vkeelkelkeeLkkieskrdeegkFkseegkevvekgqavlngLlddcfdlvedlkaqdgeek 102
                 +L+s++ k k+ee +  e+                 v+++l+++++++k   +   +e+kF+ ++++e++e+++++++g+++   +++e  ++++ ++k
  AJA92994.1  35 NLSSTIGKLKNEEYDGIEKkaknqiistttnliellVNKRLEKISNSIKIPYNILTDEEKFVIDSNDEMNERKDMIISGIINGKSKFLETTSTKH-KTK 132
                 5555555555443332222455677888888999999999999999999888888899*************************999999999986.557 PP

     DUF2408 103 kvasslqpiYd 113
                  +a ++ + +d
  AJA92994.1 133 PIAVRFVKEFD 143
                 67666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1301.29
//
Query:       AJA92995.1  [L=133]
Description: PF09969 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-37  127.0   0.5    7.1e-37  126.8   0.5    1.0  1  DUF2203   Uncharacterized conserved protein (DUF2203)


Domain annotation for each model (and alignments):
>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.5     4e-41   7.1e-37       1     122 []       3     125 ..       3     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 4e-41
     DUF2203   1 rlFtleeAnalLpllkelleelralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelveeieelGvevkdleaglvDFpakldgeevllC 98 
                 ++Ft+++An++Lpl+ ++++++++++ e+ ++e+el+ + +++++ e +  l+++l+e  +++ +++ee+ee+Gv++k+l++gl+DFp+k+ +eev+lC
  AJA92995.1   3 KYFTVQTANEVLPLVIQKYDNIKKQKMEVIKAEQELQVTLSDNDTFEkYVVLKQKLNEELSKFYKTIEELEETGVVMKGLDQGLLDFPSKRFDEEVWLC 101
                 8***********************************998887776666999************************************************ PP

     DUF2203  99 WklgEeeieywHeleeGfagRkpi 122
                 Wk+gE+ei++wHe ++Gf+gRkpi
  AJA92995.1 102 WKEGETEIKFWHEKDSGFNGRKPI 125
                 ***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1298  (0.0723967); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 943.86
//
Query:       AJA92996.1  [L=211]
Description: precorrin-8X methylmutase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-73  245.8   0.1      3e-73  245.7   0.1    1.0  1  CbiC      Precorrin-8X methylmutase


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.7   0.1   1.7e-77     3e-73       1     195 [.       8     204 ..       8     205 .. 0.98

  Alignments for each domain:
  == domain 1  score: 245.7 bits;  conditional E-value: 1.7e-77
                 HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHH..HHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HHHHHTTC-EEEECTC-HHHHH CS
        CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfela..ellrfspdaveaglealkagapivtDvemvkaGitkkrleklgnevlclladpevae 97 
                 eIe+eS++ii++e+g+++++e e+++vrR+ih+tadf++a  ++l f++da+++g++alk+g++ivtDv+ v   ++k+  + +gn+++c ++dp+ +e
  AJA92996.1   8 EIEDESMQIIESEIGSHTFNEMEWPIVRRIIHSTADFDFAreNKLLFHKDAISNGINALKNGCSIVTDVNGVIGLMNKQNPKDFGNNLICNISDPSLME 106
                 69*************************************9667899***************************************************** PP

                 HHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE----SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
        CbiC  98 lakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPvGFvgaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                  ak+ g+tr++++m+ a +e +g++vv+GnAPtALle++e+++eg vkpalv+g+PvGFv+a+esK++l+++++p+it+ GrkGGs+ A ai+naL++
  AJA92996.1 107 SAKKAGKTRAQMSMRVAEKEIDGGVVVVGNAPTALLEVMEMVREGLVKPALVVGIPVGFVSAVESKDELSKTDIPFITNIGRKGGSPCASAIINALYK 204
                 ************************************************************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1528.78
//
Query:       AJA92997.1  [L=97]
Description: hypothetical protein T478_0701 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 709.63
//
Query:       AJA92998.1  [L=616]
Description: threonine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-42  144.8   0.0    3.8e-42  143.6   0.0    1.7  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    7.4e-24   83.7   1.0    1.6e-23   82.7   1.0    1.6  1  HGTP_anticodon  Anticodon binding domain
    9.1e-17   61.6   0.1    2.3e-16   60.3   0.1    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   6.4e-46   3.8e-42       1     137 []       1     132 [.       1     132 [. 0.97

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 6.4e-46
                  -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE-STS-SSB--HHHHHHHHHH CS
  tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypyaHLssslaspevakeilkk 98 
                  mr+L++h+d+++yea+kk++k+ae+ e+k  +++e++v+F+a+E++D++   +v   a+++ik+ ++k+++kk++lypyaHLss+la+p++a +ilk 
   AJA92998.1   1 MRILQLHCDNISYEATKKEIKSAEDIEPKPVSIDEVVVCFVAIENGDNN---DVGLDAISQIKESMQKIGCKKLLLYPYAHLSSDLAAPSTALSILKL 95 
                  9***********************************************9...89******************************************** PP

                  HHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
  tRNA-Thr_ED  99 leeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                  +e++ +  +lev+raPFGw k++++++kGhpLae s+ i
   AJA92998.1  96 MESESQ--DLEVSRAPFGWTKSYNVKVKGHPLAESSKVI 132
                  *99765..58**************************976 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   1.0   2.6e-27   1.6e-23       1      93 [.     503     592 ..     503     593 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 2.6e-27
                     SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                     qv +ipl++   e++e+ + l ++L +++irv++dd+nesigk+ire+++ +i++++v+G+ke++++ ++vrdr+  + + +s+d+++++++ 
      AJA92998.1 503 QVRIIPLKD---EFMEFSQNLFDKLTEKNIRVDIDDRNESIGKRIRESEKEWIRYVLVIGDKEVNSENLSVRDRTQSDVRDISFDDFINEIQT 592
                     89*******...9***************************************************99************************996 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   3.8e-20   2.3e-16       7     178 ..     278     482 ..     273     483 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.8e-20
                   TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEE.EBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHTT.SC.. CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
  tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtk.yRdEks.dsrGLlRvreFhqkdgyvfha.easlddslrdlikaisriferlglef.. 98 
                   +++++ L+  ++ +   +  d  +  k+LP +ly++++  +R+E+s ++ GL R+r F++ d++ f++   ++ +++r  + +  ++++++g+e   
    AJA92998.1 278 DGKQLFLRFAACFGQFLIAHDMQISYKNLPYRLYEMTRYsFRREQSgELVGLRRLRAFTMPDCHAFCKdIPQAIEEFRTRFDLSRDVLKNVGIENdd 374
                   46889999999999999999998888*********99854*****98999******************6689*********************9955 PP

                   ..EEEEEEGTTSC..............................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEE CS
                   ..xxxxxxxxxxx..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  99 ..raiielmsaks..............................adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimic 163
                            ++++                              +    k ef+ +++ l+k+  ++t q +  +  +r g++++denn+  ++i+++
    AJA92998.1 375 yeM----AIRFTEdfynenkeliteivkkldkpvlvemwkerfFYFVLKWEFNYIDN-LGKASALSTDQID-VENGNRYGIEFVDENNKTINPIILH 465
                   542....33333322234455666677777777777777777333345677777777.****999999988.8999********************* PP

                   EE.EE.HHHHHHHHHHH CS
                   xx.xx.xxxxxxxxxxx RF
  tRNA-synt_2b 164 aa.ig.veRllsaileq 178
                    +  g +eR++ a+le+
    AJA92998.1 466 NSpSGaIERVIYALLEK 482
                   **9999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4128.95
//
Query:       AJA92999.1  [L=131]
Description: hypothetical protein T478_1393 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.054   13.9   1.1        3.3    8.2   0.1    2.2  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
      0.096   11.9   1.0       0.12   11.6   1.0    1.1  1  Voltage_CLC      Voltage gated chloride channel
       0.17   12.2   0.0       0.18   12.1   0.0    1.2  1  Retrotrans_gag   Retrotransposon gag protein


Domain annotation for each model (and alignments):
>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0075        45       2      26 ..      71      96 ..      70      99 .. 0.73
   2 ?    8.2   0.1   0.00056       3.3       3      26 ..     104     128 ..     102     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0075
  FeoB_associated  2 tiIVgliiaaavafvirrlikk.kkk 26
                     ++++gl+ aa+ +++i + i k kk+
       AJA92999.1 71 EVLIGLAGAAISGAAIGSYIYKiKKN 96
                     78999999999999965555553665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00056
  FeoB_associated   3 iIVgliia.aavafvirrlikkkkk 26 
                       ++g++ a +a++++ +++ kk k+
       AJA92999.1 104 AVIGGLAAsLAAGYASYKISKKIKE 128
                      5899999988***********9776 PP

>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0     2e-05      0.12      59     104 ..      75     118 ..      65     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                  BTHHHHHHHHHHHHHHHHHHTT.--SHHHHHHHHHHHHHHHHHHHT CS
  Voltage_CLC  59 GreGplvqiGAavgsglsrllklsrndrdrrlvaaGaAAGiAAaFn 104
                  G  G+++  GAa+gs++ ++ k ++  r+++ v+ G AA +AA + 
   AJA92999.1  75 GLAGAAI-SGAAIGSYIYKIKK-NSPYRKQQAVIGGLAASLAAGYA 118
                  5666655.59*********988.66775777************885 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     3e-05      0.18      48      83 ..      26      60 ..      10     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
  Retrotrans_gag 48 qleeelsslrQgtesvreYvtrfktladqldevlte 83
                    +++  l++ r+g+ ++reY+++f+   d++d ++t+
      AJA92999.1 26 DKKGALKQYRKGNLHIREYADKFTVHTDKVD-PRTD 60
                    55667999**********************9.6887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 989.15
//
Query:       AJA93000.1  [L=130]
Description: hypothetical protein T478_1412 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   14.0   0.0      0.068   13.5   0.0    1.2  1  BRF1      Brf1-like TBP-binding domain
      0.073   13.1   0.0       0.13   12.3   0.0    1.4  1  DUF4539   Domain of unknown function (DUF4539)


Domain annotation for each model (and alignments):
>> BRF1  Brf1-like TBP-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.6e-06     0.068       4      49 ..      13      58 ..      11      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.6e-06
        BRF1  4 dddeideyllseeevkiKeriWvelnkeyLeeqeekrlkeeaeeae 49
                +d+ i +++  + e +iK+ +     + yL ++e  +  ++a+   
  AJA93000.1 13 SDSNIRNCIVADTEGEIKAVMHRDGIRNYLSDEETSESLKRAATSW 58
                578****************************655444444333333 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05      0.13       9      45 ..       6      41 ..       2      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
     DUF4539  9 iiksintlnslgdalvtlkDptGeidgtihrkvleey 45
                ++k+i  ++s+     +++D  Gei++++hr+ + +y
  AJA93000.1  6 TMKRIMDSDSN-IRNCIVADTEGEIKAVMHRDGIRNY 41
                56777444444.5778999************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1010.87
//
Query:       AJA93001.1  [L=329]
Description: glycosyltransferase, group 4 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-27   96.5  16.2    1.5e-27   96.5  16.2    2.1  3  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
       0.94    8.2   5.7       0.12   11.2   0.9    2.0  2  DUF2254          Predicted membrane protein (DUF2254)
          1    9.2   4.6        2.2    8.1   0.2    2.7  3  SPC25            Microsomal signal peptidase 25 kDa subunit (


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.35   2.1e+03      33      47 ..       8      22 ..       2      73 .. 0.51
   2 !   96.5  16.2   2.5e-31   1.5e-27       2     159 ..      77     231 ..      76     232 .. 0.95
   3 ?   -2.8   0.0       0.9   5.4e+03      68      68 ..     316     316 ..     271     328 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.35
  Glycos_transf_4 33 ilaalililtldlsl 47
                     +++a++++++  ++l
       AJA93001.1  8 AIIAIVVAFFSVYGL 22
                     333333333333222 PP

  == domain 2  score: 96.5 bits;  conditional E-value: 2.5e-31
  Glycos_transf_4   2 llllltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNliDGldGlaagvs 95 
                      l+++lt+++++++G++DD + +  ++K ++ +++a++++l++    ++l+++l+ ++++++ +l+++l++++i ++ N++N iD l+G+a+g  
       AJA93001.1  77 LAVILTTFFAFIVGLIDDKKTMGGWFKPLALAFCAAPILLLGA-YDSNLDFPLF-GSVSIP-LLYMALVVFMIPIMGNTINSIDVLNGVASGFI 167
                      67899********************************988877.7788999998.888888.9999**************************** PP

  Glycos_transf_4  96 iiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlailg 159
                      +i+++al +  ++ +++e+++++l+l+++ l+f+ +++ p+k+F GDsg+++ G+ ++++ai+g
       AJA93001.1 168 TIASFALSISLFILQNYEVAIISLCLAFSSLAFYKYHKFPSKIFPGDSGAITFGAAYGAIAIIG 231
                      **************************************************************97 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.9
  Glycos_transf_4  68 l 68 
                      +
       AJA93001.1 316 I 316
                      1 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9     2e-05      0.12      40      74 ..     136     184 ..      97     187 .. 0.66
   2 ?   -4.1   0.3       0.9   5.4e+03     122     146 ..     235     259 ..     226     266 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
     DUF2254  40 e..............gaeaaralLstiagsmltvagfvfSitvvalqla 74 
                                +  ++ ++L+ +a++++t+a+f++Si +  lq +
  AJA93001.1 136 LlymalvvfmipimgNTINSIDVLNGVASGFITIASFALSISLFILQNY 184
                 0444455555555556667779*********************999975 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.9
     DUF2254 122 lsvlvalllaivsvllLiyFihhla 146
                 +  ++a+l ai++ +l++  +++++
  AJA93001.1 235 VIAAIAILPAIINSFLFLSSVKKVV 259
                 5566777777777777776666665 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2   0.00036       2.2      57      97 ..       7      47 ..       5      85 .. 0.82
   2 ?   -3.1   0.2      0.99   5.9e+03      33      43 ..     189     199 ..     164     211 .. 0.55
   3 ?    2.6   0.0     0.018   1.1e+02      63     123 ..     240     297 ..     216     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00036
       SPC25 57 pvlaiavvlYfilsgiltlystfvekntifvgkrktgskri 97
                p+++++vv++f + g+  ++++ +ek +i v   ++++k++
  AJA93001.1  7 PAIIAIVVAFFSVYGLTPFVIRALEKRNITVVDANKKEKTM 47
                67899********************9999888777776644 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.99
       SPC25  33 Gylavaiaava 43 
                   l+ a++ +a
  AJA93001.1 189 ISLCLAFSSLA 199
                 23333333333 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.018
       SPC25  63 vvlYfilsgiltlyst..fvekntifvgkrktgskriekitissslkklsptytltvsykdks 123
                  +l  i+++ l+l s   +ve  +i   k++t+++    ++++s+++++ p+  +++   +k 
  AJA93001.1 240 AILPAIINSFLFLSSVkkVVEHREI---KNPTSHT--DDWKLKSTSENHAPITLVRLLIAKKP 297
                 5555566666655443237777777...3333322..389999999*****999988775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2460.02
//
Query:       AJA93002.1  [L=398]
Description: tRNA pseudouridine synthase D [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-79  266.7   0.1    1.2e-78  264.9   0.1    1.7  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.9   0.1   6.5e-83   1.2e-78       2     416 .]       9     387 ..       8     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 264.9 bits;  conditional E-value: 6.5e-83
        TruD   2 lgielyvtdtegigGrlrespeDFiVeEieef.sgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepee 99 
                 +gi++y+t+++ i G+++++ +DF+V+Ei    + ++ ++++ + v+ ++k+++dt++++ ++ ++ g+  k +   G+KD++A T Q++  +k + ++
  AJA93002.1   9 IGISVYTTKSPSISGKIKQNENDFLVREILSEkTIDSFNNPDGHGVYLLKKSGIDTNHALIDIEKRYGLVLKSL---GLKDANAKTEQYVFTYK-KINS 103
                 89***************************7775444677778899999*********************77765...9***********99765.5568 PP

        TruD 100 lealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgk 198
                 l++ + k+ + + +g  +++++  d+ GN Fei+v++++      +++ + +   e+   + N+fG+QRFGs+rp+thlvGk i+kgd+eeA+e ++  
  AJA93002.1 104 LPEYTGKKYSAQRLGFVKKPISKKDMLGNYFEIKVSELS------NALPSFTGG-EK---ILNFFGYQRFGSKRPITHLVGKSIIKGDYEEALEYLLNF 192
                 9999*********************************62......244455443.33...89************************************* PP

        TruD 199 pfeeesedtreareavaetgdleealeelpkslryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvif 297
                 +++ +se+ +e+r++++e++  +e +e+lp s+++Er+ll++L + ++d k+A++++p +L+r++++AyqS+lFN+ ls   e   +l ep  +Dv+++
  AJA93002.1 193 SSKYDSEKNNEMRKLISERKSETEVIELLPYSMDIERNLLQQLSK-DDDPKNAIRSIPLQLRRFYIQAYQSFLFNKTLSLANEFEENLFEPEIDDVCFD 290
                 *********************************************.*************************************999*********9888 PP

        TruD 298 aeerlpdtdrlqlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlelsaeede 396
                 +++                 +++++ e     +++plvG +   ++ + + +++++leee l+++dF +++++els++G +R+++++  d++++    +
  AJA93002.1 291 KNSV--------------LGKFENIPE---QKLAVPLVGHS-YYKKSRFDYYIKKILEEELLTPKDFFIKDFQELSVEGGFRNASINYVDFAID----K 367
                 7444..............344443333...34778****95.566899******************************************8854....4 PP

        TruD 397 ltleFsLpkGsYATvvlrEi 416
                  +++F+L +GsYAT+vlrEi
  AJA93002.1 368 DLVKFQLSRGSYATIVLREI 387
                 59*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2846.84
//
Query:       AJA93003.1  [L=185]
Description: phenolic acid decarboxylase subunit B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-27   96.1   0.7    2.1e-27   95.8   0.7    1.0  1  Flavoprotein   Flavoprotein
  ------ inclusion threshold ------
      0.034   13.7   0.0      0.043   13.4   0.0    1.1  1  Y_phosphatase  Protein-tyrosine phosphatase


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.7   2.4e-31   2.1e-27       1     125 [.       1     163 [.       1     175 [. 0.89

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 2.4e-31
                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS.................TCSSHHHHHH.CTTESEEEEEEEEHHHHHHHHT CS
  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.............redpilhiel.rrwadllviaPasantlakian 83 
                   +k+++giTGs ++i++++lle Lk++gie+++v+++ Akk i  e  ++++             +++++ +++  ++++d+++++P++++tl+ ian
    AJA93003.1   1 MKLVIGITGSTGVIYGIRLLEVLKEKGIETNLVMSEWAKKCIPME--TKHDvayveslatevtdENNMAANVSSgSHKTDGMIVIPCTMKTLSSIAN 95 
                   799****************************************88..444445677776766665555555555567******************** PP

                   T--SSHH..............................HHHHHTHCCTTEEEEE.--HHCCTCSTCHHHHHHH CS
  Flavoprotein  84 Giadnll..............................tlilratakkpiliaPamnpamyenpqtlknlekl 125
                   G+ ++l+                              +l+l   a+  ++i+P + +++y+np +++ ++++
    AJA93003.1  96 GYDETLVaraagvtikevrklilvaretplsaihlenMLKL---ARLDVVIMP-PVTEFYTNPTSIDAMVDH 163
                   **********************************9999899...99*******.**************9998 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-06     0.043     135     199 ..      28      92 ..      13     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-06
                    E.EEEEESSS-SSSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHH CS
  Y_phosphatase 135 v.kqlqytnWpdhgvpesaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqlea 199
                    + + l + +W ++++p ++k+ + +++++ ++  ++++ +    s G+ +t  ++++ + ++ l++
     AJA93003.1  28 IeTNLVMSEWAKKCIPMETKHDVAYVESLATEV-TDENNMAANVSSGSHKTDGMIVIPCTMKTLSS 92 
                    3378999**************************.89999************999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1365.63
//
Query:       AJA93004.1  [L=137]
Description: hypothetical protein T478_1451 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.6   1.8       0.25   11.5   0.5    2.1  2  DUF2730   Protein of unknown function (DUF2730)
      0.058   12.4   0.0      0.069   12.2   0.0    1.0  1  CLN3      CLN3 protein
      0.073   12.2   0.4      0.089   12.0   0.4    1.1  1  TipE      Na+ channel auxiliary subunit TipE
       0.12   11.1   0.0       0.12   11.1   0.0    1.2  1  DUF2254   Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.02        88      11      68 ..      40      96 ..      33      98 .. 0.77
   2 ?   11.5   0.5   5.5e-05      0.25      38      76 ..      93     131 ..      83     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
     DUF2730 11 lavisvvvavilllldskYakredleklaekveendkrlteletkvenLPtakdlekL 68
                +av  + ++v+++++++  a r+  +    + e++++ lte e++  +L  +kdl+++
  AJA93004.1 40 MAVPIMWFMVFVIWIAQLAADRNHGADH-SHDEKKNNELTEKEITTYKLGLEKDLSDV 96
                5556677788888888888888877766.667888999******99999999999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.5e-05
     DUF2730  38 laekveendkrlteletkvenLPtakdlekLkllladlr 76 
                 l ++ + +d+ +t+l+ ++enL t++++e+++ ++ +l+
  AJA93004.1  93 LSDVHDAKDEEITHLKNEIENLKTKVEIETIRAEIYNLK 131
                 566678899**************************9987 PP

>> CLN3  CLN3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.5e-05     0.069     117     223 ..      10     114 ..       2     135 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
        CLN3 117 awssGTGaaGlvGallyalltsllglsvkatllvslvlPlllllsyflllekkkskkeakaeeee..eeyekleeeeeeee...........eeseeee 202
                 +  sG  aa l+G  ly  l    ++ ++ + ++++ +P++ ++++ +  ++  +++++ a +++  +++++l+e+e               +      
  AJA93004.1  10 TLVSGVWAAILTG--LYFPLV---DFAPSLSFIFTMAVPIMWFMVFVIWIAQLAADRNHGADHSHdeKKNNELTEKE---IttyklglekdlS------ 94 
                 5555555554443..455555...69**************9998776655554444443333333112222222222...1234444433221...... PP

        CLN3 203 lleseaasaaeeeeeees.sel 223
                   +++ a+ +e ++ +++ ++l
  AJA93004.1  95 --DVHDAKDEEITHLKNEiENL 114
                 ..11111111111111112111 PP

>> TipE  Na+ channel auxiliary subunit TipE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4     2e-05     0.089     289     361 ..      33     103 ..      26     129 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
        TipE 289 tlnlvfamaipipsfiisviylafayfviynedeeaalldkngeeediedelaetdegndnkidavneseaav 361
                 +l ++f+ma+pi  f++ vi++a       n   +    d   ++e +e e++    g ++ + +v++++ + 
  AJA93004.1  33 SLSFIFTMAVPIMWFMVFVIWIAQLAADR-NHGAD-HSHDEKKNNELTEKEITTYKLGLEKDLSDVHDAKDEE 103
                 6899*****************98643322.22222.2334445556677777777777666665554443222 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.8e-05      0.12     118     146 ..      27      58 ..       4     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
     DUF2254 118 e...vpqlsvlvalllaivsvllLiyFihhla 146
                     +p+ls+++++++ i+  ++++++i +la
  AJA93004.1  27 LvdfAPSLSFIFTMAVPIMWFMVFVIWIAQLA 58 
                 034589***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1593  (0.0888505); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 996.77
//
Query:       AJA93005.1  [L=321]
Description: 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-29  101.5   0.2      6e-29  100.8   0.2    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.1e-14   52.5   2.7      3e-12   46.5   2.7    2.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.2   6.7e-33     6e-29       2     153 .]      49     196 ..      48     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 6.7e-33
                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHH...HH CS
  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggq...qe 93 
                   iGc+             +++++  g+++ +G+ lp+A Gak+ +p+ +++a+ GDG+ l i   +++ a rrn+++t+++++N++yg+t+gq   + 
    AJA93005.1  49 IGCSGK----------TSHFINvFGVHTLHGRVLPFAQGAKISNPNLKIIAVGGDGDGLGIgAGHFVAAGRRNVDMTYIIFDNAVYGLTKGQaspTL 135
                   667776..........889999999************************************99*****************************99888 PP

                   HHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
  TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                   + g+k+ks p++++ ++v++  la a G +  ar  ++d+ +l++++ +a+++kg a+++v
    AJA93005.1 136 KLGEKTKSLPTPNTNYNVNPIGLAIASGFTfTARAYSYDIRHLKDIIIAAINHKGLAFVDV 196
                   899***************************999999***********************98 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   2.7   3.3e-16     3e-12       1      60 [.     200     284 ..     200     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.3e-16
                 XTTTXSSSXSXXXX.............X-EEEGGGST---EE...........HHHHHHHHT-----EEEEEEEE.TTS--HHHH CS
  PFO_beta_C   1 CvtFNkvnTfdwYk.............ervykleedgyDpsd...........lekAlekalewgdkiplGifYk.eekptyeer 60 
                 C+t+N++nT dw++              r+ykle+++yDp +           + +A+ k+lew+ kip+GifYk e   +y+ r
  AJA93005.1 200 CPTYNDINTRDWFNgadrvdettnkpmPRIYKLEDTDYDPVVhysdetelnqkKTQAIVKSLEWDTKIPTGIFYKnELITPYTRR 284
                 *************8444444444444459******89**************************************7777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2345.22
//
Query:       AJA93006.1  [L=346]
Description: multicopper oxidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-26   90.7   5.0    2.9e-22   78.9   0.2    2.2  2  Cu-oxidase_3  Multicopper oxidase
    8.5e-21   74.1   9.9    2.6e-10   40.2   1.4    3.1  3  Cu-oxidase_2  Multicopper oxidase
      0.008   16.3   0.0       0.19   11.8   0.0    2.6  3  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.062   13.3   0.1        3.8    7.6   0.0    2.3  2  CHB_HEX_C_1   Chitobiase/beta-hexosaminidase C-terminal domai


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.2   6.4e-26   2.9e-22      15     118 ..     102     200 ..      91     201 .. 0.91
   2 !   13.7   0.8   1.1e-05     0.048      28     117 ..     239     332 ..     230     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 6.4e-26
                   EEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEEEEEE--S-SEEEEEEE--TT...HHHTT- CS
  Cu-oxidase_3  15 revitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesftyrftvkqqagtlwYhshlsl...qqaaGl 108
                    +v+t+N+++pgpti+++egd v++++tN+ +++ s+h+hG++  +    DGv       i +g +fty+f ++   g ++Yh h++    + a+Gl
    AJA93006.1 102 YNVWTFNDSVPGPTIRATEGDLVRIHFTNEGSKPHSLHFHGIHKAEM---DGVFE----SIGTGGKFTYEFYAEP-VGLHLYHCHVHPveeHIAHGL 190
                   589***************************************98877...99988....9**************9.***********9984555*** PP

                   EEEEEEE-HH CS
  Cu-oxidase_3 109 aGaiiiedke 118
                   +Ga+i+++ke
    AJA93006.1 191 YGAYIVDPKE 200
                   *******986 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                   EEEEETT-EEEEEEEE-S..SS-B-EEEET--S-G.G.....GSCSGGG-B-T..T-EEEEEEE--S-SEEEEEEE--TTHHHTT-EEEEEEE-H CS
  Cu-oxidase_3  28 tievregdtvvvnvtNkl..dentsihwhGlqqrk.tswmDGvpgvtqcpiqp..gesftyrftvkqqagtlwYhshlslqqaaGlaGaiiiedk 117
                    ie++++++++  v+N l  d     h+hG   +      D vp + +++++   g+++  +f+ k   g +++h+h      +G +  ++++++
    AJA93006.1 239 PIEINTNQNIRAYVVNILefDAVNNFHLHGTLFHHyPAGTDTVPSGYNDMLTMsqGDRQILEFNYKY-PGLYMFHAHNTEFSEKGWVSSFLVKEN 332
                   6999**************8788899*****76555144689999999988765448899999**999.**********99878999999999876 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.9e-07    0.0018      30      62 ..     111     143 ..      83     147 .. 0.80
   2 !   20.6   0.1   6.6e-08    0.0003      95     136 ..     155     199 ..     152     200 .. 0.93
   3 !   40.2   1.4   5.9e-14   2.6e-10      20     135 ..     222     331 ..     210     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-07
                   TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS- CS
  Cu-oxidase_2  30 entnvitlpkgevveiviqnntklpHPfHlHGh 62 
                      ++i++ +g+ v+i ++n+++ pH++H+HG 
    AJA93006.1 111 VPGPTIRATEGDLVRIHFTNEGSKPHSLHFHGI 143
                   4567899999**********************6 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.6e-08
                   E-TTEEEEEEEES.S-EEEEEEESSH...HHHHTT-EEEEEEECH CS
  Cu-oxidase_2  95 vppggwvairfkadnpGvwllHCHil...wHldqGmalqfvvrpd 136
                   +  gg+++++f a+  G  l+HCH+    +H  +G++++++v+p+
    AJA93006.1 155 IGTGGKFTYEFYAEPVGLHLYHCHVHpveEHIAHGLYGAYIVDPK 199
                   6789********************99999*************987 PP

  == domain 3  score: 40.2 bits;  conditional E-value: 5.9e-14
                   EEEE...ETCCTTTSSEEEEEETTEEEEEEEEE-SSS..-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-E CS
  Cu-oxidase_2  20 seit...ngeefsentnvitlpkgevveiviqnntkl..pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpG 111
                   ++++   n  +f  + ++i+++ ++ ++ ++ n  ++     fHlHG+ f     g+++           +  +  d  ++  g++ +++f++++pG
    AJA93006.1 222 ENNFyaaNTIPFYYQHHPIEINTNQNIRAYVVNILEFdaVNNFHLHGTLFHHYPAGTDT-----------VPSGYNDMLTMSQGDRQILEFNYKYPG 307
                   2222455788999********************8888889*************999999...........89999********************** PP

                   EEEEEESSHHHHHTT-EEEEEEEC CS
  Cu-oxidase_2 112 vwllHCHilwHldqGmalqfvvrp 135
                    +++H H+++  ++G + +f+v++
    AJA93006.1 308 LYMFHAHNTEFSEKGWVSSFLVKE 331
                   *********************986 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.5   6.8e+03      79     103 ..      22      46 ..      21      46 .. 0.83
   2 !   11.8   0.0   4.3e-05      0.19      36      96 ..     115     181 ..     105     189 .. 0.86
   3 ?    1.1   0.0     0.094   4.2e+02      71      99 ..     292     321 ..     286     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.5
  Cupredoxin_1  79 tiaplkpGeYeftcdmhmdakGkli 103
                    ia+++p ++  + ++  ++ G++i
    AJA93006.1  22 IIAEETPQTFLTHTGLVIKTTGEVI 46 
                   6889999999999999888888886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.3e-05
  Cupredoxin_1  36 kievkagekvklkiknkdktpeefesed......lgeekvlapgktttitiaplkpGeYeftcdmhm 96 
                   +i + +g  v+++++n++++p+++ ++        g+ + + +g ++t ++ ++  G + ++c  h+
    AJA93006.1 115 TIRATEGDLVRIHFTNEGSKPHSLHFHGihkaemDGVFESIGTGGKFTYEFYAEPVGLHLYHCHVHP 181
                   689999*******************999666663335589***********************9987 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.094
  Cupredoxin_1  71 apgktttitiaplkpGeYeftcdmhmd.ak 99 
                    +g+ + ++++ ++pG Y f+    ++  k
    AJA93006.1 292 SQGDRQILEFNYKYPGLYMFHAHNTEFsEK 321
                   67899999************9876665555 PP

>> CHB_HEX_C_1  Chitobiase/beta-hexosaminidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.019        86      17      33 ..     120     136 ..     109     167 .. 0.82
   2 ?    7.6   0.0   0.00084       3.8      40      57 ..     237     254 ..     220     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.019
  CHB_HEX_C_1  17 atedatIyYTtDGsePt 33 
                  + + + I++T  Gs+P 
   AJA93006.1 120 EGDLVRIHFTNEGSKPH 136
                  333459**********7 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00084
  CHB_HEX_C_1  40 tgpIeitgtttikaiavd 57 
                    pIei+++ +i+a++v+
   AJA93006.1 237 HHPIEINTNQNIRAYVVN 254
                  259*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2784.21
//
Query:       AJA93007.1  [L=173]
Description: acetyltransferase (GNAT) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-15   56.9   2.4    2.9e-15   56.7   2.4    1.0  1  Acetyltransf_4  Acetyltransferase (GNAT) domain
    5.3e-15   56.3   0.1    6.5e-15   56.0   0.1    1.1  1  Acetyltransf_3  Acetyltransferase (GNAT) domain
    3.4e-05   24.1   0.0    4.3e-05   23.7   0.0    1.2  1  Acetyltransf_1  Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   2.4   4.8e-19   2.9e-15       1     154 [.       9     164 ..       9     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 4.8e-19
  Acetyltransf_4   1 iraateeDakeilaiyaey..v.vntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnk 91 
                     +ra+++eD++ ++++++++  + + +++     ++++ +fe + ++ + +  ++f+++  + +++G + l  +++  k+ +ae+s+ +  +  +k
      AJA93007.1   9 LRALEKEDLELLKKWRNDKktRiHTREFRLLNMINQKNWFESIHKQ-NPPSAIMFGIETkKQKLIGVCGLTYIDW--KNRHAEISNIISINNWQK 100
                     79**************765222123366666667777777765555.4888********9***************..***********9556777 PP

  Acetyltransf_4  92 eglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDmi 154
                     +  +++ +d l+++   e n+++l  ei+ +  ++i++++++ F+++g +++    n rw+D+ 
      AJA93007.1 101 TKEAKDTLDTLIKYGfDELNLHRLWVEIFETIPENIKLFEKMKFKKEGTLHDKLWRNSRWYDSF 164
                     7888889999999988*************9999*****************************86 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   1.1e-18   6.5e-15       3     138 .]       8     145 ..       7     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.1e-18
  Acetyltransf_3   3 lLrplteeDlealfelrsdpevmrylpe..pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgk. 94 
                      Lr l++eDle l ++r+d++++ +++e   l+  +++ w+e++ +++++ ++  + i++k+++ iG++gl++++++++ ae++ ++    w+k 
      AJA93007.1   8 NLRALEKEDLELLKKWRNDKKTRIHTREfrLLNMINQKNWFESI-HKQNPPSAIMFGIETKKQKLIGVCGLTYIDWKNRHAEISNIISINNWQKt 101
                     69***********99******88666667799999*******85.6677888899***9899978***********************8878886 PP

  Acetyltransf_3  95 GyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                       a++ +  l++y f+el+l+rl+++i ++ +  i+++ek+ f+
      AJA93007.1 102 KEAKDTLDTLIKYGFDELNLHRLWVEIFETIPENIKLFEKMKFK 145
                     9****************************************996 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   7.1e-09   4.3e-05      24     117 .]      47     144 ..      17     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7.1e-09
                     HHHHHHSTTC.EEEE..EEET.TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHH CS
  Acetyltransf_1  24 feesfsleae.gllv..aeed.geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYe 113
                     ++es +++++ + ++  +e   ++liG ++l+ i++ k+++a+i  +    ++++   ++  l++l+++ ++e ++++++++++e+    i+l+e
      AJA93007.1  47 WFESIHKQNPpSAIMfgIETKkQKLIGVCGLTYIDW-KNRHAEISNIISINNWQKTKEAKDTLDTLIKYGFDElNLHRLWVEIFETIPENIKLFE 140
                     344444444434444444443577************.******************************************99888888888***** PP

                     HTTE CS
  Acetyltransf_1 114 klGF 117
                     k+ F
      AJA93007.1 141 KMKF 144
                     9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1365.34
//
Query:       AJA93008.1  [L=270]
Description: ribosomal protein, L4/L1 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-43  147.6   0.7    3.8e-43  147.4   0.7    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.4   0.7   2.1e-47   3.8e-43       1     191 [.      16     257 ..      16     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 2.1e-47
                   EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT............STTSTT---SS---S.EEHHH CS
  Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir............spiargGgvahgpkperdyst 84 
                   +eL p+vF+++++r lih+a+ +  ++  q ++ ++ a++ev + ++++ +  G+G AR+ +i+            ++ +rgG++ah+pk+++ +++
    AJA93008.1  16 IEL-PNVFETEVNRTLIHKAYINLESHGFQKHSTKPtAGMEVVADSNDPPT--GRGVARIAKIKgggggragqageVASTRGGRQAHPPKANKVIYK 109
                   789.***********************************************..******************************************** PP

                   HHHHHHHHHHHHHHHHHHHHTT-EEEES.---.-S............S--HHHHHHHHHHTT-.........................TTSSEEEEE CS
  Ribosomal_L4  85 klnkKvrrlAlrsaLsakakqglllvvd.nleple............esktkelvellkklgl.........................ksksvLivv 143
                   klnkK+ +lAl+saL+a+++++l++ ++ ++e++e            +skt+el+++++ l++                           ks+L+vv
    AJA93008.1 110 KLNKKENKLALCSALAATTSKELVENRGhKVEGIEslpliisddiekISKTSELIKIIEDLKItqdtdrlknrkrrtgkvalrgrvskVGKSALFVV 206
                   ****************************7555666788999999999*************9988888888888888888888888888899****** PP

                   SSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHHH CS
  Ribosomal_L4 144 sekdenlvlaarnlpgvevieveslnvydllkadk....vvitksaveklee 191
                   s+ ++n+ +aa+ +pg++v+++++l+v++l+++ +    +v+tk+a+e+++e
    AJA93008.1 207 SK-SDNISKAAASIPGIDVCDAKNLSVLNLAPGGTlirlTVFTKKAIEEIAE 257
                   97.99********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2128.40
//
Query:       AJA93009.1  [L=46]
Description: hypothetical protein T478_0690 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   16.4   0.3     0.0064   16.4   0.3    1.0  1  Ferritin  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   3.6e-07    0.0064      24      60 ..       4      40 ..       1      46 [] 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-07
                HHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
    Ferritin 24 yvkgpgleglaeffdeqaeeerehadklaerilalGg 60
                  ++++ +g++++f+e+ + e + a+++a+r+++l +
  AJA93009.1  4 ETRSIDKKGFSNKFFEELDKEHDNAKEFAKRQKELKE 40
                56788999*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2052  (0.114451); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 357.39
//
Query:       AJA93010.1  [L=132]
Description: putative methylmalonyl-CoA epimerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-21   75.0   0.0    5.9e-21   74.8   0.0    1.0  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    2.9e-08   33.9   0.0    3.2e-08   33.8   0.0    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.1e-06   28.9   0.0    1.3e-06   28.7   0.0    1.1  1  Glyoxalase_3  Glyoxalase-like domain
  ------ inclusion threshold ------
      0.033   15.0   0.0      0.039   14.7   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.3e-24   5.9e-21       1     109 []       4     113 ..       4     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.3e-24
                   EEEEEE-S-HHHHHHHHHH.TT-EESS-.-E.EETTTTEEEEEEEETTEEEEEEEESSTT...-THHHTS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
  Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqr.yrdepqevdlafallgsgsvqieLieplegp...eflaehgeglhhlaywvddldaavarleeqGfev 93 
                   ++igivV+++++   ++++ l+++++ + +++++q+v+++f+++++  v+ieLiep+e++   +++ e g+g+hhl+++v+d+ + v+++ ++G +v
    AJA93010.1   4 HHIGIVVNNIKESFGELTNFLDFTETSIpVEVKSQKVNVCFLKTSD--VYIELIEPIEDNspvKTFSESGGGFHHLCFEVEDIFKEVEKMVNNGGRV 98 
                   8**********************9775538899***********99..9***********66666666***************************** PP

                   EEEEE-GGGTT-EEEE CS
  Glyoxalase_4  94 vqkgvragaagrrfay 109
                   + +   +g ++r +a+
    AJA93010.1  99 IVEP-TKGFEDRLIAF 113
                   9976.78999998887 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   7.2e-12   3.2e-08       1     116 [.       2     113 ..       2     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 7.2e-12
                 EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.TSEEEEEEEEEHCHHHHHHHHHHHTT CS
  Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee.tvhhvafialdvedvgkaldrlkeag 98 
                 +++h+ ++v+++++s    t+ L+f+ +   + + + ++++  f+  ++  iel+    ++++ k +    + ++ ++++++++ved+ k ++++  +g
  AJA93010.1   2 KLHHIGIVVNNIKESFGELTNFLDFTETSIPV-EVKSQKVNVCFLKTSDVYIELIEPIEDNSPVKTF----SeSGGGFHHLCFEVEDIFKEVEKMVNNG 95 
                 69******************************.8888******************999999999888....33899*********************** PP

                 GEEEEEEECHHCTEEEEE CS
  Glyoxalase  99 vkvvaepgrhyfgalysf 116
                 ++v  ep++ + ++l+ f
  AJA93010.1  96 GRVIVEPTKGFEDRLIAF 113
                 *********999999877 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.9e-10   1.3e-06       1     121 [.       3     118 ..       3     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.9e-10
  Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdg.YlElla.vdpeapaperprlfgldrlakgeglhtlalrtddidataarl 95 
                   l+H++++v++++e   ++++ l ft t   +  +    N ++    + Y+El++ ++++ p ++    f     ++g+g+h+l+++++di ++++++
    AJA93010.1   3 LHHIGIVVNNIKESFGELTNFLDFTETSIPVEVKSQKVNVCFLKTSDvYIELIEpIEDNSPVKT----F----SESGGGFHHLCFEVEDIFKEVEKM 91 
                   89***********************99888888877888887765556******7799999853....3....3689******************** PP

  Glyoxalase_3  96 raaGvdeagrrv..rpdg....gdlrwrllfl 121
                    ++G      rv  +p      + +++ ll +
    AJA93010.1  92 VNNGG-----RVivEPTKgfedRLIAFVLLNM 118
                   99993.....3212222223224466666555 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.8e-06     0.039      59      94 ..      74     109 ..      25     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.8e-06
  Glyoxalase_6  59 rvHldlavedldaevarlvalGArvlreprdgthgr 94 
                     Hl ++ved+ +ev+++v+ G+rv+ ep +g ++r
    AJA93010.1  74 FHHLCFEVEDIFKEVEKMVNNGGRVIVEPTKGFEDR 109
                   47************************9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 936.67
//
Query:       AJA93011.1  [L=127]
Description: PF01989 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-27   94.4   0.1    3.9e-27   93.8   0.1    1.3  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.1   2.2e-31   3.9e-27       1      80 []      21     100 ..      21     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.2e-31
                 --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--EE CS
      DUF126   1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPlv 80 
                 ++flg vd++tG+++dk+ ++  +s+++++Lv+p+g GS+vg+y +++l++n++aP A+i+ +ad  +a+G+++a+iP++
  AJA93011.1  21 INFLGAVDKKTGIIRDKKYDIFEKSMKDTVLVFPHGIGSSVGAYTIYSLKSNQSAPIAMICTKADLTVASGCALANIPMI 100
                 78****************************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 936.78
//
Query:       AJA93012.1  [L=151]
Description: ribosomal protein S19e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-47  159.9   0.0    3.1e-47  159.7   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.0   1.7e-51   3.1e-47       1     135 [.       3     137 ..       3     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.7e-51
                     TSSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS------.-THHHHHHHHH CS
  Ribosomal_S19e   1 tvkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrrgv.rpshfvkasgs 94 
                     +v+dVp++e+i++l+e Lk++  + +P wa++vKtgs+ +++p+++dW+y+R+Asi+Rk+yl+gp++v+ lr++YG  kr+ +   +h+++asg+
      AJA93012.1   3 KVYDVPQQEFISRLTEILKNE-DIPAPVWASFVKTGSHADKPPQQPDWWYTRCASIMRKIYLHGPLTVNDLRTIYGDGKRKMYyGARHHRDASGA 96 
                     59*****************98.8*****************************************************99997664789******** PP

                     TTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
  Ribosomal_S19e  95 virkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                     +ir++++ Leklg++++ +kkgr+++++G++ ld++a+e++
      AJA93012.1  97 IIRNAIHGLEKLGYLEQVEKKGRVVSRQGMQKLDKLATEIL 137
                     ***************9999*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1106.29
//
Query:       AJA93013.1  [L=183]
Description: hypothetical protein T478_0737 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.3   0.0      0.029   14.3   0.0    1.5  1  Hjc       Archaeal holliday junction resolvase (hjc)


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-06     0.029      14      83 ..      43     115 ..      24     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-06
                 T-EEEEBSCSSSSSSSS-SEEEEET..TEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHH....TCEEEEEEEETT CS
         Hjc  14 gfavvRsagSggatkplpDviAirg..dvvlviEvKsskkeriylkkeqvekllefarka....ggelllavklqg 83 
                 ++++ R  +       lpD++ +++   ++  iE Ks  ++++ +  +q+ + l++ +++      + +la+k+  
  AJA93013.1  43 DWKAFRLGSPSV---ALPDILCVNNidSIIFTIEAKSGTGTTLTVPFDQIIRCLSWTNNFtvykTRKVILAFKFLS 115
                 477777655555...5*******9832457789*************************995553445667778744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1296.69
//
Query:       AJA93014.1  [L=285]
Description: YjeF family C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-44  151.2   0.1      4e-44  150.9   0.1    1.0  1  Carb_kinase   Carbohydrate kinase
    2.2e-07   30.5   0.0    3.2e-07   30.0   0.0    1.3  1  HK            Hydroxyethylthiazole kinase family
      4e-05   23.1   0.1    0.00011   21.6   0.1    1.7  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.49   10.6   0.0    2.1  3  Crystallin    Alpha crystallin A chain, N terminal


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9   0.1   8.8e-48     4e-44       1     243 [.      30     277 ..      30     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 8.8e-48
                  EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS.....--SSS....-SEEEE-TT-S..SSHCHHHHCHHH CS
  Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqa..kilekler....ldavviGpGLg..rdekikklleev 90 
                  vlv+gGs+ y GA++l+ laalr+g++lv   + + ++ +  s++p++iv p+  ++ +  ++++ l +    +d  +iG+GL     e+ik l++  
   AJA93014.1  30 VLVVGGSYIYHGAPVLSSLAALRSGSDLVYTCVPKINAFSTRSISPDLIVIPMADSKLTrgTVNKMLGQipvdIDSAAIGMGLAiqDIEAIKLLVKSL 127
                  79***************************************************944333345566665411126889******7224577788***** PP

                  CCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-ST CS
  Carb_kinase  91 lekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlelarelaqklnavvllkgekdvivspegevlinstgssalakG 187
                  l++++ + +DA+ L +         + ++v+ TPh +Efkr+++ + + + ++r  +++++a++ + ++llkg++d+i + ++ +++n+t+++ +++G
   AJA93014.1 128 LDRNVRVSLDASSLVKEILP---IIEGQNVVVTPHSGEFKRIFGESPEtEINSRISICEKFAKNHSITILLKGQEDIITN-GDSTYTNPTSTPCMTVG 221
                  *************9865554...688899***************999867899***********************9999.9**************** PP

                  THHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT-TS-HCHHHHHHHC CS
  Carb_kinase 188 GsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkgvgmlatelskiip 243
                  G+GDvL+Gl +++L+ n+++ e+  +a++++gaa++ ++++ g  +la +l++ +p
   AJA93014.1 222 GTGDVLSGLTAGFLSRNKNMIESTSTATFVNGAAGEILQKEFGNHILASDLISVLP 277
                  ********************************************999999998887 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   7.1e-11   3.2e-07     133     229 ..     170     265 ..     112     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.1e-11
                 SSS-SHHH.HHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHHHHTT CS
          HK 133 skeaataa.vaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaaarsegs 229
                 s e++ +  +++ +k A++ ++++++ G+ D++++g ++y+    t+ ++ + ++G +l+   a fl+ +k+ ++++ +a+ +   Ag+   +++ g+
  AJA93014.1 170 SPETEINSrISICEKFAKNHSITILLKGQEDIITNGDSTYTNPTSTPCMT-VGGTGDVLSGLTAGFLSRNKNMIESTSTATFVNGAAGEI-LQKEFGN 265
                 55666664499**************************************7.9*****************************999999954.4444444 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.5e-08   0.00011     119     232 ..     152     255 ..      85     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-08
                   G-SEEE-BHHHHHHHHT---S.SHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCT CS
  Phos_pyr_kin 119 latvitPNlpEaeaLlgekik.teedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakg 214
                   +  v+tP   E +++ ge+ + + ++  + ++k++k ++ ++l+kG++         d++ +g+++++ +++  +  +  GtG++ls   a+ l+++
    AJA93014.1 152 QNVVVTPHSGEFKRIFGESPEtEINSRISICEKFAKNHSITILLKGQE---------DIITNGDSTYTNPTST-PCMTVGGTGDVLSGLTAGFLSRN 238
                   4469*************7776266788899****************97.........8888888777666655.44899****************** PP

                   SSHHHHHHHHHHHHHHHH CS
  Phos_pyr_kin 215 esleeAvkkAkeyvteai 232
                   +++ e+ ++A+ +v+ a 
    AJA93014.1 239 KNMIESTSTAT-FVNGAA 255
                   ******99985.777665 PP

>> Crystallin  Alpha crystallin A chain, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.92   4.1e+03      35      51 ..      55      71 ..      53      74 .. 0.84
   2 ?   -3.4   0.0       2.6   1.2e+04      25      31 ..     164     170 ..     163     180 .. 0.63
   3 ?   10.6   0.0   0.00011      0.49      23      46 ..     258     281 ..     248     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.92
  Crystallin 35 sdlfptsssalspfYlr 51
                sdl+ t+ + ++ f  r
  AJA93014.1 55 SDLVYTCVPKINAFSTR 71
                89999999999999887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
  Crystallin  25 DqrFGeh 31 
                  + FGe 
  AJA93014.1 164 KRIFGES 170
                 5667775 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00011
  Crystallin  23 iFDqrFGehllesdlfptsssals 46 
                 i+ + FG+h+l sdl+++++ +l+
  AJA93014.1 258 ILQKEFGNHILASDLISVLPKVLN 281
                 8899*************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1951.33
//
Query:       AJA93015.1  [L=161]
Description: ribosomal protein L24 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-16   58.2   0.1    1.5e-15   57.4   0.1    1.4  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
     0.0099   15.8   0.3      0.025   14.5   0.3    1.7  1  KOW            KOW motif
  ------ inclusion threshold ------
      0.061   13.3   3.7       0.11   12.4   3.7    1.5  1  Jak1_Phl       Jak1 pleckstrin homology-like domain


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   2.5e-19   1.5e-15       1      82 []       4     119 ..       4     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.5e-19
                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxx RF
  Ribosomal_L26   1 sssrrkqrKa.hfnapshirrklmsapLskeLrekygvrslpir................................gvtrekangttvpvgihpSk 63 
                    ss +rk r +  + a  ++ +k +s  Lsk+Lr+kyg rs +i+                                gv++ek +g++  v +h  +
     AJA93015.1   4 SSLPRKTRNQqIYYAAMQTASKQLSCALSKDLRKKYGKRSARIKegdtasiirgefagvdgkvtkisiadrgvnieGVKKEKLKGEKFDVYVHTTN 99 
                    7889999976268899******************************************************************************** PP

                    xxxxxxxx.xxxxxxxxxxx RF
  Ribosomal_L26  64 vvItklkl.DkdrkkiLerk 82 
                    +v+t l+  Dk r + Le k
     AJA93015.1 100 IVLTGLDTgDKWRINKLEGK 119
                    *****************977 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   4.2e-06     0.025       2      22 ..      49      69 ..      48      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-06
                TSEEEESSSTTTTCEEEEEEE CS
         KOW  2 GdhVkVvsGphkGktGkVvkv 22
                Gd+  +++G ++G  GkV+k+
  AJA93015.1 49 GDTASIIRGEFAGVDGKVTKI 69
                9******************98 PP

>> Jak1_Phl  Jak1 pleckstrin homology-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.7   1.9e-05      0.11      24      84 ..      92     153 ..      66     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
    Jak1_Phl  24 aeeppthevlvtG.teGiqwrlvqeeessegeksrkskekkkskkkkaeskkkkqeekekke 84 
                 +  + t ++++tG  +G +wr+ + e ++ +  +  +k k+++k++k++++kk++++ +k +
  AJA93015.1  92 DVYVHTTNIVLTGlDTGDKWRINKLEGKKATAARADDKPKTETKQEKVKEEKKDTKKATKAK 153
                 4456677888899457********99655555555555666666666665555544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2166  (0.12081); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1198.67
//
Query:       AJA93016.1  [L=95]
Description: winged helix-turn-helix [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-11   43.8   1.0    2.5e-11   43.4   1.0    1.2  1  HTH_45           Winged helix-turn-helix
    3.9e-05   23.4   0.0    5.7e-05   22.9   0.0    1.3  1  MarR_2           MarR family
    9.8e-05   22.2   0.0    0.00014   21.7   0.0    1.2  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00051   20.5   0.0    0.00065   20.1   0.0    1.3  1  HTH_27           Winged helix DNA-binding domain
    0.00062   19.9   0.1    0.00075   19.7   0.1    1.1  1  Rio2_N           Rio2, N-terminal
    0.00068   19.4   0.4    0.00084   19.1   0.4    1.1  1  DUF4364          Domain of unknown function (DUF4364)
     0.0041   17.0   0.2     0.0061   16.5   0.2    1.3  1  MarR             MarR family
     0.0042   17.4   0.2     0.0054   17.1   0.2    1.2  1  Rrf2             Transcriptional regulator
     0.0066   16.8   0.0     0.0077   16.6   0.0    1.1  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.016   15.0   0.0    1.2  1  HTH_IclR         IclR helix-turn-helix domain
      0.013   15.5   0.0      0.016   15.2   0.0    1.3  1  Cdc6_C           CDC6, C terminal winged helix domain
      0.014   15.0   0.1      0.019   14.5   0.1    1.3  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.014   14.8   0.1      0.015   14.7   0.1    1.0  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.018   15.1   0.1      0.049   13.7   0.1    1.7  1  DUF2250          Uncharacterized protein conserved in archaea
       0.02   15.0   0.0      0.026   14.6   0.0    1.2  1  Mrr_N            Mrr N-terminal domain
      0.025   14.4   0.1      0.033   14.0   0.1    1.2  1  FtsK_gamma       Ftsk gamma domain
      0.029   14.7   0.2      0.037   14.3   0.2    1.1  1  DUF2513          Hypothetical protein (DUF2513)
      0.066   13.2   0.1       0.11   12.5   0.1    1.4  1  HTH_46           Winged helix-turn-helix DNA binding
      0.085   12.6   0.0       0.11   12.2   0.0    1.4  1  RQC              RQC domain
        0.1   13.2   0.9       0.19   12.3   0.4    1.7  2  Mga              Mga helix-turn-helix domain
       0.12   12.4   0.0       0.15   12.0   0.0    1.2  1  Dimerisation2    Dimerisation domain
       0.13   12.3   0.0       0.16   11.9   0.0    1.3  1  PadR             Transcriptional regulator PadR-like family


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   1.0   3.1e-14   2.5e-11       1      75 [.       4      87 ..       4      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 3.1e-14
      HTH_45  1 rRskleIiadILea.....isegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleel 75
                +R ++eI+ dIL a     i++++a+ Tk++ kan+s ++++k L  Lv++gl+    +k+  kY++   G+++l+++k++ e+
  AJA93016.1  4 YRKQIEIVGDILYAaeeltIDQEGASITKLIQKANISHSRISKILTNLVSQGLLeqvdSKRACKYKISMTGKDFLKEYKTFSEF 87
                699*********75333336799******************************97666678889*****************987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     7e-08   5.7e-05      18      56 ..      26      62 ..      16      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-08
                TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
      MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                +g   +++ l ++ ++s+s++s+il  Lv++GL+e++++
  AJA93016.1 26 EG--ASITKLIQKANISHSRISKILTNLVSQGLLEQVDS 62
                45..68899999************************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.7e-07   0.00014      20      63 ..      25      69 ..      21      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-07
                HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEE CS
        TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYr 63
                ++ a+++++ +++++++s++ ++L +L++ Gl e +++++  +Y+
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLLEQVDSKRAcKYK 69
                5778899999***************************99665776 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     8e-07   0.00065      16      54 ..      25      63 ..      17      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8e-07
      HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                +++++++ l+++ n++ s is++l  L+ +GL+e+  ++
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLLEQVDSK 63
                678999***************************888665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   9.2e-07   0.00075      11      74 ..      14      78 ..      13      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.2e-07
      Rio2_N 11 vLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisr.ktakydGYkLtyeGyDyL 74
                +L a E    + e  + +++ + ++++++ ++k l +l+ ++l+++ ++++   Yk+++ G D+L
  AJA93016.1 14 ILYAAEELTIDQEGASITKLIQKANISHSRISKILTNLVSQGLLEQvDSKRACKYKISMTGKDFL 78
                7889999999999999******************************99999999*********99 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4     1e-06   0.00084       5      74 ..      14      82 ..      13      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
     DUF4364  5 ilYllkkvkfpltnsqlseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                ilY  +++    + + ++++i++   ++   ++++l++Lv++gl+e+ +++    yki+  Gk+ l++ +
  AJA93016.1 14 ILYAAEELTIDQEGASITKLIQKA-NISHSRISKILTNLVSQGLLEQVDSKRACKYKISMTGKDFLKEYK 82
                899999999999999****99766.5799***********************************998765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.5e-06    0.0061      15      50 ..      25      60 ..      21      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.5e-06
                STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                q+++s+++L  k ++s s ++++l+ L+ +Gl+e  
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLLEQV 60
                7899****************************9965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   6.6e-06    0.0054      23      57 ..      25      59 ..       5      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvks 57
                +e +s++++ ++ nis+s ++kil++L  +gl++ 
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLLEQ 59
                33389***************************986 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.4e-06    0.0077      24      73 ..      30      79 ..       8      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.4e-06
                     HHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXX CS
  Penicillinase_R 24 veeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeava 73
                     +++l ++ + + s +  +l++Lv +gll++  ++ra  Y   ++ +++++
       AJA93016.1 30 ITKLIQKANISHSRISKILTNLVSQGLLEQVDSKRACKYKISMTGKDFLK 79
                     3455556699******************************9999888876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     2e-05     0.016      16      51 ..      25      60 ..      21      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
    HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                +++ +++ l +++ ++ S  + +L  Lv +G++eq 
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLLEQV 60
                45669*****************************96 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     2e-05     0.016      28      75 ..      30      71 ..      23      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                HHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
      Cdc6_C 28 lCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75
                +++  +   ++++++s++l++L ++g+le   s    +  r  k++++
  AJA93016.1 30 ITKLIQKANISHSRISKILTNLVSQGLLEQVDS----K--RACKYKIS 71
                5666666789********************999....4..44444444 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-05     0.019      15      47 ..      25      57 ..      11      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
      HTH_24 15 nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                + + s++ L ++ ++S s +++ l +L+++Gl+
  AJA93016.1 25 QEGASITKLIQKANISHSRISKILTNLVSQGLL 57
                6789***************************97 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.8e-05     0.015       7      73 ..       7      71 ..       1      84 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                   -HHHHHHHHHHHHHCSSSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE- CS
  RNA_pol_Rpc34  7 klqelkkrlleelrkaseqklfsqqdLqddipslslklllsavqeLldkkllvllknsndeLvyrav 73
                   +++++ + l+++   + +q++ s ++L ++  ++s++ + +++++L++++ll+++  s+   +y++ 
     AJA93016.1  7 QIEIVGDILYAAEELTIDQEGASITKLIQK-ANISHSRISKILTNLVSQGLLEQVD-SKRACKYKIS 71
                   677888889999999988999999999999.999999999************9999.7776788875 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     6e-05     0.049      28      58 ..      33      63 ..       9      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-05
     DUF2250 28 iakeleipleevrellkkLeelGLlervegk 58
                + ++ +i+ ++++++l +L + GLle+v++k
  AJA93016.1 33 LIQKANISHSRISKILTNLVSQGLLEQVDSK 63
                34567899********************976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.2e-05     0.026      27      86 ..      17      79 ..      11      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
       Mrr_N 27 vaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespk..rgv.wkiTekGrevlk 86
                +ae++ +++e  + ++   k ++ ++r++  +t+L+ +glle+ +  r+  +ki+ +G+++lk
  AJA93016.1 17 AAEELTIDQEGASITKLIQKANISHSRISKILTNLVSQGLLEQVDskRACkYKISMTGKDFLK 79
                577778888888888877888999******************998774435**********98 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.1e-05     0.033       7      55 ..      15      63 ..      11      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-05
  FtsK_gamma  7 feeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegs 55
                +  a el ++++ aS+  l ++ +i ++R ++++  L ++G+ ++ +++
  AJA93016.1 15 LYAAEELTIDQEGASITKLIQKANISHSRISKILTNLVSQGLLEQVDSK 63
                567889***********************************99987765 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.5e-05     0.037       4      86 ..       8      82 ..       5      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
     DUF2513  4 mdlvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiR 86
                +++v diL ++eel  ++e  + +  kl + ++ s  +i+  l+ l+ +gL+e +++k+  +      ++++++G dFL + +
  AJA93016.1  8 IEIVGDILYAAEELTIDQEGASIT--KLIQKANISHSRISKILTNLVSQGLLEQVDSKRACK------YKISMTGKDFLKEYK 82
                688999******999988887664..344667788889******************999999......999********8765 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00014      0.11      26      54 ..      31      58 ..      18      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
      HTH_46 26 lkyIqkrtnLSrSsimkvLseLkkggyIe 54
                 k I ++ n+S S+i k+L +L  +g +e
  AJA93016.1 31 TKLI-QKANISHSRISKILTNLVSQGLLE 58
                5555.589**************8877665 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.11      58     101 ..      38      82 ..       8      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                 TS-HHHHHHHHHHHHHTTSE.EEE..SSSBEEE-CCGHHHHTSSS CS
         RQC  58 dlskkewrrlirqLiaegyL.eedveeygvlkltekarevlkgee 101
                 ++s + + +++  L+++g+L ++d ++   +k++  ++++lk+ +
  AJA93016.1  38 NISHSRISKILTNLVSQGLLeQVDSKRACKYKISMTGKDFLKEYK 82 
                 678999**************555555666************9765 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00023      0.19      23      55 ..      20      52 ..       6      81 .. 0.78
   2 ?   -0.9   0.0       3.1   2.5e+03      26      41 ..      77      92 ..      65      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                HHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
         Mga 23 kflfeeeevsieelaqelyiSestlkrkikeln 55
                ++ + +e  si++l+q+  iS s + +++ +l 
  AJA93016.1 20 ELTIDQEGASITKLIQKANISHSRISKILTNLV 52
                66788999********************99985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                HHHSEEEHHHHHHHCT CS
         Mga 26 feeeevsieelaqely 41
                f +e++++ e+++++ 
  AJA93016.1 77 FLKEYKTFSEFTDNFG 92
                4577778888877765 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019      0.15      15      85 ..      15      79 ..      10      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
  Dimerisation2 15 LftAceLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLv 85
                   L++A eL +     ++e  s  ++ ++ ++s++ ++ +l  +v+ gLLe+  ++ +   Y+ + + + +L 
     AJA93016.1 15 LYAAEELTI-----DQEGASITKLIQKANISHSRISKILTNLVSQGLLEQVDSK-RACKYKISMTGKDFLK 79
                   566666554.....347889999**************************66444.5799999999998886 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.16      12      74 ..      27      79 ..      14      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                HHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
        PadR 12 GyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                G  i+k +++      ++s++++ ++L+ L  +gl+e+  ++     +   Y++  +G++ l+
  AJA93016.1 27 GASITKLIQKA-----NISHSRISKILTNLVSQGLLEQVDSK-----RACKYKISMTGKDFLK 79
                77777777777.....59******************988665.....4455888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 705.40
//
Query:       AJA93017.1  [L=121]
Description: hypothetical protein T478_0040 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 854.46
//
Query:       AJA93018.1  [L=262]
Description: putative cobalt transporter subunit CbtA [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-46  158.3   5.2    3.3e-46  158.0   5.2    1.0  1  CbtA           Probable cobalt transporter subunit (CbtA)
  ------ inclusion threshold ------
       0.36   10.1   2.5        2.5    7.3   2.5    2.1  1  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.0   5.2   3.7e-50   3.3e-46       4     242 ..      29     251 ..      27     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.0 bits;  conditional E-value: 3.7e-50
        CbtA   4 lllrgllaGllAGllaflvqrlvvePlilaAeayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlgtvlanvltgvalglllaavfallegrlgk 102
                 ++++ l++G +AGl++++++ ++veP++++A+ +E+++  a ++e+ +     e + +   +r +q++ g+vla+ ++g+++++l+++vf+++++ l++
  AJA93018.1  29 FIIIVLVSGCFAGLIHGGINLAIVEPYLDQAIGIENQTLFATGEEEDT----SEFWVEYNSYRVWQKG-GQVLAGAILGTSIAALVGIVFLFARKVLPQ 122
                 68899**********************************999999877....578999999*******.****************************** PP

        CbtA 103 lsaralalllalagflavvlvPflklPpepPgvgaadtieaRqalylatvalsavalalavflarrlaargwnavlaaavaflvlvavallalPhvvea 201
                  ++ +++l+l ++++++++++Pflk+P++pP vg+++t+  R++l+l ++a+s++++++++ +++rl     n+ ++a v++++ + ++++++P+    
  AJA93018.1 123 GNNVKKTLVLSGLMWFTIFVIPFLKYPANPPTVGETETVVLRSILFLSFIAISGLGAVGFYQVYKRL----QNKKILAFVGYAAFISAVFFIMPEN--- 214
                 *******************************************************************....788**********************... PP

        CbtA 202 PqpeaaesgfpaallaqFrvaslltqavlWavlGlvfgalv 242
                 P+    e ++p +l+  Fr as+++ +v W++lGl++g ++
  AJA93018.1 215 PD----EITAPMELVDGFRGASFVAVTVYWLTLGLILGGFI 251
                 98....67*****************************9886 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.5   0.00028       2.5      78     205 ..      75     211 ..       8     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00028
                    ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........-EEECE..CTTTSCEE-SEEEC-XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50  78 a.......flkkspwqrllivlAGplanfilailvfvv........pkkske..seeekrgviGvspkpvkkegllealkegvektlkvvvltvka 156
                    +       +++ ++wq+   vlAG + +  +a lv +v        p    +  + +++  + G++  +     ++  + ++  + ++v  + + +
     AJA93018.1  75 DtsefwveYNSYRVWQKGGQVLAGAILGTSIAALVGIVflfarkvlP----QgnNVKKTLVLSGLMWFT----IFVIPFLKYPANPPTVGETETVV 162
                    03335666899999999999999999998887777766566654442....322333333333444444....56666666666666666666777 PP

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 157 lgklitgklslktlggpisiaqlaseaaeaglssflqllalisvnLgil 205
                    l++++  ++ +    g ++++q+ ++  + ++ +f+ ++a+is  ++i+
     AJA93018.1 163 LRSILFLSFIAISGLGAVGFYQVYKRLQNKKILAFVGYAAFISAVFFIM 211
                    7777777666666778899999999999999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1876.83
//
Query:       AJA93019.1  [L=136]
Description: NUDIX domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-20   71.8   0.2    5.8e-20   71.7   0.2    1.0  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.037   13.6   0.0    1.3  1  NUDIX_2   Nucleotide hydrolase


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.2   6.4e-24   5.8e-20       4     126 ..       5     125 ..       2     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 6.4e-24
                 EEEEEEEEETTSE..EEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE.EEEEEEEEEEEECSGCSST CS
       NUDIX   4 ravgvvllnekge..vLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd.eheilyvfleevegelepn 99 
                 +++g++l+n+++   +Ll+    +p ++W++++Gk+e++Etp e+A+RE++EEtG+   ++e+l+ ++++  y ++ ++ e +  ++f+  ++ +    
  AJA93019.1   5 VSAGIILFNDNEDrkFLLLN---YPSKHWDFVKGKMEKDETPHETALRETKEETGI--SDVEFLEGFEEEIEYYFYADNqEIHKKVIFFLGKTKTKDII 98 
                 799***99999667899994...78999****************************..88*****9999999999888854444477885666665566 PP

                 STTTEEEEEEEEHHHHHHHHTHCTHHH CS
       NUDIX 100 denevsevrwvpleellkeklaaesrk 126
                  ++e+ ++ w++++ +l ++ ++++++
  AJA93019.1  99 LSHEHLDYIWLEFDNALNKTTYENAKN 125
                 69**************66655555555 PP

>> NUDIX_2  Nucleotide hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-06     0.037      46      92 ..       6      52 ..       1      78 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-06
     NUDIX_2 46 veavllvhrhelphvLlLqielqefkLpggklksgedeiegLkrkLa 92
                 ++++l +++e    LlL   ++ + ++ gk++++e++ e+  r  +
  AJA93019.1  6 SAGIILFNDNEDRKFLLLNYPSKHWDFVKGKMEKDETPHETALRETK 52
                469***********************************887666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1033.48
//
Query:       AJA93020.1  [L=303]
Description: putative dihydroorotate oxidase, catalytic subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-53  181.0   0.9    3.3e-53  180.8   0.9    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    1.2e-05   24.6   0.2     0.0036   16.4   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    1.7e-05   24.4   0.1       0.02   14.3   0.0    2.3  2  His_biosynth  Histidine biosynthesis protein
    0.00057   19.0   3.5     0.0011   18.0   0.1    2.2  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0045   16.4   1.3      0.017   14.5   1.3    1.7  1  NMO           Nitronate monooxygenase
  ------ inclusion threshold ------
      0.068   12.3   7.9       0.57    9.3   4.9    3.1  2  DUF561        Protein of unknown function (DUF561)


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   0.9   1.1e-56   3.3e-53       2     295 .]       5     285 ..       4     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.1e-56
                 G-EEETTEEESSSEEE-TTSSTTSSS.HHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHHHHHHHHHHHCC.CEEE CS
      DHO_dh   2 latkvlglkfknpiglAaGfdkegee.ilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlekllkrrkeqeekkelgi 99 
                 l+t++  l++k p +lA+G+ + +   +++l ++g+ga+ ++s  ++p eG p+P++f++k +   +N++Gl n+G+++ ++ ++ +        +++i
  AJA93020.1   5 LETTLGSLTLKRPTVLASGILGISLDvFNRLHDAGAGAVVTKSLSKEPWEGYPNPTIFSVKGG-GWINAVGLSNPGAETFAKMIESND-------NVPI 95 
                 8999999**************98866156677888***************************9.9************99887776543.......59** PP

                 EEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE. CS
      DHO_dh 100 nlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkaillkvvkevskvpvlvKlaPdltdeekkdiadvllelkldgiivt 196
                 ++s  ++    +dd+ ++++k++   + + elN+S+P+++  + +++ + el ++++k+vk +++ p+++K+     +++  + +d ++  ++d+i ++
  AJA93020.1  96 VVSLVGSV---EDDFEYMIKKFEnCKVAAYELNLSCPHVAkVGLEVGDDIELVSKIIKKVKSITNSPIVAKVGL--GKSDYLATVDAAVSAGVDAITAI 189
                 *******8...************5457889*********98899****************************85..56666666666666666666666 PP

                 ..BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
      DHO_dh 197 NttvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                 N tv+ +aid++++ ++  nk GGlsG ++k+ial+ ++e++++++  ipi+g+GGi+  eDa+e i aG s+vq ++ +  + +  +++i  ++++ +
  AJA93020.1 190 N-TVRAMAIDVETQMPILSNKIGGLSGTPIKPIALRCVYEIASKFD--IPIMGCGGISNWEDAVEFILAGSSVVQFGSVMGDHWVETFSEINSGIQKYM 285
                 6.577888**************************************..********************************9999999999999999876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-06    0.0036      38     156 ..      77     187 ..      69     199 .. 0.88
   2 !    6.2   0.0    0.0016       4.8     170     200 ..     221     251 ..     213     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                 --HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTT CS
         Dus  38 reekvrirmlseeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigidde 136
                 ++ ++++ ++ e++++ p++v l+gs  +      k+ ++ ++ + +lN+ CP     + ++G     + +lv +i+k+v++ ++ P+ +k+ +g    
  AJA93020.1  77 NPGAETFAKMIESNDNVPIVVSLVGSVEDDFEYMIKKFENCKVAAYELNLSCPHVAKVGLEVG----DDIELVSKIIKKVKSITNSPIVAKVGLGKS-- 169
                 56678888899999999************************************9887777777....899**********************99987.. PP

                 TC.HHHHHHHHHHCT-SEEE CS
         Dus 137 eenalelakiveaaGaqalt 156
                   + l  ++++  aG++a+t
  AJA93020.1 170 --DYLATVDAAVSAGVDAIT 187
                 ..455677788888888887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0016
                 --CHHHHHHHHH-SS-EEEESS--SHHHHHH CS
         Dus 170 adweaIkevkqavsipviaNGdIkdaedaqa 200
                 + ++ ++e+  ++ ip+++ G+I ++eda +
  AJA93020.1 221 IALRCVYEIASKFDIPIMGCGGISNWEDAVE 251
                 667789*********************9865 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1   0.00069       2.1     166     217 ..     128     186 ..      92     192 .. 0.76
   2 !   14.3   0.0   6.8e-06      0.02      59     108 ..     220     269 ..     213     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00069
                   EEETTTTTTSS---HHHHHHHHHHH....SSEEEEESS--SHHHHHHHH...HTTCSEE CS
  His_biosynth 166 ltdidrdGtlsGpdleltkelaeav....kipviasGGvgsledlkelk...segvdav 217
                   +  ++++G + G d+el++++ ++v    + p++a  G g+ + l++++   s+gvda+
    AJA93020.1 128 CPHVAKVGLEVGDDIELVSKIIKKVksitNSPIVAKVGLGKSDYLATVDaavSAGVDAI 186
                   56899**********9988877766322367999*****99999988886657777665 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.8e-06
                   HHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
  His_biosynth  59 eanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavkn 108
                   ++ l +v eia++++ip++  GGI++ ed+ e + ag + v  g+++ ++
    AJA93020.1 220 PIALRCVYEIASKFDIPIMGCGGISNWEDAVEFILAGSSVVQFGSVMGDH 269
                   5678899*******************************999999987554 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.6     0.042   1.3e+02     171     204 ..     163     197 ..     144     223 .. 0.64
   2 !   18.0   0.1   3.8e-07    0.0011     195     269 ..     222     296 ..     214     303 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.042
                 EE-SS-ST.TBHHHHHCSB---HHHHHHHHHHHHC CS
                 xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 171 kvGiGpGs.iCttrvvagvGvpqltAvaevaeaak 204
                 kvG+G    + t     ++Gv  +tA+ +v ++a 
  AJA93020.1 163 KVGLGKSDyLATVDAAVSAGVDAITAINTVRAMAI 197
                 56666543144445555666666666666655443 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.8e-07
                 HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTB.TTSSSEEEEETTEEEEEEEETTSHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagt.eEspgeviliegrkyKeyrGmgslgam 269
                 A+  v+e+a+k+++p++  GGi++ +d v  + aG+++v  Gs++     E+ +e+     +ky e +G +++g m
  AJA93020.1 222 ALRCVYEIASKFDIPIMGCGGISNWEDAVEFILAGSSVVQFGSVMGDHwVETFSEIN-SGIQKYMERKGYATIGEM 296
                 6777899*************************************9865145555544.355667777777777777 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.3   5.6e-06     0.017     114     223 ..     159     264 ..     101     266 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.6e-06
         NMO 114 vevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaL 212
                 + v+   +gl + + +a  ++a  + +  i++++ +r+++      + +   + GG  Gtp +     ++ v ++++  diP++  GGi + ++    +
  AJA93020.1 159 PIVA--KVGLGKSDYLATVDAAVSAGVDAITAINTVRAMAIDVETQMPILSNKIGGLSGTPIK--PIALRCVYEIASKFDIPIMGCGGISNWEDAVEFI 253
                 2233..333444466666666555556666666666666666566688888999*****4433..468999***********************99999 PP

         NMO 213 alGAsgvqigt 223
                  +G s vq g+
  AJA93020.1 254 LAGSSVVQFGS 264
                 99******997 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.1   3.2e+03     187     212 ..      16      41 ..      11      49 .. 0.73
   2 ?    9.3   4.9   0.00019      0.57     173     211 ..     217     259 ..      79     286 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
      DUF561 187 lPvicasGlsdvtvplalslgasGiG 212
                  P + asG+  ++ ++   l  +G G
  AJA93020.1  16 RPTVLASGILGISLDVFNRLHDAGAG 41 
                 58889999999998887666666555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
      DUF561 173 s....tlastyeiskkvslPvicasGlsdvtvplalslgasGi 211
                 +    +l ++yei++k ++P++   G+s+    + + l  s +
  AJA93020.1 217 PikpiALRCVYEIASKFDIPIMGCGGISNWEDAVEFILAGSSV 259
                 1445699**********************99999987655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2283.88
//
Query:       AJA93021.1  [L=466]
Description: FeS assembly protein SufB [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-72  241.6   0.3    9.7e-72  241.2   0.3    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.3   5.4e-76   9.7e-72       2     218 .]     212     437 ..     211     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 5.4e-76
     UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkg 88 
                 qfertli+++eg+ev++i   +gc            +vve++++++Akl+y+++qnws+d++nl+tkra   + a++e++++++g+k+t+k+p ++l g
  AJA93021.1 212 QFERTLIIADEGSEVHYI---EGCtapvysseslhsAVVELVAHKDAKLRYTTIQNWSNDVYNLVTKRAYAYEGASVEWIDGNIGSKITMKYPGIYLMG 307
                 89****************...667777777777777*********************************9999************************** PP

     UPF0051  89 egaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgA 187
                 ++a +e  ++++a+++qh+dt+ k+ h +pnt+s+++sk+v++ ++r+++rg + v+kga++ ++ +++++Lll+++++ dt P++ei+++d++++H+A
  AJA93021.1 308 QKAYGETLSIAFAGKGQHQDTGAKMVHLAPNTTSKVTSKSVSRSTGRSTYRGLLNVAKGATNVKSTVRCDALLLDETSKTDTYPYMEINQEDATITHEA 406
                 *************************************************************************************************** PP

     UPF0051 188 tvGkideeqlfYLmsRGlseeeArrlivrgf 218
                 tvGki ++q+fYLm+RG+seeeA  liv+gf
  AJA93021.1 407 TVGKIGDDQIFYLMTRGFSEEEALTLIVNGF 437
                 ******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3344.54
//
Query:       AJA93022.1  [L=757]
Description: oligosaccharyl transferase STT3 subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-37  127.9  37.2    1.3e-36  126.5  37.2    1.7  1  STT3      Oligosaccharyl transferase STT3 subunit


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5  37.2   7.5e-41   1.3e-36      31     485 ..      48     524 ..      42     526 .. 0.79

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 7.5e-41
                 -SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC..HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS- CS
        STT3  31 sefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld..vsirevclwlpallgsLlaIpiyflvrelks 127
                  efDp++n+R+te++l+nG      ++  nw d+ +++P G r   +++ v+L  l++a+++ +++   s+ +  +++p ++gsL+aI+++ +vr+l +
  AJA93022.1  48 FEFDPFFNFRATEYILDNGT-----DAYFNWIDEKTWHPFG-RNVSETSQVTL-HLTAAFLYPIFNfgSSLYNFTILFPLVIGSLTAIVVFAFVRVLGG 139
                 69******************.....9999************.77779999999.8888888888887779***************************** PP

                 CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHHHCCSTTCHH..HHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-C CS
        STT3 128 diaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkaiktksnkisl..aviaaliiflivlaWggyailiyallllfilalLiigrfel 224
                   aGl+AAl+ +++   +sr   G++  + + +++  +++++f+ +ik +++kisl  + ia+l++ l  +aWgg+  ++++ ++lf ++l  +  +  
  AJA93022.1 140 TTAGLFAALIFSVSVPIFSRGLIGWFKSEPLGLFFAFIAMYLFVSGIKFNKGKISLikLIIAGLFLSLGLSAWGGI-LFFVIPIVLFYFSLPFFKNKDN 237
                 ********9998877788************************************9943579**************9.9*************99999999 PP

                 CHHHHH...HHHHHHHHHH..CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHHHHHHHH CS
        STT3 225 klkiav...tfsviiaflviaiivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgilsevlgligevvtalavlglial 320
                 ++ +a     +svi++ lv       ++g          g+++  +++++++ g v++     +  +++    +          ++ +  +a  g+i l
  AJA93022.1 238 FIMWAApsfSTSVILFSLVFERTTTFIIG--------YAGLALLLPTIFIIIAGIVMKF--SSERAKIRNCAIVL------ISFVTSGIGIASSGIIGL 320
                 99999976555555555554444444444........4467777788888777766666..33333333333222......222334444555555555 PP

                 CCCCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHHHCHHC.....CHHCTCHHHHHHHHHHHHHCCC-SCHCCCCCHHHHHHH CS
        STT3 321 wlgilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgiifvgl.....lleflavfvkiysvsqilfsgvvvillmltllpvlall 413
                  + + ++ ++   +  +  +  +v++++ ++l++ +  l  + if+v +gi+f+++     l  ++++f + +s+ +i++s + ++l+++  ++ +++l
  AJA93022.1 321 PSFRYLNAVN-PFLTTQDTLTDSVAEHMTTSLSLSFTFLSVFlIFSV-IGIWFLFSkktinLKTDMRIFAICSSIVAIYISSAFIRLELFA-SVGIIIL 416
                 5545555554.55677888999*********9876666665525555.78878775212215678899999999************77664.3333333 PP

                 CC....CHHHHHHHHCCHHHHHHHHHHHHHH..................................HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHH CS
        STT3 414 aa....vkiskifstykdekeakikvaakav..................................aptksnglkeslew.kantnrdsvvitwwdyghi 473
                       +  +kif+++k++ +++i     av                                   ++ sn +k+++ w k+nt++d+++ +wwdyg+ 
  AJA93022.1 417 GSigltILTQKIFEQNKQNFTKIIFP---AViiilfiipmtmpennnwltwadftpsilnggssfTNFSSNDWKDATLWlKQNTPEDAIIASWWDYGYW 512
                 33011155678888888886666664...22456788889999999******************9********************************** PP

                 HHHHHHHHHHHH CS
        STT3 474 laveadrpVtfd 485
                 +++ ++r +++d
  AJA93022.1 513 ITTLSERTTLAD 524
                 *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 5241.73
//
Query:       AJA93023.1  [L=409]
Description: glycosyltransferase family 1 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.6   0.8        6.1    7.1   0.2    2.7  2  DUF2774   Protein of unknown function (DUF2774)


Domain annotation for each model (and alignments):
>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2   0.00034       6.1      47      60 ..     191     204 ..     177     207 .. 0.89
   2 ?    4.0   0.0    0.0032        58      21      45 ..     352     376 ..     344     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00034
     DUF2774  47 rEkVVYRKrliNkk 60 
                 +EkVVY  +++N+k
  AJA93023.1 191 QEKVVYVGHFTNEK 204
                 7***********98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0032
     DUF2774  21 kkldirakdvaklwveveearekfk 45 
                 kkl++ a++ ++++  v+++ e+++
  AJA93023.1 352 KKLGLFAQNRGQIVEAVKQMYENYE 376
                 899*****************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2876.19
//
Query:       AJA93024.1  [L=65]
Description: MttA family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-10   38.0   3.0    1.2e-09   37.4   3.0    1.4  1  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   3.0   6.5e-14   1.2e-09       2      51 ..      11      61 ..      10      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 6.5e-14
                 -HHHHHHHHHHH.HHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH---XXX CS
  MttA_Hcf106  2 gapelliIlvVa.lllFGpkkLPEvaraLGktLreFkkavkeleeenekea 51
                 g  e++i+ v a +llFG+kk+PE+a+  Gk+  e+kk   e+++e ++ +
   AJA93024.1 11 GGSEWIIVIVAAgVLLFGAKKIPELAKTFGKAKGEYKKGEIEADKELKEFK 61
                 5667777665544************************98888887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 497.21
//
Query:       AJA93025.1  [L=283]
Description: sulfotransferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-16   59.2   2.3    4.7e-16   59.1   2.3    1.1  1  Sulfotransfer_1  Sulfotransferase domain
      9e-12   45.8   0.6    1.7e-08   35.1   0.6    2.9  1  Sulfotransfer_3  Sulfotransferase family
      0.003   17.1   0.4      0.005   16.4   0.4    1.3  1  Y_phosphatase    Protein-tyrosine phosphatase
     0.0072   16.2   0.1      0.015   15.1   0.1    1.8  1  Sulfotransfer_4  Sulfotransferase domain


Domain annotation for each model (and alignments):
>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   2.3     1e-19   4.7e-16       2     212 ..      30     244 ..      29     283 .] 0.78

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1e-19
                      TSEEEEESTTSSHHHHHHHHHHHHTTTCCHHHTSSGHCT-HHHSCBTTHECCTSG.CCGTTECCCHHHTTTEEHHHHHHHSTSS.EEEE...GG CS
  Sulfotransfer_1   2 ddvlivtypKSGTtwlqellslitsegdfekaeepalfnardrspfLelydlyfp.nslkppdhlrsyshvaekvvrlralesprllktHlplk 94 
                      +d++i++ +++GTt l   l  ++s+++    ++  +fn  + + ++ +y+++fp  s+k +     +++ + k+ + +     r + t + ++
       AJA93025.1  30 PDFIIIGAKRCGTTSLFSYLPEHPSIARS-HHDNMGFFND-NFHLGINWYKSFFPtISQKRK-----IEKQYGKFLAFDVT--TRYMETKITAE 114
                      79*************************99.4778888888.9*************8777777.....44444455555444..56666656666 PP

                      GS.CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBT............TSTTT-S.-HHHHHHHHHT......THSTTC-HHHHHHHHHHHTTTT CS
  Sulfotransfer_1  95 llpkslldsnlKiiylvRnpkdvavSryhfsrslk............klkepet.pfeeffdlfle......grvvcgsyfdhvkswlklrkkg 169
                       ++k   ++++Kii+++Rnp d+a+S y+ + + k            ++k  et   e+++d  le      + +  + y+ ++k w   + k+
       AJA93025.1 115 NIKKT--QPDVKIIVMLRNPIDRAYSQYNITVKEKtekldfdeaiieEMKRLETeISEKYRDRSLEfpkehrHYIKKSLYALQLKPWFDIFSKE 206
                      66555..9**********************988888877777776664444555445566666666888877999999**************** PP

                      TEEEEEHHHHHHHHHHHHHHHHHHTT--..HHHHHHHHHHTSH CS
  Sulfotransfer_1 170 nvlflrYEdlkkdpakeikkiaeFlGiplteeelekivkhlsf 212
                      ++l+l+ E+ + + ++  +ki++Fl+i        +i ++   
       AJA93025.1 207 KILVLSTEEFRDNEENIYRKIFQFLDIA-----EIQIKNKVHM 244
                      ***************************9.....3333444444 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.6   3.8e-12   1.7e-08       1     213 [.      30     233 ..      30     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.8e-12
                      -.EEEE--TTSSHHHHHHHHHTSTTEE--S--.--TT.-SBHHHHHHHHTT-S...TTTHHHHHHHHHHT--HHHHHHHHHHHHHTT-BHHHHH CS
  Sulfotransfer_3   1 P.ifivGlpRSGTTlLhrlLaahpdvripeetlfvaprllalleawskdgrelrrlldagltqeeaelphledaeepeedlqllraalasvile 93 
                      P ++i+G+ R GTT L   L +hp+++   +  + +  + ++++     g ++++     ++ +             +++  + ++  + + ++
       AJA93025.1  30 PdFIIIGAKRCGTTSLFSYLPEHPSIARSHH--DNMGFFNDNFH----LGINWYKS----FFPT------------ISQKRKIEKQYGKFLAFD 101
                      6689*********************766543..45666666766....88899983....4444............112233445555666677 PP

                      HHHHHHTTTSEEEEEESSGGG-HHHHHHHBSSEEEEEEE--H.HHHHHHHHHTT--------............--..-HHHHHHHHHHHHH.H CS
  Sulfotransfer_3  94 alarvpsyarwlvdKsPshlfrldlllelfPdAkfihlvRdpvdtvlssyvslfgkkresys............edsldeledaleewaray.e 174
                      +       +r++ +K       ++ ++++ Pd k+i+++R+p+d+++s+y   +++k+e++             e               ++ e
       AJA93025.1 102 V------TTRYMETKI-----TAENIKKTQPDVKIIVMLRNPIDRAYSQYNITVKEKTEKLDfdeaiieemkrlE--------------TEIsE 170
                      6......344433333.....5789*************************8888999998886555544433332..............33212 PP

                      HHHHHHHH........................S-TTSEEEEEHHHHHH-HHHHHHHHHHHHT- CS
  Sulfotransfer_3 175 rllaarar........................lppdrfldvrYedLvadpegtlrriyeflgl 213
                      +++++  +                        + ++++l ++ e++  + e   r+i +fl++
       AJA93025.1 171 KYRDRSLEfpkehrhyikkslyalqlkpwfdiFSKEKILVLSTEEFRDNEENIYRKIFQFLDI 233
                      222222331111122233333344444777777777777777777777777777777777776 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   1.1e-06     0.005      64     150 ..     120     206 ..     117     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-06
                    HTT--EEEEESBSEETTEESS---S-..SSTSSEEEETTEEEEEE..EEEEEESSEEEEEEEEEETTTTEEEEEEEEEEESSS-SSSSGS CS
  Y_phosphatase  64 qekvkvivmLtsleekgrekcaqYwp..eeeeesleygkikvtlk.ekekedekeyvlrelevkkkkeeseerevkqlqytnWpdhgvpe 150
                    q +vk+ivmL + +++    ++qY    +e+ e+l +++  ++ +   e+e++++y  r le  k+ ++  +++++ lq++ W d   +e
     AJA93025.1 120 QPDVKIIVMLRNPIDR---AYSQYNItvKEKTEKLDFDEAIIEEMkRLETEISEKYRDRSLEFPKEHRHYIKKSLYALQLKPWFDIFSKE 206
                    6689***********6...88888775557788999***999988877777999**********99999888888********9977554 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.4e-06     0.015       3     132 ..      33     164 ..      31     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
  Sulfotransfer_4   3 iglGlpRtGTkSlkaALeiL.gykp.vyhmeevieng.sdlkewaealeakkegkkpitredfdkllggydavvdvpaalfaeelleayPdakv 93 
                      i++G  R+GT+Sl   L +   + +  ++ + +++++ +    w + +  + ++ k+  +++  k+l+    +  + + + ae + + +Pd k+
       AJA93025.1  33 IIIGAKRCGTTSLFSYLPEHpSIARsHHDNMGFFNDNfHLGINWYKSFFPTISQ-KRKIEKQYGKFLAFDVTTRYMETKITAENIKKTQPDVKI 125
                      8899*************8742333303444556666655555555555555553.3444455555555444444556668999999******** PP

  Sulfotransfer_4  94 IlteR.dpekWlksmkktllalrsetlsrllalldpllel 132
                      I++ R + ++ + +++ t+++ +++ l +  a ++++++l
       AJA93025.1 126 IVMLRnPIDRAYSQYNITVKEKTEK-LDFDEAIIEEMKRL 164
                      *****77888888888888887765.22222223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2175.22
//
Query:       AJA93026.1  [L=64]
Description: cold-shock DNA-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   79.5   3.4    1.4e-22   79.3   3.4    1.0  1  CSD       'Cold-shock' DNA-binding domain
    1.4e-07   31.1   0.5    1.4e-07   31.1   0.5    1.1  1  OB_RNB    Ribonuclease B OB domain


Domain annotation for each model (and alignments):
>> CSD  'Cold-shock' DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   3.4   1.5e-26   1.4e-22       2      65 ..       3      62 ..       2      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.5e-26
                EEEEEEEETTTTEEEEEETTSS-EEEEETTTS-STT.TS--STSEEEEEEEECSSCEEEEEEEE CS
         CSD  2 tGtVkwfnakkgfGFItredgdkdvFvHvsaiqgdgfrsLqegqeVeFevvegkkgpeAanVtk 65
                tGtVkwfn+ kgfGFI+re++dkd+FvH +++qg+      +g++VeFev e++kgp A+ V+k
  AJA93026.1  3 TGTVKWFNQTKGFGFIERENEDKDLFVHKTEVQGQI----RDGDKVEFEVGESEKGPAAKTVKK 62
                8*********************************99....9*********************87 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.5   1.5e-11   1.4e-07       7      49 ..      12      53 ..       4      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.5e-11
                SSS-EEEEECT.TEEEEE-HHHHTTS-.TT-EEEEEEEESSSEE CS
      OB_RNB  7 kkGFGFlipdegkeDifippeqmkkam.hGDrVlvritkgdrrg 49
                 kGFGF++ + +++D+f++++++++ + +GD+V+ ++ +  +++
  AJA93026.1 12 TKGFGFIERENEDKDLFVHKTEVQGQIrDGDKVEFEVGE--SEK 53
                69*********************97665******99966..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 516.93
//
Query:       AJA93027.1  [L=163]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-22   75.8   0.3    1.3e-05   24.7   0.0    4.2  4  TPR_1            Tetratricopeptide repeat
    1.5e-17   62.2   0.0    3.1e-05   23.7   0.0    4.2  4  TPR_2            Tetratricopeptide repeat
    3.1e-16   58.1   0.7    0.00043   20.3   0.0    4.2  4  TPR_8            Tetratricopeptide repeat
    9.7e-12   44.7   0.0     0.0093   16.6   0.0    4.2  4  TPR_6            Tetratricopeptide repeat
    2.7e-11   43.0   0.1     0.0027   17.3   0.0    4.2  4  TPR_11           TPR repeat
      4e-11   42.5   0.0    1.7e-05   24.8   0.0    4.1  4  TPR_17           Tetratricopeptide repeat
      3e-09   37.0   0.0    4.3e-06   26.9   0.0    2.1  2  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    3.5e-09   36.7   0.0    7.7e-05   23.2   0.0    3.8  4  TPR_14           Tetratricopeptide repeat
    4.8e-09   36.6   0.0     0.0008   19.9   0.0    2.2  2  TPR_19           Tetratricopeptide repeat
    5.9e-09   36.4   0.0       0.03   14.9   0.0    3.1  3  TPR_16           Tetratricopeptide repeat
    2.5e-08   33.4   0.0      0.014   15.4   0.0    3.5  3  TPR_7            Tetratricopeptide repeat
    6.3e-08   32.8   0.0     0.0033   17.7   0.0    3.6  3  TPR_12           Tetratricopeptide repeat
    1.8e-05   24.7   0.1       0.51   10.5   0.0    3.9  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
    0.00031   20.8   0.0       0.21   11.8   0.0    2.6  3  TPR_9            Tetratricopeptide repeat
     0.0014   18.7   0.4        2.7    8.5   0.0    3.8  3  PPR              PPR repeat
     0.0053   17.1   0.0        3.2    8.1   0.0    2.2  2  TPR_20           Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.075   13.5   0.0        8.1    6.9   0.0    2.3  2  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
       0.11   11.7   0.0        2.8    7.1   0.0    2.1  2  TPR_15           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.3e-08   1.3e-05       8      34 .]      11      37 ..       4      37 .. 0.92
   2 !   16.5   0.1   5.6e-06    0.0055       2      25 ..      39      62 ..      38      67 .. 0.94
   3 !   24.2   0.0     2e-08     2e-05       3      33 ..      74     104 ..      72     105 .. 0.94
   4 ?    5.9   0.0     0.012        12       5      32 ..     110     137 ..     108     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                HHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  8 GnayfklgkydeAleyyekALelnPnn 34
                G++ ++lg++++Al++yek+Le +P+n
  AJA93027.1 11 GQTALNLGNPKDALAFYEKVLEQDPTN 37
                89999********************98 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 5.6e-06
                HHHHHHHHHHHHTT-HHHHHHHHH CS
       TPR_1  2 kalynlGnayfklgkydeAleyye 25
                +al+ +Gn++ k gky++A+ +y+
  AJA93027.1 39 QALFKKGNIFGKFGKYEDAIICYD 62
                5999*******************6 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2e-08
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                 +l n+G++++k ++y  A+e+++ +L++ P+
  AJA93027.1  74 SLLNKGLCFHKIEQYVPAIECFDIVLKIKPD 104
                 689***************************8 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.012
                 HHHHHHHHHTT-HHHHHHHHHHHHHHST CS
       TPR_1   5 ynlGnayfklgkydeAleyyekALelnP 32 
                 yn++  + k gk++e l+  ++ +el+ 
  AJA93027.1 110 YNMASSLIKSGKLKEGLQVLSQLIELDA 137
                 9*****************9999999985 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.1e-08   3.1e-05       5      34 .]       8      37 ..       4      37 .. 0.90
   2 !   11.8   0.0    0.0002       0.2       3      30 ..      40      67 ..      38      71 .. 0.87
   3 !   11.0   0.0   0.00037      0.36       4      33 ..      75     104 ..      73     105 .. 0.93
   4 !   10.8   0.0   0.00044      0.44       4      31 ..     109     136 ..     107     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.1e-08
       TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                   G+ +++lg++++Al+++ek+le dP+n
  AJA93027.1  8 LKSGQTALNLGNPKDALAFYEKVLEQDPTN 37
                566999**********************98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0002
       TPR_2  3 alynlGlayyklgdyeeAleafekAlel 30
                al+  G++  k g+ye+A+ +++ +l+ 
  AJA93027.1 40 ALFKKGNIFGKFGKYEDAIICYDGVLSQ 67
                89********************977765 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00037
       TPR_2   4 lynlGlayyklgdyeeAleafekAleldPn 33 
                 l n Gl+  k  +y  A+e+f+ +l++ P+
  AJA93027.1  75 LLNKGLCFHKIEQYVPAIECFDIVLKIKPD 104
                 7799************************98 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00044
       TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                  yn++ +++k+g+++e l+ + + +eld
  AJA93027.1 109 MYNMASSLIKSGKLKEGLQVLSQLIELD 136
                 79*************************8 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   4.4e-07   0.00043       2      34 .]       5      37 ..       4      37 .. 0.93
   2 !   15.0   0.1   2.1e-05     0.021       2      31 ..      39      68 ..      38      71 .. 0.88
   3 !    8.0   0.0    0.0037       3.7       4      33 ..      75     104 ..      73     105 .. 0.94
   4 !   10.7   0.1   0.00052      0.52       4      33 ..     109     138 ..     107     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4.4e-07
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34
                e++++ g++ l+lg+ + A ++yek+le dp+n
  AJA93027.1  5 ESLLKSGQTALNLGNPKDALAFYEKVLEQDPTN 37
                788999************************986 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.1e-05
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleld 31
                +a++++g+i  k g+ye A+ +y  +l+ +
  AJA93027.1 39 QALFKKGNIFGKFGKYEDAIICYDGVLSQE 68
                79*********************9888755 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0037
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                 ++n+g++ +k ++y  A+e++  +l+++pd
  AJA93027.1  75 LLNKGLCFHKIEQYVPAIECFDIVLKIKPD 104
                 789*************************98 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00052
                 HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                 +yn++s ++k g+++e  +++ + +eld +
  AJA93027.1 109 MYNMASSLIKSGKLKEGLQVLSQLIELDAS 138
                 69*************************976 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.3e-06    0.0093       1      32 [.       5      36 ..       5      37 .. 0.94
   2 ?    6.7   0.0     0.013        13       1      27 [.      39      65 ..      39      68 .. 0.88
   3 !    8.4   0.0    0.0038       3.7       3      33 .]      75     105 ..      74     105 .. 0.91
   4 !    8.1   0.0    0.0046       4.5       3      28 ..     109     134 ..     107     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.3e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  1 dAlyklalsyrklgdtdkAlealerlikeYPd 32
                ++l+k ++  ++lg++ +Al+ +e+++++ P+
  AJA93027.1  5 ESLLKSGQTALNLGNPKDALAFYEKVLEQDPT 36
                689*********99***************996 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.013
                HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  1 dAlyklalsyrklgdtdkAlealerli 27
                +Al+k +  + k g++++A+  ++ ++
  AJA93027.1 39 QALFKKGNIFGKFGKYEDAIICYDGVL 65
                69**********66******9998776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0038
                 HHHHHHHHHH.HHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   3 lyklalsyrk.lgdtdkAlealerlikeYPdS 33 
                 l++ +l++ k   ++  A+e ++ ++k  PdS
  AJA93027.1  75 LLNKGLCFHKiE-QYVPAIECFDIVLKIKPDS 105
                 8999******55.*************998887 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0046
                 HHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   3 lyklalsyrklgdtdkAlealerlik 28 
                 +y++a s++k g+  + l+ l +li+
  AJA93027.1 109 MYNMASSLIKSGKLKEGLQVLSQLIE 134
                 9*********77************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06    0.0027       8      40 ..      18      50 ..      11      52 .. 0.89
   2 !   12.1   0.0   0.00012      0.12       1      40 [.      45      84 ..      45      86 .. 0.93
   3 ?    5.8   0.0     0.011        11       4      35 ..      82     113 ..      79     116 .. 0.83
   4 !    7.7   0.0    0.0029       2.9       4      27 ..     116     139 ..     113     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
      TPR_11  8 GkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                G+ ++A++ Y+k l+ dP+n  a+++ G+++ k
  AJA93027.1 18 GNPKDALAFYEKVLEQDPTNLQALFKKGNIFGK 50
                66689************************9987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
      TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                G+++ + Gkye+Ai +Y   l    ++   ++n Gl ++k
  AJA93027.1 45 GNIFGKFGKYEDAIICYDGVLSQEKEDILSLLNKGLCFHK 84
                8888889**************************9999887 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.011
      TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                 +++  +y  Aie++   lk++Pd+ +  yn++
  AJA93027.1  82 FHKIEQYVPAIECFDIVLKIKPDSKTGMYNMA 113
                 566678888**************988888876 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0029
      TPR_11   4 yyeqGkyeeAieaYkkAlkldPdn 27 
                 + + Gk++e ++++++ ++ld ++
  AJA93027.1 116 LIKSGKLKEGLQVLSQLIELDASY 139
                 6789*****************987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.35   3.5e+02      20      33 ..      11      24 ..       4      25 .. 0.78
   2 !   24.8   0.0   1.7e-08   1.7e-05       1      33 [.      26      58 ..      26      59 .. 0.97
   3 ?    3.9   0.0     0.082        82       1      29 [.      60      88 ..      60      93 .. 0.88
   4 ?    6.8   0.0      0.01        10       5      31 ..      98     124 ..      94     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.35
      TPR_17 20 AelllknGdlmtAr 33
                +++ l++G++++A+
  AJA93027.1 11 GQTALNLGNPKDAL 24
                78889999999986 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.7e-08
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                +y+k+le+dP+n  a++ +++++ k G++++A+
  AJA93027.1 26 FYEKVLEQDPTNLQALFKKGNIFGKFGKYEDAI 58
                6******************************96 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.082
      TPR_17  1 lylkaleldPnnadaynnLAelllknGdl 29
                +y  +l +++ +  ++ n++ +++k+ ++
  AJA93027.1 60 CYDGVLSQEKEDILSLLNKGLCFHKIEQY 88
                67778999999*************99998 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.01
      TPR_17   5 aleldPnnadaynnLAelllknGdlmt 31 
                 +l++ P++   ++n+A  l k G+l++
  AJA93027.1  98 VLKIKPDSKTGMYNMASSLIKSGKLKE 124
                 68999******************9987 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.9e-05     0.029      27      80 ..       8      62 ..       2      64 .. 0.88
   2 !   26.9   0.0   4.3e-09   4.3e-06       4      81 ..      53     131 ..      50     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                HHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
      ANAPC3 27 yllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLe 80
                +  +++ +++g+ k A+ +++k  ++++++l++++ ++    k +kye+Ai +++
  AJA93027.1  8 LKSGQTALNLGNPKDALAFYEKVlEQDPTNLQALFKKGNIFGKFGKYEDAIICYD 62
                44489999*******************************999********98875 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 4.3e-09
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 +y++Ai++++ +l++e+e+  +++ ++lc+ + +qy  A+e ++   k+++ s+   y +A +l+k +k++e++++L+ 
  AJA93027.1  53 KYEDAIICYDGVLSQEKEDILSLLNKGLCFHKIEQYVPAIECFDIVlKIKPDSKTGMYNMASSLIKSGKLKEGLQVLSQ 131
                 79***********8888888889999**************************************************975 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   7.7e-08   7.7e-05       4      41 ..       7      44 ..       4      47 .. 0.89
   2 ?    2.1   0.0      0.46   4.6e+02      15      35 ..      52      72 ..      45      81 .. 0.85
   3 ?    1.7   0.0      0.62   6.1e+02      17      42 ..      88     113 ..      84     115 .. 0.81
   4 ?    5.6   0.0     0.034        33       7      32 ..     112     137 ..     109     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 7.7e-08
      TPR_14  4 llalaeallalGdpdeAiallrralalaPddaeawlll 41
                ll+ ++  l+lG+p++A+a ++++l+++P++++a++  
  AJA93027.1  7 LLKSGQTALNLGNPKDALAFYEKVLEQDPTNLQALFKK 44
                67778999*************************99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.46
      TPR_14 15 GdpdeAiallrralalaPdda 35
                G++++Ai +++ +l++  +d 
  AJA93027.1 52 GKYEDAIICYDGVLSQEKEDI 72
                899************998885 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.62
      TPR_14  17 pdeAiallrralalaPddaeawllla 42 
                 +  Ai++++ +l+  Pd+ +  + +a
  AJA93027.1  88 YVPAIECFDIVLKIKPDSKTGMYNMA 113
                 5579*************987666655 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.034
      TPR_14   7 laeallalGdpdeAiallrralalaP 32 
                 +a+ l  +G+++e +++l ++++l+ 
  AJA93027.1 112 MASSLIKSGKLKEGLQVLSQLIELDA 137
                 789999****************9875 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     8e-07    0.0008       5      57 ..      18      70 ..      14      78 .. 0.90
   2 !   14.6   0.0   3.5e-05     0.035       7      57 ..      88     138 ..      86     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8e-07
      TPR_19  5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                g++ +Ala++e++l++dp n+ a+    ++  + g +++A+ + d ++ +++ 
  AJA93027.1 18 GNPKDALAFYEKVLEQDPTNLQALFKKGNIFGKFGKYEDAIICYDGVLSQEKE 70
                99***************************************999999988877 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-05
      TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                 y  A++ +  +l+ +p++    +++A  l+++g l+e  ++L++l e d+ 
  AJA93027.1  88 YVPAIECFDIVLKIKPDSKTGMYNMASSLIKSGKLKEGLQVLSQLIELDAS 138
                 55577777779999*******************************999987 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.1e-05      0.03      36      66 ..       6      36 ..       5      38 .. 0.92
   2 !   13.9   0.0   6.5e-05     0.065       2      67 ..      43     105 ..      42     106 .. 0.92
   3 ?    4.1   0.0     0.075        75       1      27 [.     110     136 ..     110     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
      TPR_16 36 AllllgdaalrqgrlaeAaalyraalraapd 66
                +ll +g+ al +g+ ++A+a+y++ l+++p 
  AJA93027.1  6 SLLKSGQTALNLGNPKDALAFYEKVLEQDPT 36
                68899***********************997 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-05
      TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                 ++++++ + g+y+dA+  ++ +l +     ++  +ll++g+++ +   + +A++ ++  l+  pd+
  AJA93027.1  43 KKGNIFGKFGKYEDAIICYDGVLSQE---KEDILSLLNKGLCFHKIEQYVPAIECFDIVLKIKPDS 105
                 68999999******************...55556**************************999986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.075
      TPR_16   1 lalaraalragdyddAaaaleaalkrd 27 
                 +++a +++++g+  + + +l +++++d
  AJA93027.1 110 YNMASSLIKSGKLKEGLQVLSQLIELD 136
                 7899********************998 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-05     0.014       2      33 ..       7      36 ..       6      38 .. 0.87
   2 !   11.0   0.0   0.00035      0.35       2      30 ..      41      67 ..      40      73 .. 0.78
   3 ?    2.9   0.0      0.14   1.4e+02       1      28 [.      74     101 ..      74     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
       TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltkdpe 33
                Ll  +++  +lG+ ++A+ +ye+  +l+ dp+
  AJA93027.1  7 LLKSGQTALNLGNPKDALAFYEK--VLEQDPT 36
                666799999**************..9999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00035
       TPR_7  2 LlnLarlysrlGdyeeAielyeqsLaltk 30
                L+  ++++ + G+ye+Ai +y    +l  
  AJA93027.1 41 LFKKGNIFGKFGKYEDAIICYDG--VLSQ 67
                666799***************99..4444 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
       TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLal 28 
                 +Lln + ++++  +y  Aie++  +L +
  AJA93027.1  74 SLLNKGLCFHKIEQYVPAIECFDIVLKI 101
                 69999****************9886655 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.3e-06    0.0033       6      68 ..       7      61 ..       2      70 .. 0.87
   2 !    8.2   0.0    0.0029       2.9       8      72 ..      43      99 ..      38     104 .. 0.74
   3 ?    6.0   0.0     0.014        14       5      35 ..     109     138 ..     106     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
      TPR_12  6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlell 68
                l + +++ + lg+  +Al+++ek+le+      p++   +++l+  g ++ ++g+ye+A+  +
  AJA93027.1  7 LLKSGQTALNLGNPKDALAFYEKVLEQD-----PTN---LQALFKKGNIFGKFGKYEDAIICY 61
                4478899999**************9999.....987...889*****************9887 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0029
      TPR_12  8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72
                + +++  + g+y++A+ +++ +l +      ++    + +l n g ++++ ++y  A+e +  +l
  AJA93027.1 43 KKGNIFGKFGKYEDAIICYDGVLSQE-----KE---DILSLLNKGLCFHKIEQYVPAIECFDIVL 99
                56777777889999999999997776.....44...47789999999999999999988886555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.014
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarr 35 
                 ++ n+a+ l + g++ e l+ l + +e+  +
  AJA93027.1 109 MY-NMASSLIKSGKLKEGLQVLSQLIELDAS 138
                 45.**********************999755 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00051      0.51      13      38 ..      16      41 ..      14      46 .. 0.91
   2 ?    0.5   0.0      0.67   6.7e+02      13      32 ..      50      69 ..      49      72 .. 0.86
   3 ?    3.9   0.0     0.055        55      13      33 ..      84     104 ..      80     108 .. 0.92
   4 ?    4.4   0.0     0.038        38       4      34 ..     109     139 ..     106     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                HHT-HHHHHHHHHHHHHHTTS-HHHH CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEPenrQaq 38
                 lg+ ++A+ + + +Le +P n Qa+
  AJA93027.1 16 NLGNPKDALAFYEKVLEQDPTNLQAL 41
                5788899*****************97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.67
                HHT-HHHHHHHHHHHHHHTT CS
  Fis1_TPR_C 13 klgeYseArryvdalLeiEP 32
                k g+Y++A  + d +L+ E 
  AJA93027.1 50 KFGKYEDAIICYDGVLSQEK 69
                789*****999999998885 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.055
                 HHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  13 klgeYseArryvdalLeiEPe 33 
                 k+ +Y  A ++ d +L+i P+
  AJA93027.1  84 KIEQYVPAIECFDIVLKIKPD 104
                 8999****************8 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.038
                 HHHHHHHHHHHT-HHHHHHHHHHHHHHTTS- CS
  Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEPen 34 
                 +Y  A   +k g+ +e ++ + +l+e++ + 
  AJA93027.1 109 MYNMASSLIKSGKLKEGLQVLSQLIELDASY 139
                 79999999*****************999775 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.031        31      36      65 ..      11      40 ..       3      44 .. 0.86
   2 !   11.8   0.0   0.00021      0.21      10      62 ..      53     105 ..      50     107 .. 0.94
   3 !   10.8   0.0   0.00043      0.43       9      59 ..      86     136 ..      79     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
       TPR_9 36 GlllaqlGclsaAladLeaylalapdapda 65
                G+    lG+++ Ala  e  l+++p + +a
  AJA93027.1 11 GQTALNLGNPKDALAFYEKVLEQDPTNLQA 40
                788899*******************87666 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
       TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                 ++e a+ +++ +l    +d+  ++  Gl+ ++ +++  A+++++  l + pd 
  AJA93027.1  53 KYEDAIICYDGVLSQEKEDILSLLNKGLCFHKIEQYVPAIECFDIVLKIKPDS 105
                 5799*******************************************999986 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00043
       TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                 e++  a+++ + +l ++Pd+    +  +  l ++G l+++l+ L + ++l+
  AJA93027.1  86 EQYVPAIECFDIVLKIKPDSKTGMYNMASSLIKSGKLKEGLQVLSQLIELD 136
                 68889***************************************9999887 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.26   2.6e+02      13      28 ..      17      32 ..      15      34 .. 0.86
   2 ?    3.8   0.0     0.085        84       9      24 ..      47      62 ..      40      66 .. 0.88
   3 !    8.5   0.0    0.0027       2.7       6      28 ..     112     134 ..     107     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
         PPR 13 nGkleeAlelfkeMke 28
                 G++++Al ++++ +e
  AJA93027.1 17 LGNPKDALAFYEKVLE 32
                69*********99766 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.085
         PPR  9 gycknGkleeAlelfk 24
                 ++k Gk+e+A+ +++
  AJA93027.1 47 IFGKFGKYEDAIICYD 62
                699********97765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0027
         PPR   6 lIsgycknGkleeAlelfkeMke 28 
                 + s++ k+Gkl+e l+++ +++e
  AJA93027.1 112 MASSLIKSGKLKEGLQVLSQLIE 134
                 7899**************99887 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0077       7.7      11      42 ..      27      58 ..      19      70 .. 0.89
   2 !    8.1   0.0    0.0033       3.2      15      59 ..      99     143 ..      88     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0077
      TPR_20 11 leaalaanpddldarldlAlallaagryeeAl 42
                 e+ l+++p++l+a ++  +   + g+ye+A+
  AJA93027.1 27 YEKVLEQDPTNLQALFKKGNIFGKFGKYEDAI 58
                67889************************997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0033
      TPR_20  15 laanpddldarldlAlallaagryeeAleqLleilkrdrkwedda 59 
                 l+ +pd    ++++A  l++ g+ +e l+ L ++++ d +++++a
  AJA93027.1  99 LKIKPDSKTGMYNMASSLIKSGKLKEGLQVLSQLIELDASYKEQA 143
                 56678888899*****************************98765 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0081       8.1      66     121 ..       1      56 [.       1      74 [. 0.87
   2 ?    5.0   0.0     0.032        32      71     111 ..     108     148 ..      64     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0081
                      TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-S CS
  Alkyl_sulf_dimr  66 mGgaekvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqae 121
                      m++ e +l+  ++al+ g+ + a+ + ++++++dp+n +a   k +++ + g+ + 
       AJA93027.1   1 MSEIESLLKSGQTALNLGNPKDALAFYEKVLEQDPTNLQALFKKGNIFGKFGKYED 56 
                      678899*******************************9998888888888877665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.032
                      HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHH CS
  Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkad 111
                       + ++a++ +k+g+++  +++l++l++ d + +e+ +  +d
       AJA93027.1 108 GMYNMASSLIKSGKLKEGLQVLSQLIELDASYKEQAKCDID 148
                      56788999999999999999999999998888777766555 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0028       2.8     224     249 ..      14      39 ..       5      60 .. 0.74
   2 ?    2.7   0.0     0.061        60      11      36 ..     109     134 ..      98     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
      TPR_15 224 lllLgrpkkALeylrkqakenrkdpl 249
                  l Lg+pk AL++++k +++ + +  
  AJA93027.1  14 ALNLGNPKDALAFYEKVLEQDPTNLQ 39 
                 46678888888888877777666554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.061
      TPR_15  11 alklatllykqgdvkkAlevLkeaaq 36 
                  +++a+ l k g++k++l+vL + ++
  AJA93027.1 109 MYNMASSLIKSGKLKEGLQVLSQLIE 134
                 46999****************77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1171.42
//
Query:       AJA93028.1  [L=313]
Description: deoxyhypusine synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-99  330.5   0.1    8.8e-99  330.4   0.1    1.0  1  DS               Deoxyhypusine synthase
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.32   10.9   0.0    1.6  1  DUF5001          Ig-like domain
        0.2   11.7   0.0       0.34   10.9   0.0    1.3  1  Hpre_diP_synt_I  Heptaprenyl diphosphate synthase component I


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.4   0.1  1.5e-102   8.8e-99       3     287 ..      23     306 ..      21     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 330.4 bits;  conditional E-value: 1.5e-102
          DS   3 lesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgkktylgdfelddeeLrekgin 100
                 +++++++ gf+a++++e++dil +m +dekct fl++ ++++s+G+r+ii+d++k+k+ dv++tT+g +++D+++ +++ +  g+f++dd+eL +++i+
  AJA93028.1  23 FKELAQAgGFEARNVAEGVDILYNMISDEKCTKFLSFIGAIVSTGFRGIIRDMIKKKWCDVVITTCGALDHDIARHFSE-YKEGSFTMDDRELADQNIH 120
                 56677777*********************************************************************99.999**************** PP

          DS 101 Rignllvpneny.ckfedwvreildkleeeqk.vwspselikelGkeindeeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDi 197
                 R+gn+lvp e+y   +e+ v+eil+k  +e k ++s++++ +e+Gk++  e+S+lywAykndipv +p+++Dg++G q+++f+  ++++++kl+i++D 
  AJA93028.1 121 RLGNVLVPMESYgPLIEEKVQEILEKAYNEGKkEMSTADINREIGKAM-GEDSFLYWAYKNDIPVVVPGIMDGAVGSQVWMFS--QKHSDFKLNIIEDA 216
                 ************99*************99876266*************.59********************************..58899********* PP

          DS 198 relndialkakktgaiilGGGvpKhhilnanlmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                 + l+ +++ka+k+ga++lGGGvpKhh+l++n++r+g+dyavy+ttaqefdGslsga ++Ea+Swgk++++a++++++a+ T v+P++++a
  AJA93028.1 217 NFLSGLVFKAEKSGALMLGGGVPKHHTLWWNQYREGLDYAVYVTTAQEFDGSLSGALVREAISWGKVTKNATETTIHAEITTVFPFMYKA 306
                 **************************************************************************************9875 PP

>> DUF5001  Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.3e-05      0.32      11      34 ..       6      29 ..       2      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.3e-05
                TTEEEEEEEE-SSS-EEEEE-S-- CS
     DUF5001 11 tkvleveikNkSdidFeLentsey 34
                ++v+ v+i+N+Sd+d +++  +++
  AJA93028.1  6 RPVKDVDITNNSDADHIFKELAQA 29
                78999***********99987765 PP

>> Hpre_diP_synt_I  Heptaprenyl diphosphate synthase component I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.7e-05      0.34      66     108 ..      54      96 ..      42      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.7e-05
  Hpre_diP_synt_I  66 afllSlaGgllsllvmlllkklpkkklslvgiSilgavahnlg 108
                      + +lS+ G+++s+ +  +++ + kkk   v i  +ga+ h ++
       AJA93028.1  54 TKFLSFIGAIVSTGFRGIIRDMIKKKWCDVVITTCGALDHDIA 96 
                      5699**********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2128.19
//
Query:       AJA93029.1  [L=174]
Description: putative transcription factor E [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-17   61.7   0.9    4.8e-17   61.7   0.9    1.6  2  TFIIE_alpha  TFIIE alpha subunit
     0.0019   18.2   0.2     0.0053   16.8   0.0    1.9  2  zf-ACC       Acetyl-coA carboxylase zinc finger domain
     0.0023   17.7   0.0     0.0041   17.0   0.0    1.4  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0086   15.5   1.4      0.013   14.9   0.1    1.9  2  zf-ribbon_3  zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.025   14.5   0.1    1.5  1  HTH_Crp_2    Crp-like helix-turn-helix domain
      0.083   13.3   0.0       0.18   12.2   0.0    1.5  1  Rrf2         Transcriptional regulator
      0.085   13.7   1.3       0.14   13.1   0.1    2.0  2  zf-C2H2_4    C2H2-type zinc finger
       0.11   12.6   0.0       0.21   11.7   0.0    1.4  1  Sigma70_r3   Sigma-70 region 3


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.9   2.2e-20   4.8e-17      10     104 ..      16     110 ..      10     111 .. 0.95
   2 ?   -1.8   0.0       1.3   2.9e+03      87     100 ..     152     165 ..     133     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.2e-20
                  CS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHHHHHHCCCT CS
  TFIIE_alpha  10 fygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkLeeklekee 104
                  + g+e  +v  +Ll+    t+e++a  +++ +n +r++L++L++++l+  +r +de k+w  y wr   +++ + + +++++++ +L++ l+ e+
   AJA93029.1  16 IGGDEYLKVARSLLKTEDATDEEIASSTGLRINMVRRVLYDLFGKGLITGVRVKDERKGWFVYRWRSRRDEVENFIENQKKKILDRLQKRLDYEN 110
                  446999*************************************************************************************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                  HHHHHHHHHHHHHH CS
  TFIIE_alpha  87 rkleevvkkLeekl 100
                  rk+e+++k   +k+
   AJA93029.1 152 RKHEKTRKSFSKKI 165
                  45556666555555 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         3   6.7e+03       7      17 ..     122     132 ..     120     132 .. 0.57
   2 !   16.8   0.0   2.4e-06    0.0053       1      15 [.     134     148 ..     134     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3
      zf-ACC   7 CgemlykkeLe 17 
                 C+  ++ + Le
  AJA93029.1 122 CSRETFENSLE 132
                 66666666665 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
      zf-ACC   1 WtKCpsCgemlykke 15 
                 ++KCpsCg++l + +
  AJA93029.1 134 FFKCPSCGQVLKRDD 148
                 79*********9977 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0041      16      57 ..      27      68 ..      22      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
        TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                 Llk + at +eia+ +g+  + v +vL  L  kGl++ ++ 
  AJA93029.1 27 SLLKTEDATDEEIASSTGLRINMVRRVLYDLFGKGLITGVRV 68
                69**********************************987665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.87     2e+03      21      24 ..     116     119 ..     115     120 .. 0.69
   2 !   14.9   0.1   5.7e-06     0.013       4      17 ..     136     149 ..     134     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.87
  zf-ribbon_3  21 yCGt 24 
                  +CG 
   AJA93029.1 116 HCGN 119
                  7885 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.7e-06
  zf-ribbon_3   4 rCPnCGaplssddn 17 
                  +CP+CG++l+ dd+
   AJA93029.1 136 KCPSCGQVLKRDDT 149
                  8******99***96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.1e-05     0.025      21      61 ..      33      70 ..      22      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES- CS
   HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrririld 61
                + t ee+As  Gl+   v r+l +L  +gli+  + +r++d
  AJA93029.1 33 DATDEEIASSTGLRINMVRRVLYDLFGKGLIT--G-VRVKD 70
                4699***************************9..3.66666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.1e-05      0.18      25      59 ..      33      67 ..      23      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.1e-05
                -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
        Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksvr 59
                 ++ eeia+++++  ++++++l  L  +gl++ vr
  AJA93029.1 33 DATDEEIASSTGLRINMVRRVLYDLFGKGLITGVR 67
                37889**************************9876 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         4   8.9e+03       6      10 ..     122     127 ..     115     133 .. 0.53
   2 ?   13.1   0.1   6.1e-05      0.14       1      22 [.     135     157 ..     135     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4
   zf-C2H2_4   6 C.gksF 10 
                 C +++F
  AJA93029.1 122 CsRETF 127
                 655555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.1e-05
   zf-C2H2_4   1 fkCpiCgksFsskka.LlrHlkt 22 
                 fkCp Cg++ ++ ++ +++H kt
  AJA93029.1 135 FKCPSCGQVLKRDDTdIRKHEKT 157
                 8**********66667****997 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.6e-05      0.21      11      42 ..      26      55 ..      19      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-05
                HHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHH CS
  Sigma70_r3 11 reLeqelgrePtpeEiAeeLglseekVrevle 42
                r L  +   ++t+eEiA ++gl ++ Vr+vl 
  AJA93029.1 26 RSLLKTE--DATDEEIASSTGLRINMVRRVLY 55
                5555544..8********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1274.04
//
Query:       AJA93030.1  [L=256]
Description: phosphoribosylaminoimidazole carboxylase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-17   61.2   4.6    1.2e-16   60.6   4.6    1.3  1  AIRC         AIR carboxylase
     0.0082   16.8   0.1      0.016   15.9   0.1    1.5  1  NFACT-R_1    NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.051   13.3   0.9        1.5    8.6   0.6    2.2  2  DUF835       Protein of unknown function (DUF835)
       0.26   11.8   3.4        2.3    8.8   1.6    2.2  2  AF0941-like  AF0941-like


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   4.6   2.8e-20   1.2e-16       1     129 [.     122     252 ..     122     256 .] 0.86

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.8e-20
                 EEEEEESSGGGHHHHHHHHHHHHHTT-....EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE--...STTCC CS
        AIRC   1 kVgiimGSdsDlevmkkaaeilkelgv....eyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvks...kalkg 92 
                 k+gii++ +sD+ ++++   ++++++     +y+v ++  hr    l+++++    +g+++iI++AG++ +L++vv+s +++P+igvP++       kg
  AJA93030.1 122 KIGIITAGTSDIGIAEESRLMCESMNCscitSYDVGIAGLHRIFPVLKKFVK----SGVDAIIVVAGMEGALASVVSSSVNVPIIGVPTSIgygYGEKG 216
                 699*********************9996677889999999998777776666....899*******************************632246899 PP

                 HHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTT CS
        AIRC  93 ldsllSivqmPsgvpvatvaigkaknAallAaqilal 129
                 + +l +++q +s ++++ v+i+++  A+ +Aa+i+  
  AJA93030.1 217 VAALAAMLQSCS-LGLTVVNIDNGIGAGAAAAKIVNQ 252
                 *********998.566667777***********9865 PP

>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   3.5e-06     0.016      49     103 ..      66     129 ..      44     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.5e-06
   NFACT-R_1  49 lr..lsege...leeipeelleeaaqlakanSia.gnklssvdvvyvpasnlsktap....ldtG 103
                 ++  l++++   +++ip++  +++++++k+n  + ++ + +++ + v+ + ++kt+     +++G
  AJA93030.1  66 IKkvLEKTNaivVSRIPKKNYQDICNFCKKNNLKiSTGQ-NCTTILVYNKPVKKTKGkigiITAG 129
                 443433333555669*******************77777.***************9866655555 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00033       1.5       3      49 ..      57     102 ..      55     118 .. 0.80
   2 ?    2.7   0.0     0.022        97      61      86 ..     161     186 ..     150     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00033
      DUF835   3 kkkekakeilsdlvkegvkvlaitRenpkkirekvkienvkviwltk 49 
                 k+++++k+i++++ ++  ++++++R ++k+ ++  +  + + + +++
  AJA93030.1  57 KENSEVKKIIKKVLEK-TNAIVVSRIPKKNYQDICNFCKKNNLKIST 102
                 6788999******996.*********999987666776666666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.022
      DUF835  61 lekltetivkflkeaekgvvliDgle 86 
                 l+++   ++kf+k++ + ++++ g+e
  AJA93030.1 161 LHRIFPVLKKFVKSGVDAIIVVAGME 186
                 8899999*****************98 PP

>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6   0.00051       2.3      43     106 ..       2      70 ..       1      74 [. 0.64
   2 ?    3.7   0.5      0.02        88      61      96 ..      66     102 ..      42     123 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00051
                  HHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHCTT-----..........HHHHHHHHHH CS
  AF0941-like  43 dvedvleklkagdieeeeakknlklLkvyvvsqLdehykrvlelledkekkiek..........evvdeIveai 106
                  ++ d+le +k+g++  +eak   k+L +y +  +++  k  ++l  +  k i +          ev++ I+++ 
   AJA93030.1   2 NISDILESVKNGKLSTDEAK---KQLSLYTIEEIENFAK--IDLGREARKGIPEvifaerkensEVKKIIKKVL 70 
                  6789****************...6667777777766544..344444444444444445555545555555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                  HHHHHHHHHHHHHHTH.HHHHHHHHHHHHCTT----- CS
  AF0941-like  61 akknlklLkvyvvsqL.dehykrvlelledkekkiek 96 
                  +kk l++    vvs + +++y+++ ++ ++++ ki+ 
   AJA93030.1  66 IKKVLEKTNAIVVSRIpKKNYQDICNFCKKNNLKIST 102
                  4556666677788887334588888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1290  (0.0719505); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1773.08
//
Query:       AJA93031.1  [L=273]
Description: shikimate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-28   96.8   0.1    1.9e-27   95.3   0.0    1.8  2  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    1.9e-11   43.5   0.0      3e-11   42.9   0.0    1.3  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
    8.3e-10   38.9   0.1    1.4e-09   38.1   0.1    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00015   22.0   0.0    0.00026   21.3   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.03   14.9   0.1      0.051   14.2   0.1    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   0.0   5.3e-31   1.9e-27       1      83 []       7      89 ..       7      89 .. 0.99
   2 ?   -3.5   0.0       3.5   1.3e+04      25      39 ..     216     228 ..     204     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 5.3e-31
                    EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
  Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                    viG+pi+hSlSP ihnaa+++l+l+++y+a +v++ +l + +e+l++ +++G+nvTiP+K +++++ld+++++ k+igAvNt+
      AJA93031.1  7 VIGDPIEHSLSPTIHNAAYRELQLECTYIAYRVAQGDLATGIESLKKIKISGFNVTIPHKIEMMNYLDNVDDNCKKIGAVNTV 89
                    89********************************************************************************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.5
                     SEEEEEEE-SCCTHH CS
  Shikimate_dh_N  25 ngsyeafeveedele 39 
                     +++y++++++   ++
      AJA93031.1 216 DIVYKPVKTD--LIN 228
                     5556666555..444 PP

>> SDH_C  Shikimate 5'-dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   8.4e-15     3e-11       1      31 []     240     270 ..     240     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8.4e-15
                 HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
       SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                 G++ML++Q+ ++Fe+W  r++P++vM++ +l
  AJA93031.1 240 GYEMLLGQAIRSFEIWLDRKAPYDVMKRSIL 270
                 99**************************986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   3.9e-13   1.4e-09       7      84 ..     115     193 ..     109     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3.9e-13
                   HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
  Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkellaeadvvisata 84 
                   l ++k++k+ll+GaG  ++ ++  + ++++++++++NRt ++ +ela+     g +++ +++e++++  +++d ++ a +
    AJA93031.1 115 L-EIKNSKILLLGAGGASRAIVAGFQKENAREITIVNRTKTNGDELAQFSnkLGLNATSQTIEDMNSFDSNFDFIVNASS 193
                   3.699*****************************************975522255688999**************98865 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   7.2e-08   0.00026       1      77 [.     122     192 ..     122     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.2e-08
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                      +l++GaG+ ++a++   ++++    eit++ r+k++ ++la+  ++  ++a++ ++e+  +  ++     d++vn+s
       AJA93031.1 122 ILLLGAGGASRAIVAGFQKENAR--EITIVNRTKTNGDELAQFSNKLGLNATSQTIEDMNS-FDS---NFDFIVNAS 192
                      89*****************9987..****************999*************9999.554...568888876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.051       1      58 [.     121     178 ..     121     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEES...SCCCHHHHHHHHC-EEECECHHHH CS
  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansr...npekaeelaeelgvkvtavdneea 58 
                    ki ++GaG   +a++ g+++++  ++ei+++ +r   n ++++++ ++lg ++t+ + e++
     AJA93031.1 121 KILLLGAGGASRAIVAGFQKEN--AREITIV-NRtktNGDELAQFSNKLGLNATSQTIEDM 178
                    57789****************9..7777766.45011456677777888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2010.57
//
Query:       AJA93032.1  [L=147]
Description: cytochrome oxidase assembly domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-19   67.7  15.8    1.6e-14   53.8   8.9    2.0  2  COX15-CtaA       Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.17   12.0   0.0    1.2  1  PseudoU_synth_2  RNA pseudouridylate synthase
        5.4    7.0   6.2       0.72    9.9   0.4    2.2  2  SLATT_fungal     SMODS and SLOG-associating 2TM effector doma


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   5.8e-08   0.00035       2      43 ..       5      46 ..       4      48 .. 0.88
   2 !   53.8   8.9   2.6e-18   1.6e-14      74     170 ..      47     137 ..      44     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.8e-08
  COX15-CtaA  2 rwlllvlllvllvvvlGgltRltdsGlsitdWppctGalppl 43
                +++l++l++++ + ++Gg++ + + Gl +++Wp c   ++p 
  AJA93032.1  5 YLALASLVILYSLMFVGGYISAAGLGLTCPEWPLCPNGIMPN 46
                6789999999*************************8877775 PP

  == domain 2  score: 53.8 bits;  conditional E-value: 2.6e-18
  COX15-CtaA  74 aiawiEwiHRllgrllGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllalllwlalrlla 170
                 ++++iEw+HRl++ ++G+lil+ ++ +++++ + r++k   +++ +lv+ Q  lG+ ++  +L        + +a+HL++++ll+a+ l+++l +++
  AJA93032.1  47 EEYFIEWVHRLVAATTGVLILATTIGAWINRDAGRKIKFTSAFASALVVTQITLGALVIDTQL------HAVLVAVHLGIGILLFAMTLLTVLFAFR 137
                 689************************************************************......9*******************99987665 PP

>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.9e-05      0.17      36      60 ..      46      70 ..      40      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
  PseudoU_synth_2 36 eekkelklvhRLDkatsGllllAks 60
                     +e+  + +vhRL  at+G+l+lA++
       AJA93032.1 46 NEEYFIEWVHRLVAATTGVLILATT 70
                     56677899***************97 PP

>> SLATT_fungal  SMODS and SLOG-associating 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.4   0.00012      0.72       7      35 ..      77     105 ..      73     112 .. 0.92
   2 ?   -0.3   0.5      0.17     1e+03      15      43 ..     109     139 ..     105     144 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
  SLATT_fungal   7 rkaarkarltslalnlaiglQvllgAllt 35 
                   r+a rk ++ts++  ++++ Q++lgAl++
    AJA93032.1  77 RDAGRKIKFTSAFASALVVTQITLGALVI 105
                   678899********************985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
  SLATT_fungal  15 ltslalnlaiglQvllgA..lltaLgalssg 43 
                   l ++++ + +g+ +ll A  llt+L a+  g
    AJA93032.1 109 LHAVLVAVHLGIGILLFAmtLLTVLFAFRLG 139
                   4455555666666666662256777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1051.73
//
Query:       AJA93033.1  [L=201]
Description: ribosomal protein S13p/S18e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-37  128.4   0.1    2.5e-37  128.1   0.1    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0091   16.0   0.0      0.028   14.4   0.0    1.7  2  H2TH           Formamidopyrimidine-DNA glycosylase H2TH domai


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.1   0.1   2.7e-41   2.5e-37       1     128 []      10     138 ..      10     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 2.7e-41
  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdGkdshvvendlrrklre 95 
                    Rilg di g+ ++ i l +ikGiG+  a+ +l+ ++++ +++ig+lt e+i+ ie+i+en++    p+w+ nr++d+ +G+d+h+v++d+ +++r+
     AJA93033.1  10 RILGNDIHGELNMLIGLSQIKGIGYMFANSMLQVLKISPHQKIGNLTTEQISSIEKIIENPKGSDFPTWFlNRRQDMLTGEDMHLVTSDIAFNIRN 105
                    99********************************************************************************************** PP

  Ribosomal_S13  96 dieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                    d+eR+k++ s+rG RH+ GlkvRGQrT+ tgR+
     AJA93033.1 106 DVEREKTLFSWRGYRHMYGLKVRGQRTRCTGRK 138
                    *******************************95 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.1e-06     0.028      30      74 ..      23      67 ..      19      69 .. 0.88
   2 ?   -2.0   0.0      0.41   3.7e+03      61      87 ..      86     112 ..      82     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                HHCTTTSCS--HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHH CS
        H2TH 30 LLDqklvaGlGNiyadEvLfrakihPerlakslskeelellhqei 74
                L+  + + G+G ++a+ +L   ki+P+++  +l++e+++ + + i
  AJA93033.1 23 LIGLSQIKGIGYMFANSMLQVLKISPHQKIGNLTTEQISSIEKII 67
                55667899******************************9987655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.41
                 GS-HHHHHHHHHHHHHHHHHHHHTTTT CS
        H2TH  61 slskeelellhqeikevlkeaielgks 87 
                  l+ e+++l++++i+  +++ +e++k+
  AJA93033.1  86 MLTGEDMHLVTSDIAFNIRNDVEREKT 112
                 578889999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1567.30
//
Query:       AJA93034.1  [L=325]
Description: RNA-metabolizing metallo-beta-lactamase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-05   24.0   0.0    0.00014   21.7   0.0    2.0  2  RMMBL     Zn-dependent metallo-hydrolase RNA specificity doma
  ------ inclusion threshold ------
      0.013   15.6   0.1      0.033   14.4   0.1    1.6  1  DRMBL     DNA repair metallo-beta-lactamase


Domain annotation for each model (and alignments):
>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.22     2e+03      24      37 ..     234     248 ..     233     254 .. 0.69
   2 !   21.7   0.0   1.5e-08   0.00014      11      39 ..     269     297 ..     266     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.22
       RMMBL  24 elirklkprn.vilv 37 
                 ++i+++k ++ vi +
  AJA93034.1 234 NFIKHMKTKYdVITI 248
                 577777777776654 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.5e-08
       RMMBL  11 idfSgHadknellelirklkprnvilvHG 39 
                 i +S H d+nel+el++k + ++v+ +HG
  AJA93034.1 269 IPLSDHCDYNELIELVKKSEAEKVYTIHG 297
                 6689************************* PP

>> DRMBL  DNA repair metallo-beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.7e-06     0.033      30     103 ..     233     293 ..     223     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-06
       DRMBL  30 ekylkalkekfdsvlafrPtGWtkkekkkkdlekikessksrekisiyrvpYSeHSSfrELkefvkslkpkkii 103
                 ++ +k +k+k+d v+ +  +GW+ ++k                + + y++p S+H+ ++EL e vk  + +k++
  AJA93034.1 233 NNFIKHMKTKYD-VITIGFSGWANSKKF----G---F-----SRGTDYSIPLSDHCDYNELIELVKKSEAEKVY 293
                 567788888887.788899999998872....2...2.....24567*******************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2583.98
//
Query:       AJA93035.1  [L=100]
Description: SRP19 protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-14   53.7   0.2    3.7e-14   53.4   0.2    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.2   2.1e-18   3.7e-14       1      80 [.       8      89 ..       8      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 2.1e-18
                EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEE.EEEEECTTSS.TTCCEEEEEC-..........SS-C CS
       SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevv.vepeksyPrd.wanpGrVrvklkedgkevnekiknk 80
                vi+  Y++++  r++GRr++ke++v +P+++e+ +a ++ gl+ +  e++ +yP++ ++++G++ + ++e+++++ eki++k
  AJA93035.1  8 VIWLDYFNKTLPRNKGRRLSKEKCVFDPSLKELIDASNSAGLQPKeTEEQVRYPKRpYVRSGYIVLPKTEKKTTMLEKISQK 89
                79****************************************9887999*******77788****99866666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 778.73
//
Query:       AJA93036.1  [L=385]
Description: transporter, major facilitator family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-35  122.7  42.8      1e-24   87.1  19.8    2.0  2  MFS_1     Major Facilitator Superfamily
    4.1e-15   56.0  15.6    5.4e-15   55.5  15.6    1.1  1  MFS_4     Uncharacterised MFS-type transporter YbfB
    0.00039   19.0   8.5    0.00057   18.4   8.5    1.2  1  MFS_3     Transmembrane secretion effector
     0.0088   15.1  17.0       0.61    9.0  16.1    2.7  2  PUCC      PUCC protein
  ------ inclusion threshold ------
      0.067   11.5  12.6      0.033   12.5   3.9    3.0  3  OATP      Organic Anion Transporter Polypeptide (OATP) family
       0.19   11.8   4.0       0.89    9.7   0.0    3.5  3  MASE2     MASE2 domain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1  19.8   3.5e-28     1e-24       2     268 ..       9     260 ..       8     264 .. 0.85
   2 !   47.1  24.4     5e-16   1.5e-12       3     168 ..     208     370 ..     206     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 3.5e-28
       MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgag 100
                 +++++l+++++++ gp+lp + ++  g+s + +g +  + ++ ++++ l++G l +rf    +l lg+ + +++++ll++++s++ ++  rvl+G++ +
  AJA93036.1   9 YITGILIGISYGLQGPLLPVFAKNVIGASYADLGAIGFANFIPYMFFPLFVGILLNRFNNAHLLSLGIGINSISVYLLSISQSVPEIMGYRVLTGVAHA 107
                 7899***************9999***********************************9999************66666757777************** PP

       MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplv 197
                 +++p + a+i+ +++++ r r i+ ++++f  G+++gpl+g+++++++   +r +f i++ +++ ++v     +  ++ ++  ks+k        ++++
  AJA93036.1 108 FFWPPCEAIISNVSKGKTRVRNIATFTGFFTTGFMIGPLIGSVILENYDenYRFIFEIATYILVASIV---SAIGLSRNRPIVKSEK--------FSFS 195
                 *************************************************9999999999999999988...6666666666666544........4588 PP

       MFS_1 198 pawkallkdpvlwillialllfffgfsglltllplylqevlgls..glllaglllallalvgailallagrls 268
                 + +k++ k p++  +++ +++++  f ++l+  p +   ++ ++  +  ++ ++++l+ ++++i   +a++l+
  AJA93036.1 196 S-IKEIIKFPHV--IMMLIYCTA-SFGIILSIYPAF-LNDRAMTpvNIEILFFIFGLSRIITLI---MASKLA 260
                 8.9999999988..666666664.888899999998.556666647556666666666666655...566665 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 5e-16
       MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgag 100
                 ++++  +++++i+++++p a  +d  ++p  i +l+ +++l  +++ + ++ l+ +     +l+l+ ++ a+g l l+ f+ s+  ++++  l G+g +
  AJA93036.1 208 MMLIYCTASFGIILSIYP-AFLNDRAMTPVNIEILFFIFGLSRIITLIMASKLAKNT--SLTLILATFSIAAG-LGLSfFVESIVEFAIAITLLGFGFS 302
                 455566677788888888.7779999*****************************96..44555555555555.44443469999************** PP

       MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                 ++fp+ + ++   + ke  g +ig + + f++G + gp+++g++++ +g + +++++ ++++ +++l 
  AJA93036.1 303 IFFPLTLEIVLSKTRKEISGTMIGAYETVFGIGWASGPVIAGVISQFFGNETPYLVFFVIGIGVAILS 370
                 ****************************************************************9963 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5  15.6   1.8e-18   5.4e-15      11     349 ..      21     358 ..      13     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.8e-18
       MFS_4  11 sytpiLPallaeg.qlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvla 108
                 +  p+LP+  +++ + s++++g ++ aN++ Y+   l+  + l++ ++   l  g+    +++   ++ +s+  ++  R+l+Gva A+      +++ +
  AJA93036.1  21 LQGPLLPVFAKNViGASYADLGAIGFANFIPYMFFPLFVGILLNRFNNAHLLSLGIGINSISVYLLSISQSVPEIMGYRVLTGVAHAFFWPPCEAIISN 119
                 55799***99986479*****************999988877777777777999999*********************************999999999 PP

       MFS_4 109 haaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp.raalreasaaaeaakaeqkslpllalllaYglaGfG 206
                  ++ + r r +a + +    G +++ l+ +++l+   ++    + +a   +v+ +++a+ l  +++  ++++ ++++ +e  ++p ++++l Y  a fG
  AJA93036.1 120 VSKGKTRVRNIATFTGFFTTGFMIGPLIGSVILENYDENYRFIFEIATYILVASIVSAIGLSrNRPIVKSEKFSFSSIKEIIKFPHVIMMLIYCTASFG 218
                 98777777777776666799********999998888777776666666666666666666536778888888888889999***************** PP

       MFS_4 207 YiitatFlvaiardgaggalleallWllvGlaaivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlar 305
                  i+     +a+ +d+a  ++  + l +++Gl+ i+++ +  ++ak++ l  +l  a    a+g+ ls   +s++  +++  llG  f    +l+l+++ 
  AJA93036.1 219 IILSI--YPAFLNDRAMTPVNIEILFFIFGLSRIITLIMASKLAKNTSLTLIL--ATFSIAAGLGLSFFVESIVEFAIAITLLGFGFSIFFPLTLEIVL 313
                 87654..48888999999*********************99999995554444..44445889999******************************999 PP

       MFS_4 306 elappat.rrllglmTasfgigQilGpllasllaeatgslalall 349
                     ++   +++g+  ++fgig + Gp++a++++++ g+ ++ l+
  AJA93036.1 314 SKTRKEIsGTMIGAYETVFGIGWASGPVIAGVISQFFGNETPYLV 358
                 888887768999************************998877655 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   8.5   1.9e-07   0.00057      42     371 ..      36     351 ..      31     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-07
       MFS_3  42 asplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaA 140
                 as +    +  a  +P +++ +++G+l + f+  ++l  +  +  + sv l +++    +s+  ++++ +l+g+  a+  P  +A+++++ k +     
  AJA93036.1  36 ASYADLGAIGFANFIPYMFFPLFVGILLNRFNNAHLLSLGIGINSI-SVYLLSIS----QSVPEIMGYRVLTGVAHAFFWPPCEAIISNVSKGKTRVRN 129
                 555566667778899*****************99988777655444.44433333....57889************************99875554445 PP

       MFS_3 141 vaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevrksslprEkl.lealraglRftaasreikavlvRaalFglsasavl 238
                 +a  +  + +   +GP +g v++      + f ++  +y+ +  ++ ++  + ++  + +Ek+ ++++++ ++f +    i + +  +a Fg+    +l
  AJA93036.1 130 IATFTGFFTTGFMIGPLIGSVILENYDENYRFIFEIATYILVASIVSAIGLSRNRPIVKSEKFsFSSIKEIIKFPH---VIMMLIYCTASFGI----IL 221
                 5555555788899***************************99999999999999999999*994577888888765...57777777888886....78 PP

       MFS_3 239 aLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavP 337
                 ++ P    d+    ++   il+  +G+  i++ ++ s+L +  s    + la++ +A+ l    +++s++  ++++ l+G ++ + +      v   + 
  AJA93036.1 222 SIYPAFLNDRA-MTPVNIEILFFIFGLSRIITLIMASKLAKNTSLT--LILATFSIAAGLGLSFFVESIVEFAIAITLLGFGFSIFFPLTLEIVLSKTR 317
                 99999888876.569999*********************9986654..44577777777766778999999999*******999998888888888999 PP

       MFS_3 338 rWvvgRalavYltvlaGglaaGsllWGavaeals 371
                 + + g  +  Y tv+  g a G ++ G++++  +
  AJA93036.1 318 KEISGTMIGAYETVFGIGWASGPVIAGVISQFFG 351
                 99**************************998765 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.32   9.5e+02     142     159 ..      57      74 ..      12      96 .. 0.65
   2 !    9.0  16.1    0.0002      0.61      97     390 ..     101     371 ..      30     379 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
        PUCC 142 ivvgallkdytearLirv 159
                 ++vg+ll+ +++a+L+ +
  AJA93036.1  57 LFVGILLNRFNNAHLLSL 74 
                 456666666666666654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0002
        PUCC  97 lvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgallkdytearLirvvqgvalitlvlnvlalWkievkskkkkeekeeeeps 195
                 l G++      +  A+++++++ ++r + ++     ++ g +++ ++ +++l++y+e+   r++ ++a+ +lv +++++ +  ++++  k+    e+  
  AJA93036.1 101 LTGVAHAFFWPPCEAIISNVSKGKTRVRNIATFTGFFTTGFMIGPLIGSVILENYDEN--YRFIFEIATYILVASIVSAIGLSRNRPIVKS----EKF- 192
                 5666666666677777777888888887777777778888888888888888888776..5777777777777777777777665554441....111. PP

        PUCC 196 lleawlklvaekqalaflaflllgtlaffmqdviLEpYgGev..lgLtvgeTTkLtalfalGtlvGlllaglvlsrglkkarlaslgvllgllsfllli 292
                   + +++++   +  +++++l+  t++f++   iL  Y        +t  +   L  +f+l  ++ l++a+++  +      la++ +++g      l 
  AJA93036.1 193 SFSSIKEII---KFPHVIMMLIYCTASFGI---ILSIYPAFLndRAMTPVNIEILFFIFGLSRIITLIMASKLAKNTSLTLILATFSIAAG------LG 279
                 112222222...223334444555555554...4444443221124566666666667777777777777766653333333333333333......34 PP

        PUCC 293 laallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQaiaaglavllggalrdllkalaandaalayglVfaleavlliisi 390
                 l+ ++e+++ ++ ++ llG++  +f   +l ++l+ + +e +g+++Ga+  +     g++ + g +++ ++  +++  + ++y + f++ +++ i+si
  AJA93036.1 280 LSFFVESIVEFAIAITLLGFGFSIFFPLTLEIVLSKTRKEISGTMIGAYETV----FGIGWASGPVIAGVISQFFG--NETPYLVFFVIGIGVAILSI 371
                 5677889999*************************************99765....67788888888888889998..59*************99998 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.16   4.7e+02      38      86 ..      41      89 ..      36     100 .. 0.85
   2 ?    3.7   0.1     0.005        15     140     195 ..     100     155 ..      95     167 .. 0.87
   3 ?   12.5   3.9   1.1e-05     0.033     133     195 ..     285     350 ..     160     356 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 38 sgliassneignillilfvsYfggrghrPrwigigallmalgslllalP 86
                 g i  +n i ++++ lfv+ + +r + + ++ +g+ + +++ +ll++ 
  AJA93036.1 41 LGAIGFANFIPYMFFPLFVGILLNRFNNAHLLSLGIGINSISVYLLSIS 89
                5778888889999999999999999999999999999999999998765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.005
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 140 lllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                 +l G++++ +++ + + i + +k k+    +++++ + + G ++G l+Gs++l+ y
  AJA93036.1 100 VLTGVAHAFFWPPCEAIISNVSKGKTRVRNIATFTGFFTTGFMIGPLIGSVILENY 155
                 789999999999999999988888888899**********************9988 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 1.1e-05
                 x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 133 l...lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                      f +a +llG+G + +++l +  +   ++k+ s +++g++ ++  +G+a G ++++++ +++
  AJA93036.1 285 EsivEFAIAITLLGFGFSIFFPLTLEIVLSKTRKEISGTMIGAYETVFGIGWASGPVIAGVISQFF 350
                 14337999*****************************************************99987 PP

>> MASE2  MASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0003      0.89       8      75 ..      74     144 ..      70     152 .. 0.78
   2 ?    0.6   0.1       0.2     6e+02       9      28 ..     266     285 ..     264     321 .. 0.69
   3 ?   -0.4   0.2       0.4   1.2e+03       7      35 ..     331     359 ..     328     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
       MASE2   8 lGlllgaliiaaglleqhfs...lalllllvlnallwPhlayllarrsrdplrteqrlLliDallgGlwia 75 
                 lG+++ ++++    ++q ++   ++ +l  v++a++wP    ++++ s+  +r+++   +   +  G++i+
  AJA93036.1  74 LGIGINSISVYLLSISQSVPeimGYRVLTGVAHAFFWPPCEAIISNVSKGKTRVRNIATFTGFFTTGFMIG 144
                 566666666666666666664445678899*********99999999999999999988888888888887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
       MASE2   9 Glllgaliiaaglleqhfsl 28 
                  l+l+ ++iaagl    f +
  AJA93036.1 266 TLILATFSIAAGLGLSFFVE 285
                 67899999999998777663 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.4
       MASE2   7 vlGlllgaliiaaglleqhfslalllllv 35 
                 v+G+++++ +++ag+++q f  ++  l++
  AJA93036.1 331 VFGIGWASGPVIAGVISQFFGNETPYLVF 359
                 6799999999*******999866555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2595.59
//
Query:       AJA93037.1  [L=318]
Description: putative dTDP-glucose 4,6-dehydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-66  225.3   0.0    1.6e-66  225.0   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.1e-55  186.9   0.0    4.8e-55  186.7   0.0    1.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-16   60.6   0.0    1.1e-15   57.5   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.4e-14   51.6   0.0    1.1e-13   50.9   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    7.5e-09   35.1   0.0    9.5e-09   34.8   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
      6e-08   32.8   0.0    1.2e-07   31.8   0.0    1.5  2  NAD_binding_10   NAD(P)H-binding
    9.6e-08   31.5   0.1    0.00012   21.3   0.1    2.4  2  NAD_binding_4    Male sterility protein
     0.0056   16.3   0.0     0.0091   15.6   0.0    1.3  1  NmrA             NmrA-like family
     0.0075   15.7   0.0       0.02   14.4   0.0    1.7  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.0   0.0     8e-70   1.6e-66       1     332 []       4     300 ..       4     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 225.0 bits;  conditional E-value: 8e-70
                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHH CS
  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPe 96 
                    L+TG  Gfi s+++++L+e g +v+ +vrr+ss  +++i hl++        +lk+  g+++D s l +  +++  d +y+L+AqshV++s+++P 
     AJA93037.1   4 LVTGADGFIPSFVCDRLVELGANVTALVRRNSSNVIKSIPHLKT--------HLKIRWGEISDLSLLVQETKDT--DIIYHLGAQSHVQYSLHNPL 89 
                    9********************************99999999863........57999******88887766666..99****************** PP

                    HHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTS CS
  GDP_Man_Dehyd  97 ytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetf 192
                    +t+ +n +Gt+++Lea+r+  ++   ++++a+++EvYGk+++vp+tE++ + PrsPYaa K+++d ++ +y  +y++++v +++f  ++pr+    
     AJA93037.1  90 ETYVTNTVGTANVLEAARINDVR---KIVHAGSAEVYGKPNKVPITEDNELVPRSPYAAGKVASDRLMFSYFCTYDMPVVMSRFFGIYGPRQ---S 179
                    ******************98775...9****************************************************************7...7 PP

                    CCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTG CS
  GDP_Man_Dehyd 193 vtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgk 288
                    +++ i++++ +i++++ + +++G++++ Rd+ +v D ++a+ ++  ++        +g++ ++++  el++++l ++i   +            ++
     AJA93037.1 180 IEKAIPKFILKILNNE-PPVVYGDGKQSRDYMYVTDAADAYAKLGVAND------VDGQVINIGTGTELTIADLAQKILDLM------------NS 256
                    88************98.66779******************998766555......489999*************99987653............34 PP

                    GCCCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
  GDP_Man_Dehyd 289 vvvevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                    ++ ++   +  pge+ +l+ d++   ++L+W+pk+++ee+++++
     AJA93037.1 257 DLKPIFSGKINPGEAGRLFTDPTNCMKKLDWSPKIGLEEGLKNT 300
                    5667888999******************************9875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.7   0.0   2.4e-58   4.8e-55       1     241 []       3     236 ..       3     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.7 bits;  conditional E-value: 2.4e-58
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHHHTHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfieknlqgt 95 
                 +lVtGa Gfi s ++++l e g +v++l r++s++  +++++l    ++  +++ d s l +  k  + d+++hl+a+++v+ s  +p +++ +n++gt
  AJA93037.1   3 VLVTGADGFIPSFVCDRLVELGANVTALVRRNSSNVIKSIPHLkthlKIRWGEISDLSLLVQETK--DTDIIYHLGAQSHVQYSLHNPLETYVTNTVGT 99 
                 79***************************************999777777788887777777766..89****************************** PP

                 HHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHH CS
   Epimerase  96 lnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkil 194
                  n+leaar ++v+++++++S+evYGk++++p +e+    +l p+spYaa K+a+++l+ +y  +y+++++  r f +yGpr   ++ ++ ip++i kil
  AJA93037.1 100 ANVLEAARINDVRKIVHAGSAEVYGKPNKVPITEDN---ELVPRSPYAAGKVASDRLMFSYFCTYDMPVVMSRFFGIYGPR---QSIEKAIPKFILKIL 192
                 *******************************99999...9*****************************************...99************* PP

                 TTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 195 egkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 +++ + +++gdg++ Rd++yv D+a+a+  +  +  ++ +g+++niG
  AJA93037.1 193 NNE-PPVVYGDGKQSRDYMYVTDAADAYAKLGVA--NDVDGQVINIG 236
                 ***.*************************99888..456789***99 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   5.7e-19   1.1e-15       1     250 [.       3     257 ..       3     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 5.7e-19
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      vlvtGa G i s +++++++  ++   l+ r+  ++ +   +l     k++lk++     g++ d + l +  +  + d+++h  A  hV    
       AJA93037.1   3 VLVTGADGFIPSFVCDRLVELGANVTALVRRNSSNVIKSIPHL-----KTHLKIR----WGEISDLSLLVQETK--DTDIIYHLGAQSHVQYSL 85 
                      89********************999999999888776655555.....3356666....9*********99999..9***************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE..............EEEGGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTG CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvl..............iStDKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgS 174
                      +nple+  tN +gt nv+eaa  ++v+k+v               i  D    P + + a K +++ l+ ++  +    ++ +v+ Rf  + g 
       AJA93037.1  86 HNPLETYVTNTVGTANVLEAARINDVRKIVHagsaevygkpnkvpITEDNELVPRSPYAAGKVASDRLMFSYFCTY---DMPVVMSRFFGIYGP 176
                      ****************************986333333333333336678888999999999999999999998887...799************ PP

                      TTSS...HHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHHHHHHHHH.HH--SS-EEEE--.-EEEHHHHHHHH....... CS
  Polysacc_synt_2 175 rGSv...iplFkkqikeg.gpvtvTdpemtRyfmtieeavqLvlqal.alakggeifvldmGepvkivdlakalielsgle 250
                      r S+   ip+F  +i ++  pv   d +  R +m +++a++   + + a+  +g++     G  ++i+dla+++++l++ +
       AJA93037.1 177 RQSIekaIPKFILKILNNePPVVYGDGKQSRDYMYVTDAADAYAKLGvANDVDGQVINIGTGTELTIADLAQKILDLMNSD 257
                      ***8888*****9998874689999****************9888653677899999999**************9999754 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   5.5e-17   1.1e-13       1     224 [.       4     218 ..       4     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 5.5e-17
   3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegvdvvihlaslvdvag.kltedeimkvnvkGTr 97 
                 +vtG+ GF+ + ++ +Lv+l+   +v +l  r+s+++ +++ +++++  +  g + d + l + +++ d++ hl + + v+    +  e +  n  GT 
  AJA93037.1   4 LVTGADGFIPSFVCDRLVELGA--NVTALVRRNSSNVIKSIPHLKTHLkIRWGEISDLSLLVQETKDTDIIYHLGAQSHVQYsLHNPLETYVTNTVGTA 100
                 69*******************5..9999999999999999999998866889**********************9999999834455689999****** PP

   3Beta_HSD  98 nvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkl...lvpll 193
                 nvlea++ ++vr++v+  saev g+  ++ +i++       e ++ ++y+  K  +++l+ +          ++  +  R  giyG++++    + +++
  AJA93037.1 101 NVLEAARINDVRKIVHAGSAEVYGK-PNKVPITED-----NELVPRSPYAAGKVASDRLMFSYFC-----TYDMPVVMSRFFGIYGPRQSIekaIPKFI 188
                 ************************9.677788844.....45678899*****999999887665.....448999999********976511144556 PP

   3Beta_HSD 194 kqlaklglalfkigdeevlsdrvYvgNvawa 224
                  ++++++   + +gd ++  d++Yv   a+a
  AJA93037.1 189 LKILNNE-PPVVYGDGKQSRDYMYVTDAADA 218
                 6666665.778899999999****9998887 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   4.8e-12   9.5e-09       1     239 [.       1     259 [.       1     273 [. 0.83

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.8e-12
                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHHHHH-.-SEEEE------HHHHHHSHHHHHHHHT CS
  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaellkeak.pdvvvnaAAytavDkaEseeeaayavna 79 
                    m++lvtGa+G + s + ++l e g++v+al r+                ++   + + +  l++e+k  d++++++A   v    +++ + y  n 
     AJA93037.1   1 MNVLVTGADGFIPSFVCDRLVELGANVTALVRRnssnviksiphlkthlKIRWGEISDLSLLVQETKdTDIIYHLGAQSHVQYSLHNPLETYVTNT 96 
                    89****************************7777999999999999977555556666777776655278************************** PP

                    HHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH....H-SSEEEEEE-SEESS...SSS-HHHHHHHHH CS
  RmlD_sub_bind  80 eavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla....agkkalivRtswvyge...kgknfvktmlrla 167
                     +++++ eaa+  ++ +++h  +  V+   +k p +ed+e  P++ Y++ K+a  +   +    +   +++ R+  +yg     +k   k +l+ +
     AJA93037.1  97 VGTANVLEAARINDVrKIVHAGSAEVYGKPNKVPITEDNELVPRSPYAAGKVASDRLMFSyfctYDMPVVMSRFFGIYGPrqsIEKAIPKFILKIL 192
                    ***********9998469*********999***************************999443333345777999999875556788999999988 PP

                    HH-SEEEE.ESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEE CS
  RmlD_sub_bind 168 kereelkv.vaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagadseevk 239
                    +++ ++      q +   ++ d A++ ++l  +      + +v  ++   e++ +++A++il+ +++d   +k
     AJA93037.1 193 NNEPPVVYgDGKQSRDYMYVTDAADAYAKLGVANDV---DGQVINIGTGTELTIADLAQKILDLMNSD---LK 259
                    666665441556888899999999999998665554...47788888888999999999999998874...34 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.1e-11   1.2e-07       1     129 [.       7     152 ..       7     156 .. 0.75
   2 ?   -3.2   0.0       3.2   6.5e+03     164     182 ..     237     255 ..     224     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.1e-11
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHH.HC.HHHH.CTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.........HHHH...... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpe.kl.aele.aeeglevvegdvtdvedlaealkgadaVvsalggggk.........deeg...... 77 
                     GA G + + ++++l++ g  +vtalvR+ +  + ++++  + +l++  g+++d + l +  k++d+++  +++++          +         
      AJA93037.1   7 GADGFIPSFVCDRLVELG-ANVTALVRRNSsNViKSIPhLKTHLKIRWGEISDLSLLVQETKDTDIIYHLGAQSHVqyslhnpleT--Yvtntvg 98 
                     9****************5.******99744133255552238999999*******************9999777766666555440..1566667 PP

                     HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCC...HHHHHHHHHHHH CS
  NAD_binding_10  78 aknivdaakeagvkRfvlvsaigvgdevpgefgewnkell...kaylaakraaee 129
                     ++n+++aa+ ++v+++v  +++ v+   p++++ + ++ l   ++y+a k a+++
      AJA93037.1  99 TANVLEAARINDVRKIVHAGSAEVYG-KPNKVPITEDNELvprSPYAAGKVASDR 152
                     ************************95.5666665555433233455566666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                     ---EEEHHHHHHHHHHHCT CS
  NAD_binding_10 164 kggsisradVAdvlvavld 182
                     +g++ + ad+A+ ++++++
      AJA93037.1 237 TGTELTIADLAQKILDLMN 255
                     4566777777777777765 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00081       1.6       1      35 [.       5      37 ..       5      49 .. 0.90
   2 !   21.3   0.1   6.2e-08   0.00012      85     198 ..      66     165 ..      58     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00081
                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHH CS
  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksge 35
                   +TGa GF+ +++  +L++  +  ++++lvR +s++
     AJA93037.1  5 VTGADGFIPSFVCDRLVELGA--NVTALVRRNSSN 37
                   7******************99..7******98875 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.2e-08
                    HHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHH CS
  NAD_binding_4  85 aeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntYe 177
                    ++ +d+i+h +A+ ++++++++    + +N+ Gt +vle a+ ++  + ++h  +a v+g+ ++ v                 +++++      Y 
     AJA93037.1  66 TKDTDIIYHLGAQSHVQYSLHNpleTYVTNTVGTANVLEAAR-INDVRKIVHAGSAEVYGKPNK-V---------------PITEDNELVPRSPYA 144
                    5889*****************94445668**********999.556657777777766666662.2...............233334444444555 PP

                    HHHHHHHHHHHHHHHHH---E CS
  NAD_binding_4 178 qsKalaEklvrearrrsglpv 198
                      K+++++l+ +++   ++pv
     AJA93037.1 145 AGKVASDRLMFSYFCTYDMPV 165
                    555555555555555555555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.5e-06    0.0091       1      73 [.       3      77 ..       3      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.5e-06
                EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEE.E.ES-TT-HHHHHHHHTT-SEEEE--- CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvel.v.kgdlddkeslvealkgvdvvfsvtg 73
                +lv+Ga G + ++v + l++ g +v alvR  +s+++ks+ +    l +  g++ d ++lv+  k+ d ++   +
  AJA93037.1  3 VLVTGADGFIPSFVCDRLVELGANVTALVRRNSSNVIKSIPHLKTHLkIrWGEISDLSLLVQETKDTDIIYHLGA 77
                79*************************************988776663467888888888888888887776655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   9.8e-06      0.02       2      46 ..       2      47 ..       1      68 [. 0.81
   2 ?   -2.9   0.0       1.9   3.8e+03     146     160 ..     140     154 ..     135     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.8e-06
                EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHH CS
   adh_short  2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelke 46
                 vlvtGa++ I   ++++l++ Ga+v++ v r+++++ + + +lk 
  AJA93037.1  2 NVLVTGADGFIPSFVCDRLVELGANVTAlVRRNSSNVIKSIPHLKT 47
                59**************************788887777665555554 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                 BHHHHHHHHHHHHHH CS
   adh_short 146 vaaYsAsKaavaglt 160
                  ++Y+A K a + l+
  AJA93037.1 140 RSPYAAGKVASDRLM 154
                 579*****9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2242.23
//
Query:       AJA93038.1  [L=325]
Description: luciferase-like monooxygenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-56  190.1   0.0    7.6e-56  189.8   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.0   4.2e-60   7.6e-56      20     313 ..      12     296 ..       2     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 4.2e-60
  Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpavee 114
                      s+++++e+ r++ e + +  w++e++g     ++ f++l+ ++ + +  ++g+++ ++y+r+P ++A+ a t+d +s+GR++lglgt++ +++e
      AJA93038.1  12 LSIEEVLECSRKLNEIKPEVEWIPETWG-----MENFSMLGLASKENTFSKIGSSIINIYSRSPSLIAMGASTVDTISNGRLILGLGTSSVPIVE 101
                     58999***********************.....9************************************************************* PP

  Bac_luciferase 115 rrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlrag 209
                       +G ++d++++r++E+ve++r +++ge+++++G+ f++k++ ll +p  ++iP+y+aa + +++e+++ +adg+++ + p  e++e+i +++  
      AJA93038.1 102 NFHGNSFDAPVQRMKEYVEIIRLALQGEKINYSGKIFTLKDFSLLTKPIRKEIPIYLAAINQKMVEMTWDIADGVIFYLRPKNEMKETISKMQ-- 194
                     *********************************************************************************************.. PP

  Bac_luciferase 210 aaeagrdpadirvgisltvivadteeeAraea...raliagld.fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqv 300
                        + +   +i++++++ +++ ++ee+ r +a   + +++ +   y++  +  g+ +e + i ee+++n+ +g ++++p+++++ ++++Gtp+++
      AJA93038.1 195 ---RKK---KIDTALQIITCIHEDEEKSRNRAkktLSFYIAVGkIYREFLQSTGYSDEVKIINEEYKKNGLDGLQELIPEKMLDDLCIAGTPATA 283
                     ...466...9**********************666555544449*************************************************** PP

  Bac_luciferase 301 aerlaayaeagvd 313
                     +++l+a+++ g+d
      AJA93038.1 284 VKKLDAFRDVGID 296
                     ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2400.99
//
Query:       AJA93039.1  [L=386]
Description: ATPase, AAA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-12   48.4   0.0    5.6e-12   46.2   0.0    2.0  2  AAA        ATPase family associated with various cellular act
    1.7e-07   31.1   0.0    2.7e-07   30.5   0.0    1.3  1  RuvB_N     Holliday junction DNA helicase RuvB P-loop domain
    1.3e-05   25.3   0.0      5e-05   23.4   0.0    2.1  2  AAA_14     AAA domain
    0.00021   21.6   0.2      0.063   13.5   0.1    2.9  3  AAA_22     AAA domain
     0.0013   18.6   0.0     0.0039   17.1   0.0    1.9  1  Rad17      Rad17 P-loop domain
     0.0029   18.0   0.0     0.0065   16.9   0.0    1.6  1  AAA_16     AAA ATPase domain
     0.0032   17.0   0.0     0.0058   16.2   0.0    1.5  1  AAA_7      P-loop containing dynein motor region
     0.0077   16.4   0.0      0.032   14.4   0.0    2.0  2  AAA_2      AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.026   13.8   0.0    1.6  1  AAA_8      P-loop containing dynein motor region D4
      0.014   15.6   1.3      0.055   13.6   0.0    2.6  3  RFC1       Replication factor RFC1 C terminal domain
      0.017   15.7   0.0      0.055   14.0   0.0    1.9  1  AAA_18     AAA domain
      0.035   13.5   0.2          9    5.7   0.0    3.0  3  TniB       Bacterial TniB protein
      0.051   14.0   0.0       0.11   12.9   0.0    1.6  1  AAA_17     AAA domain
      0.051   13.3   0.0       0.11   12.2   0.0    1.6  1  AAA_24     AAA domain
      0.061   13.3   0.1       0.26   11.3   0.1    2.0  2  AAA_5      AAA domain (dynein-related subfamily)
      0.078   12.5   1.0        0.2   11.2   0.2    2.0  2  DUF2067    Uncharacterized protein conserved in archaea (DUF2
       0.11   11.7   0.0       0.32   10.1   0.0    1.7  2  TIP49      TIP49 P-loop domain
       0.11   12.2   0.1       0.38   10.5   0.0    1.8  2  IstB_IS21  IstB-like ATP binding protein
       0.18   11.7   0.5       0.93    9.4   0.1    2.2  2  NTPase_1   NTPase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0     6e-15   5.6e-12       1     108 [.      39     131 ..      39     146 .. 0.85
   2 ?   -1.2   0.0       2.6   2.5e+03      28      55 ..     174     200 ..     139     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 6e-15
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgv 96 
                 +ll+GppG+GKT+l+    k++g +++++++s+++      ++k+i+e+++ +  ++   +   +fiDE+d +++++       +   v++L++ l++ 
  AJA93039.1  39 LLLVGPPGIGKTTLCFLAGKQFGYDMISLNASDVR------NKKNIQEILTPVLGNQtvlGEPMIFIDEVDGIHGRS-------DYGGVEALINILKEP 124
                 69*********************************......88*********86666688789***********999.......666788888888887 PP

                 TTSSSTEEEEEE CS
         AAA  97 kkkeskviviga 108
                 +       +++a
  AJA93039.1 125 TV-----PIVLA 131
                 66.....34444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                 EEETTTCSSSSTTHHHHHHHHHHHHHHH CS
         AAA  28 eisgsellskyvgesekkirelfkeake 55 
                 +i+  +l+ k++ +s+ +ir ++++a++
  AJA93039.1 174 KINPGRLI-KLITDSKGDIRSMINSAQA 200
                 45555556.6999999999999998875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.9e-10   2.7e-07       2      97 ..       8     106 ..       7     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.9e-10
      RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnl.eekd.....vlfideih 94 
                 rP+++ + +g e+v++++   +e   k ++    +ll+GpPG+Gkttl+ +  k++g ++ +  +  + +++++  +lt +  ++      ++fide+ 
  AJA93039.1   8 RPQNIFDMVGNEDVRKQF---VEWFGKWKKGTKPLLLVGPPGIGKTTLCFLAGKQFGYDMISLNASDVRNKKNIQEILTPVlGNQTvlgepMIFIDEVD 103
                 9**************996...55555666667778*******************************************975134441111257999987 PP

      RuvB_N  95 rls 97 
                  ++
  AJA93039.1 104 GIH 106
                 654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.3e-08     5e-05       3      77 ..      37     106 ..      35     157 .. 0.75
   2 ?   -2.2   0.0       4.2   3.9e+03      30      58 ..     233     259 ..     222     299 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.3e-08
      AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                 k+l+++G+  +GKTtl++   k+      +++ +n  d r+kk+ ++  +l+ +l + +  ++ ++f+DE+  + 
  AJA93039.1  37 KPLLLVGPPGIGKTTLCFLAGKQFG---YDMISLNASDVRNKKNIQE--ILTPVLGNQTVLGEPMIFIDEVDGIH 106
                 789***************9998888...9999999999999875544..555555543335899*******8774 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
      AAA_14  30 kesilyinldderdkkladpekllelile 58 
                 + +i+ ++l  ++ +k++ +  + ++i +
  AJA93039.1 233 EARIVLFSLRIDPREKINAF--YSSIITS 259
                 55555555554444444433..2222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   6.7e-05     0.063       5      29 ..      36      60 ..      33      88 .. 0.74
   2 ?    4.9   0.0     0.031        29      85     132 ..      85     135 ..      62     140 .. 0.73
   3 ?   -0.6   0.0       1.6   1.5e+03      79     114 ..     253     294 ..     161     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
      AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                 + l+++G++G+GKTtl+    +q+
  AJA93039.1 36 TKPLLLVGPPGIGKTTLCFLAGKQF 60
                67799************97777666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.031
      AAA_22  85 alrarav..ielliiDEaqhlr..s.eealeeLrsllnlsrkgvqliLvGtpe 132
                  l ++ v   +++ iDE++ +   s    +e L ++l+  +  v+++L+G ++
  AJA93039.1  85 VLGNQTVlgEPMIFIDEVDGIHgrSdYGGVEALINILK--EPTVPIVLAGNYD 135
                 444444466789*********76537888888888899..**********985 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
      AAA_22  79 l.ealeqalrarav.ielliiDEaqhlr....seealeeLrs 114
                 + + ++ +l++ ++ ++l ii Ea+ l     + ++++ Lr 
  AJA93039.1 253 YsSIITSNLSSEKMsKALEIISEADMLYgkimKTQNWRLLRY 294
                 445566666666666777888888888654433455555544 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.1e-06    0.0039       8      87 ..       2      77 ..       1      91 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
       Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn 87
                 W eky+P+   ++       ++  ew+          + LL+ GP+G gk+t      k++g++++  ln+  +++ +n
  AJA93039.1  2 MWSEKYRPQNIFDMVGNEDVRKQFVEWFGKWKKG---TKPLLLVGPPGIGKTTLCFLAGKQFGYDMIS-LNASDVRNKKN 77
                599*******999977666666666776544333...4479999**********99999*****9985.67777676666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   6.9e-06    0.0065       5      50 ..      18      62 ..      15      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.9e-06
      AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralek 50
                 e+ ++q+ + ++++++g+   +ll+G++G+GK++l   + +++  
  AJA93039.1 18 NEDVRKQFVEWFGKWKKGT-KPLLLVGPPGIGKTTLCFLAGKQFGY 62
                5666677777788888887.7999************8665555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.2e-06    0.0058      30      88 ..      33      88 ..      18     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
       AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklek 88
                 k  kp+llvGp G GKt+++    k++    y ++++n s   + +++q+i+   l  
  AJA93039.1 33 KKGTKPLLLVGPPGIGKTTLCFLAGKQFG---YDMISLNASDVRNKKNIQEILTPVLGN 88
                56789***************988777777...********************9877765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.3e-05     0.032       6      91 ..      39     109 ..      36     150 .. 0.82
   2 ?   -1.5   0.0       2.5   2.4e+03     124     140 ..     256     272 ..     253     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                 EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG------------ CS
       AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpkessgadvS 91 
                 +ll+gp g+Gkt l     +         +i ++as++      ++ +++ +    g++ +  + ++++DE+d ih +       S
  AJA93039.1  39 LLLVGPPGIGKTTLCFLAGKQFG----YDMISLNASDVRN----KKNIQEILTPVLGNQTVLGEPMIFIDEVDGIHGR-------S 109
                 5899********98765555555....49***********....999999999889999999999***********93.......2 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                 EEEE--TTHHHHTTTS- CS
       AAA_2 124 Imtgafgsskisdesrs 140
                 I+t+++ s+k s++ ++
  AJA93039.1 256 IITSNLSSEKMSKALEI 272
                 89999999999996554 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.8e-05     0.026      27     150 ..      39     166 ..      33     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
       AAA_8  27 aLlvGvgGsGrqsltkLAafiaelelfqievtkkykekefredlkkllkkagikqkevvfllsdnqiiees...fledinnlLntGevpnLf.skeeke 121
                 +LlvG  G G+ +l+ LA    ++++++++ +   ++k+ +e l  +l +  + +++++f+ + + i   s    +e + n+L++ +vp ++  + +  
  AJA93039.1  39 LLLVGPPGIGKTTLCFLAGKQFGYDMISLNASDVRNKKNIQEILTPVLGNQTVLGEPMIFIDEVDGIHGRSdygGVEALINILKEPTVPIVLaGNYDST 137
                 79**********************************************************988888865441115788888888888887772334556 PP

       AAA_8 122 eiieelrkeakkqgvedskesllnffikr 150
                 + +++++k +k+ + +  + ++l+++++ 
  AJA93039.1 138 DKMKKIKKVVKTLQLSPLSPRFLKLYLNM 166
                 66677777777766666666666666665 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.3   2.2e+03      37      57 ..      17      37 ..       6      38 .. 0.71
   2 ?   -1.7   0.1         3   2.8e+03     132     149 ..     132     149 ..     121     152 .. 0.78
   3 ?   13.6   0.0   5.9e-05     0.055       1      23 [.     273     295 ..     273     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                EE-SS-----SHHHHHHHHHH CS
        RFC1 37 gslegrisFpswLGknSktnK 57
                g+   r +F +w+Gk  k +K
  AJA93039.1 17 GNEDVRKQFVEWFGKWKKGTK 37
                44444889*******877665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3
                 XXXXXXXXXXXXXXXXXX CS
        RFC1 132 gekkkedplkkidtkvKa 149
                 g++++ d++kki++ vK+
  AJA93039.1 132 GNYDSTDKMKKIKKVVKT 149
                 567788888999888887 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.9e-05
                 HHHHHHHHHHHTTSS-GGGHHHH CS
        RFC1   1 isdgDlvdkkirseqnWsLlpth 23 
                 is++D+++ ki ++qnW Ll++ 
  AJA93039.1 273 ISEADMLYGKIMKTQNWRLLRYL 295
                 9*******************984 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-05     0.055       2      36 ..      40      77 ..      39      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
      AAA_18  2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakeng 36
                ll G+pG GKttl+    k  g+   + n +dv  +++
  AJA93039.1 40 LLVGPPGIGKTTLCFLAGKQFGYdmiSLNASDVRNKKN 77
                689***************99988999888877766555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0095         9      35      52 ..      36      53 ..      20      64 .. 0.85
   2 ?    3.5   0.0     0.043        40     116     170 ..      90     141 ..      64     156 .. 0.70
   3 ?    0.2   0.0      0.46   4.3e+02      66      97 ..     232     263 ..     222     293 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0095
        TniB 35 mpnlllvGdsnnGKtmiv 52
                ++ lllvG++ +GKt+++
  AJA93039.1 36 TKPLLLVGPPGIGKTTLC 53
                4679***********997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.043
        TniB 116 relkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralr 170
                   l+  ++ iDE++ +  g  r+    ++al ++  e  +pivl+G  + ++ ++
  AJA93039.1  90 TVLGEPMIFIDEVDGIH-G--RSDYGGVEALINILKEPTVPIVLAGNYDSTDKMK 141
                 555667999****9998.3..334445555556666899******9988776655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.46
        TniB  66 daekvpvlvvqappkpdekrlyaaiLealgap 97 
                 +++++ ++ +++ p+ + +++y++i+++    
  AJA93039.1 232 EEARIVLFSLRIDPREKINAFYSSIITSNLSS 263
                 4555666667788888999*****99864444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.11       1      25 [.      42      66 ..      42      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                EE-TTSSHHHHHHHHHHHHTEEEEE CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthls 25
                +G+PG GK+t+c    +++g+ ++s
  AJA93039.1 42 VGPPGIGKTTLCFLAGKQFGYDMIS 66
                7***********6666889999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.11       5      22 ..      39      56 ..      36      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
      AAA_24  5 iliyGpsgiGKTtlakel 22
                +l++Gp+giGKTtl+  +
  AJA93039.1 39 LLLVGPPGIGKTTLCFLA 56
                689***********9887 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00027      0.26       1      16 [.      38      53 ..      38      69 .. 0.91
   2 ?   -1.4   0.0       2.2   2.1e+03      68      78 ..      96     106 ..      72     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                EEEEE--SSSSHHHHH CS
       AAA_5  1 dvlLvGppGtgKsela 16
                ++lLvGppG+gK++l 
  AJA93039.1 38 PLLLVGPPGIGKTTLC 53
                58***********985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                 EEEEESGGG-- CS
       AAA_5  68 ilvlDEverae 78 
                 ++++DEv+ ++
  AJA93039.1  96 MIFIDEVDGIH 106
                 46788887766 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00022       0.2      44      94 ..     134     185 ..     118     203 .. 0.89
   2 ?   -1.3   0.0       1.4   1.3e+03      99     126 ..     250     275 ..     246     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
     DUF2067  44 keikdiirrikellre.klkkekrglfkyslsdllreagapvppdvLvdaLk 94 
                 +++ d +++ik+++++ +l++ + ++ k+ l+++l + +a+++p  L++++ 
  AJA93039.1 134 YDSTDKMKKIKKVVKTlQLSPLSPRFLKLYLNMILEKENAKINPGRLIKLIT 185
                 67788899************************************99999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
     DUF2067  99 kaelreenvlktnapleevvelaerlse 126
                 +a ++  +++++n + e+  + +e +se
  AJA93039.1 250 NAFYS--SIITSNLSSEKMSKALEIISE 275
                 33333..455555555555555555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034      0.32      26      89 ..      15      73 ..       5      89 .. 0.76
   2 ?   -2.5   0.0       2.4   2.2e+03     136     189 ..     139     194 ..     125     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 26 lvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevy 89
                +vG ++ r+    +ve   + k + + +Ll+Gp+g Gkt l     k++g d   ++l++s+v 
  AJA93039.1 15 MVGNEDVRKQ---FVEWFGKWKKGTKPLLLVGPPGIGKTTLCFLAGKQFGYD--MISLNASDVR 73
                6666666664...4555555566889***********************965..5788999884 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                 ..TTS--EEEEEE-SS.-EEEEEE-HHHHHHHHHHT--TT-EEE.EETTT--EEE- CS
       TIP49 136 kekkikevkitlktak.eekklklgskiaeellkekvkegDviv.iekesGkvkkl 189
                 k kkik+v  tl+ +    + lkl  +++ e ++ k++ g +i  i  ++G ++ +
  AJA93039.1 139 KMKKIKKVVKTLQLSPlSPRFLKLYLNMILEKENAKINPGRLIKlITDSKGDIRSM 194
                 44445554444544331335567777777777777788887775255566777655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.38      42      66 ..      31      55 ..      13      70 .. 0.84
   2 ?   -2.1   0.0       2.9   2.8e+03     142     158 ..     254     270 ..     243     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
   IstB_IS21 42 sfiekkenivllGpsGvGKshlaia 66
                ++ +  + ++l+Gp+G+GK+ l   
  AJA93039.1 31 KWKKGTKPLLLVGPPGIGKTTLCFL 55
                677888899***********99764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.9
   IstB_IS21 142 siiitsnlpfaewdevl 158
                 s iitsnl+ ++ ++ l
  AJA93039.1 254 SSIITSNLSSEKMSKAL 270
                 67999999988877655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00098      0.93       3      21 ..      40      58 ..      38      78 .. 0.74
   2 ?    0.4   0.0      0.55   5.2e+02      78     129 ..      75     129 ..      55     155 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                EEE--TTSSHHHHHHHHHH CS
    NTPase_1  3 fiTGppGvGKtTlvkkvle 21
                ++ GppG+GKtTl+  + +
  AJA93039.1 40 LLVGPPGIGKTTLCFLAGK 58
                688**********976655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.55
                 HHHHHHHHHHHHHHHH.HHH-EEEE---STTGGG-H.HHHHHHHHHHT.TTSEEE CS
    NTPase_1  78 vesfeelalealrkal.seadviviDEiGkmElksk.kfkeaveevLk.sekpvl 129
                  ++++e+  ++l ++   ++ +i iDE+  +   s     ea+ ++Lk + +p++
  AJA93039.1  75 KKNIQEILTPVLGNQTvLGEPMIFIDEVDGIHGRSDyGGVEALINILKePTVPIV 129
                 4568888999998887556669999998554444431445556666664444554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2368.29
//
Query:       AJA93040.1  [L=126]
Description: hypothetical protein T478_1494 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 906.11
//
Query:       AJA93041.1  [L=443]
Description: ThiF family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-67  224.9   0.2    1.4e-66  224.3   0.2    1.2  1  ThiF             ThiF family
    2.7e-10   40.8   0.0      1e-09   38.9   0.0    2.0  2  ThiS             ThiS family
    2.8e-05   24.4   2.9    0.00038   20.7   2.9    2.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0035   17.4   0.2      0.015   15.4   0.1    2.0  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0055   17.1   0.2      0.016   15.7   0.2    1.7  1  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.017   14.7   0.2       0.32   10.6   0.1    2.3  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.052   12.9   0.0      0.095   12.1   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.3   0.2   5.6e-70   1.4e-66       2     240 ..     104     335 ..     103     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 224.3 bits;  conditional E-value: 5.6e-70
                 HHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CC CS
                 xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF   2 srqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavterit 98 
                 srq++l  +g dgq kL++skv++vG+GglG+++ + La +Gvgkl++vD D+ielsNl+Rq +f e+d+G+ K+eva+++l+++np+ve+ea++ +i+
  AJA93041.1 104 SRQVMLeqIGYDGQLKLKNSKVCVVGVGGLGNPITTRLATMGVGKLRIVDRDVIELSNLHRQTMFDEDDVGQVKVEVAQKKLKKLNPEVEIEALPISIN 202
                 68877788999**************************************************************************************** PP

                 GCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  99 detvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplctsiagnipaiatttavva 197
                 d + + +++ ++D+V+dalD++ ar+++n+acv+k ip+++++++g+ gqv++++p++t+cy+C++p    + +e+  p+c si g   +  +++++v+
  AJA93041.1 203 DYN-ASDVIDGCDVVIDALDSVNARYALNKACVEKNIPFVTGAAVGVTGQVFTVLPKETACYHCMFP----TLDEDAMPTC-SIQG---VHPPILSIVG 292
                 *65.57************************************************************9....8889999***.****...********** PP

                 HHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 198 glaalellkllsgkeklenslltqvdllesrfenvelerakks 240
                 g+ + e++ +l gk++++ +++  +dl++  f++v+  ++  +
  AJA93041.1 293 GIEVYEAVDVLIGKKPKSSEKFISIDLENLEFSSVRTFKQDAC 335
                 ***********999999999999************99887654 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   3.9e-13     1e-09      13      77 .]      17      92 ..      10      92 .. 0.88
   2 ?   -2.7   0.0       3.8   9.7e+03      21      35 ..     213     227 ..     201     241 .. 0.66

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.9e-13
                CEEEEESSTSBHHHHHHHHHHHTCHHG..........TTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS 13 eeelelaegstvaelleaLgerypela..........lerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                 e+  + e+st++e +e+++e  +  +           +  +++++Ng+++ + ++ldt+l+++Dev ilp+VaGG
  AJA93041.1 17 GEKKTELEASTLKESFEKISEIMGDDFkrkvleadgsPRSLINIYINGKNAAFdNGLDTPLNENDEVYILPAVAGG 92
                5677788999999999999777766667999999**999**************88********************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                 TSBHHHHHHHHHHHT CS
        ThiS  21 gstvaelleaLgery 35 
                  + v ++l+++++ry
  AJA93041.1 213 CDVVIDALDSVNARY 227
                 556777788888877 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   2.9   1.5e-07   0.00038       1     101 [.     125     245 ..     125     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE--TTTHHHHHHHHHTTSS CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaialdaenyeavLaallkegd 71 
                      v ++G G+ G +++  la  +    ++ ++dr+  +l +l  ++                        +v++ea  + +++y a  + ++ + d
       AJA93041.1 125 VCVVGVGGLGNPITTRLATMGVG--KLRIVDRDVIELSNLHRQTmfdeddvgqvkvevaqkklkklnPEVEIEALPISINDYNA--SDVIDGCD 214
                      6799**************99876..99*********9999999999*****************997777888888888888888..9******* PP

                      EEEE-SSGG.GHHHHHHHHHHHT-EEEESS- CS
  Sacchrp_dh_NADP  72 lvvnlsppi.ssldvlkaCietgvhyvdtsi 101
                      +v++++ ++    ++ kaC+e+ + +v+ + 
       AJA93041.1 215 VVIDALDSVnARYALNKACVEKNIPFVTGAA 245
                      *********7777**************9443 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.8e-06     0.015       9      56 ..     119     166 ..     113     189 .. 0.82
   2 ?   -1.0   0.0      0.67   1.7e+03      50      87 ..     186     224 ..     173     237 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.8e-06
                   ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
  Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                   +lk++kv+++G G +++ +++ L++ gv k+ ++ R++   ++l ++ 
    AJA93041.1 119 KLKNSKVCVVGVGGLGNPITTRLATMGVGKLRIVDRDVIELSNLHRQT 166
                   6899*********************************99998887765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                   HHHHHHHT.ET-EEEEGCGH..HHHHHT-SEEEE-SSSSS CS
  Shikimate_DH  50 kelaeelkgeeiealkleel..kellaeadvvisatasee 87 
                   k+l  e+ + e+  ++++++  +++++ +dvvi a  s +
    AJA93041.1 186 KKLNPEV-EIEALPISINDYnaSDVIDGCDVVIDALDSVN 224
                   4444444.22233344444411568999999999987755 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   6.1e-06     0.016       3      89 ..     118     240 ..     117     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.1e-06
  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele.........................elvklaeeelekd.............. 58 
                    l+lk+ kv+vvG G ++     +l+  g  k+ +v+ +v e ++                         +                          
     AJA93041.1 118 LKLKNSKVCVVGVGGLGNPITTRLATMGvGKLRIVDRDVIELSNlhrqtmfdeddvgqvkvevaqkklkK-----------Lnpeveiealpisin 202
                    6899**********************9977********85554466666666677755444444433330...........123333333333333 PP

  NAD_binding_7  59 .......legadlviaatddrelneriaeaakarrilv 89 
                           ++g d+vi a d  + + ++ +a+ +++i++
     AJA93041.1 203 dynasdvIDGCDVVIDALDSVNARYALNKACVEKNIPF 240
                    3444445************************9999986 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00012      0.32       2      52 ..     124     174 ..     123     200 .. 0.78
   2 ?    1.6   0.0     0.072   1.8e+02      45     118 ..     347     419 ..     340     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                     EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHH CS
  UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLe 52 
                     k++v+G G +G +  + la +g  ++ +vD d    ++l+++   + e +  
      AJA93041.1 124 KVCVVGVGGLGNPITTRLATMGvGKLRIVDRDVIELSNLHRQT-MFDEDDVG 174
                     8*********************7789999*9999888887654.34555544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.072
                     SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEE CS
  UDPG_MGDP_dh_N  45 piyepgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvv 118
                     p  e  Leel  +++ ++ +s t  +e +++ adv+ +a    +k  +++ Dl   +++ +   +++kkg+ vv
      AJA93041.1 347 PKQELILEELCGRNMGKRTFSITPTYEVNLDVADVTALAQEKGFKV-ENQGDLGLSMRTNDLSVNFMKKGSAVV 419
                     5567779999*****999999999***************9999999.777799999888888888888866666 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05     0.095      31      68 ..     117     155 ..      97     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                   BS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSS CS
  2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrs 68 
                   + +l++++v+++G+G +G+ +  rl+ +g+ k+ ++dr 
    AJA93041.1 117 QLKLKNSKVCVVGVGGLGNPITTRLATMGVgKLRIVDRD 155
                   4489*************************9888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3220.72
//
Query:       AJA93042.1  [L=144]
Description: acetyltransferase (GNAT) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-15   55.1   0.0    9.2e-15   54.9   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-13   51.3   0.0    1.2e-13   51.1   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    4.8e-10   39.7   0.1    7.4e-10   39.1   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.2e-05   23.6   0.0    6.3e-05   23.0   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    0.00045   20.3   0.0    0.00056   20.0   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00059   19.7   0.1      0.002   18.0   0.1    1.8  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   3.1e-18   9.2e-15      20     117 .]      36     133 ..      13     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.1e-18
                     HHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHH CS
  Acetyltransf_1  20 seeefeesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairl 111
                      +++ +++  +++  + +ae +g+++G  +l+  +      g+v++ie+++Vs+e+ g+G+G +L+  l+e+a+  +++k  l++ +     i++
      AJA93042.1  36 ALDILKKIIGNPDHIIHIAEIEGKIVGSTTLFVEQKfihDGGKVGHIEDVVVSKEFEGRGIGMKLVVSLLEKAEAMNCYKTILDCKKEL---IPF 127
                     333344454444446666*********************99*************************************77788776666...*** PP

                     HHHTTE CS
  Acetyltransf_1 112 YeklGF 117
                     Ye+ GF
      AJA93042.1 128 YERIGF 133
                     *****9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0     4e-17   1.2e-13      22     112 ..      40     139 ..      24     144 .] 0.89

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4e-17
  Acetyltransf_10  22 lrerieegealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklG 105
                      l++ i ++++++++ae +gkivG  +l  +++         hi+ ++V++e+ g+Gig +L+  ++e+ae ++   ++ ++ +++ +pfYe++G
       AJA93042.1  40 LKKIIGNPDHIIHIAEIEGKIVGSTTLfVEQKfihdggkvgHIEDVVVSKEFEGRGIGMKLVVSLLEKAEAMNCY-KTILDCKKELIPFYERIG 132
                      56667899*****************9976666799999*******************************999777.****************** PP

  Acetyltransf_10 106 Fkavgee 112
                      Fk+ +++
       AJA93042.1 133 FKQESNQ 139
                      **98554 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   2.5e-13   7.4e-10       2      75 ..      48     134 ..      47     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.5e-13
                     TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.H...TT.SEEE...EE.EEEETHHHHHHHHHHTTEE CS
  Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.a...ae.kgii...le.qlelnaekaikfYeklGFe 75 
                     ++ +++ae +gkivG   l +++         ++i+ ++V++e+ g+GiG +L+  +   ae  ++    l  + el     i+fYe+ GF+
      AJA93042.1  48 DHIIHIAEIEGKIVGSTTLFVEQkfihdggkvGHIEDVVVSKEFEGRGIGMKLVVsLlekAEaMNCYktiLDcKKEL-----IPFYERIGFK 134
                     677999*********9999999899999988778888****************963244311333332222333445.....99*******8 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.1e-08   6.3e-05      20      58 ..      75     113 ..      53     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.1e-08
  Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                      ++++v +++ ++V++e++G+Gi++kLv + l++a++ + 
       AJA93042.1  75 DGGKVGHIEDVVVSKEFEGRGIGMKLVVSLLEKAEAMNC 113
                      5666789999************************99774 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.9e-07   0.00056      41     126 ..      48     134 ..       8     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                     TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--..SSHHHHHTTT-E CS
  Acetyltransf_9  41 esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP..ssipiYrrfGye 126
                     ++ +++ae +g++vg+ +l+  +  +++   k++ + +V v  e  grg+  kL+  +le++++++   ++l      ip+Y+r G++
      AJA93042.1  48 DHIIHIAEIEGKIVGSTTLFVEQKFIHDG-GKVGHIEDVVVSKEFEGRGIGMKLVVSLLEKAEAMNCYKTILDCkkELIPFYERIGFK 134
                     57899999*********999777777764.489*********************************9999999965448*******97 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   6.8e-07     0.002      21      84 ..      79     140 ..      70     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.8e-07
                 TSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEEE CS
        FR47  21 ggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekieete 84 
                 +g +  + v +e+++rG g +lv +l ++  + +   ++      ++ i +ye++Gf++  +++
  AJA93042.1  79 VGHIEDVVVSKEFEGRGIGMKLVVSLLEKAEAMNCYKTI--LDCKKELIPFYERIGFKQESNQM 140
                 699999********************9997775444444..444567899*******9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1080.64
//
Query:       AJA93043.1  [L=50]
Description: nucleolar RNA-binding protein, Nop10p family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   81.9   3.8    2.5e-23   81.8   3.8    1.0  1  Nop10p    Nucleolar RNA-binding protein, Nop10p family
    0.00031   18.8   0.7    0.00031   18.8   0.7    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.013   15.1   1.5      0.016   14.8   1.5    1.2  1  RecR      RecR protein
        4.8    7.8   7.1        5.2    7.7   1.5    2.3  2  zf-C2H2   Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   3.8   5.7e-27   2.5e-23       1      49 [.       1      49 [.       1      50 [] 0.98

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 5.7e-27
                .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHCH CS
      Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRralK 49
                m+++lrkc++c++YTLk++c +c + tks hPa+FSPdD+y +yR+a K
  AJA93043.1  1 MRFQLRKCTECGEYTLKETCKKCDKSTKSVHPAKFSPDDRYLRYRIAEK 49
                9*********************************************998 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.7     7e-08   0.00031     616     643 ..       3      30 ..       1      44 [. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7e-08
    PolC_DP2 616 iarrkCkkCgketlearCeeCgekteek 643
                 ++ rkC++Cg+ tl+ +C++C+++t+++
  AJA93043.1   3 FQLRKCTECGEYTLKETCKKCDKSTKSV 30 
                 6789*********************985 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.5   3.5e-06     0.016      15      36 ..       4      25 ..       1      27 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                H-EE-TTT--EESSSS-CCCCS CS
        RecR 15 kvrhCsrCgnlteedlCaICsd 36
                ++r C +Cg +t ++ C  C  
  AJA93043.1  4 QLRKCTECGEYTLKETCKKCDK 25
                789***************9975 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.4     0.026   1.2e+02       2       8 ..       7      13 ..       7      17 .. 0.85
   2 ?    7.7   1.5    0.0012       5.2       2      12 ..      19      29 ..      19      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.026
                EETTTTE CS
     zf-C2H2  2 kCpdCgk 8 
                kC++Cg+
  AJA93043.1  7 KCTECGE 13
                7****95 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                EETTTTEEESS CS
     zf-C2H2  2 kCpdCgksFkr 12
                +C++C+ks k+
  AJA93043.1 19 TCKKCDKSTKS 29
                7*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 308.68
//
Query:       AJA93044.1  [L=244]
Description: hypothetical protein T478_1013 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0049   17.2   5.0     0.0049   17.2   5.0    4.0  2  THOC7           Tho complex subunit 7
  ------ inclusion threshold ------
      0.079   12.3  22.1          1    8.7   0.8    2.1  2  DUF4407         Domain of unknown function (DUF4407)
       0.29   11.4  24.6       0.55   10.5   7.5    3.4  4  FliJ            Flagellar FliJ protein
        0.5   10.1  21.9       0.58    9.9  14.2    2.5  3  DUF745          Protein of unknown function (DUF745)
       0.52   10.4   4.1         17    5.5   0.1    2.6  2  T2SSM           Type II secretion system (T2SS), protein M
       0.56   10.5  38.8         19    5.6  16.6    3.0  3  OmpH            Outer membrane protein (OmpH-like)
       0.94    9.2  39.8        1.9    8.2  26.8    2.1  2  ERM             Ezrin/radixin/moesin family
        1.3    7.4   7.2       0.92    7.9   1.3    2.6  3  Corona_S2       Coronavirus S2 glycoprotein
        2.2    7.5  22.6       0.78    9.0   8.5    2.1  2  CorA            CorA-like Mg2+ transporter protein
        2.8    8.1  15.8       0.86    9.7   0.5    3.2  3  TolA_bind_tri   TolA binding protein trimerisation
        4.1    8.1  38.6        6.2    7.5   5.9    4.0  4  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        4.6    7.6  42.6       0.93    9.8  15.5    3.1  3  Muted           Organelle biogenesis, Muted-like protein
        4.7    7.4  32.4       0.31   11.2  15.2    3.1  3  ATG16           Autophagy protein 16 (ATG16)
        4.8    7.2  48.6       0.13   12.2   5.6    4.8  5  Prefoldin_2     Prefoldin subunit
        6.5    6.9  11.5        3.6    7.8   3.8    2.8  2  RNase_H         RNase H
        6.5    7.2  37.2        1.5    9.2  25.9    2.2  2  Fez1            Fez1
        7.2    6.7  30.4        1.1    9.4   8.8    3.4  3  DUF1664         Protein of unknown function (DUF1664)
          9    3.7  36.3         18    2.7  36.3    1.4  1  DUF3584         Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   5.0   4.9e-06    0.0049      70     122 ..      33      86 ..      22      98 .. 0.86
   2 ?    1.5   4.7      0.33   3.3e+02      67      99 ..     114     146 ..      97     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.9e-06
       THOC7  70 reryeaekeeieseieavreeieelkaqLee.aratranrkeydelaekItsnp 122
                   ++++ k++ie+eie ++++i+e +++L+    ++  +rkeyde+  kI +++
  AJA93044.1  33 NTNLQKIKDDIEEEIEGLESKIKEKNERLHSiIEKIELSRKEYDEIIGKIIQSK 86 
                 5688999**********************983589999***********99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
       THOC7  67 erereryeaekeeieseieavreeieelkaqLe 99 
                 ++e+ + e++ +ei++ei +  + + el+++++
  AJA93044.1 114 SKEISNSENKLKEIQEEITKNSKINNELEEKIK 146
                 456666666666666666666666666666654 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8     0.001         1     175     240 ..      12      75 ..       4      97 .. 0.67
   2 ?    8.2  15.3    0.0014       1.4     130     258 ..     101     232 ..      75     241 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.001
     DUF4407 175 ttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaad 240
                   g+ G g   k+k + +++ +++l+++k++   +++++ l+++++e ++++++++++ + ++++ 
  AJA93044.1  12 RIGRIGMGLFSKKKSEVAQDTNTNLQKIKDD--IEEEIEGLESKIKEKNERLHSIIEKIELSRKEY 75 
                 4567888999999999999999999999999..555555555555555555444444443333333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
     DUF4407 130 a...........ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalra 217
                 +            ++e+++ e++++++q+ei++ ++  ++l+++ +        +  + v   + + k+ +++l+++++el+ +k++l + ++++++++
  AJA93044.1 101 DvikpnneniekISKEISNSENKLKEIQEEITKNSKINNELEEKIK--------KNAPSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNK 191
                 1333322222223344444444444444444444444444444444........344446666777888888888888888888888889999999999 PP

     DUF4407 218 elaeleaerakeraasqaaaaaddGllarlealdrltkeda 258
                   ++ ++  +++ +   ++++  ++ +++le + +l +++ 
  AJA93044.1 192 GEDDSKNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKER 232
                 99999999999988889999999999999999988887665 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.6      0.13   1.3e+02      57      77 ..      43      63 ..      22     101 .. 0.54
   2 ?    5.4   3.1     0.021        21       4      88 ..      51     130 ..      41     136 .. 0.70
   3 ?   10.5   7.5   0.00056      0.55      15      94 ..     104     178 ..      97     193 .. 0.91
   4 ?    7.6   3.3    0.0042       4.2      64     109 ..     196     241 ..     183     244 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
        FliJ 57 ldeaiaqqkqelaqaekqvek 77
                ++e+i+ ++++++ ++++++ 
  AJA93044.1 43 IEEEIEGLESKIKEKNERLHS 63
                333333333333333333322 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
        FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqe 88 
                 + + +e + +l +  ek+e  +++++e   ++ ++       elr ++   s+ ++ i+   +++++  k++++++++++e + e
  AJA93044.1  51 ESKIKEKNERLHSIIEKIELSRKEYDEIIGKIIQSK-----KELRSLEGSESKSNDVIKPNNENIEKISKEISNSENKLKEIQEE 130
                 567788899999999999999999999977777776.....66666666666666666666666666666666666666555444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00056
        FliJ  15 qqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklek 94 
                 + ++e++e++ +++++ +++l++ +     +e+ + ++  + l+e+i++   +++++e++ +k  ee+ + ++e++ ++k
  AJA93044.1 104 KPNNENIEKISKEISNSENKLKEIQ-----EEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMKK 178
                 5578999******************.....**********************************************9986 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0042
        FliJ  64 qkqelaqaekqvekareewqearqerkklekLkerekkeeqkeenr 109
                  k++++ a + +++  +++q  ++e++ ++ L ++e+k+  +  ++
  AJA93044.1 196 SKNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAHSETKKK 241
                 5899*********************************998776665 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.031        31     115     165 ..      28      78 ..      22     100 .. 0.76
   2 ?    5.3   7.9     0.014        14      75     148 ..     107     180 ..      63     185 .. 0.65
   3 ?    9.9  14.2   0.00058      0.58      65     182 ..     125     241 ..     121     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
      DUF745 115 aakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlekt 165
                  a+++ +n++++++  ++e++  ++ +++ ++R++++ ++++  rk+++++
  AJA93044.1  28 VAQDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIELSRKEYDEI 78 
                 566777777777777777777777777888888888888888888887764 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
      DUF745  75 eavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv 148
                 ++ +++++k++++se+++k  ++  ++  +  + l++ +k+   +++++e+ +++  +el+++++ le  kkR+
  AJA93044.1 107 NENIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMKKRL 180
                 34456666666666666666666666666666666666666666666666666666666666666666666665 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00058
      DUF745  65 eqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdle 163
                 +++++e++  +++ +e ++++++   +++  ++ +k++ ++l++ k+ l+ +k++l +++q++++ + e ++k+  +eaA + + + +k+l++  k+le
  AJA93044.1 125 KEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNKGEDDSKN-VVEAASQIISTTNKRLQDTMKELE 222
                 678999999999999**************************************************999987775.89********************** PP

      DUF745 164 ktkkaAykAacAAqeAkqk 182
                  +++   k  +A +e k+k
  AJA93044.1 223 VIRQLLDKERKAHSETKKK 241
                 ****999999999988887 PP

>> T2SSM  Type II secretion system (T2SS), protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.017        17      35      76 ..     102     143 ..     101     154 .. 0.84
   2 ?    5.4   0.9     0.018        18      41     100 ..     157     213 ..     149     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.017
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       T2SSM  35 lwqPlserieraqaelqklraqlawveeqaaevralraapas 76 
                 +++P +e ie+  +e+ +++++l++++e++++  +++++ ++
  AJA93044.1 102 VIKPNNENIEKISKEISNSENKLKEIQEEITKNSKINNELEE 143
                 799***************************999988854444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.018
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX--HHHHHHHHHHHCT--EEE CS
       T2SSM  41 erieraqaelqklraqlawveeqaaevralr.aapasalsgaaleqvvtrsarqagLalar 100
                 +++++  +el++ +++l+ +++++ e+++++ +++++  s    ++vv+++ +    + +r
  AJA93044.1 157 NEKKKIDEELNQRKKELEIMKKRLVEMKQINsKNKGEDDS----KNVVEAASQIISTTNKR 213
                 567788899*********************9555555444....44444444444444444 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  16.6     0.019        19      13     108 ..      25     120 ..      23     147 .. 0.71
   2 ?    2.8   6.0      0.14   1.4e+02      29      67 ..     111     147 ..     101     160 .. 0.49
   3 ?   -0.7  23.7       1.7   1.7e+03      15     104 ..     132     237 ..     122     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.019
                 HSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  13 espegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle.keekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikevake 108
                 +s+ +++ +++l+k + ++++e+e +e +++++ e+l    +k e +++++ e+  k  + ++   +  +  ++k+++++kp  ++i+k+ ke+   
  AJA93044.1  25 KSEVAQDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIElSRKEYDEIIGKIIQSKK-ELRSLEGSESKSNDVIKPNNENIEKISKEISNS 120
                 67889999999************************9985555542466666664444444444.222226666777777777777777777776653 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                 HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHH CS
        OmpH  29 kklqaeleakekelqklqeelqkkakklekeekeqelqk 67 
                 +k+ +e+ + e++l++ qee+ k++k   ++e e++++k
  AJA93044.1 111 EKISKEISNSENKLKEIQEEITKNSKI--NNELEEKIKK 147
                 455555555555555555555433222..2333333332 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                 HHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHHHHHHHHTTTS....-HHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH  15 pegkaaqeqlekkf..............kklqaeleakekelqklqeelqkkakkl.e..keekeqe.....lqkkeqelqqkqqqkaqelqkkqqell 91 
                 ++  +++++le+k+              kk+++el++++kel+ ++++l + ++ + +       ++     +++  q + +  +++ q+ +k+  e++
  AJA93044.1 132 TKNSKINNELEEKIkknapsvsdsenekKKIDEELNQRKKELEIMKKRLVEMKQINsKnkG----EDdsknvVEAASQIIST-TNKRLQDTMKEL-EVI 224
                 3333344444444444447777777777999999999999999999999865555422432....33344544444444444.555557777777.555 PP

                 HHHHHHHHHHHHH CS
        OmpH  92 kpildkinkaike 104
                 +++ldk +ka +e
  AJA93044.1 225 RQLLDKERKAHSE 237
                 5688888777665 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.2    0.0046       4.6      54     120 ..      24      90 ..      18     110 .. 0.79
   2 ?    8.2  26.8    0.0019       1.9       1     127 [.     111     243 ..     108     244 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
         ERM  54 qkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLkeeleeareaee 120
                 +k + a+  +++l++ + + eee e le k++e++++++ + e+ e   +e ++   ++++ +++++
  AJA93044.1  24 KKSEVAQDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIELSRKEYDEIIGKIIQSKKELR 90 
                 4555677888999999999999999999999999999999999999888888888777777776664 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0019
         ERM   1 eeaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeea....elLeqkaaeaeeeiqrlkesaekeeeekek..lerklreaeleaar 93 
                 e++ +e ++ e++Lk++qee+ k+ +  +e ee++++ a +   +e+e+    e+L+q+++e+e +++rl e ++ + ++k +   ++ +++a++ +++
  AJA93044.1 111 EKISKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKkkidEELNQRKKELEIMKKRLVEMKQINSKNKGEddSKNVVEAASQIIST 209
                 678899999*****************999999999999999999999986666789999**********998877777666431144445666777777 PP

         ERM  94 leeeserkeeeaerLkeeleeareaeeeakekll 127
                   +  +   +e e  ++ l + r+a+ e+k+kl+
  AJA93044.1 210 TNKRLQDTMKELEVIRQLLDKERKAHSETKKKLQ 243
                 77888888999999******************97 PP

>> Corona_S2  Coronavirus S2 glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.054        54     255     313 ..      10      77 ..       4      84 .. 0.79
   2 ?    7.9   1.3   0.00092      0.92     254     306 ..     106     158 ..      96     191 .. 0.87
   3 ?   -0.9   0.1      0.42   4.2e+02     248     294 ..     197     243 ..     176     244 .] 0.70

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.054
                 HHHHHHH.........HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSHHTTSSHSHHHHHHHHSCH CS
   Corona_S2 255 nkaigni.........seglatvatalakiqdvvnkqgqalnelvaqlsknfgaissviqdiydrldk 313
                 n+ ig+i         se  + + t l+ki+d ++++ + l+  +++ ++ + +i   i+   + +d+
  AJA93044.1  10 NQRIGRIgmglfskkkSEVAQDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIELSRKEYDE 77 
                 67777777777777778888999999999999999999999999999888888887777666666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00092
                 HHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHSHHTTSSHSHHHH CS
   Corona_S2 254 fnkaigniseglatvatalakiqdvvnkqgqalnelvaqlsknfgaissviqd 306
                  n+ i +is+ ++   + l++iq+ + k++++ nel ++++kn  ++s + ++
  AJA93044.1 106 NNENIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENE 158
                 58999***************************************999988665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.42
                 HHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHS CS
   Corona_S2 248 kklaasfnkaigniseglatvatalakiqdvvnkqgqalnelvaqls 294
                 k++ ++  + i+  ++ l+ + + l+ i+ +++k+ +a +e+ ++l+
  AJA93044.1 197 KNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAHSETKKKLQ 243
                 45555556666667777777777777777777777777777777776 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.5   0.00078      0.78     117     224 ..      30     133 ..      26     147 .. 0.60
   2 ?    3.9   8.7     0.029        28     128     224 ..     139     237 ..     130     244 .] 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00078
        CorA 117 deivdrlfellekleeeldeledel.edstkkeilrelaqlr.rrlvklrralapnrevlkrlla...kaddkllddedkeylrdlldelerllemlea 210
                 +  + +l ++ +++eee++ le+ + e++++   + e ++l  +++ ++   + ++++ l r l+   ++ +        + ++   +++e++++++++
  AJA93044.1  30 QDTNTNLQKIKDDIEEEIEGLESKIkEKNERLHSIIEKIELSrKEYDEIIGKIIQSKKEL-RSLEgseSKSN--------DVIKPNNENIEKISKEISN 119
                 567788889999999999999999975555554444444444266888887777777777.56662322222........2356666666666666666 PP

        CorA 211 lrerleslqdtyss 224
                   ++l  +q+++  
  AJA93044.1 120 SENKLKEIQEEITK 133
                 66666666665532 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.029
        CorA 128 ekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyss 224
                  +lee++++    +  ++++kk+i +el q +++l  +++ l +++++ ++++  +d k++ +++++ +++   +l+  +++le++r++l++ + ++s 
  AJA93044.1 139 NELEEKIKKNAPSVsdSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNKGEDDSKNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAHSE 237
                 4566666666666698999999999*****99*****************999999**********************************9987777766 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.5   0.00086      0.86       2      52 ..      43      93 ..      42      98 .. 0.93
   2 ?    5.6   3.5     0.017        17       4      71 ..     108     175 ..     106     180 .. 0.94
   3 ?    0.2   0.3      0.83   8.3e+02      41      67 ..     200     226 ..     175     235 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00086
  TolA_bind_tri  2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqle 52
                   +e+ ++ LE +++ +++ l+ + +++e  ++e +e+ G+i + + +l++le
     AJA93044.1 43 IEEEIEGLESKIKEKNERLHSIIEKIELSRKEYDEIIGKIIQSKKELRSLE 93
                   7999***********************************999999998876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
  TolA_bind_tri   4 drvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                    + ++++ + ++++++ l e+q+++ ++++  +eL  +i +++  +++ e+  +++ ++l++r ++le 
     AJA93044.1 108 ENIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEI 175
                    6799999999999**************************************************99985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.83
  TolA_bind_tri  41 iEelqyqleqleerQrdlYldlDerlr 67 
                    +E  +  ++++++r +d  ++l+   +
     AJA93044.1 200 VEAASQIISTTNKRLQDTMKELEVIRQ 226
                    455555566667777777776665544 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.0      0.01        10      13      72 ..      24      79 ..      22      91 .. 0.71
   2 ?    7.5   5.9    0.0062       6.2      29      90 ..      86     146 ..      80     148 .. 0.88
   3 ?    5.1   8.1     0.034        34      30      84 ..     135     189 ..     132     194 .. 0.87
   4 ?    3.6   6.4      0.11     1e+02      40      90 ..     193     243 ..     182     244 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.01
  HIP1_clath_bdg 13 kqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlk 72
                    k   va+ +  ++++ k+++eee+e l++    k++e++e l ++ + +e +r+e +++ 
      AJA93044.1 24 KKSEVAQDTNTNLQKIKDDIEEEIEGLES----KIKEKNERLHSIIEKIELSRKEYDEII 79
                    566799999999********999999765....666666666666666777777766554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
  HIP1_clath_bdg  29 kkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqla 90 
                     kkel ++le  +++++  ++  +e++ek+ +e+ +++++l+++++ ++++ + +++l+++++
      AJA93044.1  86 KKEL-RSLEGSESKSNDVIKPNNENIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIK 146
                     5665.4688888899999999***********************************999886 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.034
  HIP1_clath_bdg  30 keleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeq 84 
                     +++++ele+  +++   +++ + e +k+ +el+++++el+ +k+ L + +q +++
      AJA93044.1 135 SKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSK 189
                     5678899988888899999999999*********************999998876 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.11
  HIP1_clath_bdg  40 keeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqla 90 
                     ++++++ +e  ++ + + ++ l+++++el+ +++ L+++ ++ ++ +++l+
      AJA93044.1 193 EDDSKNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAHSETKKKLQ 243
                     567778888899999999**************************9999986 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   6.8    0.0089       8.8      45     112 ..      26      91 ..      19     101 .. 0.78
   2 ?    9.8  15.5   0.00093      0.93      52     136 ..      95     174 ..      90     180 .. 0.83
   3 ?    2.3   6.2      0.19   1.9e+02      47      98 ..     187     238 ..     176     244 .] 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0089
       Muted  45 kklvnelkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaewee 112
                 ++ +++++ + l+k+++ ++e+++ l++k+++ +e  + + +k  e  +++ +++  k  ++k+e  +
  AJA93044.1  26 SEVAQDTNTN-LQKIKDDIEEEIEGLESKIKEKNERLHSIIEK-IELSRKEYDEIIGKIIQSKKELRS 91 
                 5667777777.88999999999999999999999999999999.666666778887778887777665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00093
       Muted  52 keqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekveelk 136
                 +e++++ +++  +en+++++k++ ++ +k ++++++      +k+++++++ ee+ ++ +  +++ +++k+++Dee ++  +el+
  AJA93044.1  95 SESKSNDVIKPNNENIEKISKEISNSENKLKEIQEE-----ITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELE 174
                 5667778888899********************999.....4456677777777777777778999*************999986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.19
       Muted  47 lvnelkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseq 98 
                 + ++  e+ +++++e+ ++ +s++nk+l++  ++ e ++q  ++e+k +se+
  AJA93044.1 187 NSKNKGEDDSKNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAHSET 238
                 3455567778888888889999999999988877776666644444444333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.6     0.067        67      90     132 ..      33      75 ..      22      93 .. 0.45
   2 ?   11.2  15.2   0.00031      0.31      35     140 ..      86     181 ..      65     195 .. 0.62
   3 ?    0.4  11.5      0.64   6.4e+02      74     160 ..     150     235 ..     147     244 .] 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.067
       ATG16  90 laelyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                  ++l+k + + ++ +  l++++++++e+l +  e+++  ++e 
  AJA93044.1  33 NTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIELSRKEY 75 
                 3444444444444444444444444444444444444444433 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
       ATG16  35 eaenaklekaaasakssksskksakekeasasq.......snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerla 126
                 ++e ++le + ++        ++         +       + +k s++i+++e+kl++++ee ++  k ++el++++++   ++++ e++ k+ +e+l+
  AJA93044.1  86 KKELRSLEGSESK--------SN---------DvikpnneNIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELN 167
                 3333333211111........11.........0111111122345667888888888888888888888888888888888888888888888888888 PP

       ATG16 127 eleaeraaletklk 140
                 + ++e + ++++l 
  AJA93044.1 168 QRKKELEIMKKRLV 181
                 88777777777664 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.64
       ATG16  74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160
                  +++++e++ +++ eel +  k+ + +++rl+e+++  +k + +  + ++ ++++++ +++ +++l+d  +el+  ++l+++ + ++
  AJA93044.1 150 PSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNKGEDDS-KNVVEAASQIISTTNKRLQDTMKELEVIRQLLDKERKAH 235
                 5688999999***********************99877776666554.456788888888888999999999988888887666555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.6   0.00013      0.13      61      99 ..      30      68 ..      13      81 .. 0.83
   2 ?    1.0  13.6      0.41   4.1e+02      60     100 ..      99     139 ..      60     148 .. 0.81
   3 ?    4.2   9.6     0.042        42      61     103 ..     135     177 ..     132     180 .. 0.92
   4 ?    4.4   6.5     0.035        35      67     101 ..     155     189 ..     145     194 .. 0.82
   5 ?    2.7   2.9      0.12   1.2e+02       8      39 ..     212     243 ..     195     244 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2 61 eevkeeLeerketlekeiktlekqleklekeleelkeel 99
                 ++++++L++ k+++e+ei+ le+++++++++l  + e++
   AJA93044.1 30 QDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKI 68
                 466788999999999999999999999999999888876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.41
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                   ++v++  +e++e+++kei++ e++l+++++e+++  + ++
   AJA93044.1  99 SNDVIKPNNENIEKISKEISNSENKLKEIQEEITKNSKINN 139
                  56667777889999999999999999999999987554443 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.042
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
  Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                   ++++eLee++++    ++  e++++k+ +el++ k+el ++ 
   AJA93044.1 135 SKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMK 177
                  67899**********************************9875 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.035
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
  Prefoldin_2  67 Leerketlekeiktlekqleklekeleelkeelqk 101
                   e++k+++++e+++ +k+le ++k+l e+k+ + k
   AJA93044.1 155 SENEKKKIDEELNQRKKELEIMKKRLVEMKQINSK 189
                  57889999999999999999999999999986655 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.12
                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleele 39 
                  ++lq+++++l+  ++ l+++ k + ++++ l+
   AJA93044.1 212 KRLQDTMKELEVIRQLLDKERKAHSETKKKLQ 243
                  46677777777777777777777777776665 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.2      0.16   1.6e+02      13      57 ..       8      56 ..       6     152 .. 0.67
   2 ?    7.8   3.8    0.0036       3.6      33     112 ..     158     237 ..     146     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                ECTTTCEEEEEEE.CTT.....EEEEEEECCCCHHHHHHHHHHHHHHHT CS
     RNase_H 13 lgnpgeggagavl.ykeg...arnisapleeaqtnnraELsAvieaLka 57
                l+n++ g++g++l +k++   a+   ++l++ ++    E++ +   +k+
  AJA93044.1  8 LKNQRIGRIGMGLfSKKKsevAQDTNTNLQKIKDDIEEEIEGLESKIKE 56
                6788889999955244433333344555556666666666666665554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0036
                 EEEEECCCCHHHHHHHHHHHHHHH.TT.SCSEEEEEES-HHHHHHHHCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHC CS
     RNase_H  33 isapleeaqtnnraELsAvieaLk.alksdekvniytDSkYvvkgitqwvhrwkknawkttseqkpvknkdlaellkelak 112
                  ++++ e+    + EL+ + + L    ++++k +   DSk+vv+++ q++ +++k+ + +t+++ +v+ + l ++ k++ +
  AJA93044.1 158 EKKKIDEELNQRKKELEIMKKRLVeMKQINSKNKGEDDSKNVVEAASQIISTTNKRLQ-DTMKELEVIRQLLDKERKAHSE 237
                 4555553444445688888888883334556666889***********9999877555.7777779999777777766665 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   7.1      0.24   2.4e+02      31     102 ..      45     116 ..      21     122 .. 0.46
   2 ?    9.2  25.9    0.0015       1.5      30     157 ..     114     241 ..      98     244 .] 0.60

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
        Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelree 102
                 +ei  l ++++e +++l++  e+i+  +++++e   ++ + ++el+  + +++  ++ ++  +e+++++ +e
  AJA93044.1  45 EEIEGLESKIKEKNERLHSIIEKIELSRKEYDEIIGKIIQSKKELRSLEGSESKSNDVIKPNNENIEKISKE 116
                 233344444444444444444444444444444444444444444444444444444444444444444443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
        Fez1  30 lseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeae 128
                  +ei +  ++l+e++++++++ + ++elee++++ + ++   ene ++  +e +  ++++e +++ l e+++  s+++ e++++++   +++   ++++
  AJA93044.1 114 SKEISNSENKLKEIQEEITKNSKINNELEEKIKKNAPSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNKGEDDSKNVVEAASQIISTTNK 212
                 346666666777777777777777777777777777777777777766666666666666666677777766444444333333333333333344466 PP

        Fez1 129 eleelkreverlraeLkeerqkkeeqass 157
                 +l++  +e+e +r+ L +er+++ e +++
  AJA93044.1 213 RLQDTMKELEVIRQLLDKERKAHSETKKK 241
                 77777777777888888887777666554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.8    0.0011       1.1      34     121 ..      31     128 ..      22     130 .. 0.70
   2 ?    6.9   3.5    0.0061       6.1      76     118 ..     104     146 ..      92     149 .. 0.87
   3 ?   -1.7   9.2       2.7   2.7e+03      44     110 ..     160     228 ..     153     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
     DUF1664  34 vTkrslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskei...keevtevredlsei.......gedvesvkeaveglesklerie 121
                  T+ +l++  +++ +++e + +++++  ++L s i++++ + +e  ei+ +i   k+e+ ++++  s+        +e++e++++ +++ e+kl++i+
  AJA93044.1  31 DTNTNLQKIKDDIEEEIEGLESKIKEKNERLHSIIEKIELSRKEYDEIIGKIiqsKKELRSLEGSESKSndvikpnNENIEKISKEISNSENKLKEIQ 128
                 59999999999****************99**9999999999999999888763325566666544333300011114556666666777777777765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0061
     DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                 + ++e +++i++e+++ +++l+ei+e++++ +++ ++le+k++
  AJA93044.1 104 KPNNENIEKISKEISNSENKLKEIQEEITKNSKINNELEEKIK 146
                 5567889999999999999999999999999999999999997 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.7
     DUF1664  44 esvskqleqvseslaatkrhL..ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                 +++ ++l+q +++l+  k++L  +++i++ +k  d++k++ ++ ++ +++ ++ l+++ +++e ++++ 
  AJA93044.1 160 KKIDEELNQRKKELEIMKKRLveMKQINSKNKGEDDSKNVVEAASQIISTTNKRLQDTMKELEVIRQLL 228
                 678889999999999999999444689999999999999999999999999999999999999888765 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  36.3     0.018        18     285     519 ..      25     242 ..      20     244 .] 0.54

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
     DUF3584 285 vqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydr 383
                   e +++ +++l++ +d+++e+i+ l+++++++++ l+     +e++e ++k+y++  i k  +   +l s++ + ++ +  ++   e+++++ ++  +
  AJA93044.1  25 KSEVAQDTNTNLQKIKDDIEEEIEGLESKIKEKNERLHS---IIEKIELSRKEYDEI-IGKIIQSKKELRSLEGSESKSNDVIKPNNENIEKISKEISN 119
                 456778888899999999999999999999888887764...577777788888654.66666666666666666666666666666777777776666 PP

     DUF3584 384 rkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqe 482
                  + k+ke  +ee+ k+ + ++++ e+ ++            +++ ++  e++k+++ ee  + +++l+  k rl ++++ + +++    +++ +e+a +
  AJA93044.1 120 SENKLKE-IQEEITKNSKINNELEEKIKK------------NAPSVSDSENEKKKIDEELNQRKKELEIMKKRLVEMKQINSKNKGEDDSKNVVEAASQ 205
                 6666654.333333333332222222222............2233333344444444444444444444444444444444444444444445555555 PP

     DUF3584 483 elekaeaevealqaeeeqlrkkrdeadealqkaerrl 519
                  +   +++ ++  +e+e++r+  d+  +a+++ +++l
  AJA93044.1 206 IISTTNKRLQDTMKELEVIRQLLDKERKAHSETKKKL 242
                 5555555555555555555555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4162  (0.232138); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                       194  (0.0108205); expected 17.9 (0.001)
Passed Fwd filter:                       100  (0.00557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 1.48u 0.39s 00:00:01.87 Elapsed: 00:00:00.61
# Mc/sec: 1211.89
//
Query:       AJA93045.1  [L=1138]
Description: lamin tail domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.5e-14   52.0   0.2    7.5e-14   52.0   0.2    3.6  3  LTD         Lamin Tail Domain
      4e-07   30.6   1.5        1.1    9.7   0.0    5.0  5  Arrestin_C  Arrestin (or S-antigen), C-terminal domain
    0.00028   21.3   1.5        2.1    8.9   0.0    5.9  5  MG2         MG2 domain
     0.0003   21.2   0.1       0.49   10.7   0.0    3.8  4  A2M_BRD     Alpha-2-macroglobulin bait region domain
  ------ inclusion threshold ------
      0.094   12.3   0.1        1.9    8.1   0.0    2.4  2  FNIP_C      Folliculin-interacting protein C-terminus


Domain annotation for each model (and alignments):
>> LTD  Lamin Tail Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.2   2.1e-17   7.5e-14       6     107 ..       8      96 ..       3      99 .. 0.93
   2 ?   -1.6   0.0      0.92   3.3e+03      85     106 ..     250     283 ..     215     291 .. 0.62
   3 ?   -0.4   0.2       0.4   1.4e+03      31      47 ..    1105    1121 ..    1076    1134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.1e-17
         LTD   6 gdvvIsevmedgagnnanefvelyNtsskavdLsgwkledasge..ytfpngtgtlaageyvvvwsgsgttsasngskasssavwnnggdavaLydasg 102
                 +++ I+ev  +++g+++ efvelyN++s ++d sgw+++ +++   y +p+gt ++ +++ + +++               ++ +++ g++++L d+sg
  AJA93045.1   8 SQILINEVETNPPGSDTSEFVELYNPTSIDIDVSGWTISPSATWkaYEIPDGT-IISSNSFAAFTHV--------------NFWFKDFGETITLSDTSG 91 
                 79************9999************************77*********.**********999..............4568889*********** PP

         LTD 103 evvds 107
                 +++d+
  AJA93045.1  92 NLIDE 96 
                 ***97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.92
         LTD  85 savwnn............ggdavaLydasgevvd 106
                 s + +n             g++v+L+ +++++++
  AJA93045.1 250 SESTKNnleistdkesyiPGETVILFADTNSEIQ 283
                 2222223344445577778888888887777765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.4
         LTD   31 tsskavdLsgwkledas 47  
                  +ss+ +d+ +w +e  +
  AJA93045.1 1105 NSSSKIDIDNWNVEIIK 1121
                  57789******998666 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.9   6.9e+03       6      29 ..     148     171 ..     144     188 .. 0.79
   2 !    8.1   0.0   0.00099       3.5       5      24 ..     255     274 ..     251     281 .. 0.85
   3 !    5.0   0.0    0.0088        32       5      25 ..     376     396 ..     373     400 .. 0.90
   4 ?    2.1   0.0      0.07   2.5e+02       8      29 ..     503     524 ..     498     635 .. 0.79
   5 !    9.7   0.0    0.0003       1.1       6      63 ..     874     936 ..     872     972 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.9
                 EEEEEES-SEEETT--EEEEEEEE CS
  Arrestin_C   6 sleaslpkkgyvpGetipvtvkid 29 
                 sl+a+l ++ yv+ et+++  ++ 
  AJA93045.1 148 SLSATLGGTEYVFNETVTIAGSVS 171
                 789999999999999999987665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00099
                 EEEEEEES-SEEETT--EEE CS
  Arrestin_C   5 vsleaslpkkgyvpGetipv 24 
                  +le+s++k++y+pGet+ +
  AJA93045.1 255 NNLEISTDKESYIPGETVIL 274
                 589**************965 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0088
                 EEEEEEES-SEEETT--EEEE CS
  Arrestin_C   5 vsleaslpkkgyvpGetipvt 25 
                 v +++s++k+ y+ G+ i+vt
  AJA93045.1 376 VLISISTDKEIYAVGDIIKVT 396
                 7799***************98 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.07
                 EEEES-SEEETT--EEEEEEEE CS
  Arrestin_C   8 easlpkkgyvpGetipvtvkid 29 
                  ++++k++yv G+++++t ki 
  AJA93045.1 503 GLKMDKSSYVLGSSLSLTGKIL 524
                 5789*************99986 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0003
                 EEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS.......SEEEEEEEE CS
  Arrestin_C   6 sleaslpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdvcafnr.....snkkeknvv 63 
                 s++++l+k  ++ G+t++++ ki+n   ++  +++v l + +++ +f +      n+++k  v
  AJA93045.1 874 SISVNLEKDEFTSGDTVRISGKINNIYYYDSVSVRVDLPNVSEINCFEGqqcgfGNSEKKIRV 936
                 5799****************************************9998877776444444444 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.3   1.5e+04      37      57 ..      83     104 ..      82     112 .. 0.75
   2 ?   -1.8   0.0       1.3   4.6e+03      43      87 ..     189     232 ..     161     249 .. 0.56
   3 ?    2.8   0.0     0.046   1.7e+02       4      19 ..     259     274 ..     256     357 .. 0.70
   4 ?    2.5   0.1     0.057   2.1e+02      54      96 .]     441     488 ..     377     488 .. 0.42
   5 !    8.9   0.0   0.00058       2.1      61      94 ..     945     975 ..     928     978 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.3
                 EEEEE-TTSSEEEEEEE.EE-C CS
         MG2  37 kltirdpdgkevkelpl.atde 57 
                 ++t++d++g+ ++e+pl ++ e
  AJA93045.1  83 TITLSDTSGNLIDETPLiEDLE 104
                 68999********999954433 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                 TTSSEEEEEEEEE-CTTEEEEEEE--T..T--SEEEEEEEEECSTTT CS
         MG2  43 pdgkevkelplatdetggaesefalpe..aaklGeysvelsadsaee 87 
                 ++ + +k+l l  d + g++++++l++  +  +G+y v++s+   +e
  AJA93045.1 189 QGPNYFKNLALFPDRDLGFSTTLNLQKvlGFNQGSYDVKVSY---GE 232
                 444555555555555556666666666223467888888833...22 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.046
                 EEES-SEE-TT-EEEE CS
         MG2   4 vytDRglYrPgetVsl 19 
                 + tD++ Y PgetV l
  AJA93045.1 259 ISTDKESYIPGETVIL 274
                 779999******9954 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.057
                 EE-CTTEEEEEEE--TT........--SEEEEEEEEECSTTT-EEEEEEEE CS
         MG2  54 atdetggaesefalpea........aklGeysvelsadsaeeslssgsfrV 96 
                 + + +g++e+ef++ e+        ++ G+y++++   s+    +++sf+V
  AJA93045.1 441 RLNGDGTFEYEFKIVENssadenyaSSFGDYKIVV---SEYFGDGTTSFKV 488
                 44444445555555443111111113457777777...6666666666665 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.00058
                 EEEEEE--TT--SEEEEEEEEECSTTT-EEEEEE CS
         MG2  61 aesefalpeaaklGeysvelsadsaeeslssgsf 94 
                 +  +++lp++a+lG y++++   ++    +++sf
  AJA93045.1 945 FFWNYKLPKDAPLGLYTIVV---DTHFGEFEKSF 975
                 66789***************...44455555555 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0065        23       1      42 [.     257     304 ..     257     369 .. 0.78
   2 !   10.7   0.0   0.00014      0.49       1     105 [.     378     544 ..     378     565 .. 0.67
   3 ?   -1.2   0.1      0.66   2.4e+03       3      72 ..     667     735 ..     666     759 .. 0.52
   4 ?   -2.7   0.0         2     7e+03       2      19 ..     876     893 ..     875     913 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0065
                 -EEEESSSS--TTSEEEEEEE-SS-..........EE-TT-....BSS---- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxx RF
     A2M_BRD   1 lqispdkeeykvGetakltvkstfa..........tverdstlylvlsrgni 42 
                 l+is+dke+y +Get+ l  +++++          t ++++    ++  g i
  AJA93045.1 257 LEISTDKESYIPGETVILFADTNSEiqyggldytvTNPNQE----IIFEGTI 304
                 789*************9999998876666665554444444....5555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                 -EEEESSSS--TTSEEEEEEE-SS-.......EE-TT-....BSS-----.-S.............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx............................................ RF
     A2M_BRD   1 lqispdkeeykvGetakltvkstfa.......tverdstlylvlsrgnivssgek............................................ 48 
                 ++is+dke y+vG+ +k+t +s+                   v+++g + ss                                               
  AJA93045.1 378 ISISTDKEIYAVGDIIKVTGRSNDIwvedlelR---------VMQTGIL-SSSAIgsdarylapdpfdlqdrvrlngdgtfeyefkivenssadenyas 466
                 679*******************87665444444.........5555533.2332344555588888888888888888888888888888888777777 PP

                 .........................S....-EEEEEE--TT-----EEEEEE..E--CEEEEEEE----.-GGGB-EEEEE CS
                 ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     A2M_BRD  49 ........................veeidsstsfsfpvtadmaPnarvvvyyirrdgevvadsvqlpvekdfenklsvsle 105
                                         +    s+ +++ p+  +m  +++v+   +   g+ + d+ q ++ ++ +n ++++++
  AJA93045.1 467 sfgdykivvseyfgdgttsfkvveD--PESFVDVRTPLGLKMDKSSYVLGSSLSLTGK-ILDYHQAEIGNSMRNSVEITFT 544
                 7777777777776666666555331..4556677777777777777774444334456.6777777777777777777773 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.66
                 EEESSSS--TTSEEEEEEE-SS-EE-TT-....BSS-----.-S...........S........-EEEEEE--TT-----EE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xx....xxxxxxxxxxxxxxxxxxxxxx RF
     A2M_BRD   3 ispdkeeykvGetakltvkstfatverdstlylvlsrgnivssgek........ve....eidsstsfsfpvtadmaPnarv 72 
                 i+p  e++ +Ge++k++v  +             + +g+++  ++         ++    ++++ +s+s   + +m+  + v
  AJA93045.1 667 IAPSMESVVCGENLKFNVGDKL------------VVTGKVI-PKDArsltstyaDRdsdsQTSTGHSYSTNYNTAMMNYVEV 735
                 5667778888888888887433............2222221.1111112222220033335556666666666666666666 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2
                 EEEESSSS--TTSEEEEE CS
                 xxxxxxxxxxxxxxxxxx RF
     A2M_BRD   2 qispdkeeykvGetaklt 19 
                 +++++k+e+  G+t++++
  AJA93045.1 876 SVNLEKDEFTSGDTVRIS 893
                 577888899999998876 PP

>> FNIP_C  Folliculin-interacting protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00054       1.9      25      82 ..     328     384 ..     291     393 .. 0.73
   2 ?    1.3   0.0     0.064   2.3e+02      70      93 ..    1102    1125 ..    1097    1133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00054
      FNIP_C  25 LlaglcdsYvpdfVLqGvtkseeklkevlskdlssavessvldepvaEavcivaDtdk 82 
                 L+ ++++       ++G+ k  ++   + s+d+  +++s+vl+e+v+E+v+i + tdk
  AJA93045.1 328 LFMETVNPVYGTYTIEGTYK-SQNPLYYSSEDVINTSTSFVLSEDVKEDVLISISTDK 384
                 44444444444455677777.4555556678*********************999997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.064
      FNIP_C   70 vaEavcivaDtdkwtvkvlssess 93  
                  v+E++   +D+d+w+v+++  e++
  AJA93045.1 1102 VPENSSSKIDIDNWNVEIIKDEQP 1125
                  567777779*********998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.54
# Mc/sec: 6341.32
//
Query:       AJA93046.1  [L=357]
Description: aspartate-semialdehyde dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-32  112.3   0.0      5e-32  111.5   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    4.1e-28   98.2   0.1      1e-27   96.9   0.0    1.7  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
  ------ inclusion threshold ------
      0.037   14.7   0.0      0.089   13.5   0.0    1.6  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
      0.053   13.6   0.0       0.11   12.6   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
        0.1   12.2   0.3        1.9    8.1   0.0    2.4  3  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   1.4e-35     5e-32       1     181 [.     164     335 ..     164     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.4e-35
                      HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESCSE CS
  Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkileftekv 94 
                      LkPL+++ ++ ++v+++++qa+SG+Gk                     gv+ + i +N++pyi kee k  +et+++l+++++ k + ++ + v
       AJA93046.1 164 LKPLVEK-YGAKKVMMTSMQAISGGGK--------------------SGVSAMGITDNILPYIPKEEGKVRIETKKILGKLKDGKIEDADIK-V 235
                      8*****9.88*****************....................6***********************************888888776.* PP

                      EEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSHCHHSSHHHHTTC..SSSEEEEEEEEETTCTTEEE CS
  Semialdhyde_dhC  95 satcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvneeedrPtpaavagg..tnsvsVGRirkdemgdeglk 174
                      s tc+rVPv++Gh+e+v++++ +k+++ + +++ + +             pe+    ++ + rP+p++ ++   ++++s+GR++k e +d+glk
       AJA93046.1 236 SCTCTRVPVIDGHTESVFVET-EKEIDPSLAKDTFNDYnkdisvtglpsaPEKYYAFHDDPTRPQPRMEREVgdGMTTSIGRVEKEELFDNGLK 328
                      *********************.5999999999999888888******999777777777799999999997778******************** PP

                      EEEEEET CS
  Semialdhyde_dhC 175 lvvvgDN 181
                      ++  ++N
       AJA93046.1 329 YMLFSHN 335
                      *****99 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   2.9e-31     1e-27       1     118 [.       4     133 ..       4     136 .. 0.97
   2 ?   -2.5   0.0       1.9   6.7e+03      45      74 ..     217     238 ..     206     242 .. 0.52

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 2.9e-31
                     EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.............GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHH CS
  Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.............aleegkdlkvedvdeeelkevdivflalpagvskel 82 
                     +vai+G tG vGqe+++ L++hp++e++ +++s+rsaGk + +a +             ++e++k++kv +v+e +++e+d++f+a+++++++++
      AJA93046.1   4 RVAIIGVTGSVGQEFVQSLDNHPWFEVTQIAASERSAGKMYLDAIRdasgiiawdvggqIPEYIKNMKVLKVEEINVQELDLIFSAVESEAARDI 98 
                     7*******************************************99************************************************* PP

                     HHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGG CS
  Semialdhyde_dh  83 apklaeagvkviDlssdfRlkddavyvlpevnreai 118
                     + k+ ++++ vi+ ss++R+++d+++ +p +n e+ 
      AJA93046.1  99 ETKF-AKDLPVISTSSAYRYEEDVPILIPGINDEQA 133
                     ****.899************************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                     SGGGTTTECEBEEEGGGGGCTT-SEEEE-S CS
  Semialdhyde_dh  45 vkaleegkdlkvedvdeeelkevdivflal 74 
                     +k+l +         ++ +++++di ++++
      AJA93046.1 217 KKILGKL--------KDGKIEDADIKVSCT 238
                     3334444........445555566655554 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.089       1      36 [.       5      39 ..       5      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                     EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESSTH CS
  DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsnv 36
                     v+i+G TGS+G++ ++ + ++p  fev+ +aa+++ 
       AJA93046.1  5 VAIIGVTGSVGQEFVQSLDNHP-WFEVTQIAASERS 39
                     78********************.9*******95443 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.2e-05      0.11       2      37 ..       4      39 ..       3      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
                EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCS CS
      DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrkes 37
                +va++G++G +G+e v+ +++++ +e+++   +++s
  AJA93046.1  4 RVAIIGVTGSVGQEFVQSLDNHPWFEVTQIAASERS 39
                8*************************9988777663 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.9   6.8e+03      79     104 ..      75     100 ..      56     106 .. 0.62
   2 ?    1.4   0.0     0.058   2.1e+02       2      24 ..     161     183 ..     160     187 .. 0.85
   3 ?    8.1   0.0   0.00052       1.9      68      98 ..     231     261 ..     226     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                 ESSSSEEEEEEEEEESSTS-HHHHHH CS
     Gp_dh_C  79 VPtpnvsvvdlvvelekevtveevna 104
                 V  +nv   dl++   ++  + ++  
  AJA93046.1  75 VEEINVQELDLIFSAVESEAARDIET 100
                 44555666666666555555555555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.058
                 HHHHHHHHHHHEEEEEEEEEEEE CS
     Gp_dh_C   2 aplakvlndkfgikkglmttvha 24 
                 + ++k l +k+g kk++mt   a
  AJA93046.1 161 VITLKPLVEKYGAKKVMMTSMQA 183
                 56899**************8776 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00052
                 GTTTEEEEEEEESSSSEEEEEEEEEESSTS- CS
     Gp_dh_C  68 lkgkldglAvrVPtpnvsvvdlvvelekevt 98 
                  ++k++ +  rVP+++++  ++ ve+eke  
  AJA93046.1 231 ADIKVSCTCTRVPVIDGHTESVFVETEKEID 261
                 568999999******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 2057.10
//
Query:       AJA93047.1  [L=160]
Description: hypothetical protein T478_0374 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 984.11
//
Query:       AJA93048.1  [L=99]
Description: DNA-binding domain, methylated-DNA-[protein]-cysteine S-methyltransferase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-30  102.8   0.0    9.2e-30  102.6   0.0    1.1  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   5.2e-34   9.2e-30       3      80 ..       4      81 ..       2      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 5.2e-34
                   HHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
  DNA_binding_1  3 qqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80
                   ++++++ l ++p+G+vttYg++Ak+++ +++ r Vgq++++np++++vPcHRVv++dg++ggya g erk+ +L +Eg
     AJA93048.1  4 EEKIYRKLLEVPSGHVTTYGDLAKAVNLKNGQRVVGQIMKKNPFPVIVPCHRVVKSDGTIGGYAYGSERKKHMLSKEG 81
                   689**************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 606.66
//
Query:       AJA93049.1  [L=126]
Description: hypothetical protein T478_0498 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00018   21.3   0.0    0.00025   20.9   0.0    1.3  1  SprT-like      SprT-like family
     0.0045   16.8   0.0     0.0054   16.5   0.0    1.1  1  Peptidase_M76  Peptidase M76 family
      0.005   16.9   0.0     0.0077   16.3   0.0    1.3  1  DUF45          Protein of unknown function DUF45
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.077   13.0   0.0    1.2  1  Tox-MPTase5    Metallopeptidase toxin 5
       0.13   11.6   0.0       0.15   11.4   0.0    1.1  1  Aminopep       Putative aminopeptidase


Domain annotation for each model (and alignments):
>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     7e-08   0.00025      32      97 ..      54     105 ..      19     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7e-08
   SprT-like  32 taGranlkratvrhhasIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGaeFkawaa 97 
                   G          ++++I ++ k + +  e+ l+nt++HEl+H  +  +s      HG++F ++ +
  AJA93049.1  54 YYGVS------YMEKNTIFINVKKIPD--EKTLENTIVHELIHQRFPYLS------HGKRFNKLVR 105
                 33444......44559*********99..**************9874443......5777777665 PP

>> Peptidase_M76  Peptidase M76 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-06    0.0054      41      79 ..      47      89 ..      16      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
  Peptidase_M76 41 Cdekqag....gfspeegillcenrlrskehledtlahElvha 79
                   C+++  +     + ++++i +  +++ ++++le+t++hEl+h 
     AJA93049.1 47 CRTTAYKyygvSYMEKNTIFINVKKIPDEKTLENTIVHELIHQ 89
                   543322212125888889************************5 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.2e-06    0.0077     147     192 ..      60     106 ..      47     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-06
       DUF45 147 sskgkirlnwrLvkappevidYVvvHElaHllek..nHskrFwalvek 192
                  +k++i +n++ +   ++ ++  +vHEl+H + +   H+krF +lv +
  AJA93049.1  60 MEKNTIFINVKKIPD-EKTLENTIVHELIHQRFPylSHGKRFNKLVRQ 106
                 677888888887764.5567889*******9976448********987 PP

>> Tox-MPTase5  Metallopeptidase toxin 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.077      36      83 ..      52      99 ..      42     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
  Tox-MPTase5 36 ysygvnsgmakpnvgthigfkrfasrallrntvvheelhhrw..farglr 83
                 y y   s m k     +i +k++     l nt+vhe +h+r+  +++g r
   AJA93049.1 52 YKYYGVSYMEKNT--IFINVKKIPDEKTLENTIVHELIHQRFpyLSHGKR 99
                 6665567788765..47999*******************99622556655 PP

>> Aminopep  Putative aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.1e-05      0.15     146     172 ..      74     101 ..      58     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
    Aminopep 146 seeelarlifHElaHqvl.Yvkgdtafn 172
                 +e++l ++i+HEl Hq++ Y++   +fn
  AJA93049.1  74 DEKTLENTIVHELIHQRFpYLSHGKRFN 101
                 67899***********987999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 774.80
//
Query:       AJA93050.1  [L=115]
Description: hypothetical protein T478_0565 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 838.17
//
Query:       AJA93051.1  [L=692]
Description: putative minichromosome maintenance protein MCM [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-95  316.1   0.0    1.3e-94  315.5   0.0    1.2  1  MCM           MCM P-loop domain
      4e-34  117.2   0.0    7.1e-34  116.4   0.0    1.4  1  MCM_OB        MCM OB domain
    1.2e-22   80.1   0.8    2.5e-22   79.1   0.8    1.6  1  MCM_lid       MCM AAA-lid domain
    2.2e-09   37.9   0.4    2.2e-09   37.9   0.4    2.7  4  MCM_N         MCM N-terminal domain
    1.3e-05   25.2   0.0    0.00058   19.9   0.0    2.9  2  AAA_5         AAA domain (dynein-related subfamily)
    1.8e-05   24.2   0.0     0.0008   18.8   0.0    2.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0077   16.1   0.1      0.029   14.2   0.0    2.1  2  AAA_3         ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.028   14.1   1.2        0.2   11.3   0.3    2.6  2  AAA_30        AAA domain
       0.61   10.3   2.7        8.1    6.7   0.0    3.2  3  DALR_1        DALR anticodon binding domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.5   0.0   6.5e-98   1.3e-94       2     224 .]     285     506 ..     284     506 .. 0.98

  Alignments for each domain:
  == domain 1  score: 315.5 bits;  conditional E-value: 6.5e-98
                 HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSE CS
         MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaa 100
                 +++ik+l+k++d++++l++s ap+i+ghe +k++ill++ g+++++led++k+rgdinv lvgdpgtaKs++Lk++ ++apr+ ytsg+gs+aagLtaa
  AJA93051.1 285 EKMIKSLSKSPDLYQQLIDSYAPHITGHEIIKESILLLMAGSTQRELEDGSKIRGDINVFLVGDPGTAKSEMLKFCVRVAPRGLYTSGRGSTAAGLTAA 383
                 689************************************************************************************************ PP

                 EEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSS CS
         MCM 101 vvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFD 199
                 vvrd++ g f+leaGa vl d+G++ciDefdkmk edrsalhE+mEqqt si+K+GivatLnarts+laAanp++g+yd+ k+++en+nl+ +lL+rFD
  AJA93051.1 384 VVRDTN-GIFMLEAGATVLGDQGLVCIDEFDKMKAEDRSALHEVMEQQTASISKGGIVATLNARTSILAAANPMFGKYDPFKNITENVNLPVPLLTRFD 481
                 ***985.56****************************************************************************************** PP

                 EEEEE-SSTTHHHHHHHHHHHHHHH CS
         MCM 200 lifvllDkvdeekDeelaehivslh 224
                 lifv++Dk+++e+D+++a+hi++lh
  AJA93051.1 482 LIFVVRDKPSKERDTQIAKHIINLH 506
                 **********************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   3.5e-37   7.1e-34       2     125 ..     110     237 ..     109     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 3.5e-37
                 XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEEEEEEEEEE------------ CS
      MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfvdfqklklQEspeevpaGelP 95 
                 lR++++e igk+ +v+G+v rasevkp +k++vf c++ ++t  +     +l++P +C++++C+ ++++ +e+e+s+f+d+q ++lQE pe++p+G+lP
  AJA93051.1 110 LRQINAEVIGKITSVSGMVLRASEVKPLAKELVFVCPEGHRTDVLlghglSLTSPVQCSNPKCT-HRELGVEPESSRFIDVQFVRLQELPEDLPPGQLP 207
                 8*************************************9986664688888999**********.89******************************** PP

                 -EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
      MCM_OB  96 rslevileddlvdkvkPGdrvevtGiyral 125
                 + l+v++++dlvd+++PGdrv +tGi+r+ 
  AJA93051.1 208 HYLDVTVKQDLVDNARPGDRVVLTGIVRIE 237
                 ***************************985 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.8   1.3e-25   2.5e-22       1      86 [.     520     601 ..     520     602 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.3e-25
                 HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHHHHH CS
     MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeairllkes 86 
                 e+l+kY++y + +i+P+l++ea+ek+ ++Y+++R+ e+   ++ i++t+RqLe liRL++A+A+l +++ v+ +d+++ai+ll+++
  AJA93051.1 520 ETLTKYLSYVK-RINPILTKEAEEKILDYYMKMRNVEA---EEMITVTPRQLEGLIRLATARARLLMKTQVEGDDAQRAIDLLQSM 601
                 689********.***********************884...689**************************************9876 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.4   1.1e-12   2.2e-09       5      86 ..      16      92 ..      13     119 .. 0.87
   2 ?   -3.6   0.0       8.5   1.7e+04      50      62 ..     294     306 ..     290     310 .. 0.79
   3 ?   -1.8   0.1       2.4   4.7e+03      58      85 ..     526     553 ..     515     574 .. 0.65
   4 ?   -3.1   0.0       6.2   1.2e+04      57      82 ..     653     678 ..     651     684 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.1e-12
       MCM_N  5 edFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsykdd 86
                ++FL ef    +de+g++ Y+d + +m   +++ +++d++dL  + +++     enp  +l+++++a+ke++++ +p+y+++
  AJA93051.1 16 KKFLLEF----KDEKGNFRYVDDIDNMMPSKSKFINIDYNDLVLH-PDIESVFGENPDSILEAFSRAIKEILQERFPKYAKK 92
                89*****....7899***************************876.66888999***********************99987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.5
       MCM_N  50 deeLaeailenpk 62 
                 +++L++++++ + 
  AJA93051.1 294 SPDLYQQLIDSYA 306
                 6899999999886 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.4
       MCM_N  58 lenpkeylplleealkevvkklepsykd 85 
                 l++ k++ p+l + ++e + +++ +  +
  AJA93051.1 526 LSYVKRINPILTKEAEEKILDYYMKMRN 553
                 5677788888888888777777664333 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 6.2
       MCM_N  57 ilenpkeylplleealkevvkkleps 82 
                 ++e+  +  ++ ee +k++++k++++
  AJA93051.1 653 LVEELAKTEKFTEEEAKNFIRKMARD 678
                 55666666666677777777776654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   2.8e+02      54      80 ..     213     239 ..     196     276 .. 0.85
   2 !   19.9   0.0   2.9e-07   0.00058       1     122 [.     342     455 ..     342     465 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                 ...--------G-SEEEEESGGG--HH CS
       AAA_5  54 lvdsplvraaregeilvlDEveraese 80 
                  v++ lv++ar g+ +vl ++ r+e+e
  AJA93051.1 213 TVKQDLVDNARPGDRVVLTGIVRIEQE 239
                 68999******************9976 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.9e-07
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrlllee 98 
                 +v+LvG+pGt+Kse+ +   ++  r +  +   r+ t++ l+  +  + ng   l+ ++ v       ++++DE+++++ e  ++L+ ++e+++ ++ +
  AJA93051.1 342 NVFLVGDPGTAKSEMLKFCVRVAPRGL--YTSGRGSTAAGLTAAVVRDtNGIFMLEAGATV--LGDQGLVCIDEFDKMKAEDRSALHEVMEQQTASISK 436
                 69*************988777766655..45678899999999998667888888888888..77888999*************************999 PP

                 SSSEEE---......-EEEEEESS CS
       AAA_5  99 ggelvkaknddllerfrviatanp 122
                 gg +   ++      ++++a+anp
  AJA93051.1 437 GGIVATLNAR-----TSILAAANP 455
                 9988888775.....899999998 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.046        91      21      42 ..     339     360 ..     329     370 .. 0.83
   2 !   18.8   0.0     4e-07    0.0008      97     160 ..     394     457 ..     381     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.046
  Mg_chelatase  21 GgHnlllvGppGsGKtmlakrl 42 
                   G  n++lvG pG+ K+ + k  
    AJA93051.1 339 GDINVFLVGDPGTAKSEMLKFC 360
                   8889***********9776655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4e-07
  Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcp 160
                    + G+  l  +G++ +DE+ ++k++   +L e +e+++ +is+    ++  ar+ ++aa+Np  
    AJA93051.1 394 LEAGATVLGDQGLVCIDEFDKMKAEDRSALHEVMEQQTASISKGGIVATLNARTSILAAANPMF 457
                   6789999*******************************************************64 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.6   9.1e+03      21      38 ..     185     202 ..     183     206 .. 0.77
   2 !   14.2   0.0   1.4e-05     0.029      45     113 ..     383     456 ..     342     461 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.6
       AAA_3  21 kaldlefkriqftpdllP 38 
                 + +d++f r+q  p+ lP
  AJA93051.1 185 RFIDVQFVRLQELPEDLP 202
                 679999****98876555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
       AAA_3  45 evfeekekefefkkGpvf...anllladeinrappktqsalleameerqvtv..egethklpepflvlatqnPi 113
                  v+++++  f +++G+ +   + l+  de ++ ++  +sal e+me+++ ++  +g   +l+    +la+ nP+
  AJA93051.1 383 AVVRDTNGIFMLEAGATVlgdQGLVCIDEFDKMKAEDRSALHEVMEQQTASIskGGIVATLNARTSILAAANPM 456
                 566666777888888654233459999******************998765511678899*************7 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3    0.0001       0.2      18     119 ..     340     434 ..     325     448 .. 0.76
   2 ?    0.2   0.0      0.27   5.4e+02      65     128 ..     514     593 ..     505     602 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
      AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekag 116
                 d  ++l+G +Gt K+ +lk  ++++ +     +  +  g  A+ L++++  +++ i  l    +g++ l ++ l+ +DE   + +++  al + +e++ 
  AJA93051.1 340 DINVFLVGDPGTAKSEMLKFCVRVAPRG----LYTSGRGSTAAGLTAAVVRDTNGIFMLE---AGATVLGDQGLVCIDEFDKMKAEDRSALHEVMEQQT 431
                 556789*****************99966....4455566666666655555555555555...3334467789*********************99977 PP

      AAA_30 117 akv 119
                 a++
  AJA93051.1 432 ASI 434
                 765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
      AAA_30  65 elgieastiakllkrlk...............grarlepg.tllivDEagmvdtkqlaallkaaekag...akvilvGDerQl 128
                 +++i+++t+ k+l+  k               +   +  + + +   E+  v  +ql+ l++ a+++    +k  + GD++Q 
  AJA93051.1 514 KSQIDSETLTKYLSYVKrinpiltkeaeekilD---YYMKmRNVEAEEMITVTPRQLEGLIRLATARArllMKTQVEGDDAQR 593
                 556777777777766667777777776653331...22222555567888888999999999999842234666677888885 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0041       8.1      30      60 ..     279     309 ..     259     315 .. 0.78
   2 ?    0.4   0.1      0.34   6.8e+02      21      85 ..     527     590 ..     510     601 .. 0.68
   3 ?    0.4   0.1      0.36   7.1e+02      31      55 ..     645     670 ..     626     680 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0041
                 S-SHHHHHHHHHHHTHHHHHHHHHHHT-THH CS
      DALR_1  30 leeeeekeLlkalaqfpevleeaaeelephk 60 
                   ++ee++++k+l + p++ ++ +++++ph 
  AJA93051.1 279 EISPEEEKMIKSLSKSPDLYQQLIDSYAPHI 309
                 34789************************96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                 CCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTSTTSC CS
      DALR_1  21 kleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkervlkee 85 
                 ++ +  +++l++e+e+++l +  ++ +v +e + +++p +l e l+ La++  +   k++v +++
  AJA93051.1 527 SYVKRINPILTKEAEEKILDYYMKMRNVEAEEMITVTPRQL-EGLIRLATARARLLMKTQVEGDD 590
                 34444444488889999999999988888888888887765.56777777777776666666555 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.36
                 -SH.HHHHHHHHHHTHHHHHHHHHHH CS
      DALR_1  31 eee.eekeLlkalaqfpevleeaaee 55 
                 +++ eek+L+ +la+ ++  ee a++
  AJA93051.1 645 KTPvEEKQLVEELAKTEKFTEEEAKN 670
                 44559999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4601.91
//
Query:       AJA93052.1  [L=284]
Description: ABC 3 transport family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-67  226.2  37.2    5.3e-67  226.0  37.2    1.0  1  ABC-3     ABC 3 transport family
    3.1e-06   26.4  35.0    3.1e-06   26.4  35.0    1.9  2  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.0  37.2     6e-71   5.3e-67       1     256 [.       7     262 ..       7     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 6e-71
       ABC-3   1 qyeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrktklkedtaigivlsvflalglv 99 
                 +y f+q+al+a+i+v+++c+++g+f+vlrr sl+gd+++H+a++G+ ++++lgv +l+ a++v++++ ++l+ l++ tk++ d+a+++vl ++la+g++
  AJA93052.1   7 SYTFMQKALVAGIAVGIICSFMGTFLVLRRYSLFGDGIAHVAFGGISVGLFLGVFPLWTAFIVSIFGGLGLQKLRQSTKISGDSAVAVVLVSGLAVGVI 105
                 589************************************************************************************************ PP

       ABC-3 100 lvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLviallii 198
                 lvs + + +vdl+s+LfG+il is+ed i+i++i+a ++++l l+ k++l +tf+ee+Ak  gl++ ll++ +++l +++vv+++++vG++L++al+++
  AJA93052.1 106 LVSSSGGFSVDLFSFLFGSILLISNEDTIMILAISAGIIATLTLLQKQFLHLTFNEEQAKLGGLRTTLLNYAFVVLASITVVTSMRLVGILLISALIVV 204
                 *************************************************************************************************** PP

       ABC-3 199 PaatArrltrslesllivAillglvsvvaGlllSyyldlatGavivlvatllfllall 256
                 P +tA+++++ +++ + +++ ++++svv+G+l+Sy++++a++++iv++a+ +++  l+
  AJA93052.1 205 PNITAMMFGKGFKKTVFISMGIAVISVVSGILVSYSFNVAPSGTIVVIAVGILVGTLI 262
                 ***************************************************9998877 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   4.7      0.42   3.8e+03     132     171 ..      13      52 ..       7      72 .. 0.64
   2 !   26.4  35.0   3.5e-10   3.1e-06      78     307 ..      43     259 ..      40     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.42
       FecCD 132 kliLaGiavsallsaltsllllllneealesilfwllGsl 171
                 k ++aGiav++++s + ++l+l   +   + i +  +G +
  AJA93052.1  13 KALVAGIAVGIICSFMGTFLVLRRYSLFGDGIAHVAFGGI 52 
                 5577888888888888888877644444445555555554 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 3.5e-10
       FecCD  78 GissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgasw 176
                 Gi ++a  g+ ++l+l  g ++l++  +++++g+l    l     + ++ +  + ++++G+av+++l + +  +          ++   l+Gs+  +s 
  AJA93052.1  43 GIAHVAFGGISVGLFL--GVFPLWTAFIVSIFGGLGLQKLRQST-KISGDSAVAVVLVSGLAVGVILVSSSGGFS--------VDLFSFLFGSILLISN 130
                 6677777777777776..46666555555555555554444433.477888888888899999999999998888........45999*********** PP

       FecCD 177 skvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLi.vPhiarllvgadhrkllplsallGal 274
                 ++++++l++++ ++++l ll +++  l++++e+Ak  G++++ +++++++l+++ + +++ lvG++   +Li vP+i  +++g+ ++k++++s+ ++++
  AJA93052.1 131 EDTIMILAISAGIIATLTLLQKQFLHLTFNEEQAKLGGLRTTLLNYAFVVLASITVVTSMRLVGILLISALIvVPNITAMMFGKGFKKTVFISMGIAVI 229
                 ******************************************************************99998637**********************999 PP

       FecCD 275 lllladllarlllsptelpvgivtaliGapffi 307
                  ++   l++  +      p g ++ +  +++  
  AJA93052.1 230 SVVSGILVSYSFN---VAPSGTIVVIAVGILVG 259
                 9998888887773...33666555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1839.24
//
Query:       AJA93053.1  [L=79]
Description: hypothetical protein T478_0201 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 601.54
//
Query:       AJA93054.1  [L=53]
Description: zinc finger, C2H2 type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00037   20.8   0.4     0.0006   20.1   0.4    1.4  1  zf-C2H2       Zinc finger, C2H2 type
    0.00077   18.7   0.1    0.00082   18.7   0.1    1.0  1  Actin_micro   Putative actin-like family
     0.0036   18.0   0.3     0.0056   17.4   0.3    1.3  1  zf-C2H2_4     C2H2-type zinc finger
     0.0053   16.8   1.4     0.0091   16.0   1.4    1.4  1  zf-BED        BED zinc finger
     0.0062   15.1   0.1     0.0066   15.0   0.1    1.0  1  DUF629        Protein of unknown function (DUF629)
  ------ inclusion threshold ------
      0.023   15.0   0.1      0.024   15.0   0.1    1.1  1  zf-C2H2_2     C2H2 type zinc-finger (2 copies)
       0.05   13.4   0.1      0.078   12.8   0.1    1.3  1  zf-C2H2_3     zinc-finger of acetyl-transferase ESCO
      0.061   13.1   1.1       0.11   12.3   1.1    1.4  1  zf-C2H2_11    zinc-finger C2H2-type
      0.078   13.7   0.0      0.084   13.6   0.0    1.1  1  zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4     3e-07    0.0006       2      23 .]      15      37 ..      14      37 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                EETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                +C++Cg++F+ ++  +rH+++ H
  AJA93054.1 15 ECKICGMKFSEPERTMRHMMRaH 37
                7********************99 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   4.1e-07   0.00082     220     257 ..       8      46 ..       4      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.1e-07
  Actin_micro 220 lkekkefsCkvCdvkfev.ekiseHllkkHiikehvkeh 257
                   k+++ ++Ck+C++kf+  e+ + H+++ H + + vk+ 
   AJA93054.1   8 SKDTTSLECKICGMKFSEpERTMRHMMRAHSKPQRVKKR 46 
                  688999************9*************9999975 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   2.8e-06    0.0056       2      24 .]      15      37 ..      14      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                +C+iCg  Fs +++  rH+ + H
  AJA93054.1 15 ECKICGMKFSEPERTMRHMMRAH 37
                7******************9988 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.4   4.6e-06    0.0091       7      44 .]       4      38 ..       3      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.6e-06
                S----GGSS--EETTTTEE----SSTHHHHHHHHHS-H CS
      zf-BED  7 ftpvslkeqkavCryCgkilsrgggttnLkrHLrrkHp 44
                f ++s++ ++ +C++Cg ++s      + +rH+ r+H+
  AJA93054.1  4 FNRNSKDTTSLECKICGMKFSE---PERTMRHMMRAHS 38
                77889999*************9...58889***99996 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.3e-06    0.0066      48      82 ..       5      39 ..       3      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
      DUF629 48 aeenkkWrfWvCrtCsekfsdaeeckqHlvqeHva 82
                 +++k+ + + C++C  kfs++e  + H+++ H +
  AJA93054.1  5 NRNSKDTTSLECKICGMKFSEPERTMRHMMRAHSK 39
                56778888999**********************86 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.2e-05     0.024      51      75 ..      14      37 ..       2      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
   zf-C2H2_2 51 leClyCekefkslealreHmkkkgH 75
                leC +C+ +f++ e ++ Hm  + H
  AJA93054.1 14 LECKICGMKFSEPERTMRHMMRA-H 37
                77888888887888888887543.3 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.9e-05     0.078       9      24 ..       9      24 ..       4      28 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
   zf-C2H2_3  9 ksfgasqCkeCgMvYn 24
                k+ ++ +Ck CgM+++
  AJA93054.1  9 KDTTSLECKICGMKFS 24
                3433344******987 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.1   5.3e-05      0.11       1      26 [.      10      35 ..      10      37 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
  zf-C2H2_11  1 destcqCleCGlcftSqlsLsRHlfI 26
                d++++ C  CG++f+      RH+  
  AJA93054.1 10 DTTSLECKICGMKFSEPERTMRHMMR 35
                789************98888888865 PP

>> zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.084      32      64 ..      13      45 ..       5      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
  zf-C2H2_3rep 32 llqcipcgshfgnaeelwlhvlsvhpsdfklsk 64
                   l+c  cg +f++ e+ + h++ +h++  + +k
    AJA93054.1 13 SLECKICGMKFSEPERTMRHMMRAHSKPQRVKK 45
                  578999999999999999999999988776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 392.50
//
Query:       AJA93055.1  [L=87]
Description: hypothetical protein T478_0209 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0029   17.4   1.9        1.2    9.0   0.1    2.1  2  LapA_dom  Lipopolysaccharide assembly protein A domain
  ------ inclusion threshold ------
      0.043   14.0   0.0      0.089   13.0   0.0    1.5  1  DUF2749   Protein of unknown function (DUF2749)


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2   0.00021       1.9      25      40 ..       3      18 ..       1      36 [. 0.88
   2 !    9.0   0.1   0.00013       1.2      22      46 ..      47      70 ..      44      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00021
    LapA_dom 25 vafgiGallgwllslw 40
                v +g+Ga+lg+l+ l+
  AJA93055.1  3 VIIGLGAILGLLFVLP 18
                5689*********997 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
    LapA_dom 22 lllvafgiGallgwllslwsylrlr 46
                l++vaf +G ++ +l+ ++ +lr r
  AJA93055.1 47 LMIVAFTVGTVVSGLIVWL-VLRFR 70
                79***************97.66655 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.089       7      38 ..      48      80 ..      45      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
     DUF2749  7 Ivlviava.agagtilwlvvqpragtsgsgeaq 38
                ++++  v+ +++g i+wlv+  r +++ +  ++
  AJA93055.1 48 MIVAFTVGtVVSGLIVWLVLRFRESNPKAKPTS 80
                444555652689***********9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 636.95
//
Query:       AJA93056.1  [L=556]
Description: hypothetical protein T478_1068 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-66  221.8   8.3    6.8e-66  221.8   8.3    2.5  3  Topoisom_I    Eukaryotic DNA topoisomerase I, catalytic core
    2.2e-63  213.6   9.6    2.2e-63  213.6   9.6    2.5  2  Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fra
    1.8e-19   69.5   1.7    1.8e-19   69.5   1.7    3.9  3  Topo_C_assoc  C-terminal topoisomerase domain
  ------ inclusion threshold ------
      0.023   15.0   1.9       0.12   12.7   1.9    2.2  1  DUF2524       Protein of unknown function (DUF2524)
      0.046   13.7   5.6      0.036   14.0   2.5    2.4  2  DUF3137       Protein of unknown function (DUF3137)
       0.72    8.7   5.0        1.2    7.9   5.0    1.4  1  LMBR1         LMBR1-like membrane protein
        4.3    6.6  12.8         19    4.5   8.8    2.4  2  DUF4407       Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> Topoisom_I  Eukaryotic DNA topoisomerase I, catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   2.0       1.1   2.9e+03     102     147 ..      74     119 ..      53     124 .. 0.76
   2 !  221.8   8.3   2.7e-69   6.8e-66       3     225 ..     216     437 ..     214     445 .. 0.95
   3 ?   -1.8   1.1      0.59   1.5e+03     208     224 ..     457     473 ..     435     488 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                 EEEEE--HHHHHHHHHHHTT--TTSBTTTT--HHHHHHHHTTTSTT CS
  Topoisom_I 102 fntvkvdkqvyknlkifckkkkkgeevFdkintsklNkyLkelmeg 147
                 ++++++d+  +kn+  +++k+k+ +e+  k + + l +  kel e+
  AJA93056.1  74 YKKLELDDIDFKNAFNLVDKEKDAKELLTKEEKKALAAKRKELREE 119
                 4788999999999999999988888888887777777666666655 PP

  == domain 2  score: 221.8 bits;  conditional E-value: 2.7e-69
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHH---------TTS-----GGG-BGGGEEE-TT.SEEEEEEE-GGG-EE CS
  Topoisom_I   3 klkgekdfkKYekarkLkkvvekiredykkklkskeilekqlatavylidklaLrvGnekeeeeadtvGccsLrvehvklsekektitldFlGKdsiry 101
                  +k+ +d++KY+ka+ L+k +e+i++++ k+++sk+ + ++++t+++li ++a+rvG+ek+ +eadtvG ++Lr ehv+l+++   i++dFlGKds+r+
  AJA93056.1 216 GIKQDRDKAKYDKAKMLAKEIETIKNKIVKDMQSKDPKVRRISTVCWLIYRTAMRVGDEKDPDEADTVGATTLRKEHVTLTSD--AIKFDFLGKDSVRW 312
                 68*****************************************************************************9986..************** PP

                 EEEEE-...-HHHHHHHHHHHTT--TTSBTTTT--HHHHHHHHTTTSTT--TTHHHHHHHHHHHHHHHHH..--------TTHHHHHHHHHHHHHHHHH CS
  Topoisom_I 102 fntvkv...dkqvyknlkifckkkkkgeevFdkintsklNkyLkelmegLsAKvFRTYnASitlqeqLkklekievdesnvaekikayneAnreVAilc 197
                 ++tv     dkq  +nlk+++ k k+++e+F +++++++N+y k++++gL+AKvFRT+ AS+++++ L++  + +v+++++ ek+ + + An e Ai+c
  AJA93056.1 313 QETVPAignDKQFHENLKELTAKIKATDEIFGNLTSRDVNEYYKTVVKGLTAKVFRTFSASTVVSKYLNE--NGDVKKGSQMEKLYHAKLANLEAAIMC 409
                 ***9753337799*********************************************************..5899*********************** PP

                 T-EE-XXXXXXXXXXXXXXXXXXXXXXX CS
  Topoisom_I 198 nhqrsvpkqheksmeklkkkiealkedi 225
                 nh+r++pk++e+s++k +++++++++ +
  AJA93056.1 410 NHKRTIPKTFEQSLQKKRDTLKTAEKAT 437
                 *******************999988865 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.59
                 XXXXXXXXXXXXXXXXX CS
  Topoisom_I 208 eksmeklkkkiealked 224
                 +++ +k k++i ++k  
  AJA93056.1 457 DAQEKKKKERITKIKGM 473
                 22222222233333222 PP

>> Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fragment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.6   9.6   8.5e-67   2.2e-63       1     213 []       1     211 [.       1     211 [. 0.98
   2 ?   -1.1   6.7      0.44   1.1e+03      53     117 ..     404     469 ..     370     494 .. 0.57

  Alignments for each domain:
  == domain 1  score: 213.6 bits;  conditional E-value: 8.5e-67
                   ---S-EE----B---------TT--EEETTEEE---HHHHHHHHHHHHTTTSSGGG-HHHHHHHHHHHHHHHHHTT----GGGEE-HHHHHHHHHHH CS
  Topoisom_I_N   1 vkWktLehnGvlfppeYeplpknvklkydgkpvkLspeaEEvatfyaamletdyakkevFqknffkdfkkvlkekekikelekcdFskikeylekek 97 
                   +kWk LehnG+lfpp++e   k++k+k++g++v+L+ ++EE+++ +a++++t ya ++vFqknf++df k++ +k k  el+++dF++ ++ ++kek
    AJA93056.1   1 MKWKKLEHNGILFPPDFE--TKKIKIKIKGESVDLDINQEEMIYQWAKKKDTPYALDKVFQKNFVADFAKTFGKKYKKLELDDIDFKNAFNLVDKEK 95 
                   69****************..***************************************************************************** PP

                   HHHTT-----HHHH....HHHHHHHHHHHHEEEETTEEEEEE--B----EE----TT-TTTT-EE----GGG-EEE--SSS-----STT---SEEE- CS
  Topoisom_I_N  98 ekkkaltkeekkkl....keekekleekygyalldgrkekvgnfrvepPgLfrgrGehpktGklkkrvlpedvtiNigkdakvPeppaghkWkevvh 190
                   ++k+ ltkeekk+l    ke +e+++ k+g+  +dg++ +++n++ epPg+f grGehp +Gk+k +v+++dvt+N+gk+akvP      +W+++vh
    AJA93056.1  96 DAKELLTKEEKKALaakrKELREEMKVKFGTGKMDGNEVEIANYMAEPPGIFIGRGEHPLRGKWKPKVTSKDVTLNLGKEAKVPVG----NWGKIVH 188
                   ************9866667888899999********************************************************98....9****** PP

                   -TT---SEEEE-TTT--EEEEEE CS
  Topoisom_I_N 191 dntvtwlaswkeningqvkyvmL 213
                   d++++w+asw++ ++++ kyv+L
    AJA93056.1 189 DQESMWMASWTDFLTQKRKYVWL 211
                   *********************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.44
                   SGGG-HHHHHHHHHHHHHHHHHTT-.---GGGE.E-HHHHHHHHHHHHHHTT-----HHHHHHHHHH CS
  Topoisom_I_N  53 dyakkevFqknffkdfkkvlkekek.ikelekc.dFskikeylekekekkkaltkeekkklkeekek 117
                   + a    +++   k+f++ l++k+   k+ ek   ++k +e l+k +++k ++++ + kk+ke+ +k
    AJA93056.1 404 EAAIMCNHKRTIPKTFEQSLQKKRDtLKTAEKAtPWKKNEEVLKKAESTKTKTDA-QEKKKKERITK 469
                   5555555666666778888854444245444441455555555544444443333.33333333333 PP

>> Topo_C_assoc  C-terminal topoisomerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.13   3.2e+02      36      58 ..      42      66 ..      38      74 .. 0.81
   2 ?   -0.9   0.1      0.61   1.6e+03      40      57 ..     409     426 ..     402     443 .. 0.74
   3 !   69.5   1.7   6.8e-23   1.8e-19       1      69 [.     482     550 ..     482     551 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
  Topo_C_assoc 36 vawckkhdvp..iekiFsktlleKf 58
                  + w+kk d p  ++k+F+k   + f
    AJA93056.1 42 YQWAKKKDTPyaLDKVFQKNFVADF 66
                  67999999994458***99887766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.61
  Topo_C_assoc  40 kkhdvpiekiFsktlleK 57 
                    +h+  i k F ++l++K
    AJA93056.1 409 CNHKRTIPKTFEQSLQKK 426
                   567778999999999999 PP

  == domain 3  score: 69.5 bits;  conditional E-value: 6.8e-23
  Topo_C_assoc   1 kekikklklqlkdkeenkevaLgtSkinYlDPRitvawckkhdvpiekiFsktlleKfaWAmevdedfk 69 
                   ke+++kl+lql+  e++++++LgtS  nY+DPRi  +w++++  ++ek+++++l++Kf W+ + +e+++
    AJA93056.1 482 KERVEKLRLQLDLTEKTRDYNLGTSLRNYIDPRIFKSWTDEVTADWEKLYTAALQKKFLWVKSENESWQ 550
                   69************************************************************9999995 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   4.7e-05      0.12       5      75 ..     417     492 ..     414     497 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
     DUF2524   5 qsveellqkceqaieeaeeqfeeakrqehyndeeY....teAqlk.LEeavneLeklaksandqQreqLeRarlql 75 
                 + +e+ lqk  +++++ae+     k  e  ++ e     t+Aq+k   e + ++++++k++ ++Q+e++e++rlql
  AJA93056.1 417 KTFEQSLQKKRDTLKTAEKATPWKKNEEVLKKAEStktkTDAQEKkKKERITKIKGMIKKSKAKQKERVEKLRLQL 492
                 578999***********998766666555555554111156776514577899**********************8 PP

>> DUF3137  Protein of unknown function (DUF3137)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.5   1.4e-05     0.036      26      94 ..      62     129 ..      19     130 .. 0.86
   2 ?   -2.3   0.1       1.6     4e+03      10      34 ..     364     388 ..     362     427 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
     DUF3137  26 kakeskkkkekklekvkledpeFekkFeVysndqvearyiLtpalmerllelrekfkgkikasfkdnkl 94 
                  +++++k++ kk++k++l+d +F++ F+   +++ +a+ +Lt++  + l + r++ ++++k+ f  +k+
  AJA93056.1  62 FVADFAKTFGKKYKKLELDDIDFKNAFNLV-DKEKDAKELLTKEEKKALAAKRKELREEMKVKFGTGKM 129
                 556788999999****************97.7789***********************99999977765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
     DUF3137  10 adfnksfkgqtlivpk...kakeskkkk 34 
                 a++ ++f+++t++++    +      kk
  AJA93056.1 364 AKVFRTFSASTVVSKYlneN---GDVKK 388
                 66677888888886664331...22222 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.0   0.00048       1.2     220     323 ..     306     489 ..     177     517 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00048
       LMBR1 220 e....................reledllkevkklrksisesdp..lrkyleeilk............................................ 252
                                      ++l++l  ++k++++ + +     + +y ++++k                                            
  AJA93056.1 306 GkdsvrwqetvpaigndkqfhENLKELTAKIKATDEIFGNLTSrdVNEYYKTVVKgltakvfrtfsastvvskylnengdvkkgsqmeklyhaklanle 404
                 055555555555555555555555555555555555544333212446666666666666666666666666666699999999999999999999999 PP

       LMBR1 253 .........kvPeeiaeklks.....nenkteeslaklekqlikalqkrertekqwkrllekalelediiknksskekefksses 323
                          ++P+++++ l++     +  +++ + +k+e+ l+ka +++ +t +q k+  e++ +++ +ik+++ k+ke  ++ +
  AJA93056.1 405 aaimcnhkrTIPKTFEQSLQKkrdtlKTAEKATPWKKNEEVLKKAESTKTKTDAQEKKKKERITKIKGMIKKSKAKQKERVEKLR 489
                 9999999999999999999999998766668889999999999999999999999999999999999988877777666554444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.012        32     137     186 ..      90     137 ..      52     258 .. 0.79
   2 ?    4.5   8.8    0.0074        19      99     225 ..     362     498 ..     357     506 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
     DUF4407 137 eleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaak 186
                   +++ +a +   ++ +++l+a+r+e+++e++ ++gtg  ++ G++ +  
  AJA93056.1  90 LVDKEKDAKELLTKEEKKALAAKRKELREEMKVKFGTG--KMDGNEVEIA 137
                 4455555555566777889999**********999999..5667776655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0074
     DUF4407  99 leLkiFekeIdaelaeeqqeeakelkeqlaaa..ltaelaeleaqia.............alqaeidaaearldalraeaqkeldgtk.gtgttgvaGk 181
                 l+ k+F+   ++++ +++ +e+ ++k+  + +  + a+la+lea i              +lq++ d+++++ +a+  + ++e+  +  +t    +   
  AJA93056.1 362 LTAKVFRTFSASTVVSKYLNENGDVKKGSQMEklYHAKLANLEAAIMcnhkrtipktfeqSLQKKRDTLKTAEKATPWKKNEEVLKKAeST----KTKT 456
                 66788888888888999999988888766666679*********99998777777766665555555555555554444444444433222....3334 PP

     DUF4407 182 gpaakekkaqldaaqaelaelkakldatarlaalraelaeleae 225
                  +  k+kk+ +++++  +++ kak  +++r+++lr +l+  e+ 
  AJA93056.1 457 DAQEKKKKERITKIKGMIKKSKAK--QKERVEKLRLQLDLTEKT 498
                 455567888888888888888888..999999999888765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2499  (0.139383); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 3847.69
//
Query:       AJA93057.1  [L=626]
Description: glycosyltransferase, group 2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-24   84.8   0.0    1.2e-23   84.2   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.9e-19   68.5   0.2    1.5e-18   67.5   0.2    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      7e-18   65.0   0.0    1.3e-17   64.1   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    2.3e-13   50.0   0.1    4.4e-13   49.1   0.1    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0026   16.3   1.8     0.0031   16.1   0.3    1.8  2  Cellulose_synt   Cellulose synthase
  ------ inclusion threshold ------
      0.012   15.4   0.2       0.11   12.1   0.0    2.6  2  HlyIII           Haemolysin-III related
        0.1   11.6   0.3       0.23   10.4   0.3    1.5  1  CytochromB561_N  Cytochrome B561, N terminal


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   4.7e-27   1.2e-23       2     228 ..       5     232 ..       3     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 4.7e-27
  Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnl.gstgksralnealravksdlvll 93 
                      + +++  p +ne  v +++++++  q+yp ++  ++v d sd++t+e+   ++++++  + ++ ++ r + +++ k+ al++a++ ++s++v++
       AJA93057.1   5 T-ITIQLPIYNEKYVATRLVDAVCQQDYPKDKMRIMVlDDSDDDTVETMSNTVKKYQSLGFDIEHVRR-GtRTGYKAGALKHAMKSTDSEFVAI 96 
                      4.7888899****************************999*****************77777656655.4377889****************** PP

  Glyco_tranf_2_3  94 vDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg.vltlnGsgslirrevlkelegldplfllt 185
                      +D+D +    +lk++ + f+ +++g v+++  + +   +++++++al ++ ++l + +a    + ++ +nG+   +r e+ ++ +g++    l+
       AJA93057.1  97 FDADFIPPTWYLKKAMPHFAKSNIGLVQCRWgHINENYSALTQAQALNLDFHFLVEQKAKSNSKlFMNFNGTAGIWRKECIDDAGGWHT-ATLV 189
                      *******************999******998788888899**************888888777758***********************.**** PP

  Glyco_tranf_2_3 186 dDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                      +D++l++r+ + g++  ++p+ +v  + p     + +q +Rw+
       AJA93057.1 190 EDLDLSYRAQMKGWKCLFLPDIVVDAELPVQMNGAKRQQFRWA 232
                      ******************************************7 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.2   5.8e-22   1.5e-18       2     193 ..      94     306 ..      93     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 5.8e-22
  Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvl.vmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdgde 94 
                      +++ DaD  +p  +l+++  ++a  ++++vq+  + ++++ + l++ +al  + +++  +   ++++ ++ + G   ++r + ++++ggw+  +
       AJA93057.1  94 VAIFDADFIPPTWYLKKAMPHFAKSNIGLVQCRWGhINENYSALTQAQALNLDFHFLVEQKAKSNSKLFMNFNGTAGIWRKECIDDAGGWH--T 185
                      7899*******************99********9945788999999999988877777777777888888899******************..* PP

  Glyco_trans_2_3  95 ssvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.........el............eklillvrllgylgsllwsa. 166
                       ++ ED+d++ r+q+kG+++ f p+ +v  + p  +  a rQ  Rwa G           +            ++ i+l+r++ ++  l+ +  
       AJA93057.1 186 ATLVEDLDLSYRAQMKGWKCLFLPDIVVDAELPVQMNGAKRQQFRWAKGSiqcavkllgDIlvkrkiafdtklQAFIQLTRHIVFPLMLIQFIt 279
                      *************************************************876666544400443344455555555559999988777776654 PP

  Glyco_trans_2_3 167 lplhlallllfsllalalvllllllla 193
                      lp++la  +  ++++++ +l l+++la
       AJA93057.1 280 LPILLASEVNLYIVSFLPALTLATYLA 306
                      777776666666666665555555554 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   5.2e-21   1.3e-17       4     149 ..      10     157 ..       7     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 5.2e-21
                      EEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH....C-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSEE CS
  Glycos_transf_2   4 iptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak....edprvrvirreenv.GkagalnaglraatgdyilflDaDde 91 
                       p+yNe+    ++++++++q +p+++++i v+DD++ D+tve   + +k     + ++  +rr  ++  kagal ++++ +++++++++DaD +
       AJA93057.1  10 LPIYNEKYVATRLVDAVCQQdYPKDKMRIMVLDDSD-DDTVETMSNTVKkyqsLGFDIEHVRRGTRTgYKAGALKHAMKSTDSEFVAIFDADFI 102
                      79********************************99.77777655555556669999*99*99999999************************* PP

                      E-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCC CS
  Glycos_transf_2  92 pdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkg 149
                      p+  +l+k + ++ k + ++v + + +i+ +    ++++     +  +++  +++ k 
       AJA93057.1 103 PPTWYLKKAMPHFAKSNIGLVQCRWGHINENYSALTQAQA---LNLDFHFLVEQKAKS 157
                      *******************************999999986...444444444433333 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   1.7e-16   4.4e-13      13     173 .]      73     233 ..      65     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.7e-16
  Glyco_transf_21  13 vgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaaflntlagvlqa...klsglgfav 102
                      + + +K  +l +a+++   +++ i D+d + ++ yL++ + +++++++glV++     +++ ++ ++ +a+ l ++  v q    + + +   +
       AJA93057.1  73 TRTGYKAGALKHAMKSTDSEFVAIFDADFIPPTWYLKKAMPHFAKSNIGLVQCRWGHINENySALTQAQALNLDFHFLVEQKaksNSKLFMNFN 166
                      45678************************************************8776666536666666666777766655543456788999* PP

  Glyco_transf_21 103 GksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWar 173
                      G + ++r+e ++++GG      +L eD+ l+ + + +G+k  + p+ +++ ++p    +    ++q+rWa+
       AJA93057.1 167 GTAGIWRKECIDDAGGWHT--ATLVEDLDLSYRAQMKGWKCLFLPDIVVDAELPV--QMNGAKRQQFRWAK 233
                      ******************9..9*******************************96..5777899*****97 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.21   5.3e+02      19      56 ..      20      56 ..      11      61 .. 0.77
   2 !   16.1   0.3   1.2e-06    0.0031     416     540 ..     182     304 ..     172     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.21
  Cellulose_synt 19 antvlsilavdypvekvscyvsddGaalltfealaeta 56
                    +  v ++   dyp +k+ + v dd     t e++++t+
      AJA93057.1 20 TRLVDAVCQQDYPKDKMRIMVLDDSDD-DTVETMSNTV 56
                    5556678889***********999765.5777777775 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
  Cellulose_synt 416 GwiyGsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkllerl.aylnviiypftsi 509
                     Gw   ++ ed+   ++  ++Gw+ ++            p+++    +q +rwa Gs++  +     +++   +k+ +  +l a+++ + + +  +
      AJA93057.1 182 GWHTATLVEDLDLSYRAQMKGWKCLFLPD--IVVDAELPVQMNGAKRQQFRWAKGSIQCAVKLLGDILVK--RKIAFDTKLqAFIQLTRHIVFPL 272
                     8999*******************988543..4567789*********************99999999988..77777665535666665656667 PP

  Cellulose_synt 510 fllvycilpalsl.lsgkfivkelsnlasiyl 540
                     +l+ + +lp l     + +iv  l +l +  +
      AJA93057.1 273 MLIQFITLPILLAsEVNLYIVSFLPALTLATY 304
                     78888888865320334566666665555544 PP

>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       0.5   1.3e+03     128     155 ..     292     316 ..     220     356 .. 0.51
   2 ?   12.1   0.0   4.5e-05      0.11      66     129 ..     447     613 ..     441     623 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.5
      HlyIII 128 plfsrpearplravlfillgllgvipll 155
                  +   +    l  + ++++g  + + ++
  AJA93057.1 292 IV---SFLPALTLATYLAMGPGAYLLVI 316
                 22...22223333333333333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.5e-05
      HlyIII  66 ihseeklrkffaklDysgIs.lliagsylplilyal............................................................... 100
                  ++eek+ + f+kl   gI+ ++i+g y++++ ya                                                                
  AJA93057.1 447 LTKEEKMANRFYKLALGGIFaIIIIGGYMAFTGYANdvypldqsvgfldrivatsdpqsiiadinsikanlpetgnpvwifptdstnfvriqadldtml 545
                 56778999999999999998346789999999999999999********************************************************** PP

      HlyIII 101 .......................................akapkagllylslilalgvlgiisklvpl 129
                                                        +  + +  +++s+i+++++lgi+  l ++
  AJA93057.1 546 isaekiaavptdsaayhtgmldinsrsvliqenisdaipYMYVSFSNIIFSSIWIAAILGIFAVLNKK 613
                 ***********************************999988899*****************9887665 PP

>> CytochromB561_N  Cytochrome B561, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3     9e-05      0.23      21      88 ..     555     618 ..     544     625 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9e-05
  CytochromB561_N  21 pskseilalvllsiasasvllfvisredisqkaaylfvkllqivvalvailslsalikfislfkalva 88 
                      p+ s+  + ++l i s svl+     e+is +++y++v+   i+ + + i+++  ++ +++  k++++
       AJA93057.1 555 PTDSAAYHTGMLDINSRSVLIQ----ENISDAIPYMYVSFSNIIFSSIWIAAILGIFAVLNKKKQKMQ 618
                      67888899999**********9....*********************************999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4485.23
//
Query:       AJA93058.1  [L=156]
Description: aspartate carbamoyltransferase, regulatory subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-31  106.8   0.8    7.6e-31  106.2   0.8    1.3  1  PyrI       Aspartate carbamoyltransferase regulatory chain, a
      4e-16   58.7   1.6    6.2e-16   58.0   1.6    1.3  1  PyrI_C     Aspartate carbamoyltransferase regulatory chain, m
  ------ inclusion threshold ------
      0.011   15.9   1.0      0.034   14.3   0.1    2.3  3  zf-RING_7  C4-type zinc ribbon domain
      0.099   12.6   0.2       0.21   11.5   0.2    1.5  1  DUF1936    Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.8   1.7e-34   7.6e-31       2      93 ..       7      97 ..       6      98 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 1.7e-34
                -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEETTEEEEEE-- CS
        PyrI  2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIkdgevveKkkv 93
                 v++i++G+ViDHI++gk+l+vl+ L++d+ +s++ ++i+ n++s kl+kKd+ik+eg++l+ +++++la+iap+ t+niIkd+++veK++v
  AJA93058.1  7 LVRRIKDGTVIDHINEGKGLNVLEALEIDG-SSGNVITIALNMPSGKLKKKDMIKVEGRFLEGDDTNRLAVIAPSSTVNIIKDYKLVEKRRV 97
                699**************************8.7778*******************************************************98 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   1.6   1.4e-19   6.2e-16       1      45 [.     102     147 ..     102     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.4e-19
                 EEESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEH CS
      PyrI_C   1 eiegvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeise 45 
                 +ie++++C+Np CItn+ e++es ++v+dk++++lkC+YC+++++ 
  AJA93058.1 102 QIEDIFRCSNPDCITNSqEHIESIMEVIDKDNLVLKCRYCGRILDV 147
                 69***************99***********************9875 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   9.9e+03       7      21 ..       1      15 [.       1      17 [. 0.66
   2 ?   -1.6   0.0      0.75   3.3e+03      21      28 ..     104     111 ..      95     111 .. 0.73
   3 ?   14.3   0.1   7.7e-06     0.034      12      33 .]     123     145 ..     121     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                -B--CCHHHHHCCST CS
   zf-RING_7  7 melppqvlselragd 21
                me +  ++++++ g 
  AJA93058.1  1 MEQSDLLVRRIKDGT 15
                555667788888775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.75
                 TB-EE-TT CS
   zf-RING_7  21 devvtCpe 28 
                 +++++C +
  AJA93058.1 104 EDIFRCSN 111
                 46888865 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 7.7e-06
                 CHHHHHCCSTB.-EE-TTT--EE CS
   zf-RING_7  12 qvlselragde.vvtCpeCGRIL 33 
                 ++++e+  +d+ v +C +CGRIL
  AJA93058.1 123 ESIMEVIDKDNlVLKCRYCGRIL 145
                 6778888886637*********9 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   4.6e-05      0.21      22      30 ..     106     114 ..     103     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.6e-05
                 EEEES-TT- CS
     DUF1936  22 vFRCdredC 30 
                 +FRC+++dC
  AJA93058.1 106 IFRCSNPDC 114
                 7******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1260.96
//
Query:       AJA93059.1  [L=258]
Description: precorrin-4 C(11)-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-46  156.9   0.1    7.8e-46  156.7   0.1    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    0.00036   20.9   0.1    0.00064   20.1   0.1    1.4  1  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.024   14.0   0.0    1.6  1  Aldolase      KDPG and KHG aldolase
      0.047   13.5   0.0       0.11   12.3   0.0    2.0  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.1   1.7e-49   7.8e-46       1     212 [.       3     208 ..       3     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.7e-49
  TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaealaealragkdVvllvsGDPlvygtgs 97 
                   k+y+VG GpGdpel+Tv+A +++++ad++++++s+ +  +l++         ++gk  + +  + eei + l +  ++gk+V++l+ GDP vyg+ +
    AJA93059.1   3 KVYFVGCGPGDPELITVKAKKLVQKADIIVYSGSLIPPEILKYN--------KKGKIHDAAKLVREEILDLLLKNSQKGKTVIRLHDGDPAVYGAIR 91 
                   79*******************************99666666665........456777788889********************************* PP

  TP_methylase  98 elvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpglakeeereleallangdtlvllkaprklaelaelLkea.lyddtt 189
                   e ++ l++  +g+e  v+PGv+s+ a aa+lg+ lt  g +++ +    + +++ ++++++++l++++ tl+++ +++ l+++ ++ +e  +++  t
    AJA93059.1  92 EQIDNLEK--EGVESIVVPGVTSFLASAAALGTQLTLPGITQTMIitraESRTKVPKREKISELAKHQATLIFYLSVHLLNKISKEAIEGgYKK-ST 185
                   ********..999999***************************999***99999************************************5555.66 PP

  TP_methylase 190 pvavveragtedervvrgtleel 212
                   pvavv +a+++d++++ gtl+++
    AJA93059.1 186 PVAVVYKASRKDQKIILGTLTDI 208
                   ********************987 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.4e-07   0.00064      27     146 ..      55     201 ..      45     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                  HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC........................CCTEEEEEEECSSCHG.......... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxxxxxxxxxx.......... RF
  Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepllypdfvellerlakla........................vpgiritvetngtlpd.......... 90 
                  + l  eeil+++ +++  kg+ ++ l+ g+p +y  + e +++l k+                                   +g++ +          
   AJA93059.1  55 AKLVREEILDLLLKNS-QKGKTVIRLHDGDPAVYGAIREQIDNLEKEGvesivvpgvtsflasaaalgtqltL---------PGITQTmiitraesrt 142
                  567789*********6.888**************************99999**88888888885544455553.........4444445555555568 PP

                  ....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                  ....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 ....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                      +ek+ +l++   +  ++l+++ +++   ++ +++g+  +  ++++ k+ +++ k  +
   AJA93059.1 143 kvpkREKISELAKHQaTLIFYLSVHLLNKI-SKEAIEGGYKKSTPVAVVYKASRKDQKI-I 201
                  9999*********999999**********9.9999999999999999999999988883.3 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.4e-06     0.024      70     115 ..      91     136 ..      63     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-06
                 HHHHHHHHHCT-SEEEESS--HHHHHHHHHTTS-EEEEESSHHHHH CS
    Aldolase  70 aeqlaeakeaGaqfvvsPGltadllkaavdlkipllPGvstpseim 115
                 +eq+++ ++ G + +v PG+t+ l+ aa   +   lPG+++++ i 
  AJA93059.1  91 REQIDNLEKEGVESIVVPGVTSFLASAAALGTQLTLPGITQTMIIT 136
                 6899***********************************9998776 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.11      43      86 ..      77     117 ..      20     225 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                   HHHHHCH.T..THH.HHHHHHHHHHCTTESEEEE--CHHHHHHHH CS
  Asp_Glu_race  43 teaieeesgddpvl.klleaakkLekagadaiviaCnTahavade 86 
                   +   + ++gd +v+  ++e +++Lek g++ iv+++ T   +a +
    AJA93059.1  77 I---RLHDGDPAVYgAIREQIDNLEKEGVESIVVPGVTS-FLASA 117
                   3...33345557889***********************9.44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2054.96
//
Query:       AJA93060.1  [L=631]
Description: chaperone protein DnaK [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.8e-217  721.4  22.0   1.8e-195  650.6  19.3    2.2  2  HSP70     Hsp70 protein
    3.5e-19   68.8   6.9    3.5e-19   68.8   6.9    2.7  2  MreB_Mbl  MreB/Mbl protein
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.068   12.9   0.0    1.6  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
       0.18   12.2   3.3        2.1    8.8   0.6    3.3  3  DUF4376   Domain of unknown function (DUF4376)
        2.8    8.4   8.9         18    5.8   1.9    3.5  3  FtsA      Cell division protein FtsA


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   9.5e-24   3.4e-20       1      73 [.       5      82 ..       5      87 .. 0.92
   2 !  650.6  19.3  5.1e-199  1.8e-195     102     598 ..      85     581 ..      83     582 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 9.5e-24
                EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBT CS
       HSP70  1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkf 73
                +iGiDLGt ns+ +vm+ggk++ i  +eg+    ++ PsvvaF+k+ e lvGe+A+rqavtnp+nt+ ++Kr +G++f
  AJA93060.1  5 IIGIDLGTSNSAASVMQGGKPTLIPAAEGTtvagKAFPSVVAFSKDgELLVGEPARRQAVTNPDNTIREAKRKMGEDF 82
                69**************************973444678*********9*****************************98 PP

  == domain 2  score: 650.6 bits;  conditional E-value: 5.1e-199
                 EETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEE CS
       HSP70 102 eaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdv 200
                 +++g++++p+qisa++L+k+k++aea++g+++++avitvPaYfnd+qRqatkdAg+iAGL+v+Ri+NepTAa+la+G+dk++++ ++lv+D+Gggt dv
  AJA93060.1  85 KIQGKEYKPQQISAFILQKIKRDAEAFTGDTINKAVITVPAYFNDNQRQATKDAGTIAGLEVVRIINEPTAASLAFGIDKSKEDMKILVFDFGGGTLDV 183
                 5689*********************************************************************************************** PP

                 EEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHH CS
       HSP70 201 SilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakf 298
                  i+e++ Gvfev +T+gDt+lGG d+D+al++++++ef+kkegidls+d+ a+ r+ke aekaK+eLS++++te+nl++++ d +g k+l++k++Rak+
  AJA93060.1 184 TIMEMGGGVFEVMSTSGDTKLGGADMDQALIDYVIDEFRKKEGIDLSSDSTAVTRIKEGAEKAKIELSTVMETEVNLPFIAQDPSGaKNLEVKITRAKL 282
                 *************************************************************************************************** PP

                 HHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEE CS
       HSP70 299 eelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgie 397
                 e+lv+++++r+++++ kal+dakl++++i ++vl+GG tR+P v++ v++ +gke++++v+p eava GAAvqag+ +g   ++d++llDvtpL+lgie
  AJA93060.1 283 EDLVNPIVQRCKSSIDKALEDAKLSASDITKIVLIGGPTRMPIVKKFVSDTVGKEAESGVDPMEAVAFGAAVQAGIIAG-DVTSDIVLLDVTPLTLGIE 380
                 *******************************************************************************.6789*************** PP

                 ETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEE CS
       HSP70 398 tlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeiti 496
                 tlggv + +iernttipt+k ++f+taad+qtav+i+v+qger +v+dn +lgsf+l++ippaprGvpqi+V+fdidanGil+v+akd++tgk+++iti
  AJA93060.1 381 TLGGVREPIIERNTTIPTSKDKTFTTAADSQTAVTINVVQGERPMVADNVSLGSFNLTDIPPAPRGVPQINVKFDIDANGILNVTAKDMGTGKDAKITI 479
                 *************************************************************************************************** PP

                 ECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHH CS
       HSP70 497 easeglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee.aekvseaekekvesaieeLkeeleeeekeeieakteelkkvvekia 594
                 ++++++s++ei+km++dae +aeedkkkkea++ kneae+++y++ek ++++ ++k+++++  ++++ai+eLk++l ++++e+i++k+e+lk++v++++
  AJA93060.1 480 QSTTKMSDDEIKKMQEDAEGHAEEDKKKKEAVDIKNEAESFIYTTEKLVSQDlKDKIPQEKGIQITDAIKELKDSL-TQDTEQIKQKLEALKTIVNEVT 577
                 **************************************************999**********************8.8889*****************9 PP

                 HHHH CS
       HSP70 595 ekly 598
                 ++ly
  AJA93060.1 578 TELY 581
                 9887 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   6.9   9.7e-23   3.5e-19       3     316 ..       5     353 ..       3     359 .. 0.70
   2 ?    0.2   1.1     0.074   2.6e+02     219     264 ..     524     569 ..     470     584 .. 0.75

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 9.7e-23
                 EEEEEE-SSEEEEEE..TTT.........EEEEEE..ES-EEEETTT--EEEESHHHHTTTTS-GTT.E.EEE-SEETTEESSHHHHH...HHHHHHH. CS
    MreB_Mbl   3 dlgiDLGtantlvyv..kgk.........givlne..psvvAikkktkkvlavGeeAkkmlgktpgn.i.kavrPlkdGviadlevae...ellkyfi. 82 
                  +giDLGt n  + v   gk           v  +  psvvA++k+ +  l vGe A++     p+n i +a r + +  +  ++  e   + +  fi 
  AJA93060.1   5 IIGIDLGTSNSAASVmqGGKptlipaaegTTVAGKafPSVVAFSKDGE--LLVGEPARRQAVTNPDNtIrEAKRKMGEDFLYKIQGKEykpQQISAFIl 101
                 589999999876533112221111111102333223488888887655..5699999876555555416347899998877666544322266666552 PP

                 HHHHT.SS-S...S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS.-EEEEEE-SS-EEEEEEETTEEE.....EEE CS
    MreB_Mbl  83 kkvkk.kksl...skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveeps.gnmvvdiGggttevavislggiv.....tsk 171
                 +k+k+ ++++   + ++ vi+vP   ++ +r+A k+a + aG + v +i+ep aA +  g++ ++     +v d Gggt +v+++ +gg v     ts 
  AJA93060.1 102 QKIKRdAEAFtgdTINKAVITVPAYFNDNQRQATKDAGTIAGLEVVRIINEPTAASLAFGIDKSKEDmKILVFDFGGGTLDVTIMEMGGGVfevmsTSG 200
                 566654333423356789*******************************************987665156789**************985522222456 PP

                 EES-SHHHHHHHHHHHHHHHHS....EE--HHH.........HHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHH CS
    MreB_Mbl 172 svrvaGdeldeaiikyirkkyn....lliGert.........aekikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveav 257
                   +++G ++d+a+i+y+  +++    + + + +         aek kie+++++++e +       +d       ev+++ +++++ ++  v++  +++
  AJA93060.1 201 DTKLGGADMDQALIDYVIDEFRkkegIDLSSDStavtrikegAEKAKIELSTVMETEVNL--PFIAQDPSGAKNLEVKITRAKLEDLVNPIVQRCKSSI 297
                 69**************96666511114444332111111222666677776666665544..4445666666777899999999999999999999999 PP

                 HHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHH CS
    MreB_Mbl 258 kevLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtg 316
                  ++Le+++   a+di++  ivl GG + +  ++k++s+++g + + + dp+++va G++
  AJA93060.1 298 DKALEDAKLS-ASDITK--IVLIGGPTRMPIVKKFVSDTVGKEAESGVDPMEAVAFGAA 353
                 9999997643.568865..9999*********************************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.074
                 EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS CS
    MreB_Mbl 219 kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLekt 264
                 + ++  +dl   +p+e  ++ ++  + lk+++++ +e++k+ Le+ 
  AJA93060.1 524 TEKLVSQDLKDKIPQEKGIQITDAIKELKDSLTQDTEQIKQKLEAL 569
                 4456667888888888888888888888888888888888888765 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.068     145     196 ..     304     358 ..     276     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
      FGGY_C 145 d..sgkpldrlavdGGgskndllmqllAdilgvpVerpkt.aeatalGaAilAav 196
                    s ++++++++ GG ++ + + ++  d +g+  e   +  ea+a+GaA+ A++
  AJA93060.1 304 AklSASDITKIVLIGGPTRMPIVKKFVSDTVGKEAESGVDpMEAVAFGAAVQAGI 358
                 2447899*************************998876666***********986 PP

>> DUF4376  Domain of unknown function (DUF4376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.18   6.5e+02      52      79 ..     268     295 ..     230     306 .. 0.80
   2 ?    0.0   0.0       0.3   1.1e+03      18      47 ..     398     428 ..     390     439 .. 0.79
   3 ?    8.8   0.6   0.00058       2.1      45      97 ..     522     572 ..     501     575 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
     DUF4376  52 tladntvvtLtadqlialgqavaqhkqa 79 
                 + a+n  v++t ++l++l++ ++q+ ++
  AJA93060.1 268 SGAKNLEVKITRAKLEDLVNPIVQRCKS 295
                 579999*************999998665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.3
     DUF4376  18 v.nGkridtdeesrarlsgvllsaklageqg 47 
                    +k++ t ++s+  ++  + +++++++++
  AJA93060.1 398 TsKDKTFTTAADSQTAVTINVVQGERPMVAD 428
                 347899**********999999999988875 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00058
     DUF4376  45 eqgeeaWtladntvvtLtadqlialgqavaqhkqaifdrerelkaaieaaetl 97 
                  ++e+     d ++ ++ +++ i++++a+ + k++  + ++++k+++ea++t+
  AJA93060.1 522 YTTEK-LVSQDLKD-KIPQEKGIQITDAIKELKDSLTQDTEQIKQKLEALKTI 572
                 44444.66667777.8899999*****************************98 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.016        58       1      21 [.       6      26 ..       6      43 .. 0.84
   2 ?    5.8   1.9    0.0051        18       2      77 ..     173     325 ..     172     355 .. 0.64
   3 ?    0.1   0.2      0.29   1.1e+03      70      85 ..     522     576 ..     452     612 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                EEEEE-SSSEEEEEEETTEEE CS
                xxxxxxxxxxxxxxxxxxxxx RF
        FtsA  1 alvDiGagktdvavaedgalv 21
                +++D+G++ + ++v+++g+++
  AJA93060.1  6 IGIDLGTSNSAASVMQGGKPT 26
                58***************9875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0051
                 EEEE-SSSEEEEEEETTEEEE.....EEEES-...-HHHHHHH...................HHHHHT--HHHHHHHHHHH--S--............. CS
                 xxxxxxxxxxxxxxxxxxxxx.....xxxxxx...xxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxx............. RF
        FtsA   2 lvDiGagktdvavaedgalvh.....lrvigv...ggngitkd...................iakalrtaveeAerikikyGsala............. 60 
                 + D+G+g+ dv+++e+g+ v+     +        gg  +++                     ++a+    e Ae+ ki+  ++++             
  AJA93060.1 173 VFDFGGGTLDVTIMEMGGGVFevmstSG---DtklGGADMDQAlidyvidefrkkegidlssDSTAVTRIKEGAEKAKIELSTVMEtevnlpfiaqdps 268
                 569*************985544433333...14558888888887777777777777777665666677778888888887777777777777777766 PP

                 .....EEEEEHHHHH...................................GGGGSTT CS
                 .....xxxxxxxxxx...................................xxxxxxx RF
        FtsA  61 .....ekeigrkels...................................ggsalpn 77 
                      e +i+r++l+                                   g + +p 
  AJA93060.1 269 gaknlEVKITRAKLEdlvnpivqrckssidkaledaklsasditkivligGPTRMPI 325
                 666664444444444555566666655555555555555555555555555555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.29
                 H.......................................GGGGSTTHHHHHHHH CS
                 x.......................................xxxxxxxxxxxxxxx RF
        FtsA  70 s.......................................ggsalpnleelaera 85 
                                                          + +l+ l+++++++
  AJA93060.1 522 YtteklvsqdlkdkipqekgiqitdaikelkdsltqdteqIKQKLEALKTIVNEV 576
                 0222333333334444444444555555555555555554445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2318  (0.129288); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 3943.25
//
Query:       AJA93061.1  [L=62]
Description: DNA-directed RNA polymerase subunit E'' [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-13   49.1   0.7    5.5e-13   48.8   0.7    1.1  1  Spt4      Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
      0.019   14.5   5.3      0.025   14.1   5.3    1.2  1  RecR      RecR protein
       0.62    9.8   7.0        1.1    9.0   0.2    2.1  2  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.7   9.2e-17   5.5e-13       2      77 .]       5      62 .]       4      62 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 9.2e-17
        Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                 AC++C+ v+t +      Cp+C            s+++s++++G+v +++p++S++ +   l+ ++pg+YAlkv+
  AJA93061.1  5 LACRECRCVTTAKV-----CPVC-----------KSTDLSPDWNGIVLVVKPTNSKISNT--LGITKPGKYALKVT 62
                69*********999.....****...........99************************..************95 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   5.3   4.3e-06     0.025      19      37 ..       7      25 ..       4      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-06
                -TTT--EESSSS-CCCCST CS
        RecR 19 CsrCgnlteedlCaICsdp 37
                C++C+++t+  +C++C+++
  AJA93061.1  7 CRECRCVTTAKVCPVCKST 25
                ****************986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.0    0.0056        34       2      13 ..       2      13 ..       1      16 [. 0.82
   2 ?    9.0   0.2   0.00018       1.1       4      14 ..      16      26 ..      14      30 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0056
     zf-RRN7  2 ekgppCgvCgcr 13
                 k+ +C +C+c+
  AJA93061.1  2 AKELACRECRCV 13
                57899******6 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00018
     zf-RRN7  4 gppCgvCgcrs 14
                 ++C+vC +++
  AJA93061.1 16 AKVCPVCKSTD 26
                58******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 456.52
//
Query:       AJA93062.1  [L=295]
Description: hypothetical protein T478_0766 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2130.16
//
Query:       AJA93063.1  [L=339]
Description: NAD(+)/NADH kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-30  103.9   0.1    1.2e-29  103.4   0.1    1.2  1  NAD_kinase       ATP-NAD kinase
    0.00016   21.2   0.7    0.00078   18.9   0.0    2.5  3  HTH_24           Winged helix-turn-helix DNA-binding
    0.00086   19.2   0.7     0.0081   16.1   0.1    2.5  2  MarR             MarR family
     0.0017   18.8   0.1     0.0039   17.6   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain
     0.0028   17.5   0.9      0.019   14.8   0.6    2.6  2  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.023   14.2   0.0       0.04   13.3   0.0    1.3  1  TPALS            TIR- and PNP-associating SLOG family
      0.035   13.5   2.3      0.055   12.8   2.3    1.3  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
      0.088   13.2   0.4       0.26   11.6   0.2    1.9  2  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.1   5.4e-33   1.2e-29      73     275 ..      35     229 ..      12     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 5.4e-33
                 TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEES.SS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE......EEEEEEESSEE CS
  NAD_kinase  73 afadagvdliivvGGDGTaldvarllqkaeiPvlgvna.Gvkgfltefepeaaaellekllegeirvekrevldavimrskgeediadiviensvlnev 170
                 +  +++ d++ v+GGD  ++  ++ + +a+iPvlg+n   + gfl++++ +++ +l++++ + ++++e+ ++l ++i  ++           + vln+v
  AJA93063.1  35 KSKNKKSDCVFVLGGDKGVRNYFHRTFDASIPVLGINEsESDGFLSQLDLKQLPSLISRIKKMDFETEQVTRLGVKIDGKNV----------YPVLNDV 123
                 5567899****************99999*********94578********************************99977766..........789**** PP

                 EEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-.SS--EEEEETTTE CS
  NAD_kinase 171 viirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirva.srseallaldGse 268
                  +   + + l e  l v++  +  d +dg+i+stP+Gs ays+saGgp+i  + + + i  ++    + rp+Vvs+ s +++    sr  + ++ldG +
  AJA93063.1 124 AVFSSRSAMLMEHTLRVNGDEVWHDSSDGIIISTPIGSSAYSMSAGGPVIFQDSDVFGIISVNSIDITRRPLVVSNASVIEVDEIsSRLHCEVVLDGLD 222
                 *********************************************************************************87447************9 PP

                 EEEE-TT CS
  NAD_kinase 269 elelspg 275
                 +++++ +
  AJA93063.1 223 RYKVKNS 229
                 9998865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.73   1.6e+03       4      23 ..      13      32 ..      10      37 .. 0.70
   2 ?   -2.6   0.0       1.8   4.1e+03      20      30 ..     251     261 ..     245     263 .. 0.77
   3 !   18.9   0.0   3.5e-07   0.00078       7      48 .]     273     314 ..     269     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.73
      HTH_24  4 tdrkILelLqknprisqreL 23
                   +IL+ + ++ +is + +
  AJA93063.1 13 SSERILKKILDENHISSSKI 32
                56688977777788887766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
      HTH_24  20 qreLAerlglS 30 
                 ++ +A+++ l 
  AJA93063.1 251 ISAIAKKVKLA 261
                 67899999885 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 3.5e-07
      HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                  +L++L+ ++++sq+eL +++ l+  tv+  +  L e+G++k
  AJA93063.1 273 LLLKILEYEGSMSQKELVKKTMLPDRTVRLAMSHLLEKGYVK 314
                 579*************************************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   5.9e+02       2      28 ..      11      37 ..      10      41 .. 0.80
   2 !   16.1   0.1   3.6e-06    0.0081       7      58 ..     273     324 ..     268     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                -HHHHHHHHHHHHSTTEEHHHHHHHHT CS
        MarR  2 tltqfviLrilyeqgplsvseLakklg 28
                t +  +iL ++ +++ +s s+++ k++
  AJA93063.1 11 TDSSERILKKILDENHISSSKIGTKSK 37
                666668999999999999999999986 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 3.6e-06
                 HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
        MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58 
                 ++L il+++g++s++eL kk ++   tv  +  +L +kG+++++ s +D R+
  AJA93063.1 273 LLLKILEYEGSMSQKELVKKTMLPDRTVRLAMSHLLEKGYVKKKVSIRDSRQ 324
                 5899***************************************999999987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.7e-06    0.0039       9      64 ..     275     329 ..     268     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.7e-06
      HTH_27   9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64 
                 L  ++  ++ +++++l++++++ d ++  ++++L ekG+v+++ + +d r+k +++
  AJA93063.1 275 LKILE-YEGSMSQKELVKKTMLPDRTVRLAMSHLLEKGYVKKKVSIRDSRQKIYEI 329
                 44444.8899999****************************************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   2.9e+03       4      16 ..      68      80 ..      67      88 .. 0.79
   2 !   14.8   0.6   8.7e-06     0.019      12      63 ..     272     328 ..     270     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                CHHHHHCCCHCHH CS
        TrmB  4 lGLseyEakvYla 16
                lG++e E++ +l 
  AJA93063.1 68 LGINESESDGFLS 80
                89****9998875 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.7e-06
                 CHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEE CS
        TrmB  12 kvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYr 63 
                 k  l++l  +g+++ +e+ +++ +p  +v  +++ L++kG+V+++ +      k+Y+
  AJA93063.1 272 KLLLKILeYEGSMSQKELVKKTMLPDRTVRLAMSHLLEKGYVKKKVSIrdsrQKIYE 328
                 5667788678999******************************98755555566666 PP

>> TPALS  TIR- and PNP-associating SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05      0.04     117     165 ..      20      71 ..       9      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
       TPALS 117 sieddn.mtgkri..eaqarvgdalialGGgkGVsylAnkyhkagkPviPLd 165
                 +i d+n +++ +i    + + +d +++lGG+kGV    ++ ++a  Pv+ ++
  AJA93063.1  20 KILDENhISSSKIgtKSKNKKSDCVFVLGGDKGVRNYFHRTFDASIPVLGIN 71 
                 4555555777777666778899**************************9665 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.3   2.4e-05     0.055      72     146 ..     255     327 ..     215     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                    E--CCCHHHHHTSXHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEE CS
  RNA_pol_Rpc34  72 avsreeAkkktslsedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiY 146
                    a++ + A+ + +++ + +l ++i e  G     ++++ +k+ L++  v+  +  L  k+y+k+  s+  + +kiY
     AJA93063.1 255 AKKVKLAEELFNMPPSSKLLLKILEYEGS--MSQKELVKKTMLPDRTVRLAMSHLLEKGYVKKKVSIRDSRQKIY 327
                    566677999999*************9998..69****************************************** PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.5   1.2e+04      75      94 ..      74      93 ..      58     107 .. 0.61
   2 ?   11.6   0.2   0.00012      0.26      25      55 ..     287     317 ..     272     330 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.5
                     XXXXXXXXXXXXXXXXXXXX CS
  Penicillinase_R 75 avkqlldklfegsvkelvaa 94
                     +++++l++l  +++++l+++
       AJA93063.1 74 ESDGFLSQLDLKQLPSLISR 93
                     55555555555555555444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                      HT--GGG---HHHHHHHHHHHHHTTS-EEEE CS
  Penicillinase_R  25 eeleeekelaysTVktllrrLvkKgllsrek 55 
                      +el +++ l + TV+  +++L++Kg+++++ 
       AJA93063.1 287 KELVKKTMLPDRTVRLAMSHLLEKGYVKKKV 317
                      455566677799***************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2288.38
//
Query:       AJA93064.1  [L=125]
Description: hypothetical protein T478_0734 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.033   14.4   0.2      0.077   13.2   0.0    1.8  2  Response_reg  Response regulator receiver domain
      0.046   13.3   5.1      0.052   13.1   5.1    1.1  1  Cas_DxTHG     CRISPR-associated (Cas) DxTHG family
       0.16   12.2   0.9       0.55   10.5   0.2    1.8  2  OrfB_IS605    Probable transposase


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.077      31      59 ..      17      45 ..       5      57 .. 0.88
   2 ?   -3.2   0.0       1.5   9.2e+03      11      23 ..     101     113 ..      98     118 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                  SHHHHHHHHHHHHESEEEEESSCSSSEHH CS
  Response_reg 31 dgkealellkeekvdlillDinmpgmdGl 59
                  ++ + +++l+ +k d ++lD+++++++Gl
    AJA93064.1 17 NSYDIIKNLEDSKEDFLILDVELSKINGL 45
                  7788999*********************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                   HHHHHHHHHHTTE CS
  Response_reg  11 rellrqlleeegy 23 
                   r+ + + l++e++
    AJA93064.1 101 RNSIVKSLQDEKM 113
                   4455555554444 PP

>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.1   8.7e-06     0.052     219     337 ..      14     116 ..       3     123 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.7e-06
   Cas_DxTHG 219 efskalelirplellekaeklekeiveklkeeleei.eslee....eesakplellldeikkklekf..lkkqikwclekgliqqaltllreliislll 310
                 ++ ++  +i                 ++l++++e +     e    +  +k l    de+++k ++f  lkk+i+ + ++ ++ ++l+ ++e++     
  AJA93064.1  14 KILNSYDII-----------------KNLEDSKEDFlILDVElskiNGLLKVLLRKSDEFSDKNSEFskLKKKIQNYFQNYYFVEELEKMKEIY----- 90 
                 333333333.................33333333331111110000223444444666666666666777777*********************..... PP

   Cas_DxTHG 311 egedilnkkkrreeieeelknlskvek 337
                  +ed l  k  r+ i ++l+  + +++
  AJA93064.1  91 -SEDPLRVKHIRNSIVKSLQDEKMIFR 116
                 .77776666666999898866665555 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.14   8.6e+02      88     104 ..       4      20 ..       2      27 .. 0.84
   2 ?   10.5   0.2   9.2e-05      0.55      46     101 ..      49     110 ..      39     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
  OrfB_IS605  88 rkhllhklathliktlk 104
                 +++++h l +++++ ++
  AJA93064.1   4 VDEYFHDLMKKILNSYD 20 
                 7899*********9997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.2e-05
  OrfB_IS605  46 lksdykylakeiaelqsklkkskn......ykkasrklarlhrkrsrrrkhllhklathlik 101
                 l ++  +++ ++ e+++++kk +n      + +  +k++ ++ +   r+kh  ++++++l +
  AJA93064.1  49 LLRKSDEFSDKNSEFSKLKKKIQNyfqnyyFVEELEKMKEIYSEDPLRVKHIRNSIVKSLQD 110
                 55667788888888888888888888888799*************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1682  (0.0938145); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 875.95
//
Query:       AJA93065.1  [L=283]
Description: prephenate dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-26   92.5   0.3    2.8e-26   92.1   0.3    1.1  1  PDH             Prephenate dehydrogenase
    6.1e-07   29.7   0.2    3.2e-06   27.4   0.0    2.1  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    1.1e-05   26.0   0.5    3.8e-05   24.2   0.0    2.2  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    0.00011   21.7   0.1    0.00025   20.5   0.1    1.6  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0015   18.2   0.1     0.0078   15.9   0.1    2.0  1  ApbA            Ketopantoate reductase PanE/ApbA
     0.0016   18.9   0.0      0.025   15.1   0.0    2.5  2  CoA_binding_2   CoA binding domain
     0.0026   17.7   0.2     0.0075   16.2   0.0    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0077   16.7   1.2        1.1    9.7   0.2    3.3  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.026   14.6   0.0    1.6  1  DUF1392         Protein of unknown function (DUF1392)
      0.015   15.4   0.2      0.061   13.4   0.0    2.2  3  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.017   14.6   0.0      0.092   12.2   0.0    2.0  2  Epimerase       NAD dependent epimerase/dehydratase family
      0.028   14.4   1.2       0.83    9.6   0.1    2.6  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.06   12.8   0.2       0.26   10.7   0.0    2.1  2  adh_short       short chain dehydrogenase
      0.097   12.9   0.6       0.25   11.6   0.1    1.9  1  CUTL            CUT1-like DNA-binding domain of SATB
       0.12   12.6   1.5        3.2    8.1   0.2    2.4  2  Cas_Csa5        CRISPR-associated protein (Cas_Csa5)


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.3   2.4e-29   2.8e-26      34     256 ..      44     254 ..      22     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 2.4e-29
                 SEEES-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE- CS
         PDH  34 deatdd.ieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPt 131
                    +++ i+a+ + d v+l++P +++ e+++ +a+ +k++  ++D++s K k + +l ++ + ++s +  hPm+G+         ++ ++n+  +L P 
  AJA93065.1  44 K--AQSlISAILNVDYVLLSTPTKKTPEIIRLIAKEMKRESYLIDITSQKSKTATALGKIPA-KVSPICIHPMFGP--------GAKNLKNHNIVLIPI 131
                 3..34449*************************************************99988.9************........67779********** PP

                 TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH....CGGGS-HHHHHHHHHHTHHHH CS
         PDH 132 ektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt....RiaksnPelwadilleNkeav 226
                 + ++k+ l+ +k l+ +  + ++ +++ eHD+ +a++ +l+h++ ia a+ + +k +++ +  k a+  f+        i+  +Pel + i+  N e +
  AJA93065.1 132 K-DGKKELNVAKTLFPD--GNFVTIDSTEHDKKIAMILGLTHLINIAFAN-ILAKDDKISLTEKMAGTTFKAQKilaeSIMTESPELIETII-SNPE-I 224
                 9.999*********985..7899***************************.6667788899**********8776778999*********96.6998.* PP

                 HHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
         PDH 227 lealdkfikelkklkelienedaeeLvell 256
                  ++ ++f k++ +l +  ++++ ee++ ++
  AJA93065.1 225 RKVAEEFWKDVGRLLASAQEGKGEEIIDYI 254
                 **************9999999999988776 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.7e-09   3.2e-06       1     101 [.       4      99 ..       4     106 .. 0.88
   2 ?   -0.5   0.1       1.1   1.3e+03      56      95 ..     211     259 ..     169     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.7e-09
                    EEEEE--S.HHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HH CS
  NAD_binding_2   1 kigfiGlG.vMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkkgdilidgstsspe 95 
                    +i++iG G  MG+ + + + k+g++v++++ t+      va+++k a+s+ +++ ++d v++  +  k++ e+i+ +++++k++++lid ++ + +
     AJA93065.1   4 TIAIIGAGgAMGKWFSEYFSKKGFEVTGFDNTNP-----VAKNIKKAQSLISAILNVDYVLLSTPT-KKTPEIIRLIAKEMKRESYLIDITSQKSK 93 
                    5999**9549********************9954.....5566778899999999********987.7899*********************9999 PP

                    HHHHHH CS
  NAD_binding_2  96 dtrela 101
                    +++ l 
     AJA93065.1  94 TATALG 99 
                    988765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                    C.SEEEE-SSSHHHHHHHHHS.......HCCC-..-TT-EEEE-S---HH CS
  NAD_binding_2  56 l.dvvitmvkagkavdevieg.......lleal..kkgdilidgstsspe 95 
                      +++ t++++ +++++v e+       ll+++   kg+ +id  +++ e
     AJA93065.1 211 SpELIETIISN-PEIRKVAEEfwkdvgrLLASAqeGKGEEIIDYINTNKE 259
                    23555555544.45556666544445553332233566677777666654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.2e-08   3.8e-05       1      96 [.       4      89 ..       4      90 .. 0.87
   2 ?   -1.9   0.0       4.3   5.2e+03      15      47 ..     176     204 ..     161     230 .. 0.55
   3 ?   -2.7   0.0       7.6     9e+03      11      38 ..     236     260 ..     232     274 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.2e-08
                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEESS CS
  F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvisvla 96
                   +i+ii ++G mg+ + + ++++g    e++ +     +  +  a++++ k+++     a+ + d v+l+ ++++++e+++ +ak+ ++++ +i+++ 
     AJA93065.1  4 TIAIIgAGGAMGKWFSEYFSKKG---FEVT-G----FDNTNPVAKNIK-KAQS--LISAILNVDYVLLSTPTKKTPEIIRLIAKEMKRESYLIDITS 89
                   59***55689*************...9999.7....666777777775.5555..788999*********************************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                    HHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
  F420_oxidored  15 asgllaagaqpheivvansrnpekaeelaeelg 47 
                      ++la++    +i ++ +++  +  ++++ l 
     AJA93065.1 176 FANILAKD---DKISLT-EKMAGTTFKAQKILA 204
                    44455555...555533.444444444444443 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.6
                    HHHHHHHHHHTTS-GGCEEEEEESSCCC CS
  F420_oxidored  11 gealasgllaagaqpheivvansrnpek 38 
                    g+ las    +g   +ei+   + n+ek
     AJA93065.1 236 GRLLASAQEGKG---EEIIDYINTNKEK 260
                    555555444444...5555444444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.1e-07   0.00025      37     126 ..       3      87 ..       1      99 [. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                   SEEEEES-S.HHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEES CS
  2-Hacid_dh_C  37 ktvGiiGlG.rIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNt 126
                   kt++iiG+G ++G+ + +++++ g++v+++d ++   +    +  + +sl  ++ + D+v l +p t++t ++i     ++mk++++li +
    AJA93065.1   3 KTIAIIGAGgAMGKWFSEYFSKKGFEVTGFDNTNPVAK----NIKKAQSLISAILNVDYVLLSTP-TKKTPEIIRLI-AKEMKRESYLIDI 87 
                   9******96389*********************77444....3336789****************.99999999754.4889999999975 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.5e-06    0.0078       1      61 [.       5      67 ..       5     107 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.5e-06
                EEEES-S.HHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH CS
        ApbA  1 iailGaG.aiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae 61
                iai+GaG a+G  +  + +k+g +vt  ++++  ++++kk+ + ++   +  +++ ++++ ++
  AJA93065.1  5 IAIIGAGgAMGKWFSEYFSKKGFEVTGFDNTNpVAKNIKKAQSLISAILNVDYVLLSTPTKKT 67
                89***9548***********************77777***99999888755555555544444 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.025       1      79 [.       3      79 ..       3     110 .. 0.82
   2 ?    0.7   0.0      0.62   7.4e+02      20      44 ..     118     142 ..     118     170 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                   --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH.HHH- CS
  CoA_binding_2  1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea.lalg 79
                   +tia++Ga    g  g    +y+ ++g++v+    + +     k+ +sl ++  +vd v + tp ++tpei++ + ++++
     AJA93065.1  3 KTIAIIGAG---GAMGKWFSEYFSKKGFEVTGFDNTNPVAKNIKKAQSLISAILNVDYVLLSTPTKKTPEIIRLIaKEMK 79
                   7999***65...557779999***********9888777777888999997679*******************9855555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.62
                    HHHHHHHT--EEEESSS-SEETTEE CS
  CoA_binding_2  20 lryllehglpvvpVnpkeeeilgek 44 
                    +++l++h++  +p+   ++e+  +k
     AJA93065.1 118 AKNLKNHNIVLIPIKDGKKELNVAK 142
                    57999**********9999988754 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.3e-06    0.0075       1      41 [.       4      45 ..       4      96 .. 0.80
   2 ?   -2.2   0.1       2.8   3.4e+03     148     174 ..     249     275 ..     248     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.3e-06
                EEEEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
     3HCDH_N  1 kvaviGa.GtmGagiaavfasagleVvlvdiseealekalek 41
                ++a+iGa G mG+   + f ++g+eV+ +d ++  +++ +++
  AJA93065.1  4 TIAIIGAgGAMGKWFSEYFSKKGFEVTGFDNTNPVAKNIKKA 45
                69*****789********************976555443332 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                 EEEE-TT--HHHHHHHHHHHHHTT-EE CS
     3HCDH_N 148 EvvrgekTseetvatvvelakkigktp 174
                 E++   +T++e +++ v+l k+ +k +
  AJA93065.1 249 EIIDYINTNKEKISQNVDLEKSYKKLT 275
                 777788888888888888888877754 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00096       1.1       2      99 ..       5      90 ..       4     102 .. 0.68
   2 ?    1.1   0.0      0.41     5e+02      16      55 ..     224     266 ..     214     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                    EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTS...EEEE CS
  Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelapklaeagv...kviD 95
                    +ai+Ga G++G+ + ++ ++ + +e++ +  ++    k++++a        +       + ++ +vd+v+l++p + + e+ + +a++     ++iD
      AJA93065.1  5 IAIIGAGGAMGKWFSEYFSK-KGFEVTGFDNTNP-VAKNIKKA--------QSL-----ISAILNVDYVLLSTPTKKTPEIIRLIAKEMKresYLID 86
                    67888888888888887776.4566666444333.33333333........223.....3346799**********999999999555444448999 PP

                    SSST CS
  Semialdhyde_dh 96 lssd 99
                     +s+
      AJA93065.1 87 ITSQ 90
                    8875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.41
                     HHHHHCTSSEEEEEEEESTT.TTTSBHHHHSG..GGTTTECEB CS
  Semialdhyde_dh  16 lrlLeehpevelvvllsssr.saGkklaeavk..aleegkdlk 55 
                     +r ++e+++ ++ +ll+s++  +G+++ ++ +  + +  +++ 
      AJA93065.1 224 IRKVAEEFWKDVGRLLASAQeGKGEEIIDYINtnKEKISQNVD 266
                     5667788888999999999867888888887733233333333 PP

>> DUF1392  Protein of unknown function (DUF1392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.026      78     117 ..     135     174 ..     120     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
     DUF1392  78 lkkltvkkpafkLGdlveldfaekgtkqrlilGialvkks 117
                  k+l+v+k  f  G+ v++d++e+++k+ +ilG++ + + 
  AJA93065.1 135 KKELNVAKTLFPDGNFVTIDSTEHDKKIAMILGLTHLINI 174
                 47899****************************9877554 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.1e-05     0.061      13      70 ..      17      73 ..       4     111 .. 0.73
   2 ?   -2.5   0.0       4.3   5.1e+03      49      67 ..     121     139 ..     118     164 .. 0.65
   3 ?   -1.6   0.0       2.4   2.8e+03      72      90 ..     181     200 ..     135     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                HHHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-B CS
      DpaA_N 13 ylarkLaekgakvslygleleekiegvekaesleealedadviilPvpgtkdggeint 70
                +  +++++kg++v+ +    +   ++++ka+sl +a+ ++d+++l +p  k  + i+ 
  AJA93065.1 17 WFSEYFSKKGFEVTGFDN-TNPVAKNIKKAQSLISAILNVDYVLLSTPTKKTPEIIRL 73
                5668999****9999888.899999***********************8877777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                 GGG-SEEE--TT-BETTTE CS
      DpaA_N  49 ledadviilPvpgtkdgge 67 
                 l++ ++++ P+   k++ +
  AJA93065.1 121 LKNHNIVLIPIKDGKKELN 139
                 5666677777664444433 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                 S-SS-EE-.HHHHHTS-TT- CS
      DpaA_N  72 fseeklsl.eelleklkkgq 90 
                  +++k+sl e+++  + k q
  AJA93065.1 181 AKDDKISLtEKMAGTTFKAQ 200
                 35555566555554444444 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05     0.092       1      42 [.       5      46 ..       5      91 .. 0.74
   2 ?   -0.2   0.0      0.46   5.5e+02      17     101 ..     120     206 ..     118     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHH CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarled 42
                i ++Ga G +G+ + +++ +kg ev+g+d+ +   ++ ++++
  AJA93065.1  5 IAIIGAGGAMGKWFSEYFSKKGFEVTGFDNTNPVAKNIKKAQ 46
                679***************************954444333332 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.46
                 HHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S..---HHHHHHSHHHHHHHHTHHHHHHHHH CS
   Epimerase  17 allekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa..vggvaassedpadfieknlqgtlnllea 101
                 +l+++++ +i ++  +++   +  ++l    ++v++d t++++  +++   + ++ i++A   +   +++++  ++++ ++++ +  l+e 
  AJA93065.1 120 NLKNHNIVLIPIKDGKKEL--NVAKTLfpdgNFVTIDSTEHDKKIAMIL--GLTHLINIAFanILAKDDKISLTEKMAGTTFKAQKILAES 206
                 6666666666666663322..2333337788999999999998777777..7777777754346666666666666666666666666655 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4    0.0089        11       2      41 ..       5      45 ..       4      47 .. 0.89
   2 ?    9.6   0.1   0.00069      0.83      53     102 ..      38      87 ..      34      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0089
                    EEEE--.SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
  NAD_Gly3P_dh_N  2 iavlGa.GswGtalAkvlaenghevrlwvreeelieeinee 41
                    ia++Ga G+ G  ++  ++++g ev+ + + + ++++i+++
      AJA93065.1  5 IAIIGAgGAMGKWFSEYFSKKGFEVTGFDNTNPVAKNIKKA 45
                    9****8359*********************99999999876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00069
                     --TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE- CS
  NAD_Gly3P_dh_N  53 lpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsl 102
                     + +n++  + l +a+ ++d+++l  P++ + e+++ +++ +k++  l+ +
      AJA93065.1  38 VAKNIKKAQSLISAILNVDYVLLSTPTKKTPEIIRLIAKEMKRESYLIDI 87 
                     5689999**********************************999888865 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.26       1      47 [.       3      48 ..       3     100 .. 0.78
   2 ?   -0.6   0.1      0.63   7.5e+02      18      72 ..     229     282 ..     225     283 .] 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee 47
                k++ ++Ga++ +G+ +++ + k+G++v+ +d+++ ++++ +k+ +++
  AJA93065.1  3 KTIAIIGAGGAMGKWFSEYFSKKGFEVTGFDNTN-PVAKNIKKAQSL 48
                7899*************************99985.555666665554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.63
                 HHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT.SHHHHHHHHHHHH CS
   adh_short  18 kelakeGakvvvvdrseekleevakelkeegakalaiqvDvt.dreevealvekav 72 
                 +e+ k+  +++ ++ +e k ee+++ ++ + ++ +  +vD++ +++++ ++v+++ 
  AJA93065.1 229 EEFWKDVGRLL-ASAQEGKGEEIIDYINTN-KEKISQNVDLEkSYKKLTKMVNTID 282
                 55555544444.466778899999999986.5667788999877888888888775 PP

>> CUTL  CUT1-like DNA-binding domain of SATB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021      0.25      26      50 ..      34      58 ..      27      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
        CUTL 26 lqstlakecplvqSmiSsivNstYy 50
                + +  ak++   qS+iS+i N  Y 
  AJA93065.1 34 NTNPVAKNIKKAQSLISAILNVDYV 58
                667889****************996 PP

>> Cas_Csa5  CRISPR-associated protein (Cas_Csa5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.089   1.1e+02      19      57 ..      35      85 ..      31     105 .. 0.62
   2 ?    8.1   0.2    0.0027       3.2      22      78 ..     204     259 ..     197     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.089
    Cas_Csa5 19 keavakvlydaqRivqmglergeiksdtvkikek...............eyPai 57
                 ++vak +  aq ++ ++l+ + + + t     k               e   i
  AJA93065.1 35 TNPVAKNIKKAQSLISAILNVDYVLLSTP---TKktpeiirliakemkrESYLI 85
                57899999999999999999999988887...4401223333333333333334 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
    Cas_Csa5  22 vakvlydaqRivqmglergeiksdtvkikekeyPaivikkkegkkyevvGylpsded 78 
                 ++ ++ ++  ++++++++ ei+  + ++  k+  ++  +++egk  e++ y+ ++++
  AJA93065.1 204 AESIMTESPELIETIISNPEIRKVAEEF-WKDVGRLLASAQEGKGEEIIDYINTNKE 259
                 56788999999**********9988865.689**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2112.17
//
Query:       AJA93066.1  [L=304]
Description: putative malate dehydrogenase, NAD-dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-38  131.1   0.6    5.4e-38  130.3   0.6    1.4  1  Ldh_1_N        lactate/malate dehydrogenase, NAD binding doma
    8.1e-27   94.2   0.1    1.2e-26   93.6   0.1    1.2  1  Ldh_1_C        lactate/malate dehydrogenase, alpha/beta C-ter
  ------ inclusion threshold ------
      0.023   14.3   0.7       0.61    9.6   0.0    2.5  3  Glyco_hydro_4  Family 4 glycosyl hydrolase


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.6     9e-42   5.4e-38       3     141 .]       2     140 ..       1     140 [. 0.99

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 9e-42
                 EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S-SS-TTTTHHHHHHHHHHHHHH CS
     Ldh_1_N   3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitagvprkpGetRddLlkvNakIvke 100
                 ++++Ga G++G   al  a + l de+ LlDia+   +G+a+dl+h+     ++v+v++ +++e++k++++vv++ag+ rkpG+tR dLlk+Na++vk+
  AJA93066.1   2 ITIIGA-GKVGGDAALFSALRRLDDEILLLDIAEGLPQGEAMDLNHMLSEQGIDVNVKGsNNYEDMKGSKIVVVVAGAGRKPGMTRMDLLKINAGVVKD 99 
                 89****.**************************************************999*************************************** PP

                 HHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
     Ldh_1_N 101 iveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                 +v +i+k+a++a+++ v+NP d ++++++k sg++++rv+g
  AJA93066.1 100 VVGNIKKFADDAMIIPVTNPLDPMAQIAYKTSGFDRSRVFG 140
                 ***************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.1   2.1e-30   1.2e-26       3     160 ..     145     299 ..     143     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 2.1e-30
                 HHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS-HHHHHHHHHHHH CS
     Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvkakkGagsatlsmAvAgakfve 91 
                 LD+ R+k+f+ e +g + +s k+ ViG+H++          v +ipl         l +++l+e+++ ++  ++ev+k k   g++  + ++A+  ++e
  AJA93066.1 145 LDLSRFKQFIHEATGYSRESTKALVIGEHGEnmlpltrfatVSGIPL------PTLLPKEKLDEIFTATKGVAAEVIKLK---GATVHAPGNAISAMIE 234
                 9******************************9999666666556666......567899*********************...9*************** PP

                 HHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHHHH CS
     Ldh_1_C  92 allrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkkei 160
                 ++++d k+++++++ ldge+g kd   + ++vP+v+gk+Gvek+le l+lnd+e+e ++k v+  k+ +
  AJA93066.1 235 SVVQDKKQVIPVSTNLDGEYGQKD---VSIGVPAVVGKKGVEKILE-LELNDEEKEWFNKGVDSVKNAL 299
                 ************************...9******************.**************99999875 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.015        89       2      87 ..       2      82 ..       1      91 [. 0.74
   2 ?    9.6   0.0    0.0001      0.61     122     160 ..      95     133 ..      87     142 .. 0.89
   3 ?   -3.3   0.0      0.94   5.6e+03      38      52 ..     197     211 ..     195     237 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                   EEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHHCTTTCEEEEESSHHHHHTT-SEEEE---TTHHH CS
  Glyco_hydro_4  2 iviiGgGStifaklllgdlkkteelsvselaLvDideerldaiqtlakklveeagadlkieattdrkealkdadfVitairvGlek 87
                   i+iiG+G       l + l + ++    e+ L+Di e   +  +  ++++  e+g d++++   +  e +k   +V++ +  G ++
     AJA93066.1  2 ITIIGAGKVGGDAALFSALRRLDD----EILLLDIAEGLPQGEAMDLNHMLSEQGIDVNVKGSNNY-EDMKGSKIVVVVAGAGRKP 82
                   899999999999999999887664....89999999966566666678888899999988766554.4578888888777777544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0001
                    HHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTT CS
  Glyco_hydro_4 122 pvlleIakdieelcPdawvlnytNPaavvteallrlvpn 160
                    +v+ +++ +i++++ da ++  tNP+  ++++ ++++++
     AJA93066.1  95 GVVKDVVGNIKKFADDAMIIPVTNPLDPMAQIAYKTSGF 133
                    57889*****************************99875 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.94
                    HHHHHHHHHHHHHHH CS
  Glyco_hydro_4  38 eerldaiqtlakklv 52 
                    +e+ld+i+t++k + 
     AJA93066.1 197 KEKLDEIFTATKGVA 211
                    677777777665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2255.43
//
Query:       AJA93067.1  [L=55]
Description: putative lysine biosynthesis protein LysW [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00021   21.2   0.3       0.54   10.2   0.0    2.1  2  zinc_ribbon_4    zinc-ribbon domain
    0.00029   20.3   1.3     0.0004   19.9   1.3    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.002   18.0   1.0      0.003   17.4   1.0    1.3  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0028   18.0   1.0     0.0032   17.8   1.0    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0044   16.7   3.1       0.16   11.7   0.2    2.4  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.015   15.0   0.3      0.032   14.0   0.3    1.6  2  zinc_ribbon_5    zinc-ribbon domain
      0.017   15.1   0.6      0.019   15.0   0.6    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.029   14.9   0.1       0.83   10.2   0.0    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.031   14.3   0.2        1.4    9.0   0.2    2.1  2  Ogr_Delta        Ogr/Delta-like zinc finger
      0.039   13.9   0.3      0.052   13.5   0.3    1.3  1  zinc-ribbons_6   zinc-ribbons
      0.041   13.7   2.4       0.63    9.9   2.4    2.1  1  zf-HYPF          HypF finger
      0.076   13.1   0.2        0.1   12.6   0.2    1.3  1  Elf1             Transcription elongation factor Elf1 like
      0.077   13.1   0.5        5.4    7.2   0.0    2.1  2  Zn-ribbon_8      Zinc ribbon domain
       0.12   12.3   4.1       0.22   11.5   4.1    1.5  1  Prok-RING_1      Prokaryotic RING finger family 1
       0.13   11.9   1.3        3.6    7.3   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.17   12.7   1.2        1.1   10.1   0.0    2.0  2  zinc_ribbon_15   zinc-ribbon family


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00076      0.85       5      18 ..       3      16 ..       1      20 [. 0.88
   2 !   10.2   0.0   0.00048      0.54       2      16 ..      21      35 ..      21      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00076
  zinc_ribbon_4  5 CpsCkakyeiddek 18
                   Cp+C a  +i+++ 
     AJA93067.1  3 CPECDANMNIPEDA 16
                   ***********985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00048
  zinc_ribbon_4  2 kitCpsCkakyeidd 16
                   +++C  C+a yei+ 
     AJA93067.1 21 IVSCGDCGADYEIAK 35
                   699**********97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.3   3.5e-07    0.0004       1      27 [.       1      29 [.       1      34 [. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-07
                  EEETTTTCEE.CHEETSTTCE.EESSSSB CS
  TF_Zn_Ribbon  1 ykCPnCgstn.lveDpergel.vCtdCGl 27
                  + CP+C   + + eD++ ge+  C+dCG+
    AJA93067.1  1 MNCPECDANMnIPEDAAVGEIvSCGDCGA 29
                  56******999**********99*****6 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0   2.7e-06     0.003       4      33 ..       3      33 ..       3      36 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.7e-06
                    ESTTT.SBEEEEECSCCCEEEESSSS-EEES CS
  RNA_POL_M_15KD  4 CpkCg.NlLlpkedkegknfeCrqCgYeepa 33
                    Cp+C  N+ +p ++  g ++ C  Cg+ +++
      AJA93067.1  3 CPECDaNMNIPEDAAVGEIVSCGDCGADYEI 33
                    ****857777777777777***********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.0   2.9e-06    0.0032       5      45 ..       2      39 ..       1      53 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga.stpwfkiae 45
                      CP C     + ++  v +     v+C dCga  +   k+ +
       AJA93067.1  2 NCPECDANMNIPEDAAVGE----IVSCGDCGAdYEIAKKEGS 39
                     6*************99998....*********5333333333 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.015        16       2      18 ..       2      18 ..       2      19 .. 0.86
   2 !   11.7   0.2   0.00014      0.16       3      16 ..      24      37 ..      23      38 .. 0.91
   3 ?   -2.0   0.0       2.7   3.1e+03       7      17 ..      38      48 ..      38      49 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                    B-SSS--B----SSS-- CS
  DNA_RNApol_7kD  2 iCgeCgaevslkkgdpi 18
                    +C eC+a++ + + +++
      AJA93067.1  2 NCPECDANMNIPEDAAV 18
                    699******99988765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                    -SSS--B----SSS CS
  DNA_RNApol_7kD  3 CgeCgaevslkkgd 16
                    Cg+Cga+ ++ k++
      AJA93067.1 24 CGDCGADYEIAKKE 37
                    **********9986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.7
                    --B----SSS- CS
  DNA_RNApol_7kD  7 gaevslkkgdp 17
                    g++ +lk+ + 
      AJA93067.1 38 GSDIELKEAET 48
                    57889998876 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.9e-05     0.032       4      32 ..       2      28 ..       1      33 [. 0.94
   2 ?    7.0   0.1    0.0042       4.7       2      16 ..      21      35 ..      20      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-05
  zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkkVrCakCa 32
                    Cp+Cd    + ++     g  V C+ C+
     AJA93067.1  2 NCPECDANMNIPEDA--AVGEIVSCGDCG 28
                   6**************..***********8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
  zinc_ribbon_5  2 iirCpdCdtkFklvd 16
                   i++C dC+  + ++ 
     AJA93067.1 21 IVSCGDCGADYEIAK 35
                   899****99887775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   1.7e-05     0.019      72     111 ..       2      47 ..       1      48 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                 EETTTS-EEECHHH.HH....S-TTTSSS.-EEEEESSSEEEEEEE CS
        HypA  72 rCreCgkefeleek.al....rCpkCgsa.dveivsGeellvksie 111
                  C eC++++++ e+ a+    +C++Cg+  ++  ++G+++++k+ e
  AJA93067.1   2 NCPECDANMNIPEDaAVgeivSCGDCGADyEIAKKEGSDIELKEAE 47 
                 7*********77653336667******9767777889999999876 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.12   1.3e+02       8      16 ..       3      11 ..       1      16 [. 0.85
   2 ?   10.2   0.0   0.00074      0.83       5      21 ..      21      37 ..      19      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
  Zn_ribbon_recom  8 CgeCGspmt 16
                     C eC ++m 
       AJA93067.1  3 CPECDANMN 11
                     99**99996 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00074
  Zn_ribbon_recom  5 llrCgeCGspmtrrkrk 21
                     ++ Cg+CG+ +   k+ 
       AJA93067.1 21 IVSCGDCGADYEIAKKE 37
                     688******99776654 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0012       1.4       1      11 [.       2      12 ..       2      15 .. 0.90
   2 ?    3.6   0.0     0.059        66       2      23 ..      24      45 ..      23      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
   Ogr_Delta  1 rCPhCgapaaa 11
                +CP+C a++ +
  AJA93067.1  2 NCPECDANMNI 12
                6********86 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
   Ogr_Delta  2 CPhCgapaaartsrnlskdvre 23
                C  Cga   + +++  +  ++e
  AJA93067.1 24 CGDCGADYEIAKKEGSDIELKE 45
                8899999999988887777766 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   4.6e-05     0.052       2      28 ..       2      33 ..       1      40 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-05
                    --SSS-S--E.E-S....SEEE-TTT--EEEE CS
  zinc-ribbons_6  2 kCpeCqqele.krg....eqyhCeaCqedlkk 28
                    +CpeC+++++  ++    e ++C  C +d++ 
      AJA93067.1  2 NCPECDANMNiPEDaavgEIVSCGDCGADYEI 33
                    7********965447898999*****999875 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4   0.00056      0.63       2      33 ..       3      33 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00056
                -HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
     zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCGPrlsl 33
                C++C + ++ p+d     + +sC +CG  + +
  AJA93067.1  3 CPECDANMNIPEDAAV-GEIVSCGDCGADYEI 33
                9999999999998655.489*******99987 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   9.3e-05       0.1      23      61 ..       2      37 ..       1      42 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.3e-05
        Elf1 23 dCpfCnheksvevkldkkekiae.vsCkvCgesfetkvna 61
                +Cp C+++    +++ +   ++e vsC+ Cg+++e+  ++
  AJA93067.1  2 NCPECDAN----MNIPEDAAVGEiVSCGDCGADYEIAKKE 37
                79***999....77777777765279********987665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.028        31      29      35 ..       3       9 ..       1      12 [. 0.78
   2 ?    7.2   0.0    0.0048       5.4       8      19 ..      24      35 ..      14      45 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.028
  Zn-ribbon_8 29 CPeCgse 35
                 CPeC ++
   AJA93067.1  3 CPECDAN 9 
                 9***876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0048
  Zn-ribbon_8  8 CeeCghefevlq 19
                 C +Cg ++e+  
   AJA93067.1 24 CGDCGADYEIAK 35
                 888998888554 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.1   0.00019      0.22       6      30 ..       2      31 ..       1      47 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
  Prok-RING_1  6 kCpvCgkelkee.....dDiVvCpeCgtpy 30
                 +Cp C+ +++         iV C +Cg+ y
   AJA93067.1  2 NCPECDANMNIPedaavGEIVSCGDCGADY 31
                 6****999986633556679********98 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0032       3.6       5      16 ..       3      14 ..       1      17 [. 0.84
   2 ?    3.7   0.1     0.041        46       3      15 ..      22      34 ..      20      37 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0032
      zf_UBZ  5 CerCgkeipese 16
                C++C++++ ++e
  AJA93067.1  3 CPECDANMNIPE 14
                *****9998774 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
      zf_UBZ  3 ylCerCgkeipes 15
                + C +Cg+  +++
  AJA93067.1 22 VSCGDCGADYEIA 34
                57*****877665 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2      0.23   2.6e+02       2       9 ..       2       9 ..       1      20 [. 0.60
   2 ?   10.1   0.0   0.00094       1.1      36      63 ..      20      47 ..      10      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
  zinc_ribbon_15 2 lCpkCgkl 9
                    Cp+C+ +
      AJA93067.1 2 NCPECDAN 9
                   45555433 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00094
  zinc_ribbon_15 36 pylacskCkslleaskelgkeiekkess 63
                     ++ c +C++ +e+ k++g++ie ke++
      AJA93067.1 20 EIVSCGDCGADYEIAKKEGSDIELKEAE 47
                    5899************999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 377.37
//
Query:       AJA93068.1  [L=117]
Description: aminoacyl-tRNA hydrolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-39  132.5   0.0    9.4e-39  132.3   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.0   5.2e-43   9.4e-39       2     117 .]       5     117 .]       4     117 .] 0.98

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 5.2e-43
                 EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEEEETSSSSSSTTCEEEEEEE CS
        PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaalirDagrtqiepgtkTvlaig 100
                 k+v+ vr+DL+m+kGkiaaq++hA+v+ +++++k+ ++ e++++W  +gq+k+v+kv+  +eL+e+++ a +lglp + i+Dag+tqi+pgt+T++ +g
  AJA93068.1   5 KQVIAVRTDLGMGKGKIAAQVGHACVMGAEHVRKS-HP-EWFQTW-WTGQEKVVVKVSGIKELDEVKRGAIELGLPWSEITDAGHTQIAPGTTTCISVG 100
                 9*********************************8.88.8*****.89*************************************************** PP

                 EEEHHHHHHHHTTSEB- CS
        PTH2 101 PapksivdkvtgkLkll 117
                 Pap++++dkvtg+L ll
  AJA93068.1 101 PAPENLIDKVTGDLSLL 117
                 **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 839.92
//
Query:       AJA93069.1  [L=55]
Description: putative lysine biosynthesis protein LysW [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-08   33.9   3.8    2.7e-05   24.0   1.3    2.1  2  zinc_ribbon_4    zinc-ribbon domain
      9e-07   28.6   3.0    0.00021   21.0   0.8    2.0  2  zinc_ribbon_5    zinc-ribbon domain
    6.5e-05   22.2   1.0       0.18   11.3   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0002   21.2   0.7    0.00025   20.9   0.7    1.2  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00022   21.1   3.8    0.00073   19.4   3.8    1.8  1  Prok-RING_1      Prokaryotic RING finger family 1
     0.0003   20.3   1.3       0.14   11.8   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    0.00037   20.8   1.1       0.27   11.7   0.1    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
     0.0006   19.3   1.7    0.00074   19.0   1.7    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00096   19.2   3.1        0.4   10.8   0.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
     0.0011   19.2   4.9     0.0063   16.7   0.4    2.5  2  zf-RING_7        C4-type zinc ribbon domain
      0.002   18.0   5.5      0.052   13.5   2.8    2.0  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0023   17.7   1.7       0.67    9.8   0.1    2.1  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0026   17.9   0.7     0.0034   17.6   0.7    1.1  1  IBR              IBR domain, a half RING-finger domain
     0.0031   17.2   0.9       0.38   10.5   0.0    2.2  2  YacG             DNA gyrase inhibitor YacG
     0.0037   17.2   2.3          1    9.4   0.2    2.1  2  Ogr_Delta        Ogr/Delta-like zinc finger
     0.0038   16.5   2.4      0.066   12.5   3.8    1.9  2  zf-TFIIB         Transcription factor zinc-finger
      0.005   16.8   1.2       0.94    9.6   0.1    2.3  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.008   16.2   1.2       0.26   11.3   0.2    2.0  2  BssC_TutF        BssC/TutF protein
     0.0099   15.9   1.1      0.016   15.2   1.1    1.5  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.014   15.4   0.9      0.038   14.0   0.9    1.7  1  zinc-ribbons_6   zinc-ribbons
      0.015   15.0   2.2       0.17   11.7   0.2    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.016   15.3   5.0       0.78    9.9   0.4    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.017   15.1   0.2      0.023   14.6   0.2    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.017   15.1   0.3      0.018   15.0   0.3    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.018   15.1   1.3        0.7   10.0   0.1    2.1  2  zf-C2H2_6        C2H2-type zinc finger
       0.04   14.2   4.4       0.28   11.5   4.4    2.0  1  zinc_ribbon_9    zinc-ribbon
      0.047   13.7   2.6       0.88    9.6   0.2    2.1  2  CpXC             CpXC protein
      0.047   13.7   0.1        1.1    9.3   0.0    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.051   13.5   0.9        3.7    7.5   0.0    2.1  2  Cys_rich_CPXG    Cysteine-rich CPXCG
      0.051   13.3   2.5       0.16   11.7   2.5    1.7  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.061   13.3   1.2        1.2    9.2   0.2    2.1  2  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
      0.067   13.0   3.0       0.73    9.7   0.1    2.1  2  PADR1            PADR1 (NUC008) domain
      0.068   13.2   0.3       0.24   11.4   0.0    1.9  2  ADK_lid          Adenylate kinase, active site lid
      0.074   13.5   1.4        1.8    9.2   0.0    2.1  2  zf-H2C2_2        Zinc-finger double domain
        0.1   13.5   0.4        3.3    8.8   0.1    2.1  2  zf-C2H2_4        C2H2-type zinc finger
        0.1   12.4   0.2        8.3    6.3   0.0    2.1  2  zf_C2HC_14       C2HC Zing finger domain
       0.16   11.8   4.6        1.7    8.5   4.5    2.0  1  zf-HYPF          HypF finger
       0.16   12.1   0.9       0.79    9.8   0.9    1.8  1  TerY_C           TerY-C metal binding domain
       0.16   12.4   2.1        0.2   12.1   2.1    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.19   11.9   4.7        6.1    7.0   0.4    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.21   12.1   0.4        7.8    7.1   0.0    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.25   11.4   0.8       0.32   11.0   0.8    1.2  1  DUF1451          Zinc-ribbon containing domain
        0.3   10.8   4.8        7.6    6.4   4.8    2.5  1  zinc_ribbon_2    zinc-ribbon domain
       0.33   11.5   1.1        3.9    8.1   0.0    2.1  2  zf-C2H2          Zinc finger, C2H2 type
       0.36   10.8   3.3       0.55   10.2   3.3    1.4  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        1.7    8.6   5.7        4.3    7.3   0.2    2.2  2  DUF3797          Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.3     7e-08   2.7e-05       4      35 ..       3      32 ..       1      33 [. 0.91
   2 !   15.4   0.0   3.4e-05     0.013       2      16 ..      22      36 ..      22      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7e-08
  zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35
                    Cp+C a  +i+d+ + ++   v+C+ Cg++F
     AJA93069.1  3 NCPECDANMKIPDDAVEGE--IVTCPECGASF 32
                   7*************99887..89*******99 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.4e-05
  zinc_ribbon_4  2 kitCpsCkakyeidd 16
                   ++tCp+C+a +e++ 
     AJA93069.1 22 IVTCPECGASFELAK 36
                   69**********986 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.8   5.5e-07   0.00021       3      35 ..       2      32 ..       1      33 [. 0.93
   2 !   12.8   0.1   0.00019     0.073       2      16 ..      22      36 ..      21      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.5e-07
  zinc_ribbon_5  3 irCpdCdtkFklvdsklKksgkkVrCakCaevF 35
                   + Cp+Cd   k+ d+   + g  V C  C+  F
     AJA93069.1  2 TNCPECDANMKIPDDA--VEGEIVTCPECGASF 32
                   89**************..***********9766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
  zinc_ribbon_5  2 iirCpdCdtkFklvd 16
                   i+ Cp+C+  F l+ 
     AJA93069.1 22 IVTCPECGASFELAK 36
                   799********9986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0011      0.43       2      11 ..       1      10 [.       1      18 [. 0.71
   2 !   11.3   0.1   0.00045      0.18       3      10 ..      23      30 ..      21      36 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
  zf-ribbon_3  2 tvrCPnCGap 11
                 +++CP+C+a+
   AJA93069.1  1 MTNCPECDAN 10
                 7899999995 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00045
  zf-ribbon_3  3 vrCPnCGa 10
                 v+CP+CGa
   AJA93069.1 23 VTCPECGA 30
                 68999998 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.7   6.3e-07   0.00025       4      32 ..       4      33 ..       1      37 [. 0.91

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.3e-07
                    ESTTT.SBEEEEECSCCCEEEESSSS-EEE CS
  RNA_POL_M_15KD  4 CpkCg.NlLlpkedkegknfeCrqCgYeep 32
                    Cp+C  N+ +p++++eg ++ C  Cg+ ++
      AJA93069.1  4 CPECDaNMKIPDDAVEGEIVTCPECGASFE 33
                    ****769********************999 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   3.8   1.9e-06   0.00073       5      30 ..       2      32 ..       1      38 [. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.9e-06
  Prok-RING_1  5 kkCpvCgkelkeedD.....iVvCpeCgtpy 30
                 ++Cp C+ ++k  dD     iV+CpeCg+++
   AJA93069.1  2 TNCPECDANMKIPDDavegeIVTCPECGASF 32
                 58******99977654444489*******96 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0053       2.1       4      15 ..       3      14 ..       1      19 [. 0.83
   2 !   11.8   0.1   0.00036      0.14       3      16 ..      23      36 ..      21      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0053
      zf_UBZ  4 lCerCgkeipes 15
                 C++C++++ ++
  AJA93069.1  3 NCPECDANMKIP 14
                6******99887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00036
      zf_UBZ  3 ylCerCgkeipese 16
                ++C++Cg++++ ++
  AJA93069.1 23 VTCPECGASFELAK 36
                69*******99876 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0075       2.9       2      20 ..       2      19 ..       2      23 .. 0.81
   2 !   11.7   0.1    0.0007      0.27       3      29 ..      24      47 ..      23      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0075
     zf-IS66  2 rtCpcCGgllkpigedrvr 20
                ++Cp+C + + +i++d+v 
  AJA93069.1  2 TNCPECDANM-KIPDDAVE 19
                58*****987.99999775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0007
     zf-IS66  3 tCpcCGgllkpigedrvreeldipPak 29
                tCp+CG+   ++++   +e +++ Pa+
  AJA93069.1 24 TCPECGASF-ELAKA--SEGFELKPAQ 47
                7*****964.45544..5899999998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.7   1.9e-06   0.00074       3      30 ..       4      33 ..       2      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-06
                  ETTTTCEE.CHEETSTTCE.EESSSSBEEE CS
  TF_Zn_Ribbon  3 CPnCgstn.lveDpergel.vCtdCGlVle 30
                  CP+C   + +  D+ +ge+ +C++CG+  e
    AJA93069.1  4 CPECDANMkIPDDAVEGEIvTCPECGASFE 33
                  ********9*****************8666 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2     0.001       0.4       2       9 ..       3      10 ..       3      19 .. 0.78
   2 !    9.0   0.3    0.0038       1.5      17      22 ..      25      30 ..      21      33 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
     UPF0547  2 vCPeCeak 9 
                +CPeC+a 
  AJA93069.1  3 NCPECDAN 10
                7*****85 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0038
     UPF0547 17 CphCGy 22
                Cp+CG 
  AJA93069.1 25 CPECGA 30
                666665 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3      0.11        45      25      30 ..       3       8 ..       1       9 [. 0.80
   2 !   16.7   0.4   1.6e-05    0.0063      21      31 ..      20      30 ..      15      30 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.11
                E-TTT- CS
   zf-RING_7 25 tCpeCG 30
                 CpeC 
  AJA93069.1  3 NCPECD 8 
                7****6 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.6e-05
                TB-EE-TTT-- CS
   zf-RING_7 21 devvtCpeCGR 31
                +e+vtCpeCG+
  AJA93069.1 20 GEIVTCPECGA 30
                89********6 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   2.8   0.00013     0.052       4      26 ..       3      29 ..       1      33 [. 0.91
   2 !   10.3   0.0    0.0014      0.54       5      15 ..      25      35 ..      22      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
  PhnA_Zn_Ribbon  4 kCplCaSeytY....edgallvCpeCa 26
                    +Cp+C +        ++g++  CpeC+
      AJA93069.1  3 NCPECDANMKIpddaVEGEIVTCPECG 29
                    8*************************8 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
  PhnA_Zn_Ribbon  5 CplCaSeytYe 15
                    Cp+C+++++++
      AJA93069.1 25 CPECGASFELA 35
                    9****999994 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.3    0.0074       2.9       3      11 ..       3      11 ..       1      15 [. 0.82
   2 !    9.8   0.1    0.0017      0.67       2      10 ..      23      31 ..      22      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0074
                    E-SSS--EE CS
  zf-C4_Topoisom  3 kCPkCggdL 11
                     CP+C +++
      AJA93069.1  3 NCPECDANM 11
                    699999988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0017
                    EE-SSS--E CS
  zf-C4_Topoisom  2 ekCPkCggd 10
                    ++CP+Cg+ 
      AJA93069.1 23 VTCPECGAS 31
                    79*****74 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   8.7e-06    0.0034      19      48 ..       2      32 ..       1      33 [. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.7e-06
         IBR 19 kwCprpdCeaiiekseg...cksvtCskCgfef 48
                ++Cp  +C+a ++  ++    + vtC++Cg +f
  AJA93069.1  2 TNCP--ECDANMKIPDDaveGEIVTCPECGASF 32
                79**..******999996644559******998 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.031        12       2      12 ..       3      13 ..       2      18 .. 0.81
   2 !   10.5   0.0   0.00097      0.38       1      16 [.      23      38 ..      23      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.031
        YacG  2 kCPtCkkevew 12
                +CP C++++++
  AJA93069.1  3 NCPECDANMKI 13
                8****998875 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00097
        YacG  1 vkCPtCkkevewseen 16
                v+CP C++++e ++++
  AJA93069.1 23 VTCPECGASFELAKAS 38
                89*********99876 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2    0.0027         1       1      11 [.       3      13 ..       3      15 .. 0.91
   2 !    8.2   0.1    0.0064       2.5       1       8 [.      24      31 ..      24      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0027
   Ogr_Delta  1 rCPhCgapaaa 11
                +CP+C a++ +
  AJA93069.1  3 NCPECDANMKI 13
                6********87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0064
   Ogr_Delta  1 rCPhCgap 8 
                +CP+Cga 
  AJA93069.1 24 TCPECGAS 31
                6*****96 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   3.8   0.00017     0.066       1      26 [.       3      29 ..       3      29 .. 0.85
   2 !    8.5   0.1     0.003       1.2       2      16 ..      25      39 ..      24      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
    zf-TFIIB  1 kCPkCqdele.eserggveidyCpqCr 26
                +CP C ++++ + +  + ei +Cp+C+
  AJA93069.1  3 NCPECDANMKiPDDAVEGEIVTCPECG 29
                6*********54555889********7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
    zf-TFIIB  2 CPkCqdeleesergg 16
                CP C++++e ++ ++
  AJA93069.1 25 CPECGASFELAKASE 39
                *******99877743 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.022       8.5       1       7 [.       3       9 ..       3      18 .. 0.84
   2 !    9.6   0.1    0.0024      0.94       1       7 [.      24      30 ..      24      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.022
  DNA_ligase_ZBD 1 hCPvCGs 7
                   +CP+C++
      AJA93069.1 3 NCPECDA 9
                   6****86 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0024
  DNA_ligase_ZBD  1 hCPvCGs 7 
                    +CP+CG+
      AJA93069.1 24 TCPECGA 30
                    7*****7 PP

>> BssC_TutF  BssC/TutF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00066      0.26       1      17 [.       1      17 [.       1      21 [. 0.92
   2 ?    4.3   0.0       0.1        41       3      21 ..      24      42 ..      22      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00066
   BssC_TutF  1 mstCeeCkfffavPeda 17
                m++C eC   +++P+da
  AJA93069.1  1 MTNCPECDANMKIPDDA 17
                9**************98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
   BssC_TutF  3 tCeeCkfffavPedadDfe 21
                tC eC   f++ +  + fe
  AJA93069.1 24 TCPECGASFELAKASEGFE 42
                9*****9999999999888 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.1   4.1e-05     0.016      15      39 ..       4      33 ..       1      44 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.1e-05
         DZR 15 CseCgtklkavaa.....edrCpsCgekvd 39
                C+eC +++k + +       +Cp+Cg++ +
  AJA93069.1  4 CPECDANMKIPDDavegeIVTCPECGASFE 33
                888888887444477887788888887754 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9   9.6e-05     0.038       2      29 ..       3      35 ..       2      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.6e-05
                    --SSS-S--E.E-S....SEEE-TTT--EEEEE CS
  zinc-ribbons_6  2 kCpeCqqele.krg....eqyhCeaCqedlkke 29
                    +CpeC+++++  ++    e ++C +C ++++  
      AJA93069.1  3 NCPECDANMKiPDDavegEIVTCPECGASFELA 35
                    699999999865447777889999999887754 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.18        69      23      29 ..       3       9 ..       2      12 .. 0.84
   2 ?   11.7   0.2   0.00043      0.17      23      32 ..      24      33 ..      20      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
  A2L_zn_ribbon 23 vCieCga 29
                   +C+eC a
     AJA93069.1  3 NCPECDA 9 
                   7****75 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00043
  A2L_zn_ribbon 23 vCieCgasfp 32
                    C+eCgasf+
     AJA93069.1 24 TCPECGASFE 33
                   5*******97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.5     0.029        11      27      36 ..       2      11 ..       1      13 [. 0.77
   2 ?    9.9   0.4     0.002      0.78       8      16 ..      25      33 ..      23      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
  Zn-ribbon_8 27 taCPeCgsev 36
                 t CPeC +++
   AJA93069.1  2 TNCPECDANM 11
                 55****9876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
  Zn-ribbon_8  8 CeeCghefe 16
                 C eCg  fe
   AJA93069.1 25 CPECGASFE 33
                 666666666 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   5.9e-05     0.023      30      56 ..       3      32 ..       2      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-05
  OrfB_Zn_ribbon 30 tCseCgsknke...alsgrtfkCpnCgfea 56
                    +C+eC +++k    a++g+ ++Cp+Cg+++
      AJA93069.1  3 NCPECDANMKIpddAVEGEIVTCPECGASF 32
                    7********99999*************875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3   4.7e-05     0.018      71     107 ..       2      43 ..       1      48 [. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.7e-05
                 EEETTTS-EEECHHHHH.....S-TTTSSS-EEEEESSSEEE CS
        HypA  71 vrCreCgkefeleekal.....rCpkCgsadveivsGeellv 107
                 + C eC++++++ ++a+     +Cp+Cg++    ++ e++++
  AJA93069.1   2 TNCPECDANMKIPDDAVegeivTCPECGASFELAKASEGFEL 43 
                 57*********77642345567******96444444455555 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.097        38       2       9 ..       2       9 ..       1      10 [. 0.85
   2 ?   10.0   0.1    0.0018       0.7       4      12 ..      25      33 ..      24      36 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.097
   zf-C2H2_6 2 heCsvCsk 9
               ++C++C++
  AJA93069.1 2 TNCPECDA 9
               58****86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0018
   zf-C2H2_6  4 CsvCsksFp 12
                C++C++sF+
  AJA93069.1 25 CPECGASFE 33
                ********6 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.4   0.00072      0.28       7      31 ..       6      32 ..       4      32 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00072
  zinc_ribbon_9  7 qCdrfVsvspdedsd...vlCPhCgggF 31
                   +Cd +  +  d   +   v+CP+Cg  F
     AJA93069.1  6 ECDANMKIPDD-AVEgeiVTCPECGASF 32
                   89999999444.3225547******988 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.072        28      38      49 ..       2      13 ..       1      18 [. 0.74
   2 ?    9.6   0.2    0.0023      0.88      38      49 ..      23      34 ..      18      39 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.072
        CpXC 38 atCpkCgatakl 49
                + Cp+C+a+ k+
  AJA93069.1  2 TNCPECDANMKI 13
                578888887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0023
        CpXC 38 atCpkCgatakl 49
                +tCp+Cga+++l
  AJA93069.1 23 VTCPECGASFEL 34
                466666666655 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.29   1.1e+02      20      25 ..       3       8 ..       1      13 [. 0.78
   2 ?    9.3   0.0    0.0029       1.1      19      31 ..      23      36 ..      16      44 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.29
  Zn_Tnp_IS1595 20 vCPhCg 25
                    CP C 
     AJA93069.1  3 NCPECD 8 
                   5****7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
  Zn_Tnp_IS1595 19 fvCPhCgsr.kayr 31
                   ++CP Cg + ++ +
     AJA93069.1 23 VTCPECGASfELAK 36
                   68*****8877665 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.058        22       2      19 ..       3      20 ..       2      22 .. 0.88
   2 ?    7.5   0.0    0.0094       3.7       1      12 [.      23      34 ..      23      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.058
  Cys_rich_CPXG  2 qCPyCgeeievlvDlsag 19
                   +CP C +++++  D+ +g
     AJA93069.1  3 NCPECDANMKIPDDAVEG 20
                   6*********99999887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0094
  Cys_rich_CPXG  1 iqCPyCgeeiev 12
                   ++CP Cg+++e+
     AJA93069.1 23 VTCPECGASFEL 34
                   68*******986 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.5   0.00041      0.16       2      25 ..       3      30 ..       3      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                    B-SSS--B----....SSS----SSS-- CS
  DNA_RNApol_7kD  2 iCgeCgaevslk....kgdpiRCkeCGh 25
                    +C eC+a++++     +g+++ C eCG 
      AJA93069.1  3 NCPECDANMKIPddavEGEIVTCPECGA 30
                    699******99833445899*******5 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.2     0.003       1.2       1       9 [.       4      12 ..       4      13 .. 0.92
   2 ?    3.3   0.0      0.21        81       1       7 [.      25      31 ..      25      34 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.003
    PriA_CRR  1 CpnCdvslt 9 
                Cp Cd++++
  AJA93069.1  4 CPECDANMK 12
                *******97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
    PriA_CRR  1 CpnCdvs 7 
                Cp C +s
  AJA93069.1 25 CPECGAS 31
                ****997 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.5     0.066        26      13      21 ..       1       9 [.       1      16 [. 0.76
   2 ?    9.7   0.1    0.0019      0.73       6      26 ..      15      34 ..      10      42 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.066
       PADR1 13 lekCpeCke 21
                + +CpeC  
  AJA93069.1  1 MTNCPECDA 9 
                579****94 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0019
       PADR1  6 DgmlfGalekCpeCkegqlvf 26
                D  + G +  CpeC+  ++++
  AJA93069.1 15 DDAVEGEIVTCPECG-ASFEL 34
                6677899*******9.65554 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       3.5   1.4e+03       4       8 ..       4       8 ..       3      11 .. 0.74
   2 ?   11.4   0.0   0.00061      0.24       3      14 ..      24      35 ..      23      50 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.5
               -TTT- CS
     ADK_lid 4 CpkCG 8
               Cp C 
  AJA93069.1 4 CPECD 8
               88885 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00061
                E-TTT--EEETT CS
     ADK_lid  3 vCpkCGrsYhvv 14
                +Cp CG+s+ ++
  AJA93069.1 24 TCPECGASFELA 35
                8********866 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.3      0.27     1e+02      16      21 ..       3       8 ..       3      12 .. 0.84
   2 ?    9.2   0.0    0.0045       1.8      15      24 ..      23      32 ..      18      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.27
   zf-H2C2_2 16 eCplCd 21
                +Cp+Cd
  AJA93069.1  3 NCPECD 8 
                5****8 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0045
   zf-H2C2_2 15 yeCplCdkaF 24
                ++Cp+C+ +F
  AJA93069.1 23 VTCPECGASF 32
                89*****999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.47   1.8e+02       2       9 ..       3      10 ..       2      16 .. 0.79
   2 ?    8.8   0.1    0.0086       3.3       2      11 ..      24      33 ..      23      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.47
   zf-C2H2_4  2 kCpiCgks 9 
                 Cp C+++
  AJA93069.1  3 NCPECDAN 10
                6****765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0086
   zf-C2H2_4  2 kCpiCgksFs 11
                +Cp Cg+sF 
  AJA93069.1 24 TCPECGASFE 33
                6********5 PP

>> zf_C2HC_14  C2HC Zing finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.021       8.3       5      16 ..       2      13 ..       1      15 [. 0.86
   2 ?    4.6   0.1     0.071        28       6      18 ..      24      36 ..      19      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.021
  zf_C2HC_14  5 gnCkgCekqVcL 16
                +nC +C+ ++++
  AJA93069.1  2 TNCPECDANMKI 13
                8******99875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.071
  zf_C2HC_14  6 nCkgCekqVcLSk 18
                +C +C+  + L+k
  AJA93069.1 24 TCPECGASFELAK 36
                8******999976 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.5    0.0044       1.7       2      33 ..       4      34 ..       3      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0044
                -HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
     zf-HYPF  2 CedClrEykdpldRRfhaqfisCtnCGPrlsl 33
                C++C + +k p d     + ++C++CG  + l
  AJA93069.1  4 CPECDANMKIPDD-AVEGEIVTCPECGASFEL 34
                9999999999976.578899*******99876 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.9     0.002      0.79     100     124 ..      20      43 ..       1      48 [. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.002
      TerY_C 100 eeeatCpwCgkevkfgeaseegfdv 124
                  e +tCp Cg + +++ +++egf++
  AJA93069.1  20 GEIVTCPECGASFELA-KASEGFEL 43 
                 3556777777777777.45555655 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1    0.0005       0.2       5      42 ..       3      33 ..       1      53 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0005
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfk 42
                      CP C    ++  +    +     v+C +Cgas   f+
       AJA93069.1  3 NCPECDANMKIPDDAVEGE----IVTCPECGAS---FE 33
                     79***99999999977776....*********2...22 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4     0.018       7.2       2      10 ..       2      10 ..       2      12 .. 0.81
   2 ?    7.0   0.4     0.016       6.1       3       9 ..      24      30 ..      23      31 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
      zf-ACC  2 tKCpsCgem 10
                t+Cp+C + 
  AJA93069.1  2 TNCPECDAN 10
                78****986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
      zf-ACC  3 KCpsCge 9 
                 Cp+Cg+
  AJA93069.1 24 TCPECGA 30
                6999998 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.21        81       8      16 ..       4      12 ..       1      20 [. 0.81
   2 ?    7.1   0.0      0.02       7.8       5      15 ..      22      32 ..      20      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
  Zn_ribbon_recom  8 CgeCGspmt 16
                     C eC ++m+
       AJA93069.1  4 CPECDANMK 12
                     999999996 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.02
  Zn_ribbon_recom  5 llrCgeCGspm 15
                     ++ C eCG+++
       AJA93069.1 22 IVTCPECGASF 32
                     789*****987 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00083      0.32     116     140 ..       3      30 ..       1      33 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00083
     DUF1451 116 vCekCgkelal...kkteeippCpkCga 140
                 +C +C++++++      +ei +Cp+Cga
  AJA93069.1   3 NCPECDANMKIpddAVEGEIVTCPECGA 30 
                 7**********33334689*******97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.8     0.019       7.6      11      22 ..      15      31 ..       3      32 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
  zinc_ribbon_2 11 dnakF.....CpyCGtp 22
                   d+a+      Cp+CG+ 
     AJA93069.1 15 DDAVEgeivtCPECGAS 31
                   55555666669999875 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.69   2.7e+02       3       7 ..       4       8 ..       2      12 .. 0.85
   2 ?    8.1   0.0    0.0099       3.9       2      10 ..      24      32 ..      23      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.69
               ETTTT CS
     zf-C2H2 3 CpdCg 7
               Cp+C+
  AJA93069.1 4 CPECD 8
               ****8 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0099
                EETTTTEEE CS
     zf-C2H2  2 kCpdCgksF 10
                +Cp+Cg sF
  AJA93069.1 24 TCPECGASF 32
                7******99 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.3    0.0014      0.55      11      38 ..       2      30 ..       1      43 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0014
                EE-TTTTTTSEETTE.......E-TTTTT CS
   Anti-TRAP 11 tkCdaCngsGkiepe.eprasleCPkCsG 38
                t+C++C+   ki+ +  ++  + CP+C+ 
  AJA93069.1  2 TNCPECDANMKIPDDaVEGEIVTCPECGA 30
                68**********99844566789****85 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.0     0.088        34      15      23 ..       3      12 ..       1      19 [. 0.74
   2 ?    7.3   0.2     0.011       4.3      11      20 ..      20      29 ..      11      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.088
     DUF3797 15 qCPeCg.Nnk 23
                 CPeC  N k
  AJA93069.1  3 NCPECDaNMK 12
                7****73555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
     DUF3797 11 ekYvqCPeCg 20
                +  v CPeCg
  AJA93069.1 20 GEIVTCPECG 29
                55799****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 376.82
//
Query:       AJA93070.1  [L=205]
Description: pyridoxal 5'-phosphate synthase, glutaminase subunit Pdx2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-49  167.0   0.3    4.7e-49  166.8   0.3    1.0  1  SNO            SNO glutamine amidotransferase family
    4.4e-12   46.0   0.0      7e-12   45.4   0.0    1.4  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    7.8e-11   42.1   0.0    1.2e-10   41.5   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    1.8e-06   27.9   0.3    0.00013   21.8   0.2    2.7  2  Peptidase_C26  Peptidase C26
    1.8e-05   24.6   0.1    3.9e-05   23.5   0.0    1.6  2  DJ-1_PfpI      DJ-1/PfpI family
      6e-05   22.8   0.2    8.7e-05   22.3   0.2    1.2  1  Peptidase_S51  Peptidase family S51
    9.2e-05   21.7   0.0       0.36    9.9   0.0    2.2  2  BPL_N          Biotin-protein ligase, N terminal
  ------ inclusion threshold ------
      0.025   14.4   0.3       0.15   11.9   0.1    2.1  2  ChlI           Subunit ChlI of Mg-chelatase


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.3   2.1e-52   4.7e-49       1     186 [.       8     201 ..       8     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.1e-52
                 EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB..... CS
         SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelene..... 88 
                 +la+qG+v+e   a  +++ e        +vk++e++  +d+liiPGGest ++++    g +++++e+++ +  +v+G CaG+++lsk+ +       
  AJA93070.1   8 ILAVQGDVTENFLATMASMSELgidgsvIQVKTVEQISTLDGLIIPGGESTVIGQMSLVNGAIKKIKEKIESG-MPVFGICAGMVFLSKNSQDRivgnv 105
                 69*********999999888878899999*****************************************999.9*************99766555546 PP

                 SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTC.SEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHHHH CS
         SNO  89 lvktlellkvkvkrnafGrqvdsfekeldfknli.ekftavfiraPvieeilddeavkvlyeldgeivvakqkkilatsfhPelaeddirvhdyfveev 186
                 + + l++l+vk++rn+fGrq dsfe+++ ++ ++  +f +vfiraP + e +    v+vl + + +iv++kq++++at+fhPel++d + +h+ fv+ v
  AJA93070.1 106 DQPLLDILDVKIERNSFGRQKDSFEAKISMEPIGiSSFHGVFIRAPSVSETG--SGVEVLAKFNEKIVAVKQGNVIATAFHPELTKD-TSLHKSFVKLV 201
                 8889****************************9889***************9..889****************************99.99*****9865 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   3.1e-15     7e-12      29     188 ..      35     184 ..       8     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 3.1e-15
    GATase_3  29 fvplkd.eslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefek.ekltgq 125
                 ++++k+ e++ + +d +i+pGg++t+  + +l + g  ++ike++e+g+pv+giC+G+ +L+++  d           + l++Ld+++e ++  ++  +
  AJA93070.1  35 VIQVKTvEQI-STLDGLIIPGGESTVIGQMSLVN-GAIKKIKEKIESGMPVFGICAGMVFLSKNSQDRIV---GNVDQPLLDILDVKIERNSfGRQKDS 128
                 3444440455.669************99999999.999**************************988642...455899*********99986677666 PP

    GATase_3 126 vegevelaaeg.eevkGyEiHsG.rtilkekakpllkvkvggnngekdGavkksedgnvlGtYlH 188
                  e+++++++ g + + G  i+    + ++ +++ l+k+      +ek  av   ++gnv++t +H
  AJA93070.1 129 FEAKISMEPIGiSSFHGVFIRAPsVSETGSGVEVLAKF------NEKIVAV---KQGNVIATAFH 184
                 66665554444455555555543134444445555555......1333333...35777777777 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   5.1e-14   1.2e-10      18     178 ..      27     192 ..      14     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 5.1e-14
                 HHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE............EEECEE CS
      GATase  18 velgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaiefgrkvv............kekeke 99 
                  elg++  v+++++  e+     ++ dg++++gG  ++      v g+i+ ike +e+++P++GIC Gm  l + +   +v                  
  AJA93070.1  27 SELGIDGSVIQVKT-VEQ----ISTLDGLIIPGGESTVIgqmslVNGAIKKIKEKIESGMPVFGICAGMVFLSKNSQDRIVgnvdqplldildV----- 115
                 56666667777664.333....3689********888877888***********************************8886666655443331..... PP

                 EEEEEEEEEETTT.......CGGTTTTSEEEEEEEEEEEEESGCHHHTT..EEEEEEEETTEEEEEEEEETT.TEEEESSBTTSTTSTT CS
      GATase 100 hhggtmrlgddet.......allyglknevierhrHryevnpkelepag..levtakseddeelmeiiekkn.pfvgvQFHPEststpe 178
                   + + +     +        +++ + +++  +  H+  +   ++ ++g  +ev+ak  +    ++i+  k+ +++++ FHPE t  + 
  AJA93070.1 116 --KIERN-----SfgrqkdsFEAKISMEPIGISSFHGVFIRAPSVSETGsgVEVLAKF-N----EKIVAVKQgNVIATAFHPELTKDTS 192
                 ..22222.....1222223355677778999**********98555555227776666.3....34555555349********998765 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   5.8e-08   0.00013      95     216 .]      70     186 ..      29     186 .. 0.73
   2 ?    3.0   0.0     0.033        73     145     182 ..     165     202 ..     149     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.8e-08
  Peptidase_C26  95 laLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike.....laeel 185
                    ++ i++ +e+g+P++giC G+ +l      +++ ++++   l d  +   + ++ +   +k+s+ a++   e i + s+H   i+       ++++
     AJA93070.1  70 IKKIKEKIESGMPVFGICAGMVFLSKNSQDRIVGNVDQ--PLLDILDV--KIERNSFGRQKDSFEAKISM-EPIGISSFHGVFIRApsvseTGSGV 160
                    4558999*****************99999999999996..33333332..35567788899999999998.99*******9988876665577888 PP

  Peptidase_C26 186 rveAvaeDgviEaieseeakafvlgvQwHPE 216
                    +v A  +  ++ a++  +    v++  +HPE
     AJA93070.1 161 EVLAKFNEKIV-AVKQGN----VIATAFHPE 186
                    88887776655.554444....889999998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.033
  Peptidase_C26 145 saashavkvekgsllaellgseeievnslHhqaikela 182
                    +++++ v v++g ++a ++  e ++ +slH+  +k ++
     AJA93070.1 165 KFNEKIVAVKQGNVIATAFHPELTKDTSLHKSFVKLVD 202
                    5667889999*********99999999***99998776 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.7e-08   3.9e-05      60     110 ..      45      96 ..      19     100 .. 0.84
   2 ?   -2.6   0.0       1.8   4.1e+03     134     147 ..     165     179 ..     154     192 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.7e-08
                 CG-SEEEE--BHHH.HHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHT CS
   DJ-1_PfpI  60 aeyDalvlpGGrag.perlrenekvvelvkefaekgklvaaICagpqlLaaa 110
                 ++ D l++pGG++    +++  + +++ +ke  e+g +v+ ICag ++L+++
  AJA93070.1  45 STLDGLIIPGGESTvIGQMSLVNGAIKKIKEKIESGMPVFGICAGMVFLSKN 96 
                 478********9852468888889************************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                 EE-SS.SEEEETTEE CS
   DJ-1_PfpI 134 kyvdk.rvvvdgnlv 147
                 k+ +k  +v+ gn++
  AJA93070.1 165 KFNEKiVAVKQGNVI 179
                 333334455666633 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   3.9e-08   8.7e-05      59     134 ..      29      98 ..      10     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.9e-08
                    TT-EEEE--TTTS-HHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-G CS
  Peptidase_S51  59 lglevdeLelskdpeeeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesie 134
                    lg++ ++++++      +e+ +   d++++ GG+   + +    +g+ k ++e++++g++++G+ AG +  +++ +
     AJA93070.1  29 LGIDGSVIQVK-----TVEQ-ISTLDGLIIPGGESTVIGQMSLVNGAIKKIKEKIESGMPVFGICAGMVFLSKNSQ 98 
                    44444444433.....3444.666*******************************************999998876 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00016      0.36      53      98 ..      50      96 ..      43     106 .. 0.81
   2 !    9.7   0.0   0.00018       0.4     168     223 ..     145     189 ..     114     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
       BPL_N 53 lVlPgGaDlpYvr.elngegnrkikeyVekGGkylGlCAGaYygskr 98
                l++PgG  +   + +l + +++kike +e+G   +G+CAG  + sk+
  AJA93070.1 50 LIIPGGESTVIGQmSLVNGAIKKIKEKIESGMPVFGICAGMVFLSKN 96
                8999999754433134458899*******************999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
       BPL_N 168 gvFvdaeklknk...vevLArYaeeldvdsgeakkaAvvlckvgeGkalLtgvhpEfal 223
                 gvF++a +++++   vevLA+++e+              ++ v +G+++ t+ hpE + 
  AJA93070.1 145 GVFIRAPSVSETgsgVEVLAKFNEK--------------IVAVKQGNVIATAFHPELTK 189
                 99*****99998889********97..............33466788888888888765 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.6e-05      0.15      65     103 ..       4      44 ..       3      49 .. 0.88
   2 ?   -0.1   0.0      0.34   7.7e+02      84     100 ..      59      76 ..      51     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
        ChlI  65 iAigilaaleqieae..eetlflGeLsldGslrpvkgvlpi 103
                 i igila++++++++  +++  + eL++dGs+ +vk v +i
  AJA93070.1   4 IKIGILAVQGDVTENflATMASMSELGIDGSVIQVKTVEQI 44 
                 679*****999877766999***************999876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
        ChlI  84 flGeLsl.dGslrpvkgv 100
                 ++G +sl +G ++++k+ 
  AJA93070.1  59 VIGQMSLvNGAIKKIKEK 76 
                 455555434555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1331.65
//
Query:       AJA93071.1  [L=166]
Description: copper resistance protein D [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-17   61.4   2.2    9.3e-17   61.4   2.2    1.4  2  CopD           Copper resistance protein D
    0.00015   22.0   2.6    0.00015   22.0   2.6    2.0  2  DUF4149        Domain of unknown function (DUF4149)
     0.0091   16.2  11.0       0.03   14.5  11.0    1.7  1  UPF0093        Uncharacterised protein family (UPF0093)
  ------ inclusion threshold ------
      0.025   14.7   3.8      0.044   13.9   3.8    1.4  1  DUF3278        Protein of unknown function (DUF3278)
       0.34   10.7   2.5        0.3   10.9   0.5    2.0  1  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.7   9.8e+03      44      51 ..      11      18 ..       3      31 .. 0.50
   2 !   61.4   2.2   2.6e-20   9.3e-17       2     105 .]      50     160 ..      49     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
        CopD 44 llaKlall 51
                ++++ a+ 
  AJA93071.1 11 IHITSAAI 18
                33333333 PP

  == domain 2  score: 61.4 bits;  conditional E-value: 2.6e-20
        CopD   2 ralrrFsrlalaavavvlvtGvvnallrvg.lagllttayGrlllaKlalllvllalaalnrfrlvprleaa......tgaggqalrhrlrrsaalelv 93 
                 ++ rrF +lal+a+ ++++tG++ a+l ++  + l +t+yG +l++K++l+++ll+l a++ + +++ +e +       +++ q+lr+++  + ++ +v
  AJA93071.1  50 QVGRRFNKLALPALFILIATGMYQAHLVLQkSDILYETSYGHVLIIKMILVAALLVLYAVHVRIIRKDVEDKiiakemPQEQLQKLRKKIIILGEVTVV 148
                 5789************************99899999*********************************8889999997788999999*********** PP

        CopD  94 lalvvlllaaal 105
                 l++++l+laa+l
  AJA93071.1 149 LSIIILFLAAVL 160
                 **********97 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   2.6   4.3e-08   0.00015       2      90 ..      15     110 ..      14     120 .. 0.87
   2 ?    1.2   0.2      0.13   4.5e+02      26      84 ..     128     160 ..     120     165 .. 0.45

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.3e-08
     DUF4149   2 slglllGsqlwvtfvvapvlfrs.LprhqfgelqsklFplyfglglalsvlllltevavg......seklaseellqlllllvvllltllnafyle 90 
                 s+++++G+ l++++v ap+l +  +p ++  +l+ ++  +++ l l  +++l+ t +++       s  l +    ++l++ ++l+ +ll  +++ 
  AJA93071.1  15 SAAIWVGGSLFIGVVFAPILKKMsMPVEERIQLMVQVGRRFNKLALPALFILIATGMYQAhlvlqkSDILYETSYGHVLIIKMILVAALLVLYAVH 110
                 789*******************989********************************998999887666666778888888888888888777665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
     DUF4149  26 prhqfgelqsklFplyfglglalsvlllltevavgseklaseellqlllllvvllltll 84 
                 p++q  +l +k+  l  +                            +l++++++l ++l
  AJA93071.1 128 PQEQLQKLRKKIIILGEVTV--------------------------VLSIIILFLAAVL 160
                 55555555555533333222..........................2333333333333 PP

>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  11.0   8.5e-06      0.03       7     143 ..       7     159 ..       1     161 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-06
     UPF0093   7 wikalHiiavisWmAglfyLpRlfVyhaeakeks.eekevlkimerrLlkiimtpamiltlvlGlll..lalaeglvalssgWlhv...Klllvlllla 99 
                  + ++Hi +  +W+ g +++  +f    ++ + + ee+  l ++  r ++ +  pa+++ +++G+    l+l+++ + +++++ hv   K++lv++ll+
  AJA93071.1   7 LLTWIHITSAAIWVGGSLFIGVVFAPILKKMSMPvEERIQLMVQVGRRFNKLALPALFILIATGMYQahLVLQKSDILYETSYGHVliiKMILVAALLV 105
                 56789****************99999998888775655556666666666679***********8656699999777777777664445*****98888 PP

     UPF0093 100 yhlvlaklr.kk.........laagentksekfyrilNEvptlllivivllvvv 143
                 ++ v +++  k+         + +++ +k  k   il Ev ++l i+i++l+ v
  AJA93071.1 106 LYAVHVRIIrKDvedkiiakeMPQEQLQKLRKKIIILGEVTVVLSIIILFLAAV 159
                 77776665413311111111144555566666777999********99999865 PP

>> DUF3278  Protein of unknown function (DUF3278)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   3.8   1.2e-05     0.044      45     127 ..      75     156 ..      50     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
     DUF3278  45 llilslvalllakktpeselilglvltnlllvvlvsglYiliaskklglatkeveakdyekavkkivlksikfglyfaivlyl 127
                  l+l+   +l   ++ +  li++++l++ llv  ++ + i+++  + ++  ke  +++ +k  kki++ + +  ++  i+l+l
  AJA93071.1  75 HLVLQKSDILYETSYGH-VLIIKMILVAALLVLYAVHVRIIRKDVEDKIIAKEMPQEQLQKLRKKIIILGEVTVVLSIIILFL 156
                 44555555555555555.6777*********************************************9998888888888887 PP

>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   8.4e-05       0.3       6      40 ..      93     127 ..      88     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
  Brr6_like_C_C   6 llfnlllvllllylvisfvltikkDiekkleekka 40 
                    l+++++lv+ ll+l    v++i+kD+e k+ +k++
     AJA93071.1  93 LIIKMILVAALLVLYAVHVRIIRKDVEDKIIAKEM 127
                    7899************************9977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1354  (0.0755201); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1222.85
//
Query:       AJA93072.1  [L=128]
Description: PF01883 domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-16   57.8   0.1    1.2e-15   57.4   0.1    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   6.8e-20   1.2e-15       3      74 .]      11      84 ..       9      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 6.8e-20
                    HHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-T..THHHHHHHHHHHHC.STT--EEEEEE CS
  FeS_assembly_P  3 avlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacs..laeairadaeaalralpgvevveVev 74
                    ++++ L++++DPe+++++++l l+ e+di++ +V+vd+ lt+p c+  +   i++d+ + l ++ g+++v+V+v
      AJA93072.1 11 KIFDELSQIVDPEINTTITELELIDEVDINDANVKVDLHLTSPFCPavFGFKIAQDIHDNLLSIQGIDDVKVNV 84
                    79999*****************************************855568********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 916.42
//
Query:       AJA93073.1  [L=132]
Description: methionine-R-sulfoxide reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-53  179.0   0.4    3.5e-53  178.8   0.4    1.0  1  SelR          SelR domain
     0.0016   18.6   0.1     0.0035   17.5   0.1    1.6  1  Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centrom
     0.0018   18.5   0.0      0.004   17.4   0.0    1.5  1  DUF2757       Protein of unknown function (DUF2757)
     0.0031   17.9   0.6       0.35   11.3   0.1    2.2  2  DUF983        Protein of unknown function (DUF983)
  ------ inclusion threshold ------
      0.041   14.0   0.4        9.5    6.4   0.1    2.6  2  Zn-ribbon_8   Zinc ribbon domain
      0.077   12.9   3.2        1.2    9.1   0.3    2.4  2  zf-HIT        HIT zinc finger
       0.11   12.6   0.6        3.4    7.7   0.1    2.3  2  zf-C2HC5      Putative zinc finger motif, C2HC5-type
       0.21   11.1   2.3        8.2    6.0   0.3    2.5  2  zf-ribbon_3   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.8   0.4   1.5e-56   3.5e-53       1     120 [.      11     129 ..      11     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 1.5e-56
                 HHHCTSHCCHHHHHHHTT-SSTTSSSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECTTSEEEEEEETTCECEEEEEEC CS
        SelR   1 elkkkLtpeqyevlrekgterpftgeyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtslgmertevvcakcdahlGhvFe 99 
                 e+kk+Lt+e+yev+r kgte++ftg y+++k++Gvy+c++cg +Lfss++kfdsg+GwpsF+++ ++e++++ +d+s+gm r+ev c+kc++hlGhvF+
  AJA93073.1  11 EWKKELTAEEYEVCRMKGTEQAFTGMYWDCKDDGVYKCRACGVELFSSDAKFDSGTGWPSFFKPEDDEQIEYIEDRSYGMLRVEVNCKKCGSHLGHVFD 109
                 7************************************************************************************************** PP

                 TSSSSS.SEEEEE-CCCEEEE CS
        SelR 100 dgpkpttgkrycinsvslkfk 120
                 dgp+p+ ++rycinsvslk+ 
  AJA93073.1 110 DGPAPS-KLRYCINSVSLKLD 129
                 ****96.***********975 PP

>> Yippee-Mis18  Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.6e-06    0.0035       3      89 ..      46     130 ..      44     132 .] 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-06
                   EEETTTS-EEEECCCEEEEECCCEEEES---CCCEEEECEEEETTSTTEEEEEEEETTT--EEEEEEEE..CSCCCCCCCTCEEEEGGG CS
  Yippee-Mis18   3 fqCkkCktilgdslqlvsegralnivvlkkvtrnvvvgkelvtdeegkctystlsCkgCnsvlGwkYks..teeelkykrglfiletka 89 
                   ++C+ C  +l  s + +++g+ +  ++  +  +++ + +  +          +++Ck+C+s+lG ++ +  ++++l+y+++   l+ ++
    AJA93073.1  46 YKCRACGVELFSSDAKFDSGTGWPSFFKPEDDEQIEYIEDRSYG----MLRVEVNCKKCGSHLGHVFDDgpAPSKLRYCINSVSLKLDK 130
                   66777777777777777777776666666666666666666666....66789**************9844566799999999998765 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06     0.004       4      63 ..      45     105 ..      44     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                 EEEETTT--BTT-SS.TTT---SS---SSSSHHHHHHTSSS-TT-S-EEEE--HHHHHHHH CS
     DUF2757   4 hYrCrhCgkkigtle.kkeieeealgfnkLteeerqdmieyeengdikvkviCedCqeale 63 
                 +Y+Cr Cg+++ + + k +  +    f k +++e+ + ie ++ g ++v+v C +C ++l 
  AJA93073.1  45 VYKCRACGVELFSSDaKFDSGTGWPSFFKPEDDEQIEYIEDRSYGMLRVEVNCKKCGSHLG 105
                 5********99888723344444556777788888888999999************99885 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.015        33      10      24 ..      47      61 ..      44      67 .. 0.85
   2 !   11.3   0.1   0.00016      0.35       3      28 ..      89     113 ..      88     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
      DUF983 10 aCeaCgldlsharad 24
                +C+aCg +l + +a 
  AJA93073.1 47 KCRACGVELFSSDAK 61
                8********999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
      DUF983   3 gfLkvadaCeaCgldlsharaddgPa 28 
                 g L+v+ +C++Cg +l+h   ddgPa
  AJA93073.1  89 GMLRVEVNCKKCGSHLGHV-FDDGPA 113
                 6899************987.577776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0043       9.5       6      16 ..      46      54 ..      45      63 .. 0.78
   2 ?    5.2   0.0      0.01        22      27      36 ..      95     104 ..      83     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
  Zn-ribbon_8  6 YrCeeCghefe 16
                 Y+C++Cg   e
   AJA93073.1 46 YKCRACG--VE 54
                 9******..44 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
  Zn-ribbon_8  27 taCPeCgsev 36 
                  + C++Cgs++
   AJA93073.1  95 VNCKKCGSHL 104
                  3488888865 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00052       1.2       8      21 ..      40      53 ..      36      55 .. 0.89
   2 ?    3.9   0.2     0.022        49      15      22 ..      96     103 ..      94     120 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00052
                T-SB-SEE-TTT-- CS
      zf-HIT  8 CgfpakYkCpkCnt 21
                C+  + YkC+ C++
  AJA93073.1 40 CKDDGVYKCRACGV 53
                888999******97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.022
                 E-TTT--E CS
      zf-HIT  15 kCpkCntr 22 
                 +C kC+ +
  AJA93073.1  96 NCKKCGSH 103
                 7****998 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0015       3.4      28      50 ..      40      61 ..      39      63 .. 0.89
   2 ?    2.9   0.1     0.049   1.1e+02      15      25 ..      92     102 ..      86     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
    zf-C2HC5 28 CakeglskpCsfCgspllsseer 50
                C+ +g+  +C  Cg +l+ss+++
  AJA93073.1 40 CKDDGV-YKCRACGVELFSSDAK 61
                999999.9***********9876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.049
    zf-C2HC5  15 eaapnClnCGk 25 
                  +  nC +CG 
  AJA93073.1  92 RVEVNCKKCGS 102
                 56678999985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.011        25      13      26 .]      42      55 ..      41      55 .. 0.80
   2 ?    6.0   0.3    0.0036       8.2      17      24 ..      95     102 ..      94     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
  zf-ribbon_3 13 ssddnvCpyCGtkl 26
                 ++++ +C  CG +l
   AJA93073.1 42 DDGVYKCRACGVEL 55
                 577789*****875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0036
  zf-ribbon_3  17 nvCpyCGt 24 
                  ++C++CG+
   AJA93073.1  95 VNCKKCGS 102
                  58999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 958.97
//
Query:       AJA93074.1  [L=182]
Description: hypothetical protein T478_0942 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0065   16.8   3.8     0.0065   16.8   3.8    3.0  3  CPBP           CPBP intramembrane metalloprotease
  ------ inclusion threshold ------
       0.27   11.0   0.1       0.27   11.0   0.1    1.9  2  NADH_oxidored  MNLL subunit


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.14   1.3e+03      55      55 ..      67      67 ..      24      94 .. 0.57
   2 ?    2.0   1.0     0.031   2.8e+02       5      24 ..      97     116 ..      69     118 .. 0.86
   3 !   16.8   3.8   7.2e-07    0.0065      46      91 ..     123     170 ..     121     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                G CS
        CPBP 55 n 55
                +
  AJA93074.1 67 Q 67
                1 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.031
                 HHHHHHHHHHHHHHHHHHHT CS
        CPBP   5 llvfllalllapllEEllfR 24 
                 + ++++++l    +EE++fR
  AJA93074.1  97 VPLLIYMFLHINYFEEFYFR 116
                 55677788888899999999 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 7.2e-07
                 HHHHHCSGGGHHH...HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
        CPBP  46 ilFglaHlpngps...vllaalaGlvlgylylktgsllaaillHallnl 91 
                 ++++l+H+  g+     l+++ +G+v+ y+y k+g +  + ++H+++n+
  AJA93074.1 123 LVWALIHIGMGIKihmALVLIPIGFVFKYIYDKKG-IKHSYAMHFATNI 170
                 89********655335699999*************.************8 PP

>> NADH_oxidored  MNLL subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4      0.57   5.1e+03      21      26 ..      11      16 ..      10      17 .. 0.86
   2 ?   11.0   0.1     3e-05      0.27       9      30 ..     135     156 ..     126     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.57
                   HHHHHH CS
  NADH_oxidored 21 FvvGwy 26
                   F++G+y
     AJA93074.1 11 FLIGYY 16
                   99***9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3e-05
                    CCHCCCCHHHHHHHHHHHHHHH CS
  NADH_oxidored   9 rdhwvhvlvPlGFvvGwyLDkk 30 
                    + h + vl+P+GFv+ +  Dkk
     AJA93074.1 135 KIHMALVLIPIGFVFKYIYDKK 156
                    668899**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1399.08
//
Query:       AJA93075.1  [L=87]
Description: PF03685 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-27   93.9   0.7    5.3e-27   93.7   0.7    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
     0.0037   17.5   0.0        1.1    9.6   0.0    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.11   12.4   0.0    1.4  1  DUF3783   Domain of unknown function (DUF3783)
       0.11   13.0   0.7       0.31   11.5   0.4    1.8  2  DUF2497   Protein of unknown function (DUF2497)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.7   1.2e-30   5.3e-27       2      81 .]       6      85 ..       5      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.2e-30
                HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
     UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                ++ +++++++L+++++ +s+P+n ++++++ + +L++++ s++vraa+ais Ld+i++Dpn+P+++Rt++w+ vs LE+i
  AJA93075.1  6 NQAMESALQTLNQLATSHSTPKNFKKTISDLIIELQSDEYSMSVRAANAISSLDDITQDPNVPSFVRTTLWQAVSVLESI 85
                7899**************************************************************************98 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00024       1.1      25      48 ..       7      30 ..       5      34 .. 0.90
   2 !    5.8   0.0    0.0038        17      30      49 ..      54      73 ..      48      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00024
     UPF0253 25 dAiscalktLdevaanealpeevr 48
                +A++ al+tL+++a  ++ p++ +
  AJA93075.1  7 QAMESALQTLNQLATSHSTPKNFK 30
                89*****************99987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0038
     UPF0253 30 alktLdevaanealpeevre 49
                a+  Ld++ ++ ++p+ vr 
  AJA93075.1 54 AISSLDDITQDPNVPSFVRT 73
                8999************9995 PP

>> DUF3783  Domain of unknown function (DUF3783)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.5e-05      0.11      29      53 ..      20      44 ..       1      47 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
     DUF3783 29 lkAvlTptNinWtlkeLleElekEh 53
                +    Tp+N ++t+++L+ El+ + 
  AJA93075.1 20 ATSHSTPKNFKKTISDLIIELQSDE 44
                55668****************9875 PP

>> DUF2497  Protein of unknown function (DUF2497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4     7e-05      0.31       4      45 ..       1      40 [.       1      42 [. 0.88
   2 ?   -0.7   0.0      0.46     2e+03      13      25 ..      52      64 ..      44      80 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
     DUF2497  4 lseetaaavasafakLakavaakesressssgrtledlvrem 45
                +see+++a++sa+++L++ +++ +++  ++ ++t+ dl+ e+
  AJA93075.1  1 MSEENNQAMESALQTLNQLATSHSTP--KNFKKTISDLIIEL 40
                899***************99999965..58899999999885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
     DUF2497 13 asafakLakavaa 25
                a+a+++L +  ++
  AJA93075.1 52 ANAISSLDDITQD 64
                4444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 670.49
//
Query:       AJA93076.1  [L=182]
Description: hypothetical protein T478_0582 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.22   10.2   5.8       0.31    9.7   5.8    1.2  1  Presenilin  Presenilin
       0.33   10.9   0.1       0.33   10.9   0.1    2.3  3  TMCCDC2     Transmembrane and coiled-coil domain-containing p
        1.7    6.9  11.3          2    6.6  11.3    1.0  1  DUF2070     Predicted membrane protein (DUF2070)
        2.5    7.7   5.3        4.6    6.9   2.1    2.0  2  DUF4131     Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.8     7e-05      0.31      41     121 ..      71     154 ..      36     173 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 7e-05
  Presenilin  41 lvytpfeeesdstgqkllnsl.lnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsgl..llaevlkaynipl 121
                 ++ +   e+s+     l++ l lna i+ +  ++++++l+lL+ +   + i  ++i++  +++f++++l  ++  v ++++i+l
  AJA93076.1  71 FTEFVMPETSEAAFLLLIDVLgLNAGIIAVTGIFISITLILLFRFAELNSISRYFIFTISVIVFIIAMLgrFTDYVPSTFQIIL 154
                 33333333444444455555546888888888999**********************999999887654114455555555544 PP

>> TMCCDC2  Transmembrane and coiled-coil domain-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.94   4.2e+03      68      68 ..      31      31 ..       9      58 .. 0.53
   2 ?   -0.8   1.3      0.28   1.3e+03      41      79 ..      99     130 ..      73     142 .. 0.51
   3 ?   10.9   0.1   7.3e-05      0.33      35      65 ..     142     172 ..     137     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.94
     TMCCDC2 68 r 68
                r
  AJA93076.1 31 R 31
                2 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.28
     TMCCDC2  41 ptvqvilkiiflillaiGlyalwkrsirsiqkillfvit 79 
                 ++  + + i++++l+           ++si +  +f i 
  AJA93076.1  99 AVTGIFISITLILLFRFAE-------LNSISRYFIFTIS 130
                 3333444444444444433.......3333333333332 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 7.3e-05
     TMCCDC2  35 lldnlaptvqvilkiiflillaiGlyalwkr 65 
                 + d++ +t+q+il +++ + +++G++++ +r
  AJA93076.1 142 FTDYVPSTFQIILYVMYQLGMTLGIFSIMRR 172
                 5799***********************9998 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  11.3   0.00045         2      15     173 ..       9     171 ..       4     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00045
     DUF2070  15 kvsllliillalligllaflssk........lfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsallqalvllal 104
                 ++++++++ ++ll g++  + +         + + + ++l +l+++ +   + ++++   ++    ++     + ++++i++l++ +      + +  +
  AJA93076.1   9 YYTFAIVFGIGLLQGAILARGIRrkfpklkkYAKGVSIILLILFSINAAGNISKFAEPSkVEFTEFVMPETSEAAFLLLIDVLGLNAG----IIAVTGI 103
                 5677777777777777777777778887777444455555555555555555555432222222222223333333344444444333....3456789 PP

     DUF2070 105 vlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfiv 173
                 ++s++l++ +r+  l ++s++ +++++++++i+ +l+ ++ ++  s+ +++l++++ l + l+++ +++
  AJA93076.1 104 FISITLILLFRFAELNSISRYFIFTISVIVFIIAMLGRFTDYVP-STFQIILYVMYQLGMTLGIFSIMR 171
                 99************************************999999.777778888877777777776665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.03   1.4e+02       8      44 ..      16      52 ..       7      72 .. 0.51
   2 ?    6.9   2.1     0.001       4.6       4      56 ..      92     149 ..      89     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.03
     DUF4131  8 vllalllllllllllllrr....rprrrvllllllllllal 44
                + ++ll  ++l+++++ ++    +    ++ +++++ll+++
  AJA93076.1 16 FGIGLLQGAILARGIRRKFpklkK----YAKGVSIILLILF 52
                334444444444444433344322....2333333333222 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.001
     DUF4131   4 plalvllalllllllllllllrr.....rprrrvllllllllllallgfalrapqpna 56 
                 +l++ ++a+ ++++ + l+ll r       +r ++++++++ +++++   ++ + p++
  AJA93076.1  92 GLNAGIIAVTGIFISITLILLFRfaelnSISRYFIFTISVIVFIIAMLGRFTDYVPST 149
                 5666677777777766666666668898777888888888888777777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1292.18
//
Query:       AJA93077.1  [L=151]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.2e-14   51.2   0.0    1.3e-13   50.7   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    8.3e-11   41.3   1.5    1.3e-10   40.7   1.5    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    9.6e-08   31.7   0.2    1.6e-07   31.0   0.2    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00043   20.2   0.4    0.00085   19.2   0.4    1.5  1  HTH_11          HTH domain
    0.00054   19.8   0.2    0.00098   19.0   0.2    1.4  1  MarR            MarR family
      0.004   17.3   0.2     0.0059   16.7   0.2    1.3  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
  ------ inclusion threshold ------
      0.012   16.2   0.6       0.02   15.4   0.6    1.3  1  Mga             Mga helix-turn-helix domain
      0.025   14.8   0.4      0.042   14.0   0.4    1.3  1  Ribosomal_S25   S25 ribosomal protein
      0.081   13.2   1.0        1.5    9.2   0.0    2.5  3  IMCp            Inner membrane complex protein
        0.1   12.5   0.2       0.49   10.3   0.1    2.0  2  Cadherin_2      Cadherin-like


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   7.3e-17   1.3e-13      13      74 ..      79     140 ..      70     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 7.3e-17
                     HHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
  AsnC_trans_reg  13 leefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                      +e+ e l e+pe+  +  vtG +d+++ + ++dle+l+ ++++k+++++g+++tet++ le
      AJA93077.1  79 KTEIHENLLEIPEIDRIIEVTGRFDLMVGALAEDLEQLHSIVVDKIGKIDGIQNTETFVELE 140
                     5688999***************************************************9887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   1.5   7.2e-14   1.3e-10       2      48 .]       5      51 ..       4      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 7.2e-14
      HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                d++d+k+L++L+k+++is+  LA++l++  s +  r+krL+++  Ik
  AJA93077.1  5 DDLDLKLLSELKKDGSISIPLLAKKLNINASVLYSRIKRLIKKKMIK 51
                89*****************************************9997 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.2   9.1e-11   1.6e-07       2      41 ..       5      44 ..       4      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 9.1e-11
  HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                   D++D+k+L++L +d++is   LA+++++ +s    R++rL
     AJA93077.1  5 DDLDLKLLSELKKDGSISIPLLAKKLNINASVLYSRIKRL 44
                   9**************************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   4.8e-07   0.00085       4      43 ..      10      49 ..       8      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.8e-07
      HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaL.eelg 43
                ++l  L +++g is+  LA++Ln+  ++ + +Ik+L ++++
  AJA93077.1 10 KLLSEL-KKDGSISIPLLAKKLNINASVLYSRIKRLiKKKM 49
                789999.78888************************65555 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   5.5e-07   0.00098       6      50 ..       9      53 ..       7      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.5e-07
                HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
        MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                +++L  l+  g++s+  Lakkl+++ s +   ++rL+kk +i++ 
  AJA93077.1  9 LKLLSELKKDGSISIPLLAKKLNINASVLYSRIKRLIKKKMIKKF 53
                689************************************999875 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   3.3e-06    0.0059      15      55 ..      16      56 ..       9      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
  B-block_TFIIIC 15 RysGitqs.dLakeskqdprslfyrlksLekkgLIvkqsiid 55
                    +++G ++   Lak +++ ++ l++r+k L kk+ I+k +i d
      AJA93077.1 16 KKDGSISIpLLAKKLNINASVLYSRIKRLIKKKMIKKFTI-D 56
                    677777651467**************************99.4 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.6   1.1e-05      0.02      16      68 ..       6      60 ..       3      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH..HHHCHCCT-EEETT CS
         Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikel..nklLkefdleltkk 68
                +l+++ll  l ++ ++si  la++l i  s l+  ik+l  +k++k+f + + ++
  AJA93077.1  6 DLDLKLLSELKKDGSISIPLLAKKLNINASVLYSRIKRLikKKMIKKFTIDIDES 60
                57899*********************************966789*******9433 PP

>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   2.4e-05     0.042      46      89 ..      10      53 ..       5      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
  Ribosomal_S25 46 kllkevpkyklitpsvvserlkingslArraLreleekgliklv 89
                   kll+e +k   i+  +++++l+in+s+  + ++ l +k++ik+ 
     AJA93077.1 10 KLLSELKKDGSISIPLLAKKLNINASVLYSRIKRLIKKKMIKKF 53
                   899999***********************************985 PP

>> IMCp  Inner membrane complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.4   4.3e+03      47      53 ..      45      51 ..      27      60 .. 0.59
   2 ?    9.2   0.0   0.00082       1.5      59      82 ..      75      98 ..      71     102 .. 0.82
   3 ?    1.8   0.0      0.16   2.9e+02      30      53 ..     120     143 ..     115     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
        IMCp 47 vpkveik 53
                ++k +ik
  AJA93077.1 45 IKKKMIK 51
                3333333 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00082
        IMCp 59 vpkiekkikekivEvpqikevdry 82
                 pk++++i+e ++E+p+i  ++++
  AJA93077.1 75 DPKFKTEIHENLLEIPEIDRIIEV 98
                589999999999999999988765 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.16
        IMCp  30 yvdkiVeVPvivykekivpkveik 53 
                 +vdki +++ i+++e++v+ + + 
  AJA93077.1 120 VVDKIGKIDGIQNTETFVELERTE 143
                 689999999999999999876665 PP

>> Cadherin_2  Cadherin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00028      0.49      15      55 ..      22      62 ..       9      67 .. 0.86
   2 ?   -0.3   0.0      0.54   9.6e+02      14      24 ..     104     114 ..      96     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                EEEEHHHHTTS-HHHHHHTTBEEEESTSSSSEEEETTTTEE CS
  Cadherin_2 15 fvgnlakdLgLeveeLaargarvvskgnkqllqlnletgdL 55
                 +  lak L+++++ L +r  r+++k+  + ++++ +  +L
  AJA93077.1 22 SIPLLAKKLNINASVLYSRIKRLIKKKMIKKFTIDIDESQL 62
                56779*****************************9988776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.54
                 -EEEEHHHHTT CS
  Cadherin_2  14 sfvgnlakdLg 24 
                  +vg la+dL+
  AJA93077.1 104 LMVGALAEDLE 114
                 57999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1127.49
//
Query:       AJA93078.1  [L=73]
Description: transcriptional regulator, AsnC family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-09   36.0   0.0    5.5e-09   35.9   0.0    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.064   13.9   0.1      0.096   13.3   0.1    1.4  1  FtsX_ECD        FtsX extracellular domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   6.2e-13   5.5e-09      16      71 ..      15      69 ..       6      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.2e-13
                    HHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEE CS
  AsnC_trans_reg 16 feealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsi 71
                    ++++l+++ +++e + v+G +d ++ + v  l ++ +++ e ++++pgv+rtet++
      AJA93078.1 15 IAARLRKISNITESFPVSGQFDAVAVIDVTELSEIKNITTE-IQKIPGVERTETMV 69
                    7899**********************************999.************97 PP

>> FtsX_ECD  FtsX extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.096      65      94 ..      34      63 ..      11      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
    FtsX_ECD 65 pLpdsfevklkdpekleevaeelkklpgVe 94
                 + ++ ++ +++ ++++++++e++k+pgVe
  AJA93078.1 34 QFDAVAVIDVTELSEIKNITTEIQKIPGVE 63
                588899999********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 571.60
//
Query:       AJA93079.1  [L=54]
Description: hypothetical protein T478_0125 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 427.36
//
Query:       AJA93080.1  [L=311]
Description: hypothetical protein T478_1299 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2152.00
//
Query:       AJA93081.1  [L=166]
Description: hypothetical protein T478_0362 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.5   2.4       0.71   10.2   2.4    2.0  1  DUF2935   Domain of unknown function (DUF2935)
      0.079   13.3   0.4       0.44   10.9   0.1    2.1  2  Styelin   Styelin


Domain annotation for each model (and alignments):
>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.4   7.9e-05      0.71      36      87 ..      56     159 ..      50     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.9e-05
     DUF2935  36 akefkkeFekllaeavelseglv....................................................rasseleeavakLneealkltrel 82 
                 a++++++F+++l+e ++l e++                                                     ++s  ++e++a++++++ kl +e 
  AJA93081.1  56 ANAVEESFSEFLNEKISLDEYVRiaetsssqnnallmelaysdapqewqetyinriaslksfesyiietmvianlINSDGEQEQIAEIMKNIEKLKEES 154
                 89999****************988999999999999999999999999999999999999999999999999998888888889999999999999988 PP

     DUF2935  83 iqFkk 87 
                 +q+++
  AJA93081.1 155 VQYAE 159
                 88876 PP

>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.16   1.4e+03      32      46 ..      55      69 ..      45      75 .. 0.67
   2 ?   10.9   0.1   4.9e-05      0.44      18      56 ..     118     156 ..     112     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
     Styelin 32 LGDmtDeefqefmke 46
                + +  +e f ef++e
  AJA93081.1 55 VANAVEESFSEFLNE 69
                445566777777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.9e-05
     Styelin  18 ktYikaalsiakhlLGDmtDeefqefmkeveqareeeLl 56 
                   Yi  ++ ia+ +  D   e   e mk++e+ +ee ++
  AJA93081.1 118 ESYIIETMVIANLINSDGEQEQIAEIMKNIEKLKEESVQ 156
                 679999999999889999******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1989  (0.110938); expected 358.6 (0.02)
Passed bias filter:                      929  (0.0518155); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1262.06
//
Query:       AJA93082.1  [L=132]
Description: hypothetical protein T478_0948 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   15.5   9.0      0.014   15.3   9.0    1.1  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
      0.018   15.2   2.8      0.018   15.2   2.8    2.6  3  YtpI             YtpI-like protein
       0.09   12.5   8.6      0.094   12.4   5.3    1.9  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
        1.5    7.9   9.3        3.6    6.7   0.4    2.0  2  Bac_export_2     FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   9.0   3.2e-06     0.014      93     203 ..      14     129 ..       3     131 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-06
  7TMR-DISM_7TM  93 kprllklllllavllsllllllpll..pyteslslaqllallvillllligikawrkgnkparyfl.iawlllligvlidilsllg.....llpsn 180
                    kp+ll +++l +v ++ + +l+p +    + +  l++   ++++++l+++++ a++k +    +++ ia++++ ++ ++++l +++     +l+s 
     AJA93082.1  14 KPKLLIAVILTTVGALSVPVLMPHIyhGAHIWHLLLHTSGIILSVFLAILSVNAYYKMRTKKMIITtIAFMVFTAAEIVQLLDATKthvynILESP 109
                    3344444444443333333333333223333334444778888888888888888777666666667**************997774212244444 PP

  7TMR-DISM_7TM 181 ffteyllqigvllevlllslaLa 203
                       + + ++ +l+ + ll+la+ 
     AJA93082.1 110 ---SEIAHLMMLAMIGLLALAIF 129
                    ...36666666666777777765 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.2     9e+02      54      72 ..      12      30 ..       3      33 .. 0.68
   2 ?   15.2   2.8     4e-06     0.018      33      75 ..      51      93 ..      45     104 .. 0.87
   3 ?    0.2   0.1      0.19   8.4e+02      28      50 ..     104     126 ..      95     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
        YtpI 54 estvalvvgavflvlGlan 72
                es+ +l +++++  +G+ +
  AJA93082.1 12 ESKPKLLIAVILTTVGALS 30
                5666677777777777765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4e-06
        YtpI 33 kasialGlflilfginqllllestvalvvgavflvlGlanlfa 75
                 + i+l++fl+++++n++   +++  ++  + f+v+ +a++++
  AJA93082.1 51 TSGIILSVFLAILSVNAYYKMRTKKMIITTIAFMVFTAAEIVQ 93
                5789**********************************99986 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.19
        YtpI  28 kllsakasialGlflilfginql 50 
                 ++l++ ++ia  ++l+++g+ +l
  AJA93082.1 104 NILESPSEIAHLMMLAMIGLLAL 126
                 67888888998899999888754 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.048   2.2e+02     114     141 ..       2      30 ..       1      39 [. 0.71
   2 ?   12.4   5.3   2.1e-05     0.094      51     140 ..      44     128 ..      36     130 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.048
  Cation_ATPase_C 114 eslfkfsglf.snkllllaillslllqvl 141
                      e++f+++++  s++ ll+a++l+++ ++ 
       AJA93082.1   2 ENMFSYQKFAeSKPKLLIAVILTTVGALS 30 
                      57889888887778888888888865544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
  Cation_ATPase_C  51 lrriliqgllqalvtllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrre.slfkfsglfsnkllllaillslllqv 140
                      +++ l+    ++l+++l+ + +  ++++ +k+     +   t+aF+++  ++i+++l + +++  ++++ s      l+ la+++ l+l++
       AJA93082.1  44 IWHLLLHTSGIILSVFLAILSVNAYYKMRTKK-----MIITTIAFMVFTAAEIVQLLDATKTHVyNILE-SPSEIAHLMMLAMIGLLALAI 128
                      55555555555556666666666678888887.....77******************999944324444.333345566666666666655 PP

>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0008       3.6     118     183 ..       2      65 ..       1      72 [. 0.86
   2 ?    5.4   3.4     0.002       9.1     135     186 ..      75     126 ..      64     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0008
                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Bac_export_2 118 krifslrslvellksllkvvlvgavaylvlkseleellalaeldleaalelllslllkllllvlla 183
                   +++fs +++ e   +ll +v++ +v++l +   ++++++ a  ++ ++l ++  ++l+++l++l +
    AJA93082.1   2 ENMFSYQKFAESKPKLLIAVILTTVGALSVPVLMPHIYHGA--HIWHLLLHTSGIILSVFLAILSV 65 
                   79********************************9999555..67888888888888888887765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.002
                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  Bac_export_2 135 kvvlvgavaylvlkseleellalaeldleaalelllslllkllllvllallv 186
                   k+++  ++++++  +e+ +ll ++++++ ++le   +++  ++l+++++l++
    AJA93082.1  75 KMIITTIAFMVFTAAEIVQLLDATKTHVYNILESPSEIAHLMMLAMIGLLAL 126
                   5566666666666779*****************9999988777777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1347  (0.0751297); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1020.96
//
Query:       AJA93083.1  [L=364]
Description: putative chaperone protein DnaJ [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-36  125.2   0.0    3.8e-36  124.4   0.0    1.4  1  DnaJ_C         DnaJ C terminal domain
    2.7e-25   88.3   1.0    4.4e-25   87.6   1.0    1.4  1  DnaJ           DnaJ domain
      7e-12   45.5  18.9    1.2e-11   44.7  18.9    1.4  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
        8.4    6.5  20.9          6    6.9   4.3    2.6  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.0   8.5e-40   3.8e-36       3     148 .]     134     346 ..     132     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 8.5e-40
                 EEEEE-HHHHHH-.EEE.EEEE........................................................................TEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx.................................................................xxxxxxxxx RF
      DnaJ_C   3 veleisleelykGktkkikikrnvi.................................................................kkekktlev 36 
                 +e  i+le++++Gk+ ++++k+ v                                                                  +k +k l++
  AJA93083.1 134 HECYITLEDVLHGKQIELDLKKFVDcpdcngtgckpgsskstckdcggygqvrvrrnmggmilesaqpcgkcqgsgeifddpckkcqrgkVKGTKHLSF 232
                 6789****************99988****************************************************************8777889*** PP

                 EE-TT--TT-EEEETT-SSSS...S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET. CS
                 xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
      DnaJ_C  37 kipaGikdgqkirlegeGdeeg.gepGDlivtikvkphpvFkrkgndlyveveislaeallGgklevptldgkvklki...tqpgevlrikgkGmpklk 131
                 + p Gi++g+  +++geG++ + g +GDliv+++v+ph+ ++r+g dly++++is+++a lG++++v+tl+++ klki   tqp+++l+ik +G+p+++
  AJA93083.1 233 NLPSGIDNGD-YVIQGEGESIPdGDNGDLIVRVRVEPHKLYRRDGVDLYCDARISMVDATLGTEIDVKTLEKTQKLKIesgTQPNSILKIKSQGLPSQN 330
                 *********7.899****98788**************************************************************************97 PP

                 ..TEE--EEEEEEEE-- CS
                 xxxxxxxxxxxxxxxxx RF
      DnaJ_C 132 kpgkrGdlyvevkvefP 148
                  +++rGdl+v+v +e+P
  AJA93083.1 331 -SNRRGDLFVHVVIEIP 346
                 .***************9 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   1.0   9.8e-29   4.4e-25       1      63 []       6      67 ..       6      67 .. 0.99

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 9.8e-29
                HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
        DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                dyYe+Lgv+k++s de+k++Yrklalk+HPD+n k+p+a+e+Fkei+eAy vLsd+ kR  YD
  AJA93083.1  6 DYYEVLGVNKSSSPDEVKSQYRKLALKFHPDRN-KSPDAQEHFKEISEAYAVLSDSGKRDLYD 67
                8********************************.****************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7  18.9   2.8e-15   1.2e-11       1      64 [.     159     220 ..     159     223 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.8e-15
  DnaJ_CXXCXGXG   1 CkkCkGsgakkgk.kktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCk 64 
                    C++C+G+g+k+g+ k+tCk+C+G G+vr++++ +g ++ +s ++C +C+G+G+++  +d+CkkC+
     AJA93083.1 159 CPDCNGTGCKPGSsKSTCKDCGGYGQVRVRRN-MGGMILESAQPCGKCQGSGEIF--DDPCKKCQ 220
                    **********9775899********9888875.78888899**************..889****8 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   8.6     0.006        27      12      41 ..     158     184 ..     150     189 .. 0.86
   2 ?    6.9   4.3    0.0013         6      11      41 ..     200     224 ..     191     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.006
                 E-TTTTTTSEETTE......E-TTTTTSSE CS
   Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgl 41 
                  C+ Cng+G  ++    +   C +C+G g 
  AJA93083.1 158 DCPDCNGTGCKPGS---SKSTCKDCGGYGQ 184
                 7***********99...6668*****9885 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                 EE-TTTTTTSEETTE......E-TTTTTSSE CS
   Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkgl 41 
                 ++C +C+gsG+i  +      +C kC+  ++
  AJA93083.1 200 QPCGKCQGSGEIFDD------PCKKCQRGKV 224
                 68************9......9999986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2806.17
//
Query:       AJA93084.1  [L=342]
Description: PF04007 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-42  145.8   2.3      2e-42  145.5   2.3    1.0  1  DUF354         Protein of unknown function (DUF354)
     0.0032   16.4   0.1     0.0043   15.9   0.1    1.2  1  Epimerase_2    UDP-N-acetylglucosamine 2-epimerase
  ------ inclusion threshold ------
      0.027   14.7   1.2      0.027   14.7   1.2    2.4  2  RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRC


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   2.3   3.3e-46     2e-42       1     334 [.       1     338 [.       1     341 [. 0.84

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 3.3e-46
      DUF354   1 ldvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhGvt.lkekliesakrvinlskliaevkpdvalakhsvelprv 98 
                 +++w d+       +f   i+k++k+  +++ t r++ +++ + k+ +++   iGkhG     +kl+ s kr+  l+k i   +pd+ ++  s e  r+
  AJA93084.1   1 MKIWFDILTPKQYLFFEYFIQKLRKQ-HKIVSTSRKYDQVNGIRKFGSINPIIIGKHGGKdSVDKLLASLKRTELLTKKIETNRPDLLISFCSPEASRI 98 
                 58******99999**********997.57899*************9999********865167************************************ PP

      DUF354  99 afGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinvqsyeideeilkdlnlkledektilmrpepslasyl 197
                 afGl+ip +   d   a+a  kl+lp + +++ p +i ++d+k++G +   i +y+     + +++y    +       k + +ktil+rpe s a+y+
  AJA93084.1  99 AFGLGIPHIAFSDSPQAKAVMKLSLPYVTKLLTPWIIPKKDFKEFGINSRNIIQYRAIDAGVIIKNYRKTRK------RKSNVKKTILIRPEESEAAYI 191
                 **********************************************99888888***999889999986654......345577*************** PP

      DUF354 198 dadchk.dvltkiveklkdridilviprdeeq.keiyeev.dnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliek 293
                 + +++  +++ ki+ek+ d  +i+ + r++eq +e+ + + ++v +  ++v    ll   +  +G+GGtm  ea llGip++s     +  ++ +l+++
  AJA93084.1 192 KKESKTiKIIEKIIEKFPDEKKIV-LSRYKEQsNEVKRVFgKDVFIFSKPVSGKGLLDSVNCFVGSGGTMTAEAGLLGIPTISMN-SVPNRIEEFLVKN 288
                 9987654899*********99986.5676666256666553459999************************************75.568899******* PP

      DUF354 294 dlmirstdvdei...vntalr...llv.dklekkk.lie.edltdliver 334
                   +irs+  + i   v  +l    +++  k++ +k +   ed+++++++ 
  AJA93084.1 289 KIIIRSESPNRIskeVFQSLNninIINkRKQNARKlVASfEDPYQVLLKT 338
                 *****976444411122233211022212334455355589999988765 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.3e-07    0.0043     256     320 ..     246     315 ..     165     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.3e-07
                  HHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE.-TT-HHHHHHHHHHHCT-..... CS
  Epimerase_2 256 llknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvl.vgtdkeeIvaaleklled....k 320
                  ll ++++ ++  g++  Ea +lg+p++ + +  +R e    ++ ++  ++++++I +++ + l++    +
   AJA93084.1 246 LLDSVNCFVGSGGTMTAEAGLLGIPTISMNSVPNRIEEFLVKNKIIiRSESPNRISKEVFQSLNNiniiN 315
                  6677888999888*******************************9977899***********98843331 PP

>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.2   4.4e-06     0.027      29      84 ..     141     197 ..     137     206 .. 0.88
   2 ?   -1.5   0.1      0.44   2.7e+03       8      71 ..     308     316 ..     274     332 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
  RTT107_BRCT_6  29 kahGikevkvlsk.klkiedlvknekkkkkekkkspeyvliatkasqvkkfkkllke 84 
                    k++Gi++ ++++   ++   ++kn +k++k+k++ ++++li  ++s++  +kk  k+
     AJA93084.1 141 KEFGINSRNIIQYrAIDAGVIIKNYRKTRKRKSNVKKTILIRPEESEAAYIKKESKT 197
                    89**********967788999****************************99997664 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.44
  RTT107_BRCT_6   8 ikkiNlvsdipggtevissiLkahGikevkvlskklkiedlvknekkkkkekkkspeyvliatk 71 
                    +++iN+++                                                       k
     AJA93084.1 308 LNNINIIN-------------------------------------------------------K 316
                    22233332.......................................................2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2633.94
//
Query:       AJA93085.1  [L=342]
Description: cupredoxin-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-07   31.3   0.0      2e-06   27.9   0.0    2.5  2  Cupredoxin_1  Cupredoxin-like domain
    8.7e-06   26.1   0.1    8.7e-06   26.1   0.1    2.9  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    0.00014   22.0  28.3    0.00021   21.4  28.3    1.2  1  HC2           Histone H1-like nucleoprotein HC2
     0.0042   17.2   0.1        1.7    8.9   0.1    2.4  2  V-set         Immunoglobulin V-set domain
  ------ inclusion threshold ------
        0.3   10.9   4.0       0.39   10.5   4.0    1.2  1  RR_TM4-6      Ryanodine Receptor TM 4-6
        1.7    9.2   6.3        4.5    7.9   6.3    1.7  1  LPMO_10       Lytic polysaccharide mono-oxygenase, cellulose-
        8.4    6.8   7.1        1.3    9.4   2.8    1.9  2  RNA_pol_Rpc4  RNA polymerase III RPC4


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.25   6.4e+02      22      34 ..     108     120 ..      89     157 .. 0.61
   2 !   27.9   0.0   7.6e-10     2e-06      30     104 .]     254     341 ..     223     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.25
  Cupredoxin_1  22 tveitvkdggfeP 34 
                   +++itv++++++P
    AJA93085.1 108 QITITVNNNSVKP 120
                   3444444444433 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 7.6e-10
  Cupredoxin_1  30 g..........gfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                   g           ++Ps+ ++ ag   +++++n+d+ p++ +s +       +     +++++++ +t+   ++G+Y+++c  h+ ++G++iV
    AJA93085.1 254 GsgapgcetteCYTPSTATISAGG--TVTFTNTDTAPHTSTSGSaangpdgVFDTSLIMMNASFDVTL--ADAGTYTYFCMVHPWMEGTIIV 341
                   3666666666689**********8..899********9999999999999755557889999999999..**************99*****9 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.7      0.77     2e+03      33      43 ..     170     180 ..      78     234 .. 0.65
   2 !   26.1   0.1   3.4e-09   8.7e-06      14      99 .]     266     342 .]     260     342 .] 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.77
                  SSSSBEEEEET CS
  Copper-bind  33 avmgHNvvldk 43 
                   +mgH    ++
   AJA93085.1 170 SSMGHSEDSKE 180
                  44444444444 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 3.4e-09
                  EESSEEEEETTEEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEEEE CS
  Copper-bind  14 FetkeitvkkgekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvtve 99 
                  + +++ t+++g +vtf+n++  +H     +  +++g d         t+li    ++ vt+ +agtY++fC  H    M+g+++ve
   AJA93085.1 266 YTPSTATISAGGTVTFTNTDTAPHTSTSGS--AANGPDGVFD-----TSLIMMNASFDVTLADAGTYTYFCMVHP--WMEGTIIVE 342
                  889999******************765544..3334443332.....235555689*******************..69****996 PP

>> HC2  Histone H1-like nucleoprotein HC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4  28.3   8.3e-08   0.00021      83     159 ..     184     258 ..     170     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.3e-08
         HC2  83 kkvakKavAKKaaakKvvakkvvakKtvakkaaaakKpaakkavakkaaarKaa.akKavaKkaastckkkhkkkaac 159
                  ++a Ka+A Kaaa K++a  ++a K++a k aaa K+aa ka+a kaaa Kaa a+ a+aK +++ +   ++ + a+
  AJA93085.1 184 MMAADKAAAEKAAADKAAA--AAADKAAAEK-AAAEKAAAEKAAADKAAAEKAAaAAAAAAKAPMAVTVEPVAGSGAP 258
                 4667788888888888776..4567888888.8888888888888888888887344555666666655555555554 PP

>> V-set  Immunoglobulin V-set domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00066       1.7      58     107 ..      93     145 ..      71     147 .. 0.72
   2 !    6.2   0.0    0.0044        11      65      93 ..     298     332 ..     268     339 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00066
                 STTTEEEEEEGTTTEEEEEES..S..ESGGG-EEEEEEEECSSEEEEEEEEEEE CS
       V-set  58 kkgrfslrkdpskgdfsltiq..n..ltlsDsGtYtCavvpsgegvfgkgtrLt 107
                 + +++++++ +s+ d+++ti+  n  +++ D GtY++ +  ++ + ++ g rLt
  AJA93085.1  93 HHNAVKIEM-DSRLDGQITITvnNnsVKPFDDGTYFVTIDGEEVEFTQVGKRLT 145
                 566788888.6677777766532355************7666555566666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                 EEEGTTTEEEEEESS....ESGGG-EEE..EEEEE CS
       V-set  65 rkdpskgdfsltiqn....ltlsDsGtY..tCavv 93 
                 ++++   d sl ++n    +tl+D+GtY  +C+v+
  AJA93085.1 298 NGPDGVFDTSLIMMNasfdVTLADAGTYtyFCMVH 332
                 4466777778888765555899****862267764 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.0   0.00015      0.39      57     158 ..     124     233 ..      74     250 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                 XXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXX............XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX............XXXX CS
    RR_TM4-6  57 gqykvvakkseagLgDlseteaeesptpelkkkla............eeeeaeeekeeeeepeaeaeekadaengekeekeke..keeeekeseeeeee 141
                 g+y v+ +++e  ++++++  + + +  + ++k               +++ ++e+++e+e       +ad+   ek+ ++k+   ++++ ++e+   e
  AJA93085.1 124 GTYFVTIDGEEVEFTQVGKRLTIDFM--ANSQKIMiygegyksgghdMSSMGHSEDSKEHEAM----MAADKAAAEKAAADKAaaAAADKAAAEKAAAE 216
                 44666666666666666666665554..22222223455555543332222222222222222....22333333333333331111111111111111 PP

                 XXXXXXXXXXXXXXXXX CS
    RR_TM4-6 142 kkkkkkakskkkeeaea 158
                 k++ +ka ++k ++++a
  AJA93085.1 217 KAAAEKAAADKAAAEKA 233
                 12222222222222121 PP

>> LPMO_10  Lytic polysaccharide mono-oxygenase, cellulose-degrading
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.3    0.0017       4.5      42     114 ..     211     291 ..     162     297 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                 HHHTTTG-EEET.....SHHHHSSTT-TTTTTTH..........HHTT....GGGGTTSTS--...EEEESESEEEEEEEESS-S-EE CS
     LPMO_10  42 vqyeensvekek.....rlkaappdgglcgagds..........rpneaggksgldergawakpvqttytegseiefeveltapHktg 114
                 ++++ +     k     + ++++++++ + a  +          +p + +g+ g + +++  +p ++t+++g++++f+ + tapH t+
  AJA93085.1 211 EKAAAE-----KaaaekAAADKAAAEKAAAAAAAaakapmavtvEPVAGSGAPGCE-TTECYTPSTATISAGGTVTFTNTDTAPH-TS 291
                 111111.....122222222222222222211113455677775333335555544.455555789*******************.54 PP

>> RNA_pol_Rpc4  RNA polymerase III RPC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.2   3.1e+03      28      44 ..      53      69 ..      33     115 .. 0.54
   2 ?    9.4   2.8   0.00052       1.3      30      68 ..     191     229 ..     124     256 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
  RNA_pol_Rpc4 28 kseaesqsaekakaeee 44
                  +++a++ +  + +a+++
    AJA93085.1 53 APAAAPVQTPTPQAAPQ 69
                  22222222221111111 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00052
  RNA_pol_Rpc4  30 eaesqsaekakaeeeskaekasgaeaeekkskkksskkk 68 
                   +ae+++a+ka+a++++ka+ +++a+++ +++k++++k+ 
    AJA93085.1 191 AAEKAAADKAAAAAADKAAAEKAAAEKAAAEKAAADKAA 229
                   111111121111111111111111111111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1830  (0.102069); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2372.36
//
Query:       AJA93086.1  [L=259]
Description: cytidylyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-32  113.0   0.4    2.3e-32  112.7   0.4    1.1  1  CTP_transf_3  Cytidylyltransferase
     0.0086   16.5   0.0      0.028   14.8   0.0    1.7  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.4   2.5e-36   2.3e-32       2     209 ..       4     203 ..       3     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 2.5e-36
                   EEEEE-SSSSSSTTGGGSEETTE.EHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT..SEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEE CS
  CTP_transf_3   2 aIipARsgSkRlpgKnlldlggk.pliayvleaalkskafekvivaTDseeiknvakefg..asvlvtrsslesdterflevvkaflmseneeiivn 95 
                   +Ii+AR+gS+RlpgK++++l+++ p++++ le+++ s  + k+i+aT+  e +n++ +f+       +r+s e++++r ++  k+f++     iiv+
    AJA93086.1   4 CIIQARMGSSRLPGKAMKKLNNEiPMLKFQLEQLKFSRYINKIIIATTTLENDNFIIDFCeqNNLEYFRGSSEDVLDRYYNCAKKFEFP----IIVR 96 
                   8*******************9966************************************8777889**********************....**** PP

                   E-TT-TT--HHHHHHHHHHHHHSTTSSEEEEEEET...TSHHHHTSTTSTEEEETTTSBEEEEESSESSEEHHHHHCTSTTTSEEEEEEEEEEHHHH CS
  CTP_transf_3  96 lqGdnPllqeevikkaietlkenqedylstlvkkv...gkeeevlnandlkvllddagkalyfeesvipyireeplelsrrlylshagiytfrkeqp 189
                   +++dnPl+++e ++k+i + ++++ dy++t   k+   g + e++n+++l+++++d       +e+v+py  ++   ++        + y ++++  
    AJA93086.1  97 ITSDNPLIDPEIVDKVINEFLNSKCDYMTTEYPKTfplGFAVEIFNFKSLEKAWKDS-RLPSEREHVTPYLIKNKDLFE-------HKNYSYHQN-- 183
                   *****************************9876651116799***************.777899999999999988865.......666777776.. PP

                   HHHHHHSHHHHHSHHHHHT- CS
  CTP_transf_3 190 lkelvidtptseilekiekl 209
                   ++ l ++++t+++++ iek+
    AJA93086.1 184 ISHLRCTVDTDDDFKLIEKI 203
                   88888888888878777777 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.1e-06     0.028      11     148 ..       9     153 ..       8     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                   TTTT....THHHHCC.CCCCHHHHHHHHHCTT..-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-T CS
  NTP_transf_3  11 Rmgg....dKallpl.ggkpllervldalraag.vdevvvvggd....eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmP 97 
                   Rmg+     Ka+ +l ++ p+l+ +l++l+ +  ++++++++      + + + +++ ++++++ +  ++  l   +  +++  +   ++ ++ D P
    AJA93086.1   9 RMGSsrlpGKAMKKLnNEIPMLKFQLEQLKFSRyINKIIIATTTlendNFIIDFCEQNNLEYFRGS--SEDVLDRYYNCAKKF-EFPIIVRITSDNP 102
                   888756667******7778**********9886589999998664322446778888888888887..577888888888888.7899999****** PP

                   T--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGH..HHHHHHCTHT CS
  NTP_transf_3  98 lltpelverllaaaaasgadvvvptyegerghpllfrarll..salaallgdq 148
                   l++pe+v+++++++ +s++d +  +y +++  pl f  +++  ++l+++ +d+
    AJA93086.1 103 LIDPEIVDKVINEFLNSKCDYMTTEYPKTF--PLGFAVEIFnfKSLEKAWKDS 153
                   ***********************9999988..998888874337777665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1860.16
//
Query:       AJA93087.1  [L=363]
Description: ImpB/MucB/SamB family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-40  138.3   0.1    7.1e-40  136.4   0.1    1.8  2  IMS       impB/mucB/samB family
    2.6e-09   37.8   0.1    5.2e-09   36.8   0.1    1.5  1  IMS_C     impB/mucB/samB family C-terminal domain
    1.3e-07   31.5   0.0    4.7e-07   29.8   0.0    2.0  2  IMS_HHH   IMS family HHH motif
     0.0012   19.0   0.0      0.011   15.9   0.0    2.5  3  Cdd1      Pathogenicity locus


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.1   1.6e-43   7.1e-40       1     150 []       9     162 ..       9     162 .. 0.94
   2 ?   -1.1   0.0      0.38   1.7e+03     111     138 ..     269     295 ..     214     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 1.6e-43
                 EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHT.T.-EEEEEE-HHHHHHHHHHHHHHHHH-S..EEE CS
         IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcp.d.livvkvdlekyrraskkileilkrfispkvek 94 
                 iD+d Fya++e++r++++kgk v+v+  s++   +g +++++y+Ar++Gvk+g +i  ak + + + ++++++d+++y ++s+k +ei++++ ++  e 
  AJA93087.1   9 IDFDYFYAQCEEIRNSKIKGKCVAVCIFSDRggdSGAIATANYNARKFGVKSGIPIMLAKNKLKeQdAVFLPADFDYYSDMSSKGMEIIEKY-ADVFEY 106
                 8*************************999999999*************************9997546*************************.779*** PP

                 EETTEEEEE-HH.HHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHHH CS
         IMS  95 asiDEayldltg.leelaesegaalakelrkaikeelgltvsiGiasnkllAKlase 150
                 ++ DEayld+t+ +e+ +++ +++la++l+++i + l+lt+siGi++nkll+K+as+
  AJA93087.1 107 VGRDEAYLDVTKkTEMSFDN-AEHLAQQLKNEIRNSLKLTCSIGISPNKLLSKIASD 162
                 ************66666665.7*********************************96 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.38
                 HH-SHHHHHHHHHHHHHHHH---EEEEE CS
         IMS 111 aesegaalakelrkaikeelgltvsiGi 138
                 +++ +++l+++l k   +  ++  siGi
  AJA93087.1 269 QGN-VNELCAQLNKLAINDNKMYRSIGI 295
                 233.688999999999988889999987 PP

>> IMS_C  impB/mucB/samB family C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   1.1e-12   5.2e-09       2     114 ..     243     357 ..     242     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.1e-12
       IMS_C   2 vearpepksissektfpepydesk....lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtreileaalkLlrrlidepgl 95 
                 v++rp++ ++s+  t+++   +sk    l+  ++eL+++l +   +++ + r+i ++  + d + +++s+ L++p ++++e+ + a +Ll++   e+ +
  AJA93087.1 243 VKERPPTIQFSKIVTLKK---NSKelefLQGNVNELCAQLNKLAINDNKMYRSIGIQFVNEDLStKTKSRMLKNPVNSEEELKKVANQLLEEALTEQVM 338
                 67899999*********9...444334777777799999999976666699*******8666668***************************9999*** PP

       IMS_C  96 pirligvsasnlvekaesq 114
                 ++r+igv+ s++++ ++++
  AJA93087.1 339 LVRRIGVRISEFSDVEGQS 357
                 *************666654 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.1e-10   4.7e-07       2      32 .]     175     205 ..     174     205 .. 0.91
   2 ?   -3.3   0.0       3.5   1.6e+04      19      25 ..     223     229 ..     222     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
     IMS_HHH   2 ddvkefLwplpitkipGiGgklgekLeklGi 32 
                 + v++fL+pl+i++ipGiG+k+++ + +++i
  AJA93087.1 175 EQVEQFLSPLKIREIPGIGKKTEDVFTQMDI 205
                 5689********************9988887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
     IMS_HHH  19 iGgklge 25 
                 +G+k+g 
  AJA93087.1 223 FGRKTGG 229
                 69**996 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.65   2.9e+03      24      48 ..     113     137 ..     102     150 .. 0.81
   2 ?   -1.6   0.0      0.74   3.3e+03      12      43 ..     146     179 ..     135     185 .. 0.74
   3 !   15.9   0.0   2.5e-06     0.011       7      50 ..     185     228 ..     182     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.65
        Cdd1  24 elGirsveelkgedpeelyeklekl 48 
                  l++++ +e+   ++e+l ++l++ 
  AJA93087.1 113 YLDVTKKTEMSFDNAEHLAQQLKNE 137
                 6888889999999999999998865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.74
        Cdd1  12 PniGkalaedlvel..Girsveelkgedpeelye 43 
                  +iG +  + l ++  ++++++ l+  +pe++ +
  AJA93087.1 146 CSIGISPNKLLSKIasDFKKPDGLTTVKPEQVEQ 179
                 5788888888876655789999999999998755 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 2.5e-06
        Cdd1   7 elqdiPniGkalaedlvelGirsveelkgedpeelyeklekltg 50 
                 ++++iP+iGk++ + +++++i+ +eel++ d  +l +++ ++tg
  AJA93087.1 185 KIREIPGIGKKTEDVFTQMDIHIIEELRKIDVFDLNKMFGRKTG 228
                 6789*************************999999888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2660.01
//
Query:       AJA93088.1  [L=349]
Description: dimethylhistidine N-methyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-100  335.6   1.8     3e-100  335.4   1.8    1.0  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
     0.0037   17.2   0.7        0.3   11.0   0.2    2.6  2  DUF1825          Domain of unknown function (DUF1825)


Domain annotation for each model (and alignments):
>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.4   1.8  3.3e-104    3e-100       1     306 [.      43     345 ..      43     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 335.4 bits;  conditional E-value: 3.3e-104
  Methyltransf_33   1 laedvlagLsskpktlpskllYDarGselFeeitelpeYyptrtEiaiLqehaaeiaaaipaa.tlvelGsGsseKtrlLLealeaaekeltYv 93 
                      +ae+++++L++ +k++++k++YD++Gs+lF+ei++lpeYyp++ E++iLq+  +++   ++++  lvelGsGss KtrlL++ l +++k+l+Y+
       AJA93088.1  43 FAEEIRSSLQEPKKSISPKFFYDENGSKLFDEICTLPEYYPYNSETEILQSIEKKLLPYLSNEfHLVELGSGSSVKTRLLIDVLFKSQKHLQYF 136
                      6789*******99*********************************************997777********************88999***** PP

  Methyltransf_33  94 plDvseeaLeealealaaeypsleveglvgdyedglewlaslpeaederrlvlflGssigNlepeeaaafLrklraalgpgdllLlGvDlvkde 187
                      p+D+s e+L++++++l  +y++l+v+g+v +ye+gl+++++ ++   +++l++flGss+gNl+++e  +fL+++++ ++++dl+L+G+Dl+kd+
       AJA93088.1 137 PIDIS-EILDQSAKSLCMDYENLKVTGVVDTYEKGLDFIEHYDD---KPNLITFLGSSFGNLDHNEGMKFLQRINTLMKSDDLFLIGLDLKKDH 226
                      ****9.79********************************9995...9******************************99************** PP

  Methyltransf_33 188 ekleaAYndsagvtaaFnlnllerinrelgadfdledfehvaewnaeegriemylrskrdqtvrvealdltvafkagekirteiSyKyteeevr 281
                      e+l++AYnds++ ta+Fnln+l+rin+elgadf+le+feh+a++++++griemylrs  +q++++ + dl+++++++e i+te+S+K++ ++++
       AJA93088.1 227 EVLHNAYNDSQKTTAKFNLNVLKRINEELGADFNLENFEHHAVYDEQKGRIEMYLRSLSEQSITIPKSDLSITLSKDELIHTENSHKFSISQIE 320
                      ********************************************************************************************** PP

  Methyltransf_33 282 elleaaglevlkvWtdeksdfalyl 306
                      + l+++++e l++W d++++fal+l
       AJA93088.1 321 SYLKESNFEKLEMWFDSRKYFALVL 345
                      **********************998 PP

>> DUF1825  Domain of unknown function (DUF1825)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.8   0.0    0.0061        55       6      25 ..     141     160 ..     136     170 .. 0.86
   2 !   11.0   0.2   3.3e-05       0.3      14      65 ..     174     226 ..     170     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0061
     DUF1825   6 seivqqeakelfqdyqeliq 25 
                 sei+ q ak+l  dy +l +
  AJA93088.1 141 SEILDQSAKSLCMDYENLKV 160
                 9***************9965 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.3e-05
     DUF1825  14 kelfqdyqeliq.lgskygkfdreGkkifiekleelleryrilmkrlelsddf 65 
                 +e ++d  +li  lgs++g++d++    f++++++l++   +++  l+l  d 
  AJA93088.1 174 IEHYDDKPNLITfLGSSFGNLDHNEGMKFLQRINTLMKSDDLFLIGLDLKKDH 226
                 566788888886489********99999****************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2445.38
//
Query:       AJA93089.1  [L=82]
Description: hypothetical protein T478_0699 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00019   21.4   0.2    0.00024   21.1   0.2    1.2  1  DZR             Double zinc ribbon
     0.0076   15.9   0.1       0.01   15.5   0.1    1.2  1  DpnI            Dam-replacing family
     0.0085   15.9   1.6       0.94    9.4   0.0    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0093   16.1   0.1       0.41   10.8   0.0    2.2  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.022   15.0   1.6       0.95    9.7   2.3    2.2  2  C1_4            TFIIH C1-like domain
      0.052   13.2   2.4        1.3    8.7   0.6    2.4  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.055   13.9   1.0       0.77   10.3   0.1    2.2  2  zf-C2H2         Zinc finger, C2H2 type
      0.087   12.7   1.6        7.8    6.5   0.2    2.3  2  zf-LYAR         LYAR-type C2HC zinc finger
      0.098   12.4   2.3        3.2    7.6   0.4    2.4  2  zf-HYPF         HypF finger
       0.19   12.1   4.4       0.36   11.3   0.2    2.5  3  zf-IS66         zinc-finger binding domain of transposase IS6
       0.24   12.3   1.2        3.4    8.7   0.1    2.2  2  zf-C2H2_4       C2H2-type zinc finger
       0.39   10.7   3.5        3.7    7.5   3.6    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.6e-07   0.00024       9      39 ..       5      48 ..       1      55 [. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
         DZR  9 ppdarfCseCgtklkavaa.............edrCpsCgekvd 39
                +  +r+C +Cg++l  +++              ++Cp C+e+ +
  AJA93089.1  5 RRANRYCVDCGARLVYYPRlsnpkapnehrvlVYACPDCTEDFE 48
                56789********998888999999***************9865 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.8e-06      0.01      30      88 ..       7      71 ..       4      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.8e-06
                HH---TTT--SS-.....E..E--------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHH CS
        DpnI 30 knlyCpkCgskkl.....s..efennkpvaDfyCesckeefeLkskksklskkivdgaystmieri 88
                 n yC  Cg++ +     s  +  n+++v  + C +c+e+fe k k  ++++++++   +t+   i
  AJA93089.1  7 ANRYCVDCGARLVyyprlSnpKAPNEHRVLVYACPDCTEDFE-KPKMFSIKRNVTEDPLETVEIEI 71
                699******9844221112223468999*************9.88888999999988887765555 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.1     0.018        27      13      22 ..      10      19 ..       9      25 .. 0.68
   2 !    9.4   0.0   0.00063      0.94       3      18 ..      29      44 ..      27      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.018
     DUF35_N 13 rCpdCGtvqf 22
                +C dCG+  +
  AJA93089.1 10 YCVDCGARLV 19
                899**97543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00063
     DUF35_N  3 aaaegrLvgqrCpdCG 18
                a  e+r+++  CpdC 
  AJA93089.1 29 APNEHRVLVYACPDCT 44
                789************6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.055        81      26      35 ..       8      17 ..       1      20 [. 0.66
   2 !   10.8   0.0   0.00027      0.41       6      20 ..      38      54 ..      35      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.055
  Zn-ribbon_8 26 ltaCPeCgse 35
                 +  C +Cg++
   AJA93089.1  8 NRYCVDCGAR 17
                 4558899885 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00027
  Zn-ribbon_8  6 YrCeeCghefe..vlqs 20
                 Y C +C ++fe  ++ s
   AJA93089.1 38 YACPDCTEDFEkpKMFS 54
                 99*********544433 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.031        46      33      39 ..       8      14 ..       4      20 .. 0.87
   2 ?    9.7   2.3   0.00064      0.95       2      35 ..      11      47 ..      10      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.031
        C1_4 33 ndFCiDC 39
                n +C+DC
  AJA93089.1  8 NRYCVDC 14
                78***** PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00064
        C1_4  2 CygCqkk...fpklakkkkdeeltssryrCekCkndF 35
                C+ C  +   +p+l + k+ +e   ++y+C+ C +dF
  AJA93089.1 11 CVDCGARlvyYPRLSNPKAPNEHRVLVYACPDCTEDF 47
                6666544111577888888899999**********99 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6   0.00089       1.3      20      32 .]      11      23 ..       8      23 .. 0.89
   2 ?    4.0   0.0     0.027        40       1      11 [.      38      48 ..      38      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00089
                    -SSS-----B--- CS
  DNA_RNApol_7kD 20 CkeCGhRilYKkR 32
                    C +CG R++Y +R
      AJA93089.1 11 CVDCGARLVYYPR 23
                    99********766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.027
                    -B-SSS--B-- CS
  DNA_RNApol_7kD  1 YiCgeCgaevs 11
                    Y C +C ++++
      AJA93089.1 38 YACPDCTEDFE 48
                    99****99986 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.17   2.5e+02       3       7 ..      11      15 ..      10      26 .. 0.76
   2 ?   10.3   0.1   0.00052      0.77       1      16 [.      38      53 ..      38      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                ETTTT CS
     zf-C2H2  3 CpdCg 7 
                C dCg
  AJA93089.1 11 CVDCG 15
                ****9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00052
                EEETTTTEEESSHHHH CS
     zf-C2H2  1 ykCpdCgksFkrksnL 16
                y CpdC++ F  + ++
  AJA93089.1 38 YACPDCTEDFEKPKMF 53
                88********999886 PP

>> zf-LYAR  LYAR-type C2HC zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.011        17       3       8 ..      11      16 ..      10      20 .. 0.85
   2 ?    6.5   0.2    0.0052       7.8       1      12 [.      38      49 ..      38      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.011
     zf-LYAR  3 CiDCsk 8 
                C+DC+ 
  AJA93089.1 11 CVDCGA 16
                ****96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0052
     zf-LYAR  1 fsCiDCsktFdg 12
                + C DC ++F++
  AJA93089.1 38 YACPDCTEDFEK 49
                679*******86 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.02        29      24      31 ..      11      18 ..       8      21 .. 0.88
   2 ?    7.6   0.4    0.0022       3.2       2      13 ..      40      51 ..      39      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.02
                -TTTS--E CS
     zf-HYPF 24 CtnCGPrl 31
                C +CG rl
  AJA93089.1 11 CVDCGARL 18
                9*****98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                -HHHHHHHC-TT CS
     zf-HYPF  2 CedClrEykdpl 13
                C+dC ++++ p+
  AJA93089.1 40 CPDCTEDFEKPK 51
                ********9996 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.15   2.2e+02       2       9 ..       9      16 ..       3      22 .. 0.71
   2 ?   11.3   0.2   0.00024      0.36      34      45 ..      32      43 ..      31      44 .. 0.95
   3 ?   -3.4   0.1       9.4   1.4e+04      30      32 ..      69      71 ..      63      75 .. 0.46

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
     zf-IS66  2 rtCpcCGg 9 
                r C +CG+
  AJA93089.1  9 RYCVDCGA 16
                46777777 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
     zf-IS66 34 ehirpkyaCpcC 45
                eh+  +yaCp C
  AJA93089.1 32 EHRVLVYACPDC 43
                9*********** PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.4
     zf-IS66 30 frV 32
                +++
  AJA93089.1 69 IEI 71
                222 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.23   3.4e+02       2      16 ..      10      24 ..       9      26 .. 0.77
   2 ?    8.7   0.1    0.0023       3.4       1      15 [.      38      52 ..      38      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
   zf-C2H2_4  2 kCpiCgksFsskkaL 16
                +C  Cg++   + +L
  AJA93089.1 10 YCVDCGARLVYYPRL 24
                699***998777666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0023
   zf-C2H2_4  1 fkCpiCgksFsskka 15
                + Cp C++ F  +k 
  AJA93089.1 38 YACPDCTEDFEKPKM 52
                89********87765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.6    0.0025       3.7       6      31 ..      10      44 ..      10      48 .. 0.79
   2 ?    6.6   0.1    0.0049       7.3       4      15 ..      37      48 ..      34      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
  Zn_ribbon_SprT  6 rCtgCgre.ythhlsirrhn........YrCrrCk 31
                    +C++Cg + +++++ +++ +        Y C+ C 
      AJA93089.1 10 YCVDCGARlVYYPRLSNPKApnehrvlvYACPDCT 44
                    7****987356666667777999999999999997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0049
  Zn_ribbon_SprT  4 vYrCtgCgreyt 15
                    vY C++C + ++
      AJA93089.1 37 VYACPDCTEDFE 48
                    79*****98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 597.03
//
Query:       AJA93090.1  [L=53]
Description: hypothetical protein T478_0420 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00055   19.7   0.5       0.17   11.7   0.0    2.1  2  zf-RING_4       RING/Ubox like zinc-binding domain
     0.0013   18.5   1.1       0.11   12.4   0.1    2.2  2  Rad50_zn_hook   Rad50 zinc hook motif
  ------ inclusion threshold ------
      0.013   15.4   0.5        3.7    7.5   0.1    2.2  2  Prok-RING_4     Prokaryotic RING finger family 4
      0.025   14.5   0.6       0.97    9.4   0.1    2.2  2  zinc_ribbon_4   zinc-ribbon domain
      0.028   14.4   0.2      0.034   14.1   0.2    1.1  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.033   14.4   2.3        1.1    9.5   0.4    2.1  2  zinc_ribbon_9   zinc-ribbon
      0.044   14.2   0.7        2.3    8.8   0.0    2.2  2  zf-H2C2_2       Zinc-finger double domain
      0.058   13.4   1.3       0.38   10.8   1.4    1.9  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
      0.067   13.1   3.6       0.81    9.6   0.3    2.1  3  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.13   12.6   2.6        5.5    7.4   0.1    2.1  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        0.2   11.9   2.0        1.1    9.5   0.1    2.0  2  DUF4451         Domain of unknown function (DUF4451)
       0.21   11.6   2.1        5.6    7.0   0.2    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        2.2    8.8   5.7        8.9    6.9   1.4    2.2  2  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain


Domain annotation for each model (and alignments):
>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0042       5.8      36      45 ..      18      27 ..       7      28 .. 0.78
   2 !   11.7   0.0   0.00012      0.17      35      48 .]      39      52 ..      32      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
   zf-RING_4 36 eegrCPaCre 45
                ++g+CP C++
  AJA93090.1 18 TTGMCPLCKT 27
                689*****96 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
   zf-RING_4 35 eeegrCPaCreeYk 48
                ee ++CPaC +e++
  AJA93090.1 39 EERAKCPACNQEFD 52
                5799*******996 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.016        22      20      26 ..      20      26 ..      15      27 .. 0.77
   2 !   12.4   0.1   7.8e-05      0.11      12      30 ..      34      52 ..      33      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                   EE-TTT- CS
  Rad50_zn_hook 20 gcCPlCg 26
                   g CPlC+
     AJA93090.1 20 GMCPLCK 26
                   47****7 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.8e-05
                   HHHHTT-SEE-TTT--EE- CS
  Rad50_zn_hook 12 ieelkeakgcCPlCgReld 30
                   i ++ e++++CP C +e+d
     AJA93090.1 34 IGNVGEERAKCPACNQEFD 52
                   667889999*********8 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0045       6.2      32      38 ..      21      27 ..      12      32 .. 0.77
   2 ?    7.5   0.1    0.0027       3.7      28      41 ..      39      52 ..      36      53 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0045
  Prok-RING_4 32 sCPlCqr 38
                  CPlC++
   AJA93090.1 21 MCPLCKT 27
                 7****97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0027
  Prok-RING_4 28 kdlssCPlCqrris 41
                 ++ + CP C+++++
   AJA93090.1 39 EERAKCPACNQEFD 52
                 56679*****9975 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.051        71       5      14 ..      22      31 ..      21      31 .. 0.77
   2 ?    9.4   0.1    0.0007      0.97       3      13 ..      42      52 ..      39      53 .] 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.051
  zinc_ribbon_4  5 CpsCkakyei 14
                   Cp Ck+  +i
     AJA93090.1 22 CPLCKTIGRI 31
                   9999987665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0007
  zinc_ribbon_4  3 itCpsCkakye 13
                     Cp+C+ ++ 
     AJA93090.1 42 AKCPACNQEFD 52
                   46777777775 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.4e-05     0.034      17      57 ..       7      52 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
  OrfB_Zn_ribbon 17 ikveevnpay.TSktCseCgsknke....alsgrtfkCpnCgfead 57
                     k+++  p + T   C+ C  +++     ++ +++ kCp+C+ e+d
      AJA93090.1  7 QKIVKTGPKNvTTGMCPLCKTIGRIfiigNVGEERAKCPACNQEFD 52
                    56777778888*************9****************99886 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.014        19      12      28 ..      10      26 ..       7      34 .. 0.73
   2 ?    9.5   0.4   0.00083       1.1      19      31 ..      40      51 ..      29      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
  zinc_ribbon_9 12 VsvspdedsdvlCPhCg 28
                   V   p++    +CP C+
     AJA93090.1 10 VKTGPKNVTTGMCPLCK 26
                   556666666669****7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00083
  zinc_ribbon_9 19 dsdvlCPhCgggF 31
                   ++++ CP C++ F
     AJA93090.1 40 ERAK-CPACNQEF 51
                   4456.*****999 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.049        67      10      21 ..      12      26 ..       4      27 .. 0.72
   2 ?    8.8   0.0    0.0017       2.3      12      24 ..      39      51 ..      33      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.049
   zf-H2C2_2 10 tgekpy...eCplCd 21
                tg+k +    CplC+
  AJA93090.1 12 TGPKNVttgMCPLCK 26
                5666666667****6 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
   zf-H2C2_2 12 ekpyeCplCdkaF 24
                e + +Cp+C+  F
  AJA93090.1 39 EERAKCPACNQEF 51
                55669*****998 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.021        29      25      32 ..      21      28 ..      15      32 .. 0.82
   2 ?   10.8   1.4   0.00028      0.38       4      34 ..      22      52 ..      21      53 .] 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
  zf-Sec23_Sec24 25 iCnfCnhk 32
                    +C++C++ 
      AJA93090.1 21 MCPLCKTI 28
                    7****986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
  zf-Sec23_Sec24  4 CrrCraylNpfckidfggkrwiCnfCnhkne 34
                    C  C+++  +f+    g  r +C+ Cn++ +
      AJA93090.1 22 CPLCKTIGRIFIIGNVGEERAKCPACNQEFD 52
                    77788888888888999**********9877 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.016        21      37      45 ..      19      27 ..       6      31 .. 0.77
   2 ?    4.7   0.2      0.02        27      39      45 ..      21      27 ..      18      38 .. 0.68
   3 ?    9.6   0.3   0.00058      0.81      36      47 ..      40      51 ..      34      53 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                T-B-TTT-- CS
  zf-C3HC4_3 37 kkkCpiCrr 45
                +  Cp+C++
  AJA93090.1 19 TGMCPLCKT 27
                567888875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                B-TTT-- CS
  zf-C3HC4_3 39 kCpiCrr 45
                 Cp+C++
  AJA93090.1 21 MCPLCKT 27
                4666653 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00058
                TT-B-TTT--B- CS
  zf-C3HC4_3 36 rkkkCpiCrrpi 47
                +++kCp C+++ 
  AJA93090.1 40 ERAKCPACNQEF 51
                789******986 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.004       5.5      30      39 ..      18      27 ..      11      41 .. 0.78
   2 ?    5.9   0.4     0.011        16       3      13 ..      42      52 ..      40      53 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
     zf-Di19 30 kevvCPvCae 39
                + ++CP+C++
  AJA93090.1 18 TTGMCPLCKT 27
                6789****84 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
     zf-Di19  3 ftCPyCgkelt 13
                 +CP C++e++
  AJA93090.1 42 AKCPACNQEFD 52
                68999999887 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0008       1.1      18      30 ..      14      26 ..       3      36 .. 0.75
   2 ?    2.9   0.1     0.084   1.2e+02      83      93 ..      39      49 ..      30      53 .] 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
     DUF4451 18 knekkeglCpiCe 30
                 ++ + g+Cp+C+
  AJA93090.1 14 PKNVTTGMCPLCK 26
                567889******9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.084
     DUF4451 83 kegivCpkCne 93
                +e + Cp+Cn+
  AJA93090.1 39 EERAKCPACNQ 49
                45566888887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.022        30       3       9 ..      20      26 ..      18      28 .. 0.78
   2 ?    7.0   0.2    0.0041       5.6       4      12 ..      43      51 ..      39      53 .] 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.022
  PhnA_Zn_Ribbon  3 pkCplCa 9 
                    + CplC+
      AJA93090.1 20 GMCPLCK 26
                    67****6 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0041
  PhnA_Zn_Ribbon  4 kCplCaSey 12
                    kCp C+ e+
      AJA93090.1 43 KCPACNQEF 51
                    899998776 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.4    0.0065       8.9       2       8 ..      21      27 ..      21      28 .. 0.85
   2 ?    4.1   0.2     0.048        66       2      10 ..      43      51 ..      43      53 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0065
  Zn-C2H2_12  2 eCPlCse 8 
                +CPlC+ 
  AJA93090.1 21 MCPLCKT 27
                8****95 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.048
  Zn-C2H2_12  2 eCPlCseqF 10
                +CP C   F
  AJA93090.1 43 KCPACNQEF 51
                7****9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.59
# Mc/sec: 268.38
//
Query:       AJA93091.1  [L=217]
Description: nitroreductase family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-26   91.7   0.2    9.9e-14   51.7   0.0    2.1  2  Nitroreductase  Nitroreductase family
    2.1e-09   37.3   0.3     0.0004   20.0   0.0    2.8  2  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   1.1e-17   9.9e-14       2      61 ..      53     112 ..      52     117 .. 0.95
   2 !   38.2   0.0   1.6e-13   1.4e-09      98     170 .]     125     193 ..     115     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.1e-17
                     HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHH CS
  Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalell 61 
                     ++RrS+RkF+ +pv++ +++kil+aa  aP+agn q ++++ ++dk+++++l +aa+++ 
      AJA93091.1  53 ATRRSTRKFSTNPVERWKIDKILAAADSAPTAGNFQGFEIFYISDKDTKEELVKAANKQP 112
                     78*****************************************************99985 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 1.6e-13
                     --TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEEEE- CS
  Nitroreductase  98 atldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvliavGy 170
                       +  + + +++  + ++++da +aa   +LaA alGl s++ig+fde++  v++++g +   +++ l++vGy
      AJA93091.1 125 NPARVKLDFSPKVIMKFSIQDATLAAAYSQLAASALGLSSIWIGMFDEEK--VKEIIGTD--LRPTSLLCVGY 193
                     5555566778889999**********************************..********..9*********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2   5.1e-06     0.045       1      56 [.      47     103 ..      47     124 .. 0.67
   2 !   20.0   0.0   4.5e-08    0.0004      93     154 ..     155     215 ..     150     217 .] 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-06
                     -HHHHHHH--B---B--S---HHHHHHHHH-----S....S-----EE.E....... CS
  TM1586_NiRdase   1 nlyeaiekRhsvRkYkdealeeelleelkeaieeinkes.glelqlvidenkafksk 56 
                     ++++ + +R+s Rk++ +++e  +++++ +a+++  ++     +++++ + k+ k++
      AJA93091.1  47 DIFKVMATRRSTRKFSTNPVERWKIDKILAAADSAPTAGnFQGFEIFYISDKDTKEE 103
                     578999999999999999999999999999999887776333455444333333333 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 4.5e-08
                     HHHHHTT-EEEEES--SST...........T-S-EEEEE-BS----.-----HHHHBSS-GG CS
  TM1586_NiRdase  93 LkltalGlgtcWvggtykkkkakvelkkgeklvivIalGyaktklveakrkpleelcevkee 154
                     L ++alGl++ W+g+ ++++k+k  +  + +   ++ +Gy+ +k  +++r++l+el++v e+
      AJA93091.1 155 LAASALGLSSIWIGM-FDEEKVKEIIGTDLRPTSLLCVGYPIKKRPAKQRRQLKELIHVVEK 215
                     899***********7.888899899999****************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1195.99
//
Query:       AJA93092.1  [L=311]
Description: oligopeptide/dipeptide transporter, C-terminal domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-26   92.8   0.1    3.4e-26   92.4   0.1    1.2  1  ABC_tran     ABC transporter
    1.1e-18   67.5   0.1    1.9e-18   66.7   0.1    1.4  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    5.7e-05   23.1   0.8    0.00043   20.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.9e-05   21.9   2.3    0.00018   21.0   2.3    1.4  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0019   18.0   0.0     0.0028   17.4   0.0    1.3  1  PRK          Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.061   13.0   0.0        0.1   12.2   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.1   1.1e-29   3.4e-26       1     136 [.      23     177 ..      23     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 1.1e-29
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS..--S-TTSBHHHH.......... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx..xxxxxxxxxxxx.......... RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke.....qeleslrkeigvlpqe..pqlfpeltvren.......... 79 
                 l++v++ + +ge ++i Ge+ +GKStL   ++++ ++    +G+i++dg++l +      ++++  kei++++q   ++l+p  +++e+          
  AJA93092.1  23 LEDVTFAIDKGESIGIAGESACGKSTLGLSIIQMISNgkiYSGKIQFDGQSLLDipddeFDKKIRWKEISMVFQGamSSLDPVFSIQEQfdevlkqhnf 121
                 689************************99988888887889*************9988878888899********999*************99988875 PP

                 ..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  80 ..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                   +s+   + ++++l+ ++l+++v+k+ p++LSgG+kqrv +a+al+ kpk++++DEpt
  AJA93092.1 122 egDSK---QSIIQSLNSVNLDESVLKKFPHELSGGMKQRVIIAMALILKPKFVIADEPT 177
                 54444...555555555556669999999*****************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.1   6.4e-22   1.9e-18       1      65 []     228     291 ..     228     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 6.4e-22
   oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                 vE g+s+++f ep+HPYTk+Ll+s+p l +  +  + i+g +p+l + +eGC+F++RCp a+e+C
  AJA93092.1 228 VEFGDSEEIFLEPKHPYTKGLLESIPVLSKDTK-PKFIPGIPPNLVNPSEGCKFYDRCPEAMEKC 291
                 8***************************88888.999**************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.098   2.9e+02       3      22 ..      37      57 ..      35      96 .. 0.62
   2 !   20.2   0.0   1.4e-07   0.00043     235     302 ..     148     212 ..     120     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.098
      AAA_21  3 vliGpNgsGKSnL.Ldaldll 22
                ++ G  ++GKS+L L +++++
  AJA93092.1 37 GIAGESACGKSTLgLSIIQMI 57
                688999******944444444 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.4e-07
      AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                 +elS G+k+   ++ al+  +   ++++ DEp + L+  +++ ++ l+k+l++ g  +++ +H+  +l
  AJA93092.1 148 HELSGGMKQRVIIAMALILKP---KFVIADEPTTALDVLIQAQIVNLFKKLKKDGQSFMIISHDLAVL 212
                 789*****9955555555544...99*************************9977778******9887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.3   5.9e-08   0.00018     119     213 ..     125     223 ..      21     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.9e-08
                 -HHHHHHHHHCTT-STT.......CS-HHHHH..HHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSE.EEEE-SSHHHCCC-SC CS
                 xxxxxxxxxxxxxxxxx.......xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
       SMC_N 119 tkkevsellesagiske.......lLSgGekt..LvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQ.fivislreemlekadk 207
                 +k+ + + l+s++++++       +LSgG k+  ++a+aL+      kp  +++ De   aLD    +++++l+k+ +k+ Q f++is++  +l+++ +
  AJA93092.1 125 SKQSIIQSLNSVNLDESvlkkfphELSGGMKQrvIIAMALI-----LKP-KFVIADEPTTALDVLIQAQIVNLFKKLKKDGQsFMIISHDLAVLSEVAE 217
                 4455555566666655577777779****665226666666.....344.499***************************87689**********9999 PP

                 EEEEEE CS
                 xxxxxx RF
       SMC_N 208 lvgvtk 213
                  +g++ 
  AJA93092.1 218 KIGIMY 223
                 999875 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.4e-07    0.0028       2      65 ..      36     103 ..      35     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.4e-07
         PRK   2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrl....draekdleleerkrakekevsfls 65 
                 Ig+ag+S++Gk+t+   + +++ + k+ + +i+ d    l    d+++k+++ +e +  ++  +s l+
  AJA93092.1  36 IGIAGESACGKSTLGLSIIQMISNGKIYSGKIQFDGQSLLdipdDEFDKKIRWKEISMVFQGAMSSLD 103
                 9**********************999999999666655550011445555555565555555555555 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05       0.1       6      48 ..      25      65 ..      21     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                 HHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg 48
                 D+ f i +G+ ++i g++ +Gk+++  s+++  + +   iy g
   AJA93092.1 25 DVTFAIDKGESIGIAGESACGKSTLGLSIIQMIS-N-GKIYSG 65
                 88999*******************9988877752.2.356655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 1664.57
//
Query:       AJA93093.1  [L=278]
Description: oxidoreductase NAD-binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-12   47.1   0.0    5.1e-12   46.4   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    4.6e-08   33.3   0.0    7.2e-08   32.7   0.0    1.3  1  FAD_binding_6    Oxidoreductase FAD-binding domain
     0.0084   15.4   0.0      0.011   15.0   0.0    1.2  1  Methyltransf_34  Putative SAM-dependent methyltransferase
  ------ inclusion threshold ------
      0.068   13.3   0.0       0.14   12.3   0.0    1.6  2  NAD_binding_6    Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   1.1e-15   5.1e-12       2     106 ..     124     248 ..     123     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.1e-15
                    EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTT......EEEEEEE....ESSCTTTSSSEESSHHHHHHHHHHH CS
  NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpg......rlkvvav....vsreeagweggkgrvqdalleells 87 
                    ++gGtG+aP+ ++ +++ +  +dk+++v+++G+ + ++l y+  l  ++++ ++      ++ + a+     ++ +++w+g+ grv+  + e++ +
     AJA93093.1 124 VGGGTGLAPFIAFAHHFRDT-NDKRQLVVLHGASYVDELSYKRLLTDFENESKErgvdkwNFLYRAAisrpKEQYNRSWNGQVGRVESFFKENAQG 218
                    79**************9997.99**************************99999866655554444488888888899************999999 PP

                    ...........HSSTTEEEEEECSHHHHHH CS
  NAD_binding_1  88 ...........lkkeethvyvCGppgMika 106
                               ++ e+t +y+CG +g i++
     AJA93093.1 219 vspldelvgekVTPENTRIYICGYQGTIDG 248
                    99********9999*********9887665 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.6e-11   7.2e-08      12      95 ..      16     102 ..       5     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.6e-11
                    TTEEEEEEEESTTTS-----TT-EEEEEEC..ETTCCEEEEEE.BSSTTECCEEEEEEE--...TT-HHHHHHHCS-TT-EEEEEEEE- CS
  FAD_binding_6  12 edtrifrfklpsekqklglpvGqhvflrlk..ikgeaviRsYtpissenekGelellvkvy...pgGkmsqaLdelkigdtleikGPlG 95 
                    ed+ ++r+  +  +   ++ +Gq++ + l+  ++++ v R+Y+++s+ +++ ++e++++ +     G+++  L  l +gd + +  P+G
     AJA93093.1  16 EDLVVIRLVPE--NGMPKYKTGQFLTIGLPvrAENKIVKRAYSIASHAENRDYFEFVIRWVrkpLPGRVTTELFYLSVGDEVLLGDPTG 102
                    55555555443..4445899*******999777899999**********************88778***************99988887 PP

>> Methyltransf_34  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.4e-06     0.011      81     146 ..     110     175 ..      46     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-06
  Methyltransf_34  81 eeeekeekklkvlciGGGag.aElvalaallrekeeekessssslsltlvDiadWssvvkkLekait 146
                      + ++ e ++ +v+c+GGG g a ++a+a  +r++ ++k++       + vD   +++++++ e++ +
       AJA93093.1 110 KYRNGEPDNRRVVCVGGGTGlAPFIAFAHHFRDT-NDKRQLVVLHGASYVDELSYKRLLTDFENESK 175
                      2233445778*********9899*********54.44444455555678888888888888777655 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.2e-05      0.14       3      30 ..     120     147 ..     118     178 .. 0.89
   2 ?   -2.8   0.0       1.3     6e+03     135     155 ..     233     253 ..     223     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-05
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6   3 nvllvagGiGitpfisilkdllkkskke 30 
                     v+ v+gG+G++pfi ++ ++  + +k+
     AJA93093.1 120 RVVCVGGGTGLAPFIAFAHHFRDTNDKR 147
                    699******************9998854 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                    xxxxxxxxxxxxxxxxxxxxx RF
  NAD_binding_6 135 ssvgvfvCGppklvkevkklv 155
                    +++ +++CG ++ ++ v ++v
     AJA93093.1 233 ENTRIYICGYQGTIDGVMEYV 253
                    556678999998888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1583.48
//
Query:       AJA93094.1  [L=171]
Description: NUDIX-type nucleoside diphosphatase, YffH/AdpP family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.2   0.0    3.6e-18   65.9   0.0    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0     2e-22   3.6e-18       3     115 ..      34     143 ..      32     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2e-22
                 EEEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE...EEECSG CS
       NUDIX   3 rravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygdeheilyvfl...eevege 95 
                 + a++++ ++ekg+vLlv+++ + ++g   e+P+G++e+gE+p ++A RE+ EEtG++a ++++l++     +p+ g+++   e +++f+    ++e +
  AJA93094.1  34 PGAAAMLAFDEKGKVLLVKQH-RFPHGyiLEIPAGTLEKGEKPIDCAYREIIEETGYKAkKMTKLVS----YFPSVGYNK---EEIHIFVasgTKKEFD 124
                 4567777**************.999997668****************************77777777....555555555...3444444434555555 PP

                 CSSTSTTTEEEEEEEEHHHH CS
       NUDIX  96 lepndenevsevrwvpleel 115
                 l+++  +e+  v  ++++ l
  AJA93094.1 125 LKLD-NDEFITVVKMDIKRL 143
                 5555.888777755666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 965.74
//
Query:       AJA93095.1  [L=342]
Description: hypothetical protein T478_0031 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00095   18.1   0.5     0.0013   17.7   0.5    1.1  1  HTH_micro  HTH-like
     0.0041   16.6   0.0     0.0083   15.7   0.0    1.5  1  HTH_24     Winged helix-turn-helix DNA-binding
     0.0044   16.9   0.1       0.01   15.7   0.1    1.6  1  MarR       MarR family
  ------ inclusion threshold ------
      0.031   14.2   0.0      0.068   13.1   0.0    1.5  1  MarR_2     MarR family


Domain annotation for each model (and alignments):
>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   2.8e-07    0.0013      91     152 ..     278     335 ..     263     342 .] 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-07
   HTH_micro  91 keyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikink 152
                 k   +i+ f+ ++   +  ++lr+k+ +   ++  ++k+L++++lie +tk++++ +ik+ +
  AJA93095.1 278 K---DIIKFIHENGGSALESDLRKKFLLPRTTMWRAVKRLERHELIE-ITKKDQQNLIKLTN 335
                 5...799****************************************.89999999999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-06    0.0083       5      48 .]     277     321 ..     274     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
      HTH_24   5 drkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                 d++I++ + +n++    ++L ++  l+++t +r +krLe+ +lI+
  AJA93095.1 277 DKDIIKFIHENGGsALESDLRKKFLLPRTTMWRAVKRLERHELIE 321
                 899**********9**************************99996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.3e-06      0.01      12      52 ..     284     325 ..     279     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                 HHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
        MarR  12 lyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                 ++e+g+ +  s+L kk+ + ++t+ r+++rLe+++lie +k+
  AJA93095.1 284 IHENGGsALESDLRKKFLLPRTTMWRAVKRLERHELIEITKK 325
                 67777746667**************************97766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.068      12      55 ..     282     324 ..     277     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                 HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
      MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                  +++ ++g     ++l +++ l++ ++ r++krL+++ L+e ++
  AJA93095.1 282 KFIHENGGS-ALESDLRKKFLLPRTTMWRAVKRLERHELIEITK 324
                 566666665.4669**************************9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 1922.19
//
Query:       AJA93096.1  [L=121]
Description: MttA family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   40.7   0.3    1.5e-10   40.3   0.0    1.4  2  MttA_Hcf106      mttA/Hcf106 family
     0.0048   16.1   0.0      0.006   15.8   0.0    1.0  1  AI-2E_transport  AI-2E family transporter
  ------ inclusion threshold ------
      0.022   13.9   0.0      0.023   13.9   0.0    1.2  1  Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransfera
      0.032   13.5   2.3      0.038   13.3   2.3    1.1  1  Trypan_glycop    Trypanosome variant surface glycoprotein (A-
      0.053   14.1   0.7      0.076   13.6   0.6    1.4  1  OAD_gamma        Oxaloacetate decarboxylase, gamma chain


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   4.1e-14   1.5e-10       5      47 ..      14      59 ..      11     102 .. 0.81
   2 ?   -3.6   0.1         2   7.3e+03      17      20 ..     108     111 ..     108     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.1e-14
                 HHHHHHHHHH.HHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH-..- CS
  MttA_Hcf106  5 elliIlvVal.llFGpkkLPEvaraLGktLreFkkavkeleee..n 47
                 e++iI +Val llFG +kLPE+++  Gk   e+ ka  e++++  +
   AJA93096.1 14 EWMIIIFVALiLLFGTNKLPEAGKKIGKMVGEYNKAKTEMQNQinD 59
                 8888888886268****************************98540 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2
                  S-TT CS
  MttA_Hcf106  17 FGpk 20 
                  FGpk
   AJA93096.1 108 FGPK 111
                  9**9 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-06     0.006      56     128 ..      16      91 ..      10      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
  AI-2E_transport  56 vlllllvllvllvlllvplliaqltqlvkslpayidslqnilnelpslleelen...liqalkqslskilsnilss 128
                      +++++++l+ l+++  +p++ + + ++v ++ +  ++ qn++n++++ ++e+ +    +q+ +q+l+++++ ++ +
       AJA93096.1  16 MIIIFVALILLFGTNKLPEAGKKIGKMVGEYNKAKTEMQNQINDMTKAEPENPTiegPVQTERQKLERMAQTLRIN 91 
                      57999***********************************************735898888888888888887655 PP

>> Lip_A_acyltrans  Bacterial lipid A biosynthesis acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.4e-06     0.023      14      73 ..      12      66 ..       2     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-06
  Lip_A_acyltrans 14 wlvwlgiavllllallPesvlrkilkglgrlaakflkrrrkiarkNLalvfpekseaere 73
                     +  w+ i++++l+ l++ ++l +++k++g+++++ +     +a++ ++  + ++++ae+e
       AJA93096.1 12 GSEWMIIIFVALILLFGTNKLPEAGKKIGKMVGEYN-----KAKTEMQNQINDMTKAEPE 66
                     445******************************555.....6666666666666666665 PP

>> Trypan_glycop  Trypanosome variant surface glycoprotein (A-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.3   1.1e-05     0.038     265     329 ..      56     120 ..      30     121 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
  Trypan_glycop 265 alkavqeklqekvlndtaallke...............selkkaarkallkkketededieekikeafggdddnknkklw 329
                    +++++++               +               ++l   a+++  +++ ++d +++++i++ fg ++++  +k+ 
     AJA93096.1  56 QINDMTK---------------AepenptiegpvqterQKLERMAQTLRINTENKSDIELKNAIDARFGPKENSSENKFT 120
                    2222222...............2333444444555667999999*****************************9999986 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   2.1e-05     0.076      11      58 ..      16      80 ..      10     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
   OAD_gamma 11 mgvVFvvLilLslvisl......fskiikkkakkkkkkakaaaaaaaaaaaaa...........e 58
                m+++Fv+LilL    +l      ++k++  ++k+k++ + + ++ ++a+++++           +
  AJA93096.1 16 MIIIFVALILLFGTNKLpeagkkIGKMVGEYNKAKTEMQNQINDMTKAEPENPtiegpvqterqK 80
                99******************999999999999999999999988888777665676666654440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1560  (0.0870099); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 768.14
//
Query:       AJA93097.1  [L=311]
Description: hydroxymethylbilane synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-72  241.7   0.0    6.2e-72  241.4   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    7.8e-16   58.2   0.0    2.2e-15   56.8   0.0    1.8  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.0   6.9e-76   6.2e-72       1     202 [.       3     207 ..       3     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 6.9e-76
  Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke...eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlptelpeglelaavlk 92 
                     i++gtR+S+L+laq+++v ++Lk+   + ++ei++i+tkGD+++ +pL  +++kg+F ke+++a+ e+++d+aVhS+KD+p++l++ l++a+v+k
      AJA93097.1   3 IKLGTRGSPLSLAQTSWVLDELKNtnpSLTFEIEKITTKGDTDT-RPLFAMEQKGIFEKEIDRAVSEKQVDFAVHSMKDVPSDLDSSLTIACVPK 96 
                     799*******************664334448************9.8************************************************* PP

  Porphobil_deam  93 redprDvlvvks..sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAaAGLkRlgleerisevlspeellpa 185
                     re+++Dvl++++  sl+++p+g++vg+sSlRR++q++++rpdl+vk++RGn++tR++k+ e+++d+i+LA+AG++Rlg++++ s  ls++e+lp+
      AJA93097.1  97 RESVNDVLITNDgfSLDSIPSGSTVGSSSLRRAVQISRKRPDLNVKPIRGNIETRINKVTEKKIDGIVLAKAGISRLGVDTKHSL-LSKDEFLPS 190
                     *********866899***************************************************************7776665.********* PP

  Porphobil_deam 186 vgQGalavevrkedeel 202
                     +gQGala+ +r++d+++
      AJA93097.1 191 PGQGALAIICRSDDSKT 207
                     **************987 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   2.5e-19   2.2e-15       2      74 ..     221     290 ..     220     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.5e-19
                      HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHHH CS
  Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeell 74 
                      +ev aER+l ++ + GC  P+G+ya+v+ ++ l Lk  v s dg+ks+++e  +++  ++++elGkk+++el+
       AJA93097.1 221 IEVEAERSLSEHIDSGCRFPVGAYASVKSDS-LILKVGVYSMDGKKSILIEENGTI--DNPFELGKKIGNELK 290
                      589*************************989.**************8888888888..7************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2312.41
//
Query:       AJA93098.1  [L=57]
Description: hypothetical protein T478_0932 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 420.13
//
Query:       AJA93099.1  [L=101]
Description: 4Fe-4S binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-10   38.0  12.0      2e-06   27.3   0.8    2.2  2  Fer4      4Fe-4S binding domain
    8.3e-09   35.9   3.7    1.1e-08   35.5   3.7    1.2  1  Fer4_7    4Fe-4S dicluster domain
      1e-07   31.9   1.6    1.5e-07   31.4   1.6    1.3  1  Fer4_21   4Fe-4S dicluster domain
    3.5e-06   27.1   3.9    1.2e-05   25.4   4.1    1.7  2  Fer4_9    4Fe-4S dicluster domain
    8.4e-06   25.6  10.0     0.0086   16.1   0.6    2.2  2  Fer4_6    4Fe-4S binding domain
    3.4e-05   23.7   7.7      0.016   15.3   1.3    2.3  2  Fer4_2    4Fe-4S binding domain
    0.00017   21.6   8.0     0.0041   17.2   9.0    2.0  2  Fer4_10   4Fe-4S dicluster domain
    0.00021   21.5   6.5      0.075   13.6   1.7    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00028   21.4   4.4       0.12   12.9   0.4    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00062   20.7   6.2      0.057   14.4   0.1    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00078   20.2   2.8       0.13   13.2   0.6    2.1  2  Fer4_22   4Fe-4S dicluster domain
     0.0013   19.6  11.5      0.089   13.8   3.4    2.3  2  Fer4_3    4Fe-4S binding domain
     0.0024   18.3   5.8      0.018   15.4   5.8    1.9  1  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.3   5.8       0.27   11.8   5.8    2.1  1  Fer4_17   4Fe-4S dicluster domain
       0.19   12.5  10.9      1e+02    3.7  10.9    2.9  1  Fer4_15   4Fe-4S single cluster domain
        1.1    9.5  10.6        2.1    8.6   2.9    2.1  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.4     1e-05     0.011       4      18 ..      10      24 ..       7      25 .. 0.88
   2 !   27.3   0.8   1.8e-09     2e-06       2      23 ..      47      68 ..      46      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                ETTTSSS-THHHHHS CS
        Fer4  4 deekCigCGaCvevC 18
                 e +CigC +Cve+C
  AJA93099.1 10 GEQMCIGCALCVEIC 24
                5779*********** PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.8e-09
                EEETTTSSS-THHHHHSTTTEE CS
        Fer4  2 videekCigCGaCvevCPvgAI 23
                v+ +e+Ci  GaC+ vCP+ AI
  AJA93099.1 47 VFYPERCITDGACIGVCPTKAI 68
                688******************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   3.7   9.8e-12   1.1e-08       2      52 .]      14      67 ..      13      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 9.8e-12
      Fer4_7  2 CigCgaCvaaCp...vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                CigC  Cv+ C     ++++++++e  k+ +  ++ pe+C++ gaC+ vCPt+a
  AJA93099.1 14 CIGCALCVEICTslgPDVLRVKPVEGWKRGKAFVFYPERCITDGACIGVCPTKA 67
                ***********777789*******999999999*******************87 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   1.6   1.3e-10   1.5e-07       3      57 ..       9      68 ..       7      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.3e-10
     Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvl......kvvedeCvGCnlCssvCPvedci 57
                i e++CigC +C+  C   + + +++++ + +          ++C+    C+ vCP+ ++i
  AJA93099.1  9 IGEQMCIGCALCVEICTSLGPDVLRVKPVEGWkrgkafVFYPERCITDGACIGVCPT-KAI 68
                8899********************888776443333225569**************7.444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   2.2   0.00012      0.14      34      47 ..      12      25 ..       4      28 .. 0.79
   2 !   25.4   4.1   1.1e-08   1.2e-05       2      51 .]      14      68 ..      13      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
      Fer4_9 34 eaCigCgaCveaCp 47
                + CigC  Cve+C 
  AJA93099.1 12 QMCIGCALCVEICT 25
                46999999999997 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.1e-08
      Fer4_9  2 CtgCgaCveaC...pagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                C+gC  Cve C     +v + + +e+  r +a+    e+Ci+ gaC+ +Cp++ai
  AJA93099.1 14 CIGCALCVEICtslGPDVLRVKPVEGWKRGKAFVFypERCITDGACIGVCPTKAI 68
                ***********6665566777777777777665558999*************997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.0   4.3e-05     0.048       7      19 ..      12      24 ..       9      26 .. 0.92
   2 !   16.1   0.6   7.7e-06    0.0086       6      24 .]      50      68 ..      45      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
      Fer4_6  7 dkCigCgdCvrvC 19
                + CigC  Cv +C
  AJA93099.1 12 QMCIGCALCVEIC 24
                78*********** PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.7e-06
      Fer4_6  6 pdkCigCgdCvrvCPegai 24
                p++Ci  g+C+ vCP++ai
  AJA93099.1 50 PERCITDGACIGVCPTKAI 68
                89***************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.3   1.4e-05     0.016       5      21 ..       9      25 ..       4      26 .. 0.87
   2 !   12.0   0.6   0.00015      0.17       3      22 .]      46      65 ..      44      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
      Fer4_2  5 vdtdrCigCgaCvsaCP 21
                + +++CigC  Cv  C 
  AJA93099.1  9 IGEQMCIGCALCVEICT 25
                6799************5 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
      Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                +v+ ++rCi  gaC+ +CP+
  AJA93099.1 46 FVFYPERCITDGACIGVCPT 65
                7889999*744********7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   9.0   3.6e-06    0.0041       5      56 .]      10      64 ..       6      64 .. 0.81
   2 !   14.1   0.4   3.5e-05     0.039       5      23 ..      49      67 ..      45      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
     Fer4_10  5 dddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                 ++ Ci+C+ Cv+ C ++l     +v+  +  ++++a    +e+C++ gaC+ +CP
  AJA93099.1 10 GEQMCIGCALCVEIC-TSLgpdvLRVKPVEGWKRGKAFVFYPERCITDGACIGVCP 64
                5788***********.5559997666666666666666779**************9 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
     Fer4_10  5 dddtCirCgkCvkaCPadl 23
                 +++Ci  g+C  +CP+++
  AJA93099.1 49 YPERCITDGACIGVCPTKA 67
                5799************955 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   1.7   6.7e-05     0.075       2      14 ..      12      24 ..      11      30 .. 0.91
   2 !   10.6   0.2   0.00062      0.69       1      16 [.      50      65 ..      50      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.7e-05
      Fer4_4  2 erCigCgsCvaaC 14
                + CigC  Cv +C
  AJA93099.1 12 QMCIGCALCVEIC 24
                68*********** PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
      Fer4_4  1 qerCigCgsCvaaCPq 16
                +erCi  g+C+ +CP+
  AJA93099.1 50 PERCITDGACIGVCPT 65
                69*************7 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.4   0.00011      0.12       4      17 ..      12      25 ..       9      39 .. 0.86
   2 !   10.1   0.3    0.0008       0.9       4      18 ..      51      65 ..      50      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
     Fer4_13  4 dtCiacgaCvelaP 17
                + Ci+c++Cve++ 
  AJA93099.1 12 QMCIGCALCVEICT 25
                67**********94 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
     Fer4_13  4 dtCiacgaCvelaPd 18
                ++Ci +gaC  ++P 
  AJA93099.1 51 ERCITDGACIGVCPT 65
                79************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   2.0    0.0034       3.8      53      64 ..      13      24 ..       6      26 .. 0.73
   2 !   14.4   0.1   5.1e-05     0.057       1      17 [.      52      68 ..      52      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
     Fer4_16 53 aitgCdiCqdvC 64
                 ++gC+ C+++C
  AJA93099.1 13 MCIGCALCVEIC 24
                467788887777 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.1e-05
     Fer4_16  1 rCgtCgkCaevCPtnai 17
                rC+t g+C+ vCPt+ai
  AJA93099.1 52 RCITDGACIGVCPTKAI 68
                6999************9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.6   0.00011      0.13      76      93 ..       8      25 ..       3      27 .. 0.87
   2 !    7.5   0.1    0.0064       7.2       1      19 [.      52      70 ..      52      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
     Fer4_22 76 kfgesgCvGCgRCieacp 93
                 +ge++C+GC  C+e c+
  AJA93099.1  8 DIGEQMCIGCALCVEICT 25
                6799*************7 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0064
     Fer4_22  1 rClsCgaCtlvCptCsCfd 19
                rC++ gaC  vCpt   f 
  AJA93099.1 52 RCITDGACIGVCPTKAIFW 70
                7************977665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   3.4   7.9e-05     0.089       1      12 [.      14      25 ..      14      28 .. 0.92
   2 !   10.8   1.2   0.00072       0.8       1      15 []      53      67 ..      53      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.9e-05
      Fer4_3  1 CtgCgaCvevCP 12
                C+gC +Cve C 
  AJA93099.1 14 CIGCALCVEICT 25
                ***********6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00072
      Fer4_3  1 CtgCgaCvevCPvgA 15
                C+  gaC  vCP++A
  AJA93099.1 53 CITDGACIGVCPTKA 67
                77779********98 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   5.8   1.6e-05     0.018       4      64 ..      13      66 ..      12      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
      Fer4_8  4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                 Ci+C +C + C +l     + +  +g + + +    +       ++C t gaC  vCp++
  AJA93099.1 13 MCIGCALCVEICTSLGPDVLRVKPVEGWKRG-KAFVFY------PERCITDGACIGVCPTK 66
                6***********8777777666677776666.333334......89*************97 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.8   0.00024      0.27       2      58 ..      14      65 ..      13      68 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
     Fer4_17  2 CiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                Ci+C+ C++ C s+      + k+++      +++     + ++Ci+ g C  +CP 
  AJA93099.1 14 CIGCALCVEICTSLGPDVL-RVKPVEG----WKRGKAFVFYPERCITDGACIGVCPT 65
                *********9988765444.3344444....34444456899*************96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  10.9     0.092     1e+02       6      65 ..      12      69 ..       8      70 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.092
     Fer4_15  6 daCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAa.raCPvdAIr 65
                + Cigc+lCv+ ++ +     + ++   +++ ++++++v   e+  ++ A   +CP++AI+
  AJA93099.1 12 QMCIGCALCVEICTSLGPDVLRVKP---VEGWKRGKAFVFYPERCITDGACiGVCPTKAIF 69
                67***********643322223333...222333344444433333333322466666665 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.9    0.0019       2.1      84      98 ..      13      27 ..       2      42 .. 0.77
   2 ?    6.1   0.9     0.011        12      60      74 ..      52      66 ..      42      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0019
     Fer4_18 84 eciscllcidacdkv 98
                 ci c+lc++ c+++
  AJA93099.1 13 MCIGCALCVEICTSL 27
                388888888888865 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
     Fer4_18 60 dcidcescvkvcPtg 74
                 ci+ ++c+ vcPt+
  AJA93099.1 52 RCITDGACIGVCPTK 66
                6999*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 709.56
//
Query:       AJA93100.1  [L=70]
Description: hypothetical protein T478_0545 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   12.8   1.2       0.12   12.3   0.1    1.7  2  HalOD2    Halobacterial output domain 2
       0.14   12.8   0.1         14    6.4   0.0    2.0  2  RbpA      RNA polymerase-binding protein


Domain annotation for each model (and alignments):
>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.23   2.1e+03       5       8 ..      23      26 ..      18      29 .. 0.67
   2 ?   12.3   0.1   1.3e-05      0.12      30      39 ..      40      49 ..      37      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.23
      HalOD2  5 CseC 8 
                C+ C
  AJA93100.1 23 CTTC 26
                5555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.3e-05
      HalOD2 30 yvWkCtrCGe 39
                +vW+C rCG+
  AJA93100.1 40 FVWQCFRCGK 49
                9********7 PP

>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0016        14      34      60 ..       4      30 ..       1      39 [. 0.78
   2 ?    5.6   0.0    0.0028        25      50      67 ..      41      58 ..      28      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
        RbpA 34 ghetevtfaaeaevPetwecrrcGkea 60
                 ++  +++++++e+Pe+ +c +c ++ 
  AJA93100.1  4 KKKSGLPIIDSTEMPESLDCTTCLLPM 30
                56677899999**********997665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0028
        RbpA 50 twecrrcGkeakldgeep 67
                +w+c rcGk+  +++e++
  AJA93100.1 41 VWQCFRCGKKYFVHTENE 58
                8********988866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 545.65
//
Query:       AJA93101.1  [L=760]
Description: aconitate hydratase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   6.5e-145  483.7   0.0   8.9e-145  483.2   0.0    1.2  1  Aconitase    Aconitase family (aconitate hydratase)
      9e-37  126.3   0.0    1.9e-36  125.3   0.0    1.6  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
       0.13   11.0   0.0       0.21   10.2   0.0    1.3  1  DUF521       Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.2   0.0  1.5e-148  8.9e-145       1     461 []      39     482 ..      39     482 .. 0.92

  Alignments for each domain:
  == domain 1  score: 483.2 bits;  conditional E-value: 1.5e-148
   Aconitase   1 ekiwdahlvee.......egiayv...pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeealeknledefernkeryef 89 
                 eki++ hl++e       e+++yv   pdrv+lqdvtg++++ ++++a+ +             + p+++++dh+++a+++ +++++ ++ +n+e+y+f
  AJA93101.1  39 EKILAGHLEDEfldklldEKKNYVflrPDRVALQDVTGQMVMLQFMQAGLKS-----------VTLPTTVHCDHLIQARTEGKSDTKLAMYENNEVYKF 126
                 688888888555655665346666779************************9...........99********************************** PP

   Aconitase  90 LksaakafgirvvppgqGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlav 188
                 L++a++++g  +++pg+GI+Hqv+lE+ +a+pg +++gtDSHT+++gglG++a+GvGg +a++ ++g+p+el +pk +gv+l+Gk++ ++ +kD++l+v
  AJA93101.1 127 LETASSKYGAGFWNPGAGIIHQVVLEN-YAFPGGLMIGTDSHTPNAGGLGMIAVGVGGLDAAETMAGMPWELLYPKRIGVHLKGKMSGWTAPKDVILYV 224
                 ***************************.*********************************************************************** PP

   Aconitase 189 igklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlst 286
                 +gkl ++g+++ ++E+fG+gves+s++++aTi+NM+aE+GAt+++fp+d+++ +YL+ t+r+e a l +++++  +   e+++++++ +dk++e+dlst
  AJA93101.1 225 AGKLSVSGGTNSIIEYFGPGVESISCTGKATITNMGAEIGATCSIFPYDKRMETYLNSTDRKEIASLANDHTSLLQADpEVEQNPEKFFDKIIEIDLST 323
                 *************************************************************999985555555554444999***************** PP

   Aconitase 287 lepsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSe 385
                 lep+v gp++P+ a p+sel +     e+             +++  ++  k+++a+igSCTNss+ed+++  +++++a+ +g k+k  ++++v+PGSe
  AJA93101.1 324 LEPHVVGPHTPDLARPISELSN-----EI-------------DSNDYID--KISVALIGSCTNSSYEDMSRSSSVAKQAETHGIKAK--IPLLVTPGSE 400
                 *****************77764.....23.............2334455..6***************************99996555..5********* PP

   Aconitase 386 vvkayleaeGlleiLekaGfevvgagCstCignsdrle....egeaivsssNRNFegRqg..pntrayLaSPelvvaaAlaG 461
                 +++ ++e++G  ++L+++G++v++++C++Cig+++r e    e+++iv+s+NRNF gR++  ++t++++aSPe+v+a Al G
  AJA93101.1 401 QIRSTIERDGQIDTLRSIGATVLANACGPCIGQWQRPElkdgEKNSIVTSFNRNFPGRNDgkRDTMNFIASPEIVTALALGG 482
                 ************************************887777778**************53366777************976 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.0   3.1e-40   1.9e-36       3     130 ..     564     691 ..     562     692 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 3.1e-40
                  CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHT CS
  Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSSRehAAkalrll 100
                   +lk+kG++t+d++s ++++l  ++++++ ++n+ lg+ ++ + +++k+++  ++  e+  + a++yk+++ ++++++++n+GeGSSRehAA+ +r+l
   AJA93101.1 564 LILKAKGKCTTDHISPAGPWLRLRGHLDNLSDNLLLGAVNAFNDEVGKAKNILTNSIENCSQIARNYKEKNMHWIIVGDNNYGEGSSREHAAMTPRFL 661
                  57899********************************************************************************************* PP

                  TEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
  Aconitase_C 101 GikaviaeSFerIfennliknglLplefke 130
                  G  +via+SF+rI+e+nl+k+g+L l+f++
   AJA93101.1 662 GCAVVIAKSFARIHETNLKKQGILALTFEN 691
                  ***************************986 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.6e-05      0.21     298     361 ..     364     436 ..     335     452 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.6e-05
      DUF521 298 cPhlsleElre...laellkgkkkkvkvelwvttsre.vkeeaerlglveklekaGvkvlsdtC.mvv....s 361
                 c   s+e++ +   +a++ + ++ k k++l+vt + e +++++er g +++l++ G++vl++ C +++    +
  AJA93101.1 364 CTNSSYEDMSRsssVAKQAETHGIKAKIPLLVTPGSEqIRSTIERDGQIDTLRSIGATVLANACgPCIgqwqR 436
                 55556666654111677778999999******9865449*************************434454543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (760 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4905.72
//
Query:       AJA93102.1  [L=44]
Description: hypothetical protein T478_0743 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.6   2.4      0.042   13.6   2.4    1.1  1  DUF4412   Domain of unknown function (DUF4412)
      0.052   13.8   6.9      0.053   13.8   6.9    1.1  1  CEBP_ZZ   Cytoplasmic polyadenylation element-binding protein
       0.76    7.6   4.7       0.69    7.7   4.7    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2
        3.2    8.2   4.6         13    6.2   0.2    2.0  2  DUF983    Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> DUF4412  Domain of unknown function (DUF4412)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.4   9.4e-06     0.042      89     110 ..       4      25 ..       2      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-06
     DUF4412  89 veklGketikGYsCehvritsk 110
                  ek G++t kGY+Ceh + ++ 
  AJA93102.1   4 CEKCGQNTSKGYDCEHTKFEEY 25 
                 69***************98854 PP

>> CEBP_ZZ  Cytoplasmic polyadenylation element-binding protein ZZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   6.9   1.2e-05     0.053      13      49 ..       3      37 ..       1      44 [] 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
     CEBP_ZZ 13 eCeiCekakargpyfCrdlaCfkYyCetCwqrrHsae 49
                +Ce+C +++ +  y C++++ f+ yC++C+++ H   
  AJA93102.1  3 KCEKCGQNT-SKGYDCEHTK-FEEYCKECYTELHYYI 37
                7******99.4558898766.9999*********543 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.7   0.00015      0.69     632     668 ..       3      36 ..       1      44 [] 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00015
    PolC_DP2 632 rCeeCgekteeklvCkkceeeveeekcekcekeakav 668
                 +Ce+Cg++t++ + C++ +    ee c++c +e + +
  AJA93102.1   3 KCEKCGQNTSKGYDCEHTK---FEEYCKECYTELHYY 36 
                 7999999999977766554...456777777776554 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.003        13       9      19 ..       2      12 ..       1      16 [. 0.85
   2 ?    4.4   0.7     0.011        51       5      20 ..      20      35 ..      17      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
      DUF983  9 daCeaCgldls 19
                ++Ce+Cg++ s
  AJA93102.1  2 PKCEKCGQNTS 12
                79*****9876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
      DUF983  5 LkvadaCeaCgldlsh 20
                 k+++ C++C ++l+ 
  AJA93102.1 20 TKFEEYCKECYTELHY 35
                58999*****999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 312.77
//
Query:       AJA93103.1  [L=106]
Description: hypothetical protein T478_0522 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 775.96
//
Query:       AJA93104.1  [L=348]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-34  118.8   0.0    3.1e-34  118.0   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    2.6e-18   66.7   0.0    3.8e-18   66.2   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    0.00025   21.2   0.0    0.00054   20.1   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    0.00038   21.3   0.0    0.00069   20.4   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00085   19.6   0.0     0.0014   18.9   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0049   17.4   0.0      0.011   16.3   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.037   13.5   0.0      0.056   12.9   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.074   13.9   0.0       0.17   12.7   0.0    1.6  1  SGP              Sulphur globule protein
      0.078   12.9   0.0       0.18   11.7   0.0    1.6  2  NAD_binding_10   NAD(P)H-binding
        0.2   10.5   0.0       0.29    9.9   0.0    1.2  1  Mgr1             Mgr1-like, i-AAA protease complex subunit


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   0.0   1.7e-37   3.1e-34       1     120 [.       2     140 ..       2     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 1.7e-37
                     EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
  Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagvskelapklaeagvkvi 94 
                     kv+ivGa+GyvG e+lrlL +hp+ve++ ++s+++  Gk l++a ++l++ +dlk+++ d e++ +++d+vf+a+p+g++ +++++l+++g+k+i
      AJA93104.1   2 KVGIVGASGYVGGEVLRLLLSHPKVEVSMVTSRQH-VGKFLHRAQPSLRGFTDLKFSELDYEKMsDSCDLVFTAVPHGTATDIVKALYDRGMKII 95 
                     7*********************************9.**********************99999989***************************** PP

                     ESSSTTTTST...................TSEBE-HHHHGGGGGG CS
  Semialdhyde_dh  95 DlssdfRlkd...................davyvlpevnreaikk 120
                     Dls+d+Rl++                   + ++++pe++re+ikk
      AJA93104.1  96 DLSADYRLHNpedygkwygwehphpdyleKSTFGVPELHREEIKK 140
                     *******************************************97 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   2.1e-21   3.8e-18       1     184 []     158     318 ..     158     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.1e-21
                      HHHHHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESCS CS
  Semialdhyde_dhC   1 LkPLlda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkileftek 93 
                      L+PL+++ l++ +++iv+++ + SGaG+                    +g++++  ag + py+   +++++ e+++el++ a +k ++++++ 
       AJA93104.1 158 LNPLIKNdLIDTDHIIVDSKIGSSGAGAG-------------------AGTSHAMRAGVIRPYKPA-KHRHTGEIEQELSQTAGKKIKVAMSP- 230
                      89**************************5...................******************.**************************. PP

                      EEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS..TTEEEEESS....HCHHSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEET CS
  Semialdhyde_dhC  94 vsatcvrVPvlrGhseavtiklklkdveveeveellaaa..pevkvvvne....eedrPtpaavaggtnsvsVGRirkdemgdeglklvvvgDN 181
                           + V v+rG++ + ++ lk kd++ +e ++ ++++  +e +++         ++P p+  +g +n++++G ++ d ++++ l + +++DN
       AJA93104.1 231 -----HAVDVVRGILCTNHTFLK-KDIDEKELWKIYRSEysEERFIRLIRdkegLHKFPDPKFLVG-SNFCDIG-FDLDRDNNR-LIALSASDN 315
                      .....79***************7.999999999999999986777765554557789********9.9******.*****9997.********* PP

                      TTT CS
  Semialdhyde_dhC 182 llk 184
                      l+k
       AJA93104.1 316 LMK 318
                      *97 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     3e-07   0.00054       1      91 [.       1      91 [.       1      95 [. 0.63

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS......--S-BEB.SSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHTT CS
      DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg......klgvavt.ddleevlekadvliDFTtpeavlenlklalekg 91
                +kv++vGasG +G ev++++ +++++e++ + +r++       +g++l++        ++++++  d+e++ +++d +     +  + + +k+++++g
  AJA93104.1  1 MKVGIVGASGYVGGEVLRLLLSHPKVEVSMVTSRQH-------VGKFLHRAqpslrgFTDLKFSeLDYEKMSDSCDLVFTAVPHGTATDIVKALYDRG 91
                89********************************98.......4444444310000123333332456666666666644444444555555555555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.8e-07   0.00069       1      90 [.       1      95 [.       1      96 [. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.8e-07
                  EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.......HHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
  GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.......leelladpeidavivatpngtheelakaaleagkhvl 90
                  ++v+i+Ga G++g + l  l  s+++ ev  + +++       +++  +  ++d       +e++++   +d+v+ a+p gt  +++ka+  +g++++
    AJA93104.1  1 MKVGIVGAsGYVGGEVL-RLLLSHPKVEVSMVTSRQHVGKFLHRAQPSLRGFTDlkfseldYEKMSD--SCDLVFTAVPHGTATDIVKALYDRGMKII 95
                  69******999999999.6666669999998888776444444888888877777766655556666..9*************************987 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.9e-07    0.0014       1     102 [.       3     104 ..       3     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.9e-07
                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGGGHHHHHHHHHH CS
  Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnlsppissldvlkaCie 91 
                      v i+Ga G+vG  v++ll+ h +v  e+  ++  ++  + l   a  +   f+  ++   +ye+    +  + dlv  ++p   + d++ka ++
       AJA93104.1   3 VGIVGAsGYVGGEVLRLLLSHPKV--EVSMVTSRQHVGKFLH-RAqpSLRGFTDLKFSELDYEK----MSDSCDLVFTAVPHGTATDIVKALYD 89 
                      689*********************..5554444444433333.333466678999999999988....55567********************* PP

                      HT-EEEESS-....B CS
  Sacchrp_dh_NADP  92 tgvhyvdtsi....s 102
                      +g+  +d s      
       AJA93104.1  90 RGMKIIDLSAdyrlH 104
                      *******88733432 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.2e-06     0.011       1      95 [.       2      98 ..       2     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.2e-06
                   EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTS CS
  F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgk 89
                   k+gi+ ++G +g  +++ ll++   + e+ +++sr+   + ++  +++         k ++ d+e++ +++d v+ av+   +++++++l    ++g 
     AJA93104.1  2 KVGIVgASGYVGGEVLRLLLSHP--KVEVSMVTSRQH--VGKFLHRAQpslrgftdLKFSELDYEKMSDSCDLVFTAVPHGTATDIVKAL---YDRGM 92
                   79999667999*99999999996..677776655554..344444444445799999*********************************...66777 PP

                   EEEEES CS
  F420_oxidored 90 lvisvl 95
                    +i+ +
     AJA93104.1 93 KIIDLS 98
                   777765 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.056       3      53 ..       5      64 ..       3      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                EETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC........EEEE--TT-H CS
   Epimerase  3 VtGatGfiGsalvkallekg.yevigldrlssasntarledl........elveldltdr 53
                ++Ga+G++G  +++ ll++  +ev  ++++++ +++ ++++         ++ eld+ + 
  AJA93104.1  5 IVGASGYVGGEVLRLLLSHPkVEVSMVTSRQHVGKFLHRAQPslrgftdlKFSELDYEKM 64
                89******************899*******999999988877778666666666665544 PP

>> SGP  Sulphur globule protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.7e-05      0.17      50      82 ..     100     132 ..      73     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
         SGP  50 rygygapygYgypygygaPygpYgagapYgapa 82 
                 +y+ ++p +Yg  yg++ P+  Y +   +g+p 
  AJA93104.1 100 DYRLHNPEDYGKWYGWEHPHPDYLEKSTFGVPE 132
                 49999***************99*9999999996 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-05      0.18       1      72 [.       7      79 ..       7     100 .. 0.70
   2 ?   -3.6   0.0         5   8.9e+03      98     128 ..     182     209 ..     171     215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE.--T.T-CCHHHHHHTT-SEEEES---TC CS
  NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevve.gdv.tdvedlaealkgadaVvsalgggg 72
                    GA+G vG ++++ ll++ ++ev  +v + +++ ++ ++++ ++    d+  ++ d ++  + +d V++a+ +g 
      AJA93104.1  7 GASGYVGGEVLRLLLSHPKVEVS-MVTSRQHVGKFLHRAQPSLRGfTDLkFSELDYEKMSDSCDLVFTAVPHGT 79
                    9****************999985.56677777666644555444422331467899999999999999994433 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5
                     ETTTTSGCGCHHHHHHHHCCHHHHHHHHHHH CS
  NAD_binding_10  98 aigvgdevpgefgewnkellkaylaakraae 128
                     ++g+g   +g+ + +   ++++y  ak++  
      AJA93104.1 182 GAGAG---AGTSHAMRAGVIRPYKPAKHRHT 209
                     33333...35555555667788887777765 PP

>> Mgr1  Mgr1-like, i-AAA protease complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00016      0.29     316     368 ..     210     260 ..     189     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
        Mgr1 316 ekilkklsvekektkekklplsskrkeasrgiildedvkspediDleeiwsly 368
                  +i+++l   +++ k+ k+++s ++ +  rgi+  +++  ++diD +e+w++y
  AJA93104.1 210 GEIEQEL--SQTAGKKIKVAMSPHAVDVVRGILCTNHTFLKKDIDEKELWKIY 260
                 3344444..35555666677777778888***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2499.20
//
Query:       AJA93105.1  [L=697]
Description: V-type ATPase 116kDa subunit family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-26   91.4  17.5    2.1e-22   78.9   1.4    3.2  3  V_ATPase_I     V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
       0.03   14.2   0.3      0.074   12.9   0.3    1.6  1  DUF5380        Family of unknown function (DUF5380)
      0.096   13.0   5.4        3.4    8.0   0.3    4.0  3  DUF948         Bacterial protein of unknown function (DUF948)
       0.33   11.1   2.7        1.1    9.5   2.7    1.9  1  DUF624         Protein of unknown function, DUF624
       0.98    9.5   9.3        1.3    9.1   1.3    2.5  2  DivIVA         DivIVA protein
        2.7    7.7  17.2        1.2    8.8   1.4    2.5  3  DUF1351        Protein of unknown function (DUF1351)
        3.1    6.3   5.9        3.8    6.0   0.2    1.9  2  Peptidase_S46  Peptidase S46


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   1.4   8.1e-26   2.1e-22     147     416 ..     119     389 ..      18     398 .. 0.68
   2 !    6.7   3.5   0.00057       1.5     513     566 ..     463     516 ..     449     528 .. 0.90
   3 !   14.2   0.2   3.1e-06     0.008     715     810 ..     597     682 ..     592     684 .. 0.75

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 8.1e-26
  V_ATPase_I 147 eeeelleeeeelsfvaGvikrekveaferilwralrgnlfl.rqaeiee...pledpetgekve........ksvfiiffqgeqlkekikkicesfgak 233
                 e +++ ++ ++l+    v+k+ ++      l + +  nlf+ ++++i+e   +l d++     +         s+ +i++      eki k++ sf+a+
  AJA93105.1 119 EYKKEISDYTTLKETLEVVKKLNIDLTGFGLMKQFYTNLFIvQTKDIDEikkTLDDATF----NqyplntkeESALMIIADVA-NLEKILKVMRSFNAN 212
                 22222333334666666777766666666666666667665144445442214444433....12223333256666665555.5689*********** PP

  V_ATPase_I 234 lyelpeseeeree.klkeveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeat 331
                  +++pe+ e+  + ++++ e +i++ e+  ++ ++++ +++++i +++ +++   +  k + + L +     tk++ + +g++pk+ +++ +++  + +
  AJA93105.1 213 PFSIPENVEQVPTkAYATAELKIKEFEEKHKKVTKEIAKMIAKIRQDILTLHERASVAKDVLELLRKP--GGTKNFAVVQGYIPKKMEKKFKETTGKWM 309
                 *******99986505677888*******************************************9988..7899************9999998888766 PP

  V_ATPase_I 332 eessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlk 416
                      sv + +++ e +++ PT f    f ++f  i ++ Gi++  E+ p+++   ++P  +++MF D+GHGlll+ ++l++ lk
  AJA93105.1 310 -----SVVEDVSDPELSKKRPTLFDNKIFVRTFEVITQSQGIPKKGEADPTPMIALMWPIFYGLMFADVGHGLLLMGLGLVFKLK 389
                 .....44445555577899********************************************************9999987665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00057
  V_ATPase_I 513 mKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifgYlvlli 566
                 +K+s  lG+i+ +++++l++       +k+++++e iP++ +   i++ ++++i
  AJA93105.1 463 LKVSLFLGIIHIVWAFILHIRKLAKDGHKTTMFTEAIPNVTLYGGIVVIMMCAI 516
                 7***************************************99999888887776 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 3.1e-06
  V_ATPase_I 715 gciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLhWVEfqsKFykgdGykFep 810
                 +c+ +T SY RL  + L Ha L   + +   +         lg +    ++a+ +   ++++ ++egl  ++ +LRLh  Ef +K+y g   +F+ 
  AJA93105.1 597 ECLAHTISYARLGIMLLVHAALLLTVNNSYAS---------LGGMESPGALALLIGGNIGIM-MIEGLIVYIQSLRLHLYEFFTKWYDGGAQPFKQ 682
                 68899999999999999999885433333333.........333333344555666677775.67************************9999985 PP

>> DUF5380  Family of unknown function (DUF5380)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   2.9e-05     0.074       1      49 [.      73     124 ..      73     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
     DUF5380   1 levlykk.lvkkqeevkn..srlidfiskavpsGvdapvpkiaeyetfksdk 49 
                 le+l+k  + kkq++  +  ++++d i+k +p+ +dap   + + e +k + 
  AJA93105.1  73 LEILFKGtVFKKQNQELDelEKMVDEIAKKAPGIIDAPAKLLKQQEEYKKEI 124
                 78999862568887654423799******************99999999765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.12     3e+02      33      61 ..      34      62 ..      26      68 .. 0.55
   2 ?    8.0   0.3    0.0013       3.4      15      65 ..      76     126 ..      72     144 .. 0.82
   3 ?    2.3   0.3     0.077     2e+02      29      58 ..     229     258 ..     219     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
      DUF948 33 atieelekqvdpilkevedllakvnelle 61
                +t e+++ +vd il +++++ +++ e+ +
  AJA93105.1 34 STSETVTPEVDDILLKAQQTFQEIDEVIK 62
                44455555555555555555555555444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
      DUF948  15 iflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvne 65 
                 +f   v++k ++ lde++++++e+ k++ +i++  ++ll++ +e  +++++
  AJA93105.1  76 LFKGTVFKKQNQELDELEKMVDEIAKKAPGIIDAPAKLLKQQEEYKKEISD 126
                 56677999999**********************999999999987776665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.077
      DUF948  29 deaaatieelekqvdpilkevedllakvne 58 
                   a+  i+e e++ ++++ke+++++ak+++
  AJA93105.1 229 ATAELKIKEFEEKHKKVTKEIAKMIAKIRQ 258
                 556667888889999999999999998877 PP

>> DUF624  Protein of unknown function, DUF624
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.7   0.00042       1.1      12      75 ..     493     567 ..     462     568 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00042
      DUF624  12 t..........llglvvfglfPAtaAlfavvrkwirkee.dssifktFweaYKknfkksnllglillliglillv 75 
                 t          l+g++v+ ++ A+ + + v+  + + ++  ++ +  F+  + + ++ + ++g+i+++ ++++++
  AJA93105.1 493 TmfteaipnvtLYGGIVVIMMCAIGSGYDVMNMYSKIHTePVPWVTVFLGDWAQVWIITRIAGIIVIASIVVMMI 567
                 05555555555*******************98886655428999999*******************999999875 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.4     0.016        40      21      66 ..      90     135 ..      81     137 .. 0.93
   2 ?    9.1   1.3   0.00052       1.3      74     127 ..     218     271 ..     195     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXX CS
      DivIVA  21 deVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLk 66 
                 de ++  d++ak+   +++  ++l ++ +e ++++++y++l+etL+
  AJA93105.1  90 DELEKMVDEIAKKAPGIIDAPAKLLKQQEEYKKEISDYTTLKETLE 135
                 6778899************************************995 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00052
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  74 etaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqarlfr 127
                 e  e+v ++a + ael ike e+k +k+ +e ++ ++ki+++i  l ++a + +
  AJA93105.1 218 ENVEQVPTKAYATAELKIKEFEEKHKKVTKEIAKMIAKIRQDILTLHERASVAK 271
                 57899**************************************99998887765 PP

>> DUF1351  Protein of unknown function (DUF1351)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.6   6.8e+03      79     100 ..      44      65 ..      37      67 .. 0.65
   2 ?    6.6   5.4    0.0024         6      62     173 ..      80     194 ..      77     210 .. 0.85
   3 ?    8.8   1.4   0.00047       1.2      71     107 ..     235     271 ..     226     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.6
     DUF1351  79 kelekkikeaidkideqikefe 100
                 +++  k +++ ++ide ik +e
  AJA93105.1  44 DDILLKAQQTFQEIDEVIKGLE 65 
                 5555566677777777777665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
     DUF1351  62 evkkeysePideFeakikelekkikeaidkideqikefeekekeekkkevkaliselaeeaeveleei.eiqekwln....ktvslkkieeeieaakae 155
                 +v k+ ++ +de e+ ++e+ kk   +id  ++ +k+ ee +ke    ++ ++  e++++++++l+ +  +++ ++n    +t+ + +i++ + +a+ +
  AJA93105.1  80 TVFKKQNQELDELEKMVDEIAKKAPGIIDAPAKLLKQQEEYKKEISDYTTLKETLEVVKKLNIDLTGFgLMKQFYTNlfivQTKDIDEIKKTLDDATFN 178
                 688999999***********************************************************778888****9999*********99666666 PP

     DUF1351 156 kikkdreelekakaeiee 173
                 ++  +  ++e++   i+ 
  AJA93105.1 179 QYPLN--TKEESALMIIA 194
                 65444..55555555555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00047
     DUF1351  71 ideFeakikelekkikeaidkideqikefeekekeek 107
                 i+eFe+k k+++k+i ++i+ki ++i  + e+   +k
  AJA93105.1 235 IKEFEEKHKKVTKEIAKMIAKIRQDILTLHERASVAK 271
                 89************************98888776666 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0015       3.8     297     377 ..      49     134 ..      29     144 .. 0.80
   2 ?    1.9   1.6     0.026        67     352     473 ..     189     307 ..     148     324 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0015
                    HHHHHHHHHHHHHHHHH.....HHHHHHHHTTHHHHHHHHHHHHHHHHHHCT-H.HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHT CS
  Peptidase_S46 297 kyasklagleNylKnli.....Gmlealkkkkvlekkqaeeaalrawlkkdpekkekygkalselealvkekrklaersalleeae 377
                    k +++++++   +K l+     Gmle l k +v++k+++e ++l++++++ ++k+  + +a ++l + ++e++k   +++ l+e+ 
     AJA93105.1  49 KAQQTFQEIDEVIKGLEiprevGMLEILFKGTVFKKQNQELDELEKMVDEIAKKAPGIIDAPAKLLKQQEEYKKEISDYTTLKETL 134
                    5555555555555544323333***************************************************9999999998875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.026
                    HHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHH....HH-HHHHHHHHHHHHHHCHHHHCS--HHHHHH.HHHHHHHHHHHH CS
  Peptidase_S46 352 alselealvkekrklaersalleeaessgsellslarklvrlaeerekpdaereeeyqeralealekeleridkdldaevdka.vlaallkeyrek 446
                    al+ ++++ + ++ l+  + +  + +s   ++ ++++k + +ae + k+ +e++++++    +++ k +++i +d+    ++a v++  l+ +r+ 
     AJA93105.1 189 ALMIIADVANLEKILKVMRSFNANPFSIPENVEQVPTKAYATAELKIKEFEEKHKKVT----KEIAKMIAKIRQDILTLHERAsVAKDVLELLRKP 280
                    4444554444444444444444455555556777777777777777755555554444....4455555566666666667652566778888888 PP

                    S-GGG--S----SS......-S-SHHC CS
  Peptidase_S46 447 lkaerlpavdkvlgkeskgdlealvdr 473
                     ++++ + v+  + k+ +++++++  +
     AJA93105.1 281 GGTKNFAVVQGYIPKKMEKKFKETTGK 307
                    889999999999999999888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1297  (0.0723409); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 4647.63
//
Query:       AJA93106.1  [L=376]
Description: trypsin-like peptidase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-34  119.3   0.2    4.8e-34  118.4   0.2    1.5  1  Trypsin_2      Trypsin-like peptidase domain
    9.4e-18   64.8   0.2      3e-17   63.2   0.2    1.8  1  Trypsin        Trypsin
    8.7e-13   48.4   0.8    3.1e-12   46.7   0.1    2.3  3  PDZ_2          PDZ domain
    1.5e-06   28.0   2.3      0.023   14.5   0.2    3.0  3  PDZ_6          PDZ domain
    5.8e-05   22.0   0.6      0.011   14.4   0.5    2.1  2  Peptidase_S46  Peptidase S46
    0.00025   21.3   2.4       0.62   10.5   0.3    3.6  3  PDZ            PDZ domain
     0.0039   16.9   0.2     0.0099   15.6   0.1    1.8  2  Peptidase_S29  Hepatitis C virus NS3 protease
     0.0059   15.8   0.7       0.85    8.8   0.2    2.4  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
  ------ inclusion threshold ------
      0.049   13.6   0.2       0.46   10.5   0.0    2.6  2  Tricorn_PDZ    Tricorn protease PDZ domain
      0.074   12.9   0.3       0.15   11.9   0.3    1.5  1  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.2   2.7e-37   4.8e-34       1     150 []      87     225 ..      87     225 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.7e-37
   Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsealkggepvyvvGyplggeks 99 
                 GsGf+++++g+++Tn+Hvv++a+++ +         ++ dg+++ ++v+++d +lD+A++kv + +++ l+p+++g+s++lk+ge+++++G+p g  + 
  AJA93106.1  87 GSGFVYSDEGYVITNQHVVQDAKRVMI---------TFLDGEAYIGNVIGTDRDLDIAVVKV-EPTNTYLQPIKIGDSSELKVGEKIAAIGNPFGLSG- 174
                 9**************************.........**************************.**********************************9. PP

   Trypsin_2 100 gsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                  s++sGivs+  +  ++  +++ ++++qtdaa++pG+SGGpl++ +G+vvG+
  AJA93106.1 175 -SMTSGIVSQMGRlLPQETGYSIPDVIQTDAAINPGNSGGPLINMKGEVVGI 225
                 .9***********9999999999****************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.2   1.7e-20     3e-17      14     220 ..      73     251 ..      64     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.7e-20
                 TEEEEEETTC.EEEEEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCBBC CS
     Trypsin  14 wqvslsvksg.khlCgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpiclp 110
                  qvs+ ++++ + + +G+++s++ +v+T++H+v++  + +v+++       +g+   +++ +vi     +    d Dia++k++     + + +pi++ 
  AJA93106.1  73 VQVSVLRGESdGGMGSGFVYSDEgYVITNQHVVQD--AKRVMIT-----FLDGE---AYIGNVIG---TDR---DLDIAVVKVEPT---NTYLQPIKIG 152
                 455555555586678899999999**********9..4444333.....34442...34445433...333...57*********9...********** PP

                 STTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEE.SSSSCTTSE CS
     Trypsin 111 aassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPlvcsdgelvGivswg.kgcakgnrp 208
                 + ss+l+vg    ++++g+++  +   +++++ v+ + r   +++  g+  ++ ++++a     ++++G+SGGPl++++ge+vGi+++    +++   +
  AJA93106.1 153 D-SSELKVG--EKIAAIGNPFGLS--GSMTSGIVSQMGRLLPQET--GYSIPDVIQTDA-----AINPGNSGGPLINMKGEVVGINTAIqSATGEFSGI 239
                 *.7778888..7888889986666..6777777777777555553..4457999*****.....************************94444444449 PP

                 EEEEEGGGGHHH CS
     Trypsin 209 gvytkvssyldw 220
                 g++++ ++++++
  AJA93106.1 240 GFAVPSNTVKKV 251
                 999999999886 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.5     8e+03      59      73 ..      67      81 ..      62      83 .. 0.78
   2 ?   -1.9   0.0       2.4   4.2e+03       4      26 ..     123     144 ..     120     166 .. 0.64
   3 !   46.7   0.1   1.7e-15   3.1e-12       1      80 [.     264     369 ..     264     371 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.5
                S-TT-EEEEEEEETT CS
       PDZ_2 59 kkpGdtVkltvlRdg 73
                k++ + V+++vlR+ 
  AJA93106.1 67 KSEESIVQVSVLRGE 81
                677888999999975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                 .XX------..-EEEEEE-TTSG CS
       PDZ_2   4 GvsvsdeedtggvlvvsVkeggP 26 
                 G  +  ++d   + vv+V++ + 
  AJA93106.1 123 GNVIGTDRD-LDIAVVKVEPTNT 144
                 555544444.5777788877664 PP

  == domain 3  score: 46.7 bits;  conditional E-value: 1.7e-15
                 ....XX------............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHHHHHHH.TS-TT-EEEEEEEETT CS
       PDZ_2   1 pylGvsvsdeed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledlislll.kkkpGdtVkltvlRdg 73 
                 p++G+s +d+++          ++g lvvsV eg+Pa+ agl                 gD+il++dg +v + +d+   l+ +k+ Gd+  l+v R+g
  AJA93106.1 264 PWMGISGTDVDPelaevrglnsSKGFLVVSVIEGSPAETAGLLGvtetketdgrefaldGDIILSIDGETVRKISDILVHLQrEKSVGDEMVLSVNRGG 362
                 6789999999999999999999*******************6666***************************99999999998**************** PP

                 EEEEEEE CS
       PDZ_2  74 kkktvev 80 
                 + +++++
  AJA93106.1 363 EILELTM 369
                 *999876 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.4   7.9e+03      38      56 .]      61      79 ..      59      79 .. 0.80
   2 !   12.1   0.0   7.2e-05      0.13       2      16 ..     291     305 ..     290     306 .. 0.92
   3 !   14.5   0.2   1.3e-05     0.023      19      54 ..     323     358 ..     321     360 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.4
       PDZ_6 38 vaallrgsagesvvlvvrr 56
                ++++ + s++++v + v r
  AJA93106.1 61 LIDIFEKSEESIVQVSVLR 79
                5678888999999998876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.2e-05
       PDZ_6   2 VtaVdpgsPAdrAGl 16 
                 V +V++gsPA++AGl
  AJA93106.1 291 VVSVIEGSPAETAGL 305
                 89************8 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.3e-05
       PDZ_6  19 GDiilsvNGqpveglsladvaallr..gsagesvvlvv 54 
                 GDiils++G++v  +++ d+   l+   s+g ++vl v
  AJA93106.1 323 GDIILSIDGETV--RKISDILVHLQreKSVGDEMVLSV 358
                 9***********..****98655553666666666665 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0029       5.2      46      69 ..      84     107 ..      67     110 .. 0.88
   2 !   14.4   0.5   6.2e-06     0.011     626     651 ..     201     226 ..     167     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0029
                    TTTEE-EE-STT-EEEE-HHHHHH CS
  Peptidase_S46  46 lggCtasfVSpeGLvlTNHHCayg 69 
                    +g  ++ + S+eG v+TN H++++
     AJA93106.1  84 GGMGSGFVYSDEGYVITNQHVVQD 107
                    688999999***********9986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.2e-06
                    EES----TT-TT-EEE-TTS-EEEEE CS
  Peptidase_S46 626 lstnDitGGNSGSPvlngkgelvGla 651
                     +++ i  GNSG P++n kge+vG++
     AJA93106.1 201 QTDAAINPGNSGGPLINMKGEVVGIN 226
                    57888999****************97 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.58     1e+03      42      55 ..     155     168 ..     146     176 .. 0.84
   2 !    7.7   0.0    0.0026       4.6       9      44 ..     263     306 ..     254     308 .. 0.81
   3 !   10.5   0.3   0.00034      0.62      47      75 ..     323     351 ..     322     359 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.58
                 HTSSTTEEEEEETT CS
         PDZ  42 dglkvGDkIlsvNg 55 
                 + lkvG kI ++++
  AJA93106.1 155 SELKVGEKIAAIGN 168
                 449********987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0026
                 TSESSEEEEEETTSS.......SSSSEEEEEECTTSHHHHHT.S CS
         PDZ   9 rgglGfslkggsdqr.......gdkgifvsevlpggaaeadg.l 44 
                 + ++G+s+   + +         +kg+ v +v +g++ae++g l
  AJA93106.1 263 HPWMGISGTDVDPELaevrglnSSKGFLVVSVIEGSPAETAGlL 306
                 6677888887777768888888899****************966 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00034
                 TEEEEEETTEETTTSHHHHHHHHHHTTTS CS
         PDZ  47 GDkIlsvNgvdvenvsheeavqaikgskg 75 
                 GD+Ils++g++v+++s+  + ++ ++s g
  AJA93106.1 323 GDIILSIDGETVRKISDILVHLQREKSVG 351
                 9**************99888777777666 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.9   5.2e+03      72      81 ..      93     102 ..      71     111 .. 0.55
   2 !   15.6   0.1   5.5e-06    0.0099     104     147 ..     205     249 ..     177     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.9
  Peptidase_S29  72 asdlylvtrd 81 
                    + + y++t++
     AJA93106.1  93 SDEGYVITNQ 102
                    3344555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.5e-06
  Peptidase_S29 104 selkGssGsPilCdsGhvvGllvaavcsggvvkavrfv.Pvetle 147
                    +   G sG+P++  +G vvG+ +a+  + g+ + + f  P +t++
     AJA93106.1 205 AINPGNSGGPLINMKGEVVGINTAIQSATGEFSGIGFAvPSNTVK 249
                    55569********************************88998876 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0051       9.2     112     139 ..      85     110 ..      64     156 .. 0.77
   2 !    8.8   0.2   0.00047      0.85     206     229 ..     207     230 ..     166     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0051
                    SEEEEEEEECTTEEEEEEEHHHH-TSEE CS
  Peptidase_S32 112 slGsGgvftidgevvvvtashvlgdnka 139
                     +GsG v++++g   v+t  hv++d k 
     AJA93106.1  85 GMGSGFVYSDEG--YVITNQHVVQDAKR 110
                    356676666655..799******97664 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00047
                    -GGGTT-EEEETTE.EEEEEEEEE CS
  Peptidase_S32 206 kcGDsGspvvdedgelvGvhtGsn 229
                    ++G+sG p+++ +ge+vG+ t  +
     AJA93106.1 207 NPGNSGGPLINMKGEVVGINTAIQ 230
                    79*****************99754 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         1   1.8e+03      41      81 ..      42      82 ..      39      91 .. 0.84
   2 ?   10.5   0.0   0.00026      0.46      42      78 ..     322     360 ..     319     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                 .TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE-STT CS
  Tricorn_PDZ 41 reGdlilavdgepvskekgiaelLvgkagkeveLtvkrkdg 81
                 + G+++ +v g + s e ++  +++  +++ v+++v r+++
   AJA93106.1 42 NYGETVGEVTGIERSYEYSLIDIFEKSEESIVQVSVLRGES 82
                 56899999999999999999999999999999999888765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                  TT-EEEEETTEE-BTTB-HHHHHHTTTT..SEEEEEEE- CS
  Tricorn_PDZ  42 eGdlilavdgepvskekgiaelLvgkag..keveLtvkr 78 
                   Gd+il++dge+v+k ++i  +L  ++   +e+ L+v+r
   AJA93106.1 322 DGDIILSIDGETVRKISDILVHLQREKSvgDEMVLSVNR 360
                  6******************99998665322677777776 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   8.4e-05      0.15      86     120 ..     199     233 ..     170     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                   EEEEXXXXXTT-TTSEEE-TTSXEEEECEEEEEXT CS
  Peptidase_S7  86 lgitdlnlssGsSGSlvlnqnkqivgiYfatvevd 120
                   ++ td   ++G SG +++n ++++vgi  a  + +
    AJA93106.1 199 VIQTDAAINPGNSGGPLINMKGEVVGINTAIQSAT 233
                   455677889******************87766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2631.05
//
Query:       AJA93107.1  [L=62]
Description: hypothetical protein T478_0801 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   13.4   0.8      0.078   13.4   0.8    1.1  1  FAM163    FAM163 family


Domain annotation for each model (and alignments):
>> FAM163  FAM163 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   4.4e-06     0.078      33      72 ..      16      55 ..       9      62 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-06
      FAM163 33 YCCkkdeseeeeeeepefavleplacnacssevvdgsaat 72
                YC  k+++e++++++++fa+ +p+  n+ s+e ++++a++
  AJA93107.1 16 YCTMKENKEKKDKDHEHFANDDPTKFNEKSAEEIAKEAIK 55
                9*******************99998888888877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1646  (0.0918066); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 459.43
//
Query:       AJA93108.1  [L=100]
Description: hypothetical protein T478_0896 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 640.06
//
Query:       AJA93109.1  [L=320]
Description: hypothetical protein T478_1291 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.5e-05   22.9   0.0    0.00089   19.6   0.0    2.1  1  Hydrolase  haloacid dehalogenase-like hydrolase
    0.00093   19.3   3.7       0.19   11.8   3.7    2.6  1  HAD_2      Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.32   10.7   0.0    1.5  1  Phage_Nu1  Phage DNA packaging protein Nu1


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-07   0.00089       3     207 ..      20     270 ..      18     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                 EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH.HHHHHETTTE......................HHHHTHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx......................xxxxxxxxxxx RF
   Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal.tgfatfigrg......................ayaigkpewlt 78 
                  ++fD+dG+L++ ++s   +i++                i + + + ++++ g++ t+  +   +g                      a  + + e+ +
  AJA93109.1  20 SIIFDCDGVLVDIRNSYDHAINKT---------------ISAIMKELFNDEIGDVvTSKIH---FGlksvggfndevavvyaivmtlaASKKSEIEFEK 100
                 59**********************...............3333344444442222111111...12222223334445555555554334444444444 PP

                 HH..HCHHHHHHHHHHHHHHCHHHHHH.........................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT. CS
                 xx..xxxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
   Hydrolase  79 al..dippdlgaaigsaqsqgrtvall.........................................qaralavftiadplkvkpeaaeavasLkaa. 133
                      i++  ++ i s  +  ++  ++                                         q     ++ + d   v ++   ++ +Lk + 
  AJA93109.1 101 LIvdVISNANESGINSIDDYFKDRNIDlieikskldyensrkvsyihkifnqlfygpklyeeisneksQFYDEPLIDLDDI--VLDD--NLMLKLKNRf 195
                 4455555555555555555555555558888888888888888888899999********999987544344444444444..6665..6888899998 PP

                 TEEEEEEESSEHHHHH.HHHHHTT.GGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHH CS
                 xxxxxxxxxxxxxxxx.xxxxxxx.xxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   Hydrolase 134 gievvlltgdnpetae.raanqlG.ddyf.daviasdiet..vakpspegkvaaireLqgkpeevamVGDgvnDaaala 207
                 g ++  +tg  +     +  + l+ +d   ++ ++        akp+pe + + i +++ k    + +GD++ D+ + +
  AJA93109.1 196 GTKISTVTGRGKFAFSySMKKFLDnFDMEnSVFLEDR--PlnLAKPNPESLIESISKINSKC--SLYIGDSMEDLLMVQ 270
                 **********999999455555885444434444444..256****************9888..***********9975 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   3.7   3.3e-05      0.19       1     170 [.      21     271 ..      21     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
       HAD_2   1 iiFDlDgTlldteeliiqafnelleey........................................................................ 27 
                 iiFD Dg+l+d ++ + +a+n+++                                                                           
  AJA93109.1  21 IIFDCDGVLVDIRNSYDHAINKTISAImkelfndeigdvvtskihfglksvggfndevavvyaivmtlaaskkseiefeklivdvisnanesginsidd 119
                 799999999999998888888888777888899999999999999999999999999999999999999999999999999999999888777777777 PP

       HAD_2  28 ....glselseeelrkliglslrellrklgeseeeeekieellrkyneekkk...kevkpydgv...kelLeeLkea.gyklgivTsksreaveekleq 115
                        ++++ e+++++  ++   ++++ +  ++    ++l++++ +ek +   + +  +d++    +l+ +Lk++ g k+  vT + + a+  ++++
  AJA93109.1 120 yfkdR--NIDLIEIKSKLDYENSRKVSYIHKIFNQLFYGPKLYEEISNEKSQfydEPLIDLDDIvldDNLMLKLKNRfGTKISTVTGRGKFAFSYSMKK 216
                 54330..44444444444444444444444443333355555555555555544355555666633336777886554899999999999999888888 PP

       HAD_2 116 lgiesyFdvivtsedvekk..KPdpeviekaleklklkkeeviyvGDsptDieaakk 170
                 +  +  ++  v  ed   +  KP+pe++ + + k   +++  +y+GDs  D+   +k
  AJA93109.1 217 FLDNFDMENSVFLEDRPLNlaKPNPESLIESISKI--NSKCSLYIGDSMEDLLMVQK 271
                 865555555666666554445*******9999875..566789******99877665 PP

>> Phage_Nu1  Phage DNA packaging protein Nu1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.4e-05      0.32      31      91 ..      70     127 ..      47     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.4e-05
   Phage_Nu1  31 kgGGkGnevvfdtaavirWyaerdaeieneklrkeveelraaaeadldpgtieyerrrlik 91 
                 + GG   ev+   a+v+   a +++eie ekl   v+ + +a e+ ++    +y + r i 
  AJA93109.1  70 SVGGFNDEVAVVYAIVMTLAASKKSEIEFEKLI--VDVISNANESGIN-SIDDYFKDRNID 127
                 5699999*************************7..677999*****99.555788888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2478.57
//
Query:       AJA93110.1  [L=58]
Description: hypothetical protein T478_0907 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 457.06
//
Query:       AJA93111.1  [L=264]
Description: queuosine biosynthesis protein QueC-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-29  102.2   0.0    3.7e-22   79.5   0.0    2.0  2  Asn_synthase   Asparagine synthase
    1.2e-06   28.2   0.0    2.3e-06   27.3   0.0    1.7  1  QueC           Queuosine biosynthesis protein QueC
    8.2e-06   25.1   0.4      2e-05   23.8   0.1    1.8  2  NAD_synthase   NAD synthase
    0.00064   18.6   0.0     0.0015   17.4   0.0    1.7  1  tRNA_Me_trans  tRNA methyl transferase
     0.0031   17.3   0.0      0.045   13.5   0.0    2.3  2  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0     1e-25   3.7e-22      13     142 ..      31     158 ..      20     192 .. 0.89
   2 !   21.1   0.0   5.6e-08    0.0002     238     296 ..     196     258 ..     178     264 .] 0.85

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 1e-25
  Asn_synthase  13 rlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee..pfadrsaipl 107
                    ++ d  vG+ +SGG+DS+lia l++     +++  +igf  ++s ++ +akev e l+ +h  l+++ e + ++ ++v  ++ +    +++ +i+ 
    AJA93111.1  31 TTVLDNSVGVAFSGGVDSTLIAKLLDDNGY-DIHLLTIGF--PDSHDINFAKEVNEILKFKHNILEIELESFQETSEKVNDIIKTdnLSWNENSIAF 124
                   5667999********************885.*********..********************************999999999999899******** PP

  Asn_synthase 108 yllsrlakrkgvkvvLsGeGaDElfgGYpyfykaa 142
                   y++s+lak+ g+  v + +G DElf+GY+  y++a
    AJA93111.1 125 YYVSKLAKKLGISTVVTANGIDELFCGYN-AYREA 158
                   *****************************.77665 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.6e-08
  Asn_synthase 238 RvPflDhrlvevalrlppelklrg...gieKyiLRealegy.lPeeileRpKegfsapvgewk 296
                     P+lD +++ +a ++p+++k+ +    + K+  R++++   +Pe  ++++K++ +++++ +k
    AJA93111.1 196 LQPLLDENFISYAKTIPISEKIIDendLQRKHAIRKLAASCgVPEISAYKQKKALQYGSKIHK 258
                   56********************9999999***********88************999777663 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   6.5e-10   2.3e-06       4      94 ..      40     127 ..      37     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.5e-10
                 EE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-----.------...-------- CS
        QueC   4 vllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei.evpkeeleeeelpntfV 94 
                 v +SGG+DSt ++ l  ++g+ +++lt+ +   h  +++ ak++ + l+  +h+il+++ l+++++++   ++i + ++ + +e+++   +V
  AJA93111.1  40 VAFSGGVDSTLIAKLLDDNGYDIHLLTIGFPDSH--DINFAKEVNEILKF-KHNILEIE-LESFQETSEKVNDIiKTDNLSWNENSIAFYYV 127
                 679*************************998876..5789**********.********.99998877544443033334455555555555 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   5.7e-09     2e-05       3     138 ..      19     153 ..      17     176 .. 0.78
   2 ?   -2.6   0.0      0.68   2.5e+03     156     170 ..     226     240 ..     210     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5.7e-09
                   HHHHHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH-H CS
  NAD_synthase   3 eelvdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqelkeaked 98 
                   ++l d + + +k++   ++v +  SGGvDS+l+a+l  +   + + l++ +P    + +d++ a+++ e l+ + + ++i+  +++f+++ ++ ++ 
    AJA93111.1  19 NQLLDEILNSIKTTVLdNSVGVAFSGGVDSTLIAKLLDDNGYDIHLLTIGFP----DSHDINFAKEVNEILKFKHNILEIE--LESFQETSEKVNDI 109
                   66667777777777765778899************99888767777777776....6799**********99999888886..68888888888889 PP

                   HHHHHHHHHHHHHHHHHHHHHHTEEEB---BHH....HHTTT-S CS
  NAD_synthase  99 lakgNlkaRiRmailyaianklnllvlgTgnks....ElvvGyf 138
                   ++++Nl   +  ++ y++++  ++l ++T   +    El  Gy 
    AJA93111.1 110 IKTDNLSWNENSIAFYYVSKLAKKLGISTVVTAngidELFCGYN 153
                   999***************99999997776433211127777776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.68
                   HHHHHHHHHHTT--H CS
  NAD_synthase 156 KtevkeLakelnvPe 170
                   K  +++La+  +vPe
    AJA93111.1 226 KHAIRKLAASCGVPE 240
                   677889999999997 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.2e-07    0.0015       2      39 ..      37      74 ..      36     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-07
  tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeed 39
                    v va+SgGVDS++ a ll ++gy++  +++ + +++d
     AJA93111.1 37 SVGVAFSGGVDSTLIAKLLDDNGYDIHLLTIGFPDSHD 74
                   589**********************9988877766644 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.3e-05     0.045       2     104 ..      38     143 ..      37     150 .. 0.53
   2 ?    1.1   0.0     0.079   2.8e+02     114     146 ..     169     201 ..     164     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                 EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT.-EEEEEE--H......HHCTTSTCCCHHHHHHHHHHHHCHH CS
  ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckkln.ikleiekvdv......akkkgknleeaARelRYevlkealk 93 
                 v vA+SgG+DS+++ +ll ++      ++ ++++ +  ++  +  +e+ + l  k+n +++e e+++       +  k++nl  +   + +  +++++k
  AJA93111.1  38 VGVAFSGGVDSTLIAKLLDDNGY----DIHLLTIGFPDSHDINFAKEVNEILKFKHNiLEIELESFQEtsekvnDIIKTDNLSWNENSIAFYYVSKLAK 132
                 679**********9999988854....444444444333322222222222222222123333333333333333334556666666666666666666 PP

                 CCT.CEEE--- CS
  ATP_bind_3  94 kegievlllAh 104
                 k gi+ +++A 
  AJA93111.1 133 KLGISTVVTAN 143
                 66666666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.079
                 HHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT CS
  ATP_bind_3 114 llrlargsglaglagikeaseiasirlvRPlLk 146
                 +++++ ++++++++++++++++ ++r++ PlL+
  AJA93111.1 169 VMNQKLDNEKKMMIAVNNVTSLFDVRILQPLLD 201
                 5667777888999******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1299  (0.0724525); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1940.64
//
Query:       AJA93112.1  [L=94]
Description: antibiotic biosynthesis monooxygenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-07   29.4   0.0      8e-07   29.1   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase
     0.0023   18.2   0.0     0.0029   17.9   0.0    1.3  1  DUF1330   Domain of unknown function (DUF1330)


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     9e-11     8e-07       1      76 [.       1      73 [.       1      75 [. 0.95

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 9e-11
                CEEEEEEEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHH CS
         ABM  1 mviviaeirvkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaah 76
                m+++i+ei  k ++ ++f    ++ +++l ++ +G+ + +ll+s+++ +   ++ e++++++++  ++sp++ ++ 
  AJA93112.1  1 MFVAIVEIVLKDEKKDDFKTWITDSNKTL-SKFDGFVSRRLLESRDGGN--RIMVEFKDMESFQKMHSSPEHSKFA 73
                99*************************77.9****************99..7888*****************9985 PP

>> DUF1330  Domain of unknown function (DUF1330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.3e-07    0.0029      14      77 ..      16      73 ..       3      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-07
     DUF1330 14 eaykeYaalaeaalakyggrflvrggkvevlEGdeeptrlvvieFpsveaarawyeSpeYqaak 77
                +++k++   ++++l k++g  + r    + lE  ++  + +++eF+++e++++++ Spe  + +
  AJA93112.1 16 DDFKTWITDSNKTLSKFDGF-VSR----RLLES-RDGGNRIMVEFKDMESFQKMHSSPEHSKFA 73
                55666777777777777763.333....47788.7778899******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 687.27
//
Query:       AJA93113.1  [L=133]
Description: pyridoxamine 5'-phosphate oxidase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-16   59.3   0.0    5.6e-16   58.5   0.0    1.4  2  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
      7e-11   42.3   0.0      9e-11   41.9   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
    0.00099   18.7   0.1     0.0011   18.6   0.1    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
      0.014   15.7   0.5      0.021   15.1   0.5    1.2  1  Ribosomal_L34e  Ribosomal protein L34e


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   1.3e-19   5.6e-16       7      87 ..       6      87 ..       2      88 .. 0.92
   2 ?   -3.5   0.0       2.8   1.3e+04      45      62 ..     102     119 ..      98     127 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.3e-19
                    HHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT...GSEEEEEEEEEEEESCH CS
  Putative_PNPOx  7 eflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde...lgrgvrieGtaelvsdg 87
                    efl+++k+ +lAT+de+++P+++pv++ +  ++  i++ tn++++k++n++++ +v+++++      +  gv+ +Gta+l++++
      AJA93113.1  6 EFLKKEKILHLATIDEKNSPHIVPVWYMYSAKK--IYVGTNTKTQKAKNIKKHRKVSFCIDVGVnapNIFGVMGKGTAKLLKEK 87
                    9********************************..************************9988887788888889999998875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                     EEETTSHHHHHHHHH-EE CS
  Putative_PNPOx  45 atnadsrklrnleenprv 62 
                     + + d + +++l  +  +
      AJA93113.1 102 FKSLDNKSAKELLDDTDC 119
                     556666677777666555 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0     2e-14     9e-11       7     134 ..       6     125 ..       3     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2e-14
                   HHHHC-SEEEEEEEETTE.EEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEEE.EEEEEEEEEEEEE--HHHHHHH CS
  Pyridox_ox_2   7 alLdegevgrlafvddge.pvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsln.yrSVvvrGraeevtdeeekaea 100
                   ++L+++++++la+ d+++ p+i+Pv y++ ++++y+ + +++++a+ +++++ v++ +    g++        n +  V+ +G+a+++++++   ++
    AJA93113.1   6 EFLKKEKILHLATIDEKNsPHIVPVWYMYSAKKIYVGTNTKTQKAKNIKKHRkVSFCIDV--GVNAP------NiF-GVMGKGTAKLLKEKKTVNRI 93 
                   799************8888******************************55557777776..43333......449.***********999999999 PP

                   CCCHHHHHSTTTGGCSB---CCCCCT..EEEEEEEE CS
  Pyridox_ox_2 101 lellvekivpgrwenlrpptrkelka..tsvlrlki 134
                    ++++ ++    ++ l  +++kel    + ++++ +
    AJA93113.1  94 AKKILLRY----FKSLDNKSAKELLDdtDCIIEILP 125
                   99999998....776666667776543345555555 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.4e-07    0.0011       7     105 ..       5     104 ..       1     131 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
  Pyrid_ox_like   7 kelvkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsd..eskkky.vsvsGtaevvedrakieelWspvv 99 
                    +e +k+ k+  L+t++++++ +  P          +++  t+++++k+k+i+k+++v++++    +  + + v+ +Gta++ +++++++   ++++
     AJA93113.1   5 TEFLKKEKILHLATIDEKNSPHIVPVWYMYS--AKKIYVGTNTKTQKAKNIKKHRKVSFCIDVgvNAPNIFgVMGKGTAKLLKEKKTVNRIAKKIL 98 
                    6778888888899999999999999876655..568***********************9854114445564677899*********999999999 PP

  Pyrid_ox_like 100 kawfpe 105
                      +f++
     AJA93113.1  99 LRYFKS 104
                    999953 PP

>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.5   4.7e-06     0.021      16      75 ..      34      93 ..      26      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.7e-06
  Ribosomal_L34e 16 rsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRa 75
                     s+k+ +v t ++   ++++kk+ k+  C d + +   i  +  k  ++l k+kktv+R 
      AJA93113.1 34 YSAKKIYVGTNTKTQKAKNIKKHRKVSFCIDVGVNAPNIFGVMGKGTAKLLKEKKTVNRI 93
                    589999999*************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1011.84
//
Query:       AJA93114.1  [L=68]
Description: hypothetical protein T478_0567 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0026   17.5   1.2     0.0037   17.0   0.1    1.7  2  LapA_dom     Lipopolysaccharide assembly protein A domain
     0.0034   17.0   0.4     0.0034   17.0   0.4    1.5  2  Saf_2TM      SAVED-fused 2TM effector domain
  ------ inclusion threshold ------
       0.12   12.7   8.4        2.1    8.7   8.2    2.0  2  DUF308       Short repeat of unknown function (DUF308)
       0.21   11.3   1.7       0.22   11.2   1.7    1.1  1  Tetraspanin  Tetraspanin family
       0.22   11.3   2.7       0.25   11.1   2.7    1.0  1  SPC25        Microsomal signal peptidase 25 kDa subunit (SPC2


Domain annotation for each model (and alignments):
>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.41   1.5e+03      23      38 ..      12      17 ..       7      25 .. 0.51
   2 !   17.0   0.1     1e-06    0.0037      21      51 ..      36      66 ..      29      68 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.41
    LapA_dom 23 llvafgiGallgwlls 38
                l ++f           
  AJA93114.1 12 LGMFF----------V 17
                32222..........2 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1e-06
    LapA_dom 21 llllvafgiGallgwllslwsylrlrrelrr 51
                ++++v   iG++lg++  l++y+++r+ l+r
  AJA93114.1 36 TIIVVIGSIGFILGGIYLLITYMKNRKILKR 66
                68999999******************99987 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.29     1e+03      70      84 ..       8      22 ..       4      27 .. 0.78
   2 !   17.0   0.4   9.5e-07    0.0034      58      99 ..      25      66 ..      21      68 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
     Saf_2TM 70 iilvigvllivvGav 84
                + lv+g++++ vGa+
  AJA93114.1  8 TYLVLGMFFVFVGAY 22
                568889999888865 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 9.5e-07
     Saf_2TM 58 fssseipeivlaiilvigvllivvGavllilryvneakrqsk 99
                ++   +++ + +ii+vig++ +++G + l++ y++++k++++
  AJA93114.1 25 YDAGTSFQTTTTIIVVIGSIGFILGGIYLLITYMKNRKILKR 66
                56666999************99999999999**9****9988 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.0     0.049   1.7e+02      26      39 ..      10      23 ..       3      31 .. 0.70
   2 ?    8.7   8.2    0.0006       2.1      19      48 ..      32      62 ..      11      66 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.049
      DUF308 26 llfGilllvsGivq 39
                l++G+++++ G+++
  AJA93114.1 10 LVLGMFFVFVGAYS 23
                45666777666665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0006
      DUF308 19 aallalvllf.GilllvsGivqiiaafaark 48
                 +++++++++  i ++++Gi+ +i+++++rk
  AJA93114.1 32 QTTTTIIVVIgSIGFILGGIYLLITYMKNRK 62
                34444444443789************98887 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.7   6.1e-05      0.22      11      66 ..       8      51 ..       1      65 [. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.1e-05
                 XXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin 11 lfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgfl 66
                   +++g+++++vG +            ++ +s + ++++   ++v+G++ f+lg +
   AJA93114.1  8 TYLVLGMFFVFVGAYSG---------YDAGTSFQTTTTI---IVVIGSIGFILGGI 51
                 5689*********8882.........2223344455555...88888888888744 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.7   6.9e-05      0.25      28      84 ..       8      63 ..       2      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
       SPC25 28 vrLalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgiltlystfveknt 84
                + L+lG++ v++ a++  yd  ++F+ + ++++++  + fil gi+ l++++ ++++
  AJA93114.1  8 TYLVLGMFFVFVGAYS-GYDAGTSFQTTTTIIVVIGSIGFILGGIYLLITYMKNRKI 63
                5699**9988887777.677778***************************8777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 465.63
//
Query:       AJA93115.1  [L=853]
Description: DNA polymerase family B, exonuclease domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-54  183.8   2.8    8.3e-54  183.0   2.8    1.3  1  DNA_pol_B       DNA polymerase family B
    7.1e-35  120.7   5.6    1.3e-34  119.9   5.6    1.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    5.8e-08   32.9   0.5    1.3e-07   31.7   0.5    1.6  1  RNase_H_2       RNase_H superfamily
    1.1e-06   28.5   0.8    5.8e-06   26.1   0.5    2.3  2  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.0   2.8   1.8e-57   8.3e-54      10     433 ..     428     818 ..     420     839 .. 0.87

  Alignments for each domain:
  == domain 1  score: 183.0 bits;  conditional E-value: 1.8e-57
                 -HHHHHHHHHHHHHHHTTBE-B-----.--SS...........-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT CS
   DNA_pol_B  10 gqqirveslLlrlakeegfilpdrtekkgkeee..........gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaed 98 
                 g ++ + slL+ ++++++f +p r+e +gk+            +Y G++V+eP +g++ + v+v+DFaSLYPsii  +Nl+y+t+ + +ee k+     
  AJA93115.1 428 GVSQWIRSLLYYEHRKNNFLIPRRNEIEGKSAGmandavikdkKYRGGLVIEPVEGVHFD-VTVMDFASLYPSIIKVNNLSYETVRCPHEECKKNAIPG 525
                 56778999**************8666655555577778888757*************976.899***************************99755433 PP

                 ...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH..CS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHH CS
   DNA_pol_B  99 eyleveveprlvefvkksvregllpklLkdllakRkaikkelk..eekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLe 195
                               +   +++gl + ++ +l + R ++ k l   e+ +++e++l+    +alKv+ N+ YG++G++  +l+ l+ A+  T+ GR++++
  AJA93115.1 526 -----------TSHWGCTKKNGLTSLIIGSLRDLRVNYYKSLSkkENITDEERQLYTVVSQALKVILNASYGVMGAEIFPLYFLPAAEATTALGRYIIM 613
                 ...........3456778899*****************9999844333455************************************************ PP

                 HHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-.SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEES CS
   DNA_pol_B 196 ktkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkv.kdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvekt 292
                  t e  +                   +l+v YGDTDS+f++  + +++++++k++k+           + ++le++k y  ++L + KK Y g++ +  
  AJA93115.1 614 DTIEKCKGI-----------------QLEVLYGDTDSLFVKKPTvQQIDDVIKLAKK----------DHGVELEIDKEYRYVVLSNrKKNYFGVTKK-- 683
                 998888866.................99************99876999999999875..........34578***********9863777****999.. PP

                 STTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHH CS
   DNA_pol_B 293 skanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlk 391
                    +k+++KG+   +    +++k++  ++l+ l +  ++e++  ++ +++ + ++d  ++++e+++pl++++++ +lsk p++y ++   h+ +ak+l+
  AJA93115.1 684 ---GKVDVKGLTGKKSHTPPFIKTLFYELLDILAEV-ENEEQFGNAKKKVSDKIADYAKRVQEKSIPLKELTFNVTLSKAPAEYVKTIPQHIRAAKQLE 778
                 ...9***************************88888.88999999***************************************999999999999998 PP

                 HHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHH CS
   DNA_pol_B 392 krneeapevgdrisYvivekkkevkkknllaseraedpeyvl 433
                 +   ++++ gd isYv + +k  vk  +l +++ + + +y++
  AJA93115.1 779 TT--REIKKGDIISYVKILNKPGVKPVELARQDEIDSGKYME 818
                 77..79************999988777777777666666654 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   5.6   2.9e-38   1.3e-34      51     336 ..      74     359 ..      40     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 2.9e-38
                     EEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE.......TEEEEGCC--C-.S CS
  DNA_pol_B_exo1  51 vkvelvlkkslygyekkpvpylkvsvsnpnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk.......kylvraegkisncd 138
                     + +e+++ k++  +++k++p+ k+ v++p ++  ++++ s ++++v+ +e+d++y+e++l+dn++  +++y+++       + ++++e++++ ++
      AJA93115.1  74 DVIEIKTVKKIDTLKDKEIPVSKIIVTDPLAIGGTQTTQS-IRNVVESWESDIKYYENYLYDNSLIIGKYYKIEndkiiphDFEMSDETNLAMKS 167
                     45788999999999999999****************9976.**************************************999999********** PP

                     EEEEEETTTSCEETTT............CC..S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS---- CS
  DNA_pol_B_exo1 139 veidcdvddliakpke............se..pplrvlsFDIeckskkgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeed 218
                     + +d+     ++++k+            ++  p++r +s DIe+  +++++pd+++ ++++++I + + dg +        +f+lr   +ee   
      AJA93115.1 168 MLFDKLGNTGMTDTKQfeeevsnwaellNQpvPKIRRMSLDIEVETDGRRLPDVKIADKKVTAIGFEAsDGMK-------RVFVLRRDGIEEG-- 253
                     ************99999999988876664489************************************89988.......8999998773333.. PP

                     EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETT CS
  DNA_pol_B_exo1 219 feltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisg 313
                      +  +k++  +v  +e d+Ek+l+++ + ++k+y   v+++YN+d FDlpY+ nRak              + g+s+  ++ ++  ++++ ++  
      AJA93115.1 254 VNDLDKNI--QVVFYEKDQEKKLIEDAFGLVKKY--PVLITYNGDGFDLPYLYNRAK--------------RLGISEDVNPLYM--MKDSATLTK 328
                     34555555..445558899***************..*********************..............99***********..********* PP

                     SEEEEHHHHHHHH........SSSSG-SHHH CS
  DNA_pol_B_exo1 314 rihlDlyrvvkrk........lklpsYkLna 336
                      +hlDlyr++++k         k ++ +Ln+
      AJA93115.1 329 GVHLDLYRTFSNKafqiyvfsQKYSDFSLNS 359
                     ***********99666654332233555555 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.5     3e-11   1.3e-07      33     161 ..     263     412 ..     252     417 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3e-11
   RNase_H_2  33 ltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkelrkkkl.........esysLk 108
                 +  ++ e+ +e+k i+++f  l++k++ l+t+ng +FD+p+l +++k+  ++e               +  h+DL++ +++k +         + +sL 
  AJA93115.1 263 V--VFYEKDQEKKLIEDAF-GLVKKYPVLITYNGDGFDLPYLYNRAKRLGISEdvnplymmkdsatlTKGVHLDLYRTFSNKAFqiyvfsqkySDFSLN 358
                 3..34578899999***99.99************************888888888888899988877777******99977777667777766778999 PP

   RNase_H_2 109 sveke.lgierreedlsGsqavklyq..eylrtgdeellekilaYNedDvralatl 161
                 sv k  lg +  + +++ ++ + +yq  +y+ ++d  l  k+ ++Ned +++l  +
  AJA93115.1 359 SVSKGvLGEQKMDYGVEIDN-MTYYQiaKYC-QNDAYLTFKLTSFNEDLLMNLLVV 412
                 99888344444444444444.4444433777.577777778888888877777665 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.5   1.3e-09   5.8e-06      32      80 ..     266     313 ..     250     400 .. 0.62
   2 ?   -3.9   0.0         2   8.8e+03      83     111 ..     722     750 ..     713     752 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
  DNA_pol_B_exo2  32 eeessekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsap 80 
                      e+++ek+li+  f  v+k+ p l+++ng gfDlp l+ ra + g+s  
      AJA93115.1 266 YEKDQEKKLIEDAFGLVKKY-PVLITYNGDGFDLPYLYNRAKRLGISED 313
                     46789*********999877.8*******************99999853 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2
  DNA_pol_B_exo2  83 fdegdedrekkwnnylsrystrhlDLmdl 111
                     f + +++ ++k  +y +r +++++ L++l
      AJA93115.1 722 FGNAKKKVSDKIADYAKRVQEKSIPLKEL 750
                     44555567778888999988888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (853 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 5646.67
//
Query:       AJA93116.1  [L=70]
Description: hypothetical protein T478_0806 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   14.7   0.1      0.026   14.6   0.1    1.2  1  E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain


Domain annotation for each model (and alignments):
>> E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.5e-06     0.026      29      66 ..      14      52 ..       4      64 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-06
  E3_UbLigase_RBR 29 kCkVleqketkegvk.deaCgkdvaegqaglCelHYkEy 66
                      C     +  +++++ d+    + + +++glC+ HYkE 
       AJA93116.1 14 GCDADAVRSLNTKKIeDAGLRLNSSGKKSGLCKEHYKEW 52
                     5666666666554440444455667789*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 511.26
//
Query:       AJA93117.1  [L=458]
Description: NAD(P)-binding Rossmann-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-32  111.9   0.0    1.5e-31  110.2   0.0    1.7  1  Amino_oxidase  Flavin containing amine oxidoreductase
    1.2e-12   47.8   0.0    2.3e-12   46.9   0.0    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.4e-08   34.7   0.0    0.00068   19.3   0.0    2.1  2  DAO            FAD dependent oxidoreductase
    2.3e-07   31.3   1.5     0.0011   19.5   0.0    2.8  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.1e-06   28.2   0.1      0.011   15.0   0.0    2.8  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   24.7   0.2       0.01   15.0   0.5    2.1  2  FAD_binding_2  FAD binding domain
    3.9e-05   22.6   0.0    9.2e-05   21.4   0.0    1.5  1  MCRA           MCRA family
    0.00021   20.1   0.0       0.34    9.5   0.1    2.2  2  HI0933_like    HI0933-like protein
      0.001   17.7   0.5      0.056   12.0   0.1    2.1  2  GDI            GDP dissociation inhibitor
     0.0028   17.0   0.0        0.6    9.4   0.0    2.1  2  FAD_oxidored   FAD dependent oxidoreductase
     0.0093   15.1   0.4        1.4    7.9   0.0    2.3  2  GIDA           Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.024   14.6   0.0    1.5  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.046   12.1   0.0      0.058   11.8   0.0    1.2  1  FMO-like       Flavin-binding monooxygenase-like
      0.061   12.5   0.4       0.76    9.0   0.1    2.1  2  Thi4           Thi4 family
       0.18   11.8   0.2       0.45   10.5   0.0    1.7  2  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.0   1.3e-34   1.5e-31       2     446 ..      27     446 ..      26     447 .. 0.80

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.3e-34
                    HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEET.TTHHHHHHHHHTTCCCCEEEESCCGCEEEEETTEECCTTEECHHHHH CS
  Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftg.agnpllellkelgledslslpdpgapkrvlskggrefpgdlspvpae 96 
                     GL+ A+ L + G+ V+v+E +drvGGR ++ +++++++++G+++++  + ++++e+lk++++e++l+l   +   ++ ++     +  ++  p++
     AJA93117.1  27 GGLSIATLLVNDGHPVSVYEKSDRVGGRTASMKFKNHILDNGFHIMPFyKKSAIYEILKDVKIESRLKLAIVD---KIAFY-----DDGFHTYPKG 114
                    6****************************************************************99855544...44443.....6667888999 PP

                    HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCC CS
  Amino_oxidase  97 wealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpll 192
                    +++ l+      +l+ ++++++l   +l+           +++ e+ e+l   ++++   ++  ++        f+s+ f+ d  + +a ++ p++
     AJA93117.1 115 IADILK-----MSLIPFKSRISLLKILLP---------MAFTSMEKAEQLDSVPLTQ---VTSKLD--------FHSKQFF-DAVCMLAFADTPDH 184
                    999999.....455556666666666666.........5555555555566666655...555555........5555544.44678888888888 PP

                    CHHHHHTSCCCEE..............TTHTHHHHHHHHH..TTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEE CS
  Amino_oxidase 193 welegfggslllp..............rgGlsqlpealae..elrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvplgvlkailfs 271
                      l +f++ ++++               gG++++ e +a+  ++++ ++ l++  k++   ++   +v+l++ge ve D V++  p +++ + lf+
     AJA93117.1 185 ISLGEFARTIIRAnpfkggtsefaypdMGGYDRISEVMANyvKEKNSQVNLGHSIKKVLVkDRKVTGVELSTGEIVESDCVIISYPAYHAINQLFD 280
                    888888888888888888888889************************************6677799***************************** PP

                    SCC.SHHHHHHHHHS.EEEEEEEEEEEESSGGSGCSTSECE..CECCCEEETTTEEEEECCECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHH CS
  Amino_oxidase 272 Ppl.pdekaeairnl.gfgsvnkvilefdrkfwednalgqg..vlvseltttlgeafissdfpsrappgkglvllvyvggdaaneleslsdeelvq 363
                     +   d+  +   +l +++sv+ v+++  ++  +++    +   +v+e++ + g  fis+  ps +p g +l ++v ++ +  +  + +  +e+v+
     AJA93117.1 281 SGIfDDDFIKKTNRLnKTTSVVEVHFALSKQL-DER----QvvFPVGENYVSKGIFFISNITPSVSPKGEHL-IIVGTPVKPEETENPTRIKEIVS 370
                    *998999999999999***************9.332....2357****************************.66666644444435559****** PP

                    HHHHHHHHHHTGTSSTCSEEEEEECCTETTTSSSEEE.BTTH.....HHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS.HHHHHHHHHH CS
  Amino_oxidase 364 avlrdLrklfgeevpepkatlvtrWhtdplargsysyvsvgp.....ghedydplakpegdprlffAGehtsreypgt.vegAilSGlr 446
                    +  ++L+++++ + +++       W   p+a   +++v + +      ++   p+  + ++++lff G++t+   +g  ++ A +S+  
     AJA93117.1 371 KMKQELSEIYP-DFDDSLL-----WD-RPMA---WKLVEAVVkepglVWKNKMPHSVS-NVDGLFFVGDSTI--SYGIgTDSAAHSAVL 446
                    ***********.3333333.....44.6666...444444444331255555555555.9************..778889999999875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   1.9e-15   2.3e-12       1      53 [.      21      73 ..      21      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.9e-15
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EE CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifh 53
                   I+GaG++Gl++A lL ++g+ v ++ek+dr+GGr as +++++++d g hi+ 
     AJA93117.1 21 IIGAGVGGLSIATLLVNDGHPVSVYEKSDRVGGRTASMKFKNHILDNGFHIMP 73
                   9*************************************************975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.7e-07   0.00068       3      37 ..      20      57 ..      18      87 .. 0.88
   2 !   13.5   0.0   3.4e-05      0.04     153     303 ..     223     388 ..     194     434 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.7e-07
                EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGG CS
         DAO  3 viiGGGiiGlstAyeLarrg..Vtllekgdiags.gaS 37
                viiG+G+ Gls+A  L   g  V ++ek+d++g   aS
  AJA93117.1 20 VIIGAGVGGLSIATLLVNDGhpVSVYEKSDRVGGrTAS 57
                9***************999999********99943555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.4e-05
                 HHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE.EEEEEEEE--GGGHH..HHHTT..CTT..........T.SEEEEEEEEEEEEEECCTHS CS
         DAO 153 araaealGveilegtevtgleeedgkvwgve.rttpgen.daadavVnaaGawsd..llgll..kel..........d.lpispvrgqvlvlkplsekl 234
                 a+ ++++  ++ +g+ ++++  +d kv+gve   t ge+ ++ d+v+++  a+    +  l+  + +          +  +++ v   +++l++   +l
  AJA93117.1 223 ANYVKEKNSQVNLGHSIKKVLVKDRKVTGVElS-T-GEIvES-DCVIISYPAYHAinQ--LFdsG-IfdddfikktnRlNKTTSVVEVHFALSK---QL 312
                 555666666777777788876778899***532.2.777355.99*****77753331..22322.2343345443323466778888888833...33 PP

                 TGSGCSEEEEEEEETTTTEEEEEE.......TTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCG.EE CS
         DAO 235 vspaailpvpetdddgrgvyvtpr.......kdgrvlvGgtadeesgdddpevdeedidellealrklfPqlgd.vl 303
                 ++++ ++pv   +  ++g++++         k+ ++++ gt+++++ +++p+   e + ++ ++l++++P+++d +l
  AJA93117.1 313 DERQVVFPVG-ENYVSKGIFFISNitpsvspKGEHLIIVGTPVKPEETENPTRIKEIVSKMKQELSEIYPDFDDsLL 388
                 4567999999.6777888888886667788544445556666544444555888899999***********755233 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   9.1e-07    0.0011       2      63 ..      19      77 ..      18      92 .. 0.89
   2 !    9.7   0.3     0.001       1.2      41      79 ..     217     255 ..     212     261 .. 0.93
   3 ?   -2.4   0.0         6   7.2e+03      19      40 ..     293     314 ..     288     338 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.1e-07
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEE CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkv 63
                +v++G+G+ gl  A+ l + g+ V+v e sd++    +++as  +++++ +ng +++   k 
  AJA93117.1 19 AVIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVG---GRTASMKFKNHILDNGFHIMPFYKK 77
                69********************************...****************999876665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.001
                 HHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
   Pyr_redox  41 easkilqeklekngievllntkveeiegsedgvesvklk 79 
                  +s+++++++++++ +v l+++++++  ++++v++v+l+
  AJA93117.1 217 RISEVMANYVKEKNSQVNLGHSIKKVLVKDRKVTGVELS 255
                 5899********************************996 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6
                 HHTTSEEEEEESSSSSSTTSSH CS
   Pyr_redox  19 aelgkkVtvversdkllrllDe 40 
                 ++l+k ++vve +  l ++lDe
  AJA93117.1 293 NRLNKTTSVVEVHFALSKQLDE 314
                 5677778888877777777775 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     9e-06     0.011       3      38 ..      19      53 ..      17     112 .. 0.81
   2 !    9.4   0.0   0.00045      0.54     183     234 ..     216     268 ..     205     273 .. 0.93
   3 ?   -0.6   0.0      0.53   6.3e+02     265     278 ..     417     430 ..     406     448 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9e-06
                 EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegtclng 38
                  v+iG+G++Gl+ a+ l + g+ v ++e +   ++g
   AJA93117.1 19 AVIIGAGVGGLSIATLLVNDGHPVSVYE-KSDRVGG 53
                 59*************************5.3333433 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
                  HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvva 234
                  +++s+ +++++++++ +v lg+s+k++  +++k++ v+l++ge ++ d+v+++
   AJA93117.1 216 DRISEVMANYVKEKNSQVNLGHSIKKVLVKDRKVTgVELSTGEIVESDCVIIS 268
                  689*************************99999999**************986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.53
                  BESSTTEEE-GGGC CS
                  xxxxxxxxxxxxxx RF
  Pyr_redox_2 265 rtnvpgiyaiGDva 278
                   +nv+g++ +GD +
   AJA93117.1 417 VSNVDGLFFVGDST 430
                  468*********88 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.5   8.4e-06      0.01       3      39 ..      20      56 ..      19      58 .. 0.95
   2 !    7.5   0.0    0.0016       1.9     137     204 ..     212     286 ..     164     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.4e-06
                   EEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
  FAD_binding_2  3 iViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                   ++iG+G++GL+ A+ + + G+ v v ek +++gg ta
     AJA93117.1 20 VIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVGGRTA 56
                   9*********************************886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0016
                    ..HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEE..........EEEESEEEE-----GG CS
  FAD_binding_2 137 lvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrev..........rirakavvlatgGfgr 204
                    ++   ++ +++++++++ + ++   +++++++v+d++vtG++++   +g++v          +++a++ +  +g f  
     AJA93117.1 212 MGGYDRISEVMANYVKEKNSQVNLGHSIKKVLVKDRKVTGVELS---TGEIVesdcviisypAYHAINQLFDSGIFDD 286
                    677789999********************************999...7776645555566666666666666666665 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.7e-08   9.2e-05       4     251 ..      19     256 ..      17     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                 EEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-----------------CCC----B-TT-HHHHHHHTTSB-SSSTTSBHHHHHHHHHHHS----S CS
        MCRA   4 aylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldgagdpekGyvlrggreleehyeclwdLlssipSleepgasvldeieelnkedknksk 102
                 a ++G+G+++L+ A+ L++d++     + ++e+++ +gg + +++ +++  +     ++  + + ++++l+++   ++ +  ++d+i  +++  +++ k
  AJA93117.1  19 AVIIGAGVGGLSIATLLVNDGH----PVSVYEKSDRVGGRTASMKFKNHILDNGFHIMPFYKKSAIYEILKDVKIESRLKLAIVDKIAFYDDGFHTYPK 113
                 88*****************976....79*************99988885555445556677778899******9999***********99999666655 PP

                 --EEETTTEE-TTTT----C.CHHHHHHHHHCS-GGGCTT-BHHHHS-HHHHTSHHHHHHHHHHT--TT..S.BHHHHHHHHHHTGGGGGGSTT-TT-B CS
        MCRA 103 arlvekrgeeavddkklglskkdrlellkLlltkeekLedkrIedvfseeffesnFWllwsttFafqkw..h.SalElrrylrrfiheisgledlsglk 198
                   +   + + +  +++++l  k  l ++   ++k e+L+++ +++v s+  f+s+ ++    + af +   h S+ E+ r++ r      g    s + 
  AJA93117.1 114 GIADILKMSLIPFKSRISLL-KILLPMAFTSMEKAEQLDSVPLTQVTSKLDFHSKQFFDAVCMLAFADTpdHiSLGEFARTIIRANPFKGGT---SEFA 208
                 43333323455556666664.55666677778889************887777776666667777764311349999999998875555555...5556 PP

                 --SS-HHHHCCHHHHHHHHHTT-EEE-SEEEEEEEEEEE.TTEEEEEEEEEEE CS
        MCRA 199 rtkynqyeslilPlvkyLkeqgVdfqfntkVtdiefeeeeedkktvteielek 251
                   ++  y+ +   +++y ke++ +++++ +++ + ++++     +vt++el++
  AJA93117.1 209 YPDMGGYDRISEVMANYVKEKNSQVNLGHSIKKVLVKDR-----KVTGVELST 256
                 66677788999999*********************9943.....477777664 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00029      0.34       3      36 ..      19      52 ..      17      57 .. 0.93
   2 !    8.2   0.0   0.00073      0.87     103     161 ..     210     268 ..     198     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00029
                 EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                  ++iG+G  Gl  A  + + g+ V ++ek +++g
   AJA93117.1 19 AVIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVG 52
                 69****************************9998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00073
                  ETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE- CS
  HI0933_like 103 pvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlA 161
                  p+     +i +++ + +ke++ +++l +++k+v  ++ ++  v+++++e +e+d ++++
   AJA93117.1 210 PDMGGYDRISEVMANYVKEKNSQVNLGHSIKKVLVKDRKVTGVELSTGEIVESDCVIIS 268
                  555556779999*********************************99********9997 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.014        17       7      50 ..      19      62 ..      16      70 .. 0.92
   2 !   12.0   0.1   4.7e-05     0.056     220     364 ..     204     364 ..     190     387 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.014
                EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HHH CS
         GDI  7 vivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltleq 50
                ++++G+G+    ++ ll  dg+ v + ++ d  Gg +as+++++
  AJA93117.1 19 AVIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVGGRTASMKFKN 62
                5899***********************************98765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.7e-05
                 S-SEEEE.TT-TTHHHHHHHHHHHHTT-EEETS--ECEEEE-TTS-EEEEE.ETTEEEEECEE.EE-GGG-C............CCEEEEEEEEEEEEE CS
         GDI 220 kspylyp.lyGlGelpqgfarlsaiyGGtymlnkpvdevvldedgkvvGvk.seeevakakkv.icdpsylp............ekvrkvgkviraici 303
                  s + yp + G   + + +a           l +++++v++ +d kv+Gv+ s +e+++++ v i+ p+y              + ++k+ ++ ++ ++
  AJA93117.1 204 TSEFAYPdMGGYDRISEVMANYVKEKNSQVNLGHSIKKVLV-KDRKVTGVElSTGEIVESDCViISYPAYHAinqlfdsgifddDFIKKTNRLNKTTSV 301
                 56777773445667777777777777777888899999999.899*****84589999999762578***8777888888888888************* PP

                 ESS--TTSTT-SSEEEEE-GGGCTSSS-EEEEEEEGGGTSS-TT-EEEEEEEE-...-SS-HHH CS
         GDI 304 lshpipntddadsvqiiipqkqlgrksdiyvalvssahnvaakgkylaivsttv...etenpev 364
                 ++   + +++ d  q++ p       + i+ ++   +  v++kg++l iv t v   etenp+ 
  AJA93117.1 302 VEVHFALSKQLDERQVVFPVGENYVSKGIF-FISNITPSVSPKGEHLIIVGTPVkpeETENPTR 364
                 *******************87766555554.34456789*************985556777753 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0005       0.6       3     142 ..      20     172 ..      19     173 .. 0.67
   2 !    5.5   0.0    0.0074       8.9      88     127 ..     217     256 ..     186     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0005
  FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvat...dignkaeeqvvtgiareflerlrqrggarlk..krskwn....tfepevak 90 
                   v++G+g++G+  A    + G  v + e+++++GG ++s    +   d g+++  +  +  + e+l+ ++ +   +l+  ++ ++     +  p+  +
    AJA93117.1  20 VIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVGGRTASMKFKNhilDNGFHIMPFYKKSAIYEILKDVKIESRLKLAivDKIAFYddgfHTYPKGIA 116
                   8*********************************988766543111333555557777777777777755444422222222221344466777777 PP

  FAD_oxidored  91 avleeml.....aeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                    +l+  l     + + +++ll   ++++ek + +++sv + + + +  +++k f DA
    AJA93117.1 117 DILKMSLipfksRISLLKILLPMAFTSMEKAE-QLDSVPLTQVTSKLDFHSKQFFDA 172
                   77777777776555677777777777777765.777777755556777777777776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0074
  FAD_oxidored  88 vakavleemlaeagvtvllntrlvevekegkriesvtves 127
                      +v+ + ++e++ +v l++ +++v ++++++++v++ +
    AJA93117.1 217 RISEVMANYVKEKNSQVNLGHSIKKVLVKDRKVTGVELST 256
                   5678999999********************99*****965 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.1    0.0087        10       3      36 ..      20      52 ..      18      64 .. 0.86
   2 !    7.9   0.0    0.0012       1.4      97     147 ..     218     268 ..     214     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0087
                EEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
        GIDA  3 iViGgGhAGceAAlaaarlGakvlLithkldtia 36
                ++iG+G  G+  A  + + G++v  + +k d+++
  AJA93117.1 20 VIIGAGVGGLSIATLLVNDGHPVSVY-EKSDRVG 52
                89**********************99.7777666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0012
                 HHHHHHHHHHTST.TEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE- CS
        GIDA  97 yskevteklenep.nleiieeeveeliveekkvkgvvtedgetikakavvia 147
                 +s+ + +++++++ ++++   ++++++v+++kv+gv +++ge++++++v+i+
  AJA93117.1 218 ISEVMANYVKEKNsQVNL-GHSIKKVLVKDRKVTGVELSTGEIVESDCVIIS 268
                 567788888774404444.5678888899*********************97 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     2e-05     0.024       4      34 ..      21      51 ..      19      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                EE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
     3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseea 34
                +iGaG+ G +ia+++++ g++V +++ s++ 
  AJA93117.1 21 IIGAGVGGLSIATLLVNDGHPVSVYEKSDRV 51
                8************************998765 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.9e-05     0.058       4      48 ..      19      66 ..      16     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
    FMO-like  4 vaviGaGvsGlasikccleegleptcfersddiGGl...wrfkenvee 48
                  +iGaGv Gl+     +++g     +e+sd +GG     +fk++  +
  AJA93117.1 19 AVIIGAGVGGLSIATLLVNDGHPVSVYEKSDRVGGRtasMKFKNHILD 66
                569********988888899988889********96333688888654 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00064      0.76      20      57 ..      19      55 ..       7      72 .. 0.86
   2 ?    1.5   0.0      0.13   1.5e+02     100     140 ..     218     257 ..     214     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00064
                EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
        Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                 vi+GaG  GL+ a  l ++ +  v + e+s  +GG +
  AJA93117.1 19 AVIIGAGVGGLSIATLLVND-GHPVSVYEKSDRVGGRT 55
                59****************99.99*******99999965 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                 HHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEH CS
        Thi4 100 tstllskvlqlanvkllnavaveDlivregegvaGvvinwt 140
                 +s+++++ ++  n ++  + ++  ++v++ ++v+Gv +   
  AJA93117.1 218 ISEVMANYVKEKNSQVNLGHSIKKVLVKD-RKVTGVELSTG 257
                 6899999999999999999*********9.99999976654 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00038      0.45       1      49 [.      20      63 ..      20      76 .. 0.81
   2 ?   -3.3   0.0       6.6   7.9e+03     105     151 ..     223     267 ..     218     268 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvwrtdqsee 49
                   +i+GaG+ Gl++++ L++       + + ++++s   g gr ++ + +++
     AJA93117.1 20 VIIGAGVGGLSIATLLVND-----GHPVSVYEKSDRvG-GRTASMKFKNH 63
                   7*************99999.....47788999977736.88888776544 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.6
  NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvL 151
                    ++ +++ +++v++ +  ++v+  +++ +   v l++g+ ++ d V++
     AJA93117.1 223 ANYVKEKNSQVNLGHSIKKVLVKDRKVT--GVELSTGEIVESDCVII 267
                    5555555555554444444443333333..36778888888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3299.35
//
Query:       AJA93118.1  [L=177]
Description: Hsp20/alpha crystallin family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-06   26.2   1.1     0.0002   21.5   1.1    2.1  1  HSP20       Hsp20/alpha crystallin family
    5.9e-05   22.5   0.0    8.7e-05   22.0   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00056   20.3   0.0    0.00077   19.8   0.0    1.2  1  PIH1_CS     PIH1 CS-like domain
  ------ inclusion threshold ------
      0.035   14.2   0.2      0.042   13.9   0.2    1.2  1  GvpH        GvpH


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   1.1   4.4e-08    0.0002       4     101 ..      96     176 ..      93     177 .] 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.4e-08
                 SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEEEEBSS--..-------- CS
       HSP20   4 eeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvtvpkkepekkkkerkiqi 101
                 ++e+  ++ +++pg++k ++kv v+++ v + ++h   e+d ++             + + + vd d+ ka++ +G+L++t +  +++   + r++++
  AJA93118.1  96 DKEQTLKIVAEMPGVEKTDVKVFVDEDIVHIDAKHG--EKDYHVN------------VPIHHKVDSDSPKATYTNGILELTFNLDTKP---SGRSVDV 176
                 5778899*****************************..4444444............4466688999999999999999998887766...5666665 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.9e-08   8.7e-05       4      63 .]     101     163 ..      98     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.9e-08
  ArsA_HSP20   4 yvlkldLPfvdkeeidlsrsgdeLtIkig....nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                  ++++++P+v+k +++++ ++d   I ++    +++ +++   +++ + + +A++ +g Le +F
  AJA93118.1 101 LKIVAEMPGVEKTDVKVFVDEDIVHIDAKhgekDYHVNVPIHHKVDSDSP-KATYTNGILELTF 163
                 67899***********************988888999999999*****99.**********998 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.7e-07   0.00077      31      94 ..      99     163 ..      91     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
     PIH1_CS  31 kelaieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvkktklLkv 94 
                 ++l+i  e+P++ + ++vk+ v+e+ +++++k+  ++y  ++++  +vd d+ +A++ +    L+ 
  AJA93118.1  99 QTLKIVAEMPGV-EKTDVKVFVDEDIVHIDAKHgeKDYHVNVPIHHKVDSDSPKATYTNGILELTF 163
                 57889999****.6789*************999999*********************876666655 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   9.4e-06     0.042      90     161 ..      88     161 ..      41     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.4e-06
        GvpH  90 ihvetrasddsdelvvvadlpGvtdedvdvaletdeqaltlrvd..ddvverlvlddpdvaitdltlrnqvlel 161
                   ++t   d+ + l +va++pGv   dv v ++ d   +  + +  d  v+  +  + d    + t +n +lel
  AJA93118.1  88 PLIDTLVDDKEQTLKIVAEMPGVEKTDVKVFVDEDIVHIDAKHGekDYHVNVPIHHKVDSDSPKATYTNGILEL 161
                 468899999999********************988766655543113334444445555555666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1254.79
//
Query:       AJA93119.1  [L=135]
Description: low molecular weight phosphotyrosine protein phosphatase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-22   79.4   0.4    1.1e-21   77.7   0.4    1.7  1  LMWPc           Low molecular weight phosphotyrosine protein 
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.052   13.2   0.0    1.4  1  LepB_N          LepB N-terminal domain
      0.055   13.8   0.0       0.12   12.7   0.0    1.5  1  Tir_receptor_M  Translocated intimin receptor (Tir) intimin-b


Domain annotation for each model (and alignments):
>> LMWPc  Low molecular weight phosphotyrosine protein phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.4   1.8e-25   1.1e-21       1     141 [.       5     127 ..       5     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.8e-25
                 EEEEESSSSSHHHHHHHHHHHHHHHTT-CCCEEEEEEESTSTTT-B--HHHHHHHHHTTS--TT-BB-BS-HHHHHHSSEEEESSHHHHHHHHHHCCTT CS
       LMWPc   1 vlfvClgNicRSpmAealfrkelekagleekvevdSaGtgalvgkradpravevlkekgislsghvarqlskeelaelDlilamdeenkreleslapek 99 
                 +lfvC+ N++RS+mAea+frk  e      k++v+SaGt   ++ + +p +vev+ke gi++ ++ ++ ls++++++    + m    k++  +l ++ 
  AJA93119.1   5 ILFVCVENAGRSQMAEAFFRKFTEG-----KFNVNSAGTV--PSGNLNPVVVEVMKEIGIDMTNQSPKTLSQSMISSSFKTINMGCMDKESCPALFVK- 95 
                 89********************777.....7*********..**********************************9999999977777566666666. PP

                 GGGGEEEGGGGSSTSS---HTTSSHHHHHHHHHHHHHHHHHH CS
       LMWPc 100 ekakvkllgeyteqldieDPyygeieafeevldeieeavkkl 141
                 +            +++i+DP+ + ie+++e++d+i+++v ++
  AJA93119.1  96 D----------VIDWNIPDPKEKTIEQVREIRDQIKSEVLNF 127
                 3..........3589*********************999877 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.7e-06     0.052     117     159 ..      42      83 ..      15     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-06
      LepB_N 117 kllkdivskalkkipadlldketkkelakylgidsfkevsfge 159
                   l+ +v +++k+i+ d+  ++  k l++ ++ +sfk++++g 
  AJA93119.1  42 GNLNPVVVEVMKEIGIDM-TNQSPKTLSQSMISSSFKTINMGC 83 
                 678999************.999999***************984 PP

>> Tir_receptor_M  Translocated intimin receptor (Tir) intimin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.12       8      53 ..      10      54 ..       7      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
  Tir_receptor_M  8 aeaatkDqLtqeafqnPdnqkvniDenGnaiPsGeLkDDvvaqiae 53
                     e a + q+++  f++  + k n++  G  +PsG+L   vv+ ++e
      AJA93119.1 10 VENAGRSQMAEAFFRKFTEGKFNVNSAG-TVPSGNLNPVVVEVMKE 54
                    58999*****999************999.69******999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 957.80
//
Query:       AJA93120.1  [L=106]
Description: cupin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-13   48.2   0.0    8.4e-13   47.8   0.0    1.2  1  Cupin_2        Cupin domain
    6.9e-09   35.8   0.2    9.2e-09   35.4   0.2    1.1  1  CENP-C_C       Mif2/CENP-C like
      2e-05   24.8   0.0    0.00053   20.2   0.0    2.0  2  ARD            ARD/ARD' family
    0.00018   21.4   0.0    0.00027   20.8   0.0    1.2  1  AraC_binding   AraC-like ligand binding domain
    0.00058   19.5   0.0    0.00078   19.1   0.0    1.2  1  Cupin_3        Protein of unknown function (DUF861)
    0.00067   19.5   0.0     0.0008   19.2   0.0    1.1  1  EutQ           Ethanolamine utilisation protein EutQ
     0.0022   17.7   0.0     0.0027   17.4   0.0    1.1  1  DMSP_lyase     Dimethlysulfonioproprionate lyase
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.023   14.9   0.0    1.3  1  Ectoine_synth  Ectoine synthase
       0.02   14.5   0.0      0.036   13.7   0.0    1.4  1  Cupin_1        Cupin
       0.12   12.0   0.1       0.18   11.5   0.0    1.3  1  3-HAO          3-hydroxyanthranilic acid dioxygenase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   4.7e-16   8.4e-13       2      65 ..      34      95 ..      33     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.7e-16
                EEEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEE.EE-SSS-E CS
     Cupin_2  2 lvelppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrf.rNtgdepa 65
                + +l+pGe+  +  H+   e++y+leG g l++ +++++l++G ++++p+ t+H+f +N +   +
  AJA93120.1 34 VLVLKPGEEDTQLPHESD-EMYYILEGDGFLKIKNKKYKLKKGKAFFVPKDTEHYFfGNKT--KL 95
                6789****9999*****8.*************************************77776..44 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.2   5.1e-12   9.2e-09       3      83 ..      21     101 ..      20     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.1e-12
                 EEEE--TTS-EEEEEEE-TCCCEEEEE--SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT.-EEEEEE-SSS-EEEEE CS
    CENP-C_C   3 laklldkkflasGilkLppgaeKkkknskkatlvFyViqGrvevtvsktsfvigkgsvFqvPag.neysieNklnkeaklfF 83 
                 ++ +ldk  la+G+l L+pg+e ++   +++  ++y+++G+   +++++++ + kg+ F vP+   +y + Nk++ +   fF
  AJA93120.1  21 FNTFLDKDTLAAGVLVLKPGEEDTQLPHESDE-MYYILEGDGFLKIKNKKYKLKKGKAFFVPKDtEHYFFGNKTKLKILYFF 101
                 67789999************997766655555.589**************************96156888887765555554 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.061   1.1e+02      90     106 ..       6      22 ..       2      32 .. 0.88
   2 !   20.2   0.0     3e-07   0.00053      90     149 ..      48     101 ..      41     106 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.061
         ARD  90 hedeeirliveGtgyFd 106
                  +d+ ir i +G+ yF 
  AJA93120.1   6 NTDDYIRKINSGNSYFN 22 
                 689*************6 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3e-07
         ARD  90 hedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhrFtltednkvkalRlF 149
                 he +e+ +i+eG+g+     k++++    ++kG   ++P+ + h+F  +++ k+k+l +F
  AJA93120.1  48 HESDEMYYILEGDGFLK--IKNKKYK---LKKGKAFFVPKDTEHYF-FGNKTKLKILYFF 101
                 999***********965..5788898...9****************.5777888888887 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.5e-07   0.00027      25      61 ..      52      88 ..      44      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.5e-07
                  EEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEE CS
  AraC_binding 25 vihyvteGtgrlrlngrtydlgpGdlfLlppgepHdy 61
                  +  y++eG g l+++++ y l++G  f++p+++ H++
    AJA93120.1 52 EMYYILEGDGFLKIKNKKYKLKKGKAFFVPKDTEHYF 88
                  678********************************86 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.3e-07   0.00078       7      61 ..      30      85 ..      26      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.3e-07
                CEEEEEEEECEEEEECESS..EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
     Cupin_3  7 fswgiwectpGkfrltyee..dEfcyileGevkvtpeggetvelraGDlvvlpkgls 61
                  +g++  +pG+  ++ +   dE+ yileG   ++  + ++++l++G ++++pk+++
  AJA93120.1 30 LAAGVLVLKPGEEDTQLPHesDEMYYILEGDGFLKI-KNKKYKLKKGKAFFVPKDTE 85
                567888888998777765445***************.99***************985 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.5e-07    0.0008      72     144 ..      25     100 ..      13     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-07
        EutQ  72 eeskrlgaGlmemkettfdwtl..nydeidyvieGrldvlidGrkvvaeaGdviliPkgskie.fsvtdeakflyv 144
                  + + l+aG++ +k    d  l  + de+ y++eG   + i+ +k   + G+  ++Pk+++   f+   + k ly+
  AJA93120.1  25 LDKDTLAAGVLVLKPGEEDTQLphESDEMYYILEGDGFLKIKNKKYKLKKGKAFFVPKDTEHYfFGNKTKLKILYF 100
                 577889999999998777777633679*******************************987652688889999997 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0027      91     155 ..      26      89 ..      16      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
  DMSP_lyase  91 krddvalGlvllaPkvrYPdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikhamr 155
                 ++d++a+G+++l P  +  +  h+ +e+Y++l g  +++ ++++  + + G  +f +++ +h+  
  AJA93120.1  26 DKDTLAAGVLVLKPGEEDTQLPHESDEMYYILEGDGFLKIKNKK-YKLKKGKAFFVPKDTEHYFF 89 
                 68999*********99999999***********99899999998.6999*************975 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.023      55     108 ..      50     102 ..      23     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                    -EEEEEEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS.-EEEEEEEE CS
  Ectoine_synth  55 HleavycieGegeveeledgevyeikpgtlYlldkhdkHllrakk.elrlvcvFn 108
                      e  y++eG+g ++ +   ++y++k+g+ + + k+ +H+  ++k +l+++  F 
     AJA93120.1  50 SDEMYYILEGDGFLKIK--NKKYKLKKGKAFFVPKDTEHYFFGNKtKLKILYFFG 102
                    45889*******99876..79*******************998876999988775 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.036      53     113 ..      49     101 ..      44     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                 SS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEE CS
     Cupin_1  53 nateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepavaivvf 113
                  + e+ y+l+G g++ +          + kl++G +f vP+   h+++ +  +++ +++ f
  AJA93120.1  49 ESDEMYYILEGDGFLKIKNK-------KYKLKKGKAFFVPKDTEHYFFGNK-TKLKILYFF 101
                 57899*********443333.......358*****************9994.766666655 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.8e-05      0.18      41      93 ..      38      86 ..      20      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-05
                SSB--S-EEE-SS-EEEEEEES-EEEEEEETTCCCEEEE-TTEEEEE-TT--E CS
       3-HAO 41 GPnerkdyhleegeeffyqkkGdmvlkvldegkardivireGeifllParvph 93
                 P e      +e++e++y ++Gd  lk+ ++       +++G+ f++P   +h
  AJA93120.1 38 KPGEEDTQLPHESDEMYYILEGDGFLKIKNKK----YKLKKGKAFFVPKDTEH 86
                4555555556799**************98764....5699********99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 784.46
//
Query:       AJA93121.1  [L=241]
Description: hypothetical protein T478_0749 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.12   12.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.099   12.6   0.1       0.26   11.3   0.0    1.7  2  RHH_3            Ribbon-helix-helix domain
       0.17   12.6   0.0       0.32   11.7   0.0    1.5  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05      0.12      24      91 ..      81     144 ..      71     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
  Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                       g +++vD+G+G g  +   +      +l+ ++i++ e+lv+  e++ +k g +fn ++  a+  + e
       AJA93121.1  81 LGFEQIVDIGSGDGRIAYCGKT----SGLESISIEIDENLVNLQEDISKKTGVEFNPKCADATIFNFE 144
                      56789********976665555....79************************8888777666555444 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.86   5.1e+03       7      18 ..       6      17 ..       5      18 .. 0.77
   2 ?   11.3   0.0   4.4e-05      0.26       3      27 ..     106     130 ..     105     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.86
       RHH_3  7 vsidpelaekLk 18
                + i+++++  L 
  AJA93121.1  6 FVINEKQLSLLH 17
                779999998875 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.4e-05
       RHH_3   3 trttvsidpelaekLkaLSekTrIp 27 
                 +++++ id++l++  +++S+kT+++
  AJA93121.1 106 ESISIEIDENLVNLQEDISKKTGVE 130
                 799********************96 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.3e-05      0.32       1      63 [.      86     146 ..      86     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.3e-05
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTT CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedg 63 
                      ++d+G G Gr++    + +   + + ++i+e++++  +   ++ g++++  ++da+ ++fed 
       AJA93121.1  86 IVDIGSGDGRIAYCGKTSG--LESISIEIDENLVNLQEDISKKTGVEFNPKCADATIFNFEDI 146
                      89*********99999884..**************999999889999999*****99999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1696.84
//
Query:       AJA93122.1  [L=547]
Description: phenylalanine--tRNA ligase, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-36  124.6   0.1    6.1e-36  123.9   0.1    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.9e-15   56.9   0.1    1.4e-10   41.3   0.0    3.3  3  B5               tRNA synthetase B5 domain
    6.1e-14   52.1   0.4    1.1e-13   51.2   0.4    1.4  1  B3_4             B3/4 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.1     1e-39   6.1e-36       8     214 .]     350     541 ..     344     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 1e-39
  tRNA_synthFbeta   8 apttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargnedvrlFE 101
                      a+tt g++n+    ++ l+++ +g+G+ E++++s++s+k+l ++  + + ++ + ++   s+++++lR sLlp++L++l++N++ + +  +lFE
       AJA93122.1 350 ASTTIGQKNDVTIKTKLLSQTAVGLGFLEAMNSSLTSKKVLYEM-TKRNSSEIISVLDSKSQEHTILRDSLLPSMLDNLSKNIHESYP-QKLFE 441
                      556667799***********************************.688999*************************************.***** PP

  tRNA_synthFbeta 102 igkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealle.slgiekvefep.aehpalhpgrsAeikvdgkevGvlGel 193
                      +g vf k+   + ++e+ +la+v++ k+            ++ ++k+i+++ll+ +++i   e ++ ++++++ +gr A+i v+++++G +Ge+
       AJA93122.1 442 TGVVFSKR---KPIDESINLAAVIAYKD-----------TNYSEIKAIMQSLLKtNFKI-ISETKTsQNNELFTKGRHADIFVNNNKIGEIGEI 520
                      ********...689**************...........**************835888.555666577999********************** PP

  tRNA_synthFbeta 194 hpevleafdlkqrvyvfEldl 214
                        ++le+f +++ v++fE++l
       AJA93122.1 521 DSNILENFRIRTSVVGFEIKL 541
                      *******************86 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   4.1e-05      0.25       1      51 [.       4      54 ..       4      60 .. 0.94
   2 ?   -1.4   0.0      0.51     3e+03      21      31 ..     245     255 ..     168     270 .. 0.72
   3 !   41.3   0.0   2.4e-14   1.4e-10       6      66 ..     281     340 ..     276     341 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT- CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
          B5  1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDl 51
                v+l++++i+kl+  ++++++i ++L  lg++++++ +d+++++  + R+D 
  AJA93122.1  4 VELNINRIKKLVSGNVTRKQILDVLPFLGLDIESEVGDEIRIEYSPNRPDY 54
                67999*******************************************996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.51
                 HHHHHHHTT-E CS
                 xxxxxxxxxxx RF
          B5  21 iikiLkrlgce 31 
                 ++ iL+  g+e
  AJA93122.1 245 VVSILQTAGFE 255
                 55666666666 PP

  == domain 3  score: 41.3 bits;  conditional E-value: 2.4e-14
                 HHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
          B5   6 ekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyG 66 
                 +  ++++Gid+++++++ +Lk+  +++ + +++++++t+P +R D+  + Dl EE+a  yG
  AJA93122.1 281 KFTSEIIGIDMNPSNMVACLKKCRLDA-SVKGKKITCTIPRYRFDIFSPMDLTEEIALGYG 340
                 66789********************96.99999***************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.4   1.9e-17   1.1e-13      34     130 ..     114     236 ..      83     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.9e-17
                 ---HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEEEBTTS-.EEEE-T...................TSEEEETEEEEE.EETTTE CS
        B3_4  34 pinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegeklvtldgk.erelde...................edlviadsekpv.slagvm 106
                  i+ + ++++ +++ +g+      ++ +D+dki+ +++  +   + k+++l+g+ e  +de                   + ++i+dse++  s ++++
  AJA93122.1 114 AIKQLMNMQEDLHFGIGRkrkksSIGLHDADKISFPLTYTTVSRDHKFIPLNGNtEQSIDEiltntevgqnygsviesakNVPIIFDSEQKTiSFPPII 212
                 57888899999999999999999***********9***999999*******9995666699**************************988777****** PP

                 EBTTTB--TT--EEEEEEEE--HH CS
        B3_4 107 ggeeskvsedTknvfleaaafdpv 130
                 +++ + v+ +Tkn+++e++ +d++
  AJA93122.1 213 NSALTTVTPNTKNILIEVTSIDKE 236
                 *******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4069.46
//
Query:       AJA93123.1  [L=340]
Description: phosphoribosylformylglycinamidine cyclo-ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   83.4   0.0    3.5e-23   82.4   0.0    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.4e-15   57.8   0.8    2.6e-15   56.9   0.8    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.4   0.0   3.9e-27   3.5e-23       1     151 [.     175     332 ..     175     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 3.9e-27
                 STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECG.T CS
      AIRS_C   1 kpGdvliltgslGlggagtslkrkileeegldds....avqlgdvlleptliyvkralaal.kglvkaahDvTgGGLlgalaemapasgvgaeidld.k 93 
                 kp dv+i+++s+Gl+++g+sl+rk l ++   ++     ++lg++ll pt iyvk+ l a  k ++++++++Tg G    l ++    ++g ++d+  k
  AJA93123.1 175 KPNDVIIGIKSSGLHSNGYSLARKALLTKYSVKDnikgIGNLGNALLRPTEIYVKPVLEAVkKCKIHGLAHITG-GSFTKLLRL---KQIGYNLDSMpK 269
                 689********************988766443335998888*********************************.566677777...4599*****984 PP

                 HHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEEEESSSE CS
      AIRS_C  94 vpifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIGevtakeel 151
                  p++ +l      + +em++++n+G+++++++pe++ + + +i++++   + ++IG++ + +++
  AJA93123.1 270 TPALMQLIedsgvKNEEMYKTFNMGIGFCIIAPENQtKNIHKIFKKHKT-KSYEIGRISKNKGV 332
                 4444333368889***********************************8.7*******998765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.8   2.9e-19   2.6e-15       5      92 ..      57     161 ..      30     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.9e-19
                 EEEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEEEEEEESS........EEE CS
        AIRS   5 vvvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgGdtsfsne........pti 86 
                 ++ +td+++++v++    +++++iG  ++a+n++D+++ GA+P+ +++++a +     +++++v+gl ++a++  +p+vgG+t+ +++        + +
  AJA93123.1  57 LATHTDGVGTKVMIanlmKKYDTIGIDCIAMNVNDIICIGATPISFVDYIAANkndqkIFKQIVSGLVKGAKKSSMPIVGGETAIMSDliagkgfgFDL 155
                 47899******999555566777*************************************************************987656666666556 PP

                 EEEEEE CS
        AIRS  87 svtavG 92 
                 + ++vG
  AJA93123.1 156 AGMVVG 161
                 666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2766.64
//
Query:       AJA93124.1  [L=494]
Description: hypothetical protein T478_0966 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.097   12.0   0.8       0.16   11.3   0.0    1.7  2  CcmH      Cytochrome C biogenesis protein


Domain annotation for each model (and alignments):
>> CcmH  Cytochrome C biogenesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       0.4   7.1e+03      29      34 ..     269     274 ..     254     292 .. 0.50
   2 ?   11.3   0.0   8.7e-06      0.16      89     118 ..     343     372 ..     336     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.4
                 HHHHHH CS
        CcmH  29 aralse 34 
                   +l+e
  AJA93124.1 269 QMQLQE 274
                 122222 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8.7e-06
                 ---XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        CcmH  89 kPpvkastllLWlgPllllllgllvlllll 118
                 +P  +++t lLW++Pl++ ++++++l+   
  AJA93124.1 343 RPSGEMETTLLWVIPLVIGIIAAAILISKR 372
                 7999************99999887776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1633  (0.0910815); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 3849.36
//
Query:       AJA93125.1  [L=453]
Description: adenylosuccinate lyase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-45  154.7   0.5    5.6e-45  154.1   0.5    1.2  1  Lyase_1   Lyase
      2e-12   47.5   0.0    5.4e-12   46.1   0.0    1.8  1  ADSL_C    Adenylosuccinate lyase C-terminus
    0.00046   20.3   0.1     0.0012   19.0   0.1    1.7  1  ASL_C     Adenylosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   0.5   9.4e-49   5.6e-45       7     305 ..      13     292 ..       9     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 9.4e-49
                 TCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIII CS
     Lyase_1   7 adklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkv 105
                 + ++ +if e+ + +++l+     ++aa++ +  + n+++k++a++i +a++    +gk+  + ++k+ + +s +++ + l e ++e  +  +e + ++
  AJA93125.1  13 TKEMLEIFGEQKKVDYQLE-----IEAAAALSQGEINLIPKSIAKDIARAAR----SGKIT-AKRIKQLEAKSDHDTAA-LVESLAERCK--KESRPWI 98 
                 5678899999999999999.....7888888999999999999999998875....48888.999***********999.99****7777..69999** PP

                 TTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTT CS
     Lyase_1 106 htgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtav 204
                 h+g +snD v+T+ ++++++a+   + p++ +L+ +l++ a ++k  + +GrTh+q+A  + +g +++ +a+++  ++erl e++kr+l  +  g +++
  AJA93125.1  99 HYGLTSNDLVDTSNSMQMRDAI-RIIQPKVGKLALVLTKNAMKYKTLPAVGRTHGQHASIISFGLKFANWAAEMSTHLERLDEIKKRILICKTLGVVGT 196
                 **********************.55**********************************************************************7777 PP

                 SSTTTSCC.THHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHH CS
     Lyase_1 205 gtglnadp.efaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlEl 302
                 g  ++ ++ +++ +vak+l+   +     ++ ++++ +r +++e+++ l+ll + L k++ ++r l+ +e+g+v + + +++ GSS  P K+NP+++E 
  AJA93125.1 197 GSLMGKNAvKVQDRVAKKLS---L---FPAKVTTQIIPRERYAEYIFQLSLLGATLEKISIEIRNLQRTEIGEVAEHFKKGQMGSSAVPVKRNPIKSER 289
                 77776666678999999999...5...556777899**************************************************************9 PP

                 HHH CS
     Lyase_1 303 ltg 305
                 + +
  AJA93125.1 290 ISS 292
                 876 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   9.1e-16   5.4e-12       1      72 [.     363     440 ..     363     441 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 9.1e-16
                 TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC..HHCHHHHHT-GGGCCTTHHHHHHH CS
      ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk..seeeldalfdpayylgsadeivdr 72 
                 G if+e vl aL+ kg+ R  Ay+ Vq+ a +a e+   ++++L  d+ + k  +e+e++++f p+++lg+++ i++ 
  AJA93125.1 363 GQIFAEFVLEALIkKGIPRFVAYRDVQRVAFEAHEKkmnYMDALIGDKNILKslTEKEIKDIFVPEKHLGASQIIINN 440
                 789**********66************************************66*999****************99876 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     2e-07    0.0012       4     107 ..     313     422 ..     311     429 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-07
                 T--TCHHHHHTTCHHHHHHHHH..HHHHHHHHHCCEEE-HHHHHHHHHT-.GGGGHHHHHHHHHHTT-TT..HHHHHHHHHTTS.---HHHHHHHHHCS CS
       ASL_C   4 QRDLtdStvlRnlgvalahsli..alksllkglsklevneealaedLden.wevlaEaiqtvlrregiek..pYeklkeltrgk.kitkeslkefiesl 96 
                  RDL++S+  R + +++a +l+   ++ +++ +s+l++n+++++e+L  +  ++ aE +  +l ++gi++  +Y  ++++  ++ + + + ++++i + 
  AJA93125.1 313 ERDLSNSANERFT-IPMASILLdeMIETMIRIISNLQINDKRVRENLYITkGQIFAEFVLEALIKKGIPRfvAYRDVQRVAFEAhEKKMNYMDALIGDK 410
                 6*********975.78888887335899*******************865389***************9766899999987776477788899999988 PP

                 -S-HH.HHHHHH CS
       ASL_C  97 evsee.akeeLk 107
                 ++ ++ +++e+k
  AJA93125.1 411 NILKSlTEKEIK 422
                 854441455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3575.88
//
Query:       AJA93126.1  [L=140]
Description: B12 binding domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-20   71.7   0.1    6.6e-20   71.4   0.1    1.0  1  B12-binding  B12 binding domain
     0.0098   14.9   0.1      0.011   14.7   0.1    1.1  1  IMPDH        IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.015   15.4   0.0    1.3  1  Ocnus        Janus/Ocnus family (Ocnus)


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.1   1.1e-23   6.6e-20       2     114 ..      11     121 ..      10     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.1e-23
  B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel.lkrirprvkvvvGGahpsldpeet 98 
                  k+l+a++g d h++G+ vl +a+rdag+eV++ g+ +++++i++ +++e++d+v+lS+l +++ + + ++v++ +k++  +v vv GG++p+ d +  
   AJA93126.1  11 KILVAKLGLDGHDRGALVLCRAFRDAGMEVIYSGLFATPDRIAQIVEDEDADAVALSLLNGAHGTLFPRVVKElKKKKITDVLVVGGGVIPEEDKKA- 107
                  799**********************************************************************95555589*************999. PP

  B12-binding  99 leaklgiddvvvgege 114
                  le+  g +   +g g+
   AJA93126.1 108 LEK-AG-VSGNFGPGT 121
                  554.66.555667765 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.9e-06     0.011     107     169 ..      50     115 ..      34     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-06
                 HHHHHHHH.TT-SEEEEE-STS.SSHHHHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SE CS
                 xxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 107 ervkalve.agvdvlvvdsahg.hsekvleavkeikkkvee.veviaGnvataegakaLieagada 169
                 +r++++ve +++d++++   +g h +   ++vke+kkk  + v v++G v  +e  kaL +ag+ +
  AJA93126.1  50 DRIAQIVEdEDADAVALSLLNGaHGTLFPRVVKELKKKKITdVLVVGGGVIPEEDKKALEKAGVSG 115
                 566666652789****99988834556678999999776544*********************975 PP

>> Ocnus  Janus/Ocnus family (Ocnus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.5e-06     0.015      42      89 ..      72     119 ..      54     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
       Ocnus  42 yhadifekveeeleklg.levkclGGGriehdeekkkikvYGysqtfGk 89 
                  h   f +v +el+k++  +v ++GGG i  + +kk ++  G+s +fG 
  AJA93126.1  72 AHGTLFPRVVKELKKKKiTDVLVVGGGVIPEE-DKKALEKAGVSGNFGP 119
                 68899999******998457889999999765.7899**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1125.47
//
Query:       AJA93127.1  [L=237]
Description: glycosyltransferase, group 2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-26   91.1   0.0      9e-26   90.7   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    2.7e-10   40.5   0.0      4e-10   40.0   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    9.2e-05   22.0   0.0    0.00012   21.6   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0013   18.3   0.2     0.0026   17.4   0.2    1.4  1  DUF166           Domain of unknown function
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.025   14.3   0.0    1.5  1  CAP59_mtransfer  Cryptococcal mannosyltransferase 1
      0.019   14.9   0.2      0.081   12.8   0.0    2.0  2  MT-A70           MT-A70
      0.055   13.3   0.0       0.19   11.5   0.0    1.8  2  RVT_3            Reverse transcriptase-like
      0.074   12.4   0.0       0.48    9.8   0.0    2.0  2  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
       0.13   12.8   0.0       0.22   12.0   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   4.5e-29     9e-26       2     168 ..       5     173 ..       4     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 4.5e-29
                      EEEEESS-TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS....EEEEEESS CS
  Glycos_transf_2   2 vviptyNeektlletlesllaq..dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd....yilflDaD 89 
                      +viptyNe++t++ +++ l +   +  ++++++++DD+S+D+t++i++el  ++++++vi+r ++ G+++a+ +g+r+   +    +i+ +DaD
       AJA93127.1   5 IVIPTYNEAETIPSLIKELFEKikQLVEKLDVLIIDDSSPDGTADIVRELGGKYDKITVIQRAKKMGLGAAYKEGFRYILDKldseLIVQMDAD 98 
                      9*******9999999999999888889**************************************************998888888******** PP

                      EEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
  Glycos_transf_2  90 depdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealee 168
                      + ++p  ++ ++e++++ ++   +++r + +++   +   ++      + + + k   k+++ + ++++++++++ le+
       AJA93127.1  99 HSHQPSEIPNMLEKIKNFDY--LIASRHVEGSDIVGWGIGRK--ATHSVAGAIAKACAKIEINDSTSGFRMFKKKTLER 173
                      *****************666..66666665555555555544..57899999999999999999999999999998876 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     2e-13     4e-10       4     112 ..       3     113 ..       2     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2e-13
  Glyco_tranf_2_3   4 lavlVptfneedvlgevlesll.aqey..prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk....sdl 90 
                      la+++pt+ne++++ +++ +l  +++     ++v +++d s ++t++ ++el  ++++  ++v+++a++ g  g+  a++e++r +     s+l
       AJA93127.1   3 LAIVIPTYNEAETIPSLIKELFeKIKQlvEKLDVLIIDDSSPDGTADIVRELGGKYDK--ITVIQRAKKMGL-GA--AYKEGFRYILdkldSEL 91 
                      79********************777744677*************************77..6******98886.44..568****865455599* PP

  Glyco_tranf_2_3  91 vllvDdDtvvePdtlkrllqff 112
                      ++ +D+D   +P  ++ +l  +
       AJA93127.1  92 IVQMDADHSHQPSEIPNMLEKI 113
                      ************9998877665 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   6.2e-08   0.00012       2     110 ..       5     115 ..       4     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.2e-08
  Glyco_tranf_2_2   2 vviplraseer.hyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska....esdlvlFlDa 90 
                      +vip +++ e+ + +   + +k k+  e+++++++dd S++ +++ v+ +  +  ++ + +   k  +l+aa   G+ +      s+l++ +Da
       AJA93127.1   5 IVIPTYNEAETiPSLIKELFEKIKQLVEKLDVLIIDDSSPDGTADIVRELGGKYDKITVIQR-AKKMGLGAAYKEGFRYIldklDSELIVQMDA 97 
                      89**9999887344455568888999*************************99999975555.6899*********9764222289******** PP

  Glyco_tranf_2_2  91 DcfissDkfekilklitikk 110
                      D    + ++ ++l+  +ik+
       AJA93127.1  98 DHSHQPSEIPNMLE--KIKN 115
                      *9999988888887..5555 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.3e-06    0.0026      28     110 ..       7      93 ..       1      97 [. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
      DUF166  28 vavvevpeeldefiedpeelLpe.lkeaDiviaytlhpDlllelaekakekkvkalivpaeapk....aglrkelkekleelgievav 110
                 + +++ +e+++ +i +  e +++ +++ D++i  +  pD ++++++++  +k++ + v + a+k    a+ +++++  l++l+ e++v
  AJA93127.1   7 IPTYNEAETIPSLIKELFEKIKQlVEKLDVLIIDDSSPDGTADIVRELG-GKYDKITVIQRAKKmglgAAYKEGFRYILDKLDSELIV 93 
                 44566677***************99************************.55555555555555478888888999999888877765 PP

>> CAP59_mtransfer  Cryptococcal mannosyltransferase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.025       3      66 ..       4      66 ..       2      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
  CAP59_mtransfer  3 fiAanlynneellpewleallelirfLgpenvfvSiyesgskdgtkeaLraleaelealgvers 66
                      i++  yn++e +p+++++l+e i+ L  e++ v i+++ s dgt++++r+l  + ++++v ++
       AJA93127.1  4 AIVIPTYNEAETIPSLIKELFEKIKQL-VEKLDVLIIDDSSPDGTADIVRELGGKYDKITVIQR 66
                     5788899********************.89999********************99999987655 PP

>> MT-A70  MT-A70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.73   1.5e+03     133     157 ..      12      36 ..       3      39 .. 0.76
   2 ?   12.8   0.0   4.1e-05     0.081     118     150 ..      83     115 ..      63     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.73
                 TTTSS-THHHHHHHHHCTCS-EEEE CS
      MT-A70 133 ehsrKPpelfellehllesarkLel 157
                 e    P+++ el e++ +  +kL++
  AJA93127.1  12 EAETIPSLIKELFEKIKQLVEKLDV 36 
                 5555699999999999999999875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.1e-05
                 B-TTSSBSEEEEE-CTTTSS-THHHHHHHHHCT CS
      MT-A70 118 inknvdtdliisperehsrKPpelfellehlle 150
                 i  + d++li+ +   hs+ P+e++++le++ +
  AJA93127.1  83 ILDKLDSELIVQMDADHSHQPSEIPNMLEKIKN 115
                 445679***********************9974 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1   2.2e+03      83     103 ..      16      36 ..       5      40 .. 0.76
   2 ?   11.5   0.0   9.5e-05      0.19      46      96 ..      66     115 ..      42     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
       RVT_3  83 ksselanlldeirkllksfes 103
                   s ++ l ++i++l++++++
  AJA93127.1  16 IPSLIKELFEKIKQLVEKLDV 36 
                 667788999999999999876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.5e-05
       RVT_3  46 qALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirk 96 
                 +A  +GL +a k g+r +  + Ds+ +vq   + ++ + se+ n+l++i++
  AJA93127.1  66 RAKKMGLGAAYKEGFRYILDKLDSELIVQMDADHSH-QPSEIPNMLEKIKN 115
                 66679**************************99998.**********9975 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.23   4.6e+02     119     140 ..      25      46 ..      20      70 .. 0.85
   2 ?    9.8   0.0   0.00024      0.48     120     188 ..      79     148 ..      60     153 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.23
                     GGGTTTCCC-SEEEEESS-TT- CS
  Ribul_P_3_epim 119 ealeyllekldlvllmsvePgf 140
                     e +++l+ekld++++  + P+ 
      AJA93127.1  25 EKIKQLVEKLDVLIIDDSSPDG 46 
                     6789999999999998888875 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00024
                     GGTTTCCC-SEEEEESS-TT-SS-.---CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT- CS
  Ribul_P_3_epim 120 aleyllekldlvllmsvePgfgGQ.kFipevlekikkvrklidekeldlkievDGGvkldnieqiaeaga 188
                      ++y+l+kld  l+   + + + Q + ip++lekik+   li++++++    v  G+  ++++ +a a a
      AJA93127.1  79 GFRYILDKLDSELIVQMDADHSHQpSEIPNMLEKIKNFDYLIASRHVEGSDIVGWGIGRKATHSVAGAIA 148
                     579*******************99667*****************99999999999***999999987755 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.22       2      49 ..      11      67 ..      10     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
  Glyco_tranf_2_4  2 neadiLpefla....hhlalgfdr..ilvydndstDgtrailke....lpevkllhvd 49
                     nea+++p+ ++     +++l +++  +l++d+ s Dgt++i++e    ++++++++  
       AJA93127.1 11 NEAETIPSLIKelfeKIKQL-VEKldVLIIDDSSPDGTADIVRElggkYDKITVIQRA 67
                     77777777777332234444.443339***************9943333445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 1907.62
//
Query:       AJA93128.1  [L=186]
Description: putative cytidylate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-11   43.8   0.0    5.3e-11   43.2   0.0    1.4  1  AAA_18           AAA domain
    6.6e-09   36.3   0.0    1.3e-08   35.3   0.0    1.5  1  AAA_17           AAA domain
    1.2e-07   32.0   0.1    8.1e-07   29.3   0.1    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
    9.4e-07   28.8   0.0    0.00023   21.0   0.0    2.2  2  Cytidylate_kin   Cytidylate kinase
    2.8e-05   24.3   0.3    9.4e-05   22.6   0.0    2.0  3  ADK              Adenylate kinase
    6.6e-05   23.1   0.2    0.00029   21.0   0.2    1.9  1  SKI              Shikimate kinase
    0.00012   22.5   0.1    0.00039   20.8   0.2    1.9  2  AAA              ATPase family associated with various cellul
    0.00054   20.2   0.0    0.00079   19.7   0.0    1.3  1  AAA_28           AAA domain
    0.00066   20.0   0.0     0.0007   19.9   0.0    1.3  1  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0013   18.9   0.0     0.0024   18.0   0.0    1.7  1  AAA_33           AAA domain
     0.0029   17.1   0.8      0.063   12.7   0.1    2.1  2  KTI12            Chromatin associated protein KTI12
     0.0042   16.8   0.0      0.008   15.9   0.0    1.4  1  AAA_24           AAA domain
     0.0058   17.0   0.0     0.0095   16.3   0.0    1.5  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
       0.01   15.7   0.1       0.23   11.3   0.0    2.4  2  dNK              Deoxynucleoside kinase
      0.011   15.5   0.0      0.019   14.7   0.0    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.013   15.8   0.0      0.019   15.4   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.014   15.3   0.2      0.063   13.2   0.0    1.9  2  Rad17            Rad17 P-loop domain
      0.049   12.9   0.1       0.86    8.8   0.0    2.1  2  Zeta_toxin       Zeta toxin
       0.07   13.4   0.0       0.14   12.4   0.0    1.5  1  AAA_22           AAA domain
      0.097   12.6   0.0       0.15   12.0   0.0    1.4  1  NTPase_1         NTPase
       0.11   11.8   0.0        9.9    5.5   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   6.2e-14   5.3e-11       1     118 [.       5     127 ..       5     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.2e-14
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.......aldeskrldedkldklldaleenssaleegknlvidghlaele 87 
                 I+++G+p+ GKtt+ak L+k+ ++     g++l+++a+e g + + d+        ++ ++++++ ++++k+ ++l +  +     +n+vi +    ++
  AJA93128.1   5 IVVSGPPAIGKTTVAKGLAKEFNLnylsgGDILKELASEQGFSSSGDDWwdtedgmKFLNQRKENSEFDKKVDEKLIQLFE----KGNVVITSYTLPWL 99 
                 89*******************87788***************9999888888999**6666666666666666666666543....46668888877777 PP

      AAA_18  88 seaakdikkvvLtaspeelleRlekRgyeea 118
                  ++ ++    +L+   e  ++R+++R++ + 
  AJA93128.1 100 IDSGIK---LWLDGTVENSAKRMQNRDNLDE 127
                 777775...9****************97654 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.6e-11   1.3e-08       2      79 ..       9      94 ..       8     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.6e-11
                E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTT.......SHSSHHHHC.TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE- CS
      AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgg.......lakardemr.klpleekkelqkeaaekiaeeakkkgvlvdgh 79
                G+P  GK+t+++ l++++++ +ls Gd+l e a+++g         +++d m+  ++ +e+ e++k++ ek+ +  +k++v+++ +
  AJA93128.1  9 GPPAIGKTTVAKGLAKEFNLNYLSGGDILKELASEQGfsssgddWWDTEDGMKfLNQRKENSEFDKKVDEKLIQLFEKGNVVITSY 94
                9***********************************94443333123344444335667788999999999999889999998765 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   9.5e-10   8.1e-07       4     177 ..       7     166 ..       4     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 9.5e-10
  Cytidylate_kin2   4 IsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldeklddelfeaqervirelaaee 96 
                      +s+  + g++t+++ LA++++l++++  +i++e+a+e g+s +     d +    +fl++           ++++d++    +e++i+   ++ 
       AJA93128.1   7 VSGPPAIGKTTVAKGLAKEFNLNYLSGgDILKELASEQGFSSSGDDWWDTEDG-MKFLNQR----KE----NSEFDKK---VDEKLIQLFEKG- 87 
                      56666779******************99*************998877777555.5566432....21....2333333...445666655444. PP

  Cytidylate_kin2  97 svVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgqdw.gdaenYdlvlnt 177
                      +vVi        L  ++  ++ +l+++ e+ +kr++ r +l+e+ a   ++++ ++++  yk++++ +  +d + +d +++t
       AJA93128.1  88 NVVITSYTLP-WL--IDSGIKLWLDGTVENSAKRMQNRDNLDESSALAVVNKRFNENKLIYKNLYNFEFgDDLSVFDKIIQT 166
                      8888765443.33..4457*************************************************95566778877776 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.7e-07   0.00023       1      37 [.       5      41 ..       5      66 .. 0.91
   2 ?    5.7   0.0     0.013        11      97     153 ..      71     124 ..      57     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
  Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                    i + GP + GK +va+ la++++l+yl+ g + + la
      AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNYLSGGDILKELA 41
                    6789**************************9987766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.013
                     HHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHH CS
  Cytidylate_kin  97 avRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlka 153
                     ++ +++ +kl +l +k++vv+     +   + d+ +K++ld  ve  akR  +  ++
      AJA93128.1  71 EFDKKVDEKLIQLFEKGNVVITSY--TLPWLIDSGIKLWLDGTVENSAKRMQNR-DN 124
                     566778888888889999888754..5556789************999875443.33 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-07   9.4e-05       1      37 [.       7      43 ..       7      53 .. 0.89
   2 ?   -2.9   0.0       7.8   6.7e+03      42      55 ..      77      90 ..      62     102 .. 0.55
   3 ?   -3.0   0.0       8.1   6.9e+03     126     135 ..     132     141 ..     106     151 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-07
                EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHC CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevks 37
                + G+P+ GK t+a+ l+k+++l+ ls Gd+l++  ++
  AJA93128.1  7 VSGPPAIGKTTVAKGLAKEFNLNYLSGGDILKELASE 43
                57*****************************987655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.8
                HHHHHHHHHTTSS- CS
                xxxxxxxxxxxxxx RF
         ADK 42 Gkeakevmdkgelv 55
                 +++ ++ +kg++v
  AJA93128.1 77 DEKLIQLFEKGNVV 90
                23333444455444 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.1
                 HHHHHHHHHH CS
                 xxxxxxxxxx RF
         ADK 126 etvkkRlety 135
                   v+kR++++
  AJA93128.1 132 AVVNKRFNEN 141
                 3344555544 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   3.4e-07   0.00029       3     144 ..      13     158 ..      11     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.4e-07
                 SSHHHHHHHHHHHHTSEEEEHHHHH.....HHHHTS-HHHHHHHHHHHHH..HHHHHHHHHHHCCCS.SEEEEE-TTGGGSHHHHHHHHHHSEEEEEE- CS
         SKI   3 aGKstvGkllAkklglefiDlDeli.....ekrtgksiaeifeeegeegF..relEsevlkelleee.glViatGGGavlseenrellkekgiviyLdv 93 
                  GK+tv+k lAk+ +l+++   +++     e+ +  s  +  + e+  +F  +++E   +++ ++e+    +  G  +++s    +l+  +gi ++Ld 
  AJA93128.1  13 IGKTTVAKGLAKEFNLNYLSGGDILkelasEQGFSSSGDDWWDTEDGMKFlnQRKENSEFDKKVDEKlIQLFEKGNVVITSYTLPWLID-SGIKLWLDG 110
                 6*****************98766654445566777899999999999999443456666788888876778888777777777777777.********* PP

                 -HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSS CS
         SKI  94 sleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdesee 144
                 ++e+ ++r++++++   l e+s   ++ ++ + e + +y+++ +  + ++ +
  AJA93128.1 111 TVENSAKRMQNRDN---LDESSA-LAVVNKRFnENKLIYKNLYNFEFGDDLS 158
                 **************...666666.5666666657777777766665555544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   4.6e-07   0.00039       2      37 ..       6      39 ..       5      88 .. 0.80
   2 ?   -0.6   0.0         2   1.7e+03      74     106 ..      66      91 ..      39     110 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.6e-07
                EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS CS
         AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk 37
                +++Gpp +GKT++ak +ake++ ++  +sg ++l++
  AJA93128.1  6 VVSGPPAIGKTTVAKGLAKEFNLNY--LSGGDILKE 39
                789*****************76654..566666644 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                 HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEE CS
         AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivi 106
                 r +++se++++v ++L++ +++ +       vi
  AJA93128.1  66 R-KENSEFDKKVDEKLIQLFEKGNV------VI 91 
                 3.56777777777777777765433......44 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   9.3e-07   0.00079       2      62 ..       5      69 ..       4      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.3e-07
      AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwv.edllafaervlee 62
                iv++G++  GKTt+++ La++ + +++   ++  e+ +e++++  ++  w  ed ++f  ++ e+
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEfNLNYLsgGDILKELASEQGFSSSGDDWWDtEDGMKFLNQRKEN 69
                9******************8885554445999999999999877776677778888888776554 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.2e-07    0.0007       2      42 ..       5      45 ..       4     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.2e-07
   Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisdgn 42
                i+v G+P  GKt+ a  Lak+++  +l+  ++++e  s+++
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNYLSGGDILKELASEQG 45
                9***************************9999999888765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.8e-06    0.0024       2      46 ..       5      49 ..       5     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.8e-06
      AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqskt 46
                +++ G+p+ GK+t+a++l+k+     ls  ++++ l+ ++  s +
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNYLSGGDILKELASEQGFSSS 49
                5789*****************999999998888888876655444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   7.4e-05     0.063       4      26 ..       5      27 ..       4      57 .. 0.88
   2 ?    3.0   0.1     0.066        57     111     141 ..      58      88 ..      47      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                EEEE--TTSSHHHHHHHHHHHHH CS
       KTI12  4 vvltGlPssGKstrakeLakale 26
                +v++G P+ GK+t+ak Lak+++
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFN 27
                89******************997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.066
                 HHHHHHHHTT-S..S-HHHHHHHHHH---TT CS
       KTI12 111 vlvkwneereekeeyekelldaLiqRyeePd 141
                   +k+ ++r+e++e++k++ ++Liq +e+ +
  AJA93128.1  58 DGMKFLNQRKENSEFDKKVDEKLIQLFEKGN 88 
                 5567778999999***************865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.4e-06     0.008       1      41 [.       1      66 [.       1      79 [. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-06
      AAA_24  1 kklkiliyGpsgiGKTtlakelgpkplfi..........................dtekGlksldad 41
                ++++i++ Gp+ iGKTt+ak l  k + +                          dte+G+k l+ +
  AJA93128.1  1 MSKSIVVSGPPAIGKTTVAKGL-AKEFNLnylsggdilkelaseqgfsssgddwwDTEDGMKFLNQR 66
                5789*****************9.44444445577777777777777777777777777777766665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05    0.0095       1      46 [.       5      56 ..       5      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl........klkkkdsvysrnpeddfwdg 46
                  i+++Gp+ +GK+t+ak Lak++  ++        +l +++ +   ++ dd+wd 
    AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNYlsggdilkELASEQGF--SSSGDDWWDT 56
                  789*******************96656777776433333333..5799999986 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.23       1      26 [.       5      30 ..       5      44 .. 0.92
   2 ?    2.2   0.0      0.17   1.4e+02     127     149 ..     106     128 ..      62     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                EEEEESTTSSHHHHHHHHHCCSTCEE CS
         dNK  1 ivveGnIgaGKstlvklLskklgvkv 26
                ivv+G+ + GK+t++k L+k+++ + 
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNY 30
                89*******************99775 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.17
                 EEEE--HHHHHHHHHHCTTCCCT CS
         dNK 127 iYLkasletclerikkRgreeek 149
                  +L+ ++e+  +r+++R++ +e 
  AJA93128.1 106 LWLDGTVENSAKRMQNRDNLDES 128
                 5899999***********99987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-05     0.019      36      61 ..       5      30 ..       2      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
      RuvB_N 36 vllyGpPGlGkttlakiiakelgvkl 61
                ++++GpP +Gktt+ak +ake++ + 
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNY 30
                789******************98764 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.2e-05     0.019      25      51 ..       3      29 ..       1      87 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
      AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                 ++++sG++++GK+++++ l+++++ +
  AJA93128.1  3 KSIVVSGPPAIGKTTVAKGLAKEFNLN 29
                5899**************999987765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.4e-05     0.063      48      74 ..       5      31 ..       2      93 .. 0.78
   2 ?    0.1   0.1      0.77   6.5e+02      76     142 ..     107     170 ..     100     186 .] 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-05
       Rad17 48 LLisGPsGCgkstvvkvLskelgiklr 74
                +++sGP+  gk+tv k L+ke+  ++ 
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEFNLNYL 31
                579******************988775 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.77
       Rad17  76 wlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkdakylklqklGddlrtdkklilvedlP 142
                 wl+++   e + ++ + +  ++  s +    + f+e +L   +   ++  Gddl    k+i  + + 
  AJA93128.1 107 WLDGTV--ENSAKRMQNRDNLDESSALAVVNKRFNENKLIYKNLYNFE-FGDDLSVFDKIIQTDGIN 170
                 555555..5555566666666666666666667777777766665666.788888888888777776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0     0.001      0.86      17      45 ..       3      29 ..       2      40 .. 0.86
   2 ?    1.9   0.0      0.14   1.2e+02      65     109 ..      73     117 ..      64     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
  Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgn 45
                k+i+++G p+ GK+++a+ l++e+  + n
  AJA93128.1  3 KSIVVSGPPAIGKTTVAKGLAKEF--NLN 29
                6899******************98..444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.14
  Zeta_toxin  65 lkadpkkaseltqkdaselvekllqeaiengyniivegtlrspdv 109
                  k+ ++k  +l++k   +++  +l ++i+ g+ + ++gt ++  +
  AJA93128.1  73 DKKVDEKLIQLFEKGNVVITSYTLPWLIDSGIKLWLDGTVENSAK 117
                 4567888889999999999999*****************998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.14       6      30 ..       3      27 ..       2      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
      AAA_22  6 gilvvtGesGtGKTtllrrlleqld 30
                +++vv G++ +GKTt+++ l+++++
  AJA93128.1  3 KSIVVSGPPAIGKTTVAKGLAKEFN 27
                589***************9999885 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.15       2      39 ..       5      41 ..       4      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                ++++Gpp +GKtT+ k ++++  + ++  gG + +e  
  AJA93128.1  5 IVVSGPPAIGKTTVAKGLAKEF-NLNYLSGGDILKELA 41
                89**************999998.677777777777765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.012       9.9      24      43 ..       4      23 ..       2      32 .. 0.89
   2 ?    4.1   0.0     0.031        26     108     138 ..      59      92 ..      55      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.012
  Mg_chelatase 24 nlllvGppGsGKtmlakrlp 43
                  ++++ Gpp  GKt +ak l+
    AJA93128.1  4 SIVVSGPPAIGKTTVAKGLA 23
                  68999***********9886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.031
  Mg_chelatase 108 GvLfLD...ElpefkrkvlevLRePledgevtis 138
                   G+ fL+   E +ef++kv e L + +e+g+v+i+
    AJA93128.1  59 GMKFLNqrkENSEFDKKVDEKLIQLFEKGNVVIT 92 
                   666664333889*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1341.85
//
Query:       AJA93129.1  [L=139]
Description: hypothetical protein T478_0674 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.089   13.1   0.0       0.11   12.7   0.0    1.4  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.3e-06      0.11       1      33 [.       1      33 [.       1     113 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-06
                     EEEEEEEEEESS-HHHHHHHHTTTTGGGGT-TT CS
  Polyketide_cyc2  1 mvkvtvsvviaappekVwalvsdfenwprWhpe 33
                     m k++ ++ i+a+ ek ++++++fen+++  pe
       AJA93129.1  1 MLKISFERKINADIEKSFDIITNFENFQKLFPE 33
                     568889999*******************98663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1101.78
//
Query:       AJA93130.1  [L=155]
Description: 50S ribosomal protein L30P [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-11   41.9   0.1      1e-10   41.3   0.1    1.3  1  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.096   12.4   0.1         11    5.6   0.0    2.1  2  VPS28          VPS28 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.1   1.2e-14     1e-10       1      51 []       5      55 ..       5      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.2e-14
                   EEEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51
                   ++V+ri ++++vp +   t++lL L k + ++ +++   +i  mL+kV+h+V
     AJA93130.1  5 YLVVRISGTADVPYWATTTMNLLKLEKKHrAVIIPEIDNTIG-MLRKVQHYV 55
                   58***************************9999999988885.********9 PP

>> VPS28  VPS28 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.002        18     108     146 ..      22      64 ..      14      75 .. 0.79
   2 ?    5.6   0.0    0.0012        11     107     139 ..      81     113 ..      70     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.002
       VPS28 108 TlmDalkLnlkakdqlhplLsdLveslnklekl....ekdfeg 146
                 T+m  lkL+ k++  + p++ + +  l+k+++     e d+e+
  AJA93130.1  22 TTMNLLKLEKKHRAVIIPEIDNTIGMLRKVQHYvawqELDVET 64 
                 99**********************9999994333333555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0012
       VPS28 107 ITlmDalkLnlkakdqlhplLsdLveslnklek 139
                 IT  D   L++k++d+l   L++  +sl+kl+ 
  AJA93130.1  81 ITPEDITALGYKSVDELASALAEGKTSLTKLKP 113
                 88889999***************9999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1146.71
//
Query:       AJA93131.1  [L=206]
Description: hypothetical protein T478_0458 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1572.01
//
Query:       AJA93132.1  [L=93]
Description: hypothetical protein T478_0294 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 730.02
//
Query:       AJA93133.1  [L=149]
Description: ribosomal protein S9 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-31  109.1   0.2    2.2e-31  108.9   0.2    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.2   1.2e-35   2.2e-31       2     121 .]      11     149 .]      10     149 .] 0.91

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 1.2e-35
                   ECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS..SEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHH............H CS
  Ribosomal_S9   2 rrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg..kfdvfvkvkgGGlsgqaeAirlgiaraLvalek............e 84 
                    rK+s+A+v i++g gki++n+ +le  ++ e +re +l+pl+++g++   k+d+ ++v+gGG++gqa+A +++++raL+ ++k            +
    AJA93133.1  11 SRKTSSAHVFITKGVGKIRINNIPLEM-IEPESSREVILAPLEIIGEEIrdKVDISIRVRGGGFMGQAYASATAMSRALIGWTKskkepkdhpfnkS 106
                   69*************************.888**************9865668******************************865666666667644 PP

                   HHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
  Ribosomal_S9  85 ekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                   ++++L+      ++ l+  D+R++E+kK+g ++AR++ q+s+R
    AJA93133.1 107 TRQQLRekiadyDKYLISGDARRKEPKKFGGPGARRRKQKSYR 149
                   4999998888888****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1087.62
//
Query:       AJA93134.1  [L=67]
Description: ribosomal protein L29 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-12   46.1   7.8    4.3e-12   45.8   7.8    1.1  1  Ribosomal_L29    Ribosomal L29 protein
     0.0054   16.8   4.1      0.028   14.4   0.6    2.1  2  DUF1192          Protein of unknown function (DUF1192)
     0.0069   16.8   5.4     0.0082   16.5   5.4    1.1  1  Snapin_Pallidin  Snapin/Pallidin
  ------ inclusion threshold ------
      0.026   13.5   2.7      0.029   13.4   2.7    1.0  1  Ran-binding      RanGTP-binding protein
      0.028   14.4   0.1      0.028   14.4   0.1    1.0  1  PilJ             Type IV pili methyl-accepting chemotaxis tra
       0.16   10.8   3.2       0.17   10.8   3.2    1.0  1  FemAB            FemAB family
       0.49   11.0   7.9        0.5   11.0   1.5    2.1  2  GTP-bdg_M        GTP-binding GTPase Middle Region


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   7.8   1.7e-15   4.3e-12       2      56 ..       8      63 ..       7      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.7e-15
                   HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS.-CHHHHHHHHHHHHHHHHHHH CS
  Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqle.npsrirkvRkdIARikTvlre 56
                    +rel++++L+++++++k+eL +L+   a g+l   +++irkv+k++AR++T l+e
     AJA93134.1  8 SIRELNEKDLRDRIVQMKTELSKLKTEDAKGTLRkETGKIRKVKKEVARLMTRLNE 63
                   69*******************************779******************98 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.6   1.1e-05     0.028      15      45 ..       7      37 ..       2      44 .. 0.86
   2 ?    4.2   0.2     0.018        46      28      45 ..      46      63 ..      44      67 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
     DUF1192 15 qDLslLSveELeerIalLeaEIaRleaaiak 45
                + +  L+ ++L++rI +++ E  +l+++ ak
  AJA93134.1  7 KSIRELNEKDLRDRIVQMKTELSKLKTEDAK 37
                6778999******************998665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
     DUF1192 28 rIalLeaEIaRleaaiak 45
                 I + ++E+aRl + + +
  AJA93134.1 46 KIRKVKKEVARLMTRLNE 63
                58999*******988765 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   5.4   3.2e-06    0.0082      29      84 ..      14      66 ..       5      67 .] 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
  Snapin_Pallidin 29 QeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84
                      ++L++++ +++++L +l+ ++      +l++   K++++kk++ +l +rl+++kk
       AJA93134.1 14 EKDLRDRIVQMKTELSKLKTEDA---KGTLRKETGKIRKVKKEVARLMTRLNEVKK 66
                     578*************9999888...99*************************997 PP

>> Ran-binding  RanGTP-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.7   1.1e-05     0.029      89     138 ..      15      63 ..       3      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
  Ran-binding  89 ksLkkeieelgerleeaaekeekskkkeeekeelkkviedikeLLkriee 138
                  k+L++ i++++++l+++ ++   + + ++e+ +++kv +++ +L++r++e
   AJA93134.1  15 KDLRDRIVQMKTELSKLKTEDA-KGTLRKETGKIRKVKKEVARLMTRLNE 63 
                  79***************77666.566889999***************997 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.1e-05     0.028      40      93 ..      10      66 ..       1      67 [] 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
        PilJ 40 aaearaqlretiaqfdrtlaalrlgdpapgllvpae...avraqleaveqlWqelkk 93
                ++ + ++lr++i q+ + l  l+  d++ +l + ++   +v++++++++++ +e kk
  AJA93134.1 10 RELNEKDLRDRIVQMKTELSKLKTEDAKGTLRKETGkirKVKKEVARLMTRLNEVKK 66
                566789**********************88888877777777777777777777665 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.2   6.5e-05      0.17     245     296 ..      15      66 ..       2      67 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.5e-05
       FemAB 245 kelqekleklekklakleekleknpekkkkkklkelekqlaslekelkeaee 296
                 k+l+ ++ +++++l+kl+ + +k + +k++ k+++++k++a+l ++l+e+++
  AJA93134.1  15 KDLRDRIVQMKTELSKLKTEDAKGTLRKETGKIRKVKKEVARLMTRLNEVKK 66 
                 345555556888888888877777779**********************986 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.5   0.00019       0.5      48      73 ..      11      36 ..       7      44 .. 0.87
   2 ?    4.2   1.0     0.025        65      51      70 ..      47      66 ..      35      67 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                HHHHHHHHHHHHHHHHHHHHHHHHHH CS
   GTP-bdg_M 48 eldrrlireriaklkkeLekvkkkre 73
                el+++ +r+ri ++k+eL+k+k++ +
  AJA93134.1 11 ELNEKDLRDRIVQMKTELSKLKTEDA 36
                8999*****************98765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                HHHHHHHHHHHHHHHHHHHH CS
   GTP-bdg_M 51 rrlireriaklkkeLekvkk 70
                 r++++ +a+l ++L++vkk
  AJA93134.1 47 IRKVKKEVARLMTRLNEVKK 66
                48889999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1425  (0.0794802); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 495.46
//
Query:       AJA93135.1  [L=128]
Description: hypothetical protein T478_0592 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 945.07
//
Query:       AJA93136.1  [L=97]
Description: hypothetical protein T478_0617 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0057   16.4   0.3     0.0064   16.2   0.3    1.0  1  Tetraspanin  Tetraspanin family
  ------ inclusion threshold ------
      0.011   15.9   2.3       0.15   12.2   0.4    2.1  2  YtpI         YtpI-like protein
      0.047   13.9   5.2        2.4    8.4   1.5    2.1  2  DUF3784      Domain of unknown function (DUF3784)
       0.07   12.8   0.2       0.12   12.1   0.2    1.4  1  Neurensin    Neurensin
       0.38   10.8   4.7          3    7.9   4.7    2.0  1  DUF3185      Protein of unknown function (DUF3185)
        2.1    7.9   5.3          3    7.4   1.6    2.0  2  Saf_2TM      SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.1e-06    0.0064       2      75 ..      12      94 ..      11      96 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXX............XXX.....................XXXXXXXXXXXXXXXXXXXXXXX CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Tetraspanin  2 kyllfffnllfwligivllavGvwlrl............khaeaalacllsesaedpailaillivvGvllfllgflGcigalken 75
                 kyl+ + n  ++ igi+ll++G  +++            +++ +a    ++++ ++     i+ + vG +++l g + +i+++ +n
   AJA93136.1 12 KYLVNIQNSTWFFIGIILLILGSFVTIfdypqiqyfenmDSEMYATLESEQKEIHNRL---IIEFSVGLVILLAGGASFIMSFFKN 94
                 8*********************55555799***9997653332222222333333333...3467777788888877777776665 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4     5e-05      0.15      50      85 ..      14      49 ..       4      51 .. 0.84
   2 ?    3.9   0.1      0.02        60      56      77 ..      70      91 ..      63      97 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-05
        YtpI 50 llllestvalvvgavflvlGlanlfaGiraykhyrp 85
                l++ ++   +++g+++l+lG + ++  + + +++++
  AJA93136.1 14 LVNIQNSTWFFIGIILLILGSFVTIFDYPQIQYFEN 49
                56677777899*****************99999976 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
        YtpI 56 tvalvvgavflvlGlanlfaGi 77
                 +++ vg+v+l+ G a+++  +
  AJA93136.1 70 IIEFSVGLVILLAGGASFIMSF 91
                678889********99998765 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.5   0.00082       2.4      54      87 ..       5      38 ..       1      41 [. 0.63
   2 ?    7.4   0.1    0.0016       4.8      26      63 ..      55      92 ..      53      97 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00082
     DUF3784 54 gilflllgllsaiesealliialiviiiiviyli 87
                +++ +l  +l +i++++++ i++i++i++++++i
  AJA93136.1  5 SLIHFLKKYLVNIQNSTWFFIGIILLILGSFVTI 38
                5566677777666666666666776666666555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
     DUF3784 26 Yntmskeekekydekklsrfmgivllligilflllgll 63
                Y t+  e+ke  +   +   +g v+ll g + ++++++
  AJA93136.1 55 YATLESEQKEIHNRLIIEFSVGLVILLAGGASFIMSFF 92
                899999999999999999******************99 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.9e-05      0.12      45     115 ..      23      92 ..      11      97 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
   Neurensin  45 lvvgtlvlllGvtallvGylvprrlelvksegelvvvDkqaiefnnaLdtlklaGavllclGglllalsll 115
                 + +g+++l+lG  + +  y   + +e +   + +  + ++  e  n L +   +G+v+l +Gg+ +++s++
  AJA93136.1  23 FFIGIILLILGSFVTIFDYPQIQYFENM-DSEMYATLESEQKEIHNRLIIEFSVGLVILLAGGASFIMSFF 92 
                 7899999999999999999999999999.555566666666665556666667899999999999999986 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.7   0.00099         3       3      32 ..      25      54 ..      24      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00099
     DUF3185  3 iGiiLlvaGivLlvfGynasdSlgsqvsea 32
                iGiiLl++G +  +f y + + +++  se+
  AJA93136.1 25 IGIILLILGSFVTIFDYPQIQYFENMDSEM 54
                9**************995555544444444 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.6     0.001         3      66      90 ..      17      41 ..       3      49 .. 0.84
   2 ?    2.8   0.1     0.027        82      60      90 ..      60      91 ..      43      97 .] 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
     Saf_2TM 66 ivlaiilvigvllivvGavllilry 90
                i + + ++ig++l+++G +  i +y
  AJA93136.1 17 IQNSTWFFIGIILLILGSFVTIFDY 41
                567789****************999 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.027
     Saf_2TM 60 sse.ipeivlaiilvigvllivvGavllilry 90
                s++  ++  l+i + +g +++++G    i  +
  AJA93136.1 60 SEQkEIHNRLIIEFSVGLVILLAGGASFIMSF 91
                55555555555555666555555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 739.74
//
Query:       AJA93137.1  [L=251]
Description: hydrolase, TatD family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-45  153.8   0.0    5.8e-45  153.7   0.0    1.0  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
      0.032   13.6   0.0        0.4    9.9   0.0    2.0  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7   0.0   6.5e-49   5.8e-45       2     254 ..       6     249 ..       5     250 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 6.5e-49
                 EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET.- CS
  TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhskvvaiGeiGLDy.y 99 
                 DaH+Hl ++e+++d + il+ ++  +++a++ v+ + ++s+++ +l +k++n v + +G HP  +++ se + e +++    +++ +++iGeiGLD  y
  AJA93137.1   6 DAHIHLSDPEYKSDIDMILNYMDLLKIKACC-VSMDIETSNETMALYEKSKN-VLPFIGTHPEMAQKSSEPVYELIEK----NNEIISGIGEIGLDRtY 98 
                 ***********************99999985.8999*************999.*********9999766555554444....6999***********88 PP

                 CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GG CS
  TatD_DNase 100 sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpld 198
                  ++e++++ q++vF +ql+lA+++++p++iH+rk+  d+ eil +++ ++  + lH+f g++ ++k +++  y++s++ ll++ n  + + l+ + + +
  AJA93137.1  99 INSEDEWKIQKDVFSKQLSLAEKFNKPVSIHSRKTLSDIFEILPSYKIPG--ILLHWFDGNKSQLKTAMENEYFVSYGPLLVYAN--DKQVLLSKTDPS 193
                 9999******************************************9887..9******************************55..556677****** PP

                 GEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
  TatD_DNase 199 rlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                 rlLiETD P      ++ k  e  +v+ v+ + +++   ++e l +++++N+k+++
  AJA93137.1 194 RLLIETDGPVRFSRCFEYKTTEIMFVPSVLFCASKILHTSYENLLTQIEDNSKKFL 249
                 **********99988988***********************************986 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.5e-05       0.4      88     160 ..      50     138 ..       4     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.5e-05
                   S................GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHH CS
  Amidohydro_1  88 r................gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiHaletkgeve 160
                                      +++s+ ++e +++   e+i g ++ +++ ++++ +  + ++++  ++ l++a+k ++pv+iH   t  +++
    AJA93137.1  50 LyeksknvlpfigthpeMAQKSSEPVYELIEKN-NEIISGIGEIGLDrTYINSEDEWKIQKDVFSKQLSLAEKFNKPVSIHSRKTLSDIF 138
                   344444444444444443334445555555555.67788888999999*********************************977666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1507.55
//
Query:       AJA93138.1  [L=194]
Description: MobA-like NTP transferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-16   61.1   0.0    1.8e-16   60.9   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    1.4e-10   41.3   0.0    1.9e-10   40.8   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    0.00035   20.2   0.1     0.0006   19.5   0.0    1.5  1  NTP_transferase  Nucleotidyl transferase
    0.00084   19.3   0.2     0.0038   17.2   0.2    2.0  1  CTP_transf_3     Cytidylyltransferase
     0.0042   16.3   0.8     0.0042   16.3   0.8    1.6  2  CofC             Guanylyl transferase CofC like
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.26   10.7   0.0    1.4  1  DUF4851          Domain of unknown function (DUF4851)


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0     6e-20   1.8e-16       1     123 [.       3     125 ..       3     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6e-20
                   EEEEEESS-TTTTTTHHHHCC.CCCCHHHHHHHHHCTT.-.CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEE CS
  NTP_transf_3   1 aviLAGGrSsRmggdKallpl.ggkpllervldalraagv.devvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvla 93 
                   ++++AGG+++Rm++dK  l l  +kpl+ +v+dal+ +++ ++++ v+ +  ++ ++ l + +v+++e    g + +  l + l+++  +d+v+v++
    AJA93138.1   3 GLVMAGGKGTRMQSDKEKLLLeYKKPLVLHVVDALKNSNCfEKIIAVTSPnsPQTQKILIENDVKIIETL--GDNFVTDLNSILKKL--DDYVFVTS 95 
                   68************99999998899*************86599999986655889999999********8..89***********98..8******* PP

                   TT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
  NTP_transf_3  94 cDmPlltpelverllaaaaasgadvvvpty 123
                   +D+Pll++++v++++ a  +++  + v+t+
    AJA93138.1  96 GDLPLLDENIVKQIVSASNPKKIWTSVVTT 125
                   *****************9877766655554 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   6.5e-14   1.9e-10       3     118 ..       3     114 ..       1     127 [. 0.86

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.5e-14
                 EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE-.-SSHHHHHHHHHHTTSSTTSEEEE--T CS
        IspD   3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaG.GdeRaesVlnglkalegeakfVLvHDa 100
                  ++ A G+G+Rm+++++K++le k ++l+ h vdal +s+  +ki+ v s++  ++++++l ++++++++  Gd+     +  lk   + +++V v  +
  AJA93138.1   3 GLVMAGGKGTRMQSDKEKLLLEYK-KPLVLHVVDALKNSNCFEKIIAVTSPNS-PQTQKILIENDVKIIETlGDNFVTDLNSILK---KLDDYVFVTSG 96 
                 5899******************86.89*******************9999999.9**************8646666555555444...45678****** PP

                 T-TT--HHHHHHHHHHHH CS
        IspD 101 ARpllkaadiaellaaae 118
                   pll ++ +++++ a++
  AJA93138.1  97 DLPLLDENIVKQIVSASN 114
                 **********99999876 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     2e-07    0.0006       2      69 ..       3      65 ..       2     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2e-07
                     EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSG CS
  NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegs 69
                     ++++aGG+GtR+    ++   kl++ ++k +l+ +++ +l ns++ e i+ +t+ +s+  ++ l e++
       AJA93138.1  3 GLVMAGGKGTRM----QSDKEKLLLEYKK-PLVLHVVDALKNSNCFEKIIAVTSPNSPQTQKILIEND 65
                     79*********9....5788899999999.************99988899999999888887766554 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.3e-06    0.0038      24     138 ..      27     133 ..      12     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                   EEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHHHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
  CTP_transf_3  24 kpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterflevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqe 120
                   kpl+ +v++a+++s  fek i+a +s +  ++ k +     +  + +e+  + f+  +  +l + +++++  + Gd Pll+e  +k+++++ + +  
    AJA93138.1  27 KPLVLHVVDALKNSNCFEK-IIAVTSPNSPQTQKILI---ENDVKIIETLGDNFVTDLNSILKK-LDDYVFVTSGDLPLLDENIVKQIVSASNPK-- 116
                   9******************.88988888877777664...344444555566677777777777.6777999***************99998877.. PP

                   SSEEEEEEETTSHHHHTS CS
  CTP_transf_3 121 dylstlvkkvgkeeevln 138
                    ++ t v+ ++++++ ln
    AJA93138.1 117 -KIWTSVVTTKSFQSSLN 133
                   .45666666666666555 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   1.4e-06    0.0042      33     114 ..      29     114 ..      12     126 .. 0.70
   2 ?   -2.3   0.1      0.68     2e+03      78      94 ..     158     174 ..     142     189 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
        CofC  33 mlldvidalkr...ld.vlvv.s...edeevleyaldelgvevvkek.ekdlntavekafeeieekeviiipsdiPlikkedvkdllelek 114
                 ++l v+dalk+    + ++ v s    + + +  + d++ +e++ ++   dln+ ++k      ++ v ++  d+Pl++++ vk+++  ++
  AJA93138.1  29 LVLHVVDALKNsncFEkIIAVtSpnsPQTQKILIENDVKIIETLGDNfVTDLNSILKKL-----DDYVFVTSGDLPLLDENIVKQIVSASN 114
                 55566666665332334333312111122333456778888999999889999999999.....899******************998765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.68
        CofC  78 avekafeeieekeviii 94 
                 +  k f ++ee+ +ii 
  AJA93138.1 158 TQIKNFDSVEEDYLIIN 174
                 33333444444444443 PP

>> DUF4851  Domain of unknown function (DUF4851)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.7e-05      0.26     141     177 ..      14      50 ..      11      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.7e-05
     DUF4851 141 aefrkvKlvlEYREPlpsalgeaakdaveagelpvie 177
                 ++  k Kl+lEY+ Pl+ ++ +a+k++  +++  ++ 
  AJA93138.1  14 MQSDKEKLLLEYKKPLVLHVVDALKNSNCFEKIIAVT 50 
                 556799*******************999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1216.76
//
Query:       AJA93139.1  [L=501]
Description: hypothetical protein T478_0432 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2958.77
//
Query:       AJA93140.1  [L=478]
Description: IMP dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.4e-146  485.8   7.3   7.3e-146  485.6   7.3    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    7.9e-22   77.5   2.1    9.1e-11   42.0   0.2    2.7  2  CBS           CBS domain
    4.6e-10   39.4   5.7      7e-06   25.6   3.6    2.3  2  NMO           Nitronate monooxygenase
    4.7e-06   25.9   7.2    9.1e-06   24.9   7.2    1.7  1  FMN_dh        FMN-dependent dehydrogenase
    1.9e-05   24.3   3.7     0.0043   16.5   0.1    3.0  3  His_biosynth  Histidine biosynthesis protein
    0.00028   20.2   0.6    0.00028   20.2   0.6    2.0  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.017   14.5   3.1      0.018   14.3   0.2    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
      0.048   12.8   4.0      0.088   11.9   4.0    1.5  1  Glu_synthase  Conserved region in glutamate synthase
      0.069   12.6   0.5       0.15   11.5   0.2    1.7  2  PEP_mutase    Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.6   7.3  3.7e-149  7.3e-146       1     345 []       6     473 ..       6     473 .. 0.98

  Alignments for each domain:
  == domain 1  score: 485.6 bits;  conditional E-value: 3.7e-149
                 E--GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS................ CS
                 xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
       IMPDH   1 gltfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkrs................ 82 
                 g+tfddvllvp++s+++++ +++l+t+l+++iklniPlvsa+mdtvtes+mA+++ar+Ggig+ih+ l+iee+ae+v kvkrs                
  AJA93140.1   6 GFTFDDVLLVPKFSDITSRsQTNLSTNLSRNIKLNIPLVSANMDTVTESTMATTMARQGGIGIIHRFLTIEEEAEQVLKVKRSgsvmidnpyqisseks 104
                 68****************989****************************************************************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
       IMPDH  83 ................................................................................................... 82 
                                                                                                                    
  AJA93140.1 105 ieeaidlmnekevsgllvvdpdsklvgvlterdvlfesinskksvselmtkdvissnenttldeakdilkshrieklplvndknhivglyttqdilnie 203
                 *************************************************************************************************** PP

                 ..TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STT CS
                 ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH  83 ..pnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsi 179
                   pna+kd+kgr lvgaavgvk d l+r +al+ ag+d++vvd+ahghse+ +++vk+ikk+++++e+iaGnvata+g+++Li+ag+davkvG+G+Gsi
  AJA93140.1 204 nfPNASKDKKGRPLVGAAVGVKGDFLDRTEALLGAGADAIVVDIAHGHSENAISTVKNIKKAFPDCELIAGNVATAQGTEDLIKAGVDAVKVGVGSGSI 302
                 *************************************************************************************************** PP

                 BHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 180 CttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryf 278
                 C+trv++g GvpqltAv+++ae+ kk+++p+i+DGG ++sgd +kAlaaGa++vmlGs+l gt+Espg++i+ +g++yK y Gm+slga +++++++ +
  AJA93140.1 303 CITRVITGSGVPQLTAVMDCAEIGKKYDIPIISDGGTRTSGDATKALAAGASSVMLGSMLGGTDESPGSTITKNGKRYKFYSGMASLGAARRRKSKEVT 401
                 ******************************************************************************************776566555 PP

                 -...-....-SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                 x.xxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 279 q.kke....klvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                 q ++e     +v+eGve++vpykg+v +++ q++gg+rsg++y+G ++i++++++a+f+++++ag++es++H
  AJA93140.1 402 QaDTEddlnDYVAEGVEAMVPYKGTVIDILVQITGGIRSGLSYCGGHDIKQMQTNAEFIKMSRAGFAESQPH 473
                 6322245779*************************************************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.2   4.6e-14   9.1e-11       2      53 ..      89     140 ..      87     143 .. 0.94
   2 !   34.2   0.1   1.3e-11   2.7e-08       1      53 [.     149     201 ..     149     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 4.6e-14
                 HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                 g++m +++  ++ + ++eea++lm ek+vs+l+VVd d klvG++t+rD+l 
  AJA93140.1  89 GSVMIDNPYQISSEKSIEEAIDLMNEKEVSGLLVVDPDSKLVGVLTERDVLF 140
                 57999*******************9999*******9999***********95 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 1.3e-11
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                 V+++mt+dv++ +++ttl ea ++++++++  lP V++ +++vG+ t  D+l+
  AJA93140.1 149 VSELMTKDVISSNENTTLDEAKDILKSHRIEKLPLVNDKNHIVGLYTTQDILN 201
                 89***********************9999*******99999**********96 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.3e-05     0.026       4      78 ..      33     110 ..      30     175 .. 0.80
   2 !   25.6   3.6   3.5e-09     7e-06     138     239 ..     271     376 ..     206     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
         NMO   4 ltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvka....ltdkPfgvnlflpkkdaad 78 
                 l+  +k + p+v + m  +++  +a   + +Gg+G++    lt  + a+++ kvk+    ++d+P+++    + ++a d
  AJA93140.1  33 LSRNIKLNIPLVSANMDTVTESTMATTMARQGGIGIIH-RFLTIEEEAEQVLKVKRsgsvMIDNPYQISSEKSIEEAID 110
                 666788899****************************9.99***99999*99999744445677887766555555555 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3.5e-09
         NMO 138 vliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvp.....qvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkes 231
                 ++ + +++++    ++++G Da+ v G  +G    t+ + + g  +L +     ++ +  diP+i  GG  +  +   aLa+GAs v +g+ + +t+es
  AJA93140.1 271 LIAGNVATAQGTEDLIKAGVDAVKV-GVGSGSICITRVITGSGVPQLTAvmdcaEIGKKYDIPIISDGGTRTSGDATKALAAGASSVMLGSMLGGTDES 368
                 345679999999999999**99766.77777766666665555444433000114555566************************************** PP

         NMO 232 dakdahkk 239
                 + + ++k+
  AJA93140.1 369 PGSTITKN 376
                 **999985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   7.2   4.6e-09   9.1e-06     204     300 ..     255     359 ..      44     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.6e-09
                 -HHHHHHHHHHHS.SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT---HHHCHHHHHHHH......SS-EEEESS--SHHHHHHHHHT CS
      FMN_dh 204 twddikwlreqtk.lplvvKGvltaedakraveaGvdgivvSNHGG.....RqldgapatidvLpeiveavg..g..rievlvDgGirrGsDvlkAlal 292
                   +++k+++++ +  +l+   v ta+  + +++aGvd++ v    G     R + g  + +  L ++++ ++  +  +i+++ DgG r+  D+ kAla 
  AJA93140.1 255 AISTVKNIKKAFPdCELIAGNVATAQGTEDLIKAGVDAVKVGVGSGsicitRVITG--SGVPQLTAVMDCAEigKkyDIPIISDGGTRTSGDATKALAA 351
                 45577888887765788888999******************999996666655544..34444545544333212368********************* PP

                 T-SEEEES CS
      FMN_dh 293 GAdavllG 300
                 GA+ v+lG
  AJA93140.1 352 GASSVMLG 359
                 *******9 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.3    0.0011       2.2      29     102 ..     226     296 ..     220     311 .. 0.79
   2 !   16.5   0.1   2.2e-06    0.0043      65     105 ..     322     362 ..     307     421 .. 0.83
   3 ?   -1.5   0.1      0.71   1.4e+03      72      84 ..     428     440 ..     414     442 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                   TSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEES CS
  His_biosynth  29 gdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviig 102
                   gd ++  +++  +gad + vvD+  a+ ++e+ ++ v++i +++     + G + + +  e+l++ag+d v +g
    AJA93140.1 226 GDFLDRTEALLGAGADAI-VVDI--AHGHSENAISTVKNIKKAFPDCELIAGNVATAQGTEDLIKAGVDAVKVG 296
                   566666666666777765.78**..8999999***********6555556777***************966554 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.2e-06
                   HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
  His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                    +ei ++ +ip+  +GG r+  d++++l aga+ v++g++ 
    AJA93140.1 322 CAEIGKKYDIPIISDGGTRTSGDATKALAAGASSVMLGSML 362
                   46889999******************************985 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.71
                   -SSEEEEESSSSS CS
  His_biosynth  72 vfipvqvGGGIrs 84 
                   ++i vq+ GGIrs
    AJA93140.1 428 IDILVQITGGIRS 440
                   6788999999997 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.43   8.6e+02     230     275 ..     255     298 ..     252     311 .. 0.79
   2 !   20.2   0.6   1.4e-07   0.00028     240     277 ..     328     363 ..     308     376 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.43
                 HHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH CS
      DHO_dh 230 alkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvyta 275
                 a+ ++ +++k +  +  +I+ G + +++   + i+aG  +v+v+ +
  AJA93140.1 255 AISTVKNIKKAFP-DCELIA-GNVATAQGTEDLIKAGVDAVKVGVG 298
                 6777777777776.778886.99999*99999*****999998865 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.4e-07
                 HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHH CS
      DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalv 277
                 +   +ipiI+ GG  ++ Da   + aGAs v +++ l 
  AJA93140.1 328 KY--DIPIISDGGTRTSGDATKALAAGASSVMLGSMLG 363
                 44..5*****************************9985 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.33   6.6e+02     194     224 ..     236     266 ..     216     284 .. 0.75
   2 ?   14.3   0.2   9.2e-06     0.018     167     208 ..     322     363 ..     297     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.33
                 HHTT-SEEEESHHHHTSSSHHHHHHHHHHHH CS
        ThiG 194 melGadavllntavaeakdpvamArafklav 224
                 +  Gada++++ a  ++++ ++  + +k+a 
  AJA93140.1 236 LGAGADAIVVDIAHGHSENAISTVKNIKKAF 266
                 56899******99999999999988888874 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.2e-06
                 HHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
        ThiG 167 lkiiieeakvPvivDAGigspsdaaqamelGadavllntava 208
                    i ++ ++P+i D G +++ da++a+  Ga++v+l + + 
  AJA93140.1 322 CAEIGKKYDIPIISDGGTRTSGDATKALAAGASSVMLGSMLG 363
                 45677899****************************988765 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   4.0   4.4e-05     0.088     222     304 ..     284     360 ..     239     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                   HHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
  Glu_synthase 222 gvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                    + ka++d++++  +  G     + +i  +G+P ++a+        e g +  + +i dGg +t+ d  kala GA +v +g+
    AJA93140.1 284 DLIKAGVDAVKVG-VGSGS-ICITRVITGSGVPQLTAVMDCA----EIGKKYDIPIISDGGTRTSGDATKALAAGASSVMLGS 360
                   2566666766663.22222.3456788999****99998875....56888899*************************9997 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   7.5e-05      0.15     158     224 ..     228     300 ..     219     311 .. 0.72
   2 ?   -2.6   0.0       1.6   3.1e+03     164     174 ..     347     357 ..     313     378 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
  PEP_mutase 158 aieRaraYaeAGAdgvfvpglqkdae.....iaelvaav.dvplnvvplkgtlsvaelaelGvarislgnhll 224
                  ++R +a + AGAd+++v  ++  +e     ++++ +a+ d+ l++    ++  +++l ++Gv  + +g    
  AJA93140.1 228 FLDRTEALLGAGADAIVVDIAHGHSEnaistVKNIKKAFpDCELIAGNVATAQGTEDLIKAGVDAVKVGVGSG 300
                 589**************9877444333101255555666446665555455799************9997665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.6
  PEP_mutase 164 aYaeAGAdgvf 174
                   ++AGA+ v+
  AJA93140.1 347 KALAAGASSVM 357
                 33445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2795.31
//
Query:       AJA93141.1  [L=367]
Description: putative ferrous iron transport protein B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-29   99.7   2.9    1.8e-28   98.6   2.9    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      4e-23   81.7   0.0    1.3e-22   80.0   0.0    1.9  1  MMR_HSR1      50S ribosome-binding GTPase
    2.9e-21   75.3   0.1    1.1e-20   73.5   0.0    2.0  2  TGS           TGS domain
      2e-16   59.9   4.4    9.5e-14   51.2   0.2    2.6  3  FeoB_N        Ferrous iron transport protein B
    2.7e-07   30.6   3.2    0.00069   19.6   0.1    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00023   21.2   4.4      0.089   12.8   0.4    3.1  3  Dynamin_N     Dynamin family
     0.0019   17.7   1.6       0.12   11.9   0.1    2.4  2  Arf           ADP-ribosylation factor family
     0.0065   15.9   0.1     0.0065   15.9   0.1    2.1  2  SRPRB         Signal recognition particle receptor beta subun
     0.0074   15.9   6.3      0.082   12.5   0.4    2.7  3  Ras           Ras family
  ------ inclusion threshold ------
      0.022   13.7   0.5       0.13   11.2   0.3    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.033   14.4   0.5       0.18   12.0   0.1    2.2  2  AAA_33        AAA domain
      0.079   13.2   0.5       0.28   11.4   0.0    2.2  2  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.087   13.1   0.3      0.087   13.1   0.3    2.1  2  AAA_28        AAA domain
       0.11   12.8   0.4       0.61   10.5   0.1    2.3  2  AAA_16        AAA ATPase domain
       0.13   11.9   0.0       0.26   10.9   0.0    1.5  1  GSHPx         Glutathione peroxidase


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   2.9   1.5e-31   1.8e-28       1     105 [.     184     290 ..     184     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.5e-31
  MMR_HSR1_Xtn   1 kgGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare..pnsvviSaekelnlde 95 
                   +gGi ++++vkl+k++e+  k+il+ y++++a+v+ired++ ++l+d+i+gn++Y +++++lNKiDl++++ +++++++   + +++Sa++++n++e
    AJA93141.1 184 TGGIAVAQQVKLKKMSEKLLKEILNIYGYTSARVVIREDIESEQLVDFINGNKTYAKAITILNKIDLVDDKFVKDVSKKlkTDFIPTSADSNKNINE 280
                   59***************************************************************************96547*************** PP

  MMR_HSR1_Xtn  96 LkekiweeLn 105
                   Lke+i++eL+
    AJA93141.1 281 LKERIYNELQ 290
                   ********97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   1.1e-25   1.3e-22       2      92 ..      66     156 ..      65     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.1e-25
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkp 92 
                 v+++G p vGKStL+n+ltg+k+ v+++++tT++++ g ++++g +i+++D+pG+i+gas++kglgk++l++ + ad++llv+d+  + +++
  AJA93141.1  66 VVFIGLPSVGKSTLLNRLTGSKSAVGAFQFTTLTVVPGVMNYRGARIQVLDLPGIIKGASTGKGLGKRILSVARsADIVLLVLDVF-QPYHE 156
                 89*********************************************************************99978********88.43433 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.8   3.4e+03      12      30 ..     249     267 ..     246     270 .. 0.74
   2 !   73.5   0.0   8.8e-24   1.1e-20       1      60 []     292     365 ..     292     365 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                 EEETTB-HHHHHHHHSTTH CS
         TGS  12 dlprgatveDfAykIhrsl 30 
                 dl   + v+D+ +k+++++
  AJA93141.1 249 DLVDDKFVKDVSKKLKTDF 267
                 5556667899999999886 PP

  == domain 2  score: 73.5 bits;  conditional E-value: 8.8e-24
                 EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEEE CS
         TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIvt 60 
                 irvy+ P+G + d      +++g tv D+++k+hr l+k+f+ +lV+G       qrvgl+hvL d+dv++I++
  AJA93141.1 292 IRVYLrPKGGETDfkepliVRKGNTVTDVCNKLHRNLKKDFRFGLVWGksvkfggQRVGLKHVLIDEDVLTIIK 365
                 89**********************************************************************97 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       3.1   3.7e+03     122     149 ..      29      56 ..      17      58 .. 0.72
   2 !   51.2   0.2   7.9e-17   9.5e-14       2     107 ..      65     169 ..      64     219 .. 0.85
   3 !   10.2   0.1   0.00034       0.4     106     156 .]     239     285 ..     225     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                 TEEE-HHHHHHHHTS-EEEEBTTTTBTH CS
      FeoB_N 122 gieidlkkLsekLgvpvvktsakkkegi 149
                  ++  ++kL+++ + + vk sakk++g+
  AJA93141.1  29 LLKAKIAKLKREQEAEQVKKSAKKQDGF 56 
                 4566778899999999999999999886 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 7.9e-17
                 EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEGGGHHHHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdvvvnvvdatnlernLyLtl 99 
                 tv+++G p vGk+tl+n+ltg+k+ vg ++ +t     g ++++g +++++DlPGi  ++  s+ + + +++l   +++d+v+ v+d  +   + +L++
  AJA93141.1  65 TVVFIGLPSVGKSTLLNRLTGSKSAVGAFQFTTLTVVPGVMNYRGARIQVLDLPGI--IKGASTGKGLGKRILSvARSADIVLLVLDVFQPYHEDVLIT 161
                 799****************************************************9..789999999999999757889*********99999999999 PP

                 HHHHTTSS CS
      FeoB_N 100 qllelgvp 107
                 +l ++g++
  AJA93141.1 162 ELGNIGIR 169
                 99888765 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00034
                 SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
      FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                 ++ + +ln+id +++k +    k +s+kL+++ ++tsa ++++i+el+++i
  AJA93141.1 239 AKAITILNKIDLVDDKFV----KDVSKKLKTDFIPTSADSNKNINELKERI 285
                 678899999999998875....68999********************9976 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   5.8e-07   0.00069      67     125 ..      33      88 ..       8      97 .. 0.74
   2 !   11.3   0.5   0.00019      0.23      44     101 ..     236     289 ..     189     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.8e-07
                  HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
  RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                  ++++  ++ + e ++ sak+++g++   ++  d t+v++G   vGKStL+n+l+++ + 
   AJA93141.1  33 KIAKLKREQEAEQVKKSAKKQDGFD--VKRTGDATVVFIGLPSVGKSTLLNRLTGS-KS 88 
                  4455556666777777777777776..3566789*******************998.44 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00019
                  HTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSE CS
  RsgA_GTPase  44 ekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdkt 101
                  ++ ++ + +lnKiDl++++     +k+  ++l ++++ +sa+++++++elke++ +++
   AJA93141.1 236 KTYAKAITILNKIDLVDDKF----VKDVSKKLKTDFIPTSADSNKNINELKERIYNEL 289
                  556788899*********99....667777788899***************9998876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3         4   4.8e+03      59      79 ..      28      48 ..       5      56 .. 0.47
   2 !   12.8   0.4   7.5e-05     0.089       1      25 [.      66      90 ..      66     102 .. 0.79
   3 !    8.5   0.0    0.0016       1.9     102     138 ..     111     150 ..     103     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4
                T-EB--CHHHHHHHHHHHHHH CS
   Dynamin_N 59 ekkledfsevreeieketeki 79
                     ++ ++++e+e+e+ k+
  AJA93141.1 28 GLLKAKIAKLKREQEAEQVKK 48
                333344444444444444443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.5e-05
                EEEEEBTTTTHHHHHHHHHTS--S- CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilp 25
                ++++G  S GKS++ln L+g++  +
  AJA93141.1 66 VVFIGLPSVGKSTLLNRLTGSKSAV 90
                7899****************98544 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0016
                 SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEET CS
   Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsa 138
                 ++ ++DlPG+++ +   +   + + + +++adi+l+v++ 
  AJA93141.1 111 RIQVLDLPGIIKGASTGKglgKRILSVARSADIVLLVLDV 150
                 68899*******9999998999999999*********986 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   9.7e-05      0.12      14      67 ..      63     119 ..      51     123 .. 0.74
   2 ?    4.7   0.2     0.015        18     102     145 ..     226     268 ..     194     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                 EEEEEEEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEEE-S CS
         Arf  14 elrilllGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwDvGG 67 
                 ++ ++++GL + GK+T+l++l+  + +    +  T+      +++++ +++v D+ G
  AJA93141.1  63 DATVVFIGLPSVGKSTLLNRLTGSKSAVgafQFTTLTVVPGVMNYRGARIQVLDLPG 119
                 6789*****************987765444333444444445667888888888766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.015
                 HHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGS CS
         Arf 102 eeLkalleeeelkevallvlaNKqDlpealseeelrellgleel 145
                 e+L  +++ ++   ++ + + NK+Dl ++   ++++++l+ + +
  AJA93141.1 226 EQLVDFINGNKT-YAKAITILNKIDLVDDKFVKDVSKKLKTDFI 268
                 556666665554.45566778****************9987765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4       2.6   3.1e+03     138     173 ..      24      57 ..      10      60 .. 0.56
   2 !   15.9   0.1   5.4e-06    0.0065       4      60 ..      64     121 ..      61     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                 HHHHHHHHHCHHHHHH------T....T-------- CS
       SRPRB 138 EkElnkiierrskalkeldeeedksavlakkgkdFk 173
                 E+ ++ + + + + lk   +e +++ + akk ++F+
  AJA93141.1  24 EHHIGLL-KAKIAKLKRE-QEAEQVKKSAKKQDGFD 57 
                 4444433.4455555554.44444555566666776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.4e-06
                 -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-G CS
       SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGhe 60 
                  +v+++Gl   GK +l++rLt  +           +++  v + +g +++++D+PG  
  AJA93141.1  64 ATVVFIGLPSVGKSTLLNRLTGSKSAVGAFQFtTLTVVPGVMNYRGARIQVLDLPGII 121
                 589*****************988655555555366677777899************65 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       6.9   8.3e+03     129     145 ..      36      52 ..      10      56 .. 0.60
   2 !    6.4   0.1    0.0052       6.2       2      22 ..      66      86 ..      65     101 .. 0.89
   3 !   12.5   0.4   6.9e-05     0.082     104     159 ..     238     288 ..     188     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.9
                 HHHHHHTSEEEEEBTTT CS
         Ras 129 elakelglkfletSAkt 145
                 +l +e++++ ++ SAk+
  AJA93141.1  36 KLKREQEAEQVKKSAKK 52 
                 34444444555555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0052
                EEEEESTTSSHHHHHHHHHHS CS
         Ras  2 lvlvGdsavGKtslllrfvkd 22
                +v++G  +vGK++ll+r + +
  AJA93141.1 66 VVFIGLPSVGKSTLLNRLTGS 86
                799*************98865 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 6.9e-05
                 TSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
         Ras 104 nvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellre 159
                   + + + nK+Dl +      + +++++k+l++ f+ tSA +n+n++e+ e++ +e
  AJA93141.1 238 YAKAITILNKIDLVD-----DKFVKDVSKKLKTDFIPTSADSNKNINELKERIYNE 288
                 345555666676665.....555678899*******************98888776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00011      0.13      24      55 ..      59      89 ..      38     112 .. 0.81
   2 ?   -0.5   0.0       0.4   4.7e+02     199     232 ..     259     292 ..     220     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
        MeaB 24 akaGraqvvGltGvPGaGkstlvealglelrr 55
                +++G a+vv + G+P +Gkstl+++l+ +  +
  AJA93141.1 59 KRTGDATVV-FIGLPSVGKSTLLNRLTGSKSA 89
                689999988.67*************9866555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.4
                 TBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHH CS
        MeaB 199 kekeWrpkvlktsavegeGidelvdaieehrevl 232
                  +k+ ++  + tsa+ ++ i+el ++i +  +++
  AJA93141.1 259 VSKKLKTDFIPTSADSNKNINELKERIYNELQFI 292
                 4777888899999999999*99999998766655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.18       2      22 ..      66      86 ..      65      98 .. 0.88
   2 ?   -0.3   0.0       0.9   1.1e+03      34      64 ..     264     293 ..     208     316 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
      AAA_33  2 vllvGlpGsGKstlaerllkk 22
                v+++Glp +GKstl+ rl   
  AJA93141.1 66 VVFIGLPSVGKSTLLNRLTGS 86
                79**************99755 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.9
      AAA_33  34 rrrlfgtdqqsktdytrvldrlyqilnelar 64 
                 ++   +t  +s ++ +++++r+y+ l +++r
  AJA93141.1 264 KTDFIPTSADSNKNINELKERIYNEL-QFIR 293
                 22222244444445555666666666.5555 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.28       2      24 ..      66      88 ..      65     117 .. 0.85
   2 ?   -2.3   0.0       4.1   4.9e+03     100     119 ..     230     249 ..     199     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                EEEESSTTSSHHHHHHCHCT-CC CS
         Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                vv++G  +vGK++ll+r++ +k 
  AJA93141.1 66 VVFIGLPSVGKSTLLNRLTGSKS 88
                89****************97765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.1
                 HHHHHHCSSS-EEEEEE-TT CS
         Roc 100 kelkkvagkspvilvgnkiD 119
                 + ++ + + +++i + nkiD
  AJA93141.1 230 DFINGNKTYAKAITILNKID 249
                 44555555667788888888 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.9   2.3e+03      28      69 ..      12      51 ..       5      56 .. 0.66
   2 ?   13.1   0.3   7.3e-05     0.087       2      20 ..      66      84 ..      65     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.9
      AAA_28 28 pEaareileeklakgedalpwvedllafaervleeqleeeaa 69
                 E++r+ l++ ++ + + l++  ++ ++++++++eq+++ a+
  AJA93141.1 12 DEIHRTQLNKATEHHIGLLKA--KIAKLKREQEAEQVKKSAK 51
                688888888888887776665..5777777777777665554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.3e-05
      AAA_28  2 ivitGgestGKTtlleaLa 20
                +v++G +s GK+tll++L+
  AJA93141.1 66 VVFIGLPSVGKSTLLNRLT 84
                9*****************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00051      0.61      20      45 ..      60      84 ..      37     102 .. 0.76
   2 ?   -1.6   0.0       2.6   3.2e+03     124     149 ..     132     156 ..     116     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
      AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                r+g+   v+++G + vGKs+l+++l 
  AJA93141.1 60 RTGD-ATVVFIGLPSVGKSTLLNRLT 84
                3344.7899*************9986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
      AAA_16 124 krllallsrderplvlvlDdlqwade 149
                 kr+l+ +++ ++ ++lvlD +q   e
  AJA93141.1 132 KRILSVARS-ADIVLLVLDVFQPYHE 156
                 466677777.6669999999995555 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.26      33      97 ..     185     252 ..     168     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                 STTHH.HHHHHHHHHHHHGGGTEEEEEEEE-TTTT---S-GGGHHHTSSHT..TT-SSEEB--BBSSS CS
       GSHPx  33 Cglte.qykeleelqkrykdkglvilgfPCnqfgkqepgsdeeikkfrqgk..yevtfellekievnG 97 
                  g++  q  +l+++ +++ ++ l i g+   +   +e  + e++  f +g+  y    ++l+ki+   
  AJA93141.1 185 GGIAVaQQVKLKKMSEKLLKEILNIYGYTSARVVIREDIESEQLVDFINGNktYAKAITILNKIDLVD 252
                 4444448899*************************************998778***********9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2538.95
//
Query:       AJA93142.1  [L=313]
Description: NAD(P)H-binding protein, PF13460 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-30  105.8   0.0      3e-30  105.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.7e-24   86.2   0.1    1.2e-23   84.1   0.1    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.3e-18   67.1   0.0    1.8e-18   66.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.9e-15   56.8   0.1    2.7e-15   56.3   0.1    1.3  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    8.3e-14   51.2   0.1    1.2e-13   50.7   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    5.8e-07   29.6   0.0    8.2e-07   29.1   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.9e-06   27.6   0.0    8.1e-06   26.1   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    2.6e-05   23.5   0.5    0.00086   18.6   0.5    2.7  1  NAD_binding_4    Male sterility protein
    0.00016   21.6   0.0    0.00054   19.9   0.0    1.8  1  KR               KR domain
     0.0036   15.6   0.0      0.005   15.1   0.0    1.1  1  Mesothelin       Pre-pro-megakaryocyte potentiating factor pr
     0.0096   15.5   0.0      0.016   14.7   0.0    1.4  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.034   14.2   0.1    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.038   14.7   0.0       0.28   11.9   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
      0.086   12.3   0.0       0.15   11.5   0.0    1.5  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   0.0   2.3e-33     3e-30       1     241 []       4     237 ..       4     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 2.3e-33
                 EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHHHSHHHHHHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl........elveldltdrsalerlfkeeqpdavihlAavggvaassedpadfiek 90 
                 i++ G++G+iG+ l+++lle++ ++++ +drl  +  ++ +  +        ++++ d+++ + ++ +++    d+v++lAa  g +   ++p++ ++ 
  AJA93142.1   4 IILSGGAGYIGTKLTEHLLENTdHTIVIVDRLDFKLDENFK--KntysnnrvSFHKEDIRNLDFMNSIIE--SNDYVVNLAALVGEPLCKIKPEEAVDV 98 
                 6789******************999*******554444444..344889999******************..67********9999999********** PP

                 HTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHH CS
   Epimerase  91 nlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipal 189
                 n++ + nl+  ++++++k++++ls+++ YG+ +e+    + ++g+l p+s Ya +K+  ek + +    +  na+ilr+ + yG   g  + + +++ +
  AJA93142.1  99 NFEAAKNLAILCKEKNIKKFIQLSTCSNYGQAKEM----VDEDGELFPTSLYAETKVNLEKFLIK----NIPNATILRCATAYGLSVGRMRFDLLVSDF 189
                 ******************************88884....44456899**************9996....44678************888888999999* PP

                 HHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEEES CS
   Epimerase 190 irkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyniG 241
                 i+ + ++k ++ ++   +  R+ ++v+D+ +ai l ++h   gd  ++yn+G
  AJA93142.1 190 IKEAWLEK-QINVFM-PEVHRPIVHVSDISTAISLCIDH--HGDLSRVYNVG 237
                 ******99.999997.7899*******************..788899****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   9.1e-27   1.2e-23       3     332 .]       7     297 ..       5     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 9.1e-27
                    ETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHH CS
  GDP_Man_Dehyd   3 TGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAAqshVdvsfekPeyt 98 
                     G+aG+iG  l+e+Lle+  + ++iv+r +  +   +++  k++    ++++++hk D+++ + +++++++   d v+nLAA    +    kPe+ 
     AJA93142.1   7 SGGAGYIGTKLTEHLLENTDHTIVIVDRLDF-K---LDENFKKNT-YSNNRVSFHKEDIRNLDFMNSIIESN--DYVVNLAALVGEPLCKIKPEEA 95 
                    6****************98877777666543.2...333333333.45789********************9..9**********99999****** PP

                    HHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCC CS
  GDP_Man_Dehyd  99 aevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvt 194
                    ++vn+ ++ +L  ++++ ++   ++f+q St   YG+++e  ++E+  + P+s Ya +K+  + + ++   +  +  +       ++   g+    
     AJA93142.1  96 VDVNFEAAKNLAILCKEKNI---KKFIQLSTCSNYGQAKE-MVDEDGELFPTSLYAETKVNLEKFLIKNIPNATILRC----ATAYGLSVGRMRFD 183
                    ***************99776...59************985.679****************988777655554455555....55555555555566 PP

                    CHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGC CS
  GDP_Man_Dehyd 195 rkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvv 290
                     ++++++ ++ l+kq  +++   +  R   hv+D+ +a+ l + +           ++++v++ ++     ++++i  +              + +
     AJA93142.1 184 LLVSDFIKEAWLEKQ--INVFMPEVHRPIVHVSDISTAISLCIDHHG------DLSRVYNVGSSNQNY---TKREIAEK-------------VSSR 255
                    89999**99999886..555667779***************998765......467888888766633...33333222.............2234 PP

                    CCEECGG--SS--SB--B-THHHHHHH----SS-HHHHHHHH CS
  GDP_Man_Dehyd 291 vevdpkyfrpgevdlllgdaskakeeLgWkpkvsfeelvrem 332
                     +v  + + +++ + ++ + +++k+eL+++ k+  e++++em
     AJA93142.1 256 LNVPLNIVEKEDKRDYIVNFDRIKNELNFSTKFLAEDGIEEM 297
                    555556677788899999999999999999999999999998 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.4e-21   1.8e-18       2     252 ..       3     277 ..       2     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.4e-21
                    EEEEESTTSHHHHHHHHHCTT.TSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlae.eglevlaltre.....................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaay 75 
                    ki++ G+ G +G++L++ l e  ++ ++ ++r                      + d+++ + +++++++   d vvn+AA      +  ++e+a 
     AJA93142.1   3 KIILSGGAGYIGTKLTEHLLEnTDHTIVIVDRLdfkldenfkkntysnnrvsfhKEDIRNLDFMNSIIES--NDYVVNLAALVGEPLCKIKPEEAV 96 
                    7999************988772455555556669**********************************99..789********************* PP

                    HHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESS.....SSS-HHHHHHH CS
  RmlD_sub_bind  76 avnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvyge.....kgknfvktmlr 165
                     vn ea+++lA ++++ ++ ++i++St   + G++k+   ed e  P ++Y++tK++ E+   ++ ++a+i+R +  yg      +   +v+ +++
     AJA93142.1  97 DVNFEAAKNLAILCKEKNIkKFIQLSTCSNY-GQAKEMVDEDGELFPTSLYAETKVNLEKFLIKNIPNATILRCATAYGLsvgrmRFDLLVSDFIK 191
                    ******************846******8877.777888****************************************875544333446899999 PP

                    HHHH-SEEEEESS-EE--.EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-.EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS-- CS
  RmlD_sub_bind 166 lakereelkvvaDqlgsP.TsardlAevllqllekaaeekelagvyHlanege.tswlefArailkeagadseevkpistaeyptpAkR 252
                     a  +++++v+   + +P  ++ d++ ++   +++  +   l++vy ++++++  ++ e+A+++ +++++  + v+  ++ +y  + +R
     AJA93142.1 192 EAWLEKQINVFMPEVHRPiVHVSDISTAISLCIDHHGD---LSRVYNVGSSNQnYTKREIAEKVSSRLNVPLNIVEKEDKRDYIVNFDR 277
                    9999**************44789999999988888876...89****98877769************9998888888877777666666 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1   2.1e-18   2.7e-15       1     128 [.       4     123 ..       4     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.1e-18
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      ++++G++G iG +l++++l+++ ++i++++r ++kl+e  k++  ++++++++++      d+r+ + +++++e  + d+v++ AAl   Pl+ 
       AJA93142.1   4 IILSGGAGYIGTKLTEHLLENTDHTIVIVDRLDFKLDENFKKN--TYSNNRVSFH----KEDIRNLDFMNSIIE--SNDYVVNLAALVGEPLCK 89 
                      6789********************************9877776..5677778777....78*************..9***************** PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliSt 128
                       +p ea++ N  +++n++  ++e+++kk++ +St
       AJA93142.1  90 IKPEEAVDVNFEAAKNLAILCKEKNIKKFIQLST 123
                      *********************************9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.1   9.4e-17   1.2e-13       3     159 ..       7     159 ..       5     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 9.4e-17
   3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdv.agkltedeimkvnvkGTr 97 
                  GgaG++G +l ++L++  + +++ ++D    + +++ ++++ + n+ ++++ D+++ d ++  +e+ d v+ la+lv     k++ +e  +vn +  +
  AJA93142.1   7 SGGAGYIGTKLTEHLLENTD-HTIVIVDrldFKLDENFKKNTYSNNRVSFHKEDIRNLDFMNSIIESNDYVVNLAALVGEpLCKIKPEEAVDVNFEAAK 104
                 6***************9997.5555555433888888888888889999**************************9875415589************** PP

   3Beta_HSD  98 nvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                 n+   c+++++++++  S+++  g+   ++e++  dE+ e    +++ y+e+K   Ek+++k
  AJA93142.1 105 NLAILCKEKNIKKFIQLSTCSNYGQ---AKEMV--DEDGE--LFPTSLYAETKVNLEKFLIK 159
                 ************************9...99999..56544..45778999999999987765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   6.4e-10   8.2e-07       1     144 [.       8     170 ..       8     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.4e-10
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHH.HH....CTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.....--TCC.......HHHH. CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklae.le....aeeglevvegdvtdvedlaealkgadaVvsal.....ggggk.......deeg. 77 
                     G+ G +G +l+++ll++++h+++++ R   kl+e ++    ++++++  + d+ + + + + ++  d Vv  +                    + 
      AJA93142.1   8 GGAGYIGTKLTEHLLENTDHTIVIVDRLDFKLDEnFKkntySNNRVSFHKEDIRNLDFMNSIIESNDYVVNLAalvgeP---LckikpeeA--Vd 97 
                     999***************99999888877677531223334679***********************876666344440...255554331..14 PP

                     .....HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCC.HHHHHHHHHHHHHHHHSSSEEEEEEE- CS
  NAD_binding_10  78 .....aknivdaakeagvkRfvlvsaigvgdevpgefgewnkell.kaylaakraaeellrasgldwTivrpg 144
                          akn++  +ke+++k+f+ +s+   + ++++ ++e  + +  + y++ k   e+ l +   + Ti+r +
      AJA93142.1  98 vnfeaAKNLAILCKEKNIKKFIQLSTCSNYGQAKEMVDEDGELFPtSLYAETKVNLEKFLIKNIPNATILRCA 170
                     45566*********************99998888888887666551444566888899998888888888875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   6.3e-09   8.1e-06       5      77 ..       9      80 ..       4      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.3e-09
                     --SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
  Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkegdlvvnls 77
                     GaG++G  ++e l+++ d+  +i+++dr + kl++ ++k   ++ r+++++ d+ n +  + ++++++d vvnl+
       AJA93142.1  9 GAGYIGTKLTEHLLENTDH--TIVIVDRLDFKLDENFKKNtySNNRVSFHKEDIRNLDF-MNSIIESNDYVVNLA 80
                     88*****************..9**************99889999**************9.*************98 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   6.7e-07   0.00086       1     149 [.       6     136 ..       6     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.7e-07
                    EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHHHHHHHH--EEEE--S CS
  NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedlqelaeevdviihsaA 96 
                    l G+ G++G+ L e LL++t++ +i+++ R +       +l+e+++    ++       +r+++ + D+ + ++      ++ ++e+ d +++ aA
     AJA93142.1   6 LSGGAGYIGTKLTEHLLENTDH-TIVIVDRLDF------KLDENFK----KNTY---SNNRVSFHKEDIRNLDF------MNSIIESNDYVVNLAA 81 
                    5699999999999999999874.5555444332......2322222....2222...47789999999988776......788999********** PP

                    S-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--S CS
  NAD_binding_4  97 tvn...fdepykellrvNveGtrevlelakklkklkvllhvST..ayvngeregevee 149
                     v     + + +e+++vN e+++++  l+k+ + +  +++ ST   y   + ++ v+e
     AJA93142.1  82 LVGeplCKIKPEEAVDVNFEAAKNLAILCKEKNIK-KFIQLSTcsNYG--QAKEMVDE 136
                    **73324447889*****************77666.*******63333..33334443 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.2e-07   0.00054       3     139 ..       4     126 ..       2     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.2e-07
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                  ++ GG+G +G++l+++l+e+  +++v++ R    d + ++++++ + ++ +v++ + D+ + d +++++e+ +        v++ A ++ + l + + 
  AJA93142.1   4 IILSGGAGYIGTKLTEHLLENTDHTIVIVDRL---DFKLDENFKKNTYSNNRVSFHKEDIRNLDFMNSIIESND-------YVVNLAALVGEPLCKIKP 92 
                 5789***************************9...4444557888889999******************99876.......578888877766655555 PP

                 HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHH CS
          KR 102 aedleqvlapKvkGawnLhelledesldffvlfSSiag 139
                 +e+++      +++a+nL  l+++++++ f+ +S +++
  AJA93142.1  93 EEAVDV----NFEAAKNLAILCKEKNIKKFIQLSTCSN 126
                 544443....4566888888888888888888887776 PP

>> Mesothelin  Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-06     0.005      56     124 ..      77     145 ..      61     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX CS
  Mesothelin  56 snlaslspslllgftcaevsglsiervkelavalkqknitlradqlrclarrlskhlapedldalpldl 124
                  nla+l  + l+ +  +e  ++  e +k+la+  k+kni+   +   c     +k +++ed + +p  l
  AJA93142.1  77 VNLAALVGEPLCKIKPEEAVDVNFEAAKNLAILCKEKNIKKFIQLSTCSNYGQAKEMVDEDGELFPTSL 145
                 6899************************************9999999*****************99877 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.016       1     225 [.       4     256 ..       4     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S.....-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.............S-HHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt.....kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.............skeied 81 
                 I+  G++G++G  ++++ll++  ++ ++v  +     ++ + ++ +++ v + k+d+ + + ++++++  d v    ++              + + e 
  AJA93142.1   4 IILSGGAGYIGTKLTEHLLENTDHTIVIVDRLdfkldENFKKNTYSNNRVSFHKEDIRNLDFMNSIIESNDYVVNLAALVgeplckikpeeavDVNFEA 102
                 6677****************777777777766477655556666777888888*******************9998888789999****9999999999 PP

                 HHHHHHHHHHHS-SEEE....EEE---GG.GT....SSS---TTTHHHHHHHHHHHHCTS-EEEEEE.-EEGGG-BS....SS-SS-BEEE-TTS.-EE CS
        NmrA  82 gkklvdAakeaGvkhfi....ySslgddndrs...naeepavphfdsKaeieeyvralgipytfvya.gffmenfls....llaqlkvgdtappedkvt 168
                  k+l+   ke  +k+fi     S++g++++ +      +p     ++K++ e+ + +   ++t++++ +++   + +    ll+  ++++    e++++
  AJA93142.1 103 AKNLAILCKEKNIKKFIqlstCSNYGQAKEMVdedGELFPTSLYAETKVNLEKFLIKNIPNATILRCaTAYGLSVGRmrfdLLVSDFIKEAW-LEKQIN 200
                 ****************9555535566555444110344566555678999999887776677877551566544433111144443444444.445899 PP

                 EEESS-TTS-EE-HHHHHHHHHHHHHHHHHHH.TTEEEEE-SEEE-HHHHHHHHHHHH CS
        NmrA 169 llgpgnpkavlldaeeDiGafvikilkdprkl.kgkriklagntlsgneivelfekki 225
                 + +p+    ++++++ Di +++   +++  +l  +  +  +++ ++  ei+e  + ++
  AJA93142.1 201 VFMPEV--HRPIVHVSDISTAISLCIDHHGDLsRVYNVGSSNQNYTKREIAEKVSSRL 256
                 999988..5666799*************99998888899999999***9999887765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.6e-05     0.034      19      93 ..       9      80 ..       1     121 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                  S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HH CS
  Shikimate_DH 19 GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepileke 93
                  GaG +++++++hLl+++ + +v++ R   +   l e++k++ ++  +++  ke +++ d + s + s++++++ +
    AJA93142.1  9 GAGYIGTKLTEHLLENTDHTIVIVDRLDFK---LDENFKKNTYSNNRVSFHKEDIRNLDFMNSIIESNDYVVNLA 80
                  9*************************8876...566777778889999999999999999999999999998765 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.28       7      69 ..       9      77 ..       5     107 .. 0.76
   2 ?   -0.7   0.0       1.9   2.4e+03      51      91 ..     168     208 ..     148     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                     TTSHHHHHHHCTS..T.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTT...TEEEEE CS
  Methyltransf_25  7 GtGrltlalakrl..g.kakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedg...sfDlvv 69
                     G G +  +l ++l  + +++++ vD  +  l++  +++  ++ +v+f++ d+++l+f ++   s D+vv
       AJA93142.1  9 GAGYIGTKLTEHLleNtDHTIVIVDRLDFKLDENFKKNTYSNNRVSFHKEDIRNLDFMNSiieSNDYVV 77
                     566666666666554248********99999888888878888************99553222556665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                      EESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHH CS
  Methyltransf_25  51 vqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiar 91 
                      +++ a  l+    +fDl vs +  + + ++++  ++ e++r
       AJA93142.1 168 RCATAYGLSVGRMRFDLLVSDFIKEAWLEKQINVFMPEVHR 208
                      56677778888999999999555444445667777777766 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.15       3      70 ..       4      72 ..       2     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
   adh_short  3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvek 70
                ++  G+++ IG ++ ++l+++  +++v vdr + kl e  k+    ++++ + + D+++ + ++ ++e 
  AJA93142.1  4 IILSGGAGYIGTKLTEHLLENTDHTIViVDRLDFKLDENFKKNTYSNNRVSFHKEDIRNLDFMNSIIES 72
                788899999***********98888888***********999888899**********99999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2190.70
//
Query:       AJA93143.1  [L=99]
Description: hypothetical protein T478_0808 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-09   38.0   5.9    1.6e-09   37.9   5.9    1.0  1  Ribosomal_S25   S25 ribosomal protein
     0.0041   17.0   0.1     0.0041   17.0   0.1    1.8  2  MarR            MarR family
     0.0046   16.5   0.1     0.0062   16.1   0.1    1.2  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0082   15.9   0.1      0.016   15.0   0.1    1.5  1  LacI            Bacterial regulatory proteins, lacI family
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.018   14.9   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.033   12.6   2.8      0.035   12.5   2.8    1.0  1  SID-1_RNA_chan  dsRNA-gated channel SID-1
      0.047   13.6   0.0      0.056   13.4   0.0    1.2  1  DUF977          Bacterial protein of unknown function (DUF977
      0.097   12.6   0.0       0.13   12.2   0.0    1.2  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   5.9   7.1e-13   1.6e-09       4      99 ..       4      95 ..       1      97 [. 0.86

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.1e-13
  Ribosomal_S25  4 kakkakaaaakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvskhraqviYt 99
                   k k  +++++++ggk k KK  k+ + dk +  v++++e  +k++   ++ k it   ++ + ++++s A ++L++ +++g +k+v   + ++iY 
     AJA93143.1  4 KNKSVSSSEKSQGGKDKAKK-DKKDHSDKKEVDVFINEEQANKII---KSSKAITIQDLARQANVKISTANAFLKKALAEGAVKKVGGFSGHYIYQ 95
                   55666666777888887555.577778888889***********8...5789******************************************95 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       0.7   1.6e+03      51      59 .]      26      34 ..      25      34 .. 0.87
   2 !   17.0   0.1   1.8e-06    0.0041      11      47 ..      46      82 ..      45      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.7
                EETTSTTSE CS
        MarR 51 kspeDrRev 59
                k+++D++ev
  AJA93143.1 26 KDHSDKKEV 34
                899****98 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.8e-06
                HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
        MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                i++++ ++++++La++ +v++st+  +l++   +G +
  AJA93143.1 46 IIKSSKAITIQDLARQANVKISTANAFLKKALAEGAV 82
                7999************************997777766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.8e-06    0.0062      18      48 .]      53      83 ..      45      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
      HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                i++++LA++ ++ +st n+ lk+   eG +k
  AJA93143.1 53 ITIQDLARQANVKISTANAFLKKALAEGAVK 83
                9***********************9999775 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   7.3e-06     0.016       1      23 [.      54      76 ..      54      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.3e-06
                -HHHHHHHCTS-HHHHHHHCTTS CS
        LacI  1 tikDVArlAGVSkaTVSrvLnnk 23
                ti+D+Ar+A+V  +T+  +L+++
  AJA93143.1 54 TIQDLARQANVKISTANAFLKKA 76
                9***************9999986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   8.1e-06     0.018      20      65 ..      50      97 ..      39      99 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-06
                HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE- CS
        TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYrav 65
                ++  t++++a++++v  s+++  L++ +  G V+++ g    ++Y+++
  AJA93143.1 50 SKAITIQDLARQANVKISTANAFLKKALAEGAVKKVGGFsgHYIYQPA 97
                677899*****************************9865668888876 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.8   1.5e-05     0.035     161     222 ..       6      67 ..       1      82 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
  SID-1_RNA_chan 161 sesaseslesvssavrsesessveeesdydtleeiesdknvirtkkvlvvsdlsrkdkrvle 222
                     ++ +s+++++  +   ++++++ +++++ d++ + e+ +++i++ k+++++dl+r+ + + +
      AJA93143.1   6 KSVSSSEKSQGGKDKAKKDKKDHSDKKEVDVFINEEQANKIIKSSKAITIQDLARQANVKIS 67 
                     3344444555555566667777779*****************************97765543 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05     0.056      20      60 ..      46      86 ..      26      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
      DUF977 20 lvkkneritisdleritGvgrtsvrkylvdvlerGdlirpG 60
                ++k  + iti+dl r   v+  +++ +l+ +l+ G + + G
  AJA93143.1 46 IIKSSKAITIQDLARQANVKISTANAFLKKALAEGAVKKVG 86
                6899999****************************987766 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.8e-05      0.13      21      54 ..      52      85 ..      36      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 21 dltvgelarrlglsksavsrilkrLvaaGLverr 54
                 +t+++lar  +++ s+++  lk++ a G v ++
  AJA93143.1 52 AITIQDLARQANVKISTANAFLKKALAEGAVKKV 85
                38***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2082  (0.116125); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 781.85
//
Query:       AJA93144.1  [L=146]
Description: hypothetical protein T478_0909 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.3   0.0      0.071   12.9   0.0    1.4  1  RVT_3     Reverse transcriptase-like


Domain annotation for each model (and alignments):
>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     4e-06     0.071      34      99 ..      44     109 ..      15     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
       RVT_3  34 lqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirkllk 99 
                  ++  s+++A + ++ +GL +        + v +Dsk  ++ ++g ek++++ ++  +  i++l +
  AJA93144.1  44 KNNEESRFVALHVGIYWGLGVNIIKNNDVVNVMCDSKIMFEIMTGAEKIDNDIINDKVYFINQLTN 109
                 57788999*********************************************9999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1115.64
//
Query:       AJA93145.1  [L=448]
Description: nucleotide sugar dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-40  138.9   0.3    3.3e-40  137.7   0.1    1.7  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    3.9e-22   78.7   0.0    2.2e-21   76.2   0.0    2.1  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    3.4e-21   75.2   0.1    6.6e-21   74.3   0.1    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    2.8e-06   26.8   0.1      0.081   12.3   0.0    3.2  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    0.00012   22.3   0.0    0.00047   20.4   0.0    2.0  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00036   20.5   0.1       0.01   15.8   0.0    2.9  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0032   17.5   0.8        4.6    7.4   0.1    3.2  3  DpaA_N          Dipicolinate synthase subunit A N-terminal do
     0.0036   17.2   0.0     0.0094   15.8   0.0    1.7  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0054   17.0   0.2      0.011   16.0   0.2    1.4  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.029   14.0   0.0    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.072   13.4   0.2        1.1    9.6   0.0    2.7  3  TrkA_N          TrkA-N domain
      0.082   12.3   0.1       0.17   11.2   0.1    1.5  1  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.7   0.1   2.2e-43   3.3e-40       2     183 ..      17     198 ..      16     202 .. 0.95
   2 ?   -2.1   0.0       1.6   2.4e+03      51      84 ..     306     339 ..     293     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 137.7 bits;  conditional E-value: 2.2e-43
                     EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS-.-TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-TTTTCB CS
  UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy.epgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskkkgkaa 95 
                     k++viG G +Gl+ta+ +a+ g e igvDi+e+ v+++nsgk+p+  epg +++  ++++++++s+tt++ekav ++d+++++ +TP+++ ++ +
      AJA93145.1  17 KVCVIGIGRIGLPTALSFAKSGLETIGVDINESLVQNINSGKFPLKdEPGYDKIFDDVIKNKKFSATTNIEKAVPNSDLVLLSLPTPMDE-NNVP 110
                     8*******************************************9659******************************************.9999 PP

                     -THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE------TTSHHHHHHS-S-EEEEESSCHHHHH CS
  UDPG_MGDP_dh_N  96 DlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnPEflregsavkdllnpdrvviGveekkaeaa 183
                     D +++ ++  +++e+l+ +++v+v+ST+ +g  e+ + +++ + ++ k + +f + ++PE  ++g++++d+ n +r v+G +++ ++ +
      AJA93145.1 111 DYSALRTVGMKLSEVLSPNSLVIVESTIEPGFIEDEMVSLISKSDRLKiNDNFFIGVCPENANPGEILHDFTNLPRLVGGINQNITQ-I 198
                     *********************************99999999988888889******************************9988766.4 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                     HHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-- CS
  UDPG_MGDP_dh_N  51 LeelvkkavesgrlsfttdvekaveeadvifiaV 84 
                     ++e + ++v +  l + ++++++++ea ++++ +
      AJA93145.1 306 INEKMPEHVINLTLDGFQECNQNIKEATILILGI 339
                     4556666666788889999999999999999876 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.3e+03      51      73 ..      77      99 ..      58     117 .. 0.75
   2 !   76.2   0.0   1.5e-24   2.2e-21       1     104 [.     335     431 ..     335     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                    BTCCEEES-CHHHHTT-SEEEE- CS
  UDPG_MGDP_dh_C 51 ekgvevvdsleealkgadaivil 73
                    +k+ + ++++e+a+ ++d++++ 
      AJA93145.1 77 NKKFSATTNIEKAVPNSDLVLLS 99
                    45677788999999999999875 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 1.5e-24
                     EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-E CS
  UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpav 95 
                     +ilG+++K++++D+  +pa  ii++L+e g+ v iyDP++k+ +v       g+++ ++l++ + ++da++i+t hdefk+l+l+k+ + mk+++
      AJA93145.1 335 LILGISYKPNVKDIQLTPAEIIIKKLQELGVTVCIYDPYFKDVDVF------GIKSEKNLDDIIPNVDAAIIVTGHDEFKKLELSKFSQ-MKNKI 422
                     69****************************************8874......799*******************************965.***** PP

                     EEESSS-CC CS
  UDPG_MGDP_dh_C  96 vfDgrnvld 104
                     ++D+r++++
      AJA93145.1 423 LIDTRGIIE 431
                     ******987 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   4.4e-24   6.6e-21       1      93 [.     218     308 ..     218     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.4e-24
  UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgleaelleavrevNe 93 
                   +tA ++Kl+ N+f++++I++i ela ++e+lgid++ V+ea++++ +  +++++pg GvGG clp   ++L+++a++ + +++++e+ r++Ne
    AJA93145.1 218 KTANAVKLTTNVFRDINIAYISELALMFEKLGIDTNIVLEAAKKKYN--FQVHYPGSGVGGPCLPINSYQLLNTARRTNSNLSIIESGRKINE 308
                   589******************************************99..79*****************************************8 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   5.4e-05     0.081      35      70 ..      14      49 ..       4      63 .. 0.85
   2 ?    1.3   0.0      0.13     2e+02      79     108 ..      79     109 ..      66     121 .. 0.72
   3 !    9.0   0.0   0.00055      0.83      51     120 ..     356     421 ..     353     429 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                  TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
  2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                  +  +v++iG+GrIG  +a  +++ g++ i++d +++
    AJA93145.1 14 KSLKVCVIGIGRIGLPTALSFAKSGLETIGVDINES 49
                  56689***************************9876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                   TC.EECSHHHHHHH-SEEEE-S--STTTTTS CS
  2-Hacid_dh_C  79 gv.elvsleellaesDivslhlpltpetrhl 108
                   ++   +++e+++ +sD v l lp   + +++
    AJA93145.1  79 KFsATTNIEKAVPNSDLVLLSLPTPMDENNV 109
                   33246799**************987666665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00055
                   HHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTT CS
  2-Hacid_dh_C  51 vakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhlinaeelakmkkg 120
                   ++k+l+++g+ v +yd++ k+   ++  g++ + +l++++ + D  ++++   ++  + ++ +++++mk++
    AJA93145.1 356 IIKKLQELGVTVCIYDPYFKD---VDVFGIKSEkNLDDIIPNVDAAIIVTG--HDEFKKLELSKFSQMKNK 421
                   7899**************883...6688885555**********9877665..333444677778888865 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.1e-07   0.00047       1      94 [.      17     140 ..      17     150 .. 0.93
   2 ?   -2.1   0.0       2.5   3.7e+03      15      26 ..     357     368 ..     305     406 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.1e-07
                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....................EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....................akaaesieelvasldvvitmvkagkavdevieg 75 
                    k+ +iG+G +G + al ++k+g ++++++ +++ v+++ + +                     ++a+++ie++v + d+v++ ++   + ++v + 
     AJA93145.1  17 KVCVIGIGRIGLPTALSFAKSGLETIGVDINESLVQNINSGKfplkdepgydkifddviknkkFSATTNIEKAVPNSDLVLLSLPTPMDENNVPDY 112
                    689****************************9999999988899*******************9********************999998888777 PP

                    .........HCCC--TT-EEEE-S---H CS
  NAD_binding_2  76 .........llealkkgdilidgstssp 94 
                             l e l++++++i  st++p
     AJA93145.1 113 salrtvgmkLSEVLSPNSLVIVESTIEP 140
                    77888888899999***********987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                    HHHHHHTT-EEE CS
  NAD_binding_2  15 alnllkagykva 26 
                    +++l++ g +v+
     AJA93145.1 357 IKKLQELGVTVC 368
                    334444444455 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     7e-06      0.01       1      82 [.      17     105 ..      17     156 .. 0.83
   2 ?    1.0   0.0      0.26   3.8e+02      34      79 ..     296     341 ..     286     357 .. 0.85
   3 ?   -1.8   0.0       1.8   2.7e+03      57     108 ..     382     432 ..     376     441 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7e-06
                     -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS.......SBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHH CS
  NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineeh.......envkyLpgiklpenlvattdlaealkgadiivlvvPsqal 82 
                     k++v+G G  G   A ++a+ g e+     +e l+++in+ +          k ++++  +++  att++++a+ ++d+++l +P+ + 
      AJA93145.1  17 KVCVIGIGRIGLPTALSFAKSGLETIGVDINESLVQNINSGKfplkdepGYDKIFDDVIKNKKFSATTNIEKAVPNSDLVLLSLPTPMD 105
                     79************************************986522211113456788899999***********************8654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                     HHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---H CS
  NAD_Gly3P_dh_N  34 lieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPs 79 
                      +  i++ ++ ++ +p++ ++ +l   ++ ++ +k+a+i++l ++ 
      AJA93145.1 296 NLSIIESGRKINEKMPEHVINLTLDGFQECNQNIKEATILILGISY 341
                     566777778878889999***********************99975 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.8
                     EEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE.ET CS
  NAD_Gly3P_dh_N  57 lvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi.ee 108
                     ++ +++l++ + ++d  ++v  +  +++   +l+++ + k ++++ ++Gi e+
      AJA93145.1 382 IKSEKNLDDIIPNVDAAIIVTGHDEFKKL--ELSKFSQMKNKILIDTRGIiEP 432
                     56778889999999999999999988876..5666666667777777777544 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0     0.004       5.9      34      93 ..      75     133 ..      67     157 .. 0.79
   2 ?   -1.8   0.0       2.2   3.3e+03      45      60 ..     325     340 ..     300     350 .. 0.63
   3 !    7.4   0.1    0.0031       4.6      14      57 ..     356     400 ..     353     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.004
                 S-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BSS-SS-EE-HHHHHTS-TT-EEE CS
      DpaA_N  34 ekiegvekaesleealedadviilPvpgtkdggeintpfseeklsleelleklkkgqllf 93 
                  k++++  ++++e+a+ ++d+++l +p   d++++   +s+ + +  +l e l++++l++
  AJA93145.1  75 IKNKKFSATTNIEKAVPNSDLVLLSLPTPMDENNVPD-YSALRTVGMKLSEVLSPNSLVI 133
                 5678889999*****************9999999998.5555544467777777777765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                 GGS-GGG-SEEE--TT CS
      DpaA_N  45 leealedadviilPvp 60 
                  ++ +++a ++il + 
  AJA93145.1 325 CNQNIKEATILILGIS 340
                 3444555555555554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0031
                 HHHHHHHTT-EEEEE..S-TSSS-BTTEEEE-GGGS-GGG-SEEE- CS
      DpaA_N  14 larkLaekgakvsly..gleleekiegvekaesleealedadviil 57 
                 +++kL+e g +v++y   + ++    g++ +++l++ + ++d+ i 
  AJA93145.1 356 IIKKLQELGVTVCIYdpYF-KDVDVFGIKSEKNLDDIIPNVDAAII 400
                 79*************5444.5666669***********99999885 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.3e-06    0.0094       1      82 [.      17      96 ..      17     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.3e-06
                EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH.C-SEE CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav.dadlv 82
                kv viG G +G   a  fa++gle+  vdi+e+ +++ ++     l+      k+ ++ +    ++ s+tt++e+av + dlv
  AJA93145.1 17 KVCVIGIGRIGLPTALSFAKSGLETIGVDINESLVQNINSGKF-PLKDEPGYDKIFDDVI--KNKKFSATTNIEKAVpNSDLV 96
                699****************************998887655433.3444444444442222..234455556666666666655 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   7.3e-06     0.011       3      43 ..     220     260 ..     219     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.3e-06
  NAD_binding_11   3 GqavKlvnnlllainlaaasEalvlaekaGldpekvlevin 43 
                     ++avKl  n+   in+a +sE  ++ ek+G+d + vle+ +
      AJA93145.1 220 ANAVKLTTNVFRDINIAYISELALMFEKLGIDTNIVLEAAK 260
                     689*********************************99865 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.9e-05     0.029       1      88 [.      18     112 ..      18     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                 EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT.CEEEEEECEEECCH.....SCCCCS-ESEEEE-SSGGGHHHHHHHH CS
        ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg.geeilrppealsae.....ekselepidlvivtvKayqteealeei 88 
                 ++++G+G iG   a + ak g + + ++ ++  ++++++  + l++e   ++i+ +  +  +       ++   + dlv++++++  +e+++ ++
  AJA93145.1  18 VCVIGIGRIGLPTALSFAKSGLETIGVDINEsLVQNINSGKFPLKDEPgYDKIFDDVIKNKKFsattnIEKAVPNSDLVLLSLPTPMDENNVPDY 112
                 69**********************************************7444444444433335556656678999*****99999888887776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00071       1.1       1      38 [.      18      55 ..      18      63 .. 0.86
   2 ?   -3.5   0.0       8.2   1.2e+04      99     114 ..     239     254 ..     219     256 .. 0.73
   3 ?   -0.0   0.0      0.67     1e+03      61      76 ..     393     408 ..     391     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH CS
      TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelr 38
                + +iG Gr+G   a  + ++g + +++d +e+ v+++ 
  AJA93145.1 18 VCVIGIGRIGLPTALSFAKSGLETIGVDINESLVQNIN 55
                579****************6535*********999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.2
                 GGGHHHHHHHTTSEEE CS
      TrkA_N  99 pehaellkklgadvvi 114
                 +e a +++klg+d+ i
  AJA93145.1 239 SELALMFEKLGIDTNI 254
                 4556678888888765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.67
                 GGESEEEE-SSSHHHH CS
      TrkA_N  61 ekadaviaatgddean 76 
                  ++da i++tg+de++
  AJA93145.1 393 PNVDAAIIVTGHDEFK 408
                 688999****999865 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.17      17      47 ..      14      44 ..       4      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                HTSEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 17 rdskvllvGaGglGsellknLalsGvgkltl 47
                ++ kv+++G+G +G + +  +a+sG++ + +
  AJA93145.1 14 KSLKVCVIGIGRIGLPTALSFAKSGLETIGV 44
                468***********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3267.32
//
Query:       AJA93146.1  [L=237]
Description: signal peptidase I [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-07   29.3   0.3    6.1e-07   29.3   0.3    2.0  2  Peptidase_S24    Peptidase S24-like
     0.0091   16.2   4.9      0.028   14.6   0.8    2.2  2  TrbC             TrbC/VIRB2 family
  ------ inclusion threshold ------
      0.012   15.9   0.5      0.028   14.7   0.0    1.9  2  MscL             Large-conductance mechanosensitive channel, 
      0.023   13.5   0.1      0.034   12.9   0.1    1.2  1  Ureide_permease  Ureide permease
       0.14   12.4   2.1       0.59   10.5   0.1    2.2  2  Sigma_reg_N      Sigma factor regulator N-terminal
       0.17   10.2   0.4       0.23    9.8   0.4    1.3  1  SID-1_RNA_chan   dsRNA-gated channel SID-1
       0.29   12.1   5.8       0.25   12.3   0.9    2.4  2  DUF4834          Domain of unknown function (DUF4834)


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   2.4e-10   6.1e-07       2      46 ..      39      91 ..      38     109 .. 0.84
   2 ?   -2.4   0.1       1.8   4.7e+03      42      56 ..     161     175 ..     151     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.4e-10
                   XXSSTTCCTXXTTXEEEEE...CTS---TTSEEEEEETTCE.....-EEEEEE CS
  Peptidase_S24  2 vpGdSMeptlldGdlilVd...kfsepkrGdivvfrlpgee.....eayiKrv 46
                   v ++SM p l+  d+i+V+   +f+++++Gdi+vf  p+       +++++rv
     AJA93146.1 39 VSSGSMIPALEVYDVIVVEgntPFEDIEKGDIIVFYSPKLYeqgkeRVIVHRV 91
                   89*****************777777**********777655555567777777 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                    EEEEEEEETTEEEEE CS
  Peptidase_S24  42 yiKrviglpgdrvll 56 
                     +K + g++++++++
     AJA93146.1 161 VVKHFAGKEKKKIEF 175
                    688888888888874 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.8   1.1e-05     0.028      46      73 ..       5      32 ..       1      45 [. 0.87
   2 ?    3.3   0.2     0.037        95      45      73 ..     140     168 ..     136     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
        TrbC 46 vdfltgplakviatiaiivaGimlafgr 73
                +++l ++++++++ ia+i++G++++fg 
  AJA93146.1  5 TKSLIKDVVIIVVAIAVIWLGLQAVFGT 32
                7899999*******************97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.037
        TrbC  45 ivdfltgplakviatiaiivaGimlafgr 73 
                 i++ l+ p+ ++i+ ++i v+ ++ ++g+
  AJA93146.1 140 ITQILQPPINYIIIAVIIGVMVVKHFAGK 168
                 78999999888888888877766666665 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.3   3.4e+03      38      46 ..      12      20 ..       3      48 .. 0.57
   2 ?   14.7   0.0   1.1e-05     0.028      68      95 ..     140     183 ..     101     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
        MscL 38 iimpligll 46
                ++  ++++ 
  AJA93146.1 12 VVIIVVAIA 20
                332222222 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-05
        MscL  68 ygafiqavinFliiafvi.Flivkaink...............k 95 
                 + +++q  in++iia++i  ++vk +                 +
  AJA93146.1 140 ITQILQPPINYIIIAVIIgVMVVKHFAGkekkkiefqytkdssE 183
                 46788999**********99999887764333333333322220 PP

>> Ureide_permease  Ureide permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.3e-05     0.034     100     165 ..     141     210 ..     129     232 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
  Ureide_permease 100 aeilfpGvacfliavllgsavhssnaadnkeklskskseekeetkeeekkeeesekkkee....kdleeg 165
                      ++il p +   +iav++g +v +  a  +k+k++ + ++ ++e +e  +++ee++ ++++    k++ ++
       AJA93146.1 141 TQILQPPINYIIIAVIIGVMVVKHFAGKEKKKIEFQYTKDSSEVNEPDNNSEENKDESTDntlhKEIADD 210
                      58999****************9999999999998665555555444333333332222221222222222 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.21   5.3e+02      10      30 ..       6      26 ..       5      35 .. 0.71
   2 ?   10.5   0.1   0.00023      0.59      24      62 ..     151     191 ..     148     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
  Sigma_reg_N 10 ksilrivlislivlllifvil 30
                 ks+++ v+i+++++ +i++ l
   AJA93146.1  6 KSLIKDVVIIVVAIAVIWLGL 26
                 677887888888888777766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
  Sigma_reg_N  24 llifvil.vvtllylaekegnkl.revlelaveitsPNvyv 62 
                  ++i vi+ v+  +++a ke++k+  +++++ +e+ +P+   
   AJA93146.1 151 IIIAVIIgVMVVKHFAGKEKKKIeFQYTKDSSEVNEPDNNS 191
                  55666666***************888899999999998664 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4     9e-05      0.23     116     200 ..     129     212 ..      74     236 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9e-05
  SID-1_RNA_chan 116 ksvyvvavllvllvllsfllltllvvivekvre................sseekrvkessssesaseslesvssavrsesessveeesdydtlee 194
                     + +yvv+ + +++ +l + + +++++++  v+                 +                +++++v+ +++++se++ +e++d+   +e
      AJA93146.1 129 QVEYVVPQVGYITQILQPPINYIIIAVIIGVMVvkhfagkekkkiefqyT----------------KDSSEVN-EPDNNSEENKDESTDNTLHKE 206
                     44567777666666666555555554444333322233332233322220................2222222.233333333333333333333 PP

  SID-1_RNA_chan 195 iesdkn 200
                     i  d++
      AJA93146.1 207 IADDSD 212
                     332222 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.17   4.4e+02      12      33 ..      12      33 ..       8      43 .. 0.80
   2 ?   12.3   0.9   9.7e-05      0.25      15      88 ..     151     218 ..     139     235 .. 0.43

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.17
     DUF4834 12 iailviglsilsvilrtvfglg 33
                ++i+v+++++++  l++vfg++
  AJA93146.1 12 VVIIVVAIAVIWLGLQAVFGTS 33
                5678888888888888888865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.7e-05
     DUF4834  15 lviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetkeegeiieeersekeakrkkiFekd 88 
                 ++i+++i  ++++ + g+ ++k +  +++k+ +++ n++ ++s++++ +++++ + ++e   +  ++ k Fe++
  AJA93146.1 151 IIIAVIIGVMVVKHFAGKEKKKIEF-QYTKD-SSEVNEPDNNSEENKDESTDN-TLHKEIADD--SD-KSFENN 218
                 3444444444444443433333333.33333.333333333332222222222.222221111..12.444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1616  (0.0901333); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1741.44
//
Query:       AJA93147.1  [L=731]
Description: translation elongation factor aEF-2 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-59  201.2   0.6    1.9e-59  200.5   0.6    1.4  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    2.9e-22   78.5   0.0      1e-21   76.7   0.0    2.0  2  EFG_C            Elongation factor G C-terminus
      8e-21   73.9   0.7    1.9e-20   72.7   0.7    1.7  1  EFG_II           Elongation Factor G, domain II
    1.7e-18   66.5   0.0    1.3e-17   63.7   0.0    2.4  2  EFG_IV           Elongation factor G, domain IV
    1.3e-13   51.1   0.2    3.9e-13   49.6   0.2    1.9  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    0.00098   19.2   0.0     0.0026   17.8   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.39   10.4   0.0    1.6  1  E3_UbLigase_EDD  E3 ubiquitin ligase EDD


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.6   7.4e-63   1.9e-59       2     183 ..      19     243 ..      18     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 7.4e-63
                 CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEE CS
    GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..ketkkylinliDtPGHvdFskevirglrvlDgav 98 
                 +irn+g+i+hvDhGKtT++d+Ll+++g+is   ++a+++ ++D++k+E+ergiTi  a+++l+  ++ ++y in+iDtPGHvdFs  vir+lr++Dgav
  AJA93147.1  19 KIRNFGVIAHVDHGKTTMSDSLLAHSGIISP--STAGSALAMDSMKAEQERGITIVQANVTLHyqQDDDDYVINMIDTPGHVDFSGRVIRSLRAIDGAV 115
                 79*****************************..67788899*********************975699******************************* PP

                 EEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH................HHHHHHHHHTTTTTEEEEEEBTTTTBTH CS
    GTP_EFTU  99 lvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk................eeklekygekgekevpvvfgSalkgegv 181
                 +v+daveG+++qte+v r+ l+e+v++++ iNK+Drl++el+ ++e+++++l  +                +ek+++      ++ +v fgSa++++++
  AJA93147.1 116 VVCDAVEGIMTQTETVTRMSLEERVRPVLYINKIDRLIKELRLTPEKMQETLAGVvanfnelidtyaedeyKEKWKVSI----QDGSVTFGSAKDKWAI 210
                 ****************************************************777999977777666544444444444....5667**********88 PP

                 H...............................H CS
    GTP_EFTU 182 k...............................t 183
                 +                               +
  AJA93147.1 211 NvdimkkkgvtfndvieaysdsgkvedlvekaP 243
                 866666666666655555555555555555550 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       6.6   1.7e+04      16      33 ..      99     116 ..      96     125 .. 0.79
   2 !   76.7   0.0   4.1e-25     1e-21       1      86 [.     620     704 ..     620     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.6
                 CCCCCHHHHHHHCT-EEE CS
       EFG_C  16 eyvgkvisdlssrrGeie 33 
                 +++g+vi +l +  G + 
  AJA93147.1  99 DFSGRVIRSLRAIDGAVV 116
                 789999999988777765 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 4.1e-25
                 EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE--HHHH CS
       EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevpgdkl 86 
                 vllEP+  +e++vp++++g+v s l+ +rG+++dm+q+ +++ i+ +e+P+ e+++ ++++r  T+G+++++++f+ + +vp++++
  AJA93147.1 620 VLLEPMLAIEVRVPTDLIGNVSSVLQGKRGKVLDMQQK-GATSIVIGEVPAVETFDISEKMRGQTAGKAMWNTHFKAWTPVPKSIA 704
                 59************************************.*******************************************9986 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   0.7   7.4e-24   1.9e-20       1      73 [.     387     458 ..     387     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 7.4e-24
      EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                 ++ePv+++aiepk  +d  kl ++L++l+ EDp l ++ dee++eti++GmG lHl+++v+ +k   kve+ +
  AJA93147.1 387 VSEPVVQMAIEPKHPKDLPKLVEVLRKLTIEDPNLVIKIDEESGETIMAGMGVLHLDVAVNLIKDA-KVEIVT 458
                 689*********************************************************999875.888876 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.36   9.1e+02       3      41 ..     463     495 ..     461     507 .. 0.62
   2 !   63.7   0.0   5.1e-21   1.3e-17      11     120 ..     511     617 ..     505     618 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                 CESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTT CS
      EFG_IV   3 VayrEtirkpvkereeklkkqsggdgqyakvileiePle 41 
                 ++yrEti+  ++    +++k     +   k+ +++ePle
  AJA93147.1 463 INYRETINGGCE---PVMAKS---PNRHNKIFMKVEPLE 495
                 899999999888...444443...223335555555554 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 5.1e-21
                 S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEEEEE--T..TTC-HHHHHH CS
      EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLldgslhe..vdsseaafkp 107
                 k++ke +++l + +g++++ ak++++++      gn++++ tkg+q  +e  ++   Gf e++ eG l++e+v+++k+t++  + he   +++ +++ p
  AJA93147.1 511 KDKKETAQILRD-KGWSPDVAKKVMRFDSR----GNVMINGTKGVQFVDESTDSLLSGFDEVMSEGGLTKEQVRNCKFTFTHFVPHEdtAHRGLSQIGP 604
                 677778888888.8**************95....9**************************************************************** PP

                 HHCHHHHHHHHCC CS
      EFG_IV 108 aarralkeallkA 120
                 a+rra+ +a+l+A
  AJA93147.1 605 ASRRACLAAFLSA 617
                 **********998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.2   1.5e-16   3.9e-13       1      73 [.     306     372 ..     306     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.5e-16
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  G va gr++sGt+k G+++ i   dt+++   +r++s+  f+ +++e+v +  aG+i a+ gl d +++G+t+
   AJA93147.1 306 GPVAIGRLFSGTIKDGQTINI--IDTKRE---GRVQSVNFFMSNVREQVGELGAGNIPALLGLTD-VRAGQTI 372
                  679******************..***999...*********************************.******9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     1e-06    0.0026       7     114 .]      28     148 ..      22     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1e-06
                 STTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE...ETTEE....EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEE CS
    MMR_HSR1   7 rpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk...lkgke....ielvDtpGliegaseekglgkaflaleeadlillv 82 
                 +   GK+t+  +l+                 +  +++++ g T+     +++       +    i+++DtpG ++        g+ +++l+  d +++v
  AJA93147.1  28 HVDHGKTTMSDSLLAhsgiispstagsalamDSMKAEQERGITIVQANVTLHyqqD---DddyvINMIDTPGHVD------FSGRVIRSLRAIDGAVVV 117
                 55668888888887533333343433333223556666666666666666653321...134459*******666......467777777778****** PP

                 EETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  83 vdaseeklkpldeeleelleeakkplilvlnk 114
                 +da  e++  + e++ ++  e++ + +l++nk
  AJA93147.1 118 CDAV-EGIMTQTETVTRMSLEERVRPVLYINK 148
                 **99.668888888888876655555666665 PP

>> E3_UbLigase_EDD  E3 ubiquitin ligase EDD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.39       6      25 ..     631     650 ..     627     655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
  E3_UbLigase_EDD   6 evPeeLieqvQvVLqgKSRq 25 
                      +vP +Li +v  VLqgK  +
       AJA93147.1 631 RVPTDLIGNVSSVLQGKRGK 650
                      69***************655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4756.91
//
Query:       AJA93148.1  [L=169]
Description: iron-sulfur cluster assembly accessory protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-22   80.2   0.0    1.6e-22   79.8   0.0    1.2  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.8   0.0   8.9e-27   1.6e-22       3     110 ..      63     163 ..      61     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 8.9e-27
                  EEE-HHHHHHHHHHHHCTTEC...EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGGGHHHS.TTEEEEEEEETTEEEEE CS
  Fe-S_biosyn   3 itlteaAaeklkkllaedkke...lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksyslvfldeglvldfvedlgtlgLk 97 
                  +t+t+ Aaek+k+++ae++++   lr++v+ gg       Cs g +y + + +e+ ee+d v+e ng+kv+v+s+s   l +g ++d+ e+l+++g+k
   AJA93148.1  63 VTITAPAAEKIKEFMAEEDGNpqyLRIYVQGGG-------CS-GLSYGMGFEKEA-EEDDRVIEENGVKVLVDSMSIDHL-NGANVDYIESLMGSGFK 150
                  79***************99888***********.......**.************.************************.***************** PP

                  EETCCEEEEEEEE CS
  Fe-S_biosyn  98 sdngilddnvglg 110
                   +n++++ ++++g
   AJA93148.1 151 INNPNVTKSCSCG 163
                  ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1288.43
//
Query:       AJA93149.1  [L=432]
Description: translation elongation factor EF-1, subunit alpha [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-46  156.7   0.0      7e-46  156.2   0.0    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      4e-35  120.5   0.1    8.6e-35  119.4   0.1    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.5e-16   60.5   0.2    6.2e-16   58.5   0.2    2.1  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.5e-05   24.8   0.8      4e-05   23.4   0.8    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.021   14.4   0.1    1.3  1  NIF3         NIF3 (NGG1p interacting factor 3)
      0.082   13.0   0.0        0.4   10.8   0.0    2.0  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   2.3e-49     7e-46       1     190 [.       4     220 ..       4     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 2.3e-49
                 TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST..............HCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
    GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv..............lDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                 k+++n++i gh+D GK+T++++ l+++g +++++ +a   e                  +D+ k+ErergiTi+ a  ++e  t k++++liD+PGH+d
  AJA93149.1   4 KPHLNMIITGHIDNGKSTTMGHFLMDLGVVDQRTIDAhaaE---SektgkgdtfkyawvMDNIKDERERGITIDLAFQKFE--TPKFNYTLIDAPGHRD 97 
                 579******************************99995542...2345899999***************************..**************** PP

                 GHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEE CS
    GTP_EFTU  83 FskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKmDrl...kaelkeiveevkqklsrkeeklekygekgekevpv 170
                 F+k++i+g++ +D+avlv++a+ G       +  q +e++ l++++gv  iiv+iNKmD     ++ +k  ve+ k  l      +++ g+k + evp+
  AJA93149.1  98 FIKNMITGASEADCAVLVLSAKPGetdtaiaPGGQAREHAFLLKTLGVGqIIVAINKMDDSnfaEDAYKAAVEKGK-GL------IKSCGYKPD-EVPF 188
                 *****************************99*****************99*********99665555555555555.55......8999***96.**** PP

                 EEEBTTTTBTHH............HHHHHHHH CS
    GTP_EFTU 171 vfgSalkgegvk............tllealve 190
                 +++S++kg+++             tllea+++
  AJA93149.1 189 IPVSGWKGDNLVkksenmgwysgkTLLEAFDD 220
                 *********87766667777777788888776 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.1   2.9e-38   8.6e-35       4     111 ..     321     426 ..     318     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.9e-38
                  EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE--TTTHCCCCEEEEECTTC CS
  GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpialekgseypqlGrFaiReggr 101
                   +++f+Aq++++++  +t+i  gY+pv++++ta+v+++++e+l k++++t+   e++p+f+k Gd++iv++++ +p  +e+++e+p++GrFa+R++g 
   AJA93149.1 321 VAKEFKAQIIVIHH--PTAIAPGYTPVMHAHTAQVAATITEFLGKINPQTGAMDEENPKFLKVGDSAIVKIRPVRPTPIETFQEFPEMGRFALRDMGA 416
                  689***********..********************************************************************************** PP

                  EEEEEEEEEE CS
  GTP_EFTU_D3 102 TvaaGvvtei 111
                  T+aaGvv+ei
   AJA93149.1 417 TIAAGVVKEI 426
                  ********99 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.2   2.1e-19   6.2e-16       1      73 [.     246     312 ..     246     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 2.1e-19
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  Gtv  grv++G +k+G+++++  ++++ +   ++i+s+e +h+++  a+ag+n+G+++++++ +d i++Gd+l
   AJA93149.1 246 GTVPVGRVETGLMKPGQKIVV--MPSGAQ---GEIKSIESHHAELPSAEAGDNIGFNLRGIEKKD-IKRGDVL 312
                  99*******************..666677...9********************************.******9 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.8   1.3e-08     4e-05      21      85 ..     250     312 ..     240     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                  EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-EE CS
  GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdil 85 
                  vG +v +G +kpg k++       Gei++i++++ +l  a+aG++++  ++g    ++ik gd+l
   AJA93149.1 250 VG-RVETGLMKPGQKIVVMPSGAQGEIKSIESHHAELPSAEAGDNIGFNLRGIE-KKDIKRGDVL 312
                  88.9**********9876544477***************************965.899**99998 PP

>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   7.1e-06     0.021       5      66 ..     278     339 ..     274     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
        NIF3   5 vleelaplelaeswDnvGlqvg.dpek..evkkvllaldlteevleeAiekgadliithHPlifk 66 
                 + +  a+l  ae  Dn+G+ +    +k  +   vl + d+ ++v++e ++   + i+ hHP+ + 
  AJA93149.1 278 IESHHAELPSAEAGDNIGFNLRgIEKKdiKRGDVLGTPDAPPAVAKEFKA---QIIVIHHPTAIA 339
                 556689999**********99854444245556***********888765...********9764 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013       0.4      22      87 ..      61     122 ..       8     154 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                 STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT..T CS
    MMR_HSR1  22 ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvdas..e 87 
                 ++ + +++ g T+d  + ++++ + +++l+D pG  +    +  +++ +    ead ++lv++a+  e
  AJA93149.1  61 DNIKDERERGITIDLAFQKFETPKFNYTLIDAPG--H----RDFIKNMITGASEADCAVLVLSAKpgE 122
                 34555666788888888888877788********..3....234666666677789999999866431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2959.37
//
Query:       AJA93150.1  [L=346]
Description: 3-dehydroquinate synthase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-104  350.2   1.9   1.2e-104  350.0   1.9    1.0  1  DHQS      3-dehydroquinate synthase II


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.0   1.9  6.9e-109  1.2e-104      15     352 .]      12     346 .]       2     346 .] 0.89

  Alignments for each domain:
  == domain 1  score: 350.0 bits;  conditional E-value: 6.9e-109
        DHQS  15 rkelvtaaleagvdavlveeedaekvkelgkik.viakeeddavlvgkddleklkkakkvaalveikskeeeeeaaeaake.adyvivelkdwtvIPlE 111
                  +++v++  ++gv+++ ++   +  +++ +k+k v+++++ d v+ gkd   k  k kk ++ ++i s+++ + + e+ak+  d+vi+e+kdw++IPlE
  AJA93150.1  12 LNKFVKNLEDEGVKHIYAD--PKLITNKKSKMKtVFTTSNADYVVLGKD--GKKVKGKKNGKQFKILSNKDIDGVYETAKKgLDFVIIEVKDWKIIPLE 106
                 5567777778899999998..4445556667772444446689999999..34444578899999999999888877766659**************** PP

        DHQS 112 nliAalqgeetkiiaavksaeeAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcslmkegeGmLvGs 210
                 n+iA+l++ +tki++++k+++e + ++++L+ G+dgv+++t ++ e++e+     +  +++ +Lk+a++t+++evg g+RvcvDt+s++++geGmL+Gs
  AJA93150.1 107 NIIAKLHKIHTKIFTIAKNQKEVRKMFSILDVGVDGVIFQTGSIGEVQETLV---NLGTKSFDLKTAKITEIQEVGDGERVCVDTASMLHKGEGMLIGS 202
                 ****************************************998777776655...4566789************************************* PP

        DHQS 211 ssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktreavvGRvKiEkRPlllveaeaegkkvstilQnaeti 309
                  ++ +fLvh E++ s++ ++RPFRVNAGavh+Y+l p+g+TkYLseL++G+evl+ ++kGk+r+a +GR+KiEkRP+ll++a++ ++   +i Q+aeti
  AJA93150.1 203 RANFMFLVHNESVGSSFTSPRPFRVNAGAVHCYTLSPDGNTKYLSELETGSEVLILNSKGKARRAAIGRCKIEKRPMLLIKAKVGNEIGGIIAQDAETI 301
                 *************************************************************************************************** PP

        DHQS 310 rlvtedgkaisvteLkeGdevlvylee.kaRHfGiki.eEtiiEk 352
                 r v+ +g+ +svt+Lk+Gd vl++ +e ++RHfG+++ +E i+Ek
  AJA93150.1 302 RFVKANGQLVSVTHLKKGDSVLAFSKEaSGRHFGMEVaDEYILEK 346
                 **********************98766489******955999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2449.89
//
Query:       AJA93151.1  [L=78]
Description: hypothetical protein T478_0519 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.031   14.2   0.8      0.035   14.0   0.8    1.0  1  HSDR_N       Type I restriction enzyme R protein N terminus (
      0.036   14.2   0.6      0.041   14.0   0.6    1.1  1  DUF1874      Domain of unknown function (DUF1874)
      0.044   14.3   2.5      0.049   14.2   2.5    1.1  1  AF0941-like  AF0941-like


Domain annotation for each model (and alignments):
>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   5.9e-06     0.035      44      99 ..       7      65 ..       2      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                HHHHHHHHHHHHHHHH-HHHHHHHHTT--HHHHHHHHHTS-EE.EE..TS-EEEEESS- CS
      HSDR_N 44 evaleknlreqlgalnikkltkrlalsdgnkefyellkegkvk.fk..egrkknikLiD 99
                ++ + k+l++ l+++n  ++t++    ++n++++++l+eg+++ ++  ++ kk i+L++
  AJA93151.1  7 KEEMIKDLENILAKINALEVTAKDEEAKANVKILRKLTEGQIHsINefDHLKKAIDLLT 65
                578999**********9999999999*****************8889999999999975 PP

>> DUF1874  Domain of unknown function (DUF1874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   6.9e-06     0.041      44      96 ..       4      56 ..       3      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.9e-06
                -HHHHHHHHHHHT-----------B-TT-EEEEEEE-----------HHHHHH CS
     DUF1874 44 HeataellselldveikvnRieiklekgdkaivlklkeRleEgkvltkeelek 96
                H    e++++l ++  k n  e++ ++++    +k+ ++l Eg++ + +e ++
  AJA93151.1  4 HAPKEEMIKDLENILAKINALEVTAKDEEAKANVKILRKLTEGQIHSINEFDH 56
                66677999***************************************999887 PP

>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.5   8.1e-06     0.049      37      97 ..       7      74 ..       1      78 [] 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.1e-06
                 HHHHHHHHHHHHHHHHTTSS-..HHHHHHHHHHHHHHHHHTHHH.....HHHHHHHHHHCTT-----H CS
  AF0941-like 37 eelfrsdvedvleklkagdie..eeeakknlklLkvyvvsqLde.....hykrvlelledkekkieke 97
                 +e +++d+e++l k++a +++  +eeak n+k+L+     q+++     h k+ ++ll  + ++++++
   AJA93151.1  7 KEEMIKDLENILAKINALEVTakDEEAKANVKILRKLTEGQIHSinefdHLKKAIDLLTMQLFDVKDK 74
                 566899**********999763389*********9888777763222336677777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1457  (0.081265); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 574.43
//
Query:       AJA93152.1  [L=282]
Description: hypothetical protein T478_1239 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1583  (0.0882927); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1857.64
//
Query:       AJA93153.1  [L=73]
Description: AN1-like Zinc finger [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-11   43.3   6.7    4.5e-11   42.7   6.7    1.2  1  zf-AN1        AN1-like Zinc finger
  ------ inclusion threshold ------
       0.29   11.5   4.6        1.4    9.3   4.6    1.9  1  Transp_Tc5_C  Tc5 transposase C-terminal domain
       0.47   11.4   5.3       0.52   11.3   1.8    2.2  2  zf-C2H2_4     C2H2-type zinc finger
       0.71    9.7   6.2       0.71    9.7   0.9    2.1  2  PSI_integrin  Integrin plexin domain


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   6.7     1e-14   4.5e-11       1      38 [.       6      41 ..       5      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1e-14
      zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrlpedHdCkkl 38
                C++  C+  + +pf+C yC+  FC +HrlpedH C kl
  AJA93153.1  6 CAY--CGDMVDIPFECTYCKDPFCDEHRLPEDHRCVKL 41
                885..******************************986 PP

>> Transp_Tc5_C  Tc5 transposase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.6   0.00032       1.4      29      63 .]       5      38 ..       2      38 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00032
  Transp_Tc5_C 29 dCkiegCselafi..kCarCkellCFdHfvvsekhlC 63
                   C+   C+++  i   C +Ck+ +C +H +  e h C
    AJA93153.1  5 RCAY--CGDMVDIpfECTYCKDPFCDEHRL-PEDHRC 38
                  5666..7777655448************88.477777 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       0.2     9e+02       2       8 ..       5      11 ..       5      14 .. 0.80
   2 ?   11.3   1.8   0.00012      0.52       1      19 [.      17      36 ..      17      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
   zf-C2H2_4  2 kCpiCgk 8 
                +C +Cg 
  AJA93153.1  5 RCAYCGD 11
                69***85 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
   zf-C2H2_4  1 fkCpiCgksFsskkaL.lrH 19
                f+C++C+ +F++ ++L  +H
  AJA93153.1 17 FECTYCKDPFCDEHRLpEDH 36
                89*********999986666 PP

>> PSI_integrin  Integrin plexin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3      0.02        89      17      24 ..       4      11 ..       2      14 .. 0.82
   2 ?    9.7   0.9   0.00016      0.71      18      36 ..      18      40 ..      13      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.02
  PSI_integrin 17 psCaWCkq 24
                  ++Ca+C +
    AJA93153.1  4 ERCAYCGD 11
                  58****76 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00016
  PSI_integrin 18 sCaWCkqenft....sessRCds 36
                  +C++Ck++  +    +e +RC +
    AJA93153.1 18 ECTYCKDPFCDehrlPEDHRCVK 40
                  7******9554777889999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 498.03
//
Query:       AJA93154.1  [L=410]
Description: phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-57  193.5   5.1    8.4e-56  188.7   5.4    2.3  2  DFP              DNA / pantothenate metabolism flavoprotein
    5.7e-34  117.1   0.3    5.7e-34  117.1   0.3    2.2  2  Flavoprotein     Flavoprotein
     0.0017   18.7   1.3      0.079   13.4   0.2    2.8  2  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.075   12.9   0.1       0.15   12.0   0.1    1.5  1  NAD_binding_10   NAD(P)H-binding
      0.077   12.6   1.3       0.21   11.2   0.3    2.2  2  Glyco_trans_4_5  Glycosyl-transferase family 4


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.047   1.7e+02      33      62 ..      39      70 ..      36     106 .. 0.61
   2 !  188.7   5.4   2.3e-59   8.4e-56       1     183 [.     196     379 ..     196     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.047
                HHHHHHHHHTT-EEEEEE-S-SS-..--TT-E CS
         DFP 33 yalAeaaaarGaeVtlvsgpvsle..tpegve 62
                ++lA+ +++ G +V+ v ++ s++  +p+ ++
  AJA93154.1 39 IELARLLMRHGGNVKCVMSNASTKliKPDYMK 70
                689**************999654411454433 PP

  == domain 2  score: 188.7 bits;  conditional E-value: 2.3e-59
                 TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHHTT-.SEEEE---S--EEES CS
         DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveealkea.divimaAAvaDyrpk 98 
                 l+gkk+l+taGpT+E+iD+VR+i+N+SSGk+G  lA++++++Ga+Vtlv gp + e p+g+++++v+s++em++av+ealk++ di+im+AA +Dy +k
  AJA93154.1 196 LRGKKILMTAGPTVEKIDSVRVITNQSSGKTGTLLASELISAGAKVTLVYGPGTSEPPKGAKIIRVNSVDEMNKAVKEALKKKfDIAIMTAAASDYVVK 294
                 689*************************************************8889999********************98878*************** PP

                 -------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS....-HHHHHHHHHHHTT-SEEEEEEGGGTTGGG-SS-EEE CS
         DFP  99 eaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaete....ellenareklerkgldlivaNdvskeeagfgsdenev 183
                 +a ++Kik   +++e++++l+k p+i+  + ++k+k+ +lvGF+aet+    el+++a++kl++ ++d+ivaNd++++  + + + ne+
  AJA93154.1 295 NAISSKIKS--DKKEINVKLVKAPKIIDII-KNKQKEIFLVGFKAETDiskkELVSRAKKKLKDSKADMIVANDIGRN-YNKDPNYNEI 379
                 ********6..5678***************.67777889*******977899************************87.3344445555 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.1   0.3   1.6e-37   5.7e-34       1     157 [.      23     189 ..      23     190 .. 0.95
   2 ?   -0.6   2.0      0.28   9.9e+02      20      52 ..     271     314 ..     262     366 .. 0.54

  Alignments for each domain:
  == domain 1  score: 117.1 bits;  conditional E-value: 1.6e-37
                   EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHH..CTTESEEEEEEEEHHHHHHHHTT--SS CS
  Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhiel..rrwadllviaPasantlakianGiadn 88 
                   k+i+l++ Gsvaa+k +el + L ++g +v++v+++a++k+i+++++k+a+        +++++hiel   ++ dll+++P +antl+k+a Gi d+
    AJA93154.1  23 KNIVLCVAGSVAAYKSIELARLLMRHGGNVKCVMSNASTKLIKPDYMKWATgnnvitkLTGDMEHIELadYKRSDLLIVYPSTANTLGKLATGIDDT 119
                   69*******************************************999999*******9*********55569************************ PP

                   HHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHHHT................GHHHHHHHHHHCHH CS
  Flavoprotein  89 lltlilra..takkpiliaPamnpamyenpqtlknlekleegvtvikPsegdigkgkmaeieeivgkildk 157
                   +++++l +  ++k pi++  am+ +myen +++kn++ l++++ +++P+ + +gk+k++e+e+++  +l+k
    AJA93154.1 120 PISTVLTVafGSKIPIIMGLAMHRSMYENAAVKKNMNFLRKKIDFVSPQ-MIEGKAKAPEPEDVLLFVLKK 189
                   **99995558***************************************.78999********99888876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                   HHHHHHTTEEEEEEESCHHHHCCHHGGS................T CS
  Flavoprotein  20 lekLkkegievqvvltkaAkkfiskeklklaa............r 52 
                   +++  k+++++ ++  +a+  ++++  ++ ++            +
    AJA93154.1 271 VKEALKKKFDIAIMTAAASDYVVKNA-ISSKIksdkkeinvklvK 314
                   44444567777655555555555544.322222333334444440 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.04   1.4e+02       4      51 ..      19      72 ..      18     119 .. 0.58
   2 !   13.4   0.2   2.2e-05     0.079      16      91 ..     224     310 ..     222     323 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.04
  NAD_binding_7  4 dlkgkkvlvvGgGevAark....vrklleagakvtvv.apevkeele.elvkla 51
                   +l gk++++  +G+vAa k    +r l++ g +v+ v ++++++ ++ + +k+a
     AJA93154.1 19 ELAGKNIVLCVAGSVAAYKsielARLLMRHGGNVKCVmSNASTKLIKpDYMKWA 72
                   57899999999******9944444556678888875414444444334333343 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.2e-05
  NAD_binding_7  16 GevAarkvrklleagakvtvvapevkeele..........elvklaeeelekdlegad...lviaatddrelneriaeaakarrilvnv 91 
                    G+ ++  ++ l++agakvt+v    ++  e          + v+  ++ +++ l++ +   +  aa +d  ++++i  ++k+ ++ +nv
     AJA93154.1 224 GKTGTLLASELISAGAKVTLVYGPGTS--EppkgakiirvNSVDEMNKAVKEALKKKFdiaIMTAAASDYVVKNAISSKIKSDKKEINV 310
                    6666667889*********98555333..233566333332222223444544554333448899999************986666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     4e-05      0.15       3      85 ..     223     322 ..     222     378 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                     TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-..CCHHHHHHT.T-S.EEEES---TCCHHHH................ CS
  NAD_binding_10   3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtd..vedlaealk.gad.aVvsalggggkdeeg................ 77 
                     +Gk+G ll++el+++g  +vt++     + +     +g++++ ++  d   ++++ealk   d a+++a++++   +++                
      AJA93154.1 223 SGKTGTLLASELISAG-AKVTLVYGPGTSEP----PKGAKIIRVNSVDemNKAVKEALKkKFDiAIMTAAASDYVVKNAisskiksdkkeinvkl 312
                     8**************5.9**99886655555....467777776555522467777776356834444444333322222333333334444455 PP

                     ..HHHHHHHH CS
  NAD_binding_10  78 ..aknivdaa 85 
                       a +i+d  
      AJA93154.1 313 vkAPKIIDII 322
                     5555555555 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.82   2.9e+03      22      43 ..      39      60 ..      26      66 .. 0.72
   2 ?   11.2   0.3   5.9e-05      0.21      24      84 ..     230     301 ..     228     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.82
  Glyco_trans_4_5 22 melatlLrsvgaevvvltlskk 43
                     +ela lL   g +v ++  +  
       AJA93154.1 39 IELARLLMRHGGNVKCVMSNAS 60
                     5788888888888877766555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.9e-05
  Glyco_trans_4_5  24 latlLrsvgaevvvltlskkgg...........llkeladrgikvleakaeelfklalkaDlvvlntvvaak 84 
                      la++L s+ga+v+++     ++           ++ e++++  ++l++k + ++ +a+ +D vv n++ +  
       AJA93154.1 230 LASELISAGAKVTLVYGPGTSEppkgakiirvnSVDEMNKAVKEALKKKFDIAIMTAAASDYVVKNAISSKI 301
                      799************99999989999*****9999*******************************987553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1195  (0.0666518); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3047.23
//
Query:       AJA93155.1  [L=218]
Description: ribosomal protein L1p/L10e family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-41  141.7   0.9      3e-41  141.4   0.9    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
      0.095   13.0   0.1       0.44   10.8   0.0    2.0  2  IGPD          Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.9   3.4e-45     3e-41       4     203 ..      18     207 ..      11     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 3.4e-45
                   HS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHHHHHTCCH-SEEEEE CS
  Ribosomal_L1   4 hakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfeakrkllkefdlflad 100
                    +++kf+es e++++l+++++kk    +++ i+Lp+ + k++ +c+ + ++      +ak+a+  ++v++ + ++k  ++++a rkl++++d+flad
    AJA93155.1  18 EKERKFKESLELYITLKDIDVKK-GFAFNEVIQLPNQMSKPAAVCVMASGDMGL---KAKDAK-ADEVLDNDGVNKLAEDKRATRKLINKYDFFLAD 109
                   33679***********9999777.678**************************9...777777.77899999999999999**************** PP

                   GGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEE CS
  Ribosomal_L1 101 drimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiy 197
                    ++mp ++k LG+ +g+r+kmP+pv      ++ + + + +++  ++ vr++++ ++s+kvG +++++ ++a+N++av+++l  k p++ kni++ +
    AJA93155.1 110 TKLMPVVGKSLGQLLGPRGKMPTPV--P--FNAPIDAFLSRFKT-SIRVRVKNSLSISCKVGDTEMDEHHVAANAMAVINNLRGKFPNGDKNIRKYM 201
                   *************************..6..4678**********.9*************************************************** PP

                   EEETTS CS
  Ribosomal_L1 198 lkttms 203
                   +kttm+
    AJA93155.1 202 IKTTMG 207
                   *****9 PP

>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.15   1.3e+03      37     101 ..      33     105 ..      21     124 .. 0.61
   2 ?   10.8   0.0   4.9e-05      0.44      11      59 ..     149     198 ..     132     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                 HHHHHHHHHHHHHHHS..-SSB--EEEEEEE........ETTEEEEEEEE--SS-EEE--..-SB--TT.--H CS
        IGPD  37 vedvgialGqalkealgdkrgikRfgsallp........mDealaevaldlsgrpylvleaelkrekigeldt 101
                 + d+ +  G a++e ++  +++++ + +++           +a a  +ld  g   l  +++ +r+ i+++d 
  AJA93155.1  33 LKDIDVKKGFAFNEVIQLPNQMSKPAAVCVMasgdmglkAKDAKADEVLDNDGVNKLAEDKRATRKLINKYDF 105
                 5666666666666666655555554433333233333336666667777776666666666666666666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 4.9e-05
                 HHHHHHHT--EEEEEE.ESSH...HHHHHHHHHHHHHHHHHHS..-SSB- CS
        IGPD  11 dqlakhggfdlkvkvk.gdlevddHhtvedvgialGqalkealgdkrgik 59 
                 +++    + +l++++k gd+e+d+Hh+  + + ++ +   +  +  ++i+
  AJA93155.1 149 TSIRVRVKNSLSISCKvGDTEMDEHHVAANAMAVINNLRGKFPNGDKNIR 198
                 44555556678999999**********99988887666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1580.77
//
Query:       AJA93156.1  [L=118]
Description: putative queuosine biosynthesis protein QueD [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-24   85.8   0.0    2.3e-24   85.7   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase
  ------ inclusion threshold ------
      0.067   13.8   0.2       0.12   12.9   0.2    1.4  1  CAAP1     Caspase activity and apoptosis inhibitor 1


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.0   2.6e-28   2.3e-24       5     121 ..       8     116 ..       4     118 .] 0.94

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 2.6e-28
                 EEEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-....STCTTBSS-HHHHHHHHHHHHHCTTTEECCCC-CCHHCCS.--HHHHHHHHHHHHHHHHG CS
        PTPS   5 efeFdaaHrlrkhegkcrnlHGHnykvevtvegee....ldetgmvvdfgelkealkeileelDhkflnaddpeleellspTaEnlaklifeelkerlq 99 
                  fe+d aH+lr+h+ kc++ HGH+ ++ v+v+g++      e++mv+ f+++k++  e +e+lDh++ln   + ++    pT+En+ ++if++lk+++ 
  AJA93156.1   8 SFEIDFAHTLRGHP-KCGKPHGHTSRIIVEVQGDVkkggSYEENMVIEFDKMKKLCWETIEQLDHRNLN---ELFDF---PTSENITEWIFDNLKDKV- 98 
                 699**********9.*******************9888888999*************************...66664...******************. PP

                 CCCGCEEEEEEEEETTEEEEEE CS
        PTPS 100 ekevklskvrvwEtpnswaeyr 121
                      l++v+++E  n+++e++
  AJA93156.1  99 ----PLHSVKFFEGTNKYCEIT 116
                 ....9**************986 PP

>> CAAP1  Caspase activity and apoptosis inhibitor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.3e-05      0.12      38      60 ..      53      75 ..      51      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
       CAAP1 38 lsleelkelCleqLeglskkrll 60
                ++++++k+lC+e +e+l++++l 
  AJA93156.1 53 IEFDKMKKLCWETIEQLDHRNLN 75
                6899***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 880.59
//
Query:       AJA93157.1  [L=522]
Description: von Willebrand factor type A domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-05   22.9   0.0    0.00025   21.3   0.0    1.7  1  VWA             von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.02   15.0   0.4      0.043   13.9   0.4    1.5  1  GerPC           Spore germination protein GerPC
      0.024   14.8   0.0      0.062   13.5   0.0    1.6  1  Myb_DNA-bind_2  Rap1 Myb domain
       0.04   13.9   0.0       0.12   12.3   0.0    1.8  3  VWA_3           von Willebrand factor type A domain
      0.056   13.6   0.2        2.1    8.4   0.0    2.9  2  vWA-TerF-like   vWA found in TerF C terminus


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0     7e-08   0.00025       2     146 ..     350     487 ..     350     501 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7e-08
                 EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTG.SGGGGSSC-HHHHHHHHHHHHHHHHGT CS
         VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnl.kysgggttntgkalkyaleklfkssag 98 
                 iv++lD S+s++++++e  k++ + l e l     ++ +++  f++   ++++ l +  + ++ +sa ++l ++s +     g+ l++++++++    +
  AJA93157.1 350 IVILLDHSSSVSDQQIE-YKKATIGLCEVLA--FLKIDFSVYAFNTVdRQVVCWLVKPAEMKWNNSAAKRLaQISAN----GGTPLAEVYDRMLPVLTS 441
                 8**********777775.6888889999999..77788888888877444445555555666666666665322333....444555666655555555 PP

                 SSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEESSSHHHH CS
         VWA  99 aRenakkviilltdGksnd.gdpkeaaneakeqgikvfavGvgnadeke 146
                    + + +++ l+dG++ d + +k  +++ ++ gik+ a+Gvg ++  +
  AJA93157.1 442 ---KKPDIFLTLSDGEPADaNAVKLILKSYRSLGIKMTAIGVGRDTFSA 487
                 ...4467**********9977*********************9887655 PP

>> GerPC  Spore germination protein GerPC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.2e-05     0.043       5     144 ..     231     364 ..     225     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
       GerPC   5 ekqleelqeeleelkkkpatsiekieYkFDqLKvekLeGTLNiGlnPsdlgksiedfaveqaktvapeneaeselfqeiqeeveayLeeeapelleele 103
                 +k  ++l++el ++  ++a+    i  +FD++K e+ +   N Gl P+++g     +++ + ++v++++  +++l+++++++  ++ +   +e + + e
  AJA93157.1 231 QKITKNLESELGKIDPNKAMAGLEIAKEFDLIKDETKK-NENKGLIPETIG-----IQIPNPTNVDETKIYDQDLISSLKNRFREWKTGWKEEHVISGE 323
                 556678999999999999999999999******98866.57*********4.....55666666666677789999************99999999999 PP

       GerPC 104 kqyeveldeeyrefileDikkQldsRikyYlkqvaaeeeee 144
                 +  e +  e +++  + Dikk ++sRi   l++ ++ ++++
  AJA93157.1 324 DFDEESYLEGFHKPFVTDIKKSIKSRIVILLDHSSSVSDQQ 364
                 9999999999999999*************999744333333 PP

>> Myb_DNA-bind_2  Rap1 Myb domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.7e-05     0.062      13      47 ..      93     124 ..      80     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.7e-05
  Myb_DNA-bind_2  13 ilkyvkekerspasvkGnkiwkelekkhltrHsWQ 47 
                     +l+ +   er++ +  G kiw+ ++++ + + sWQ
      AJA93157.1  93 LLNSI---ERRRVELVGRKIWQGMDEELIFNYSWQ 124
                     44444...999999********************* PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       3.7   1.3e+04      26      45 ..      17      36 ..       9      40 .. 0.79
   2 ?   -3.7   0.0       2.8   9.9e+03      54      84 ..     219     250 ..     212     262 .. 0.71
   3 ?   12.3   0.0   3.4e-05      0.12       2     135 ..     349     480 ..     348     496 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.7
       VWA_3 26 valrqLptndkiavllfgtk 45
                +++r  ++ndki v + + k
  AJA93157.1 17 FLIRRWSENDKIIVTMSPKK 36
                67899999999998876665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.8
       VWA_3  54 ravsaaelqealqkike.lelslgasnlegaL 84 
                 ++v +++ ++a qki + le +lg  ++ +a+
  AJA93157.1 219 MVVTPQDFEKAVQKITKnLESELGKIDPNKAM 250
                 66677777777777765577777877777765 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.4e-05
       VWA_3   2 evvivvDvsssmsaen.klvkdaLsvalrqLptnd.kiavllfgtkprplfpg.sravsaaelqealqkikelelslgasnlegaLkealrqpakpgev 97 
                 ++vi++D sss+s+++ +  k+++  + + L   +  ++v +f t +r++ +   + ++ +    a++ ++++++  g+++l+ + ++ l      + +
  AJA93157.1 349 RIVILLDHSSSVSDQQiEYKKATI-GLCEVLAFLKiDFSVYAFNTVDRQVVCWlVKPAEMKWNNSAAKRLAQISA-NGGTPLAEVYDRMLPVLT-SKKP 444
                 8*************9955555555.56788888777*********99999976477888889999**********.***********9998653.3678 PP

       VWA_3  98 rsvilltDgssaqgeervsdlisrarekirfhalglgs 135
                 +  + l+Dg +   ++ +++li ++ + + + ++++g 
  AJA93157.1 445 DIFLTLSDGEP--ADANAVKLILKSYRSLGIKMTAIGV 480
                 88888999996..4455788888877775555555554 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.071   2.6e+02     170     199 ..     290     319 ..     287     320 .. 0.86
   2 ?    8.4   0.0   0.00058       2.1      45     147 ..     387     486 ..     347     502 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.071
  vWA-TerF-like 170 didkvsdaeLYdrLlsefpeWlkaarekgi 199
                    d +k+ d++L + L + f eW +  +e+++
     AJA93157.1 290 DETKIYDQDLISSLKNRFREWKTGWKEEHV 319
                    456899***************998888776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00058
  vWA-TerF-like  45 vwlfaskakrlpdvtladlee.yvkeeeegllelkklggvneeapvleevlekvrk.epaelptlvlFitDGgvkkkkeiekalreaskepiFwqF 138
                    v++f++  +++    ++ +e  + +++++ l ++++ gg +     l+ev +++    ++++p + l ++DG+ +++++++ +l++  ++ i    
     AJA93157.1 387 VYAFNTVDRQVVCWLVKPAEMkWNNSAAKRLAQISANGG-TP----LAEVYDRMLPvLTSKKPDIFLTLSDGEPADANAVKLILKSYRSLGIKMTA 477
                    555555555544444444433144444444444443333.44....45555555544457789********************************* PP

  vWA-TerF-like 139 vglgkseyg 147
                    +g+g+  + 
     AJA93157.1 478 IGVGRDTFS 486
                    *****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3426.15
//
Query:       AJA93158.1  [L=110]
Description: hypothetical protein T478_0610 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 835.61
//
Query:       AJA93159.1  [L=193]
Description: hypothetical protein T478_0665 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.54   10.2   2.6        1.7    8.5   0.2    2.5  2  DUF1418   Protein of unknown function (DUF1418)
        7.2    6.5  11.3       0.91    9.4   6.6    1.9  2  DUF4118   Domain of unknown function (DUF4118)


Domain annotation for each model (and alignments):
>> DUF1418  Protein of unknown function (DUF1418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.034     3e+02      18      48 ..      24      54 ..       6      94 .. 0.73
   2 ?    8.5   0.2   0.00019       1.7       5      37 ..      93     125 ..      89     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.034
     DUF1418 18 GliLLvlayLsvndylsLPgplsskeaaivm 48
                G   L  ++++++++l +P+    k++ + m
  AJA93159.1 24 GGFALFSSFFAIDQMLDIPAGTFYKTIGVTM 54
                5556677788888888888766666665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00019
     DUF1418   5 gklPrsvlilevlGliLLvlayLsvndylsLPg 37 
                  ++P++++     Gli++ la+L ++ ++  P 
  AJA93159.1  93 VTVPKAIITGVWTGLIVFTLAFLPIHMFVMTPM 125
                 578*************************99885 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.6    0.0001      0.91       7      69 ..      69     128 ..      60     137 .. 0.79
   2 ?   -2.5   0.1      0.48   4.3e+03      38      54 ..     159     175 ..     155     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0001
     DUF4118   7 llalatllallldkllslanivllfllavllvallgglgpgllaallsvllfnyfftpPyftl 69 
                  + +a l++++    +  +ni   f l+++  a+++g++ gl++  l++l +  f + P ++ 
  AJA93159.1  69 HMGVAALIGAMY---FLASNIWRFFRLVTVPKAIITGVWTGLIVFTLAFLPIHMFVMTPMMEV 128
                 333444444444...5479****************************************8865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.48
     DUF4118  38 vallgglgpgllaalls 54 
                  al++ +++g++a +++
  AJA93159.1 159 NALILHIIYGAIAGFVG 175
                 57777788888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1295.66
//
Query:       AJA93160.1  [L=217]
Description: hypothetical protein T478_1361 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.004   17.5   0.0     0.0074   16.6   0.0    1.4  1  DUF2383   Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.14   11.9   0.0    1.1  1  AMO       Ammonia monooxygenase
       0.15   12.3   1.8       0.31   11.4   1.8    1.4  1  TSC22     TSC-22/dip/bun family


Domain annotation for each model (and alignments):
>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-06    0.0074      36      71 ..     160     195 ..     155     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                 HHHHHHHHHHHHHHHHHHHHHCT------------- CS
     DUF2383  36 leriaeereeaaeeLqseiralggepedggslagkl 71 
                 +er +++ +  ++eLq+ i++l++eped+++++g +
  AJA93160.1 160 FEREVNDLRGDIRELQETINELKEEPEDDNGMSGMI 195
                 889999999************************975 PP

>> AMO  Ammonia monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.3e-05      0.14      13      52 ..       3      42 ..       1      68 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.3e-05
                HHHHHHHHHHHHHHHHHHHHHHHHS-SSSSS-GGG--TTH CS
         AMO 13 kidlivlvilflvvlggyhihqmllaGdWdfWvdwkdrrl 52
                k+ li+l+++  ++l + ++hq+  +Gd+   +dwk++ +
  AJA93160.1  3 KTYLIALFLISPLMLNSAFAHQSDSVGDYRIEIDWKNKPI 42
                566899999999************************9854 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.8   5.2e-05      0.31      15      36 ..     163     184 ..     161     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
       TSC22  15 eVevLkekIkeLeernseleeE 36 
                 eV+ L+  I+eL+e+++el+eE
  AJA93160.1 163 EVNDLRGDIRELQETINELKEE 184
                 8*******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1593.10
//
Query:       AJA93161.1  [L=342]
Description: alcohol dehydrogenase, catalytic domain, GroES-like family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-21   76.4   1.9      3e-21   75.3   1.9    1.6  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.6e-18   66.9   0.1    2.4e-18   66.4   0.1    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    2.6e-13   50.0   0.2    4.2e-13   49.3   0.2    1.2  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    7.7e-06   27.0   0.2    1.4e-05   26.2   0.2    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   1.9   6.8e-25     3e-21       1     104 [.      24     125 ..      24     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 6.8e-25
                 TTEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-..SSSHHHHTT-GGG-TTBEETTTSS-SSSBS CS
       ADH_N   1 pgevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvveplisc..geCaaCkegeenlCeeakllgvsldGgfae 97 
                 p+e+lik++++giCgsD++ + g      ++ + lGHE +Gev ++g++++++k+GdrV+ +++++c  ++C++C++g+e++C+++   +++  G +a+
  AJA93161.1  24 PNELLIKMQSCGICGSDVEKVFG---KYGQPSMRLGHEPAGEVIKIGDAISDFKIGDRVFTHHHVACysKDCHECSHGNETMCKQYYQSNLNPCG-LAD 118
                 5899*****************99...46777789*********************************5556**************9999999555.555 PP

                 EEEECGG CS
       ADH_N  98 yvvvpek 104
                  +vvpe 
  AJA93161.1 119 NYVVPEW 125
                 5555554 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   5.3e-22   2.4e-18       2     129 ..     176     303 ..     175     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 5.3e-22
                 HHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEE.. CS
  ADH_zinc_N   2 vGlaavqlAkalGa.eviavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeee.. 96 
                  G++ v lAk +G+ +++++d ++ +l+++kk+ +  +    ++ +lv+++ + t + gvdv++ ++ s +++++a+kl+++gG++v++G+++++ +  
  AJA93161.1 176 TGMMHVLLAKYFGFsKIFCMDLNDFRLDFVKKFDVITIRS--DDpNLVQKVTDDT-TIGVDVAIVATSSLHAFQDAIKLVRKGGTVVMFGVPSKGATte 271
                 79*******************************8544433..4559*********.89*********************************55554448 PP

                 EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
  ADH_zinc_N  97 fdlrnlllkeksilGsllgslreefkealdlla 129
                 +d++ +  ke+si+ +  +s   + k+al+l++
  AJA93161.1 272 IDMSVVYSKEISIVTTYAAS-DMDTKKALELIS 303
                 ********************.999999999986 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2   9.3e-17   4.2e-13       6     210 ..     146     340 ..     142     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 9.3e-17
  Glu_dehyd_C   6 LvEPisiveKaielaeasrsafewe.pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretp.vdeipe.asee 100
                  L+EP++   +a+       s+f+++  +++ +lG G+ G++   +l a+  g++++++++    +d ++d+v++ +   + s+  + v+++++ ++  
   AJA93161.1 146 LIEPLACCVRAW-------SKFKYQkNDTVAILGVGPTGMMH--VLLAKYFGFSKIFCMDL---NDFRLDFVKKFDVITIRSDDPNlVQKVTDdTTIG 231
                  677777777666.......456655146899**********9..4444579********96...6789*********999998765377776516779 PP

  Glu_dehyd_C 101 mdlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvvdldelee 197
                  +d+ + aT s ++  +ai+ ++  G +++ Gvp++  + e+d++ + ++       +v +  a+    ++a++ +++ + + +++lvt+++ ld+ ++
   AJA93161.1 232 VDVAIVATSSLHAFQDAIKLVRKGGTVVMFGVPSKGaTTEIDMSVVYSK----EISIVTTYAASDMDTKKALELISSGNVD-VKSLVTHKYSLDDSQK 324
                  **********99999******************9865999*99988776....5678999999999999999988876665.799************* PP

  Glu_dehyd_C 198 Afe...dddetiKtvv 210
                  Afe   ++d  +K ++
   AJA93161.1 325 AFEhakTGDSAMKIII 340
                  **94445667777776 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   3.1e-09   1.4e-05      14     133 .]     224     340 ..     209     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.1e-09
                   HHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHHHHHHHH..----EEE CS
  ADH_zinc_N_2  14 feaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaalieeGk..lrpvvdr 108
                   ++++t   gvDv++ ++ + +++++++k++++gG++v+ g p  s++   +  +    s  ++ +++  as   d  ++ ++li++G+  ++  v++
    AJA93161.1 224 VTDDT-TIGVDVAIVATSSLHAFQDAIKLVRKGGTVVMFGVP--SKGATTEIDMSVVYSKEISIVTTYAAS-DMD-TKKALELISSGNvdVKSLVTH 315
                   33444.468*****9999666669999***888***999864..333333333333344444444443344.445.9***********777899999 PP

                   EEEGGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2 109 vfpleeaaeAhrylesgrarGKiVl 133
                    ++l++ ++A+++ ++g    Ki++
    AJA93161.1 316 KYSLDDSQKAFEHAKTGDSAMKIII 340
                   9****************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2596.49
//
Query:       AJA93162.1  [L=320]
Description: hypothetical protein T478_1269 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.9   1.0       0.03   14.2   1.0    1.3  1  TMEM154   TMEM154 protein family
        0.2   11.7   0.2        0.6   10.2   0.2    1.7  1  DUF1664   Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   3.3e-06      0.03      10      78 ..     248     316 ..     240     320 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-06
     TMEM154  10 taletatleeesadatsaasteseslkqeeakeslssaelsnesdqlelvlmiiiPlvllillllvvii 78 
                 t +e a l+ee+++ +s  s  s+ l+ +    s s +++++ s+ql+ +l  i+ ++++il l +vii
  AJA93162.1 248 TKTELANLKEETSTFGSSLSDASSNLDDSVVLISDSVGNIEEGSSQLNALLFPIVASIAIILALQIVII 316
                 55677889999999999999999999999**********************999999987776666665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   6.7e-05       0.6      62     105 ..     225     268 ..     218     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.7e-05
     DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                 + L+++i  + +++ e ++i  e+k e+++++e++s++g+ ++ 
  AJA93162.1 225 NVLTQDISGISAQILELNQILDETKTELANLKEETSTFGSSLSD 268
                 5699********************************99976543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2319.67
//
Query:       AJA93163.1  [L=187]
Description: ammonia monooxygenase/methane monooxygenase, subunit C [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   47.8   6.6    1.4e-12   47.5   6.6    1.1  1  AmoC      Ammonia monooxygenase/methane monooxygenase, subuni
     0.0051   16.4   0.3     0.0075   15.9   0.3    1.2  1  RTA1      RTA1 like protein


Domain annotation for each model (and alignments):
>> AmoC  Ammonia monooxygenase/methane monooxygenase, subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   6.6   1.5e-16   1.4e-12      96     242 ..      13     156 ..       2     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.5e-16
        AmoC  96 elkryltlllwlvvyalavyWGasffte..qdgtWhqtvirdtdftPshiiefylsyPiyiilgvaaflyaktrlPlf...akglslpylvlvagplmi 189
                 e++r+ +  +wlvv a++    as  ++   dg+ hqt ird  ftP+h   +  s+ +   lg++       ++P++   +++++  + +++ g l +
  AJA93163.1  13 EIQRLKK--IWLVVIAMGSTA-ASVEVDnfVDGSLHQTSIRDSAFTPAHWWLY--SHFVALPLGWGFAAIYDRKVPVLrgpNNSMNTGLKMTILGYLAT 106
                 5555443..466666665544.3333331249*****************7643..4445555677766556678888733357788899********** PP

        AmoC 190 lpnvglnewGhtfWfmeelfvaPLhwgfvvlgWaalavlGvalqvlarlsell 242
                 +  +g+ne  h fWf+ee+f+ P hw f +   + +a++G ++ v+  +++l+
  AJA93163.1 107 MFTIGVNEMWH-FWFVEEIFAVPNHWMFNMG--VVVAFMGALAYVVRVYARLV 156
                 *********99.9**************9763..45666676666666555555 PP

>> RTA1  RTA1 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   8.3e-07    0.0075     101     185 ..      91     179 ..      84     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-07
        RTA1 101 eaklGeniiiaGlalQvvvlvvFlllaldFllrvr...kskkfkkfllalyaavlliliRsiyRvvElaeGw.dgylithEvyfyvLda 185
                 ++++G +++i G +  +++++v  + ++ F+ ++    +++ f++ +++ ++  l+ ++R   R+vEl     + +    E+y ++L++
  AJA93163.1  91 SMNTGLKMTILGYLATMFTIGVNEMWHFWFVEEIFavpNHWMFNMGVVVAFMGALAYVVRVYARLVELGAETpGENPYVAEMYKMALEG 179
                 389**********************************98899**************************887734456778999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1371.98
//
Query:       AJA93164.1  [L=160]
Description: peptidyl-prolyl cis-trans isomerase, cyclophilin-type [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-51  174.0   0.0      3e-51  173.8   0.0    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.8   0.0   1.7e-55     3e-51       2     157 ..       4     157 ..       3     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 1.7e-55
  Pro_isomerase   2 vdietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEitsklkhkrGalamartg 97 
                    v+iet+ +G+i ++L ++ aP+tv+ F+kl+++gfYdgt FhRvi+gfm+qgGdp++k++++++++  g   +++++E+ s+ +h +G+++mar+ 
     AJA93164.1   4 VKIETN-HGNILFNLLPELAPETVRSFVKLTTDGFYDGTLFHRVIPGFMIQGGDPNTKDPNMKSQWGMGGPGFNVKAEF-SSRSHLEGIVSMARA- 96 
                    79***7.*****************************************************888885555568*******.7889**********9. PP

  Pro_isomerase  98 kepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkivsae 157
                     +p+sagsqFfI++k+ ++ld++ytvFG+V+eGmdv  kie++++d+ + p+++ k+ +++
     AJA93164.1  97 TDPDSAGSQFFIVTKDSTFLDREYTVFGEVTEGMDVAHKIESLDRDGnDCPHEDAKMLKVS 157
                    79*********************************************99****99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1113.35
//
Query:       AJA93165.1  [L=191]
Description: AAA domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-10   41.5   0.5    2.8e-10   40.8   0.1    1.5  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.065   13.4   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.038   13.9   0.1       0.26   11.2   0.0    2.1  2  NTPase_1         NTPase
      0.042   13.6   0.1      0.088   12.5   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.061   13.7   0.4        0.2   12.1   0.4    1.9  1  AAA              ATPase family associated with various cellul
      0.088   13.1   0.0       0.22   11.8   0.0    1.8  2  AAA_22           AAA domain
       0.09   12.5   0.0       0.33   10.6   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   1.1e-13   2.8e-10       2     129 ..      11     127 ..      10     128 .. 0.86
   2 ?   -2.2   0.0       2.2   5.6e+03      57      67 ..     157     167 ..     132     186 .. 0.55

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-13
      AAA_18   2 lltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaele.seaakdikkv 97 
                 ++tG pGvGK t+a+   k +  +  + +++ a e+gl +  d+       ++d++kl++ +++l+         + l+i ghla ++ +e++++++ +
  AJA93165.1  11 VITGNPGVGKHTIADLFTKQNsSYqIFDINKFAIEKGLGEQTDDG-----IEVDTKKLKNEIQKLNL--------EKLLIVGHLAPYVlDESNIEYV-I 95 
                 69*****************98555988888888888888877777.....89999997777777777........6678888888877699999999.* PP

      AAA_18  98 vLtaspeelleRlekRgyeeakikeneeaeil 129
                 +L+ +p el++  ekR+y++ kiken  +e l
  AJA93165.1  96 ILRKNPYELIKIYEKRKYQNQKIKENAGSEVL 127
                 **************************988876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.2
      AAA_18  57 ldklldaleen 67 
                 l++++d+++++
  AJA93165.1 157 LKRIQDIMNNQ 167
                 33333333332 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05     0.065      20      60 ..       6      44 ..       2      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                     -SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH- CS
  Sigma54_activ_2 20 sklpvfltGekGsgkelvArlLhknsgpwleifvverlakl 60
                     + +++ +tG++G gk ++A l+ k+++   +if++++ a +
       AJA93165.1  6 NYVNLVITGNPGVGKHTIADLFTKQNSS-YQIFDINKFA-I 44
                     567899*******************999.9999996544.4 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.26       2      18 ..      10      26 ..       9      40 .. 0.84
   2 ?   -0.1   0.0      0.29   7.5e+02      25      64 ..     121     161 ..     112     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                EEEE--TTSSHHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvkk 18
                ++iTG+pGvGK T+ + 
  AJA93165.1 10 LVITGNPGVGKHTIADL 26
                79***********9875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                 ..GGGEEEEEEEEE-.------EEEEEET.T--EEEEEETT CS
    NTPase_1  25 ssgvkvgGfyteevr.eggrrigFkivdlasgeegiLarve 64 
                 + g +v G+++++   + g+   F++ + ++  e iL r +
  AJA93165.1 121 NAGSEVLGVIANDSItSFGKEKSFEVDATDKTPEVILKRIQ 161
                 34788888888764438888889998888888888887776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.4e-05     0.088      49     137 ..       9     101 ..       3     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
   IstB_IS21  49 nivllGpsGvGKshlaialgveavr.aglsvl.fvrvedLveelk..rarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekr 137
                 n+v++G +GvGK  +a  + ++    + + +  f   + L e+    ++ +  kl++++++l   +lli+  l+   ld+ + e++  + ++ 
  AJA93165.1   9 NLVITGNPGVGKHTIADLFTKQNSSyQIFDINkFAIEKGLGEQTDdgIEVDTKKLKNEIQKLNLEKLLIVGHLAPYVLDESNIEYVIILRKNP 101
                 9****************9999887745566652555566887776334667789999999999999***999999999998888776655555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   7.8e-05       0.2       2      43 ..      11      52 ..      10     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.8e-05
                EEESSTTSSHHHHHHHHHHH.HTHEEEEEETTTCSSSSTTHHH CS
         AAA  2 llyGppGtGKTllakavake.lgvefleisgsellskyvgese 43
                +++G+pG+GK ++a    k+ ++ +++ i+   +  k +ge+ 
  AJA93165.1 11 VITGNPGVGKHTIADLFTKQnSSYQIFDINKFAIE-KGLGEQT 52
                689*************9999334667777776666.6555543 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.7e-05      0.22       8      34 ..      10      36 ..       6      96 .. 0.80
   2 ?   -1.5   0.0       1.1   2.8e+03      74      85 ..     152     163 ..     104     178 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-05
      AAA_22  8 lvvtGesGtGKTtllrrlleqldeeak 34
                lv+tG +G+GK t +  +++q+  ++ 
  AJA93165.1 10 LVITGNPGVGKHTIADLFTKQNSSYQI 36
                79*******************976654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
      AAA_22  74 sseellealeqa 85 
                 + e +l+++++ 
  AJA93165.1 152 TPEVILKRIQDI 163
                 222222333333 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.33      23      61 ..       8      44 ..       2      53 .. 0.72
   2 ?   -1.3   0.0      0.61   1.6e+03     111     134 ..     124     147 ..     116     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                     S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
  Sigma54_activat 23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61
                     ++++itG+ G+GK ++a++  ++++  + ++  +n  ai
       AJA93165.1  8 VNLVITGNPGVGKHTIADLFTKQNS--SYQIFDINKFAI 44
                     7899*************99876554..344555665555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.61
                      HHHHHHHHHSEEESBTSSSEEE-- CS
  Sigma54_activat 111 ekLlrvlqegevervGsskeikvd 134
                      +++l v+ + +++  G++k+ +vd
       AJA93165.1 124 SEVLGVIANDSITSFGKEKSFEVD 147
                      678999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1433.30
//
Query:       AJA93166.1  [L=313]
Description: PEFG-CTERM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.055   13.5   0.1    2.0  2  NHL           NHL repeat
      0.071   13.5   0.0        0.2   12.1   0.0    1.7  1  PDZ           PDZ domain
      0.085   13.0   0.0       0.33   11.1   0.0    2.0  2  Cupredoxin_1  Cupredoxin-like domain
      0.095   13.2   0.0       0.62   10.5   0.0    2.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.3e+04      15      22 ..     125     132 ..     123     133 .. 0.78
   2 ?   13.5   0.1   1.2e-05     0.055       6      24 ..     205     223 ..     205     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                 EEEEECCC CS
         NHL  15 iyVaDsen 22 
                 i+ aDse+
  AJA93166.1 125 ILAADSET 132
                 78899986 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.2e-05
                 EEEEETTTEEEEEECCCTE CS
         NHL   6 GvavdsnGdiyVaDsenhr 24 
                 +++v++nG+i+ aD++ hr
  AJA93166.1 205 DITVSQNGEIILADNGAHR 223
                 699***************8 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05       0.2      20      59 ..      36      72 ..      28      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                TTSSSSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETT CS
         PDZ 20 sdqrgdkgifvsevlpggaaeadglkvGDkIlsvNgvdve 59
                +    ++g+ v+++   +a +++  +vGDkI+  Ng d  
  AJA93166.1 36 RGS-SQPGCEVTNLCFVPAIATA--NVGDKIIFLNGDDAP 72
                333.579******9999999999..9**********9875 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.4e-05      0.33      31     104 .]      49     125 ..      25     125 .. 0.72
   2 ?   -2.9   0.0       1.7   7.6e+03      26      26 ..     190     190 ..     170     224 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
  Cupredoxin_1  31 gfePskievkagekvklkiknkdktpeefesed.......lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkliV 104
                    f P+  +++ g   k+ + n d+ p++ +s +       ++ +   +pg  ++  + + +pG+++++c  h+ + G+l++
    AJA93166.1  49 CFVPAIATANVGD--KIIFLNGDDAPHTSTSGNptsgpdgIWDSGLQQPGVDFV--FMATTPGTFDYFCMVHPWMAGQLVI 125
                   5666666666666..677777777777777766666666555544444555544..5579*************99***996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
  Cupredoxin_1  26 t 26 
                   +
    AJA93166.1 190 E 190
                   2 PP

>> Copper-bind  Copper binding proteins, plastocyanin/azurin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00014      0.62       9      97 ..      45     124 ..      39     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                  TETSEEESSEEEEETTEEEEEEEESSSSBEEEEET.TSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETTTTTTTSEEEEE CS
  Copper-bind   9 sgdlqFetkeitvkkgekvtfvnlavmgHNvvldk.dgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsPHaaagMkgkvt 97 
                   ++l F ++  t + g+k+ f+n ++ +H     +  + p+g+ ++         l  +G  +    +++gt+++fC  H    M g+++
   AJA93166.1  45 VTNLCFVPAIATANVGDKIIFLNGDDAPHTSTSGNpTSGPDGIWDSG--------LQQPGVDFVFMATTPGTFDYFCMVHP--WMAGQLV 124
                  5678999999999****************766554333334443333........4558999*9999***********999..5788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2428.68
//
Query:       AJA93167.1  [L=377]
Description: membrane protein, putative [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2700.32
//
Query:       AJA93168.1  [L=291]
Description: sulfotransferase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-22   79.2   1.9    4.5e-22   78.8   1.9    1.1  1  Sulfotransfer_1  Sulfotransferase domain
    2.8e-10   41.0   0.0    2.6e-07   31.2   0.0    2.9  1  Sulfotransfer_3  Sulfotransferase family
    0.00026   21.0   1.6    0.00065   19.7   1.6    1.6  1  Sulfotransfer_2  Sulfotransferase family
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.041   13.3   0.0    1.6  2  SRPRB            Signal recognition particle receptor beta su
       0.16   11.7   0.0       0.36   10.6   0.0    1.5  1  PduV-EutP        Ethanolamine utilisation - propanediol utili


Domain annotation for each model (and alignments):
>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   1.9   1.2e-25   4.5e-22       2     226 ..      37     267 ..      36     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 1.2e-25
                      TSEEEEESTTSSHHHHHHHHHHHHTTTCCHHHTSSGHCT-.HHHSCBTTHECCTSGCCGTTECCCHHHTTTEEHHHHHHHSTSS.EEEE...GG CS
  Sulfotransfer_1   2 ddvlivtypKSGTtwlqellslitsegdfekaeepalfna.rdrspfLelydlyfpnslkppdhlrsyshvaekvvrlralesprllktHlplk 94 
                      + ++i++  K+GTt l+  l +++++++   ++e+ +fn+ +d+ +   +y+ +fp slk++  l+++s+ ++ + ++  l    l     +++
       AJA93168.1  37 PNFIIIGEAKCGTTSLYNYLIQHPNIESS-LTKEINFFNWsYDKPK--NWYRAHFPTSLKKK-MLKRFSNKQIITGEATPL---YL-----FHS 118
                      5689************************9.589*******888888..89999***555555.234455444444444444...33.....344 PP

                      GS.CHH..HHTT-EEEEEE--HHHHHHHHHHHHHHBTTSTTT-S-HHHHHHHHHT.....................THSTTC-HHHHHHHHHHH CS
  Sulfotransfer_1  95 llpksl..ldsnlKiiylvRnpkdvavSryhfsrslkklkepetpfeeffdlfle.....................grvvcgsyfdhvkswlkl 165
                      l+pk +  + + +K+i+++Rnp ++a+S yh    +   +e+ t f+e++++ ++                       v+ g y+ h+k w+ l
       AJA93168.1 119 LVPKRIfqMLPEVKLIICLRNPIERAYSHYHDL-GIRLGEEQRT-FDEAIETEIQslkqknynildsdygfssrlyQYVSRGVYLPHIKLWMNL 210
                      77777623579*******************998.7776677777.9988888888888888889999999999999****************** PP

                      TTTTTEEEEEHHHHHHHHHHHHHHHHHHTT--..HHHHHHHHHHTSHHHHHTETTTSSTTS CS
  Sulfotransfer_1 166 rkkgnvlflrYEdlkkdpakeikkiaeFlGiplteeelekivkhlsfenmksnpvsnkskl 226
                      + ++++lf++ E+l  ++ +++++++eFl+ +    +++ i  + +f+  k +p++n+++ 
       AJA93168.1 211 FSRDQILFVKTEELNNNTSESVNRVFEFLDTK----KFNGIDVKERFNVSKYKPMNNSTRE 267
                      ********************************....*********************8663 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   7.4e-11   2.6e-07       1     213 [.      37     241 ..      37     245 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.4e-11
                      -.EEEE--TTSSHHHHHHHHHTSTTEE--S--.--TT.-SBHHHHHHHHTT-S...TTTHHHHHHHHHHT--HHHHHHHHHHHHHTT-BHHHHH CS
  Sulfotransfer_3   1 P.ifivGlpRSGTTlLhrlLaahpdvripeetlfvaprllalleawskdgrelrrlldagltqeeaelphledaeepeedlqllraalasvile 93 
                      P ++i+G  + GTT L + L +hp +++     +++  +        ++ ++++r   a++  +                  l ++ l++++ +
       AJA93168.1  37 PnFIIIGEAKCGTTSLYNYLIQHPNIESSLTK-EINF-FNWS----YDKPKNWYR---AHFPTS------------------LKKKMLKRFSNK 103
                      6689*********************9998666.3332.2222....234456666...433333..................444555555555 PP

                      HHHHHHTTTSEEEEEESSGGG-HHHHHHHBSSEEEEEEE--H.HHHHHHHHHT...T----------..-HHHHHHHHHHHHH....HHHHHHH CS
  Sulfotransfer_3  94 alarvpsyarwlvdKsPshlfrldlllelfPdAkfihlvRdpvdtvlssyvsl...fgkkresysedsldeledaleewaray....erllaar 180
                      ++  +++ +  +     +h    +++++++P+ k+i+ +R+p+++++s y  l    g++++++     + +e++++  +++     ++ + + 
       AJA93168.1 104 QII-TGEATPLY----LFHSLVPKRIFQMLPEVKLIICLRNPIERAYSHYHDLgirLGEEQRTFD----EAIETEIQSLKQKNynilDSDYGFS 188
                      532.33333433....36888999**************************888111133333343....2333223333222201113333333 PP

                      HH....................S-TTSEEEEEHHHHHH-HHHHHHHHHHHHT- CS
  Sulfotransfer_3 181 ar....................lppdrfldvrYedLvadpegtlrriyeflgl 213
                       r                    +  d++l v+ e+L ++  + ++r+ efl+ 
       AJA93168.1 189 SRlyqyvsrgvylphiklwmnlFSRDQILFVKTEELNNNTSESVNRVFEFLDT 241
                      335556666888888888999*****************************985 PP

>> Sulfotransfer_2  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.6   1.8e-07   0.00065      18     223 ..      46     266 ..      38     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
  Sulfotransfer_2  18 Kvasttfkrvlvrlig.......k.kctknrpsinetwlfsrrstgwshglfadltelssteipkrld.k.....................yfk 81 
                      K++ t++ ++l+   +       + ++++   +++++w + ++ t  +++ ++++   s+++i   ++ +                        
       AJA93168.1  46 KCGTTSLYNYLIQHPNiessltkEiNFFNWSYDKPKNWYRAHFPTSLKKKMLKRF---SNKQI---ITgEatplylfhslvpkrifqmlpeVKL 133
                      9999999999999877878888777888888888888888888777777777777...33444...332266789***************9999 PP

  Sulfotransfer_2  82 filvRdPfeRllSayrnkcvgdkergatwkgrlivckgr..lpacyegddwsgvsfeeFleclsnlapersrnnrhwapacd.lctpcladydl 172
                      +i++R+P+eR  S y +  ++  e ++t+ ++ i   ++  ++++y+ +d +    +++ +++s           h++  ++ +  +   +  +
       AJA93168.1 134 IICLRNPIERAYSHYHDLGIRLGEEQRTF-DEAIETEIQslKQKNYNILDSDYGFSSRLYQYVSRGV-----YLPHIKLWMNlFS-RD--QILF 218
                      *****************999777777777.8888888887444445444666678888999999988.....5557666667455.33..3445 PP

  Sulfotransfer_2 173 vgkyetleedrnailrllallnlknvavfgltefprktqtanttrrsnstr 223
                      v++ e  +++++++ r  +   l ++++ g++  +r   ++ +   +nstr
       AJA93168.1 219 VKTEELNNNTSESVNRVFEF--LDTKKFNGIDVKERFNVSKYKPM-NNSTR 266
                      55555444444444444444..33455666666666433222222.33333 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.041       4      73 ..      37     103 ..      34     123 .. 0.78
   2 ?   -2.7   0.0      0.93   3.3e+03     133     148 ..     162     177 ..     154     191 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 -EEEEE-STTSSHHHHHHHHHHS.S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHH CS
       SRPRB   4 pavllvGlsdsGKTslftrLttd.svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkak 73 
                 p+++++G  ++G Tsl++ L +  +++++ t   + +  ++  +k +++  + fP   +l++k+l+++ +k
  AJA93168.1  37 PNFIIIGEAKCGTTSLYNYLIQHpNIESSLTKEINFFNWSY--DKPKNWYRAHFPT--SLKKKMLKRFSNK 103
                 789*******************9455555555577788888..7778888888884..6666666665544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.93
                 HHHHHHHHHHHHHHCH CS
       SRPRB 133 ikdaLEkElnkiierr 148
                   +a+E E++ + ++ 
  AJA93168.1 162 FDEAIETEIQSLKQKN 177
                 5678888888887654 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.36       4      50 ..      39      86 ..      37      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
   PduV-EutP  4 illiGkvgsGKttLtqal.kgeelkYkktqaiefsdeviDtPGeylen 50
                 ++iG+ ++G t+L + l ++ +++ + t+ i+f +   D P ++   
  AJA93168.1 39 FIIIGEAKCGTTSLYNYLiQHPNIESSLTKEINFFNWSYDKPKNWYRA 86
                589***********998725579**************99999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2194.21
//
Query:       AJA93169.1  [L=366]
Description: radical SAM domain protein, CofH subfamily [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-19   70.0   0.0    2.9e-18   66.8   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
    0.00074   18.9   0.0      0.044   13.1   0.0    2.3  2  BKACE        beta-keto acid cleavage enzyme
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.26   11.4   0.0    1.7  2  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   4.8e-22   2.9e-18       2     163 ..      63     232 ..      62     236 .. 0.88
   2 ?    0.6   0.0      0.11   6.5e+02     111     144 ..     321     352 ..     298     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 4.8e-22
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC........CCTEEEEEEECSSCHG CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla........vpgiritvetngtlpd 90 
                  + t+ C+  C  Ca++++ + e+++++l++++i++ v ++ ++ g +++ i+gg +p+l+ d++e +  ++k +            +i++ +  t+ +
   AJA93169.1  63 NYTNLCAASCQMCAFYRK-GGEDDAYTLTPDQIEKRVAAA-KDLGaTEVHIVGGFHPDLQLDYYEQMMSAIKQKhpdmtikaFTAAEIFFLSKLTKNS 158
                  67999************7.*********************.7***9999999999******************9999999888888888888888877 PP

                  .HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHH CS
                  .xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 .eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleel 163
                   +e+l rl+ +g       g+e +++++  k+++++ t +++l+++e ++++gik++v++++g+  e  e+++++
   AJA93169.1 159 iPEILSRLKAAGlDSMPGGGAELFHPDVRSKIIRGKCTGQQWLDTIEVAHNLGIKSNVTMLYGHI-EKPEHVVDH 232
                  9***********77788999*******7788888*********************6666665555.666666655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                  SSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 111 aaddekvlklmnrghtfeevlealeklreagikr 144
                  a+++e + +   +++t++ +le+  +++e g k+
   AJA93169.1 321 AFSEE-IYRAA-GKPTNSSLLELATLAKEIGRKP 352
                  34555.99999.8999********9999999875 PP

>> BKACE  beta-keto acid cleavage enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   7.4e-06     0.044      23      82 ..      89     144 ..      72     165 .. 0.89
   2 !    3.2   0.0    0.0075        45     210     264 ..     301     354 ..     271     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-06
                 -SHHHHHHHHHHHHHHTESEEEE-EE-TTTS-EE--HHHHHHHHHHHHHHHTTSEEEE-S CS
       BKACE  23 vtpeeiaeeaveaaeaGAaivHlHaRdpedgrpsldpelyrevlarirekepdviinltt 82 
                 +tp++i + +++a + GA+ vH+        +p l++++y++++++i++k+pd+ i+  t
  AJA93169.1  89 LTPDQIEKRVAAAKDLGATEVHIVGGF----HPDLQLDYYEQMMSAIKQKHPDMTIKAFT 144
                 69*******************996655....589********************997655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0075
                 GHHHHHHHHHHTT-EEEESTT..T-SEEETTEE-S-HHHHHHHHHHHHHHTT-EB-- CS
       BKACE 210 aqlplaaaalalGghvRvGlE..DnlylkkgelaksNaelVeravriarelgreiat 264
                    +la+ al+ Gg+  vG      +y  ++  +++N  l e ++++a+e+gr++ +
  AJA93169.1 301 YGTKLAQVALSHGGNDLVGTAfsEEIY--RAAGKPTNSSLLE-LATLAKEIGRKPIQ 354
                 45689999*******888876226666..6778888999997.6789******9976 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.3e-05      0.26       4      92 ..      64     149 ..      60     169 .. 0.74
   2 ?   -3.7   0.0       2.1   1.2e+04      79      95 ..     263     279 ..     257     293 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
     Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhye.nkkellklvkrlkeeypekkiwletngtle 92 
                  ++ C  sC++C    +  ++     t +++e+++  + +++  + ++ ++GG  +h+  + +   ++++ +k++ p++ i+  t + + 
  AJA93169.1  64 YTNLCAASCQMCAFYRKGGEDDAYTLTPDQIEKRV--AAAKDLGATEVHIVGG--FHPDlQLDYYEQMMSAIKQKHPDMTIKAFTAAEIF 149
                 5789********97776666666666667777777..6777788899******..666514555667999999999******99998765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.1
     Fer4_14  79 pekkiwletngtleiel 95 
                 +e+k++ e++  +++++
  AJA93169.1 263 KEHKVTHESSSIYDLKI 279
                 35677777766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2701.26
//
Query:       AJA93170.1  [L=216]
Description: DSBA-like thioredoxin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-31  108.7   0.1    4.1e-31  108.4   0.1    1.1  1  Thioredoxin_4  Thioredoxin
    7.5e-17   61.7   0.1    1.5e-15   57.5   0.1    2.0  1  DSBA           DSBA-like thioredoxin domain
    1.8e-14   54.1   0.1    2.9e-14   53.4   0.1    1.3  1  Thioredoxin_2  Thioredoxin-like domain
    3.9e-06   26.7   0.1      8e-06   25.7   0.0    1.5  2  Thioredoxin_5  Thioredoxin
  ------ inclusion threshold ------
       0.02   14.9   0.0       0.85    9.6   0.0    2.3  2  Thioredoxin    Thioredoxin
       0.14   12.5   0.9        1.7    9.1   0.6    2.3  2  Thioredoxin_8  Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.1   1.4e-34   4.1e-31       4     165 ..      42     211 ..      40     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.4e-34
                    SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTH....HHH CS
  Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysq....qee 94 
                    ++ ++GnpdA++t++e+ d++C  C kf+ e+  k+ +  i+t++v f++rdfpl++ + s+ a+ a+ ca++++  +f++++  ly++     + 
     AJA93170.1  42 GTTILGNPDAKITIVEFGDYQCTFCYKFHDETMkKIDQAHIKTENVNFVYRDFPLNGPQ-SILASEASYCAQKQN--KFWEYHNTLYDNwggeNTG 134
                    6789*************************998769***********************8.************998..9999999999885554222 PP

                    TTS-HHH..HH......H.HHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE.TTEE...E-TT--HHHHHHHHT CS
  Thioredoxin_4  95 waeslke..la.aealdk.dekfeacleeekldalveaeskeakkagiestPtfii.ngek...veepqtyeelkalid 165
                    w ++  +  +  a+++      f++cle+++++++v  + + a++ gi +tP+f+i n+     + ++q++e+++++++
     AJA93170.1 135 WITK--NvlIGfANDIRLdLDSFSQCLENSEFKQKVLDNEQFAREIGIDATPSFLIfNDSElyrIIGAQPFEKFEQALQ 211
                    2222..2222245555543677**********************************96665355689********9998 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.1     5e-19   1.5e-15       1     193 []      54     211 ..      54     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 5e-19
                 EEEEEEBTTBHHHHHHH.HHHHHHHHHC...CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgk.erleklaars...pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef D++C +Cy +  e ++k+++++   ++v++v+r+f+l g                                           +s  a  + + 
  AJA93170.1  54 TIVEFGDYQCTFCYKFHdETMKKIDQAHiktENVNFVYRDFPLNGP------------------------------------------QSILASEASYC 110
                 799***********98526789999888*9888*************..........................................9********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE.TTC..EEEESSSSHHHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv.dgk..rmvfGadrldtlada 191
                 a+++++  ++ ++l++   +e++   ++++l  +a++  ld +++ + le++++k++v +n++ a+++g+  +P +++ +++  + + Ga++++++++a
  AJA93170.1 111 AQKQNKFWEYHNTLYDNWGGENTGWITKNVLIGFANDIRLDLDSFSQCLENSEFKQKVLDNEQFAREIGIDATPSFLIfNDSelYRIIGAQPFEKFEQA 209
                 ******************************************************************************96667**************** PP

                 HH CS
        DSBA 192 la 193
                 l+
  AJA93170.1 210 LQ 211
                 97 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   9.8e-18   2.9e-14       4     109 .]      50     210 ..      47     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 9.8e-18
  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd......................... 65 
                    + k ++v f d +C +C k+++e+++         ++v++ +++fp  +p++  +++a +ca+ ++k ++                          
     AJA93170.1  50 DAKITIVEFGDYQCTFCYKFHDETMKKidqahiktENVNFVYRDFPlNGPQSILASEASYCAQKQNKFWEYhntlydnwggentgwitknvligfa 145
                    57999*****************555555******************99999**************9777778999999999999************ PP

  Thioredoxin_2  66 ......................ieenvelarkygvrgtPtivfldgkeivarlpGyvpaeeleall 109
                                          + +n+++ar+ g+++tP++++++ + +++r+ G+ p+e++e++l
     AJA93170.1 146 ndirldldsfsqclensefkqkVLDNEQFAREIGIDATPSFLIFNDS-ELYRIIGAQPFEKFEQAL 210
                    ****************************************7766666.599************987 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.7   2.1e+03       8      25 ..      63      80 ..      58     122 .. 0.74
   2 !   25.7   0.0   2.7e-09     8e-06     110     167 ..     135     192 ..     102     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.7
  Thioredoxin_5  8 cseCweiEpelkklkvey 25
                   c  C+++  e +k ++++
     AJA93170.1 63 CTFCYKFHDETMKKIDQA 80
                   777777777777666553 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 2.7e-09
  Thioredoxin_5 110 iskeellleiaekaglDveefkeDlesklakkafqcDlklakemgvtevPtlvffnen 167
                      ++++l+  a++++lD++ f + le +  k++     ++a+e+g++ +P++ +fn++
     AJA93170.1 135 WITKNVLIGFANDIRLDLDSFSQCLENSEFKQKVLDNEQFAREIGIDATPSFLIFNDS 192
                    44559********************97777777777789*****************43 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.033     1e+02      18      48 ..      51      81 ..      35      96 .. 0.73
   2 ?    9.6   0.0   0.00028      0.85      59     102 ..     169     211 ..     155     212 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.033
                 SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCT CS
  Thioredoxin 18 kklvlveFyApwCghCkalaPeleklaeelk 48
                 +k  +veF    C+ C ++  e +k  ++ +
   AJA93170.1 51 AKITIVEFGDYQCTFCYKFHDETMKKIDQAH 81
                 67899***********999877665544443 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00028
                  TTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHH CS
  Thioredoxin  59 denedlakkyevegiPtlklfkngkevkkyegarekeklaaflk 102
                   +ne+ a+++++++ P +++f++++   ++ ga++ ek+++ l+
   AJA93170.1 169 LDNEQFAREIGIDATPSFLIFNDSE-LYRIIGAQPFEKFEQALQ 211
                  578999***************9998.778889999898888776 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6   0.00055       1.7       2      40 ..      52      91 ..      50     128 .. 0.86
   2 ?    1.3   0.0      0.15   4.5e+02      66      91 ..     164     191 ..     138     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00055
                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHH.TTSEEEEE CS
  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkk.kkkveivy 40
                   k++++ fg+++c  c +f+ + ++  ++ +    +v++vy
     AJA93170.1 52 KITIVEFGDYQCTFCYKFHDETMKKIDQAHIkTENVNFVY 91
                   89*****************997766665554499999998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                    E-TT-..HHHHTT-S--TT-SEEEEE-T CS
  Thioredoxin_8  66 fddkk..rnklkkkynvkaiPtlvvldk 91 
                    f++k   +++++++ ++ a P++++ + 
     AJA93170.1 164 FKQKVldNEQFAREIGIDATPSFLIFND 191
                    555533378999999******9999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1627.17
//
Query:       AJA93171.1  [L=424]
Description: ammonium transporter [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.6e-111  371.7  31.4     4e-111  371.5  31.4    1.0  1  Ammonium_transp  Ammonium Transporter Family


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.5  31.4  2.3e-115    4e-111       1     399 []       9     403 ..       9     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 371.5 bits;  conditional E-value: 2.3e-115
                      HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-.TTTTSCCGCCTTCCHHH......H CS
  Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign.lglsaagvqdetlldgl......f 87 
                      a++l++ +lv++m + ++l+e+gl r+knv++il + ++ la+ ++++++fGysl+fg s    g+ign  + + +g+++++ l+g+      f
       AJA93171.1   9 AWMLVAGMLVLLMIPALGLFESGLLRKKNVVSILSQIIFGLALLSVMWFVFGYSLSFGPS--QDGMIGNlDNAFIKGIPWDEPLEGMtipgvlF 100
                      7*********************************************************99..9******755667888888888888788888* PP

                      HHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.SSHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTT CS
  Ammonium_transp  88 flfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeggwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfegk 181
                      + fq++fa+++  + sg +aer+kf+++++f+ +++ l+y p++hw+wg ggwla+lgv+ DfAg++v+H+  g+a+Laaa+vlg+r+g +   
       AJA93171.1 101 VKFQMMFACITPLLLSGTIAERMKFKSFIIFISVWSALIYYPLVHWIWG-GGWLAELGVV-DFAGGIVIHTSVGMAALAAAIVLGQRRGFG--- 189
                      *************************************************.**********.****************************99... PP

                      TSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HH CS
  Ammonium_transp 182 eeaikghnlpfavlGtllLwfgWfgFNaGsaltankrararaavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepw 275
                      +    +h++p+avlG+ lLw+gWfg NaGsalt  +  ++ +a++T lA++++al+++ +s++++gk++++  +nG++AGl++iT+a ++v++ 
       AJA93171.1 190 PAINIPHSIPIAVLGASLLWLGWFGLNAGSALTSGALPAN-IALVTHLASSVSALIWVGFSWMRTGKPSIVAGINGAIAGLAGITPASGFVSVE 282
                      88889***********************************.***************************************************** PP

                      HHHHHHHHHHHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHCSSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Ammonium_transp 276 gAliiGlvAgvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaekvvaskisggllsgegkqlvvqligilvilayafvvtlill 369
                      +A++i +  g++s+ gv ++++klkidD+ldv +vHg++Gi+G+la gifa       +  +g+l+g+  ql++q++gi v++++ f+ t+++l
       AJA93171.1 283 HAFVIAIAIGIFSYGGVVLIRDKLKIDDALDVSSVHGIAGIVGALAIGIFASAA---IGGVDGWLYGNPDQLWIQAVGIGVAAVLGFGGTWLIL 373
                      ****************************************************97...468999******************************* PP

                      HHHHHHTTSB--HHHHHHSHHHHHHSSSSB CS
  Ammonium_transp 370 lllklllgLrvseeeeevglDvaehgetay 399
                       ++k ++g+rv++e e +glD+aehge+ay
       AJA93171.1 374 QVMKRTIGIRVDPEVEDMGLDLAEHGEAAY 403
                      ****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3068.31
//
Query:       AJA93172.1  [L=136]
Description: thioredoxin [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-31  107.9   0.1    3.2e-31  107.4   0.1    1.3  1  Thioredoxin    Thioredoxin
    2.1e-08   34.4   0.6    2.9e-06   27.5   0.0    2.6  3  Thioredoxin_8  Thioredoxin-like
    3.7e-08   33.2   0.4    4.6e-08   32.9   0.4    1.1  1  Thioredoxin_9  Thioredoxin
    5.3e-08   33.3   0.2    2.4e-07   31.2   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    1.5e-06   27.8   0.0    1.8e-06   27.5   0.0    1.2  1  OST3_OST6      OST3 / OST6 family, transporter family
      4e-05   23.6   0.2    0.00016   21.7   0.0    2.0  3  Thioredoxin_3  Thioredoxin domain
    0.00017   20.6   0.0     0.0002   20.4   0.0    1.0  1  Phosducin      Phosducin
     0.0002   21.1   0.1    0.00075   19.2   0.1    1.7  2  Redoxin        Redoxin
    0.00082   19.3   0.1     0.0024   17.8   0.1    1.8  1  AhpC-TSA       AhpC/TSA family
     0.0017   18.2   0.1     0.0028   17.5   0.1    1.3  1  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.013   15.7   0.3      0.031   14.4   0.2    1.7  1  Thioredoxin_7  Thioredoxin-like
      0.038   14.0   0.1       0.12   12.3   0.0    1.7  2  HyaE           Hydrogenase-1 expression protein HyaE
      0.039   14.4   0.1       0.21   12.0   0.0    2.0  2  DUF836         Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.1   2.3e-34   3.2e-31       2      94 ..      32     122 ..      31     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 2.3e-34
                  EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HH CS
  Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarek 94 
                  v++lt++nF++e+++ ++l+lv+F+A+wCg+Ck++ P ++++a+++k +v++a+v+vd+ +d+a ky+v++iPt+++fkng+ +++++ga  +
   AJA93172.1  32 VMELTSQNFNQEISN-NDLLLVDFWAEWCGPCKSMHPIFTRMAKKYK-QVRFARVNVDNAQDIAMKYGVQSIPTFIMFKNGEIANQMVGAVGE 122
                  7899***********.*******************************.*****************************************9765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.2   5.8e+03      77      81 ..      20      24 ..       7      42 .. 0.55
   2 !   27.5   0.0   2.1e-09   2.9e-06       1      47 [.      47      90 ..      46      95 .. 0.90
   3 !    7.8   0.0     0.003       4.2      67      92 ..      85     109 ..      81     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                   -S--T CS
  Thioredoxin_8 77 kynvk 81
                   + n++
     AJA93172.1 20 QQNIN 24
                   22333 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.1e-09
                   .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-H CS
  Thioredoxin_8  1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkke 47
                   ++++l+ f+a+wc pck ++p  +++ +k+k   +v++  v++d+ +
     AJA93172.1 47 NDLLLVDFWAEWCGPCKSMHPIFTRMAKKYK---QVRFARVNVDNAQ 90
                   5899**************************8...8999999998865 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.003
                    -TT-HHHHTT-S--TT-SEEEEE-TT CS
  Thioredoxin_8  67 ddkkrnklkkkynvkaiPtlvvldkn 92 
                    + ++ + ++ ky+v++iPt++   kn
     AJA93172.1  85 NVDNAQDIAMKYGVQSIPTFIMF-KN 109
                    5567889999*********7655.44 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.4   3.3e-11   4.6e-08      14     107 ..      18     110 ..       2     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.3e-11
                    HHHHHHHHHHHHHHHH---HHHHHT.--S-EEEEE.E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
  Thioredoxin_9  14 enkermlrvykkvelseeteekiks.iekklkilv.ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildee 107
                     ++++++++++++ ++e t++  ++ i+++  +lv + ++wCg +  + P++ ++a+  +++ +  +  d+ +++  +y   g ++iPt+i+++++
     AJA93172.1  18 LKQQNINNILNETPVMELTSQNFNQeISNNDLLLVdFWAEWCGPCKSMHPIFTRMAKKYKQVRFARVNVDNAQDIAMKY---GVQSIPTFIMFKNG 110
                    679999***********999954441444444444489*****************************************...99********9876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   1.8e-10   2.4e-07       3     100 ..      45     120 ..      42     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-10
  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.fldgkeivarlp 97 
                    +n+  +lv+f++++C+ Ck ++  +  +   +++       +++ ++ v+++ a++              a kygv++ Pt++ f +g+ i+++++
     AJA93172.1  45 SNNDLLLVDFWAEWCGPCKSMHPIFTRM--AKKY-------KQVRFARVNVDNAQDI-------------AMKYGVQSIPTFImFKNGE-IANQMV 117
                    578889*****************88877..4444.......4568999999999987.............589********77588888.****** PP

  Thioredoxin_2  98 Gyv 100
                    G+v
     AJA93172.1 118 GAV 120
                    *98 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.3e-09   1.8e-06      45     105 ..      58     110 ..      16     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.3e-09
   OST3_OST6  45 kCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppk 105
                  C +C+ ++p f+ +ak +++          Fa+v++d+++d+ +k+g++s+P +++f+  
  AJA93172.1  58 WCGPCKSMHPIFTRMAKKYKQV--------RFARVNVDNAQDIAMKYGVQSIPTFIMFKNG 110
                 4****************99988........5***************************974 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.4     6e+03      35      42 ..      19      26 ..       6      35 .. 0.53
   2 !   21.7   0.0   1.1e-07   0.00016      10      58 ..      59     111 ..      52     121 .. 0.87
   3 ?   -0.9   0.0       1.3   1.7e+03      19      39 ..     115     135 ..     108     136 .] 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.4
                   CCTTHHHH CS
  Thioredoxin_3 35 kvtdfeei 42
                   k +++++i
     AJA93172.1 19 KQQNINNI 26
                   33444444 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 1.1e-07
                    STTCHHHHHHHHHHCHCC.TCECEEECCTTHHHH.HHCT-SSSSEE..ECTTC CS
  Thioredoxin_3  10 CakCpklekavkeaaaek.gikaevekvtdfeei.ekygVmsvPal..vidgk 58 
                    C  C+ +  +++++a++  ++ +  ++v + ++i +kygV+s+P+   + +g+
     AJA93172.1  59 CGPCKSMHPIFTRMAKKYkQVRFARVNVDNAQDIaMKYGVQSIPTFimFKNGE 111
                    999**************956************************983333565 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                    HHHHHCHCCTCECEEECCTTH CS
  Thioredoxin_3  19 avkeaaaekgikaevekvtdf 39 
                     +  a+ e+gi++ ++k t++
     AJA93172.1 115 QMVGAVGEPGIHMICKKFTEN 135
                    556688899999999998876 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.5e-07    0.0002      98     215 ..       2     117 ..       1     127 [. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.5e-07
                 --HHHHHHHHHHHHHHH.HHH.H-------SEEE--SHHHHHHHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-TTSEEEEEEHHHH.--TTS CS
   Phosducin  98 ddeeflrkyrkqrmdem.rqk.lskgprfkfvlelesgeqfldtidkeqkitlivvhiyedgvkgtealnssliclaaeyptvkfckvkasvi.gasdr 193
                 +dee+ ++ +k++++++ +q+ ++   +   v+el s  +f + i  +    l++v  + +    ++++   +  +a +y  v+f +v+  +    + +
  AJA93172.1   2 EDEEL-ENIKKKQLEDLlKQQnINNILNETPVMELTSQ-NFNQEISNN---DLLLVDFWAEWCGPCKSMHPIFTRMAKKYKQVRFARVNVDNAqDIAMK 95 
                 56665.44555555554144414445556678888874.577767654...5899**********************************988625789* PP

                 S-TTT-SEEEEEETTEEEEEET CS
   Phosducin 194 fsrdvlpallvykagellsnfv 215
                 +  + +p+++++k ge+ +++v
  AJA93172.1  96 YGVQSIPTFIMFKNGEIANQMV 117
                 ****************988776 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   5.4e-07   0.00075      26      72 ..      45      88 ..      23      96 .. 0.72
   2 ?    1.0   0.0      0.22     3e+02      89     127 ..      84     112 ..      77     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.4e-07
                HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESS CS
     Redoxin 26 fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadn 72
                 ++  ++v f++  +c++C+  hp ++  a+++k+    +  v++dn
  AJA93172.1 45 SNNDLLLVDFWAE-WCGPCKSMHPIFTRMAKKYKQV--RFARVNVDN 88
                4444578899999.**********999998886654..444455555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                 EEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEE CS
     Redoxin  89 vlsDgsaaftkalGlrleedaseglrtpryavidedgkv 127
                 v +D  ++++ ++G++          +p+++++ ++g +
  AJA93172.1  84 VNVDNAQDIAMKYGVQ---------SIPTFIMF-KNGEI 112
                 5679999999999988.........88888876.45555 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.8e-06    0.0024       9      73 ..      34      92 ..      26     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                EEESTTCEE.EECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHH CS
    AhpC-TSA  9 elknadget.vslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspesh 73
                el+ +++++ +s    +++ +++ f+++ wc +C+   p + ++++++k   v    v+vd+ +++
  AJA93172.1 34 ELTSQNFNQeIS----NNDLLLVDFWAE-WCGPCKSMHPIFTRMAKKYK--QVRFARVNVDNAQDI 92
                555554433244....345699******.*******************9..778888888887755 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     2e-06    0.0028     131     203 ..      49     111 ..      34     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
        TraF 131 ygLlfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpks 203
                   L+ F ++ c+ c+ + pi  ++a+ky +     V+vd+ ++  ++          ++gv+++P++++++  +
  AJA93172.1  49 LLLVDFWAEWCGPCKSMHPIFTRMAKKYkQVRFARVNVDNAQD--IAM---------KYGVQSIPTFIMFKNGE 111
                 4566689999******************7789999*****999..777.........9***********99875 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.3e-05     0.031      20      81 ..      50     107 ..      44     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                    EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-..--SSEEEEE CS
  Thioredoxin_7  20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde..qgvPvvafl 81 
                    +lv+f a+wc++C+ +   f      k+   +++ + rv+v++ ++ i +++   q +P+++++
     AJA93172.1  50 LLVDFWAEWCGPCKSMHPIFTRM--AKK--YKQVRFARVNVDNAQD-I-AMKYgvQSIPTFIMF 107
                    899*************9888766..444..3677777777777777.3.444334669999887 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.4   1.9e+03      12      32 ..       7      27 ..       2      39 .. 0.68
   2 ?   12.3   0.0   8.9e-05      0.12      55      96 ..      74     113 ..      63     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                EEE-CCCHHHHHHHHSEEEEE CS
        HyaE 12 aevdadtlddflkaagdavll 32
                +++ +++l+d+lk++ +  +l
  AJA93172.1  7 ENIKKKQLEDLLKQQNINNIL 27
                556667777777776665544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.9e-05
                 CT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEE CS
        HyaE  55 kaFpnalraavvadreqeealaerfgvlktPsllflrdgeyl 96 
                 k+++++  a v    ++ + +a ++gv+  P+++++++ge+ 
  AJA93172.1  74 KKYKQVRFARVNV--DNAQDIAMKYGVQSIPTFIMFKNGEIA 113
                 5555554444444..66778999***************9976 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.84   1.2e+03      49      53 ..      29      33 ..       3      53 .. 0.49
   2 ?   12.0   0.0   0.00015      0.21       8      49 ..      57      99 ..      51     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.84
                TTTEE CS
      DUF836 49 eipvl 53
                e+pv+
  AJA93172.1 29 ETPVM 33
                33333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                TT-HHHHHHHHHHHH.HCCCTTEEEEEEETTT-CCCHCCCCTT CS
      DUF836  8 pgChlCeqakekLke.lkleegleleviDIakdeeleakYgle 49
                + C+ C++++ +  + +k+ ++++  ++++++ ++  +kYg++
  AJA93172.1 57 EWCGPCKSMHPIFTRmAKKYKQVRFARVNVDNAQDIAMKYGVQ 99
                56**********9994555566******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 900.06
//
Query:       AJA93173.1  [L=200]
Description: orotate phosphoribosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-12   45.8   0.3    5.9e-12   45.4   0.3    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.05   13.1   0.1       0.07   12.6   0.1    1.2  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.3   6.6e-16   5.9e-12      14     131 ..      48     158 ..      42     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 6.6e-16
                   EEEETTEEEEEE..--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHH CS
  Pribosyltran  14 avarlaaeilee..yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaale 108
                   +  + +++++ e   +++   +v +++gG+++a  la e+  pl yvrk+ ++++++  +            +  ++k l+++D++++Gg++++a++
    AJA93173.1  48 KMIKGLQNLIAEdiGFENFHSLVSVPTGGLVVAASLATEILKPLIYVRKQAKEHGTGKAVE---------GVICHDMKLLMIEDVVTSGGSVINAIK 135
                   556667777777777788889*******************99******************5.........56899********************** PP

                   HHHCC-BSEEEEEEEEE-HHHHH CS
  Pribosyltran 109 lLkekgpeevriavlvdkpatee 131
                    +ke+++ +  + ++vd+++++ 
    AJA93173.1 136 SIKEEKMVVTDAYAVVDRMEGAT 158
                   ****************9999865 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   7.8e-06      0.07     106     174 ..      99     169 ..      96     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-06
    PRTase_2 106 tdhllyaedeellaaakelvLvDDEistGktalnliralqeklpr..kryvvvslvdwrseedeaafaale 174
                 ++h   ++ e ++ ++ +l+++ D +++G +++n i++++e+ +   + y+vv  ++  +e+ +a+  +l+
  AJA93173.1  99 KEHGTGKAVEGVICHDMKLLMIEDVVTSGGSVINAIKSIKEEKMVvtDAYAVVDRMEGATEALQAEGVKLH 169
                 55666666777888999**********************99844335888888776666666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1474.33
//
Query:       AJA93174.1  [L=225]
Description: DSBA-like thioredoxin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-29  101.8   0.0    5.4e-29  101.5   0.0    1.1  1  Thioredoxin_4  Thioredoxin
      2e-09   37.5   0.3    8.7e-08   32.2   0.3    2.1  1  DSBA           DSBA-like thioredoxin domain
    3.3e-07   30.7   0.0    5.7e-07   30.0   0.0    1.4  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.022   14.4   0.0    1.2  1  Thioredoxin_5  Thioredoxin
      0.031   14.6   0.0        2.1    8.7   0.0    2.3  1  Thioredoxin_8  Thioredoxin-like
       0.15   12.0   0.0       0.21   11.5   0.0    1.2  1  Autophagy_N    Autophagocytosis associated protein (Atg3), N-


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   0.0   1.8e-32   5.4e-29       4     165 ..      50     222 ..      47     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 1.8e-32
                    SSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTHHHHTTS- CS
  Thioredoxin_4   4 tdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysqqeewaes 98 
                    + +v+G++dA++t++e  d++C  C+ ++ee+  ++++ y++tGk  ++++d+p+ ++  s+ a+ a  ca +++  ++++++ +l++ qe+    
     AJA93174.1  50 DAPVLGSKDATITIVEVGDYQCHMCKLWFEETRpQIIKNYVETGKANLVFIDMPFLGRD-STPASEATYCADDQG--KYWEYHSMLFTYQEDEIDG 142
                    5689****************************99************************8.**************9..8888999999998887776 PP

                    .......HHHHH.....HHHHHTS-------HHHHHHHHHHH.HHHT--SS-EEEE.....TTEEE-TT--HHHHHHHHT CS
  Thioredoxin_4  99 .......lkelaaealdkdekfeacleeekldalveaeskea.kkagiestPtfii.....ngekveepqtyeelkalid 165
                           l+++a + + ++e+f++c+  ++ +a v  ++++a k+ g +stPtf+i       +k+ ++++y+++ +++d
     AJA93174.1 143 gwananrLQAFALNLGLDMEQFDKCMITDDHRAHVNFNMQMAkKEFGANSTPTFVIvgptgEAQKIVGAHPYSTFVSVLD 222
                    677644444455556677************************8889**********777543345778999999999888 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.3   2.9e-11   8.7e-08       2     192 ..      63     221 ..      62     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.9e-11
                 EEEEEBTTBHHHHHHHHHH.HHHHHHC...CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHHH CS
        DSBA   2 vdeffDvlCPyCylgkerl.eklaars...pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarlllaa 96 
                 ++e  D++C+ C+l +e+  +++++++    ++++v+ ++++ g                                           +st a  +++ a
  AJA93174.1  63 IVEVGDYQCHMCKLWFEETrPQIIKNYvetGKANLVFIDMPFLGR------------------------------------------DSTPASEATYCA 119
                 555666666666665444313455555664446666666666666..........................................9*********** PP

                 HHHHGHHHHHHHHHHHHHTSSS-.....TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHH.HTT-SSSSEEEE...TTC.EEEESSSSH CS
        DSBA  97 gaeglaekvvrelfealwsegqa.....itddqellevaekaGldaeeldealeseavkeavrentaaaq.slgvtGvPtvvv...dgk.rmvfGadrl 185
                   +g    +++e++  l++ +++        ++ l+++a ++Gld+e++d+ + ++++  +v+ n+++a+ + g++ +Pt+v+    g+ + ++Ga ++
  AJA93174.1 120 DDQG----KYWEYHSMLFTYQEDeidggWANANRLQAFALNLGLDMEQFDKCMITDDHRAHVNFNMQMAKkEFGANSTPTFVIvgpTGEaQKIVGAHPY 214
                 ***7....78888888888887732222345667*********************************996269**********666334689******* PP

                 HHHHHHH CS
        DSBA 186 dtladal 192
                  t+ + l
  AJA93174.1 215 STFVSVL 221
                 9998866 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.9e-10   5.7e-07       7     108 ..      61     220 ..      54     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.9e-10
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd............................ 65 
                     ++v + d +C  Ck+  +e++++         + +   +++p l++++ p+++a +ca+++ k ++                             
     AJA93174.1  61 ITIVEVGDYQCHMCKLWFEETRPQiiknyvetGKANLVFIDMPfLGRDSTPASEATYCADDQGKYWEYhsmlftyqedeidggwananrlqafaln 156
                    566667799***********99999988885533333334666********************999999*************************** PP

  Thioredoxin_2  66 ....................ieenvelark.ygvrgtPtivfldgkeivarlpGyvpaeeleal 108
                                        ++ n++ a+k +g ++tPt+v+  ++ ++ +++G+ p   +  +
     AJA93174.1 157 lgldmeqfdkcmitddhrahVNFNMQMAKKeFGANSTPTFVIVGPTGEAQKIVGAHPYSTFVSV 220
                    ******************************9********9999999788999***998888665 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.5e-06     0.022     114     185 ..     148     218 ..     135     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-06
  Thioredoxin_5 114 ellleiaekaglDveefkeDlesklakkafqcDlkla.kemgvtevPtlvffneneeeeglkveglksyevye 185
                    + l++ a + glD+e+f + + ++      +  +++a ke+g +++Pt+v++    ++e  k+ g ++y++++
     AJA93174.1 148 NRLQAFALNLGLDMEQFDKCMITDDHRAHVNFNMQMAkKEFGANSTPTFVIVG--PTGEAQKIVGAHPYSTFV 218
                    56788999*************9999999999999999459************9..888889999999998875 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0007       2.1      74      94 ..     177     204 ..      58     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0007
                    H.......TT-S--TT-SEEEEE-TT-B CS
  Thioredoxin_8  74 l.......kkkynvkaiPtlvvldknge 94 
                    +       kk+++ ++ Pt+v++++ ge
     AJA93174.1 177 VnfnmqmaKKEFGANSTPTFVIVGPTGE 204
                    2333333488888899999999998875 PP

>> Autophagy_N  Autophagocytosis associated protein (Atg3), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.9e-05      0.21      33      82 ..      64     123 ..      60     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
  Autophagy_N  33 vaAGDyLvhkfptWsWasaeeskrksyLPkdKqfLvtrnVpcykRakql...........e 82 
                  v+ GDy +h+++ W  +++ ++  k+y  ++K  Lv  + p   R ++             
   AJA93174.1  64 VEVGDYQCHMCKLW-FEETRPQIIKNYVETGKANLVFIDMPFLGRDSTPaseatycaddqG 123
                  789**********9.577899***************9999998887776555544443331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1590.81
//
Query:       AJA93175.1  [L=49]
Description: hypothetical protein T478_0281 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1225  (0.0683251); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 347.90
//
Query:       AJA93176.1  [L=122]
Description: rRNA processing protein, FCF1 family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-14   53.7   0.2    2.8e-14   53.4   0.2    1.0  1  PIN_9     PIN like domain
    1.3e-05   25.5   0.0    1.7e-05   25.2   0.0    1.1  1  Fcf1      Fcf1
  ------ inclusion threshold ------
      0.044   14.1   2.5      0.074   13.3   2.5    1.4  1  PIN_4     PIN domain
      0.053   13.5   0.0      0.083   12.9   0.0    1.4  1  HypA      Hydrogenase/urease nickel incorporation, metallocha
      0.082   12.7   0.2       0.15   11.8   0.1    1.6  1  DUF5615   Domain of unknown function (DUF5615)
       0.11   12.5   1.1       0.88    9.6   0.2    2.2  2  Imm43     Immunity protein 43


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.2   9.3e-18   2.8e-14       1     112 [.       4     112 ..       4     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 9.3e-18
       PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDdailelakeldaavlvTnDreL 99 
                 vi Dt++L+  ++  ++ ++ +e  +g+  ++vpk v +ELe+l  ag++ ++   +  l+  ++ ++ ++++++aD ail++ ke +  +++T D+eL
  AJA93176.1   4 VISDTSFLIHFATHRIKNIDSIETEIGTLSFIVPKIVKKELEHL--AGDPDKKIISEQTLDFIKNFKTNDIDGSNADAAILDFIKENR-SIVATMDKEL 99 
                 899*****************************************..9999***********************************998.6666****** PP

       PIN_9 100 kkrllekgipvil 112
                 k++++++g  +++
  AJA93176.1 100 KNKIKQSGSSILS 112
                 *******998876 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.6e-09   1.7e-05       9      99 .]      34     122 .]      29     122 .] 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.6e-09
                 EEEEHHHHHHHHHCT........-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTSTT--EEEEE--EEEE-- CS
        Fcf1   9 pliTqCviaeleklgkk......lkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrkipgvPilyikrsvmvlEk 99 
                 +++ + v +ele+l  +       +++l++   ++ +k n  ++ +ad  +++ +k    ++r ivAt Dk+l++++++  g  il i++ ++vlE+
  AJA93176.1  34 FIVPKIVKKELEHLAGDpdkkiiSEQTLDF---IKNFKTNDIDGSNADAAILDFIK----ENRSIVATMDKELKNKIKQ-SGSSILSIHNDKIVLEN 122
                 566777888999988552222333334444...445566667789***********....4799*************87.6999***********95 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.5   2.5e-05     0.074       2      80 ..       5     102 ..       4     121 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
       PIN_4   2 VlDTnvlLhdpe.alksf......keehdvviPitVleELdklKkgsse....relarlarqanrlldelleke...............sgrlkvqtsa 74 
                 + DT++l+h  +  +k++       + +  ++P +V +EL++l  + ++    +       q+++++++ + +                + r  v t +
  AJA93176.1   5 ISDTSFLIHFAThRIKNIdsieteIGTLSFIVPKIVKKELEHLAGDPDKkiisE-------QTLDFIKNFKTNDidgsnadaaildfikENRSIVATMD 96 
                 779****9976525666688888888999******************9533330.......55666655544444455555555555554444555555 PP

       PIN_4  75 eelpee 80 
                 +el+++
  AJA93176.1  97 KELKNK 102
                 555543 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.083      19      54 ..      15      50 ..       3      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                CCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC CS
        HypA 19 keaaarkvtkvkvevGelsgvepeaLefafellaeg 54
                ++++++++++++ e+G+ls ++p++++  +e la +
  AJA93176.1 15 ATHRIKNIDSIETEIGTLSFIVPKIVKKELEHLAGD 50
                467889**********************99999843 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.1e-05      0.15      35      66 ..      76     107 ..      52     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
     DUF5615  35 asDeeileyAkeedriivTkDkDFgellllgg 66 
                   D +il++ ke+  i+ T Dk   + ++++g
  AJA93176.1  76 NADAAILDFIKENRSIVATMDKELKNKIKQSG 107
                 68********************9888877766 PP

>> Imm43  Immunity protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00029      0.88      43      67 ..      47      72 ..      26      91 .. 0.71
   2 ?    2.5   0.1     0.046   1.4e+02      55      83 ..      81     110 ..      74     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00029
       Imm43 43 ys.hsklkivSdefldllkefklsdk 67
                +      ki+S++ ld++k+fk+ d 
  AJA93176.1 47 LAgDPDKKIISEQTLDFIKNFKTNDI 72
                44456789**************9986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.046
       Imm43  55 fldllkefklsdkyekaklkilsk.kgesl 83 
                 +ld++ke++       ++lk  +k  g+s+
  AJA93176.1  81 ILDFIKENRSIVATMDKELKNKIKqSGSSI 110
                 799****99766544444444433044444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 997.17
//
Query:       AJA93177.1  [L=218]
Description: antioxidant, AhpC/TSA family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-06   26.0   0.1    0.00094   19.1   0.0    2.5  2  AhpC-TSA       AhpC/TSA family
      7e-06   25.8   0.0     0.0055   16.4   0.0    2.3  2  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.015   15.6   0.0        5.4    7.4   0.0    2.6  2  Thioredoxin_8  Thioredoxin-like


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.6e-07   0.00094       1     106 [.       4     115 ..       4     128 .. 0.77
   2 !    4.5   0.0    0.0051        30     104     123 ..     174     199 ..     133     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-07
                 TTSB----EEEST.TCEEEECHHHTTSEEEEEEESTST-CCHH.HHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H....SSEEEE-TTSHH CS
    AhpC-TSA   1 vgdkapdfelkna.dgetvslsdykgkpvvlffypkdwcpvCt.telpalaklyeefkergvevigvsvdspeshkkfiekes...lnfpllsDeegkv 94 
                 +g+kap+ +l ++ +g + ++++  +++ ++ +++  +cp+C  + +p++ + y++fk  g++v+gv +  ++  k++ e  +    + +++ D ++++
  AJA93177.1   4 IGEKAPNLKLGKWvQGMETNFDKEGDNVKLVEVFQV-NCPGCFmHSIPEIINIYQKFKGDGLTVMGVATAFEDYDKNTLENLEmllTTGEVVGD-TKQA 100
                 79********97735666666655557778888888.*****62579**********************9999999999999988666677777.5566 PP

                 HHHTT-EETT...TT CS
    AhpC-TSA  95 akaygvlkee...kg 106
                   +yg lk+    ++
  AJA93177.1 101 LSQYGQLKDGklpYK 115
                 677887755544444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0051
                 T......TTECSCEEEEE-TTSBEEE CS
    AhpC-TSA 104 e......kglalratfvidkegkiry 123
                 +      +   +++t+++d++g++r 
  AJA93177.1 174 AetfemySLQGTPSTILVDRKGVLRD 199
                 0333343555899*********9985 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.3e-07    0.0055       3      83 ..       5      87 ..       3     140 .. 0.77
   2 !    7.8   0.0   0.00043       2.6      94     134 ..     173     204 ..     132     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.3e-07
                TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH...T CS
     Redoxin  3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkefwgk...e 83
                g+kaP+++l +   +g +++ ++  +++++v ++    cP C    + ++ ++++++k  g +v +v ++ +++ k+ +++   +
  AJA93177.1  5 GEKAPNLKL-GKWVQGMETNFDKEGDNVKLVEVFQV-NCPGCFMHSIpEIINIYQKFKGDGLTVMGVATAFEDYDKNTLENlemL 87
                899*****9.5599*********7777778888887.*****766666*******************999999988877775442 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00043
                 TSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESS CS
     Redoxin  94 saaftkalGlrleedaseglrtpryavidedgkvvylevep 134
                 sa+ ++++ l+         +tp+++++d++g+++ +  ++
  AJA93177.1 173 SAETFEMYSLQ---------GTPSTILVDRKGVLRDVSFGQ 204
                 44555555555.........9*************9987665 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0029        18       7      42 ..      35      70 ..      28      90 .. 0.77
   2 ?    7.4   0.0    0.0009       5.4      62      93 ..     163     195 ..     131     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0029
                   EE--SSSHHH.HHHHHHHHHHHHHHHHTTSEEEEEEE CS
  Thioredoxin_8  7 yfgaswcppc.kaftpklkelyeklkkkkkveivyvs 42
                    ++  +cp c ++ +p+++++y+k+k ++++ +  v 
     AJA93177.1 35 EVFQVNCPGCfMHSIPEIINIYQKFK-GDGLTVMGVA 70
                   556678998769*************9.6777766654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0009
                    EE.EE-TT-.HHHHTT-S--TT-SEEEEE-TT- CS
  Thioredoxin_8  62 lsvpfddkk.rnklkkkynvkaiPtlvvldkng 93 
                    +   f++k+ + +  ++y +++ P+++++d++g
     AJA93177.1 163 VKGYFKSKEySAETFEMYSLQGTPSTILVDRKG 195
                    44467787757788****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1629.15
//
Query:       AJA93178.1  [L=53]
Description: hypothetical protein T478_1343 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.2   0.5    0.00026   21.0   0.5    1.1  1  DZR             Double zinc ribbon
    0.00066   19.2   1.2       0.69    9.6   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0013   18.0   0.8     0.0071   15.6   0.2    2.0  2  zf-TFIIB        Transcription factor zinc-finger
     0.0016   18.7   1.9     0.0039   17.4   1.8    1.7  2  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
     0.0021   17.5   1.1      0.098   12.2   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0025   17.1   3.2       0.77    9.3   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0046   17.2   3.0       0.29   11.4   0.5    2.1  2  zf-LITAF-like   LITAF-like zinc ribbon domain
     0.0049   16.9   3.9      0.022   14.8   0.1    2.5  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.008   16.4   0.2      0.012   15.9   0.2    1.3  1  LIM             LIM domain
  ------ inclusion threshold ------
      0.013   15.5   0.4      0.014   15.4   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.025   14.3   3.8        1.5    8.6   0.4    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.027   14.4   1.6         10    6.2   0.1    2.0  1  zinc-ribbons_6  zinc-ribbons
      0.029   14.3   3.2       0.15   12.0   1.3    2.0  1  DUF4428         Domain of unknown function (DUF4428)
      0.032   14.3   1.3      0.087   13.0   1.3    1.7  1  Zn-ribbon_8     Zinc ribbon domain
      0.033   14.3   0.5        1.5    9.0   0.0    2.1  2  SR1P            SR1 protein
      0.058   13.3   2.9       0.42   10.5   2.9    1.9  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.075   13.1   2.0       0.47   10.6   0.1    2.1  2  UPF0547         Uncharacterised protein family UPF0547
      0.076   13.3   1.3        1.5    9.1   0.1    2.0  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.13   12.4   1.9        4.9    7.3   0.3    2.0  2  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
       0.16   11.9   3.8       0.46   10.5   3.8    1.7  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.21   11.6   5.0        1.6    8.8   2.5    2.1  2  zf-BED          BED zinc finger
       0.23   12.0   4.0        3.8    8.2   0.2    2.3  2  zf-C2H2         Zinc finger, C2H2 type
       0.25   11.4   4.2        4.5    7.3   0.8    2.3  2  YhfH            YhfH-like protein
       0.33   11.9   4.8        3.8    8.6   0.5    2.7  2  zf-C2H2_4       C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.5   3.5e-07   0.00026      13      40 ..       5      43 ..       2      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.5e-07
         DZR 13 rfCseCgtklkavaa...........edrCpsCgekvdp 40
                ++C++Cg+k++ ++            +++CpsC++ ++ 
  AJA93178.1  5 IVCGKCGEKISTMKMlksvkdvlkhyNNKCPSCNQTLST 43
                68*******998777999****************99765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00092      0.69       3      14 ..       5      16 ..       3      20 .. 0.84
   2 !    8.9   0.1    0.0015       1.1       4      17 ..      33      46 ..      31      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00092
      zf_UBZ  3 ylCerCgkeipe 14
                ++C +Cg++i++
  AJA93178.1  5 IVCGKCGEKIST 16
                69********97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0015
      zf_UBZ  4 lCerCgkeipesel 17
                 C+ C++++++se+
  AJA93178.1 33 KCPSCNQTLSTSEF 46
                7*********9986 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.32   2.4e+02       2       6 ..       7      11 ..       6      29 .. 0.67
   2 !   15.6   0.2   9.5e-06    0.0071       1      15 [.      33      47 ..      33      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.32
    zf-TFIIB  2 CPkCq 6 
                C kC+
  AJA93178.1  7 CGKCG 11
                55565 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 9.5e-06
    zf-TFIIB  1 kCPkCqdeleeserg 15
                kCP+C+++l +se++
  AJA93178.1 33 KCPSCNQTLSTSEFS 47
                8************96 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   5.3e-06    0.0039       1      46 [.       1      43 [.       1      47 [. 0.87
   2 ?    3.8   0.1     0.093        70       7      25 ..      34      52 ..      33      53 .] 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.3e-06
  Chordopox_RPO7  1 mvfplvCstCGrDlseeryrLlvkkkkLkdvlatvkrkC..CrlkLst 46
                    m  ++vC  CG+ +s  + +     k++kdvl+ +++kC  C   Lst
      AJA93178.1  1 MSVEIVCGKCGEKISTMKML-----KSVKDVLKHYNNKCpsCNQTLST 43
                    6679***********98764.....789***********888888888 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.093
  Chordopox_RPO7  7 CstCGrDlseeryrLlvkk 25
                    C +C + ls   + L v++
      AJA93178.1 34 CPSCNQTLSTSEFSLDVEE 52
                    99***********998876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00013     0.098      17      30 ..       2      15 ..       1      22 [. 0.85
   2 ?    4.7   0.1     0.028        21       2       9 ..      33      40 ..      32      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                  TTCEEESSSSBEEE CS
  TF_Zn_Ribbon 17 rgelvCtdCGlVle 30
                  + e+vC++CG+ + 
    AJA93178.1  2 SVEIVCGKCGEKIS 15
                  6699******9986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                  EETTTTCE CS
  TF_Zn_Ribbon  2 kCPnCgst 9 
                  kCP C+ t
    AJA93178.1 33 KCPSCNQT 40
                  8****976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0015       1.2      17      26 .]       5      14 ..       3      14 .. 0.87
   2 !    9.3   0.4     0.001      0.77       3      14 ..      32      43 ..      31      45 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
  zf-ribbon_3 17 nvCpyCGtkl 26
                 +vC +CG+k+
   AJA93178.1  5 IVCGKCGEKI 14
                 79*****986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.001
  zf-ribbon_3  3 vrCPnCGa.plss 14
                 ++CP+C++ + s+
   AJA93178.1 32 NKCPSCNQtL-ST 43
                 5899999944.65 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.012       9.1      55      68 ..       3      16 ..       1      18 [. 0.65
   2 !   11.4   0.5   0.00038      0.29      50      68 ..      25      43 ..      18      45 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
  zf-LITAF-like 55 vehyCpnCgallgt 68
                   ve  C++Cg+++ t
     AJA93178.1  3 VEIVCGKCGEKIST 16
                   66677777777765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00038
  zf-LITAF-like 50 dslkdvehyCpnCgallgt 68
                   d lk+ + +Cp+C+++l t
     AJA93178.1 25 DVLKHYNNKCPSCNQTLST 43
                   5578888899999999976 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.13     1e+02       4       9 ..       7      12 ..       5      17 .. 0.79
   2 ?   -2.2   0.0       6.4   4.8e+03      14      21 ..      24      31 ..      23      31 .. 0.78
   3 !   14.8   0.1     3e-05     0.022       3      16 ..      33      46 ..      32      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
      zf-ACC  4 CpsCge 9 
                C +Cge
  AJA93178.1  7 CGKCGE 12
                889987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
      zf-ACC 14 keLernly 21
                k++ ++++
  AJA93178.1 24 KDVLKHYN 31
                88888886 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3e-05
      zf-ACC  3 KCpsCgemlykkeL 16
                KCpsC+++l + e+
  AJA93178.1 33 KCPSCNQTLSTSEF 46
                9********98886 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.6e-05     0.012       1      41 [.       7      46 ..       7      53 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                -TTT--BE-TTTEEEEETTEEEETTTSB-TTT-SB-CTT.C CS
         LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCsdCqkeLkegsf 41
                C +C++ki+  +++ +++d   H +  +C +C+++L++ +f
  AJA93178.1  7 CGKCGEKISTMKMLKSVKDVLKHYNN-KCPSCNQTLSTSEF 46
                **************999999999885.9********99984 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.4   1.9e-05     0.014      68      95 ..       2      40 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                --EEEETTTS-EEECHH..HHH..........S-TTTSSS CS
        HypA 68 pvkvrCreCgkefelee..kal..........rCpkCgsa 95
                +v++ C +Cg+++++ +  k            +Cp+C+++
  AJA93178.1  2 SVEIVCGKCGEKISTMKmlK-SvkdvlkhynnKCPSCNQT 40
                57899********9775332.257889999*******985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4     0.002       1.5       2       9 ..       7      14 ..       6      16 .. 0.74
   2 ?    6.9   0.2    0.0071       5.3       1      10 [.      33      42 ..      33      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
  zinc_ribbon_2  2 CpnCGael 9 
                   C +CG+++
     AJA93178.1  7 CGKCGEKI 14
                   88888887 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0071
  zinc_ribbon_2  1 fCpnCGaelq 10
                   +Cp+C  +l+
     AJA93178.1 33 KCPSCNQTLS 42
                   8****98876 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.014        10      28      43 ..       3      18 ..       1      24 [. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                    EEEE-SSS-S---EEE CS
  zinc-ribbons_6 28 kealCpeCeqelevlk 43
                    +e +C +C+++++++k
      AJA93178.1  3 VEIVCGKCGEKISTMK 18
                    5778999999988876 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3   0.00021      0.15      21      39 ..       5      22 ..       4      33 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
     DUF4428 21 yvCkdClkKlseflsdvki 39
                +vC +C +K+s+++ + k+
  AJA93178.1  5 IVCGKCGEKISTMK-MLKS 22
                69999999995552.3332 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.3   0.00012     0.087       7      36 ..       6      41 ..       3      43 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
  Zn-ribbon_8  7 rCeeCghefevlqsis.dap.....ltaCPeCgsev 36
                  C +Cg++   +   +  ++     + +CP+C++++
   AJA93178.1  6 VCGKCGEKISTMKMLKsVKDvlkhyNNKCPSCNQTL 41
                 7*****9999665544333367887888****9865 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.002       1.5       4      16 ..       5      17 ..       4      21 .. 0.90
   2 ?    3.8   0.1     0.083        62       6      15 ..      34      43 ..      33      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
        SR1P  4 IvCqtCnatIdhf 16
                IvC +C++ I ++
  AJA93178.1  5 IVCGKCGEKISTM 17
                9********9886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.083
        SR1P  6 CqtCnatIdh 15
                C +Cn+t  +
  AJA93178.1 34 CPSCNQTLST 43
                999***9876 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.9   0.00056      0.42      25      48 ..       6      42 ..       4      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00056
                E-HHHHHHHHH.............TT-B-TTT--B-- CS
  zf-C3HC4_3 25 lCeeCaekllk.............rkkkCpiCrrpie 48
                +C +C ek+                ++kCp C++  +
  AJA93178.1  6 VCGKCGEKISTmkmlksvkdvlkhYNNKCPSCNQTLS 42
                7888888887678888888888899********9876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.27     2e+02       2      11 ..       6      15 ..       6      16 .. 0.76
   2 ?   10.6   0.1   0.00062      0.47       2      12 ..      33      43 ..      32      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
     UPF0547  2 vCPeCeakvP 11
                vC  C +k++
  AJA93178.1  6 VCGKCGEKIS 15
                5778999987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
     UPF0547  2 vCPeCeakvPv 12
                +CP C +++++
  AJA93178.1 33 KCPSCNQTLST 43
                7*******997 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1       0.1        77      32      45 ..       5      19 ..       2      32 .. 0.53
   2 ?    9.1   0.1     0.002       1.5       4      23 ..      33      52 ..      30      53 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
     zf-Di19 32 vvCPvCaekvt.kdl 45
                 vC  C ek++ + +
  AJA93178.1  5 IVCGKCGEKIStMKM 19
                566666655331233 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
     zf-Di19  4 tCPyCgkeltvkeLveHved 23
                +CP C+++l+++e+   ve+
  AJA93178.1 33 KCPSCNQTLSTSEFSLDVEE 52
                7**********999888776 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.025        19      55      67 ..       7      19 ..       1      27 [. 0.65
   2 ?    7.3   0.3    0.0066       4.9      25      40 ..      29      44 ..      20      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
   DiS_P_DiS 55 CraCkakislryp 67
                C +C++kis + +
  AJA93178.1  7 CGKCGEKISTMKM 19
                5555555555444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0066
   DiS_P_DiS 25 kprSrCpkCghklkwl 40
                + + +Cp+C+++l+  
  AJA93178.1 29 HYNNKCPSCNQTLSTS 44
                45789****9999876 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.8   0.00062      0.46      18      48 ..       5      45 ..       1      50 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00062
    zf-C2HC5 18 pnClnCGkiiCakegls..........kpCsfCgspllsse 48
                  C +CG  i +++ l+          ++C++C++ l +se
  AJA93178.1  5 IVCGKCGEKISTMKMLKsvkdvlkhynNKCPSCNQTLSTSE 45
                5799999988888888778888889999*******998765 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.5    0.0021       1.6      17      44 .]       5      35 ..       2      35 .. 0.86
   2 ?    6.4   0.4     0.012       8.8      12      29 ..      27      44 ..      18      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                -EETTTTEE----...SSTHHHHHHHHHS-H CS
      zf-BED 17 avCryCgkilsrg...ggttnLkrHLrrkHp 44
                +vC  Cg+++s      +++   +H + k+p
  AJA93178.1  5 IVCGKCGEKISTMkmlKSVKDVLKHYNNKCP 35
                89*********98888888888888888887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                GGSS--EETTTTEE---- CS
      zf-BED 12 lkeqkavCryCgkilsrg 29
                lk+ + +C  C+ +ls +
  AJA93178.1 27 LKHYNNKCPSCNQTLSTS 44
                799***********9976 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2     0.005       3.8       2      17 ..       6      21 ..       5      31 .. 0.88
   2 ?    5.2   0.4     0.045        33       2      13 ..      33      44 ..      33      46 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.005
                EETTTTEEESSHHHHH CS
     zf-C2H2  2 kCpdCgksFkrksnLk 17
                +C++Cg++ ++  +Lk
  AJA93178.1  6 VCGKCGEKISTMKMLK 21
                7*****9999988887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.045
                EETTTTEEESSH CS
     zf-C2H2  2 kCpdCgksFkrk 13
                kCp C+++ +++
  AJA93178.1 33 KCPSCNQTLSTS 44
                7******99887 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.8    0.0061       4.5      16      26 ..       7      17 ..       6      19 .. 0.84
   2 ?    5.3   0.1     0.026        19      30      37 .]      30      37 ..      21      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0061
        YhfH 16 CteCGkeieEq 26
                C +CG++i  +
  AJA93178.1  7 CGKCGEKISTM 17
                *******9865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.026
        YhfH 30 YgneCekC 37
                Y+n+C +C
  AJA93178.1 30 YNNKCPSC 37
                9*****99 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.095        71       2      17 ..       6      21 ..       5      32 .. 0.79
   2 ?    8.6   0.5     0.005       3.8       2      13 ..      33      44 ..      32      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.095
   zf-C2H2_4  2 kCpiCgksFsskkaLl 17
                 C  Cg+  s+ k L+
  AJA93178.1  6 VCGKCGEKISTMKMLK 21
                5999998888877764 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.005
   zf-C2H2_4  2 kCpiCgksFssk 13
                kCp C+++ s++
  AJA93178.1 33 KCPSCNQTLSTS 44
                8*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1124  (0.0626917); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 401.93
//
Query:       AJA93179.1  [L=192]
Description: hypothetical protein T478_1400 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.043   13.8   0.7        0.1   12.6   0.7    1.6  1  Minor_capsid_2  Minor capsid protein


Domain annotation for each model (and alignments):
>> Minor_capsid_2  Minor capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   5.7e-06       0.1      74     108 ..     144     179 ..     126     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-06
  Minor_capsid_2  74 aekkgkvkftkyttPgtgkeWdkk.Akakevedwke 108
                      +k+  + + ky +P  g  Wdk+ A++   +dw +
      AJA93179.1 144 LDKFTDIDILKYRKPNGGIDWDKYhAERRRKRDWTR 179
                     4554458999**************9*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1479  (0.0824921); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1436.41
//
Query:       AJA93180.1  [L=382]
Description: polysaccharide biosynthesis protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0002   21.5  11.1     0.0002   21.5  11.1    4.4  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
       0.75    8.9  35.9        1.7    7.8  18.0    2.8  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
       0.76    9.1  46.0       0.17   11.3  25.2    2.9  2  Polysacc_synt    Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2  11.7       1.4   8.2e+03      60     112 ..      49     101 ..      15     125 .. 0.58
   2 ?   -9.1  15.4         3   1.8e+04      22     139 ..     123     246 ..     106     251 .. 0.62
   3 ?   -1.0   7.8      0.28   1.7e+03      56     115 ..     230     287 ..     195     296 .. 0.68
   4 !   21.5  11.1   3.3e-08    0.0002       2      81 ..     299     378 ..     298     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
  Polysacc_synt_C  60 iatvlallvvavln...lyalrrllgiklellrrllkpllaalvmgivvyllllll 112
                      ia+++++++ +  +   ++++ + l+i+    +  +  +++++v++ +v+++   +
       AJA93180.1  49 IASAISYIALFGSQntiIVFAAKNLKIQS---TLYFISIISSVVLSTIVIIVIPSF 101
                      66677777777666544666666666666...222244555555555533232222 PP

  == domain 2  score: -9.1 bits;  conditional E-value: 3
  Polysacc_synt_C  22 LqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr.llgikl.....ellrrllkpllaalvmgiv..vyl 107
                      L g +   ++ k++++  ++ ++l + ++++fg   +++a  +++l+++  +++  +  ++ ++l      ++++ + +ll++ + g +  v  
       AJA93180.1 123 LLGKKLYSTYSKYVILQKILTICLGISFLHFFGFESIIFALGFSYLFYLKRIIRNFQEmKIDFSLlrsklGFITNNYILLLSSGLHGQIdkV-- 214
                      45555556677888999999999999999999999999999999998886665555544566666766665566666777777777777432.. PP

  Polysacc_synt_C 108 llllllgllllaalalllavlvgalvYlllll 139
                      l+  llg++ l +++l+++ +v + +  ++++
       AJA93180.1 215 LVAPLLGFTVLGNFSLGMQFIVVMSIISGIIF 246
                      44444444444444555555444444444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.28
  Polysacc_synt_C  56 vGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgl 115
                      +G+ +  v + + ++++ + +++  +++     r  +  ++++++++i+ +++l  ++++
       AJA93180.1 230 LGMQFIVVMSIISGIIFKYLLAQDATNVEN--NRLKILSVICSIIISILGMIFLPTIIEI 287
                      566666777777777777888888888877..4444566777777777755455554444 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 3.3e-08
  Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrll 81 
                      ++i+++ ii++s+++++ s L g    k++l   + g+ v +i  ++l   + i+G+ai+ vl+ +v +v+  + ++rl+
       AJA93180.1 299 IQIMCIHIIPTSIAVIFESKLLGQLNSKYVLAGRLSGLGVMVIGMIILGSVYDIIGIAISLVLSSIVLCVIFAIGVQRLT 378
                      89*********************************************************************999998876 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  18.0   0.00028       1.7       6     232 ..      35     245 ..      30     252 .. 0.83
   2 ?    4.7  10.9    0.0025        15      40     160 ..     252     373 ..     242     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00028
  Polysacc_synt_3   6 LspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfynqpelvtvlrvlalvlilsglss 99 
                      + p+++G +  ++ + s ++ ++ +G ++ +i     + +  st++ ++++++++++++++++   i sfy+ ++        ++ l+   +++
       AJA93180.1  35 IEPSEYGEIQWLIGIASAISYIALFGSQNTIIVFAAKNLKIQSTLYFISIISSVVLSTIVIIV---IPSFYEIDI--------GILLFAYVINA 117
                      79********************************99999999****************99987...5589*9984........44444455555 PP

  Polysacc_synt_3 100 vqeallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkelfsfglklllsnllnyl 193
                      +    l  +  +++ +k+ ++ ++++++++i   l  +g  ++++   +s l+ l  ++   +   ++k++++ l++ ++f  +  +  l   l
       AJA93180.1 118 LAIGDLLGKKLYSTYSKYVILQKILTICLGISF-LHFFGFESIIFALGFSYLFYLKRII---RNFQEMKIDFSLLRSKLGFITNNYILLLSSGL 207
                      556666666779*******************97.6789*****9987777666554433...3334666788899******************* PP

  Polysacc_synt_3 194 arnldnlliGkvlssaaLGlYsvakrlaslpvaeitsvi 232
                        ++d++l++ +l+ + LG +s +++++ +++++i+ +i
       AJA93180.1 208 HGQIDKVLVAPLLGFTVLGNFSLGMQFI-VVMSIISGII 245
                      *************************987.5667777776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0025
  Polysacc_synt_3  40 edlteedlstvftfnlvlgllialvlfllaplias.fynqpe.lvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaiv 131
                      +d+t+ + +++  ++++ +++i+++ +++ p i + f+ + + + + ++++ + +i +++ ++ e++l  +l+ k + + +l +  v+vi  i+
       AJA93180.1 252 QDATNVENNRLKILSVICSIIISILGMIFLPTIIEiFFPKFImISDAIQIMCIHIIPTSIAVIFESKLLGQLNSKYVLAGRLSGLGVMVIGMII 345
                      566666677888899********99888887776625555442578*************************************99999887777 PP

  Polysacc_synt_3 132 lAllglgvwALvigtllssllslvllwla 160
                      l    + +  ++i+ +lss++ +v++ + 
       AJA93180.1 346 LGS-VYDIIGIAISLVLSSIVLCVIFAIG 373
                      765.5678889999999999999998765 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  25.2   2.8e-05      0.17       3     259 ..       8     243 ..       7     249 .. 0.78
   2 ?   -1.9  20.9      0.29   1.7e+03      24     185 ..     214     371 ..     195     377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
  Polysacc_synt   3 kgvivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlvllfllllli 98 
                    k+v  + ++ +i   l++++ +yla  + p ++G  + ++ i++ ++ ++ +G  ++++ + ak+ +    ++l++++++++++++ +++++++ +
     AJA93180.1   8 KDVGKIGTGDVIGTALGAIFWFYLASQIEPSEYGEIQWLIGIASAISYIALFGSQNTIIVFAAKNLK--IQSTLYFISIISSVVLSTIVIIVIPSF 101
                    56667789999*******************************************************8..899999999988888888888888888 PP

  Polysacc_synt  99 aaflglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfrp 194
                            + + + il ++++   ++a+ ++ l+  +   +y    ++++++  ++l ++++  f+ + ++++++ +++l   +++  ++r   ++
     AJA93180.1 102 --------YEIDIGILLFAYV---INALAIGDLLGKKLYSTYSKY-VILQKILTICLGISFLHFFG-FESIIFALGFSYL---FYLKRIIR---NF 178
                    ........5555555555555...555555566666555555544.56666666667777777777.6666666655554...34555555...56 PP

  Polysacc_synt 195 rfvilslklvrellsfsapltisslaillytyidsillglllgaeavGiYnaayqllvaisglla 259
                    ++++++ +l r  l f ++  i  l++ l  +id +l + llg +++G+++++ q+ v+ s++  
     AJA93180.1 179 QEMKIDFSLLRSKLGFITNNYILLLSSGLHGQIDKVLVAPLLGFTVLGNFSLGMQFIVVMSIISG 243
                    77777678889999999999999999999999999999999999999999999999998887655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.29
  Polysacc_synt  24 vylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllvllvlvllfllllliaa.....flglpelavlylil 114
                    v++a +lg +  G ++l + +++ ++i+++  +   l +     +      +l +l+v+ ++++++l +++l++i +     f + ++    ++i+
     AJA93180.1 214 VLVAPLLGFTVLGNFSLGMQFIVVMSIISGIIFKYLLAQDATNVE----NNRLKILSVICSIIISILGMIFLPTIIEiffpkFIMISD---AIQIM 302
                    77888999999********************99999988654444....5789999*******************9984444444433...36666 PP

  Polysacc_synt 115 almllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivsl 185
                     + + +  + ++f + l+ +l + ky++  +++  l++++  +i +  ++di ++++++vl+++v  ++++
     AJA93180.1 303 CIHIIPTSIAVIFESKLLGQL-NSKYVLAGRLS-GLGVMVIGMIILGSVYDIIGIAISLVLSSIVLCVIFA 371
                    666666677777777777666.57887777765.5666666666667777799999999999998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2708.39
//
Query:       AJA93181.1  [L=221]
Description: SNARE-like domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-14   55.0   3.6      1e-14   55.0   3.6    2.5  3  SNARE_assoc    SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.11   12.8   1.6       0.64   10.3   0.2    2.1  2  Glycophorin_A  Glycophorin A


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2      0.17   1.6e+03      70      82 ..      22      34 ..      10      41 .. 0.73
   2 !   55.0   3.6   1.1e-18     1e-14       1     116 [.      34     147 ..      32     151 .. 0.90
   3 ?   -0.4   0.2      0.17   1.5e+03       8      24 ..     179     195 ..     174     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.17
  SNARE_assoc 70 allllrllpivPr 82
                 + +++ l+p+vP+
   AJA93181.1 22 VSFFGSLIPFVPI 34
                 4567777777775 PP

  == domain 2  score: 55.0 bits;  conditional E-value: 1.1e-18
  SNARE_assoc   1 lPsevll..vaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvka...lerlverygflallllrllpivPrdlvnyvaGltr 93 
                  +Ps +ll  + +G  f+l +  +++++ a++++ + ++++      +++rk++sek+ ++   ++rlv++yg+ a++++  +pi P+d++ +++Gl++
   AJA93181.1  34 IPSFILLvtMSVGNQFDLHILAIIAAVTATVAKQIIFVIS------YGGRKIMSEKTKQRmlpFQRLVKKYGAAAAFVAAATPI-PDDIIYVPLGLAK 124
                  6777777679999**************************6......45688888888888899********************7.8************ PP

  SNARE_assoc  94 vsfkrFflatfiGsipwalvyay 116
                  +++ rFf+at+ G+++ +  ++ 
   AJA93181.1 125 YNPLRFFIATLTGKLVLCYAIVI 147
                  **************998776665 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.17
  SNARE_assoc   8 vaaGvlfglllgtlvts 24 
                  +++ v+fg +++ +v++
   AJA93181.1 179 IIGIVVFGAVMTAVVVL 195
                  44555556655554443 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   7.1e-05      0.64      58      86 ..      51      80 ..      42      92 .. 0.78
   2 ?    1.5   0.1     0.037   3.3e+02      51      76 ..     170     197 ..     153     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.1e-05
                   TTHHHHHHHHHHHHHH.HHHHHHHHHHTHS CS
  Glycophorin_A 58 lvitliifgvmAgvig.tillisYlirRli 86
                   l i  ii +v A v   +i++isY  r+++
     AJA93181.1 51 LHILAIIAAVTATVAKqIIFVISYGGRKIM 80
                   67999*********8625788***999864 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.037
                    SSSSSS-TTHHHHHH..HHHHHHHHHHH CS
  Glycophorin_A  51 lvhdFselvitliif..gvmAgvigtil 76 
                       d + + i++i++  +vm +v+  +l
     AJA93181.1 170 EDLDDPTPIIIGIVVfgAVMTAVVVLML 197
                    5556678888888644569988876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1564.07
//
Query:       AJA93182.1  [L=77]
Description: hypothetical protein T478_0656 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 463.10
//
Query:       AJA93183.1  [L=61]
Description: hypothetical protein T478_0067 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0017   18.6   1.5     0.0017   18.6   1.5    1.4  1  IBR             IBR domain, a half RING-finger domain
     0.0039   17.2   2.6      0.059   13.4   0.2    2.0  2  CpXC            CpXC protein
     0.0075   16.4   2.5      0.013   15.6   2.5    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.015   15.3   0.5      0.016   15.2   0.5    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.016   15.3   0.3      0.017   15.1   0.3    1.1  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.018   15.0   5.4       0.65   10.0   5.4    2.2  1  zinc_ribbon_4   zinc-ribbon domain
      0.019   14.4   2.1        2.5    7.6   0.3    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.02   14.6   2.0      0.069   12.9   1.8    1.8  2  Ribosomal_S27e  Ribosomal protein S27
      0.028   14.4   0.8        5.1    7.1   0.1    2.0  2  zf-DNL          DNL zinc finger
       0.03   14.3   0.3      0.046   13.7   0.3    1.2  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
      0.033   14.1   1.6      0.046   13.6   1.6    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.04   13.6   1.1        3.4    7.5   0.1    2.2  2  YacG            DNA gyrase inhibitor YacG
      0.067   13.4   2.8        1.5    9.0   0.1    2.2  2  zf-RING_7       C4-type zinc ribbon domain
      0.067   13.3   0.5      0.074   13.1   0.5    1.1  1  DUF2614         Zinc-ribbon containing domain
      0.095   12.7   2.3        1.4    9.0   0.1    2.1  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.11   13.2   4.6        4.2    8.1   0.5    2.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.11   12.4   5.6       0.43   10.6   0.5    2.1  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.12   12.1   2.8       0.25   11.1   2.8    1.5  1  zinc_ribbon_5   zinc-ribbon domain
       0.13   12.8   0.0       0.16   12.5   0.0    1.1  1  DUF4830         Domain of unknown function (DUF4830)
       0.13   11.0   0.4       0.15   10.8   0.4    1.2  1  tRNA-synt_1g    tRNA synthetases class I (M)
       0.17   11.9   2.8        3.9    7.5   0.0    2.2  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.21   11.7   2.4        9.5    6.3   0.1    2.0  2  Thioredoxin_3   Thioredoxin domain
       0.27   11.2   5.6        1.9    8.4   1.0    2.2  2  DUF3797         Domain of unknown function (DUF3797)
       0.45   10.7   6.0        3.5    7.8   6.1    2.0  1  Zn-ribbon_8     Zinc ribbon domain
       0.61   10.4   5.9        1.2    9.5   0.4    2.2  2  zinc_ribbon_9   zinc-ribbon


Domain annotation for each model (and alignments):
>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.5   2.3e-06    0.0017      20      47 ..       8      33 ..       5      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
         IBR 20 wCprpdCeaiieksegcksvtCskCgfe 47
                 Cp  +Ce++++ +++ ++vtC++C+fe
  AJA93183.1  8 RCP--ECENVAKVNDELTKVTCPHCKFE 33
                6*9..***********999*******97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.015        11      36      50 ..       5      19 ..       2      22 .. 0.79
   2 !   13.4   0.2   8.2e-05     0.059      32      58 ..      19      45 ..      16      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
        CpXC 36 featCpkCgatakle 50
                ++a+Cp+C++ ak++
  AJA93183.1  5 LDARCPECENVAKVN 19
                6789****9998876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.2e-05
        CpXC 32 dgslfeatCpkCgatakleapllyhdp 58
                +++l+++tCp+C  + +++  l + + 
  AJA93183.1 19 NDELTKVTCPHCKFEKTYDEYLEIMKD 45
                789**********99999887766543 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.5   1.8e-05     0.013      13      39 ..       4      30 ..       3      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
  Auto_anti-p27 13 MLaetCpvC.gvPLmrdrkggkvyCvaC 39
                   ML++ Cp+C +v  + d   +kv C+ C
     AJA93183.1  4 MLDARCPECeNVAKVNDE-LTKVTCPHC 30
                   *********999999996.5699***** PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   2.2e-05     0.016      70      96 ..       6      34 ..       2      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                EEEETTTS-EEECHHH..HHS-TTTSSS- CS
        HypA 70 kvrCreCgkefeleek..alrCpkCgsad 96
                 +rC eC++  +++++  +++Cp+C+ ++
  AJA93183.1  6 DARCPECENVAKVNDEltKVTCPHCKFEK 34
                689*****999977644689*****9765 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   2.4e-05     0.017      40      81 ..       7      49 ..       2      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
  Zn_Tnp_IS91 40 yeCeeCghekivyfsCksrhCpsCqkkat.eewlekqqeellp 81
                  +C+eC++  +v     +  Cp+C+ ++t +e+le ++++ ++
   AJA93183.1  7 ARCPECENVAKVNDELTKVTCPHCKFEKTyDEYLEIMKDQAVN 49
                 68**********************9766626677766666655 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   5.4   0.00091      0.65       3      32 ..       7      31 ..       5      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00091
  zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCg 32
                    +Cp+C+ + +++de      +kv+C++C+
     AJA93183.1  7 ARCPECENVAKVNDE-----LTKVTCPHCK 31
                   589999988777775.....799******6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0067       4.8       4      13 ..       8      17 ..       6      22 .. 0.77
   2 ?    7.6   0.3    0.0035       2.5       3      23 ..      25      31 ..      23      33 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0067
  zf-ribbon_3  4 rCPnCGapls 13
                 rCP+C ++++
   AJA93183.1  8 RCPECENVAK 17
                 8999988755 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0035
  zf-ribbon_3  3 vrCPnCGaplssddnvCpyCG 23
                 v+C              p+C 
   AJA93183.1 25 VTC--------------PHCK 31
                 455..............5553 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.8   9.6e-05     0.069       4      32 ..       3      30 ..       1      32 [. 0.88
   2 ?    4.8   0.4     0.032        23       6      18 ..      23      35 ..      18      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-05
                    -EEEEE-TTTS-EEEEESS-SS-EEESSS CS
  Ribosomal_S27e  4 kFldvkCpdCenetvvFshaatvvkCisC 32
                    + ld +Cp+Cen   v +   t v+C  C
      AJA93183.1  3 YMLDARCPECENVAKVNDE-LTKVTCPHC 30
                    7799***********9876.6899**999 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                    EEEE-TTTS-EEE CS
  Ribosomal_S27e  6 ldvkCpdCenetv 18
                     +v Cp C+ e++
      AJA93183.1 23 TKVTCPHCKFEKT 35
                    5899****87765 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0071       5.1      30      45 ..       8      23 ..       6      25 .. 0.89
   2 ?    6.4   0.1     0.011       8.2      29      54 ..      25      50 ..      23      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0071
      zf-DNL 30 qCpgCknrHliaDnLg 45
                +Cp+C+n   + D+L 
  AJA93183.1  8 RCPECENVAKVNDELT 23
                8*******99999996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
      zf-DNL 29 vqCpgCknrHliaDnLgwfedkkkti 54
                v+Cp+Ck +      L++++d++ ++
  AJA93183.1 25 VTCPHCKFEKTYDEYLEIMKDQAVNM 50
                89*****9999999999999887775 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   6.4e-05     0.046       9      38 ..       5      32 ..       3      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                CEEE-TTTTTTSEETTE......E-TTTTT CS
   Anti-TRAP  9 LEtkCdaCngsGkiepeeprasleCPkCsG 38
                L+  C++C+   k++ e   + + CP+C+ 
  AJA93183.1  5 LDARCPECENVAKVNDE--LTKVTCPHCKF 32
                7889*******999988..999******95 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.6   6.5e-05     0.046      30      55 ..       8      33 ..       7      39 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
  OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                    +C+eC  + k +++  +++Cp+C+fe
      AJA93183.1  8 RCPECENVAKVNDELTKVTCPHCKFE 33
                    6**********9************98 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.024        17       2      14 ..       8      20 ..       7      23 .. 0.79
   2 ?    7.5   0.1    0.0047       3.4       1      14 [.      25      38 ..      25      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
        YacG  2 kCPtCkkevewse 14
                +CP C++  ++++
  AJA93183.1  8 RCPECENVAKVND 20
                8****99877665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0047
        YacG  1 vkCPtCkkevewse 14
                v+CP+Ck e +++e
  AJA93183.1 25 VTCPHCKFEKTYDE 38
                89*****9988876 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4     0.048        34      24      29 ..       7      12 ..       5      13 .. 0.91
   2 ?    9.0   0.1    0.0021       1.5      21      29 ..      20      30 ..      14      31 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
                EE-TTT CS
   zf-RING_7 24 vtCpeC 29
                ++CpeC
  AJA93183.1  7 ARCPEC 12
                69**** PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0021
                TB-..EE-TTT CS
   zf-RING_7 21 dev..vtCpeC 29
                de+  vtCp+C
  AJA93183.1 20 DELtkVTCPHC 30
                666779***** PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5    0.0001     0.074      68     101 ..       7      42 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
     DUF2614  68 vvcpeceketkvlGrvd..lcmhcdepltldksleG 101
                  +cpece+ +kv        c hc+   t d+ le 
  AJA93183.1   7 ARCPECENVAKVNDELTkvTCPHCKFEKTYDEYLEI 42 
                 68*********966543226***********99995 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5     0.083        60      22      25 ..       9      12 ..       5      14 .. 0.69
   2 ?    9.0   0.1    0.0019       1.4       5      15 ..      27      44 ..      25      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.083
  PhnA_Zn_Ribbon 22 CpeC 25
                    CpeC
      AJA93183.1  9 CPEC 12
                    6666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0019
  PhnA_Zn_Ribbon  5 CplCaSeytY.......e 15
                    Cp+C+ e tY        
      AJA93183.1 27 CPHCKFEKTYdeyleimK 44
                    999999999965555553 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3      0.01       7.2       3      14 ..       7      18 ..       6      25 .. 0.76
   2 ?    8.1   0.5    0.0059       4.2       3      15 ..      25      37 ..      23      39 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
     zf-ISL3  3 hrCPnCgsktvv 14
                 rCP+C ++ +v
  AJA93183.1  7 ARCPECENVAKV 18
                59*****99633 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0059
     zf-ISL3  3 hrCPnCgsktvvk 15
                 +CP+C+  + ++
  AJA93183.1 25 VTCPHCKFEKTYD 37
                69****9888776 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5     0.044        31      20      27 ..       8      15 ..       5      20 .. 0.79
   2 ?   10.6   0.5   0.00061      0.43      18      30 ..      24      36 ..      20      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.044
  Zn_Tnp_IS1595 20 vCPhCgsr 27
                   +CP C++ 
     AJA93183.1  8 RCPECENV 15
                   7****985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00061
  Zn_Tnp_IS1595 18 gfvCPhCgsrkay 30
                   +++CPhC+ +k y
     AJA93183.1 24 KVTCPHCKFEKTY 36
                   689*****99877 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.8   0.00035      0.25       3      32 ..       7      31 ..       5      32 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
  zinc_ribbon_5  3 irCpdCdtkFklvdsklKksgkkVrCakCa 32
                    rCp+C+   k+ d+       kV C +C 
     AJA93183.1  7 ARCPECENVAKVNDEL-----TKVTCPHCK 31
                   59**********9998.....99******5 PP

>> DUF4830  Domain of unknown function (DUF4830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00022      0.16      12      44 ..      18      51 ..      14      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00022
     DUF4830 12 kpietkevkiPk.efeevyaeynelqkdiGldLe 44
                 + e  +v+ P+ +fe++y ey e++kd+ ++++
  AJA93183.1 18 VNDELTKVTCPHcKFEKTYDEYLEIMKDQAVNMA 51
                55677889999757999**************996 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00021      0.15     123     155 ..       9      43 ..       3      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                   ETTTTEE..E-GGG-EE........-TTS-EE-TT CS
  tRNA-synt_1g 123 cpkderf..lpdryvegtCPkckseeargdqceec 155
                   cp++e+    +d+  ++tCP+ck e+ +++  e +
    AJA93183.1   9 CPECENVakVNDELTKVTCPHCKFEKTYDEYLEIM 43 
                   55555432268999***********9998776655 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0054       3.9       1      11 [.       8      18 ..       8      23 .. 0.87
   2 ?    4.6   0.7     0.046        33       1       6 [.      26      31 ..      26      34 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0054
   Ogr_Delta  1 rCPhCgapaaa 11
                rCP+C++ a +
  AJA93183.1  8 RCPECENVAKV 18
                7*****99875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.046
   Ogr_Delta  1 rCPhCg 6 
                +CPhC+
  AJA93183.1 26 TCPHCK 31
                6****6 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.014       9.8       7      23 ..       6      22 ..       3      26 .. 0.81
   2 ?    6.3   0.1     0.013       9.5       8      31 ..      25      50 ..      21      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                   SSSSTTCHHHHHHHHHH CS
  Thioredoxin_3  7 gpgCakCpklekavkea 23
                   +  C++C++++k+  e+
     AJA93183.1  6 DARCPECENVAKVNDEL 22
                   678******99998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                   SSSTTCH..HHHHHHHHHCHCCTCEC CS
  Thioredoxin_3  8 pgCakCp..klekavkeaaaekgika 31
                    +C++C+  k++    e+++++ +++
     AJA93183.1 25 VTCPHCKfeKTYDEYLEIMKDQAVNM 50
                   57*****9999988888888887665 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0    0.0027       1.9      14      28 ..       7      21 ..       4      25 .. 0.75
   2 ?    5.7   0.2     0.019        13      14      23 ..      25      34 ..      21      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0027
     DUF3797 14 vqCPeCgNnkvlNse 28
                + CPeC N    N e
  AJA93183.1  7 ARCPECENVAKVNDE 21
                68******7555544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
     DUF3797 14 vqCPeCgNnk 23
                v CP C+ +k
  AJA93183.1 25 VTCPHCKFEK 34
                79****9776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1    0.0048       3.5       7      33 ..       8      31 ..       6      36 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
  Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCg 33
                 rC eC ++  v     +  +++CP+C+
   AJA93183.1  8 RCPECENVAKVND---ELTKVTCPHCK 31
                 7888885555444...444777****5 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.7      0.11        75      23      29 ..       8      14 ..       5      15 .. 0.77
   2 ?    9.5   0.4    0.0016       1.2      19      28 ..      20      31 ..      14      33 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
  zinc_ribbon_9 23 lCPhCgg 29
                    CP+C++
     AJA93183.1  8 RCPECEN 14
                   4****75 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
  zinc_ribbon_9 19 dsd..vlCPhCg 28
                   d+   v+CPhC+
     AJA93183.1 20 DELtkVTCPHCK 31
                   4443369****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 357.51
//
Query:       AJA93184.1  [L=414]
Description: cysteine desulfurase, SufS family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.9e-153  508.5   0.2   1.1e-152  508.3   0.2    1.0  1  Aminotran_5      Aminotransferase class-V
    0.00034   19.3   0.1    0.00061   18.4   0.1    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0014   18.0   0.0     0.0016   17.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0057   15.7   0.0     0.0093   15.0   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.3   0.2  2.5e-156  1.1e-152       1     371 []      29     401 ..      29     401 .. 0.99

  Alignments for each domain:
  == domain 1  score: 508.3 bits;  conditional E-value: 2.5e-156
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTSEEEEETTS CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslars.lkpgdeivvteae 97 
                  +y+d+aAttqkp++V+da+++yy+++n+n+hr+vh l++e t+a+e++r+ va+++n+e++ eiif++Gtte+inlva++++r  +++gd iv+te e
   AJA93184.1  29 VYFDNAATTQKPNQVIDAISDYYQNHNSNIHRAVHALAEESTEAFEDTRDIVAKFLNIEDSREIIFVRGTTEGINLVAYAWGRDnVNEGDIIVTTEYE 126
                  7************************************************************************************************* PP

                  HGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
  Aminotran_5  98 hhanlvpwqelakrtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                  hh+n+vpwq l ++++a++k+i +d++gel ld+l+++l+  k+klv+++h+snv+Gti pv+ei++ +k++g+ vl+Daaq+v+h++++++++g+Df
   AJA93184.1 127 HHSNIVPWQLLTQEKKAQLKYIDIDDNGELMLDQLDDYLStGKVKLVTFSHMSNVLGTISPVKEIVSKCKNAGVKVLIDAAQSVPHMKVNLNEIGCDF 224
                  ***************************************769******************************************************** PP

                  EEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC CS
  Aminotran_5 195 lafsghKllgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlk 292
                  ++fsghK+lgPtG+Gvl+++ke+lek+ p+l+gg+m++ev   ett+++ p+kfeaGTpn+a++ig+++a++yle+ig+e+i+khe el++y+le++k
   AJA93184.1 225 FVFSGHKMLGPTGVGVLWAKKEILEKMSPFLGGGDMIREVHKYETTWNDLPYKFEAGTPNIADVIGFAEAIKYLEKIGMENIRKHELELTKYALEEMK 322
                  ************************************************************************************************** PP

                  TSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
  Aminotran_5 293 slpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                  ++pg++lyg+++ e+r ++vsfnf++vh++dv+tl+d+eg+a+rsGhhcaq+lm+ l++++t RaS+yiynt+eevd l
   AJA93184.1 323 KIPGITLYGTKEPEKRGGVVSFNFNSVHPHDVGTLIDKEGVAIRSGHHCAQVLMEKLNVAATNRASFYIYNTKEEVDVL 401
                  ****************************************************************************976 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.4e-07   0.00061      88     201 ..     114     234 ..     106     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-07
                      S-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHH.HHCCT.....TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
  Cys_Met_Meta_PP  88 lkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleele.kaike.....ntklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                      +++Gd iv++++ + +     + ++++ + + k++d +d  el   ++++     ++klv +  ++n l  +  +++i++ +k+agv v++D++
       AJA93184.1 114 VNEGDIIVTTEYEHHSNIVPWQLLTQEKKAQLKYIDIDDNGELMlDQLDDylstgKVKLVTFSHMSNVLGTISPVKEIVSKCKNAGVKVLIDAA 207
                      6788989998888888888888888889999999999876554312333333337*************************************** PP

                      TTHT.TTS-GGGGT-SEEEEETTTTTT CS
  Cys_Met_Meta_PP 176 fasp.llqrplklgaDivvhSaTKylg 201
                       + p + ++  + g+D  v S+ K lg
       AJA93184.1 208 QSVPhMKVNLNEIGCDFFVFSGHKMLG 234
                      ****555666689********999886 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.6e-07    0.0016      91     216 ..     138     282 ..      56     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-07
                      HHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHH CS
  Beta_elim_lyase  91 aelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivke 184
                       + + ++l+ ++++++G++ l++l + +        k+kl++     n+  G++ +   ++e+   +k+ g+++++D+A     + ++++ + e
       AJA93184.1 138 TQEKKAQLKYIDIDDNGELMLDQLDDYLST--G---KVKLVTFSHMSNV-LGTISP---VKEIVSKCKNAGVKVLIDAAQS---VPHMKVNLNE 219
                      4556788899999999*************9..3...69*****999997.566655...6778899************965...5677999999 PP

                      HHTTSSEEEEESSSTT--SS-.EEEEE-HH.................................... CS
  Beta_elim_lyase 185 mfsyvDsvtmslkKdllanvG.gvlafrddel.................................e 216
                      +  ++D +++s+ K  l + G gvl  +++ l                                  
       AJA93184.1 220 I--GCDFFVFSGHKM-LGPTGvGVLWAKKEILekmspflgggdmirevhkyettwndlpykfeagT 282
                      9..7**********7.56799899998888546666666665555555555555555555555550 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.1e-06    0.0093     194     234 ..     211     252 ..     168     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-06
                 -BHHHHHHT.T-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
        SelA 194 Ptvqealae.GvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                 P+++ +l+e G+d   fsG k+lG    G++  kke++ek+ 
  AJA93184.1 211 PHMKVNLNEiGCDFFVFSGHKMLGPTGVGVLWAKKEILEKMS 252
                 6666655544*****************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2456.04
//
Query:       AJA93185.1  [L=233]
Description: di-trans,poly-cis-decaprenylcistransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-70  237.6   0.1    1.3e-70  237.4   0.1    1.0  1  Prenyltransf     Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.062   13.5   0.5       0.12   12.6   0.4    1.6  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.076   13.5   2.3       0.14   12.6   0.8    1.9  2  PIN_12           PIN domain
       0.14   12.3   0.0       0.27   11.4   0.0    1.4  1  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.4   0.1   2.9e-74   1.3e-70       1     224 []       8     232 ..       8     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 237.4 bits;  conditional E-value: 2.9e-74
                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHHHHHHHHHTTEEEEEESSGGG CS
  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellkeelkellkegvrvrviGdlel 94 
                   i+DGNrRwAk++  + +e+Gh +Ga+a++++l++c e+++k++t+Y++S eN+ R++ee+d+l++l+    e+l ++   +++k+++rv++iG +el
    AJA93185.1   8 ILDGNRRWAKRNL-TIQEKGHFKGADAVENLLDWCEEFDIKIITLYVLSAENLDRKNEELDYLYDLIYkrlEKLYND--PRIHKNKMRVKAIGTIEL 101
                   89********999.77777************************************************7454444444..49**************** PP

                   S-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHHHHCTSTT..T.SSS-SEEEEESS--S-TTSSTTTT CS
  Prenyltransf  95 lpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideetlekhlytaka.lpdpDlliRtsGeeRlSnFllwql 189
                   lpe+++e l ++ e tk+ nk   lnia++Yg+++e+v+av+++  + ++ + + +ei++e +e++lyt++  + +pD+++RtsGe+R+S+Fllwq+
    AJA93185.1 102 LPESIKEVLGRLDEVTKNYNK-HFLNIAIAYGGQNELVDAVKKIGMKIKNGELDaKEINKEVIESNLYTSHLpQSSPDMILRTSGEKRMSGFLLWQS 197
                   *****************6666.**********************6555544444367899********97778899********************* PP

                   TT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
  Prenyltransf 190 ayselyfldvlWPdfskedllealleyqkrerrfg 224
                   aysel+fld +WP+f+k dl++a++++qkr+rr+g
    AJA93185.1 198 AYSELVFLDIFWPEFRKIDLMRAIRTFQKRKRRIG 232
                   *********************************87 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   2.8e-05      0.12      16      98 ..      89     163 ..      70     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                   HHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N  16 eklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaele 98 
                   +k+      ++ + ++  l e  +e+  +l+e+ ++ N+   +I+ a       +el++ vk+++ ++k+ e + ke+++e+ 
    AJA93185.1  89 NKM-----RVKAIGTIELLPESIKEVLGRLDEVTKNYNKHFLNIAIAYGG---QNELVDAVKKIGMKIKNGELDAKEINKEVI 163
                   333.....455688888899999***********************9974...689***********************9986 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   3.2e-05      0.14      10     111 ..      23     128 ..      17     149 .. 0.75
   2 ?    4.1   0.2     0.013        58      42      89 ..     113     164 ..     112     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.2e-05
      PIN_12  10 deffrlseeealkklleliesgkiklivpdivldEflknrekkieeskkle.kalks...lsklksakkklnekkkllslkeikkkieekveeslkkll 104
                 +e+ ++++++a+++ll+ +e+ +ik+i+  +   E l  +++++++   l+ k l++     ++ ++k+++++  +++ l e  k++  +++e+ k++ 
  AJA93185.1  23 QEKGHFKGADAVENLLDWCEEFDIKIITLYVLSAENLDRKNEELDYLYDLIyKRLEKlynDPRIHKNKMRVKAIGTIELLPESIKEVLGRLDEVTKNYN 121
                 5567888899***********************************996666666666655689999999999999998888888888888555544333 PP

      PIN_12 105 ekleaik 111
                 + + +i 
  AJA93185.1 122 KHFLNIA 128
                 3333344 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
      PIN_12  42 ldEflknrekkiees.......kklekalkslsklksakkklnekkkllslkeik 89 
                 ldE+ kn++k++ ++       ++l +a+k+   ++ ++k+ +   k++ ++ i+
  AJA93185.1 113 LDEVTKNYNKHFLNIaiayggqNELVDAVKK---IGMKIKNGELDAKEINKEVIE 164
                 69***********996665443333333333...333333333333322223333 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.9e-05      0.27      13      86 ..      80     161 ..      78     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                      XXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHH......HHHHHHHHHHHHHT...-BTCCG-S--HH CS
  Cob_adeno_trans  13 lvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLee......iqneLfdlgaelatp..ekkkekkkitee 86 
                      l++  r++K++ rv+a+Gt++ l   i  ++  l+e ++++++++ +       qneL+d+ +++ ++  + + ++k+i++e
       AJA93185.1  80 LYNDPRIHKNKMRVKAIGTIELLPESIKEVLGRLDEVTKNYNKHFLNiaiaygGQNELVDAVKKIGMKikNGELDAKEINKE 161
                      78899******************99999999888888666666665534444469999999999987654333333344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1662.42
//
Query:       AJA93186.1  [L=56]
Description: hypothetical protein T478_0217 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.077   12.9   0.0        0.1   12.5   0.0    1.1  1  DUF1899   Domain of unknown function (DUF1899)


Domain annotation for each model (and alignments):
>> DUF1899  Domain of unknown function (DUF1899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-06       0.1      12      47 ..      16      51 ..      15      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-06
     DUF1899 12 fgkpakkeecydnirvsknawdsnlikaNpkflAvn 47
                f+k  ++eec+++i v+  +   + +   +kf+A+ 
  AJA93186.1 16 FCKKGRHEECMKEIPVNAKSEGPHECTFDTKFIACK 51
                89999*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 448.68
//
Query:       AJA93187.1  [L=220]
Description: fructose-6-phosphate aldolase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-58  198.5   0.1    1.4e-57  195.3   0.1    2.2  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase
     0.0013   17.8   0.1     0.0014   17.8   0.1    1.1  1  FMN_dh    FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.053   12.7   0.0      0.069   12.3   0.0    1.2  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.1   2.3e-61   1.4e-57       1     284 [.       3     213 ..       3     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 2.3e-61
                 EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S-EEEE-S-...-SHHHHHHHHH CS
     TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadgrvslEVdarlsddteatieeAr 99 
                 ++lDta++++i+k+ + + ++g+TtNPsl++k  ++  + ++a+eei ++                      +  +g vslEV++   +d+++++ee++
  AJA93187.1   3 IFLDTANIDDIRKYNDMGLLDGITTNPSLLAK--EGG-DPHAAMEEITRI----------------------I--KGDVSLEVVS---TDYDGMMEEGK 71 
                 79******************************..545.788999999977......................6..9*********...*********** PP

                 HHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-SEEEEBHHHHHTTT............S-HHHHHHHHHHHHHHHT- CS
     TAL_FSA 100 rlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagasviSpFvgRiddllkkleekdklkgkddgvalvkeiynyykklgy 198
                 +l +  e  +v++K+P+t +G+kA+k  +++Gi vnvTl+Fs++qal+aa+aga+++SpF+gR+dd++            + g+ l++ei + + ++++
  AJA93187.1  72 KLREYGE--HVVVKCPMTGDGLKACKSFSEQGIPVNVTLVFSANQALLAAKAGAKYVSPFIGRLDDIG------------HTGMDLIREIKQVFSNYDF 156
                 ***9888..***********************************************************............89***************** PP

                 S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHHHHHT--HHH...............................HHHHHHHHHHHHHHH CS
     TAL_FSA 199 sTkvmaasfrnveeve..elagcdtvTippkllealakhgktsekleeeeieklleklfrlginedavaeelldegikkFakdlekll 284
                 +T+++ as+r++++v   +++g+d+vT+p+++l+++  h++t                               d+g+k+F +d++kl+
  AJA93187.1 157 KTEILVASVRHPQHVVdaAKIGADVVTLPAAVLAKMLGHSLT-------------------------------DKGLKAFLADWNKLQ 213
                 ****************9************************9...............................666666666666665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.3e-07    0.0014     217     303 ..     102     188 ..      27     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-07
                 SEEEEEEE-SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH.....SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
      FMN_dh 217 lplvvKGvltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavgg...rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                 +p+ v  v +a+ a +a++aG++  +vS   GR  d  ++ +d + ei +   +   ++e+lv + +r+ ++v+ A  +GAd+v l  ++
  AJA93187.1 102 IPVNVTLVFSANQALLAAKAGAK--YVSPFIGRLDDIGHTGMDLIREIKQVFSNydfKTEILVAS-VRHPQHVVDAAKIGADVVTLPAAV 188
                 6777777999***********99..59*********************9999988889*****85.9*****************986555 PP

>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.2e-05     0.069     205     267 ..     141     202 ..     111     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEE CS
         TGT 205 eellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegel 267
                  +l++ +++v ++++ +  +++  v +P+ +++a + G+D+++ +++ ++   g+ lt++g l
  AJA93187.1 141 MDLIREIKQVFSNYDFKTEILVASVRHPQHVVDAAKIGADVVTLPAAVLAKMLGHSLTDKG-L 202
                 56777788888888888889999***********************************999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1703.19
//
Query:       AJA93188.1  [L=131]
Description: methylmalonyl-CoA epimerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-24   85.4   0.0    3.4e-24   85.2   0.0    1.0  1  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
    1.7e-12   47.6   0.0    1.8e-12   47.6   0.0    1.0  1  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    7.2e-10   39.2   0.0    7.5e-10   39.2   0.0    1.0  1  Glyoxalase_3  Glyoxalase-like domain
    0.00072   20.3   0.0    0.00093   20.0   0.0    1.1  1  Glyoxalase_6  Glyoxalase-like domain
  ------ inclusion threshold ------
       0.15   11.7   0.0       0.18   11.5   0.0    1.1  1  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.0   9.6e-28   3.4e-24       1     109 []       4     113 ..       4     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 9.6e-28
                   EEEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT....-THHHTS-EEEEEEEEES-HHHHHHHHCTTTEEE CS
  Glyoxalase_4   1 dQigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegp....eflaehgeglhhlaywvddldaavarleeqGfev 93 
                   d+i+i+V+D+ea ++ ++++lG+++++  ++e+++v++a+  + +g  +ieL++p +++    +fl+++g+glhh a+++d++d  v+r+e  G+++
    AJA93188.1   4 DHIAIAVNDVEASAKVYQKALGIDEIEFETVESEGVKVAIIPMENG--RIELMQPTKDDspikKFLDKKGPGLHHMALETDNIDGEVERMEGCGVQF 98 
                   6********************************************9..9********99777788888****************************9 PP

                   EEEEE-GGGTT-EEEE CS
  Glyoxalase_4  94 vqkgvragaagrrfay 109
                   + k vr+g ag+++++
    AJA93188.1  99 LGK-VRPGSAGTKVTF 113
                   997.5*********98 PP

>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0     5e-16   1.8e-12       1     115 [.       2     112 ..       2     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 5e-16
                 EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHCHHHHHHHHHHHTTG CS
  Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdvedvgkaldrlkeagv 99 
                 +idh+a++v+d+e+s++ Y+k+LG + ++ +    e eg++ a +  ++g+iel+    ++++ k++  + +++ +++++al++++++  ++r++  gv
  AJA93188.1   2 KIDHIAIAVNDVEASAKVYQKALGIDEIEFET--VESEGVKVAIIPMENGRIELMQPTKDDSPIKKF--LDKKGPGLHHMALETDNIDGEVERMEGCGV 96 
                 69****************************99..999************************999999..55579************************* PP

                 EEEEEEECHHCTEEEE CS
  Glyoxalase 100 kvvaepgrhyfgalys 115
                 ++ +++     g  ++
  AJA93188.1  97 QFLGKVRPGSAGTKVT 112
                 **99987776666665 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.1e-13   7.5e-10       1     110 [.       3     105 ..       3     131 .] 0.80

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.1e-13
  Glyoxalase_3   1 lDHvvlavpdleeaaarfarrlGftvtpggehpglgtaNalvmfgdgYlEllavdpeapaperprlfgldrlakgeglhtlalrtddidataarlra 97 
                   +DH+ +av+d e+ a+ ++++lG+  ++    ++ g + a++++ +g +El+++  +  +   ++ f ld+  kg+glh++al+td+id +++r++ 
    AJA93188.1   3 IDHIAIAVNDVEASAKVYQKALGIDEIEFETVESEGVKVAIIPMENGRIELMQPTKDDSP--IKK-F-LDK--KGPGLHHMALETDNIDGEVERMEG 93 
                   7************************9999999999*****************97444443..344.4.455..8**********************9 PP

  Glyoxalase_3  98 aGvdeagrrvrpd 110
                    Gv+ +++ vrp 
    AJA93188.1  94 CGVQ-FLGKVRPG 105
                   9996.77767663 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.6e-07   0.00093       2      94 ..       6     109 ..       5     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.6e-07
  Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree.aaledpegvgpaaedaatllfqrvpe..........paknrvHldlavedldaevarlvalGArvlrep 87 
                   ++++++d++a a+ +++alg +  + e ++ e  +++    e++   l+q++++          ++    H+ l+++++d ev+r++ +G + l++ 
    AJA93188.1   6 IAIAVNDVEASAKVYQKALGIDEIEFEtVESEGVKVAIIPMENGRIELMQPTKDdspikkfldkKGPGLHHMALETDNIDGEVERMEGCGVQFLGKV 102
                   8999****************98877775444444444444566666666666667888888865333458********************9998888 PP

  Glyoxalase_6  88 rdgthgr 94 
                   r g +g+
    AJA93188.1 103 RPGSAGT 109
                   8877665 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     5e-05      0.18       1      48 [.      24      71 ..      24      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5e-05
  DDE_Tnp_ISL3  1 lgiDEislkkghkyvtvvvdllvdggrlldilpgRkketlkaflesls 48
                  lgiDEi +++ ++   +v+ + ++ gr+  + p+++ + +k+fl++ +
    AJA93188.1 24 LGIDEIEFETVESEGVKVAIIPMENGRIELMQPTKDDSPIKKFLDKKG 71
                  8*********999878888888999*******************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1011.91
//
Query:       AJA93189.1  [L=447]
Description: hypothetical protein T478_0978 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.041   13.3   0.4        1.4    8.2   0.1    2.5  2  DUF5305      Family of unknown function (DUF5305)
       0.11   12.5   7.6       0.19   11.7   7.6    1.4  1  Trypan_PARP  Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00016       1.4      30      83 ..      72     123 ..      54     128 .. 0.79
   2 ?    2.3   0.0      0.01        93     113     142 ..     309     338 ..     290     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00016
     DUF5305  30 lseyndrieeieeelglsvgtseltvvlevnvegeidgesieesktsrlpiplt 83 
                 ++e++dri+   ++lg s+  +++ ++++++++g   g ++++++++ l++++t
  AJA93189.1  72 VNELRDRINYQISQLGSSAAITDVQIDYDTKLTG--RGLNTSIDYKIILTMSIT 123
                 799****************99*999999999999..555555555555555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.01
     DUF5305 113 laegilliilgllaliglvvlirriiftss 142
                 + ++++ ii+g+++++g+  ++++i+ +++
  AJA93189.1 309 TGQFPVMIIYGMAGMAGIGGIAVFIVSEKK 338
                 3347999***********999999777654 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.6   2.2e-05      0.19      47     101 ..     376     428 ..     345     440 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
  Trypan_PARP  47 tkvsdddtngt....dpepepepepepepepepepepetepeeepepepepepepepep 101
                  +++++dd +      d +p+ e++ e      p p +et+ e+ p +e++ ep p  e 
   AJA93189.1 376 AHLKSDDYEHHrsvyDENPQVEQKTE------PAPAEETKTEPAPAEETKTEPAPAEET 428
                  33444444443112233333333333......333333333333333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3124.85
//
Query:       AJA93190.1  [L=585]
Description: ATP-dependent DNA ligase domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-57  192.6   2.0    5.8e-57  192.6   2.0    2.1  2  DNA_ligase_A_M   ATP dependent DNA ligase domain
    1.3e-39  136.2   1.5    1.3e-39  136.2   1.5    2.2  2  DNA_ligase_A_N   DNA ligase N terminus
      1e-20   74.1   0.0      2e-20   73.2   0.0    1.5  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    2.8e-09   37.5   0.2    5.1e-09   36.6   0.2    1.5  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.085   12.9   0.0        0.4   10.8   0.0    2.1  2  DNA_ligase_OB_2  DNA ligase OB-like domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.89   3.2e+03     137     170 ..     184     217 ..     179     220 .. 0.86
   2 !  192.6   2.0   1.6e-60   5.8e-57       1     204 []     227     425 ..     227     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                     HHHHHHHHHB--BTTTEEE--EEEESSHHHHHHH CS
  DNA_ligase_A_M 137 eRrklLeeilkesedrvelaeslevkdveeleel 170
                     e r+++e++ + s+d  ++ae ++++ vee+e++
      AJA93190.1 184 ENREIIENAYNVSSDLGKVAEVISTRGVEEIEKF 217
                     6688999999999999999999999999999987 PP

  == domain 2  score: 192.6 bits;  conditional E-value: 1.6e-60
                     -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHH CS
  DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGElvavdketgeilpfqk 95 
                     pmLA ++ks e++++k+ +++f +E+K+DGeRaq+hk++dk+++fSR+l+ it+++p++v+++++++  +  +vil++E+va++ ++g +lpfq+
      AJA93190.1 227 PMLADRIKSGEETVEKF-QEKFAAEYKLDGERAQIHKQKDKIEIFSRSLEIITSYYPDIVEKISKLIISE--DVILEAEVVAMNSNSGDFLPFQE 318
                     9****************.89999*******************************************9986..8********************** PP

                     HCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-C CS
  DNA_ligase_A_M  96 lasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaeslevkdveeleelleeaiseglEGlvvKnpdsk 190
                     l++r ++k+++ee+++++++ + +FD+L+ +g++ +d+ ++eRr+lLe+i+ +++d  +l+ ++ +++ e++ e+le++i++g+EGl++K  ds+
      AJA93190.1 319 LMHR-RRKYEIEEAVTKYPITVNFFDVLFSEGKNCMDMRYEERRELLEKII-KQDDFARLIPMSIIESKEQVLEVLENSINSGCEGLMLKHLDST 411
                     ****.999*******************************************.9****************************************** PP

                     C-TTCEEEEEEEEE CS
  DNA_ligase_A_M 191 YepgkrsknwlKvK 204
                     Y++g r++nwlK+K
      AJA93190.1 412 YRAGIRGSNWLKLK 425
                     ************99 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   1.5   3.7e-43   1.3e-39       1     173 []       2     176 ..       2     176 .. 0.96
   2 ?   -0.2   0.2       0.3   1.1e+03      79     140 ..     189     274 ..     180     302 .. 0.49

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 3.7e-43
                     BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HHHHHHHHHHHS-HHH CS
  DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskkkikdalakvgDlge 91 
                     +F+ ++++f+++e+ t+krle ++il ++++++    ++ +++a++L    l P+++g e+gi e+l+++a+++ +g++ kki+d+++k gDlg+
      AJA93190.1   2 KFSIISDAFQQMEA-TTKRLELTDILVKLIQEIP---EDVIAKAIYLiqgkLRPNFEGVELGIAEKLVMRAMSKSSGIPLKKIEDDYNKGGDLGQ 92 
                     59999*********.899************8864...568***************************************99************** PP

                     HHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
  DNA_ligase_A_N  92 vaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriilkdlriglsektvldala 173
                     +ae++l+++ ++ ++++ +t+e+v+++L k+++  gkgs++ k+k ++++l+ a+p+E k++ +i+l+ lr+g++e+tv+dala
      AJA93190.1  93 TAENILQQKIQTtFASEVITLEKVYDTLFKISKLeGKGSQEMKMKYVSSMLNDATPQESKFILKILLGTLRLGIAENTVMDALA 176
                     ******998888899999*************9889***********************************************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.3
                     HHHHHHHHS-HHHHHHHHHCCHHHH------BH................HHHHHHHHHHHH-........STTHHHHHHHHHHHHH CS
  DNA_ligase_A_N  79 ikdalakvgDlgevaeevlskrstlakksplti................eevnelLdklaaa........gkgsedekkkilkkll 140
                     i++a++   Dlg+vae +  +  +  +k ++ +                e v+++ +k aa+        +  ++++k++i+++ l
      AJA93190.1 189 IENAYNVSSDLGKVAEVISTRGVEEIEKFQIKLfspirpmladriksgeETVEKFQEKFAAEykldgeraQIHKQKDKIEIFSRSL 274
                     56666667788888655544443333333333355555555555555555555555555533444422222223444444444444 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   5.7e-24     2e-20       1      99 []     450     560 ..     450     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5.7e-24
                     GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG.GGEECTTCE.SS---HHHHTTEEE-TT-EEEEEESEEECTSSSTT...... CS
  DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk.elerkkppf.aekvpeeekrdvWvePelvveVkfaeitasgkyka...... 85 
                     r+g++g+lll  y+  ++ + +++kvgtGf+d++l++l++ l+ ++  kk+p   ++ +    +dvW+ePelv+e+ ++eit+s+ +k+      
      AJA93190.1 450 RTGKYGTLLLSTYNdeEDVFPSICKVGTGFTDESLDQLYQILSpKVTLKKNPRiVSEME----ADVWFEPELVIEIVASEITQSPIHKTaldkik 540
                     6899**********76666***********************97555555555134444....459***************************** PP

                     .....EECT-EEE.EE-TTS CS
  DNA_ligase_A_C  86 .....slRfPrfk.rlReDk 99 
                          +lRfP f+ ++R++k
      AJA93190.1 541 egtglALRFPKFTgKIRTEK 560
                     ***********997888876 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.2   1.4e-12   5.1e-09       2     161 .]     246     425 ..     245     425 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.4e-12
                 EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.....SS...............TTSS... CS
  RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig....hsi.............kygglpk.. 79 
                 ++ ++ KlDG++++i+++k+ + ++sRs ++ +           ++ +  +k+ + + +e++il  E++     +               k        
  AJA93190.1 246 KFAAEYKLDGERAQIHKQKDkIEIFSRSLEIiT----------SYYPDIVEKISKLIISEDVILEAEVVAmnsnS-GdflpfqelmhrrrK-----Yei 328
                 688999************777**********42..........333344456667777999*********86641.144433333333332.....044 PP

                 .........EEEEEEEEEEECTTBECE--HHHHHHHHHCCT.......B..EEEEE.SS.HHHHHCCC.H.HHHTC--EEEEEESSSSBE.TTE.BSEE CS
  RNA_ligase  80 .........efyvFdifdirdkeeqrylspdevealakglg.......tvpvlyegkfl.aaeellelll.skgnkrEGlVikpeselyk.nkg.raif 158
                              Fd++  +  ++   + ++e+++l++++         +p+     ++   e++le l+ s ++ +EGl +k+ +++y+   + ++++
  AJA93190.1 329 eeavtkypiTVNFFDVLFSE-GKNCMDMRYEERRELLEKIIkqddfarLIPMS----IIeSKEQVLEVLEnSINSGCEGLMLKHLDSTYRaGIRgSNWL 422
                 44566655566779999554.569999******66666332334433333333....2223333333322345669**************9999***** PP

                 EEE CS
  RNA_ligase 159 Kvk 161
                 K+k
  AJA93190.1 423 KLK 425
                 *97 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011       0.4       2      32 ..     446     482 ..     445     496 .. 0.86
   2 ?   -1.6   0.0      0.81   2.9e+03      57      63 ..     547     553 ..     539     555 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                      ...EEEEEEEEEEEEE.TTEE......EEE-SS--HH CS
  DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsda 32 
                      GkG+  g+ G ll +t ++++       k+G+G++d+
       AJA93190.1 446 GKGRRTGKYGTLLLSTYNDEEdvfpsiCKVGTGFTDE 482
                      9***************877644555669********8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                      -EEEEEE CS
  DNA_ligase_OB_2  57 pRfPsfl 63 
                      +RfP+f 
       AJA93190.1 547 LRFPKFT 553
                      9****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4057.63
//
Query:       AJA93191.1  [L=196]
Description: SIS domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-20   72.4   0.1    4.7e-20   72.0   0.1    1.1  1  SIS_2        SIS domain
    2.4e-11   43.6   0.2    1.6e-09   37.7   0.1    2.2  2  SIS          SIS domain
     0.0043   17.1   0.2       0.38   10.9   0.0    2.2  2  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.029   14.1   0.1        0.4   10.4   0.0    2.1  2  MAF_flag10   Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.1     1e-23   4.7e-20       8     138 .]      16     147 ..      11     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1e-23
                 HHHHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--.GGGSSSSST..THHHHHTT-TTHHHHHHHH..TT--T CS
       SIS_2   8 eilerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferial.palalhtdaeatkssalerdegyakqilrl..vrlkp 103
                 + +++i+++q + iek  e++  + ++++k+++fG+G+Sa  ++++a ++ +   ++     +a+ l+++  +   +a ++d  y ++++++    l++
  AJA93191.1  16 NCISKIKSEQLDIIEKILEVLETARKTNQKIILFGNGGSASTSSHFASDLQKTSIVDNANRfRAICLTDN--IPVLTAWANDTSYEDIFSSQleNFLDS 112
                 67999**********************************************8877766665155666554..5888888888888888888833346** PP

                 T-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
       SIS_2 104 gDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                  Dv l iS sGn+++vv+a+e a+++g+k+i lt+
  AJA93191.1 113 DDVVLAISGSGNSPNVVKAVELANKMGAKTISLTG 147
                 *********************************97 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0094        42       6      31 ..      44      69 ..      39      84 .. 0.88
   2 !   37.7   0.1   3.6e-13   1.6e-09      49     107 ..     108     166 ..      93     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0094
                SEEEEEESHHHHHHHHHHHHHHHHHH CS
         SIS  6 kriyvlGaGtsyaiakelalkleeig 31
                ++i+++G G s+++ + +a  l++++
  AJA93191.1 44 QKIILFGNGGSASTSSHFASDLQKTS 69
                49**************9999998876 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 3.6e-13
                 GG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEEEEE CS
         SIS  49 alideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyinae 107
                 + +d+dd+v++is sg+++++v+a+ela++ gak+i++T+++g  l++ ++++l i+ +
  AJA93191.1 108 NFLDSDDVVLAISGSGNSPNVVKAVELANKMGAKTISLTGKDGGMLSKISKINLNIPNS 166
                 5799**********************************************888888765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   8.4e-05      0.38      15      54 ..      28      68 ..      22      81 .. 0.83
   2 !    4.3   0.0    0.0097        44       3      64 ..     110     169 ..     108     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
                 E-TTHHHHHHHHHHTT-EEEEEE--.-SS-HHHHHHHHHHT CS
  Hydrolase_6 15 aipgaaealnalraagkpvvllTNn.sskseeeyakklekl 54
                 +i++  e+l++ r+++ +++l+ N+ s ++ +++a +l+k 
   AJA93191.1 28 IIEKILEVLETARKTNQKIILFGNGgSASTSSHFASDLQKT 68
                 789999******************94556677888888775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0097
                  EESTTTSEE..TTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEE CS
  Hydrolase_6   3 fDidGvLwr..gdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvv 64 
                  +D d v++   g+   p++++a++  +++g +++ lT + +    +++ k++k++++i  ++++
   AJA93191.1 110 LDSDDVVLAisGSGNSPNVVKAVELANKMGAKTISLTGKDG----GMLSKISKINLNIPNSDML 169
                  5667776643388889*******************997543....4466666666666666665 PP

>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.025   1.1e+02      15      67 ..      32      85 ..      19     130 .. 0.64
   2 ?   10.4   0.0     9e-05       0.4     102     166 ..      83     150 ..      72     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.025
  MAF_flag10 15 lkellnkfkg.nkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkeg 67
                + e+l++ ++ n+++i++g+G S   + ++ ++l++  ++  a++   ++l  +
  AJA93191.1 32 ILEVLETARKtNQKIILFGNGGSASTSSHFASDLQKTSIVDNANRFRAICLTDN 85
                445555443348999999999887777777777766666655555555555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9e-05
  MAF_flag10 102 gvnpellkkykgpkiflvtgstqalelleeekne...ilfgGgsv.antaldlAvklgfkeIiliGqDl 166
                 ++n+ +l ++ +   +    s q le++ +++++   i ++G s     a++lA k+g+k+I l G D 
  AJA93191.1  83 TDNIPVLTAWANDTSYEDIFSSQ-LENFLDSDDVvlaISGSGNSPnVVKAVELANKMGAKTISLTGKDG 150
                 55666666666665553333333.55555555556764444433213459****************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1347.00
//
Query:       AJA93192.1  [L=353]
Description: PhoU domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-18   66.5  10.5    6.3e-17   61.8   1.1    2.6  2  PhoU            PhoU domain
    2.5e-06   27.3   0.0    7.9e-06   25.7   0.0    1.9  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.31   11.4   5.7          9    6.7   4.1    3.4  2  Syntaxin_2      Syntaxin-like protein


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   1.1   1.1e-20   6.3e-17       2      88 ..     151     241 ..     150     242 .. 0.93
   2 !    8.9   2.6   0.00035       2.1       7      88 ..     262     333 ..     256     334 .. 0.68

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.1e-20
                 HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriardlERigDhavniaer 88 
                 +rm++ +++m+++++ a+e++d e+a+e++ +ddei+r+ + ++r l+ al   + l++    +  +++++ ri+++ ERi+Dh+  ia+ 
  AJA93192.1 151 NRMFKSTSNMFSETMHAIEKGDSEYAQEIVHMDDEINRFSYYLTRNLVMALDDANILSAlgleKTSQAIGYKRIITCVERIADHISTIAKV 241
                 89*************************************************77777777777888899*********************97 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00035
                 HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavniaer 88 
                  + e +d+++++++e++   a++     +ei++l +e  ++l++  +       + ++ + + ++++   Ri D++ +i+e 
  AJA93192.1 262 KTIELFDKTMTLISERNYSQAEKH---AEEIEALIDET-NALVKSTK-T-----NSEASIVYQNLIYQNRRILDYILDISEV 333
                 567889999999999997777555...45555554443.33233332.2.....2344577999***************997 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.3e-09   7.9e-06       3      38 ..      18      54 ..      17      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.3e-09
                    ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCC CS
  MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd.kiil 38
                    +G+++ +++Pk + ++l+++ Gd+  ++ +++ +i l
      AJA93192.1 18 GGSTYVISLPKKWIEKLNLKNGDSMQIVNNPNnSITL 54
                    79*************************9999877776 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.16   9.5e+02      43      67 ..     151     176 ..     129     193 .. 0.80
   2 ?    6.7   4.1    0.0015         9       2      62 ..     232     309 ..     204     325 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
  Syntaxin_2  43 nelikktnellkklsqldnsssds.q 67 
                 n+++k t++ +++ ++ +++++++ +
  AJA93192.1 151 NRMFKSTSNMFSETMHAIEKGDSEyA 176
                 78999999999999999888865452 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
  Syntaxin_2   2 ssnlqkinsnvstleklvkq.....Lgtkkdteelr............eklhelieeinelikktnellkklsqldns 62 
                 ++++++i++ v  +ek +++     ++t + t el             +++++  eei  li +tn+l+k+ +++++ 
  AJA93192.1 232 ADHISTIAKVVVDMEKNISKtpkdiINTYQKTIELFdktmtlisernySQAEKHAEEIEALIDETNALVKSTKTNSEA 309
                 445555555555555555543333333333333333455555555555777777777777777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2637.75
//
Query:       AJA93193.1  [L=384]
Description: aminotransferase, class V [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-31  109.7   0.0    1.9e-31  109.4   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.025   13.1   0.1      0.037   12.6   0.1    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   2.1e-35   1.9e-31       4     338 ..       6     325 ..       3     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 2.1e-35
                  BTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGG CS
  Aminotran_5   4 dsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhan 101
                  + +++t++p++V +a+             s+ h++ ++ + +ee+ ++ ++++++e +   +  sGt+ a ++ + +l   +k++d++++ +++  ++
   AJA93193.1   6 MLPGPTNVPERVTRAMVTP----------SINHRSDDFVELYEECVDNTKKIFETEGDAVCLSASGTG-ATECSVVNL---VKKDDKVIIPVNGEFST 89 
                  5689999999999999888..........99*************************955556666666.*********...***************** PP

                  THHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEE CS
  Aminotran_5 102 lvpwqelakrtgakvkvipldeegeldldelekll..nektklvaithvsnvtGt.iqpveeigklakkkgalvlvDaaqavghipidvkklgvDfla 196
                  +  +q+++ + g  +  i+ +++ + + d+++++   n+++k+ +  +++++tGt i+ +++i++l  +++ ++++D+++ vg  ++ ++k+g+D+++
   AJA93193.1  90 R-LAQQIEWAGGQAI-RIQTEPGVNATFDQVKEAFdnNKDVKAFYCVWNETSTGTmINYLDRIKDLTSRNDSYYVLDGVSIVGGEELHMDKWGIDIAM 185
                  *.9*****9988888.67888**************65599********************************************************** PP

                  EETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEE.EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_5 197 fsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eett.faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerl 291
                   +++K +  P+Gi+ +++  +  + +e   + + +++ +++ +++   + +p+     Tp  + +++ ++a++++ e g+e+  ++++  +++l+++l
   AJA93193.1 186 TGAQKaFACPPGISPICINGRTRKYMEDNPPNTMYFNLPRYfKYYEeAKHTPF-----TPALPVLYAYREAMRIILEEGMEKRIQRHRICSDALYSGL 278
                  *****9999*****************999999999999999866662666666.....9*************************************** PP

                  CTSTTEEEES.-B-CTCBSEEEEEE.TTCSHHHHHHHHHHT.TEEEEEE CS
  Aminotran_5 292 kslpgvrlygpdkaerrasivsfnf.kgvhaedvatlLdee.gIavrsG 338
                  ++++ + +  +d++ r++ ++++n+ +g++ + ++  L+++  I v +G
   AJA93193.1 279 SAIGLTPF--ADENSRSTVVIALNYlDGLEDKIFRDTLAKKfRILVAGG 325
                  ********..566777777788877778888888889999988988887 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.1e-06     0.037      66     195 ..      51     187 ..      39     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-06
                      T-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTH....HHTTCEEEEESTTSHHHHHHHCCTTEE.....EEEEESS-TTT CS
  Cys_Met_Meta_PP  66 ggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvl....kklgievkfvdtsdleelekaikentk.....lvylEtptnpl 150
                      +g+a+++ +sG++A+++++++l+k+ d++++  +   +t rl +++     + + i+++    + ++++++a+++n +     +v+ Et t  +
       AJA93193.1  51 EGDAVCLSASGTGATECSVVNLVKKDDKVIIPVNGEFST-RLAQQIEwaggQAIRIQTEPGVNATFDQVKEAFDNNKDvkafyCVWNETSTGTM 143
                      57888899********************99876543333.3333332111134566666666689999***99996432233358889999999 PP

                      T----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEE CS
  Cys_Met_Meta_PP 151 lkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhS 195
                      ++ +D  +i +l+  ++   v+D + + +    +  k+g+Di +  
       AJA93193.1 144 INYLD--RIKDLTSRNDSYYVLDGVSIVGgEELHMDKWGIDIAMTG 187
                      99988..666777777777777765444324445555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3043.48
//
Query:       AJA93194.1  [L=578]
Description: radical SAM domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-10   42.0   0.0    2.6e-10   41.0   0.0    1.6  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.4e-14   2.6e-10       1     159 [.     272     454 ..     272     462 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.4e-14
                  EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGS.............TTHHHHHHHHHHTC..CCTEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.............xxxxxxxxxxxxxx..xxxxxxxx RF
  Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggeplly.............pdfvellerlakla..vpgiritv 82 
                  v+v+rgC ++C+fC+++      +  r+ s+e++++e++ +  +kg  +  ++++++ ++y             +d  e+l++++     +    ++ 
   AJA93194.1 272 VEVMRGCGRGCKFCDVT-----LRSLRYYSPEKVKKEIEVN-IKKGgMDRAWIHSDDIFVYgmdirtaknmepnRDALEDLFKAIMSTgvKHTNPTHG 363
                  689**************.....69*****************.67777**************8888888888877777777777777755555555555 PP

                  EECSSCHGHHHHHHHHHTT......-SEEEEEEBSSSHH.......HHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT.TSHHH CS
                  xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
  Radical_SAM  83 etngtlpdeeklerllelg......vdrvslgleaadde.......kvlklmnrghtfeevlealeklreagikrvvdrivglpG.endee 159
                  + +g   de+ +  l +        ++ ++ g e+++ +       + l +  + +    v+e++++l+e+ + + ++ i+gl + e  e+
   AJA93194.1 364 TLSGAIADERLVPSLSKITragpdnLTGIQCGFETGSTRliekyadRKLAPYSPDEWHWVVKEGVKTLNENYWIPAFTLIMGLDNdEQPED 454
                  555555555555555554455599***************88887774455554767779*************9999999998874133355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 4479.02
//
Query:       AJA93195.1  [L=402]
Description: phosphoglycerate kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-100  337.3   0.8   1.2e-100  337.1   0.8    1.0  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.1   0.8  6.6e-105  1.2e-100       2     377 ..       7     383 ..       6     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 337.1 bits;  conditional E-value: 6.6e-105
                 GGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHTT-EEEESSTTSHHHHHHHH CS
         PGK   2 kdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellgkeVkfvedvvgeeveeaia 99 
                 +++d+k+k+vl+RvD+N+p++ +  +i  ++ri++ ++Ti++l  +gak+v++sH+gr+ g+++ + ++++a++L++  +k+V++v dv+g+ ++++i+
  AJA93195.1   7 DNFDVKDKTVLLRVDMNCPIHPDtCEILGTKRIEEVVETINAL--DGAKIVVISHQGRV-GRDDFVGMEEHAKQLEKFSNKKVRYVADVIGSLAQKEIK 102
                 789*****************99889******************..9************9.89************************************* PP

                 T-TTT-EEEES-GGGSTTTTTT-H..H.....HHHHHHHT-SEEEE--GGGTTS--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES CS
         PGK 100 elkegevllLeNvrfykeEeknde..e.....lakklasladvyVnDAFgtahrahaStvgiakvlsaaaGllmekElealskvlenperplvailGGa 191
                 e+k+ e++lL+N+r  +eE+ + +  e     ++++l +l+d+++ D+F +ahr h S+vg+a+vl+++aG+l+ekE++ l+++l+  + p++++lGG+
  AJA93195.1 103 EMKNDEIILLDNLRLCAEENYEFSleEsartiMVQRLKDLFDLFILDSFPSAHRTHPSLVGFAQVLPTCAGRLLEKEVKQLDNILTVAKSPFTVVLGGS 201
                 *******************7442233123456**********************************99******************************* PP

                 -HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B-TTSS--GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEE.ECCG--TT-EEE CS
         PGK 192 kvsdkikvienLlekv..dkliigGgmantFlkaqgleigkslveedklelakellekakkkgvkillpvDvvvakeeaekeakvv.eveaipedemal 287
                 kv+d++k i+ L++k   d+++++G++ n+Fl+aqg  i   l+ +d+ e++++  +   ++ + + +pvD++v+k+     ++v  +v+++ +d++++
  AJA93195.1 202 KVDDRLKAIKLLIKKEraDHVLLTGVIGNVFLRAQGR-IKFPLNIKDEDEMVASAHSLIGDHPDVFSTPVDIAVNKDG----KRVEiDVRDLAKDDEIF 295
                 *************98666****************994.55666655566677777777777779***********832....233348999******** PP

                 EE-HHHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
         PGK 288 DigpktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                 Dig+kt+e+++++i++a tv++ Gp+G+fe e+f+ GTk++++ +a++   a+si++Gg+  +a+++++l++kvsh+St+GgA++++L+g
  AJA93195.1 296 DIGTKTLEHYSKIISSAGTVFMSGPAGFFEKENFQFGTKSMLESIADSM--ATSIISGGHLTSALRQFNLTEKVSHISTAGGALVRYLTG 383
                 ***********************************************85..6************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2755.21
//
Query:       AJA93196.1  [L=155]
Description: transcriptional regulator MntR family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-18   64.8   1.4    7.4e-18   64.5   0.7    1.6  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      1e-17   63.9   0.2    2.4e-17   62.8   0.0    1.7  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    3.6e-05   23.7   0.0     0.0015   18.4   0.0    2.4  2  HTH_6           Helix-turn-helix domain, rpiR family
    0.00017   22.0   0.0     0.0014   19.1   0.0    2.2  2  HTH_27          Winged helix DNA-binding domain
    0.00018   21.2   0.0     0.0037   17.0   0.0    2.7  3  LexA_DNA_bind   LexA DNA binding domain
    0.00027   20.8   0.0    0.00049   19.9   0.0    1.4  1  MarR_2          MarR family
    0.00041   20.2   0.0    0.00082   19.3   0.0    1.5  1  MarR            MarR family
     0.0026   17.7   0.0      0.006   16.5   0.0    1.8  1  HTH_12          Ribonuclease R winged-helix domain
     0.0029   17.5   0.1     0.0054   16.6   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0048   17.1   1.6       0.15   12.4   0.1    2.3  2  DUF2683         Protein of unknown function (DUF2683)
     0.0049   17.0   0.1     0.0084   16.2   0.1    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.005   16.8   0.4     0.0089   16.0   0.4    1.5  1  HTH_45          Winged helix-turn-helix
     0.0058   16.6   0.0      0.012   15.6   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0087   16.9   0.2      0.033   15.1   0.2    2.0  1  DUF2624         Protein of unknown function (DUF2624)
  ------ inclusion threshold ------
      0.041   14.2   0.6       0.37   11.2   0.2    2.3  2  WYL_3           WYL domain
      0.069   12.3   0.1        0.1   11.7   0.1    1.2  1  TRM             N2,N2-dimethylguanosine tRNA methyltransferas
      0.085   12.7   0.1       0.23   11.3   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.7     7e-21   7.4e-18       3      59 ..      25      81 ..      23      82 .. 0.96
   2 ?   -3.0   0.0       8.1   8.5e+03      26      35 ..      89      98 ..      87      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 7e-21
                    -HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
  Fe_dep_repress  3 vestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                    +++ EdYLe+I +l + k+++ t d+++ +nvs++sV++mlkkL+ +G++eyeky g
      AJA93196.1 25 SDRVEDYLEVISELVDMKGYAATLDISRYMNVSAPSVTKMLKKLDAEGFLEYEKYYG 81
                    789****************************************************88 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.1
                    HHHHHHHTS- CS
  Fe_dep_repress 26 kdlaerLnvs 35
                    +++ae ++++
      AJA93196.1 89 QRIAEMIKQK 98
                    5788888876 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   5.8e+03      44      52 ..      24      32 ..      13      38 .. 0.55
   2 !   62.8   0.0   2.2e-20   2.4e-17       1      64 [.      85     147 ..      85     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                   S-HHHHHHH CS
  Fe_dep_repr_C 44 lseelierl 52
                   +s+++++ l
     AJA93196.1 24 ISDRVEDYL 32
                   344444433 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 2.2e-20
                    -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TT CS
  Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPh 64 
                    TekG+++A+ ++++h +l +f+ ++lg+ +e+a ++Ae +Eh+l++++i+++++++ f++ +P+
     AJA93196.1  85 TEKGQRIAEMIKQKHGILLEFF-EILGIGKEIANQDAEGIEHHLNPKTIRQIRKFVTFFKANPK 147
                    9*********************.*************************************9995 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.5e-06    0.0015      23      65 ..      33      75 ..      15      77 .. 0.85
   2 ?    2.7   0.0      0.11   1.2e+02      13      28 ..      83      98 ..      77     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                HHHHH-S---TT--HHHHHHHTT--HHHHHHHH---S-SSHHH CS
       HTH_6 23 eyilaspdkaielsikalAkaaavSeativrfakkLGfkGFse 65
                e+i + +d   + +  +++  ++vS ++++++ kkL+++GF e
  AJA93196.1 33 EVISELVDMKGYAATLDISRYMNVSAPSVTKMLKKLDAEGFLE 75
                566666666677788899***********************87 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.11
                ---HHHHHHHHHHHH- CS
       HTH_6 13 kltksekkiaeyilas 28
                +lt+  ++iae+i+++
  AJA93196.1 83 NLTEKGQRIAEMIKQK 98
                689999*******986 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.3e-06    0.0014      20      68 .]      46      88 ..      31      88 .. 0.83
   2 ?    0.2   0.0       1.1   1.1e+03      12      28 ..     123     139 ..     121     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
      HTH_27 20 kladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                +  d+++++nv++ ++ ++lkkL + G++   ++e   ++  + lT+kG
  AJA93196.1 46 ATLDISRYMNVSAPSVTKMLKKLDAEGFL---EYE---KYYGINLTEKG 88
                5569*************************...444...77888999998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
      HTH_27  12 irhrrrrkkladlcgrl 28 
                 i+h +++k+++++++++
  AJA93196.1 123 IEHHLNPKTIRQIRKFV 139
                 678999*******9876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.5e-06    0.0037       5      58 ..      25      76 ..      22      79 .. 0.90
   2 ?   -0.8   0.0       1.3   1.3e+03       3      17 ..      83      97 ..      82      99 .. 0.86
   3 ?   -0.1   0.0      0.77   8.1e+02      19      37 ..     123     141 ..     112     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.5e-06
                   -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
  LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                   ++r ++ l++i + ++ +gy+ +  +i+r ++++ + +v + Lk+L   G++e 
     AJA93196.1 25 SDRVEDYLEVISELVDMKGYAATL-DISRYMNVS-APSVTKMLKKLDAEGFLEY 76
                   6777889**************987.8******97.778*************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                   ---HHHHHHHHHHHH CS
  LexA_DNA_bind  3 kLTerQrevldlika 17
                   +LTe+ +++ ++ik+
     AJA93196.1 83 NLTEKGQRIAEMIKQ 97
                   599999999999997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.77
                    HHHHSS---HHHHHHHHTS CS
  LexA_DNA_bind  19 ieetgypPsireiaralgl 37 
                    ie++  p +ir+i + + +
     AJA93196.1 123 IEHHLNPKTIRQIRKFVTF 141
                    5555567788888776665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.7e-07   0.00049      13      54 ..      37      77 ..      31      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.7e-07
                HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
      MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                +L +  g+  +  ++ r++++s ++v+++lk+L a G++e++
  AJA93196.1 37 ELVDMKGY-AATLDISRYMNVSAPSVTKMLKKLDAEGFLEYE 77
                55556665.46669*************************987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   7.7e-07   0.00082      21      48 ..      47      75 ..      31      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.7e-07
                H.HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
        MarR 21 s.eLakklgvskstvtrvldrLekkGlie 48
                + ++ + ++vs ++vt++l++L  +G++e
  AJA93196.1 47 TlDISRYMNVSAPSVTKMLKKLDAEGFLE 75
                35899**********************97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.7e-06     0.006      29      63 ..      55      89 ..      30      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
      HTH_12 29 digeravRyrLrkleergltrrvgyagreltEkGl 63
                ++++ +v   L+kl+ +g+ +   y g +ltEkG 
  AJA93196.1 55 NVSAPSVTKMLKKLDAEGFLEYEKYYGINLTEKGQ 89
                7788899999***********************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.1e-06    0.0054      16      56 ..      37      78 ..      31      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
        TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                 L+ ++g a + +i++  +v+ ++v ++L++L   G+ e ek
  AJA93196.1 37 ELVdMKGYAATLDISRYMNVSAPSVTKMLKKLDAEGFLEYEK 78
                577778899999*************************99775 PP

>> DUF2683  Protein of unknown function (DUF2683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.064        68      11      45 ..       4      37 ..       1      47 [. 0.85
   2 !   12.4   0.1   0.00014      0.15       6      59 ..      82     138 ..      80     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.064
     DUF2683 11 esnriieivKakydlkdksaAidllieqyaeyllE 45
                ++ r ++ +Ka ++  +k + i   +e+y e + E
  AJA93196.1  4 KTSRRLDSIKAAHE-SEKTISISDRVEDYLEVISE 37
                57788999*****9.67899999999***999987 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00014
     DUF2683   6 vdisDesnriieivKakydlkdks...aAidllieqyaeyllEaElkPefvekirni 59 
                 ++++++ +ri e++K k+ +  +      i + i + + ++ E  l+P+ +++ir+ 
  AJA93196.1  82 INLTEKGQRIAEMIKQKHGILLEFfeiLGIGKEIANQDAEGIEHHLNPKTIRQIRKF 138
                 89*****************9877611156677777778899999******9999875 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     8e-06    0.0084       9      77 ..      30      99 ..      22     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8e-06
     DUF2250  9 lalkvlkhlkkanvdYa..ksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhH 77
                ++l+v+  l  ++  Ya  + i+++++++   v+++lkkL   G le+ +   i+ te+  + ++  +++H
  AJA93196.1 30 DYLEVISELVDMKG-YAatLDISRYMNVSAPSVTKMLKKLDAEGFLEYEKYYGINLTEKGQRIAEMIKQKH 99
                56777777777765.441246899*******************************************9999 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   8.4e-06    0.0089       7      71 ..      34      97 ..      26     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.4e-06
      HTH_45  7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklke 71
                +i+++ + + +g a    i    n s   + k+L++L  +g+++  +     lTekG+++ e +k+
  AJA93196.1 34 VISELVD-M-KGYAATLDISRYMNVSAPSVTKMLKKLDAEGFLEYeKYYGINLTEKGQRIAEMIKQ 97
                5555444.2.5666667889999********************883556689********999876 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.1e-05     0.012      26      55 ..      49      79 ..      43      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                HHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
   HTH_Crp_2 26 elAsmlGltretvsrilseLkreglis.rgr 55
                +++++++++  +v+++l++L  eg ++  ++
  AJA93196.1 49 DISRYMNVSAPSVTKMLKKLDAEGFLEyEKY 79
                89************************95343 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   3.1e-05     0.033       1      47 [.      54      99 ..      54     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-05
     DUF2624  1 MniiqqlVnqklnsiTaeellkyakqygveltksqAekivkilrekk 47
                Mn+    V + l+++ ae +l+y k yg++lt++  + i++++++k+
  AJA93196.1 54 MNVSAPSVTKMLKKLDAEGFLEYEKYYGINLTEK-GQRIAEMIKQKH 99
                888888899***********************87.689999999985 PP

>> WYL_3  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00035      0.37      13      57 ..      36      80 ..      29      81 .. 0.75
   2 ?    0.8   0.0      0.61   6.5e+02      23      42 ..     107     124 ..      90     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
       WYL_3 13 kdgvtkedyAkkLgIadkiak.aessagaleklmqTseYkKyeaYl 57
                 ++v  + yA++L I+  ++  a s ++ l+kl   + +  ye+Y+
  AJA93196.1 36 SELVDMKGYAATLDISRYMNVsAPSVTKMLKKL-DAEGFLEYEKYY 80
                67888999*************555666666665.566666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
       WYL_3  23 kkLgIadkiakaessagale 42 
                 + LgI ++ia  ++ a+++e
  AJA93196.1 107 EILGIGKEIA--NQDAEGIE 124
                 5699999998..56666665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.9e-05       0.1     289     350 ..      13      73 ..       4      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                 HHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....T CS
         TRM 289 leeaekekeeelkkrvkklLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgf 350
                  ++ e+ek+ +++ rv+  L++i+e l+d  +y  + ++++ +++s+p+++k+ ++l + gf
  AJA93196.1  13 KAAHESEKTISISDRVEDYLEVISE-LVDMKGYAATLDISRYMNVSAPSVTKMLKKLDAEGF 73 
                 444555556666**********986.5*******************************9999 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.23      16      47 .]      45      76 ..      32      76 .. 0.82
   2 ?   -2.7   0.0       5.3   5.6e+03      33      37 ..     124     128 ..     123     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
       HTH_5 16 lcvcelaeelglsqstvShHLkkLreaGLVek 47
                +   ++++++++s + v   LkkL  +G++e+
  AJA93196.1 45 AATLDISRYMNVSAPSVTKMLKKLDAEGFLEY 76
                56669***********************9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                 HHHHH CS
       HTH_5  33 ShHLk 37 
                  hHL+
  AJA93196.1 124 EHHLN 128
                 57775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1146.39
//
Query:       AJA93197.1  [L=196]
Description: precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-16   59.9   0.1    3.2e-16   59.5   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    6.3e-14   52.2   0.4    7.9e-14   51.9   0.4    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.5e-11   44.8   0.0    3.1e-11   43.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.8e-11   42.3   2.0    7.6e-11   41.9   2.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.9e-10   40.5   0.2    3.5e-10   39.6   0.1    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    5.6e-09   36.1   0.7    7.4e-09   35.7   0.7    1.2  1  Methyltransf_18  Methyltransferase domain
      3e-08   34.3   0.1    6.9e-08   33.1   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
    5.5e-08   32.5   0.0    9.5e-08   31.8   0.0    1.5  1  MTS              Methyltransferase small domain
    9.1e-08   31.7   0.1    1.3e-07   31.2   0.1    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
      1e-07   32.5   0.0    1.9e-07   31.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    3.2e-07   29.7   0.1    3.8e-07   29.5   0.1    1.2  1  Methyltransf_3   O-methyltransferase
    6.7e-07   29.1   0.0    1.1e-06   28.5   0.0    1.5  2  Cons_hypoth95    Conserved hypothetical protein 95
      7e-07   28.9   0.1    1.8e-06   27.6   0.1    1.7  2  Methyltransf_4   Putative methyltransferase
    1.6e-06   28.1   0.0    1.8e-06   27.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.9e-05   24.3   0.2      4e-05   23.3   0.1    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    3.1e-05   24.9   0.0    4.5e-05   24.4   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
    4.8e-05   23.1   0.1    0.00086   19.0   0.0    2.1  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    4.9e-05   23.1   0.1     0.0004   20.1   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    0.00015   21.6   0.0    0.00018   21.3   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00018   21.6   0.0     0.0019   18.3   0.0    1.9  2  FtsJ             FtsJ-like methyltransferase
    0.00023   21.0   0.0    0.00027   20.8   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00047   20.2   0.0    0.00059   19.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
    0.00049   19.6   0.0    0.00071   19.1   0.0    1.2  1  AviRa            RRNA methyltransferase AviRa
     0.0014   18.4   0.2     0.0025   17.5   0.0    1.5  2  N6_N4_Mtase      DNA methylase
     0.0014   18.2   0.0     0.0019   17.8   0.0    1.3  1  Methyltransf_5   MraW methylase family
      0.002   17.5   0.1     0.0032   16.8   0.1    1.3  1  GidB             rRNA small subunit methyltransferase G
     0.0025   17.4   0.2     0.0041   16.7   0.2    1.6  1  DOT1             Histone methylation protein DOT1
     0.0028   17.1   0.1     0.0042   16.5   0.1    1.4  1  Spermine_synth   Spermine/spermidine synthase domain
  ------ inclusion threshold ------
      0.012   15.2   0.0       0.02   14.5   0.0    1.4  1  NodS             Nodulation protein S (NodS)
      0.016   15.0   0.2      0.027   14.2   0.2    1.4  1  Methyltransf_16  Lysine methyltransferase
      0.024   13.5   0.0      0.037   12.9   0.0    1.3  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.037   13.2   0.0      0.048   12.8   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
       0.04   13.5   0.0      0.056   13.0   0.0    1.2  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
      0.068   12.2   0.1        0.1   11.6   0.1    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.075   12.3   0.0        0.1   11.9   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
      0.085   12.3   0.0       0.24   10.9   0.0    1.7  2  CheR             CheR methyltransferase, SAM binding domain


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.1   6.5e-19   3.2e-16       3     123 ..      39     156 ..      37     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 6.5e-19
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkile 95 
                       g +vlD+GCG+G  t e+a ++ + ++v+G+Di+++aiel ++n++k g++n+++ +g++ e +++l    + D i+  ++     d ++i e
       AJA93197.1  39 AGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEkISEL---PQADTIFIGGTG---GDTKDIVE 126
                      6789*****************999***************************************88876...578999998664...88888888 PP

  Methyltransf_31  96 eiervlkpggilliedpr..llaelpakve 123
                        ++ +++gg+++i  +   +l+ +++ +e
       AJA93197.1 127 LCQDKVQSGGRIVIGVILieTLYSVLQTIE 156
                      888899999998876554334444445554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.4   1.6e-16   7.9e-14      66     194 ..      32     165 ..      13     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.6e-16
                 HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGGG-SEEEEEESSB...BSS--HHHHH CS
        PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyeekaPYdaihvgaa...apeiPealid 161
                 +   +l++g+ vL++G+GsG  t+  a  v+e+g+v++++  ++ +e +k+nl+k +++n ++v+g  ++   e    d+i++g +   +++i e   d
  AJA93197.1  32 ISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEKISELPQADTIFIGGTggdTKDIVELCQD 130
                 4444599***************************************************************************9876233578999999* PP

                 TEEEEEEEEEEESB..SSSEEEEEEEEETTTEEEE CS
        PCMT 162 QLkeGGrlvvPvge..eeeQvlklvdkkadgkvvi 194
                 ++++GGr+v+ v    +   vl+ ++k + +++ i
  AJA93197.1 131 KVQSGGRIVIGVILieTLYSVLQTIEKLNFESIDI 165
                 **********9987656677888888887666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   6.3e-14   3.1e-11       1      70 [.      43     114 ..      43     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 6.3e-14
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                      vLd+GcG+G +t ++a ++ +++kv+gvDi+++++e +++++e+ g+ n ++v+g+a++   e  + D +++
       AJA93197.1  43 VLDIGCGSGSVTVEAAIQVeESGKVIGVDIDPNAIELTKKNLEKFGIsNYTLVEGNAKEKISELPQADTIFI 114
                      9*****************9659********************99999**********664444456777766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   2.0   1.5e-13   7.6e-11     158     282 ..      36     165 ..      22     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.5e-13
        PrmA 158 lvkegeevlDvGtGSGiLai.aaakL.gakkvvavDiDevAvkvakeNaelNkveaklev..alseellkeekadvivaNILaevlielaedikklvke 252
                  + +g++vlD+G+GSG  ++ aa ++ +  kv++vDiD+ A++ +k+N+e+ ++++   v  +++e++ +  +ad i+         +++e  +  v++
  AJA93197.1  36 RLSAGQTVLDIGCGSGSVTVeAAIQVeESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVegNAKEKISELPQADTIFIGGTGGDTKDIVELCQDKVQS 134
                 577899**********999944555524679*************************665633456666667899******9*999************** PP

        PrmA 253 ggllilSGilkekaeevaealeq.gfeleev 282
                 gg++++  il e   +v +++e+ +fe +++
  AJA93197.1 135 GGRIVIGVILIETLYSVLQTIEKlNFESIDI 165
                 *******************999889998776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.1   7.1e-13   3.5e-10      46     120 ..      38     112 ..      23     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.1e-13
                      --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
  Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                        g++vlD+ +G+g ++++ + +v+e+gkv+++Di++n ++ ++k l++ g +n  ++ +na+e   e    D++
       AJA93197.1  38 SAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEKISELPQADTI 112
                      4699**********************************************************8755554445544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.7   1.5e-11   7.4e-09      13     115 ..      38     140 ..      30     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.5e-11
  Methyltransf_18  13 ekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGleklkeee.vdtvviaGmGgelileILeeak 104
                      + g++v+DiG+  g ++++++ + +   kvi +Di ++++e  k+n+ek g++ + +++ ++  ek++e   +dt+ i G Gg++  +I+e ++
       AJA93197.1  38 SAGQTVLDIGCGSGSVTVEAAiQVEESGKVIGVDIDPNAIELTKKNLEKFGIS-NYTLVEGNAKEKISELPqADTIFIGGTGGDT-KDIVELCQ 129
                      57899*************8653889999************************6.689999*******97655***********97.78999998 PP

  Methyltransf_18 105 eklkkikklil 115
                      +k+++  ++++
       AJA93197.1 130 DKVQSGGRIVI 140
                      88887777665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.4e-10   6.9e-08       1      84 [.      44     126 ..      44     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-10
  Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdire 84 
                      L+iGcG+Gs++ + + +  +  +++gvDi+p+aie +k+ l k +  n + ve +a++ +++ +  + D++++ ++   +kdi e
       AJA93197.1  44 LDIGCGSGSVTVEAAIQVeESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEKISELP--QADTIFIGGTGGDTKDIVE 126
                      8*********999988888999999*********************************999888..9****99988777777665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   1.9e-10   9.5e-08      31      94 ..      39     104 ..      19     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.9e-10
                 TCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST CS
         MTS  31 lsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vevvasdvleeve 94 
                 + ++vlD+GcG G +++++a + +e   v  vd+d +A+e++k+nle+ +++  ++v+ ++ e+++
  AJA93197.1  39 AGQTVLDIGCGSGSVTVEAAIQVEESGkVIGVDIDPNAIELTKKNLEKFGISnYTLVEGNAKEKIS 104
                 4678*************99977776555*********************99988888888887776 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.1   2.6e-10   1.3e-07      53     130 ..      30     111 ..      22     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.6e-10
                 HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH-..-EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---..--SE CS
        CMAS  53 lileklelkpGmtlLdiGcGWGslvrraveryd..vkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde..kvdr 130
                 + + k +l +G+t+LdiGcG Gs++++a+ + +   kv+g+ +  +  +l+kk++++ ++++ + v+    e ++e  + d 
  AJA93197.1  30 IQISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEesGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEKISElpQADT 111
                 5678999*******************99876542279**********************99988887777776666655555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.8e-10   1.9e-07       1      65 [.      44     112 ..      44     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.8e-10
                      EEET-TTSHHHHHHH...HTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC....TSS-TT-EEEE CS
  Methyltransf_11   1 LdvGcGtGrlaeala...krgarvvgvDlskemlklakekaseegl.kvefvvadaek....lpfednsfDlv 65 
                      Ld+GcG+G+++ + a   +  ++v+gvD+++++++l k++ ++ g+ + ++v+++a++    lp    + D +
       AJA93197.1  44 LDIGCGSGSVTVEAAiqvEESGKVIGVDIDPNAIELTKKNLEKFGIsNYTLVEGNAKEkiseLP----QADTI 112
                      8**************6554449*********************999999999999996321133....34444 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   7.7e-10   3.8e-07      45     156 ..      37     141 ..      17     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.7e-10
                     HHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHH CS
  Methyltransf_3  45 lvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkklpefDfifvDaDkssyvny 139
                     l+  + vl+iG   G   +  a+++ e Gk++ +did++a e+++k ++k g+ +   l eg+a++ + el + +       if+     + +  
      AJA93197.1  37 LSAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISN-YTLVEGNAKEKISELPQAD------TIFIGGTGGDTKDI 124
                     6677899**********************************************87.57999***99998886654......57877777777777 PP

                     HHHHHHTEEEEEEEEEE CS
  Methyltransf_3 140 yeklleLvkvGgliaiD 156
                      e + + v+ Gg i+i 
      AJA93197.1 125 VELCQDKVQSGGRIVIG 141
                     77777777777777665 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   2.1e-09   1.1e-06      41     119 ..      39     114 ..      24     172 .. 0.87
   2 ?   -2.3   0.0         6     3e+03      67      91 ..     142     167 ..     136     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.1e-09
                    CC-EEEETT-TTSHHHHHHHHT..T-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSR..gakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                     g++vLD+ +GsG++ +EA+    +  k++ v+ d++a+++ k+nle++++++  + +  +a+e++++l+    + d +f+
     AJA93197.1  39 AGQTVLDIGCGSGSVTVEAAIQveESGKVIGVDIDPNAIELTKKNLEKFGISN-YTLVEGNAKEKISELP----QADTIFI 114
                    5789***************976225668999********************97.9999999999998884....5577776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                    EEEEES-HHHHHHHHH.HHCCCT--T CS
  Cons_hypoth95  67 avlvekdkeavkilke.nleelklee 91 
                    ++l+e+  ++++++++ n e++++++
     AJA93197.1 142 VILIETLYSVLQTIEKlNFESIDITQ 167
                    56666666666666544666665553 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   3.6e-09   1.8e-06       3      66 ..      41     105 ..      39     112 .. 0.89
   2 ?   -2.1   0.0       4.5   2.3e+03     102     138 ..     127     162 ..     121     174 .. 0.50

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.6e-09
                     EEEEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHH CS
  Methyltransf_4   3 pvvleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvlle 66 
                      +vl+iGcG+G+++v+ A + + + +++G++i  + ++   k+ e+ +++N  +++g+a + ++e
      AJA93197.1  41 QTVLDIGCGSGSVTVEAAIQvEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEKISE 105
                     579***************77256679*********************************888866 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.5
                     HHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEEE CS
  Methyltransf_4 102 elarvLkkgGvlelaTDveeyaeemlkvleeeplfer 138
                       +++ + gG +++   + e  + +l+ +e+  +fe+
      AJA93197.1 127 LCQDKVQSGGRIVIGVILIETLYSVLQTIEKL-NFES 162
                     45555555555554444444444444444443.3433 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   3.6e-09   1.8e-06      19      62 ..      36      90 ..      21     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.6e-09
  Methyltransf_23 19 klraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae........k 62
                     +l ag+ vLdiGcG+G+++ +++ ++    +v+gvD++p+a+e+ +        +
       AJA93197.1 36 RLSAGQTVLDIGCGSGSVTVEAAIQVEesgKVIGVDIDPNAIELTKknlekfgiS 90
                     467889************999999876778*************987666666662 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1     8e-08     4e-05       2      66 ..      41     107 ..      40     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8e-08
  Methyltransf_15   2 rvilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklk 66 
                      +++lD+ +G+G  +++ a +     kvi+++i+++ ++++++N e +g+s+  tlv g+ +e +++l 
       AJA93197.1  41 QTVLDIGCGSGSVTVEAAIQveeSGKVIGVDIDPNAIELTKKNLEKFGISN-YTLVEGNAKEKISELP 107
                      579*********99998887455459**********************986.5889999888777654 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   9.1e-08   4.5e-05       2     103 ..      45     140 ..      44     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.1e-08
  Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealaslaagsiDllfiDgghaaeavledleall 92 
                       iG  +G  ++ + +a++  + g+++ vd dp   +a +l ++   +   ++ +l++++++e +++l   + D +fi g   + ++++ +e+++
       AJA93197.1  45 DIG--CGSGSVTVEAAIQVEESGKVIGVDIDP---NAIELTKKnleKFGISNYTLVEGNAKEKISELP--QADTIFIGGT--GGDTKDIVELCQ 129
                      799..7777777777788888889********...544444443333555569***************..89*****986..9*********** PP

  Methyltransf_24  93 prlapggvvlf 103
                      +++++gg +++
       AJA93197.1 130 DKVQSGGRIVI 140
                      *******9885 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.7e-06   0.00086       8      71 ..      39     102 ..      35     116 .. 0.89
   2 ?    2.3   0.0      0.22   1.1e+02      19      73 ..     117     175 ..     106     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.7e-06
                      TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCC CS
  Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarki 71 
                       ++t+lD+ ++ G+ T   a  ++++g+v+ vd++ + ++  ++nl+++g+ n +++e+ a++ 
       AJA93197.1  39 AGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEK 102
                      5799*************999889**********************************9998764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                      TSHHHHHHHHHTTTT....SEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHH CS
  Methyltr_RsmB-F  19 PGgKTthiaelmknk....gtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73 
                       Gg T  i el ++k    g++v   +  e l +v +++++L+ +++ +++  + k  k
       AJA93197.1 117 TGGDTKDIVELCQDKvqsgGRIVIGVILIETLYSVLQTIEKLNFESIDITQITIGKSRK 175
                      58888888888655422336788888888899999999999999999888876665555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1     8e-07    0.0004      26     109 ..      37      97 ..      24     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8e-07
                 --TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE CS
     UPF0020  26 wkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsq 109
                 + +g++ lD  CGsG++ +Eaa+++++                         k++g+D+d+++++ +++N+ek g+++   ++ 
  AJA93197.1  37 LSAGQTVLDIGCGSGSVTVEAAIQVEESG-----------------------KVIGVDIDPNAIELTKKNLEKFGISNYTLVEG 97 
                 56789999999***************999.......................69*********************998766554 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   3.5e-07   0.00018      33     174 ..      32     170 ..      16     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.5e-07
       GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDavfLDlPa..Pweaip 129
                 i k +l  G  v++ G Gsgs++   a  v+  G++  ++   + +e  ++++++ ++s+++ v+     ke   +e+  ++D++f+        + ++
  AJA93197.1  32 ISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGN--AKEKI-SEL-PQADTIFIGGTGgdTKDIVE 126
                 4577999******************************************************999875..45555.567.799****9865411445666 PP

       GCD14 130 haakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevll 174
                    +++ ++ggr+      ie +    +++++l+f  i+  ++ +
  AJA93197.1 127 LCQDKV-QSGGRIVIGVILIETLYSVLQTIEKLNFESIDITQITI 170
                 677777.999***99999**************9999988877765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.8e-06    0.0019      19      71 ..      37     100 ..      25     113 .. 0.76
   2 ?    1.4   0.0      0.62   3.1e+02     118     159 ..     125     167 ..     121     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.8e-06
                 S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHH..TTEEEECS-CC CS
        FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgdit 71 
                 ++ g+tv+D+g++ G+ +  ++ +++++gkv++vD+ p+         +++  ++ t+++g+ +
  AJA93197.1  37 LSAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNaieltkknlEKFgiSNYTLVEGNAK 100
                 5689**************9999999999********9997766654331223356666666654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.62
                 HCCHCCCCECCCEEEECCCHCCCHHHHHHH.HHCCEEEEEEEE CS
        FtsJ 118 lelalkllkpggtfvlkifrgeeteallkq.lkkfFekvsvvk 159
                 +el+ + ++ gg +v+ ++  e   ++l++  k  Fe++++++
  AJA93197.1 125 VELCQDKVQSGGRIVIGVILIETLYSVLQTiEKLNFESIDITQ 167
                 7899999**********99999999999996669999999876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   5.4e-07   0.00027      98     162 ..      37     101 ..      20     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.4e-07
                 --TT-EEEETT-TTTCCHHHCCHH.TTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG CS
      Met_10  98 veegevVvdvfAGiGpfaipiaky.skakrvlaidlnPesvkylkeniklNkvekvvkpileDgre 162
                  + g++V+d+  G G  ++ +a    +  +v+++d++P+++++ k+n++   ++++   +++ ++e
  AJA93197.1  37 LSAGQTVLDIGCGSGSVTVEAAIQvEESGKVIGVDIDPNAIELTKKNLEKFGISNYT-LVEGNAKE 101
                 5789***************98865156789******************998888876.45555554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.2e-06   0.00059      24      93 ..      38     103 ..      23     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.2e-06
  Methyltransf_32  24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeat 93 
                      s+ +tv+D+G+G g  +   a  ++e + kv+g+d+  + +e ++k  ek+g  + ++    e++ +e++
       AJA93197.1  38 SAGQTVLDIGCGSGSVTVEAAI-QVEESGKVIGVDIDPNAIELTKKNLEKFG--I-SNYTLVEGNAKEKI 103
                      55689**************999.8889********************99999..5.55555555555554 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.4e-06   0.00071      41     100 ..      28      85 ..      17     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
       AviRa  41 ralellekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkNLs 100
                 ra+++ + +  +a+ t+ D  CG++  +tv + ++ ++  kv++ D+d +++el+kkNL+
  AJA93197.1  28 RAIQISKGRL-SAGQTVLDIGCGSGS-VTVEAAIQVEESGKVIGVDIDPNAIELTKKNLE 85 
                 6666664444.4789**********8.699999*************************97 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.1e-06    0.0025     191     231 .]      39      82 ..      11      82 .. 0.81
   2 ?   -2.6   0.0       7.2   3.6e+03      38      74 ..     124     159 ..     121     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.1e-06
                  TT-EEEETT-TTTH.HHHHHH..HTT-EEEEEESSHHHHHHHHH CS
  N6_N4_Mtase 191 kgdivlDpFaGSGt.Tavaak..elgrkfiGieieeeyvelaek 231
                   g++vlD  +GSG+ T++aa+  e++ k iG++i+++++el++k
   AJA93197.1  39 AGQTVLDIGCGSGSvTVEAAIqvEESGKVIGVDIDPNAIELTKK 82 
                  499*********9846666663356677************9986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.2
                  HHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT CS
  N6_N4_Mtase  38 vlkevrrvLkddgsifiniddseikkelkaladeifg 74 
                  +++++ +  + +g i+i +  +e+ +  +++  e+++
   AJA93197.1 124 IVELCQDKVQSGGRIVIGVILIETLY-SVLQTIEKLN 159
                  66788888888888888877766655.4444444444 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.8e-06    0.0019      19      84 ..      38     106 ..      19     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                     -TT-EEEES--TTSHHHHHHHTT--TT.EEEEEES-HHHHHHHTT.....-.--EEEEES-G.GGHHHH CS
  Methyltransf_5  19 kedgvyiDaTlGaggHsealLeqlsel.rligidrDksalarakerLkefe.krltlvkgnf.kelkea 84 
                      ++++ +D   G+g  + +   q++e  ++ig+d+D++a++ +k++L++f   ++tlv+gn  ++++e 
      AJA93197.1  38 SAGQTVLDIGCGSGSVTVEAAIQVEESgKVIGVDIDPNAIELTKKNLEKFGiSNYTLVEGNAkEKISEL 106
                     5677889999999998877766777766**********************83559***99985555544 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   6.5e-06    0.0032      49     145 ..      41     139 ..      24     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.5e-06
                 C-.EEEETSTTTTTHHHHHHH-TT.SEEEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC.TTTTT-EEEEEEC-S.SSHHHHHHHHCCCEEEEEEE CS
        GidB  49 rdkviDvGsGaGlPGipLaiarpe.lkltLleslekkiaFLeevkeelklenveivearaee.kqeeekydvvtsRAl.aslnelteillkllkeggli 144
                 + +v+D+G G G   +  ai  +e  k++ ++ +   i+  ++  e+++++n++ ve +a e   e  + d++ + +  +  ++++e+++ ++++gg+i
  AJA93197.1  41 Q-TVLDIGCGSGSVTVEAAIQVEEsGKVIGVDIDPNAIELTKKNLEKFGISNYTLVEGNAKEkISELPQADTIFIGGTgGDTKDIVELCQDKVQSGGRI 138
                 2.5*****************7665157999******************************8878999********99835899**************99 PP

                 E CS
        GidB 145 l 145
                 +
  AJA93197.1 139 V 139
                 8 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   8.3e-06    0.0041      35      89 ..      32      87 ..      23     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.3e-06
                HHHTT--TT-EEEEES-TTSHHHHHHHHHH--S.EEEEEE--HHHHHHHHHHHHHH CS
        DOT1 35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgck.lsvGvEimdnaselaekqkeel 89
                ++k  l+  ++ +D+G G G v++ aa +v+   + +Gv+i  na el++k+ e +
  AJA93197.1 32 ISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEESgKVIGVDIDPNAIELTKKNLEKF 87
                567789999*******************997542789************9988776 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.4e-06    0.0042      19      70 ..      40      92 ..      24     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                    T-EEEEESSTTSHHHHHH.TTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCG CS
  Spermine_synth 19 pkevLiiGGgDGgvlrev.vkhntvekitlvdiDqkvidfskkflpslaisaf 70
                     + vL iG g G v+ e  ++ +   k+  vdiD ++i++ kk+l ++ is++
      AJA93197.1 40 GQTVLDIGCGSGSVTVEAaIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNY 92
                    578999*******9999625777789**********************99944 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.1e-05      0.02      38      88 ..      33      87 ..      13     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
        NodS 38 slaqgsia.dalevGcaaGalterlapyck...rltvvdvveeaiararervkes 88
                s++  s++  +l++Gc +G++t++ a+  +   ++  vd+ ++ai+ +++ +++ 
  AJA93197.1 33 SKGRLSAGqTVLDIGCGSGSVTVEAAIQVEesgKVIGVDIDPNAIELTKKNLEKF 87
                33333333258***************98652225667899********9998874 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   5.5e-05     0.027      43      91 ..      36      86 ..      21     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.5e-05
  Methyltransf_16 43 nelsklsvlELGsGtGlvGlavaell.peakviltDlee.llellkkniel 91
                     + +++++vl++G G+G v + +a ++ ++ kvi  D++  ++el kkn+e 
       AJA93197.1 36 RLSAGQTVLDIGCGSGSVTVEAAIQVeESGKVIGVDIDPnAIELTKKNLEK 86
                     4567899****************998799*******9876*********97 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.5e-05     0.037     116     223 ..      40     146 ..      32     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                     T-EEEEET-TTSHHHHH..HHHCT-SEEEE..E---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES-GGG-S-HHHHHHHHH CS
  Methyltransf_9 116 grtildvGcgnGyhlwr..mvgegaklvvG..idPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmGvlyhrrsPldhllqlk 206
                     g+t+ld+Gcg+G       +  e++  v+G  idP+ + l++ + ++k+ g  + + +   + e++ el   dt+f  G     +     +   +
      AJA93197.1  40 GQTVLDIGCGSGSVTVEaaIQVEESGKVIGvdIDPNAIELTK-KNLEKF-GISNYTLVEGNAKEKISELPQADTIFIGGTGGDTKD---IVELCQ 129
                     799*********988761145677778888335688777765.566665.455555555678889999999999998887555543...333345 PP

                     CTEEEEEEEEEEEE-BS CS
  Methyltransf_9 207 dqlvkgGelvletlvie 223
                     d++++gG +v+  + ie
      AJA93197.1 130 DKVQSGGRIVIGVILIE 146
                     77777777777666665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.6e-05     0.048      37     103 ..      27      92 ..      10     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                 ...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGE CS
         TRM  37 irqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeiv 103
                 ir +++ k +l++  +vld   +sG  ++  a  v++  +v+  Di ++A+el k+N +   +++ +
  AJA93197.1  27 IRAIQISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEESGKVIGVDIDPNAIELTKKNLEKFGISN-Y 92 
                 56677777777888999****************************************88877776.2 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.056     104     161 ..      37      95 ..      30     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
        FmrO 104 lPapasvlDvaCgLnpLavpw.lllaadatylasDidsdlvefldrflalvevegrvev 161
                 l a ++vlD++Cg   ++v   ++       ++ Did + +e+ ++ l+  ++ +   v
  AJA93197.1  37 LSAGQTVLDIGCGSGSVTVEAaIQVEESGKVIGVDIDPNAIELTKKNLEKFGISNYTLV 95 
                 66789**************8615566667889**************9998888776555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021       0.1      24      79 ..      33      93 ..      22     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                HHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCCEE CS
      RrnaAD 24 dklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdeklk 79
                +k  l+  +tvl+ig G G  T+e a ++    +v  + +d++ ++l++k+l+    ++ +
  AJA93197.1 33 SKGRLSAGQTVLDIGCGSGSVTVEAAIQVeesGKVIGVDIDPNAIELTKKNLEkfGISNYT 93
                45556699***************98655555589999999999999999988855455555 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002       0.1      45     102 ..      38      89 ..      23     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
    N6_Mtase  45 ksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgi 102
                 + g++v+D  cGsg++ v+a+ +++      ++ ++ G+++++++++L+k Nl   gi
  AJA93197.1  38 SAGQTVLDIGCGSGSVTVEAAIQVE------ESGKVIGVDIDPNAIELTKKNLEKFGI 89 
                 56788***************99985......5667889***********999866665 PP

>> CheR  CheR methyltransferase, SAM binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00047      0.24      14      82 ..      22      82 ..      12      89 .. 0.80
   2 ?   -1.9   0.0       3.9     2e+03     156     175 ..     123     142 ..     120     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                HHHHCCH.HHHHHHHTSSSEEEEEES-TTTHHHHHHHHHHHCHSTTTSSS-EEEEEEESSCHHHHHHHH CS
        CheR 14 elekevlepllakaknekrvriwsagcssGeEpYslAmllketlpkaaklkvkilAtDidlkvlekAka 82
                  ++e+   +++k + +   +++ +gc+sG  +   A+ ++e          k++++Did +++e +k+
  AJA93197.1 22 ITKEEIRAIQISKGRLSAGQTVLDIGCGSGSVTVEAAIQVEE-----S---GKVIGVDIDPNAIELTKK 82
                556677766777777778899*********988888888888.....3...489**********98876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.9
                 HHHHHHHCCEEEEEEEEE-T CS
        CheR 156 kvlerfaeklkpgglLllGh 175
                 +++e  ++k++ gg++++G 
  AJA93197.1 123 DIVELCQDKVQSGGRIVIGV 142
                 67777788999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1338.10
//
Query:       AJA93198.1  [L=266]
Description: putative translation initiation factor IF-2 subunit alpha [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-15   57.5   2.1    1.7e-15   57.1   0.1    2.1  3  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
      6e-14   52.1   0.6    1.2e-13   51.2   0.6    1.6  1  S1           S1 RNA binding domain
     0.0058   17.2   0.9      0.029   15.0   0.2    2.3  2  EXOSC1       Exosome component EXOSC1/CSL4
  ------ inclusion threshold ------
      0.014   15.5   0.1       0.07   13.2   0.0    2.3  2  S1_2         S1 domain
        0.5   10.6   4.8       0.24   11.5   1.2    2.1  2  COG5         Golgi transport complex subunit 5


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.9   3.2e+03      39      55 ..     102     118 ..      56     126 .. 0.65
   2 !   57.1   0.1   4.7e-19   1.7e-15       4     115 ..     123     227 ..     120     228 .. 0.90
   3 ?   -0.5   0.0      0.35   1.3e+03      32      54 ..     227     249 ..     222     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.9
                  THHHHHHCTHHHHHHT- CS
  EIF_2_alpha  39 veeaLveiikkklkpqk 55 
                   e+ ++++i++k k ++
   AJA93198.1 102 KEQGILKNIQEKSKLTT 118
                  34445566666655555 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 4.7e-19
                  CTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHST.S..TTSSSEEEEEEE CS
  EIF_2_alpha   4 evgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkageeasneeeveeeeevkik 100
                  ++  k+  ky+++yda+ ++ai++   +++l+++++v+ ++ e+i  k+k + v++r+ +e++  +++Gve I++ Lk +e+  +e     + +++i+
   AJA93198.1 123 DLEDKFLSKYDSVYDAMlNIAIKGSGEIEDLKLQKKVITTI-EDICSKMKLPSVELRGILEISNNQSNGVELIQKTLKDAEN--TE-----DAKIEIT 212
                  56778999******************************997.567778******************************4444..44.....59***** PP

                  ESSSSEEEEEEEES. CS
  EIF_2_alpha 101 liapPeYvltvetld 115
                  + ++P+Y+l++ ++d
   AJA93198.1 213 YLGAPKYRLSLVSQD 227
                  *********998887 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.35
                  HTTS-TTTHHHHHHCTHHHHHHT CS
  EIF_2_alpha  32 kleipeeveeaLveiikkklkpq 54 
                  +++  e+  + ++e+i+k++k q
   AJA93198.1 227 DFKTAEKSLKPILEKIEKNVKKQ 249
                  55667788889999999999987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.6   3.4e-17   1.2e-13       2      75 .]       9      83 ..       8      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 3.4e-17
                STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                pe+ge+v ++Vt+++++Ga+V l+  n+++gf+++se++    v++ ++ +++G++  + v kv++ r++i+ls+k
  AJA93198.1  9 PETGEIVIATVTKISDHGAYVTLDeyNKIQGFLHVSEIAPG-WVRKVNKYVREGEKKVLLVKKVERGRKEIDLSLK 83
                899************************************99.9*******************************86 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   8.2e-06     0.029       1      76 [.       8      85 ..       8     171 .. 0.86
   2 ?    0.6   0.1      0.23   8.4e+02      34      87 ..     178     233 ..     149     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                -S-TT-EEEEEEEEEESSEEEEEEEEECTBSBCCCEEECCCTTSS--STS.TTSSCCHCTEEETTS....STTTT.SEEEE CS
      EXOSC1  1 lPkegdvVLarvtrlrkkqalveilsvegennvlsdsgvgangegavkei.eagggldsllsvatv....ssdlgetfkai 76
                lP+ g++V+a vt+++ + a+v +      n++ + ++v++   g v+++ + + ++++++   +      +++++++k i
  AJA93198.1  8 LPETGEIVIATVTKISDHGAYVTLDEY---NKIQGFLHVSEIAPGWVRKVnKYVREGEKKVLLVKKvergRKEIDLSLKQI 85
                8********************987666...789999*********999998777666655444333366667777777765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.23
                 CCEEECCCTTSS--STS.TTSSCCHCTEEETTSSTTTT..SEEEEEECCCTECCSS CS
      EXOSC1  34 lsdsgvgangegavkei.eagggldsllsvatvssdlge.tfkaiirsqdvRatek 87 
                  +++ +++n+++ v+ i ++  +++++   +  ++ lg  +++  + sqd +++ek
  AJA93198.1 178 RGILEISNNQSNGVELIqKTLKDAENTEDAKIEITYLGApKYRLSLVSQDFKTAEK 233
                 46777888888888777666666666544444444444325666666666666655 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05      0.07       2      32 ..      12      44 ..      11      49 .. 0.83
   2 ?   -2.4   0.0       1.5   5.4e+03      18      32 ..      57      70 ..      54      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
        S1_2  2 GkintlkvlretdfgyfLqkdesgev..lLpkk 32
                G+i+ ++v++++d g++++ de++++  +L+ +
  AJA93198.1 12 GEIVIATVTKISDHGAYVTLDEYNKIqgFLHVS 44
                99*****************99998874456555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
        S1_2 18 fLqkdesgevlLpkk 32
                ++ ++e ++vlL kk
  AJA93198.1 57 YVREGE-KKVLLVKK 70
                666777.88888765 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.2   6.8e-05      0.24      34     102 ..      67     135 ..      49     143 .. 0.90
   2 ?   -0.4   0.1      0.34   1.2e+03      54      82 ..     232     247 ..     184     258 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.8e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHH CS
        COG5  34 plkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeea 102
                  +k+++ + +e+d  l+q+ +++ ++ l  +++ ++++++l++++++ +  ++ +e l+ k l +y+++
  AJA93198.1  67 LVKKVERGRKEIDLSLKQISKDQRKKKLLDVKRFEKEQGILKNIQEKSKLTTKQIEDLEDKFLSKYDSV 135
                 5799******************99999999***********************************9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        COG5  54 tsnhleLlehlskskslssvlselkssle 82 
                  ++ ++             +l++++++++
  AJA93198.1 232 EKSLKP-------------ILEKIEKNVK 247
                 222222.............4444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1789  (0.0997825); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1809.75
//
Query:       AJA93199.1  [L=39]
Description: hypothetical protein T478_0496 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.28s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 290.49
//
Query:       AJA93200.1  [L=530]
Description: phosphoenolpyruvate carboxykinase (ATP) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.6e-218  726.1   0.0   1.8e-218  725.9   0.0    1.0  1  PEPCK_ATP  Phosphoenolpyruvate carboxykinase


Domain annotation for each model (and alignments):
>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.9   0.0    1e-222  1.8e-218       2     464 ..      21     482 ..      20     483 .. 0.99

  Alignments for each domain:
  == domain 1  score: 725.9 bits;  conditional E-value: 1e-222
                 -EEES--HHHHHHHHHHTTS-EE-TTS-EEE--TT--S--GGGEEEE--TTTTTTS-BTTTBEEE-HHHHHHHHHHHHHHHHTS-EEEEEEEE-SSTTT CS
   PEPCK_ATP   2 kvirnlsvaeLveealkreegkltstgalvvetgkktgRspkdkfiVedeetedkiwWgkvnkpiseekfealkekvleylkekelyvvdafagadpky 100
                 +++rnl+v++Lve++++++eg ltstg+l+v+tgk+tgRsp+d++i+ d+et+++i+Wg+vn+++ +ekf+++ ek+ ++ ++k+ly++d+f+gad++ 
  AJA93200.1  21 SIHRNLPVEKLVEQSIETNEGMLTSTGSLSVKTGKYTGRSPQDRYIIYDDETHETIDWGDVNRQFPTEKFNSVFEKMKKHAEGKDLYIFDGFVGADKEN 119
                 699************************************************************************************************ PP

                 -EEEEEEES-HHHHHHHHHHSBGGS-S-TTT---SEEEEEETT----HHHH--SSS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHHHTT-EEE CS
   PEPCK_ATP 101 rlkvrviterawqalfvknllirpteeeleefepdftilnapefkadpekdglnsetvvalnlekklvlilgteYaGEikKsifsvmnyllpkkgvlsm 199
                 rl++rv++++awq+lf+++l++rp++eele+++pdfti+++ +f++ pe dg++++ ++++nl+kk+vli+gt+YaGE+kKs+f+vmnyl+pkk+v++m
  AJA93200.1 120 RLAIRVVNDHAWQNLFCRQLFVRPSNEELESHDPDFTIVCLNDFETIPEIDGTRTNIFILINLSKKIVLIGGTNYAGEMKKSMFAVMNYLMPKKDVFPM 218
                 *************************************************************************************************** PP

                 EEEEEE-T.TS-EEEEEE-TTSSHHHHH-BTTB-EEESSEEEE-SS-EEES-SEEEEE-TT--TTTSHHHHHHHSTT-EEES-EE-TTT--EETT--SS CS
   PEPCK_ATP 200 hcsanvgekkgdvalfFGLSGtGKTtLsadperkligdDehgwsdegvfniegGcYaKtidLskekepeiynairfgavlENvvldeetrevdfddtsl 298
                 hcsan+g k+gd+alfFGLSGtGKT+Lsadper+ligdDehgws++gvfn+egGcYaK+i+L++++ep+i+nai+ gavlENvv++++t ++dfdd sl
  AJA93200.1 219 HCSANIG-KEGDTALFFGLSGTGKTSLSADPERMLIGDDEHGWSQNGVFNFEGGCYAKCINLNEDAEPQIWNAIKSGAVLENVVVNKDTLKPDFDDGSL 316
                 *******.677**************************************************************************************** PP

                 -S--EEEEEGGGSSSB-TTSEE--EEEEEEEE--TTS-S-SEEEE-HHHHHHHHHH-EEEE-----------EEEE-GGG-GGG-SS-HHHHHHHHHHH CS
   PEPCK_ATP 299 teNtrvaypiehienakeesvaghpkniifLtadafgvlPpvskLtkeqamyhFlsGytakvaGtergvtepeatFsacfgapFlplhpteyaelLaek 397
                 teNtr+ayp+++i+ a+ +s++ghpk iifLtada gvlPpvskLtke am+hF+sGyt+k+aGterg++ep+atFsacfg+pF+p+++++ya++L+ek
  AJA93200.1 317 TENTRAAYPLDYIPGAVIPSIGGHPKVIIFLTADALGVLPPVSKLTKESAMFHFMSGYTSKLAGTERGIKEPKATFSACFGSPFMPRPASVYAKMLGEK 415
                 *************************************************************************************************** PP

                 HHHH--EEEEEE-SEESSSTTTSEE--HHHHHHHHHHHHTTCCCTS-EEE-TTT--EEES-BTTC-G CS
   PEPCK_ATP 398 lekhnakvyLvNtGwtggaygvgkrislkatraiikaildgeleavefekdpvfglevptevpgvps 464
                 + +hn+ vyL+NtGw+gg+ygvgkris+k++ra+++a+l+g+++ ++f++d++f+l+vpte+pgvps
  AJA93200.1 416 ILEHNTVVYLINTGWSGGPYGVGKRISIKYSRAMVTAALTGKFDLIKFRHDDTFNLDVPTECPGVPS 482
                 *****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3473.68
//
Query:       AJA93201.1  [L=397]
Description: glycosyltransferase, group 1 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-37  128.3   0.0    4.6e-37  127.2   0.0    1.6  2  Glycos_transf_1  Glycosyl transferases group 1
    5.8e-22   78.6   0.0    1.1e-21   77.7   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    9.7e-14   51.7   0.0    3.2e-13   50.0   0.0    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
    2.8e-07   30.8   0.0      1e-06   29.0   0.0    1.9  2  Glyco_trans_1_2  Glycosyl transferases group 1
    6.9e-07   29.4   1.0    1.9e-06   28.0   0.4    2.1  2  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0077   16.7   0.0      0.014   15.8   0.0    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.5   7.4e+03     114     127 ..     117     130 ..     116     131 .. 0.84
   2 !  127.2   0.0   1.5e-40   4.6e-37       7     169 ..     202     366 ..     197     369 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.5
                      HTT--EEEETTTTH CS
  Glycos_transf_1 114 aaglpviasnaggp 127
                      ++++p i+s+ gg+
       AJA93201.1 117 KLKIPLIVSDQGGL 130
                      5789******9996 PP

  == domain 2  score: 127.2 bits;  conditional E-value: 1.5e-40
                      HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCC.HCSCEEEEEES..STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEEE CS
  Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkq.lnpnvklviaG.ngeeekelkklaeelelsdnviflgevsredleellknadifvl 98 
                      +k++ + + k+il+vgr++k Kg+++li+a+  ++ + + +++ lvi G +  +ek +++l+++ +ls+++ ++++ +r+d+++ +  +  +vl
       AJA93201.1 202 FKEKYQITSKFILFVGRFSKSKGIETLIHALNIIQTDqKFSDTILVIMGvDFGYEKDMEELIKKFNLSKRIMVIKNPPRKDVISAYGESEFLVL 295
                      555555689************************986669******************************************************* PP

                      EESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHH CS
  Glycos_transf_1  99 psisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgena 169
                      ps++E  ++v+lE++a+++pvi++n+ g++ +v+d+++G+lv+p n+ +la+ai+kll d++lr r+g  +
       AJA93201.1 296 PSHWELSPLVPLESFAFKKPVISTNSHGIPFTVQDNKNGILVEPDNPPQLADAIEKLLLDDNLRIRMGLSG 366
                      ****************************************************************9998666 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   3.6e-25   1.1e-21       3     134 .]     212     355 ..     210     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 3.6e-25
                      EEEEES---GG.GTHHHHHHHHHHHH.H.H...EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEEEE--..---SH CS
  Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d...vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvfvaPs..egfgl 85 
                       ilfvGr+  + kg++ l++a+  ++ + +     lvi+G +   ++++eel++  +l++r+ +      +d+ +++ ++  +v+Ps  e  +l
       AJA93201.1 212 FILFVGRF-SKSKGIETLIHALNIIQTDqKfsdTILVIMGVDFgYEKDMEELIKkfNLSKRIMVIKNPprKDVISAYGESEFLVLPShwELSPL 304
                      69******.556**************443244699*****44366679999887699999977777666699****************9999** PP

                      HHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
  Glyco_trans_1_4  86 kllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                      + lE++a+++pv++t+  gi+ +v  ++ng+lv+p++p +la+ai++Ll d
       AJA93201.1 305 VPLESFAFKKPVISTNSHGIPFTVqdNKNGILVEPDNPPQLADAIEKLLLD 355
                      **********************99988*********************965 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.1e-16   3.2e-13       1     169 [.      16     194 ..      16     195 .. 0.76
   2 ?   -1.4   0.0      0.68     2e+03     145     164 ..     259     277 ..     256     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.1e-16
  Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev........elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaal.ga 86 
                     +GG+   +++Lar+    Gh+Vt++t + d   + +         e v  ++  +  + +  l+ +    ++ +++++ kpD++H+ +  +   +
      AJA93201.1  16 FGGIVFLAVDLAREISNIGHDVTIYTTDLDFSNGPNKfnknlprnEKVEKFVINR-THVWFSLKLFFINTSMFKQIQKDKPDIIHTIGLRSYqSL 109
                     59***********************999998888887776665432222222222.22222222222233456677778******9987664244 PP

  Glyco_transf_4  87 allalrrrlgiplVltvHglye....krllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                      +l++ ++l+ipl+++  g        ++   +l+ l+++ +++ ++++++a  v a  e++++ +++  + +++++ +i nGv+le
      AJA93201.1 110 TALKISKKLKIPLIVSDQGGLTthpfLKHSSIFLRILYKIQNYFVKQIINHATIVSAANEYEKNIFLD-IN-KNSNVQIIRNGVNLE 194
                     45555558********99999988887888889999999999999999********************.77.679**********98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
  Glyco_transf_4 145 adelrerygvppekitVipn 164
                      +el+++++++ ++i Vi n
      AJA93201.1 259 MEELIKKFNLS-KRIMVIKN 277
                     5778888**99.8*****99 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   6.1e+03      46      57 ..     255     267 ..     252     268 .. 0.82
   2 !   29.0   0.0   3.4e-10     1e-06      13      89 ..     304     382 ..     292     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
  Glyco_trans_1_2  46 fe.dleelaekir 57 
                      +e d+eel++k++
       AJA93201.1 255 YEkDMEELIKKFN 267
                      6779999999986 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 3.4e-10
  Glyco_trans_1_2  13 lrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhraeq 89 
                      l+ +E  a+  +++++ ++g++  ++++k +il+e  ++ +la++i++ll ++ +r +++  ++++v++e++++  a++
       AJA93201.1 304 LVPLESFAFKKPVISTNSHGIPFTVQDNKNGILVEpdNPPQLADAIEKLLLDDNLRIRMGLSGYNFVHEECNCVSMAKN 382
                      6789********************************************************************9998876 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.4   6.4e-10   1.9e-06      14     136 ..      24     158 ..      11     161 .. 0.71
   2 ?   -1.8   0.0      0.95   2.8e+03      98     111 ..     240     253 ..     195     275 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.4e-10
  Glyco_trans_4_2  14 lrlakeLakrgyeVhvitpkkga..kdele....aegihvhrlkvd...rkgpleylkaf.klkklikkikPDvvhahyakpy.gllgslaarl 96 
                      + la+e+++ g++V++ t + +     +++      + +v ++ ++   ++++l+++ ++ +++k i+k+kPD++h++   +y  l +  ++++
       AJA93201.1  24 VDLAREISNIGHDVTIYTTDLDFsnGPNKFnknlPRNEKVEKFVINrthVWFSLKLFFINtSMFKQIQKDKPDIIHTIGLRSYqSLTALKISKK 117
                      5578899999999999886433212222220001334466666444444777****998779*********************65556556677 PP

  Glyco_trans_4_2  97 sgvipvvlsvwGldv.lkfpkksk.lkklllklalkkatkvi 136
                      ++ ip+++s +G  + + f k s  + ++l+k+  + ++++i
       AJA93201.1 118 LK-IPLIVSDQGGLTtHPFLKHSSiFLRILYKIQNYFVKQII 158
                      77.88887777654437775555579*******999999988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.95
  Glyco_trans_4_2  98 gvipvvlsvwGldv 111
                      +++ ++l + G d+
       AJA93201.1 240 KFSDTILVIMGVDF 253
                      34444555555555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.7e-06     0.014       1     146 [.      17     177 ..      17     190 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
  Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt........papapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvhahspt.. 83 
                      gGi   + +lar+    Gh+Vt++t        p++ ++  +++e    v  + + r++  + +l+  +   +++ + ++ +pd++h+ ++   
       AJA93201.1  17 GGIVFLAVDLAREISNIGHDVTIYTtdldfsngPNKFNKNLPRNE---KVEKFVINRTH-VWFSLKLFFINTSMFkQIQKDKPDIIHTIGLRsy 106
                      78888899*****************87776554444444443322...34455566665.3344443333333433239********9995422 PP

  Glyco_trans_4_4  84 aglaarlarrrrgiplvvtlhglllrrg.....sgavrrly...ralerrllrradavlvvseaeaeelra 146
                       +l a+ ++ + +ipl+v+ +g l++++     s ++r ly     + + ++++a  v +  e+e   + +
       AJA93201.1 107 QSLTALKISKKLKIPLIVSDQGGLTTHPflkhsSIFLRILYkiqNYFVKQIINHATIVSAANEYEKNIFLD 177
                      455555555588*******9986655444433444444444444556778888888888888877766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2951.73
//
Query:       AJA93202.1  [L=139]
Description: putative translation initiation factor aIF-2, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-30  103.1   0.0      1e-29  102.8   0.0    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.002   18.5   0.8     0.0027   18.0   0.8    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0039   16.7   1.3     0.0072   15.8   1.3    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0068   16.4   0.4      0.011   15.7   0.4    1.4  1  Elf1             Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
       0.18   11.2   2.5        0.3   10.5   2.5    1.4  1  zf-TFIIB         Transcription factor zinc-finger
       0.21   11.6   2.4         30    4.6   0.1    3.3  3  zinc_ribbon_4    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.0   3.4e-33     1e-29       5     117 .]      21     131 ..      17     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 3.4e-33
                   CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHHHHTSTSSSTSTCEEEC CS
  eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyieeyVlCkeCkspetele 101
                   +++ +r+++p+++++ egk kt+++Nf++  kaL+rdp+ +l+yl+ke+++ ++   ++++i+ gk + +++++l+  y+++yV C++C+sp+t++e
    AJA93202.1  21 SSSGKRFELPPIDITWEGK-KTILRNFADFPKALRRDPNTILQYLSKEFAVPADR-VGDKAIFVGKRDPDDFSRLFGIYLKDYVECPTCQSPDTKVE 115
                   57789**************.********************************998.899************************************** PP

                   CSSSCEEEEESSSTCE CS
  eIF-5_eIF-2B 102 keerllvlkCkaCgak 117
                   ke+r+++l C+aCgak
    AJA93202.1 116 KENRISFLICEACGAK 131
                   **************85 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.8   9.2e-07    0.0027       5      38 ..     103     133 ..      99     139 .] 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.2e-07
  Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCga.st 38 
                       CP C +++++++ +++ +    + +C+ Cga st
       AJA93202.1 103 ECPTCQSPDTKVEKENRIS----FLICEACGAkST 133
                      7************999999....9********443 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.3   2.4e-06    0.0072       3      27 ..     104     130 ..     102     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                   ETTTTCEEC.HEETSTTCE.EESSSSB CS
  TF_Zn_Ribbon   3 CPnCgstnl.veDpergel.vCtdCGl 27 
                   CP C s+++ ve ++r  + +C++CG+
    AJA93202.1 104 CPTCQSPDTkVEKENRISFlICEACGA 130
                   ******99547778888888******7 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   3.8e-06     0.011      19      58 ..      99     135 ..      94     139 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.8e-06
        Elf1  19 ptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetk 58 
                 + + +Cp C++    + k++k+++i  + C+ Cg++ ++k
  AJA93202.1  99 KDYVECPTCQSP---DTKVEKENRISFLICEACGAKSTIK 135
                 66779*******...89*****************998876 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.5    0.0001       0.3       2      26 ..     104     129 ..     103     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
    zf-TFIIB   2 CPkCqdeleeser.ggveidyCpqCr 26 
                 CP+Cq++ +++e+ + + +  C++C+
  AJA93202.1 104 CPTCQSPDTKVEKeNRISFLICEACG 129
                 ******9999999555*********7 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.17     5e+02      10      23 ..      66      79 ..      65      82 .. 0.84
   2 ?    4.2   0.2     0.013        40       3      10 ..     102     109 ..     101     117 .. 0.82
   3 ?    4.6   0.1      0.01        30       4      14 ..     124     134 ..     122     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.17
  zinc_ribbon_4 10 akyeiddeklpakg 23
                   ++++++++++ +k+
     AJA93202.1 66 KEFAVPADRVGDKA 79
                   79*******99886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
  zinc_ribbon_4   3 itCpsCka 10 
                    ++Cp C++
     AJA93202.1 102 VECPTCQS 109
                    67888875 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.01
  zinc_ribbon_4   4 tCpsCkakyei 14 
                     C++C+ak +i
     AJA93202.1 124 ICEACGAKSTI 134
                    6******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1060.03
//
Query:       AJA93203.1  [L=374]
Description: PF07431 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-121  404.6   3.2   3.7e-121  404.5   3.2    1.0  1  DUF1512   Protein of unknown function (DUF1512)
  ------ inclusion threshold ------
       0.12   12.8   0.5       0.37   11.3   0.1    1.9  2  ANAPC2    Anaphase promoting complex (APC) subunit 2


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.5   3.2  4.1e-125  3.7e-121       2     356 .]      22     373 ..      21     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.5 bits;  conditional E-value: 4.1e-125
     DUF1512   2 isliifllllill.llglnqklqlavllrdiekklakleklaeeakkkvvellkklg..kedpkklverlleffviePvdlePtgivkrlehllrtsed 97 
                 ++++i++l +i++ ++g  q++ql++ +++i+k++ kl+++++++kk++++++k++   k+dp+k +++++++f+i+Pvd++P+gi+++++hl+r++ed
  AJA93203.1  22 LMMLIWILPVIIFvFYG--QRIQLMISSNEIKKDIGKLDEYTTSTKKDFLNYVKNNLtsKSDPSKKLDSFFDYFTIMPVDMDPNGIITKINHLIRSRED 118
                 799*****999997777..***********************************9988899************************************** PP

     DUF1512  98 klkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlqmllplllklaeayekalkaflkgkPvGDgaGplvaakllek 196
                  ++ +++ ++++ ++ve s+++++lei+++l+l +k  rH++l+akk+kn+ l+l lqm++p+++++a a+++a+ a+++g+P+GDg+Gp+++++++  
  AJA93203.1 119 FIRLQINGMFSNLSSVELSKLQNLLEIVTTLQLFHKHTRHLYLTAKKQKNFPLILPLQMMIPFIMEEALALKDAMPAIKNGQPIGDGIGPMIVGQMMLG 217
                 *************************************************************************************************98 PP

     DUF1512 197 kekksleaakdtviaevelegrkvivvkaeGpgstvGrlgeavekiveklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatky 295
                 ++k+  +aa +tv++++++e+r+++++kaeGp +tvGr+g+++eki++ +  k+dl+i++DA lkLEGE+++s+a+G+G+aiG++G+e++kiE++at++
  AJA93203.1 218 TTKE--SAAFETVWSKTTFEDRELFLMKAEGPNATVGRPGDGLEKIISIK--KPDLVIMIDASLKLEGEDSASIAKGFGAAIGGIGTERFKIEEIATRN 312
                 8877..99****************************************99..*********************************************** PP

     DUF1512 296 gipldaviikmsleeAitaMtkeiaeavdkavervkeiikektkegetvivvGvGNtvGva 356
                 +ip+ a+++k+s++eAit Mt++ia++++++ ++++++i+e+t++g++++v+GvGNt+Gv+
  AJA93203.1 313 NIPILALVVKQSIHEAITLMTEDIANSAKTVKDELHQMIRENTTSGQSILVIGVGNTIGVS 373
                 ***********************************************************95 PP

>> ANAPC2  Anaphase promoting complex (APC) subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.2e-05      0.37       2      25 ..     124     147 ..     124     164 .. 0.89
   2 ?   -2.6   0.0      0.91   8.2e+03      30      48 ..     335     353 ..     325     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.2e-05
      ANAPC2   2 IvgMLtNlgslpleRIhsmLkmfv 25 
                 I+gM  Nl+s++l++++++L+++ 
  AJA93203.1 124 INGMFSNLSSVELSKLQNLLEIVT 147
                 89******************9876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.91
      ANAPC2  30 gydisdeeLkefLdelvke 48 
                 ++  s +++k+ L+++++e
  AJA93203.1 335 DIANSAKTVKDELHQMIRE 353
                 4555667777778888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2447.10
//
Query:       AJA93204.1  [L=368]
Description: tetratricopeptide repeat protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-19   67.2   0.0    3.7e-05   23.5   0.0    4.4  4  TPR_2       Tetratricopeptide repeat
    7.8e-16   57.2   0.7     0.0043   16.8   0.2    4.5  4  TPR_1       Tetratricopeptide repeat
    7.1e-11   42.6   0.0      6e-06   26.8   0.0    2.4  2  TPR_16      Tetratricopeptide repeat
    7.6e-11   41.3   1.6     0.0042   17.2   0.1    4.8  4  TPR_8       Tetratricopeptide repeat
    1.1e-10   41.0   0.1      0.083   12.6   0.0    4.3  4  TPR_11      TPR repeat
    2.3e-10   40.1   0.7     0.0008   19.6   0.0    3.7  3  TPR_17      Tetratricopeptide repeat
    4.7e-10   39.8   0.1    5.5e-06   26.8   0.0    2.3  2  TPR_19      Tetratricopeptide repeat
    3.7e-09   36.6   0.1     0.0052   17.5   0.0    4.2  4  TPR_14      Tetratricopeptide repeat
    7.9e-07   29.3   0.3     0.0056   17.2   0.0    4.3  4  TPR_6       Tetratricopeptide repeat
    8.1e-06   26.0   0.0       0.11   12.8   0.0    3.1  3  TPR_12      Tetratricopeptide repeat
    1.6e-05   25.0   0.0      0.011   15.9   0.0    2.7  4  TPR_9       Tetratricopeptide repeat
    3.4e-05   24.0   0.1    5.6e-05   23.3   0.1    1.4  1  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    0.00076   19.5   0.0       0.22   11.6   0.0    3.2  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
  ------ inclusion threshold ------
      0.025   14.9   0.2        4.1    7.8   0.0    3.3  3  TPR_20      Tetratricopeptide repeat
      0.034   14.2   0.1         51    4.2   0.0    3.6  3  TPR_7       Tetratricopeptide repeat
       0.14   11.9   0.6        1.9    8.2   0.0    2.5  3  YfiO        Outer membrane lipoprotein


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   8.5e-05     0.096       4      34 .]      28      58 ..      26      58 .. 0.95
   2 !   13.3   0.0   6.2e-05      0.07       2      31 ..      60      89 ..      59      92 .. 0.92
   3 !   23.5   0.0   3.3e-08   3.7e-05       1      34 []      93     126 ..      93     126 .. 0.96
   4 !   12.4   0.0   0.00012      0.13       3      31 ..     129     157 ..     127     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-05
       TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                l+  G  +++  ++eeA+e fe  l+ dPn+
  AJA93204.1 28 LFKKGINLMADEKLEEAVENFEMILRADPND 58
                7899*************************97 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.2e-05
       TPR_2  2 ealynlGlayyklgdyeeAleafekAleld 31
                ea   lG++ ++l+d+ eA + ++k l +d
  AJA93204.1 60 EAMLKLGYSRFHLDDHSEAMRVYDKILDID 89
                78899**********************998 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 3.3e-08
       TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                 +ea++   l+ y++++y++Al++ ekA+  dP++
  AJA93204.1  93 PEAWNLKSLVNYEKKNYAKALDCVEKAIDSDPTY 126
                 69******************************85 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00012
       TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                 a+yn G+ +  l++  + lea+++++e+d
  AJA93204.1 129 AWYNKGCYLSMLNQVPDSLEALKRSIEID 157
                 8**************************98 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00051      0.57       6      34 .]      30      58 ..      26      58 .. 0.86
   2 !    9.8   0.0   0.00064      0.72       2      31 ..      60      89 ..      59      92 .. 0.90
   3 !   16.8   0.2   3.8e-06    0.0043       2      34 .]      94     126 ..      93     126 .. 0.88
   4 !   15.7   0.0   8.9e-06      0.01       3      31 ..     129     157 ..     128     160 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                 +G  ++  +k++eA+e +e  L+ +Pn+
  AJA93204.1 30 KKGINLMADEKLEEAVENFEMILRADPND 58
                5677778889*****************97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00064
                HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1  2 kalynlGnayfklgkydeAleyyekALeln 31
                +a   lG+  f+l ++ eA   y+k L ++
  AJA93204.1 60 EAMLKLGYSRFHLDDHSEAMRVYDKILDID 89
                677789**********************98 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 3.8e-06
                 HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
       TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                 +a++ + ++ +++++y +Al++ ekA+  +P++
  AJA93204.1  94 EAWNLKSLVNYEKKNYAKALDCVEKAIDSDPTY 126
                 677777788899*******************86 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 8.9e-06
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
       TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                 a+yn+G  +  l++  + le+ ++ +e++
  AJA93204.1 129 AWYNKGCYLSMLNQVPDSLEALKRSIEID 157
                 9***************************9 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   5.4e-09     6e-06       2      64 ..      30      89 ..      29      95 .. 0.92
   2 !   13.4   0.0     8e-05      0.09       8      63 ..     104     156 ..     101     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.4e-09
      TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraa 64
                +++  +++  + ++A++ +e  l++d   P ++eA+l lg +++++ ++ eA  +y++ l+ +
  AJA93204.1 30 KKGINLMADEKLEEAVENFEMILRAD---PNDVEAMLKLGYSRFHLDDHSEAMRVYDKILDID 89
                5678899999****************...*****************************99876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8e-05
      TPR_16   8 lragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                 ++ ++y++A+   e a+++d   P    A++++g  +  ++ +++ ++++++ ++ 
  AJA93204.1 104 YEKKNYAKALDCVEKAIDSD---PTYGMAWYNKGCYLSMLNQVPDSLEALKRSIEI 156
                 6789****************...************************999987765 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        30       5      34 .]      29      58 ..      26      58 .. 0.84
   2 !   10.7   0.0   0.00047      0.52       2      31 ..      60      89 ..      59      90 .. 0.95
   3 !   17.2   0.1   3.7e-06    0.0042       2      33 ..      94     125 ..      93     126 .. 0.95
   4 ?    3.8   0.0     0.073        82       3      31 ..     129     157 ..     129     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                HHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
       TPR_8  5 ynlgsiylklgdyeeAkeyyekaleldpdn 34
                +++g  ++  +++eeA+e +e  l++dp++
  AJA93204.1 29 FKKGINLMADEKLEEAVENFEMILRADPND 58
                666667778899***************986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00047
                CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleld 31
                ea+++lg+  + l d+ eA+ +y k l++d
  AJA93204.1 60 EAMLKLGYSRFHLDDHSEAMRVYDKILDID 89
                7999***********************997 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.7e-06
                 CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
       TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                 ea+++++++  ++++y +A  + eka++ dp+
  AJA93204.1  94 EAWNLKSLVNYEKKNYAKALDCVEKAIDSDPT 125
                 89****************************97 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.073
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                 a+yn+g+ ++ l++   + e++++ +e+d
  AJA93204.1 129 AWYNKGCYLSMLNQVPDSLEALKRSIEID 157
                 7*********9999999999999999998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   7.4e-05     0.083       8      37 ..      39      68 ..      34      73 .. 0.90
   2 !    9.1   0.0   0.00091         1       9      40 ..      74     105 ..      68     107 .. 0.86
   3 !   11.2   0.1   0.00021      0.23       5      35 ..     104     134 ..     101     137 .. 0.95
   4 ?    4.4   0.0     0.026        30       8      28 ..     141     161 ..     139     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.4e-05
      TPR_11  8 GkyeeAieaYkkAlkldPdnaeayynLGla 37
                 k+eeA+e+++  l+ dP+++ea ++LG+ 
  AJA93204.1 39 EKLEEAVENFEMILRADPNDVEAMLKLGYS 68
                69**************************86 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00091
      TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                 +  eA+ +Y k l++d +n+ea++   l+ y+
  AJA93204.1  74 DHSEAMRVYDKILDIDVTNPEAWNLKSLVNYE 105
                 678********************987777776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00021
      TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayynLG 35 
                 ye+ +y +A+ + +kA++ dP++  a+yn G
  AJA93204.1 104 YEKKNYAKALDCVEKAIDSDPTYGMAWYNKG 134
                 99**************************988 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.026
      TPR_11   8 GkyeeAieaYkkAlkldPdna 28 
                 ++ ++++ea+k+ +++d +na
  AJA93204.1 141 NQVPDSLEALKRSIEIDVKNA 161
                 78999************9998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00093         1       5      32 ..      51      78 ..      47      80 .. 0.82
   2 !    7.1   0.1    0.0071         8       2      33 ..      82     113 ..      81     114 .. 0.93
   3 !   19.6   0.0   7.1e-07    0.0008       3      29 ..     117     143 ..     115     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00093
      TPR_17  5 aleldPnnadaynnLAelllknGdlmtA 32
                 l+ dPn+++a+  L++   ++ d+ +A
  AJA93204.1 51 ILRADPNDVEAMLKLGYSRFHLDDHSEA 78
                6899************988887777665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
      TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                 y k l++d +n++a+n++  + ++++++++A+
  AJA93204.1  82 YDKILDIDVTNPEAWNLKSLVNYEKKNYAKAL 113
                 899999*******************9999996 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 7.1e-07
      TPR_17   3 lkaleldPnnadaynnLAelllknGdl 29 
                 +ka++ dP++  a++n++ +l+++++ 
  AJA93204.1 117 EKAIDSDPTYGMAWYNKGCYLSMLNQV 143
                 8**********************9984 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   4.9e-09   5.5e-06       1      66 [.      35     100 ..      35     102 .. 0.97
   2 !   11.0   0.0   0.00043      0.48       3      58 ..     105     160 ..     103     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 4.9e-09
      TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlA 66 
                 l+a+++++eA++ +e +l +dp++ ea l L    + l +  eA+++ d++++ d  ++++++L+ 
  AJA93204.1  35 LMADEKLEEAVENFEMILRADPNDVEAMLKLGYSRFHLDDHSEAMRVYDKILDIDVTNPEAWNLKS 100
                 7999**********************************************************9985 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00043
      TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallal.gqldeAealLdalpeedpdd 58 
                 + ++ya Al+  e+a++ dp ++ a++    ++l++ +q+ +  ++L++  e d ++
  AJA93204.1 105 EKKNYAKALDCVEKAIDSDPTYGMAWY-NKGCYLSMlNQVPDSLEALKRSIEIDVKN 160
                 6789***********************.666777777***********999988875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00024      0.27      11      42 ..      35      66 ..      28      68 .. 0.90
   2 !   17.5   0.0   4.6e-06    0.0052       2      40 ..      60      98 ..      59     102 .. 0.93
   3 ?    5.7   0.0     0.029        32      14      40 ..     106     132 ..     100     134 .. 0.88
   4 ?   -0.3   0.0       2.4   2.7e+03      15      35 ..     141     161 ..     136     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
      TPR_14 11 llalGdpdeAiallrralalaPddaeawllla 42
                l+a ++++eA++ ++ +l+++P+d ea l l+
  AJA93204.1 35 LMADEKLEEAVENFEMILRADPNDVEAMLKLG 66
                788899*********************99997 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.6e-06
      TPR_14  2 eallalaeallalGdpdeAiallrralalaPddaeawll 40
                ea l+l+   ++l+d+ eA+++++++l+ + +++eaw l
  AJA93204.1 60 EAMLKLGYSRFHLDDHSEAMRVYDKILDIDVTNPEAWNL 98
                78899********************************65 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.029
      TPR_14  14 lGdpdeAiallrralalaPddaeawll 40 
                   ++++A+++ ++a++ +P+   aw+ 
  AJA93204.1 106 KKNYAKALDCVEKAIDSDPTYGMAWYN 132
                 5799*****************999986 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.4
      TPR_14  15 GdpdeAiallrralalaPdda 35 
                  +  +++++l+r ++ + ++a
  AJA93204.1 141 NQVPDSLEALKRSIEIDVKNA 161
                 556677888888888877765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.069        78       3      32 ..      28      57 ..      26      58 .. 0.80
   2 !   17.2   0.0     5e-06    0.0056       1      28 [.      60      87 ..      60      89 .. 0.95
   3 ?    2.3   0.0       0.3   3.3e+02      11      32 ..     104     125 ..      99     126 .. 0.82
   4 ?   -1.5   0.0       4.6   5.1e+03       9      25 ..     135     152 ..     129     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.069
                HHHHHHHHHH.HHHHHHHHHHHHHHHHH-TT CS
       TPR_6  3 lyklalsyrk.lgdtdkAlealerlikeYPd 32
                l+k +  + +   + ++A+e +e +++  P+
  AJA93204.1 28 LFKKGINLMAdE-KLEEAVENFEMILRADPN 57
                566666666645.99************9998 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  1 dAlyklalsyrklgdtdkAlealerlik 28
                +A++kl++s++ l+d+++A++ ++++++
  AJA93204.1 60 EAMLKLGYSRFHLDDHSEAMRVYDKILD 87
                7************************986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.3
                 HHHHHHHHHHHHHHHHHHH-TT CS
       TPR_6  11 rklgdtdkAlealerlikeYPd 32 
                 ++ ++++kAl+  e+ i++ P+
  AJA93204.1 104 YEKKNYAKALDCVEKAIDSDPT 125
                 5555********9999999885 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.6
                 HHHH.HHHHHHHHHHHHH CS
       TPR_6   9 syrk.lgdtdkAlealer 25 
                 +y++ l++  ++leal+r
  AJA93204.1 135 CYLSmLNQVPDSLEALKR 152
                 677657888899999987 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0011       1.3      15      74 ..      37      88 ..      27      89 .. 0.70
   2 !   11.8   0.0   0.00021      0.23       2      73 ..      59     121 ..      58     122 .. 0.80
   3 !   12.8   0.0   9.9e-05      0.11       5      74 ..      95     156 ..      89     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
      TPR_12 15 rlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                + ++++eA e++e  l++         p+ ++++  Lg   + l+++ eA + + + l+i
  AJA93204.1 37 ADEKLEEAVENFEMILRAD--------PNDVEAMLKLGYSRFHLDDHSEAMRVYDKILDI 88
                4444444444444444444........557999999999999999999999999999887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00021
      TPR_12   2 vatalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                 v ++l +l+   ++l ++ eA + ++k l+i   + +p+      + +  + + ++ ++y++Al+  e+a++
  AJA93204.1  59 VEAML-KLGYSRFHLDDHSEAMRVYDKILDID--VTNPE------AWNLKSLVNYEKKNYAKALDCVEKAID 121
                 56677.99999999***99*999999999999..53343......466666677789999999999999975 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 9.9e-05
      TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                 a+n   +v ++ ++y++Al++ eka++          p +  + +n g ++++l++  + le+l+++++i
  AJA93204.1  95 AWNLKSLVNYEKKNYAKALDCVEKAIDS--------DPTYGMAWYNKGCYLSMLNQVPDSLEALKRSIEI 156
                 5666777788888888888888888444........456899*************************998 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.2e-05     0.035       7      71 ..      37     101 ..      33     103 .. 0.89
   2 !   15.9   0.0   9.4e-06     0.011       8      60 ..      72     124 ..      63     129 .. 0.94
   3 ?    6.1   0.0     0.011        12       7      57 ..     105     155 ..      98     162 .. 0.85
   4 ?   -2.8   0.0       6.6   7.4e+03       6      54 ..     288     302 ..     284     313 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
       TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeairaq 71 
                   e+ e+a +  e++l  +P+d+e  +  G  +++l++ s+A++  +  l+++  +p+a  ++++
  AJA93204.1  37 ADEKLEEAVENFEMILRADPNDVEAMLKLGYSRFHLDDHSEAMRVYDKILDIDVTNPEAWNLKSL 101
                 668999**************************************999999998888887777666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9.4e-06
       TPR_9   8 eedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                  +d+++a++v++ +l ++   pe +    l++++  ++++Al++ e +++ +p
  AJA93204.1  72 LDDHSEAMRVYDKILDIDVTNPEAWNLKSLVNYEKKNYAKALDCVEKAIDSDP 124
                 589***********************************************999 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.011
       TPR_9   7 reedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                 +++++++al +ve  +  +P     ++  G  l  l+++   l++L + ++
  AJA93204.1 105 EKKNYAKALDCVEKAIDSDPTYGMAWYNKGCYLSMLNQVPDSLEALKRSIE 155
                 578899999999999999999999999999999999999999999988776 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 6.6
       TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLea 54 
                 i++ed e++                                  ++ ++a
  AJA93204.1 288 IENEDLEKT----------------------------------VESFDA 302
                 555555554..................................444444 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1     5e-08   5.6e-05       4      81 ..      40     118 ..      37     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5e-08
                 -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
      ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                 ++++A+  +e +l a++++ e+ + l+++ +++ ++ +A+++++k  +++ ++++++ l+  + ++ k+y +A+++ ek
  AJA93204.1  40 KLEEAVENFEMILRADPNDVEAMLKLGYSRFHLDDHSEAMRVYDKIlDIDVTNPEAWNLKSLVNYEKKNYAKALDCVEK 118
                 67899999*****9**************************************************************998 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   1.6e+03      17      36 ..      41      60 ..      39      64 .. 0.82
   2 !   11.6   0.0   0.00019      0.22      12      45 ..      70     103 ..      60     105 .. 0.89
   3 ?    4.9   0.0     0.024        27      11      33 ..     103     125 ..     100     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                HHHHHHHHHHHHHHTTS-HH CS
  Fis1_TPR_C 17 YseArryvdalLeiEPenrQ 36
                 +eA +  +++L+ +P+   
  AJA93204.1 41 LEEAVENFEMILRADPNDVE 60
                578999999******99755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                 HHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHH CS
  Fis1_TPR_C  12 yklgeYseArryvdalLeiEPenrQaqsLkelie 45 
                 + l ++seA+r  d +L i+  n  a +Lk+l++
  AJA93204.1  70 FHLDDHSEAMRVYDKILDIDVTNPEAWNLKSLVN 103
                 55889**************************986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.024
                 HHHHT-HHHHHHHHHHHHHHTTS CS
  Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPe 33 
                 +y  ++Y +A+ +v+  +  +P 
  AJA93204.1 103 NYEKKNYAKALDCVEKAIDSDPT 125
                 78889***********9999985 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0036       4.1       7      43 ..      44      80 ..      29      96 .. 0.84
   2 ?    2.2   0.0       0.2   2.2e+02       6      62 ..     111     167 ..     105     186 .. 0.87
   3 ?    0.6   0.0      0.67   7.5e+02      60      74 ..     342     356 ..     326     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0036
      TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAle 43
                 ++++e  l a+p+d++a+l+l    ++  ++ eA+ 
  AJA93204.1 44 AVENFEMILRADPNDVEAMLKLGYSRFHLDDHSEAMR 80
                577788889999******9999999999999999985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
      TPR_20   6 pelaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkweddaark 62 
                 + l+ +e+a+ ++p+   a ++    l + +++ ++le+L + ++ d k +++a+++
  AJA93204.1 111 KALDCVEKAIDSDPTYGMAWYNKGCYLSMLNQVPDSLEALKRSIEIDVKNARKAVKD 167
                 567778899999999999999999999999999999999999999999999999886 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.67
      TPR_20  60 arkqllkifealgsq 74 
                  +k++l++fe ++ +
  AJA93204.1 342 NKKKMLELFENMEMT 356
                 599*******98874 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.3   3.4e+02      14      35 ..      40      59 ..      35      60 .. 0.83
   2 ?    3.6   0.0      0.07        78       4      30 ..      64      90 ..      61      95 .. 0.79
   3 ?    4.2   0.0     0.045        51      14      32 ..     108     124 ..     105     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.3
       TPR_7 14 dyeeAielyeqsLaltkdpeda 35
                + eeA+e +e    l+ dp+d+
  AJA93204.1 40 KLEEAVENFEM--ILRADPNDV 59
                679********..999998886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.07
       TPR_7  4 nLarlysrlGdyeeAielyeqsLaltk 30
                 L+  ++ l d++eA ++y + L ++ 
  AJA93204.1 64 KLGYSRFHLDDHSEAMRVYDKILDIDV 90
                577777889************877765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.045
       TPR_7  14 dyeeAielyeqsLaltkdp 32 
                 +y++A+++ e+  a+++dp
  AJA93204.1 108 NYAKALDCVEK--AIDSDP 124
                 8**********..***998 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0017       1.9       5      69 ..      25      86 ..      22      97 .. 0.87
   2 ?    0.8   0.0      0.31   3.5e+02      52     112 ..     103     167 ..      96     173 .. 0.68
   3 ?   -2.1   0.1       2.4   2.7e+03      47      70 ..     282     305 ..     279     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
        YfiO  5 aselYekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFl 69
                   l++kg + +++++ +eA++++e +    P+     +a+l+l y+ ++ +d +ea+  +++ l
  AJA93204.1 25 RDRLFKKGINLMADEKLEEAVENFEMILRADPN---DVEAMLKLGYSRFHLDDHSEAMRVYDKIL 86
                5689*********************99998776...5689*****************99988765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                 HHHTT-HHHHHHHHHHHHHH-SSSTTHHHHHHHHHH..HHHHHHSHSC.....TTTS-THHHHHHHHH CS
        YfiO  52 yykdadyaealasaerFlrlyPthknvdyvlYlrgl..salaqarell.....rskrdpesarqafed 112
                 +y++++ya+al+ +e+ +   Pt      ++Y +g   s l+q+ + l       + d ++ar+a++d
  AJA93204.1 103 NYEKKNYAKALDCVEKAIDSDPTYG---MAWYNKGCylSMLNQVPDSLealkrSIEIDVKNARKAVKD 167
                 6999999999999999998888754...4555555433555555555544454446677777777765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.4
                 HHHHHHHHTT-HHHHHHHHHHHHH CS
        YfiO  47 dliyAyykdadyaealasaerFlr 70 
                 ++  A+ +++d++++++s + +++
  AJA93204.1 282 QTTMAAIENEDLEKTVESFDAYIN 305
                 567789999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2284.27
//
Query:       AJA93205.1  [L=246]
Description: phosphoglycerol geranylgeranyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-53  181.9   0.1    1.5e-53  181.5   0.1    1.0  1  PcrB          PcrB family
    2.4e-09   37.0   0.2    1.7e-07   31.0   0.0    2.1  2  His_biosynth  Histidine biosynthesis protein
      9e-06   24.9   0.5      3e-05   23.2   0.5    1.7  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0005   20.1   0.3      0.011   15.9   0.1    2.2  2  DpaA_N        Dipicolinate synthase subunit A N-terminal doma
    0.00071   18.8   0.0       0.48    9.5   0.0    2.1  2  Dus           Dihydrouridine synthase (Dus)
     0.0077   15.6   1.0       0.27   10.5   0.1    2.1  2  ThiG          Thiazole biosynthesis protein ThiG
     0.0077   15.1   0.2      0.065   12.1   0.1    2.0  2  Trp_syntA     Tryptophan synthase alpha chain
     0.0083   15.3   0.2      0.089   12.0   0.0    2.3  3  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
       0.01   15.1   0.1       0.11   11.8   0.0    2.1  2  TMP-TENI      Thiamine monophosphate synthase
      0.027   13.7   1.9        1.3    8.1   0.0    2.7  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.076   12.4   3.6        3.8    6.8   0.3    2.1  2  NMO           Nitronate monooxygenase
       0.15   11.4   0.9       0.67    9.3   0.1    2.2  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.5   0.1     1e-56   1.5e-53      10     224 ..      21     242 ..      11     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 1e-56
                 EEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEEETTBSSTTTTTHHHHHHHHH CS
        PcrB  10 tklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnvegvvryaDalFvmsllnsanadWivgahalglkk 102
                 +++D e  ++d +v+ +    + g+ ++++gGs+   + ++ ++v+ lk    +++Pi+l+p+n++gvv++aDa+ + sl+ns+n+++i+ a+alg+ +
  AJA93205.1  21 VLIDSEVSQIDSAVKLAkdvEQIGAASILVGGSSatdQMEMAEVVKNLKSA--VNIPIILFPGNITGVVPQADAILFSSLMNSENPYYITQAQALGAPN 117
                 689999999**999987553567999******9955566677777777777..9********************************************* PP

                 HHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHH CS
        PcrB 103 vkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkev 198
                 v k+   +e+l+ +Ylv+  ++ +  v++++ ++ +k++iaa++ laa+++g+r++YlEa sGa+ +v  e++a+++k+ +  livGGGir+a +Ak  
  AJA93205.1 118 VLKFG--LEPLPTSYLVIGEGTSAWFVGNVRgIPFDKPKIAAAYSLAAQFFGMRFVYLEAgSGAKTNVtPEMVATVRKVFQGFLIVGGGIRDAQTAKSL 214
                 *****..*************************************************************989999999999999**************** PP

                 HCC.SSEEEE-CHHHHHH.HCHHHHHHH CS
        PcrB 199 vea.ADvivvGnvveekd.erkidaile 224
                   a AD++v+G+++e+++  +k+ +i++
  AJA93205.1 215 TDAgADALVIGTLLEDSKnLEKLTEIAK 242
                 ****************995467777776 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.018        27      27      77 ..      29      77 ..      21      86 .. 0.74
   2 !   31.0   0.0   1.1e-10   1.7e-07      41     118 ..     163     243 ..     147     246 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.018
                  ETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
  His_biosynth 27 yagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77
                    ++ v+lak+ e+ ga  + v   +a  + + ++ ++v+++ ++v+ip+ 
    AJA93205.1 29 QIDSAVKLAKDVEQIGAASILVGGSSA--TDQMEMAEVVKNLKSAVNIPII 77
                  556778888888888888887766544..4677788888888888888875 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.1e-10
                   HT-SEEEEEEHHHHC.TTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH..H-THHHHHHHHH CS
  His_biosynth  41 egadelhvvDldaak.egreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaav..knpelikelaek 118
                   +++  + +v l+a + +++++  ++v+++++ ++  + vGGGIr+ +++++l +agad ++igt     kn e ++e+a++
    AJA93205.1 163 AQFFGMRFVYLEAGSgAKTNVTPEMVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALVIGTLLEdsKNLEKLTEIAKA 243
                   5555566777777653556666699999999999******************************86511555556666665 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.5     2e-08     3e-05      48     173 ..      34     225 ..      13     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                 HHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS.............................................................TTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................................xxx RF
       IMPDH  48 semAialareGgigvihknlsieeqaeevkkvkrs.............................................................pna 85 
                  ++A  + + G+ +++    s+++q+e+ + vk+                                                                 
  AJA93205.1  34 VKLAKDVEQIGAASILVGGSSATDQMEMAEVVKNLksavnipiilfpgnitgvvpqadailfsslmnsenpyyitqaqalgapnvlkfgleplptsYLV 132
                 567888888999999999999999999999999888899999999999999999999999999999999999999999999999999999999765444 PP

                 XBXTTSXB-EEEEE-S..STTHHHHHHHHHHT..T-SEEEEE-STSSSHHHH.HHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                 xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH  86 akdekgrllvgaavgv..kedalervkalvea..gvdvlvvdsahghsekvl.eavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                   + +    vg   g+   + +++ +  l+++  g+ ++ +++  g +++v+ e+v++++k ++   +++G + +a+ ak+L +agada+ +G
  AJA93205.1 133 IGEGTSAWFVGNVRGIpfDKPKIAAAYSLAAQffGMRFVYLEAGSGAKTNVTpEMVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALVIG 225
                 5577778888876555114455556666666444788999999999998886589********9999***********************999 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.12   1.7e+02      13      56 ..      35      78 ..      17      86 .. 0.58
   2 !   15.9   0.1   7.1e-06     0.011       2      50 ..     198     245 ..     197     246 .] 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                HHHHHHHHTT-EEEEES-.TSSS-BTTEEEE-GGGS-GGG-SEEE CS
      DpaA_N 13 ylarkLaekgakvslygl.eleekiegvekaesleealedadvii 56
                +la+  ++ ga   l+g  + ++++e +e +++l++a+ +  +i+
  AJA93205.1 35 KLAKDVEQIGAASILVGGsSATDQMEMAEVVKNLKSAV-NIPIIL 78
                33444444443333332235566666666666666665.555555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.1e-06
                 EEEESB-HHHHHHHHHHHHTT-EEEEES-TSSS-BTTEEEE-GGGS-GG CS
      DpaA_N   2 iaviGGDaRqlylarkLaekgakvslygleleekiegvekaesleeale 50 
                 ++++GG  R++ +a++L++ ga+  ++g  l e  +++ek +++++a++
  AJA93205.1 198 FLIVGGGIRDAQTAKSLTDAGADALVIGT-LLEDSKNLEKLTEIAKAIK 245
                 79***************************.8888889999999988886 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0014       2.2     138     193 ..      31      84 ..      21      97 .. 0.81
   2 !    9.5   0.0   0.00032      0.48     174     214 ..     187     226 ..     177     238 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
                 C.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEE.ESS-- CS
         Dus 138 enalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipvia.NGdIk 193
                 + a++lak ve+ Ga+ + v g ++ ++ e     e +k++k av+ip+i   G+I+
  AJA93205.1  31 DSAVKLAKDVEQIGAASILVGGSSATDQMEM---AEVVKNLKSAVNIPIILfPGNIT 84 
                 5789*****************9988887776...3679**********985256665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00032
                 HHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESC CS
         Dus 174 aIkevkqavsipviaNGdIkdaedaqaileetGadgvmigr 214
                  ++ v++ ++  +i+ G+I+da+ a+  ++  Gad+++ig 
  AJA93205.1 187 MVATVRKVFQGFLIVGGGIRDAQTAKSLTDA-GADALVIGT 226
                 6889999999999*************99998.*******95 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.017        26     134     181 ..      34      79 ..      26     105 .. 0.82
   2 !   10.5   0.1   0.00018      0.27     160     216 ..     181     237 ..     157     246 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                 HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEE CS
        ThiG 134 lvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivD 181
                 + la+ +e++G+a+++  ++       ++ +e++k + + +++P+i+ 
  AJA93205.1  34 VKLAKDVEQIGAASILVGGSSAT--DQMEMAEVVKNLKSAVNIPIILF 79 
                 56899999999999998888754..44677889999999999999975 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00018
                 --S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHH CS
        ThiG 160 GllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvam 216
                   +++e++ ++++ ++  +iv  Gi+ ++ a    + Gada+++ t +  +k+  ++
  AJA93205.1 181 TNVTPEMVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALVIGTLLEDSKNLEKL 237
                 346788888888888999999999999999999999999999999999888886554 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.12   1.8e+02     177     201 ..      52      76 ..      28      82 .. 0.60
   2 !   12.1   0.1   4.3e-05     0.065     184     229 ..     182     228 ..     167     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                 STTSSB-TTHHHHHHHHHHCTSS-E CS
   Trp_syntA 177 gaenavaaevdelverlkkltavPv 201
                 g +++ ++e+ e+v++lk++ + P+
  AJA93205.1  52 GSSATDQMEMAEVVKNLKSAVNIPI 76 
                 3333444444444444444444443 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.3e-05
                 TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHH CS
   Trp_syntA 184 aevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSal 229
                 + + e+v++++k+ +  + vG Gi++++++k+++ ++ad+ ++G  l
  AJA93205.1 182 NVTPEMVATVRKVFQGFLIVGGGIRDAQTAKSLTdAGADALVIGTLL 228
                 44568999999999999*****************9*********866 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.15   2.2e+02     218     251 ..      34      65 ..      13      69 .. 0.62
   2 ?   -3.6   0.0       3.2   4.8e+03     120     136 ..     103     119 ..     101     119 .. 0.87
   3 !   12.0   0.0   5.9e-05     0.089     199     251 ..     184     238 ..     151     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                 S-SHHHHHHHCCTT-SEEEES.HHHHC-TTHHHHH CS
        IGPS 218 iktredveklkeegvnafLvG.eslmrqedvekai 251
                 +k ++   ++++ g+ ++LvG +s ++q ++++ +
  AJA93205.1  34 VKLAK---DVEQIGAASILVGgSSATDQMEMAEVV 65 
                 33344...445556668888624455555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.2
                 SHHHHHHHHHCT-SEEE CS
        IGPS 120 deyqieearalgadaiL 136
                 ++y i++a+alga  +L
  AJA93205.1 103 NPYYITQAQALGAPNVL 119
                 589999*****998887 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 5.9e-05
                 HHHHCHCC-TT..SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
        IGPS 199 teeLaklvpkd..vllvaeSGiktredveklkeegvnafLvGeslmrqedvekai 251
                 t e++++v+k    +l+   Gi++++++++l+++g++a+ +G+ l +++++ek +
  AJA93205.1 184 TPEMVATVRKVfqGFLIVGGGIRDAQTAKSLTDAGADALVIGTLLEDSKNLEKLT 238
                 55555556533226889999**************************999998765 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.16   2.3e+02     109     152 ..      37      75 ..      27      84 .. 0.61
   2 ?   11.8   0.0   7.5e-05      0.11      85     127 ..     187     229 ..     181     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.16
    TMP-TENI 109 aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiP 152
                 a+ +e+ ga  i vG   +Td  ++a     e +k+l++a++iP
  AJA93205.1  37 AKDVEQIGAASILVGGSSATDQMEMA-----EVVKNLKSAVNIP 75 
                 55566666666666666666666665.....3345555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.5e-05
    TMP-TENI  85 pvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifp 127
                  va++r++++  li+G  + + + a+ + ++gad +++G++ +
  AJA93205.1 187 MVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALVIGTLLE 229
                 5899***********************************9865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.016        24     157     180 ..      35      59 ..      18      73 .. 0.72
   2 ?   -0.0   0.1      0.28   4.2e+02      22      36 ..      63      77 ..      58      83 .. 0.84
   3 ?    8.1   0.0    0.0009       1.3     146     178 ..     198     230 ..     158     246 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                 HHHHHHHTT--SEEEE-HH.HH-HH CS
        NanE 157 ekakkaieiGvdavvvGsa.itrle 180
                 ++ak++ +iG++++ vG++  t   
  AJA93205.1  35 KLAKDVEQIGAASILVGGSsATDQM 59 
                 57999*********99875144444 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                HHHHHHHTT--S-EE CS
        NanE 22 edikaikavvdlPii 36
                e +k++k++v++Pii
  AJA93205.1 63 EVVKNLKSAVNIPII 77
                55889999******9 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0009
                 -EEEES---SHHHHHHHHTT--SEEEE-HHHH- CS
        NanE 146 kviaeGrintPekakkaieiGvdavvvGsaitr 178
                 ++i+ G i   + ak+ ++ G+da+v+G+ +  
  AJA93205.1 198 FLIVGGGIRDAQTAKSLTDAGADALVIGTLLED 230
                 5899999*********************97754 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0025       3.8     141     197 ..      29      77 ..      21      85 .. 0.80
   2 ?    6.4   0.2    0.0033       4.9     181     223 ..     184     226 ..     174     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
         NMO 141 ptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPvi 197
                  + s+vk a+ ve+ Ga ++ v G+ a     t +    +  ++v++ ++av+iP+i
  AJA93205.1  29 QIDSAVKLAKDVEQIGAASILVGGSSA-----TDQ---MEMAEVVKNLKSAVNIPII 77 
                 56689999999*****99999866654.....223...35789*************9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0033
         NMO 181 lfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                 + ++v++v+++ +  +i  GGi d++  +    +GA +  igt
  AJA93205.1 184 TPEMVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALVIGT 226
                 5567888888888889999999999999999999999999999 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.39   5.8e+02     127     142 ..      61      76 ..      20      94 .. 0.60
   2 ?    9.3   0.1   0.00045      0.67     126     166 ..     183     223 ..     181     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                   GHHHHCTSTTS...EE CS
  G3P_antiterm 127 vpkvikeikkelkipi 142
                   +++v+k++k++++ipi
    AJA93205.1  61 MAEVVKNLKSAVNIPI 76 
                   2333333333333333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00045
                   GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
  G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                   + p++++ ++k ++  +i GG i++ ++ +++ +aGa+a  
    AJA93205.1 183 VTPEMVATVRKVFQGFLIVGGGIRDAQTAKSLTDAGADALV 223
                   45999********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1748.27
//
Query:       AJA93206.1  [L=39]
Description: hypothetical protein T478_1355 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 289.21
//
Query:       AJA93207.1  [L=63]
Description: hypothetical protein T478_0338 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 476.59
//
Query:       AJA93208.1  [L=228]
Description: peptidase propeptide and YpeB domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-07   30.6   0.0    9.1e-07   29.4   0.0    1.7  1  PepSY     Peptidase propeptide and YPEB domain
    0.00048   20.5   9.5    0.00093   19.6   9.5    1.5  1  DUF3106   Protein of unknown function (DUF3106)


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     1e-10   9.1e-07       2      60 ..      56     112 ..      55     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1e-10
                 S-HHHHHHHHHHHSTTE.EEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEETTT--EE CS
       PepSY   2 iseeqAlaiAlaavpgk.iieielededdgrlvYevelstaepegpeyevfiDAkTGkvl 60 
                 is+ +A++ A++avp++ +i+ +l    +g+lvY+v   +  +++++ +v++DA TG+ l
  AJA93208.1  56 ISLVDAMSTAEEAVPDSkAIYGKLTVI-NGYLVYKVVMMD--DNRGHNKVLVDAGTGEQL 112
                 8999*************9*********.*********665..899999999*******88 PP

>> DUF3106  Protein of unknown function (DUF3106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   9.5     1e-07   0.00093      16     101 ..     120     217 ..     111     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1e-07
     DUF3106  16 aeewnelspeqreklleiaerykkltpee....qkrlqermeewakLspeqreqarenyqklk....qLppeer....eelrekweeyqkLppeerkk 101
                 ++++++ ++  +++  ++++ +k +tpe+    +++++e  ++w+++s ++r+++  ++ ++k    +++ +e+    +e++e+w+e+  L+pee+k+
  AJA93208.1 120 KDSYKNKRSYDKKHNKKMKDYFKGMTPEQvaekKQQFKEMGDAWKSISLQDRATMIIHFMQMKmqwdTMSDDEKelkkQEMKEQWKEFLPLSPEEKKQ 217
                 56788888999999*************8733335666666689****************999998888998865222279*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1711  (0.095432); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1874.93
//
Query:       AJA93209.1  [L=432]
Description: hypothetical protein T478_0649 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0027   17.8   6.4     0.0027   17.8   6.4    3.1  2  DHR10         Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
      0.036   14.2  19.5       0.18   11.9   8.5    2.8  2  Mod_r         Modifier of rudimentary (Mod(r)) protein
      0.047   14.1   8.7        1.6    9.2   1.8    2.5  2  SLX9          Ribosome biogenesis protein SLX9
      0.076   13.1  19.3       0.18   11.9   1.6    4.5  4  DUF1664       Protein of unknown function (DUF1664)
        0.1   12.8   0.2        0.1   12.8   0.2    2.5  2  Uds1          Up-regulated During Septation
       0.13   12.0  10.9       0.12   12.2   3.1    2.8  2  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
       0.19   12.1   1.0         38    4.7   0.0    3.4  2  FlgM          Anti-sigma-28 factor, FlgM
       0.23   11.8   2.2        2.3    8.5   0.1    3.3  3  Med15_fungi   Mediator complex subunit 15
       0.39    8.8  23.9        1.1    7.3   4.7    2.4  2  EzrA          Septation ring formation regulator, EzrA
       0.55   10.3  16.6        1.9    8.5   7.0    2.5  2  ADIP          Afadin- and alpha -actinin-Binding
       0.67   10.1   5.6         13    5.9   0.1    2.6  2  SAM_KSR1      SAM like domain present in kinase suppressor RA
       0.69    9.9   7.5       0.36   10.8   0.5    3.9  3  DUF438        Family of unknown function (DUF438)
        1.2    8.7  11.7        1.3    8.5   4.2    2.3  2  Exonuc_VII_L  Exonuclease VII, large subunit
        1.5    9.3  20.0        1.5    9.2   8.1    3.0  3  Fez1          Fez1
        1.6    9.3   6.0        1.6    9.3   0.4    3.2  2  Arc_PepC_II   Archaeal Peptidase A24 C-terminus Type II
        1.9    8.4  13.7        1.1    9.2   1.8    3.2  2  STAT_alpha    STAT protein, all-alpha domain
        1.9    8.7  10.2        1.2    9.3   2.4    3.4  3  SesA          N-terminal domain on NACHT_NTPase and P-loop NT
        3.4    7.5   5.7        2.2    8.1   1.7    2.9  2  DivIC         Septum formation initiator
        4.1    7.3   8.3       0.52   10.2   0.9    3.2  3  DASH_Dam1     DASH complex subunit Dam1
        4.1    6.6  17.0        4.6    6.4   2.5    2.8  2  TMPIT         TMPIT-like protein
        4.8    7.9  12.4        6.7    7.4   2.9    3.3  3  DUF2203       Uncharacterized conserved protein (DUF2203)
        4.9    7.1   5.7        5.6    6.9   0.9    2.8  2  DUF489        Protein of unknown function (DUF489)
        5.5    7.6   8.4        2.5    8.7   1.3    3.5  2  YtxH          YtxH-like protein
        6.4    7.1  13.7        1.5    9.1   3.5    3.4  3  DUF641        Plant protein of unknown function (DUF641)
        6.5    7.5  14.2    1.4e+04   -3.2  13.5    3.5  0  FliD_N        Flagellar hook-associated protein 2 N-terminus


Domain annotation for each model (and alignments):
>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   6.4   3.7e-06    0.0027      10      84 ..     157     231 ..     152     238 .. 0.93
   2 ?    1.4   1.1      0.43   3.1e+02       2      51 ..     369     419 ..     368     427 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-06
       DHR10  10 elaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlq 84 
                  l+el    +e+ + id ++  e+ ++ + +ll   e+ l+kl + + +++el+  l+ek+ +  + e++++ ++
  AJA93209.1 157 DLKELSDDLKEVDELIDIFNITENSVQTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIE 231
                 67889999999*******************************************************999988665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.43
       DHR10   2 eslaeekeelaelErkarelqakidalqvvekdlrsci.klleeieaelak 51 
                 +sl+ + ++l+  E    +++ k++++++ + +l +++ ++l+eie++l+ 
  AJA93209.1 369 KSLQTAEKNLKHEESDVSDISSKLKVFEEETLELTHALpTILHEIETNLKD 419
                 688899999999999999999999999988888866553678888888765 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.5   0.00025      0.18       5      82 ..     155     232 ..     151     250 .. 0.90
   2 ?    9.3   0.9    0.0016       1.1      28      88 ..     325     389 ..     308     423 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
       Mod_r   5 keeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeq 82 
                 +++L+el +d + +++l++  + +++  +   ell + e+++ek  ++e +++el+s+l+ek +++++ e+e ++ e+
  AJA93209.1 155 TNDLKELSDDLKEVDELIDIFNITENSVQTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIEN 232
                 799***************87799999*****************7777799*******************999998776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
       Mod_r  28 vkqlkeekeellaeneslaeknlslepeleelrselqeklee.....lkelekefeekeqeldell 88 
                 vk++ ++k+++  e++++    +s ++++e ++ e+++kle+     l+++ek+++  e++ ++++
  AJA93209.1 325 VKDISKSKDSI-VEIKNIIPTLISTKEKFETKKHEFTSKLENfdsksLQTAEKNLKHEESDVSDIS 389
                 77778888877.788888888888888888888888888887443334444444444444444433 PP

>> SLX9  Ribosome biogenesis protein SLX9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.8    0.0022       1.6      40      90 ..     150     213 ..     122     266 .. 0.67
   2 ?    8.8   0.7    0.0029       2.1       4      43 ..     346     383 ..     343     425 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
        SLX9  40 pskklvtdlesLadaLpdle.....................eeegekkekkekeqaqqgkvkkaekslkskp 90 
                  skkl +dl++L d L++++                     +    ++++ ek ++++ +v+    +lks++
  AJA93209.1 150 YSKKLTNDLKELSDDLKEVDelidifnitensvqtinellsS----REKTLEKLSKRELRVN----ELKSSL 213
                 589****************99999998776555444322221....1111222222222222....222222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
        SLX9   4 lsKkdKrkiKheaflsKieksisksaskkkkkrkrrpskk 43 
                  s k+K   K+ +f sK+e+   +++ ++++k+ + ++ +
  AJA93209.1 346 ISTKEKFETKKHEFTSKLEN-FDSKSLQTAEKNLKHEE-S 383
                 5779****************.44444444444433222.2 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.35   2.5e+02      60      95 ..      43      78 ..      30     104 .. 0.85
   2 ?    5.6   0.1     0.022        15      56     113 ..     117     175 ..     110     186 .. 0.78
   3 ?    3.5   2.4     0.093        67      45     100 ..     191     250 ..     171     270 .. 0.46
   4 ?   11.9   1.6   0.00025      0.18      50     116 ..     345     412 ..     331     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.35
     DUF1664 60 tkrhLssridrvdkkldeqkeiskeikeevtevred 95
                 k  L+s+i++  +++d q e++ +i++e++e + d
  AJA93209.1 43 RKGTLASEIKSHRNRIDPQREVILKIANELSEDELD 78
                578999**********************99886555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.022
     DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeev.tevredlseigedvesvkeavegl 113
                 ++ + k+  ++ i++v++ l + ++++++ + +  +++ +dl+e+++d+++v+e++  +
  AJA93209.1 117 DVMRFKKASTAGINKVGDMLGKHSKVIHHFAPKYsKKLTNDLKELSDDLKEVDELIDIF 175
                 56667888888999999999999998888887652579999999999999999988655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.093
     DUF1664  45 svskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeik.eevtevredlseig 100
                 s  k le++s     +++ k  L+++ d++ k  +e k+i ++ + +e t+v+++lse +
  AJA93209.1 191 SREKTLEKLSkreLRVNELKSSLAEKNDNITKFENEIKDIENSPNyKEYTDVKSQLSECD 250
                 222334444421123455555555555555555555555544432244555555555555 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00025
     DUF1664  50 leqvseslaatkrhLssridrvdkk.ldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                 l + +e+ ++ k++++s++++ d+k l+  ++  k+ +++v++++++l+ ++e+  ++ +a  ++ ++
  AJA93209.1 345 LISTKEKFETKKHEFTSKLENFDSKsLQTAEKNLKHEESDVSDISSKLKVFEEETLELTHALPTILHE 412
                 55677899999************8637777788899999**************998888776665444 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   2.0      0.57   4.1e+02      24     106 ..     159     228 ..     144     257 .. 0.55
   2 ?   12.8   0.2   0.00014       0.1       7     118 ..     288     405 ..     285     406 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.57
        Uds1  24 eelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdelasele 106
                 +el+ +lk ++e ++  + +   e+++++  + Ls++  +++++   s+       ++   ++ +++lae +  + ++++e++
  AJA93209.1 159 KELSDDLKEVDELIDIFNIT---ENSVQTINELLSSRE-KTLEK--LSK-------RELRVNELKSSLAEKNDNITKFENEIK 228
                 45555555555555555555...555555555555555.33333..111.......111233333334444444444444443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
        Uds1   7 tAlvdsqefeiLsleeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksak.......ssaarsnskssreslakaeeelaeserkv 98 
                 tA + s+ +++L++  +  +k  l ++++ +++ +  ++  +k +d+ +++++    ++ s+k       ++ +++ ++++++sl++ae++l++ e+ v
  AJA93209.1 288 TATLASSPYDVLDTANIPGIKNILDSITTGIDSGSVSVKDISKSKDSIVEIKNII-PTLISTKekfetkkHEFTSKLENFDSKSLQTAEKNLKHEESDV 385
                 7888999999999999999999999999999999999999999999999999998.777776678888885666678889999**************** PP

        Uds1  99 delaselekleeraaevrrr 118
                  +++s+l+  ee+  e+ + 
  AJA93209.1 386 SDISSKLKVFEEETLELTHA 405
                 ************99988765 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.1   0.00017      0.12      88     173 ..     147     233 ..     127     237 .. 0.84
   2 ?    3.8   1.0     0.062        44     131     167 ..     355     392 ..     308     420 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
  Bacillus_HBL  88 yktlveavdkkdkaellellekLqee..iqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                   +++ +++  ++d +el+++l++  e   i ++ +++ q+i+eL + ++k+ ++ ++ +  v+el+s la ++ +i + +nei+d++++
    AJA93209.1 147 APKYSKKL-TNDLKELSDDLKEVDELidIFNITENSVQTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENS 233
                   55555555.5667788888888876444899999999************************************************987 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.062
  Bacillus_HBL 131 lklklakdsknFktdv.deltsilagdsgvisqlqnei 167
                    k +++++ +nF+++  +++++ l+ ++ ++s++  ++
    AJA93209.1 355 KKHEFTSKLENFDSKSlQTAEKNLKHEESDVSDISSKL 392
                   12234444444443322455555555555555544444 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3     0.098        70       5      38 ..     189     214 ..     176     216 .. 0.79
   2 ?    4.7   0.0     0.053        38       3      35 ..     275     309 ..     274     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.098
        FlgM   5 iSeaakalqkakqaaaaapevreekVaelKeaIa 38 
                 +S++ k+l k+++        re +V+elK+ +a
  AJA93209.1 189 LSSREKTLEKLSK--------RELRVNELKSSLA 214
                 4666666655555........99*******9987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.053
        FlgM   3 VeiSeaakalqkakqaaaaap.e.vreekVaelKe 35 
                 V+iS++ k+l+ + + +a++p +  +++ +  +K+
  AJA93209.1 275 VHISSHDKELKDLTATLASSPyDvLDTANIPGIKN 309
                 89*******************98788888877776 PP

>> Med15_fungi  Mediator complex subunit 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0033       2.3      33      73 ..     152     192 ..     137     207 .. 0.86
   2 ?   -0.6   0.1       2.2   1.6e+03       2      42 ..     208     249 ..     200     261 .. 0.77
   3 ?    0.5   0.0         1   7.3e+02      41      91 ..     330     362 ..     323     374 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0033
  Med15_fungi  33 aaikqqlqeiqqmlarvdaliplfykltkneeavkrLlqmr 73 
                  ++ ++ l+e+++ l++vd+li +f +  ++++ + +Ll+ r
   AJA93209.1 152 KKLTNDLKELSDDLKEVDELIDIFNITENSVQTINELLSSR 192
                  5677899******************************9988 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.2
  Med15_fungi   2 qlkeklkqiyeevaknavrlkpitn.lspeqKaaikqqlqei 42 
                  +lk+ l + +++++k + + k+i+n    +++  +k+ql e+
   AJA93209.1 208 ELKSSLAEKNDNITKFENEIKDIENsPNYKEYTDVKSQLSEC 249
                  566667777778888888888888877777888888888877 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1
  Med15_fungi  41 eiqqmlarvdaliplfykltkneeavkrLlqmrimlkeqleklpqdqftik 91 
                  ++++ + +++++ip+++                   ke +e +++ +ft k
   AJA93209.1 330 KSKDSIVEIKNIIPTLIST-----------------KEKFE-TKKHEFTSK 362
                  5555555555555555555.................44444.444444444 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.9    0.0039       2.8      64     166 ..     145     246 ..     129     304 .. 0.73
   2 ?    7.3   4.7    0.0016       1.1     167     245 ..     349     427 ..     307     431 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0039
                 HHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHH...HHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHH CS
        EzrA  64 ewkkkwdeiktkklpeieellfeaeelldkykfkkakkklaeleeeldeveekikkile...elkelteseeknreeieklkekYrelrkkllanrfsy 159
                  +  k+ +  t++l+e+++ l e++el+d +++ +  +++++++e l++ e++++k+ +    ++el++s  ++ + i+k +++ ++++++ +   ++y
  AJA93209.1 145 HFAPKYSKKLTNDLKELSDDLKEVDELIDIFNITE--NSVQTINELLSSREKTLEKLSKrelRVNELKSSLAEKNDNITKFENEIKDIENSPN--YKEY 239
                 56678888889999999999999999999999864..55555555555555555555442227999999999999999999999999988643..4445 PP

                 HHHHHHH CS
        EzrA 160 gealeel 166
                  +++++l
  AJA93209.1 240 TDVKSQL 246
                 5555544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                 HHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SG CS
        EzrA 167 ekqleniekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemkeegYal 245
                 ++++e+ + ef++  e  +++  ++a++ lk  e+++++++++++ + e  +el++ lp  l+e++++ k+ ++  Y +
  AJA93209.1 349 KEKFETKKHEFTSKLENFDSKSLQTAEKNLKHEESDVSDISSKLKVFEEETLELTHALPTILHEIETNLKDVTATSYTI 427
                 5677777777877777778888888888899999999999999999999999999999999999998888888888876 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.0    0.0027       1.9      36     108 ..     180     253 ..     172     290 .. 0.77
   2 ?    7.2   1.4    0.0067       4.8      28     111 ..     329     413 ..     308     427 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0027
        ADIP  36 aiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerela.lvqakerqlekklktle 108
                 + + +i++Ll +r++ le   + + ++++l+++++ ++ +i + +++ ++ e+        + +++  +  ++e
  AJA93209.1 180 NSVQTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENSPNyKEYTDVKSQLSECDSEE 253
                 66899*********************************************999866444444444444555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0067
        ADIP  28 ekveeniaaiinviysLlqardrdleqreslnetirkleaeier.lqskierlktqleqlerelalvqakerqlekklktleqkl 111
                  k++++i++i n+i  L+  +++    + +++ ++++ ++ + +  +++ +  +  +++  ++l++ ++++ +l+ +l t  + +
  AJA93209.1 329 SKSKDSIVEIKNIIPTLISTKEKFETKKHEFTSKLENFDSKSLQtAEKNLKHEESDVSDISSKLKVFEEETLELTHALPTILHEI 413
                 57899*****************999999999999999887665515667777779999999****99999999998887755554 PP

>> SAM_KSR1  SAM like domain present in kinase suppressor RAS 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.6     0.024        17      38     114 ..     140     216 ..     134     231 .. 0.56
   2 ?    5.9   0.1     0.018        13      89     125 ..     370     406 ..     338     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
    SAM_KSR1  38 sKlvkyfSeqllaksklaereranelqkypelkqWLrvvglsqetleail.nkklsleelLkmseeelkqllsevqae 114
                 sK+++ f+ +  +k     +e +++l++ +el +  ++ + s +t++ +l ++ ++le+l  + e  +++l s++  +
  AJA93209.1 140 SKVIHHFAPKYSKKLTNDLKELSDDLKEVDELIDIFNITENSVQTINELLsSREKTLEKL-SKRELRVNELKSSLAEK 216
                 677777777777776666666677777777776666666666666655431344555543.22332333333333333 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
    SAM_KSR1  89 kklsleelLkmseeelkqllsevqaeeeelrRllaAm 125
                  +++ e+ Lk +e+++ ++ s++++ eee+  l++A+
  AJA93209.1 370 SLQTAEKNLKHEESDVSDISSKLKVFEEETLELTHAL 406
                 5678899***************************998 PP

>> DUF438  Family of unknown function (DUF438)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   1.1e+03      11      30 ..      95     114 ..      89     121 .. 0.81
   2 ?   -1.3   0.6       2.9   2.1e+03       5      32 ..     196     224 ..     193     233 .. 0.66
   3 ?   10.8   0.5    0.0005      0.36       1      51 [.     338     389 ..     338     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
      DUF438  11 gesleevkeefkellkevsa 30 
                 +e + ++k+ef + + +++ 
  AJA93209.1  95 KEVISAIKKEFGTPFPDINN 114
                 566889*****999999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
      DUF438   5 lkrLhkges.leevkeefkellkevsaeE 32 
                 l++L k e  ++e+k+ ++e+ ++++  E
  AJA93209.1 196 LEKLSKRELrVNELKSSLAEKNDNITKFE 224
                 77777766558899998888888887643 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0005
      DUF438   1 LkellkrLhk.gesleevkeefkellkevsaeEIsqaEqeLieeGipveeiq 51 
                 +k+++  L + +e++e+ k+ef ++l++ +   +  aE++L  e  +v++i 
  AJA93209.1 338 IKNIIPTLIStKEKFETKKHEFTSKLENFDSKSLQTAEKNLKHEESDVSDIS 389
                 57888776542888****************************9999999885 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.2    0.0019       1.3     142     257 ..     151     292 ..     131     302 .. 0.55
   2 ?    4.7   0.8     0.027        19     140     184 ..     354     398 ..     302     429 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
  Exonuc_VII_L 142 kaeleeqleelerrlek.....aikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk.ekleekkerl 232
                   +++l+++l+el++ l++      i +  e++ q +++l s+ ++  e+l++++ r++el+++l +  + +++k +++++ ++++ + +++++ k++l
    AJA93209.1 151 SKKLTNDLKELSDDLKEvdeliDIFNITENSVQTINELLSSREKTLEKLSKRELRVNELKSSLAE-KNDNITKFENEIKDIENSPNyKEYTDVKSQL 246
                   34555566666665555222222334446666666666666666777777777777777777777.6667777777777777555344444444444 PP

  Exonuc_VII_L 233 .......kklkerle....................lleekkerleeleekle 257
                                 +                    ++++++++l+ l+++l+
    AJA93209.1 247 secdseeV------KirhhvndeftkisrplgkfvHISSHDKELKDLTATLA 292
                   22222111......11122223444444444455557777777776666664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.027
  Exonuc_VII_L 140 pdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeel 184
                    +k+e++++le+++++  + ++++l+++++ ++ ++s+lk  ee 
    AJA93209.1 354 TKKHEFTSKLENFDSKSLQTAEKNLKHEESDVSDISSKLKVFEEE 398
                   223333333333333333333333333333333333333222221 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.7   1.2e+03      39      79 ..      50      92 ..      31     183 .. 0.47
   2 ?    9.2   8.1    0.0021       1.5      31     104 ..     186     261 ..     152     295 .. 0.64
   3 ?    5.8   2.4     0.024        17      28     107 ..     330     410 ..     324     426 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
        Fez1 39 qlrelrakleekeeeikeleesleektlelevcenelqrk..k 79
                +++  r++++ + e i ++ ++l+e +l+ ++++  +q +  +
  AJA93209.1 50 EIKSHRNRIDPQREVILKIANELSEDELDPDKLDPHFQIMvnR 92
                5555555555555555555555555555544444444433221 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0021
        Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.....kseaellrekvekleeelkelreels 104
                 +e+++   +   + +kl+++e +++el++sl ek++++ + ene++        +e + ++ +++++++e  ++r++++
  AJA93209.1 186 NELLS---SREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIenspnYKEYTDVKSQLSECDSEEVKIRHHVN 261
                 33333...33446678889999999999999999999999999988873333222222223333444444444444333 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.024
        Fez1  28 qklseivalkaqlrelrakleekeeeikeleeslee.ktlelevcenelqrkkseaellrekvekleeelkelreelsels 107
                 +  + iv++k+ +  l ++ e+ e++ +e+ ++le+  +++l++ e++l++++s+++ ++ k++ +eee+ el ++l +  
  AJA93209.1 330 KSKDSIVEIKNIIPTLISTKEKFETKKHEFTSKLENfDSKSLQTAEKNLKHEESDVSDISSKLKVFEEETLELTHALPTIL 410
                 555667777776666666666666666666666655245678999**************************9999987754 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.7      0.72   5.2e+02      13      23 ..     131     141 ..      87     260 .. 0.66
   2 ?    9.3   0.4    0.0022       1.6       2      61 ..     340     399 ..     339     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.72
  Arc_PepC_II  13 kvkellkkflf 23 
                  kv ++l k+ +
   AJA93209.1 131 KVGDMLGKHSK 141
                  23333333333 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0022
  Arc_PepC_II   2 kllymligyrvkvkellkkflflleefeekdgkikrkfisvekeldeelrkelkkykkkg 61 
                  +++  li ++ k ++ +++f   le+f+ k  ++ +k ++ e+++ ++++++lk ++++ 
   AJA93209.1 340 NIIPTLISTKEKFETKKHEFTSKLENFDSKSLQTAEKNLKHEESDVSDISSKLKVFEEET 399
                  56667889999999999**************************************99986 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   4.4      0.19   1.3e+02      10      71 ..     153     212 ..     147     269 .. 0.67
   2 ?    9.2   1.8    0.0015       1.1       8      88 ..     328     415 ..     325     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
  STAT_alpha  10 elrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqk 71 
                 +l +  +e+  d++++ ++ + F++  +++q + +e  +s +k+l+ +  + +  +n+L+ +
  AJA93209.1 153 KLTNDLKELSDDLKEVDELIDIFNITENSVQTI-NELLSSREKTLE-KLSKRELRVNELKSS 212
                 677788888889999999999999998888888.333333333222.222222233333222 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
  STAT_alpha   8 leelrskvqeteqdirkLedeqeeFdfqyqelqkl....eqeraesekkelkkqkellqqmlna...LdqkRkelvdklkellnlles 88 
                 ++++++++ e+++ i +L ++ e+F+ + +e++++    ++++ ++++k+lk ++  + +  ++     ++  el ++l  +l+++e+
  AJA93209.1 328 ISKSKDSIVEIKNIIPTLISTKEKFETKKHEFTSKlenfDSKSLQTAEKNLKHEESDVSDISSKlkvFEEETLELTHALPTILHEIET 415
                 6788999999*************************99997888888888899999888887777222444444444444444444444 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.4    0.0017       1.2      10      92 ..     157     239 ..     153     254 .. 0.87
   2 ?    0.9   0.0      0.71   5.1e+02      34      69 ..     303     338 ..     301     369 .. 0.65
   3 ?    0.6   0.3      0.82   5.9e+02      41      89 ..     370     419 ..     357     428 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
        SesA  10 aaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapapadsrl 92 
                  + +l d +k++ +l   F+  +++++++ e L++ +++le+ ++ e   +++k++l++ ++++tk e+  + ++ +p+ +++
  AJA93209.1 157 DLKELSDDLKEVDELIDIFNITENSVQTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENSPNYKEY 239
                 567888999****************************************999***************9999988766665554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.71
        SesA  34 rLplvqetLedaksqlesskldedtesaikpvlesc 69 
                 ++p ++++L+++++ ++s++ + ++ s+ k+++ + 
  AJA93209.1 303 NIPGIKNILDSITTGIDSGSVSVKDISKSKDSIVEI 338
                 577788888888888888877776655544333333 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.82
        SesA  41 tLedaksqlesskldedtesa.ikpvlesckekatkleeifekvapapad 89 
                  L++a+++l+++++d ++ s+ +k   e+  e  ++l +i+ +++ + +d
  AJA93209.1 370 SLQTAEKNLKHEESDVSDISSkLKVFEEETLELTHALPTILHEIETNLKD 419
                 68888888888888877666546666666666666666776666555554 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       4.6   3.3e+03      29      44 ..     154     169 ..     149     176 .. 0.49
   2 ?    8.1   1.7     0.003       2.2      14      58 ..     194     238 ..     188     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.6
                 HHHHHHHHHHHHHHHH CS
       DivIC  29 lqaelaklkaeneeLe 44 
                 l+++l++l+++ +e +
  AJA93209.1 154 LTNDLKELSDDLKEVD 169
                 3444444444333333 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                 XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
       DivIC  14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58 
                 k+l ++++ +  +++l+  la++++ + + e e+kd +++++y e
  AJA93209.1 194 KTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENSPNYKE 238
                 567788899999*****************************9976 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   0.00073      0.52       1      38 [.     154     191 ..     154     192 .. 0.94
   2 ?   -0.3   0.1       1.3   9.6e+02       3      22 ..     211     230 ..     195     234 .. 0.66
   3 ?   -1.9   0.1       4.3   3.1e+03      25      32 ..     388     395 ..     362     421 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
   DASH_Dam1   1 lepafaeLaDsletLdknledLqqihesLsdfNeSFas 38 
                 l++ ++eL+D l+++d+ ++ ++ +++s+++ Ne ++s
  AJA93209.1 154 LTNDLKELSDDLKEVDELIDIFNITENSVQTINELLSS 191
                 57899*****************************9987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.3
   DASH_Dam1   3 pafaeLaDsletLdknledL 22 
                  ++ae +D+++++++ ++d+
  AJA93209.1 211 SSLAEKNDNITKFENEIKDI 230
                 45556666666666666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
   DASH_Dam1  25 ihesLsdf 32 
                 i+ +L+ f
  AJA93209.1 388 ISSKLKVF 395
                 44444333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   6.9      0.02        14       3      81 ..     157     233 ..     152     294 .. 0.62
   2 ?    6.4   2.5    0.0064       4.6       9      86 ..     347     421 ..     332     428 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
       TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                 +++el++++ke+ e  + ++ + +++ + ++++ ++ +k  ++l++ + ++++lk+s+ +e+++++++ ++e+k+++++
  AJA93209.1 157 DLKELSDDLKEVDELIDIFNITENSV-QTINELLSSREKTLEKLSKRELRVNELKSSL-AEKNDNITKFENEIKDIENS 233
                 56777777777777664443333333.2333333333333444444455555555554.34455555555555554443 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0064
       TMPIT   9 kefkeleetakeykqkleels.klqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeve 86 
                 +  +++e++++e+++kle+   k+ ++  k++k+++ ++++++s+lk ++++    + e ++ l + l+e++++lk+v 
  AJA93209.1 347 STKEKFETKKHEFTSKLENFDsKSLQTAEKNLKHEESDVSDISSKLKVFEEE----TLELTHALPTILHEIETNLKDVT 421
                 4456677777778888877741445666677778888888888888877765....45555555555555555555554 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.9    0.0094       6.7       7      80 ..     160     231 ..     152     265 .. 0.79
   2 ?    4.4   1.9     0.084        60      11      80 ..     188     231 ..     181     304 .. 0.64
   3 ?    5.5   0.6     0.038        27       7      70 ..     337     393 ..     327     423 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0094
     DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                 e  + L +++el++ ++ +++ ++++ e l++ +++ e  + +++e +++el++++ e  ++i+++  e+kd+e
  AJA93209.1 160 ELSDDLKEVDELIDIFNITENSVQTINELLSSREKTLE--KLSKRELRVNELKSSLAEKNDNITKFENEIKDIE 231
                 55556777777777777777777777666666666644..4788888999999999999999999999999986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.084
     DUF2203  11 lLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                 lL   +++le+l + + +                          ++el++++ e  ++i+++  e+kd+e
  AJA93209.1 188 LLSSREKTLEKLSKRELR--------------------------VNELKSSLAEKNDNITKFENEIKDIE 231
                 444444444444444444..........................44444444444444444444444443 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.038
     DUF2203   7 eAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeie 70 
                 e ++++p+l ++ e++ ++++e++++ e+ ++++ ++       +e++l++ e+ ++++ ++++
  AJA93209.1 337 EIKNIIPTLISTKEKFETKKHEFTSKLENFDSKSLQT-------AEKNLKHEESDVSDISSKLK 393
                 3344555555555555555555555555444444444.......44444333333333333332 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9    0.0078       5.6      57     119 ..     180     241 ..     166     249 .. 0.84
   2 ?   -0.7   0.0       1.7   1.2e+03      43      84 ..     389     429 ..     378     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0078
                 HHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTS CS
      DUF489  57 lGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehfdllh 119
                 + ++t++e l++++k +  +l +  l + +l+++L+++++ ++k +++i+ ie+  ++ ++++
  AJA93209.1 180 NSVQTINELLSSREK-TLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENSPNYKEYTD 241
                 567888888888887.57799999*****************************9988877765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                 SSHHHHTTS.GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHH CS
      DUF489  43 estedvygg.lanlklGletlleqlekekkkkdaeltryalsl 84 
                 +s ++v+++ + +l+++l t+l+ +e++ k  d++ t+y++sl
  AJA93209.1 389 SSKLKVFEEeTLELTHALPTILHEIETNLK--DVTATSYTISL 429
                 567889999888999999999999998877..88999998876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.3    0.0035       2.5      18      70 ..     146     220 ..     146     255 .. 0.79
   2 ?    0.8   1.0         1   7.2e+02      38      52 ..     349     363 ..     282     403 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0035
        YtxH  18 lAPksGketRkdlkekaddlkekakelleeakeka.......................kekaedlkekvkekadel 70 
                 +APk  k++ +dlke  ddlk  ++el++ ++ +                        + ++++lk++++ek d +
  AJA93209.1 146 FAPKYSKKLTNDLKELSDDLK-EVDELIDIFNITEnsvqtinellssrektleklskrELRVNELKSSLAEKNDNI 220
                 8***************99996.567777777666666788888877777777776654333666666666666655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1
        YtxH  38 kekakelleeakeka 52 
                 kek++  ++e+ +k 
  AJA93209.1 349 KEKFETKKHEFTSKL 363
                 222222222222222 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.1   7.8e+02      73     114 ..      44      85 ..      28      96 .. 0.81
   2 ?    9.1   3.5    0.0021       1.5      49     121 ..     164     233 ..     149     239 .. 0.81
   3 ?    2.1   1.0      0.33   2.3e+02      71     123 ..     347     400 ..     323     413 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.1
      DUF641  73 eseleaeiqeqrsllktyeitvkkleaelkakdseieeLkek 114
                 + +l++ei+ +r+ ++++  ++ k+ +el++ + + ++L  +
  AJA93209.1  44 KGTLASEIKSHRNRIDPQREVILKIANELSEDELDPDKLDPH 85 
                 567899999999999999999999999999888877777655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
      DUF641  49 eLkklselkrlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeks 121
                 +Lk++ el + +  ++++    ++ +el +  ++  ++l   e +v++l++ l +k+ +i++ +++++++e+s
  AJA93209.1 164 DLKEVDELIDIFNITENSV---QTINELLSSREKTLEKLSKRELRVNELKSSLAEKNDNITKFENEIKDIENS 233
                 5777777777777764433...567777778888899999****************************99876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.33
      DUF641  71 aeeseleaeiqeqrsllktyei.tvkkleaelkakdseieeLkekLeeaeksnk 123
                  +++++e++ +e  s+l+  +   ++  e++lk+ +s+++ + +kL+  e+++ 
  AJA93209.1 347 STKEKFETKKHEFTSKLENFDSkSLQTAEKNLKHEESDVSDISSKLKVFEEETL 400
                 455556666666555565554314556677777777777777777776665554 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   [No individual domains that satisfy reporting thresholds (although complete target did)]



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1618  (0.0902449); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.46
# Mc/sec: 2834.16
//
Query:       AJA93210.1  [L=531]
Description: hypothetical protein T478_1486 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3559.95
//
Query:       AJA93211.1  [L=404]
Description: hypothetical protein T478_0423 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.4   10.9   3.5       0.46   10.7   0.1    2.8  3  YozE_SAM_like  YozE SAM-like fold
        3.3    7.8   5.9         27    4.8   0.1    3.7  3  YpjP           YpjP-like protein


Domain annotation for each model (and alignments):
>> YozE_SAM_like  YozE SAM-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   5.1e-05      0.46      13      33 ..      21      41 ..      15      51 .. 0.87
   2 ?   -0.6   0.0      0.18   1.6e+03       3      16 ..     239     252 ..     231     261 .. 0.56
   3 ?   -3.5   0.2       1.4   1.3e+04       2      11 ..     335     344 ..     335     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.1e-05
                   --SHHHHHHHHHHT-TTS-TT CS
  YozE_SAM_like 13 sedpvgelAenafkDksFPkq 33
                   +e ++++l e++ +Dk+FPkq
     AJA93211.1 21 EEKEIAKLSEKIDEDKEFPKQ 41
                   7899****************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                    HHHHHTT--S--SH CS
  YozE_SAM_like   3 Yqflmtfrnpsedp 16 
                    Y++l+ +  p++ p
     AJA93211.1 239 YEYLQLQTVPDNFP 252
                    55555555555555 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.4
                    HHHHHHTT-- CS
  YozE_SAM_like   2 FYqflmtfrn 11 
                    F ++l+tf +
     AJA93211.1 335 FQNYLTTFMG 344
                    7799999987 PP

>> YpjP  YpjP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3     0.046   4.1e+02      12      50 ..      18      64 ..       6     103 .. 0.69
   2 ?    4.8   0.1     0.003        27      27      86 ..     178     237 ..     154     268 .. 0.74
   3 ?    2.7   0.1     0.014   1.2e+02      50      79 ..     339     368 ..     273     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.046
        YpjP 12 eeaeeqsllKlGkkiaekie........defeeeilpkieevieell 50
                e  ee+ + Kl +ki e  e        ++f++ei+p+i + +ee +
  AJA93211.1 18 EIDEEKEIAKLSEKIDEDKEfpkqfiglESFSKEIFPDICKKVEEFT 64
                44566777777777765433222222236788899999988888765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.003
        YpjP  27 aekiedefeeeilpkieevieellekveeekleeleisekpasgkgEkifhiynkktked 86 
                 +e++e+ ++ ++   + e+i + +++  +e+ ++ +i+ +  +++  ki+   ++++ ++
  AJA93211.1 178 KEQVESGYKGALKMTMVEEIVHSTQDNLQEDNKNAAINVNSINEELAKIILNLDEDSTKN 237
                 568889999888766666555555555566667888888888888777765555555554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.014
        YpjP  50 lekveeekleeleisekpasgkgEkifhiy 79 
                 l++   ++++++++ ++ +++ +Ek+f+ +
  AJA93211.1 339 LTTFMGTDFSSYKVRKNMGKELTEKVFNKF 368
                 455566788889999999999999999743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.60
# Mc/sec: 2037.29
//
Query:       AJA93212.1  [L=478]
Description: putative amidophosphoribosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-12   45.8   0.0    1.3e-11   44.8   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    8.1e-12   45.1   0.0    1.7e-11   44.1   0.0    1.6  1  GATase_7      Glutamine amidotransferase domain
    8.7e-08   31.8   0.0    1.5e-07   31.1   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0004   19.4   0.0    0.00082   18.4   0.0    1.5  1  GATase_4      Glutamine amidotransferases class-II
     0.0094   14.7   0.0      0.054   12.2   0.0    2.2  3  GATase_2      Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   3.6e-15   1.3e-11       7     128 ..      65     192 ..      57     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.6e-15
    GATase_6   7 aslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll...eelG.....eevl.erlrGm 95 
                 ++ + ++ a++HvR ++vg ++ e+aqP+  + + l ++hNG+i+n++el++ +    + + +  sDt v ++ l+   +e G        l ++++G 
  AJA93212.1  65 SEEYASHSAIGHVRYSTVGKSDLESAQPL--KVKDLCVAHNGTISNVEELSNLVGG-CTFTPQNASDTLVAAQrLVsliTENGklgnaLSILkNEMVGS 160
                 44456779*************99999***..*************************.99999********99965599955555646656666788888 PP

    GATase_6  96 fafaiwdkrentlilardrlgvkplyyavdesg 128
                 f f + + + + ++ ard  g +p++ + +e+g
  AJA93212.1 161 FCFTFLS-DDDAVFAARDPKGFRPMVLGHKEQG 192
                 8776554.89999999*********99988443 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   4.8e-15   1.7e-11      10     122 ..      87     205 ..      76     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 4.8e-15
    GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAfaiwdeeekrlllaRDrlGi 99 
                  ++aQP+     ++l++++nG+i N +el +      ++ ++ sDt v ++ l +         + +  + +++ G+f+f  + +++  +++aRD+ G+
  AJA93212.1  87 LESAQPLKV---KDLCVAHNGTISNVEELSNLVGGCTFTPQNASDTLVAAQRLVSlitengklgNALSILKNEMVGSFCFTFLSDDD-AVFAARDPKGF 181
                 4789***94...789*****************99999999*******9766555568889987766777779*********998887.9********** PP

    GATase_7 100 kPLyygedk.gdallfaSelkall 122
                 +P+ +g+++ g+  +++Se +a+ 
  AJA93212.1 182 RPMVLGHKEqGNVHIVTSESSAIS 205
                 ********999999******9986 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.1e-11   1.5e-07      29     124 ..     281     386 ..     259     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.1e-11
                   GGEEEEEEETTTHHHHHHHHHHSTT-EE.-EEEEEE-TTT--EE..................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC- CS
  Pribosyltran  29 kpdvvvgiargGvpfakiladeLevpla.yvrkvkyrpdgseeaargssdes..........rlledpagkkVliVDDildtGgTllaalelLkekg 114
                     dvv++++  + p a   a+eL+++++  ++k +y+++g     +     s             e +++k+++++DD l  G++ +a++++L++ g
    AJA93212.1 281 DADVVIPVPDSARPAALGFAQELGIQFDeGLLKDRYSKKGPLRSFIEPHQ-SdrieinrwiiPIREVIEDKHIIVIDDSLVRGTSSKAIIKALRRSG 376
                   459*************************8999999999888877654433.3699****************************************** PP

                   BSEEEEEEEE CS
  Pribosyltran 115 peevriavlv 124
                   + ++  +v +
    AJA93212.1 377 ARKISMMVTY 386
                   ***9998875 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.3e-07   0.00082      69     187 ..      68     177 ..      35     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-07
    GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelasrfekaepsaeeleralaela 163
                   s+ ++ H+R  t G+  le ++p    l+ ++   AHnG+++++++ +      +f+P    D+ +a   l++ ++++        ++l +al+ l 
  AJA93212.1  68 YASHSAIGHVRYSTVGKSDLESAQP----LKVKDLCVAHNGTISNVEELSnlvgGCTFTPQNASDTLVAAQRLVSLITEN--------GKLGNALSILK 154
                 67999******************99....6789**********9988877666656899999999888776666555544........47888888888 PP

    GATase_4 164 keiaelGvfnlllsdgralfahas 187
                 +e+     f++ lsd +a+fa ++
  AJA93212.1 155 NEMVGSFCFTF-LSDDDAVFAARD 177
                 88876666655.688888888766 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.4   1.4e+03       8      33 ..      10      35 ..       6      37 .. 0.77
   2 !   12.2   0.0   1.5e-05     0.054     199     239 ..      66     110 ..      60     126 .. 0.87
   3 ?   -1.8   0.0      0.27   9.9e+02     336     395 ..     166     224 ..     160     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.4
                -SSS--BSHHHHHHHHHHHHGGGGS- CS
    GATase_2  8 elkgkkshkivekalealenleHRGa 33
                 + ++ + +++   ++al+ l+HRG 
  AJA93212.1 10 GIYSEGDVNVIPMVIDALRALQHRGQ 35
                5566667788889999********95 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.5e-05
                 TT--BSEEEEEE---SSSS--GGGSSS-SS....EEEEE--TTHH CS
    GATase_2 199 eelesalalvHsRfstntfPsWelaqPlRl....laHnGEintlr 239
                 ee+ s+ a+ H R+st      e aqPl++    +aHnG i  ++
  AJA93212.1  66 EEYASHSAIGHVRYSTVGKSDLESAQPLKVkdlcVAHNGTISNVE 110
                 7899************************9655559*****98776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.27
                 EE-SSEEEEEE-TT--S--EEEEETT-.-EEEESSTTSS---GGGEEEEEE--TT-EEEEE CS
    GATase_2 336 ftdGkvvgavLDRnGLRPaRylvtkdd.lvvlasEvGvldleeeevvekgrlqPGrmllvd 395
                 ++d   v a  D  G RP      +++ + +++sE+  +    +++v+   + PG+++ + 
  AJA93212.1 166 LSDDDAVFAARDPKGFRPMVLGHKEQGnVHIVTSESSAISAIGAKLVR--DVVPGELIKIS 224
                 578888899999999999998877665155889999887776666665..46788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 2711.58
//
Query:       AJA93213.1  [L=55]
Description: ribosomal L40e family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-07   28.6   5.9    1.1e-06   28.4   5.9    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0012   18.9   0.6     0.0013   18.7   0.6    1.2  1  DZR             Double zinc ribbon
     0.0032   17.1   0.1     0.0048   16.6   0.1    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0032   17.7   1.2     0.0035   17.5   1.2    1.1  1  zf-AD           Zinc-finger associated domain (zf-AD)
  ------ inclusion threshold ------
      0.014   16.2   0.3      0.015   16.0   0.3    1.1  1  zinc_ribbon_15  zinc-ribbon family
       0.02   14.9   0.4      0.021   14.9   0.4    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.04   13.8   2.5      0.046   13.6   2.5    1.1  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.072   12.5   0.7        0.1   12.0   0.7    1.3  1  zf-ribbon_3     zinc-ribbon domain
       0.13   11.8   0.5       0.13   11.8   0.5    1.0  1  CTV_P23         Citrus tristeza virus (CTV) P23 protein
        9.5    6.2   8.3        1.2    9.1   2.8    2.0  2  zf-trcl         Probable zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   5.9   6.1e-10   1.1e-06       6      48 ..       9      48 ..       4      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 6.1e-10
  Ribosomal_L40e  6 rqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                    +q+AqK + + +iC  C Arl + At Cr  kC +s +lr K 
      AJA93213.1  9 KQIAQKARLHMKICISCGARLDMSATRCR--KC-RSTQLRLKN 48
                    79***************************..89.788999885 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.6   7.2e-07    0.0013      11      35 ..      18      40 ..       6      50 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.2e-07
         DZR 11 darfCseCgtklkavaaedrCpsCg 35
                + + C  Cg++l+   +++rC +C 
  AJA93213.1 18 HMKICISCGARLD--MSATRCRKCR 40
                3345555555554..3445555554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.7e-06    0.0048       2      20 ..      22      40 ..      21      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
  zinc_ribbon_2  2 CpnCGaelqdnakFCpyCG 20
                   C +CGa l+  a+ C +C+
     AJA93213.1 22 CISCGARLDMSATRCRKCR 40
                   99****************8 PP

>> zf-AD  Zinc-finger associated domain (zf-AD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.2     2e-06    0.0035      37      75 ..      10      48 ..       4      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
       zf-AD 37 elepddslpekiCesCleklqefyeFrekcveanellqe 75
                ++ ++  l +kiC+sC ++l+   + ++kc+ ++  l++
  AJA93213.1 10 QIAQKARLHMKICISCGARLDMSATRCRKCRSTQLRLKN 48
                5668889999************************99986 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.3   8.5e-06     0.015      53      85 ..       7      39 ..       1      40 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-06
  zinc_ribbon_15 53 lgkeiekkessekkeCknCgkeveeefkyCpkC 85
                    l+k+i +k++ ++k+C +Cg++++ + + C kC
      AJA93213.1  7 LKKQIAQKARLHMKICISCGARLDMSATRCRKC 39
                    567888888889********************* PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.4   1.1e-05     0.021      71     100 ..      20      47 ..       4      55 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                 EEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
        HypA  71 vrCreCgkefeleekalrCpkCgsadveiv 100
                   C +Cg++ +++  a+rC kC s++++++
  AJA93213.1  20 KICISCGARLDMS--ATRCRKCRSTQLRLK 47 
                 46*******9988..469*******99874 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.5   2.6e-05     0.046      22      45 ..      18      41 ..       8      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                EEEE-HHHHHHHHHTT-B-TTT-- CS
  zf-C3HC4_3 22 HlvlCeeCaekllkrkkkCpiCrr 45
                H+ +C +C  +l  + ++C  Cr+
  AJA93213.1 18 HMKICISCGARLDMSATRCRKCRS 41
                9***********99*********7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   5.7e-05       0.1       2      22 ..      19      39 ..      18      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
  zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyC 22
                 ++ C +CGa + + +++ C +C
   AJA93213.1 19 MKICISCGArL-DMSATRCRKC 39
                 78999****66.********** PP

>> CTV_P23  Citrus tristeza virus (CTV) P23 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   7.2e-05      0.13      52      94 ..       9      48 ..       3      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
     CTV_P23 52 knsyqgarfrariigvcvdcgrkhdkalkterkckvnntqsqn 94
                k+  q ar+      +c+ cg + d ++   rkc+  + + +n
  AJA93213.1  9 KQIAQKARLHM---KICISCGARLDMSATRCRKCRSTQLRLKN 48
                55556666654...57******************987766555 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.29   5.1e+02       6      12 ..      21      27 ..      18      29 .. 0.77
   2 ?    9.1   2.8   0.00065       1.2      30      43 ..      30      43 ..      26      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.29
     zf-trcl  6 tCkdCga 12
                +C +Cga
  AJA93213.1 21 ICISCGA 27
                6888887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00065
     zf-trcl 30 dnepkRCkaCRkar 43
                d  ++RC++CR+ +
  AJA93213.1 30 DMSATRCRKCRSTQ 43
                5679*******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 350.76
//
Query:       AJA93214.1  [L=425]
Description: hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-72  243.3   3.6    3.9e-72  242.6   3.6    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    1.2e-50  171.3   0.0    2.3e-50  170.4   0.0    1.5  1  ThiP_synth    Thiamine-phosphate synthase
    4.9e-07   29.4   0.0    8.5e-07   28.6   0.0    1.4  1  PfkB          pfkB family carbohydrate kinase
    5.2e-06   26.1   0.4      1e-05   25.2   0.4    1.5  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.047   14.1   0.1       0.14   12.6   0.1    1.8  1  Goodbye       fungal STAND N-terminal Goodbye domain
      0.065   12.8   0.3        0.2   11.2   0.3    1.8  1  GerE          Bacterial regulatory proteins, luxR family


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.6   3.6   1.3e-75   3.9e-72       1     243 [.      10     244 ..      10     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 242.6 bits;  conditional E-value: 1.3e-75
                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE---SS CS
  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaeklkkykvpvVlDPVmva 97 
                   D+s+GAGiq D+ktf++++vyg++vita+t qntk+++e++p++a+ +++qle++l+d+++da+KiGm+++a+ii+++ +++k++k+p+++DP++ +
    AJA93214.1  10 DPSSGAGIQSDIKTFENHNVYGFTVITAITSQNTKKISEIMPISAKNIKSQLESILTDFQIDAIKIGMVYDASIIKTINTVIKNQKCPIIVDPIIES 106
                   9************************************************************************************************ PP

                   CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S CS
  Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietk 194
                   ++ + ll+++a++ +k+ ++plat+itPN +Ea+ L+g      ++m++aak++++lgak+V+i+G +   ++++++d++++ ++ ++l++++i+  
    AJA93214.1 107 TTKKILLKKSALSDYKKMIIPLATIITPNKKEAKILSG-----YSKMEDAAKEIQRLGAKNVIITGFRE--SKNEIEDFVMEAGNNYILKGKKIK-I 195
                   *************************************9.....89**********************95..566678******************.9 PP

                   --BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BSTSSS- CS
  Phos_pyr_kin 195 nthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelgkgag 243
                    +hG+GC +s++i+a+la ++s+ eA   Akeyv+++ik++ +lgkg++
    AJA93214.1 196 INHGSGCNYSASITASLASKKSIYEATIIAKEYVYQSIKKSKNLGKGVK 244
                   99*******************************************9976 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.0   7.8e-54   2.3e-50       7     164 ..     262     422 ..     256     423 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 7.8e-54
                 HHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT--EEEEEE--HHHHHHHCCTTSEEE CS
  ThiP_synth   7 elleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevraainirydekilealeelglkvv 105
                   ++++++++kliPe+++N++++++++k+++ v++++GR+v+ +++v+ +ge  fg+s+hva++++++ k+++++r+aini+y++ki+ ++++ ++ v 
  AJA93214.1 262 IDFQNIKNVSKLIPECQTNFVFSKNKPKTVKNVLGISGRLVKSGNNVVQAGELVFGGSQHVATAVIEVSKKFSNIRSAINIKYEPKIITNAKKHKMLVL 360
                 568999********************************************************************************************* PP

                 E--CCCS-CCC....T-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESSHHHHHHHHH CS
  ThiP_synth 106 efdreeepeev....gstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkdaeevvekvl 164
                 +++r++e++++    +s+++wg++++++++ +pd+iy++G++GkEpmi+v+g++++evv+k++
  AJA93214.1 361 SYNRKDESKNSklkeNSSISWGISSCLKSD-TPDIIYHKGDFGKEPMIIVFGATPTEVVKKIK 422
                 **********99999************999.7*****************************97 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   2.8e-10   8.5e-07     146     278 ..      82     221 ..      48     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.8e-10
                 HHHHHHHHHHHHTTEEEEEECESSSHH..........HHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEE CS
        PfkB 146 avleelaeaaknggtfdpnlldplgaq..........fkeallell.aladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGal 233
                 ++ +++ ++ kn++  +p+++dp +++          +++++++++ +la++++pn +E+++l+g +   +e+a++ ++     gak+v++t   e   
  AJA93214.1  82 SIIKTINTVIKNQK--CPIIVDPIIESttkkillkksALSDYKKMIiPLATIITPNKKEAKILSGYS--KMEDAAKEIQR---LGAKNVIITGFRESKN 173
                 56788899999999..99999999999999999999999****************************..88888888877...7999***994332222 PP

                 EEE.....TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHH CS
        PfkB 234 vve.....kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleea 278
                   e      +++++ +  +k+k+++  G G  + ++++a+l++ ks+ ea
  AJA93214.1 174 EIEdfvmeAGNNYILKG-KKIKIIN-HGSGCNYSASITASLASKKSIYEA 221
                 22222222444444444.6666665.366666666666666666666555 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.4   3.4e-09     1e-05       2     220 ..       4     231 ..       3     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.4e-09
                  EEEE-BTTCHHHHHHHHHHHHCTT..-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSSHCHHHHCHHHCCCCS-E CS
  Carb_kinase   2 lvigGsedytGAallaalaalrlg..aglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrdekikklleevlekdepl 97 
                  l igGs+  +GA++ + + + +     g + + +   + ++  s +  + +++++ ++  +il +  ++da+ iG+  ++   ik +   + ++++p+
   AJA93214.1   4 LSIGGSDPSSGAGIQSDIKTFENHnvYGFTVITAITSQNTKKISEIMPISAKNIK-SQLESILTDF-QIDAIKIGMVYDASI-IKTINTVIKNQKCPI 98 
                  569**************99987543388888877777777777777888899999.4555677777.999999999665544.466777788899999 PP

                  EEEGGGGGSGGGG.............TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEE..ESTTSEEEECTTEEEEE----GG CS
  Carb_kinase  98 viDAdgLnllaqkne..........lserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvll..kgekdvivspegevlinstgssa 183
                  ++D   +   ++k+           +     ++i+TP+kkE k L++ +   ed   e++r  a+++  +     k e +  v ++g+ +i++  +  
   AJA93214.1  99 IVDP-IIESTTKKILlkksalsdykKMIIPLATIITPNKKEAKILSGYSK-MEDAAKEIQRLGAKNVIITGFResKNEIEDFVMEAGNNYILKGKKIK 194
                  9995.3344444333444454323333334589****************9.99999999999999887776651133444466679999999999999 PP

                  G-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHH CS
  Carb_kinase 184 lakGGsGDvLaGligalLaqneasyeaaiaaawlhga 220
                      GsG   + +i a La++++ yea i a + + +
   AJA93214.1 195 IINHGSGCNYSASITASLASKKSIYEATIIAKEYVYQ 231
                  99*************************9999876644 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.6e-05      0.14      16     104 ..     257     340 ..     247     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
     Goodbye  16 lkdealkelssvedllkqieaekdkfeefrekkeklkealkkilspiqllggiaaqgasmaFgPaslcfnAvsyLikaakkvseiydai 104
                 l  +++ +++++ +++k i + + +f  f+++k k  +++  i   + + g+ ++q+ +++Fg ++ + +Av   i++ kk s+i +ai
  AJA93214.1 257 L-SHSIIDFQNIKNVSKLIPECQTNFV-FSKNKPKTVKNVLGISGRLVKSGNNVVQAGELVFGGSQHVATAV---IEVSKKFSNIRSAI 340
                 5.56677889999999***99999998.66666666666666777777789999999***********9997...89999999998888 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   6.8e-05       0.2      18      43 ..      41      66 ..      37      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.8e-05
                S-HHHHHHHHTS-HHHHHHHHHHHHH CS
        GerE 18 ksnkeIAeelniSekTVkvhksnimk 43
                + +k+I+e++ iS+k++k+++++i++
  AJA93214.1 41 QNTKKISEIMPISAKNIKSQLESILT 66
                579*******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1256  (0.0700541); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2995.47
//
Query:       AJA93215.1  [L=115]
Description: hypothetical protein T478_0764 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 873.47
//
Query:       AJA93216.1  [L=68]
Description: hypothetical protein T478_0514 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.014   14.5   7.4      0.016   14.3   7.4    1.0  1  DUF973     Protein of unknown function (DUF973)
       0.04   14.1   2.0      0.046   13.9   2.0    1.0  1  RDD        RDD family
      0.075   12.7   2.3      0.075   12.7   2.3    2.5  2  DUF3149    Protein of unknown function (DUF3149)
        0.2   11.0   0.9       0.34   10.2   0.5    1.6  2  YndJ       YndJ-like protein
       0.31   11.2   2.9       0.51   10.5   2.9    1.3  1  Pox_A14    Poxvirus virion envelope protein A14
       0.47   10.5   7.7        4.6    7.3   0.9    2.2  2  DUF3185    Protein of unknown function (DUF3185)
        1.4    8.7   4.8        2.9    7.6   4.8    1.8  1  Neurensin  Neurensin
        1.6    8.9   3.9        1.1    9.5   0.3    2.0  2  UL41A      Herpesvirus UL41A
        5.2    7.3   5.7        0.8    9.9   0.8    1.8  2  DUF2371    Uncharacterised conserved protein (DUF2371)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.4   7.8e-06     0.016     101     148 ..       4      60 ..       1      62 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
      DUF973 101 ltliligaiiiiigvilaivsll............slilslillgviilligiilaliGq 148
                 l +i+ g+i++i+g+i +    +            + ++  i+ g+ii++ig+il+liG+
  AJA93216.1   4 LSIIIPGVILVIFGIIFNF---QgqgmvgpetsfmYQNQDWIDNGIIISMIGVILILIGY 60 
                 5678888888888877544...366788999999999999*******************8 PP

>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   2.3e-05     0.046       9      64 ..       4      62 ..       1      63 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.3e-05
         RDD  9 lAfliDlvllliislllallivall.......nakasaneavagslllllllvlllvllvyql 64
                l+ +i +v+l+i+++++++             +++  +n+++  + +++ ++ ++l+l+ y++
  AJA93216.1  4 LSIIIPGVILVIFGIIFNFQ----GqgmvgpeTSFMYQNQDWIDNGIIISMIGVILILIGYFV 62
                45555555555555555555....35556*****************************99986 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   6.8       1.2   2.3e+03      15      25 ..      10      20 ..       1      23 [. 0.82
   2 ?   12.7   2.3   3.8e-05     0.075      16      36 ..      46      66 ..      45      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
     DUF3149 15 iVIvftigmga 25
                +VI++++g++ 
  AJA93216.1 10 GVILVIFGIIF 20
                58999999986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.8e-05
     DUF3149 16 VIvftigmgaffiryFirKmk 36
                +I+ +ig++++ i+yF+ K k
  AJA93216.1 46 IIISMIGVILILIGYFVEKKK 66
                79***************9965 PP

>> YndJ  YndJ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.35   6.9e+02     160     174 ..       6      20 ..       3      24 .. 0.81
   2 ?   10.2   0.5   0.00017      0.34     150     176 ..      37      64 ..      11      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
        YndJ 160 vvlvgpllvavGitv 174
                 +++ g++lv  Gi +
  AJA93216.1   6 IIIPGVILVIFGIIF 20 
                 577799999999987 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
        YndJ 150 k.sklyklaavvvlvgpllvavGitvsd 176
                 + + + +  +++ ++g++l+++G++v +
  AJA93216.1  37 QnQDWIDNGIIISMIGVILILIGYFVEK 64 
                 24778999999**************975 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.9   0.00026      0.51      13      63 ..       5      61 ..       2      66 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
     Pox_A14 13 tvliaGiiLLilacifafvdfskststtdkawral.....s.ivsFilgivillgll 63
                +++i G+iL+i  +if f     ++++t  +++         i+s i  i+il+g +
  AJA93216.1  5 SIIIPGVILVIFGIIFNFQGQGMVGPETSFMYQNQdwidnGiIISMIGVILILIGYF 61
                6899**************999999988776665441111131444444455556655 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9    0.0023       4.6       4      18 ..      10      24 ..       2      30 .. 0.68
   2 ?    7.3   1.0    0.0024       4.8       4      20 ..      45      61 ..      44      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
     DUF3185  4 GiiLlvaGivLlvfG 18
                G+iL++ Gi++ ++G
  AJA93216.1 10 GVILVIFGIIFNFQG 24
                566666666666655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0024
     DUF3185  4 GiiLlvaGivLlvfGyn 20
                Gii+  +G++L+  Gy 
  AJA93216.1 45 GIIISMIGVILILIGYF 61
                89999999999999996 PP

>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   4.8    0.0015       2.9      48      68 ..      45      65 ..       3      68 .] 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0015
   Neurensin 48 gtlvlllGvtallvGylvprr 68
                g+++ ++Gv+ +l+Gy v ++
  AJA93216.1 45 GIIISMIGVILILIGYFVEKK 65
                999**************9987 PP

>> UL41A  Herpesvirus UL41A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.29   5.8e+02      22      34 ..       7      19 ..       2      25 .. 0.70
   2 ?    9.5   0.3   0.00053       1.1      13      35 ..      40      62 ..      33      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.29
       UL41A 22 gmigvvcfvfgvf 34
                 + gv+  +fg++
  AJA93216.1  7 IIPGVILVIFGII 19
                4558888888874 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00053
       UL41A 13 gyvdmnvcigmigvvcfvfgvfi 35
                 ++d  + i migv+ +++g f+
  AJA93216.1 40 DWIDNGIIISMIGVILILIGYFV 62
                579999**************997 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.28   5.6e+02      45      57 ..       8      20 ..       2      44 .. 0.62
   2 ?    9.9   0.8    0.0004       0.8      47      67 ..      45      65 ..      36      68 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.28
     DUF2371 45 llGllvllvGiam 57
                + G+++++ Gi +
  AJA93216.1  8 IPGVILVIFGIIF 20
                3455555555543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
     DUF2371 47 GllvllvGiamavlgywpkka 67
                G++++++G+ + ++gy+ +k+
  AJA93216.1 45 GIIISMIGVILILIGYFVEKK 65
                9***************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 496.02
//
Query:       AJA93217.1  [L=147]
Description: hypothetical protein T478_1070 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0024   17.9   2.2     0.0024   17.9   2.2    1.5  1  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
     0.0026   17.5   2.4     0.0045   16.8   2.4    1.3  1  Leptin           Leptin
  ------ inclusion threshold ------
      0.023   14.5   2.4       0.52   10.1   0.5    2.2  2  YqgF             Holliday-junction resolvase-like of SPT6
      0.036   14.0   0.3      0.077   13.0   0.3    1.6  1  DUF3161          Protein of unknown function (DUF3161)
      0.039   14.4   0.1      0.051   14.0   0.1    1.3  1  DSPn             Dual specificity protein phosphatase, N-term
        1.8    9.2   6.4        1.1    9.8   1.2    2.6  2  FeoB_Cyto        FeoB cytosolic helical domain


Domain annotation for each model (and alignments):
>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.2   8.1e-07    0.0024      99     187 ..       6      98 ..       1     102 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.1e-07
  HIGH_NTase1_ass  99 tievlkeelendn.pledi.rdeekiletvneldldelldlnlldeklankliekr...pyesieeikeaiprgfskhykerilsvLeakiekd 187
                       +++l++e+e+ +  ++ + ++ ek++  +  l ++    ++ l+ kl++ ++e++   + e i+ i++++ + fsk  +  ils L   i+k 
       AJA93217.1   6 SLKLLDSEFEKFQkIIDSMpKNSEKMIPDIVSLYFQA-TMVETLSKKLTQDISESKqqtHLEKINKIQKYVYENFSKSLHPVILSQLVNSIQKS 98 
                      6788999998888466666977777777777766766.578999*******977664447899************************9999986 PP

>> Leptin  Leptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.4   1.5e-06    0.0045      48     141 ..       5     104 ..       2     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                 SSHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHH...HHHHHHHHHHTT---------S-GGGGHHHH....-BTTB-HHHHHHHHHHHHHHHHHHHG CS
      Leptin  48 eslskmdqtLavyqqilsslpseevvqisnDlenL...rallkllatsksCelekaseletleslekvl....easlystevvaLeRlqksLlellkqL 139
                 +sl  +d   + +q+i+ s+p +   ++  D+  L    +++++l+   + +++++++  +le+++k++    e++  s   v L+ l +s+++  ++L
  AJA93217.1   5 NSLKLLDSEFEKFQKIIDSMPKNS-EKMIPDIVSLyfqATMVETLSKKLTQDISESKQQTHLEKINKIQkyvyENFSKSLHPVILSQLVNSIQKSTNDL 102
                 689999***************755.455567777733357999999999999999988888888877641112678899999******99999988887 PP

                 GG CS
      Leptin 140 dl 141
                  l
  AJA93217.1 103 KL 104
                 65 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00017      0.52      31     100 ..       2      69 ..       1      84 [. 0.87
   2 ?    4.6   0.1    0.0084        25      19      50 ..      84     116 ..      75     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                 -EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHHHHHHHHHHTTB-TTS-B-- CS
        YqgF  31 evvdslklaareedrekkakfvetlkkfllskkPdvigvsGenrdaqkliedvkevlhekeqdsrlstvg 100
                 +v +slkl + e+++   +k ++++ k  +++ Pd++++  + +  + l +++ + ++e +q+++l+ ++
  AJA93217.1   2 DVANSLKLLDSEFEK--FQKIIDSMPKNSEKMIPDIVSLYFQATMVETLSKKLTQDISESKQQTHLEKIN 69 
                 678899997777765..67889999**********************************99999998886 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0084
                 S-E.EEEEE-TTS-EEEEEEE-S-TT-SS-SHH CS
        YqgF  19 dai.icvlvngeGevvdslklaareedrekkak 50 
                 +++ ++ lvn     +++lkl  ++++ + k+ 
  AJA93217.1  84 HPViLSQLVNSIQKSTNDLKLLGQNSEAKTKEI 116
                 55515779************9555544443332 PP

>> DUF3161  Protein of unknown function (DUF3161)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.6e-05     0.077      21      73 ..      60     116 ..      57     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
     DUF3161  21 rrraklddinliykalydiavkkgsclPvekseltq......mnlkvfGqtGekkiakl 73 
                 ++++ l++in+i k++y+   k     Pv  s+l +      ++lk+ Gq  e+k + +
  AJA93217.1  60 KQQTHLEKINKIQKYVYENFSKSL--HPVILSQLVNsiqkstNDLKLLGQNSEAKTKEI 116
                 56789*************998855..4555555443111122589********999987 PP

>> DSPn  Dual specificity protein phosphatase, N-terminal half
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.051      15      69 ..      55     116 ..      31     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
        DSPn  15 k.pketenvhyfsid..delvYenFyaDFGPlnlaqlyrfcvkvnkkL....kskelskkki 69 
                 + +++++++h+ +i+  +++vYenF +   P+ l+ql++ ++k ++ L    +++e+++k+i
  AJA93217.1  55 DiSESKQQTHLEKINkiQKYVYENFSKSLHPVILSQLVNSIQKSTNDLkllgQNSEAKTKEI 116
                 2245567788888887789********************99999988744454555555655 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.2   0.00038       1.1      40      85 ..      51      98 ..       4     102 .. 0.78
   2 ?    1.7   0.3      0.13   3.9e+02      43      59 ..     115     131 ..      99     147 .] 0.47

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
   FeoB_Cyto 40 elleelk..edpelraeveearkeleaelgedledvIvdarykfiegi 85
                +l++ ++  +++   +++++++k++ ++++++l  vI +++++ i++ 
  AJA93217.1 51 KLTQDISesKQQTHLEKINKIQKYVYENFSKSLHPVILSQLVNSIQKS 98
                4444555545578899**************************999875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
   FeoB_Cyto  43 eelkedpelraeveear 59 
                 e +++++ l +e++e+ 
  AJA93217.1 115 EIIENEARLYKELRELM 131
                 34444344444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2146  (0.119694); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 968.92
//
Query:       AJA93218.1  [L=212]
Description: isopentenyl-diphosphate delta-isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-18   66.6   0.0    3.2e-18   66.0   0.0    1.3  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   1.8e-22   3.2e-18       1     124 [.      29     154 ..      29     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.8e-22
                 EEEEEEEEEEEETTSEEEEEEES..SSSTTT.EE.SSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE.EEECS CS
       NUDIX   1 klrravgvvllnekgevLlvrrs..kkpfpg.We.lPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeheilyvfl.eeveg 94 
                 kl+ra+ ++++n++g++Ll+rrs  k  +pg W+ +++ + ++gEt+   A R++ EE+G+++ ++ ++++++y  py+++   e+e++ +++   ++ 
  AJA93218.1  29 KLHRAFTALIFNKEGKLLLTRRSdsKMLWPGeWDgTVASHPREGETYVSSAERRMPEEIGITC-QMNYVNKFEYHVPYKDIGS-ENEVCGTLVgVVDDF 125
                 589******************************88**************************99.8899999********9999.788886666333333 PP

                 GCSSTSTTTEEEEEEEEHHHHHHHHTHCTH CS
       NUDIX  95 elepndenevsevrwvpleellkeklaaes 124
                 +     ++e+s+++w++++el k++l+++ 
  AJA93218.1 126 DESSLIKDEISAIKWISPNEL-KTELENNL 154
                 4344478**************.77766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1542.56
//
Query:       AJA93219.1  [L=309]
Description: protoheme IX farnesyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-36  125.7  21.0    2.4e-36  125.3  21.0    1.2  1  UbiA             UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.13   11.7   1.4         18    4.9   0.0    3.3  3  ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
        6.6    4.9  11.5        5.1    5.3  10.1    1.5  1  DUF2070          Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3  21.0     4e-40   2.4e-36       2     249 ..      25     291 ..      24     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 4e-40
        UbiA   2 lipalvglalaaggspdl....llllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkeali.faivllilgllll.......alll 88 
                 l+++++g a++a +  ++     +++l+l+g+++ +a+an+l +y Dr+iD  mert+ RP++s ri p+e  + f++vl+ ++++++        ++ 
  AJA93219.1  25 LVFTAFGTAITASNIYNIeisiATWALMLFGVAAGSASANTLTNYHDRDIDEVMERTKGRPIPSKRIFPAEKARdFGLVLAGISIACAfgiafttSFWN 123
                 77888888888888888778889****************************************999987765555*************99999988888 PP

        UbiA  89 npltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.sllalllalavflltwaialandlrdregDrkagiktlpvvlGr 185
                 + ++ ++++++l+   ++Y++  lKr + l++++gg+++g p+++g+aavt +  +   l++a +vf+++  +++a  l+ r++++k+ +++l++vl +
  AJA93219.1 124 GMWCGIFMVFGLADNiLIYSH-ALKRKSQLNIILGGFSGGAPAMIGYAAVTLTGlWDFGLIMAGLVFIWIPMHIWALTLHFRDDYQKVKVPMLTAVLSE 221
                 899999******9999****8.***************************766665555566666678888888888888889999************99 PP

        UbiA 186 kaaril...lalllavllla........llllllalllllylllalllaalallraarlvrrrdakkaakfflfl 249
                 k+++++    +++++    +         + ++   ++ +yl+ a+++++l+++ +a++v + ++k+ + +f ++
  AJA93219.1 222 KTSARViaaTTVMMV----VfsivpfflTTDTGEPVMSEVYLYTAIASGVLMVALSAWVVSKPTEKASWVLF-KF 291
                 999996443333333....33543433222233346677899999*********************999999.43 PP

>> ATP1G1_PLM_MAT8  ATP1G1/PLM/MAT8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.006        36      15      34 ..      99     120 ..      95     121 .. 0.79
   2 ?    4.9   0.0    0.0029        18      17      26 ..     181     190 ..     177     211 .. 0.81
   3 ?   -2.2   0.0      0.47   2.8e+03      20      35 ..     264     279 ..     263     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.006
                      HHHHHHHHH..HHHHHHHHHHC CS
  ATP1G1_PLM_MAT8  15 lgGLifAgl..LfivGiliilS 34 
                        GL++Ag+  +++ Gi+  +S
       AJA93219.1  99 DFGLVLAGIsiACAFGIAFTTS 120
                      56*****954499999998766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0029
                      HHHHHHHHHH CS
  ATP1G1_PLM_MAT8  17 GLifAglLfi 26 
                      GLi+Agl fi
       AJA93219.1 181 GLIMAGLVFI 190
                      9********9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.47
                      HHHHHHHHHHHHHHCC CS
  ATP1G1_PLM_MAT8  20 fAglLfivGiliilSk 35 
                       +g+L ++  ++++Sk
       AJA93219.1 264 ASGVLMVALSAWVVSK 279
                      5799999999999997 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  10.1   0.00085       5.1      28     148 ..     167     304 ..     138     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.00085
     DUF2070  28 igllaflssk.......lfgillfglpalvaflltlpvlrilggr.......ltykrslflalltelivviisllaillsall..qalvllalvlslal 110
                 ig++a++          + g++++ +p+ + +l ++  +++ + +       l  k s+ + ++t++++v++s+++ +l++ +  + ++  +l  ++a+
  AJA93219.1 167 IGYAAVTLTGlwdfgliMAGLVFIWIPMHIWALTLHFRDDYQKVKvpmltavLSEKTSARVIAATTVMMVVFSIVPFFLTTDTgePVMSEVYLYTAIAS 265
                 3333333333556677789999999999999999989999988888887776666677999999************99998888766777788888*** PP

     DUF2070 111 vfalrllvlvavsdesllkav.lpaliqpllailllvly 148
                  + ++ l  ++vs+ +++ ++ l  +  p+la+l++ l+
  AJA93219.1 266 GVLMVALSAWVVSKPTEKASWvLFKFSSPYLAVLFIALM 304
                 ***************999999666777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2266.66
//
Query:       AJA93220.1  [L=237]
Description: MIP family channel protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-51  174.3  17.4    3.6e-51  174.0  17.4    1.0  1  MIP       Major intrinsic protein


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.0  17.4     2e-55   3.6e-51       9     226 ..       5     224 ..       1     225 [. 0.88

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 2e-55
                 HHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHHHHHHTTSSSHHHHHHHHHHHHHHHHHHH CS
         MIP   9 ravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTlallvarkisllrailYivaQllGaivaa 107
                 ra lAE++at+ lvf+g  s++  ++ +  ++ l +  +  ++l++g  ++  vy++++iSGaH+NPavT+ ++++++i+++ +i Yi  Q++Gai+a+
  AJA93220.1   5 RAWLAEAIATYALVFFGPLSVILSAAWY-GDG-LSTEAIIFISLGHGGIIVFMVYAFGHISGAHINPAVTIPMMITKQIDVKNGIGYILFQIMGAIIAT 101
                 899****************888444444.434.44458999********************************************************** PP

                 HHHHHHCHHH...HHHTTTTSSSSST..TSSHHHHHHHHHHHHHHHHHHHHHHCSTTSSSSTCHGHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHH CS
         MIP 108 allklltkgl...esraglfanslkp..glsagqalvvEiiltfvLvlvvfaltddkrkvslgelaplaigllvaliilvgipltGaamNpArslgpav 201
                 ++l++l+ +    +     +   +++  g s++++lvvEiiltf+Lv+v++ ++ ++++ +  ++ + aig +v+l +lvg+pltGa+mNpArs+ pav
  AJA93220.1 102 LTLQALFPEIgkkV--FWGAHGGPSEliGNSMMSGLVVEIILTFFLVVVIYMVAVHTKAPK--QIYGGAIGGMVFLLHLVGVPLTGASMNPARSFSPAV 196
                 *******9984321..222222333311568899*********************999998..99********************************** PP

                 HHTH...STTTTHHHHHHHHHHHHHHHH CS
         MIP 202 vlnk...fedhwvylvGPliGailgalv 226
                 v+ +   +e  w y+vGP+iG+i+g++v
  AJA93220.1 197 VSGDaglWEVQWLYWVGPIIGGIIGGVV 224
                 ***9999******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1786.70
//
Query:       AJA93221.1  [L=398]
Description: MacB-like periplasmic core domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-18   65.3   2.3    1.9e-17   63.5   0.7    2.3  2  FtsX      FtsX-like permease family
    8.1e-15   55.7   1.0    1.3e-14   55.0   1.0    1.3  1  MacB_PCD  MacB-like periplasmic core domain
  ------ inclusion threshold ------
       0.26   11.6  12.0        5.6    7.3   8.1    2.6  2  DUF4064   Protein of unknown function (DUF4064)


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17     1e+03      29      53 ..      22      49 ..      16      78 .. 0.58
   2 !   63.5   0.7   3.2e-21   1.9e-17       2      96 .]     297     391 ..     296     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
        FtsX 29 tlvalviGlgl...gllaaqllsdvlls 53
                +++a  iG+++    +++ q ++d +  
  AJA93221.1 22 AVLAVSIGILVihvNFVIFQGIYDAIIR 49
                2333333322222255555555555555 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 3.2e-21
        FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsiskilkkep 96 
                 reig++ra+G+k+k++l ++++++++i+++++ +G+g+gl+++ +      ++ +s +l ++ ++  ++++++l+++la+la+++++++++k +p
  AJA93221.1 297 REIGVMRAIGAKRKDILMVFILQGMIIGAIGAGAGTGIGLAYTTYAKETNMQFGGSLALEVNYNWPKIAETALLAFFLAMLASIYPSYRATKLQP 391
                 9********************************************99999999999************************************998 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   1.0   2.3e-18   1.3e-14       4     188 ..      22     230 ..      18     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2.3e-18
    MacB_PCD   4 tvLGiaiGvaaviaivslgeglqasvlsqisdl..gnlvtvtpgkgsgeslsdpdvealrr....evp.veavapvv.......tvrgggsg..eee.. 84 
                 +vL++ iG+ ++ + +++ +g+ +++ ++++d   g+   ++++  + ++++ ++v    +    +vp v++++p++           ++ g  +ee  
  AJA93221.1  22 AVLAVSIGILVIHVNFVIFQGIYDAIIRDMTDYrfGD---IFVSHEEEATIERSHV-VY-TnwfeRVPlVQSATPRLsgsadieF---RSMGkfNEEfd 112
                 89*****************************886666...4444333444444433.21.1222259********9865443321...11112322233 PP

    MacB_PCD  85 vtvvgvdp..dyfkvfglklaeGrffteadlrggpnvvvigeelaerlf..pvGdtirl...........kpftVvGvledppgsgsalgddavylplt 168
                 v vvgv+p  d +   ++      +++e +   ++n++v+ge++ae+l   +vGd+++l           k+f V+G+ ++  g+g    d++v++ + 
  AJA93221.1 113 VPVVGVEPvsDILA-SKI----HTTISEGQYVYARNSIVVGETVAEDLGgvRVGDNLKLimtnqggeeesKRFVVTGISKTAGGQG---FDTSVIIHID 203
                 67788774324444.334....2334444455699************99*99*****************999******84442333...3799***966 PP

    MacB_PCD 169 tl........qrrsitvrlkdgadleaa 188
                 +l        +++si+v+l++    eaa
  AJA93221.1 204 SLrslldrpdESNSIFVKLNEKNP-EAA 230
                 65344676655677*****98654.444 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.004        24       9      36 ..      18      45 ..      15      74 .. 0.87
   2 ?    7.3   8.1   0.00093       5.6       2      93 ..     263     354 ..     263     357 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.004
     DUF4064  9 glIGgilgillglllllflfllssgefs 36
                +lIG++l + +g+l++ + f++ +g ++
  AJA93221.1 18 SLIGAVLAVSIGILVIHVNFVIFQGIYD 45
                58****************9999998766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00093
     DUF4064   2 rkaeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalllkknkk.vsGilf 93 
                 r++  +++lIG  +g+ ++ ++++++ ++  ++++ e + + a+ ++  +  + f+ + +i+ +++a   + +g++ + + k  +  ++G+l 
  AJA93221.1 263 RSGIAMINLIGY-FGMGSSAFAIVTIQMMLVNSKTREIGVMRAIGAKRKDILMVFILQGMIIGAIGAGAGTGIGLAYTTYAKETNMqFGGSLA 354
                 5667899****9.*********************************************************************77777999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2978.72
//
Query:       AJA93222.1  [L=412]
Description: adenosylhomocysteinase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-59  199.4   0.0    5.2e-30  104.6   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    2.1e-50  170.9   0.3    2.1e-50  170.9   0.3    1.7  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    1.6e-07   30.9   0.1    4.6e-07   29.4   0.1    1.8  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    6.9e-06   25.7   0.0    1.2e-05   24.9   0.0    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00092   19.5   0.3     0.0034   17.6   0.1    2.1  3  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.077   12.3   8.9      0.093   12.0   3.3    3.0  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.13   12.1   0.6       0.39   10.6   0.6    1.9  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.0     2e-33   5.2e-30       3     143 ..       3     138 ..       1     143 [. 0.95
   2 !   94.0   0.0   3.6e-30   9.2e-27     179     285 ..     141     409 ..     133     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 2e-33
                 B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--HHHHHHHCCTTEEEE--TT-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase   3 kvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqdeaaaaiaeagvpvfawkget 101
                 kvk+ +la+ G+   e a + m  l ++ ++ +++kplkg+ ia +lh+t +t+vL+   ++lGa+v  +  n   tqd++aa +a++g+ ++aw g+t
  AJA93222.1   3 KVKNPKLAKQGKISYEWARTHMDILDNTLTRLKKSKPLKGVTIAFCLHITKETSVLLMGAKELGANVAVCGGNPLTTQDHIAAFLATQGIHIYAWNGQT 101
                 8999*********************************************************************************************** PP

                 HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase 102 leeywwcieqalkwaedekepnlilDdGGDltllvhkgvkee 143
                 ++ey wc++q+l++     +p li DdG D+   vh  +k++
  AJA93222.1 102 NKEYDWCLDQVLNH-----KPSLICDDGADMNVKVHFDKKFK 138
                 ************65.....7**************99876655 PP

  == domain 2  score: 94.0 bits;  conditional E-value: 3.6e-30
                 C--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH......................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................................... RF
   AdoHcyase 179 kikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD......................................................... 220
                 ki G +eett+Gv r++ ++k+gkL+ p + vnd+ tk  fD                                                         
  AJA93222.1 141 KILGSTEETTAGVTRVQAMEKQGKLKYPVVIVNDADTKHMFDnrygtgqstidgylramgllftskkivvvgygwvgrgvaersrgmggkvivteidpv 239
                 6889*********************************************************************************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
   AdoHcyase 221 ................................................................................................... 220
                                                                                                                    
  AJA93222.1 240 kaleahmdgfdvmpmsqaakigqifitttgmtsvirkehllsmkdgsvvgnvghfdveidtkflleksksvrevrpsldecvlrngrkiyligkgrlan 338
                 *************************************************************************************************** PP

                 ......S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCC CS
                 ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   AdoHcyase 221 ......hpsfvmsasftnqvlaqielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyi 285
                       hp  vm++sf+nq+l+ + +fk++kk+ kk +++pk++D ++a   l++l++k+++ltkeq +y 
  AJA93222.1 339 lvaaegHPPEVMAQSFSNQILSLLYIFKNHKKMGKKTMIVPKEIDRQIAVDALKALDVKIDKLTKEQKKYA 409
                 *********************************************************************95 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.3   8.4e-54   2.1e-50       1     161 [.     183     343 ..     183     344 .. 0.99
   2 ?   -2.7   0.1       2.2   5.6e+03     111     133 ..     381     403 ..     365     409 .. 0.63

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 8.4e-54
                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SSSSSSB-HHH CS
  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtttGnkdiitleh 96 
                    n yg+ +s +dg  ra  +l++ k++vv+GyG vG+G a+  +g+G +vivte+dP+ al a m+Gf+v+ + +++k ++i++tttG + +i++eh
     AJA93222.1 183 NRYGTGQSTIDGYLRAMGLLFTSKKIVVVGYGWVGRGVAERSRGMGGKVIVTEIDPVKALEAHMDGFDVMPMSQAAKIGQIFITTTGMTSVIRKEH 278
                    78********************************************************************************************** PP

                    HCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS- CS
  AdoHcyase_NAD  97 lkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgcat 161
                    l +mkd ++v+n+Ghfd eid++ l ++++++ ev+p +d+++l++g+ki l+ +Grl nl +a 
     AJA93222.1 279 LLSMKDGSVVGNVGHFDVEIDTKFLLEKSKSVREVRPSLDECVLRNGRKIYLIGKGRLANLVAAE 343
                    *************************************************************9886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                    STTTTBTHHHHHTTT-EEEEEET CS
  AdoHcyase_NAD 111 hfdseidvaaleanalkkeevkp 133
                      d +i v+al+a ++k++++  
     AJA93222.1 381 EIDRQIAVDALKALDVKIDKLTK 403
                    45667777777777777766654 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.8e-10   4.6e-07      29     129 ..     198     294 ..     174     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.8e-10
                   GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEE CS
  2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiN 125
                    +g   + k++ ++G+G +G+ va+r +++g kvi+++  + k  e++  g++++ + ++ +  +i + ++      + +i +e+l +mk+g+++ N
    AJA93222.1 198 AMGLLFTSKKIVVVGYGWVGRGVAERSRGMGGKVIVTEIDPVKALEAHMDGFDVMPMSQAAKIGQIFITTT----GMTSVIRKEHLLSMKDGSVVGN 290
                   56667789********************************9977777777776666666555555544433....445799**************** PP

                   SS-G CS
  2-Hacid_dh_C 126 taRG 129
                   ++  
    AJA93222.1 291 VGHF 294
                   9975 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   4.8e-09   1.2e-05       3      99 ..     204     296 ..     202     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.8e-09
                 HTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHH CS
        IlvN   3 kgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeeiepnlkegkalafahGfni 99 
                 ++kki+v+GyG  G+  a+  r  g +v+v+  +   ++ +A+ +gf+v+ +++a+k  ++ ++    + +++v+++e   ++k+g+++     f++
  AJA93222.1 204 TSKKIVVVGYGWVGRGVAERSRGMGGKVIVTEIDPV-KALEAHMDGFDVMPMSQAAKIGQIFIT---TTGMTSVIRKEHLLSMKDGSVVGNVGHFDV 296
                 68****************************988877.6778*************9998876554...456777888887888888887776666666 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.5   9.1e+03      59      68 ..      61      70 ..      28      88 .. 0.64
   2 ?   -3.0   0.0       3.4   8.8e+03      87     100 ..     163     176 ..     144     183 .. 0.48
   3 !   17.6   0.1   1.3e-06    0.0034       1      44 [.     208     251 ..     208     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                TGGGESEEEE CS
      TrkA_N 59 giekadavia 68
                g+++  a +a
  AJA93222.1 61 GAKELGANVA 70
                3333333333 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
                 TSSSEEEEEESSGG CS
      TrkA_N  87 npkkkiiaraqdpe 100
                  + k+ ++ ++d++
  AJA93222.1 163 GKLKYPVVIVNDAD 176
                 22233333333333 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.3e-06
                 EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
      TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                 i+++G+G vGr +ae+ +  gg +v+v + d+ ++ e+  +g++v
  AJA93222.1 208 IVVVGYGWVGRGVAERSRGmGG-KVIVTEIDPVKALEAHMDGFDV 251
                 89*****************888.5********9999999888876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2     3e+03      47      59 ..      62      74 ..      44      96 .. 0.66
   2 ?   12.0   3.3   3.6e-05     0.093      28     124 ..     205     288 ..     189     299 .. 0.76
   3 ?   -2.3   0.1      0.86   2.2e+03      48      82 ..     369     403 ..     365     410 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                 HHHTT-EEEEEES CS
  AlaDh_PNT_C 47 akglgakVtvlDv 59
                 ak+lga+V v+  
   AJA93222.1 62 AKELGANVAVCGG 74
                 4555555555444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 3.6e-05
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEE CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVi 124
                    k++v+G G +G   ++ ++g+g kV v++++p ++ + +  g   v         +++a+k  ++ i+t          ++++e++ sMk+gsV+
   AJA93222.1 205 SKKIVVVGYGWVGRGVAERSRGMGGKVIVTEIDPVKALEAHMDGFD-V-------MPMSQAAKIGQIFITT-----TGMTSVIRKEHLLSMKDGSVV 288
                  5699***************************999765444433333.2.......2233444444566776.....4566799************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.86
                  HHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH CS
  AlaDh_PNT_C  48 kglgakVtvlDvrparleqleslgakfvevlksqe 82 
                  k++g k++++ ++++r+  +++l+a  v++ k ++
   AJA93222.1 369 KKMGKKTMIVPKEIDRQIAVDALKALDVKIDKLTK 403
                  78999999999999999999998888777744443 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00015      0.39       1      38 [.     207     244 ..     207     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                 EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
     3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                 k+ v+G G +G+g+a+     g +V +++i++ ++ +a
  AJA93222.1 207 KIVVVGYGWVGRGVAERSRGMGGKVIVTEIDPVKALEA 244
                 689***************************98665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2670.02
//
Query:       AJA93223.1  [L=153]
Description: hypothetical protein T478_0871 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.067   12.5   0.0      0.079   12.3   0.0    1.1  1  Guanylate_cyc_2  Guanylylate cyclase
       0.17   11.5   0.0       0.27   10.8   0.0    1.3  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> Guanylate_cyc_2  Guanylylate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.8e-06     0.079      96     191 ..       3     104 ..       1     112 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-06
  Guanylate_cyc_2  96 lfkkakeagievekrsvsveelvehlasgk..vaivLvnaalLkcdlcksnkllselrkllsrkseytGhyvvlcGydakekk....llyrnPa 183
                      +fk+ k  +  v+++s+s +el e+l  ++   a+  +++ + + ++++ + ++s +++ ++r  +  G y+vl G d +e+       +  P 
       AJA93223.1   3 KFKTIKVGNSFVSTTSISKKELDEYLGFSRikNAMFEIDSGKDENRVISGRAIISRMEGEFTRLRQIYGNYIVLYGIDGDEEWknrqTRFVRPV 96 
                      67777777888999999999999999766655899999999999999999999999*********************97654222224445566 PP

  Guanylate_cyc_2 184 ssdkvcsi 191
                      + d+v ++
       AJA93223.1  97 YTDQVLRL 104
                      66666555 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     3e-05      0.27      80     110 ..      87     117 ..      78     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3e-05
                      EEEEEE-S--BTTCEEEEEEEEEEEEEEEEE CS
  MaoC_dehydratas  80 eikvrFtkpVlpgdtlkvelevvgkrdvrkt 110
                        + rF++pV++++ l+ + + ++krd++++
       AJA93223.1  87 NRQTRFVRPVYTDQVLRLKYTISDKRDIDDE 117
                      5678**********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1154.96
//
Query:       AJA93224.1  [L=183]
Description: arginine decarboxylase, pyruvoyl-dependent [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-57  192.4   0.0      5e-57  192.2   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.0   2.8e-61     5e-57       2     162 .]       6     182 ..       5     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 2.8e-61
    PvlArgDC   2 PkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrliaaavgvaipkdekkgGyiaE 100
                  k++flt+G+g ++++l+sF+ AL+dAgI+ +N+v +SSi+Pp+a++++++eglk+++pG+i++++++r+++nep+r+i+a+vg+a+pkd++++Gy++E
  AJA93224.1   6 AKELFLTRGIGVHEDKLTSFEYALRDAGIAGTNIVLISSIFPPKAKLIPKKEGLKKIKPGQILFTIYSRNQTNEPHRMISASVGLALPKDRTRYGYLSE 104
                 6899*********************************************************************************************** PP

    PvlArgDC 101 ysgfgeseeeaeeeaeelaaemlattrgl................leekiietkeievaaveakvekygtvlaaavfv 162
                 y +fg++e++a+++ae+ aa+mla+ +g+                +++ki+++++i+++a+++k++k++tv++aa+++
  AJA93224.1 105 YDAFGQNEKQAGDYAEDIAAQMLASSLGIpfdidkswdekrqqwsISGKIYKSQNITMTAKGDKSGKWTTVFSAACLI 182
                 *************************9999***************9999****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1337.09
//
Query:       AJA93225.1  [L=370]
Description: glucose/sorbosone dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-77  259.0   0.0    9.4e-77  258.5   0.0    1.1  1  GSDH      Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
      0.015   15.5   0.1        9.1    6.9   0.0    3.1  2  Reg_prop  Two component regulator propeller
        0.1   12.9   0.7       0.51   10.7   0.7    2.3  1  DUF5122   Domain of unknown function (DUF5122) beta-propeller


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.5   0.0   1.6e-80   9.4e-77       1     329 [.      55     355 ..      55     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 258.5 bits;  conditional E-value: 1.6e-80
                 -S-EEEEEE-TTS-EEEEETTTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE-SS..-EEEE CS
        GSDH   1 lehPwslaflpdgrlLvtersGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararlsedeaaledl 99 
                 +++Pws+af  d+r++v+e+sG++++v+++g l +p+ ++ +      gGll++++hpdf +n+ +Y +++   ee+++ +++v+r++ +++  + ++ 
  AJA93225.1  55 FDKPWSIAFD-DDRIFVSEKSGKIQIVTSSGVLDSPLITL-RTPEIFGGGLLGITTHPDFTNNHFLYAYHTY--EENEKLWNKVIRITEKDN--KSTEI 147
                 689******8.56********************8888877.34455679**********************5..599999*********999..9999* PP

                 EEEEEEE---TT-------EEE-TTS-EEEE---TT-.GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEE CS
        GSDH 100 evifrqepkvesgahfGsrlafgpdgtLfvtvGdrsk.reeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwe 197
                  +i++++p   s+ ++G+ + fgpdg+L+v++G  s+  +e+q+l+s +Gkilrln+dG++p+dnp       ++ ++++GhRnp G+a+++  g++++
  AJA93225.1 148 ITILDKIPG--SAFSNGGVIKFGPDGKLYVGTGSVSDfLNESQNLNSLAGKILRLNDDGTIPSDNPYE-----ESYVFTLGHRNPTGFAWNNL-GTMFA 238
                 *********..899***********************999***************************5.....89****************99.***** PP

                 EEE--SSSEEEEEE-TT-B--TTT-S......S-.....-S-TTS---SEEETT---EEEEEEE........TTEEEEEETTTTEEEEEEEEEEEEEEE CS
        GSDH 198 sEhGprggDelnlieaGknYGWplvsygeeYsgkkigesetreglekpvlvwtpsiapsglafytgdafpewkgdllvggLksqsllrleldegekvve 296
                 +E Gp+++De+nli+aG+nYGWp+v+             ++++++ +p+ +++p++ p+g++fy+gd++ + ++++++++ k+++l +++++e+   v+
  AJA93225.1 239 TESGPTKNDEINLITAGSNYGWPEVQC-----------FSNNDNFVNPLECFDPGLEPGGIIFYSGDKL-DINDEMILASQKATNLFKVQISEN--DVN 323
                 *************************93...........356789*************************.8********************954..688 PP

                 EEEEEESS-.-EEEEEE-TTS-EEEEE-TTTTT CS
        GSDH 297 eerlleelgeriRdVeqgpdGalyvltdeedgk 329
                  er+l+ lg riRdV+qgpdG++y++t ++dgk
  AJA93225.1 324 LERILSGLG-RIRDVAQGPDGYVYIITTNTDGK 355
                 8999*****.*********************97 PP

>> Reg_prop  Two component regulator propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0056        33      12      23 ..     167     178 ..     156     179 .. 0.83
   2 ?    6.9   0.0    0.0015       9.1       6      24 .]     333     351 ..     328     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0056
                 E-TTSCEEEEES CS
    Reg_prop  12 eDsdGrlWvGte 23 
                   +dG+l+vGt 
  AJA93225.1 167 FGPDGKLYVGTG 178
                 579*******96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0015
                 CEEEEEE-TTSCEEEEESS CS
    Reg_prop   6 nvtaileDsdGrlWvGteg 24 
                 +++++++ +dG++++ t++
  AJA93225.1 333 RIRDVAQGPDGYVYIITTN 351
                 899************9986 PP

>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.7   8.5e-05      0.51       2      32 ..     169     206 ..     168     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.5e-05
     DUF5122   2 pDGKIlVaGsftsy.......ngssdfalvRLnaDGsl 32 
                 pDGK++V+  + s+        +s +  ++RLn DG++
  AJA93225.1 169 PDGKLYVGTGSVSDflnesqnLNSLAGKILRLNDDGTI 206
                 9***988877775679********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2701.51
//
Query:       AJA93226.1  [L=93]
Description: hypothetical protein T478_0827 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00036   20.8   1.2    0.00041   20.6   1.2    1.2  1  Med30           Mediator complex subunit 30
     0.0055   15.9   0.2     0.0055   15.9   0.2    1.0  1  Glyco_hydro_99  Glycosyl hydrolase family 99
  ------ inclusion threshold ------
      0.011   13.8   0.4      0.012   13.6   0.4    1.0  1  Prominin        Prominin
      0.017   14.5   2.4       0.02   14.2   2.4    1.0  1  ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
      0.044   14.0   2.3       0.05   13.8   1.8    1.4  1  Fib_alpha       Fibrinogen alpha/beta chain family
       0.26    9.9   3.8       0.27    9.8   3.8    1.0  1  FapA            Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> Med30  Mediator complex subunit 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.2   1.4e-07   0.00041      13      79 ..      19      85 ..       5      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
       Med30 13 vqdivsrtqelfqllkavqlpngrtqskhqaqdrkkklqeqlrqlkvlfkkLrliYekckencqgle 79
                + d++++ +++ + l ++ ++n  +    +  +   k+q+++++ + l +k+++iY++  +++++ +
  AJA93226.1 19 LMDMLKNWNDIRTRLVNIEPNNPMNEMFDKMIQDLVKIQNHTKNYRTLLEKMKQIYDEFSKESKEWH 85
                679*********************99999999999************************99997665 PP

>> Glyco_hydro_99  Glycosyl hydrolase family 99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   1.9e-06    0.0055     120     176 ..      34      88 ..       5      93 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-06
                     EEE---TT--HHHHHHHHHHHHHHHTTSTTB--BTTB-EEEETTGGGS-HHHHHHHH CS
  Glyco_hydro_99 120 fhiepyssrdaqnlrenikklidkyGnhpafyrkkgkplfyiydsylikpsewakll 176
                       iep ++  ++ + + i++l+ k  nh   yr+    +  iyd +  +++ew++ +
      AJA93226.1  34 VNIEP-NNPMNEMFDKMIQDLV-KIQNHTKNYRTLLEKMKQIYDEFSKESKEWHEKY 88 
                     57999.7777888888999987.689***************************9765 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   4.1e-06     0.012     358     414 ..      16      73 ..       5      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-06
    Prominin 358 aevvpdlkkalakgreqikklakkip.realdavisdlenterssktfddvvekyeky 414
                 + ++ d+ k+ +++r+ + +++ + p +e+ d++i+dl ++++++k++   +ek+ ++
  AJA93226.1  16 ELLLMDMLKNWNDIRTRLVNIEPNNPmNEMFDKMIQDLVKIQNHTKNYRTLLEKMKQI 73 
                 566779999*********************************************9875 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.4   6.7e-06      0.02     148     237 ..       7      86 ..       2      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.7e-06
  ALIX_LYPXL_bnd 148 kldelkaereqllkdlkekaendDitpklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdse 237
                      ldel  e+e ll d+   +  +Di+++l++ + +    n ++++f+++++    +  ++++  +   +ll++ +++++ef++++k+  e
      AJA93226.1   7 ALDELVTEQELLLMDML--KNWNDIRTRLVNIEPN----NPMNEMFDKMIQ----DLVKIQNHTKNYRTLLEKMKQIYDEFSKESKEWHE 86 
                     68999999999988885..67788******99999....888999999999....55556666699999*************99887555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.8   1.7e-05      0.05      31      82 ..      40      91 ..      28      93 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha 31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikks 82
                + +++  +k+ ++l +i+n tk+ ++l +++k+++ e  k++k+  + + ks
  AJA93226.1 40 NPMNEMFDKMIQDLVKIQNHTKNYRTLLEKMKQIYDEFSKESKEWHEKYDKS 91
                56788999*******************************9999888888877 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.8   9.1e-05      0.27     330     410 ..       3      83 ..       1      92 [. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.1e-05
        FapA 330 ldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                 +++ +l+e ++e e +l ++ ++ ++++ ++  +++ +  +++  ++ ++l k+++  +++++ le+++++++e ++e ++
  AJA93226.1   3 IKQDALDELVTEQELLLMDMLKNWNDIRTRLVNIEPNNPMNEMFDKMIQDLVKIQNHTKNYRTLLEKMKQIYDEFSKESKE 83 
                 566678888888899999999999999999888888666999999999999999999999999999999999998888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2258  (0.125941); expected 358.6 (0.02)
Passed bias filter:                      835  (0.0465726); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 637.78
//
Query:       AJA93227.1  [L=57]
Description: hypothetical protein T478_0066 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 356.36
//
Query:       AJA93228.1  [L=119]
Description: hypothetical protein T478_0663 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 817.35
//
Query:       AJA93229.1  [L=265]
Description: hypothetical protein T478_1023 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.026   13.2   1.9      0.033   12.9   1.9    1.0  1  Med15         ARC105 or Med15 subunit of Mediator complex non
       0.11   12.6   0.4       0.33   11.1   0.1    2.0  2  DUF2613       Protein of unknown function (DUF2613)
       0.16   12.1   0.4       0.29   11.3   0.4    1.5  1  DUF2407_C     DUF2407 C-terminal domain
       0.28   11.6   2.1       0.38   11.2   2.1    1.2  1  RNA_pol_Rpc4  RNA polymerase III RPC4


Domain annotation for each model (and alignments):
>> Med15  ARC105 or Med15 subunit of Mediator complex non-fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.9   7.4e-06     0.033     249     323 ..     138     208 ..     123     228 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-06
       Med15 249 nqqkqqldqvrgpadaqaqmqqqaqanagmnpqqmagaqaqv.arqqqqaqqqaqqsqlgalanqmqqmaqGdrqa 323
                  q++q++d     a+aqa++ +qa+a+a +++q+    +a+  a +++qa+ +++++  +   n m+    Gd+ +
  AJA93229.1 138 EQKQQDVDAA---AKAQAEADAQAEAEAAAKAQAESDTKAEAeAAAKAQAEIDVKNAEEEKIENMMNTC--GDGTV 208
                 3444444443...44444444444444444444444444442144444444444433333333334333..44433 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   9.4e+03      39      50 ..      37      48 ..      30      48 .. 0.78
   2 ?   11.1   0.1   7.3e-05      0.33       3      23 ..     228     248 ..     227     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
     DUF2613 39 avnadsalLgsv 50
                  na++++L sv
  AJA93229.1 37 DYNANNVVLKSV 48
                468999999887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.3e-05
     DUF2613   3 lgPaaaSaVaGivlGvvavfg 23 
                 +gP + S+V+G  lG+v  ++
  AJA93229.1 228 TGPLIYSIVIGMSLGIVIMMI 248
                 69**************98765 PP

>> DUF2407_C  DUF2407 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   6.4e-05      0.29      32     112 ..     172     250 ..     136     260 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
   DUF2407_C  32 tpdtmpsdleeeeeeelreLEerWidstanaeeaaeaeeegeaakeeensvdseeskanedlliGlliGfflglfalllll 112
                 t+ +  +  + + e ++++ Ee+ i++  n+    +  e+ge   +  +   +++   +  l++ ++iG+ lg++ +++l+
  AJA93229.1 172 TKAEAEAAAKAQAEIDVKNAEEEKIENMMNTCGDGTVYENGECVLSPME-K-NASDFRTGPLIYSIVIGMSLGIVIMMILW 250
                 2222222334444477888888888888876666554444444433222.2.333334678999**********9988886 PP

>> RNA_pol_Rpc4  RNA polymerase III RPC4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1   8.5e-05      0.38      25      81 ..     142     199 ..     105     230 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
  RNA_pol_Rpc4  25 eddkseaesqs.aekakaeeeskaekasgaeaeekkskkksskkkkkkkskalklksl 81 
                   +d++ +a++q+ a+ ++++e++++++a++++++e++  +k++++ ++k+++++k +++
    AJA93229.1 142 QDVDAAAKAQAeADAQAEAEAAAKAQAESDTKAEAEAAAKAQAEIDVKNAEEEKIENM 199
                   2222222222202222222222222333333333333334444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2644  (0.147471); expected 358.6 (0.02)
Passed bias filter:                     1337  (0.0745719); expected 358.6 (0.02)
Passed Vit filter:                       204  (0.0113782); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.36s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 1564.38
//
Query:       AJA93230.1  [L=79]
Description: hypothetical protein T478_0372 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 493.30
//
Query:       AJA93231.1  [L=314]
Description: ABC transporter, ATP-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-29  102.5   0.0    6.1e-29  101.3   0.0    1.6  1  ABC_tran      ABC transporter
    3.3e-11   43.6   1.4    2.7e-06   27.4   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.3e-06   29.0   0.7    4.6e-06   27.3   0.4    2.0  2  DUF4162       Domain of unknown function (DUF4162)
    1.2e-05   25.3   0.5     0.0098   15.6   0.4    2.9  1  AAA_15        AAA ATPase domain
    8.4e-05   23.2   0.1    0.00014   22.4   0.1    1.6  1  AAA_23        AAA domain
    0.00035   20.2   0.2    0.00072   19.2   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   14.5   0.7      0.065   12.1   0.1    1.9  2  AAA_10        AAA-like domain
      0.017   14.1   0.1      0.031   13.2   0.1    1.3  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.017   14.9   0.0      0.038   13.8   0.0    1.6  1  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.034   13.5   0.1      0.072   12.5   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.043   13.3   1.5        2.7    7.4   0.1    2.7  3  SMC_N         RecF/RecN/SMC N terminal domain
      0.057   13.7   0.3       0.29   11.4   0.2    2.2  2  AAA_22        AAA domain
      0.075   12.9   0.3       0.17   11.8   0.3    1.6  1  RsgA_GTPase   RsgA GTPase
      0.095   12.9   0.1       0.16   12.2   0.1    1.4  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.15   11.8   0.0       0.21   11.3   0.0    1.3  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   5.1e-32   6.1e-29       2     136 ..      20     162 ..      19     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 5.1e-32
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdeeiek 87 
                 + +sl++k g++ +++G+nGaGKSt++kll+ l+ pt+G++ + g d  + +l + r++igv+ q+p+   +l+v+++             +++++ e+
  AJA93231.1  20 DGISLEIKSGQVFGFLGPNGAGKSTVIKLLTTLMPPTKGKLSVLGIDAAKSPL-EIRRKIGVVLQQPSYEMTLSVENSldkygmmwdvdkkTRKQRTEE 117
                 789**********************************************9555.56889**************98888**********99888889*** PP

                 HHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  88 alsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +l+++gl+++++++       LS Gq++rv++ar ++ + +ll+lDEpt
  AJA93231.1 118 LLTSFGLQDIRKKKN----DDLSIGQRRRVQVAREFMHDMELLFLDEPT 162
                 *********999998....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   1.2e-05     0.014       2      22 ..      32      52 ..      31     118 .. 0.88
   2 !   27.4   0.0   2.3e-09   2.7e-06     259     297 ..     154     193 ..     111     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
      AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                 ++ GpNg+GKS+++++l  l
  AJA93231.1 32 FGFLGPNGAGKSTVIKLLTTL 52
                5789*************9766 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.3e-09
      AAA_21 259 sllliDEpEngLHPkllrrllell.kelsrngaQviltTH 297
                  ll++DEp  gL+P++ r ll++l k+ +++g  ++ tTH
  AJA93231.1 154 ELLFLDEPTVGLDPSARRDLLDFLkKQVQKTGLTIFYTTH 193
                 79**********************777777********** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.9   8.3e+03      47      62 ..     167     182 ..     162     188 .. 0.76
   2 !   27.3   0.4   3.8e-09   4.6e-06       2      81 .]     218     306 ..     218     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.9
                 ---------------E CS
     DUF4162  47 eeaanellkaltsgve 62 
                  +a+++ll+ l+++v+
  AJA93231.1 167 PSARRDLLDFLKKQVQ 182
                 5688899999988776 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.8e-09
                 -HHHHHTTS.-SSEEEEE.....--.-----..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHHH CS
     DUF4162   2 tleeiKrsy.gknrieve.....ad.aeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                 +++e+K+++ ++++i++      +   + l  +p+   e+e e  ++++  ++ e++  ++lk l +++++i+ ++ ++  L++IF+++v
  AJA93231.1 218 SPNELKNRFgREKTIKINltktsNSiTDLLSGIPDcKIELEPEP-TITINSSNsEVVLMNVLKILnQNNITINDLSAIPTNLEEIFLKVV 306
                 579******77778889997764334666667799556666665.799999999***********77*********************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   8.2e-06    0.0098      25     177 ..      31     251 ..      19     289 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.2e-06
      AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekkn.............................................................kkvikiek 62 
                 +  + G+N++GKS+++++l  +   ++  +                                                             +       
  AJA93231.1  31 VFGFLGPNGAGKSTVIKLLTTLMPPTKG-KlsvlgidaakspleirrkigvvlqqpsyemtlsvensldkygmmwdvdkktrkqrteelltS------- 121
                 5668899999999999999999887722.246777777777777777777777777777777775555555555544444444444444441....... PP

      AAA_15  63 edleifeniseskdikIdvef...........................aek...ekakeyektlkskekkkadlllkkkesdlkktikdkklklkknel 131
                                     f                           + +    + +e  + l++++++     lkk  +++  ti+  +  l++ e+
  AJA93231.1 122 --------------------FglqdirkkknddlsigqrrrvqvarefMHDmelLFLDEPTVGLDPSARRDLLDFLKKQVQKTGLTIFYTTHVLSEAEY 200
                 ....................2333333444444444444444444433222335666666666777777777777777777777777777777788888 PP

      AAA_15 132 sdekisvekkks.....kkelpkekeeklekekeelkidkedlkklikkle 177
                  +++i + +k +     + +  k++   +++ k +l ++++++++l++ + 
  AJA93231.1 201 LCDNIAIINKGKilavdSPNELKNRFGREKTIKINLTKTSNSITDLLSGIP 251
                 888877777776554444444444444444444444444555555554444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.2e-07   0.00014      18     115 ..      28     129 ..      18     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
      AAA_23  18 skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese....gkvkay.veltfenkdgrytrsiererelskkkgkttkkaklel 111
                 s  ++ + GpNGaGK+T++  ++  +   +++ls   g ++ ks  ei  +     ++++y ++l++en  ++  + + ++  ++  k +t    + ++
  AJA93231.1  28 SGQVFGFLGPNGAGKSTVIKLLTTLMPPTKGKLSVL-GIDAAKSPLEIRRKigvvLQQPSYeMTLSVENSLDK--YGMMWDVDKKTRKQRTEELLTSFG 123
                 557999**************9999988877777764.889999999887777665555555566666665554..566666666655555544444444 PP

      AAA_23 112 lei..d 115
                 l++  +
  AJA93231.1 124 LQDirK 129
                 433222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2     6e-07   0.00072      15      50 ..      22      57 ..      18      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6e-07
      AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                 ++ei+  +++ + Gp+G+GKST++  +++l+ p+k
  AJA93231.1 22 ISLEIKSGQVFGFLGPNGAGKSTVIKLLTTLMPPTK 57
                5677775559999************88888887766 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.4e-05     0.065      25     123 ..      33     134 ..      16     184 .. 0.80
   2 ?    0.8   0.1      0.16   1.9e+02      44     114 ..     204     282 ..     196     301 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
      AAA_10  25 liiGdlGnGKSvlakllvlyisllggk..aliiDpkkerekfketlpe.iakkinvvtLdseeenegvLdPlvllk..eekeaeslaedilel..llgv 116
                  ++G+ G+GKS ++kll   +   +gk  +l iD  k   + ++++   +++    +tL+   en  +Ld + ++   ++k  ++  e++l+   l+++
  AJA93231.1  33 GFLGPNGAGKSTVIKLLTTLMPPTKGKlsVLGIDAAKSPLEIRRKIGVvLQQPSYEMTLS--VEN--SLDKYGMMWdvDKKTRKQRTEELLTSfgLQDI 127
                 589******************999987336889*****9999**9966256666667888..556..89999888656666666666777776577788 PP

      AAA_10 117 kkkesek 123
                 +kk+++ 
  AJA93231.1 128 RKKKNDD 134
                 7776654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
      AAA_10  44 yisllg.gkaliiDpkke.rekf..ketlpe.iakkinvvt.Ldse.eenegvLdPlvllk.eekeaeslaedilelll 114
                 +i++++ gk+l +D  +e +++f   +t++  ++k+ n +t L s+  + + +L+P   +  +  ++e +  ++l++l+
  AJA93231.1 204 NIAIINkGKILAVDSPNElKNRFgrEKTIKInLTKTSNSITdLLSGiPDCKIELEPEPTITiNSSNSEVVLMNVLKILN 282
                 454443399*****99997777843334433466666666435444477777777643333233366666666666655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.6e-05     0.031      29      68 ..      29      68 ..      15      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
        MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                 qv G+ G  GaGkst+++ l++ +     + +vl +D +
  AJA93231.1 29 GQVFGFLGPNGAGKSTVIKLLTTLMPPTKGKLSVLGIDAA 68
                5899*********************999999******975 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.038       2      39 ..      35      72 ..      34      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
  ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeel 39
                +Gp G+GK+t ++ l+ +++ ++ ++ v+ +D A + l
  AJA93231.1 35 LGPNGAGKSTVIKLLTTLMPPTKGKLSVLGIDAAKSPL 72
                7*******************************998755 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     6e-05     0.072      26      52 ..      33      59 ..      10      92 .. 0.78
   2 ?   -3.0   0.0       3.4     4e+03     109     138 ..     155     189 ..     152     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
  Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplsee 52
                   ++Gp G+GK+ ++k l++l+pp + +
    AJA93231.1 33 GFLGPNGAGKSTVIKLLTTLMPPTKGK 59
                  589*******************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.4
  Mg_chelatase 109 vLfLDEl.....pefkrkvlevLRePledgevtis 138
                   +LfLDE      p  +r+ l+ L++ ++++ +ti 
    AJA93231.1 155 LLFLDEPtvgldPSARRDLLDFLKKQVQKTGLTIF 189
                   57888842222355667777777777777666665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0023       2.7      28      42 ..      33      47 ..      15      60 .. 0.79
   2 ?    4.0   0.1     0.024        28     136     195 ..     134     188 ..      77     211 .. 0.67
   3 ?   -1.3   0.0         1   1.2e+03     112     138 ..     264     292 ..     250     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0023
                EEEESTTSSHHHHHH CS
                xxxxxxxxxxxxxxx RF
       SMC_N 28 aivGpNGSGKsnlld 42
                  +GpNG+GKs ++ 
  AJA93231.1 33 GFLGPNGAGKSTVIK 47
                468*********986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                 CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                  LS G++  v +a       ++   l +lDe    LD + ++ + ++lk++ +++ +  i
  AJA93231.1 134 DLSIGQRRRVQVARE----FMHDMELLFLDEPTVGLDPSARRDLLDFLKKQVQKTGLT-I 188
                 677777766655444....455667899*********************998765433.3 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                 EETTE..EE-HHHHHHHHHCTT-STTCS- CS
                 xxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 112 kingk..evtkkevsellesagiskelLS 138
                 +in +  ev   +v ++l++ +i+++ LS
  AJA93231.1 264 TINSSnsEVVLMNVLKILNQNNITINDLS 292
                 45444004445788888888888888777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00024      0.29      11      91 ..      35     132 ..      26     193 .. 0.55
   2 ?   -2.1   0.0       3.6   4.3e+03      39      59 ..     228     249 ..     215     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
      AAA_22  11 tGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsstsskdllrellralglelka......................erls 74 
                  G+ G+GK+t+++ l+   +      +             +                +++r++   l+++  +                      + ++
  AJA93231.1  35 LGPNGAGKSTVIKLLTTLMPPT----KgklsvlgidaaksP---------------LEIRRKIGVVLQQPSYEmtlsvensldkygmmwdvdkktRKQR 114
                 59**************998643....212234444444440...............5555555555554444444444444444444444444445556 PP

      AAA_22  75 seell.ealeqalrarav 91 
                 +eell +   q +r+++ 
  AJA93231.1 115 TEELLtSFGLQDIRKKKN 132
                 666655555666655555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
      AAA_22  39 rpevvfvtlpsst.sskdllre 59 
                 r ++++++l++ + s +dll+ 
  AJA93231.1 228 REKTIKINLTKTSnSITDLLSG 249
                 7789999999999888888765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00014      0.17      94     121 ..      23      51 ..       5      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                  HHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallp 121
                  + ++k+ ++  ++G+ G+GKSt+i+ l+ 
   AJA93231.1  23 SLEIKSgQVFGFLGPNGAGKSTVIKLLTT 51 
                  55566659999*************99875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.16      62      89 ..     151     178 ..     138     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
     SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                 ++++l+fLDE   +lD+  ++ ll++l+
  AJA93231.1 151 HDMELLFLDEPTVGLDPSARRDLLDFLK 178
                 6799*********************998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.21      16      54 ..      28      65 ..      22     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
      AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrviglAp 54
                sg +v    Gp G+GK+t++k l+ ++   +g++ +l  
  AJA93231.1 28 SG-QVFGFLGPNGAGKSTVIKLLTTLMPPTKGKLSVLGI 65
                44.488889**************9999888666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 1888.85
//
Query:       AJA93232.1  [L=368]
Description: DnaJ domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-09   36.3   0.0    9.1e-09   35.3   0.0    1.6  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   5.1e-13   9.1e-09       3      54 ..       6      53 ..       4      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 5.1e-13
                HHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHT CS
        DnaJ  3 YeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLs 54
                YeiLg+++ as +eI++a+r+lal +H D+      ++e+F  i++A+e L+
  AJA93232.1  6 YEILGITEGASRNEIRSAFRNLALTHHADRG----GQDEEFIIIKQAFEDLK 53
                *******************************....77899*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2323.82
//
Query:       AJA93233.1  [L=92]
Description: winged helix-turn-helix [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-16   58.8   0.2    4.5e-16   58.6   0.2    1.1  1  HTH_45           Winged helix-turn-helix
    0.00029   21.1   0.1    0.00041   20.6   0.1    1.2  1  Rrf2             Transcriptional regulator
    0.00061   19.3   0.0    0.00074   19.0   0.0    1.1  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit
     0.0016   18.5   0.1     0.0021   18.1   0.1    1.3  1  Mrr_N            Mrr N-terminal domain
     0.0027   17.5   0.1     0.0032   17.2   0.1    1.2  1  DUF4364          Domain of unknown function (DUF4364)
     0.0069   16.5   0.2       0.01   16.0   0.2    1.3  1  HTH_34           Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.033   12.6   0.1      0.033   12.6   0.1    1.1  1  DUF505           Protein of unknown function (DUF505)
      0.043   14.3   0.1      0.059   13.9   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
      0.046   14.4   0.0      0.062   14.0   0.0    1.1  1  RPA_C            Replication protein A C terminal
      0.082   12.2   0.0      0.085   12.1   0.0    1.0  1  Mannosyl_trans2  Mannosyltransferase (PIG-V)
       0.13   12.2   0.0       0.18   11.7   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.2   2.7e-19   4.5e-16       1      76 [.       3      85 ..       3      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.7e-19
      HTH_45  1 rRskleIiadILeais...egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleela 76
                +R++++I+ad+L +++   +++ k T+++ kanLs ++l+k+++ L+  gli     +  +++v+TekG+++le+++++ +la
  AJA93233.1  3 YRTSMQIVADVLTVTEqtgQEGIKTTSLLTKANLSHSRLEKFVKNLTGAGLInkieFDGRHTFVITEKGRQYLESYQKFSDLA 85
                6***********9998433455689**************************9666444789******************9875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.5e-07   0.00041       1      57 [.       1      56 [.       1      60 [. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                X---HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
        Rrf2  1 MklsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                M + ++++++  +l++ ++  +e+ ++++++ ++ n+s+s lek +++L+ agl++ 
  AJA93233.1  1 MTYRTSMQIVADVLTVTEQTGQEG-IKTTSLLTKANLSHSRLEKFVKNLTGAGLINK 56
                8899999*********99999999.******************************85 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.6e-07   0.00074      91     134 ..      13      56 ..       3      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-07
                    HHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEE CS
  RNA_pol_Rpc34  91 VysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiks 134
                    V+ + e++G+eGI +  + +k nL +s ++k +k+L + ++i +
     AJA93233.1  13 VLTVTEQTGQEGIKTTSLLTKANLSHSRLEKFVKNLTGAGLINK 56 
                    78899*********************************999976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   1.3e-06    0.0021      29      86 ..      12      76 ..       3      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
       Mrr_N 29 erfglseeeraellpsgkq....trfknrvgWartyLkkagllespk...rgvwkiTekGrevlk 86
                + + ++e+  +e +++       ++ ++r+    ++L+ agl+++ +   r ++ iTekGr++l+
  AJA93233.1 12 DVLTVTEQTGQEGIKTTSLltkaNLSHSRLEKFVKNLTGAGLINKIEfdgRHTFVITEKGRQYLE 76
                55555555555555444323344777888888999********9999988************997 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     2e-06    0.0032      27      74 ..      32      79 ..      13      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
     DUF4364 27 eneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfe 74
                 +  ++   l++++++L+ +gli++ e ++++++ iTekG++ le  +
  AJA93233.1 32 TKANLSHSRLEKFVKNLTGAGLINKIEFDGRHTFVITEKGRQYLESYQ 79
                566677778999*******************************99766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   6.2e-06      0.01      13      74 ..      23      80 ..       9      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.2e-06
      HTH_34 13 deadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74
                + ++ ++l ++ +++ ++L + +k L  ag i+ ++ef+g+    ++ iT++Gr+  ++y k
  AJA93233.1 23 EGIKTTSLLTKANLSHSRLEKFVKNLTGAGLIN-KIEFDGR---HTFVITEKGRQYLESYQK 80
                455666677777888888889999******886.89****9...7889********999965 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     2e-05     0.033     365     408 ..      40      81 ..      11      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
      DUF505 365 dlreaLysLesfeLieseveekgkevyvlTeyGekvledqekkl 408
                  l++  ++L + +Li++  e +g++++v+Te+G++ le  + k+
  AJA93233.1  40 RLEKFVKNLTGAGLINKI-EFDGRHTFVITEKGRQYLESYQ-KF 81 
                 57788899*******998.789***************9764.45 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.6e-05     0.059       9      68 .]      14      71 ..       5      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
      HTH_27  9 Lhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                L + + ++ + ++ + l  + n++ s   + +k Lt +GL+  ++ e d+r ++v +T+kG
  AJA93233.1 14 LTVTEQTGQEGIKtTSLLTKANLSHSRLEKFVKNLTGAGLI--NKIEFDGRHTFV-ITEKG 71
                4555555666666678888899*******************..555666777766.78888 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.8e-05     0.062      51      97 ..       7      54 ..       2      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                HHHHHHHHHH..SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
       RPA_C 51 aqqvlnlikq.speseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                 q+v ++++  ++ ++eG++   +  k +ls + +++ v++L ++G+i
  AJA93233.1  7 MQIVADVLTVtEQTGQEGIKTTSLLTKANLSHSRLEKFVKNLTGAGLI 54
                5789999998899*********************************98 PP

>> Mannosyl_trans2  Mannosyltransferase (PIG-V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05     0.085       7      82 ..       3      80 ..       1      90 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
  Mannosyl_trans2  7 yavlsrllvllLviLfrialipddtsealnppcl..laspslvdslvekllenlvsWDsvyflkiaenGyeyeheyaf 82
                     y  +++++  +L++  ++ +   +t+ +l +  l       +v++l+   l n + +D  + + i+e+G +y + y  
       AJA93233.1  3 YRTSMQIVADVLTVTEQTGQEGIKTTSLLTKANLshSRLEKFVKNLTGAGLINKIEFDGRHTFVITEKGRQYLESYQK 80
                     555666677777777777777777777887776533345689******************************998853 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.18      24      56 ..      26      58 ..      21      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
        TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerek 56
                +++ +  ++++++s+  + +++L  +Gl+++++
  AJA93233.1 26 KTTSLLTKANLSHSRLEKFVKNLTGAGLINKIE 58
                67788899**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 668.28
//
Query:       AJA93234.1  [L=199]
Description: ferritin-like protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-20   72.2   0.0    5.6e-20   71.7   0.0    1.1  1  Ferritin  Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   3.1e-24   5.6e-20       3     136 ..      34     172 ..      32     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.1e-24
                 HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......C-SSSSCSSHHHHHHHHHHHHHHH CS
    Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......ieapkefgsveevleaalehekkv 95 
                 +L    + e+ta+y++ ++  ++ g++ eg++  +++   e + h++ ++eri +lGg+ + + + + +      ++ pk+ ++++++le++l++e+ +
  AJA93234.1  34 QLITNASVEFTAYYYFTNLRMHATGMEGEGIKGIIEDARLEDLSHFESCIERIFQLGGSLPNDAQAFIKmsgcefLKLPKNPTDIKAILEKCLKAEQGA 132
                 66667789**************************************************9999999888899998654455566**************** PP

                 HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin  96 teslrelielaeeegDpatadfledfleeqeeheweleall 136
                 + +  ++++++  + Dpat+d+++d+l e+ ehe ++ +ll
  AJA93234.1 133 IVNWDKVCKMTFGK-DPATYDIAKDILMEEIEHESWFLELL 172
                 ************96.*********************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1579.06
//
Query:       AJA93235.1  [L=287]
Description: FAH family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-69  233.8   0.0    2.1e-69  233.5   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
      0.042   14.7   0.0       0.12   13.3   0.0    1.8  1  DUF2437        Domain of unknown function (DUF2437)


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.5   0.0   2.3e-73   2.1e-69       1     218 []      79     284 ..      79     284 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.5 bits;  conditional E-value: 2.3e-73
                    .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTEEEEEEEEEEE- CS
  FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedaiaGytllnDvsa 96 
                    ki+c ++ny++h++e +    +pp+     ep++ +k++++l g +++i  P+++++ldyE ELa++igk+++++ s eeA+d+i+Gy++lnDvsa
     AJA93235.1  79 KIICLAFNYKDHAEEQK---LTPPK-----EPAIVNKPRTALNGTNAEIICPNFVKELDYEIELALIIGKKCKNI-SEEEAMDVIFGYMILNDVSA 165
                    69*************86...66888.....899******************************************.9******************* PP

                    SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S CS
  FAA_hydrolase  97 RdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspaeliahlsagltLepGdliltGTpsgvgaeee 192
                    Rd+qa +k   +++++ksfd+f+p Gpwi+t+de++dp++l+l++ +ng+ +qds+t++m  +++ +i+ ls+ +tLepGd+i+tGT +gv  ++ 
     AJA93235.1 166 RDIQAMDK---QFTRAKSFDGFAPCGPWITTKDEIDDPQNLKLTTKINGQIRQDSTTSNMFIKIPSIISILSKSITLEPGDIISTGTAAGVALNNP 258
                    *******9...9*******************************************************************************98899 PP

                    --EE--TT-EEEEEETTTEEEEEEE. CS
  FAA_hydrolase 193 slkflkdgDeveveieglGelrnrVa 218
                    + ++lkdgD++e+eie++G+++n+V+
     AJA93235.1 259 NIPYLKDGDHIEMEIEKIGTIQNKVR 284
                    ************************96 PP

>> DUF2437  Domain of unknown function (DUF2437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05      0.12       1      23 [.       1      23 [.       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                -EEEEEEETTEEEEEEEE.EEEE CS
     DUF2437  1 MriaRFshgggpryGvlegdtvv 23
                M+iaR+ ++++  +G++++++++
  AJA93235.1  1 MKIARVVKSDRETFGLVKDGKIA 23
                ******************88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2400.69
//
Query:       AJA93236.1  [L=103]
Description: hypothetical protein T478_0459 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   14.0   2.3        1.3    9.0   0.1    2.3  2  JmjN      jmjN domain


Domain annotation for each model (and alignments):
>> JmjN  jmjN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   7.2e-05       1.3       4      25 ..      36      58 ..      34      60 .. 0.86
   2 ?    4.7   0.4    0.0017        30       8      18 ..      64      74 ..      62      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.2e-05
                ---HHHHC.-HHHHHHHHHHHHC CS
        JmjN  4 yPTeeEFk.dplkYiekieplge 25
                 P+++EF+    +Y +ki pl e
  AJA93236.1 36 NPSKDEFReKTVEYFSKIVPLLE 58
                5******76*********98765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0017
                HHHC-HHHHHH CS
        JmjN  8 eEFkdplkYie 18
                +EF+d + Y++
  AJA93236.1 64 KEFEDINHYMK 74
                7********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 772.93
//
Query:       AJA93237.1  [L=1380]
Description: HYR domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-59  195.7  64.5      1e-06   29.0   1.8   12.6 12  HYR              HYR domain
    9.9e-30  101.1   6.1    6.3e-05   22.8   0.2    6.9  6  NHL              NHL repeat
      3e-12   46.3  44.1    5.5e-07   29.4  16.4    4.2  4  HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 co
    9.1e-12   44.9   6.7        3.4    7.9   0.3    9.3 10  DUF5011          Domain of unknown function (DUF5011)
    1.6e-11   43.9   0.5        3.9    7.3   0.1    9.0 11  Big_3_4          Domain of unknown function
    2.7e-11   43.2  14.3    3.5e-07   29.7   2.4    3.2  3  DUF5128          6-bladed beta-propeller
    3.4e-07   30.1   0.3      0.032   13.8   0.0    4.3  3  SGL              SMP-30/Gluconolactonase/LRE-like region
    3.8e-07   29.3  28.4       0.38    9.5   0.1    7.3  8  REJ              REJ domain
    8.5e-07   28.5   0.9    0.00039   19.8   0.1    2.5  2  TolB_like        TolB-like 6-blade propeller-like
     0.0048   16.6  16.1         17    5.1   0.3    7.5  8  ChitinaseA_N     Chitinase A, N-terminal domain
  ------ inclusion threshold ------
      0.037   14.0   1.6        6.6    6.6   0.1    4.1  5  Phytase-like     Esterase-like activity of phytase
       0.53   10.3   0.0       0.53   10.3   0.0    8.1 12  SBBP             Beta-propeller repeat
        3.3    7.4  56.8       0.38   10.4   0.6   10.4 12  Big_3_3          Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> HYR  HYR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.5e-05      0.02       2      81 .]     339     413 ..     338     413 .. 0.78
   2 !   16.9   0.2   4.2e-06    0.0058       1      71 [.     414     480 ..     414     486 .. 0.86
   3 !   21.5   0.1   1.6e-07   0.00022      36      80 ..     522     566 ..     491     567 .. 0.87
   4 !   17.8   0.1   2.2e-06    0.0031      46      80 ..     607     641 ..     568     642 .. 0.70
   5 !   19.5   0.4   6.5e-07    0.0009       1      81 []     643     719 ..     643     719 .. 0.82
   6 !   18.8   0.1   1.1e-06    0.0015      37      78 ..     752     793 ..     721     796 .. 0.83
   7 !   29.0   1.8   7.3e-10     1e-06       2      81 .]     798     874 ..     797     874 .. 0.87
   8 !   26.6   0.3   4.2e-09   5.8e-06       1      81 []     875     951 ..     875     951 .. 0.81
   9 ?    3.6   0.4      0.06        83       1      73 [.     952    1020 ..     952    1028 .. 0.70
  10 !   20.6   0.8   3.1e-07   0.00043       2      81 .]    1030    1105 ..    1029    1105 .. 0.78
  11 !   25.6   2.6   8.1e-09   1.1e-05       1      81 []    1106    1182 ..    1106    1182 .. 0.82
  12 !   19.6   1.3   6.1e-07   0.00085       1      76 [.    1183    1254 ..    1183    1259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
         HYR   2 DttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81 
                 D + P++ +p+ i   ve   + +++   e  a+d sg     s t++  +sFp G++t+  +a D +gn a  + tVt+
  AJA93237.1 339 DFQKPVILVPEDI--LVEATGPLTSIDIGEAMATDESG---IYSLTNNAPSSFPLGINTIIWTAVDGAGNMAIASQTVTI 413
                 7778888888884..5666667777778899999**99...33344445589********************98888886 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.2e-06
         HYR   1 vDttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgn 71 
                 +D tpP+++ ++ i  +++  +s+  v  t p++ d +g   ++s+t+   + Fp G+t Vt +a+D  gn
  AJA93237.1 414 QDSTPPKISAIDDISLEAKS-SSQNLVTLTIPEIYDEVG---VMSTTNDAPEVFPLGETIVTWTATDVIGN 480
                 599**********8777664.455568899999999999...8899999999***************9998 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.6e-07
         HYR  36 dnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVt 80 
                  +s+ ++++s t+     Fp G+t Vt +a+D sgn+ s ++t+t
  AJA93237.1 522 ETSDDVEVISVTNDAPTVFPLGETIVTWTATDSSGNSSSQSYTIT 566
                 5678899*******************************9999997 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 2.2e-06
         HYR  46 rtaqpGdsFpvGsttVtyvaeDesgneasCkFtVt 80 
                  t+     Fp G+t Vt +a+D sgn+as + t+ 
  AJA93237.1 607 LTNDAPTVFPLGETIVTWTATDSSGNSASATQTII 641
                 34444578********************9998875 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 6.5e-07
         HYR   1 vDttpPtvkcpnnivrtvelgkstvev.ffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81 
                 vDtt P +  p+n   t+e +++ +++    e +a+d+sg  + ++++ +p + Fp G+t Vt +a+D  gn+ s +  +tv
  AJA93237.1 643 VDTTSPILIAPEN--LTIEAESTLTQIeNLGEFVAEDISG--ITTVTNDAP-EVFPLGETIVTWTATDDYGNSISNTQSITV 719
                 7************..888888888888357899*******..444445555.69******************9877776665 PP

  == domain 6  score: 18.8 bits;  conditional E-value: 1.1e-06
         HYR  37 nsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFt 78 
                 +s+ ++++s t+     Fp G+t Vt +a+D sgn+as + +
  AJA93237.1 752 ASDDVEVISITNDAPTVFPLGETIVTWTATDSSGNSASDSQQ 793
                 455788999999999*********************976555 PP

  == domain 7  score: 29.0 bits;  conditional E-value: 7.3e-10
         HYR   2 DttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81 
                 Dtt P++  pn i+ ++  +k++ve+    pt +d++++  ++++ a p   Fp G+t Vt +a+D sgn+as + t+tv
  AJA93237.1 798 DTTIPSIIAPNDIQVEI-YDKLGVEIDTGIPTSDDVIDSQPVITNDA-P-TVFPLGETIVTWTATDSSGNSASATQTITV 874
                 9***********65555.79******************666555444.4.69************************9998 PP

  == domain 8  score: 26.6 bits;  conditional E-value: 4.2e-09
         HYR   1 vDttpPtvkcpnn.ivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81 
                 vDtt P +  p++ i+  ++ + + v++     + +d+++    +s t+   + Fp G+t Vt +a+D sgn+as + t+tv
  AJA93237.1 875 VDTTSPILIAPESiIQEAINHEANPVRIGIS--EYTDIMD---ITSITNDAPEVFPLGETIVTWTATDSSGNSASATQTITV 951
                 79***********555667777777777665..5678877...44555566679************************9998 PP

  == domain 9  score: 3.6 bits;  conditional E-value: 0.06
         HYR    1 vDttpPtvkcpnn.ivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgnea 73  
                  vDtt P+v+  ++  +  +  + + ve+     ta+dn   ++ +s t+     F+ G+t ++  + D  gn+ 
  AJA93237.1  952 VDTTSPVVENFDSlTFEATAQNANLVEIP--LITASDN---TEIISITNDAPVLFEFGTTIINWSVVDIIGNQS 1020
                  68999999877772333333333333333..3455555...668888899999***************999985 PP

  == domain 10  score: 20.6 bits;  conditional E-value: 3.1e-07
         HYR    2 DttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81  
                  Dtt Pt+  p      ve++ +++e    e  +  +s+q++  + t+     Fp G+t +  +a+D sgn+as + t+tv
  AJA93237.1 1030 DTTLPTIISPVD----VEVEATSMENNLVEFGFAEASDQVEISTITNDAPTVFPLGETIIIWTATDSSGNSASATQTITV 1105
                  899999977776....566666666555566666666666666777777799************************9998 PP

  == domain 11  score: 25.6 bits;  conditional E-value: 8.1e-09
         HYR    1 vDttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCkFtVtv 81  
                  vDtt P+++ p+ni+  ++  k++  v  ++ ++ d++  ++ ++++    + ++ G+t Vt +a+D sgn+as + t+tv
  AJA93237.1 1106 VDTTAPVITTPENITSNATS-KLNNIVELEQISVIDSIS-TVQITNN--APSYYEFGETIVTWTATDSSGNSASATQTITV 1182
                  7************8888765.566678888888888877.5555544..4567888*********************9998 PP

  == domain 12  score: 19.6 bits;  conditional E-value: 6.1e-07
         HYR    1 vDttpPtvkcpnnivrtvelgkstvevffteptakdnsgqaalvsrtaqpGdsFpvGsttVtyvaeDesgneasCk 76  
                  vDtt P+++ p+ni  +v+  ++++ +     t++d+++  + + + + +   Fp G+t Vt +a+D+ gn+ s  
  AJA93237.1 1183 VDTTAPVITTPQNI--IVDAVNTETLLEIGSATIDDIID-DRPIIT-NDSPTVFPLGETIVTWTATDKFGNTSSSL 1254
                  7************3..4555566666778999*******.444444.455589******************98765 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     8e-08   0.00011       1      28 []      37      64 ..      37      64 .. 0.96
   2 !   22.8   0.2   4.6e-08   6.3e-05       1      28 []      84     110 ..      84     110 .. 0.97
   3 !   14.5   0.0   1.9e-05     0.027       1      28 []     130     157 ..     130     157 .. 0.94
   4 !    9.8   0.1   0.00062      0.86       1      24 [.     177     199 ..     177     203 .. 0.78
   5 !   10.8   0.0    0.0003      0.41       3      27 ..     223     247 ..     223     248 .. 0.93
   6 !   18.0   0.0   1.5e-06     0.002       1      28 []     268     295 ..     268     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8e-08
                BSSEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL  1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28
                f +P+ +a ds +++yV+D +n+rvq+F
  AJA93237.1 37 FLSPQHLAFDSENNVYVTDLGNSRVQKF 64
                778999*********************9 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 4.6e-08
                 BSSEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28 
                 f +P+G+av s+  ++V D++nh +q+F
  AJA93237.1  84 FGHPTGIAV-SDEFVFVVDNKNHNIQKF 110
                 889******.8****************9 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 1.9e-05
                 BSSEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28 
                 f +P+G+ v++   +yV Ds+n r+q+F
  AJA93237.1 130 FKSPRGIIVSDYESVYVVDSGNARIQKF 157
                 6789999999999**************9 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00062
                 BSSEEEEEEETTTEEEEEECCCTE CS
         NHL   1 fnyPhGvavdsnGdiyVaDsenhr 24 
                 f +P ++a+ +++ iyV+D + + 
  AJA93237.1 177 FVSPVDIAI-NSDKIYVTDPNQNK 199
                 678******.6********55544 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.0003
                 SEEEEEEETTTEEEEEECCCTEEEE CS
         NHL   3 yPhGvavdsnGdiyVaDsenhrvqv 27 
                 yP+G+  d  +++y+ D++n+r+ +
  AJA93237.1 223 YPEGIIFDEEDNFYIVDYRNNRIIH 247
                 79********************976 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 1.5e-06
                 BSSEEEEEEETTTEEEEEECCCTEEEEE CS
         NHL   1 fnyPhGvavdsnGdiyVaDsenhrvqvF 28 
                 f +P +va++++G ++++D+  hr+q+F
  AJA93237.1 268 FKFPKDVAISNDGYLFITDTQGHRIQKF 295
                 789************************9 PP

>> HemolysinCabind  RTX calcium-binding nonapeptide repeat (4 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.5   4.8e+03      18      25 ..     257     264 ..     256     265 .. 0.47
   2 !   22.6   7.2   5.5e-08   7.6e-05       2      34 ..    1274    1306 ..    1273    1306 .. 0.97
   3 !   29.4  16.4     4e-10   5.5e-07       2      36 .]    1301    1335 ..    1301    1335 .. 0.97
   4 !   18.9  13.2   8.2e-07    0.0011       2      35 ..    1328    1361 ..    1327    1362 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.5
  HemolysinCabind  18 iyGgaGnD 25 
                      i+G  GnD
       AJA93237.1 257 IFGQMGND 264
                      44444554 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.5e-08
  HemolysinCabind    2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnD 34  
                       G++ +D+l+G+a  D i++++G+D+++G++GnD
       AJA93237.1 1274 GSEEDDILIGTALSDLIFANGGDDIISGDKGND 1306
                       8999****************************9 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 4e-10
  HemolysinCabind    2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDtl 36  
                       G+ GnD + +g+G+D+i+G++GnD ++G +GnD++
       AJA93237.1 1301 GDKGNDCILAGDGDDIIFGNQGNDHISGQGGNDII 1335
                       889******************************97 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 8.2e-07
  HemolysinCabind    2 GgdGnDtlvGgaGnDtiyGgaGnDtlyGGaGnDt 35  
                       G +GnD++ G +G D+++Gg G D+++GG++ Dt
       AJA93237.1 1328 GQGGNDIIKGQSGEDFVFGGLGLDVIDGGDDIDT 1361
                       899*****************************98 PP

>> DUF5011  Domain of unknown function (DUF5011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.4   8.9e+03      47      70 ..     389     412 ..     388     413 .. 0.85
   2 ?    0.8   0.0       0.4   5.5e+02      50      66 ..     546     562 ..     538     566 .. 0.82
   3 !    6.7   0.0    0.0055       7.6      50      71 .]     621     642 ..     616     642 .. 0.90
   4 ?   -1.1   0.0       1.5   2.1e+03      50      71 .]     698     719 ..     693     719 .. 0.82
   5 ?    1.8   0.0      0.19   2.7e+02      50      71 .]     775     796 ..     768     796 .. 0.83
   6 !    7.0   0.0    0.0047       6.4      50      71 .]     853     874 ..     838     874 .. 0.92
   7 !    6.9   0.0    0.0049       6.7      50      71 .]     930     951 ..     924     951 .. 0.90
   8 ?    4.6   0.0     0.026        35      51      71 .]    1085    1105 ..    1079    1105 .. 0.89
   9 !    7.9   0.3    0.0025       3.4      44      71 .]    1155    1182 ..    1134    1182 .. 0.80
  10 ?   -0.0   0.0      0.72   9.9e+02      50      71 .]    1238    1259 ..    1233    1259 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.4
                 EEEEEEEEEE-TTSEEEEEEEEEE CS
     DUF5011  47 GtYtitYtvtdssgneatvtRtVk 70 
                 G  ti  t+ d +gn a ++ tV+
  AJA93237.1 389 GINTIIWTAVDGAGNMAIASQTVT 412
                 66689999*******999999997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.4
                 EEEEEEE-TTSEEEEEE CS
     DUF5011  50 titYtvtdssgneatvt 66 
                  +t t+tdssgn+++ +
  AJA93237.1 546 IVTWTATDSSGNSSSQS 562
                 699*********99876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0055
                 EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011  50 titYtvtdssgneatvtRtVkV 71 
                  +t t+tdssgn+a++t t++V
  AJA93237.1 621 IVTWTATDSSGNSASATQTIIV 642
                 599*****************98 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.5
                 EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011  50 titYtvtdssgneatvtRtVkV 71 
                  +t t+td +gn+ + t  ++V
  AJA93237.1 698 IVTWTATDDYGNSISNTQSITV 719
                 5899********9988877776 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.19
                 EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011  50 titYtvtdssgneatvtRtVkV 71 
                  +t t+tdssgn+a+ + +++V
  AJA93237.1 775 IVTWTATDSSGNSASDSQQISV 796
                 699**********998777766 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0047
                 EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011  50 titYtvtdssgneatvtRtVkV 71 
                  +t t+tdssgn+a++t t++V
  AJA93237.1 853 IVTWTATDSSGNSASATQTITV 874
                 699*****************98 PP

  == domain 7  score: 6.9 bits;  conditional E-value: 0.0049
                 EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011  50 titYtvtdssgneatvtRtVkV 71 
                  +t t+tdssgn+a++t t++V
  AJA93237.1 930 IVTWTATDSSGNSASATQTITV 951
                 599*****************98 PP

  == domain 8  score: 4.6 bits;  conditional E-value: 0.026
                  EEEEEE-TTSEEEEEEEEEEE CS
     DUF5011   51 itYtvtdssgneatvtRtVkV 71  
                  i  t+tdssgn+a++t t++V
  AJA93237.1 1085 IIWTATDSSGNSASATQTITV 1105
                  7789***************98 PP

  == domain 9  score: 7.9 bits;  conditional E-value: 0.0025
                  TS-EEEEEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011   44 skvGtYtitYtvtdssgneatvtRtVkV 71  
                   + G+  +t t+tdssgn+a++t t++V
  AJA93237.1 1155 YEFGETIVTWTATDSSGNSASATQTITV 1182
                  56677789******************98 PP

  == domain 10  score: -0.0 bits;  conditional E-value: 0.72
                  EEEEEEE-TTSEEEEEEEEEEE CS
     DUF5011   50 titYtvtdssgneatvtRtVkV 71  
                   +t t+td+ gn+++   t++V
  AJA93237.1 1238 IVTWTATDKFGNTSSSLQTISV 1259
                  5999*********998777766 PP

>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.2   3.1e+03      34      61 ..     466     493 ..     464     512 .. 0.87
   2 ?   -0.1   0.0      0.54   7.4e+02      34      53 ..     543     565 ..     536     582 .. 0.76
   3 !    6.3   0.0    0.0056       7.7      34      63 ..     618     647 ..     608     685 .. 0.78
   4 ?   -1.7   0.0       1.7   2.4e+03      34      50 ..     695     711 ..     692     725 .. 0.82
   5 ?   -0.2   0.0       0.6   8.3e+02      34      61 ..     772     799 ..     766     815 .. 0.84
   6 ?    4.7   0.0     0.018        25      34      62 ..     850     878 ..     843     897 .. 0.90
   7 !    6.1   0.0    0.0063       8.7      34      78 ..     927     972 ..     922     994 .. 0.78
   8 ?   -0.9   0.1      0.99   1.4e+03      33      73 ..    1003    1042 ..     992    1072 .. 0.73
   9 ?    3.8   0.0     0.034        46      34      62 ..    1081    1109 ..    1070    1138 .. 0.84
  10 !    7.3   0.1    0.0028       3.9      29      63 ..    1153    1187 ..    1131    1217 .. 0.75
  11 ?   -3.8   0.0       7.8   1.1e+04      34      50 ..    1235    1251 ..    1234    1253 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
     Big_3_4  34 GeyvvellaedeaGnqayiakllyvvdi 61 
                 Ge +v   a d  Gn + +++ +  vd 
  AJA93237.1 466 GETIVTWTATDVIGNISNLSQSIILVDS 493
                 899************9999887777765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.54
     Big_3_4  34 GeyvvellaedeaGn...qayia 53 
                 Ge +v   a d +Gn   q+y  
  AJA93237.1 543 GETIVTWTATDSSGNsssQSYTI 565
                 99************944444543 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0056
     Big_3_4  34 GeyvvellaedeaGnqayiakllyvvdien 63 
                 Ge +v   a d +Gn a  ++ + vvd+  
  AJA93237.1 618 GETIVTWTATDSSGNSASATQTIIVVDTTS 647
                 99************************9864 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.7
     Big_3_4  34 GeyvvellaedeaGnqa 50 
                 Ge +v   a d+ Gn  
  AJA93237.1 695 GETIVTWTATDDYGNSI 711
                 999***********975 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.6
     Big_3_4  34 GeyvvellaedeaGnqayiakllyvvdi 61 
                 Ge +v   a d +Gn a  ++ + v+d+
  AJA93237.1 772 GETIVTWTATDSSGNSASDSQQISVIDT 799
                 99*************9977666666665 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.018
     Big_3_4  34 GeyvvellaedeaGnqayiakllyvvdie 62 
                 Ge +v   a d +Gn a  ++ + vvd+ 
  AJA93237.1 850 GETIVTWTATDSSGNSASATQTITVVDTT 878
                 99************************985 PP

  == domain 7  score: 6.1 bits;  conditional E-value: 0.0063
     Big_3_4  34 GeyvvellaedeaGnqayiakllyvvdien.icvevrpldylsekl 78 
                 Ge +v   a d +Gn a  ++ + vvd+   +  +   l + + ++
  AJA93237.1 927 GETIVTWTATDSSGNSASATQTITVVDTTSpVVENFDSLTFEATAQ 972
                 99************************98761444455565555555 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 0.99
     Big_3_4   33 dGeyvvellaedeaGnqayiakllyvvdienicvevrpldy 73  
                   G  +++    d  Gnq+ + + + ++d+ +  + + p+d 
  AJA93237.1 1003 FGTTIINWSVVDIIGNQSVVEQQIDIIDTTL-PTIISPVDV 1042
                  47788888999999*****999998888754.344555554 PP

  == domain 9  score: 3.8 bits;  conditional E-value: 0.034
     Big_3_4   34 GeyvvellaedeaGnqayiakllyvvdie 62  
                  Ge ++   a d +Gn a  ++ + vvd+ 
  AJA93237.1 1081 GETIIIWTATDSSGNSASATQTITVVDTT 1109
                  999***********************986 PP

  == domain 10  score: 7.3 bits;  conditional E-value: 0.0028
     Big_3_4   29 PldedGeyvvellaedeaGnqayiakllyvvdien 63  
                   + e Ge +v   a d +Gn a  ++ + vvd+  
  AJA93237.1 1153 SYYEFGETIVTWTATDSSGNSASATQTITVVDTTA 1187
                  56678**************************9865 PP

  == domain 11  score: -3.8 bits;  conditional E-value: 7.8
     Big_3_4   34 GeyvvellaedeaGnqa 50  
                  Ge +v   a d+ Gn +
  AJA93237.1 1235 GETIVTWTATDKFGNTS 1251
                  899***********975 PP

>> DUF5128  6-bladed beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   3.2e-07   0.00044      62     135 ..      48     118 ..      39     120 .. 0.94
   2 !   29.7   2.4   2.6e-10   3.5e-07      55     130 ..     133     207 ..     125     214 .. 0.88
   3 ?    0.3   1.1      0.22     3e+02      62     127 ..     232     296 ..     222     318 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.2e-07
     DUF5128  62 dkrifvlDsaknnlfvFdkkGkfvrkIgaqGeGPgEYlqindfiidksnesIyildfmknkiltYdLegykfie 135
                 ++ ++v+D  ++++  Fd +G+f  + g++G+  gE+   + +++   +e ++++d +++ i ++ L+g +fi+
  AJA93237.1  48 ENNVYVTDLGNSRVQKFDSTGNFLIEWGNRGSSDGEFGHPTGIAVS--DEFVFVVDNKNHNIQKFTLDG-EFIS 118
                 5789*****************************************9..888****************99.**97 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.6e-10
     DUF5128  55 iskikvvd.krifvlDsaknnlfvFdkkGkfvrkIgaqGeGPgEYlqindfiidksnesIyildfmknkiltYdLeg 130
                 +  i v+d + ++v+Ds ++++  F+ +G+f++  g+ G+  g++++  d++i+ +  +Iy+ d+ +nki+++dLeg
  AJA93237.1 133 PRGIIVSDyESVYVVDSGNARIQKFTLDGEFISGFGQSGKRGGNFVSPVDIAINSD--KIYVTDPNQNKIIVFDLEG 207
                 556666676899******************************************55..5****************98 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.22
     DUF5128  62 dkrifvlDsaknnlfvFdkkGkfvrkIgaqGeGPgEYlqindfiidksnesIyildfmknkiltYd 127
                 ++  +++D ++n++  +++ G   +  g++G+  g +   +d +i  ++ +++i d ++++i +++
  AJA93237.1 232 EDNFYIVDYRNNRIIHYNEFGVSLSIFGQMGNDNGHFKFPKDVAIS-NDGYLFITDTQGHRIQKFS 296
                 3555666666666666666666666666666666666666666666.3446666666666665554 PP

>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0029         4     189     217 ..      43      71 ..      38      77 .. 0.90
   2 !   13.8   0.0   2.3e-05     0.032     145     215 ..     187     253 ..     181     259 .. 0.82
   3 ?   -1.7   0.0       1.2   1.7e+03     190     211 ..     275     296 ..     261     302 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
         SGL 189 lavDaeGnvwvAvwgggkvvrfdpdGkli 217
                 la D+e+nv+v+ +g+++v++fd  G+ +
  AJA93237.1  43 LAFDSENNVYVTDLGNSRVQKFDSTGNFL 71 
                 689*********************99876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.3e-05
         SGL 145 gktlYlaDsltrkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGk 215
                 ++++Y++D  ++ki ++d++ + +++ n    + +k+   +p G++ D+e+n ++  +++++++++++ G 
  AJA93237.1 187 SDKIYVTDPNQNKIIVFDLEGNLENIFNDS--IGGKP--IYPEGIIFDEEDNFYIVDYRNNRIIHYNEFGV 253
                 5689***************76666555555..33444..56**************************9886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
         SGL 190 avDaeGnvwvAvwgggkvvrfd 211
                 a+ ++G+++++  +g+++++f+
  AJA93237.1 275 AISNDGYLFITDTQGHRIQKFS 296
                 4444555555555555555444 PP

>> REJ  REJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0058       8.1     175     206 ..     392     422 ..     367     442 .. 0.76
   2 ?   -1.6   0.1      0.65     9e+02     161     205 ..     531     575 ..     512     580 .. 0.84
   3 !    8.0   0.1   0.00078       1.1     158     206 ..     603     651 ..     590     666 .. 0.85
   4 ?   -2.3   0.0       1.1   1.5e+03     161     205 ..     760     804 ..     751     807 .. 0.83
   5 !    9.5   0.1   0.00027      0.38     158     206 ..     835     883 ..     823     905 .. 0.85
   6 !    6.9   0.1    0.0017       2.3     161     205 ..     915     959 ..     910     961 .. 0.87
   7 !    7.3   0.6    0.0013       1.8     158     206 ..    1066    1114 ..    1043    1134 .. 0.77
   8 !    6.9   1.8    0.0017       2.3     157     205 ..    1142    1190 ..    1115    1221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0058
         REJ 175 ynftltvskrsrksasteqtilvvdgepplvs 206
                   +++ v +++ ++a ++qt++++d+ pp++s
  AJA93237.1 392 TIIWTAV-DGAGNMAIASQTVTIQDSTPPKIS 422
                 4444444.555559***************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.65
         REJ 161 sltfpaselvanltynftltvskrsrksasteqtilvvdgepplv 205
                 s+t +a ++ +  +  +t t++++s +s+s + ti+ vd  +p++
  AJA93237.1 531 SVTNDAPTVFPLGETIVTWTATDSSGNSSSQSYTITFVDTIIPEI 575
                 667777777777788999999999999**********99999987 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00078
         REJ 158 stssltfpaselvanltynftltvskrsrksasteqtilvvdgepplvs 206
                 ++  lt +a ++ +  +  +t t++++s +sas++qti vvd   p+++
  AJA93237.1 603 QNAELTNDAPTVFPLGETIVTWTATDSSGNSASATQTIIVVDTTSPILI 651
                 5667888888888888999***********************9998875 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.1
         REJ 161 sltfpaselvanltynftltvskrsrksasteqtilvvdgepplv 205
                 s+t +a ++ +  +  +t t++++s +sas +q i v d  +p +
  AJA93237.1 760 SITNDAPTVFPLGETIVTWTATDSSGNSASDSQQISVIDTTIPSI 804
                 566677777777788899999999999999999999999999987 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.00027
         REJ 158 stssltfpaselvanltynftltvskrsrksasteqtilvvdgepplvs 206
                 s++++t +a ++ +  +  +t t++++s +sas++qti+vvd   p+++
  AJA93237.1 835 SQPVITNDAPTVFPLGETIVTWTATDSSGNSASATQTITVVDTTSPILI 883
                 5678888999999999999***********************9998764 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0017
         REJ 161 sltfpaselvanltynftltvskrsrksasteqtilvvdgepplv 205
                 s+t +a e+ +  +  +t t++++s +sas++qti+vvd   p v
  AJA93237.1 915 SITNDAPEVFPLGETIVTWTATDSSGNSASATQTITVVDTTSPVV 959
                 56777888888888999**********************988865 PP

  == domain 7  score: 7.3 bits;  conditional E-value: 0.0013
         REJ  158 stssltfpaselvanltynftltvskrsrksasteqtilvvdgepplvs 206 
                  + s++t +a ++ +  +  +  t++++s +sas++qti+vvd   p ++
  AJA93237.1 1066 EISTITNDAPTVFPLGETIIIWTATDSSGNSASATQTITVVDTTAPVIT 1114
                  557888888888888888888899999999**********999988765 PP

  == domain 8  score: 6.9 bits;  conditional E-value: 0.0017
         REJ  157 sstssltfpaselvanltynftltvskrsrksasteqtilvvdgepplv 205 
                   st ++t +a + ++  +  +t t++++s +sas++qti+vvd   p +
  AJA93237.1 1142 ISTVQITNNAPSYYEFGETIVTWTATDSSGNSASATQTITVVDTTAPVI 1190
                  45667777777777777999***********************999864 PP

>> TolB_like  TolB-like 6-blade propeller-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0027       3.7       9      93 ..      28     111 ..      21     119 .. 0.84
   2 !   19.8   0.1   2.8e-07   0.00039      14     152 ..     126     261 ..     123     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0027
   TolB_like   9 kvialkslymryPfrikvkdd.ilvilDlhgddffyaysypelqfvssfakrGrgpeemlsaeefriskdslwvldkskltaakii 93 
                 ++   ks ++ +P +++   +  +++ Dl +++ +  +  +  +f+ + ++rG + +e+  +  + +s+++++v+d+ + +++k+ 
  AJA93237.1  28 QAGIFKSGFFLSPQHLAFDSEnNVYVTDLGNSR-VQKFD-STGNFLIEWGNRGSSDGEFGHPTGIAVSDEFVFVVDNKNHNIQKFT 111
                 55566888999999999765559999***9999.88886.46789******************************98888888775 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.8e-07
   TolB_like  14 kslymryPfrikvkdd.ilvilDlhgddffyaysypelqfvssfakrGrgpeemlsaeefriskdslwvldkskltaakiifnkkdlsiqrqeelidld 111
                 ++ ++++P  i v+d   ++++D  + + +  + + + +f+s f++ G+  ++++s+  + i+ d+++v d ++ ++  ++      + ++ e++ ++ 
  AJA93237.1 126 DNGFFKSPRGIIVSDYeSVYVVDSGNAR-IQKFTL-DGEFISGFGQSGKRGGNFVSPVDIAINSDKIYVTDPNQNKIIVFDL-----EGNL-ENIFNDS 216
                 567999*****99998577788876666.999998.679*******************************977444433333.....2222.2333333 PP

   TolB_like 112 ksilri....ldl.tdstFivsdysgdsrfllvdrdgkllkkakei 152
                     +i    + + ++  F + dy  ++r+   ++ g  l+ ++++
  AJA93237.1 217 IGGKPIypegIIFdEEDNFYIVDY-RNNRIIHYNEFGVSLSIFGQM 261
                 333333111244588999999999.788888888777766666655 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   2.5e+03      90     110 ..     550     570 ..     541     571 .. 0.85
   2 ?    3.7   0.0     0.032        44      88     111 ..     623     646 ..     608     665 .. 0.84
   3 ?   -2.1   0.0         2   2.7e+03      90     110 ..     702     722 ..     690     725 .. 0.85
   4 ?    1.8   0.0      0.12   1.7e+02      88     110 ..     777     799 ..     763     813 .. 0.86
   5 ?    3.3   0.0     0.043        59      89     111 ..     856     878 ..     843     895 .. 0.85
   6 ?    3.6   0.0     0.036        49      88     112 ..     932     956 ..     917     978 .. 0.81
   7 ?    2.4   0.2     0.083   1.1e+02      91     111 ..    1089    1109 ..    1077    1129 .. 0.87
   8 ?    5.1   0.3     0.012        17      73     111 ..    1148    1186 ..    1118    1204 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
  ChitinaseA_N  90 elCdaeGCsksapkeivvaDt 110
                    + d++G s+s++ +i+  Dt
    AJA93237.1 550 TATDSSGNSSSQSYTITFVDT 570
                   67899************9998 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
  ChitinaseA_N  88 evelCdaeGCsksapkeivvaDtD 111
                   +  + d++G s+sa+++i+v Dt 
    AJA93237.1 623 TWTATDSSGNSASATQTIIVVDTT 646
                   556789****************96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2
  ChitinaseA_N  90 elCdaeGCsksapkeivvaDt 110
                    + d  G s s++++i+v Dt
    AJA93237.1 702 TATDDYGNSISNTQSITVLDT 722
                   56788999***********99 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.12
  ChitinaseA_N  88 evelCdaeGCsksapkeivvaDt 110
                   +  + d++G s+s++++i v Dt
    AJA93237.1 777 TWTATDSSGNSASDSQQISVIDT 799
                   556789****************9 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.043
  ChitinaseA_N  89 velCdaeGCsksapkeivvaDtD 111
                     + d++G s+sa+++i+v Dt 
    AJA93237.1 856 WTATDSSGNSASATQTITVVDTT 878
                   56789****************96 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.036
  ChitinaseA_N  88 evelCdaeGCsksapkeivvaDtDG 112
                   +  + d++G s+sa+++i+v Dt  
    AJA93237.1 932 TWTATDSSGNSASATQTITVVDTTS 956
                   556789****************965 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.083
  ChitinaseA_N   91 lCdaeGCsksapkeivvaDtD 111 
                    + d++G s+sa+++i+v Dt 
    AJA93237.1 1089 ATDSSGNSASATQTITVVDTT 1109
                    6799***************96 PP

  == domain 8  score: 5.1 bits;  conditional E-value: 0.012
  ChitinaseA_N   73 esatfkvkkgGryqlevelCdaeGCsksapkeivvaDtD 111 
                    +++  ++ + G+  ++  + d++G s+sa+++i+v Dt 
    AJA93237.1 1148 TNNAPSYYEFGETIVTWTATDSSGNSASATQTITVVDTT 1186
                    44455677778888899999*****************96 PP

>> Phytase-like  Esterase-like activity of phytase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         2   2.8e+03      73     101 ..      43      71 ..      42      78 .. 0.90
   2 ?    0.4   0.0      0.35   4.9e+02      72     103 ..      89     119 ..      80     125 .. 0.88
   3 ?    1.1   0.0      0.23   3.1e+02      72     103 ..     135     166 ..     132     172 .. 0.90
   4 ?    6.6   0.1    0.0048       6.6      60      98 ..     219     252 ..     179     264 .. 0.74
   5 ?   -3.4   0.0       5.4   7.4e+03      73      95 ..     274     296 ..     271     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2
  Phytase-like  73 iavapdgtfwvssEggpfilefdadGkll 101
                   +a++++++++v++ g+ ++ +fd +G++l
    AJA93237.1  43 LAFDSENNVYVTDLGNSRVQKFDSTGNFL 71 
                   688999********************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
  Phytase-like  72 giavapdgtfwvssEggpfilefdadGkllre 103
                   giav +d+ ++v++  ++ i +f++dG+++++
    AJA93237.1  89 GIAV-SDEFVFVVDNKNHNIQKFTLDGEFISK 119
                   7888.888899999999**********99876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.23
  Phytase-like  72 giavapdgtfwvssEggpfilefdadGkllre 103
                   gi v++ ++++v++ g+ +i +f++dG++++ 
    AJA93237.1 135 GIIVSDYESVYVVDSGNARIQKFTLDGEFISG 166
                   78888999*******************99765 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0048
  Phytase-like  60 gapfpkkglDpEgiavapdgtfwvssEggpfilefdadG 98 
                   g     k + pEgi ++++++f++++ ++++i++++  G
    AJA93237.1 219 G-----KPIYPEGIIFDEEDNFYIVDYRNNRIIHYNEFG 252
                   3.....4448*************************9766 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 5.4
  Phytase-like  73 iavapdgtfwvssEggpfilefd 95 
                   +a+++dg +++++ +g++i +f+
    AJA93237.1 274 VAISNDGYLFITDTQGHRIQKFS 296
                   57789999999999999999997 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038      0.53      14      29 ..      39      54 ..      38      59 .. 0.92
   2 ?    5.4   0.1     0.013        18      10      29 ..     219     238 ..     216     238 .. 0.86
   3 ?    0.3   0.0      0.51     7e+02      14      29 ..     270     285 ..     260     285 .. 0.89
   4 ?   -3.2   0.0       6.4   8.8e+03      12      24 ..     362     374 ..     357     374 .. 0.76
   5 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..     551     558 ..     551     558 .. 0.89
   6 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..     626     633 ..     626     633 .. 0.89
   7 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..     780     787 ..     780     787 .. 0.89
   8 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..     858     865 ..     858     865 .. 0.89
   9 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..     935     942 ..     935     942 .. 0.89
  10 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..    1089    1096 ..    1089    1096 .. 0.89
  11 ?   -2.6   0.1       4.1   5.6e+03      19      26 ..    1166    1173 ..    1166    1173 .. 0.89
  12 ?   -2.7   0.1       4.6   6.3e+03      13      21 ..    1191    1199 ..    1187    1200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
        SBBP 14 ygngIavDsnGNiYvt 29
                +++++a+Ds+ N+Yvt
  AJA93237.1 39 SPQHLAFDSENNVYVT 54
                6899***********9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
        SBBP  10 gastygngIavDsnGNiYvt 29 
                 g+ +y+ gI +D++ N Y++
  AJA93237.1 219 GKPIYPEGIIFDEEDNFYIV 238
                 6669************9996 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.51
        SBBP  14 ygngIavDsnGNiYvt 29 
                 +++++a+  +G+ ++t
  AJA93237.1 270 FPKDVAISNDGYLFIT 285
                 899***********98 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6.4
        SBBP  12 stygngIavDsnG 24 
                  ++g  +a+D++G
  AJA93237.1 362 IDIGEAMATDESG 374
                 348999****998 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 4.1
        SBBP  19 avDsnGNi 26 
                 a+Ds+GN+
  AJA93237.1 551 ATDSSGNS 558
                 89*****5 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 4.1
        SBBP  19 avDsnGNi 26 
                 a+Ds+GN+
  AJA93237.1 626 ATDSSGNS 633
                 89*****5 PP

  == domain 7  score: -2.6 bits;  conditional E-value: 4.1
        SBBP  19 avDsnGNi 26 
                 a+Ds+GN+
  AJA93237.1 780 ATDSSGNS 787
                 89*****5 PP

  == domain 8  score: -2.6 bits;  conditional E-value: 4.1
        SBBP  19 avDsnGNi 26 
                 a+Ds+GN+
  AJA93237.1 858 ATDSSGNS 865
                 89*****5 PP

  == domain 9  score: -2.6 bits;  conditional E-value: 4.1
        SBBP  19 avDsnGNi 26 
                 a+Ds+GN+
  AJA93237.1 935 ATDSSGNS 942
                 89*****5 PP

  == domain 10  score: -2.6 bits;  conditional E-value: 4.1
        SBBP   19 avDsnGNi 26  
                  a+Ds+GN+
  AJA93237.1 1089 ATDSSGNS 1096
                  89*****5 PP

  == domain 11  score: -2.6 bits;  conditional E-value: 4.1
        SBBP   19 avDsnGNi 26  
                  a+Ds+GN+
  AJA93237.1 1166 ATDSSGNS 1173
                  89*****5 PP

  == domain 12  score: -2.7 bits;  conditional E-value: 4.6
        SBBP   13 tygngIavD 21  
                  t++++I vD
  AJA93237.1 1191 TTPQNIIVD 1199
                  89******9 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.65     9e+02      29      67 ..     342     380 ..     333     384 .. 0.81
   2 ?    2.7   0.1     0.064        88      11      70 ..     385     443 ..     376     456 .. 0.80
   3 ?    5.0   0.1     0.013        17      13      71 ..     464     521 ..     453     534 .. 0.80
   4 ?   -2.5   0.0       2.6   3.6e+03     126     145 ..     547     566 ..     537     573 .. 0.73
   5 ?   10.4   0.6   0.00028      0.38      13      77 ..     616     679 ..     604     688 .. 0.86
   6 ?    1.0   0.2      0.21   2.9e+02      13      56 ..     693     735 ..     683     763 .. 0.70
   7 ?   -1.4   0.0       1.2   1.6e+03      15      48 ..     772     804 ..     766     814 .. 0.67
   8 ?    3.9   0.9     0.028        39      13      85 ..     848     917 ..     843     921 .. 0.84
   9 ?    5.0   1.7     0.013        18      13      85 ..     925     994 ..     920     996 .. 0.77
  10 ?    8.2   3.5    0.0013       1.8      13      82 ..    1079    1148 ..    1068    1151 .. 0.83
  11 ?    2.4   1.5     0.079   1.1e+02      18      68 ..    1161    1209 ..    1152    1225 .. 0.69
  12 ?   -2.2   0.0         2   2.8e+03     126     142 ..    1239    1255 ..    1229    1260 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.65
     Big_3_3  29 nqvtksllstilvdntpPtvsi.segkkisdgavvkglen 67 
                  +v + +  +ilv+ t P  si   ++  +d++ +++l n
  AJA93237.1 342 KPVILVPE-DILVEATGPLTSIdIGEAMATDESGIYSLTN 380
                 55555555.899*******9998888999999*9*99986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.064
     Big_3_3  11 elpeGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlri 70 
                 + p G  +++ +a d  +n +  s +    +d tpP +s  ++ + + ++  ++l+ l i
  AJA93237.1 385 SFPLGINTIIWTAVDGAGNMAIASQT-VTIQDSTPPKISAIDDISLEAKSSSQNLVTLTI 443
                 56788888888888998888877776.5568*******9988888888888888887776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
     Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlrit 71 
                 p G+  ++ +a+d  +n  ++s +  ilvd t+P ++ se+  i+ +++ +++ +l+i 
  AJA93237.1 464 PLGETIVTWTATDVIGNISNLSQS-IILVDSTAPRIAFSEDLIIEASSLEENILELVIP 521
                 67777777899******9999887.9***********9888888877777777777774 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.6
     Big_3_3 126 ltvkaeDeagNaktkaskFe 145
                 +t +a+D+ gN + ++ + +
  AJA93237.1 547 VTWTATDSSGNSSSQSYTIT 566
                 57788899998887776655 PP

  == domain 5  score: 10.4 bits;  conditional E-value: 0.00028
     Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladald 77 
                 p G+  ++ +a+d  +n +  + +  i+vd+t+P +  +e+ +i+ ++++ ++enl   +a+++ 
  AJA93237.1 616 PLGETIVTWTATDSSGNSASATQT-IIVVDTTSPILIAPENLTIEAESTLTQIENLGEFVAEDIS 679
                 667777777999999999888776.89*********99******************999998875 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.21
     Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkki 56 
                 p G+  ++ +a+d ++n + ++ +   ++d+ +P++  +++ + 
  AJA93237.1 693 PLGETIVTWTATDDYGNSISNTQS-ITVLDTISPVIMAPSDFQL 735
                 667777777999999999988877.5567999999887554443 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 1.2
     Big_3_3  15 GkynlvlaakdtfnnqvtksllstilvdntpPtv 48 
                 G+  ++ +a+d  +n +  s +   ++d+t P++
  AJA93237.1 772 GETIVTWTATDSSGNSASDSQQ-ISVIDTTIPSI 804
                 5555555777777777766665.55677777776 PP

  == domain 8  score: 3.9 bits;  conditional E-value: 0.028
     Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldkskltsia 85 
                 p G+  ++ +a+d  +n +  + +   +vd+t+P +     ++i ++a+ ++ + +ri + + +d   +tsi+
  AJA93237.1 848 PLGETIVTWTATDSSGNSASATQT-ITVVDTTSPILIA--PESIIQEAINHEANPVRIGISEYTDIMDITSIT 917
                 567777777999999998887776.5679*****9866..78999999999*********9999999999986 PP

  == domain 9  score: 5.0 bits;  conditional E-value: 0.013
     Big_3_3  13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenlritladaldkskltsia 85 
                 p G+  ++ +a+d  +n +  + +   +vd+t+P+v+ ++  + + +a+ ++ + ++i l  a+d++++ si+
  AJA93237.1 925 PLGETIVTWTATDSSGNSASATQT-ITVVDTTSPVVENFD--SLTFEATAQNANLVEIPLITASDNTEIISIT 994
                 667777777999999998887776.6689*******9854..5666777777777888888888888787775 PP

  == domain 10  score: 8.2 bits;  conditional E-value: 0.0013
     Big_3_3   13 peGkynlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenl.ritladaldksklt 82  
                  p G+  ++ +a+d  +n +  + +   +vd+t+P+++ +e+ + +  + ++++++l +i++ d++ + ++t
  AJA93237.1 1079 PLGETIIIWTATDSSGNSASATQT-ITVVDTTAPVITTPENITSNATSKLNNIVELeQISVIDSISTVQIT 1148
                  667777777999999998887776.6689*********998888888999999999458999999887776 PP

  == domain 11  score: 2.4 bits;  conditional E-value: 0.079
     Big_3_3   18 nlvlaakdtfnnqvtksllstilvdntpPtvsisegkkisdgavvkglenl 68  
                   ++ +a+d  +n +  + +   +vd+t+P+++   ++ i d +  ++l ++
  AJA93237.1 1161 IVTWTATDSSGNSASATQT-ITVVDTTAPVITT-PQNIIVDAVNTETLLEI 1209
                  4455889999998877766.5689*******98.44555666666665555 PP

  == domain 12  score: -2.2 bits;  conditional E-value: 2
     Big_3_3  126 ltvkaeDeagNaktkas 142 
                  +t +a+D++gN++ + +
  AJA93237.1 1239 VTWTATDKFGNTSSSLQ 1255
                  57789999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.85u 0.30s 00:00:01.14 Elapsed: 00:00:00.46
# Mc/sec: 9001.03
//
Query:       AJA93238.1  [L=306]
Description: oligopeptide ABC transporter, oligopeptide-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-23   81.8   0.0    7.6e-23   81.3   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein
  ------ inclusion threshold ------
      0.046   13.4   0.0        1.3    8.8   0.0    2.5  2  Fis1_TPR_N    Fis1 N-terminal tetratricopeptide repeat
       0.14   12.3   0.1       0.46   10.6   0.1    2.0  1  V-ATPase_H_C  V-ATPase subunit H
       0.18   12.1   0.9       0.39   11.0   0.1    1.9  2  Mis14         Kinetochore protein Mis14 like


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   1.7e-26   7.6e-23       1     236 [.       6     266 ..       6     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.7e-26
                   EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....................TS-BSBESSSB-H....HHHHHH--SEEEE-GGG...... CS
  Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..................aivevgadgeidv....EklaalkPDlvilskgl...... 69 
                   i+s  ps te+ ++lGa +k++gv + +++p+da ++++                  +i++++  ge  +      + +++PDl+i+++        
    AJA93238.1   6 IISFLPSATELIYELGAQEKLFGVTHECNYPSDATNKPKviesvfepenmssleidkKICDLSEKGEDIYklvaQNVSNARPDLIISQEICevcsay 102
                   6677799*****************************9999997777777777766666677777777666999999*************99999999 PP

                   ....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHH CS
  Peripla_BP_2  70 .gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlld 165
                     +++ ++e+l+++ + + + +    +++ + ++ ++e  ++ ++++++v+ ++s+++++++   s  +++vl   + ++    +++s++++ ++++
    AJA93238.1 103 tNQVKNAIEILDEKPEIYSMSPHDI-QGILKCVEDIAEKIDEVKRGNEIVNSLNSRIEEIRNVKISS-RPKVLGIEWLNP----FFTSGHWVPEMVE 193
                   ***********************97.*************************************9999.666666666666....************* PP

                   TS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
  Peripla_BP_2 166 algieniaaeskkseyeeisaEqilasdpdvifvsgr...aeadnktgleflkenpllaelpAvkngrVyalds 236
                   + g+ n++    ++++ +   E+i ++dpd+++ +++        ++  + lk++p +++l+Avk+++V+a+d+
    AJA93238.1 194 ISGGVNMITKT-GEHSRKMEIEEIEKEDPDILILMPCgfdVQRTVSEYEKNLKNDPRWSQLKAVKERKVFAVDA 266
                   *******9999.***************************999999999**********************9987 PP

>> Fis1_TPR_N  Fis1 N-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00028       1.3      11      28 ..      98     115 ..      96     116 .. 0.95
   2 ?    1.5   0.0     0.052   2.3e+02      20      31 ..     278     289 ..     272     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00028
  Fis1_TPR_N  11 vkSknredqqeGiaLLee 28 
                 v+S ++++++  i++L e
  AJA93238.1  98 VCSAYTNQVKNAIEILDE 115
                 9***************87 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.052
  Fis1_TPR_N  20 qeGiaLLeelyr 31 
                   Gi++L+ +++
  AJA93238.1 278 ITGIEILAKILH 289
                 68******9985 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0001      0.46      42     115 ..     104     175 ..      92     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
  V-ATPase_H_C  42 kllkkLiklleeskdktvlavalnDigelvkllpegkkvleklkaKekimellehedeevkyeALkavqkllvq 115
                   + +k+ i++l  ++++++ ++  +Di+ ++k +++  + ++++k  ++i++ l+++ ee++   + +  k+l+ 
    AJA93238.1 104 NQVKNAIEIL--DEKPEIYSMSPHDIQGILKCVEDIAEKIDEVKRGNEIVNSLNSRIEEIRNVKISSRPKVLGI 175
                   6789999999..57899***************************************999998777666666655 PP

>> Mis14  Kinetochore protein Mis14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.6e-05      0.39      69     132 ..     100     166 ..      97     167 .. 0.82
   2 ?   -1.9   0.0      0.89     4e+03      94     111 ..     221     248 ..     200     258 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.6e-05
                 HHHHHHCCCHHHHHHCT--HHHHH--.......------SSSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       Mis14  69 eayakelkaeleeldeyleainelek.....qekkdpeeddededekerleelvkqyeeslkslkelke 132
                 +ay++++k+++e+lde +++i +++        k+  e+ +e++de +r +e+v+  ++ ++++ ++k+
  AJA93238.1 100 SAYTNQVKNAIEILDE-KPEIYSMSPhdiqgILKC-VEDIAEKIDEVKRGNEIVNSLNSRIEEIRNVKI 166
                 69**************.****99999777644444.455578889999999999999999999988875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.89
                 -............------SSSHHHHHH CS
       Mis14  94 k..........qekkdpeeddededeke 111
                            + +   +e +++ + ++
  AJA93238.1 221 PdililmpcgfDVQRTVSEYEKNLKNDP 248
                 1333333344444444444444444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2249.04
//
Query:       AJA93239.1  [L=103]
Description: putative translation initiation factor eIF-1A [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-19   67.9   1.5    6.3e-19   67.5   1.5    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.098   12.5   1.0        1.9    8.4   0.0    2.4  2  Myosin_N  Myosin N-terminal SH3-like domain
       0.13   12.5   0.0       0.15   12.3   0.0    1.2  1  MCM6_C    MCM6 C-terminal winged-helix domain


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   1.5   1.1e-22   6.3e-19       1      64 []      21      84 ..      21      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.1e-22
                EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TT.EEEEES- CS
      eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydlt.kGrIvyr 64
                ge++g+Vi++lg++++ V+++d   ++ ++i+gk++++iwi+ +d+V++ ++++  t +G+Iv+r
  AJA93239.1 21 GEMYGRVIKLLGSDQVLVKCTD-DITRRGRIRGKLKRRIWIRDNDVVVIAPWDFKETeRGDIVWR 84
                69******************96.*******************************9888*****98 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00031       1.9      16      36 ..      25      46 ..      18      47 .. 0.87
   2 ?    2.5   0.2     0.021   1.3e+02       1       8 [.      55      62 ..      55      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00031
                EEEEEEES.SEEEEEETTSEEE CS
    Myosin_N 16 GeIkeeeG.dkvtVetedGktv 36
                G++++  G d+v V+++d+ t+
  AJA93239.1 25 GRVIKLLGsDQVLVKCTDDITR 46
                78999999899*****998776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                SEEEEETT CS
    Myosin_N  1 KklVWVpD 8 
                K+++W++D
  AJA93239.1 55 KRRIWIRD 62
                9*****99 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      54      87 ..      15      48 ..       6      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
      MCM6_C 54 eeleeekklvekvlkrLvkdkvLlevreeaeese 87
                  l ee +++ +v+k L +d+vL++ +++ + + 
  AJA93239.1 15 IRLAEEGEMYGRVIKLLGSDQVLVKCTDDITRRG 48
                568999*********************9988743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 740.40
//
Query:       AJA93240.1  [L=224]
Description: queuosine biosynthesis protein QueC [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-51  172.8   0.1    7.7e-51  172.6   0.1    1.0  1  QueC             Queuosine biosynthesis protein QueC
    2.1e-06   27.6   0.0      3e-06   27.2   0.0    1.1  1  Asn_synthase     Asparagine synthase
     0.0016   17.8   0.1     0.0021   17.4   0.1    1.1  1  Arginosuc_synth  Arginosuccinate synthase
     0.0039   16.8   0.1      0.011   15.3   0.0    1.7  2  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.019   14.1   0.0      0.024   13.7   0.0    1.2  1  NAD_synthase     NAD synthase
       0.06   13.2   0.1        3.2    7.7   0.0    3.0  4  DUF1737          Domain of unknown function (DUF1737)
       0.13   12.0   0.0       0.24   11.1   0.0    1.4  1  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   0.1     3e-54   7.7e-51       1     209 [.       3     214 ..       3     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 3e-54
                 EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGS..CGGG-----------...--------TTH CS
        QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelg..gsaLtdeeievpkeeleeeelpntfVpaR 97 
                 kav++lSGGlDS+ +++  +k+g++++ +tf Ygqr+++e++aak+iak l+++ehkild+ ++kel   ++ Lt++++++p+     +   +  Vp R
  AJA93240.1   3 KAVIILSGGLDSA-CMVSYLKKGYQLYGITFAYGQRASEEIKAAKRIAKLLKLKEHKILDIGFMKELYgdSNVLTSTKKKMPS-----TFEYSIVVPIR 95 
                 79**********8.5566677789*******************************************8334557777777777.....5556789**** PP

                 HHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH........HTS--EEE-TTT.T--HHHHHHHH.HHTTHHHHH-B-STTS CS
        QueC  98 NliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg........edkkieieaPli.dlsKaeivklg.kelgvpleetlsCYeg 186
                 N+ifls+a+++a +l+ae +++G+++ d + YPDcr+ef +++++aln g          k+i+i  P   ++sK++ +k g kelg ++ +t+sCY +
  AJA93240.1  96 NAIFLSIATAWAFTLNAELVAYGAQKGD-TKYPDCRPEFTRKIQTALNQGeydgiknkIRKEIKIWSPYSeNISKSDLIKKGyKELGNEIFKTWSCYLS 193
                 ****************************.89************************9987899******97369******9985789************9 PP

                 .-BTTTTSSSHHHHHHHHHHHHH CS
        QueC 187 eeegkaCgeCdaCalRkkgfeea 209
                 ++   +Cg+C++C+ Rk +f++a
  AJA93240.1 194 GK--VQCGKCESCNNRKIAFAKA 214
                 55..59**************986 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   1.2e-09     3e-06      22      77 ..       6      59 ..       2      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.2e-09
  Asn_synthase 22 alLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtel 77
                  + LSGGlDS+  ++++++  +    tF+ g   ++s+e+k+ak++a+ l+++ +++
    AJA93240.1  6 IILSGGLDSACMVSYLKKGYQLYGITFAYGQ--RASEEIKAAKRIAKLLKLKEHKI 59
                  68****************9976666666666..******************98765 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   8.1e-07    0.0021       2     113 ..       6     119 ..       5     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.1e-07
  Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGqe.eedldevkekalklgavksvvvDa...keefvedyifpaikanalYedrYllgtalaRP 91 
                      +  sGGlD ++++++lk+ ++     ++   Gq  +e+++++k+ a+ l  +++ + D+   ke + +  ++++ k +     +Y ++  +   
       AJA93240.1   6 IILSGGLDSACMVSYLKKGYQ--LYGITFAYGQRaSEEIKAAKRIAKLLKLKEHKILDIgfmKELYGDSNVLTSTKKKMPSTFEYSIVVPIRNA 97 
                      567**************9885..555555668762599********999999999999644356666677888888777777778888887777 PP

  Arginosuc_synth  92 liakklvevakkegaeavahGc 113
                      +      + a   +ae va+G+
       AJA93240.1  98 IFLSIATAWAFTLNAELVAYGA 119
                      7777777777778888888776 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.4e-06     0.011       5      60 ..       3      56 ..       1     119 [. 0.81
   2 ?   -1.1   0.0      0.47   1.2e+03      45      80 ..     149     185 ..     138     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.4e-06
        ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyq 60
                k++ +lSgG+DS       lk+G +   +++  +   + e+i+  +++a+ll   +
  AJA93240.1  3 KAVIILSGGLDSACMV-SYLKKGYQLYGITFA-YGQRASEEIKAAKRIAKLLKLKE 56
                7999********8654.468***********5.88899999999999*99987544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.47
        ThiI  45 aiekveklaellaeyqtsl.evklvvvdfkevlkeil 80 
                  ++k++k  ++++ y+ ++ +  l+   +ke+ +ei 
  AJA93240.1 149 IKNKIRKEIKIWSPYSENIsKSDLIKKGYKELGNEIF 185
                 5789999999999998764256777777877777775 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.5e-06     0.024      19      88 ..       2      69 ..       1     105 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.5e-06
                  SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-.--HHHHHHH CS
  NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkti.dikpivraf 88
                  k++v+ lSGG+DS+      +k     +  ++ +   +   e++++a+ +a+ l+++ ++i di  + + +
    AJA93240.1  2 KKAVIILSGGLDSACMVSYLKKGY---QLYGITFAYGQRASEEIKAAKRIAKLLKLKEHKIlDIGFMKELY 69
                  789999*******97555555555...89******999999************999877653676555555 PP

>> DUF1737  Domain of unknown function (DUF1737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0012       3.2      22      31 ..      20      29 ..      17      46 .. 0.81
   2 ?   -2.6   0.0       2.1   5.3e+03      28      40 ..      67      79 ..      67      82 .. 0.76
   3 ?    1.6   0.0       0.1   2.6e+02      14      26 ..     132     144 ..     128     144 .. 0.92
   4 ?   -2.8   0.0       2.4   6.1e+03      21      31 ..     171     181 ..     170     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
     DUF1737 22 aLneGWqlyG 31
                +L++G+qlyG
  AJA93240.1 20 YLKKGYQLYG 29
                8********9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
     DUF1737 28 qlyGspsitfdga 40
                +lyG+  +++  +
  AJA93240.1 67 ELYGDSNVLTSTK 79
                6999999988777 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.1
     DUF1737  14 efcerVtqaLneG 26 
                 ef  +++ aLn+G
  AJA93240.1 132 EFTRKIQTALNQG 144
                 799*********9 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.4
     DUF1737  21 qaLneGWqlyG 31 
                 + +++G++ +G
  AJA93240.1 171 DLIKKGYKELG 181
                 56899999777 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.6e-05      0.24       2      50 ..       4      48 ..       3      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.6e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHH CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelv 50
                +++ +SgGlDS +++  l+k  +     l  i++ +g r +e  + a+ +
  AJA93240.1  4 AVIILSGGLDSACMVSYLKKGYQ-----LYGITFAYGQRaSEEIKAAKRI 48
                57889*************99855.....6777778887732333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1633.30
//
Query:       AJA93241.1  [L=236]
Description: PAC2 family protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-28   98.6   0.0    5.8e-28   98.4   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   3.2e-32   5.8e-28       1     211 [.      20     222 ..      20     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 3.2e-32
                 EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEE.TTT.SEEEEEEE...E-HSCHHHHHHHHHHHHHHHT CS
        PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyak.dsgsrdllvlqg...repilqyeefakalldwaeel 95 
                 L+ Gfp+ G    +a++ Li++ ++e  + ids+  +p     p+ ++++g +    r++++ d    ++ ++ +    +  ++  + a+ +ldwaee 
  AJA93241.1  20 LVNGFPSSGITSAIATESLINTSNFELQANIDSEK-FP-----PISVIKNGMPNYATRIFVNrD---LKVGIFSSfltLDVTMHR-TAARMMLDWAEEK 108
                 789********************************.**.....********999*****99977...99******9644444444.58999******** PP

                 TESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT.....-CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHH CS
        PAC2  96 gvkevvvLggldageradvphtrpekvtgaatdeelleel.ees.....eyggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskl 188
                 +++++v  +++    ++       ++v+g+a++ + + +l e +     ++++i gi+g+Ll+++++rg ++++ll+++++++pd ka+a l e +sk+
  AJA93241.1 109 KCSTIV--SSITVKGSN------DVEVFGVASTGNARGKLvE-NgitmvDHATIPGISGILLNEGASRGQDVIVLLVSSNKEIPDFKATANLCETFSKI 198
                 ******..899876664......459***********99955.3477899************************************************* PP

                 H.T---HCHHHHHHHHHHHHHHHH CS
        PAC2 189 l.glevdtedLeedaeeleeqlee 211
                 + g+++++++Le++++ +eeql++
  AJA93241.1 199 IpGISCNMTKLENESKIIEEQLQQ 222
                 *9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1715.05
//
Query:       AJA93242.1  [L=348]
Description: tyrosine--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-42  144.6   0.0    5.2e-42  144.2   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2   0.0   2.9e-46   5.2e-42       3     291 ..      32     326 ..      30     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 2.9e-46
                   HS--EEEEEEETSSS-BGGGHHHH.HHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTEEEEETHHHHTTH. CS
  tRNA-synt_1b   3 erplrvysGidPTgklHlGylvpl.kklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpekaevvlqsewlehl. 97 
                   +++ + y G + +g lHlG l+++  k+ ++ kag+++++++aD+h++i+d+   +++++ k +++++ a      +++ p  +++v++++ ++++ 
    AJA93242.1  32 NSKPKHYIGLEISGFLHLGSLISTgFKINDFMKAGIDCTVFLADWHTLINDKLGGNLETISKVSKYYADA-----FRLVCP-GVNIVMGTDLYDSKk 122
                   567899*************777773799*************************99***************.....444444.377888888776654 PP

                   HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBST CS
  tRNA-synt_1b  98 elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgl 194
                   e++  l +++k+++l+r ++  +++ r e++e+i l+ ++Yp +qaaDi  l+ d+v  G+DQ+++  l r++ ++++ k     p+++ + ll+gl
    AJA93242.1 123 EYWAELVKFTKHMTLARTMRTLTIMGRSENEEKIDLAKLLYPPMQAADIHSLDLDIVHAGMDQRKIHMLVREIFPKMKWK----VPVAVHHSLLPGL 215
                   9*****************************99*********************************************999....8888888888777 PP

                   TS........SSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC.SHHHHHHH.HHTHHH....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHH CS
  tRNA-synt_1b 195 dG........ekKmSKSagnsaIfLddekesvkkkiqkavtdsde.evekllkl.ktelsn....elierleavsgkkpkreaeellaeevtklvhg 277
                   ++          KmSKS++ns If+  + +++kkki+k  ++ +  e+  +l++ +  ++       ier e+++g+ +++++eel+a++++k++h+
    AJA93242.1 216 TQpkgdstteLGKMSKSDPNSGIFIHNSDDEIKKKINKGWCEEGLtENNPVLEIaRQIVFHeydsISIERPEKFGGNVTYNSYEELEADFAQKNLHP 312
                   653333332235**************************99999877444444441333333555479****************************** PP

                   HHHHHHHHHHHHHH CS
  tRNA-synt_1b 278 gdlkkalaealnel 291
                   gdlk+ + e + ++
    AJA93242.1 313 GDLKNTVGEHMVKI 326
                   ******99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2629.73
//
Query:       AJA93243.1  [L=382]
Description: putative NAD(P)H-quinone oxidoreductase subunit H [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-74  250.6   0.0    2.9e-58  197.1   0.0    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.1   0.0   1.6e-62   2.9e-58       2     166 ..     137     302 ..     137     312 .. 0.96
   2 !   51.9   0.0   3.1e-18   5.6e-14     200     271 .]     311     382 .]     304     382 .] 0.96

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 1.6e-62
                     TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHHTT CS
  Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskeealelgl 96 
                     lG+ t+f++   +Re ++dl+e++tGaR+t++y+++GGv++D+p+++ + + + ++++ek+++e+ +++ +n+i+k+Rt++ gvls+e+a++lg+
      AJA93243.1 137 LGHSTMFMWPAGDRELLIDLMEKITGARVTHAYFIPGGVRNDVPANFEDVCLRQVNYFEKRIKEYADIFYDNPILKARTEDTGVLSREDAIRLGT 231
                     69********************************************************************************************* PP

                     -SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--..S-SB- CS
  Complex1_49kDa  97 tGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe.gpvla 166
                     tG vlRasGv+yD+R +epY++Ydeld +  v ++gD+y+R  v    m +S++Ii+qalek+p+ g++ +
      AJA93243.1 232 TGSVLRASGVDYDVRVKEPYDVYDELDVHTNVLKAGDSYARSKVPWLDMLESCNIIRQALEKMPKsGSIRT 302
                     ***************************************************************98566554 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 3.1e-18
                     -SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
  Complex1_49kDa 200 pkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                     + gevy++vE+++G  g+y++s+++ +pyrlk+   sf nl al++llkge+l  ++a++ sl++   e+DR
      AJA93243.1 311 KLGEVYRRVESGRGAAGCYIISKEKPEPYRLKLSVGSFRNLIALPYLLKGEKLGNMPAVYWSLNYWPVEADR 382
                     459******************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2689.78
//
Query:       AJA93244.1  [L=252]
Description: ABC transporter, permease protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-23   82.1  15.5    3.9e-23   82.1  15.5    1.5  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.15   2.7e+03      44      56 ..      52      64 ..      10      74 .. 0.42
   2 !   82.1  15.5   2.2e-27   3.9e-23       1     172 [.      75     233 ..      75     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.15
  BPD_transp_1 44 vilsilghlilpv 56
                  +++ ++g++++ +
    AJA93244.1 52 SLFYGIGTSMWRL 64
                  3333444444443 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 2.2e-27
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                   g++lGi++a  r  ++++ +  l+  l+s+Ps+++++l +       ++g +  ++i++++++a++ v+++++ ++++++ +++eaar +Ga+  q+
    AJA93244.1  75 GMMLGIFMA--RVETVNQTIGSLVLGLQSIPSVAWVPLAI------LWFGLTDSGIIFVTAIGAIFAVTINTYTGVKNIDPSFIEAARNMGAKGGQL 163
                   789******..*****************************......9************************************************** PP

  BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlva 172
                   + ++++P+a+p++itg+   +++++ g + +e+l+s  Glg ll    + +d+s+ +     a+ ++++ + +++
    AJA93244.1 164 VTTILIPAAFPYMITGFKQGWAFAWRGVIGAELLFSFLGLGFLLNVGRQLNDVSQVI-----AMMLVIMGIGILI 233
                   ******************************************************555.....3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1706.78
//
Query:       AJA93245.1  [L=335]
Description: putative bifunctional phosphoglucose/phosphomannose isomerase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-34  117.3   0.0    9.7e-34  116.6   0.0    1.4  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    1.7e-06   27.9   0.3    3.2e-06   27.0   0.1    1.6  2  SIS         SIS domain
  ------ inclusion threshold ------
       0.14   11.7   0.0        2.5    7.5   0.0    2.1  2  ECH_2       Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   1.6e-37   9.7e-34       2     152 .]     191     335 .]     190     335 .] 0.97

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.6e-37
                 G-HHHHHHHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........HHHHHHHHTTTS CS
  bact-PGI_C   2 knpakqlAlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkraeivkelaeerg 100
                 +n + +lA+++++ +p+iy   + l++aA+Rfkn l+en+K++++++ + ea hn iv++    e+k++++ +l+r +++  ++k+r +++ e++ +++
  AJA93245.1 191 DNTSLELAKWIND-IPLIYY-PWGLQSAAIRFKNSLQENSKMHVITEDVIEACHNGIVAW----EKKSKIKPILIRGKDDFIKTKERWQVLIEFFDKEN 283
                 788999*****98.******.***************************************....89**********88889****************** PP

                 SEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH.. CS
  bact-PGI_C 101 vrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKeel 152
                 +++ e+++  ++ l+++++li+l+D+ S+y  +l+++DP+pv +Id++K++l
  AJA93245.1 284 IEFFEINSISGNILSKIVNLIFLFDYCSIYHGVLNNIDPSPVRSIDYIKNKL 335
                 *************************************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   5.4e-10   3.2e-06       6      88 ..      42     119 ..      37     162 .. 0.80
   2 ?   -3.7   0.0       1.7     1e+04      22      42 ..     219     239 ..     214     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.4e-10
                 SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEES CS
         SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITd 88 
                 +++++ G+G s++i++ ++  l +  +i+v  ++ +     + +++d++ lv+  s sg+t++++a +e ak+ +a+i a+ +
  AJA93245.1  42 NHVVFSGMGGSGSIGDVISSIL-SKENIHVTTVKGYH----IPNNLDKNSLVVTTSISGNTRETLAILENAKKTDAHIAAFSS 119
                 89********************.67778888888777....3448*********************************99874 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                 HHHHHHHHHHTSEEEEEEHHH CS
         SIS  22 elalkleeiggivvevedase 42 
                  ++  l+e ++++v  ed  e
  AJA93245.1 219 RFKNSLQENSKMHVITEDVIE 239
                 566666666677766666555 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.02   1.2e+02      47      62 ..     115     130 ..      91     180 .. 0.85
   2 ?    7.5   0.0   0.00042       2.5       6      45 ..     224     263 ..     221     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.02
                 SECE--B--HHHHHHH CS
       ECH_2  47 kafCAGgDvralyeaa 62 
                  af++GgD++++ +++
  AJA93245.1 115 AAFSSGGDIENFCSKN 130
                 49*******9988765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00042
                 E--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESS CS
       ECH_2   6 LnrpkalNaLslemvralkealkewekddevklvvlkgag 45 
                 L+  +++++++ ++++a ++ + +wek++++k ++++g+ 
  AJA93245.1 224 LQENSKMHVITEDVIEACHNGIVAWEKKSKIKPILIRGKD 263
                 788999********************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2289.87
//
Query:       AJA93246.1  [L=128]
Description: hypothetical protein T478_0754 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 955.85
//
Query:       AJA93247.1  [L=390]
Description: glucose/sorbosone dehydrogenase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-83  280.7   0.1    2.1e-83  280.4   0.1    1.1  1  GSDH      Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
      0.034   14.5   0.1        3.2    8.1   0.0    3.3  2  DUF5122   Domain of unknown function (DUF5122) beta-propeller


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.4   0.1   2.3e-87   2.1e-83       1     328 [.      32     340 ..      32     345 .. 0.93

  Alignments for each domain:
  == domain 1  score: 280.4 bits;  conditional E-value: 2.3e-87
                 -S-EEEEEE-TTS-EEEEETTTEEEEEE.TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...TTSSEEEEEEEEE-SS..-EEEE CS
        GSDH   1 lehPwslaflpdgrlLvtersGrlrlvkadgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeekggagtavararlsedeaaledl 99 
                 l++Pw++ f+p+g++ ++er+Gr++ +++ g+  + i+++p+   + +gG l++al+p+f+e++ +Y++ ++   e +  +++v ++++++d  +l d+
  AJA93247.1  32 LNNPWEMVFAPNGDIYFSERDGRVWKIENFGEA-KVIQTFPKS-GSYEGGTLGLALDPNFEETKKIYIYQTN--LELEFFQNKVFSFTVDGD--ELVDM 124
                 689*************************99*99.9*****987.7899***********************5..58888899*******999..***** PP

                 EEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE-TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEE CS
        GSDH 100 evifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrlnkdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwes 198
                 +++ +++p      h G+r+afgpd++L++t+Gd+ ++  +qdlss +Gkilr+n+dGs+p+dnpf      +++i+syGhRnpqG+a+++d g L +s
  AJA93247.1 125 QTVIDDIPG--APWHDGGRIAFGPDDKLYITTGDAVNPGWSQDLSSLAGKILRINSDGSIPDDNPFD-----SSAIFSYGHRNPQGIAWNED-GMLVSS 215
                 *********..889****************************************************4.....799****************9.****** PP

                 EE--SSS.....EEEEEE-TT-B--TTT-S......S-.....-S-TTS---SE.EETT---EEEEEEE........TTEEEEEETTTTEEEEEEEEEE CS
        GSDH 199 EhGprgg.....DelnlieaGknYGWplvsygeeYsgkkigesetreglekpvl.vwtpsiapsglafytgdafpewkgdllvggLksqsllrleldeg 291
                 EhGp+g+     De+n+i +GknYGWp v       g+     ++++++ +p++ + ++++apsg++fy++d++++++g++lvg+L+ q+l++l+++++
  AJA93247.1 216 EHGPSGEmgyghDEINVIVKGKNYGWPKVV------GD-----SSDDSFVNPIIhSGEQTWAPSGMIFYNSDKISSLEGKFLVGALRGQHLMVLDVAND 303
                 *****9999999*****************9......33.....67788999987578999************************************99* PP

                 EEEEEEEEEE.ESS-.-EEEEEE-TTS-EEEEE-TTTT CS
        GSDH 292 ekvveeerll.eelgeriRdVeqgpdGalyvltdeedg 328
                 +++ ++e+++  ++g riR  + ++dG ly+lt + d 
  AJA93247.1 304 GSLISAEKMFeGDFG-RIRTAQINSDGVLYLLTANGDN 340
                 ********9956666.****************986554 PP

>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00036       3.2      10      32 ..     161     182 ..     146     182 .. 0.86
   2 ?    2.6   0.0      0.02   1.8e+02      16      32 ..     315     331 ..     302     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00036
     DUF5122  10 GsftsyngssdfalvRLnaDGsl 32 
                 G++  + +s +  ++R+n+DGs+
  AJA93247.1 161 GWSQ-DLSSLAGKILRINSDGSI 182
                 5566.67888999********96 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.02
     DUF5122  16 ngssdfalvRLnaDGsl 32 
                 ++ ++++ + +n+DG l
  AJA93247.1 315 GDFGRIRTAQINSDGVL 331
                 4556999********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2703.20
//
Query:       AJA93248.1  [L=385]
Description: methionine adenosyltransferase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-71  237.8   0.2    5.8e-71  236.9   0.0    1.6  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    5.5e-47  158.9   0.0    2.2e-46  157.0   0.0    2.0  2  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
    9.5e-41  138.5   0.9    3.1e-40  136.8   0.1    2.2  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 
  ------ inclusion threshold ------
       0.15   10.9   1.1       0.98    8.1   0.2    2.3  2  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.9   8.6e+03      65      98 ..     170     204 ..     167     212 .. 0.54
   2 !  236.9   0.0   1.3e-74   5.8e-71       1     138 []     233     372 ..     233     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.9
                      EEEEE-TT-SS-SE.EEEEE-S-BSS-HHHHHHHH CS
  S-AdoMet_synt_C  65 vqlsYaigvaepvs.isvetfgtekvseeeiaeiv 98 
                      v + Y  +  ++++ i ++t+++ ++++eei++ +
       AJA93248.1 170 VSIRYEDDKPKAIEaIVLSTQHSPEITNEEISSQL 204
                      55555555555554144455555567777775443 PP

  == domain 2  score: 236.9 bits;  conditional E-value: 1.3e-74
                      S-TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEEEEE-S-BSS-HHHH CS
  S-AdoMet_synt_C   1 iGgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepvsisvetfgtekvseeei 94 
                      iGgp+gdaGltgrkiivd+Ygg+++hgggafsgKdp+kvDrsa+y++ryvakn+vaagla+++evq++Yaigvaepvs++v+tfgt+k+se++i
       AJA93248.1 233 IGGPHGDAGLTGRKIIVDSYGGMGRHGGGAFSGKDPSKVDRSACYMCRYVAKNIVAAGLADRCEVQVAYAIGVAEPVSLMVNTFGTNKISEDKI 326
                      8********************************************************************************************* PP

                      HHHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--..T-TTS. CS
  S-AdoMet_synt_C  95 aeivkevfdlrpaaiieeldLkkpiykktaayghfgre..elpwek 138
                      +e+v+++fd+rpa+i+e+ldLk+piykktaayghfgr+  e++wek
       AJA93248.1 327 EELVNNNFDMRPAGIVEQLDLKRPIYKKTAAYGHFGRNepEFNWEK 372
                      *************************************98899**97 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.79   3.6e+03      46      71 ..      31      56 ..      20      93 .. 0.64
   2 !  157.0   0.0   4.9e-50   2.2e-46       1     120 []     115     231 ..     115     231 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.79
  S-AdoMet_synt_M 46 eylrpDaKsqvtveYeeelkpvrvdt 71
                     eyl+ D  s+v ve  +++  v v  
       AJA93248.1 31 EYLKGDPNSRVAVETMTTTDFVGVAG 56
                     57777888888887743444444433 PP

  == domain 2  score: 157.0 bits;  conditional E-value: 4.9e-50
  S-AdoMet_synt_M   1 eigAgDqGimfGYAtdeteelmPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistqhdeevsqeklredlkek 94 
                      e+gAgDqG+mfGYA++eteelmPlpillahkl+++l+++rk+++l++ rpD+Ksqv+++Ye + kp+ ++++v+stqh++e+++e+++++l+e+
       AJA93248.1 115 EQGAGDQGLMFGYASNETEELMPLPILLAHKLTKKLTDVRKNNQLPWARPDGKSQVSIRYE-DDKPKAIEAIVLSTQHSPEITNEEISSQLIEH 207
                      69**********************************************************5.88****************************** PP

  S-AdoMet_synt_M  95 vikkvlkeelldekktkllinptGkF 120
                      vik+v+  +l +e ++k+++nptGkF
       AJA93248.1 208 VIKPVC-GDLWNE-NIKIHVNPTGKF 231
                      ******.777766.6**********9 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8   0.1     7e-44   3.1e-40       1      99 []       4     102 ..       4     102 .. 0.99
   2 ?   -0.7   0.1      0.51   2.3e+03      18      55 ..     279     316 ..     277     383 .. 0.60

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 7e-44
  S-AdoMet_synt_N   1 kylftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittkakvdiekivrevikeigYekeelgfdaktcevlval 94 
                      +ylftsesV+eGHPDkv+d isd+ild++lk dp++rva+et++tt++v vage+t+ka++die+++r++i+eigY++ +l+fd ++cev+v+l
       AJA93248.1   4 NYLFTSESVTEGHPDKVCDMISDSILDEYLKGDPNSRVAVETMTTTDFVGVAGEVTSKASFDIESVIRKTITEIGYDNPDLKFDSHSCEVMVKL 97 
                      69******************************************************************************************** PP

  S-AdoMet_synt_N  95 eeqsp 99 
                      + qsp
       AJA93248.1  98 DPQSP 102
                      ****7 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
  S-AdoMet_synt_N  18 adqisdaildailkedpkarvacetlvttglvvvagei 55 
                      +  ++ +i+ a l++  + +va  + v++ + +++  +
       AJA93248.1 279 CRYVAKNIVAAGLADRCEVQVAYAIGVAEPVSLMVNTF 316
                      66666666666666666666666555554433333333 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2   0.00022      0.98      25      44 ..      13      32 ..       6      61 .. 0.80
   2 ?    1.4   0.1     0.025   1.1e+02      96     172 ..      60     136 ..      44     337 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00022
                     -TTSHHHHHHHHHHHHHHHH CS
  AdoMet_Synthase 25 GiGHPDsiaDgiaeavsral 44
                       GHPD+++D i++++  ++
       AJA93248.1 13 TEGHPDKVCDMISDSILDEY 32
                     57************997766 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.025
                      .EEE--HHHHHHHHHHHHHHHH-SS--TTTS.EEEEEEEEEEEEHHHHHHCH-SS..-BESSSEEEEEEES--HHHHH CS
  AdoMet_Synthase  96 egekipveeialeaakeylkenlraldlekd.vivdvklgkgsadLkdvferkkkevplaNDtSfgvgyaplselekl 172
                      ++ ++++e+++ +++ e   +n + l+++++   v vkl + s  + + ++ ++++ + a D  +  gya   + e +
       AJA93248.1  60 SKASFDIESVIRKTITEIGYDN-PDLKFDSHsCEVMVKLDPQSPHISQGVTGTDEKEQGAGDQGLMFGYASNETEELM 136
                      5666777777777777744444.4466665425677777777777765444444545778888888888765544432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2760.05
//
Query:       AJA93249.1  [L=572]
Description: glutamate--tRNA ligase [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-75  254.1   0.0    2.2e-75  253.5   0.0    1.3  1  tRNA-synt_1c     tRNA synthetases class I (E and Q), catalyti
    7.5e-27   94.3   0.7    6.8e-26   91.2   0.0    2.3  2  tRNA-synt_1c_C   tRNA synthetases class I (E and Q), anti-cod
  ------ inclusion threshold ------
       0.12   12.3  10.1        4.3    7.3   0.2    4.2  4  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
        5.7    7.5   7.9         41    4.7   2.3    3.4  4  PP2C_C           Protein serine/threonine phosphatase 2C, C-t


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.5   0.0   4.9e-79   2.2e-75       2     313 ..     103     407 ..     102     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 253.5 bits;  conditional E-value: 4.9e-79
                   -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE- CS
  tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvce 98 
                   + tRf+P P+Gy+HiGhakaa+++  +Ak ++Gk+ilR+eDT+p  e  e+ ++i+  ++wlgik+ + + + sd +d+l+k a+++ik+  AYvc 
    AJA93249.1 103 IITRFPPAPNGYPHIGHAKAAVISEEYAKMHGGKLILRFEDTNPGTERLEYYAAIKVGMDWLGIKY-DSVEHVSDNLDILYKKADQIIKSNDAYVCT 198
                   78****************************************************************.66**************************** PP

                   STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHH CS
  tRNA-synt_1c  99 ctkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvid 194
                   c+++ + + r+e   +++k  ++++een kl+++   ++ +++++a +R++ +++s  +++rD+   ri+ +    h +  +k+++ PtYdfa +i 
    AJA93249.1 199 CSQDSISKDRRE--MIECKCTKQSIEENEKLWHKMHDEKGFKEGQALLRFRGNMQSGnTTMRDPALFRINTKR---HARQEQKYKVWPTYDFAGIIF 290
                   **********99..6666689***********77777889***************999***************...********************* PP

                   HHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCC CS
  tRNA-synt_1c 195 DaleeithvlrteefldntpkyiwllealglevppfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreel 291
                   D++ +++h++r +ef+ +++ +  +l++lg+e+ +fi+ + rl le+  +SK  l+ l+++ +v   dd+r+++l++lrr+G+ pe+ ++++ + +l
    AJA93249.1 291 DSISKVSHAMRSKEFELRKELHHTILDKLGMEKSEFIF-FGRLDLEGMPVSKSALKPLIENGKVPWYDDPRLPTLEGLRRRGIRPEAVKKFVLSLGL 386
                   ********************************777765.89******************************************************** PP

                   CSSS.EEEEHHHHHHHHHHHHH CS
  tRNA-synt_1c 292 iksfdlnresksleafdrkkLe 313
                   +k++ +     sleaf++k ++
    AJA93249.1 387 TKND-TVSPFASLEAFNKKIID 407
                   ****.8889999*****99775 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.077   3.4e+02      62     104 ..     187     228 ..     174     234 .. 0.67
   2 !   91.2   0.0   1.5e-29   6.8e-26       3     172 ..     412     560 ..     410     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.077
  tRNA-synt_1c_C  62 eevrLkelynikveevekdesgevte.lkleydgesleearkkk 104
                     + ++  ++y+ ++++ +   s++  e +++++ ++s+ee++k  
      AJA93249.1 187 QIIKSNDAYVCTCSQDSI--SKDRREmIECKCTKQSIEENEKLW 228
                     556667889999965532..333333477999999999987654 PP

  == domain 2  score: 91.2 bits;  conditional E-value: 1.5e-29
  tRNA-synt_1c_C   3 RymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveevekdesgevtelkleydgesl 97 
                     R+ +V++p +++++nlp   + ele+p+hp   +lg+r+v+++++++i+ eDa++lk+ge +rL +++++k+ e      g+  +l +e+ +e+ 
      AJA93249.1 412 RLHMVRKPKEMKVTNLP---SNELELPNHPT-IDLGKRTVTVNDSVMIDGEDANELKKGESIRLLGIGIFKIVED-----GS--NLTAEFISENA 495
                     8999************9...689********.8***************************************654.....33..34477887666 PP

  tRNA-synt_1c_C  98 eearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepalanlkkgdivQfeRiGyfr 172
                        ++ +++i+Wv+  e+++ ++ + d+Lf     + +++n+dslk++ eg++e+a  +lk gd +Qf R+Gy+r
      AJA93249.1 496 ---ENIEKKIQWVA-GEPIKLKIIVPDQLF-----FGETFNEDSLKEI-EGYVEQAYLELKDGDEIQFIRFGYCR 560
                     ...46777******.69****9*******7.....3588*******96.************************98 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.054   2.4e+02       6      29 ..      55      78 ..      51      84 .. 0.84
   2 ?   -0.3   0.0      0.22     1e+03       4      23 ..     171     190 ..     171     192 .. 0.90
   3 ?    7.3   0.2   0.00095       4.3      31      64 ..     461     497 ..     458     501 .. 0.77
   4 ?    6.7   0.1    0.0015       6.7      16      58 ..     528     570 ..     525     572 .] 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.054
  HU-CCDC81_bac_2  6 siaeaegisyeeAlqkiekeveel 29
                      ++e ++is ee +++ie+   el
       AJA93249.1 55 VVSEINQISLEEQQKEIEEKFPEL 78
                     688999************987776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
  HU-CCDC81_bac_2   4 ansiaeaegisyeeAlqkie 23 
                      ++++++  +i y++A q i+
       AJA93249.1 171 VEHVSDNLDILYKKADQIIK 190
                      6899************9997 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.00095
  HU-CCDC81_bac_2  31 qeLeeegrveleniGeLslneegk...leFepseagn 64 
                      +eL++++++ l +iG +++ e+g+    eF  ++a+n
       AJA93249.1 461 NELKKGESIRLLGIGIFKIVEDGSnltAEFISENAEN 497
                      69*****************999852224566655555 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0015
  HU-CCDC81_bac_2  16 eeAlqkiekeveelkqeLeeegrveleniGeLslneegkleFe 58 
                      e+ l++ie +ve+   eL+++ ++++ + G  +  + ++++F+
       AJA93249.1 528 EDSLKEIEGYVEQAYLELKDGDEIQFIRFGYCRKESTHQVIFT 570
                      67899*************************9999999999997 PP

>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2   5.3e+03      15      40 ..      21      45 ..      15      66 .. 0.50
   2 ?    4.7   2.3    0.0092        41      22      65 ..      65     110 ..      37     130 .. 0.73
   3 ?   -3.0   0.1       2.3     1e+04      28      57 ..     204     234 ..     201     236 .. 0.72
   4 ?    4.3   0.0     0.012        56       5      37 ..     288     320 ..     288     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
      PP2C_C 15 eeavkkEkeldekleervkeiiekee 40
                +e ++++k + +k+  +v e+ + + 
  AJA93249.1 21 HEGQTRDKTILAKIMGNVPELRQ-KA 45
                44444445555555555555544.22 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0092
      PP2C_C  22 keldekleervkeiie.keekkeeldlekvlkvLa.sedipnlPpG 65 
                 +e ++++ee+  e++e k+ek+++ +l   lk+++ +e i+++Pp 
  AJA93249.1  65 EEQQKEIEEKFPELLEvKKEKPQKESLLPALKNIEgKEIITRFPPA 110
                 577899**********544455555555555555555559999984 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.3
      PP2C_C  28 leervkeiie.keekkeeldlekvlkvLase 57 
                 + +  +e+ie k +k++  + ek+ + +++e
  AJA93249.1 204 ISKDRREMIEcKCTKQSIEENEKLWHKMHDE 234
                 6667788888777777777778888887766 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.012
      PP2C_C   5 vafpgaPkvseeavkkEkeldekleervkeiie 37 
                 ++f+++ kvs+ + +kE el ++l++ + + + 
  AJA93249.1 288 IIFDSISKVSHAMRSKEFELRKELHHTILDKLG 320
                 78**********************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3770.67
//
Query:       AJA93250.1  [L=65]
Description: hypothetical protein T478_0243 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 481.88
//
Query:       AJA93251.1  [L=230]
Description: hypothetical protein T478_1379 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.5   0.9        1.4   10.0   0.2    2.3  2  SRC-1     Steroid receptor coactivator


Domain annotation for each model (and alignments):
>> SRC-1  Steroid receptor coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   7.8e-05       1.4      35      71 ..      37      71 ..       8      77 .. 0.66
   2 ?    1.5   0.0     0.037   6.6e+02      56      70 ..     124     138 ..     104     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.8e-05
       SRC-1 35 dssagvtspssgvssssssssasssssLqEkHkILHk 71
                + +  +    s +++s+s++ ++ s+s+ Ek kIL k
  AJA93251.1 37 QRAIIHHL--SNSTNSASKTRTAISQSIAEKNKILWK 71
                33333333..34447777778889***********88 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.037
       SRC-1  56 asssssLqEkHkILH 70 
                 + +  s+ Ek kIL 
  AJA93251.1 124 SLAIDSMSEKKKILK 138
                 556789*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1742.64
//
Query:       AJA93252.1  [L=398]
Description: tryptophan synthase, beta subunit [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-47  161.1   1.0    4.4e-47  160.9   1.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.9   1.0   2.5e-51   4.4e-47       3     294 .]      54     375 ..      52     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 160.9 bits;  conditional E-value: 2.5e-51
                 GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHH.HHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-...HHHHHH CS
        PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgae.yllarlkegtgaktvveassGNhgralAaaaallGlkvtivvpadas...pekval 96 
                 ++ +pTP+  +++l+k +g++ ++lK+E+l ++g++K++     +l++ + g +++ ++e+++G+hg+a+A+a+a lGlk++i++   ++   +++v +
  AJA93252.1  54 YAGRPTPIYFARNLTKTVGGAkIYLKREDLLHGGAHKINNTLgQALLAKRMG-KKRIIAETGAGQHGVATAMACASLGLKAEIYMGYVDTirqKQNVFR 151
                 6789***********************************9995555556666.9999999999*********************8888886668***** PP

                 HHHTT-EEEEECCHHHHHHHHHHHHHHH.....STTCEE--TTT..SHH..HHHH.HHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT- CS
        PALP  97 lrllGaevvevggdydeavaaaaelaae.....gegaylvsqfd..npt..vieg.ygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdv 185
                 ++llGa+v+ v+++ ++ ++a++e+ ++     +  +yl+ +    +p+   +   ++ ig Ei++q+++ p+av+++vGgG+++ G+  +l +  ++ 
  AJA93252.1 152 MELLGAKVHAVKSGSKTLKDAINEAMRDwitnvDSTYYLLGSAVgpHPYplMVRDfQAVIGVEIKKQMKKIPNAVIACVGGGSNAIGTFYPLID--TNA 248
                 ***********999999999999999999888744455544444464446655555*************************************8..556 PP

                 EEEEEEEC..TTCGGTTCC..S..S.SS..B................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-H CS
        PALP 186 rvigvepe..gsdalarsl..ragrrvtvpvs...............dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregivvep 265
                 ++ig+e+   g+ +  +s+   ag+   ++ +               ++i  gl+ + +++++  l d+   e+ +v+d+e+++a   l r+egi++  
  AJA93252.1 249 KIIGIEAGgkGVKTKLHSAplTAGKKGVLHGMmtylmqdkdgqisetHSISAGLDYPGVGPEHAYLKDENRVEYKAVTDDEVIDAFLILTRTEGIIPAL 347
                 8****998554444444444444444444444888888888888888**********9999999999******************************** PP

                 HHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
        PALP 266 ssaaalaalklreagelkegdrvvviltg 294
                  sa+a+a +  +  +++k+++++vv l+g
  AJA93252.1 348 ESAHAIAHA-IKISKKMKKNESIVVTLSG 375
                 *********.9****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2797.18
//
Query:       AJA93253.1  [L=65]
Description: putative Zn-ribbon RNA-binding protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00012   22.0   4.6    0.00012   22.0   4.6    2.5  3  DUF1610         Domain of unknown function (DUF1610)
    0.00049   20.3   8.0       0.06   13.7   0.2    2.1  2  C1_2            C1 domain
    0.00089   19.7   3.9     0.0012   19.3   3.9    1.2  1  zf-CHY          CHY zinc finger
  ------ inclusion threshold ------
       0.57   10.4   9.7        3.2    8.0   5.5    2.8  2  zf-B_box        B-box zinc finger
        1.8    8.3  15.7         53    3.6   0.3    3.7  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
          3    7.8   9.9          4    7.3   0.6    3.0  3  ZZ              Zinc finger, ZZ type
        4.4    7.6  11.2        6.1    7.1   2.5    2.5  2  zf-AN1          AN1-like Zinc finger
        6.7    6.8   8.9        1.7    8.6   0.1    3.0  3  Gin             Inhibitor of sigma-G Gin
        9.5    6.2  12.8        1.1    9.2   2.0    3.4  3  Nudix_N_2       Nudix N-terminal


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   4.6   5.8e-08   0.00012       1      22 [.      16      37 ..      16      37 .. 0.96
   2 ?   -4.5   2.4         9   1.8e+04       1       4 [.      45      48 ..      45      48 .. 0.63
   3 ?    0.4   0.8      0.34   6.8e+02       1       5 [.      57      61 ..      57      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 5.8e-08
     DUF1610  1 CtSCGaelaprEravvFpCPNC 22
                C  C++ + p+ + v+F+CP+C
  AJA93253.1 16 CNGCNRHIMPGDNNVKFICPEC 37
                778******************* PP

  == domain 2  score: -4.5 bits;  conditional E-value: 9
     DUF1610  1 CtSC 4 
                C SC
  AJA93253.1 45 CGSC 48
                6677 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.34
     DUF1610  1 CtSCG 5 
                C SCG
  AJA93253.1 57 CESCG 61
                88**9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2     3e-05      0.06       7      38 ..       2      37 ..       1      42 [. 0.75
   2 !   10.7   2.4   0.00025       0.5      18      41 ..      42      63 ..      38      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
        C1_2  7 LtlskgedssesfnCsaCgrk...idgff...YsCseC 38
                L l+ ++++ +   C++C r    +  ++   ++C+eC
  AJA93253.1  2 LDLDGNSPKISLPVCNGCNRHimpG--DNnvkFICPEC 37
                55666677777889*******8553..33458****** PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00025
        C1_2 18 sfnCsaCgrkidgffYsCseCdfs 41
                 ++C  C++      Y+C+ C fs
  AJA93253.1 42 IWRCGSCREAA--APYKCESCGFS 63
                589******95..44***99*996 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   3.9   5.8e-07    0.0012      22      73 ..      16      61 ..      10      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.8e-07
      zf-CHY 22 CreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                C+ C +    h +   +  +++c +C  e      C++C++ +a y+C+ C 
  AJA93253.1 16 CNGCNR----HIMPGDNNVKFICPECPDE--LIWRCGSCREAAAPYKCESCG 61
                777776....9999999999******997..8999****************7 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.099     2e+02      24      30 ..      14      20 ..      12      25 .. 0.67
   2 ?    8.0   5.5    0.0016       3.2       4      24 ..      32      51 ..      29      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.099
    zf-B_box 24 plCeeCs 30
                p+C+ C+
  AJA93253.1 14 PVCNGCN 20
                6777772 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
    zf-B_box  4 tkCpeHknkpatlfCedCqqp 24
                 +Cpe++  ++++ C +C++ 
  AJA93253.1 32 FICPECP-DELIWRCGSCREA 51
                5899999.9999999999874 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   9.1     0.051     1e+02      24      51 ..      15      49 ..       4      52 .. 0.64
   2 ?    3.6   0.3     0.027        53      44      52 ..      54      62 ..      49      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.051
  zinc_ribbon_10 24 ICskChsh.....nGlap..keeleevkyrCpkCg 51
                    +C+ C+ h     n++    +e ++e+ +rC +C+
      AJA93253.1 15 VCNGCNRHimpgdNNVKFicPECPDELIWRCGSCR 49
                    67777777444433433355677777777777776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.027
  zinc_ribbon_10 44 kyrCpkCga 52
                     y+C +Cg+
      AJA93253.1 54 PYKCESCGF 62
                    6******96 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.083   1.7e+02       7      12 ..      16      21 ..      14      26 .. 0.80
   2 ?    7.3   0.6     0.002         4       4      27 ..      31      50 ..      28      52 .. 0.89
   3 ?    3.8   0.4     0.025        51       5      12 ..      55      62 ..      51      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.083
                -TTT-S CS
          ZZ  7 CdgCse 12
                C+gC  
  AJA93253.1 16 CNGCNR 21
                999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.002
                -EE-TTT-S..EESSEEEESSSSS CS
          ZZ  4 kytCdgCseapligvRyhclrcsd 27
                k++C +C      +  ++c +c++
  AJA93253.1 31 KFICPECPD----ELIWRCGSCRE 50
                789999999....999******97 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.025
                EE-TTT-S CS
          ZZ  5 ytCdgCse 12
                y+C+ C++
  AJA93253.1 55 YKCESCGF 62
                89999997 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.6     0.013        26       1      19 [.      16      37 ..      16      40 .. 0.76
   2 ?    7.1   2.5    0.0031       6.1       1      20 [.      45      61 ..      44      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
      zf-AN1  1 CsfksCkkkd.....flpfkCryC 19
                C+  +C++++     ++ f C++C
  AJA93253.1 16 CN--GCNRHImpgdnNVKFICPEC 37
                66..89999977665455****99 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0031
      zf-AN1  1 CsfksCkkkdflpfkCryCg 20
                C   sC++    p+kC++Cg
  AJA93253.1 45 CG--SCREAAA-PYKCESCG 61
                55..7999997.*******8 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.045        89      19      28 ..      15      24 ..      12      29 .. 0.87
   2 ?    8.6   0.1   0.00087       1.7      17      28 ..      31      42 ..      28      43 .. 0.87
   3 ?   -1.6   1.2       1.4   2.8e+03      26      26 ..      51      51 ..      45      60 .. 0.47

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                EEHHHHHHHH CS
         Gin 19 ICeeCekkiv 28
                +C+ C++ i+
  AJA93253.1 15 VCNGCNRHIM 24
                7*****9997 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00087
                --EEHHHHHHHH CS
         Gin 17 kfICeeCekkiv 28
                kfIC eC ++++
  AJA93253.1 31 KFICPECPDELI 42
                8******99986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                H CS
         Gin 26 k 26
                +
  AJA93253.1 51 A 51
                2 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0   0.00056       1.1      11      28 ..      20      37 ..      14      38 .. 0.88
   2 ?   -0.3   0.2      0.54   1.1e+03      24      28 ..      44      48 ..      43      51 .. 0.75
   3 ?    2.4   0.3     0.075   1.5e+02      25      30 ..      57      62 ..      55      62 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00056
                EEE--TT-SS-EEEETTT CS
   Nudix_N_2 11 elripdgDnreRlvCpaC 28
                +++i +gDn   ++Cp C
  AJA93253.1 20 NRHIMPGDNNVKFICPEC 37
                578999************ PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.54
                EETTT CS
   Nudix_N_2 24 vCpaC 28
                +C +C
  AJA93253.1 44 RCGSC 48
                58888 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.075
                ETTTTE CS
   Nudix_N_2 25 CpaCgt 30
                C++Cg+
  AJA93253.1 57 CESCGF 62
                888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 461.08
//
Query:       AJA93254.1  [L=99]
Description: ribosomal protein L21e [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-19   68.6   1.9    4.4e-19   68.2   1.9    1.1  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   1.9   2.4e-23   4.4e-19       3      99 ..       9      97 ..       4      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.4e-23
                    -S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETTE..EEEEEE-GGGEEE- CS
  Ribosomal_L21e  3 nskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvggkileKriivriehlkks 99
                    +s+g+++++r++++k    kg   +s +lrey++Gd+  ++id+s +kg ph+ryhGk+g v +v++r   v++ +k+g+k   K++i+r +h+k++
      AJA93254.1  9 RSHGFKHKSRSVMTK----KGPRGVSFLLREYNVGDRALVQIDSSQHKGLPHRRYHGKVGLVTEVGRRH--VVLDVKLGEK--SKTLITRLDHIKPF 97
                    789999999999885....89999**************************************8888875..68899*****..************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 725.04
//
Query:       AJA93255.1  [L=279]
Description: apurinic endonuclease (APN1) [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-35  120.9   0.0    1.1e-34  119.7   0.0    1.5  2  AP_endonuc_2    Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.016   14.9   0.2       0.18   11.5   0.1    2.5  3  DUF5537         Family of unknown function (DUF5537)
      0.018   13.3   0.0      0.026   12.8   0.0    1.2  1  ACC_central     Acetyl-CoA carboxylase, central region
       0.14   11.8   0.0        1.6    8.3   0.0    2.0  2  Ala_racemase_N  Alanine racemase, N-terminal domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   2.5e-38   1.1e-34       2     210 .]      18     237 ..      17     237 .. 0.95
   2 ?   -1.7   0.0      0.36   1.6e+03     111     136 ..     240     265 ..     240     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.5e-38
                   HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGB CS
  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraielaaaLGapllvlhpGtag 95 
                   + a e G  ++++f+r+++++ ++  + +e++++++ ld+ ++   + ++++ +   +    + +  e+s++ + ++++++ +LG+p+lv+h G   
    AJA93255.1  18 DNAVERGCSAFQVFTRSPRSWFAKdlDLDEAKAYKEKLDASDIDRMATCAHMPYLPNLSTPED-EgYEKSIKSMIEEVKRCDKLGIPYLVTHLG--- 110
                   678999**************************************9999999999997765344.25999*************************... PP

                   CTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTT.EEEEEEHHHHHHH......TTTHHHHHHHHHGG. CS
  AP_endonuc_2  96 agpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspn.vgvclDtgHllia......eedvddalraladr. 182
                   ++ +++ee  ++rl ++lne+a+   k++v ++lE++ag+ ++ g   +++a+++ + ++ + +gvclDt+H++ a      ++ v ++++++++  
    AJA93255.1 111 SHKGSGEENGIKRLTSALNEVAKT--KADVIILLENTAGQKNSVGSdfKQFAEIFAQCKPAKkFGVCLDTCHAFVAgydlrtKAAVKKTMKEFDETv 205
                   ************************..****************9999************99999********************************** PP

                   ....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
  AP_endonuc_2 183 ....ikhvHikDakgdlgagrdrhvpigeGei 210
                       +k++H++D+kg+l+++ drh  ig Gei
    AJA93255.1 206 glknLKILHLNDSKGELNSNLDRHNHIGLGEI 237
                   ******************************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                   HHHHHHHHHHHHHTSEEEEE--TTTT CS
  AP_endonuc_2 111 eslneladyaekegvklalEtlagsg 136
                   e+l e++++  k+ + ++lEt   ++
    AJA93255.1 240 EGLGEIVKIMNKNKIPIVLETPIDDT 265
                   67889999999999999999865555 PP

>> DUF5537  Family of unknown function (DUF5537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.1e-05      0.18      34      68 ..      44      78 ..      24      99 .. 0.73
   2 ?    0.8   0.0     0.079   3.6e+02      50      91 ..      91     132 ..      82     157 .. 0.68
   3 ?   -1.0   0.0      0.27   1.2e+03      19      54 ..     175     211 ..     164     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
     DUF5537 34 vletqkikkeyttafgleelkeclkmpylpelqsc 68
                 l+  k  ke   a  ++ +  c +mpylp+l + 
  AJA93255.1 44 DLDEAKAYKEKLDASDIDRMATCAHMPYLPNLSTP 78
                467788999999*******************9653 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.079
     DUF5537  50 leelkeclk..mpylpelqscskslsssplevpkrllraeaevs 91 
                 +ee+k c k  +pyl     ++k   s   +  krl  a  ev+
  AJA93255.1  91 IEEVKRCDKlgIPYLVTHLGSHK--GSGEENGIKRLTSALNEVA 132
                 79999996622688876544444..3445556677777777765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.27
     DUF5537  19 sldscllfesswk.kavletqkikkeyttafgleelk 54 
                  ld+c  f + +  ++    +k  ke+  + gl++lk
  AJA93255.1 175 CLDTCHAFVAGYDlRTKAAVKKTMKEFDETVGLKNLK 211
                 5777777777764233445677888999999999887 PP

>> ACC_central  Acetyl-CoA carboxylase, central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.8e-06     0.026      28      89 ..     164     227 ..     150     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-06
                  TTSCHHHHHHHHCHHHHHHHHT-S..HTTTCCHHHHHHHHHHTSTCHHHHHHHHHHCCCTTTS- CS
  ACC_central  28 vgekphqrlaallsaleniLaGYd..nqakiketlkeLievLrdpeLPllelqevlsalsgrlP 89 
                   + kp++++  +l++++++ aGYd  ++a +k+t+ke+ e++  ++L +l l++    l++ l+
   AJA93255.1 164 AQCKPAKKFGVCLDTCHAFVAGYDlrTKAAVKKTMKEFDETVGLKNLKILHLNDSKGELNSNLD 227
                  4569*********************9999*********************99999888888776 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00037       1.6     134     197 ..      87     147 ..      82     156 .. 0.85
   2 ?    3.7   0.0    0.0089        40     103     202 ..     128     225 ..     126     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                     HHHHHHHHHHTTTEEEEEEE-S-SSTTSTSHHHHHHHHHHHHHHHHHHHTTGGGSEEEEESHHH CS
  Ala_racemase_N 134 leellealaalpglrleglmtHfasadepdeeteaqlarfeealeelekaglrppvvslanSaa 197
                     +++++e+++++++l +  l+tH++s +   +  e+ ++r++ al+e++k   ++ ++ l n+a+
      AJA93255.1  87 IKSMIEEVKRCDKLGIPYLVTHLGSHKG--SGEENGIKRLTSALNEVAK-TKADVIILLENTAG 147
                     67899********************997..36888************74.45557888888886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0089
                     HHHHHHHTTS-EEEEEEBESSSS.SSSBSCHHHHHHHHHHHHTTTEEEEEEE-S-SST..TSTS.HHHHHHHHHHHHHHHHHHHTTGGGSEEEEE CS
  Ala_racemase_N 103 laaaareagkplrvhlkidtgmg.RlGftpeeleellealaalpglrleglmtHfasa..depd.eeteaqlarfeealeelekaglrppvvsla 193
                     l+++a+ ++  + ++l+   g     G + ++++e++++++ ++++ ++  + H   a  d ++ +++++ ++ f+e +        + ++++l 
      AJA93255.1 128 LNEVAK-TKADVIILLENTAGQKnSVGSDFKQFAEIFAQCKPAKKFGVCLDTCHAFVAgyDLRTkAAVKKTMKEFDETVGLK-----NLKILHLN 216
                     566664.344444444444454467899999************999999999999999553333446666777777776533.....57799999 PP

                     SHHHHHHSG CS
  Ala_racemase_N 194 nSaaillaa 202
                      S + l+ +
      AJA93255.1 217 DSKGELNSN 225
                     999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2067.06
//
Query:       AJA93256.1  [L=150]
Description: ASCH domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-12   48.4   0.1    1.8e-12   47.8   0.1    1.3  1  ASCH            ASCH domain
  ------ inclusion threshold ------
      0.087   12.7   1.2       0.25   11.3   0.7    2.0  2  Phage_integr_3  Archaeal phage integrase
       0.15   11.8   0.0       0.25   11.1   0.0    1.4  1  Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.1   3.1e-16   1.8e-12       1     105 [.       4     110 ..       4     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 3.1e-16
                 EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCC................CTSEEEEEEEEEEEEEE.HHHHHHHHHCHCC---HCHHHHHH CS
        ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalk................ptgralgivevtkvevk.pfeevteehalkegesleewrevh 82 
                 ls++q++a+li++GkKt+e r+w+++    rg++l++aa +                 tg ++g+v++++v+++ + +e++++ ++            h
  AJA93256.1   4 LSICQPFAELIIQGKKTIELRKWNTK---FRGEFLVHAAKNileddckrmkispkavTTGAIIGKVNLVDVKKYdSDKELKADKKK------------H 87 
                 799***********************...99******9999******************************999777777666665............7 PP

                 HCCHHHHHCCEEEEEEEEEEEEE CS
        ASCH  83 eefyeeeseeyedelvvveefel 105
                 +++ ++ +++y ++l  ++++++
  AJA93256.1  88 YSISDNTKNKYGFILEKPKKLRV 110
                 77777777766666666666655 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   8.9e+02      65      96 ..      26      58 ..      15      67 .. 0.72
   2 ?   11.3   0.7   4.1e-05      0.25      32      86 ..      58     113 ..      36     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                    E-SSS-EEEEEEESS---.....--B--HHHHH CS
  Phage_integr_3 65 lekgeKkafyiylptela.kelerlelseeavk 96
                    ++ + + +f ++  +++     +r+++s +av+
      AJA93256.1 26 WNTKFRGEFLVHAAKNILeDDCKRMKISPKAVT 58
                    556666777777777765477888888888876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.1e-05
                     HH---HHHHHHH.HHS..GGG-EEETTEEEEEEEE-SSS-EEEEEEESS---.... CS
  Phage_integr_3  32 fsGiRLkevlkl.LreyDpekliveddiarYpialekgeKkafyiylptelakele 86 
                      +G+ + +v  + +++yD++k +  d+  +Y+i+ + ++K  f + +p++l+  +e
      AJA93256.1  58 TTGAIIGKVNLVdVKKYDSDKELKADKKKHYSISDNTKNKYGFILEKPKKLRVPIE 113
                     5555555554333789*****************************99999986555 PP

>> Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.1e-05      0.25      16      37 ..      97     118 ..      72     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.1e-05
  Nitr_red_bet_C  16 eadgllpaveslRiPveYLAnL 37 
                     +   +l++ ++lR+P+eYL +L
      AJA93256.1  97 KYGFILEKPKKLRVPIEYLGKL 118
                     333389999**********887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1207.02
//
Query:       AJA93257.1  [L=70]
Description: hypothetical protein T478_0353 [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0049   16.7   4.4      0.058   13.3   4.4    2.1  1  zinc_ribbon_4    zinc-ribbon domain
  ------ inclusion threshold ------
      0.022   15.1   2.0      0.048   14.0   2.0    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.05   13.6   0.9      0.073   13.1   0.9    1.3  1  DZR              Double zinc ribbon
      0.063   13.3   0.4      0.075   13.1   0.4    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.066   12.9   3.4        0.2   11.4   3.4    1.7  1  Ribosomal_S27e   Ribosomal protein S27
      0.098   12.7   0.7       0.14   12.2   0.7    1.2  1  zinc_ribbon_6    Zinc-ribbon
       0.13   12.3   1.6        2.8    8.0   0.2    2.0  2  CpXC             CpXC protein
       0.16   12.1   1.8       0.23   11.6   1.8    1.4  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.24   10.9   5.2        8.8    5.9   5.2    2.2  1  zf-ribbon_3      zinc-ribbon domain
       0.31   10.9   3.3          9    6.2   0.7    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.51    9.9   4.3        3.2    7.4   0.5    2.5  2  Sgf11            Sgf11 (transcriptional regulation protein)
          2    8.9   3.0         20    5.7   0.2    2.1  2  DUF983           Protein of unknown function (DUF983)
        9.8    6.1   6.8        3.2    7.7   0.9    2.3  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   4.4   4.2e-05     0.058       1      32 [.       1      27 [.       1      28 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
  zinc_ribbon_4  1 MkitCpsCkakyeiddeklpakgvkvrCskCg 32
                   Mki Cp+Ck     +d+ l+++ + v C+kCg
     AJA93257.1  1 MKIKCPKCK-----EDAELAPDFSYVECKKCG 27
                   *********.....688899999********8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.0   3.5e-05     0.048       5      43 ..       4      32 ..       3      50 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfki 43
                      CP C+++a+l  +   +     +v+C++Cg    ++++
       AJA93257.1  4 KCPKCKEDAELAPD--FS-----YVECKKCGL---DMSY 32
                     5********99866..43.....89******9...3333 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.9   5.3e-05     0.073      29      49 .]       3      27 ..       1      31 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
         DZR 29 drCpsCgekvdpearf....CpeCG 49
                ++Cp+C+e++++   f    C++CG
  AJA93257.1  3 IKCPKCKEDAELAPDFsyveCKKCG 27
                6899999998888888889999998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   5.4e-05     0.075      70      94 ..       2      28 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.4e-05
                EEEETTTS-EEECHHH..HHS-TTTSS CS
        HypA 70 kvrCreCgkefeleek..alrCpkCgs 94
                k++C +C+++ el+ +   ++C+kCg 
  AJA93257.1  2 KIKCPKCKEDAELAPDfsYVECKKCGL 28
                799*********998555679****85 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4   0.00015       0.2       6      33 ..       1      27 [.       1      31 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                    EEEE-TTTS-EEEEESS-SS-EEESSST CS
  Ribosomal_S27e  6 ldvkCpdCenetvvFshaatvvkCisCg 33
                    +++kCp+C++         ++v+C +Cg
      AJA93257.1  1 MKIKCPKCKEDAE-LAPDFSYVECKKCG 27
                    89******98765.4566799******9 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7    0.0001      0.14      29      54 ..       2      27 ..       1      32 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
  zinc_ribbon_6 29 kilCnDCekksevkfhvlglkCkeCg 54
                   ki C  C++  e +  + ++ Ck+Cg
     AJA93257.1  2 KIKCPKCKEDAELAPDFSYVECKKCG 27
                   79***********************6 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0021       2.8      37      56 ..       2      21 ..       1      22 [. 0.83
   2 ?    6.1   0.1    0.0078        11      35      60 ..      18      43 ..      14      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0021
        CpXC 37 eatCpkCgatakleapllyh 56
                +++CpkC ++a+l  ++ y+
  AJA93257.1  2 KIKCPKCKEDAELAPDFSYV 21
                67899999999999888886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0078
        CpXC 35 lfeatCpkCgatakleapllyhdpek 60
                +  ++C kCg + ++   ++y+ +++
  AJA93257.1 18 FSYVECKKCGLDMSYGEYVRYVAHSE 43
                77899******999999999987665 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.8   0.00016      0.23       1      27 [.       4      31 ..       4      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
    zf-Mss51  1 lCPvpkhkqt.apkhvdfeCpdCGipty 27
                +CP +k++ + ap    +eC++CG+ + 
  AJA93257.1  4 KCPKCKEDAElAPDFSYVECKKCGLDMS 31
                6****9999878888889******9665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.2    0.0064       8.8       2      24 ..       2      28 ..       1      30 [. 0.59

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
  zf-ribbon_3  2 tvrCPnCGa.p.lssd..dnvCpyCGt 24
                 +++CP+C++   l++d   + C++CG 
   AJA93257.1  2 KIKCPKCKEdAeLAPDfsYVECKKCGL 28
                 689999996544444311455777776 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.7    0.0066         9       1       9 [.       3      11 ..       3      13 .. 0.83
   2 ?    5.2   0.1     0.014        19      28      35 ..      20      27 ..      16      31 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0066
     TFIIS_C  1 akCpkCgsr 9 
                +kCpkC+++
  AJA93257.1  3 IKCPKCKED 11
                69****975 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.014
     TFIIS_C 28 fykCtkCg 35
                +++C+kCg
  AJA93257.1 20 YVECKKCG 27
                67788886 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.037        51       5      11 ..       3       9 ..       1      11 [. 0.84
   2 ?    7.4   0.5    0.0023       3.2       4      22 ..      20      41 ..      17      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.037
                EE-TTTS CS
       Sgf11  5 vtCpnCg 11
                ++Cp C+
  AJA93257.1  3 IKCPKCK 9 
                79****8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                EEE-TTTSSEEEGG...GHHHH CS
       Sgf11  4 yvtCpnCgRqiaas...RFApH 22
                yv+C+ Cg +++ +   R+++H
  AJA93257.1 20 YVECKKCGLDMSYGeyvRYVAH 41
                9*******98886533366666 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.041        57       8      22 ..       2      16 ..       1      21 [. 0.80
   2 ?    5.7   0.2     0.014        20      10      19 ..      22      31 ..      19      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.041
      DUF983  8 adaCeaCgldlshar 22
                + +C++C++d + a+
  AJA93257.1  2 KIKCPKCKEDAELAP 16
                568******988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.014
      DUF983 10 aCeaCgldls 19
                +C++Cgld+s
  AJA93257.1 22 ECKKCGLDMS 31
                7*******97 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6      0.18   2.5e+02      14      20 ..       3       9 ..       1       9 [. 0.80
   2 ?    7.7   0.9    0.0023       3.2      10      21 ..      17      28 ..      15      43 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
   zf-C2H2_3 14 sqCkeCg 20
                 +C++C+
  AJA93257.1  3 IKCPKCK 9 
                57****6 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
   zf-C2H2_3 10 sfgasqCkeCgM 21
                +f+ ++Ck+Cg+
  AJA93257.1 17 DFSYVECKKCGL 28
                577889****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 522.17
//
Query:       AJA93258.1  [L=61]
Description: DDE Tnp 1-like zinc-ribbon [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0078   16.6   0.6      0.014   15.9   0.6    1.4  1  zf-C2H2          Zinc finger, C2H2 type
  ------ inclusion threshold ------
       0.01   16.6   0.8      0.018   15.8   0.6    1.5  2  zf-C2H2_4        C2H2-type zinc finger
      0.016   16.0   0.9      0.026   15.3   0.9    1.3  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
      0.017   15.4   0.5      0.019   15.3   0.5    1.1  1  zf-C2H2_2        C2H2 type zinc-finger (2 copies)
      0.049   12.8   0.4      0.053   12.7   0.4    1.0  1  Actin_micro      Putative actin-like family
      0.063   13.3   2.3       0.11   12.5   2.3    1.5  1  zf-BED           BED zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   4.6e-06     0.014       3      23 .]      18      39 ..      16      39 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-06
                ETTTTEEESSHHHHHHHHHC.C CS
     zf-C2H2  3 CpdCgksFkrksnLkrHirt.H 23
                C++C+    +++ L+rH+++ H
  AJA93258.1 18 CKVCDLELHQPERLERHMKKaH 39
                ********************99 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.6     6e-06     0.018       2      24 .]      17      39 ..      16      39 .. 0.95
   2 ?   -3.1   0.0         6   1.8e+04       9      14 ..      48      53 ..      47      55 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6e-06
   zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                +C++C+   + +++L rH+k+ H
  AJA93258.1 17 ICKVCDLELHQPERLERHMKKAH 39
                7*******************988 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
   zf-C2H2_4  9 sFsskk 14
                 Fs+k 
  AJA93258.1 48 EFSTKG 53
                588886 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.9   8.9e-06     0.026       8      25 ..       7      24 ..       6      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.9e-06
  Tnp_zf-ribbon_2  8 kkkikkeTriiCqeCdvp 25
                     kkk+ k+T++iC+ Cd  
       AJA93258.1  7 KKKDDKKTNTICKVCDLE 24
                     7999999********954 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.5   6.3e-06     0.019      50      82 ..      15      46 ..       4      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-06
   zf-C2H2_2 50 kleClyCekefkslealreHmkkkgHckineee 82
                + +C +C+ e ++ e l+ Hmk k H +++e++
  AJA93258.1 15 NTICKVCDLELHQPERLERHMK-KAHGNVPEKK 46
                579*******99*********7.5688876543 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.8e-05     0.053     214     249 ..       4      40 ..       3      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
  Actin_micro 214 frkleelkekkefsCkvCdvkfev.ekiseHllkkHi 249
                  f k ++ ++k++  CkvCd + ++ e+++ H++k H 
   AJA93258.1   4 FGKKKKDDKKTNTICKVCDLELHQpERLERHMKKAHG 40 
                  55666667788889*******9999***********7 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.3   3.7e-05      0.11      12      43 ..      11      39 ..       4      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                GGSS--EETTTTEE----SSTHHHHHHHHHS- CS
      zf-BED 12 lkeqkavCryCgkilsrgggttnLkrHLrrkH 43
                 k+++++C+ C  +l       +L rH++++H
  AJA93258.1 11 DKKTNTICKVCDLELHQ---PERLERHMKKAH 39
                589*********99988...7**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 486.55
//
Query:       AJA93259.1  [L=269]
Description: DSBA-like thioredoxin domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-30  104.2   0.1    1.5e-29  103.3   0.1    1.4  1  Thioredoxin_4  Thioredoxin
    3.7e-15   56.2   2.2    9.1e-14   51.7   2.2    2.1  1  DSBA           DSBA-like thioredoxin domain
    1.1e-06   29.1   0.1    2.5e-06   27.9   0.1    1.6  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.039   13.8   0.0      0.063   13.1   0.0    1.3  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.1   3.3e-33   1.5e-29       5     155 ..      94     248 ..      91     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 3.3e-33
                    SEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TTHHHHHHHHHHHHTH....HHHT CS
  Thioredoxin_4   5 diviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcageespeaflaikallysq....qeew 95 
                    ++++Gnp+A +t++e+ d++C  C  ++ ++e k++e y+ +Gkv +i++d+ + +   s+ aa aa+cage++  +f++++  ly++    ++ w
     AJA93259.1  94 SPILGNPNAEITLVEFGDYQCHFCNVYFHNTEhKIFENYVMEGKVNVIFKDYTIIGPD-SVVAAHAAHCAGEQG--KFWEYHNTLYNNwdgeETGW 186
                    689***********************7777777*******************888887.9**************..99999999999977765556 PP

                    TS-HHH...HH.....HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEE...TTEEE-TT- CS
  Thioredoxin_4  96 aeslke...laaealdkdekfeacleeekldalveaeskeakkagiestPtfii...ngekveepq 155
                    a + ++   +a+e   ++ +f++c +e k+++l+++   +a+ +g+++tP f++   n ++v   q
     AJA93259.1 187 AGQ-ENvvrFAQENNLNMNQFMDCNNELKYQNLIANSNSDAQSLGLTGTPAFFVistNSQQV---Q 248
                    666.33344778899999***********************************966655553...2 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   2.2     2e-17   9.1e-14       1     190 [.     105     261 ..     105     264 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 2e-17
                 EEEEEEBTTBHHHHHHHHHHH.HHHHHC...CTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerle.klaars...pdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarllla 95 
                 t++ef D++C++C + +++ e k+ +++    +v+v ++++ + g                                           +s  aa++++ 
  AJA93259.1 105 TLVEFGDYQCHFCNVYFHNTEhKIFENYvmeGKVNVIFKDYTIIGP------------------------------------------DSVVAAHAAHC 161
                 6899***********999987245555599777*************..........................................*********** PP

                 HHHHHGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE...TTC..EEEESSSSHHHHH CS
        DSBA  96 agaeglaekvvrelfealwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv...dgk..rmvfGadrldtla 189
                 ag++g+  ++ ++l++   +e +    +++++++a++  l+++++    ++ ++++ ++ +   aqslg+tG+P+++v   + +  ++++Ga++++ ++
  AJA93259.1 162 AGEQGKFWEYHNTLYNNWDGEETGWAGQENVVRFAQENNLNMNQFMDCNNELKYQNLIANSNSDAQSLGLTGTPAFFVistNSQqvQTISGAQPFEVFE 260
                 ******************************************************************************997554679*********998 PP

                 H CS
        DSBA 190 d 190
                 +
  AJA93259.1 261 R 261
                 7 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   5.6e-10   2.5e-06       4     108 ..     101     262 ..      99     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.6e-10
  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel........ddvtvrvllfp.lkpsfepkavaiwcakekkkafkd......................... 65 
                    n + +lv f d +C +C     +++           +v+v+  ++  ++p+++ +a a  ca e+ k ++                          
     AJA93259.1 101 NAEITLVEFGDYQCHFCNVYFHNTEHKifenyvmeGKVNVIFKDYTiIGPDSVVAAHAAHCAGEQGKFWEYhntlynnwdgeetgwagqenvvrfa 196
                    67789999********986544444444555898878888877777*******************96666688888888889999999******** PP

  Thioredoxin_2  66 ......................ieenvelarkygvrgtPtivfldgk.eivarlpGyvpaeeleal 108
                                          i+ ++  a+++g++gtP+++++  + + v ++ G+ p+e +e +
     AJA93259.1 197 qennlnmnqfmdcnnelkyqnlIANSNSDAQSLGLTGTPAFFVISTNsQQVQTISGAQPFEVFERI 262
                    ******************************************999999999**********99875 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.063     152     210 ..     193     251 ..     187     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
        TraF 152 qafadkyglev.raVsvdgrplpelpn.arvdkgqaarlgvkrtPalvlvdpksqkvvpva 210
                  +fa++ +l + ++++++++    ++n +  +++ a+ lg++ tPa+++++ +sq+v  ++
  AJA93259.1 193 VRFAQENNLNMnQFMDCNNELK--YQNlIANSNSDAQSLGLTGTPAFFVISTNSQQVQTIS 251
                 5677777777745788888877..4453567899999*******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1939.32
//
Query:       AJA93260.1  [L=402]
Description: geranylgeranyl reductase family [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-15   55.7   0.4    1.3e-14   54.5   0.2    1.7  2  FAD_oxidored    FAD dependent oxidoreductase
    5.4e-15   55.5   0.1    2.5e-14   53.3   0.1    1.9  1  FAD_binding_3   FAD binding domain
    6.3e-14   52.3   1.3    4.1e-07   29.9   0.9    2.3  2  DAO             FAD dependent oxidoreductase
    1.1e-13   51.1   2.0    2.3e-08   33.5   0.4    2.1  2  FAD_binding_2   FAD binding domain
    1.6e-10   40.4   0.9    0.00015   20.7   0.0    2.4  2  Trp_halogenase  Tryptophan halogenase
    3.3e-09   36.0   1.9    4.3e-08   32.3   0.3    2.1  2  HI0933_like     HI0933-like protein
    1.7e-08   33.9   0.0    2.6e-08   33.3   0.0    1.3  1  Lycopene_cycl   Lycopene cyclase protein
    2.6e-08   33.4   1.5    6.5e-08   32.2   1.5    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.5e-07   30.1   1.4      4e-07   29.5   0.3    1.7  2  GIDA            Glucose inhibited division protein A
    2.6e-05   24.4   0.2    5.2e-05   23.4   0.2    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.1e-05   24.0   1.1     0.0031   18.1   0.2    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    6.6e-05   22.4   0.4     0.0032   16.9   0.1    2.1  2  GMC_oxred_N     GMC oxidoreductase
    0.00012   21.4   0.6    0.00036   19.8   0.1    1.9  2  Thi4            Thi4 family
    0.00012   21.4   0.0    0.00022   20.6   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00047   19.5   1.0    0.00087   18.6   1.0    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0023   17.9   0.1     0.0042   17.0   0.1    1.4  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0048   17.1   0.0      0.011   16.0   0.0    1.6  1  TrkA_N          TrkA-N domain
     0.0083   16.6   0.0      0.023   15.1   0.0    1.8  1  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.061   13.8   0.0        0.1   13.1   0.0    1.4  1  XdhC_C          XdhC Rossmann domain


Domain annotation for each model (and alignments):
>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.2   1.3e-17   1.3e-14       1     145 [.       7     154 ..       7     183 .. 0.82
   2 ?   -1.5   0.0       1.3   1.2e+03     134     191 ..     300     353 ..     291     399 .. 0.64

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.3e-17
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrq......rggarlkkrskwn.....tfep 86 
                   DvvVvGGgpaG  AA  Aa++G +v+L+e+++ +  ++   +v+++   k       gi +e ++ +++      +++ +++     +     + ++
    AJA93260.1   7 DVVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVRTSGVTWISDIK-----KFGIPEECYNPIKKfsfcspKNSVKISG----EiakaaVLDV 94 
                   9********************************97666666666666644.....79**********9964433222222222....13344599** PP

  FAD_oxidored  87 evakavleemlaeagvtvllntrlvevekeg.kriesvtveskegrktirAkvfiDATgd 145
                   +   + l +  + +g ++++ t ++ev k++ +++ +v+++s+ +++++++kv+iDA+g 
    AJA93260.1  95 RKTYRFLANRAKTSGSELFTSTNVTEVLKDNtGKCVGVIAKSDGKQIQFNSKVVIDASGF 154
                   *****************************8636799999976667*************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
  FAD_oxidored 134 irAkvfiDATgdGdlaalaGvpyrvGresreetgepaagtlmfrlegveggeedekvq 191
                   ++++v+ DA  +Gd  +++  py+  ++   e + + ag+ + r+ g+    +d++++
    AJA93260.1 300 VAGQVTADAIKNGDTTEASLNPYEKEWKRAIESKINSAGKVQNRWVGL----TDDEWD 353
                   667777777777777777777777766666654444555555555555....333333 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   2.7e-17   2.5e-14       2     316 ..       6     303 ..       5     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.7e-17
                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHHCHHCST CS
  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsdtpkaradlelesspe 97 
                     dV++VG+GpaG ++a++ ++ G  v l+ek ++ +++ r +g++   +  +++ G+ +++++        +++  ++    pk +++++   +  
     AJA93260.1   6 FDVVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVRTSGVTW--ISDIKKFGIPEECYNPI------KKFSFCS----PKNSVKIS--GEIA 87 
                    59****************************************9865..7799*******998765......4455555....45566665..9999 PP

                    -CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEE CS
  FAD_binding_3  98 rvtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfd 193
                    + +v+ + ++ r L+++a+  g ++  +t+v+ +++d++g    v  k++g++ ++++k ++ a G+ S ++k+lg   + ++    +  +++ f+
     AJA93260.1  88 KAAVLDVRKTYRFLANRAKTSGSELFTSTNVTEVLKDNTGKCVGVIAKSDGKQIQFNSKVVIDASGFVSVIAKELGYVTQWKK----F-GAGAEFE 178
                    9***************************************************************************6633222....2.3567778 PP

                    C-SCCCTTC..CEEEEECCTTEE..EEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETT CS
  FAD_binding_3 194 adlsdivep..lvlilsaesrgv..mviPlentlerfyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgr 285
                    ++++++ ++  + +++++ s+     + P+++ +++++ +   +++ + +++ + +e + ++l  i +   ++     +  +  ++ + +k   ++
     AJA93260.1 179 VKTEKLEHDnwWLMVGQEYSPAGyaWIFPTSK-DTARIGVGIGKPDSDVDPTVRLNELLEKKLGPIKDLGNIEKIEFHYG-LIPNDGLSRKTVYDN 272
                    88887777755444444433333457888888.56556665555555555555555555555555555555544333333.334556667777777 PP

                    EEE-GGGTEEE-STTSHHHHHHHHHHHHHHH CS
  FAD_binding_3 286 vflaGDAaHihpPtgGqGlNtaiqDavnLaw 316
                    + l+GD+a    P    G+  ai+     + 
     AJA93260.1 273 LILVGDSAGQANPLVLEGIRYAIRFGEVAGQ 303
                    7777777777777666666666665555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.9   4.4e-10   4.1e-07       1      44 [.       7      50 ..       7      73 .. 0.91
   2 !   20.6   0.0   2.8e-07   0.00027     139     311 ..      88     260 ..      75     308 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.4e-10
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgll 44
                dvv++GGG +G+s+A+ +a+ g  V+l+ek+++++  ++ r+sg+ 
  AJA93260.1  7 DVVVVGGGPAGSSAAHMAAKSGctVALIEKEKEIA--QTVRTSGVT 50
                9******************************9998..888888875 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.8e-07
                 TEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEE.EEEETCEEEEEEECT.EEE.E.EEEEEEE--GGGHHHHHTTCTT....TSEEEEEEEEEEEEEE CS
         DAO 139 dtgqvdpakltaalaraaealGveilegtevtgl.eeedgkvwgverttp.gen.d.aadavVnaaGawsdllgllkel....dlpispvrgqvlvlkp 229
                  ++++d +k  ++la++a++ G e+++ t+vt++ +++ gk +gv  +++ g + +   + v+ a G  s ++   kel    + + +   g  + +  
  AJA93260.1  88 KAAVLDVRKTYRFLANRAKTSGSELFTSTNVTEVlKDNTGKCVGV-IAKSdGKQiQfNSKVVIDASGFVSVIA---KELgyvtQWK-KFGAGAEFEV-- 179
                 56889****************************734444888999.455557764333356*****9776455...5552212111.2233333444.. PP

                 CCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHH.HHHHHHHHHHHHSGGGCGEEE..EEEEEEE CS
         DAO 230 lseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdee.didellealrklfPqlgdvlr..kwaGlrp 311
                 ++ekl++ +  l v      ++++  ++p+ +++ ++G      +++d+ +vd+  +++elle+    + +lg++++    +Gl p
  AJA93260.1 180 KTEKLEHDNWWLMV-GqEYSPAGYAWIFPTSKDTARIGVG---IGKPDS-DVDPTvRLNELLEKKLGPIKDLGNIEKieFHYGLIP 260
                 22333333222233.2477778888888887788888765...345555.333332567777766666666777774435557777 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.4   2.5e-11   2.3e-08       1      49 [.       7      54 ..       7      63 .. 0.92
   2 !   17.1   0.1   2.4e-06    0.0023     143     203 ..      97     156 ..      84     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.5e-11
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl 49
                   Dv+V+G+G AG +AA+ aa+ G +va++eke+e   +t+  +G  ++++
     AJA93260.1  7 DVVVVGGGPAGSSAAHMAAKSGCTVALIEKEKE-IAQTVRTSGVTWISD 54
                   9*******************************9.5699999***99987 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.4e-06
                    HHHHHHHHHHTCTEEEEESEEEEEEEEC.TTEEEEEEEEETTTTCEEEEEESEEEE-----G CS
  FAD_binding_2 143 llarlvesarkagvdfqerteadeLive.dgrvtGavvenpesgrevrirakavvlatgGfg 203
                        l+++a+  g +++++t+++e++ + +g+++G++++  ++g++ ++++k v++a+g ++
     AJA93260.1  97 TYRFLANRAKTSGSELFTSTNVTEVLKDnTGKCVGVIAK--SDGKQIQFNSKVVIDASGFVS 156
                    56678999*999**************96366********..****************99766 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   1.2e-06    0.0012       1      60 [.       7      62 ..       7      73 .. 0.80
   2 !   20.7   0.0   1.6e-07   0.00015     141     369 ..      82     328 ..      64     335 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHHHT--H CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrlLgide 60
                    ++v+vGGG+aG+ aA + ak +   ++v l+e+e+     v  + ++ i  +   +gi+e
      AJA93260.1  7 DVVVVGGGPAGSSAAHMAAKSG---CTVALIEKEKEIAQTVRTSGVTWISDIK-KFGIPE 62
                    69**************999999...9*******98777777777776666653.346655 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.6e-07
                     S-B-S--EEEE-HHHHHHHHHHHHHHCT-EEE.E--EEEEEE-TTS-EEEE.EETTS-EEE-..SEEEE-SGGG-IIIIIIT---EEE-TTT--- CS
  Trp_halogenase 141 glsalsyAyhldaalyakfLrrvaearGvtrv.egkvvevqldedgrvesl.rledgrevea..dlfiDcsGfrgllieqaLktgfedwsdvLlt 231
                      + +++ A  ld ++  +fL + a+  G +   +++v+ev  d++g+  ++   +dg+++++    +iD+sGf + + ++   + +++w + +  
      AJA93260.1  82 ISGEIAKAAVLDVRKTYRFLANRAKTSGSELFtSTNVTEVLKDNTGKCVGViAKSDGKQIQFnsKVVIDASGFVSVIAKEL--GYVTQW-KKFGA 173
                     55678888889999**************99751567777777887776665155679887652279*********999996..445555.55656 PP

                     -EEEEEEEE--H..---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS..-HHHHHHHH.HHHCT--TTTS-.EEEE---EE......ES-S CS
  Trp_halogenase 232 drAlavqvesee..lvepytrataekaGWtWkiPLqhrlgn.Gyvyssaha..dddeAlael.laeldgkleaep.rkirfttGr......rkqa 313
                          v++e+ e      + +     aG  W  P ++ +   G+   +     d    l+el +++l+ +++  + +ki+f+ G        +++
      AJA93260.1 174 GAEFEVKTEKLEhdNWWLMVGQEYSPAGYAWIFPTSKDTARiGVGIGKPDSdvDPTVRLNELlEKKLGPIKDLGNiEKIEFHYGLipndglSRKT 268
                     666666666666554555556777889*******9987666666665555500555555565156677777777789*****9999999998888 PP

                     EETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHHHH CS
  Trp_halogenase 314 wvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnrevar 369
                        n++++G+++g  +Pl   +i  + +    a +  +  + ++   +a+++ +++e +r
      AJA93260.1 269 VYDNLILVGDSAGQANPLVLEGIRYAIRfgevAGQVTADAIKNGDTTEASLNPYEKEWKR 328
                     889**************9988887776544433334444444444445555556555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   4.5e-11   4.3e-08       1      43 [.       6      48 ..       6      51 .. 0.97
   2 ?    3.0   0.1     0.035        33     113     166 ..      99     156 ..      93     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.5e-11
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                 +dv+v+GgG+AG  aA  aak g+ V+l+ek+k++++ +++sG
   AJA93260.1  6 FDVVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVRTSG 48
                 59****************************************9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.035
                  HHHHHHHHHHT-EEE-S--EEEEECETTE.E.EEEE..TTEEEEESE.EEE.----SS CS
  HI0933_like 113 dallkelkeagvklrletevksvekeedgkf.rvkt.kseeeleadk.lvl.AtGGlS 166
                  ++l +++k +g +l ++t+v++v k+++gk   v + +++++++ ++ +v+ A+G  S
   AJA93260.1  99 RFLANRAKTSGSELFTSTNVTEVLKDNTGKCvGVIAkSDGKQIQFNSkVVIdASGFVS 156
                  7899*******************98887754144443566666654413333666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.7e-11   2.6e-08       1     175 [.       7     192 ..       7     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.7e-11
  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny...vWsdefedlgaleecvehsWsgtivylddgkkillgraYgrv.sskrlkee 92 
                    Dvvv+G+GpAg s A+    ak g  v lie  +++  + +    +W    +  g  eec +   +      ++  ki  + a + v   ++  + 
     AJA93260.1   7 DVVVVGGGPAGSSAAHMA--AKSGCTVALIEKEKEIAQTVRTsgvTWISDIKKFGIPEECYNPIKKFSFCSPKNSVKISGEIAKAAVlDVRKTYRF 100
                    9************99999..***********99988766665222666666666657788777766555555555555555555544155667788 PP

  Lycopene_cycl  93 llerlvengv.klleakvesveeeeages..lvvleggr..kirarlvvdarglaslkkarrlgl..Q..tf.yGvevevdnppfdldkmvlM 175
                    l++r  ++g   +++  v++v +++ g+   +++ ++g+  + ++++v+da+g + +  a++lg+  Q  +f  G e ev++++ + d+  lM
     AJA93260.1 101 LANRAKTSGSeLFTSTNVTEVLKDNTGKCvgVIAKSDGKqiQFNSKVVIDASG-FVSVIAKELGYvtQwkKFgAGAEFEVKTEKLEHDNWWLM 192
                    88888866651567778********977612466678994444689*******.777755555551121133357788888777777777777 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   1.5   6.9e-11   6.5e-08       1     111 [.       6     156 ..       6     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 6.9e-11
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH.......................................H CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................x RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeias.......................................e 58 
                  +dvvv+GgGpAG +aa+ +a++g+ v+l+e +++   +++ +  +++  +++++  ++                                       +
   AJA93260.1   6 FDVVVVGGGPAGSSAAHMAAKSGCTVALIEkEKEIAQTVRTSGVTWISDIKKFGIPEEcynpikkfsfcspknsvkisgeiakaavldvrktyrflaN 103
                  69***************************953333444555555555555555543337779999999999999999999999888888888887764 PP

                  HHHCHHHHCCCCHCCTCEEEEESC..EEEEETEEECTCEEEEEESEEEE---EEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  59 vvkklnqgielllgeevvkidpgk..kkvklekkkegdeekiaydklvlAtGssp 111
                    k  ++++ + ++  v+++ +++  k+v + +k++g++ ++  + ++ A+G+ +
   AJA93260.1 104 RAKTSGSELFTSTN--VTEVLKDNtgKCVGVIAKSDGKQIQFNSKVVIDASGFVS 156
                  44444444444444..666665554378888777777766666677777998765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.3   4.2e-10     4e-07       1      38 [.       7      43 ..       7      64 .. 0.89
   2 ?   -1.1   0.0      0.79   7.5e+02     116     149 ..     116     153 ..      74     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.2e-10
                CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT-- CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiael 38
                dv+V+GgG AG+ AA  aa++G+ v+Li +k ++ia+ 
  AJA93260.1  7 DVVVVGGGPAGSSAAHMAAKSGCTVALI-EKEKEIAQT 43
                79**************************.666666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.79
                 S-EEEEEECT.TEEEE.EEETTS-EEEEC..EEEE--T CS
        GIDA 116 eeveelivee.kkvkg.vvtedgetikak..avviatG 149
                  +v+e++ ++ +k+ g + ++dg++i+ +  +v+ a+G
  AJA93260.1 116 TNVTEVLKDNtGKCVGvIAKSDGKQIQFNskVVIDASG 153
                 45666655445777773455667766544315555666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.2   5.5e-08   5.2e-05       1      31 [.      10      40 ..      10      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.5e-08
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                   +vG+G +G++aA+ +ak g+ v l+ek   +
     AJA93260.1 10 VVGGGPAGSSAAHMAAKSGCTVALIEKEKEI 40
                   8**************************9877 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   3.2e-06    0.0031       2      35 ..       8      41 ..       7      55 .. 0.91
   2 ?    4.3   0.0     0.064        61      46      79 ..     101     135 ..      94     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.2e-06
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                vvvvGgG  g  +A ++a+ g+ V ++e ++++ 
  AJA93260.1  8 VVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIA 41
                8*****************************9987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.064
                 HHHHHHHTTEEEECSEEEEEEEEETTS.EEEEEEE CS
   Pyr_redox  46 lqeklekngievllntkveeiegsedg.vesvklk 79 
                 l+++ +  g e+ ++t+v+e+ +++ g   +v  k
  AJA93260.1 101 LANRAKTSGSELFTSTNVTEVLKDNTGkCVGVIAK 135
                 67888999****************99988888876 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.036        34       1      35 [.       6      39 ..       6      57 .. 0.87
   2 !   16.9   0.1   3.4e-06    0.0032     198     257 ..     100     155 ..      95     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.036
  GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleaggr 35
                 +d +v+ggG ags  Aa ++++   +v ++e + +
   AJA93260.1  6 FDVVVVGGGPAGSS-AAHMAAKSGCTVALIEKEKE 39
                 6889**********.***************98765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.4e-06
  GMC_oxred_N 198 wLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvvaaGal 257
                  +L +  +  ++e+ t+++++ + l+++++++vGV a++++++   ++ ++k+v+ a+G +
   AJA93260.1 100 FLANRAKTSGSELFTSTNVTEV-LKDNTGKCVGVIAKSDGKQ---IQFNSKVVIDASGFV 155
                  566677778*************.7779**********99999...899999999999877 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   3.8e-07   0.00036      17      50 ..       5      37 ..       1      53 [. 0.87
   2 ?   -1.0   0.0       0.9   8.5e+02     112     166 ..     109     152 ..      87     170 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.8e-07
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                + Dvv+vG+G++G +aa++ ak+ +  va++e++
  AJA93260.1  5 NFDVVVVGGGPAGSSAAHMAAKS-GCTVALIEKE 37
                57*****************9999.*******986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.9
                 TEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE-- CS
        Thi4 112 nvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdat 166
                 +  l++++ v +++  +  +  Gv+ ++   +++            ++kvv+da+
  AJA93260.1 109 GSELFTSTNVTEVLKDNTGKCVGVIAKSDGKQIQF-----------NSKVVIDAS 152
                 55555555555554444445555555544444444...........344444444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.3e-07   0.00022      30      76 ..       7      53 ..       5      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                 EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECE CS
  AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfve 76
                  v+v+GgG aG +A+++a++ g +V +++++++ ++ +++ g ++++
   AJA93260.1  7 DVVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVRTSGVTWIS 53
                 59**********************************99998877765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.0   9.2e-07   0.00087       1     134 [.       9     154 ..       9     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.2e-07
  Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkg.nignsiyr....ypkemtfispsftsekleipdlnaiseetspafs...lkeeklsrkealeYlrev 90 
                  +++G+GPaG +aa+ + k+g  ++  +Ek+ +i ++++     +  + + +   + +    i+++ + s+++s ++s    k   l  ++  ++l++ 
   AJA93260.1   9 VVVGGGPAGSSAAHMAAKSGC-TVALIEKEkEIAQTVRTsgvtWISDIKKFGIPE-ECYNPIKKFSFCSPKNSVKISgeiAKAAVLDVRKTYRFLANR 104
                  79*******************.799****98899888742222666665555432.222345566677777776555322233455566666777777 PP

  Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfev..etske....tyeAkkviiAtGe 134
                  ak+   +  + ++V++v k+++g  v   ++++    ++++k vi A G+
   AJA93260.1 105 AKTSGSELFTSTNVTEVLKDNTGKCVgvIAKSDgkqiQFNSKVVIDASGF 154
                  77777778888888888887766443112222223456667777777665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.4e-06    0.0042       2      40 ..       8      46 ..       7      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-06
                EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
     3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                v v+G G  G++ a+++a++g++V l++ ++e++++++ 
  AJA93260.1  8 VVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVRT 46
                89*****************************99998775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.1e-05     0.011       1      45 [.       8      52 ..       8      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEE CS
      TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevv 45
                ++++G G  G+s a+   + g+  v +i+k++e ++++r  g++++
  AJA93260.1  8 VVVVGGGPAGSSAAHMAAKsGCT-VALIEKEKEIAQTVRTSGVTWI 52
                79*****************8885.****************999887 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.4e-05     0.023       8      58 ..       6      54 ..       4     115 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
  NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekd 58
                     v+vvGgG+ + + ++  +++g++v ++ +e  +e+ ++v+ +  +  +d
     AJA93260.1  6 FDVVVVGGGPAGSSAAHMAAKSGCTVALIEKE--KEIAQTVRTSGVTWISD 54
                   579*****************************..56666666443333333 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011       0.1       1      38 [.       8      45 ..       8     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG CS
      XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefatker 38
                +v++G+g+ + + a++aa+ g++v ++++++e+a++ r
  AJA93260.1  8 VVVVGGGPAGSSAAHMAAKSGCTVALIEKEKEIAQTVR 45
                689***************************99886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2761.04
//
Query:       AJA93261.1  [L=186]
Description: putative segregation and condensation protein B [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-34  119.2   0.3    1.5e-34  118.9   0.3    1.1  1  SMC_ScpB     Segregation and condensation complex subunit Scp
  ------ inclusion threshold ------
      0.015   15.3   0.1       0.74    9.9   0.0    2.3  2  HTH_20       Helix-turn-helix domain
      0.019   15.3   0.1      0.023   15.0   0.1    1.3  1  DUF5013      Domain of unknown function (DUF5013)
       0.02   14.8   0.1        1.5    8.8   0.0    2.5  2  TBPIP        TBPIP/Hop2 winged helix domain
      0.033   14.1   0.1      0.089   12.8   0.1    1.7  1  Y_Y_Y        Y_Y_Y domain
      0.043   13.8   0.4       0.24   11.4   0.1    2.1  2  PadR         Transcriptional regulator PadR-like family
      0.096   12.3   0.0       0.15   11.7   0.0    1.3  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.3   5.8e-38   1.5e-34       1     155 [.      12     162 ..      12     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 5.8e-38
    SMC_ScpB   1 aiiEAiLfvageplsleeLakilels.keeveealeeLkeeyeeedrglelvev.aggyrlvtkpelaevvkklvkekkktrLsqaaletLaiIaykqp 97 
                 a+iE++L++ag+pls+e+L ++ +++ ++++ ++l +L ++ +++ +++e+ ++ +g y +++kpe+++ + + + +  ++ L +a+ +tL++Iay+qp
  AJA93261.1  12 ARIESALYSAGRPLSVEDLIRASGTEsRKTTLNLLTKLIQKTKSSFKAIEITNLpDGSYVFQLKPEYSSTIGRKYAS--RPMLAKATQKTLSYIAYEQP 108
                 58*********************97779**************************999**************999998..8******************* PP

    SMC_ScpB  98 vtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglksle 155
                 ++++++ e+RG  ++s+++ L++ ++ie++     +gr  +Y+tTekF +yfg++  +
  AJA93261.1 109 ISSKQLVEVRGTGVYSHLKDLTQLDFIEHQT----VGRYKIYTTTEKFRKYFGIQGDD 162
                 *****************************99....9******************9754 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.037        94      11      34 ..      10      34 ..       7      50 .. 0.78
   2 ?    9.9   0.0   0.00029      0.74      26      61 .]     110     142 ..      90     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.037
                HHHHHHHHH.STCTTB-HHHHHHHH CS
      HTH_20 11 vRrrilraL.araegltaselaerl 34
                  +ri++aL + +++l++++l ++ 
  AJA93261.1 10 ATARIESALySAGRPLSVEDLIRAS 34
                6689*****99999****9998875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00029
                 -HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
      HTH_20  26 taselaerldlskntlsyHLrvLeeagLvevvregr 61 
                 + ++l e   ++ + ++ HL+ L + +++e +++gr
  AJA93261.1 110 SSKQLVE---VRGTGVYSHLKDLTQLDFIEHQTVGR 142
                 5555555...78889******************997 PP

>> DUF5013  Domain of unknown function (DUF5013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   8.9e-06     0.023      45     108 ..      39     104 ..      14     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.9e-06
     DUF5013  45 kegaisletgwdnaaieNgkiYQtvtLpaGkYelsvtvaeengqnsn..gtaylvvakgstLPdle 108
                  +++++l t+  ++     k    ++Lp G+Y ++ +++ +++++ +  +   l+ a+++tL+ ++
  AJA93261.1  39 RKTTLNLLTKLIQKTKSSFKAIEITNLPDGSYVFQLKPEYSSTIGRKyaSRPMLAKATQKTLSYIA 104
                 56666666655566666677778899**************999999999999*********98765 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00058       1.5       1      46 [.       9      53 ..       9      60 .. 0.79
   2 ?    3.6   0.1     0.024        62      29      60 ..     116     147 ..     106     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00058
       TBPIP  1 eaeelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdeg 46
                ea + ++  l++  rP+sv+d + + + +  Kt+    L +L ++ 
  AJA93261.1  9 EATARIESALYSAGRPLSVEDLIRASGTESRKTTL-NLLTKLIQKT 53
                68899*******************99999888875.4555665555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.024
       TBPIP  29 klgKtavqkaLdeLvdegkiieKeyGKqkiYl 60 
                 ++ +t v   L  L + + i   + G  kiY 
  AJA93261.1 116 EVRGTGVYSHLKDLTQLDFIEHQTVGRYKIYT 147
                 6778889999999******************7 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-05     0.089      26      46 ..      54      75 ..      47      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                STS..EEEEES--SEEEEEEEE CS
       Y_Y_Y 26 dysq.easytnlppGdYtlkVk 46
                ++s   +++tnlp G+Y++++k
  AJA93261.1 54 KSSFkAIEITNLPDGSYVFQLK 75
                333359*************986 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.37   9.4e+02      31      54 ..      15      38 ..       3      48 .. 0.78
   2 ?   11.4   0.1   9.5e-05      0.24      25      72 ..     113     155 ..     106     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.37
                HHHHHHHHHHHHHTTSEEEEEE-S CS
        PadR 31 eGslYpaLkrLekeglvesewees 54
                e+ lY a + L+ e+l+ ++ +es
  AJA93261.1 15 ESALYSAGRPLSVEDLIRASGTES 38
                788999999999999999987776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.5e-05
                 T-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
        PadR  25 gllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72 
                  l+e+  + +Y  Lk+L + +++e++ +      + k+Y+ T++ r++
  AJA93261.1 113 QLVEVRGTGVYSHLKDLTQLDFIEHQTVG-----RYKIYTTTEKFRKY 155
                 567788889*****************874.....89******987665 PP

>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.15      48      88 ..      37      77 ..      29      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                 -SS--HHHHHHHHHHHTTEEEEEEEEEEEETTEEEEEEEEE CS
  DNase-RNase 48 ppRPlthDLlasllealgakvervvItdledgtfyAelvlr 88
                  +R +t +Ll++l+++++ + + ++It+l dg +  +l+ +
   AJA93261.1 37 ESRKTTLNLLTKLIQKTKSSFKAIEITNLPDGSYVFQLKPE 77
                 67999*****************************9888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1327.95
//
Query:       AJA93262.1  [L=169]
Description: acetyltransferase (GNAT) domain protein [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-19   70.2   0.0    3.2e-19   70.0   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.3e-11   44.9   1.8    1.5e-11   44.7   1.8    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.2e-10   41.7   0.1    1.4e-10   41.4   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.9e-06   27.0   0.0    1.3e-05   24.9   0.0    1.8  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    3.1e-05   23.9   0.2      4e-05   23.5   0.2    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0035   17.7   0.3     0.0054   17.1   0.3    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.056   12.8   0.0      0.074   12.4   0.0    1.2  1  YmdB             YmdB-like protein
       0.07   13.5   1.7       0.15   12.4   1.7    1.6  1  Pox_polyA_pol_N  Poxvirus poly(A) polymerase N-terminal domai


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   1.4e-22   3.2e-19       2     138 .]       5     141 ..       4     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.4e-22
  Acetyltransf_3   2 LlLrplteeDlealfelrsdpevmrylpe..pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedeeaelgymlaps.fwg 93 
                     + L  ++++Dl  ++++r+++++ ++ ++   l+ e +++w++++ ++es+++ + +    k++ ++G+ gl +++++++ a++ ++l++s  +g
      AJA93262.1   5 IELSGIKKADLSVIVKWRNNHDILKFNTQyfLLNMEHQKKWFDEINQKESKSKMFVFKY--KNK-IVGVGGLIHIDNKNKNADIAIILGESkLHG 96 
                     567888999**9**************666689***********9766655555555555..555.9***********************8889** PP

  Acetyltransf_3  94 kGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                     kG++t a++ l++y f+++gl+r+ a+i + Ne S +++ekl f+
      AJA93262.1  97 KGLGTKALQLLVDYGFKKMGLHRIGAEIFEYNEISLKLFEKLNFK 141
                     ******************************************996 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   1.8   6.7e-15   1.5e-11       3     151 ..       9     157 ..       7     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 6.7e-15
  Acetyltransf_4   3 aateeDakeilaiyaeyvvntaitfeyevssveefekfleal.d.sekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglg 95 
                      ++++D+  i +++++ ++ ++ t++     +e  +k+ +++ +   k+ +f   ++ +ivG   l  ++   k++ a + + l e +   +glg
      AJA93262.1   9 GIKKADLSVIVKWRNNHDILKFNTQY-FLLNMEHQKKWFDEInQkESKSKMFVFKYKNKIVGVGGLIHIDN--KNKNADIAIILGESKLHGKGLG 100
                     5899***********99997777766.588999999*****943455689999999***************..***********99999****** PP

  Acetyltransf_4  96 relidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwi 151
                      + +++l+++  k+++++++ aei+  ne+s +++++l F+++ + +++    g+w 
      AJA93262.1 101 TKALQLLVDYGfKKMGLHRIGAEIFEYNEISLKLFEKLNFKKEVEMRDYLWRDGKWW 157
                     **********88*************************************99999996 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   6.3e-14   1.4e-10      20     117 .]      45     140 ..      21     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.3e-14
                     HHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHH CS
  Acetyltransf_1  20 seee.feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikkivlaveedndaairlY 112
                     +++e  ++      +  +v ++ ++++G  +l  i++ k+++a i  +   ++ +gkGlG++ l+ l+++ +++ g+++i ++++e n+ + +l+
      AJA93262.1  45 WFDEiNQKE---SKSKMFVFKYKNKIVGVGGLIHIDN-KNKNADIAIILGESKLHGKGLGTKALQLLVDYGFKKmGLHRIGAEIFEYNEISLKLF 135
                     222212222...44499999*****************.9999999999999999********************999****************** PP

                     HHTTE CS
  Acetyltransf_1 113 eklGF 117
                     ekl F
      AJA93262.1 136 EKLNF 140
                     **998 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   5.8e-09   1.3e-05       3     142 ..      12     145 ..      11     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.8e-09
                     GGGHHHHHHHCTSCCCHHHH----..-HHHHHHHHHHHC..STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTT CS
  Acetyltransf_8   3 eaDlellhrWmnrprvaewweeag..tleevrellakld.adphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargk 94 
                     +aDl ++ +W n+  + ++  +    + e+++++ ++++ ++ +s+ ++  ++++ vg   + ++++          +    i +++ge + +gk
      AJA93262.1  12 KADLSVIVKWRNNHDILKFNTQYFllNMEHQKKWFDEINqKESKSKMFVFKYKNKIVGVGGLIHIDNK---------NKNADIAIILGESKLHGK 97 
                     57888999999999998888888744344555544444426777888888888888888888877777.........56667789********** PP

                     TCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEE CS
  Acetyltransf_8  95 glttallralvhylfadprtrrvvvEPdvrNerairllekaGfekeke 142
                     gl+t+ l+ lv+y f++ +  r+ +E    Ne +++l+ek+ f+ke e
      AJA93262.1  98 GLGTKALQLLVDYGFKKMGLHRIGAEIFEYNEISLKLFEKLNFKKEVE 145
                     *******************************************99866 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   1.8e-08     4e-05      20     111 ..      43     145 ..      20     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.8e-08
  Acetyltransf_10  20 ealrerie..egealllvaeeggkivGvi...elrdgs...hisllfVdpeyrgqGigkaLleaveee.aekdgikl.eltvnasp.yavpfYe 102
                      +++ ++i+  e++ +++v++ ++kivGv+    +++++    i+ +  +++ +g+G+g++ l+ + ++ ++k+g++    ++ + +    +++e
       AJA93262.1  43 KKWFDEINqkESKSKMFVFKYKNKIVGVGgliHIDNKNknaDIAIILGESKLHGKGLGTKALQLLVDYgFKKMGLHRiGAEIFEYNeISLKLFE 136
                      4444455235788999**********87732255444477888888889***************************9988888888899***** PP

  Acetyltransf_10 103 klGFkavge 111
                      kl Fk+  e
       AJA93262.1 137 KLNFKKEVE 145
                      ****98765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   2.4e-06    0.0054       2      76 .]      55     142 ..      54     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                     TEEEEEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHHH......TTSEEE.....EEEEEETHHHHHHHHHHTTEEE CS
  Acetyltransf_7   2 kgevfVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLlea......aekgii.....leqlelnaekaikfYeklGFee 76 
                     k+++fV + ++kivG  +l ++d     a+i  +    + +gkG+G++ l++      ++ g++     +      +e ++k++ekl F++
      AJA93262.1  55 KSKMFVFKYKNKIVGVGGLIHIDnknknADIAIILGESKLHGKGLGTKALQLlvdygfKKMGLHrigaeI---FEYNEISLKLFEKLNFKK 142
                     5789***********99999998877666666688888*************7555555223322222212...223336799*******85 PP

>> YmdB  YmdB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.3e-05     0.074      23      73 ..      78     131 ..      69     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
        YmdB  23 kkeykidfviangEnaaggkGltkkeaeellkagvdviTl...Gnhvwdkkeil 73 
                 +k++++d+ i+ gE   +gkGl +k ++ l+++g   + l   G  +++ +ei 
  AJA93262.1  78 NKNKNADIAIILGESKLHGKGLGTKALQLLVDYGFKKMGLhriGAEIFEYNEIS 131
                 578899****************************98765322255555555554 PP

>> Pox_polyA_pol_N  Poxvirus poly(A) polymerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.7   6.9e-05      0.15      28      75 ..      20      66 ..      11      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-05
                     GHHHHHHHHHS-HHHHHHHHHHHHHHH-TTSSS-THHHHHHHHHHTTG CS
  Pox_polyA_pol_N 28 qvrniqkilnfdkdiflsLlkknkkkffkdlklseseikkrileyfsk 75
                     + rn + il+f+++ fl  +   +kk+f ++++ es+ k  + +y  k
       AJA93262.1 20 KWRNNHDILKFNTQYFLLNM-EHQKKWFDEINQKESKSKMFVFKYKNK 66
                     6789999*******998655.567899***********9999999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1202.79
//
Query:       AJA93263.1  [L=95]
Description: sugar efflux transporter for intercellular exchange [ammonia-oxidizing marine archaeon V2]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-11   42.7   3.4    5.1e-11   42.5   3.4    1.0  1  MtN3_slv  Sugar efflux transporter for intercellular exchange
    7.5e-06   25.6   0.4    7.5e-06   25.6   0.4    1.5  2  PQ-loop   PQ loop repeat
  ------ inclusion threshold ------
      0.011   16.0   2.3      0.011   16.0   2.3    1.9  2  DUF996    Protein of unknown function (DUF996)
      0.032   13.9   1.8      0.037   13.7   1.8    1.1  1  MASE3     Membrane-associated sensor domain
      0.042   14.3   2.4        0.6   10.6   3.3    1.9  2  DUF1211   Protein of unknown function (DUF1211)
      0.056   13.6   7.9       0.61   10.3   7.9    2.1  1  DUF3784   Domain of unknown function (DUF3784)
        1.2    9.6   5.5       0.29   11.6   1.3    1.9  2  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> MtN3_slv  Sugar efflux transporter for intercellular exchange
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   3.4     2e-14   5.1e-11       2      84 ..       6      88 ..       5      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2e-14
    MtN3_slv  2 llgllcvvftvavFlsPlsilrkiikkksveelsfllflagllsallWllYGllkkdaliiivNlvgvlleliylllflvyak 84
                +lg++++   v+     ++++ + +k+k+ e++s  l++a + +a+lWl+YG+ ++d +ii vN+  ++l ++ l++ l y+k
  AJA93263.1  6 TLGIVAIAAGVLILIGWVPQIIQGYKTKKLEDVSKYLVIAIFSGAALWLVYGIEIDDVYIIGVNVAAMFLTMTVLIMKLKYEK 88
                79***********************************************************************9999888865 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.4   2.9e-09   7.5e-06       4      53 ..       9      58 ..       6      59 .. 0.92
   2 ?   -2.6   0.1       1.9   4.8e+03      35      45 ..      70      80 ..      66      84 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-09
     PQ-loop  4 ilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllyli 53
                i+ +++ vl l+  +PQii+ yk+k  e +S + ++  ++G  l+l+y i
  AJA93263.1  9 IVAIAAGVLILIGWVPQIIQGYKTKKLEDVSKYLVIAIFSGAALWLVYGI 58
                5678888999*************************************975 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
     PQ-loop 35 ilflllwllGd 45
                +  ++l ++  
  AJA93263.1 70 VAAMFLTMTVL 80
                45555555544 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   2.3   4.3e-06     0.011      72     118 ..      14      58 ..       2      69 .. 0.76
   2 ?    1.7   0.6      0.12     3e+02      70      97 ..      66      92 ..      58      95 .] 0.50

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
      DUF996  72 llllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGa 118
                   +l+ +i +v++ii+++  kk +e ++k++ + +F+ a+l+++ G 
  AJA93263.1  14 AGVLI-LIGWVPQIIQGYKTKK-LEDVSKYLVIAIFSGAALWLVYGI 58 
                 33332.4789*****9998877.7899****************9995 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
      DUF996 70 illlllvliiayvlliisavflkksyel 97
                i++ ++++ +++ +++i  + + k++e 
  AJA93263.1 66 IGVNVAAM-FLTMTVLIMKLKYEKAFES 92
                44444444.3334444445555566655 PP

>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.8   1.4e-05     0.037     113     186 ..       9      80 ..       3      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
       MASE3 113 lvtlllllsifypkifPalfiegsGlTpfkiisEyliilllllalllllrrrkkfekkvlrlllaalvllilse 186
                 +v++++ ++i+  +++P++ i+g  + ++  +s yl+i+++  a+l l+   +  + +++ + +aa++l++   
  AJA93263.1   9 IVAIAAGVLIL-IGWVPQI-IQGYKTKKLEDVSKYLVIAIFSGAALWLVYGIEIDDVYIIGVNVAAMFLTMTVL 80 
                 33444444444.7999*97.89**9*************************999999999999999999998755 PP

>> DUF1211  Protein of unknown function (DUF1211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.3   0.00023       0.6       2      54 ..       2      57 ..       1      82 [. 0.73
   2 ?    1.8   0.2      0.13   3.3e+02      12      23 ..      75      86 ..      65      94 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                HHHHHHHHHHHHHHHHHHHS-.--...HHHHHHHHHHTHHHHHHHHHHHHHHHHHHH CS
     DUF1211  2 leafsDavfAIaiTLlvleik.vp...eeellaallellpsllayllsFlvvasfWl 54
                l  f+ +++AIa+ +l+l i  vp   ++ ++++l + ++ l++ ++s + ++ ++ 
  AJA93263.1  2 LDEFTLGIVAIAAGVLIL-IGwVPqiiQGYKTKKLEDVSKYLVIAIFSGAALWLVYG 57
                567999************.75478777777788888888888888888777777664 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                HHHHHHHHHS-- CS
     DUF1211 12 IaiTLlvleikv 23
                 ++T+l++++k+
  AJA93263.1 75 LTMTVLIMKLKY 86
                345555555544 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.9   0.00024      0.61       2      81 ..       6      74 ..       5      87 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
     DUF3784  2 ilallflilGilflkgkganLiaGYntmskeekekydekklsrfmgivllligilflllgllsaiesealliialiviii 81
                 l+++++++G+l+l g  ++ i GY+t++ e   ky          i+++  ++l+l+ g+     +++++i++ ++ + 
  AJA93263.1  6 TLGIVAIAAGVLILIGWVPQIIQGYKTKKLEDVSKY--------LVIAIFSGAALWLVYGIE---IDDVYIIGVNVAAMF 74
                5899*********************98444443333........223333333444444444...555555555554333 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.3   0.00011      0.29       8      59 ..       6      55 ..       3      63 .. 0.66
   2 ?   -0.2   0.2      0.52   1.3e+03      13      27 ..      72      86 ..      61      91 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
     DUF2583  8 llGnvlmglGlllmvaslaysvlnqlpelelpellaeaallgifiGallWla 59
                 lG v ++ G+l++++ +    ++   + +  e +++  +++if Ga lWl+
  AJA93263.1  6 TLGIVAIAAGVLILIGWVPQI-IQGY-KTKKLEDVSKYLVIAIFSGAALWLV 55
                566666777776666555543.3333.33444456777899**********7 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.52
     DUF2583 13 lmglGlllmvaslay 27
                 m l + ++++ l y
  AJA93263.1 72 AMFLTMTVLIMKLKY 86
                355555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 719.75
//
[ok]
